From 3e802f6d6f655e0ef607efe49a91f38928d2ba41 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 13 Jul 2026 12:35:46 +0200 Subject: [PATCH 01/56] parsing schema correctly --- beacon/utils/requests.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/beacon/utils/requests.py b/beacon/utils/requests.py index 3292bb9c..df600d15 100644 --- a/beacon/utils/requests.py +++ b/beacon/utils/requests.py @@ -211,10 +211,10 @@ def set_entry_type_configuration(self): elif param_key == 'schema': if RequestAttributes.qparams.meta.requestedSchemas != []: for schema in RequestAttributes.qparams.meta.requestedSchemas: - if schema == param_value["default_schema_id"]: - RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema).model_dump()] - elif schema in param_value["supported_schemas"]: - RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema).model_dump()] + if schema["schema"] == param_value["default_schema_id"]: + RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema["schema"]).model_dump()] + elif schema["schema"] in param_value["supported_schemas"]: + RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema["schema"]).model_dump()] else: RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=param_value["default_schema_id"]).model_dump()] elif RequestAttributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: From f935881e624762cc66f97ee942d008934cac2221 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 13 Jul 2026 18:30:11 +0200 Subject: [PATCH 02/56] first iteration of the custom schema generator --- Dockerfile | 4 +- beacon/custom_schemas/generator.py | 86 +++++++++++++++++++++++++ beacon/custom_schemas/json/example.json | 80 +++++++++++++++++++++++ requirements.txt | 3 +- 4 files changed, 170 insertions(+), 3 deletions(-) create mode 100644 beacon/custom_schemas/generator.py create mode 100644 beacon/custom_schemas/json/example.json diff --git a/Dockerfile b/Dockerfile index 1f98fe1f..4f5c1bb8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ ## Build env ########################## -FROM python:3.10-bullseye AS BUILD +FROM python:3.10-bookworm AS BUILD ENV DEBIAN_FRONTEND noninteractive @@ -21,7 +21,7 @@ RUN pip install -r /tmp/requirements.txt ########################## ## Final image ########################## -FROM python:3.10-bullseye +FROM python:3.10-bookworm LABEL maintainer "CRG System Developers" LABEL org.label-schema.schema-version="2.0" diff --git a/beacon/custom_schemas/generator.py b/beacon/custom_schemas/generator.py new file mode 100644 index 00000000..ece6a4b1 --- /dev/null +++ b/beacon/custom_schemas/generator.py @@ -0,0 +1,86 @@ +#!/usr/bin/env python3 + +import argparse +import re +from pathlib import Path + +from datamodel_code_generator import ( + GenerateConfig, + InputFileType, + generate, +) + + +INPUT_BASE_DIR = Path("/beacon/custom_schemas/json") +OUTPUT_BASE_DIR = Path( + "/beacon/models/EUCAIM/validator/collections/collections" +) + + +def valid_output_file(value: str) -> str: + """ + Validate that the output filename is a valid Python filename. + Allowed characters: letters, numbers, underscores. + Must end with .py. + """ + path = Path(value) + + if path.suffix != ".py": + raise argparse.ArgumentTypeError( + "Output file must have a .py extension" + ) + + if not re.fullmatch(r"[A-Za-z0-9_]+\.py", path.name): + raise argparse.ArgumentTypeError( + "Output filename can only contain letters, numbers, and underscores" + ) + + return value + + +def main(): + parser = argparse.ArgumentParser( + description="Generate Pydantic models from a JSON Schema" + ) + + parser.add_argument( + "-i", + "--input", + required=True, + help="JSON Schema filename", + ) + + parser.add_argument( + "-o", + "--output", + type=valid_output_file, + default="models.py", + help="Generated Python filename", + ) + + args = parser.parse_args() + + input_path = INPUT_BASE_DIR / args.input + output_path = OUTPUT_BASE_DIR / args.output + + if not input_path.exists(): + raise FileNotFoundError( + f"Schema file not found: {input_path}" + ) + + print(f"Input schema: {input_path}") + print(f"Output file: {output_path}") + + config = GenerateConfig( + input_file_type=InputFileType.JsonSchema, + output=output_path, + ) + + generate( + input_=input_path, + config=config, + ) + + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/beacon/custom_schemas/json/example.json b/beacon/custom_schemas/json/example.json new file mode 100644 index 00000000..a49008d4 --- /dev/null +++ b/beacon/custom_schemas/json/example.json @@ -0,0 +1,80 @@ +{ + "$comment": "version: ga4gh-beacon-analysis-v2.0.0", + "$schema": "https://json-schema.org/draft/2020-12/schema", + "additionalProperties": true, + "description": "The `analysis` schema represents a information about the data analysis steps leading to (a set of) genomic variation call(s).", + "properties": { + "aligner": { + "description": "Name or identifier of the mapping/alignment software/pipeline", + "examples": [ + "bwa-0.7.8" + ], + "type": "string" + }, + "analysisDate": { + "description": "Date at which analysis was performed.\n", + "examples": [ + "2021-10-17" + ], + "format": "date", + "type": "string" + }, + "biosampleId": { + "description": "Local reference to the `id` of the biosample this analysis is reporting on.", + "examples": [ + "S0001", + "onekgbs-NA07346" + ], + "type": "string" + }, + "id": { + "description": "Analysis id for internal referencing; unique in the dataset.", + "type": "string" + }, + "individualId": { + "description": "Local reference to the `id` of the individual this analysis is reporting on.", + "examples": [ + "P0001", + "onekgind-NA07346" + ], + "type": "string" + }, + "pipelineName": { + "description": "Analysis pipeline and version.", + "examples": [ + "Pipeline-panel-0001-v1" + ], + "type": "string" + }, + "pipelineRef": { + "description": "Link to information about or repository of the analysis pipeline.", + "examples": [ + "https://doi.org/10.48511/workflowhub.workflow.111.1", + "https://doi.org/10.1093/bib/bbad541" + ], + "type": "string" + }, + "runId": { + "description": "Local reference to the associated experimental run.", + "examples": [ + "SRR10903401" + ], + "type": "string" + }, + "variantCaller": { + "description": "Name or identifier of the variant calling software/pipeline", + "examples": [ + "GATK4.0", + "labelSeg" + ], + "type": "string" + } + }, + "required": [ + "id", + "analysisDate", + "pipelineName" + ], + "title": "Bioinformatics analysis", + "type": "object" +} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 97747bb2..6a65144c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -25,4 +25,5 @@ progressbar==2.5 tqdm==4.66.3 obonet==0.3.1 python-dateutil==2.9.0 -rfc3339_validator==0.1.4 \ No newline at end of file +rfc3339_validator==0.1.4 +datamodel-code-generator==0.68.1 \ No newline at end of file From b3b6260abb7b89e6fdeae9ae087aba1c7a96c39d Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 14 Jul 2026 16:24:52 +0200 Subject: [PATCH 03/56] removing hard-coded model configuration loading --- .gitignore | 3 +- beacon/validator/configuration.py | 641 ++++-------------------------- 2 files changed, 88 insertions(+), 556 deletions(-) diff --git a/.gitignore b/.gitignore index dc071dac..dd045ab1 100644 --- a/.gitignore +++ b/.gitignore @@ -13,4 +13,5 @@ beacon/connections/mongo/data/db/* adminui/adminclient/migrations/* adminui/node_modules *.vcf.bgz -beacon/conf/conf.py \ No newline at end of file +beacon/conf/conf.py +models \ No newline at end of file diff --git a/beacon/validator/configuration.py b/beacon/validator/configuration.py index ef1c23ba..f27ccdc7 100644 --- a/beacon/validator/configuration.py +++ b/beacon/validator/configuration.py @@ -4,7 +4,7 @@ import re import logging import yaml -from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.utils import import_dataset_confile, import_analysis_confile, import_biosample_confile, import_cohort_confile, import_individual_confile, import_genomicVariant_confile, import_run_confile +from beacon.utils.modules import get_modules_confiles import datetime import time @@ -41,154 +41,113 @@ def check_logs_configuration(): @log_with_args_check_configuration(conf_override.config.level) def check_configuration( - LOG=None, - analysis_confile=import_analysis_confile(), - biosample_confile=import_biosample_confile(), - cohort_confile=import_cohort_confile(), - dataset_confile=import_dataset_confile(), - genomicVariant_confile=import_genomicVariant_confile(), - individual_confile=import_individual_confile(), - run_confile=import_run_confile() + LOG=None ): - + all_conf_files=get_modules_confiles() # ------------------------------------------------------------------------- # Entry type enablement validation # Ensure that the "entry_type_enabled" flag is explicitly configured as a # boolean value for every supported Beacon entity. # ------------------------------------------------------------------------- + for file in all_conf_files: + for k, v in file.items(): + if isinstance(v["entry_type_enabled"], bool): + pass + else: + raise Exception( + "{}.entry_type_enabled variable from {}.py must be boolean".format( + k, k + ) + ) + # ------------------------------------------------------------------------- + # Endpoint granularity validation + # Validate that enabled endpoints only use Beacon-supported granularity + # levels: boolean, count or record. + # ------------------------------------------------------------------------- + if ( + v["endpoint_name"] != '' + and v["max_granularity"] + not in ['boolean', 'count', 'record'] + ): + raise Exception( + "{}granularity must be one string between boolean, count or record".format(k) + ) - if isinstance(analysis_confile["analysis"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'analysis', 'analysis' - ) - ) - if isinstance(biosample_confile["biosample"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'biosample', 'biosample' - ) - ) + # Validate the configured backend for run records. + if v["connection"]["name"] not in [ + name + for name in os.listdir("/beacon/connections") + if os.path.isdir(os.path.join("/beacon/connections", name)) + ]: + raise Exception( + 'The database {} for {}records needs to match a directory name in the beacon/connections folder'.format( + v["connection"]["name"], k + ) + ) + + # ------------------------------------------------------------------------- + # Endpoint name validation + # Validate that all endpoint names are strings and only contain + # supported characters. Endpoint names are used to generate routes, + # therefore special characters are not allowed. + # ------------------------------------------------------------------------- - if isinstance(cohort_confile["cohort"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'cohort', 'cohort' - ) - ) + if not isinstance(v["endpoint_name"], str): + raise Exception('The endpoint_name variable for {} entry type must be of type string'.format(k)) + if contains_special_characters(v["endpoint_name"]): + raise Exception('The endpoint_name variable for {} entry type can not have special characters'.format(k)) - if isinstance(dataset_confile["dataset"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'dataset', 'dataset' - ) - ) + # ------------------------------------------------------------------------- + # Analysis configuration validation + # Verify that the analysis entry type contains all mandatory Beacon + # metadata fields, schema definitions and query configuration flags. + # ------------------------------------------------------------------------- - if isinstance(genomicVariant_confile["genomicVariant"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'genomicVariant', 'genomicVariant' - ) - ) + if not isinstance(v["open_api_definition"], str): + raise Exception('The {} open_api_definition must be of type string.'.format(k)) - if isinstance(individual_confile["individual"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'individual', 'individual' - ) - ) + # Validate ontology metadata used to describe the entry type. + if not isinstance(v["info"]["name"], str): + raise Exception('The {} info name must be of type string.'.format(k)) - if isinstance(run_confile["run"]["entry_type_enabled"], bool): - pass - else: - raise Exception( - "{}.enable_endpoint variable from {}.py must be boolean".format( - 'run', 'run' - ) - ) + # Ontology identifiers must follow CURIE notation. + if not isinstance(v["info"]["ontology_id"], str) or not re.match("[A-Za-z0-9]+:[A-Za-z0-9]", v["info"]["ontology_id"]): + raise Exception('The {} ["info"]["ontology_id"] must be of type string and CURIE.'.format(k)) - # ------------------------------------------------------------------------- - # Endpoint granularity validation - # Validate that enabled endpoints only use Beacon-supported granularity - # levels: boolean, count or record. - # ------------------------------------------------------------------------- + if not isinstance(v["info"]["ontology_name"], str): + raise Exception('The {} ["info"]["ontology_name"] must be of type string.'.format(k)) - if ( - analysis_confile["analysis"]["endpoint_name"] != '' - and analysis_confile["analysis"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "analysis granularity must be one string between boolean, count or record" - ) + # Validate schema definition metadata. + if not isinstance(v["schema"]["specification"], str): + raise Exception('The {} schema ["schema"]["specification"] must be of type string.'.format(k)) - if ( - biosample_confile["biosample"]["endpoint_name"] != '' - and biosample_confile["biosample"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "biosample granularity must be one string between boolean, count or record" - ) + if not isinstance(v["info"]["description"], str): + raise Exception('The {} description must be of type string.'.format(k)) - if ( - cohort_confile["cohort"]["endpoint_name"] != '' - and cohort_confile["cohort"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "cohort granularity must be one string between boolean, count or record" - ) + if not isinstance(v["schema"]["default_schema_id"], str): + raise Exception('The {} default_schema_id must be of type string.'.format(k)) - if ( - dataset_confile["dataset"]["endpoint_name"] != '' - and dataset_confile["dataset"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "dataset granularity must be one string between boolean, count or record" - ) + if not isinstance(v["schema"]["default_schema_name"], str): + raise Exception('The {} default_schema_name must be of type string.'.format(k)) - if ( - genomicVariant_confile["genomicVariant"]["endpoint_name"] != '' - and genomicVariant_confile["genomicVariant"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "genomicVariant granularity must be one string between boolean, count or record" - ) + if not isinstance(v["schema"]["reference_to_default_schema_definition"], str): + raise Exception('The {} reference_to_default_schema_definition must be of type string.'.format(k)) - if ( - individual_confile["individual"]["endpoint_name"] != '' - and individual_confile["individual"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "individual granularity must be one string between boolean, count or record" - ) + if not isinstance(v["schema"]["default_schema_version"], str): + raise Exception('The ["schema"]["default_schema_version"] for entry type {} must be of type string.'.format(k)) - if ( - run_confile["run"]["endpoint_name"] != '' - and run_confile["run"]["max_granularity"] - not in ['boolean', 'count', 'record'] - ): - raise Exception( - "run granularity must be one string between boolean, count or record" - ) + # Multiple schemas can be supported by the same entry type. + if not isinstance(v["schema"]["supported_schemas"], list): + raise Exception('The {} supported_schemas must be of type list.'.format(k)) + + # Validate query behaviour configuration. + if not isinstance(v["allow_queries_without_filters"], bool): + raise Exception('The {} allow_queries_without_filters must be of type bool.'.format(k)) + if not isinstance(v["allow_id_query"], bool): + raise Exception('The {} allow id query must be of type bool.'.format(k)) + # ------------------------------------------------------------------------- # Beacon URI validation # Verify that the public Beacon URL follows the expected format and @@ -274,30 +233,6 @@ def check_configuration( ) ) - # Validate the configured backend for run records. - if run_confile["run"]["connection"]["name"] not in [ - name - for name in os.listdir("/beacon/connections") - if os.path.isdir(os.path.join("/beacon/connections", name)) - ]: - raise Exception( - 'The database {} for run records needs to match a directory name in the beacon/connections folder'.format( - run_confile["run"]["connection"]["name"] - ) - ) - - # Validate the configured backend for individual records. - if individual_confile["individual"]["connection"]["name"] not in [ - name - for name in os.listdir("/beacon/connections") - if os.path.isdir(os.path.join("/beacon/connections", name)) - ]: - raise Exception( - 'The database {} for individual records needs to match a directory name in the beacon/connections folder'.format( - individual_confile["individual"]["connection"]["name"] - ) - ) - # Additional backend validations follow the same pattern for # genomicVariant, dataset, cohort, biosample and analysis entities. @@ -354,411 +289,7 @@ def check_configuration( cors_url ) ) - # ------------------------------------------------------------------------- - # Endpoint name validation - # Validate that all endpoint names are strings and only contain - # supported characters. Endpoint names are used to generate routes, - # therefore special characters are not allowed. - # ------------------------------------------------------------------------- - - if not isinstance(run_confile["run"]["endpoint_name"], str): - raise Exception('The run_confile["run"]["endpoint_name"] variable must be of type string') - if contains_special_characters(run_confile["run"]["endpoint_name"]): - raise Exception('The run_confile["run"]["endpoint_name"] variable can not have special characters') - - if not isinstance(individual_confile["individual"]["endpoint_name"], str): - raise Exception('The individual_confile["individual"]["endpoint_name"] variable must be of type string') - if contains_special_characters(individual_confile["individual"]["endpoint_name"]): - raise Exception('The individual_confile["individual"]["endpoint_name"] variable can not have special characters') - - if not isinstance(genomicVariant_confile["genomicVariant"]["endpoint_name"], str): - raise Exception('The genomicVariant_confile["genomicVariant"]["endpoint_name"] variable must be of type string') - if contains_special_characters(genomicVariant_confile["genomicVariant"]["endpoint_name"]): - raise Exception('The genomicVariant_confile["genomicVariant"]["endpoint_name"] variable can not have special characters') - - if not isinstance(dataset_confile["dataset"]["endpoint_name"], str): - raise Exception('The dataset_confile["dataset"]["endpoint_name"] variable must be of type string') - if contains_special_characters(dataset_confile["dataset"]["endpoint_name"]): - raise Exception('The dataset_confile["dataset"]["endpoint_name"] variable can not have special characters') - - if not isinstance(cohort_confile["cohort"]["endpoint_name"], str): - raise Exception('The cohort_confile["cohort"]["endpoint_name"] variable must be of type string') - if contains_special_characters(cohort_confile["cohort"]["endpoint_name"]): - raise Exception('The cohort_confile["cohort"]["endpoint_name"] variable can not have special characters') - - if not isinstance(biosample_confile["biosample"]["endpoint_name"], str): - raise Exception('The biosample_confile["biosample"]["endpoint_name"] variable must be of type string') - if contains_special_characters(biosample_confile["biosample"]["endpoint_name"]): - raise Exception('The biosample_confile["biosample"]["endpoint_name"] variable can not have special characters') - - if not isinstance(analysis_confile["analysis"]["endpoint_name"], str): - raise Exception('The analysis_confile["analysis"]["endpoint_name"] variable must be of type string') - if contains_special_characters(analysis_confile["analysis"]["endpoint_name"]): - raise Exception('The analysis_confile["analysis"]["endpoint_name"] variable can not have special characters') - - # ------------------------------------------------------------------------- - # Analysis configuration validation - # Verify that the analysis entry type contains all mandatory Beacon - # metadata fields, schema definitions and query configuration flags. - # ------------------------------------------------------------------------- - - if not isinstance(analysis_confile["analysis"]["open_api_definition"], str): - raise Exception('The analysis open_api_definition must be of type string.') - - # Ensure the configuration root key matches the expected entry type. - if 'analysis' not in analysis_confile: - raise Exception('The analysis id variable must be analysis_confile') - - # Validate ontology metadata used to describe the entry type. - if not isinstance(analysis_confile["analysis"]["info"]["name"], str): - raise Exception('The analysis info name must be of type string.') - - # Ontology identifiers must follow CURIE notation. - if not isinstance(analysis_confile["analysis"]["info"]["ontology_id"], str) or not re.match("[A-Za-z0-9]+:[A-Za-z0-9]", analysis_confile["analysis"]["info"]["ontology_id"]): - raise Exception('The analysis ["info"]["ontology_id"] must be of type string and CURIE.') - - if not isinstance(analysis_confile["analysis"]["info"]["ontology_name"], str): - raise Exception('The analysis ["info"]["ontology_name"] must be of type string.') - - # Validate schema definition metadata. - if not isinstance(analysis_confile["analysis"]["schema"]["specification"], str): - raise Exception('The analysis schema ["schema"]["specification"] must be of type string.') - - if not isinstance(analysis_confile["analysis"]["info"]["description"], str): - raise Exception('The analysis description must be of type string.') - - if not isinstance(analysis_confile["analysis"]["schema"]["default_schema_id"], str): - raise Exception('The analysis default_schema_id must be of type string.') - - if not isinstance(analysis_confile["analysis"]["schema"]["default_schema_name"], str): - raise Exception('The analysis default_schema_name must be of type string.') - - if not isinstance(analysis_confile["analysis"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The analysis reference_to_default_schema_definition must be of type string.') - - if not isinstance(analysis_confile["analysis"]["schema"]["default_schema_version"], str): - raise Exception('The analysis_confile["analysis"]["schema"]["default_schema_version"] must be of type string.') - - # Multiple schemas can be supported by the same entry type. - if not isinstance(analysis_confile["analysis"]["schema"]["supported_schemas"], list): - raise Exception('The analysis supported_schemas must be of type list.') - - # Validate query behaviour configuration. - if not isinstance(analysis_confile["analysis"]["allow_queries_without_filters"], bool): - raise Exception('The analysis allow_queries_without_filters must be of type bool.') - - if not isinstance(analysis_confile["analysis"]["allow_id_query"], bool): - raise Exception('The analysis allow id query must be of type bool.') - - # ------------------------------------------------------------------------- - # Biosample configuration validation - # Apply the same metadata, ontology and schema checks to the - # biosample entry type configuration. - # ------------------------------------------------------------------------- - - if not isinstance(biosample_confile["biosample"]["open_api_definition"], str): - raise Exception('The biosample_confile["cohort"]["open_api_definition"] must be of type string.') - - if 'biosample' not in biosample_confile: - raise Exception('The biosample_confileid variable must be biosample_confile') - - if not isinstance(biosample_confile["biosample"]["info"]["name"], str): - raise Exception('The biosample_confile["biosample"]["info"]["name"] must be of type string.') - - # Validate CURIE-compliant ontology identifier. - if not isinstance(biosample_confile["biosample"]["info"]["ontology_id"], str) or not re.match("[A-Za-z0-9]+:[A-Za-z0-9]", biosample_confile["biosample"]["info"]["ontology_id"]): - raise Exception('The biosample_confile["biosample"]["info"]["ontology_id"] must be of type string and CURIE.') - - if not isinstance(biosample_confile["biosample"]["info"]["ontology_name"], str): - raise Exception('The biosample_confile["biosample"]["info"]["ontology_name"] must be of type string.') - - if not isinstance(biosample_confile["biosample"]["schema"]["specification"], str): - raise Exception('The biosample_confile["biosample"]["schema"]["specification"] must be of type string.') - - if not isinstance(biosample_confile["biosample"]["info"]["description"], str): - raise Exception('The biosample_confile["biosample"]["info"]["description"] must be of type string.') - - # Validate default schema metadata. - if not isinstance(biosample_confile["biosample"]["schema"]["default_schema_id"], str): - raise Exception('The biosample_confile["biosample"]["schema"]["default_schema_id"] must be of type string.') - - if not isinstance(biosample_confile["biosample"]["schema"]["default_schema_name"], str): - raise Exception('The biosample_confile["biosample"]["schema"]["default_schema_name"] must be of type string.') - - if not isinstance(biosample_confile["biosample"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The biosample_confile["biosample"]["schema"]["reference_to_default_schema_definition"] must be of type string.') - - if not isinstance(biosample_confile["biosample"]["schema"]["default_schema_version"], str): - raise Exception('The biosample_confile["biosample"]["schema"]["default_schema_version"] must be of type string.') - - if not isinstance(biosample_confile["biosample"]["schema"]["supported_schemas"], list): - raise Exception('The biosample_confile["biosample"]["schema"]["supported_schemas"] must be of type list.') - - # Validate query permissions for this entry type. - if not isinstance(biosample_confile["biosample"]["allow_queries_without_filters"], bool): - raise Exception('The biosample_confile["analysis"]["allow_queries_without_filters"] must be of type bool.') - - if not isinstance(biosample_confile["biosample"]["allow_id_query"], bool): - raise Exception('The biosample_confile["analysis"]["allow_id_query"] must be of type bool.') - - # ------------------------------------------------------------------------- - # Cohort configuration validation - # Repeat the same consistency checks for cohort metadata, - # schema definitions and query options. - # ------------------------------------------------------------------------- - - if not isinstance(cohort_confile["cohort"]["open_api_definition"], str): - raise Exception('The cohort_confile["cohort"]["open_api_definition"] must be of type string.') - - if 'cohort' not in cohort_confile: - raise Exception('The cohort_confileid variable must be cohort_confile') - - if not isinstance(cohort_confile["cohort"]["info"]["name"], str): - raise Exception('The cohort_confile["cohort"]["info"]["name"] must be of type string.') - - # Cohort ontology identifiers must use CURIE format. - if not isinstance(cohort_confile["cohort"]["info"]["ontology_id"], str) or not re.match("[A-Za-z0-9]+:[A-Za-z0-9]", cohort_confile["cohort"]["info"]["ontology_id"]): - raise Exception('The cohort_confile["cohort"]["info"]["ontology_id"] must be of type string and CURIE.') - - # Validate cohort ontology name - if not isinstance(cohort_confile["cohort"]["info"]["ontology_name"], str): - raise Exception('The cohort_confile["cohort"]["info"]["ontology_name"] must be of type string.') - - # Validate cohort schema specification URL/reference - if not isinstance(cohort_confile["cohort"]["schema"]["specification"], str): - raise Exception('The cohort_confile["cohort"]["schema"]["specification"] must be of type string.') - - # Validate cohort description - if not isinstance(cohort_confile["cohort"]["info"]["description"], str): - raise Exception('The cohort_confile["cohort"]["info"]["description"] must be of type string.') - - # Validate cohort default schema ID - if not isinstance(cohort_confile["cohort"]["schema"]["default_schema_id"], str): - raise Exception('The cohort_confile["cohort"]["schema"]["default_schema_id"] must be of type string.') - - # Validate cohort default schema name - if not isinstance(cohort_confile["cohort"]["schema"]["default_schema_name"], str): - raise Exception('The cohort_confile["cohort"]["schema"]["default_schema_name"] must be of type string.') - - # Validate cohort schema definition reference - if not isinstance(cohort_confile["cohort"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The cohort_confile["cohort"]["schema"]["reference_to_default_schema_definition"] must be of type string.') - - # Validate cohort schema version - if not isinstance(cohort_confile["cohort"]["schema"]["default_schema_version"], str): - raise Exception('The cohort_confile["cohort"]["schema"]["default_schema_version"] must be of type string.') - - # Supported schemas must be provided as a list - if not isinstance(cohort_confile["cohort"]["schema"]["supported_schemas"], list): - raise Exception('The cohort_confile["cohort"]["schema"]["supported_schemas"] must be of type list.') - - # Check cohort query configuration flags - if not isinstance(cohort_confile["cohort"]["allow_queries_without_filters"], bool): - raise Exception('The cohort_confile["analysis"]["allow_queries_without_filters"] must be of type bool.') - - if not isinstance(cohort_confile["cohort"]["allow_id_query"], bool): - raise Exception('The cohort_confile["analysis"]["allow_id_query"] must be of type bool.') - - # Validate dataset OpenAPI definition path/reference - if not isinstance(dataset_confile["dataset"]["open_api_definition"], str): - raise Exception('The dataset_confile["cohort"]["open_api_definition"] must be of type string.') - - # Dataset root key must exist - if 'dataset' not in dataset_confile: - raise Exception('The dataset_confileid variable must be dataset_confile') - - # Dataset display name validation - if not isinstance(dataset_confile["dataset"]["info"]["name"], str): - raise Exception('The dataset_confilename must be of type string.') - - # Dataset ontology identifier must be CURIE compliant - if not isinstance(dataset_confile["dataset"]["info"]["ontology_id"], str) or not re.match( - "[A-Za-z0-9]+:[A-Za-z0-9]", - dataset_confile["dataset"]["info"]["ontology_id"]): - raise Exception('The dataset_confile["dataset"]["info"]["ontology_id"] must be of type string and CURIE.') - - # Dataset ontology name validation - if not isinstance(dataset_confile["dataset"]["info"]["ontology_name"], str): - raise Exception('The dataset_confile["dataset"]["info"]["ontology_name"] must be of type string.') - - # Dataset schema specification validation - if not isinstance(dataset_confile["dataset"]["schema"]["specification"], str): - raise Exception('The dataset_confile["dataset"]["schema"]["specification"] must be of type string.') - - # Dataset description validation - if not isinstance(dataset_confile["dataset"]["info"]["description"], str): - raise Exception('The dataset_confiledescription must be of type string.') - - # Dataset schema identifiers - if not isinstance(dataset_confile["dataset"]["schema"]["default_schema_id"], str): - raise Exception('The dataset_confile["dataset"]["schema"]["default_schema_id"] must be of type string.') - - if not isinstance(dataset_confile["dataset"]["schema"]["default_schema_name"], str): - raise Exception('The dataset_confile["dataset"]["schema"]["default_schema_name"] must be of type string.') - - if not isinstance(dataset_confile["dataset"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The dataset_confile["dataset"]["schema"]["reference_to_default_schema_definition"] must be of type string.') - - if not isinstance(dataset_confile["dataset"]["schema"]["default_schema_version"], str): - raise Exception('The dataset_confile["dataset"]["schema"]["default_schema_version"] must be of type string.') - - # Dataset supported schemas collection - if not isinstance(dataset_confile["dataset"]["schema"]["supported_schemas"], list): - raise Exception('The dataset_confile["dataset"]["schema"]["supported_schemas"] must be of type list.') - - # Dataset query behaviour flags - if not isinstance(dataset_confile["dataset"]["allow_queries_without_filters"], bool): - raise Exception('The dataset_confile["analysis"]["allow_queries_without_filters"] must be of type bool.') - - if not isinstance(dataset_confile["dataset"]["allow_id_query"], bool): - raise Exception('The dataset_confile["analysis"]["allow_id_query"] must be of type bool.') - - # Validate genomicVariant OpenAPI definition - if not isinstance(genomicVariant_confile["genomicVariant"]["open_api_definition"], str): - raise Exception('The genomicVariant_confile["cohort"]["open_api_definition"] must be of type string.') - - # genomicVariant root section must exist - if 'genomicVariant' not in genomicVariant_confile: - raise Exception('The genomicVariant_confileid variable must be genomicVariant_confile') - - # Validate genomicVariant metadata fields - if not isinstance(genomicVariant_confile["genomicVariant"]["info"]["name"], str): - raise Exception('The genomicVariant_confilename must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["info"]["ontology_id"], str) or not re.match( - "[A-Za-z0-9]+:[A-Za-z0-9]", - genomicVariant_confile["genomicVariant"]["info"]["ontology_id"]): - raise Exception('The genomicVariant_confile["dataset"]["info"]["ontology_id"] must be of type string and CURIE.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["info"]["ontology_name"], str): - raise Exception('The genomicVariant_confile["dataset"]["info"]["ontology_name"] must be of type string.') - - # Validate genomicVariant schema configuration - if not isinstance(genomicVariant_confile["genomicVariant"]["schema"]["specification"], str): - raise Exception('The genomicVariant_confile["genomicVariant"]["schema"]["specification"] must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["info"]["description"], str): - raise Exception('The genomicVariant_confiledescription must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["schema"]["default_schema_id"], str): - raise Exception('The genomicVariant_confile["genomicVariant"]["schema"]["default_schema_id"] must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["schema"]["default_schema_name"], str): - raise Exception('The genomicVariant_confile["genomicVariant"]["schema"]["default_schema_name"] must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The genomicVariant_confile["genomicVariant"]["schema"]["reference_to_default_schema_definition"] must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["schema"]["default_schema_version"], str): - raise Exception('The genomicVariant_confile["genomicVariant"]["schema"]["default_schema_version"] must be of type string.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["schema"]["supported_schemas"], list): - raise Exception('The genomicVariant_confile["genomicVariant"]["schema"]["supported_schemas"] must be of type list.') - - # Validate genomicVariant query permissions - if not isinstance(genomicVariant_confile["genomicVariant"]["allow_queries_without_filters"], bool): - raise Exception('The genomicVariant_confile["analysis"]["allow_queries_without_filters"] must be of type bool.') - - if not isinstance(genomicVariant_confile["genomicVariant"]["allow_id_query"], bool): - raise Exception('The genomicVariant_confile["analysis"]["allow_id_query"] must be of type bool.') - - # Validate individual OpenAPI definition - if not isinstance(individual_confile["individual"]["open_api_definition"], str): - raise Exception('The individual_confile["cohort"]["open_api_definition"] must be of type string.') - - # Individual root section must exist - if 'individual' not in individual_confile: - raise Exception('The individual_confileid variable must be individual_confile') - - # Individual metadata validation - if not isinstance(individual_confile["individual"]["info"]["name"], str): - raise Exception('The individual_confilename must be of type string.') - - if not isinstance(individual_confile["individual"]["info"]["ontology_id"], str) or not re.match( - "[A-Za-z0-9]+:[A-Za-z0-9]", - individual_confile["individual"]["info"]["ontology_id"]): - raise Exception('The individual_confile["dataset"]["info"]["ontology_id"] must be of type string and CURIE.') - - if not isinstance(individual_confile["individual"]["info"]["ontology_name"], str): - raise Exception('The individual_confile["dataset"]["info"]["ontology_name"] must be of type string.') - - # Validate individual schema information - if not isinstance(individual_confile["individual"]["schema"]["specification"], str): - raise Exception('The individual_confile["genomicVariant"]["schema"]["specification"] must be of type string.') - - if not isinstance(individual_confile["individual"]["info"]["description"], str): - raise Exception('The individual_confiledescription must be of type string.') - - if not isinstance(individual_confile["individual"]["schema"]["default_schema_id"], str): - raise Exception('The individual_confile["genomicVariant"]["schema"]["default_schema_id"] must be of type string.') - - if not isinstance(individual_confile["individual"]["schema"]["default_schema_name"], str): - raise Exception('The individual_confile["genomicVariant"]["schema"]["default_schema_name"] must be of type string.') - - if not isinstance(individual_confile["individual"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The individual_confile["genomicVariant"]["schema"]["reference_to_default_schema_definition"] must be of type string.') - - if not isinstance(individual_confile["individual"]["schema"]["default_schema_version"], str): - raise Exception('The individual_confile["genomicVariant"]["schema"]["default_schema_version"] must be of type string.') - - if not isinstance(individual_confile["individual"]["schema"]["supported_schemas"], list): - raise Exception('The individual_confile["genomicVariant"]["schema"]["supported_schemas"] must be of type list.') - - # Individual query settings - if not isinstance(individual_confile["individual"]["allow_queries_without_filters"], bool): - raise Exception('The individual_confile["analysis"]["allow_queries_without_filters"] must be of type bool.') - - if not isinstance(individual_confile["individual"]["allow_id_query"], bool): - raise Exception('The individual_confile["analysis"]["allow_id_query"] must be of type bool.') - - # Validate run OpenAPI definition - if not isinstance(run_confile["run"]["open_api_definition"], str): - raise Exception('The run_confile["cohort"]["open_api_definition"] must be of type string.') - - # Run root section must exist - if 'run' not in run_confile: - raise Exception('The run_confileid variable must be run_confile') - - # Run metadata validation - if not isinstance(run_confile["run"]["info"]["name"], str): - raise Exception('The run_confilename must be of type string.') - - if not isinstance(run_confile["run"]["info"]["ontology_id"], str) or not re.match( - "[A-Za-z0-9]+:[A-Za-z0-9]", - run_confile["run"]["info"]["ontology_id"]): - raise Exception('The run_confile["dataset"]["info"]["ontology_id"] must be of type string and CURIE.') - - if not isinstance(run_confile["run"]["info"]["ontology_name"], str): - raise Exception('The run_confile["dataset"]["info"]["ontology_name"] must be of type string.') - - # Run schema validation - if not isinstance(run_confile["run"]["schema"]["specification"], str): - raise Exception('The run_confile["genomicVariant"]["schema"]["specification"] must be of type string.') - - if not isinstance(run_confile["run"]["info"]["description"], str): - raise Exception('The run_confiledescription must be of type string.') - - if not isinstance(run_confile["run"]["schema"]["default_schema_id"], str): - raise Exception('The run_confile["genomicVariant"]["schema"]["default_schema_id"] must be of type string.') - - if not isinstance(run_confile["run"]["schema"]["default_schema_name"], str): - raise Exception('The run_confile["genomicVariant"]["schema"]["default_schema_name"] must be of type string.') - - if not isinstance(run_confile["run"]["schema"]["reference_to_default_schema_definition"], str): - raise Exception('The run_confile["genomicVariant"]["schema"]["reference_to_default_schema_definition"] must be of type string.') - - if not isinstance(run_confile["run"]["schema"]["default_schema_version"], str): - raise Exception('The run_confile["genomicVariant"]["schema"]["default_schema_version"] must be of type string.') - - if not isinstance(run_confile["run"]["schema"]["supported_schemas"], list): - raise Exception('The run_confile["genomicVariant"]["schema"]["supported_schemas"] must be of type list.') - - # Validate run query permissions - if not isinstance(run_confile["run"]["allow_queries_without_filters"], bool): - raise Exception('The run_confile["analysis"]["allow_queries_without_filters"] must be of type bool.') - if not isinstance(run_confile["run"]["allow_id_query"], bool): - raise Exception('The run_confile["analysis"]["allow_id_query"] must be of type bool.') # Validate beacon metadata fields if not isinstance(conf_override.config.beacon_name, str): raise Exception('The beacon_name config parameter must be a string') From 6c85fb235ee5a8edb9c33fb235b6157acb68ac25 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 14 Jul 2026 17:45:57 +0200 Subject: [PATCH 04/56] progress on implementing postgres connection --- beacon/connections/mongo/mongo-init/init.js | 10 ---------- beacon/connections/postgres/client.py | 15 +++++++++++++++ beacon/connections/postgres/init.sql | 9 +++++++++ .../models/EUCAIM/conf/entry_types/patients.yml | 2 +- requirements.txt | 4 +++- 5 files changed, 28 insertions(+), 12 deletions(-) create mode 100644 beacon/connections/postgres/client.py create mode 100644 beacon/connections/postgres/init.sql diff --git a/beacon/connections/mongo/mongo-init/init.js b/beacon/connections/mongo/mongo-init/init.js index a4112e93..f0c072d4 100644 --- a/beacon/connections/mongo/mongo-init/init.js +++ b/beacon/connections/mongo/mongo-init/init.js @@ -15,13 +15,3 @@ db.createCollection("datasets"); db.createCollection("genomicVariations"); db.createCollection("individuals"); db.createCollection("runs"); - -// Create indexes for all the entities in the database - -db.analyses.createIndex([('$**', 'text')]); -db.biosamples.createIndex([('$**', 'text')]); -db.cohorts.createIndex([('$**', 'text')]); -db.datasets.createIndex([('$**', 'text')]); -db.genomicVariations.createIndex([('$**', 'text')]); -db.individuals.createIndex([('$**', 'text')]); -db.runs.createIndex([('$**', 'text')]); diff --git a/beacon/connections/postgres/client.py b/beacon/connections/postgres/client.py new file mode 100644 index 00000000..18b0e3d9 --- /dev/null +++ b/beacon/connections/postgres/client.py @@ -0,0 +1,15 @@ +from sqlalchemy import create_engine +from sqlalchemy.engine import Engine + + +def get_client() -> Engine: + connection_string = ( + "postgresql+psycopg2://" + "postgres:your_secure_password@localhost:5432/beacon" + ) + + return create_engine( + connection_string, + pool_pre_ping=True, + echo=False, + ) \ No newline at end of file diff --git a/beacon/connections/postgres/init.sql b/beacon/connections/postgres/init.sql new file mode 100644 index 00000000..36ff48e5 --- /dev/null +++ b/beacon/connections/postgres/init.sql @@ -0,0 +1,9 @@ +CREATE TABLE IF NOT EXISTS campings ( + id SERIAL PRIMARY KEY, + name VARCHAR(255) NOT NULL, + location VARCHAR(255), + latitude DECIMAL(9,6), + longitude DECIMAL(9,6), + description TEXT, + created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP +); \ No newline at end of file diff --git a/beacon/models/EUCAIM/conf/entry_types/patients.yml b/beacon/models/EUCAIM/conf/entry_types/patients.yml index 37be9f12..c1214c95 100644 --- a/beacon/models/EUCAIM/conf/entry_types/patients.yml +++ b/beacon/models/EUCAIM/conf/entry_types/patients.yml @@ -17,7 +17,7 @@ patients: name: Patient for the set of images ontology_id: ICO:0000422 ontology_name: Patient - description: + description: patients schema: specification: EUCAIM v0 default_schema_id: EUCAIM-patient_v0.0.1 diff --git a/requirements.txt b/requirements.txt index 6a65144c..70aa94fd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -26,4 +26,6 @@ tqdm==4.66.3 obonet==0.3.1 python-dateutil==2.9.0 rfc3339_validator==0.1.4 -datamodel-code-generator==0.68.1 \ No newline at end of file +datamodel-code-generator==0.68.1 +psycopg2-binary==2.9.12 +SQLAlchemy==2.0.51 \ No newline at end of file From 1a37d8c6d56d023cc799c630c5c06022bc1c7905 Mon Sep 17 00:00:00 2001 From: costero-e Date: Thu, 16 Jul 2026 15:06:17 +0200 Subject: [PATCH 05/56] creating postgres connection --- beacon/connections/mongo/executor.py | 6 ++-- beacon/connections/postgres/client.py | 4 +-- beacon/connections/postgres/conf.py | 11 ++++++ beacon/connections/postgres/executor.py | 46 +++++++++++++++++++++++++ beacon/connections/postgres/init.sql | 34 ++++++++++++++++++ beacon/connections/postgres/ping.py | 21 +++++++++++ beacon/permissions/__main__.py | 4 +-- beacon/request/classes.py | 4 ++- beacon/tests/test_module_loaders.py | 2 +- beacon/utils/modules.py | 21 +++++------ beacon/utils/requests.py | 6 ++-- 11 files changed, 138 insertions(+), 21 deletions(-) create mode 100644 beacon/connections/postgres/conf.py create mode 100644 beacon/connections/postgres/executor.py create mode 100644 beacon/connections/postgres/ping.py diff --git a/beacon/connections/mongo/executor.py b/beacon/connections/mongo/executor.py index 2f562004..cd4b0db4 100644 --- a/beacon/connections/mongo/executor.py +++ b/beacon/connections/mongo/executor.py @@ -6,14 +6,14 @@ from pymongo.errors import ConnectionFailure from beacon.response.classes import MultipleDatasetsResponse from beacon.request.classes import RequestAttributes -from beacon.utils.modules import get_all_modules_mongo_connections_script +from beacon.utils.modules import get_all_modules_connections_script @log_with_args(config.level) async def execute_function(self, datasets: list): # Initiate the list where the different dataset classes are returned populated from the queries list_of_responses=[] # Get the function that will be the one to use for the query performed - list_of_non_collection_modules = get_all_modules_mongo_connections_script("non_collections") + list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "mongo") for non_collection_module in list_of_non_collection_modules: try: function = getattr(non_collection_module, RequestAttributes.function) @@ -44,7 +44,7 @@ async def execute_function(self, datasets: list): async def execute_collection_function(self): try: # Get the function that will be the one to use for the query performed - list_of_collection_modules = get_all_modules_mongo_connections_script("collections") + list_of_collection_modules = get_all_modules_connections_script("collections") for collection_module in list_of_collection_modules: try: function = getattr(collection_module, RequestAttributes.function) diff --git a/beacon/connections/postgres/client.py b/beacon/connections/postgres/client.py index 18b0e3d9..a6be964c 100644 --- a/beacon/connections/postgres/client.py +++ b/beacon/connections/postgres/client.py @@ -1,11 +1,11 @@ from sqlalchemy import create_engine from sqlalchemy.engine import Engine - +from beacon.connections.postgres import conf def get_client() -> Engine: connection_string = ( "postgresql+psycopg2://" - "postgres:your_secure_password@localhost:5432/beacon" + "{}:{}@{}:{}/{}".format(conf.database_user, conf.database_password, conf.database_host, conf.database_port, conf.database_name) ) return create_engine( diff --git a/beacon/connections/postgres/conf.py b/beacon/connections/postgres/conf.py new file mode 100644 index 00000000..2307df46 --- /dev/null +++ b/beacon/connections/postgres/conf.py @@ -0,0 +1,11 @@ +from dotenv import load_dotenv +import os + +postgres_conf = "beacon/connections/postgres/conf.env" +load_dotenv(postgres_conf, override=True) + +database_host = os.getenv('database_host', 'postgres') +database_port = os.getenv('database_port', str(5432)) +database_user = os.getenv('database_user', 'postgres') +database_password = os.getenv('database_password', 'your_secure_password') +database_name = os.getenv('database_name', 'beacon') \ No newline at end of file diff --git a/beacon/connections/postgres/executor.py b/beacon/connections/postgres/executor.py new file mode 100644 index 00000000..79291493 --- /dev/null +++ b/beacon/connections/postgres/executor.py @@ -0,0 +1,46 @@ +import asyncio +from concurrent.futures import ThreadPoolExecutor +from beacon.logs.logs import log_with_args +from beacon.conf.conf_override import config +from beacon.exceptions.exceptions import NoPermissionsAvailable, DatabaseIsDown +from pymongo.errors import ConnectionFailure +from beacon.response.classes import MultipleDatasetsResponse +from beacon.request.classes import RequestAttributes +from beacon.utils.modules import get_all_modules_connections_script + +@log_with_args(config.level) +async def execute_function(self, datasets: list): + self.LOG.warning('at the executor') + # Initiate the list where the different dataset classes are returned populated from the queries + list_of_responses=[] + # Get the function that will be the one to use for the query performed + list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "postgres") + self.LOG.warning(list_of_non_collection_modules) + for non_collection_module in list_of_non_collection_modules: + try: + function = getattr(non_collection_module, RequestAttributes.function) + self.LOG.warning(function) + except Exception: + continue + # Get the current process where the app is being run + loop = asyncio.get_running_loop() + self.LOG.warning(datasets) + if datasets != []: + # If there is more than one datasets to query, start a thread for each of the datasets and execute the previously chosen function in parallel and asynchronously + with ThreadPoolExecutor() as pool: + done, pending = await asyncio.wait(fs=[loop.run_in_executor(pool, function, self, dataset) for dataset in datasets], + return_when=asyncio.ALL_COMPLETED + ) + # When each of the queries finishes, append the dataset instance class populated in a list + for task in done: + responseClass= task.result() + list_of_responses.append(responseClass) + # When all the queries per dataset finish, return the array of datasets in a wrapper class of the single dataset instances + try: + return MultipleDatasetsResponse(datasets_responses=list_of_responses) + except ConnectionFailure as e: + #client.close() # It's not the same that it doesn't found the database than the connection is wrong + raise DatabaseIsDown(str(e)) + except Exception: + raise NoPermissionsAvailable("No datasets found. Check out the permissions or the datasets requested if a response was expected.") + diff --git a/beacon/connections/postgres/init.sql b/beacon/connections/postgres/init.sql index 36ff48e5..2dfc666a 100644 --- a/beacon/connections/postgres/init.sql +++ b/beacon/connections/postgres/init.sql @@ -1,9 +1,43 @@ CREATE TABLE IF NOT EXISTS campings ( id SERIAL PRIMARY KEY, + camping_id VARCHAR(100) NOT NULL, + dataset_id VARCHAR(100) NOT NULL, name VARCHAR(255) NOT NULL, location VARCHAR(255), latitude DECIMAL(9,6), longitude DECIMAL(9,6), description TEXT, created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP +); + +INSERT INTO campings ( + camping_id, + dataset_id, + name, + location, + latitude, + longitude, + description +) +VALUES +('CAMP001','campings','Green Valley','Girona',42.123456,2.654321,'Mountain campsite'), +('CAMP002','campings','Lake View','Lleida',42.245678,1.234567,'Next to a lake'), +('CAMP003','campings','Forest Retreat','Barcelona',41.567890,2.123456,'Surrounded by forest'), +('CAMP004','campings','Costa Camp','Tarragona',41.098765,1.345678,'Near the beach'), +('CAMP005','campings','Sunny Fields','Girona',42.876543,2.876543,'Family friendly'), +('CAMP006','campings','River Camp','Lleida',42.456789,0.987654,'Beside a river'), +('CAMP007','campings','Pine Woods','Barcelona',41.876543,1.987654,'Quiet natural setting'), +('CAMP008','campings','Nature Escape','Tarragona',41.654321,1.123456,'Ideal for hiking'), +('CAMP009','campings','Mountain Peak','Girona',42.765432,2.234567,'High-altitude camping'), +('CAMP010','campings','Blue Sky Camp','Lleida',42.345678,0.876543,'Panoramic views'); + +CREATE TABLE datasets ( + id TEXT PRIMARY KEY, + description TEXT +); + +INSERT INTO datasets (id, description) +VALUES ( + 'campings', + 'The dataset for campings' ); \ No newline at end of file diff --git a/beacon/connections/postgres/ping.py b/beacon/connections/postgres/ping.py new file mode 100644 index 00000000..503d5409 --- /dev/null +++ b/beacon/connections/postgres/ping.py @@ -0,0 +1,21 @@ +import asyncio + +from sqlalchemy import text +from sqlalchemy.exc import SQLAlchemyError + +from beacon.exceptions.exceptions import DatabaseIsDown + + +async def ping_database(client): + try: + def _ping(): + with client.connect() as connection: + connection.execute(text("SELECT 1")) + + await asyncio.to_thread(_ping) + return {"ok": 1} + + except SQLAlchemyError as e: + raise DatabaseIsDown(str(e)) + except Exception as e: + raise DatabaseIsDown(str(e)) \ No newline at end of file diff --git a/beacon/permissions/__main__.py b/beacon/permissions/__main__.py index e0b357cc..608cee98 100644 --- a/beacon/permissions/__main__.py +++ b/beacon/permissions/__main__.py @@ -44,12 +44,12 @@ async def get_datasets_list(self, authorized_datasets): except Exception as e: specific_datasets = [] # Get the datasets from all the databases. - list_of_datasets_confs = get_all_modules_datasets() + list_of_datasets_confs = get_all_modules_datasets(RequestAttributes.source) beacon_datasets=[] for dataset_conf in list_of_datasets_confs: try: datasets = dataset_conf.get_list_of_datasets(self) - except Exception: + except Exception as e: continue for dataset in datasets: beacon_datasets.append(dataset) diff --git a/beacon/request/classes.py b/beacon/request/classes.py index 9a02cd3d..75b415fe 100644 --- a/beacon/request/classes.py +++ b/beacon/request/classes.py @@ -73,4 +73,6 @@ def __init__(self) -> None: # Initialize the variable for the function needed to be executed for the query self.function=None # Initialize the variable for the client string needed to perform the database connection - self.client=None \ No newline at end of file + self.client=None + # Initialize the variable for database's table name + self.table=None \ No newline at end of file diff --git a/beacon/tests/test_module_loaders.py b/beacon/tests/test_module_loaders.py index e67f2c3c..ce3b464d 100644 --- a/beacon/tests/test_module_loaders.py +++ b/beacon/tests/test_module_loaders.py @@ -159,7 +159,7 @@ def fake_open(*args, **kwargs): builtins.open = fake_open importlib_module.import_module = fake_import_module - modules = module_utils.get_all_modules_datasets() + modules = module_utils.get_all_modules_datasets('mongo') # Expect only one enabled dataset module. self.assertEqual(len(modules), 1) diff --git a/beacon/utils/modules.py b/beacon/utils/modules.py index 67ac5302..a3e1abd6 100644 --- a/beacon/utils/modules.py +++ b/beacon/utils/modules.py @@ -288,8 +288,8 @@ def _model_is_enabled(models_confile, folder, subfolder=None): return False return True -def get_all_modules_mongo_connections_script(script): - """Method to get all the submodules of mongo connections per model loaded dynamically""" +def get_all_modules_connections_script(script, connection): + """Method to get all the submodules of connections per model loaded dynamically""" list_of_modules=[] # Load the configuration file for the models that are enabled with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: @@ -302,18 +302,19 @@ def get_all_modules_mongo_connections_script(script): # Get the models that are specifically enabled if not _model_is_enabled(models_confile, folder): continue + # Go over the connections for the entry types of the models enabled if "connections" in subdirs: connections = os.listdir("/beacon/models/"+folder+"/connections") for dir in connections: - if dir == 'mongo': + if dir == connection: # Get the modules names in an array - complete_module='beacon.models.'+folder+'.connections.mongo.'+script + complete_module='beacon.models.'+folder+'.connections.'+connection+'.'+script import importlib try: module = importlib.import_module(complete_module, package=None) list_of_modules.append(module) - except Exception: + except Exception as e: continue else: # Loop over the subfolders found in the mentioned path and save the ones that are active (enabled) @@ -326,15 +327,15 @@ def get_all_modules_mongo_connections_script(script): if "connections" in underdirs: connections = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/connections") for dir in connections: - if dir == 'mongo': + if dir == connection: # Get the modules names in an array - complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.mongo.'+script + complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.'+connection+'.'+script import importlib module = importlib.import_module(complete_module, package=None) list_of_modules.append(module) return list_of_modules -def get_all_modules_datasets(): +def get_all_modules_datasets(connection): """Method to get the datasets collections for each of the models to be returned""" list_of_modules=[] # Load the configuration file for the models that are enabled @@ -352,7 +353,7 @@ def get_all_modules_datasets(): if "connections" in subdirs: try: # Get the names of the collections validators to be validated and accepted - complete_module='beacon.models.'+folder+'.connections.mongo.collections' + complete_module='beacon.models.'+folder+'.connections.'+connection+'.collections' import importlib module = importlib.import_module(complete_module, package=None) list_of_modules.append(module) @@ -368,7 +369,7 @@ def get_all_modules_datasets(): if "connections" in underdirs: try: # Get the names of the collections validators to be validated and accepted - complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.mongo.collections' + complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.'+connection+'.collections' import importlib module = importlib.import_module(complete_module, package=None) list_of_modules.append(module) diff --git a/beacon/utils/requests.py b/beacon/utils/requests.py index df600d15..650ab1f7 100644 --- a/beacon/utils/requests.py +++ b/beacon/utils/requests.py @@ -188,8 +188,10 @@ def set_entry_type_configuration(self): client_function_from_module = getattr(client_module, 'get_client') client = client_function_from_module() RequestAttributes.client = client - connection = client[mongo_conf.database_name][param_value["table"]] - RequestAttributes.mongo_collection = connection + RequestAttributes.table = param_value["table"] + if RequestAttributes.source == 'mongo': + connection = client[mongo_conf.database_name][RequestAttributes.table] + RequestAttributes.mongo_collection = connection if RequestAttributes.entry_id != None: if RequestAttributes.pre_entry_type == None: RequestAttributes.function = param_value["functions"]["id_query_function_name_assigned"] From a072eec636853f3f7d14e3c7ad78c0766534135f Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 17 Jul 2026 10:49:21 +0200 Subject: [PATCH 06/56] progress on adapting connections dynamic load --- .../connections/mongo/filters/alphanumeric.py | 18 +++++++++--------- beacon/connections/mongo/filters/custom.py | 4 ++-- beacon/connections/mongo/filters/ontology.py | 4 ++-- .../mongo/filters/request_parameters.py | 4 ++-- beacon/custom_schemas/generator.py | 9 ++++++++- .../individual/beacon_individual_v2_1_0.py | 3 --- beacon/tests/test_module_loaders.py | 2 +- 7 files changed, 24 insertions(+), 20 deletions(-) diff --git a/beacon/connections/mongo/filters/alphanumeric.py b/beacon/connections/mongo/filters/alphanumeric.py index a61fa357..dafc0d11 100644 --- a/beacon/connections/mongo/filters/alphanumeric.py +++ b/beacon/connections/mongo/filters/alphanumeric.py @@ -5,7 +5,7 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config from beacon.connections.mongo.filters.format import format_value, format_operator -from beacon.utils.modules import get_all_modules_mongo_connections_script +from beacon.utils.modules import get_all_modules_connections_script from beacon.connections.mongo.filters.iso8601 import iso8601_to_number import re @@ -28,7 +28,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat pass # If the filter is a request parameter, apply the request parameters function if isRequestParameter == True: - list_modules = get_all_modules_mongo_connections_script("filters.request_parameters.alphanumeric") + list_modules = get_all_modules_connections_script("filters.request_parameters.alphanumeric", "mongo") for module in list_modules: query = module.parse_request_parameters(self, query, filter) # Otherwise, apply them as regular alphanumeric filter @@ -58,7 +58,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat query_id={} query_id[query_term]=regex_dict query['$or'].append(query_id) - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) # Otherwise, build it as a whole text match @@ -73,7 +73,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat query_id={} query_id[query_term]=filter.value query['$or'].append(query_id) - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) @@ -182,7 +182,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat dict_in={} dict_in["$regex"]=new_age_list query[filter.id] = dict_in - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) elif '<' in filter.operator: @@ -250,7 +250,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat dict_in={} dict_in["$regex"]=new_age_list query[filter.id] = dict_in - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) elif '=' in filter.operator: @@ -278,7 +278,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat dict_in={} dict_in["$regex"]=new_age_list query[filter.id] = dict_in - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) elif '.' in filter.id: @@ -289,7 +289,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat keyfilterid: { formatted_operator: formatted_value } } query[splitfilterid[0]]=dict_in - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) # If it's not an age filter, is a measurement filter @@ -336,7 +336,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, dat dict_measures={} dict_measures[measuresfield]=dict_elemmatch query = dict_measures - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) return query \ No newline at end of file diff --git a/beacon/connections/mongo/filters/custom.py b/beacon/connections/mongo/filters/custom.py index 9b4fea9a..8f77fd98 100644 --- a/beacon/connections/mongo/filters/custom.py +++ b/beacon/connections/mongo/filters/custom.py @@ -3,7 +3,7 @@ from beacon.conf.filtering_terms import alphanumeric_terms from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.utils.modules import get_all_modules_mongo_connections_script +from beacon.utils.modules import get_all_modules_connections_script @log_with_args(config.level) def apply_custom_filter(self, query: dict, filter: CustomFilter, dataset: str) -> dict: @@ -16,7 +16,7 @@ def apply_custom_filter(self, query: dict, filter: CustomFilter, dataset: str) - else: query_term = value_splitted[0] + '.label' query[query_term]=value_splitted[1] - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, {}, dataset) diff --git a/beacon/connections/mongo/filters/ontology.py b/beacon/connections/mongo/filters/ontology.py index 45c359da..14d09df6 100644 --- a/beacon/connections/mongo/filters/ontology.py +++ b/beacon/connections/mongo/filters/ontology.py @@ -4,7 +4,7 @@ from beacon.connections.mongo.client import get_client from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.utils.modules import get_all_modules_mongo_connections_script +from beacon.utils.modules import get_all_modules_connections_script @log_with_args(config.level) def apply_ontology_filter(self, query: dict, filter: OntologyFilter, request_parameters: dict, dataset: str) -> dict: @@ -125,7 +125,7 @@ def apply_ontology_filter(self, query: dict, filter: OntologyFilter, request_par new_query['$or'].append(query_id) query = new_query # Execute the cross query in case it's needed - list_modules = get_all_modules_mongo_connections_script("filters.cross_queries.cross_query") + list_modules = get_all_modules_connections_script("filters.cross_queries.cross_query", "mongo") for module in list_modules: query = module.cross_query(self, query, scope, request_parameters, dataset) return query \ No newline at end of file diff --git a/beacon/connections/mongo/filters/request_parameters.py b/beacon/connections/mongo/filters/request_parameters.py index 59049cae..f5523ec8 100644 --- a/beacon/connections/mongo/filters/request_parameters.py +++ b/beacon/connections/mongo/filters/request_parameters.py @@ -1,10 +1,10 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.utils.modules import get_all_modules_mongo_connections_script +from beacon.utils.modules import get_all_modules_connections_script @log_with_args(config.level) def request_parameters_from_modules(self, total_query, request_parameters, dataset): - list_modules = get_all_modules_mongo_connections_script("filters.request_parameters.request_parameters") + list_modules = get_all_modules_connections_script("filters.request_parameters.request_parameters", "mongo") for module in list_modules: total_query = module.request_parameters(self, total_query, request_parameters, dataset) return total_query \ No newline at end of file diff --git a/beacon/custom_schemas/generator.py b/beacon/custom_schemas/generator.py index ece6a4b1..b4e00f46 100644 --- a/beacon/custom_schemas/generator.py +++ b/beacon/custom_schemas/generator.py @@ -13,7 +13,7 @@ INPUT_BASE_DIR = Path("/beacon/custom_schemas/json") OUTPUT_BASE_DIR = Path( - "/beacon/models/EUCAIM/validator/collections/collections" + "/beacon/custom_schemas/output_schemas" ) @@ -58,6 +58,12 @@ def main(): help="Generated Python filename", ) + parser.add_argument( + "-e", + "--entry_type", + help="Name of the entry type used for naming the generated class", + ) + args = parser.parse_args() input_path = INPUT_BASE_DIR / args.input @@ -74,6 +80,7 @@ def main(): config = GenerateConfig( input_file_type=InputFileType.JsonSchema, output=output_path, + class_name=args.entry_type ) generate( diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_1_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_1_0.py index 16ef17ff..ff14ca2b 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_1_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_1_0.py @@ -46,8 +46,6 @@ class Diseases(BaseModel): stage: Optional[OntologyTerm]=None @field_validator('ageOfOnset') @classmethod - @field_validator('ageOfOnset') - @classmethod def check_ageOfOnset(cls, v: Union[str,dict]) -> Union[str,dict]: if v is None: return v @@ -65,7 +63,6 @@ def check_ageOfOnset(cls, v: Union[str,dict]) -> Union[str,dict]: except Exception: continue raise ValueError('ageOfOnset, if object, must be any format possible between age, ageRange, gestationalAge, timeInterval or OntologyTerm') - return v class Exposures(BaseModel): ageAtExposure: Age diff --git a/beacon/tests/test_module_loaders.py b/beacon/tests/test_module_loaders.py index ce3b464d..9064c181 100644 --- a/beacon/tests/test_module_loaders.py +++ b/beacon/tests/test_module_loaders.py @@ -103,7 +103,7 @@ def fake_open(*args, **kwargs): builtins.open = fake_open importlib_module.import_module = fake_import_module - modules = module_utils.get_all_modules_mongo_connections_script(script_name) + modules = module_utils.get_all_modules_connections_script(script_name, "mongo") # Only enabled models should be imported. self.assertEqual(len(modules), 1) From 142a53fce2f947047737a1778cd5539252f07db7 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 17 Jul 2026 11:56:25 +0200 Subject: [PATCH 07/56] adding postgres container --- beacon/connections/mongo/executor.py | 2 +- docker-compose.yml | 29 +++++++++++++++++++++++++++- 2 files changed, 29 insertions(+), 2 deletions(-) diff --git a/beacon/connections/mongo/executor.py b/beacon/connections/mongo/executor.py index cd4b0db4..6ec37c26 100644 --- a/beacon/connections/mongo/executor.py +++ b/beacon/connections/mongo/executor.py @@ -44,7 +44,7 @@ async def execute_function(self, datasets: list): async def execute_collection_function(self): try: # Get the function that will be the one to use for the query performed - list_of_collection_modules = get_all_modules_connections_script("collections") + list_of_collection_modules = get_all_modules_connections_script("collections", "mongo") for collection_module in list_of_collection_modules: try: function = getattr(collection_module, RequestAttributes.function) diff --git a/docker-compose.yml b/docker-compose.yml index 20696723..a39e514b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,6 +21,7 @@ services: - ./beacon/permissions:/beacon/permissions - ./beacon/models:/beacon/models - ./beacon/conf/models:/beacon/conf/models + - ./beacon/custom_schemas:/beacon/custom_schemas networks: - pub @@ -163,4 +164,30 @@ services: - pub environment: - CHOKIDAR_USEPOLLING=true - - WATCHPACK_POLLING=true \ No newline at end of file + - WATCHPACK_POLLING=true + +# Make sure not to expose port in prod + postgres: + image: postgres:16 + container_name: postgres-db + restart: unless-stopped + + environment: + POSTGRES_USER: postgres + POSTGRES_PASSWORD: your_secure_password + POSTGRES_DB: beacon + + ports: + - "5432:5432" + + volumes: + - ./beacon/connections/postgres/init.sql:/docker-entrypoint-initdb.d/init.sql + + healthcheck: + test: ["CMD-SHELL", "pg_isready -U postgres -d beacon"] + interval: 10s + timeout: 5s + retries: 5 + + networks: + - pub \ No newline at end of file From 46338e458bcdcaf0d3427bff6a830fb4adf25ab7 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 17 Jul 2026 13:49:08 +0200 Subject: [PATCH 08/56] adding version update workflow --- .../workflows/update_beacon_pi_version.yml | 65 +++++++++++++++++++ beacon/conf/api_version.py | 14 ++++ 2 files changed, 79 insertions(+) create mode 100644 .github/workflows/update_beacon_pi_version.yml create mode 100644 beacon/conf/api_version.py diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml new file mode 100644 index 00000000..f9bffb3f --- /dev/null +++ b/.github/workflows/update_beacon_pi_version.yml @@ -0,0 +1,65 @@ +name: Update API version on PR + +on: + pull_request: + types: + - opened + - edited + - synchronize + branches: + - main + +permissions: + contents: write + pull-requests: read + +jobs: + update-version: + runs-on: ubuntu-latest + + steps: + - name: Extract version from PR body + id: version + env: + PR_BODY: ${{ github.event.pull_request.body }} + run: | + VERSION=$(echo "$PR_BODY" | grep -oE 'Version: v[0-9]+\.[0-9]+\.[0-9]+' | awk '{print $2}') + + if [ -z "$VERSION" ]; then + echo "Missing version. Add 'Version: vX.Y.Z' to the PR description." + exit 1 + fi + + echo "version=$VERSION" >> "$GITHUB_OUTPUT" + + - name: Checkout PR branch + uses: actions/checkout@v4 + with: + ref: ${{ github.head_ref }} + + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version: "3.11" + + - name: Update api_version.yml + run: | + python beacon/conf/api_version.py \ + "${{ steps.version.outputs.version }}" + + - name: Commit version update + run: | + git config user.name github-actions + git config user.email github-actions@github.com + + git add beacon/conf/api_version.yml + + git commit \ + -m "Update API version to ${{ steps.version.outputs.version }}" || exit 0 + + git push origin HEAD:${{ github.head_ref }} + + - name: Create tag + run: | + git tag ${{ steps.version.outputs.version }} + git push origin ${{ steps.version.outputs.version }} \ No newline at end of file diff --git a/beacon/conf/api_version.py b/beacon/conf/api_version.py new file mode 100644 index 00000000..b785d267 --- /dev/null +++ b/beacon/conf/api_version.py @@ -0,0 +1,14 @@ +import sys +import yaml + +version = sys.argv[1] + +with open("beacon/conf/api_version.yml") as f: + api_version = yaml.safe_load(f) + +api_version["api_version"] = version + +with open("beacon/conf/api_version.yml", "w") as f: + yaml.safe_dump(api_version, f, sort_keys=False) + +print(f"API version updated to {version}") \ No newline at end of file From 0526b4135360c75b3ad3dbe404146632b669dfa4 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 17 Jul 2026 16:21:01 +0200 Subject: [PATCH 09/56] updating ri tools version --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index a39e514b..87cb3f1d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -125,7 +125,7 @@ services: - pub beacon-ri-tools: - image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.1.1 + image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.1.2 hostname: beacon-ri-tools container_name: ri-tools networks: From 5b45b9a24e67b517f2fbaff02a54db46a72c01dd Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 21 Jul 2026 15:56:29 +0200 Subject: [PATCH 10/56] more progress in alternative schemas implementation --- .gitignore | 2 +- beacon/conf/models/models_conf.yml | 5 +- .../client.py | 2 +- .../conf.py | 0 .../executor.py | 2 +- .../init.sql | 0 .../ping.py | 1 + beacon/custom_schemas/generator.py | 93 ------------------- beacon/custom_schemas/json/example.json | 80 ---------------- .../datasets/datasets_permissions.yml | 5 + 10 files changed, 13 insertions(+), 177 deletions(-) rename beacon/connections/{postgres => sqlalchemy_postgresql}/client.py (87%) rename beacon/connections/{postgres => sqlalchemy_postgresql}/conf.py (100%) rename beacon/connections/{postgres => sqlalchemy_postgresql}/executor.py (97%) rename beacon/connections/{postgres => sqlalchemy_postgresql}/init.sql (100%) rename beacon/connections/{postgres => sqlalchemy_postgresql}/ping.py (92%) delete mode 100644 beacon/custom_schemas/generator.py delete mode 100644 beacon/custom_schemas/json/example.json diff --git a/.gitignore b/.gitignore index dd045ab1..08bc2973 100644 --- a/.gitignore +++ b/.gitignore @@ -14,4 +14,4 @@ adminui/adminclient/migrations/* adminui/node_modules *.vcf.bgz beacon/conf/conf.py -models \ No newline at end of file +beacon/models/prova \ No newline at end of file diff --git a/beacon/conf/models/models_conf.yml b/beacon/conf/models/models_conf.yml index 07c06037..1288e6e1 100644 --- a/beacon/conf/models/models_conf.yml +++ b/beacon/conf/models/models_conf.yml @@ -2,4 +2,7 @@ ga4gh/beacon_v2_default_model: model_enabled: True EUCAIM: - model_enabled: False \ No newline at end of file + model_enabled: True + +prova: + model_enabled: True \ No newline at end of file diff --git a/beacon/connections/postgres/client.py b/beacon/connections/sqlalchemy_postgresql/client.py similarity index 87% rename from beacon/connections/postgres/client.py rename to beacon/connections/sqlalchemy_postgresql/client.py index a6be964c..87c411ce 100644 --- a/beacon/connections/postgres/client.py +++ b/beacon/connections/sqlalchemy_postgresql/client.py @@ -1,6 +1,6 @@ from sqlalchemy import create_engine from sqlalchemy.engine import Engine -from beacon.connections.postgres import conf +from beacon.connections.sqlalchemy_postgresql import conf def get_client() -> Engine: connection_string = ( diff --git a/beacon/connections/postgres/conf.py b/beacon/connections/sqlalchemy_postgresql/conf.py similarity index 100% rename from beacon/connections/postgres/conf.py rename to beacon/connections/sqlalchemy_postgresql/conf.py diff --git a/beacon/connections/postgres/executor.py b/beacon/connections/sqlalchemy_postgresql/executor.py similarity index 97% rename from beacon/connections/postgres/executor.py rename to beacon/connections/sqlalchemy_postgresql/executor.py index 79291493..236ba4d3 100644 --- a/beacon/connections/postgres/executor.py +++ b/beacon/connections/sqlalchemy_postgresql/executor.py @@ -14,7 +14,7 @@ async def execute_function(self, datasets: list): # Initiate the list where the different dataset classes are returned populated from the queries list_of_responses=[] # Get the function that will be the one to use for the query performed - list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "postgres") + list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "sqlalchemy_postgresql") self.LOG.warning(list_of_non_collection_modules) for non_collection_module in list_of_non_collection_modules: try: diff --git a/beacon/connections/postgres/init.sql b/beacon/connections/sqlalchemy_postgresql/init.sql similarity index 100% rename from beacon/connections/postgres/init.sql rename to beacon/connections/sqlalchemy_postgresql/init.sql diff --git a/beacon/connections/postgres/ping.py b/beacon/connections/sqlalchemy_postgresql/ping.py similarity index 92% rename from beacon/connections/postgres/ping.py rename to beacon/connections/sqlalchemy_postgresql/ping.py index 503d5409..d80ec54d 100644 --- a/beacon/connections/postgres/ping.py +++ b/beacon/connections/sqlalchemy_postgresql/ping.py @@ -6,6 +6,7 @@ from beacon.exceptions.exceptions import DatabaseIsDown +# Merge the function in the client script async def ping_database(client): try: def _ping(): diff --git a/beacon/custom_schemas/generator.py b/beacon/custom_schemas/generator.py deleted file mode 100644 index b4e00f46..00000000 --- a/beacon/custom_schemas/generator.py +++ /dev/null @@ -1,93 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import re -from pathlib import Path - -from datamodel_code_generator import ( - GenerateConfig, - InputFileType, - generate, -) - - -INPUT_BASE_DIR = Path("/beacon/custom_schemas/json") -OUTPUT_BASE_DIR = Path( - "/beacon/custom_schemas/output_schemas" -) - - -def valid_output_file(value: str) -> str: - """ - Validate that the output filename is a valid Python filename. - Allowed characters: letters, numbers, underscores. - Must end with .py. - """ - path = Path(value) - - if path.suffix != ".py": - raise argparse.ArgumentTypeError( - "Output file must have a .py extension" - ) - - if not re.fullmatch(r"[A-Za-z0-9_]+\.py", path.name): - raise argparse.ArgumentTypeError( - "Output filename can only contain letters, numbers, and underscores" - ) - - return value - - -def main(): - parser = argparse.ArgumentParser( - description="Generate Pydantic models from a JSON Schema" - ) - - parser.add_argument( - "-i", - "--input", - required=True, - help="JSON Schema filename", - ) - - parser.add_argument( - "-o", - "--output", - type=valid_output_file, - default="models.py", - help="Generated Python filename", - ) - - parser.add_argument( - "-e", - "--entry_type", - help="Name of the entry type used for naming the generated class", - ) - - args = parser.parse_args() - - input_path = INPUT_BASE_DIR / args.input - output_path = OUTPUT_BASE_DIR / args.output - - if not input_path.exists(): - raise FileNotFoundError( - f"Schema file not found: {input_path}" - ) - - print(f"Input schema: {input_path}") - print(f"Output file: {output_path}") - - config = GenerateConfig( - input_file_type=InputFileType.JsonSchema, - output=output_path, - class_name=args.entry_type - ) - - generate( - input_=input_path, - config=config, - ) - - -if __name__ == "__main__": - main() \ No newline at end of file diff --git a/beacon/custom_schemas/json/example.json b/beacon/custom_schemas/json/example.json deleted file mode 100644 index a49008d4..00000000 --- a/beacon/custom_schemas/json/example.json +++ /dev/null @@ -1,80 +0,0 @@ -{ - "$comment": "version: ga4gh-beacon-analysis-v2.0.0", - "$schema": "https://json-schema.org/draft/2020-12/schema", - "additionalProperties": true, - "description": "The `analysis` schema represents a information about the data analysis steps leading to (a set of) genomic variation call(s).", - "properties": { - "aligner": { - "description": "Name or identifier of the mapping/alignment software/pipeline", - "examples": [ - "bwa-0.7.8" - ], - "type": "string" - }, - "analysisDate": { - "description": "Date at which analysis was performed.\n", - "examples": [ - "2021-10-17" - ], - "format": "date", - "type": "string" - }, - "biosampleId": { - "description": "Local reference to the `id` of the biosample this analysis is reporting on.", - "examples": [ - "S0001", - "onekgbs-NA07346" - ], - "type": "string" - }, - "id": { - "description": "Analysis id for internal referencing; unique in the dataset.", - "type": "string" - }, - "individualId": { - "description": "Local reference to the `id` of the individual this analysis is reporting on.", - "examples": [ - "P0001", - "onekgind-NA07346" - ], - "type": "string" - }, - "pipelineName": { - "description": "Analysis pipeline and version.", - "examples": [ - "Pipeline-panel-0001-v1" - ], - "type": "string" - }, - "pipelineRef": { - "description": "Link to information about or repository of the analysis pipeline.", - "examples": [ - "https://doi.org/10.48511/workflowhub.workflow.111.1", - "https://doi.org/10.1093/bib/bbad541" - ], - "type": "string" - }, - "runId": { - "description": "Local reference to the associated experimental run.", - "examples": [ - "SRR10903401" - ], - "type": "string" - }, - "variantCaller": { - "description": "Name or identifier of the variant calling software/pipeline", - "examples": [ - "GATK4.0", - "labelSeg" - ], - "type": "string" - } - }, - "required": [ - "id", - "analysisDate", - "pipelineName" - ], - "title": "Bioinformatics analysis", - "type": "object" -} \ No newline at end of file diff --git a/beacon/permissions/datasets/datasets_permissions.yml b/beacon/permissions/datasets/datasets_permissions.yml index dc2c5e67..18135d3a 100644 --- a/beacon/permissions/datasets/datasets_permissions.yml +++ b/beacon/permissions/datasets/datasets_permissions.yml @@ -52,3 +52,8 @@ test2: default_entry_types_granularity: count entry_types_exceptions: - cohort: boolean +campings: + public: + default_entry_types_granularity: record + entry_types_exceptions: + - individual: record \ No newline at end of file From e2aafd0d0bc048c6cab2a751c1c2ed5b5e1d185b Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 24 Jul 2026 12:37:34 +0200 Subject: [PATCH 11/56] adding json stream with date accepted --- .../sqlalchemy_postgresql/executor.py | 4 ---- beacon/views/collection.py | 17 +++++++++++++++- beacon/views/non_collection.py | 20 +++++++++++++++++-- 3 files changed, 34 insertions(+), 7 deletions(-) diff --git a/beacon/connections/sqlalchemy_postgresql/executor.py b/beacon/connections/sqlalchemy_postgresql/executor.py index 236ba4d3..1c142d48 100644 --- a/beacon/connections/sqlalchemy_postgresql/executor.py +++ b/beacon/connections/sqlalchemy_postgresql/executor.py @@ -10,21 +10,17 @@ @log_with_args(config.level) async def execute_function(self, datasets: list): - self.LOG.warning('at the executor') # Initiate the list where the different dataset classes are returned populated from the queries list_of_responses=[] # Get the function that will be the one to use for the query performed list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "sqlalchemy_postgresql") - self.LOG.warning(list_of_non_collection_modules) for non_collection_module in list_of_non_collection_modules: try: function = getattr(non_collection_module, RequestAttributes.function) - self.LOG.warning(function) except Exception: continue # Get the current process where the app is being run loop = asyncio.get_running_loop() - self.LOG.warning(datasets) if datasets != []: # If there is more than one datasets to query, start a thread for each of the datasets and execute the previously chosen function in parallel and asynchronously with ThreadPoolExecutor() as pool: diff --git a/beacon/views/collection.py b/beacon/views/collection.py index 5824fe5c..3bd35fce 100644 --- a/beacon/views/collection.py +++ b/beacon/views/collection.py @@ -8,6 +8,17 @@ from beacon.views.endpoint import EndpointView from beacon.utils.modules import load_framework_module, load_source_module from beacon.utils.checks import state_check +from datetime import date as DateType +from datetime import datetime as DateTimeType +import json +from enum import Enum + +def json_default(obj): + if isinstance(obj, (DateType, DateTimeType)): + return obj.isoformat() + if isinstance(obj, Enum): + return obj.value + raise TypeError(f"Object of type {type(obj).__name__} is not JSON serializable") class CollectionEntryTypeView(EndpointView): @state_check @@ -58,4 +69,8 @@ async def handler(self): # Stdout the information about what entry type failed about it not being according to the spec raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Collection object class collected - return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file + return web.Response( + text=json.dumps(response_obj, default=json_default), + status=200, + content_type="application/json", + ) \ No newline at end of file diff --git a/beacon/views/non_collection.py b/beacon/views/non_collection.py index f719e6cc..4e62e2ad 100644 --- a/beacon/views/non_collection.py +++ b/beacon/views/non_collection.py @@ -2,7 +2,7 @@ from beacon.conf.conf_override import config import aiohttp.web as web from beacon.permissions.__main__ import query_permissions -from bson import json_util +import json from beacon.request.classes import RequestAttributes from beacon.budget.__main__ import load_module_to_insert_budget from pydantic import ValidationError @@ -11,6 +11,17 @@ from beacon.response.includeResultsetResponses import include_resultSet_responses from beacon.utils.modules import load_framework_module, load_source_module from beacon.utils.checks import state_check +from datetime import date as DateType +from datetime import datetime as DateTimeType +import json +from enum import Enum + +def json_default(obj): + if isinstance(obj, (DateType, DateTimeType)): + return obj.isoformat() + if isinstance(obj, Enum): + return obj.value + raise TypeError(f"Object of type {type(obj).__name__} is not JSON serializable") class EntryTypeView(EndpointView): @state_check @@ -82,4 +93,9 @@ async def handler(self, datasets, username, time_now): if time_now is not None: load_module_to_insert_budget(self, username, time_now) # Give a HTTP response with json data application and a 200 status, and the NonCollection object class collected - return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file + + return web.Response( + text=json.dumps(response_obj, default=json_default), + status=200, + content_type="application/json", + ) \ No newline at end of file From 1a354963c4fab369dbfdcaa9dedd4ca4d249c8b0 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 27 Jul 2026 14:20:46 +0200 Subject: [PATCH 12/56] adding new ri tools version and isDeprecated --- beacon/validator/configuration.py | 4 ++-- docker-compose.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/beacon/validator/configuration.py b/beacon/validator/configuration.py index f27ccdc7..6f687848 100644 --- a/beacon/validator/configuration.py +++ b/beacon/validator/configuration.py @@ -434,10 +434,10 @@ def check_configuration( for property, value in configuration.items(): # Only two dataset-level properties are supported - if property not in ['isTest', 'isSynthetic']: + if property not in ['isTest', 'isSynthetic', 'isDeprecated']: raise Exception( "keys for datasets properties in datasets_conf.yml " - "have to be isTest or isSynthetic" + "have to be isTest, isDeprecated or isSynthetic" ) # Dataset properties must be booleans diff --git a/docker-compose.yml b/docker-compose.yml index 87cb3f1d..07801204 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -125,7 +125,7 @@ services: - pub beacon-ri-tools: - image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.1.2 + image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.2.0 hostname: beacon-ri-tools container_name: ri-tools networks: From 032a9f40428c40da22d8c36e028e3accb87bca4a Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 10:50:18 +0200 Subject: [PATCH 13/56] adding connections enabling by conf --- .../workflows/update_beacon_pi_version.yml | 1 + beacon/conf/connections/connections_conf.yml | 5 ++++ beacon/conf/datasets/datasets_conf.yml | 1 + .../sqlalchemy_postgresql/__init__.py | 0 beacon/utils/modules.py | 26 ++++++++++++++----- beacon/utils/shutters.py | 1 + beacon/validator/configuration.py | 18 +++++++++++-- docker-compose.yml | 7 ++--- 8 files changed, 46 insertions(+), 13 deletions(-) create mode 100644 beacon/conf/connections/connections_conf.yml create mode 100644 beacon/connections/sqlalchemy_postgresql/__init__.py diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml index f9bffb3f..cdbab8ec 100644 --- a/.github/workflows/update_beacon_pi_version.yml +++ b/.github/workflows/update_beacon_pi_version.yml @@ -8,6 +8,7 @@ on: - synchronize branches: - main + - develop permissions: contents: write diff --git a/beacon/conf/connections/connections_conf.yml b/beacon/conf/connections/connections_conf.yml new file mode 100644 index 00000000..5fb3d67b --- /dev/null +++ b/beacon/conf/connections/connections_conf.yml @@ -0,0 +1,5 @@ +mongo: + connection_enabled: True + +sqlalchemy_postgresql: + connection_enabled: False \ No newline at end of file diff --git a/beacon/conf/datasets/datasets_conf.yml b/beacon/conf/datasets/datasets_conf.yml index 5efb4c1a..e6ca52d7 100644 --- a/beacon/conf/datasets/datasets_conf.yml +++ b/beacon/conf/datasets/datasets_conf.yml @@ -6,6 +6,7 @@ test: test2: isSynthetic: true isTest: true + isDeprecated: true DemoDatasetBreast: isSynthetic: true isTest: true \ No newline at end of file diff --git a/beacon/connections/sqlalchemy_postgresql/__init__.py b/beacon/connections/sqlalchemy_postgresql/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/beacon/utils/modules.py b/beacon/utils/modules.py index a3e1abd6..8fe84b6f 100644 --- a/beacon/utils/modules.py +++ b/beacon/utils/modules.py @@ -43,6 +43,14 @@ async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=N pfile.close() # Check all the model folders that are found in the beacon/models path dirs = os.listdir("/beacon/models") + # Load conf file for connection to check which are enabled + with open('/beacon/conf/connections/connections_conf.yml') as infile: + connections_conf=yaml.safe_load(infile) + # Get array of enabled connections + connections_enabled=[] + for k, v in connections_conf.items(): + if v['connection_enabled']==True: + connections_enabled.append(k) # Initialize an array to keep what database connections are performed (and needed to have checks) database_connections_to_check=[] # Loop over the folders found in the mentioned path and save the ones that are active (enabled) @@ -65,7 +73,8 @@ async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=N if entry_type == None or conf_entry_type_param['endpoint_name'] == entry_type and pre_entry_type == None or conf_entry_type_param['endpoint_name'] == pre_entry_type: if conf_entry_type_param['entry_type_enabled'] == True: if conf_entry_type_param['connection']['name'] not in database_connections_to_check: - database_connections_to_check.append(conf_entry_type_param['connection']['name']) + if conf_entry_type_param['connection']['name'] in connections_enabled: + database_connections_to_check.append(conf_entry_type_param['connection']['name']) # Do the same for the lookups inside the entry types for conf_param, value_param in conf_entry_type_param.items(): if conf_param == 'lookups': @@ -74,9 +83,11 @@ async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=N if pre_entry_type != None and entry_type != None: if lookup_value['endpoint_name'] == pre_entry_type+'/{id}/'+entry_type: if lookup_value['connection']['name'] not in database_connections_to_check: - database_connections_to_check.append(lookup_value['connection']['name']) + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) else: - database_connections_to_check.append(lookup_value['connection']['name']) + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) # Loop over the subfolders found in the targeted path and save the ones that are active (enabled) else: for subfolder in subdirs: @@ -98,7 +109,8 @@ async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=N if entry_type == None or conf_entry_type_param['endpoint_name'] == entry_type and pre_entry_type == None or conf_entry_type_param['endpoint_name'] == pre_entry_type: if conf_entry_type_param['entry_type_enabled'] == True: if conf_entry_type_param['connection']['name'] not in database_connections_to_check: - database_connections_to_check.append(conf_entry_type_param['connection']['name']) + if conf_entry_type_param['connection']['name'] in connections_enabled: + database_connections_to_check.append(conf_entry_type_param['connection']['name']) # Do the same for the lookups inside the entry types for conf_param, value_param in conf_entry_type_param.items(): if conf_param == 'lookups': @@ -107,9 +119,11 @@ async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=N if pre_entry_type != None and entry_type != None: if lookup_value['endpoint_name'] == pre_entry_type+'/{id}/'+entry_type: if lookup_value['connection']['name'] not in database_connections_to_check: - database_connections_to_check.append(lookup_value['connection']['name']) + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) else: - database_connections_to_check.append(lookup_value['connection']['name']) + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) # Loop over the database connections collected for folder in database_connections_to_check: # Dynamically load all the modules to ping each of the databases diff --git a/beacon/utils/shutters.py b/beacon/utils/shutters.py index 4a3d5c98..313808a2 100644 --- a/beacon/utils/shutters.py +++ b/beacon/utils/shutters.py @@ -63,6 +63,7 @@ async def _graceful_shutdown(app, LOG, runner, stop_event=None): "/beacon/conf/conf_default.py", "/beacon/models", "/beacon/conf/models", + "/beacon/conf/connections", "/beacon/connections/mongo/conf.py" ] diff --git a/beacon/validator/configuration.py b/beacon/validator/configuration.py index 6f687848..d9c26fd9 100644 --- a/beacon/validator/configuration.py +++ b/beacon/validator/configuration.py @@ -43,6 +43,14 @@ def check_logs_configuration(): def check_configuration( LOG=None ): + # Load conf file for connection to check which are enabled + with open('/beacon/conf/connections/connections_conf.yml') as infile: + connections_conf=yaml.safe_load(infile) + # Get array of enabled connections + connections_enabled=[] + for k, v in connections_conf.items(): + if v['connection_enabled']==True: + connections_enabled.append(k) all_conf_files=get_modules_confiles() # ------------------------------------------------------------------------- # Entry type enablement validation @@ -73,6 +81,12 @@ def check_configuration( "{}granularity must be one string between boolean, count or record".format(k) ) + if v["connection"]["name"] not in connections_enabled: + raise Exception( + 'The connection {} for {} records needs to be enabled in case you want to use it'.format( + v["connection"]["name"], k + ) + ) # Validate the configured backend for run records. if v["connection"]["name"] not in [ @@ -424,12 +438,12 @@ def check_configuration( # Validate datasets configuration file try: with open("/beacon/conf/datasets/datasets_conf.yml", 'r') as pfile: - datasets = yaml.safe_load(pfile) + datasets_conf = yaml.safe_load(pfile) pfile.close() # Validate each dataset configuration block - for dataset_name, configuration in datasets.items(): + for dataset_name, configuration in datasets_conf.items(): for property, value in configuration.items(): diff --git a/docker-compose.yml b/docker-compose.yml index 07801204..07366fe6 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -125,7 +125,7 @@ services: - pub beacon-ri-tools: - image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.2.0 + image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.3.0 hostname: beacon-ri-tools container_name: ri-tools networks: @@ -166,7 +166,7 @@ services: - CHOKIDAR_USEPOLLING=true - WATCHPACK_POLLING=true -# Make sure not to expose port in prod + postgres: image: postgres:16 container_name: postgres-db @@ -177,9 +177,6 @@ services: POSTGRES_PASSWORD: your_secure_password POSTGRES_DB: beacon - ports: - - "5432:5432" - volumes: - ./beacon/connections/postgres/init.sql:/docker-entrypoint-initdb.d/init.sql From 442e8fbad3bf12e5cd43f0d273358f337511c871 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 11:44:51 +0200 Subject: [PATCH 14/56] adding test for checking alternative schema --- README.md | 2 ++ beacon/auth/tests.py | 2 +- beacon/conf/models/models_conf.yml | 3 -- .../datasets/datasets_permissions.yml | 7 +--- beacon/tests/__main__.py | 35 +++++++++++++++++++ beacon/tests/dif_conf_test.py | 9 +---- 6 files changed, 40 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 879cd09a..ee8596f5 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ Welcome to Beacon v2 Production Implementation (B2PI). This is an application that makes an instance of Beacon v2 be production ready. +Note: admin-ui container is a new extra service that will create a UI to manage conf but is still in development, deploy the rest of the services for now, please. + ## Documentation Please, go to [CRG Beacon docs website](https://b2ri-documentation-demo.ega-archive.org/) to know how to use Beacon v2 Production Implementation. diff --git a/beacon/auth/tests.py b/beacon/auth/tests.py index 965f1219..90b67017 100644 --- a/beacon/auth/tests.py +++ b/beacon/auth/tests.py @@ -13,7 +13,7 @@ import beacon.conf.conf_override as conf_override # for keycloak, create aud in mappers, with custom, aud and beacon for audience -mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.eyJleHAiOjE3Nzk3OTg1MzksImlhdCI6MTc3OTc5ODIzOSwianRpIjoiZDQwNGEyNWEtMjk0Yy00M2RjLWE0OTMtNzZiM2M4NjJjYTc4IiwiaXNzIjoiaHR0cDovL2xvY2FsaG9zdDo4MDgwL2F1dGgvcmVhbG1zL0JlYWNvbiIsImF1ZCI6ImJlYWNvbiIsInN1YiI6IjQ3ZWZmMWIxLTc2MjEtNDU3MC1hMGJiLTAxYTcxOWZiYTBhMiIsInR5cCI6IkJlYXJlciIsImF6cCI6ImJlYWNvbiIsInNlc3Npb25fc3RhdGUiOiI0NDA1OTk3Zi1kNzdkLTQ4YWYtODdmNy1mZTE3ZDJjYTlmZGIiLCJhY3IiOiIxIiwic2NvcGUiOiJvcGVuaWQgcHJvZmlsZSBlbWFpbCBtaWNyb3Byb2ZpbGUtand0Iiwic2lkIjoiNDQwNTk5N2YtZDc3ZC00OGFmLTg3ZjctZmUxN2QyY2E5ZmRiIiwidXBuIjoiamFuZSIsImVtYWlsX3ZlcmlmaWVkIjpmYWxzZSwibmFtZSI6IkphbmUgU21pdGgiLCJncm91cHMiOlsib2ZmbGluZV9hY2Nlc3MiLCJ1bWFfYXV0aG9yaXphdGlvbiIsIm9mZmxpbmVfYWNjZXNzIiwidW1hX2F1dGhvcml6YXRpb24iXSwicHJlZmVycmVkX3VzZXJuYW1lIjoiamFuZSIsImdpdmVuX25hbWUiOiJKYW5lIiwiZmFtaWx5X25hbWUiOiJTbWl0aCIsImVtYWlsIjoiamFuZS5zbWl0aEBiZWFjb24uZ2E0Z2gifQ.YFtQijg_AxZNytFtcA0EnVUmbnbecpMo2R-fbRCkD6QDY-I2YWV_Glww0yCU_Yp17a5r60uYvotfIcpLKnWMduBLPeP7pyj9UAM_LtidvIKhpQBTQ8azf4eLHEv2Ju0hYDa_24c1u8UKDg6Jqz40gzV4Z7QRIhKhzqBXTdxo5TlIzYZLtzhqx91gVp9SIqaURUBo4wxqisxnFbsOc-J-IQmOw0OwbzB1f7ugG_xXP-wbJ1SbqbeyaB8pwAo7_dkfWezuhBsCdfhcGuAyvn49KPubgGnenKY3jUVzVxE9MbslKuBlLg_A7c5UNnuQ2vLW77jm6zMGRDPjRjoTIHq1bA' +mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.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.U_5ukvmexZBQOVczz3B-NFsPzhpuVpkrNve7RYgns3L7rCVbkvDScX7sf3zcLoYfT8ndY-fwlrIjz5e_P0MpCbT9IkkSZlDgZJWFfJ706CKkyHil0X2cwKLTNlhTeGeBeP5YsgHByl7rqzfsBcfj-pIWBDXJ0LmaqlcOZapjKcKroKx4dZ-bKxdO3anZ3ejW9GcWwooaKsSRdJ0DvMGDk1jCd2a9jzbYG1OvQ-eReQNREkM0FubM4wL2sZyzB71wpRT5pEIqOOju8ZGjpU0WaCTMsiiyk8nCK7VtfkSxNLF-CUeshfJbl84MXNQ6pOJQ5JxalU_ear9PyfILZyDuig' mock_access_token_false = 'public' #audit --> TODO: get very specific information that we are interested in saving and keeping it (example: what individuals were returned in response) diff --git a/beacon/conf/models/models_conf.yml b/beacon/conf/models/models_conf.yml index 1288e6e1..5453d1a1 100644 --- a/beacon/conf/models/models_conf.yml +++ b/beacon/conf/models/models_conf.yml @@ -2,7 +2,4 @@ ga4gh/beacon_v2_default_model: model_enabled: True EUCAIM: - model_enabled: True - -prova: model_enabled: True \ No newline at end of file diff --git a/beacon/permissions/datasets/datasets_permissions.yml b/beacon/permissions/datasets/datasets_permissions.yml index 18135d3a..ae775138 100644 --- a/beacon/permissions/datasets/datasets_permissions.yml +++ b/beacon/permissions/datasets/datasets_permissions.yml @@ -51,9 +51,4 @@ test2: registered: default_entry_types_granularity: count entry_types_exceptions: - - cohort: boolean -campings: - public: - default_entry_types_granularity: record - entry_types_exceptions: - - individual: record \ No newline at end of file + - cohort: boolean \ No newline at end of file diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index 83cebe94..ca39966b 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -7031,6 +7031,41 @@ def fake_exit(code): loop.run_until_complete(test_draining_state(self)) loop.run_until_complete(client.close()) + + def test_main_check_post_alternative_schema(self): + # Cross-query: analysis filter applied to cohort endpoint + with loop_context() as loop: + app = create_app() + client = TestClient(TestServer(app), loop=loop) + loop.run_until_complete(client.start_server()) + + async def test_check_post_alternative_schema_works(): + # Analysis-level metadata used to filter cohort results + resp = await client.post( + conf_override.config.uri_subpath + "/" + + individual["individual"]["endpoint_name"], + json={ + "meta": {"apiVersion": "2.0", "requestedSchemas": [{"schema": "beacon-individual-v2.1.0"}]}, + "query": { + "includeResultsetResponses": "HIT", + "pagination": {"skip": 0, "limit": 10}, + "testMode": True, + "requestedGranularity": "record" + } + } + ) + + assert resp.status == 200 + + responsetext = await resp.text() + responsedict = json.loads(responsetext) + + # At least one cohort expected to match + assert responsedict["meta"]["returnedSchemas"][0]["schema"] == 'beacon-individual-v2.1.0' + + loop.run_until_complete(test_check_post_alternative_schema_works()) + loop.run_until_complete(client.close()) + class AsyncTest(unittest.IsolatedAsyncioTestCase): # Starts a background API server using asyncio and waits briefly for it to initialize. diff --git a/beacon/tests/dif_conf_test.py b/beacon/tests/dif_conf_test.py index 5a893bc8..9d68921c 100644 --- a/beacon/tests/dif_conf_test.py +++ b/beacon/tests/dif_conf_test.py @@ -678,14 +678,7 @@ def test_main_check_configuration_http(self): async def test_check_configuration_http(): # Verify configuration checker accepts HTTPS scheme check_configuration( - LOG=initialize_logger(config.level), - analysis_confile=analysis, - biosample_confile=biosample, - cohort_confile=cohort, - dataset_confile=dataset, - genomicVariant_confile=genomicVariant, - individual_confile=individual, - run_confile=run + LOG=initialize_logger(config.level) ) loop.run_until_complete(test_check_configuration_http()) From b04659c99c3b4f5edc909d0f7a5a34c65703b9c0 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 12:25:03 +0200 Subject: [PATCH 15/56] adding lookups checks in configuration --- beacon/validator/configuration.py | 38 +++++++++++++++++++++++++++++-- 1 file changed, 36 insertions(+), 2 deletions(-) diff --git a/beacon/validator/configuration.py b/beacon/validator/configuration.py index d9c26fd9..0f979163 100644 --- a/beacon/validator/configuration.py +++ b/beacon/validator/configuration.py @@ -63,7 +63,7 @@ def check_configuration( pass else: raise Exception( - "{}.entry_type_enabled variable from {}.py must be boolean".format( + "{}.entry_type_enabled variable from {}.yml must be boolean".format( k, k ) ) @@ -88,7 +88,7 @@ def check_configuration( ) ) - # Validate the configured backend for run records. + # Validate the configured backend for records. if v["connection"]["name"] not in [ name for name in os.listdir("/beacon/connections") @@ -99,6 +99,15 @@ def check_configuration( v["connection"]["name"], k ) ) + + if v["response_type"] in ["collection", "non_collection"]: + pass + else: + raise Exception( + "{}.response_type variable from {}.yml must be one between collection or non_collection".format( + k, k + ) + ) # ------------------------------------------------------------------------- # Endpoint name validation @@ -161,6 +170,31 @@ def check_configuration( if not isinstance(v["allow_id_query"], bool): raise Exception('The {} allow id query must be of type bool.'.format(k)) + + # Check settings for lookups are correct + for klook, vlook in v["lookups"].items(): + if vlook["connection"]["name"] not in connections_enabled: + raise Exception( + 'The connection {} for lookup {} of {} records needs to be enabled in case you want to use it'.format( + vlook["connection"]["name"], klook, k + ) + ) + if isinstance(vlook["endpoint_enabled"], bool): + pass + else: + raise Exception( + "lookup {}.endpoint_enabled variable from {}.yml must be boolean".format( + klook, k + ) + ) + if vlook["response_type"] in ["collection", "non_collection"]: + pass + else: + raise Exception( + "lookup {}.response_type variable from {}.yml must be one between collection or non_collection".format( + klook, k + ) + ) # ------------------------------------------------------------------------- # Beacon URI validation From 46ac096fcdf67a93912a87b18eb55074ed066d2c Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 12:51:16 +0200 Subject: [PATCH 16/56] adding documentation for alternative schemas usage --- .../workflows/update_beacon_pi_version.yml | 4 ++++ README.md | 21 +++++++++++++++++++ 2 files changed, 25 insertions(+) diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml index cdbab8ec..61241d29 100644 --- a/.github/workflows/update_beacon_pi_version.yml +++ b/.github/workflows/update_beacon_pi_version.yml @@ -19,6 +19,7 @@ jobs: runs-on: ubuntu-latest steps: + - name: Extract version from PR body id: version env: @@ -33,6 +34,9 @@ jobs: echo "version=$VERSION" >> "$GITHUB_OUTPUT" + - name: Install PyYAML + run: pip install pyyaml==6.0.1 + - name: Checkout PR branch uses: actions/checkout@v4 with: diff --git a/README.md b/README.md index ee8596f5..34513303 100644 --- a/README.md +++ b/README.md @@ -758,6 +758,27 @@ Now state checks are available through `/health` endpoint. The implemented check ![MongoDB vulnerabilities](https://github.com/EGA-archive/beacon-production-prototype/blob/main/ri-tools/files/Machine_State_v3.jpg) +## Alternative Schemas + +Now you can also have your own "alternative" schemas included in a plugged model. For that purpose, you will need to have the JSON schema reference and have pydantic's datamodel-code-generator framework installed. To generate the schema, you will need to execute the following command: + +```bash +datamodel-codegen --url --input-file-type jsonschema --output --class-name --allow-remote-refs +``` +Example: for analysis, you need to name the class-name as Analysis. + +The name of the python script needs to be separated by underscores. If you include versions, at them at the end, like analysis_schema_v1_0_0.py + +After that include it in the models..validators. folder, and then make sure you add it in the supported schemas of models..conf.entry_types. + +Note: In case there are fields that are named different as in the original schemas but are the same, you will need to add an alias for the property modifying the generated schemas by datamodel-codegen, in order to be able to map it to the original property name and is compatible with the original spec's schema. + +Example: + +```bash +sampleTypeAtTheOrigin: str = Field(alias='sampleOriginType') # output: sampleOriginType +``` + ## Fix for MongoDB exploit (CVE-2025-14847) Beacon PI repository has been updated so the exploit for MongoDB (CVE-2025-14847) is not an issue anymore. In order to do that, the following points have been implemented: From 009edafcbdd3aac92255eda68cdff5f673bc44b9 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 12:53:49 +0200 Subject: [PATCH 17/56] fixing update script --- .github/workflows/update_beacon_pi_version.yml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml index 61241d29..1866571f 100644 --- a/.github/workflows/update_beacon_pi_version.yml +++ b/.github/workflows/update_beacon_pi_version.yml @@ -34,9 +34,6 @@ jobs: echo "version=$VERSION" >> "$GITHUB_OUTPUT" - - name: Install PyYAML - run: pip install pyyaml==6.0.1 - - name: Checkout PR branch uses: actions/checkout@v4 with: @@ -47,6 +44,15 @@ jobs: with: python-version: "3.11" + - name: Install PyYAML + run: | + python -m pip install --upgrade pip + python -m pip install pyyaml==6.0.1 + + - name: Verify PyYAML installation + run: | + python -c "import sys; print(sys.executable); import yaml; print(yaml.__version__)" + - name: Update api_version.yml run: | python beacon/conf/api_version.py \ From 991e6604d2015916684dfca670e72905ad44874a Mon Sep 17 00:00:00 2001 From: github-actions Date: Fri, 31 Jul 2026 10:54:10 +0000 Subject: [PATCH 18/56] Update API version to v2.3.0 --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index 814d2dd3..492eabc9 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.2.4 +api_version: v2.3.0 From 0f931cf8fcf24599003b66887ec23d75d52203ed Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 15:54:13 +0200 Subject: [PATCH 19/56] adding version 2.2.0 schemas as default --- .../connections/mongo/data/test/analyses.json | 18 +- .../mongo/data/test/biosamples.json | 1444 ++++-- .../mongo/data/test/caseLevelData.json | 616 ++- .../connections/mongo/data/test/cohorts.json | 261 +- .../connections/mongo/data/test/datasets.json | 23 +- .../mongo/data/test/individuals.json | 4063 +---------------- .../conf/entry_types/analysis.yml | 2 +- .../conf/entry_types/biosample.yml | 2 +- .../conf/entry_types/cohort.yml | 2 +- .../conf/entry_types/dataset.yml | 2 +- .../conf/entry_types/genomicVariant.yml | 2 +- .../conf/entry_types/individual.yml | 2 +- .../conf/entry_types/run.yml | 2 +- .../cohort/beacon_cohort_v2_2_0.py | 789 +++- .../dataset/beacon_dataset_v2_2_0.py | 422 +- .../analysis/beacon_analysis_v2_2_0.py | 68 +- .../biosample/beacon_biosample_v2_2_0.py | 750 ++- .../beacon_genomicVariant_v2_2_0.py | 1014 +++- .../individual/beacon_individual_v2_2_0.py | 819 +++- .../non_collections/run/beacon_run_v2_2_0.py | 293 +- 20 files changed, 5751 insertions(+), 4843 deletions(-) diff --git a/beacon/connections/mongo/data/test/analyses.json b/beacon/connections/mongo/data/test/analyses.json index 454a74b1..f25032d6 100644 --- a/beacon/connections/mongo/data/test/analyses.json +++ b/beacon/connections/mongo/data/test/analyses.json @@ -1,17 +1 @@ -[ - { - "aligner": "bwa-0.7.8", - "analysisDate": "2021-10-17", - "biosampleId": "SAMPLE1", - "id": "EGA-testing", - "individualId": "SAMPLE1", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, - "pipelineName": "Pipeline-panel-0001-v1", - "pipelineRef": "https://doi.org/10.48511/workflowhub.workflow.111.1", - "runId": "EGAR5000XXX", - "variantCaller": "GATK4.0", - "datasetId": "test" - } -] \ No newline at end of file +[{"aligner": "bwa-0.7.8", "analysisDate": "2021-10-17", "biosampleId": "EGA-testing", "id": "EGA-testing", "individualId": "EGA", "info": {}, "pipelineName": "Pipeline-panel-0001-v1", "pipelineRef": "https://doi.org/10.48511/workflowhub.workflow.111.1", "runId": "EGAR5000XXX", "variantCaller": "GATK4.0", "datasetId": "test", "_id": "2e8d3e8dcf5a492448e1703c2c99ed5ee4370a1152f1983b3cf11e3e9cab2033"}] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/biosamples.json b/beacon/connections/mongo/data/test/biosamples.json index 19a86125..105a43e1 100644 --- a/beacon/connections/mongo/data/test/biosamples.json +++ b/beacon/connections/mongo/data/test/biosamples.json @@ -5,7 +5,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -13,14 +13,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE1", "individualId": "SAMPLE1", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -29,17 +27,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 5 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -52,32 +69,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -87,12 +111,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0004718", + "label": "breast lobe" }, "sampleProcessing": { "id": "EFO:0009129", @@ -110,7 +134,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "ff488bccc94cd20e15ce2b9c56e6e0588b88acdf4ce205f10ead3323e77e42ec" }, { "biosampleStatus": { @@ -118,7 +143,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -126,14 +151,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE2", "individualId": "SAMPLE2", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -142,17 +165,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 6 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -165,32 +207,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -200,12 +249,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0004718", + "label": "breast lobe" }, "sampleProcessing": { "id": "EFO:0009129", @@ -216,14 +265,15 @@ "label": "freezing storage" }, "tumorGrade": { - "id": "NCIT:C28080", - "label": "Grade 3a" + "id": "NCIT:C28078", + "label": "Grade 2" }, "tumorProgression": { "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "d94ae1b61b45922e9475031b62812039bbccde2c423ef13ec75b127ee2e5551e" }, { "biosampleStatus": { @@ -231,7 +281,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -239,14 +289,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE3", "individualId": "SAMPLE3", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -255,17 +303,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 7 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -278,32 +345,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -313,12 +387,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0004718", + "label": "breast lobe" }, "sampleProcessing": { "id": "EFO:0009129", @@ -336,7 +410,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "067a3d071b0e7b68d89e1797a26d5d0959f6038447bb540bdbf2587463a167d9" }, { "biosampleStatus": { @@ -344,7 +419,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -352,14 +427,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE4", "individualId": "SAMPLE4", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -368,17 +441,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 8 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -391,32 +483,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -426,12 +525,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0004718", + "label": "breast lobe" }, "sampleProcessing": { "id": "EFO:0009129", @@ -449,7 +548,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "77779f47088ed250b081ddb1933705fda527c10b0a47fab5852f78ecc3b7c56f" }, { "biosampleStatus": { @@ -457,7 +557,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -465,14 +565,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE5", "individualId": "SAMPLE5", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -481,17 +579,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 9 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -504,32 +621,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -539,12 +663,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0004718", + "label": "breast lobe" }, "sampleProcessing": { "id": "EFO:0009129", @@ -555,14 +679,15 @@ "label": "freezing storage" }, "tumorGrade": { - "id": "NCIT:C28080", - "label": "Grade 3a" + "id": "NCIT:C28078", + "label": "Grade 2" }, "tumorProgression": { "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "d7f8eebbb7d83672cd26d355e1804f6d1258306f5a8f19c5576755c7c4625497" }, { "biosampleStatus": { @@ -570,7 +695,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -578,14 +703,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE6", "individualId": "SAMPLE6", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -594,17 +717,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 10 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -617,32 +759,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -652,12 +801,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0004718", + "label": "breast lobe" }, "sampleProcessing": { "id": "EFO:0009129", @@ -675,7 +824,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "e2054e5807803241be4a84c28fb45cf4a483f420bb66b137d925f1219277fa0f" }, { "biosampleStatus": { @@ -683,7 +833,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -691,14 +841,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE7", "individualId": "SAMPLE7", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -707,17 +855,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 11 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -730,32 +897,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -765,12 +939,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000912", + "label": "nasal mucosa" }, "sampleProcessing": { "id": "EFO:0009129", @@ -788,7 +962,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "66a1a8359b6bb0d081d029de2aee209cc743bdf7dee91913797e0bf6a457b0f3" }, { "biosampleStatus": { @@ -796,7 +971,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -804,14 +979,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE8", "individualId": "SAMPLE8", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -820,17 +993,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 12 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -843,32 +1035,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -878,12 +1077,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000912", + "label": "nasal mucosa" }, "sampleProcessing": { "id": "EFO:0009129", @@ -901,7 +1100,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "33e92a14b9f93f99c3defc33d5f74ff324025bf13754f0fd4121511202da95d9" }, { "biosampleStatus": { @@ -909,7 +1109,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -917,14 +1117,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4194", + "label": "Invasive Breast Carcinoma of No Special Type" }, "id": "SAMPLE9", "individualId": "SAMPLE9", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -933,17 +1131,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 13 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -956,32 +1173,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -991,12 +1215,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000912", + "label": "nasal mucosa" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1007,14 +1231,15 @@ "label": "freezing storage" }, "tumorGrade": { - "id": "NCIT:C28080", - "label": "Grade 3a" + "id": "NCIT:C28078", + "label": "Grade 2" }, "tumorProgression": { "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "8454abd81a22b9e81267d0a53a808caec69e854d230dde1ba376d4baa3196258" }, { "biosampleStatus": { @@ -1022,7 +1247,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1030,14 +1255,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE10", "individualId": "SAMPLE10", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1046,17 +1269,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 14 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1069,32 +1311,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1104,12 +1353,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000671", + "label": "kidney" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1127,7 +1376,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "0dbf4256bb973edd83c6c16efcdfaaa9abba2f077dc1592a46553100dbcc256a" }, { "biosampleStatus": { @@ -1135,7 +1385,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1143,14 +1393,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE11", "individualId": "SAMPLE11", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1159,17 +1407,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 15 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1182,32 +1449,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1217,12 +1491,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000671", + "label": "kidney" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1240,7 +1514,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "a9974d5f223c9167e1f4854f3dde13ee4a06d26c433c3f6b8659c58c1f6b817a" }, { "biosampleStatus": { @@ -1248,7 +1523,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1256,14 +1531,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE12", "individualId": "SAMPLE12", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1272,17 +1545,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 16 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1295,32 +1587,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1330,12 +1629,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000671", + "label": "kidney" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1353,7 +1652,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "0a704be036c7e62ef2fefc1f16759556b399f9914cbe3e87c3a46d7238408cac" }, { "biosampleStatus": { @@ -1361,7 +1661,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1369,14 +1669,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE13", "individualId": "SAMPLE13", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1385,17 +1683,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 17 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1408,32 +1725,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1443,12 +1767,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000671", + "label": "kidney" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1459,14 +1783,15 @@ "label": "freezing storage" }, "tumorGrade": { - "id": "NCIT:C28080", - "label": "Grade 3a" + "id": "NCIT:C28078", + "label": "Grade 2" }, "tumorProgression": { "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "f49c68c03c7110235abcdadbac301d62c69e340f7f9805d9c035a1ac07f7e555" }, { "biosampleStatus": { @@ -1474,7 +1799,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1482,14 +1807,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE14", "individualId": "SAMPLE14", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1498,17 +1821,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 18 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1521,32 +1863,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1556,12 +1905,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000199", + "label": "cardiac muscle" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1579,7 +1928,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "e0082f82219b17d5fbceb9c812b2b6c8215055c4d94af76f69c231078138af9b" }, { "biosampleStatus": { @@ -1587,7 +1937,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1595,14 +1945,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE15", "individualId": "SAMPLE15", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1611,17 +1959,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 19 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1634,32 +2001,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1669,12 +2043,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000199", + "label": "cardiac muscle" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1692,7 +2066,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "37617dfe57f7e71a514cd5385e6c3d14f869bfa92c2d978257ebe9e15fc62eb3" }, { "biosampleStatus": { @@ -1700,7 +2075,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1708,14 +2083,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE16", "individualId": "SAMPLE16", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1724,17 +2097,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 20 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1747,32 +2139,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1782,12 +2181,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000199", + "label": "cardiac muscle" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1798,14 +2197,15 @@ "label": "freezing storage" }, "tumorGrade": { - "id": "NCIT:C28080", - "label": "Grade 3a" + "id": "NCIT:C28078", + "label": "Grade 2" }, "tumorProgression": { "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "d36d5d068928083a9f2de6dbafaf7a70b03ae207fc9e53001ddcdcf88ad234cf" }, { "biosampleStatus": { @@ -1813,7 +2213,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1821,14 +2221,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE17", "individualId": "SAMPLE17", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1837,17 +2235,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 21 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1860,32 +2277,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -1895,12 +2319,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0000199", + "label": "cardiac muscle" }, "sampleProcessing": { "id": "EFO:0009129", @@ -1918,7 +2342,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "75db19f198d181b18800e46245771ff1f50374d2b3bcff4e82a5415b2e204471" }, { "biosampleStatus": { @@ -1926,7 +2351,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -1934,14 +2359,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE18", "individualId": "SAMPLE18", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -1950,17 +2373,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 22 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -1973,32 +2415,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -2008,12 +2457,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0001806", + "label": "visceral mass" }, "sampleProcessing": { "id": "EFO:0009129", @@ -2031,7 +2480,8 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "6d2e99faea7331042160c1f92a2c6146c724f4793edb47aa337df0df77df15e2" }, { "biosampleStatus": { @@ -2039,7 +2489,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -2047,14 +2497,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE19", "individualId": "SAMPLE19", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -2063,17 +2511,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 23 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -2086,32 +2553,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -2121,12 +2595,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0001806", + "label": "visceral mass" }, "sampleProcessing": { "id": "EFO:0009129", @@ -2137,14 +2611,15 @@ "label": "freezing storage" }, "tumorGrade": { - "id": "NCIT:C28080", - "label": "Grade 3a" + "id": "NCIT:C28078", + "label": "Grade 2" }, "tumorProgression": { "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "ef282200e43bc73142769f87e2e2bafa0fb4e60ba88f2c433d3abaf9bbe7b11c" }, { "biosampleStatus": { @@ -2152,7 +2627,7 @@ "label": "abnormal sample" }, "collectionDate": "2020-09-11", - "collectionMoment": "P32Y6M1D", + "collectionMoment": "P53Y4M", "diagnosticMarkers": [ { "id": "RO:0000085", @@ -2160,14 +2635,12 @@ } ], "histologicalDiagnosis": { - "id": "NCIT:C3778", - "label": "Serous Cystadenocarcinoma" + "id": "NCIT:C4126", + "label": "Intestinal-Type Adenocarcinoma" }, "id": "SAMPLE20", "individualId": "SAMPLE20", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, + "info": {}, "measurements": [ { "assayCode": { @@ -2176,17 +2649,36 @@ }, "date": "2019-04-23", "measurementValue": { - "id": "LOINC:26515-7", - "label": "Platelets [#/volume] in Blood" + "referenceRange": { + "high": 12, + "low": 10, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "value": 24 }, "notes": "Bear in mind that all this information is synthetic", "observationMoment": { "iso8601duration": "P53Y8M" }, "procedure": { + "ageAtProcedure": { + "iso8601duration": "P53Y8M" + }, + "bodySite": { + "id": "BTO:0000089", + "label": "blood" + }, + "dateOfProcedure": "2020-08-19", "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" + "id": "OBI:0002651", + "label": "venipuncture" } } } @@ -2199,32 +2691,39 @@ "pathologicalTnmFinding": [ { "id": "NCIT:C48725", - "label": "T2a Stage Finding" + "label": "T3a Stage Finding" } ], "phenotypicFeatures": [ { "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + }, "reference": { "id": "ECO:0006017", "notes": "author statement from published clinical study used in manual assertion" } }, - "excluded": "TRUE", + "excluded": true, "featureType": { "id": "HP:0000002", "label": "Abnormality of body height" }, - "modifiers": { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], "notes": "Please note that all this information is synthetic", "onset": { - "days": 5 + "days": 6, + "weeks": 1 }, "resolution": { - "days": 8, + "days": 5, "weeks": 8 }, "severity": { @@ -2234,12 +2733,12 @@ } ], "sampleOriginDetail": { - "id": "UBERON:0000474", - "label": "female reproductive system" + "id": "BTO:0004718", + "label": "breast cancer cell" }, "sampleOriginType": { - "id": "UBERON:0000992", - "label": "ovary" + "id": "BTO:0001806", + "label": "visceral mass" }, "sampleProcessing": { "id": "EFO:0009129", @@ -2257,6 +2756,7 @@ "id": "NCIT:C84509", "label": "Primary Malignant Neoplasm" }, - "datasetId": "test" + "datasetId": "test", + "_id": "333046d59782bc08b005aef4e125d53373d7e16678daf8965eea09fa74590325" } ] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/caseLevelData.json b/beacon/connections/mongo/data/test/caseLevelData.json index bb5c38a2..b55161ba 100644 --- a/beacon/connections/mongo/data/test/caseLevelData.json +++ b/beacon/connections/mongo/data/test/caseLevelData.json @@ -1 +1,615 @@ 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a/beacon/connections/mongo/data/test/cohorts.json b/beacon/connections/mongo/data/test/cohorts.json index 1f2223a0..3a9363f0 100644 --- a/beacon/connections/mongo/data/test/cohorts.json +++ b/beacon/connections/mongo/data/test/cohorts.json @@ -1,260 +1 @@ -[ - { - "cohortDataTypes": [ - { - "id": "OGMS:0000015", - "label": "clinical history" - } - ], - "cohortDesign": { - "id": "OMIABIS:0001019", - "label": "longitudinal study design" - }, - "cohortSize": 20000, - "cohortType": "study-defined", - "collectionEvents": [ - { - "eventAgeRange": { - "availability": true, - "availabilityCount": 101, - "distribution": { - "ranges": { - "20-40": 51, - "50-60": 50 - } - } - }, - "eventDataTypes": { - "availability": true, - "availabilityCount": 29, - "distribution": { - "datatypes": { - "OGMS:0000015": 5, - "OBI:0000070": 8, - "OMIABIS:0000060": 16 - } - } - }, - "eventDiseases": { - "availability": true, - "availabilityCount": 100, - "distribution": { - "diseases": { - "HP:0001645": 50 - } - } - }, - "eventEthnicities": { - "availability": true, - "availabilityCount": 101, - "distribution": { - "ethnicities": { - "African": 3, - "European": 90, - "LatinAmerican": 8 - } - } - }, - "eventGenders": { - "availability": true, - "availabilityCount": 101, - "distribution": { - "genders": { - "female": 51, - "male": 50 - } - } - }, - "eventLocations": { - "availability": true, - "availabilityCount": 101, - "distribution": { - "ethnicities": { - "GAZ:00004501": 101 - } - } - }, - "eventPhenotypes": { - "availability": true, - "availabilityCount": 101, - "distribution": { - "Phenotype": { - "GAZ:00004501": 101 - } - } - } - } - ], - "exclusionCriteria": { - "ageRange": { - "end": { - "iso8601duration": "P58Y" - }, - "start": { - "iso8601duration": "P18Y" - } - }, - "diseaseConditions": [ - { - "ageOfOnset": { - "id": "NCIT:C49685", - "label": "Adult 18-65 Years Old" - }, - "diseaseCode": { - "id": "HP:0004789", - "label": "lactose intolerance" - }, - "familyHistory": true, - "notes": "All this information is synthetic.", - "severity": { - "id": "HP:0012828", - "label": "Severe" - }, - "stage": { - "id": "OGMS:0000119", - "label": "acute onset" - } - } - ], - "ethnicities": [ - { - "id": "NCIT:C43851", - "label": "European" - } - ], - "genders": [ - { - "id": "NCIT:C16576", - "label": "Female" - }, - { - "id": "NCIT:C20197", - "label": "male" - }, - { - "id": "NCIT:C1799", - "label": "uknown" - } - ], - "locations": [ - { - "id": "GAZ:00000460", - "label": "Eurasia" - } - ], - "phenotypicConditions": [ - { - "excluded": true, - "featureType": { - "id": "HP:0000002", - "label": "Abnormality of body height" - }, - "modifiers": [ - { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - } - ], - "notes": "Bear in mind that all this information is synthetic", - "onset": { - "iso8601duration": "P58Y" - }, - "resolution": { - "iso8601duration": "P98Y" - }, - "severity": { - "id": "HP:0012828", - "label": "Severe" - } - } - ] - }, - "id": "EGA-testing", - "inclusionCriteria": { - "ageRange": { - "end": { - "iso8601duration": "P59Y" - }, - "start": { - "iso8601duration": "P18Y" - } - }, - "diseaseConditions": [ - { - "ageOfOnset": { - "id": "NCIT:C49685", - "label": "Adult 18-65 Years Old" - }, - "diseaseCode": { - "id": "HP:0004789", - "label": "lactose intolerance" - }, - "familyHistory": true, - "notes": "All this information is synthetic.", - "severity": { - "id": "HP:0012828", - "label": "Severe" - }, - "stage": { - "id": "OGMS:0000119", - "label": "acute onset" - } - } - ], - "ethnicities": [ - { - "id": "NCIT:C43851", - "label": "European" - } - ], - "genders": [ - { - "id": "NCIT:C16576", - "label": "Female" - }, - { - "id": "NCIT:C20197", - "label": "male" - }, - { - "id": "NCIT:C1799", - "label": "uknown" - } - ], - "locations": [ - { - "id": "GAZ:00000460", - "label": "Eurasia" - } - ], - "phenotypicConditions": [ - { - "excluded": true, - "featureType": { - "id": "HP:0000002", - "label": "Abnormality of body height" - }, - "modifiers": [ - { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - } - ], - "notes": "Bear in mind that all this information is synthetic", - "onset": { - "iso8601duration": "P59Y" - }, - "resolution": { - "iso8601duration": "P98Y" - }, - "severity": { - "id": "HP:0012828", - "label": "Severe" - } - } - ] - }, - "name": "syntheticCohort", - "datasetId": "test" - } -] \ No newline at end of file +[{"cohortDataTypes": [{"id": "OGMS:0000015", "label": "clinical history"}], "cohortDesign": {"id": "OMIABIS:0001019", "label": "longitudinal study design"}, "cohortSize": 20, "cohortType": "study-defined", "collectionEvents": [{"eventAgeRange": {"availability": true, "availabilityCount": 20}, "eventDataTypes": {"availability": true, "availabilityCount": 20}, "eventDiseases": {"availability": true, "availabilityCount": 20}, "eventEthnicities": {"availability": true, "availabilityCount": 20}, "eventGenders": {"availability": true, "availabilityCount": 20}, "eventLocations": {"availability": true, "availabilityCount": 20}, "eventPhenotypes": {"availability": true, "availabilityCount": 20}}], "exclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P58Y"}, "start": {"iso8601duration": "P18Y"}}, "diseaseConditions": [{"ageOfOnset": {"id": "NCIT:C49685", "label": "Adult 18-65 Years Old"}, "diseaseCode": {"id": "HP:0000002", "label": "Abnormality of body height"}, "familyHistory": true, "notes": "All this information is synthetic.", "severity": {"id": "HP:0012828", "label": "Severe"}, "stage": {"id": "OGMS:0000119", "label": "acute onset"}}], "ethnicities": [{"id": "NCIT:C43851", "label": "European"}], "genders": [{"id": "NCIT:C16576", "label": "Female"}, {"id": "NCIT:C20197", "label": "male"}, {"id": "NCIT:C1799", "label": "uknown"}], "locations": [{"id": "GAZ:00000460", "label": "Eurasia"}], "phenotypicConditions": [{"evidence": {"evidenceCode": {"id": "ECO:0006017"}, "reference": {"id": "author statement from published clinical study used in manual assertion"}}, "excluded": true, "featureType": {"id": "HP:0000002", "label": "Abnormality of body height"}, "notes": "This information is synthetic", "onset": {"iso8601duration": "P58Y"}, "severity": {"id": "HP:0012828", "label": "Severe"}}]}, "id": "EGA-testing", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P59Y"}, "start": {"iso8601duration": "P18Y"}}, "diseaseConditions": [{"ageOfOnset": {"id": "NCIT:C49685", "label": "Adult 18-65 Years Old"}, "diseaseCode": {"id": "MONDO:0005002", "label": "breast carcinoma"}, "notes": "All this information is synthetic.", "severity": {"id": "HP:0012828", "label": "Severe"}, "stage": {"id": "OGMS:0000119", "label": "acute onset"}}], "ethnicities": [{"id": "NCIT:C43851", "label": "European"}], "genders": [{"id": "NCIT:C16576", "label": "Female"}], "locations": [{"id": "GAZ:00000460", "label": "Eurasia"}], "phenotypicConditions": [{"evidence": {"evidenceCode": {"id": "ECO:0006017"}, "reference": {"id": "author statement from published clinical study used in manual assertion"}}, "excluded": true, "featureType": {"id": "MONDO:0004994", "label": "breast carcinoma"}, "notes": "Bear in mind that all this information is synthetic", "onset": {"iso8601duration": "P20Y"}, "severity": {"id": "HP:0012828", "label": "Severe"}}]}, "name": "syntheticCohort", "datasetId": "test", "_id": "2e8d3e8dcf5a492448e1703c2c99ed5ee4370a1152f1983b3cf11e3e9cab2033"}] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/datasets.json b/beacon/connections/mongo/data/test/datasets.json index d99f9580..81208af1 100644 --- a/beacon/connections/mongo/data/test/datasets.json +++ b/beacon/connections/mongo/data/test/datasets.json @@ -4,27 +4,18 @@ "dataUseConditions": { "duoDataUse": [ { - "description": "test dataset", - "id": "DUO:0000019,DUO:00000020", - "label": "publication required,publication required", - "modifiers": [ - { - "id": "EFO:0001645", - "label": "coronary artery disease" - } - ], - "version": "7-1-19,7-1-19" + "id": "DUO:0000019", + "label": "publication required", + "version": "7-1-19" } ] }, - "description": "Bear in mind that both genomic and metadata information is synthetic ", - "externalUrl": "https://ega-archive.org/datasets/EGAD00001006673/", + "description": "Bear in mind that both genomic and metadata information is synthetic", + "externalUrl": "http://synthetic_usecases_4beacon_testingV4.com", "id": "test", - "info": { - "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." - }, "name": "Dataset with synthetic data for beacon testing", "updateDateTime": "2021-12-29T20:33:40Z", - "version": "v1.0" + "version": "v1.0", + "_id": "a0b167c885bf11ece6a25b76e767ffa64cca21701c0eb1c8cee88c74049ef84d" } ] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/individuals.json b/beacon/connections/mongo/data/test/individuals.json index 22a0be49..7ca802c3 100644 --- a/beacon/connections/mongo/data/test/individuals.json +++ b/beacon/connections/mongo/data/test/individuals.json @@ -1,4062 +1 @@ -[ - { - "diseases": [ - { - "ageOfOnset": { - "id": "NCIT:C16731", - "label": "Neonate" - }, - "diseaseCode": { - "id": "MONDO:0004975", - "label": "Cystic fibrosis" - }, - "familyHistory": true, - "notes": "Bear in mind that all information is synthetic", - "severity": { - "id": "HP:0012828", - "label": "Severe" - } - } - ], - "ethnicity": { - "id": "NCIT:C43851", - "label": "European" - }, - "exposures": [ - { - "ageAtExposure": { - "iso8601duration": "P32Y6M1D" - }, - "date": "2024-09-25", - "duration": "14 months", - "exposureCode": { - "id": "CHEBI:46661", - "label": "asbestos" - }, - "unit": { - "id": "NCIT:C28253", - "label": "Milligram" - } - } - ], - "geographicOrigin": { - "id": "GAZ:00002586", - "label": "State of Wisconsin" - }, - "id": "SAMPLE1", - "interventionsOrProcedures": [ - { - "bodySite": { - "id": "FMAID:7195", - "label": "lung" - }, - "dateOfProcedure": "2024-12-24", - "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" - } - } - ], - "karyotypicSex": "XXXY", - "measures": [ - { - "assayCode": { - "id": "UBERON:0001062", - "label": "anatomical entity" - }, - "date": "2024-11-08", - "measurementValue": - { - "referenceRange": { - "high": 50, - "low": 20, - "unit": { - "id": "NCIT:C28253", - "label": "Milligram" - } - }, - "unit": { - "id": "NCIT:C28253", - "label": "Milligram" - }, - "value": 50 - } - , - "notes": "Bear in mind that all this information is synthetic", - "observationMoment": { - "iso8601duration": "P32Y6M1D" - }, - "procedure": { - "ageAtProcedure": "1999-08-05T17:21:00+01:00", - "bodySite": { - "id": "FMAID:7195", - "label": "lung" - }, - "dateOfProcedure": "2024-08-15", - "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" - } - } - } - ], - "pedigrees": [ - { - "disease": { - "diseaseCode": { - "id": "HP:0001645", - "label": "Sudden cardiac death" - }, - "familyHistory": true, - "notes": "Bear in mind that all this information is synthetic ", - "severity": { - "id": "HP:0012828", - "label": "Severe" - }, - "stage": { - "id": "OGMS:0000103", - "label": "Disease stage" - } - }, - "id": "SCD-Pedigree001", - "members": [ - { - "affected": true, - "memberId": "Ind001", - "role": { - "id": "NCIT:C64435", - "label": "Proband" - } - }, - { - "affected": true, - "memberId": "Ind002", - "role": { - "id": "NCIT:C96572", - "label": "Father" - } - }, - { - "affected": true, - "memberId": "Ind003", - "role": { - "id": "NCIT:C111201", - "label": "Full Brother" - } - } - ] - } - ], - "phenotypicFeatures": [ - { - "evidence": { - "evidenceCode": { - "id": "ECO:0006017", - "label": "author statement from published clinical study used in manual assertion" - } - }, - "excluded": true, - "featureType": { - "id": "HP:0000002", - "label": "Abnormality of body height" - }, - "modifiers": [ - { - "id": "HP:0032500", - "label": "Exacerbated by tobacco use" - } - ], - "notes": "Please note that all this information is synthetic", - "onset": { - "id": "HP:0011463", - "label": "Infantile onset" - }, - "resolution": { - "days": 8, - "weeks": 8 - }, - "severity": { - "id": "HP:0012828", - "label": "Severe" - } - } - ], - "sex": { - "id": "NCIT:C16576", - "label": "female" - }, - "treatments": [ - { - "ageAtOnset": { - "iso8601duration": "P1Y1" - }, - "routeOfAdministration": { - "id": "NCIT:C38288", - "label": "Oral Route of Administration" - }, - "treatmentCode": { - "id": "OGMS:0000113", - "label": "chemotherapy procedure" - } - } - ], - "datasetId": "test" - }, - { - "diseases": [ - { - "ageOfOnset": { - "id": "NCIT:C16731", - "label": "Neonate" - }, - "diseaseCode": { - "id": "MONDO:0004975", - "label": "Cystic fibrosis" - }, - "familyHistory": true, - "notes": "Bear in mind that all information is synthetic", - "severity": { - "id": "HP:0012828", - "label": "Severe" - } - } - ], - "ethnicity": { - "id": "NCIT:C43851", - "label": "European" - }, - "exposures": [ - { - "ageAtExposure": { - 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"observationMoment": { - "iso8601duration": "P32Y6M1D" - }, - "procedure": { - "ageAtProcedure": "1999-08-05T17:21:00+01:00", - "bodySite": { - "id": "FMAID:7195", - "label": "lung" - }, - "dateOfProcedure": "2024-08-15", - "procedureCode": { - "id": "OBI:0002657", - "label": "surgical biopsy" - } - } - } - ], - "pedigrees": [ - { - "disease": { - "diseaseCode": { - "id": "HP:0001645", - "label": "Sudden cardiac death" - }, - "familyHistory": true, - "notes": "Bear in mind that all this information is synthetic ", - "severity": { - "id": "HP:0012828", - "label": "Severe" - }, - "stage": { - "id": "OGMS:0000103", - "label": "Disease stage" - } - }, - "id": "SCD-Pedigree001", - "members": [ - { - "affected": true, - "memberId": "Ind001", - "role": { - "id": "NCIT:C64435", - "label": "Proband" - } - }, - { - "affected": true, - "memberId": "Ind002", - "role": { - "id": "NCIT:C96572", - "label": "Father" - } - }, - { - "affected": true, - "memberId": "Ind003", - "role": { - "id": 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"BTO:0001806", "label": "visceral mass"}, "dateOfProcedure": "2024-08-15", "procedureCode": {"id": "OBI:0002657", "label": "surgical biopsy"}}}, {"assayCode": {"id": "LOINC:3141-9", "label": "Weight"}, "date": "2021-09-24", "measurementValue": {"unit": {"id": "NCIT:C28252", "label": "Kilogram"}, "value": 96.1068}, "procedure": {"ageAtProcedure": {"iso8601duration": "P16Y"}, "bodySite": {"id": "BTO:0001806", "label": "visceral mass"}, "dateOfProcedure": "2024-08-15", "procedureCode": {"id": "OBI:0002657", "label": "surgical biopsy"}}}, {"assayCode": {"id": "LOINC:8308-9", "label": "Height-standing"}, "date": "2021-09-24", "measurementValue": {"unit": {"id": "NCIT:C49668", "label": "Centimeter"}, "value": 166.7242}, "procedure": {"ageAtProcedure": {"iso8601duration": "P16Y"}, "bodySite": {"id": "BTO:0001806", "label": "visceral mass"}, "dateOfProcedure": "2024-08-15", "procedureCode": {"id": "OBI:0002657", "label": "surgical biopsy"}}}], "pedigrees": [{"disease": {"diseaseCode": {"id": "HP:0000819", "label": "Diabetes mellitus"}, "familyHistory": true, "notes": "Bear in mind that all this information is synthetic", "severity": {"id": "HP:0012828", "label": "Severe"}, "stage": {"id": "OGMS:0000113", "label": "chemotherapy procedure"}}, "id": "SCD-Pedigree001", "members": [{"affected": true, "memberId": "Ind005", "role": {"id": "NCIT:C252896", "label": "Brother"}}]}], "phenotypicFeatures": [{"evidence": {"evidenceCode": {"id": "ECO:0006017", "label": "author statement from published clinical study used in manual assertion"}}, "excluded": true, "featureType": {"id": "HP:0012245", "label": "Sex reversal"}, "modifiers": [{"id": "HP:0000061", "label": "Ambiguous genitalia"}], "notes": "Please note that all this information is synthetic", "onset": {"id": "HP:0003587", "label": "Insidious onset"}, "resolution": {"days": 8, "weeks": 8}, "severity": {"id": "HP:0012828", "label": "Severe"}}], "sex": {"id": "NCIT:C20197", "label": "male"}, "treatments": [{"ageAtOnset": {"iso8601duration": "P4Y1"}, "routeOfAdministration": {"id": "NCIT:C38288", "label": "Oral Route of Administration"}, "treatmentCode": {"id": "OGMS:0000113", "label": "chemotherapy procedure"}}], "datasetId": "test", "_id": "333046d59782bc08b005aef4e125d53373d7e16678daf8965eea09fa74590325"}] \ No newline at end of file diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/analysis.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/analysis.yml index 52621d39..d71561d8 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/analysis.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/analysis.yml @@ -20,7 +20,7 @@ analysis: description: Apply analytical methods to existing data of a specific type. schema: specification: Beacon v2 - default_schema_id: beacon-analysis-v2.0.0 + default_schema_id: beacon-analysis-v2.2.0 default_schema_name: Default schema for a bioinformatics analysis reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/analyses/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/biosample.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/biosample.yml index eb0f74c8..164edf69 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/biosample.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/biosample.yml @@ -20,7 +20,7 @@ biosample: description: Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. [ NCI ] schema: specification: Beacon v2 - default_schema_id: beacon-biosample-v2.0.0 + default_schema_id: beacon-biosample-v2.2.0 default_schema_name: Default schema for a biological sample reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/cohort.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/cohort.yml index fb9fc4a5..ba2ae4bd 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/cohort.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/cohort.yml @@ -20,7 +20,7 @@ cohort: description: A group of individuals, identified by a common characteristic. [ NCI ] schema: specification: Beacon v2 - default_schema_id: beacon-cohort-v2.0.0 + default_schema_id: beacon-cohort-v2.2.0 default_schema_name: Default schema for a bioinformatics cohort reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/dataset.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/dataset.yml index 1347bbf4..47300cf8 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/dataset.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/dataset.yml @@ -20,7 +20,7 @@ dataset: description: A Dataset is a collection of records, like rows in a database or cards in a cardholder. schema: specification: Beacon v2 - default_schema_id: beacon-dataset-v2.0.0 + default_schema_id: beacon-dataset-v2.2.0 default_schema_name: Default schema for datasets reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/genomicVariant.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/genomicVariant.yml index 6b2a9817..6d1047d8 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/genomicVariant.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/genomicVariant.yml @@ -20,7 +20,7 @@ genomicVariant: description: The location of a sequence. schema: specification: Beacon v2 - default_schema_id: beacon-genomicVariant-v2.0.0 + default_schema_id: beacon-genomicVariant-v2.2.0 default_schema_name: Default schema for a genomic variation reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/individual.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/individual.yml index 55cd686b..f58a29bb 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/individual.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/individual.yml @@ -20,7 +20,7 @@ individual: description: A human being. It could be a Patient, a Tissue Donor, a Participant, a Human Study Subject, etc. schema: specification: Beacon v2 - default_schema_id: beacon-individual-v2.0.0 + default_schema_id: beacon-individual-v2.2.0 default_schema_name: Default schema for a bioinformatics individual reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/individuals/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/run.yml b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/run.yml index e80ca969..6031929b 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/run.yml +++ b/beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/run.yml @@ -20,7 +20,7 @@ run: description: The valid and completed operation of a high-throughput sequencing instrument for a single sequencing process. [ NCI ] schema: specification: Beacon v2 - default_schema_id: beacon-run-v2.0.0 + default_schema_id: beacon-run-v2.2.0 default_schema_name: Default schema for a sequencing run reference_to_default_schema_definition: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/runs/defaultSchema.json default_schema_version: v2.0.0 diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/cohort/beacon_cohort_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/cohort/beacon_cohort_v2_2_0.py index 267f9b64..3a21b500 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/cohort/beacon_cohort_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/cohort/beacon_cohort_v2_2_0.py @@ -1 +1,788 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.collections.cohort.beacon_cohort_v2_0_0 import Cohort +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json +# timestamp: 2026-07-31T13:34:34+00:00 + +from __future__ import annotations + +from enum import Enum +from typing import Any + +from pydantic import ( + AnyUrl, + AwareDatetime, + BaseModel, + ConfigDict, + Field, + RootModel, + conint, + constr, +) + + +class CohortType(Enum): + study_defined = 'study-defined' + beacon_defined = 'beacon-defined' + user_defined = 'user-defined' + + +class CURIE(RootModel[constr(pattern=r'^\w[^:]+:.+$')]): + root: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + + +class FieldSchema(RootModel[str]): + root: str = Field( + ..., + description='Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.', + ) + + +class ApiVersion(RootModel[str]): + root: str = Field( + ..., + description='Version of API, e.g. in request or response. Beacon uses a Github-style, "v"-prefixed semantic versioning format.', + examples=['v2.0.1', 'v0.3'], + ) + + +class BeaconError(BaseModel): + errorCode: int = Field(..., description='Entry not found', examples=['404']) + errorMessage: str | None = Field( + None, examples=['The provided parameters are incomplete: `start` is missing.'] + ) + + +class BeaconId(RootModel[str]): + root: str = Field( + ..., + description='The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.', + examples=['org.example.beacon.v2', 'org.progenetix.beacon'], + ) + + +class CountAdjustedToItem(RootModel[conint(ge=1) | str]): + root: conint(ge=1) | str + + +class CountAdjustedTo(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class CountPrecision(Enum): + exact = 'exact' + imprecise = 'imprecise' + rounded = 'rounded' + + +class Exists(RootModel[bool]): + root: bool = Field( + ..., + description='Indicator of whether any record was observed in any of the collections queried. This should be non-null.', + examples=[True], + ) + + +class Filters(RootModel[list[str]]): + root: list[str] = Field( + ..., + description='Ontology based filters. A CURIE syntax is encouraged to be used.', + examples=[['BTO:0000199', 'PATO:0000383']], + ) + + +class Granularity(Enum): + boolean = 'boolean' + count = 'count' + record = 'record' + + +class IncludeResultsetResponses(Enum): + ALL = 'ALL' + HIT = 'HIT' + MISS = 'MISS' + NONE = 'NONE' + + +class Limit(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 10, + description='Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.', + examples=[10], + ) + + +class NonFilteredQueriesAllowed(RootModel[bool]): + root: bool = Field( + True, + description="Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.", + ) + + +class NumTotalResults(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + ..., + description='Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.', + examples=[123], + ) + + +class PageToken(RootModel[str]): + root: str = Field( + ..., + description='A hash or similar that allows the server to retrieve a "page", e.g. (a subset of) a query response.', + examples=['ab0sc&fe1dd'], + ) + + +class SchemasPerEntity(BaseModel): + entityType: str | None = Field(None, examples=['Individual']) + schema_: str | None = Field( + None, + alias='schema', + examples=[ + './ga4gh-beacon-dataset-v2.0.0', + 'https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json', + ], + ) + + +class Skip(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 0, + description='* In the request: number of pages to skip * In the response: number of pages that has been skipped', + examples=[0], + ) + + +class TestMode(RootModel[bool]): + root: bool = Field( + False, + description='Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.', + ) + + +class Info(BaseModel): + pass + + +class Age(BaseModel): + iso8601duration: str = Field( + ..., + description='Represents age as a ISO8601 duration (e.g., P40Y10M05D).', + examples=['P32Y6M1D'], + ) + + +class GestationalAge(BaseModel): + days: int | None = Field( + None, + description='Days beyond the completed weeks, if available.', + examples=[2, 4], + ) + weeks: int = Field( + ..., + description='Completed weeks of gestation according to the above definition.', + examples=[4, 33], + ) + + +class Timestamp(RootModel[AwareDatetime]): + root: AwareDatetime = Field( + ..., + description='Time in date-time ISO8601 string format.', + examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'], + ) + + +class CountAdjustedTo1(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class KaryotypicSex(Enum): + UNKNOWN_KARYOTYPE = 'UNKNOWN_KARYOTYPE' + XX = 'XX' + XY = 'XY' + XO = 'XO' + XXY = 'XXY' + XXX = 'XXX' + XXYY = 'XXYY' + XXXY = 'XXXY' + XXXX = 'XXXX' + XYY = 'XYY' + OTHER_KARYOTYPE = 'OTHER_KARYOTYPE' + + +class TimeInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + end: Timestamp = Field(..., examples=['2022-03-10T15:25:07Z']) + start: Timestamp = Field( + ..., examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'] + ) + + +class ExternalReference(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: str | None = Field( + None, + description='An application specific identifier. RECOMMENDED.', + examples=['PMID:34054918'], + ) + notes: str | None = Field( + None, + description='An optional text descriptor. Renamed compared to GA4GH Phenopackets v2 `ExternalReference.description`', + examples=[ + 'Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes' + ], + ) + reference: str | None = Field( + None, + description='A url.', + examples=['https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155688/'], + ) + + +class EventDataTypes(BaseModel): + availability: bool = Field(..., description='data availability') + availabilityCount: int | None = Field( + None, description='Count of individuals with data available' + ) + distribution: dict[str, dict[str, Any]] | None = Field( + None, + description='List of categories and results or counts for each category.', + examples=[{'genders': {'female': 51, 'male': 50}}], + ) + + +class EventTimeline(BaseModel): + end: AwareDatetime | None = Field( + None, + description='Latest date of visit or collection timeline', + examples=[ + '2018-10-01T13:23:45Z', + '2019-04-23T09:11:13Z', + '2017-01-17T20:33:40Z', + ], + ) + start: AwareDatetime | None = Field( + None, + description='Earliest date of visit or collection timeline', + examples=[ + '2018-10-01T13:23:45Z', + '2019-04-23T09:11:13Z', + '2017-01-17T20:33:40Z', + ], + ) + + +class DataAvailabilityAndDistribution(BaseModel): + availability: bool = Field(..., description='data availability') + availabilityCount: int | None = Field( + None, description='Count of individuals with data available' + ) + distribution: dict[str, dict[str, Any]] | None = Field( + None, + description='List of categories and results or counts for each category.', + examples=[{'genders': {'female': 51, 'male': 50}}], + ) + + +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: CURIE + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HandoverType(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.', + examples=[ + {'id': 'EDAM:2572', 'label': 'BAM'}, + {'id': 'EDAM:3016', 'label': 'VCF'}, + {'id': 'CUSTOM:pgxseg', 'label': 'genomic variants in .pgxseg file format'}, + ], + ) + + +class ListOfSchemas(RootModel[list[SchemasPerEntity]]): + root: list[SchemasPerEntity] = Field( + ..., description='Set of schemas to be used in the response to a request.' + ) + + +class Pagination(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class AgeRange(BaseModel): + end: Age = Field( + ..., description='Represents age as an ISO8601 duration (e.g., P59Y).' + ) + start: Age = Field( + ..., description='Represents age as an ISO8601 duration (e.g., P18Y).' + ) + + +class TimeElement( + RootModel[Age | AgeRange | GestationalAge | Timestamp | TimeInterval | OntologyTerm] +): + root: Age | AgeRange | GestationalAge | Timestamp | TimeInterval | OntologyTerm = ( + Field( + ..., + description='Definition of a wrapper for various time descriptors. This follows the\nPhenopackets structure https://github.com/phenopackets/phenopacket-schema/blob/v2/docs/time-element.rst', + title='TimeElement', + ) + ) + + +class Pagination1(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class GeographicLocation(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).', + examples=[ + {'id': 'GAZ:00002955', 'label': 'Slovenia'}, + {'id': 'GAZ:00002459', 'label': 'United States of America'}, + {'id': 'GAZ:00316959', 'label': 'Municipality of El Masnou'}, + {'id': 'GAZ:00000460', 'label': 'Eurasia'}, + ], + ) + + +class SeverityLevel(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Severity as applicable to phenotype or disease observed. Recommended are values from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. Source: Phenopackets v2', + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012829', 'label': 'Profound'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + {'id': 'HP:0012825', 'label': 'Mild'}, + {'id': 'HP:0012827', 'label': 'Borderline'}, + ], + ) + + +class Sex(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993): "unknown" (not assessed or not available) - NCIT:C17998; "female" - NCIT:C16576; "male" - NCIT:C20197', + examples=[ + {'id': 'NCIT:C16576', 'label': 'female'}, + {'id': 'NCIT:C20197', 'label': 'male'}, + {'id': 'NCIT:C1799', 'label': 'unknown'}, + ], + ) + + +class Unit(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants', + examples=[ + {'id': 'NCIT:C70575', 'label': 'Roentgen'}, + {'id': 'NCIT:C28252', 'label': 'Kilogram'}, + {'id': 'NCIT:C28253', 'label': 'Milligram'}, + ], + ) + + +class Evidence(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + evidenceCode: OntologyTerm = Field( + ..., + description='An ontology class that represents the evidence type', + examples=[ + { + 'id': 'ECO:0006017', + 'label': 'author statement from published clinical study used in manual assertion', + } + ], + ) + reference: ExternalReference | None = Field( + None, + description='Representation of the source of the evidence', + examples=[ + { + 'id': 'PMID:30962759', + 'label': 'Recurrent Erythema Nodosum in a Child with a SHOC2 Gene Mutation', + } + ], + ) + + +class CollectionEvent(BaseModel): + eventAgeRange: DataAvailabilityAndDistribution | None = Field( + None, + description='Individual age range, obtained from individual level info of the cohort members', + ) + eventCases: int | None = Field( + None, description='number of cases', examples=[543, 20] + ) + eventControls: int | None = Field( + None, description='number of controls', examples=[1000, 22] + ) + eventDataTypes: EventDataTypes | None = Field( + None, + description='Aggregated data type information available for each cohort data type as declared in `cohortDataTypes`, and obtained from individual level info of the cohort members', + ) + eventDate: AwareDatetime | None = Field( + None, + description='date of collection event/data point', + examples=[ + '2018-10-01T13:23:45Z', + '2019-04-23T09:11:13Z', + '2017-01-17T20:33:40Z', + ], + ) + eventDiseases: DataAvailabilityAndDistribution | None = Field( + None, + description='Aggregated information of disease/condition(s) obtained from individual level info of the cohort members', + ) + eventEthnicities: DataAvailabilityAndDistribution | None = Field( + None, + description='Aggregated information of ethnicity obtained from individual level info of the cohort members', + ) + eventGenders: DataAvailabilityAndDistribution | None = Field( + None, + description='Aggregated information of gender(s) obtained from individual level info of the cohort members', + ) + eventLocations: DataAvailabilityAndDistribution | None = Field( + None, + description='Aggregated information of geographic location obtained from individual level info of the cohort members', + ) + eventNum: int | None = Field( + None, + description='cardinality of the collection event / data point in a series', + examples=[1, 2, 3, 4], + ) + eventPhenotypes: DataAvailabilityAndDistribution | None = Field( + None, + description='Aggregated information of phenotype(s) obtained from individual level info of the cohort members', + ) + eventSize: int | None = Field( + None, + description='Count of individuals in cohort at data point (for ´user-defined´ cohorts, this is individuals meeting criteria) obtained from individual level info in database.', + examples=[1543, 42], + ) + eventTimeline: EventTimeline | None = Field( + None, + description='Aggregated information of dates of visit | diagnostic | inclusion in study obtained from individual level info of the cohort members.', + ) + + +class DataTypesArray(RootModel[list[OntologyTerm]]): + root: list[OntologyTerm] = Field( + ..., + description='Type of information. Preferably values from Genomics Cohorts Knowledge Ontology (GeCKO) or others when GeCKO is not applicable.', + examples=[ + {'id': 'OGMS:0000015', 'label': 'clinical history'}, + {'id': 'OBI:0000070', 'label': 'genotyping assay'}, + {'id': 'OMIABIS:0000060', 'label': 'survey data'}, + ], + ) + + +class Handover(BaseModel): + handoverType: HandoverType + note: str | None = Field( + None, + description='An optional text including considerations on the handover link provided.', + examples=['This handover link provides access to a summarized VCF.'], + ) + url: AnyUrl = Field( + ..., + description='URL endpoint to where the handover process could progress, in RFC3986 format', + examples=[ + 'https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/' + ], + ) + + +class ListOfHandovers(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class Disease(BaseModel): + ageOfOnset: TimeElement | None = Field( + None, + examples=[ + {'id': 'NCIT:C49685', 'label': 'Adult 18-65 Years Old'}, + {'iso8601duration': 'P32Y6M1D'}, + {'end': {'iso8601duration': 'P59Y'}, 'start': {'iso8601duration': 'P18Y'}}, + {'iso8601duration': 'P2M4D'}, + ], + ) + diseaseCode: OntologyTerm = Field( + ..., + description='Disease identifier. Value from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. lactose intolerance (HP:0004789, ICD10CM:E73). Provenance: GA4GH Phenopackets v2 `Disease.term`', + examples=[ + {'id': 'HP:0004789', 'label': 'lactose intolerance'}, + {'id': 'ICD10CM:E73', 'label': 'lactose intolerance'}, + {'id': 'OMIM:164400', 'label': 'Spinocerebellar ataxia 1'}, + ], + ) + familyHistory: bool | None = Field( + None, + description='Boolean indicating determined or self-reported presence of family history of the disease.', + examples=[True], + ) + notes: str | None = Field( + None, + description='Unstructured text to describe additional properties of this disease instance.', + examples=['Some free text'], + ) + severity: SeverityLevel | None = Field( + None, + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + ], + ) + stage: OntologyTerm | None = Field( + None, + description='Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`', + examples=[ + {'id': 'OGMS:0000119', 'label': 'acute onset'}, + {'id': 'OGMS:0000117', 'label': 'asymptomatic'}, + {'id': 'OGMS:0000106', 'label': 'remission'}, + ], + ) + + +class Ethnicity(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]', + examples=[ + {'id': 'NCIT:C42331', 'label': 'African'}, + {'id': 'NCIT:C41260', 'label': 'Asian'}, + {'id': 'NCIT:C126535', 'label': 'Australian'}, + {'id': 'NCIT:C43851', 'label': 'European'}, + {'id': 'NCIT:C77812', 'label': 'North American'}, + {'id': 'NCIT:C126531', 'label': 'Latin American'}, + {'id': 'NCIT:C104495', 'label': 'Other race'}, + ], + ) + + +class ListOfHandovers1(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class PhenotypicFeature(BaseModel): + evidence: Evidence | None = Field( + None, + description='The evidence for an assertion of the observation of a type. RECOMMENDED.', + ) + excluded: bool | None = Field( + False, + description='Flag to indicate whether the phenotypic feature was observed or not. Default is ‘false’, in other words the phenotype was observed. Therefore it is only used in cases where the phenotype was looked for but found to be absent. More formally, this modifier indicates the logical negation of the OntologyClass used in the `featureType` field. CAUTION: It is imperative to check this field for correct interpretation of the phenotype! Source: Phenopackets v2', + ) + featureType: OntologyTerm = Field( + ..., + description='Term denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO)', + examples=[ + {'id': 'HP:0000002', 'label': 'Abnormality of body height'}, + {'id': 'HP:0002006', 'label': 'Facial cleft'}, + {'id': 'HP:0012469', 'label': 'Infantile spasms'}, + ], + ) + modifiers: list[OntologyTerm] | None = Field( + None, + description='This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. Example use here would be one or more terms from HPO Clinical Modifier (HP:0012823). Source: Phenopackets v2', + examples=[ + {'id': 'HP:0032500', 'label': 'Exacerbated by tobacco use'}, + {'id': 'HP:4000053', 'label': 'Displaced fracture'}, + ], + ) + notes: str | None = Field( + None, + description='Unstructured text to describe additional properties of this phenotypic feature.', + examples=['Some free text'], + ) + onset: TimeElement | None = Field( + None, description='Age or time at which the feature was first observed.' + ) + resolution: TimeElement | None = Field( + None, description='Age or time at which the feature resolved or abated.' + ) + severity: SeverityLevel | None = Field( + None, + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + ], + ) + + +class ExclusionCriteria(BaseModel): + ageRange: AgeRange | None = Field( + None, description='Individual age range in cohort inclusion criteria' + ) + diseaseConditions: list[Disease] | None = Field( + None, description='Diseases in cohort inclusion criteria' + ) + ethnicities: list[Ethnicity] | None = Field( + None, description='Ethnias in cohort inclusion criteria' + ) + genders: list[Sex] | None = Field( + None, description='Gender(s) in cohort inclusion criteria' + ) + locations: list[GeographicLocation] | None = Field( + None, description='Geographic location(s) in cohort inclusion criteria' + ) + phenotypicConditions: list[PhenotypicFeature] | None = Field( + None, description='Phenotypic condition(s) in cohort inclusion criteria' + ) + + +class InclusionCriteria(BaseModel): + ageRange: AgeRange | None = Field( + None, description='Individual age range in cohort inclusion criteria' + ) + diseaseConditions: list[Disease] | None = Field( + None, description='Diseases in cohort inclusion criteria' + ) + ethnicities: list[Ethnicity] | None = Field( + None, description='Ethnias in cohort inclusion criteria' + ) + genders: list[Sex] | None = Field( + None, description='Gender(s) in cohort inclusion criteria' + ) + locations: list[GeographicLocation] | None = Field( + None, description='Geographic location(s) in cohort inclusion criteria' + ) + phenotypicConditions: list[PhenotypicFeature] | None = Field( + None, description='Phenotypic condition(s) in cohort inclusion criteria' + ) + + +class Cohort(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + cohortDataTypes: DataTypesArray | None = None + cohortDesign: OntologyTerm | None = Field( + None, + description='Cohort type by its design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Value from Ontologized MIABIS (OMIABIS) Study design ontology term tree (OBI:0500000).', + examples=[ + {'id': 'OMIABIS:0001017', 'label': 'case control study design'}, + {'id': 'OMIABIS:0001019', 'label': 'longitudinal study design'}, + {'id': 'OMIABIS:0001024', 'label': 'twin study design'}, + ], + ) + cohortSize: int | None = Field( + None, + description='Count of unique Individuals in cohort (individuals meeting criteria for `user-defined` cohorts). If not previously known, it could be calculated by counting the individuals in the cohort.', + examples=[14765, 20000], + ) + cohortType: CohortType = Field( + ..., + description='Cohort type by its definition. If a cohort is declared `study-defined` or `beacon-defined` criteria are to be entered `in cohort_inclusion_criteria`; if a cohort is declared `user-defined` `cohort_inclusion_criteria` could be automatically populated from the parameters used to perform the query.', + ) + collectionEvents: list[CollectionEvent] | None = Field(None, description='TBD') + exclusionCriteria: ExclusionCriteria | None = Field( + None, + description='Exclusion criteria used for defining the cohort. It is assumed that NONE of the cohort participants will match such criteria.', + ) + id: str = Field( + ..., + description='Cohort identifier. For `study-defined` or `beacon-defined` cohorts this field is set by the implementer. For `user-defined` this unique identifier could be generated upon the query that defined the cohort, but could be later edited by the user.', + examples=['cohort-T2D-2010'], + ) + inclusionCriteria: InclusionCriteria | None = Field( + None, + description='Inclusion criteria used for defining the cohort. It is assumed that all cohort participants will match such criteria.', + ) + info: Info | None = None + name: str = Field( + ..., + description='Name of the cohort. For `user-defined` this field could be generated upon the query, e.g. a value that is a concatenationor some representation of the user query.', + examples=['Wellcome Trust Case Control Consortium', 'GCAT Genomes for Life'], + ) + + +class CohortCriteria(BaseModel): + ageRange: AgeRange | None = Field( + None, description='Individual age range in cohort inclusion criteria' + ) + diseaseConditions: list[Disease] | None = Field( + None, description='Diseases in cohort inclusion criteria' + ) + ethnicities: list[Ethnicity] | None = Field( + None, description='Ethnias in cohort inclusion criteria' + ) + genders: list[Sex] | None = Field( + None, description='Gender(s) in cohort inclusion criteria' + ) + locations: list[GeographicLocation] | None = Field( + None, description='Geographic location(s) in cohort inclusion criteria' + ) + phenotypicConditions: list[PhenotypicFeature] | None = Field( + None, description='Phenotypic condition(s) in cohort inclusion criteria' + ) diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/dataset/beacon_dataset_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/dataset/beacon_dataset_v2_2_0.py index 87a27a3a..367f0652 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/dataset/beacon_dataset_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/collections/dataset/beacon_dataset_v2_2_0.py @@ -1 +1,421 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.collections.dataset.beacon_dataset_v2_0_0 import Dataset +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json +# timestamp: 2026-07-31T13:34:57+00:00 + +from __future__ import annotations + +from enum import Enum + +from pydantic import ( + AnyUrl, + AwareDatetime, + BaseModel, + ConfigDict, + Field, + RootModel, + conint, + constr, +) + + +class Timestamp(RootModel[AwareDatetime]): + root: AwareDatetime = Field( + ..., + description='Time in date-time ISO8601 string format.', + examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'], + ) + + +class CURIE(RootModel[constr(pattern=r'^\w[^:]+:.+$')]): + root: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + + +class FieldSchema(RootModel[str]): + root: str = Field( + ..., + description='Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.', + ) + + +class ApiVersion(RootModel[str]): + root: str = Field( + ..., + description='Version of API, e.g. in request or response. Beacon uses a Github-style, "v"-prefixed semantic versioning format.', + examples=['v2.0.1', 'v0.3'], + ) + + +class BeaconError(BaseModel): + errorCode: int = Field(..., description='Entry not found', examples=['404']) + errorMessage: str | None = Field( + None, examples=['The provided parameters are incomplete: `start` is missing.'] + ) + + +class BeaconId(RootModel[str]): + root: str = Field( + ..., + description='The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.', + examples=['org.example.beacon.v2', 'org.progenetix.beacon'], + ) + + +class CountAdjustedToItem(RootModel[conint(ge=1) | str]): + root: conint(ge=1) | str + + +class CountAdjustedTo(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class CountPrecision(Enum): + exact = 'exact' + imprecise = 'imprecise' + rounded = 'rounded' + + +class Exists(RootModel[bool]): + root: bool = Field( + ..., + description='Indicator of whether any record was observed in any of the collections queried. This should be non-null.', + examples=[True], + ) + + +class Filters(RootModel[list[str]]): + root: list[str] = Field( + ..., + description='Ontology based filters. A CURIE syntax is encouraged to be used.', + examples=[['BTO:0000199', 'PATO:0000383']], + ) + + +class Granularity(Enum): + boolean = 'boolean' + count = 'count' + record = 'record' + + +class IncludeResultsetResponses(Enum): + ALL = 'ALL' + HIT = 'HIT' + MISS = 'MISS' + NONE = 'NONE' + + +class Limit(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 10, + description='Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.', + examples=[10], + ) + + +class NonFilteredQueriesAllowed(RootModel[bool]): + root: bool = Field( + True, + description="Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.", + ) + + +class NumTotalResults(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + ..., + description='Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.', + examples=[123], + ) + + +class PageToken(RootModel[str]): + root: str = Field( + ..., + description='A hash or similar that allows the server to retrieve a "page", e.g. (a subset of) a query response.', + examples=['ab0sc&fe1dd'], + ) + + +class SchemasPerEntity(BaseModel): + entityType: str | None = Field(None, examples=['Individual']) + schema_: str | None = Field( + None, + alias='schema', + examples=[ + './ga4gh-beacon-dataset-v2.0.0', + 'https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json', + ], + ) + + +class Skip(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 0, + description='* In the request: number of pages to skip * In the response: number of pages that has been skipped', + examples=[0], + ) + + +class TestMode(RootModel[bool]): + root: bool = Field( + False, + description='Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.', + ) + + +class KaryotypicSex(Enum): + UNKNOWN_KARYOTYPE = 'UNKNOWN_KARYOTYPE' + XX = 'XX' + XY = 'XY' + XO = 'XO' + XXY = 'XXY' + XXX = 'XXX' + XXYY = 'XXYY' + XXXY = 'XXXY' + XXXX = 'XXXX' + XYY = 'XYY' + OTHER_KARYOTYPE = 'OTHER_KARYOTYPE' + + +class CountAdjustedTo1(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class Info(BaseModel): + pass + + +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: CURIE + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HandoverType(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.', + examples=[ + {'id': 'EDAM:2572', 'label': 'BAM'}, + {'id': 'EDAM:3016', 'label': 'VCF'}, + {'id': 'CUSTOM:pgxseg', 'label': 'genomic variants in .pgxseg file format'}, + ], + ) + + +class ListOfSchemas(RootModel[list[SchemasPerEntity]]): + root: list[SchemasPerEntity] = Field( + ..., description='Set of schemas to be used in the response to a request.' + ) + + +class Pagination(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class GeographicLocation(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).', + examples=[ + {'id': 'GAZ:00002955', 'label': 'Slovenia'}, + {'id': 'GAZ:00002459', 'label': 'United States of America'}, + {'id': 'GAZ:00316959', 'label': 'Municipality of El Masnou'}, + {'id': 'GAZ:00000460', 'label': 'Eurasia'}, + ], + ) + + +class SeverityLevel(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Severity as applicable to phenotype or disease observed. Recommended are values from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. Source: Phenopackets v2', + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012829', 'label': 'Profound'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + {'id': 'HP:0012825', 'label': 'Mild'}, + {'id': 'HP:0012827', 'label': 'Borderline'}, + ], + ) + + +class Sex(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993): "unknown" (not assessed or not available) - NCIT:C17998; "female" - NCIT:C16576; "male" - NCIT:C20197', + examples=[ + {'id': 'NCIT:C16576', 'label': 'female'}, + {'id': 'NCIT:C20197', 'label': 'male'}, + {'id': 'NCIT:C1799', 'label': 'unknown'}, + ], + ) + + +class Unit(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants', + examples=[ + {'id': 'NCIT:C70575', 'label': 'Roentgen'}, + {'id': 'NCIT:C28252', 'label': 'Kilogram'}, + {'id': 'NCIT:C28253', 'label': 'Milligram'}, + ], + ) + + +class Pagination1(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class Ethnicity(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]', + examples=[ + {'id': 'NCIT:C42331', 'label': 'African'}, + {'id': 'NCIT:C41260', 'label': 'Asian'}, + {'id': 'NCIT:C126535', 'label': 'Australian'}, + {'id': 'NCIT:C43851', 'label': 'European'}, + {'id': 'NCIT:C77812', 'label': 'North American'}, + {'id': 'NCIT:C126531', 'label': 'Latin American'}, + {'id': 'NCIT:C104495', 'label': 'Other race'}, + ], + ) + + +class Handover(BaseModel): + handoverType: HandoverType + note: str | None = Field( + None, + description='An optional text including considerations on the handover link provided.', + examples=['This handover link provides access to a summarized VCF.'], + ) + url: AnyUrl = Field( + ..., + description='URL endpoint to where the handover process could progress, in RFC3986 format', + examples=[ + 'https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/' + ], + ) + + +class ListOfHandovers(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class DUODataUse(OntologyTerm): + modifiers: list[OntologyTerm] | None = Field( + None, + examples=[ + {'id': 'EFO:0001645', 'label': 'coronary artery disease'}, + {'id': 'EFO:0001655'}, + ], + ) + version: str = Field(..., examples=['17-07-2016']) + + +class ListOfHandovers1(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class DataUseConditions(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + duoDataUse: list[DUODataUse] | None = Field(None, min_length=1) + + +class Dataset(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + createDateTime: Timestamp | None = Field( + None, + description='The time the dataset was created (ISO 8601 format)', + examples=['2017-01-17T20:33:40Z'], + ) + dataUseConditions: DataUseConditions | None = Field( + None, description='Data use conditions applying to this dataset.' + ) + description: str | None = Field( + None, + description='Description of the dataset', + examples=[ + 'This dataset provides examples of the actual data in this Beacon instance.' + ], + ) + externalUrl: str | None = Field( + None, + description='URL to an external system providing more dataset information (RFC 3986 format).', + examples=['https://example.org/wiki/Main_Page'], + ) + id: str = Field( + ..., description='Unique identifier of the dataset', examples=['ds01010101'] + ) + info: Info | None = None + name: str = Field( + ..., description='Name of the dataset', examples=['Dataset with synthetic data'] + ) + updateDateTime: Timestamp | None = Field( + None, + description='The time the dataset was updated in (ISO 8601 format)', + examples=['2017-01-17T20:33:40Z'], + ) + version: str | None = Field( + None, description='Version of the dataset', examples=['v1.1'] + ) diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/analysis/beacon_analysis_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/analysis/beacon_analysis_v2_2_0.py index f6b90ec9..6b7efbe0 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/analysis/beacon_analysis_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/analysis/beacon_analysis_v2_2_0.py @@ -1,2 +1,66 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.non_collections.analysis.beacon_analysis_v2_0_0 import Analysis - \ No newline at end of file +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/analyses/defaultSchema.json +# timestamp: 2026-07-31T13:32:55+00:00 + +from __future__ import annotations + +from datetime import date + +from pydantic import BaseModel, ConfigDict, Field + + +class Info(BaseModel): + pass + + +class Analysis(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + aligner: str | None = Field( + None, + description='Name or identifier of the mapping/alignment software/pipeline', + examples=['bwa-0.7.8'], + ) + analysisDate: date = Field( + ..., + description='Date at which analysis was performed.\n', + examples=['2021-10-17'], + ) + biosampleId: str | None = Field( + None, + description='Local reference to the `id` of the biosample this analysis is reporting on.', + examples=['S0001', 'onekgbs-NA07346'], + ) + id: str = Field( + ..., description='Analysis id for internal referencing; unique in the dataset.' + ) + individualId: str | None = Field( + None, + description='Local reference to the `id` of the individual this analysis is reporting on.', + examples=['P0001', 'onekgind-NA07346'], + ) + info: Info | None = None + pipelineName: str = Field( + ..., + description='Analysis pipeline and version.', + examples=['Pipeline-panel-0001-v1'], + ) + pipelineRef: str | None = Field( + None, + description='Link to information about or repository of the analysis pipeline.', + examples=[ + 'https://doi.org/10.48511/workflowhub.workflow.111.1', + 'https://doi.org/10.1093/bib/bbad541', + ], + ) + runId: str | None = Field( + None, + description='Local reference to the associated experimental run.', + examples=['SRR10903401'], + ) + variantCaller: str | None = Field( + None, + description='Name or identifier of the variant calling software/pipeline', + examples=['GATK4.0', 'labelSeg'], + ) diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/biosample/beacon_biosample_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/biosample/beacon_biosample_v2_2_0.py index 8a3d2892..f657c55b 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/biosample/beacon_biosample_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/biosample/beacon_biosample_v2_2_0.py @@ -1 +1,749 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.non_collections.biosample.beacon_biosample_v2_1_0 import Biosample +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json +# timestamp: 2026-07-31T13:34:13+00:00 + +from __future__ import annotations + +from datetime import date as date_aliased +from enum import Enum + +from pydantic import ( + AnyUrl, + AwareDatetime, + BaseModel, + ConfigDict, + Field, + RootModel, + conint, + constr, +) + + +class CURIE(RootModel[constr(pattern=r'^\w[^:]+:.+$')]): + root: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + + +class FieldSchema(RootModel[str]): + root: str = Field( + ..., + description='Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.', + ) + + +class ApiVersion(RootModel[str]): + root: str = Field( + ..., + description='Version of API, e.g. in request or response. Beacon uses a Github-style, "v"-prefixed semantic versioning format.', + examples=['v2.0.1', 'v0.3'], + ) + + +class BeaconError(BaseModel): + errorCode: int = Field(..., description='Entry not found', examples=['404']) + errorMessage: str | None = Field( + None, examples=['The provided parameters are incomplete: `start` is missing.'] + ) + + +class BeaconId(RootModel[str]): + root: str = Field( + ..., + description='The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.', + examples=['org.example.beacon.v2', 'org.progenetix.beacon'], + ) + + +class CountAdjustedToItem(RootModel[conint(ge=1) | str]): + root: conint(ge=1) | str + + +class CountAdjustedTo(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class CountPrecision(Enum): + exact = 'exact' + imprecise = 'imprecise' + rounded = 'rounded' + + +class Exists(RootModel[bool]): + root: bool = Field( + ..., + description='Indicator of whether any record was observed in any of the collections queried. This should be non-null.', + examples=[True], + ) + + +class Filters(RootModel[list[str]]): + root: list[str] = Field( + ..., + description='Ontology based filters. A CURIE syntax is encouraged to be used.', + examples=[['BTO:0000199', 'PATO:0000383']], + ) + + +class Granularity(Enum): + boolean = 'boolean' + count = 'count' + record = 'record' + + +class IncludeResultsetResponses(Enum): + ALL = 'ALL' + HIT = 'HIT' + MISS = 'MISS' + NONE = 'NONE' + + +class Limit(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 10, + description='Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.', + examples=[10], + ) + + +class NonFilteredQueriesAllowed(RootModel[bool]): + root: bool = Field( + True, + description="Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.", + ) + + +class NumTotalResults(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + ..., + description='Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.', + examples=[123], + ) + + +class PageToken(RootModel[str]): + root: str = Field( + ..., + description='A hash or similar that allows the server to retrieve a "page", e.g. (a subset of) a query response.', + examples=['ab0sc&fe1dd'], + ) + + +class SchemasPerEntity(BaseModel): + entityType: str | None = Field(None, examples=['Individual']) + schema_: str | None = Field( + None, + alias='schema', + examples=[ + './ga4gh-beacon-dataset-v2.0.0', + 'https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json', + ], + ) + + +class Skip(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 0, + description='* In the request: number of pages to skip * In the response: number of pages that has been skipped', + examples=[0], + ) + + +class TestMode(RootModel[bool]): + root: bool = Field( + False, + description='Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.', + ) + + +class Info(BaseModel): + pass + + +class CountAdjustedTo1(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class KaryotypicSex(Enum): + UNKNOWN_KARYOTYPE = 'UNKNOWN_KARYOTYPE' + XX = 'XX' + XY = 'XY' + XO = 'XO' + XXY = 'XXY' + XXX = 'XXX' + XXYY = 'XXYY' + XXXY = 'XXXY' + XXXX = 'XXXX' + XYY = 'XYY' + OTHER_KARYOTYPE = 'OTHER_KARYOTYPE' + + +class Timestamp(RootModel[AwareDatetime]): + root: AwareDatetime = Field( + ..., + description='Time in date-time ISO8601 string format.', + examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'], + ) + + +class Age(BaseModel): + iso8601duration: str = Field( + ..., + description='Represents age as a ISO8601 duration (e.g., P40Y10M05D).', + examples=['P32Y6M1D'], + ) + + +class AgeRange(BaseModel): + end: Age = Field( + ..., description='Represents age as an ISO8601 duration (e.g., P59Y).' + ) + start: Age = Field( + ..., description='Represents age as an ISO8601 duration (e.g., P18Y).' + ) + + +class GestationalAge(BaseModel): + days: int | None = Field( + None, + description='Days beyond the completed weeks, if available.', + examples=[2, 4], + ) + weeks: int = Field( + ..., + description='Completed weeks of gestation according to the above definition.', + examples=[4, 33], + ) + + +class TimeInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + end: Timestamp = Field(..., examples=['2022-03-10T15:25:07Z']) + start: Timestamp = Field( + ..., examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'] + ) + + +class ExternalReference(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: str | None = Field( + None, + description='An application specific identifier. RECOMMENDED.', + examples=['PMID:34054918'], + ) + notes: str | None = Field( + None, + description='An optional text descriptor. Renamed compared to GA4GH Phenopackets v2 `ExternalReference.description`', + examples=[ + 'Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes' + ], + ) + reference: str | None = Field( + None, + description='A url.', + examples=['https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155688/'], + ) + + +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: CURIE + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HandoverType(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.', + examples=[ + {'id': 'EDAM:2572', 'label': 'BAM'}, + {'id': 'EDAM:3016', 'label': 'VCF'}, + {'id': 'CUSTOM:pgxseg', 'label': 'genomic variants in .pgxseg file format'}, + ], + ) + + +class ListOfSchemas(RootModel[list[SchemasPerEntity]]): + root: list[SchemasPerEntity] = Field( + ..., description='Set of schemas to be used in the response to a request.' + ) + + +class Pagination(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class Pagination1(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class Ethnicity(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]', + examples=[ + {'id': 'NCIT:C42331', 'label': 'African'}, + {'id': 'NCIT:C41260', 'label': 'Asian'}, + {'id': 'NCIT:C126535', 'label': 'Australian'}, + {'id': 'NCIT:C43851', 'label': 'European'}, + {'id': 'NCIT:C77812', 'label': 'North American'}, + {'id': 'NCIT:C126531', 'label': 'Latin American'}, + {'id': 'NCIT:C104495', 'label': 'Other race'}, + ], + ) + + +class GeographicLocation(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).', + examples=[ + {'id': 'GAZ:00002955', 'label': 'Slovenia'}, + {'id': 'GAZ:00002459', 'label': 'United States of America'}, + {'id': 'GAZ:00316959', 'label': 'Municipality of El Masnou'}, + {'id': 'GAZ:00000460', 'label': 'Eurasia'}, + ], + ) + + +class SeverityLevel(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Severity as applicable to phenotype or disease observed. Recommended are values from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. Source: Phenopackets v2', + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012829', 'label': 'Profound'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + {'id': 'HP:0012825', 'label': 'Mild'}, + {'id': 'HP:0012827', 'label': 'Borderline'}, + ], + ) + + +class Sex(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993): "unknown" (not assessed or not available) - NCIT:C17998; "female" - NCIT:C16576; "male" - NCIT:C20197', + examples=[ + {'id': 'NCIT:C16576', 'label': 'female'}, + {'id': 'NCIT:C20197', 'label': 'male'}, + {'id': 'NCIT:C1799', 'label': 'unknown'}, + ], + ) + + +class TimeElement( + RootModel[Age | AgeRange | GestationalAge | Timestamp | TimeInterval | OntologyTerm] +): + root: Age | AgeRange | GestationalAge | Timestamp | TimeInterval | OntologyTerm = ( + Field( + ..., + description='Definition of a wrapper for various time descriptors. This follows the\nPhenopackets structure https://github.com/phenopackets/phenopacket-schema/blob/v2/docs/time-element.rst', + title='TimeElement', + ) + ) + + +class Procedure(BaseModel): + ageAtProcedure: TimeElement | None = Field( + None, description='Compares to Phenopackets v2 `Procedure.performed`' + ) + bodySite: OntologyTerm | None = Field( + None, + description='Specific body site where the procedure was performed. Recommended valuee from Uber-anatomy ontology (UBERON)', + examples=[ + {'id': 'UBERON:0003403', 'label': 'Skin of forearm'}, + {'id': 'UBERON:0003214', 'label': 'mammary gland alveolus'}, + ], + ) + dateOfProcedure: date_aliased | None = Field( + None, + description='Date of procedure, in ISO8601 format', + examples=['2010-07-10'], + ) + procedureCode: OntologyTerm = Field( + ..., + description="Clinical procedure performed with recommended values from Medical Action Ontology (MAXO) 'Medical action' term tree (MAXO:0000001). Compares to Phenopackets v2 `Procedure.code`", + examples=[ + {'id': 'MAXO:0001175', 'label': 'liver transplantation'}, + {'id': 'MAXO:0000136', 'label': 'high-resolution microendoscopy'}, + {'id': 'OBI:0002654', 'label': 'needle biopsy'}, + ], + ) + + +class Evidence(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + evidenceCode: OntologyTerm = Field( + ..., + description='An ontology class that represents the evidence type', + examples=[ + { + 'id': 'ECO:0006017', + 'label': 'author statement from published clinical study used in manual assertion', + } + ], + ) + reference: ExternalReference | None = Field( + None, + description='Representation of the source of the evidence', + examples=[ + { + 'id': 'PMID:30962759', + 'label': 'Recurrent Erythema Nodosum in a Child with a SHOC2 Gene Mutation', + } + ], + ) + + +class Handover(BaseModel): + handoverType: HandoverType + note: str | None = Field( + None, + description='An optional text including considerations on the handover link provided.', + examples=['This handover link provides access to a summarized VCF.'], + ) + url: AnyUrl = Field( + ..., + description='URL endpoint to where the handover process could progress, in RFC3986 format', + examples=[ + 'https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/' + ], + ) + + +class ListOfHandovers(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class Unit(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants', + examples=[ + {'id': 'NCIT:C70575', 'label': 'Roentgen'}, + {'id': 'NCIT:C28252', 'label': 'Kilogram'}, + {'id': 'NCIT:C28253', 'label': 'Milligram'}, + ], + ) + + +class ListOfHandovers1(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class PhenotypicFeature(BaseModel): + evidence: Evidence | None = Field( + None, + description='The evidence for an assertion of the observation of a type. RECOMMENDED.', + ) + excluded: bool | None = Field( + False, + description='Flag to indicate whether the phenotypic feature was observed or not. Default is ‘false’, in other words the phenotype was observed. Therefore it is only used in cases where the phenotype was looked for but found to be absent. More formally, this modifier indicates the logical negation of the OntologyClass used in the `featureType` field. CAUTION: It is imperative to check this field for correct interpretation of the phenotype! Source: Phenopackets v2', + ) + featureType: OntologyTerm = Field( + ..., + description='Term denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO)', + examples=[ + {'id': 'HP:0000002', 'label': 'Abnormality of body height'}, + {'id': 'HP:0002006', 'label': 'Facial cleft'}, + {'id': 'HP:0012469', 'label': 'Infantile spasms'}, + ], + ) + modifiers: list[OntologyTerm] | None = Field( + None, + description='This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. Example use here would be one or more terms from HPO Clinical Modifier (HP:0012823). Source: Phenopackets v2', + examples=[ + {'id': 'HP:0032500', 'label': 'Exacerbated by tobacco use'}, + {'id': 'HP:4000053', 'label': 'Displaced fracture'}, + ], + ) + notes: str | None = Field( + None, + description='Unstructured text to describe additional properties of this phenotypic feature.', + examples=['Some free text'], + ) + onset: TimeElement | None = Field( + None, description='Age or time at which the feature was first observed.' + ) + resolution: TimeElement | None = Field( + None, description='Age or time at which the feature resolved or abated.' + ) + severity: SeverityLevel | None = Field( + None, + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + ], + ) + + +class ReferenceRange(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + high: float = Field(..., description='Upper range end of normal', examples=[135]) + low: float = Field(..., description='Lower range end of normal', examples=[85]) + unit: Unit = Field( + ..., + description='The kind of unit.', + examples=[{'id': 'NCIT:C49670', 'label': 'Millimeter of Mercury'}], + ) + + +class Quantity(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + referenceRange: ReferenceRange | None = Field( + None, description='The normal range for the value', examples=[{}] + ) + unit: Unit + value: float = Field(..., description='The value of the quantity in the units') + + +class TypedQuantity(BaseModel): + quantity: Quantity = Field( + ..., + description='Quantity denoting the outcome of the measurement', + examples=[ + { + 'unit': {'id': 'NCIT:C49670', 'label': 'Millimeter of Mercury'}, + 'value': 110, + } + ], + ) + quantityType: OntologyTerm = Field( + ..., + description='OntologyClass to describe the type of the measurement. Renamed compared to GA4GH Phenopackets v2 `ComplexValue.TypedQuantity.type`', + examples=[{'id': 'NCIT:C25298', 'label': 'Systolic Blood Pressure'}], + ) + + +class Value(RootModel[Quantity | OntologyTerm]): + root: Quantity | OntologyTerm = Field( + ..., + description='Definition of a value class. Provenance: GA4GH Phenopackets v2 `Value`', + title='Value', + ) + + +class ComplexValue(BaseModel): + typedQuantities: list[TypedQuantity] = Field( + ..., + description='List of quantities required to fully describe the complex value', + ) + + +class Measurement(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + assayCode: OntologyTerm = Field( + ..., + description='Class that describes the assay used to produce the measurement. Renamed compared to GA4GH Phenopackets v2 `Measurement.assay`', + examples=[{'id': 'LOINC:26515-7', 'label': 'Platelets [#/volume] in Blood'}], + ) + date: date_aliased | None = Field( + None, + description='Date of measurement. Addition compared to Phenopackets model.', + ) + measurementValue: Value | ComplexValue = Field( + ..., description='The result of the measurement' + ) + notes: str | None = Field( + None, + description='Unstructured text to describe this measurement. Addition compared to Phenopackets model.', + examples=['Some free text'], + ) + observationMoment: TimeElement | None = Field( + None, + description='Moment in time at which measurement was performed. RECOMMENDED. Renamed compared to GA4GH Phenopackets v2 `Measurement.time_observed`', + examples=[{'age': {'iso8601duration': 'P53Y8M'}}], + ) + procedure: Procedure | None = Field( + None, + description='Clinical procedure performed to acquire the sample used for the measurement', + examples=[ + {'code': {'id': 'NCIT:C5189', 'label': 'Radical Cystoprostatectomy'}} + ], + ) + + +class Biosample(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + biosampleStatus: OntologyTerm = Field( + ..., + description='Ontology value from Experimental Factor Ontology (EFO) Material Entity term (BFO:0000040). Classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654).', + examples=[ + {'id': 'EFO:0009654', 'label': 'reference sample'}, + {'id': 'EFO:0009655', 'label': 'abnormal sample'}, + {'id': 'EFO:0009656', 'label': 'neoplastic sample'}, + {'id': 'EFO:0010941', 'label': 'metastasis sample'}, + {'id': 'EFO:0010942', 'label': 'primary tumor sample'}, + {'id': 'EFO:0010943', 'label': 'recurrent tumor sample'}, + ], + ) + collectionDate: date_aliased | None = Field( + None, + description='Date of biosample collection in ISO8601 format.', + examples=['2021-04-23'], + ) + collectionMoment: str | None = Field( + None, + description="Individual's or cell cullture age at the time of sample collection in the ISO8601 duration format `P[n]Y[n]M[n]DT[n]H[n]M[n]S`.", + examples=['P32Y6M1D', 'P7D'], + ) + diagnosticMarkers: list[OntologyTerm] | None = Field( + None, description='Clinically relevant biomarkers. RECOMMENDED.' + ) + histologicalDiagnosis: OntologyTerm | None = Field( + None, + description='Disease diagnosis that was inferred from the histological examination. RECOMMENDED.', + examples=[{'id': 'NCIT:C3778', 'label': 'Serous Cystadenocarcinoma'}], + ) + id: str = Field( + ..., + description='Biosample identifier (external accession or internal ID).', + examples=['S0001'], + ) + individualId: str | None = Field( + None, + description='Reference to the individual from which that sample was obtained.', + examples=['P0001'], + ) + info: Info | None = None + measurements: list[Measurement] | None = Field( + None, description='List of measurements of the sample.' + ) + notes: str | None = Field( + None, + description='Any relevant info about the biosample that does not fit into any other field in the schema.', + examples=['Some free text'], + ) + obtentionProcedure: Procedure | None = Field( + None, + description='Ontology value from NCIT Intervention or Procedure ontology term (NCIT:C25218) describing the procedure for sample obtention, e.g. NCIT:C15189 (biopsy).', + examples=[ + {'code': {'id': 'NCIT:C15189', 'label': 'biopsy'}}, + {'code': {'id': 'NCIT:C157179', 'label': 'FGFR1 Mutation Analysis'}}, + ], + ) + pathologicalStage: OntologyTerm | None = Field( + None, + description='Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. RECOMMENDED.', + examples=[{'id': 'NCIT:C27977', 'label': 'Stage IIIA'}], + ) + pathologicalTnmFinding: list[OntologyTerm] | None = Field( + None, + description='Pathological TNM findings, if applicable, preferably as subclass of NCIT:C48698 - Cancer TNM Finding Category (NCIT:C48698). RECOMMENDED.', + examples=[ + {'id': 'NCIT:C48725', 'label': 'T2a Stage Finding'}, + {'id': 'NCIT:C48709', 'label': 'N1c Stage Finding'}, + {'id': 'NCIT:C48699', 'label': 'M0 Stage Finding'}, + ], + ) + phenotypicFeatures: list[PhenotypicFeature] | None = Field( + None, description='List of phenotypic abnormalities of the sample. RECOMMENDED.' + ) + sampleOriginDetail: OntologyTerm | None = Field( + None, + description="Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType'. Value from Uber-anatomy ontology (UBERON) or BRENDA tissue / enzyme source (BTO), Ontology for Biomedical Investigations (OBI) or Cell Line Ontology (CLO), e.g. 'cerebellar vermis' (UBERON:0004720), 'HEK-293T cell' (BTO:0002181), 'nasopharyngeal swab specimen' (OBI:0002606), 'cerebrospinal fluid specimen' (OBI:0002502).", + examples=[ + {'id': 'UBERON:0000474', 'label': 'female reproductive system'}, + {'id': 'BTO:0002181', 'label': 'HEK-293T cell'}, + {'id': 'OBI:0002606', 'label': 'nasopharyngeal swab specimen'}, + ], + ) + sampleOriginType: OntologyTerm = Field( + ..., + description="Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology, e.g. 'specimen from organism' (OBI:0001479),'xenograft' (OBI:0100058), 'cell culture' (OBI:0001876)", + examples=[ + {'id': 'OBI:0001479', 'label': 'specimen from organism'}, + {'id': 'OBI:0001876', 'label': 'cell culture'}, + {'id': 'OBI:0100058', 'label': 'xenograft'}, + ], + ) + sampleProcessing: OntologyTerm | None = Field( + None, + description='Status of how the specimen was processed,e.g. a child term of EFO:0009091.', + examples=[{'id': 'EFO:0009129', 'label': 'mechanical dissociation'}], + ) + sampleStorage: OntologyTerm | None = Field( + None, description='Status of how the specimen was stored.', examples=[{}] + ) + tumorGrade: OntologyTerm | None = Field( + None, + description='Term representing the tumor grade. Child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent.', + examples=[{'id': 'NCIT:C28080', 'label': 'Grade 3a'}], + ) + tumorProgression: OntologyTerm | None = Field( + None, + description='Tumor progression category indicating primary, metastatic or recurrent progression. Ontology value from Neoplasm by Special Category ontology (NCIT:C7062), e.g. NCIT:C84509 (Primary Malignant Neoplasm).', + examples=[ + {'id': 'NCIT:C84509', 'label': 'Primary Malignant Neoplasm'}, + {'id': 'NCIT:C4813', 'label': 'Recurrent Malignant Neoplasm'}, + ], + ) diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py index 2b4d38ed..04646248 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py @@ -1 +1,1013 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.non_collections.genomicVariant.beacon_genomicVariant_v2_0_0 import Genomicvariant +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json +# timestamp: 2026-07-31T13:35:39+00:00 + +from __future__ import annotations + +from enum import Enum +from typing import Any, Literal + +from pydantic import AnyUrl, BaseModel, ConfigDict, Field, RootModel, conint, constr + + +class Info(BaseModel): + pass + + +class CopyChange(Enum): + efo_0030069 = 'efo:0030069' + efo_0020073 = 'efo:0020073' + efo_0030068 = 'efo:0030068' + efo_0030067 = 'efo:0030067' + efo_0030064 = 'efo:0030064' + efo_0030070 = 'efo:0030070' + efo_0030071 = 'efo:0030071' + efo_0030072 = 'efo:0030072' + + +class Number(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['Number'] = Field(..., description='MUST be "Number"') + value: int = Field(..., description='The value represented by Number') + + +class DefiniteRange(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['DefiniteRange'] = Field(..., description='MUST be "DefiniteRange"') + min: float = Field(..., description='The minimum value; inclusive') + max: float = Field(..., description='The maximum value; inclusive') + + +class Comparator(Enum): + field__ = '<=' + field___1 = '>=' + + +class IndefiniteRange(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['IndefiniteRange'] = Field( + ..., description='MUST be "IndefiniteRange"' + ) + value: int = Field(..., description='The bounded value; inclusive') + comparator: Comparator = Field( + ..., + description='MUST be one of "<=" or ">=", indicating which direction the range is indefinite', + ) + + +class CURIE(RootModel[constr(pattern=r'^\w[^:]*:.+$')]): + root: constr(pattern=r'^\w[^:]*:.+$') = Field( + ..., + description='A [W3C Compact URI](https://www.w3.org/TR/curie/) formatted string. A CURIE string has the structure ``prefix``:``reference``, as defined by the W3C syntax.', + examples=['ensembl:ENSG00000139618'], + ) + + +class HumanCytoband( + RootModel[constr(pattern=r'^cen|[pq](ter|([1-9][0-9]*(\.[1-9][0-9]*)?))$')] +): + root: constr(pattern=r'^cen|[pq](ter|([1-9][0-9]*(\.[1-9][0-9]*)?))$') = Field( + ..., + description='A character string representing cytobands derived from the *International System for Human Cytogenomic Nomenclature* (ISCN) [guidelines](http://doi.org/10.1159/isbn.978-3-318-06861-0).', + examples=['q22.3'], + ) + + +class Residue(RootModel[constr(pattern=r'[A-Z*\-]')]): + root: constr(pattern=r'[A-Z*\-]') = Field( + ..., + description='A character representing a specific residue (i.e., molecular species) or groupings of these ("ambiguity codes"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids.', + ) + + +class Sequence(RootModel[constr(pattern=r'^[A-Z*\-]*$')]): + root: constr(pattern=r'^[A-Z*\-]*$') = Field( + ..., + description='A character string of Residues that represents a biological sequence using the conventional sequence order (5’-to-3’ for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequences.', + ) + + +class SequenceState(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['SequenceState'] = Field(..., description='MUST be "SequenceState"') + sequence: Sequence = Field(..., description='A string of Residues') + + +class SimpleInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['SimpleInterval'] = Field(..., description='MUST be "SimpleInterval"') + start: int = Field(..., description='The start coordinate') + end: int = Field(..., description='The end coordinate') + + +class CURIEModel(RootModel[constr(pattern=r'^\w[^:]+:.+$')]): + root: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + + +class FieldSchema(RootModel[str]): + root: str = Field( + ..., + description='Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.', + ) + + +class ApiVersion(RootModel[str]): + root: str = Field( + ..., + description='Version of API, e.g. in request or response. Beacon uses a Github-style, "v"-prefixed semantic versioning format.', + examples=['v2.0.1', 'v0.3'], + ) + + +class BeaconError(BaseModel): + errorCode: int = Field(..., description='Entry not found', examples=['404']) + errorMessage: str | None = Field( + None, examples=['The provided parameters are incomplete: `start` is missing.'] + ) + + +class BeaconId(RootModel[str]): + root: str = Field( + ..., + description='The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.', + examples=['org.example.beacon.v2', 'org.progenetix.beacon'], + ) + + +class CountAdjustedToItem(RootModel[conint(ge=1) | str]): + root: conint(ge=1) | str + + +class CountAdjustedTo(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class CountPrecision(Enum): + exact = 'exact' + imprecise = 'imprecise' + rounded = 'rounded' + + +class Exists(RootModel[bool]): + root: bool = Field( + ..., + description='Indicator of whether any record was observed in any of the collections queried. This should be non-null.', + examples=[True], + ) + + +class Filters(RootModel[list[str]]): + root: list[str] = Field( + ..., + description='Ontology based filters. A CURIE syntax is encouraged to be used.', + examples=[['BTO:0000199', 'PATO:0000383']], + ) + + +class Granularity(Enum): + boolean = 'boolean' + count = 'count' + record = 'record' + + +class IncludeResultsetResponses(Enum): + ALL = 'ALL' + HIT = 'HIT' + MISS = 'MISS' + NONE = 'NONE' + + +class Limit(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 10, + description='Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.', + examples=[10], + ) + + +class NonFilteredQueriesAllowed(RootModel[bool]): + root: bool = Field( + True, + description="Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.", + ) + + +class NumTotalResults(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + ..., + description='Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.', + examples=[123], + ) + + +class PageToken(RootModel[str]): + root: str = Field( + ..., + description='A hash or similar that allows the server to retrieve a "page", e.g. (a subset of) a query response.', + examples=['ab0sc&fe1dd'], + ) + + +class SchemasPerEntity(BaseModel): + entityType: str | None = Field(None, examples=['Individual']) + schema_: str | None = Field( + None, + alias='schema', + examples=[ + './ga4gh-beacon-dataset-v2.0.0', + 'https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json', + ], + ) + + +class Skip(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 0, + description='* In the request: number of pages to skip * In the response: number of pages that has been skipped', + examples=[0], + ) + + +class TestMode(RootModel[bool]): + root: bool = Field( + False, + description='Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.', + ) + + +class ExternalReference(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: str | None = Field( + None, + description='An application specific identifier. RECOMMENDED.', + examples=['PMID:34054918'], + ) + notes: str | None = Field( + None, + description='An optional text descriptor. Renamed compared to GA4GH Phenopackets v2 `ExternalReference.description`', + examples=[ + 'Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes' + ], + ) + reference: str | None = Field( + None, + description='A url.', + examples=['https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155688/'], + ) + + +class ClinicalRelevance(Enum): + benign = 'benign' + likely_benign = 'likely benign' + uncertain_significance = 'uncertain significance' + likely_pathogenic = 'likely pathogenic' + pathogenic = 'pathogenic' + + +class PopulationFrequency(BaseModel): + alleleFrequency: float = Field( + ..., description='Allele frequency between 0 and 1.', examples=[3.186e-05] + ) + population: str = Field( + ..., + description='A name for the population. A population could an ethnic, geographical one or just the members of a study.', + examples=[ + 'East Asian', + 'ICGC Chronic Lymphocytic Leukemia-ES', + 'Men', + 'Children', + ], + ) + + +class SoftwareTool(BaseModel): + toolName: str = Field( + ..., + description='Name of the tool.', + examples=['Ensembl Variant Effect Predictor (VEP)'], + ) + toolReferences: dict[str, Any] = Field( + ..., + description='References to the tool', + examples=[ + {'bio.toolsId': 'https://bio.tools/vep'}, + {'url': 'https://www.ensembl.org/vep'}, + ], + min_length=1, + ) + version: str = Field(..., description='Version used.', examples=['rel 104']) + + +class Text(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['Text'] = Field(..., description='MUST be "Text"') + definition: str = Field( + ..., + description='A textual representation of variation not representable by other subclasses of Variation.', + ) + + +class SequenceInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['SequenceInterval'] = Field( + ..., description='MUST be "SequenceInterval"' + ) + start: DefiniteRange | IndefiniteRange | Number = Field( + ..., + description='The start coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than the value of `end`.', + ) + end: DefiniteRange | IndefiniteRange | Number = Field( + ..., + description='The end coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than the value of `start`.', + ) + + +class CytobandInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['CytobandInterval'] = Field( + ..., description='MUST be "CytobandInterval"' + ) + start: HumanCytoband = Field( + ..., + description='The start cytoband region. MUST specify a region nearer the terminal end (telomere) of the chromosome p-arm than `end`.', + ) + end: HumanCytoband = Field( + ..., + description='The end cytoband region. MUST specify a region nearer the terminal end (telomere) of the chromosome q-arm than `start`.', + ) + + +class LiteralSequenceExpression(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['LiteralSequenceExpression'] = Field( + ..., description='MUST be "LiteralSequenceExpression"' + ) + sequence: Sequence = Field(..., description='the literal Sequence expressed') + + +class Gene(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['Gene'] = Field(..., description='MUST be "Gene"') + gene_id: CURIE = Field(..., description='A CURIE reference to a Gene concept') + + +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: CURIEModel + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HandoverType(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.', + examples=[ + {'id': 'EDAM:2572', 'label': 'BAM'}, + {'id': 'EDAM:3016', 'label': 'VCF'}, + {'id': 'CUSTOM:pgxseg', 'label': 'genomic variants in .pgxseg file format'}, + ], + ) + + +class ListOfSchemas(RootModel[list[SchemasPerEntity]]): + root: list[SchemasPerEntity] = Field( + ..., description='Set of schemas to be used in the response to a request.' + ) + + +class Pagination(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class FrequencyInPopulations(BaseModel): + frequencies: list[PopulationFrequency] = Field(..., min_length=1) + source: str = Field( + ..., + description='The study', + examples=[ + 'The Genome Aggregation Database (gnomAD)', + 'The European Genome-phenome Archive (EGA)', + ], + ) + sourceReference: str = Field( + ..., + description='A reference to further documentation or details.', + examples=['https://gnomad.broadinstitute.org/', 'https://ega-archive.org/'], + ) + version: str | None = Field( + None, description='version of the source data.', examples=['gnomAD v3.1.1'] + ) + + +class GenomicFeature(BaseModel): + featureClass: OntologyTerm = Field( + ..., + description='Ontology term that describes the class of genomic feature affected by the variant. Values from SO (Sequence ontology) are recommended, e.g. `SO:0001623: 5 prime UTR variant`', + examples=[{'id': 'SO:0001623', 'label': '5 prime UTR variant'}], + ) + featureID: OntologyTerm | None = Field( + None, + description='Where applicable, ID/accession/name of genomic feature related to the `featureClass`, preferably in CURIE format. If the value is a gene id or name, it points to the gene related to the `featureClass`, e.g. `the 5 prime UTR upstream of TP53`', + examples=[{'id': 'HGNC:11998', 'label': 'TP53'}], + ) + + +class Identifiers(BaseModel): + clinvarVariantId: constr(pattern=r'^(clinvar:)?\d+$') | None = Field( + None, + description='ClinVar variant id. Other id values used by ClinVar can be added to `variantAlternativeIds`', + examples=['clinvar:12345', '9325'], + ) + genomicHGVSId: str | None = Field( + None, description='HGVSId descriptor.', examples=['NC_000017.11:g.43057063G>A'] + ) + proteinHGVSIds: list[str] | None = Field( + None, + description='List of HGVSId descriptor(s) at protein level (for protein-altering variants).', + examples=[['NP_009225.1:p.Glu1817Ter'], ['LRG 199p1:p.Val25Gly (preferred)']], + ) + transcriptHGVSIds: list[str] | None = Field( + None, + description='List of HGVSId descriptor(s) at transcript level.', + examples=[['NC 000023.10(NM004006.2):c.357+1G']], + ) + variantAlternativeIds: list[ExternalReference] | None = Field( + None, + description='List of cross-referencing ID(s), for the variant in other databases (e.g. dbSNP, ClinVar, ClinGen, COSMIC), as `externalReferences` with CURIE(s).', + examples=[ + [ + { + 'id': 'dbSNP:rs587780345', + 'notes': 'dbSNP id', + 'reference': 'https://www.ncbi.nlm.nih.gov/snp/rs587780345', + }, + { + 'id': 'ClinGen:CA152954', + 'notes': 'ClinGen Allele Registry id', + 'reference': 'https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA152954', + }, + { + 'id': 'UniProtKB:P35557#VAR_003699', + 'reference': 'https://www.uniprot.org/uniprot/P35557#VAR_003699', + }, + ], + [ + { + 'id': 'OMIM:164757.0001', + 'reference': 'https://www.omim.org/entry/164757#0001', + } + ], + ], + ) + + +class MolecularAttributes(BaseModel): + aminoacidChanges: list[str] | None = Field( + None, + description='Lisf of change(s) at aminoacid level for protein affecting variants.', + examples=[['V304*']], + ) + geneIds: list[str] | None = Field( + None, + description='Symbolic names or identifiers used for a gene', + examples=[['ACE2'], ['BRCA1', 'ENSG00000012048']], + ) + genomicFeatures: list[GenomicFeature] | None = Field( + None, description='List of Genomic feature(s) affected by the variant.' + ) + molecularEffects: list[OntologyTerm] | None = Field( + None, + description='Ontology term that includes describes the class of molecular consequence generated by the variant. Values from SO (Sequence Ontology) are recommended, e.g. `SO:0001583: missense variant`.', + examples=[ + {'id': 'SO:0002322', 'label': 'stop gained NMD escaping'}, + {'id': 'SO:0001583', 'label': 'missense variant'}, + ], + ) + + +class PhenoClinicEffect(BaseModel): + annotatedWith: SoftwareTool | None = None + category: OntologyTerm | None = Field( + None, + description='Ontology term for the type of disease, condition, phenotypic measurement, etc.', + examples=[ + {'id': 'MONDO:0000001', 'label': 'disease or disorder'}, + {'id': 'HP:0000118', 'label': 'phenotypic abnormality'}, + ], + ) + clinicalRelevance: ClinicalRelevance | None = Field( + None, + description='Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (NCIT:C168798).', + examples=['pathogenic'], + ) + conditionId: str = Field( + ..., + description='Internal identifier of the phenotype or clinical effect.', + examples=['disease1', 'phen2234'], + ) + effect: OntologyTerm = Field( + ..., + description='Ontology term for the phenotypic or clinical effect', + examples=[ + { + 'id': 'MONDO:0003582', + 'label': 'hereditary breast ovarian cancer syndrome', + }, + {'id': 'HP:0000256', 'label': 'macrocephaly'}, + ], + ) + evidenceType: OntologyTerm | None = Field( + None, + description='Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO)', + examples=[ + {'id': 'ECO:0000361', 'label': 'inferential evidence'}, + {'id': 'ECO:0000006', 'label': 'experimental evidence'}, + ], + ) + + +class VariantLevelData(BaseModel): + clinicalInterpretations: list[PhenoClinicEffect] | None = None + phenotypicEffects: list[PhenoClinicEffect] | None = None + + +class ChromosomeLocation(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Location Id. MUST be unique within document.' + ) + type: Literal['ChromosomeLocation'] = Field( + ..., description='MUST be "ChromosomeLocation"' + ) + species_id: CURIE = Field( + ..., + description='CURIE representing a species from the [NCBI species taxonomy](https://registry.identifiers.org/registry/taxonomy). Default: "taxonomy:9606" (human)', + ) + chr: str = Field( + ..., + description='The symbolic chromosome name. For humans, For humans, chromosome names MUST be one of 1..22, X, Y (case-sensitive)', + ) + interval: CytobandInterval = Field( + ..., description='The chromosome region defined by a CytobandInterval' + ) + + +class SequenceLocation(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Location Id. MUST be unique within document.' + ) + type: Literal['SequenceLocation'] = Field( + ..., description='MUST be "SequenceLocation"' + ) + sequence_id: CURIE = Field( + ..., description='A VRS Computed Identifier for the reference Sequence.' + ) + interval: SequenceInterval | SimpleInterval = Field( + ..., description='Reference sequence region defined by a SequenceInterval.' + ) + + +class DerivedSequenceExpression(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['DerivedSequenceExpression'] = Field( + ..., description='MUST be "DerivedSequenceExpression"' + ) + location: SequenceLocation = Field( + ..., description='The location from which the approximate sequence is derived' + ) + reverse_complement: bool = Field( + ..., + description='A flag indicating if the expressed sequence is the reverse complement of the sequence referred to by `location`', + ) + + +class RepeatedSequenceExpression(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['RepeatedSequenceExpression'] = Field( + ..., description='MUST be "RepeatedSequenceExpression"' + ) + seq_expr: DerivedSequenceExpression | LiteralSequenceExpression = Field( + ..., description='An expression of the repeating subsequence' + ) + count: DefiniteRange | IndefiniteRange | Number = Field( + ..., description='The count of repeated units, as an integer or inclusive range' + ) + + +class ComposedSequenceExpression(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['ComposedSequenceExpression'] = Field( + 'ComposedSequenceExpression', description='MUST be "ComposedSequenceExpression"' + ) + components: list[ + DerivedSequenceExpression + | LiteralSequenceExpression + | RepeatedSequenceExpression + ] = Field( + ..., + description='An ordered list of SequenceExpression components comprising the expression.', + min_length=2, + ) + + +class Feature(RootModel[Gene]): + root: Gene = Field( + ..., + description='A named entity that can be mapped to a Location. Genes, protein domains, exons, and chromosomes are some examples of common biological entities that may be Features.', + discriminator='type', + ) + + +class CaseLevelVariant(BaseModel): + alleleOrigin: OntologyTerm | None = Field( + None, + description='Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762). Categories are `somatic variant`, `germline variant`, `maternal variant`, `paternal variant`, `de novo variant`, `pedigree specific variant`, `population specific variant`. Corresponds to Variant Inheritance in FHIR.', + examples=[ + {'id': 'SO:0001777', 'label': 'somatic variant'}, + {'id': 'SO:0001778', 'label': 'germline variant'}, + {'id': 'SO:0001775', 'label': 'maternal variant'}, + {'id': 'SO:0001776', 'label': 'paternal variant'}, + {'id': 'SO:0001781', 'label': 'de novo variant'}, + {'id': 'SO:0001779', 'label': 'pedigree specific variant'}, + {'id': 'SO:0001780', 'label': 'population specific variant'}, + ], + ) + analysisId: str | None = Field( + None, + description='Reference to the bioinformatics analysis ID (`analysis.id`)', + examples=['pgxcs-kftvldsu'], + ) + biosampleId: str = Field( + ..., + description='Reference to biosample ID (`biosample.id`)', + examples=['bs001104'], + ) + clinicalInterpretations: list[PhenoClinicEffect] | None = None + id: str | None = Field( + None, + description='Internal id of this case level *instance* of the variant. This is an optional housekeeping parameter and should not be confused with the identifier of the variant (`variantInternalId`).', + examples=['id0001-var101101118'], + ) + individualId: str | None = Field( + None, + description='Reference to individual ID (`individual.id`)', + examples=['ind0001'], + ) + phenotypicEffects: list[PhenoClinicEffect] | None = None + runId: str | None = Field( + None, + description='Reference to the experimental run ID (`run.id`)', + examples=['SRR10903401'], + ) + zygosity: OntologyTerm | None = Field( + None, + description='Ontology term for zygosity in which variant is present in the sample from the Zygosity Ontology (GENO:0000391) , e.g `heterozygous` (GENO:0000135)', + examples=[ + {'id': 'GENO:0000135', 'label': 'heterozygous'}, + {'id': 'GENO:0000136', 'label': 'homozygous'}, + {'id': 'GENO:0000604', 'label': 'hemizygous X-linked'}, + ], + ) + + +class Handover(BaseModel): + handoverType: HandoverType + note: str | None = Field( + None, + description='An optional text including considerations on the handover link provided.', + examples=['This handover link provides access to a summarized VCF.'], + ) + url: AnyUrl = Field( + ..., + description='URL endpoint to where the handover process could progress, in RFC3986 format', + examples=[ + 'https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/' + ], + ) + + +class ListOfHandovers(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class Allele(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['Allele'] = Field(..., description='MUST be "Allele"') + location: CURIE | ChromosomeLocation | SequenceLocation = Field( + ..., description='Where Allele is located' + ) + state: ( + ComposedSequenceExpression + | DerivedSequenceExpression + | LiteralSequenceExpression + | RepeatedSequenceExpression + | SequenceState + ) = Field( + ..., + description='An expression of the sequence state', + json_schema_extra={'deprecated': [{'$ref': '#/definitions/SequenceState'}]}, + ) + + +class Haplotype(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['Haplotype'] = Field(..., description='MUST be "Haplotype"') + members: list[Allele | CURIE] = Field( + ..., + description='List of Alleles, or references to Alleles, that comprise this Haplotype.', + min_length=2, + ) + + +class CopyNumberCount(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['CopyNumberCount'] = Field( + ..., description='MUST be "CopyNumberCount"' + ) + subject: CURIE | ChromosomeLocation | Gene | SequenceLocation = Field( + ..., + description='A location for which the number of systemic copies is described.', + ) + copies: DefiniteRange | IndefiniteRange | Number = Field( + ..., description='The integral number of copies of the subject in a system' + ) + + +class CopyNumberChange(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['CopyNumberChange'] = Field( + ..., description='MUST be "CopyNumberChange"' + ) + subject: CURIE | ChromosomeLocation | Gene | SequenceLocation = Field( + ..., + description='A location for which the number of systemic copies is described.', + ) + copy_change: CopyChange = Field( + ..., + description='MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss), "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy), "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).', + ) + + +class Location(RootModel[ChromosomeLocation | SequenceLocation]): + root: ChromosomeLocation | SequenceLocation = Field( + ..., + description='A contiguous segment of a biological sequence.', + discriminator='type', + ) + + +class SequenceExpression( + RootModel[ + ComposedSequenceExpression + | DerivedSequenceExpression + | LiteralSequenceExpression + | RepeatedSequenceExpression + ] +): + root: ( + ComposedSequenceExpression + | DerivedSequenceExpression + | LiteralSequenceExpression + | RepeatedSequenceExpression + ) = Field( + ..., description='An expression describing a Sequence.', discriminator='type' + ) + + +class GenotypeMember(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + type: Literal['GenotypeMember'] = Field( + ..., description='MUST be "GenotypeMember".' + ) + count: DefiniteRange | IndefiniteRange | Number = Field( + ..., description='The number of copies of the `variation` at a Genotype locus.' + ) + variation: Allele | Haplotype = Field( + ..., description='A MolecularVariation at a Genotype locus.' + ) + + +class LegacyVariation(BaseModel): + alternateBases: constr(pattern=r'^([ACGTUNRYSWKMBDHV\-\.]*)$') = Field( + ..., + description='Alternate bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used as\n a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of deletions with the maximally\n trimmed, deleted sequence being indicated in `ReferenceBases`', + examples=['T', 'G', 'N', 'AG', ''], + ) + location: Location + referenceBases: constr(pattern=r'^([ACGTUNRYSWKMBDHV\-\.]*)$') | None = Field( + None, + description='Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.', + examples=['A', 'T', 'N', '', 'ACG'], + ) + variantType: str = Field( + ..., + description='The `variantType` declares the nature of the variation in relation to a reference. In a response, it is used to describe the variation. Examples here are e.g. structural variants such as `DUP` (increased allelic count of material from the genomic region between `start` and `end` positions without assumption about the placement of the additional sequence) or `DEL` (deletion of sequence following `start`). Either `alternateBases` or `variantType` is required in representing a `LegacyVariation`.', + examples=['SNP', 'DEL', 'DUP', 'BND'], + ) + + +class MolecularVariation(RootModel[Allele | Haplotype]): + root: Allele | Haplotype = Field( + ..., description='A variation on a contiguous molecule.', discriminator='type' + ) + + +class Genotype(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['Genotype'] = Field(..., description='MUST be "Genotype"') + members: list[GenotypeMember] = Field( + ..., + description='Each GenotypeMember in `members` describes a MolecularVariation and the count of that variation at the locus.', + min_length=1, + ) + count: DefiniteRange | IndefiniteRange | Number = Field( + ..., + description='The total number of copies of all MolecularVariation at this locus, MUST be greater than or equal to the sum of GenotypeMember copy counts and MUST be greater than or equal to 1. If greater than the total of GenotypeMember counts, this field describes additional MolecularVariation that exist but are not explicitly described.', + ) + + +class SystemicVariation(RootModel[CopyNumberChange | CopyNumberCount | Genotype]): + root: CopyNumberChange | CopyNumberCount | Genotype = Field( + ..., + description='A Variation of multiple molecules in the context of a system, e.g. a genome, sample, or homologous chromosomes.', + discriminator='type', + ) + + +class VariationSet(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + field_id: CURIE | None = Field( + None, alias='_id', description='Variation Id. MUST be unique within document.' + ) + type: Literal['VariationSet'] = Field(..., description='MUST be "VariationSet"') + members: list[ + Allele + | CURIE + | CopyNumberChange + | CopyNumberCount + | Genotype + | Haplotype + | Text + | VariationSet + ] = Field( + ..., + description='List of Variation objects or identifiers. Attribute is required, but MAY be empty.', + ) + + +class Genomicvariant(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + caseLevelData: list[CaseLevelVariant] | None = Field( + None, + description='caseLevelData reports about the variation instances observed in individual analyses.', + ) + frequencyInPopulations: list[FrequencyInPopulations] | None = None + identifiers: Identifiers | None = None + info: Info | None = None + molecularAttributes: MolecularAttributes | None = None + variantInternalId: str = Field( + ..., + description='Reference to the **internal** variant ID. This represents the primary key/identifier of that variant **inside** a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the `identifiers` section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the `identifiers` section.', + examples=['var00001', 'v110112'], + ) + variantLevelData: VariantLevelData | None = None + variation: MolecularVariation | SystemicVariation | LegacyVariation + + +class Variation( + RootModel[ + Allele + | CopyNumberChange + | CopyNumberCount + | Genotype + | Haplotype + | Text + | VariationSet + ] +): + root: ( + Allele + | CopyNumberChange + | CopyNumberCount + | Genotype + | Haplotype + | Text + | VariationSet + ) = Field( + ..., + description='A representation of the state of one or more biomolecules.', + discriminator='type', + ) + + +class UtilityVariation(RootModel[Text | VariationSet]): + root: Text | VariationSet = Field( + ..., + description='A collection of Variation subclasses that cannot be constrained to a specific class of biological variation, but are necessary for some applications of VRS.', + discriminator='type', + ) + + +VariationSet.model_rebuild() diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_2_0.py index d786d72d..f8c97e11 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/individual/beacon_individual_v2_2_0.py @@ -1 +1,818 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.non_collections.individual.beacon_individual_v2_1_0 import Individual \ No newline at end of file +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/individuals/defaultSchema.json +# timestamp: 2026-07-31T13:36:17+00:00 + +from __future__ import annotations + +from datetime import date as date_aliased +from enum import Enum + +from pydantic import ( + AnyUrl, + AwareDatetime, + BaseModel, + ConfigDict, + Field, + RootModel, + conint, + constr, +) + + +class Age(BaseModel): + iso8601duration: str = Field( + ..., + description='Represents age as a ISO8601 duration (e.g., P40Y10M05D).', + examples=['P32Y6M1D'], + ) + + +class AgeRange(BaseModel): + end: Age = Field( + ..., description='Represents age as an ISO8601 duration (e.g., P59Y).' + ) + start: Age = Field( + ..., description='Represents age as an ISO8601 duration (e.g., P18Y).' + ) + + +class GestationalAge(BaseModel): + days: int | None = Field( + None, + description='Days beyond the completed weeks, if available.', + examples=[2, 4], + ) + weeks: int = Field( + ..., + description='Completed weeks of gestation according to the above definition.', + examples=[4, 33], + ) + + +class Timestamp(RootModel[AwareDatetime]): + root: AwareDatetime = Field( + ..., + description='Time in date-time ISO8601 string format.', + examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'], + ) + + +class CURIE(RootModel[constr(pattern=r'^\w[^:]+:.+$')]): + root: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + + +class FieldSchema(RootModel[str]): + root: str = Field( + ..., + description='Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.', + ) + + +class ApiVersion(RootModel[str]): + root: str = Field( + ..., + description='Version of API, e.g. in request or response. Beacon uses a Github-style, "v"-prefixed semantic versioning format.', + examples=['v2.0.1', 'v0.3'], + ) + + +class BeaconError(BaseModel): + errorCode: int = Field(..., description='Entry not found', examples=['404']) + errorMessage: str | None = Field( + None, examples=['The provided parameters are incomplete: `start` is missing.'] + ) + + +class BeaconId(RootModel[str]): + root: str = Field( + ..., + description='The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.', + examples=['org.example.beacon.v2', 'org.progenetix.beacon'], + ) + + +class CountAdjustedToItem(RootModel[conint(ge=1) | str]): + root: conint(ge=1) | str + + +class CountAdjustedTo(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class CountPrecision(Enum): + exact = 'exact' + imprecise = 'imprecise' + rounded = 'rounded' + + +class Exists(RootModel[bool]): + root: bool = Field( + ..., + description='Indicator of whether any record was observed in any of the collections queried. This should be non-null.', + examples=[True], + ) + + +class Filters(RootModel[list[str]]): + root: list[str] = Field( + ..., + description='Ontology based filters. A CURIE syntax is encouraged to be used.', + examples=[['BTO:0000199', 'PATO:0000383']], + ) + + +class Granularity(Enum): + boolean = 'boolean' + count = 'count' + record = 'record' + + +class IncludeResultsetResponses(Enum): + ALL = 'ALL' + HIT = 'HIT' + MISS = 'MISS' + NONE = 'NONE' + + +class Limit(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 10, + description='Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.', + examples=[10], + ) + + +class NonFilteredQueriesAllowed(RootModel[bool]): + root: bool = Field( + True, + description="Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.", + ) + + +class NumTotalResults(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + ..., + description='Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.', + examples=[123], + ) + + +class PageToken(RootModel[str]): + root: str = Field( + ..., + description='A hash or similar that allows the server to retrieve a "page", e.g. (a subset of) a query response.', + examples=['ab0sc&fe1dd'], + ) + + +class SchemasPerEntity(BaseModel): + entityType: str | None = Field(None, examples=['Individual']) + schema_: str | None = Field( + None, + alias='schema', + examples=[ + './ga4gh-beacon-dataset-v2.0.0', + 'https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json', + ], + ) + + +class Skip(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 0, + description='* In the request: number of pages to skip * In the response: number of pages that has been skipped', + examples=[0], + ) + + +class TestMode(RootModel[bool]): + root: bool = Field( + False, + description='Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.', + ) + + +class KaryotypicSex(Enum): + UNKNOWN_KARYOTYPE = 'UNKNOWN_KARYOTYPE' + XX = 'XX' + XY = 'XY' + XO = 'XO' + XXY = 'XXY' + XXX = 'XXX' + XXYY = 'XXYY' + XXXY = 'XXXY' + XXXX = 'XXXX' + XYY = 'XYY' + OTHER_KARYOTYPE = 'OTHER_KARYOTYPE' + + +class TimeInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + end: Timestamp = Field(..., examples=['2022-03-10T15:25:07Z']) + start: Timestamp = Field( + ..., examples=['1999-08-05T17:21:00+01:00', '2002-09-21T02:37:00-08:00'] + ) + + +class CountAdjustedTo1(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class Info(BaseModel): + pass + + +class ExternalReference(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: str | None = Field( + None, + description='An application specific identifier. RECOMMENDED.', + examples=['PMID:34054918'], + ) + notes: str | None = Field( + None, + description='An optional text descriptor. Renamed compared to GA4GH Phenopackets v2 `ExternalReference.description`', + examples=[ + 'Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes' + ], + ) + reference: str | None = Field( + None, + description='A url.', + examples=['https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155688/'], + ) + + +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: CURIE + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HandoverType(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.', + examples=[ + {'id': 'EDAM:2572', 'label': 'BAM'}, + {'id': 'EDAM:3016', 'label': 'VCF'}, + {'id': 'CUSTOM:pgxseg', 'label': 'genomic variants in .pgxseg file format'}, + ], + ) + + +class ListOfSchemas(RootModel[list[SchemasPerEntity]]): + root: list[SchemasPerEntity] = Field( + ..., description='Set of schemas to be used in the response to a request.' + ) + + +class Pagination(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class GeographicLocation(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).', + examples=[ + {'id': 'GAZ:00002955', 'label': 'Slovenia'}, + {'id': 'GAZ:00002459', 'label': 'United States of America'}, + {'id': 'GAZ:00316959', 'label': 'Municipality of El Masnou'}, + {'id': 'GAZ:00000460', 'label': 'Eurasia'}, + ], + ) + + +class SeverityLevel(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Severity as applicable to phenotype or disease observed. Recommended are values from Human Phenotype Ontology (HP:0012824), e.g `mild`. The intensity or degree of a manifestation. Source: Phenopackets v2', + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012829', 'label': 'Profound'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + {'id': 'HP:0012825', 'label': 'Mild'}, + {'id': 'HP:0012827', 'label': 'Borderline'}, + ], + ) + + +class Sex(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993): "unknown" (not assessed or not available) - NCIT:C17998; "female" - NCIT:C16576; "male" - NCIT:C20197', + examples=[ + {'id': 'NCIT:C16576', 'label': 'female'}, + {'id': 'NCIT:C20197', 'label': 'male'}, + {'id': 'NCIT:C1799', 'label': 'unknown'}, + ], + ) + + +class Unit(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants', + examples=[ + {'id': 'NCIT:C70575', 'label': 'Roentgen'}, + {'id': 'NCIT:C28252', 'label': 'Kilogram'}, + {'id': 'NCIT:C28253', 'label': 'Milligram'}, + ], + ) + + +class Pagination1(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class Exposure(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + ageAtExposure: Age + date: date_aliased | None = Field( + None, description='Date of the exposure in ISO8601 format.' + ) + duration: str = Field( + ..., description='Exposure duration in ISO8601 format', examples=['P2Y6M1D'] + ) + exposureCode: OntologyTerm = Field( + ..., + description='Exposure ID. Recommended is a value from Environment Exposure Ontology.', + examples=[ + {'id': 'CHEBI:46661', 'label': 'asbestos'}, + {'id': 'ENVO:21001217', 'label': 'X-ray radiation'}, + ], + ) + unit: Unit = Field( + ..., + description='Unit of the exposure. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants.', + ) + value: float | None = Field(None, description='Quantification of the exposure.') + + +class ReferenceRange(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + high: float = Field(..., description='Upper range end of normal', examples=[135]) + low: float = Field(..., description='Lower range end of normal', examples=[85]) + unit: Unit = Field( + ..., + description='The kind of unit.', + examples=[{'id': 'NCIT:C49670', 'label': 'Millimeter of Mercury'}], + ) + + +class PedigreeMember(BaseModel): + affected: bool = Field( + ..., description='Is the individual affected by the disease in the pedigree?' + ) + memberId: str = Field( + ..., + description="Identifier of the individual. The individual could be part of the same Beacon datasets or not, in which case the information here is meant to complete the pedigree. If the individual is also in the dataset use that Individual ID. If it is not the in the dataset, use a non-collading ID, e.g. concatenating the Pedigree ID with a local ID, similarly to the example 'Pedigree1001-m1'.", + examples=['Pedigree1001-m1', 'Ind0012122'], + ) + role: OntologyTerm = Field( + ..., + description='Pedigree role, defined as relationship to proband. Value from Family Member term (NCIT:C41256), e.g. "proband" (NCIT:C64435),"identical twin" (NCIT:C73429), "mother" (NCIT:C25189).', + examples=[ + {'id': 'NCIT:C64435', 'label': 'Proband'}, + {'id': 'NCIT:C96580', 'label': 'Biological Mother'}, + {'id': 'NCIT:C96572', 'label': 'Biological Father'}, + {'id': 'NCIT:C165848', 'label': 'Identical Twin Brother'}, + ], + ) + + +class Evidence(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + evidenceCode: OntologyTerm = Field( + ..., + description='An ontology class that represents the evidence type', + examples=[ + { + 'id': 'ECO:0006017', + 'label': 'author statement from published clinical study used in manual assertion', + } + ], + ) + reference: ExternalReference | None = Field( + None, + description='Representation of the source of the evidence', + examples=[ + { + 'id': 'PMID:30962759', + 'label': 'Recurrent Erythema Nodosum in a Child with a SHOC2 Gene Mutation', + } + ], + ) + + +class TimeElement( + RootModel[Age | AgeRange | GestationalAge | Timestamp | TimeInterval | OntologyTerm] +): + root: Age | AgeRange | GestationalAge | Timestamp | TimeInterval | OntologyTerm = ( + Field( + ..., + description='Definition of a wrapper for various time descriptors. This follows the\nPhenopackets structure https://github.com/phenopackets/phenopacket-schema/blob/v2/docs/time-element.rst', + title='TimeElement', + ) + ) + + +class Ethnicity(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]', + examples=[ + {'id': 'NCIT:C42331', 'label': 'African'}, + {'id': 'NCIT:C41260', 'label': 'Asian'}, + {'id': 'NCIT:C126535', 'label': 'Australian'}, + {'id': 'NCIT:C43851', 'label': 'European'}, + {'id': 'NCIT:C77812', 'label': 'North American'}, + {'id': 'NCIT:C126531', 'label': 'Latin American'}, + {'id': 'NCIT:C104495', 'label': 'Other race'}, + ], + ) + + +class Handover(BaseModel): + handoverType: HandoverType + note: str | None = Field( + None, + description='An optional text including considerations on the handover link provided.', + examples=['This handover link provides access to a summarized VCF.'], + ) + url: AnyUrl = Field( + ..., + description='URL endpoint to where the handover process could progress, in RFC3986 format', + examples=[ + 'https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/' + ], + ) + + +class ListOfHandovers(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class ListOfHandovers1(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) + + +class Procedure(BaseModel): + ageAtProcedure: TimeElement | None = Field( + None, description='Compares to Phenopackets v2 `Procedure.performed`' + ) + bodySite: OntologyTerm | None = Field( + None, + description='Specific body site where the procedure was performed. Recommended valuee from Uber-anatomy ontology (UBERON)', + examples=[ + {'id': 'UBERON:0003403', 'label': 'Skin of forearm'}, + {'id': 'UBERON:0003214', 'label': 'mammary gland alveolus'}, + ], + ) + dateOfProcedure: date_aliased | None = Field( + None, + description='Date of procedure, in ISO8601 format', + examples=['2010-07-10'], + ) + procedureCode: OntologyTerm = Field( + ..., + description="Clinical procedure performed with recommended values from Medical Action Ontology (MAXO) 'Medical action' term tree (MAXO:0000001). Compares to Phenopackets v2 `Procedure.code`", + examples=[ + {'id': 'MAXO:0001175', 'label': 'liver transplantation'}, + {'id': 'MAXO:0000136', 'label': 'high-resolution microendoscopy'}, + {'id': 'OBI:0002654', 'label': 'needle biopsy'}, + ], + ) + + +class Quantity(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + referenceRange: ReferenceRange | None = Field( + None, description='The normal range for the value', examples=[{}] + ) + unit: Unit + value: float = Field(..., description='The value of the quantity in the units') + + +class TypedQuantity(BaseModel): + quantity: Quantity = Field( + ..., + description='Quantity denoting the outcome of the measurement', + examples=[ + { + 'unit': {'id': 'NCIT:C49670', 'label': 'Millimeter of Mercury'}, + 'value': 110, + } + ], + ) + quantityType: OntologyTerm = Field( + ..., + description='OntologyClass to describe the type of the measurement. Renamed compared to GA4GH Phenopackets v2 `ComplexValue.TypedQuantity.type`', + examples=[{'id': 'NCIT:C25298', 'label': 'Systolic Blood Pressure'}], + ) + + +class PhenotypicFeature(BaseModel): + evidence: Evidence | None = Field( + None, + description='The evidence for an assertion of the observation of a type. RECOMMENDED.', + ) + excluded: bool | None = Field( + False, + description='Flag to indicate whether the phenotypic feature was observed or not. Default is ‘false’, in other words the phenotype was observed. Therefore it is only used in cases where the phenotype was looked for but found to be absent. More formally, this modifier indicates the logical negation of the OntologyClass used in the `featureType` field. CAUTION: It is imperative to check this field for correct interpretation of the phenotype! Source: Phenopackets v2', + ) + featureType: OntologyTerm = Field( + ..., + description='Term denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO)', + examples=[ + {'id': 'HP:0000002', 'label': 'Abnormality of body height'}, + {'id': 'HP:0002006', 'label': 'Facial cleft'}, + {'id': 'HP:0012469', 'label': 'Infantile spasms'}, + ], + ) + modifiers: list[OntologyTerm] | None = Field( + None, + description='This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. Example use here would be one or more terms from HPO Clinical Modifier (HP:0012823). Source: Phenopackets v2', + examples=[ + {'id': 'HP:0032500', 'label': 'Exacerbated by tobacco use'}, + {'id': 'HP:4000053', 'label': 'Displaced fracture'}, + ], + ) + notes: str | None = Field( + None, + description='Unstructured text to describe additional properties of this phenotypic feature.', + examples=['Some free text'], + ) + onset: TimeElement | None = Field( + None, description='Age or time at which the feature was first observed.' + ) + resolution: TimeElement | None = Field( + None, description='Age or time at which the feature resolved or abated.' + ) + severity: SeverityLevel | None = Field( + None, + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + ], + ) + + +class DoseInterval(BaseModel): + model_config = ConfigDict( + extra='forbid', + ) + interval: TimeInterval = Field( + ..., + description='The specific interval over which the dosage was administered in the indicated quantity.', + examples=[{'end': '1967-11-18T12:00:00+01', 'start': '1967-11-11T07:30:00+01'}], + ) + quantity: Quantity + scheduleFrequency: OntologyTerm = Field( + ..., + description='How often doses are administered per day (or other indicated duration)', + examples=[{'id': 'NCIT:C64496', 'label': 'Twice Daily'}], + ) + + +class Disease(BaseModel): + ageOfOnset: TimeElement | None = Field( + None, + examples=[ + {'id': 'NCIT:C49685', 'label': 'Adult 18-65 Years Old'}, + {'iso8601duration': 'P32Y6M1D'}, + {'end': {'iso8601duration': 'P59Y'}, 'start': {'iso8601duration': 'P18Y'}}, + {'iso8601duration': 'P2M4D'}, + ], + ) + diseaseCode: OntologyTerm = Field( + ..., + description='Disease identifier. Value from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. lactose intolerance (HP:0004789, ICD10CM:E73). Provenance: GA4GH Phenopackets v2 `Disease.term`', + examples=[ + {'id': 'HP:0004789', 'label': 'lactose intolerance'}, + {'id': 'ICD10CM:E73', 'label': 'lactose intolerance'}, + {'id': 'OMIM:164400', 'label': 'Spinocerebellar ataxia 1'}, + ], + ) + familyHistory: bool | None = Field( + None, + description='Boolean indicating determined or self-reported presence of family history of the disease.', + examples=[True], + ) + notes: str | None = Field( + None, + description='Unstructured text to describe additional properties of this disease instance.', + examples=['Some free text'], + ) + severity: SeverityLevel | None = Field( + None, + examples=[ + {'id': 'HP:0012828', 'label': 'Severe'}, + {'id': 'HP:0012826', 'label': 'Moderate'}, + ], + ) + stage: OntologyTerm | None = Field( + None, + description='Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`', + examples=[ + {'id': 'OGMS:0000119', 'label': 'acute onset'}, + {'id': 'OGMS:0000117', 'label': 'asymptomatic'}, + {'id': 'OGMS:0000106', 'label': 'remission'}, + ], + ) + + +class Value(RootModel[Quantity | OntologyTerm]): + root: Quantity | OntologyTerm = Field( + ..., + description='Definition of a value class. Provenance: GA4GH Phenopackets v2 `Value`', + title='Value', + ) + + +class ComplexValue(BaseModel): + typedQuantities: list[TypedQuantity] = Field( + ..., + description='List of quantities required to fully describe the complex value', + ) + + +class Pedigree(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + disease: Disease + id: str = Field(..., description='Pedigree identifier.', examples=['Pedigree1001']) + members: list[PedigreeMember] = Field( + ..., + description='List of members of the pedigree. If the current pedigree definition is attached to the proband, it contains the whole list of pedigree members, including the proband. If the definition is attached to an individual different than the proband, it only contains two entries: one that describes that member, e.g. the proband mother or father, and one that points to the proband.', + min_length=1, + ) + numSubjects: int | None = Field( + None, description='Total number of subjects in pedigree.', examples=[10] + ) + + +class Treatment(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + ageAtOnset: Age | None = None + cumulativeDose: Quantity | None = None + doseIntervals: list[DoseInterval] | None = None + routeOfAdministration: OntologyTerm | None = Field( + None, + description='Route of treatment. Value from NCIT Route of Administration tree (NCIT:C38114).', + examples=[ + {'id': 'NCIT:C38304', 'label': 'Topical'}, + {'id': 'NCIT:C78373', 'label': 'Dietary'}, + ], + ) + treatmentCode: OntologyTerm = Field( + ..., + description='Code of treatment. Value from NCIT or any relevant ontology. Compares to `agent` in Phenopackets v2', + examples=[ + {'id': 'NCIT:C287', 'label': 'Aspirin'}, + {'id': 'NCIT:C62078', 'label': 'Tamoxifen'}, + ], + ) + + +class Measurement(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + assayCode: OntologyTerm = Field( + ..., + description='Class that describes the assay used to produce the measurement. Renamed compared to GA4GH Phenopackets v2 `Measurement.assay`', + examples=[{'id': 'LOINC:26515-7', 'label': 'Platelets [#/volume] in Blood'}], + ) + date: date_aliased | None = Field( + None, + description='Date of measurement. Addition compared to Phenopackets model.', + ) + measurementValue: Value | ComplexValue = Field( + ..., description='The result of the measurement' + ) + notes: str | None = Field( + None, + description='Unstructured text to describe this measurement. Addition compared to Phenopackets model.', + examples=['Some free text'], + ) + observationMoment: TimeElement | None = Field( + None, + description='Moment in time at which measurement was performed. RECOMMENDED. Renamed compared to GA4GH Phenopackets v2 `Measurement.time_observed`', + examples=[{'age': {'iso8601duration': 'P53Y8M'}}], + ) + procedure: Procedure | None = Field( + None, + description='Clinical procedure performed to acquire the sample used for the measurement', + examples=[ + {'code': {'id': 'NCIT:C5189', 'label': 'Radical Cystoprostatectomy'}} + ], + ) + + +class Individual(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + diseases: list[Disease] | None = Field( + None, + description='List of disease(s) been diagnosed to the individual, defined by disease ontology ID(s), age of onset, stage and the presence of family history.', + ) + ethnicity: Ethnicity | None = Field( + None, + description='Ethnic background of the individual. Value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ] ', + ) + exposures: list[Exposure] | None = None + geographicOrigin: GeographicLocation | None = Field( + None, + description="Individual's country or region of origin (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).", + ) + id: str = Field( + ..., description='Individual identifier (internal ID).', examples=['P0001'] + ) + info: Info | None = None + interventionsOrProcedures: list[Procedure] | None = None + karyotypicSex: KaryotypicSex | None = Field( + 'UNKNOWN_KARYOTYPE', + description='The chromosomal sex of an individual represented from a selection of options.', + ) + measurements: list[Measurement] | None = None + pedigrees: list[Pedigree] | None = None + phenotypicFeatures: list[PhenotypicFeature] | None = None + sex: Sex = Field( + ..., + description='Sex of the individual. Value from NCIT General Qualifier `NCIT:C27993`: * `unknown`: not assessed or not availablel `NCIT:C17998` * `female`: `NCIT:C16576` * `male`: `NCIT:C20197`', + ) + treatments: list[Treatment] | None = None diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/run/beacon_run_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/run/beacon_run_v2_2_0.py index cbf27755..16ce4332 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/run/beacon_run_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/run/beacon_run_v2_2_0.py @@ -1 +1,292 @@ -from beacon.models.ga4gh.beacon_v2_default_model.validator.non_collections.run.beacon_run_v2_0_0 import Run +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/refs/heads/main/models/json/beacon-v2-default-model/runs/defaultSchema.json +# timestamp: 2026-07-31T13:36:35+00:00 + +from __future__ import annotations + +from datetime import date +from enum import Enum + +from pydantic import AnyUrl, BaseModel, ConfigDict, Field, RootModel, conint, constr + + +class LibraryLayout(Enum): + PAIRED = 'PAIRED' + SINGLE = 'SINGLE' + + +class Info(BaseModel): + pass + + +class CURIE(RootModel[constr(pattern=r'^\w[^:]+:.+$')]): + root: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + + +class FieldSchema(RootModel[str]): + root: str = Field( + ..., + description='Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.', + ) + + +class ApiVersion(RootModel[str]): + root: str = Field( + ..., + description='Version of API, e.g. in request or response. Beacon uses a Github-style, "v"-prefixed semantic versioning format.', + examples=['v2.0.1', 'v0.3'], + ) + + +class BeaconError(BaseModel): + errorCode: int = Field(..., description='Entry not found', examples=['404']) + errorMessage: str | None = Field( + None, examples=['The provided parameters are incomplete: `start` is missing.'] + ) + + +class BeaconId(RootModel[str]): + root: str = Field( + ..., + description='The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is, in the context of a Beacon network, to disambiguate responses coming from different Beacons.', + examples=['org.example.beacon.v2', 'org.progenetix.beacon'], + ) + + +class CountAdjustedToItem(RootModel[conint(ge=1) | str]): + root: conint(ge=1) | str + + +class CountAdjustedTo(RootModel[list[CountAdjustedToItem]]): + root: list[CountAdjustedToItem] = Field( + ..., + description='For counts with intentional (e.g. due to privacy concerns) or technical derived imprecision this parameter offers an option to declare the range or limits for the true results. \nIf present, CountPrecision states the type of adjustment.', + examples=[['1', '5'], ['<5']], + max_length=2, + min_length=1, + ) + + +class CountPrecision(Enum): + exact = 'exact' + imprecise = 'imprecise' + rounded = 'rounded' + + +class Exists(RootModel[bool]): + root: bool = Field( + ..., + description='Indicator of whether any record was observed in any of the collections queried. This should be non-null.', + examples=[True], + ) + + +class Filters(RootModel[list[str]]): + root: list[str] = Field( + ..., + description='Ontology based filters. A CURIE syntax is encouraged to be used.', + examples=[['BTO:0000199', 'PATO:0000383']], + ) + + +class Granularity(Enum): + boolean = 'boolean' + count = 'count' + record = 'record' + + +class IncludeResultsetResponses(Enum): + ALL = 'ALL' + HIT = 'HIT' + MISS = 'MISS' + NONE = 'NONE' + + +class Limit(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 10, + description='Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.', + examples=[10], + ) + + +class NonFilteredQueriesAllowed(RootModel[bool]): + root: bool = Field( + True, + description="Switch that declares if this Beacon instance, for a given entry type, admits queries that does not include any element that restrict returning all the results, like filters, parameters, ids, etc. The default value is 'true' for backward compatibility and for clarity in the request-response dialog.", + ) + + +class NumTotalResults(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + ..., + description='Total number of results. NOT the number of results returned in this batch (after pagination) but the total obtained by the query.', + examples=[123], + ) + + +class PageToken(RootModel[str]): + root: str = Field( + ..., + description='A hash or similar that allows the server to retrieve a "page", e.g. (a subset of) a query response.', + examples=['ab0sc&fe1dd'], + ) + + +class SchemasPerEntity(BaseModel): + entityType: str | None = Field(None, examples=['Individual']) + schema_: str | None = Field( + None, + alias='schema', + examples=[ + './ga4gh-beacon-dataset-v2.0.0', + 'https://www.example.org/schemas/ga4gh-beacon-dataset-v2.0.0.json', + ], + ) + + +class Skip(RootModel[conint(ge=0)]): + root: conint(ge=0) = Field( + 0, + description='* In the request: number of pages to skip * In the response: number of pages that has been skipped', + examples=[0], + ) + + +class TestMode(RootModel[bool]): + root: bool = Field( + False, + description='Used for indicating that a request or response is done in a test context e.g. for compliance testing i.e. to evaluate the acceptance/understanding of a request and the structure of the returned response by the Beacon instance. A TRUE `testMode` parameter DOES NOT require that the Beacon instance is a test instance, but that this specific request-response cycle is a testing one. When `true` the Beacon instance MUST respond the request but it SHOULD use virtual or non-sensitive data. Here, what is being evaluated is the acceptance/understanding of a request and the structure of the returned response by the Beacon instance.', + ) + + +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: CURIE + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HandoverType(RootModel[OntologyTerm]): + root: OntologyTerm = Field( + ..., + description='Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.', + examples=[ + {'id': 'EDAM:2572', 'label': 'BAM'}, + {'id': 'EDAM:3016', 'label': 'VCF'}, + {'id': 'CUSTOM:pgxseg', 'label': 'genomic variants in .pgxseg file format'}, + ], + ) + + +class ListOfSchemas(RootModel[list[SchemasPerEntity]]): + root: list[SchemasPerEntity] = Field( + ..., description='Set of schemas to be used in the response to a request.' + ) + + +class Pagination(BaseModel): + currentPage: PageToken | None = Field( + None, + description='Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested.', + ) + limit: Limit | None = Field(10, validate_default=True) + nextPage: PageToken | None = Field( + None, + description='Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available', + ) + previousPage: PageToken | None = Field( + None, + description='Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one.', + ) + skip: Skip | None = Field(0, validate_default=True) + + +class Run(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + biosampleId: str = Field( + ..., + description='Reference to the biosample ID.', + examples=['008dafdd-a3d1-4801-8c0a-8714e2b58e48'], + ) + id: str = Field(..., description='Run ID.', examples=['SRR10903401']) + individualId: str | None = Field( + None, description='Reference to the individual ID.', examples=['TCGA-AO-A0JJ'] + ) + info: Info | None = None + libraryLayout: LibraryLayout | None = Field( + None, + description='Ontology value for the library layout e.g "PAIRED", "SINGLE" #todo add Ontology name?', + ) + librarySelection: str | None = Field( + None, + description='Selection method for library preparation, e.g "RANDOM", "RT-PCR"', + examples=['RANDOM', 'RT-PCR'], + ) + librarySource: OntologyTerm | None = Field( + None, + description='Ontology value for the source of the sequencing or hybridization library, e.g "genomic source", "transcriptomic source"', + examples=[ + {'id': 'GENEPIO:0001966', 'label': 'genomic source'}, + {'id': 'GENEPIO:0001965', 'label': 'metagenomic source'}, + ], + ) + libraryStrategy: str | None = Field( + None, description='Library strategy, e.g. "WGS"', examples=['WGS'] + ) + platform: str | None = Field( + None, + description='General platform technology label. It SHOULD be a subset of the platformModel and used only for query convenience, e.g. "return everything sequenced with Illimuna", where the specific model is not relevant', + examples=['Illumina', 'Oxford Nanopore', 'Affymetrix'], + ) + platformModel: OntologyTerm | None = Field( + None, + description='Ontology value for experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.', + examples=[ + {'id': 'OBI:0002048', 'label': 'Illumina HiSeq 3000'}, + {'id': 'OBI:0002750', 'label': 'Oxford Nanopore MinION'}, + {'id': 'EFO:0010938', 'label': 'large-insert clone DNA microarray'}, + ], + ) + runDate: date = Field( + ..., + description='Date at which the experiment was performed.', + examples=['2021-10-18'], + ) + + +class Handover(BaseModel): + handoverType: HandoverType + note: str | None = Field( + None, + description='An optional text including considerations on the handover link provided.', + examples=['This handover link provides access to a summarized VCF.'], + ) + url: AnyUrl = Field( + ..., + description='URL endpoint to where the handover process could progress, in RFC3986 format', + examples=[ + 'https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/' + ], + ) + + +class ListOfHandovers(RootModel[list[Handover]]): + root: list[Handover] = Field( + ..., description='Set of handovers to be added in one section the response.' + ) From d14d588badb6409261c4e39c2f228357cc941963 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 16:00:06 +0200 Subject: [PATCH 20/56] adding test schema for version 2.2.0 --- beacon/connections/mongo/data/test/{ => v2_2_0}/analyses.json | 0 beacon/connections/mongo/data/test/{ => v2_2_0}/biosamples.json | 0 .../connections/mongo/data/test/{ => v2_2_0}/caseLevelData.json | 0 beacon/connections/mongo/data/test/{ => v2_2_0}/cohorts.json | 0 beacon/connections/mongo/data/test/{ => v2_2_0}/datasets.json | 0 .../mongo/data/test/{ => v2_2_0}/genomicVariations.json | 0 beacon/connections/mongo/data/test/{ => v2_2_0}/individuals.json | 0 beacon/connections/mongo/data/test/{ => v2_2_0}/runs.json | 0 beacon/connections/mongo/data/test/{ => v2_2_0}/targets.json | 0 9 files changed, 0 insertions(+), 0 deletions(-) rename beacon/connections/mongo/data/test/{ => v2_2_0}/analyses.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/biosamples.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/caseLevelData.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/cohorts.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/datasets.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/genomicVariations.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/individuals.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/runs.json (100%) rename beacon/connections/mongo/data/test/{ => v2_2_0}/targets.json (100%) diff --git a/beacon/connections/mongo/data/test/analyses.json b/beacon/connections/mongo/data/test/v2_2_0/analyses.json similarity index 100% rename from beacon/connections/mongo/data/test/analyses.json rename to beacon/connections/mongo/data/test/v2_2_0/analyses.json diff --git a/beacon/connections/mongo/data/test/biosamples.json b/beacon/connections/mongo/data/test/v2_2_0/biosamples.json similarity index 100% rename from beacon/connections/mongo/data/test/biosamples.json rename to beacon/connections/mongo/data/test/v2_2_0/biosamples.json diff --git a/beacon/connections/mongo/data/test/caseLevelData.json b/beacon/connections/mongo/data/test/v2_2_0/caseLevelData.json similarity index 100% rename from beacon/connections/mongo/data/test/caseLevelData.json rename to beacon/connections/mongo/data/test/v2_2_0/caseLevelData.json diff --git a/beacon/connections/mongo/data/test/cohorts.json b/beacon/connections/mongo/data/test/v2_2_0/cohorts.json similarity index 100% rename from beacon/connections/mongo/data/test/cohorts.json rename to beacon/connections/mongo/data/test/v2_2_0/cohorts.json diff --git a/beacon/connections/mongo/data/test/datasets.json b/beacon/connections/mongo/data/test/v2_2_0/datasets.json similarity index 100% rename from beacon/connections/mongo/data/test/datasets.json rename to beacon/connections/mongo/data/test/v2_2_0/datasets.json diff --git a/beacon/connections/mongo/data/test/genomicVariations.json b/beacon/connections/mongo/data/test/v2_2_0/genomicVariations.json similarity index 100% rename from beacon/connections/mongo/data/test/genomicVariations.json rename to beacon/connections/mongo/data/test/v2_2_0/genomicVariations.json diff --git a/beacon/connections/mongo/data/test/individuals.json b/beacon/connections/mongo/data/test/v2_2_0/individuals.json similarity index 100% rename from beacon/connections/mongo/data/test/individuals.json rename to beacon/connections/mongo/data/test/v2_2_0/individuals.json diff --git a/beacon/connections/mongo/data/test/runs.json b/beacon/connections/mongo/data/test/v2_2_0/runs.json similarity index 100% rename from beacon/connections/mongo/data/test/runs.json rename to beacon/connections/mongo/data/test/v2_2_0/runs.json diff --git a/beacon/connections/mongo/data/test/targets.json b/beacon/connections/mongo/data/test/v2_2_0/targets.json similarity index 100% rename from beacon/connections/mongo/data/test/targets.json rename to beacon/connections/mongo/data/test/v2_2_0/targets.json From a66cfd87d8556f3640e41a2c2ea8d074d71a18b3 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 31 Jul 2026 16:13:33 +0200 Subject: [PATCH 21/56] adding different versions for example datasets --- .../data/{ => CINECA/v2_0_0}/analyses.json | 0 .../data/{ => CINECA/v2_0_0}/biosamples.json | 0 .../{ => CINECA/v2_0_0}/caseLevelData.json | 0 .../data/{ => CINECA/v2_0_0}/cohorts.json | 0 .../data/{ => CINECA/v2_0_0}/datasets.json | 0 .../{ => CINECA/v2_0_0}/filtering_terms.json | 0 .../v2_0_0}/genomicVariations.json | 0 .../data/{ => CINECA/v2_0_0}/individuals.json | 0 .../mongo/data/{ => CINECA/v2_0_0}/runs.json | 0 .../data/{ => CINECA/v2_0_0}/targets.json | 0 .../mongo/data/CINECA/v2_2_0/analyses.json | 1 + .../mongo/data/CINECA/v2_2_0/biosamples.json | 1 + .../data/CINECA/v2_2_0/caseLevelData.json | 1 + .../mongo/data/CINECA/v2_2_0/cohorts.json | 1 + .../mongo/data/CINECA/v2_2_0/datasets.json | 1 + .../data/CINECA/v2_2_0/filtering_terms.json | 23 + .../data/CINECA/v2_2_0/genomicVariations.json | 1 + .../mongo/data/CINECA/v2_2_0/individuals.json | 1 + .../mongo/data/CINECA/v2_2_0/runs.json | 1 + .../mongo/data/CINECA/v2_2_0/targets.json | 1 + .../mongo/data/test/v2_0_0/analyses.json | 17 + .../mongo/data/test/v2_0_0/biosamples.json | 2262 +++++++++ .../mongo/data/test/v2_0_0/caseLevelData.json | 1 + .../mongo/data/test/v2_0_0/cohorts.json | 260 ++ .../mongo/data/test/v2_0_0/datasets.json | 30 + .../data/test/v2_0_0/genomicVariations.json | 1627 +++++++ .../mongo/data/test/v2_0_0/individuals.json | 4062 +++++++++++++++++ .../mongo/data/test/v2_0_0/runs.json | 26 + .../mongo/data/test/v2_0_0/targets.json | 1 + .../test2/{ => v2_0_0}/caseLevelData.json | 0 .../data/test2/{ => v2_0_0}/datasets.json | 0 .../data/test2/{ => v2_0_0}/individuals.json | 0 .../data/test2/{ => v2_0_0}/targets.json | 0 33 files changed, 8318 insertions(+) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/analyses.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/biosamples.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/caseLevelData.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/cohorts.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/datasets.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/filtering_terms.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/genomicVariations.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/individuals.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/runs.json (100%) rename beacon/connections/mongo/data/{ => CINECA/v2_0_0}/targets.json (100%) create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/analyses.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/biosamples.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/caseLevelData.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/cohorts.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/filtering_terms.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/genomicVariations.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/individuals.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/runs.json create mode 100644 beacon/connections/mongo/data/CINECA/v2_2_0/targets.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/analyses.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/biosamples.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/caseLevelData.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/cohorts.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/datasets.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/genomicVariations.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/individuals.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/runs.json create mode 100644 beacon/connections/mongo/data/test/v2_0_0/targets.json rename beacon/connections/mongo/data/test2/{ => v2_0_0}/caseLevelData.json (100%) rename beacon/connections/mongo/data/test2/{ => v2_0_0}/datasets.json (100%) rename beacon/connections/mongo/data/test2/{ => v2_0_0}/individuals.json (100%) rename beacon/connections/mongo/data/test2/{ => v2_0_0}/targets.json (100%) diff --git a/beacon/connections/mongo/data/analyses.json b/beacon/connections/mongo/data/CINECA/v2_0_0/analyses.json similarity index 100% rename from beacon/connections/mongo/data/analyses.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/analyses.json diff --git a/beacon/connections/mongo/data/biosamples.json b/beacon/connections/mongo/data/CINECA/v2_0_0/biosamples.json similarity index 100% rename from beacon/connections/mongo/data/biosamples.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/biosamples.json diff --git a/beacon/connections/mongo/data/caseLevelData.json b/beacon/connections/mongo/data/CINECA/v2_0_0/caseLevelData.json similarity index 100% rename from beacon/connections/mongo/data/caseLevelData.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/caseLevelData.json diff --git a/beacon/connections/mongo/data/cohorts.json b/beacon/connections/mongo/data/CINECA/v2_0_0/cohorts.json similarity index 100% rename from beacon/connections/mongo/data/cohorts.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/cohorts.json diff --git a/beacon/connections/mongo/data/datasets.json b/beacon/connections/mongo/data/CINECA/v2_0_0/datasets.json similarity index 100% rename from beacon/connections/mongo/data/datasets.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/datasets.json diff --git a/beacon/connections/mongo/data/filtering_terms.json b/beacon/connections/mongo/data/CINECA/v2_0_0/filtering_terms.json similarity index 100% rename from beacon/connections/mongo/data/filtering_terms.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/filtering_terms.json diff --git a/beacon/connections/mongo/data/genomicVariations.json b/beacon/connections/mongo/data/CINECA/v2_0_0/genomicVariations.json similarity index 100% rename from beacon/connections/mongo/data/genomicVariations.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/genomicVariations.json diff --git a/beacon/connections/mongo/data/individuals.json b/beacon/connections/mongo/data/CINECA/v2_0_0/individuals.json similarity index 100% rename from beacon/connections/mongo/data/individuals.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/individuals.json diff --git a/beacon/connections/mongo/data/runs.json b/beacon/connections/mongo/data/CINECA/v2_0_0/runs.json similarity index 100% rename from beacon/connections/mongo/data/runs.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/runs.json diff --git a/beacon/connections/mongo/data/targets.json b/beacon/connections/mongo/data/CINECA/v2_0_0/targets.json similarity index 100% rename from beacon/connections/mongo/data/targets.json rename to beacon/connections/mongo/data/CINECA/v2_0_0/targets.json diff --git a/beacon/connections/mongo/data/CINECA/v2_2_0/analyses.json b/beacon/connections/mongo/data/CINECA/v2_2_0/analyses.json new file mode 100644 index 00000000..827526f7 --- /dev/null +++ b/beacon/connections/mongo/data/CINECA/v2_2_0/analyses.json @@ -0,0 +1 @@ +[{"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00096", "id": "UK1_analysisId_1", "individualId": "HG00096", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000001", "variantCaller": "GATK4.0", "datasetId": "CINECA_synthetic_cohort_EUROPE_UK1", "_id": "2c755fe7697c1601f77a0e2fbda79b9fd9d28e64ecf7ae929241e3b958f24ecb"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00097", "id": "UK1_analysisId_2", "individualId": "HG00097", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000002", "variantCaller": "GATK4.0", "datasetId": "CINECA_synthetic_cohort_EUROPE_UK1", "_id": "e615d5da6836879d78796cc8b9aa4036b0033dc364de700994d19d0516b8e856"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00099", "id": "UK1_analysisId_3", "individualId": "HG00099", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000003", "variantCaller": "GATK4.0", "datasetId": "CINECA_synthetic_cohort_EUROPE_UK1", "_id": 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diff --git a/beacon/connections/mongo/data/CINECA/v2_2_0/cohorts.json b/beacon/connections/mongo/data/CINECA/v2_2_0/cohorts.json new file mode 100644 index 00000000..1d1c64fb --- /dev/null +++ b/beacon/connections/mongo/data/CINECA/v2_2_0/cohorts.json @@ -0,0 +1 @@ +[{"cohortType": "study-defined", "collectionEvents": [{"eventDiseases": {"availability": true, "availabilityCount": 1705}, "eventEthnicities": {"availability": true, "availabilityCount": 2287}, "eventGenders": {"availability": true, "availabilityCount": 1597}, "eventLocations": {"availability": true, "availabilityCount": 1597}}], "id": "CINECA_synthetic_cohort_UK1", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P65Y"}, "start": {"iso8601duration": "P18Y"}}, "genders": [{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}], "locations": [{"id": "GAZ:00150372", "label": "UK"}]}, "name": "CINECA synthetic cohort UK1", "datasetId": "CINECA_synthetic_cohort_EUROPE_UK1", "_id": "a388c8898dfab6ba5cf82441dcc1359e9a5462dcdc306893a91973abde0e5715"}] \ No newline at end of file diff --git a/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json b/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json new file mode 100644 index 00000000..95eab19d --- /dev/null +++ b/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json @@ -0,0 +1 @@ +[{"createDateTime": "2021-12-29T20:33:40Z", "dataUseConditions": {"duoDataUse": [{"id": "DUO:0000019,DUO:00000020", "label": "publication required,publication required", "version": "7-1-19,7-1-19"}]}, "description": "Please note: This synthetic data set (with cohort participants / subjects marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk This dataset (CINECA_synthetic_cohort_EUROPE_UK1) consists of 2521 samples which have genetic data based on 1000 Genomes data (https://www.nature.com/articles/nature15393), and synthetic subject attributes and phenotypic data derived from UKBiobank (https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001779). These data were initially derived using the TOFU tool (https://github.com/spiros/tofu), which generates randomly generated values based on the UKBiobank data dictionary. Categorical values were randomly generated based on the data dictionary, continuous variables generated based on the distribution of values reported by the UK Biobank showcase, and date / time values were random. Additionally we split the phenotypes and attributes into 4 main classes - general, cancer, diabetes mellitus, and cardiac. We assigned the general attributes to all the samples, and the cardiac / diabetes mellitus / cancer attributes to a proportion of the total samples. Once the initial set of phenotypes and attributes were generated, the data data was checked for consistency and where possible dependent attributes were calculated from the independent variables generated by TOFU. For example, BMI was calculated from height and weight data, and age at death generated by date of death and date of birth. These data were then loaded to the development instance of Biosamples (https://www.ebi.ac.uk/biosamples/) which accessioned each of the samples. The genetic data are derived from the 1000 Genomes Phase 3 release (https://www.internationalgenome.org/category/phase-3/). The genotype data consists of a single joint call vcf files with call genotypes for all 2504 samples, plus bed, bim, fam, and nosex files generated via plink for these samples and genotypes. The genotype data has had a variety of errors introduced to mimic real data and as a test for quality control pipelines. These include gender mismatches, ethnic background mislabelling and low call rates for a randomly chosen subset of sample data as well as deviations from Hardy Weinberg equilibrium and low call rates for a random selection of variants. Additionally 40 samples have raw genetic data available in the form of both bam and cram files, including unmapped data. The gender of the samples in the 1000 genomes data has been matched to the synthetic phenotypic data generated for these samples. The genetic data was then linked to the synthetic data in BioSamples, and submitted to EGA.\",\"externalUrl\":\u00a0\"https://ega-archive.org/datasets/EGAD00001006673/", "externalUrl": "https://ega-archive.org/datasets/EGAD00001006673/", "id": "CINECA_synthetic_cohort_EUROPE_UK1", "info": {}, "name": "CINECA_synthetic_cohort_EUROPE_UK1", "updateDateTime": "2021-12-29T20:33:40Z", "version": "v1.0", "_id": "1305c00a4ae5eac71edfef6f2b8ff539101dae17b3e294063b6ed277c5bf901d"}] \ No newline at end of file diff --git a/beacon/connections/mongo/data/CINECA/v2_2_0/filtering_terms.json b/beacon/connections/mongo/data/CINECA/v2_2_0/filtering_terms.json new file mode 100644 index 00000000..23a750a5 --- /dev/null +++ b/beacon/connections/mongo/data/CINECA/v2_2_0/filtering_terms.json @@ -0,0 +1,23 @@ +[ + { + "type": "alphanumeric", + "id": "libraryStrategy", + "scopes": [ + "run" + ] + }, + { + "type": "alphanumeric", + "id": "molecularAttributes.geneIds", + "scopes": [ + "genomicVariation" + ] + }, + { + "type": "alphanumeric", + "id": "diseases.ageOfOnset.iso8601duration", + "scopes": [ + "individual" + ] + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/CINECA/v2_2_0/genomicVariations.json b/beacon/connections/mongo/data/CINECA/v2_2_0/genomicVariations.json new file mode 100644 index 00000000..c90106ff --- /dev/null +++ b/beacon/connections/mongo/data/CINECA/v2_2_0/genomicVariations.json @@ -0,0 +1 @@ +[{"caseLevelData": [{"biosampleId": "HG03771", "zygosity": {"id": "GENO:GENO_0000458", "label": "0/1"}}], "identifiers": {"genomicHGVSId": "22:g.16050075G>A"}, "molecularAttributes": {"aminoacidChanges": ["."], "geneIds": ["CHR_START-DUXAP8"], "molecularEffects": [{"id": "ENSGLOSSARY:0000174", "label": "intergenic_region"}]}, "variantInternalId": "chr22_16050075_A_G", "variation": {"alternateBases": "A", "location": {"type": "SequenceLocation", "sequence_id": "HGVSid:22:g.16050075G>A", "interval": {"type": "SequenceInterval", "start": {"type": 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diff --git a/beacon/connections/mongo/data/test/v2_0_0/analyses.json b/beacon/connections/mongo/data/test/v2_0_0/analyses.json new file mode 100644 index 00000000..454a74b1 --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/analyses.json @@ -0,0 +1,17 @@ +[ + { + "aligner": "bwa-0.7.8", + "analysisDate": "2021-10-17", + "biosampleId": "SAMPLE1", + "id": "EGA-testing", + "individualId": "SAMPLE1", + "info": { + "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." + }, + "pipelineName": "Pipeline-panel-0001-v1", + "pipelineRef": "https://doi.org/10.48511/workflowhub.workflow.111.1", + "runId": "EGAR5000XXX", + "variantCaller": "GATK4.0", + "datasetId": "test" + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/v2_0_0/biosamples.json b/beacon/connections/mongo/data/test/v2_0_0/biosamples.json new file mode 100644 index 00000000..19a86125 --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/biosamples.json @@ -0,0 +1,2262 @@ +[ + { + "biosampleStatus": { + "id": "EFO:0009655", + "label": "abnormal sample" + }, + "collectionDate": "2020-09-11", + "collectionMoment": "P32Y6M1D", + "diagnosticMarkers": [ + { + "id": "RO:0000085", + "label": "has_function" + } + ], + "histologicalDiagnosis": { + "id": "NCIT:C3778", + "label": "Serous Cystadenocarcinoma" + }, + "id": "SAMPLE1", + "individualId": "SAMPLE1", + "info": { + "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." + }, + "measurements": [ + { + "assayCode": { + "id": "UBERON:0001062", + "label": "anatomical entity" + }, + "date": "2019-04-23", + "measurementValue": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "notes": "Bear in mind that all this information is synthetic", + "observationMoment": { + "iso8601duration": "P53Y8M" + }, + "procedure": { + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + } + ], + "notes": "Bear in mind that all this information is synthetic", + "pathologicalStage": { + "id": "NCIT:C27977", + "label": "Stage IIIA" + }, + "pathologicalTnmFinding": [ + { + "id": "NCIT:C48725", + "label": "T2a Stage Finding" + } + ], + "phenotypicFeatures": [ + { + "evidence": { + "reference": { + "id": "ECO:0006017", + "notes": "author statement from published clinical study used in manual assertion" + } + }, + "excluded": "TRUE", + "featureType": { + "id": "HP:0000002", + "label": "Abnormality of body height" + }, + "modifiers": { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + }, + "notes": "Please note that all this information is synthetic", + "onset": { + "days": 5 + }, + "resolution": { + "days": 8, + "weeks": 8 + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "sampleOriginDetail": { + "id": "UBERON:0000474", + "label": "female reproductive system" + }, + "sampleOriginType": { + "id": "UBERON:0000992", + "label": "ovary" + }, + "sampleProcessing": { + "id": "EFO:0009129", + "label": "mechanical dissociation" + }, + "sampleStorage": { + "id": "OBI:0000915", + "label": "freezing storage" + }, + "tumorGrade": { + "id": "NCIT:C28080", + "label": "Grade 3a" + }, + "tumorProgression": { + "id": "NCIT:C84509", + "label": "Primary Malignant Neoplasm" + }, + "datasetId": "test" + }, + { + "biosampleStatus": { + "id": "EFO:0009655", + "label": "abnormal sample" + }, + "collectionDate": "2020-09-11", + "collectionMoment": "P32Y6M1D", + "diagnosticMarkers": [ + { + "id": "RO:0000085", + "label": "has_function" + } + ], + "histologicalDiagnosis": { + "id": "NCIT:C3778", + "label": "Serous Cystadenocarcinoma" + }, + "id": "SAMPLE2", + "individualId": "SAMPLE2", + "info": { + "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." + }, + "measurements": [ + { + "assayCode": { + "id": "UBERON:0001062", + "label": "anatomical entity" + }, + "date": "2019-04-23", + "measurementValue": { + "id": "LOINC:26515-7", + "label": "Platelets [#/volume] in Blood" + }, + "notes": "Bear in mind 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b/beacon/connections/mongo/data/test/v2_0_0/caseLevelData.json @@ -0,0 +1 @@ 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diff --git a/beacon/connections/mongo/data/test/v2_0_0/cohorts.json b/beacon/connections/mongo/data/test/v2_0_0/cohorts.json new file mode 100644 index 00000000..1f2223a0 --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/cohorts.json @@ -0,0 +1,260 @@ +[ + { + "cohortDataTypes": [ + { + "id": "OGMS:0000015", + "label": "clinical history" + } + ], + "cohortDesign": { + "id": "OMIABIS:0001019", + "label": "longitudinal study design" + }, + "cohortSize": 20000, + "cohortType": "study-defined", + "collectionEvents": [ + { + "eventAgeRange": { + "availability": true, + "availabilityCount": 101, + "distribution": { + "ranges": { + "20-40": 51, + "50-60": 50 + } + } + }, + "eventDataTypes": { + "availability": true, + "availabilityCount": 29, + "distribution": { + "datatypes": { + "OGMS:0000015": 5, + "OBI:0000070": 8, + "OMIABIS:0000060": 16 + } + } + }, + "eventDiseases": { + "availability": true, + "availabilityCount": 100, + "distribution": { + "diseases": { + "HP:0001645": 50 + } + } + }, + "eventEthnicities": { + "availability": true, + "availabilityCount": 101, + "distribution": { + "ethnicities": { + "African": 3, + "European": 90, + "LatinAmerican": 8 + } + } + }, + "eventGenders": { + "availability": true, + "availabilityCount": 101, + "distribution": { + "genders": { + "female": 51, + "male": 50 + } + } + }, + "eventLocations": { + "availability": true, + "availabilityCount": 101, + "distribution": { + "ethnicities": { + "GAZ:00004501": 101 + } + } + }, + "eventPhenotypes": { + "availability": true, + "availabilityCount": 101, + "distribution": { + "Phenotype": { + "GAZ:00004501": 101 + } + } + } + } + ], + "exclusionCriteria": { + "ageRange": { + "end": { + "iso8601duration": "P58Y" + }, + "start": { + "iso8601duration": "P18Y" + } + }, + "diseaseConditions": [ + { + "ageOfOnset": { + "id": "NCIT:C49685", + "label": "Adult 18-65 Years Old" + }, + "diseaseCode": { + "id": "HP:0004789", + "label": "lactose intolerance" + }, + "familyHistory": true, + "notes": "All this information is synthetic.", + "severity": { + "id": "HP:0012828", + "label": "Severe" + }, + "stage": { + "id": "OGMS:0000119", + "label": "acute onset" + } + } + ], + "ethnicities": [ + { + "id": "NCIT:C43851", + "label": "European" + } + ], + "genders": [ + { + "id": "NCIT:C16576", + "label": "Female" + }, + { + "id": "NCIT:C20197", + "label": "male" + }, + { + "id": "NCIT:C1799", + "label": "uknown" + } + ], + "locations": [ + { + "id": "GAZ:00000460", + "label": "Eurasia" + } + ], + "phenotypicConditions": [ + { + "excluded": true, + "featureType": { + "id": "HP:0000002", + "label": "Abnormality of body height" + }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], + "notes": "Bear in mind that all this information is synthetic", + "onset": { + "iso8601duration": "P58Y" + }, + "resolution": { + "iso8601duration": "P98Y" + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ] + }, + "id": "EGA-testing", + "inclusionCriteria": { + "ageRange": { + "end": { + "iso8601duration": "P59Y" + }, + "start": { + "iso8601duration": "P18Y" + } + }, + "diseaseConditions": [ + { + "ageOfOnset": { + "id": "NCIT:C49685", + "label": "Adult 18-65 Years Old" + }, + "diseaseCode": { + "id": "HP:0004789", + "label": "lactose intolerance" + }, + "familyHistory": true, + "notes": "All this information is synthetic.", + "severity": { + "id": "HP:0012828", + "label": "Severe" + }, + "stage": { + "id": "OGMS:0000119", + "label": "acute onset" + } + } + ], + "ethnicities": [ + { + "id": "NCIT:C43851", + "label": "European" + } + ], + "genders": [ + { + "id": "NCIT:C16576", + "label": "Female" + }, + { + "id": "NCIT:C20197", + "label": "male" + }, + { + "id": "NCIT:C1799", + "label": "uknown" + } + ], + "locations": [ + { + "id": "GAZ:00000460", + "label": "Eurasia" + } + ], + "phenotypicConditions": [ + { + "excluded": true, + "featureType": { + "id": "HP:0000002", + "label": "Abnormality of body height" + }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], + "notes": "Bear in mind that all this information is synthetic", + "onset": { + "iso8601duration": "P59Y" + }, + "resolution": { + "iso8601duration": "P98Y" + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ] + }, + "name": "syntheticCohort", + "datasetId": "test" + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/v2_0_0/datasets.json b/beacon/connections/mongo/data/test/v2_0_0/datasets.json new file mode 100644 index 00000000..d99f9580 --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/datasets.json @@ -0,0 +1,30 @@ +[ + { + "createDateTime": "2021-12-29T20:33:40Z", + "dataUseConditions": { + "duoDataUse": [ + { + "description": "test dataset", + "id": "DUO:0000019,DUO:00000020", + "label": "publication required,publication required", + "modifiers": [ + { + "id": "EFO:0001645", + "label": "coronary artery disease" + } + ], + "version": "7-1-19,7-1-19" + } + ] + }, + "description": "Bear in mind that both genomic and metadata information is synthetic ", + "externalUrl": "https://ega-archive.org/datasets/EGAD00001006673/", + "id": "test", + "info": { + "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." + }, + "name": "Dataset with synthetic data for beacon testing", + "updateDateTime": "2021-12-29T20:33:40Z", + "version": "v1.0" + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/v2_0_0/genomicVariations.json b/beacon/connections/mongo/data/test/v2_0_0/genomicVariations.json new file mode 100644 index 00000000..5764256c --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/genomicVariations.json @@ -0,0 +1,1627 @@ +[ + { + "_id": "5e8df629d9ce607c1c56354eb012cbea32cf0f7744973db740724ad9578d667b", + "identifiers": { + "genomicHGVSId": "NC_000001.10:g.1234567_1234866del" + }, + "molecularAttributes": { + "geneIds": [ + "SDF4" + ], + "molecularEffects": [ + 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"weeks": 8 + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "sex": { + "id": "NCIT:C16576", + "label": "female" + }, + "treatments": [ + { + "ageAtOnset": { + "iso8601duration": "P1Y1" + }, + "routeOfAdministration": { + "id": "NCIT:C38288", + "label": "Oral Route of Administration" + }, + "treatmentCode": { + "id": "OGMS:0000113", + "label": "chemotherapy procedure" + } + } + ], + "datasetId": "test" + }, + { + "diseases": [ + { + "ageOfOnset": { + "id": "NCIT:C16731", + "label": "Neonate" + }, + "diseaseCode": { + "id": "MONDO:0004975", + "label": "Cystic fibrosis" + }, + "familyHistory": true, + "notes": "Bear in mind that all information is synthetic", + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "ethnicity": { + "id": "NCIT:C43851", + "label": "European" + }, + "exposures": [ + { + "ageAtExposure": { + "iso8601duration": "P32Y6M1D" + }, + "date": "2024-09-25", + "duration": "14 months", + "exposureCode": { + "id": "CHEBI:46661", + "label": "asbestos" + }, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + } + ], + "geographicOrigin": { + "id": "GAZ:00002586", + "label": "State of Wisconsin" + }, + "id": "SAMPLE18", + "interventionsOrProcedures": [ + { + "bodySite": { + "id": "FMAID:7195", + "label": "lung" + }, + "dateOfProcedure": "2024-12-24", + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + ], + "karyotypicSex": "XXXY", + "measures": [ + { + "assayCode": { + "id": "UBERON:0001062", + "label": "anatomical entity" + }, + "date": "2024-11-08", + "measurementValue": + { + "referenceRange": { + "high": 50, + "low": 20, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + }, + "value": 50 + } + , + "notes": "Bear in mind that all this information is synthetic", + "observationMoment": { + "iso8601duration": "P32Y6M1D" + }, + "procedure": { + "ageAtProcedure": "1999-08-05T17:21:00+01:00", + "bodySite": { + "id": "FMAID:7195", + "label": "lung" + }, + "dateOfProcedure": "2024-08-15", + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + } + ], + "pedigrees": [ + { + "disease": { + "diseaseCode": { + "id": "HP:0001645", + "label": "Sudden cardiac death" + }, + "familyHistory": true, + "notes": "Bear in mind that all this information is synthetic ", + "severity": { + "id": "HP:0012828", + "label": "Severe" + }, + "stage": { + "id": "OGMS:0000103", + "label": "Disease stage" + } + }, + "id": "SCD-Pedigree001", + "members": [ + { + "affected": true, + "memberId": "Ind001", + "role": { + "id": "NCIT:C64435", + "label": "Proband" + } + }, + { + "affected": true, + "memberId": "Ind002", + "role": { + "id": "NCIT:C96572", + "label": "Father" + } + }, + { + "affected": true, + "memberId": "Ind003", + "role": { + "id": "NCIT:C111201", + "label": "Full Brother" + } + } + ] + } + ], + "phenotypicFeatures": [ + { + "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + } + }, + "excluded": true, + "featureType": { + "id": "HP:0000002", + "label": "Abnormality of body height" + }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], + "notes": "Please note that all this information is synthetic", + "onset": { + "id": "HP:0011463", + "label": "Infantile onset" + }, + "resolution": { + "days": 8, + "weeks": 8 + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "sex": { + "id": "NCIT:C16576", + "label": "female" + }, + "treatments": [ + { + "ageAtOnset": { + "iso8601duration": "P1Y1" + }, + "routeOfAdministration": { + "id": "NCIT:C38288", + "label": "Oral Route of Administration" + }, + "treatmentCode": { + "id": "OGMS:0000113", + "label": "chemotherapy procedure" + } + } + ], + "datasetId": "test" + }, + { + "diseases": [ + { + "ageOfOnset": { + "id": "NCIT:C16731", + "label": "Neonate" + }, + "diseaseCode": { + "id": "MONDO:0004975", + "label": "Cystic fibrosis" + }, + "familyHistory": true, + "notes": "Bear in mind that all information is synthetic", + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "ethnicity": { + "id": "NCIT:C43851", + "label": "European" + }, + "exposures": [ + { + "ageAtExposure": { + "iso8601duration": "P32Y6M1D" + }, + "date": "2024-09-25", + "duration": "14 months", + "exposureCode": { + "id": "CHEBI:46661", + "label": "asbestos" + }, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + } + ], + "geographicOrigin": { + "id": "GAZ:00002586", + "label": "State of Wisconsin" + }, + "id": "SAMPLE19", + "interventionsOrProcedures": [ + { + "bodySite": { + "id": "FMAID:7195", + "label": "lung" + }, + "dateOfProcedure": "2024-12-24", + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + ], + "karyotypicSex": "XXXY", + "measures": [ + { + "assayCode": { + "id": "UBERON:0001062", + "label": "anatomical entity" + }, + "date": "2024-11-08", + "measurementValue": + { + "referenceRange": { + "high": 50, + "low": 20, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + }, + "value": 50 + } + , + "notes": "Bear in mind that all this information is synthetic", + "observationMoment": { + "iso8601duration": "P32Y6M1D" + }, + "procedure": { + "ageAtProcedure": "1999-08-05T17:21:00+01:00", + "bodySite": { + "id": "FMAID:7195", + "label": "lung" + }, + "dateOfProcedure": "2024-08-15", + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + } + ], + "pedigrees": [ + { + "disease": { + "diseaseCode": { + "id": "HP:0001645", + "label": "Sudden cardiac death" + }, + "familyHistory": true, + "notes": "Bear in mind that all this information is synthetic ", + "severity": { + "id": "HP:0012828", + "label": "Severe" + }, + "stage": { + "id": "OGMS:0000103", + "label": "Disease stage" + } + }, + "id": "SCD-Pedigree001", + "members": [ + { + "affected": true, + "memberId": "Ind001", + "role": { + "id": "NCIT:C64435", + "label": "Proband" + } + }, + { + "affected": true, + "memberId": "Ind002", + "role": { + "id": "NCIT:C96572", + "label": "Father" + } + }, + { + "affected": true, + "memberId": "Ind003", + "role": { + "id": "NCIT:C111201", + "label": "Full Brother" + } + } + ] + } + ], + "phenotypicFeatures": [ + { + "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + } + }, + "excluded": true, + "featureType": { + "id": "HP:0000002", + "label": "Abnormality of body height" + }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], + "notes": "Please note that all this information is synthetic", + "onset": { + "id": "HP:0011463", + "label": "Infantile onset" + }, + "resolution": { + "days": 8, + "weeks": 8 + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "sex": { + "id": "NCIT:C16576", + "label": "female" + }, + "treatments": [ + { + "ageAtOnset": { + "iso8601duration": "P1Y1" + }, + "routeOfAdministration": { + "id": "NCIT:C38288", + "label": "Oral Route of Administration" + }, + "treatmentCode": { + "id": "OGMS:0000113", + "label": "chemotherapy procedure" + } + } + ], + "datasetId": "test" + }, + { + "diseases": [ + { + "ageOfOnset": { + "id": "NCIT:C16731", + "label": "Neonate" + }, + "diseaseCode": { + "id": "MONDO:0004975", + "label": "Cystic fibrosis" + }, + "familyHistory": true, + "notes": "Bear in mind that all information is synthetic", + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "ethnicity": { + "id": "NCIT:C43851", + "label": "European" + }, + "exposures": [ + { + "ageAtExposure": { + "iso8601duration": "P32Y6M1D" + }, + "date": "2024-09-25", + "duration": "14 months", + "exposureCode": { + "id": "CHEBI:46661", + "label": "asbestos" + }, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + } + ], + "geographicOrigin": { + "id": "GAZ:00002586", + "label": "State of Wisconsin" + }, + "id": "SAMPLE20", + "interventionsOrProcedures": [ + { + "bodySite": { + "id": "FMAID:7195", + "label": "lung" + }, + "dateOfProcedure": "2024-12-24", + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + ], + "karyotypicSex": "XXXY", + "measures": [ + { + "assayCode": { + "id": "UBERON:0001062", + "label": "anatomical entity" + }, + "date": "2024-11-08", + "measurementValue": + { + "referenceRange": { + "high": 50, + "low": 20, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + } + }, + "unit": { + "id": "NCIT:C28253", + "label": "Milligram" + }, + "value": 50 + } + , + "notes": "Bear in mind that all this information is synthetic", + "observationMoment": { + "iso8601duration": "P32Y6M1D" + }, + "procedure": { + "ageAtProcedure": "1999-08-05T17:21:00+01:00", + "bodySite": { + "id": "FMAID:7195", + "label": "lung" + }, + "dateOfProcedure": "2024-08-15", + "procedureCode": { + "id": "OBI:0002657", + "label": "surgical biopsy" + } + } + } + ], + "pedigrees": [ + { + "disease": { + "diseaseCode": { + "id": "HP:0001645", + "label": "Sudden cardiac death" + }, + "familyHistory": true, + "notes": "Bear in mind that all this information is synthetic ", + "severity": { + "id": "HP:0012828", + "label": "Severe" + }, + "stage": { + "id": "OGMS:0000103", + "label": "Disease stage" + } + }, + "id": "SCD-Pedigree001", + "members": [ + { + "affected": true, + "memberId": "Ind001", + "role": { + "id": "NCIT:C64435", + "label": "Proband" + } + }, + { + "affected": true, + "memberId": "Ind002", + "role": { + "id": "NCIT:C96572", + "label": "Father" + } + }, + { + "affected": true, + "memberId": "Ind003", + "role": { + "id": "NCIT:C111201", + "label": "Full Brother" + } + } + ] + } + ], + "phenotypicFeatures": [ + { + "evidence": { + "evidenceCode": { + "id": "ECO:0006017", + "label": "author statement from published clinical study used in manual assertion" + } + }, + "excluded": true, + "featureType": { + "id": "HP:0000002", + "label": "Abnormality of body height" + }, + "modifiers": [ + { + "id": "HP:0032500", + "label": "Exacerbated by tobacco use" + } + ], + "notes": "Please note that all this information is synthetic", + "onset": { + "id": "HP:0011463", + "label": "Infantile onset" + }, + "resolution": { + "days": 8, + "weeks": 8 + }, + "severity": { + "id": "HP:0012828", + "label": "Severe" + } + } + ], + "sex": { + "id": "NCIT:C16576", + "label": "female" + }, + "treatments": [ + { + "ageAtOnset": { + "iso8601duration": "P1Y1" + }, + "routeOfAdministration": { + "id": "NCIT:C38288", + "label": "Oral Route of Administration" + }, + "treatmentCode": { + "id": "OGMS:0000113", + "label": "chemotherapy procedure" + } + } + ], + "datasetId": "test" + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/v2_0_0/runs.json b/beacon/connections/mongo/data/test/v2_0_0/runs.json new file mode 100644 index 00000000..3d4019ed --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/runs.json @@ -0,0 +1,26 @@ +[ + { + "biosampleId": "SAMPLE1", + "id": "EGA-testing", + "individualId": "SAMPLE1", + "info": { + "info": { + "info": "Bothmetadataandgenomicvariationsinformationaresynthetic." + } + }, + "libraryLayout": "PAIRED", + "librarySelection": "RANDOM", + "librarySource": { + "id": "GENEPIO:0001966", + "label": "genomic source" + }, + "libraryStrategy": "WGS", + "platform": "Illumina", + "platformModel": { + "id": "OBI:0002048", + "label": "Illumina HiSeq 3000" + }, + "runDate": "2021-10-18", + "datasetId": "test" + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/v2_0_0/targets.json b/beacon/connections/mongo/data/test/v2_0_0/targets.json new file mode 100644 index 00000000..eefd0e65 --- /dev/null +++ b/beacon/connections/mongo/data/test/v2_0_0/targets.json @@ -0,0 +1 @@ +[{"_id":"9f86d081884c7d659a2feaa0c55ad015a3bf4f1b2b0b822cd15d6c15b0f00a08","datasetId":"test","biosampleIds":["SAMPLE1","SAMPLE2","SAMPLE3","SAMPLE4","SAMPLE5","SAMPLE6","SAMPLE7","SAMPLE8","SAMPLE9","SAMPLE10","SAMPLE11","SAMPLE12","SAMPLE13","SAMPLE14","SAMPLE15","SAMPLE16","SAMPLE17","SAMPLE18","SAMPLE19","SAMPLE20"]}] diff --git a/beacon/connections/mongo/data/test2/caseLevelData.json b/beacon/connections/mongo/data/test2/v2_0_0/caseLevelData.json similarity index 100% rename from beacon/connections/mongo/data/test2/caseLevelData.json rename to beacon/connections/mongo/data/test2/v2_0_0/caseLevelData.json diff --git a/beacon/connections/mongo/data/test2/datasets.json b/beacon/connections/mongo/data/test2/v2_0_0/datasets.json similarity index 100% rename from beacon/connections/mongo/data/test2/datasets.json rename to beacon/connections/mongo/data/test2/v2_0_0/datasets.json diff --git a/beacon/connections/mongo/data/test2/individuals.json b/beacon/connections/mongo/data/test2/v2_0_0/individuals.json similarity index 100% rename from beacon/connections/mongo/data/test2/individuals.json rename to beacon/connections/mongo/data/test2/v2_0_0/individuals.json diff --git a/beacon/connections/mongo/data/test2/targets.json b/beacon/connections/mongo/data/test2/v2_0_0/targets.json similarity index 100% rename from beacon/connections/mongo/data/test2/targets.json rename to beacon/connections/mongo/data/test2/v2_0_0/targets.json From 5b66900288c18a713cd1af43c6d79f7ea4c77a06 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 3 Aug 2026 09:49:09 +0200 Subject: [PATCH 22/56] addressing org info to be an object --- beacon/framework/validator/v2_0_0/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/framework/validator/v2_0_0/info.py b/beacon/framework/validator/v2_0_0/info.py index 3be1ef1d..bd237c0a 100644 --- a/beacon/framework/validator/v2_0_0/info.py +++ b/beacon/framework/validator/v2_0_0/info.py @@ -9,7 +9,7 @@ class BeaconOrganization(BaseModel): contactUrl: Optional[str]=conf_override.config.org_contact_url if conf_override.config.org_contact_url != "" else None description: Optional[str]=conf_override.config.org_description if conf_override.config.org_description != "" else None id: str=conf_override.config.org_id - info: Optional[str]=conf_override.config.org_info if conf_override.config.org_info != "" else None + info: Optional[Dict]={"organizationInfo": conf_override.config.org_info} if conf_override.config.org_info != "" else None logoUrl: Optional[str]=conf_override.config.org_logo_url if conf_override.config.org_logo_url != "" else None name: str=conf_override.config.org_name welcomeUrl: Optional[str]=conf_override.config.org_welcome_url if conf_override.config.welcome_url != "" else None From 398b737c0cdba49b2d0348562b449c0c6f968d73 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 3 Aug 2026 10:27:22 +0200 Subject: [PATCH 23/56] fixing test data --- beacon/connections/mongo/Makefile | 2 +- .../mongo/data/CINECA/v2_2_0/datasets.json | 23 ++++++++++++++++++- .../mongo/data/test/v2_2_0/analyses.json | 17 +++++++++++++- 3 files changed, 39 insertions(+), 3 deletions(-) diff --git a/beacon/connections/mongo/Makefile b/beacon/connections/mongo/Makefile index aefd5b28..5154bc17 100644 --- a/beacon/connections/mongo/Makefile +++ b/beacon/connections/mongo/Makefile @@ -1,4 +1,4 @@ -DATA_PATH = /data/test +DATA_PATH = /data/test/v2_2_0 build: docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file $(DATA_PATH)/datasets.json --collection datasets diff --git a/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json b/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json index 95eab19d..2284815c 100644 --- a/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json +++ b/beacon/connections/mongo/data/CINECA/v2_2_0/datasets.json @@ -1 +1,22 @@ -[{"createDateTime": "2021-12-29T20:33:40Z", "dataUseConditions": {"duoDataUse": [{"id": "DUO:0000019,DUO:00000020", "label": "publication required,publication required", "version": "7-1-19,7-1-19"}]}, "description": "Please note: This synthetic data set (with cohort participants / subjects marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk This dataset (CINECA_synthetic_cohort_EUROPE_UK1) consists of 2521 samples which have genetic data based on 1000 Genomes data (https://www.nature.com/articles/nature15393), and synthetic subject attributes and phenotypic data derived from UKBiobank (https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001779). These data were initially derived using the TOFU tool (https://github.com/spiros/tofu), which generates randomly generated values based on the UKBiobank data dictionary. Categorical values were randomly generated based on the data dictionary, continuous variables generated based on the distribution of values reported by the UK Biobank showcase, and date / time values were random. Additionally we split the phenotypes and attributes into 4 main classes - general, cancer, diabetes mellitus, and cardiac. We assigned the general attributes to all the samples, and the cardiac / diabetes mellitus / cancer attributes to a proportion of the total samples. Once the initial set of phenotypes and attributes were generated, the data data was checked for consistency and where possible dependent attributes were calculated from the independent variables generated by TOFU. For example, BMI was calculated from height and weight data, and age at death generated by date of death and date of birth. These data were then loaded to the development instance of Biosamples (https://www.ebi.ac.uk/biosamples/) which accessioned each of the samples. The genetic data are derived from the 1000 Genomes Phase 3 release (https://www.internationalgenome.org/category/phase-3/). The genotype data consists of a single joint call vcf files with call genotypes for all 2504 samples, plus bed, bim, fam, and nosex files generated via plink for these samples and genotypes. The genotype data has had a variety of errors introduced to mimic real data and as a test for quality control pipelines. These include gender mismatches, ethnic background mislabelling and low call rates for a randomly chosen subset of sample data as well as deviations from Hardy Weinberg equilibrium and low call rates for a random selection of variants. Additionally 40 samples have raw genetic data available in the form of both bam and cram files, including unmapped data. The gender of the samples in the 1000 genomes data has been matched to the synthetic phenotypic data generated for these samples. The genetic data was then linked to the synthetic data in BioSamples, and submitted to EGA.\",\"externalUrl\":\u00a0\"https://ega-archive.org/datasets/EGAD00001006673/", "externalUrl": "https://ega-archive.org/datasets/EGAD00001006673/", "id": "CINECA_synthetic_cohort_EUROPE_UK1", "info": {}, "name": "CINECA_synthetic_cohort_EUROPE_UK1", "updateDateTime": "2021-12-29T20:33:40Z", "version": "v1.0", "_id": "1305c00a4ae5eac71edfef6f2b8ff539101dae17b3e294063b6ed277c5bf901d"}] \ No newline at end of file +[ + { + "createDateTime": "2021-12-29T20:33:40Z", + "dataUseConditions": { + "duoDataUse": [ + { + "id": "DUO:0000019,DUO:00000020", + "label": "publication required,publication required", + "version": "7-1-19,7-1-19" + } + ] + }, + "description": "Please note: This synthetic data set (with cohort participants / subjects marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk This dataset (CINECA_synthetic_cohort_EUROPE_UK1) consists of 2521 samples which have genetic data based on 1000 Genomes data (https://www.nature.com/articles/nature15393), and synthetic subject attributes and phenotypic data derived from UKBiobank (https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001779). These data were initially derived using the TOFU tool (https://github.com/spiros/tofu), which generates randomly generated values based on the UKBiobank data dictionary. Categorical values were randomly generated based on the data dictionary, continuous variables generated based on the distribution of values reported by the UK Biobank showcase, and date / time values were random. Additionally we split the phenotypes and attributes into 4 main classes - general, cancer, diabetes mellitus, and cardiac. We assigned the general attributes to all the samples, and the cardiac / diabetes mellitus / cancer attributes to a proportion of the total samples. Once the initial set of phenotypes and attributes were generated, the data data was checked for consistency and where possible dependent attributes were calculated from the independent variables generated by TOFU. For example, BMI was calculated from height and weight data, and age at death generated by date of death and date of birth. These data were then loaded to the development instance of Biosamples (https://www.ebi.ac.uk/biosamples/) which accessioned each of the samples. The genetic data are derived from the 1000 Genomes Phase 3 release (https://www.internationalgenome.org/category/phase-3/). The genotype data consists of a single joint call vcf files with call genotypes for all 2504 samples, plus bed, bim, fam, and nosex files generated via plink for these samples and genotypes. The genotype data has had a variety of errors introduced to mimic real data and as a test for quality control pipelines. These include gender mismatches, ethnic background mislabelling and low call rates for a randomly chosen subset of sample data as well as deviations from Hardy Weinberg equilibrium and low call rates for a random selection of variants. Additionally 40 samples have raw genetic data available in the form of both bam and cram files, including unmapped data. The gender of the samples in the 1000 genomes data has been matched to the synthetic phenotypic data generated for these samples. The genetic data was then linked to the synthetic data in BioSamples, and submitted to EGA.\",\"externalUrl\": \"https://ega-archive.org/datasets/EGAD00001006673/", + "externalUrl": "https://ega-archive.org/datasets/EGAD00001006673/", + "id": "CINECA_synthetic_cohort_EUROPE_UK1", + "info": {}, + "name": "CINECA_synthetic_cohort_EUROPE_UK1", + "updateDateTime": "2021-12-29T20:33:40Z", + "version": "v1.0", + "_id": "1305c00a4ae5eac71edfef6f2b8ff539101dae17b3e294063b6ed277c5bf901d" + } +] \ No newline at end of file diff --git a/beacon/connections/mongo/data/test/v2_2_0/analyses.json b/beacon/connections/mongo/data/test/v2_2_0/analyses.json index f25032d6..22119ced 100644 --- a/beacon/connections/mongo/data/test/v2_2_0/analyses.json +++ b/beacon/connections/mongo/data/test/v2_2_0/analyses.json @@ -1 +1,16 @@ -[{"aligner": "bwa-0.7.8", "analysisDate": "2021-10-17", "biosampleId": "EGA-testing", "id": "EGA-testing", "individualId": "EGA", "info": {}, "pipelineName": "Pipeline-panel-0001-v1", "pipelineRef": "https://doi.org/10.48511/workflowhub.workflow.111.1", "runId": "EGAR5000XXX", "variantCaller": "GATK4.0", "datasetId": "test", "_id": "2e8d3e8dcf5a492448e1703c2c99ed5ee4370a1152f1983b3cf11e3e9cab2033"}] \ No newline at end of file +[ + { + "aligner": "bwa-0.7.8", + "analysisDate": "2021-10-17", + "biosampleId": "SAMPLE1", + "id": "EGA-testing", + "individualId": "SAMPLE1", + "info": {}, + "pipelineName": "Pipeline-panel-0001-v1", + "pipelineRef": "https://doi.org/10.48511/workflowhub.workflow.111.1", + "runId": "EGAR5000XXX", + "variantCaller": "GATK4.0", + "datasetId": "test", + "_id": "2e8d3e8dcf5a492448e1703c2c99ed5ee4370a1152f1983b3cf11e3e9cab2033" + } +] \ No newline at end of file From 1564001ca175538cfc1f3df1724185077dfae93d Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 3 Aug 2026 17:50:58 +0200 Subject: [PATCH 24/56] adapting tests to new v2.2.0 datasets --- .../mongo/extract_filtering_terms.py | 9 +- beacon/tests/__main__.py | 85 ++++++++++--------- 2 files changed, 46 insertions(+), 48 deletions(-) diff --git a/beacon/connections/mongo/extract_filtering_terms.py b/beacon/connections/mongo/extract_filtering_terms.py index 05f6dfbd..ea737542 100644 --- a/beacon/connections/mongo/extract_filtering_terms.py +++ b/beacon/connections/mongo/extract_filtering_terms.py @@ -42,6 +42,7 @@ def get_ontology_field_name(ontology_id:str, term_id:str, collection:str, fields query['$or'].append(fieldquery) # Execute the query results = client['beacon'].get_collection(collection).find(query).limit(1) + # Get the results in a dictionary and extract the labels of the ontologies try: results = list(results) @@ -244,7 +245,7 @@ def insert_all_ontology_terms_used(): }) insert_zygosity_terms() elif entity == 'individual': - individuals_fields=['diseases.ageOfOnset.id','diseases.diseaseCode.id','diseases.severity.id','diseases.stage.id','ethnicity.id','exposures.exposureCode.id','exposures.unit.id','geographicOrigin.id','interventionsOrProcedures.ageAtProcedure.id','interventionsOrProcedures.bodySite.id','interventionsOrProcedures.procedureCode.id','measures.assayCode.id','measures.measurementValue.id','measures.measurementValue.typedQuantities.quantity.unit.id','measures.measurementValue.unit.id','measures.observationMoment.id','measures.procedure.bodySite.id','measures.procedure.procedureCode.id','pedigrees.disease.diseaseCode.id','pedigrees.disease.severity.id','pedigrees.disease.stage.id','pedigrees.id','pedigrees.members.role.id','phenotypicFeatures.evidence.evidenceCode.id','phenotypicFeatures.evidence.reference.id','phenotypicFeatures.featureType.id','phenotypicFeatures.modifiers.id','phenotypicFeatures.onset.id','phenotypicFeatures.resolution.id','phenotypicFeatures.severity.id','sex.id','treatments.cumulativeDose.referenceRange.id','treatments.doseIntervals.id','treatments.routeOfAdministration.id','treatments.treatmentCode.id'] + individuals_fields=['diseases.ageOfOnset.id','diseases.diseaseCode.id','diseases.severity.id','diseases.stage.id','ethnicity.id','exposures.exposureCode.id','exposures.unit.id','geographicOrigin.id','interventionsOrProcedures.ageAtProcedure.id','interventionsOrProcedures.bodySite.id','interventionsOrProcedures.procedureCode.id','measurements.assayCode.id','measurements.measurementValue.id','measurements.measurementValue.typedQuantities.quantity.unit.id','measurements.measurementValue.unit.id','measurements.observationMoment.id','measurements.procedure.bodySite.id','measurements.procedure.procedureCode.id','pedigrees.disease.diseaseCode.id','pedigrees.disease.severity.id','pedigrees.disease.stage.id','pedigrees.id','pedigrees.members.role.id','phenotypicFeatures.evidence.evidenceCode.id','phenotypicFeatures.evidence.reference.id','phenotypicFeatures.featureType.id','phenotypicFeatures.modifiers.id','phenotypicFeatures.onset.id','phenotypicFeatures.resolution.id','phenotypicFeatures.severity.id','sex.id','treatments.cumulativeDose.referenceRange.id','treatments.doseIntervals.id','treatments.routeOfAdministration.id','treatments.treatmentCode.id'] insert_found_terms(individuals, individuals_fields) for alphanumeric_term in alphanumeric_terms_individuals: alphanumterms.append({ @@ -334,8 +335,6 @@ def get_filtering_object(terms_ids: list, collection, fields): ontology = onto.split(':') ontology_id = ontology[0] term_id = ontology[1] - #if ontology_id not in ontologies: - #ontologies[ontology_id] = load_ontology(ontology_id) if ontology_id.isupper(): field_dict = get_ontology_field_name(ontology_id, term_id, collection.name, fields) else: @@ -346,8 +345,6 @@ def get_filtering_object(terms_ids: list, collection, fields): value_id=None if 'measurements.assayCode' in field: value_id = label - if 'measures.assayCode' in field: - value_id = label ontology_label = label if field is not None: if onto not in list_of_ontologies: @@ -394,7 +391,7 @@ def get_filtering_object(terms_ids: list, collection, fields): }) print(terms) - except Exception: + except Exception as e: pass return terms diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index ca39966b..dd214e26 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -2731,7 +2731,7 @@ async def test_check_post_cross_query_g_variants_individuals_is_working(): responsedict = json.loads(responsetext) # Expect aggregated cross-query result size - assert responsedict["responseSummary"]["numTotalResults"] == 40 + assert responsedict["responseSummary"]["numTotalResults"] == 38 loop.run_until_complete(test_check_post_cross_query_g_variants_individuals_is_working()) loop.run_until_complete(client.close()) @@ -2764,7 +2764,7 @@ async def test_check_post_cross_query_biosamples_individuals_is_working(): responsedict = json.loads(responsetext) # Expect biosample results for matching individuals - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 16 assert resp.status == 200 loop.run_until_complete(test_check_post_cross_query_biosamples_individuals_is_working()) @@ -2903,7 +2903,7 @@ async def test_check_alphanumeric_equal_query_is_working(): responsedict = json.loads(responsetext) # Expect deterministic match count for exact filter - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 13 loop.run_until_complete(test_check_alphanumeric_equal_query_is_working()) loop.run_until_complete(client.close()) @@ -2945,7 +2945,7 @@ async def test_check_alphanumeric_like_query_is_working(): responsedict = json.loads(responsetext) # Pattern match should still resolve to same dataset subset - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 13 loop.run_until_complete(test_check_alphanumeric_like_query_is_working()) loop.run_until_complete(client.close()) @@ -2987,7 +2987,8 @@ async def test_check_alphanumeric_not_like_query_is_working(): responsedict = json.loads(responsetext) # Expect no matching records due to exclusion filter - assert responsedict["responseSummary"]["exists"] == False + assert responsedict["responseSummary"]["exists"] == True + assert responsedict["responseSummary"]["numTotalResults"] == 7 loop.run_until_complete(test_check_alphanumeric_not_like_query_is_working()) loop.run_until_complete(client.close()) @@ -3029,7 +3030,8 @@ async def test_check_alphanumeric_not_query_is_working(): responsedict = json.loads(responsetext) # No matching individuals expected - assert responsedict["responseSummary"]["exists"] == False + assert responsedict["responseSummary"]["exists"] == True + assert responsedict["responseSummary"]["numTotalResults"] == 7 loop.run_until_complete(test_check_alphanumeric_not_query_is_working()) loop.run_until_complete(client.close()) @@ -3053,7 +3055,7 @@ async def test_check_iso8601duration_gt_query_is_working(): { "id": "exposures.ageAtExposure.iso8601duration", "operator": ">", - "value": "31" + "value": "21" } ], "includeResultsetResponses": "HIT", @@ -3070,7 +3072,7 @@ async def test_check_iso8601duration_gt_query_is_working(): responsedict = json.loads(responsetext) # Expect deterministic count of matching exposures above threshold - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 10 loop.run_until_complete(test_check_iso8601duration_gt_query_is_working()) loop.run_until_complete(client.close()) @@ -3093,7 +3095,7 @@ async def test_check_iso8601duration_ls_query_is_working(): { "id": "exposures.ageAtExposure.iso8601duration", "operator": "<", - "value": "33" + "value": "22" } ], "includeResultsetResponses": "HIT", @@ -3111,7 +3113,7 @@ async def test_check_iso8601duration_ls_query_is_working(): # Validate that matching individuals exist and count is as expected assert responsedict["responseSummary"]["exists"] == True - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 10 loop.run_until_complete(test_check_iso8601duration_ls_query_is_working()) loop.run_until_complete(client.close()) @@ -3174,7 +3176,7 @@ async def test_check_measurement_value_query_is_working(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": ">", "value": "44", "scope": "individual" @@ -3215,9 +3217,9 @@ async def test_check_measurement_value_query_does_not_find_results(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": ">", - "value": "50", + "value": "250", "scope": "individual" } ], @@ -3253,7 +3255,7 @@ async def test_check_custom_query_is_working(): "meta": {"apiVersion": "2.0"}, "query": { "filters": [ - {"id": "sampleOriginType:ovary"} + {"id": "sampleOriginType:breast lobe"} ], "includeResultsetResponses": "HIT", "pagination": {"skip": 0, "limit": 10}, @@ -3311,7 +3313,7 @@ async def test_check_filters_as_request_parameter_working(): assert resp.status == 200 responsetext = await resp.text() responsedict = json.loads(responsetext) - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 16 loop.run_until_complete(test_check_filters_as_request_parameter_working()) loop.run_until_complete(client.close()) @@ -3333,7 +3335,6 @@ async def test_check_datasets_list_query_is_working(): "requestParameters": { "datasets": ["test"] }, - "filters": [], "includeResultsetResponses": "HIT", "pagination": {"skip": 0, "limit": 101}, "testMode": True, @@ -3543,7 +3544,7 @@ async def test_check_individuals_variants(): assert resp.status == 200 responsetext = await resp.text() responsedict = json.loads(responsetext) - assert responsedict["responseSummary"]["numTotalResults"] == 16 + assert responsedict["responseSummary"]["numTotalResults"] == 14 loop.run_until_complete(test_check_individuals_variants()) loop.run_until_complete(client.close()) @@ -3762,7 +3763,7 @@ async def test_check_biosamples_variants(): responsedict = json.loads(responsetext) # Validate filtered biosample-linked variant results - assert responsedict["responseSummary"]["numTotalResults"] == 7 + assert responsedict["responseSummary"]["numTotalResults"] == 5 loop.run_until_complete(test_check_biosamples_variants()) loop.run_until_complete(client.close()) @@ -4255,7 +4256,7 @@ async def test_check_geneId_individual_filter(): responsedict = json.loads(responsetext) # Expect 17 biosample-level results - assert responsedict["responseSummary"]["numTotalResults"] == 17 + assert responsedict["responseSummary"]["numTotalResults"] == 13 loop.run_until_complete(test_check_geneId_individual_filter()) loop.run_until_complete(client.close()) @@ -4291,7 +4292,7 @@ async def test_check_geneId_individual_filter(): responsedict = json.loads(responsetext) # Expect biosamples matching both individual filter + geneId constraint - assert responsedict["responseSummary"]["numTotalResults"] == 17 + assert responsedict["responseSummary"]["numTotalResults"] == 13 loop.run_until_complete(test_check_geneId_individual_filter()) loop.run_until_complete(client.close()) @@ -4569,7 +4570,7 @@ async def test_check_runs_variants(): "query": { "filters": [ { - "id": "MONDO:0004975", + "id": "MONDO:0004989", "scope": "individual", "includeDescendantTerms": True } @@ -4587,7 +4588,7 @@ async def test_check_runs_variants(): responsedict = json.loads(responsetext) # Expect expanded ontology query to return multiple matched individuals - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 3 loop.run_until_complete(test_check_runs_variants()) loop.run_until_complete(client.close()) @@ -5061,7 +5062,7 @@ async def test_check_post_individuals_with_filter_is_working(): # Validate filtered results exist and match expected count assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 40 + assert responsedict["responseSummary"]["numTotalResults"] == 38 loop.run_until_complete(test_check_post_individuals_with_filter_is_working()) loop.run_until_complete(client.close()) @@ -5222,7 +5223,7 @@ async def test_check_individuals_with_request_parameters_and_filters(): # Ensure combined filtering + coordinate query works correctly assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 15 + assert responsedict["responseSummary"]["numTotalResults"] == 12 loop.run_until_complete(test_check_individuals_with_request_parameters_and_filters()) loop.run_until_complete(client.close()) @@ -5267,7 +5268,7 @@ async def test_check_get_double_filters(): resp = await client.get( conf_override.config.uri_subpath + "/" + individual["individual"]["endpoint_name"] + - "?filters=NCIT:C16576,NCIT:C16731" + "?filters=NCIT:C16576,BTO:0004718" ) assert resp.status == 200 @@ -5277,7 +5278,7 @@ async def test_check_get_double_filters(): # Ensure combined filters still return valid matches assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 4 loop.run_until_complete(test_check_get_double_filters()) loop.run_until_complete(client.close()) @@ -5354,7 +5355,7 @@ async def test_check_measurement_value_query_is_not_working(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": ">", "value": "44", "scope": "individual" @@ -5397,7 +5398,7 @@ async def test_check_measurement_value_query_is_working(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": ">", "value": "44", "scope": "individual" @@ -5519,7 +5520,7 @@ async def test_check_measurement_value_query_is_not_working(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": ">", "value": "44", "scope": "individual" @@ -5562,7 +5563,7 @@ async def test_check_similarity_high(): "query": { "filters": [ { - "id": "MONDO:0004975", + "id": "MONDO:0004989", "scope": "individual", # Strict similarity expansion "similarity": "high" @@ -5582,7 +5583,7 @@ async def test_check_similarity_high(): responsedict = json.loads(responsetext) # High similarity still returns expanded matches - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 3 loop.run_until_complete(test_check_similarity_high()) loop.run_until_complete(client.close()) @@ -5605,7 +5606,7 @@ async def test_check_similarity_medium(): "query": { "filters": [ { - "id": "MONDO:0004975", + "id": "MONDO:0004989", "scope": "individual", "similarity": "medium" } @@ -5624,7 +5625,7 @@ async def test_check_similarity_medium(): responsedict = json.loads(responsetext) # Medium similarity yields same expected match count - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 3 loop.run_until_complete(test_check_similarity_medium()) loop.run_until_complete(client.close()) @@ -5647,7 +5648,7 @@ async def test_check_similarity_low(): "query": { "filters": [ { - "id": "MONDO:0004975", + "id": "MONDO:0004989", "scope": "individual", "similarity": "low" } @@ -5666,7 +5667,7 @@ async def test_check_similarity_low(): responsedict = json.loads(responsetext) # Low similarity still returns same aggregate match count in this dataset - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 3 loop.run_until_complete(test_check_similarity_low()) loop.run_until_complete(client.close()) @@ -5686,7 +5687,7 @@ async def test_check_synonyms(): "meta": {"apiVersion": "2.0"}, "query": { "filters": [ - {"id": "DOID:1485", "scope": "individual"} + {"id": "NCIT:C4872", "scope": "individual"} ], "includeResultsetResponses": "HIT", "pagination": {"skip": 0, "limit": 10}, @@ -5702,7 +5703,7 @@ async def test_check_synonyms(): responsedict = json.loads(responsetext) # Synonym expansion should increase matched result set - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 3 loop.run_until_complete(test_check_synonyms()) loop.run_until_complete(client.close()) @@ -6090,7 +6091,7 @@ def test_main_check_post_cross_query_individuals_g_variants_is_not_working(self) loop.run_until_complete(client.start_server()) async def test_check_post_cross_query_individuals_g_variants_is_not_working(): - # Mis-scoped filter (individual scope incorrectly used for anatomical entity) + # Mis-scoped filter (individual scope incorrectly used for Height-standing) resp = await client.post( conf_override.config.uri_subpath + "/" + genomicVariant["genomicVariant"]["endpoint_name"], @@ -6099,7 +6100,7 @@ async def test_check_post_cross_query_individuals_g_variants_is_not_working(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": "=", "value": "GATK3.0", "scope": "individual" @@ -6142,7 +6143,7 @@ async def test_check_post_cross_query_individuals_runs_is_not_working(): "query": { "filters": [ { - "id": "anatomical entity", + "id": "Height-standing", "operator": "=", "value": "GATK3.0", "scope": "individual" @@ -6585,7 +6586,7 @@ async def test_check_iso8601duration_gt_query_is_working(): { "id": "exposures.ageAtExposure.iso8601duration", "operator": ">", - "value": "P31Y" + "value": "P21Y" } ], "includeResultsetResponses": "HIT", @@ -6602,7 +6603,7 @@ async def test_check_iso8601duration_gt_query_is_working(): responsedict = json.loads(responsetext) # Expected deterministic result count for duration-based filter - assert responsedict["responseSummary"]["numTotalResults"] == 20 + assert responsedict["responseSummary"]["numTotalResults"] == 10 loop.run_until_complete(test_check_iso8601duration_gt_query_is_working()) loop.run_until_complete(client.close()) From 1c69849b774c504b358b2077eb6b1e7e329feef6 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 3 Aug 2026 17:52:53 +0200 Subject: [PATCH 25/56] only update version at PR to main --- .github/workflows/update_beacon_pi_version.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml index 1866571f..f9d381be 100644 --- a/.github/workflows/update_beacon_pi_version.yml +++ b/.github/workflows/update_beacon_pi_version.yml @@ -8,7 +8,6 @@ on: - synchronize branches: - main - - develop permissions: contents: write From 363e9f04d345c74c7ce82e06565caab664b8cbf8 Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 3 Aug 2026 17:54:19 +0200 Subject: [PATCH 26/56] modifying version to make action succeed --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index 492eabc9..14e4b344 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.3.0 +api_version: v2.2.5 From ce16c466885deb5bbdf348584b1d6c53e77fdb9c Mon Sep 17 00:00:00 2001 From: github-actions Date: Mon, 3 Aug 2026 15:55:53 +0000 Subject: [PATCH 27/56] Update API version to v2.3.0 --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index 14e4b344..492eabc9 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.2.5 +api_version: v2.3.0 From f5b0688a67b22c9baf50c19c065c6ca8327bb568 Mon Sep 17 00:00:00 2001 From: costero-e Date: Wed, 2 Sep 2026 17:16:25 +0200 Subject: [PATCH 28/56] progress on new descendants script --- beacon/connections/mongo/get_descendants.py | 151 +++++++------------- 1 file changed, 53 insertions(+), 98 deletions(-) diff --git a/beacon/connections/mongo/get_descendants.py b/beacon/connections/mongo/get_descendants.py index be8a314e..4c9182f7 100644 --- a/beacon/connections/mongo/get_descendants.py +++ b/beacon/connections/mongo/get_descendants.py @@ -5,6 +5,8 @@ from urllib.error import HTTPError import progressbar from beacon.connections.mongo.client import get_client +import requests +import json class MyProgressBar: def __init__(self): @@ -21,41 +23,10 @@ def __call__(self, block_num: int, block_size: int, total_size: int): else: self.pbar.finish() -def load_ontology(ontology_id: str): - if ontology_id.isalpha(): - print(ontology_id) - url_alt = "https://www.ebi.ac.uk/efo/EFO.obo" - url = "http://purl.obolibrary.org/obo/{}.obo".format(ontology_id.lower()) - path = "/beacon/connections/mongo/ontologies/{}.obo".format(ontology_id) - try: - if not os.path.exists(path): - full_path = os.path.realpath(__file__) - print(full_path) - urllib.request.urlretrieve(url, path, MyProgressBar()) - except HTTPError: - # TODO: Handle error in case the HTTP address could not be reached. - pass - except ValueError: - # TODO: Handle error in case there was a wrong ontology trying to be mapped. - pass - except Exception: - pass - try: - if os.stat(path).st_size == 0: - try: - urllib.request.urlretrieve(url_alt, path, MyProgressBar()) - except HTTPError: - # TODO: Handle error in case the HTTP address could not be reached. - pass - except ValueError: - # TODO: Handle error in case there was a wrong ontology trying to be mapped. - pass - except Exception: - pass - return '{}'.format(ontology_id) - - def get_descendants_and_similarities(): + list_of_ontology_families=[] + similarity_high=[] + dict_of_ontology_families={} client=get_client() try: client['beacon'].drop_collection("similarities") @@ -72,74 +43,58 @@ def get_descendants_and_similarities(): array_of_ontologies.append(ft_doc["id"]) for ontology in array_of_ontologies: ontology_list = ontology.split(':') - load_ontology(ontology_list[0]) - url = "/beacon/connections/mongo/ontologies/{}.obo".format(ontology_list[0].lower()) - list_of_cousins = [] - list_of_brothers = [] - list_of_uncles = [] - list_of_grandpas = [] - url_alt = "https://www.ebi.ac.uk/efo/EFO.obo" - try: - graph = obonet.read_obo(url) - except Exception: - graph = obonet.read_obo(url_alt) - try: - descendants = networkx.ancestors(graph, ontology) - except Exception: - descendants = '' - descendants=list(descendants) - - print(descendants) - - - try: - tree = [n for n in graph.successors(ontology)] - for onto in tree: - predecessors = [n for n in graph.successors(onto)] - successors = [n for n in graph.predecessors(onto)] - list_of_brothers.append(successors) - list_of_grandpas.append(predecessors) - similarity_high=[] - similarity_medium=[] - similarity_low=[] - for llista in list_of_grandpas: - for item in llista: - uncles = [n for n in graph.predecessors(item)] - list_of_uncles.append(uncles) - for uncle in uncles: - cousins = [n for n in graph.predecessors(uncle)] - if ontology not in cousins: - list_of_cousins.append(cousins) + if ontology_list[0] not in dict_of_ontology_families: + dict_of_ontology_families[ontology_list[0]]=[ontology_list[1]] + else: + dict_of_ontology_families[ontology_list[0]].append(ontology_list[1]) + for ontology_id, ontology_codes_list in dict_of_ontology_families.items(): + list_of_existing_descendants = [] + for code in ontology_codes_list: + parent=None + #url = f"https://api-evsrest.nci.nih.gov/api/v1/concept/{ontology_id.lower()}/{code}/descendants" + url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" + data = requests.get(url).json() + if "_embedded" in data: + list_of_descendants_full=data["_embedded"]["terms"] + for descendant in list_of_descendants_full: + if descendant["obo_id"] in ontology_codes_list: + list_of_existing_descendants.append(descendant["obo_id"]) - for llista in list_of_brothers: - for item in llista: - similarity_high.append(item) - similarity_medium.append(item) - similarity_low.append(item) + print(f"\n===== {ontology_id}:{code} =====") + print(list_of_existing_descendants) - for llista in list_of_cousins: - for item in llista: - similarity_medium.append(item) - similarity_low.append(item) + ancestors_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" + ancestors_data = requests.get(ancestors_url).json() + if "_embedded" in ancestors_data: + list_of_ancestors_full=data["_embedded"]["terms"] + for ancestor in list_of_ancestors_full: + ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ancestor["obo_id"]}" + ancestor_descendants_data = requests.get(ancestor_descendants_url).json() + if "_embedded" in ancestor_descendants_data: + list_of_ancestor_descendants_full=data["_embedded"]["terms"] + for ancestor_descendant in list_of_ancestor_descendants_full: + if ancestor_descendant["obo_id"] == ontology_id+":"+code: + parent = ancestor_descendant["obo_id"] + similarity_high = list_of_ancestor_descendants_full + break + similarity_high.remove[ontology_id+":"+code] + definitive_similarity_high=[] + for similar_high_ontology in similarity_high: + if similar_high_ontology in ontology_codes_list: + definitive_similarity_high.append(similar_high_ontology) - for llista in list_of_uncles: - for item in llista: - similarity_low.append(item) - - except Exception: - similarity_high=[] - similarity_medium=[] - similarity_low=[] - dict={} - dict['id']=ontology - dict['descendants']=descendants - dict['similarity_high']=similarity_high - dict['similarity_medium']=similarity_medium - dict['similarity_low']=similarity_low - - client['beacon'].similarities.insert_one(dict) - print("succesfully retrieved descendants from {}".format(ontology)) + """ + dict={} + dict['id']=ontology + dict['descendants']=descendants + dict['similarity_high']=similarity_high + dict['similarity_medium']=similarity_medium + dict['similarity_low']=similarity_low + + client['beacon'].similarities.insert_one(dict) + """ + print("succesfully retrieved descendants from {}".format(ontology)) get_descendants_and_similarities() From 3fe12f5a31b8ad7137e9fccc502acdb6a586d275 Mon Sep 17 00:00:00 2001 From: costero-e Date: Wed, 2 Sep 2026 17:42:53 +0200 Subject: [PATCH 29/56] descendants progress in similarity --- beacon/connections/mongo/get_descendants.py | 56 +++++++++++++-------- 1 file changed, 35 insertions(+), 21 deletions(-) diff --git a/beacon/connections/mongo/get_descendants.py b/beacon/connections/mongo/get_descendants.py index 4c9182f7..eacc0ac2 100644 --- a/beacon/connections/mongo/get_descendants.py +++ b/beacon/connections/mongo/get_descendants.py @@ -23,9 +23,24 @@ def __call__(self, block_num: int, block_size: int, total_size: int): else: self.pbar.finish() +def get_all_ancestors(ontology_id, code, data): + similarity_high=[] + ancestors_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" + ancestors_data = requests.get(ancestors_url).json() + if "_embedded" in ancestors_data: + list_of_ancestors_full=data["_embedded"]["terms"] + for ancestor in list_of_ancestors_full: + ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ancestor["obo_id"]}" + ancestor_descendants_data = requests.get(ancestor_descendants_url).json() + if "_embedded" in ancestor_descendants_data: + list_of_ancestor_descendants_full=data["_embedded"]["terms"] + for ancestor_descendant in list_of_ancestor_descendants_full: + if ancestor_descendant["obo_id"] == ontology_id+":"+code: + similarity_high = list_of_ancestor_descendants_full + return similarity_high + def get_descendants_and_similarities(): list_of_ontology_families=[] - similarity_high=[] dict_of_ontology_families={} client=get_client() try: @@ -50,7 +65,6 @@ def get_descendants_and_similarities(): for ontology_id, ontology_codes_list in dict_of_ontology_families.items(): list_of_existing_descendants = [] for code in ontology_codes_list: - parent=None #url = f"https://api-evsrest.nci.nih.gov/api/v1/concept/{ontology_id.lower()}/{code}/descendants" url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" data = requests.get(url).json() @@ -63,25 +77,25 @@ def get_descendants_and_similarities(): print(f"\n===== {ontology_id}:{code} =====") print(list_of_existing_descendants) - ancestors_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" - ancestors_data = requests.get(ancestors_url).json() - if "_embedded" in ancestors_data: - list_of_ancestors_full=data["_embedded"]["terms"] - for ancestor in list_of_ancestors_full: - ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ancestor["obo_id"]}" - ancestor_descendants_data = requests.get(ancestor_descendants_url).json() - if "_embedded" in ancestor_descendants_data: - list_of_ancestor_descendants_full=data["_embedded"]["terms"] - for ancestor_descendant in list_of_ancestor_descendants_full: - if ancestor_descendant["obo_id"] == ontology_id+":"+code: - parent = ancestor_descendant["obo_id"] - similarity_high = list_of_ancestor_descendants_full - break - similarity_high.remove[ontology_id+":"+code] - definitive_similarity_high=[] - for similar_high_ontology in similarity_high: - if similar_high_ontology in ontology_codes_list: - definitive_similarity_high.append(similar_high_ontology) + similarity_high = get_all_ancestors(ontology_id, code, data) + similarity_high.remove[ontology_id+":"+code] + definitive_similarity_high=[] + for similar_high_ontology in similarity_high: + if similar_high_ontology in ontology_codes_list: + definitive_similarity_high.append(similar_high_ontology) + + definitive_similarity_low=[] + for similar_high_ontology in definitive_similarity_high: + split_similar_high = similar_high_ontology.split(":") + similarity_medium = get_all_ancestors(split_similar_high[0], split_similar_high[1], data) + similarity_medium.remove(similar_high_ontology) + + definitive_similarity_medium=[] + for similar_medium_ontology in similarity_medium: + if similar_medium_ontology in ontology_codes_list: + definitive_similarity_medium.append(similar_medium_ontology) + + """ From 328cab42a502e5047a61b83df18cb4d4ea75893c Mon Sep 17 00:00:00 2001 From: costero-e Date: Thu, 3 Sep 2026 10:42:09 +0200 Subject: [PATCH 30/56] progress on similar ontologies --- beacon/connections/mongo/get_descendants.py | 46 ++++++++++++--------- 1 file changed, 26 insertions(+), 20 deletions(-) diff --git a/beacon/connections/mongo/get_descendants.py b/beacon/connections/mongo/get_descendants.py index eacc0ac2..9087a84f 100644 --- a/beacon/connections/mongo/get_descendants.py +++ b/beacon/connections/mongo/get_descendants.py @@ -23,21 +23,28 @@ def __call__(self, block_num: int, block_size: int, total_size: int): else: self.pbar.finish() -def get_all_ancestors(ontology_id, code, data): +def discard_non_scanned_ontologies(list_of_all_ontologies, ontology_codes_list): + definitive_list=[] + for similar_ontology in list_of_all_ontologies: + if similar_ontology in ontology_codes_list: + definitive_list.append(similar_ontology) + return definitive_list + +def get_all_ancestors_descendants(ontology_id, code, data): similarity_high=[] - ancestors_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" + ancestors_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/ancestors?id={ontology_id}:{code}" ancestors_data = requests.get(ancestors_url).json() if "_embedded" in ancestors_data: list_of_ancestors_full=data["_embedded"]["terms"] for ancestor in list_of_ancestors_full: - ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ancestor["obo_id"]}" + ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/ancestors?id={ancestor["obo_id"]}" ancestor_descendants_data = requests.get(ancestor_descendants_url).json() if "_embedded" in ancestor_descendants_data: list_of_ancestor_descendants_full=data["_embedded"]["terms"] for ancestor_descendant in list_of_ancestor_descendants_full: if ancestor_descendant["obo_id"] == ontology_id+":"+code: similarity_high = list_of_ancestor_descendants_full - return similarity_high + return similarity_high, list_of_ancestor_descendants_full def get_descendants_and_similarities(): list_of_ontology_families=[] @@ -74,30 +81,29 @@ def get_descendants_and_similarities(): if descendant["obo_id"] in ontology_codes_list: list_of_existing_descendants.append(descendant["obo_id"]) - print(f"\n===== {ontology_id}:{code} =====") - print(list_of_existing_descendants) - - similarity_high = get_all_ancestors(ontology_id, code, data) + similarity_high, similarity_low = get_all_ancestors_descendants(ontology_id, code, data) similarity_high.remove[ontology_id+":"+code] - definitive_similarity_high=[] - for similar_high_ontology in similarity_high: - if similar_high_ontology in ontology_codes_list: - definitive_similarity_high.append(similar_high_ontology) + definitive_similarity_high=discard_non_scanned_ontologies(similarity_high, ontology_codes_list) - definitive_similarity_low=[] for similar_high_ontology in definitive_similarity_high: split_similar_high = similar_high_ontology.split(":") - similarity_medium = get_all_ancestors(split_similar_high[0], split_similar_high[1], data) + similarity_medium, cousins_ancestors_list = get_all_ancestors_descendants(split_similar_high[0], split_similar_high[1], data) similarity_medium.remove(similar_high_ontology) - definitive_similarity_medium=[] - for similar_medium_ontology in similarity_medium: - if similar_medium_ontology in ontology_codes_list: - definitive_similarity_medium.append(similar_medium_ontology) + definitive_similarity_medium=discard_non_scanned_ontologies(similarity_medium, ontology_codes_list) + + definitive_similarity_low=discard_non_scanned_ontologies(similarity_low, ontology_codes_list) - - + print(f"\n===== {ontology_id}:{code} =====") + print('-----DESCENDANTS-----') + print(list_of_existing_descendants) + print('-----SIMILARITY_HIGH-----') + print(definitive_similarity_high) + print('-----SIMILARITY_MEDIUM-----') + print(definitive_similarity_medium) + print('-----SIMILARITY_LOW-----') + print(definitive_similarity_low) """ dict={} dict['id']=ontology From 8eb258d32574e85478ce35c6059ba9427c0e418a Mon Sep 17 00:00:00 2001 From: costero-e Date: Thu, 3 Sep 2026 13:09:23 +0200 Subject: [PATCH 31/56] finished first iteration of new get_descendants script --- beacon/connections/mongo/get_descendants.py | 107 ++++++++++++-------- requirements.txt | 1 - 2 files changed, 67 insertions(+), 41 deletions(-) diff --git a/beacon/connections/mongo/get_descendants.py b/beacon/connections/mongo/get_descendants.py index 9087a84f..3f1d3213 100644 --- a/beacon/connections/mongo/get_descendants.py +++ b/beacon/connections/mongo/get_descendants.py @@ -1,12 +1,8 @@ -import obonet -import networkx -import os -import urllib.request -from urllib.error import HTTPError import progressbar from beacon.connections.mongo.client import get_client import requests -import json +import tqdm +from beacon.connections.mongo.conf import database_name class MyProgressBar: def __init__(self): @@ -30,35 +26,42 @@ def discard_non_scanned_ontologies(list_of_all_ontologies, ontology_codes_list): definitive_list.append(similar_ontology) return definitive_list -def get_all_ancestors_descendants(ontology_id, code, data): - similarity_high=[] +def get_all_ancestors_descendants(ontology_id, code): + ancestors_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/ancestors?id={ontology_id}:{code}" ancestors_data = requests.get(ancestors_url).json() if "_embedded" in ancestors_data: - list_of_ancestors_full=data["_embedded"]["terms"] + list_of_ancestors_full=ancestors_data["_embedded"]["terms"] for ancestor in list_of_ancestors_full: - ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/ancestors?id={ancestor["obo_id"]}" + ancestor_descendants_url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/children?id={ancestor['obo_id']}" ancestor_descendants_data = requests.get(ancestor_descendants_url).json() if "_embedded" in ancestor_descendants_data: - list_of_ancestor_descendants_full=data["_embedded"]["terms"] + list_of_ancestor_descendants_full=ancestor_descendants_data["_embedded"]["terms"] + list_of_ancestors_descendants=[] + is_list=False for ancestor_descendant in list_of_ancestor_descendants_full: + list_of_ancestors_descendants.append(ancestor_descendant["obo_id"]) if ancestor_descendant["obo_id"] == ontology_id+":"+code: - similarity_high = list_of_ancestor_descendants_full - return similarity_high, list_of_ancestor_descendants_full + is_list=True + if is_list==True: + return list_of_ancestors_descendants, list_of_ancestors_full + else: + return None, None + return None, list_of_ancestors_full def get_descendants_and_similarities(): list_of_ontology_families=[] dict_of_ontology_families={} client=get_client() try: - client['beacon'].drop_collection("similarities") + client[database_name].drop_collection("similarities") except Exception: - client['beacon'].create_collection(name="similarities") + client[database_name].create_collection(name="similarities") try: - client['beacon'].validate_collection("similarities") + client[database_name].validate_collection("similarities") except Exception: - db=client['beacon'].create_collection(name="similarities") - filtering_docs=client['beacon'].filtering_terms.find({"type": "ontology"}) + db=client[database_name].create_collection(name="similarities") + filtering_docs=client[database_name].filtering_terms.find({"type": "ontology"}) array_of_ontologies=[] for ft_doc in filtering_docs: if ft_doc["id"] not in array_of_ontologies: @@ -69,9 +72,15 @@ def get_descendants_and_similarities(): dict_of_ontology_families[ontology_list[0]]=[ontology_list[1]] else: dict_of_ontology_families[ontology_list[0]].append(ontology_list[1]) + i=0 + j=0 for ontology_id, ontology_codes_list in dict_of_ontology_families.items(): + pbar = tqdm.tqdm(total=len(ontology_codes_list)) list_of_existing_descendants = [] for code in ontology_codes_list: + definitive_similarity_high=[] + definitive_similarity_medium=[] + definitive_similarity_low=[] #url = f"https://api-evsrest.nci.nih.gov/api/v1/concept/{ontology_id.lower()}/{code}/descendants" url = f"https://www.ebi.ac.uk/ols4/api/ontologies/{ontology_id.lower()}/descendants?id={ontology_id}:{code}" data = requests.get(url).json() @@ -80,21 +89,35 @@ def get_descendants_and_similarities(): for descendant in list_of_descendants_full: if descendant["obo_id"] in ontology_codes_list: list_of_existing_descendants.append(descendant["obo_id"]) + similarity_high, similarity_low = get_all_ancestors_descendants(ontology_id, code) - similarity_high, similarity_low = get_all_ancestors_descendants(ontology_id, code, data) - similarity_high.remove[ontology_id+":"+code] - definitive_similarity_high=discard_non_scanned_ontologies(similarity_high, ontology_codes_list) - - for similar_high_ontology in definitive_similarity_high: - split_similar_high = similar_high_ontology.split(":") - similarity_medium, cousins_ancestors_list = get_all_ancestors_descendants(split_similar_high[0], split_similar_high[1], data) - similarity_medium.remove(similar_high_ontology) - - definitive_similarity_medium=discard_non_scanned_ontologies(similarity_medium, ontology_codes_list) - - definitive_similarity_low=discard_non_scanned_ontologies(similarity_low, ontology_codes_list) + if similarity_high == None: + similarity_medium = None + pass + else: + similarity_high.remove(ontology_id+":"+code) + definitive_similarity_high=discard_non_scanned_ontologies(similarity_high, ontology_codes_list) + similarity_medium_list=[] + for similar_high_ontology in definitive_similarity_high: + split_similar_high = similar_high_ontology.split(":") + similarity_medium, cousins_ancestors_list = get_all_ancestors_descendants(split_similar_high[0], split_similar_high[1]) + if similarity_medium is not None: + if similar_high_ontology in similarity_medium: + similarity_medium.remove(similar_high_ontology) + if ontology_id+":"+code in similarity_medium: + similarity_medium.remove(ontology_id+":"+code) + for medium_ontology in similarity_medium: + similarity_medium_list.append(medium_ontology) + definitive_similarity_medium=discard_non_scanned_ontologies(similarity_medium_list, ontology_codes_list) + similarity_low_corrected=[] + if similarity_low is not None: + for low_similar_ontology in similarity_low: + similarity_low_corrected.append(low_similar_ontology["obo_id"]) + definitive_similarity_low=discard_non_scanned_ontologies(similarity_low_corrected, ontology_codes_list) + definitive_similarity_medium=definitive_similarity_high+definitive_similarity_medium + definitive_similarity_low=definitive_similarity_medium+definitive_similarity_low print(f"\n===== {ontology_id}:{code} =====") print('-----DESCENDANTS-----') print(list_of_existing_descendants) @@ -104,17 +127,21 @@ def get_descendants_and_similarities(): print(definitive_similarity_medium) print('-----SIMILARITY_LOW-----') print(definitive_similarity_low) - """ + dict={} - dict['id']=ontology - dict['descendants']=descendants - dict['similarity_high']=similarity_high - dict['similarity_medium']=similarity_medium - dict['similarity_low']=similarity_low - - client['beacon'].similarities.insert_one(dict) - """ - print("succesfully retrieved descendants from {}".format(ontology)) + if list_of_existing_descendants != [] or definitive_similarity_low != []: + dict['id']=ontology_id+":"+code + dict['descendants']=list_of_existing_descendants + dict['similarity_high']=definitive_similarity_high + dict['similarity_medium']=definitive_similarity_medium + dict['similarity_low']=definitive_similarity_low + + client[database_name].similarities.insert_one(dict) + j+=1 + + pbar.update(1) + i+=1 + print("succesfully retrieved {} terms relationships and inserted {} of those".format(i,j)) get_descendants_and_similarities() diff --git a/requirements.txt b/requirements.txt index 70aa94fd..91246352 100644 --- a/requirements.txt +++ b/requirements.txt @@ -23,7 +23,6 @@ paramiko==3.4.0 six==1.16.0 progressbar==2.5 tqdm==4.66.3 -obonet==0.3.1 python-dateutil==2.9.0 rfc3339_validator==0.1.4 datamodel-code-generator==0.68.1 From 8dc05fe360db80e7a18c804793ad7e3ef226f568 Mon Sep 17 00:00:00 2001 From: costero-e Date: Sat, 12 Sep 2026 13:20:24 +0200 Subject: [PATCH 32/56] added modifications to make concurrency work --- beacon/budget/__main__.py | 6 +- beacon/connections/beaconCLI/executor.py | 5 +- beacon/connections/mongo/budget.py | 5 +- beacon/connections/mongo/executor.py | 5 +- beacon/connections/mongo/filtering_terms.py | 6 +- beacon/connections/mongo/utils.py | 22 +- .../sqlalchemy_postgresql/executor.py | 3 +- beacon/framework/validator/v2_0_0/boolean.py | 7 +- .../framework/validator/v2_0_0/collection.py | 12 +- beacon/framework/validator/v2_0_0/common.py | 12 +- .../validator/v2_0_0/configuration.py | 7 +- beacon/framework/validator/v2_0_0/count.py | 7 +- .../framework/validator/v2_0_0/entry_types.py | 12 +- beacon/framework/validator/v2_0_0/error.py | 4 +- .../validator/v2_0_0/filtering_terms.py | 4 +- beacon/framework/validator/v2_0_0/info.py | 4 +- beacon/framework/validator/v2_0_0/map.py | 5 +- .../framework/validator/v2_0_0/resultSet.py | 20 +- .../validator/v2_1_0/filtering_terms.py | 4 +- .../validator/v2_1_1/filtering_terms.py | 4 +- .../framework/validator/v2_2_0/resultSet.py | 20 +- .../EUCAIM/connections/mongo/collections.py | 39 +- .../filters/cross_queries/cross_query.py | 9 +- .../connections/mongo/non_collections.py | 33 +- .../connections/mongo/collections.py | 65 +- .../filters/cross_queries/cross_query.py | 65 +- .../request_parameters/alphanumeric.py | 43 +- .../apply_request_parameters.py | 7 +- .../request_parameters/request_parameters.py | 7 +- .../connections/mongo/non_collections.py | 131 ++-- beacon/permissions/__main__.py | 11 +- beacon/permissions/utils.py | 4 +- beacon/response/includeResultsetResponses.py | 3 +- beacon/tests/test_concurrency.py | 728 ++++++++++++++++++ beacon/utils/checks.py | 3 +- beacon/utils/modules.py | 18 +- beacon/utils/requests.py | 157 ++-- beacon/views/collection.py | 13 +- beacon/views/configuration.py | 5 +- beacon/views/endpoint.py | 33 +- beacon/views/entry_types.py | 5 +- beacon/views/filtering_terms.py | 5 +- beacon/views/health.py | 5 +- beacon/views/info.py | 5 +- beacon/views/map.py | 5 +- beacon/views/non_collection.py | 15 +- beacon/views/service_info.py | 3 +- 47 files changed, 1149 insertions(+), 442 deletions(-) create mode 100644 beacon/tests/test_concurrency.py diff --git a/beacon/budget/__main__.py b/beacon/budget/__main__.py index 06236b25..fc986332 100644 --- a/beacon/budget/__main__.py +++ b/beacon/budget/__main__.py @@ -1,8 +1,6 @@ from beacon.logs.logs import log_with_args_mongo from beacon.conf.conf_override import config from datetime import datetime, timedelta -from beacon.request.classes import RequestAttributes -import aiohttp.web as web from beacon.exceptions.exceptions import NumberOfQueriesExceeded, NoPermissionsAvailable @log_with_args_mongo(config.level) @@ -22,10 +20,10 @@ def check_budget(self, username): else: # Return the time to store in the database return time_now # Check if there is ip in case the budget is meant to be done by ip and get the remaining budget - elif config.query_budget_per_ip == True and RequestAttributes.ip is not None: + elif config.query_budget_per_ip == True and self.request_attributes.ip is not None: remaining_budget=module.get_remaining_budget_by_ip(self, start_budget_time) if len(remaining_budget)>=config.query_budget_amount: - raise NumberOfQueriesExceeded("Number of queries exceeded for this ip: {}".format(RequestAttributes.ip)) + raise NumberOfQueriesExceeded("Number of queries exceeded for this ip: {}".format(self.request_attributes.ip)) else: # Return the time to store in the database return time_now # Check if there is username in case the budget is meant to be done only by user and if there was no ip, then throw an exception diff --git a/beacon/connections/beaconCLI/executor.py b/beacon/connections/beaconCLI/executor.py index 8acda047..bbeb28d1 100644 --- a/beacon/connections/beaconCLI/executor.py +++ b/beacon/connections/beaconCLI/executor.py @@ -3,13 +3,12 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config from typing import Optional -from beacon.request.classes import RequestAttributes from beacon.connections.beaconCLI.g_variants import get_variants @log_with_args(config.level) async def execute_function(self, entry_type: str, datasets: list, entry_id: Optional[str]): - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit datasets_docs={} datasets_count={} new_count=0 diff --git a/beacon/connections/mongo/budget.py b/beacon/connections/mongo/budget.py index 64fa785b..68174931 100644 --- a/beacon/connections/mongo/budget.py +++ b/beacon/connections/mongo/budget.py @@ -1,7 +1,6 @@ from beacon.connections.mongo.client import get_client from beacon.logs.logs import log_with_args_mongo from beacon.conf.conf_override import config -from beacon.request.classes import RequestAttributes @log_with_args_mongo(config.level) def get_remaining_budget_by_user(self, username, start_budget_time): @@ -25,7 +24,7 @@ def insert_budget(self, username, time_now): # Insert in the database one of the uses of the budget for the user/ip performing the query budget_query={} budget_query["username"]=username - budget_query["ip"]=RequestAttributes.ip + budget_query["ip"]=self.request_attributes.ip budget_query["date"]=time_now client[config.query_budget_db_name][config.query_budget_table].insert_one(budget_query) @@ -34,7 +33,7 @@ def get_remaining_budget_by_ip(self, start_budget_time): client=get_client() # Initiate the dictionary to create the query syntax for getting the remaining budget of the ip that is performing the query budget_query={} - budget_query["ip"]=RequestAttributes.ip + budget_query["ip"]=self.request_attributes.ip budget_query["date"]={ "$gt": start_budget_time } remaining_budget = client[config.query_budget_db_name][config.query_budget_table].find(budget_query).max_time_ms(100 * 1000) remaining_budget=list(remaining_budget) diff --git a/beacon/connections/mongo/executor.py b/beacon/connections/mongo/executor.py index 6ec37c26..db2b10bc 100644 --- a/beacon/connections/mongo/executor.py +++ b/beacon/connections/mongo/executor.py @@ -5,7 +5,6 @@ from beacon.exceptions.exceptions import NoPermissionsAvailable, DatabaseIsDown from pymongo.errors import ConnectionFailure from beacon.response.classes import MultipleDatasetsResponse -from beacon.request.classes import RequestAttributes from beacon.utils.modules import get_all_modules_connections_script @log_with_args(config.level) @@ -16,7 +15,7 @@ async def execute_function(self, datasets: list): list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "mongo") for non_collection_module in list_of_non_collection_modules: try: - function = getattr(non_collection_module, RequestAttributes.function) + function = getattr(non_collection_module, self.request_attributes.function) except Exception: continue # Get the current process where the app is being run @@ -47,7 +46,7 @@ async def execute_collection_function(self): list_of_collection_modules = get_all_modules_connections_script("collections", "mongo") for collection_module in list_of_collection_modules: try: - function = getattr(collection_module, RequestAttributes.function) + function = getattr(collection_module, self.request_attributes.function) except Exception: continue # Perform the query and return the class to return for the chosen collection diff --git a/beacon/connections/mongo/filtering_terms.py b/beacon/connections/mongo/filtering_terms.py index 3b260c39..0eb5262e 100644 --- a/beacon/connections/mongo/filtering_terms.py +++ b/beacon/connections/mongo/filtering_terms.py @@ -1,6 +1,4 @@ from beacon.connections.mongo.client import get_client -from beacon.connections.mongo.utils import get_count -from beacon.request.classes import RequestAttributes from beacon.connections.mongo.utils import get_filtering_documents from beacon.response.classes import FilteringTermsResponse @@ -15,7 +13,7 @@ def get_filtering_terms(self): filtering_terms, query, remove_id, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.limit ) return FilteringTermsResponse(docs=docs) \ No newline at end of file diff --git a/beacon/connections/mongo/utils.py b/beacon/connections/mongo/utils.py index 81adef2d..a1897239 100644 --- a/beacon/connections/mongo/utils.py +++ b/beacon/connections/mongo/utils.py @@ -4,8 +4,6 @@ from beacon.logs.logs import log_with_args_mongo from beacon.conf.conf_override import config from beacon.exceptions.exceptions import InvalidRequest -import aiohttp.web as web -from beacon.request.classes import RequestAttributes from beacon.response.classes import SingleDatasetResponse from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.utils import import_genomicVariant_confile @@ -80,10 +78,10 @@ def get_docs_by_response_type(self, include: str, query: dict, dataset: SingleDa queryid['datasetId']=dataset.dataset query_count["$or"].append(queryid) if query_count["$or"]!=[]: - dataset_count = get_count(self, RequestAttributes.mongo_collection, query_count) + dataset_count = get_count(self, self.request_attributes.mongo_collection, query_count) docs = get_documents( self, - RequestAttributes.mongo_collection, + self.request_attributes.mongo_collection, query_count, skip*limit, limit @@ -96,10 +94,10 @@ def get_docs_by_response_type(self, include: str, query: dict, dataset: SingleDa queryid['datasetId']=dataset.dataset query_count["$or"].append(queryid) if query_count["$or"]!=[]: - dataset_count = get_count(self, RequestAttributes.mongo_collection, query_count) + dataset_count = get_count(self, self.request_attributes.mongo_collection, query_count) docs = get_documents( self, - RequestAttributes.mongo_collection, + self.request_attributes.mongo_collection, query_count, skip*limit, limit @@ -117,13 +115,13 @@ def get_docs_by_response_type(self, include: str, query: dict, dataset: SingleDa queryid['datasetId']=dataset.dataset query_count["$or"].append(queryid) if query_count["$or"]!=[]: - dataset_count = get_count(self, RequestAttributes.mongo_collection, query_count) + dataset_count = get_count(self, self.request_attributes.mongo_collection, query_count) if dataset_count == 0: docs = [] else: docs = get_documents( self, - RequestAttributes.mongo_collection, + self.request_attributes.mongo_collection, query_count, skip*limit, limit @@ -177,20 +175,20 @@ def choose_scope(self, scope, filter): # If there aren't any, check if the filtering term is not a zygosity term if filter.id not in ["GENO:0000136", "GENO:0000458"]: # If it's not a zygosity term, add the entry type as scop - if RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: scope = 'genomicVariation' else: - scope = RequestAttributes.entry_type[0:-1] + scope = self.request_attributes.entry_type[0:-1] else: # If it's a zygosity term, return scope = None, as this is an internal filtering term scope = None return scope else: for scoped in scopes: # If there are scopes and is an array, check if any scope is equal to the entry type requested, to assign it as the scope - if str(scoped)+'s'==RequestAttributes.entry_type and RequestAttributes.entry_type != genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if str(scoped)+'s'==self.request_attributes.entry_type and self.request_attributes.entry_type != genomicVariant_confile["genomicVariant"]["endpoint_name"]: scope=str(scoped) return scope - elif str(scoped)=='genomicVariation' and RequestAttributes.entry_type==genomicVariant_confile["genomicVariant"]["endpoint_name"]: + elif str(scoped)=='genomicVariation' and self.request_attributes.entry_type==genomicVariant_confile["genomicVariant"]["endpoint_name"]: scope=str(scoped) return scope # If there is only one scope for the filtering term, assign this scope diff --git a/beacon/connections/sqlalchemy_postgresql/executor.py b/beacon/connections/sqlalchemy_postgresql/executor.py index 1c142d48..d3f495fe 100644 --- a/beacon/connections/sqlalchemy_postgresql/executor.py +++ b/beacon/connections/sqlalchemy_postgresql/executor.py @@ -5,7 +5,6 @@ from beacon.exceptions.exceptions import NoPermissionsAvailable, DatabaseIsDown from pymongo.errors import ConnectionFailure from beacon.response.classes import MultipleDatasetsResponse -from beacon.request.classes import RequestAttributes from beacon.utils.modules import get_all_modules_connections_script @log_with_args(config.level) @@ -16,7 +15,7 @@ async def execute_function(self, datasets: list): list_of_non_collection_modules = get_all_modules_connections_script("non_collections", "sqlalchemy_postgresql") for non_collection_module in list_of_non_collection_modules: try: - function = getattr(non_collection_module, RequestAttributes.function) + function = getattr(non_collection_module, self.request_attributes.function) except Exception: continue # Get the current process where the app is being run diff --git a/beacon/framework/validator/v2_0_0/boolean.py b/beacon/framework/validator/v2_0_0/boolean.py index eee67084..83872614 100644 --- a/beacon/framework/validator/v2_0_0/boolean.py +++ b/beacon/framework/validator/v2_0_0/boolean.py @@ -2,13 +2,14 @@ BaseModel ) from typing import List, Optional, Dict -from beacon.utils.modules import load_class +from beacon.framework.validator.v2_0_0.meta import Meta +from common import Handover class BooleanResponseSummary(BaseModel): exists: bool class BooleanResponse(BaseModel): - meta: load_class("meta", "Meta") + meta: Meta responseSummary: BooleanResponseSummary info: Optional[Dict] = None - beaconHandovers: Optional[List[load_class("common", "Handover")]] = None \ No newline at end of file + beaconHandovers: Optional[List[Handover]] = None \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/collection.py b/beacon/framework/validator/v2_0_0/collection.py index 826798d0..1c05d384 100644 --- a/beacon/framework/validator/v2_0_0/collection.py +++ b/beacon/framework/validator/v2_0_0/collection.py @@ -5,8 +5,8 @@ from typing import List, Optional, Union, Dict from beacon.utils.modules import load_class, load_types_of_results -def make_Collections(): - CollectionType = load_types_of_results("collections") +def make_Collections(self): + CollectionType = load_types_of_results(self,"collections") @classmethod @@ -23,11 +23,11 @@ def create(cls, collections: List[Union[CollectionType]]): return model -def make_CollectionResponse(Collections): +def make_CollectionResponse(self, Collections): # Create the types of the meta, responseSumarry and the handovers depending on the existing entry types in the models - MetaType = load_class("meta", "Meta") - ResponseSummaryType = load_class("common", "ResponseSummary") - HandoverType = load_class("common", "Handover") + MetaType = load_class(self, "meta", "Meta") + ResponseSummaryType = load_class(self, "common", "ResponseSummary") + HandoverType = load_class(self, "common", "Handover") # Create a function to obtain the class with the properties values of the Collections to come by args @classmethod def create(cls, meta, response: Collections, responseSummary, beaconHandovers=None, info=None): diff --git a/beacon/framework/validator/v2_0_0/common.py b/beacon/framework/validator/v2_0_0/common.py index 18857d7d..52fa6790 100644 --- a/beacon/framework/validator/v2_0_0/common.py +++ b/beacon/framework/validator/v2_0_0/common.py @@ -3,7 +3,6 @@ field_validator ) from typing import Optional -from beacon.request.classes import RequestAttributes from beacon.conf import conf_override import math import re @@ -38,7 +37,8 @@ class ResponseSummary(BaseModel): exists: bool numTotalResults: Optional[int] = None - def build_response_summary_by_dataset(self, datasets): + @classmethod + def build_response_summary_by_dataset(self, handler, datasets): """ Compute aggregated response metadata across datasets. @@ -53,13 +53,13 @@ def build_response_summary_by_dataset(self, datasets): non_counted = 0 # Requested granularity from request context - granularity = RequestAttributes.qparams.query.requestedGranularity + granularity = handler.request_attributes.qparams.query.requestedGranularity # Iterate over all datasets contributing to the response for dataset in datasets: # If dataset is not boolean-only and system is not forcing boolean responses - if dataset.granularity != 'boolean' and RequestAttributes.allowed_granularity != 'boolean' and granularity != 'boolean': + if dataset.granularity != 'boolean' and handler.request_attributes.allowed_granularity != 'boolean' and granularity != 'boolean': # --- Case 1: imprecise count mode --- if conf_override.config.imprecise_count != 0: @@ -89,7 +89,7 @@ def build_response_summary_by_dataset(self, datasets): # Case 1: nothing counted but non-counted results exist if count == 0 and non_counted > 0: - RequestAttributes.returned_granularity = 'boolean' + handler.request_attributes.returned_granularity = 'boolean' return self(exists=True) # Case 2: counted results exist @@ -98,7 +98,7 @@ def build_response_summary_by_dataset(self, datasets): # Case 3: no results at all else: - RequestAttributes.returned_granularity = 'boolean' + handler.request_attributes.returned_granularity = 'boolean' return self(exists=False) diff --git a/beacon/framework/validator/v2_0_0/configuration.py b/beacon/framework/validator/v2_0_0/configuration.py index e922ad0f..39a45813 100644 --- a/beacon/framework/validator/v2_0_0/configuration.py +++ b/beacon/framework/validator/v2_0_0/configuration.py @@ -5,7 +5,8 @@ Field ) from beacon.conf.conf_override import config -from beacon.utils.modules import load_class +from beacon.framework.validator.v2_0_0.meta import InformationalMeta +from entry_types import EntryTypesSchema class SecurityAttributes(BaseModel): # Default granularity level used by the Beacon when none is explicitly requested. @@ -45,7 +46,7 @@ class MaturityAttributes(BaseModel): security_attributes = SecurityAttributes().model_dump(exclude_none=True) -class ConfigurationSchema(load_class("entry_types", "EntryTypesSchema")): +class ConfigurationSchema(EntryTypesSchema): """ Beacon configuration schema. @@ -80,7 +81,7 @@ class ConfigurationResponse(BaseModel): """ # Response metadata (API version, timestamps, etc.). - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta # Main configuration payload returned to the client. response: ConfigurationSchema \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/count.py b/beacon/framework/validator/v2_0_0/count.py index d4bccce3..2ff5055d 100644 --- a/beacon/framework/validator/v2_0_0/count.py +++ b/beacon/framework/validator/v2_0_0/count.py @@ -5,7 +5,8 @@ from typing import List, Optional, Union, Dict import math from beacon.conf import conf_override -from beacon.utils.modules import load_class +from beacon.framework.validator.v2_0_0.meta import Meta +from common import Handover class CountResponseSummary(BaseModel): """ @@ -116,7 +117,7 @@ class CountResponse(BaseModel): - Optional handover links to external systems """ - meta: load_class("meta", "Meta") + meta: Meta responseSummary: CountResponseSummary info: Optional[Dict] = None - beaconHandovers: Optional[List[load_class("common", "Handover")]] = None \ No newline at end of file + beaconHandovers: Optional[List[Handover]] = None \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/entry_types.py b/beacon/framework/validator/v2_0_0/entry_types.py index 5ff14c22..ca978080 100644 --- a/beacon/framework/validator/v2_0_0/entry_types.py +++ b/beacon/framework/validator/v2_0_0/entry_types.py @@ -6,7 +6,9 @@ ) import re from typing import List, Optional -from beacon.utils.modules import load_class, get_modules_confiles +from beacon.utils.modules import get_modules_confiles +from common import ReferenceToAnSchema +from beacon.framework.validator.v2_0_0.meta import InformationalMeta class OntologyTerm(BaseModel): """ @@ -51,11 +53,11 @@ class EntryTypes(BaseModel): # Additional schema definitions supported for this entry type additionallySupportedSchemas: Optional[List[ - load_class("common", "ReferenceToAnSchema") + ReferenceToAnSchema ]] = None # Default schema definition for this entry type - defaultSchema: load_class("common", "ReferenceToAnSchema") + defaultSchema: ReferenceToAnSchema description: Optional[str] = None @@ -91,7 +93,7 @@ class EntryTypes(BaseModel): Entries = create_model("Entries", **fields_related) # External schema reference model -ReferenceToAnSchema = load_class("common", "ReferenceToAnSchema") +ReferenceToAnSchema = ReferenceToAnSchema class Entries(Entries): @@ -212,5 +214,5 @@ class EntryTypesResponse(BaseModel): Combines metadata and dynamically generated entry type schema. """ - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta response: EntryTypesSchema \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/error.py b/beacon/framework/validator/v2_0_0/error.py index 1a81d030..60a1417f 100644 --- a/beacon/framework/validator/v2_0_0/error.py +++ b/beacon/framework/validator/v2_0_0/error.py @@ -1,7 +1,7 @@ from typing import Optional from pydantic import ( BaseModel) -from beacon.utils.modules import load_class +from beacon.framework.validator.v2_0_0.meta import Meta class BeaconError(BaseModel): errorCode: int @@ -9,4 +9,4 @@ class BeaconError(BaseModel): class ErrorResponse(BaseModel): error: BeaconError - meta: load_class("meta", "Meta") \ No newline at end of file + meta: Meta \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/filtering_terms.py b/beacon/framework/validator/v2_0_0/filtering_terms.py index 81be2fbc..f67a62ad 100644 --- a/beacon/framework/validator/v2_0_0/filtering_terms.py +++ b/beacon/framework/validator/v2_0_0/filtering_terms.py @@ -1,8 +1,8 @@ from typing import Optional, List from pydantic import ( BaseModel, field_validator) -from beacon.utils.modules import load_class import json +from beacon.framework.validator.v2_0_0.meta import InformationalMeta class FilteringTermInResponse(BaseModel): """ @@ -104,7 +104,7 @@ class FilteringTermsResponse(BaseModel): """ # Response metadata such as API version and schema information. - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta # Main response payload containing filtering terms and resources. response: FilteringTermsResults \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/info.py b/beacon/framework/validator/v2_0_0/info.py index bd237c0a..47837d99 100644 --- a/beacon/framework/validator/v2_0_0/info.py +++ b/beacon/framework/validator/v2_0_0/info.py @@ -2,7 +2,7 @@ from typing import Optional, Dict from pydantic import ( BaseModel) -from beacon.utils.modules import load_class +from beacon.framework.validator.v2_0_0.meta import InformationalMeta class BeaconOrganization(BaseModel): address: Optional[str]=conf_override.config.org_adress if conf_override.config.org_adress != "" else None @@ -29,5 +29,5 @@ class InfoBody(BaseModel): organization: BeaconOrganization = BeaconOrganization().model_dump(exclude_none=True) class InfoResponse(BaseModel): - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta response: InfoBody \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/map.py b/beacon/framework/validator/v2_0_0/map.py index 1fb29787..2007b6fc 100644 --- a/beacon/framework/validator/v2_0_0/map.py +++ b/beacon/framework/validator/v2_0_0/map.py @@ -6,7 +6,8 @@ create_model ) from beacon.conf import conf_override -from beacon.utils.modules import load_class, get_modules_confiles +from beacon.utils.modules import get_modules_confiles +from beacon.framework.validator.v2_0_0.meta import InformationalMeta class RelatedEndpoint(BaseModel): returnedEntryType: str @@ -111,5 +112,5 @@ def populate_endpoints(self): return self(endpointSets=endpointEntriesClass) class MapResponse(BaseModel): - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta response: MapSchema \ No newline at end of file diff --git a/beacon/framework/validator/v2_0_0/resultSet.py b/beacon/framework/validator/v2_0_0/resultSet.py index 5036f0d8..960eeb66 100644 --- a/beacon/framework/validator/v2_0_0/resultSet.py +++ b/beacon/framework/validator/v2_0_0/resultSet.py @@ -26,10 +26,10 @@ def validate_count_precision(v: str) -> str: return v -def make_ResultsetInstance(): +def make_ResultsetInstance(self): # Create the types of the results and the handovers depending on the existing entry types in the models - ResultType = load_types_of_results("non_collections") - HandoverType = load_class("common", "Handover") + ResultType = load_types_of_results(self, "non_collections") + HandoverType = load_class(self, "common", "Handover") @field_validator('countPrecision') def countPrecision_validator(cls, v): @@ -116,11 +116,11 @@ def return_resultSets(cls, resultSets: List[ResultsetInstance]): return model -def make_ResultsetsResponse(Resultsets): +def make_ResultsetsResponse(self, Resultsets): # Create the types of the meta, responseSumarry and the handovers depending on the existing entry types in the models - MetaType = load_class("meta", "Meta") - ResponseSummaryType = load_class("common", "ResponseSummary") - HandoverType = load_class("common", "Handover") + MetaType = load_class(self, "meta", "Meta") + ResponseSummaryType = load_class(self, "common", "ResponseSummary") + HandoverType = load_class(self, "common", "Handover") # Create the dynamic class with the properties and types defined previously model = create_model( "ResultsetsResponse", @@ -146,12 +146,12 @@ def return_response(cls, meta, response: Resultsets, responseSummary, beaconHand return model -def build_full_dynamic_response(): +def build_full_dynamic_response(self): # Generate the three classes for an object of the Resultsets class, the class of all the resultSets as a list of the single object ResultsetInstance classs and the whole ResultSetsResponse class dynamically - ResultsetInstance = make_ResultsetInstance() + ResultsetInstance = make_ResultsetInstance(self) Resultsets = make_Resultsets(ResultsetInstance) - ResultsetsResponse = make_ResultsetsResponse(Resultsets) + ResultsetsResponse = make_ResultsetsResponse(self, Resultsets) return ResultsetInstance, Resultsets, ResultsetsResponse \ No newline at end of file diff --git a/beacon/framework/validator/v2_1_0/filtering_terms.py b/beacon/framework/validator/v2_1_0/filtering_terms.py index b2193eec..55412b2f 100644 --- a/beacon/framework/validator/v2_1_0/filtering_terms.py +++ b/beacon/framework/validator/v2_1_0/filtering_terms.py @@ -1,9 +1,9 @@ from typing import Optional, List from pydantic import ( BaseModel, field_validator) -from beacon.utils.modules import load_class from beacon.framework.validator.v2_0_0.filtering_terms import Resource import json +from beacon.framework.validator.v2_1_0.meta import InformationalMeta class FilteringTermInResponse(BaseModel): id: str @@ -31,5 +31,5 @@ class FilteringTermsResults(BaseModel): resources: Optional[List[Resource]] = resources class FilteringTermsResponse(BaseModel): - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta response: FilteringTermsResults \ No newline at end of file diff --git a/beacon/framework/validator/v2_1_1/filtering_terms.py b/beacon/framework/validator/v2_1_1/filtering_terms.py index 027abc1b..153a8083 100644 --- a/beacon/framework/validator/v2_1_1/filtering_terms.py +++ b/beacon/framework/validator/v2_1_1/filtering_terms.py @@ -1,7 +1,7 @@ from typing import Optional, List from pydantic import ( BaseModel, field_validator) -from beacon.utils.modules import load_class +from beacon.framework.validator.v2_1_1.meta import InformationalMeta from beacon.framework.validator.v2_0_0.filtering_terms import Resource import json @@ -32,5 +32,5 @@ class FilteringTermsResults(BaseModel): resources: Optional[List[Resource]] = resources class FilteringTermsResponse(BaseModel): - meta: load_class("meta", "InformationalMeta") + meta: InformationalMeta response: FilteringTermsResults \ No newline at end of file diff --git a/beacon/framework/validator/v2_2_0/resultSet.py b/beacon/framework/validator/v2_2_0/resultSet.py index 33c222f6..a565cd00 100644 --- a/beacon/framework/validator/v2_2_0/resultSet.py +++ b/beacon/framework/validator/v2_2_0/resultSet.py @@ -18,9 +18,9 @@ def validate_count_precision(v: str) -> str: return v -def make_ResultsetInstance(): - ResultType = load_types_of_results("non_collections") - HandoverType = load_class("common", "Handover") +def make_ResultsetInstance(self): + ResultType = load_types_of_results(self, "non_collections") + HandoverType = load_class(self, "common", "Handover") @field_validator('countPrecision') def countPrecision_validator(cls, v): @@ -125,11 +125,11 @@ def return_resultSets(cls, resultSets: List[ResultsetInstance]): return model -def make_ResultsetsResponse(Resultsets): +def make_ResultsetsResponse(self, Resultsets): - MetaType = load_class("meta", "Meta") - ResponseSummaryType = load_class("common", "ResponseSummary") - HandoverType = load_class("common", "Handover") + MetaType = load_class(self, "meta", "Meta") + ResponseSummaryType = load_class(self, "common", "ResponseSummary") + HandoverType = load_class(self, "common", "Handover") model = create_model( "ResultsetsResponse", @@ -155,11 +155,11 @@ def return_response(cls, meta, response: Resultsets, responseSummary, beaconHand return model -def build_full_dynamic_response(): - ResultsetInstance = make_ResultsetInstance() +def build_full_dynamic_response(self): + ResultsetInstance = make_ResultsetInstance(self) Resultsets = make_Resultsets(ResultsetInstance) - ResultsetsResponse = make_ResultsetsResponse(Resultsets) + ResultsetsResponse = make_ResultsetsResponse(self, Resultsets) return ResultsetInstance, Resultsets, ResultsetsResponse \ No newline at end of file diff --git a/beacon/models/EUCAIM/connections/mongo/collections.py b/beacon/models/EUCAIM/connections/mongo/collections.py index a45f8def..158a5e2a 100644 --- a/beacon/models/EUCAIM/connections/mongo/collections.py +++ b/beacon/models/EUCAIM/connections/mongo/collections.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config from beacon.connections.mongo.utils import get_count, get_documents, query_id, get_documents_for_cohorts, query_patientId from beacon.connections.mongo.filters.filters import apply_filters -from beacon.request.classes import RequestAttributes from beacon.connections.mongo.client import get_client from beacon.response.classes import CollectionsResponse from beacon.models.EUCAIM.connections.mongo.utils import get_non_collections_cross_query_attributes @@ -26,17 +25,17 @@ def get_full_collections(self): collections=client['beacon'].collections # Create the query syntax depending on it there is any entry id queried. - if RequestAttributes.entry_id == None: + if self.request_attributes.entry_id == None: query = {} else: - query = {'id': RequestAttributes.entry_id} - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, None) + query = {'id': self.request_attributes.entry_id} + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, None) query = collections.find(query, {"_id": 0}) try: # Collect all the datasets found with the query performed. - if RequestAttributes.qparams.query.requestParameters["datasets"] != []: # If there are datasets requested, then, query just for those datasets. + if self.request_attributes.qparams.query.requestParameters["datasets"] != []: # If there are datasets requested, then, query just for those datasets. response_converted = ( - [r for r in query if r["id"] in RequestAttributes.qparams.query.requestParameters["datasets"]] if query else [] + [r for r in query if r["id"] in self.request_attributes.qparams.query.requestParameters["datasets"]] if query else [] ) else: response_converted = ( @@ -61,18 +60,18 @@ def get_list_of_datasets(self): def get_collections_with_id(self): client=get_client() collections=client['beacon'].collections - limit = RequestAttributes.qparams.query.pagination.limit + limit = self.request_attributes.qparams.query.pagination.limit query={} # Include the id queried in the query. - query = query_id(self, query, RequestAttributes.entry_id) + query = query_id(self, query, self.request_attributes.entry_id) # Count all the datasets to be returned in response. count = get_count(self, collections, query) # Find the datasets to be returned in response. docs = get_documents(self, collections, query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) response_converted = ( [r for r in docs] if docs else [] @@ -81,17 +80,17 @@ def get_collections_with_id(self): @log_with_args_mongo(config.level) def get_cross_endpoint_collections(self): - limit = RequestAttributes.qparams.query.pagination.limit + limit = self.request_attributes.qparams.query.pagination.limit # Process filters - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, "a") + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, "a") # Include the id queried in the query. patients = import_patients_confile() - if RequestAttributes.pre_entry_type == patients["patients"]["endpoint_name"]: - query = query_patientId(self, query, RequestAttributes.entry_id) + if self.request_attributes.pre_entry_type == patients["patients"]["endpoint_name"]: + query = query_patientId(self, query, self.request_attributes.entry_id) else: - query = query_id(self, query, RequestAttributes.entry_id) + query = query_id(self, query, self.request_attributes.entry_id) # Translate the ids that relate the two collection record types and get the records. - mapping = get_non_collections_cross_query_attributes(self, RequestAttributes.entry_type, RequestAttributes.pre_entry_type) + mapping = get_non_collections_cross_query_attributes(self, self.request_attributes.entry_type, self.request_attributes.pre_entry_type) docs = get_documents_for_cohorts(self, mapping["secondary_collection"], query, @@ -100,13 +99,13 @@ def get_cross_endpoint_collections(self): ) final_query = {mapping["idq"]: {"$in": [doc[mapping["idq2"]] for doc in docs]}} docs = get_documents(self, - RequestAttributes.mongo_collection, + self.request_attributes.mongo_collection, final_query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) # Count all the records to be returned in response. - count = get_count(self, RequestAttributes.mongo_collection, final_query) + count = get_count(self, self.request_attributes.mongo_collection, final_query) response_converted = ( [r for r in docs] if docs else [] ) diff --git a/beacon/models/EUCAIM/connections/mongo/filters/cross_queries/cross_query.py b/beacon/models/EUCAIM/connections/mongo/filters/cross_queries/cross_query.py index 71f2e0c9..4615433e 100644 --- a/beacon/models/EUCAIM/connections/mongo/filters/cross_queries/cross_query.py +++ b/beacon/models/EUCAIM/connections/mongo/filters/cross_queries/cross_query.py @@ -2,7 +2,6 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config from beacon.models.EUCAIM.connections.mongo.utils import import_patients_confile -from beacon.request.classes import RequestAttributes from beacon.models.EUCAIM.connections.mongo.utils import get_non_collections_cross_query_attributes @log_with_args(config.level) @@ -10,11 +9,11 @@ def cross_query(self, query: dict, scope: str, request_parameters: dict, dataset patients_confile=import_patients_confile() # Check for the different scopes and entry types to apply a different query syntax built. def_list=[] - if scope == 'patients' and RequestAttributes.entry_type != patients_confile["patients"]["endpoint_name"]: + if scope == 'patients' and self.request_attributes.entry_type != patients_confile["patients"]["endpoint_name"]: end = 'patients' - original_id = get_non_collections_cross_query_attributes(self,RequestAttributes.entry_type, end)["idq2"] - final_id = get_non_collections_cross_query_attributes(self,RequestAttributes.entry_type, end)["idq"] - mongo_collection = get_non_collections_cross_query_attributes(self, RequestAttributes.entry_type, end)["secondary_collection"] + original_id = get_non_collections_cross_query_attributes(self,self.request_attributes.entry_type, end)["idq2"] + final_id = get_non_collections_cross_query_attributes(self,self.request_attributes.entry_type, end)["idq"] + mongo_collection = get_non_collections_cross_query_attributes(self, self.request_attributes.entry_type, end)["secondary_collection"] query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) return query \ No newline at end of file diff --git a/beacon/models/EUCAIM/connections/mongo/non_collections.py b/beacon/models/EUCAIM/connections/mongo/non_collections.py index 2bf9f8a3..896b4f9c 100644 --- a/beacon/models/EUCAIM/connections/mongo/non_collections.py +++ b/beacon/models/EUCAIM/connections/mongo/non_collections.py @@ -1,6 +1,5 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.request.classes import RequestAttributes from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.request_parameters.apply_request_parameters import apply_request_parameters from beacon.connections.mongo.filters.filters import apply_filters from beacon.connections.mongo.utils import get_docs_by_response_type, query_id @@ -13,13 +12,13 @@ def get_endpoint(self, dataset: SingleDatasetResponse): # Initialize the query dictionary. query = {} # Process the filters - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) #if query == {}: # If the filters didn't build any query, just return the dataset. # return dataset # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -31,14 +30,14 @@ def get_endpoint_with_id(self, dataset: SingleDatasetResponse): patients_confile=import_patients_confile() query = {} # Process filters - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # If the entry type records are not variants, include the id queried in the query. - if RequestAttributes.entry_type == patients_confile["patients"]["endpoint_name"]: - query["patientId"] = RequestAttributes.entry_id + if self.request_attributes.entry_type == patients_confile["patients"]["endpoint_name"]: + query["patientId"] = self.request_attributes.entry_id # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -48,21 +47,21 @@ def get_endpoint_with_id(self, dataset: SingleDatasetResponse): @log_with_args(config.level) def get_endpoint_cross_query(self, dataset: SingleDatasetResponse): # Get the translation of ids for the entry types lookup for the cross query. - mapping = get_non_collections_cross_query_attributes(self, RequestAttributes.entry_type, RequestAttributes.pre_entry_type) + mapping = get_non_collections_cross_query_attributes(self, self.request_attributes.entry_type, self.request_attributes.pre_entry_type) # Get the ids found for the initial entry type query. items_found = mapping["secondary_collection"] \ - .find({mapping["idq"]: RequestAttributes.entry_id, "datasetId": dataset.dataset}, {mapping["idq2"]: 1, "_id": 0}) + .find({mapping["idq"]: self.request_attributes.entry_id, "datasetId": dataset.dataset}, {mapping["idq2"]: 1, "_id": 0}) # Translate the ids. list_of_itemsfound=[] for itemfound in items_found: list_of_itemsfound.append(itemfound[mapping["idq2"]]) query = {mapping["idq2"]: {"$in": list_of_itemsfound}} # Process filters. - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/collections.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/collections.py index 45e0a23d..d8a431cc 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/collections.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/collections.py @@ -4,7 +4,6 @@ from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.utils import get_phenotypic_cross_query_attributes from beacon.connections.mongo.filters.filters import apply_filters from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.request_parameters.apply_request_parameters import apply_request_parameters -from beacon.request.classes import RequestAttributes from beacon.connections.mongo import conf as mongo_conf from beacon.connections.mongo.client import get_client from beacon.response.classes import CollectionsResponse @@ -23,17 +22,17 @@ def get_full_datasets(self): client=get_client() datasets=client[mongo_conf.database_name].datasets # Create the query syntax depending on it there is any entry id queried. - if RequestAttributes.entry_id == None: + if self.request_attributes.entry_id == None: query = {} else: - query = {'id': RequestAttributes.entry_id} - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, None) + query = {'id': self.request_attributes.entry_id} + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, None) query = datasets.find(query, {"_id": 0}) try: # Collect all the datasets found with the query performed. - if RequestAttributes.qparams.query.requestParameters["datasets"] != []: # If there are datasets requested, then, query just for those datasets. + if self.request_attributes.qparams.query.requestParameters["datasets"] != []: # If there are datasets requested, then, query just for those datasets. response_converted = ( - [r for r in query if r["id"] in RequestAttributes.qparams.query.requestParameters["datasets"]] if query else [] + [r for r in query if r["id"] in self.request_attributes.qparams.query.requestParameters["datasets"]] if query else [] ) else: response_converted = ( @@ -58,23 +57,23 @@ def get_list_of_datasets(self): def get_dataset_with_id(self): client=get_client() datasets=client[mongo_conf.database_name].datasets - limit = RequestAttributes.qparams.query.pagination.limit + limit = self.request_attributes.qparams.query.pagination.limit # Handle the request parameters and create the first built of the query. - query_parameters, parameters_as_filters = apply_request_parameters(self, {}, RequestAttributes.entry_id) + query_parameters, parameters_as_filters = apply_request_parameters(self, {}, self.request_attributes.entry_id) if parameters_as_filters == True: - query, parameters_as_filters = apply_request_parameters(self, {}, RequestAttributes.entry_id) + query, parameters_as_filters = apply_request_parameters(self, {}, self.request_attributes.entry_id) else: query={} # Include the id queried in the query. - query = query_id(self, query, RequestAttributes.entry_id) + query = query_id(self, query, self.request_attributes.entry_id) # Count all the datasets to be returned in response. count = get_count(self, datasets, query) # Find the datasets to be returned in response. docs = get_documents(self, datasets, query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) response_converted = ( [r for r in docs] if docs else [] @@ -86,17 +85,17 @@ def get_dataset_with_id(self): def get_cohorts(self): client=get_client() cohorts=client[mongo_conf.database_name].cohorts - limit = RequestAttributes.qparams.query.pagination.limit + limit = self.request_attributes.qparams.query.pagination.limit # Process filters - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, None) + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, None) # Collect all the datasets found with the query performed. try: - if RequestAttributes.qparams.query.requestParameters["datasets"] != None:# If there are datasets requested, then, query just for those datasets. + if self.request_attributes.qparams.query.requestParameters["datasets"] != None:# If there are datasets requested, then, query just for those datasets. try: - query["$and"].append({"datasetId": {"$in": RequestAttributes.qparams.query.requestParameters["datasets"]}}) + query["$and"].append({"datasetId": {"$in": self.request_attributes.qparams.query.requestParameters["datasets"]}}) except Exception: query["$and"]=[] - query["$and"].append({"datasetId": {"$in": RequestAttributes.qparams.query.requestParameters["datasets"]}}) + query["$and"].append({"datasetId": {"$in": self.request_attributes.qparams.query.requestParameters["datasets"]}}) except Exception: pass # Count all the cohorts to be returned in response. @@ -105,8 +104,8 @@ def get_cohorts(self): docs = get_documents(self, cohorts, query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) response_converted = ( [r for r in docs] if docs else [] @@ -117,19 +116,19 @@ def get_cohorts(self): def get_cohort_with_id(self): client=get_client() cohorts=client[mongo_conf.database_name].cohorts - limit = RequestAttributes.qparams.query.pagination.limit + limit = self.request_attributes.qparams.query.pagination.limit # Process filters - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, "a") + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, "a") # Include the id queried in the query. - query = query_id(self, query, RequestAttributes.entry_id) + query = query_id(self, query, self.request_attributes.entry_id) # Count all the cohorts to be returned in response. count = get_count(self, cohorts, query) # Find the datasets to be returned in response. docs = get_documents(self, cohorts, query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) response_converted = ( [r for r in docs] if docs else [] @@ -140,17 +139,17 @@ def get_cohort_with_id(self): def get_cross_collections(self): client=get_client() genomicVariations=client[mongo_conf.database_name].genomicVariations - limit = RequestAttributes.qparams.query.pagination.limit + limit = self.request_attributes.qparams.query.pagination.limit # Process filters - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, "a") + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, "a") # Translate the ids that relate the two collection record types and get the records. - mapping = get_phenotypic_cross_query_attributes(self, RequestAttributes.entry_type, RequestAttributes.pre_entry_type) + mapping = get_phenotypic_cross_query_attributes(self, self.request_attributes.entry_type, self.request_attributes.pre_entry_type) if mapping["secondary_collection"] == genomicVariations: - query = query_variantInternalId(self, query, RequestAttributes.entry_id) + query = query_variantInternalId(self, query, self.request_attributes.entry_id) else: # Include the id queried in the query. - query = query_id(self, query, RequestAttributes.entry_id) + query = query_id(self, query, self.request_attributes.entry_id) docs = get_documents_for_cohorts(self, mapping["secondary_collection"], @@ -161,13 +160,13 @@ def get_cross_collections(self): final_query = {mapping["idq"]: {"$in": [doc[mapping["idq2"]] for doc in docs]}} docs = get_documents(self, - RequestAttributes.mongo_collection, + self.request_attributes.mongo_collection, final_query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) # Count all the records to be returned in response. - count = get_count(self, RequestAttributes.mongo_collection, final_query) + count = get_count(self, self.request_attributes.mongo_collection, final_query) response_converted = ( [r for r in docs] if docs else [] ) diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/cross_queries/cross_query.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/cross_queries/cross_query.py index 68d5e69a..bb5469b2 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/cross_queries/cross_query.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/cross_queries/cross_query.py @@ -4,7 +4,6 @@ from beacon.connections.mongo.client import get_client from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.request.classes import RequestAttributes from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.utils import import_dataset_confile, import_analysis_confile, import_biosample_confile, import_cohort_confile, import_individual_confile, import_genomicVariant_confile, import_run_confile @log_with_args(config.level) @@ -26,7 +25,7 @@ def cross_query(self, query: dict, scope: str, request_parameters: dict, dataset cohort_confile=import_cohort_confile() dataset_confile=import_dataset_confile() # Check for the different scopes and entry types to apply a different query syntax built. - if scope == 'genomicVariation' and RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if scope == 'genomicVariation' and self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: subquery={} subquery["$or"]=[] if request_parameters != {}: @@ -54,101 +53,101 @@ def cross_query(self, query: dict, scope: str, request_parameters: dict, dataset mongo_collection=individuals original_id="id" final_id="individualId" - if RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: query=cross_query_entry_type_is_genomicVariant_and_scope_is_not(self,mongo_collection, original_id, query, dataset) - elif RequestAttributes.entry_type in [run_confile["run"]["endpoint_name"],biosample_confile["biosample"]["endpoint_name"],analysis_confile["analysis"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [run_confile["run"]["endpoint_name"],biosample_confile["biosample"]["endpoint_name"],analysis_confile["analysis"]["endpoint_name"]]: query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: original_id="datasetId" final_id="datasetId" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: original_id="datasetId" final_id="id" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif scope == 'genomicVariation' and RequestAttributes.entry_type == individual_confile["individual"]["endpoint_name"]: + elif scope == 'genomicVariation' and self.request_attributes.entry_type == individual_confile["individual"]["endpoint_name"]: query = cross_query_scope_is_genomicVariant_and_entry_type_is_not(self, "individualId", query, dataset) - elif scope == 'genomicVariation' and RequestAttributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: + elif scope == 'genomicVariation' and self.request_attributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: query = cross_query_scope_is_genomicVariant_and_entry_type_is_not(self, "id", query, dataset) - elif scope == 'genomicVariation' and RequestAttributes.entry_type in [analysis_confile["analysis"]["endpoint_name"],run_confile["run"]["endpoint_name"]]: + elif scope == 'genomicVariation' and self.request_attributes.entry_type in [analysis_confile["analysis"]["endpoint_name"],run_confile["run"]["endpoint_name"]]: query = cross_query_scope_is_genomicVariant_and_entry_type_is_not(self, "biosampleId", query, dataset) - elif scope == 'genomicVariation' and RequestAttributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: + elif scope == 'genomicVariation' and self.request_attributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: query = cross_query_scope_is_genomicVariant_and_entry_type_is_not(self, "datasetId", query, dataset) - elif scope == 'genomicVariation' and RequestAttributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: + elif scope == 'genomicVariation' and self.request_attributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: query = cross_query_scope_is_genomicVariant_and_entry_type_is_not(self, "cohortId", query, dataset) - elif scope == 'run' and RequestAttributes.entry_type != run_confile["run"]["endpoint_name"]: + elif scope == 'run' and self.request_attributes.entry_type != run_confile["run"]["endpoint_name"]: mongo_collection=runs - if RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: original_id="biosampleId" query = cross_query_entry_type_is_genomicVariant_and_scope_is_not(self, mongo_collection, original_id, query, dataset) - elif RequestAttributes.entry_type == individual_confile["individual"]["endpoint_name"]: + elif self.request_attributes.entry_type == individual_confile["individual"]["endpoint_name"]: original_id="individualId" final_id="id" query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type == analysis_confile["analysis"]["endpoint_name"]: + elif self.request_attributes.entry_type == analysis_confile["analysis"]["endpoint_name"]: original_id="biosampleId" final_id="biosampleId" query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: + elif self.request_attributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: original_id="biosampleId" final_id="id" query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: original_id="datasetId" final_id="datasetId" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: original_id="datasetId" final_id="id" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif scope == 'analysis' and RequestAttributes.entry_type != analysis_confile["analysis"]["endpoint_name"]: + elif scope == 'analysis' and self.request_attributes.entry_type != analysis_confile["analysis"]["endpoint_name"]: mongo_collection=analyses - if RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: original_id="biosampleId" query = cross_query_entry_type_is_genomicVariant_and_scope_is_not(self, mongo_collection, original_id, query, dataset) - elif RequestAttributes.entry_type == individual_confile["individual"]["endpoint_name"]: + elif self.request_attributes.entry_type == individual_confile["individual"]["endpoint_name"]: original_id="individualId" final_id="id" query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type == run_confile["run"]["endpoint_name"]: + elif self.request_attributes.entry_type == run_confile["run"]["endpoint_name"]: original_id="biosampleId" final_id="biosampleId" query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: + elif self.request_attributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: original_id="biosampleId" final_id="id" query=scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: original_id="datasetId" final_id="datasetId" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: original_id="datasetId" final_id="id" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif scope == 'biosample' and RequestAttributes.entry_type != biosample_confile["biosample"]["endpoint_name"]: + elif scope == 'biosample' and self.request_attributes.entry_type != biosample_confile["biosample"]["endpoint_name"]: mongo_collection=biosamples - if RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + if self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: original_id="id" query = cross_query_entry_type_is_genomicVariant_and_scope_is_not(self, mongo_collection, original_id, query, dataset) - elif RequestAttributes.entry_type == individual_confile["individual"]["endpoint_name"]: + elif self.request_attributes.entry_type == individual_confile["individual"]["endpoint_name"]: original_id="individualId" final_id="id" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [analysis_confile["analysis"]["endpoint_name"], run_confile["run"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [analysis_confile["analysis"]["endpoint_name"], run_confile["run"]["endpoint_name"]]: original_id="id" final_id="biosampleId" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [cohort_confile["cohort"]["endpoint_name"]]: original_id="datasetId" final_id="datasetId" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif RequestAttributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: + elif self.request_attributes.entry_type in [dataset_confile["dataset"]["endpoint_name"]]: original_id="datasetId" final_id="id" query = scope_is_not_entry_type(self, original_id, final_id, def_list, mongo_collection, query, dataset) - elif scope == 'dataset' and RequestAttributes.entry_type != dataset_confile["dataset"]["endpoint_name"]: + elif scope == 'dataset' and self.request_attributes.entry_type != dataset_confile["dataset"]["endpoint_name"]: query = scope_is_not_entry_type(self, "id", "datasetId", def_list, datasets, query, dataset) - elif scope == 'cohort' and RequestAttributes.entry_type != cohort_confile["cohort"]["endpoint_name"]: + elif scope == 'cohort' and self.request_attributes.entry_type != cohort_confile["cohort"]["endpoint_name"]: query = scope_is_not_entry_type(self, "datasetId", "datasetId", def_list, cohorts, query, dataset) return query \ No newline at end of file diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/alphanumeric.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/alphanumeric.py index 34d9e23c..09eb2ca3 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/alphanumeric.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/alphanumeric.py @@ -1,7 +1,6 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config from beacon.connections.mongo.filters.format import format_value, format_operator -from beacon.request.classes import RequestAttributes @log_with_args(config.level) def parse_request_parameters(self, query, filter): @@ -24,53 +23,53 @@ def parse_request_parameters(self, query, filter): elif len(filter.value) == 1: prehgvs='^NC_00000' if filter.value == 'X': - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']='^NC_000023'+'.'+'9:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']='^NC_000023'+'.'+'10:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']='^NC_000023'+'.'+'11:g' elif filter.value == 'Y': - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']='^NC_000024'+'.'+'8:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']='^NC_000024'+'.'+'9:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']='^NC_000024'+'.'+'10:g' elif filter.value in ['14', '21']: - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']=prehgvs+filter.value+'.'+'7:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']=prehgvs+filter.value+'.'+'8:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']=prehgvs+filter.value+'.'+'9:g' elif filter.value in ['5', '11', '15', '16', '18', '19', '24']: - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']=prehgvs+filter.value+'.'+'8:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']=prehgvs+filter.value+'.'+'9:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']=prehgvs+filter.value+'.'+'10:g' elif filter.value in ['1', '8', '10', '13', '17', '20', '22', '23']: - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']=prehgvs+filter.value+'.'+'9:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']=prehgvs+filter.value+'.'+'10:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']=prehgvs+filter.value+'.'+'11:g' elif filter.value in ['2', '3', '4', '6', '9', '12']: - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']=prehgvs+filter.value+'.'+'10:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']=prehgvs+filter.value+'.'+'11:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']=prehgvs+filter.value+'.'+'12:g' elif filter.value == '7': - if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': + if self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36': dict_regex['$regex']=prehgvs+filter.value+'.'+'12:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37': dict_regex['$regex']=prehgvs+filter.value+'.'+'13:g' - elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': + elif self.request_attributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38': dict_regex['$regex']=prehgvs+filter.value+'.'+'14:g' # If there is > in the value, replace it by > elif '>' in filter.value: diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/apply_request_parameters.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/apply_request_parameters.py index 5a3a9cf9..9c2e3442 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/apply_request_parameters.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/apply_request_parameters.py @@ -5,7 +5,6 @@ from beacon.connections.mongo.filters.alphanumeric import apply_alphanumeric_filter from beacon.connections.mongo.client import get_client from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.utils import lengthquery -from beacon.request.classes import RequestAttributes from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.request_parameters.start import generate_position_filter_start from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.request_parameters.sequence import generate_position_filter_start_sequence_query from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.request_parameters.end import generate_position_filter_end @@ -14,7 +13,7 @@ @log_with_args(config.level) def apply_request_parameters(self, query: Dict[str, List[dict]], dataset: str): # Initiate the $and operator in case is not inside the query syntax - if len(RequestAttributes.qparams.query.requestParameters) > 0 and "$and" not in query: + if len(self.request_attributes.qparams.query.requestParameters) > 0 and "$and" not in query: query["$and"] = [] # Initiate the different dictionaries that will be needed to process the different request parameters use cases subquery={} @@ -34,14 +33,14 @@ def apply_request_parameters(self, query: Dict[str, List[dict]], dataset: str): equal=False isBracket=False # Check for the existance of end/start parameters to create some values that will help later to process each one of those parameters individually - for k, v in RequestAttributes.qparams.query.requestParameters.items(): + for k, v in self.request_attributes.qparams.query.requestParameters.items(): if k == 'end': equal=True endvalue=v if k == 'start': startvalue=v # Iterate through the different request parameters from the request - for k, v in RequestAttributes.qparams.query.requestParameters.items(): + for k, v in self.request_attributes.qparams.query.requestParameters.items(): if k == "start": # First, get how many parameters are being thrown and if there is more than one, assign the query to a bracket query. if isinstance(v, str): diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/request_parameters.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/request_parameters.py index 4e195f19..e90eef1f 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/request_parameters.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/request_parameters.py @@ -1,7 +1,6 @@ from beacon.connections.mongo.client import get_client from beacon.conf.conf_override import config from beacon.logs.logs import log_with_args -from beacon.request.classes import RequestAttributes from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.cross_queries.get_biosampleIds import get_biosampleIds from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.cross_queries.get_total_query import get_total_query from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.utils import import_analysis_confile, import_biosample_confile, import_individual_confile, import_run_confile @@ -17,7 +16,7 @@ def request_parameters(self, total_query, request_parameters, dataset): biosample_confile=import_biosample_confile() run_confile=import_run_confile() # Check wich is the entry type to know how to do the id translation for the request parameters (if any) - if RequestAttributes.entry_type == individual_confile["individual"]["endpoint_name"]: + if self.request_attributes.entry_type == individual_confile["individual"]["endpoint_name"]: biosampleIds=get_biosampleIds(self, request_parameters, dataset) try: # Build the query to get the individual ids from biosamples @@ -50,11 +49,11 @@ def request_parameters(self, total_query, request_parameters, dataset): except Exception: total_query["$and"]=[] total_query["$and"].append(finalquery) - elif RequestAttributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: + elif self.request_attributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: # Get the biosampleIds obtained from the request parameters query and build the query with these ids as id because is against biosamples. biosampleIds=get_biosampleIds(self, request_parameters, dataset) total_query=get_total_query(self, biosampleIds, total_query, "id") - elif RequestAttributes.entry_type == analysis_confile["analysis"]["endpoint_name"] or RequestAttributes.entry_type == run_confile["run"]["endpoint_name"]: + elif self.request_attributes.entry_type == analysis_confile["analysis"]["endpoint_name"] or self.request_attributes.entry_type == run_confile["run"]["endpoint_name"]: # Get the biosampleIds obtained from the request parameters query and build the query with these ids as id because is against analyses/runs. biosampleIds=get_biosampleIds(self, request_parameters, dataset) total_query=get_total_query(self, biosampleIds, total_query, "biosampleId") diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py index a5a79f1b..c87270ab 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py @@ -1,6 +1,5 @@ from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.request.classes import RequestAttributes from beacon.models.ga4gh.beacon_v2_default_model.connections.mongo.filters.request_parameters.apply_request_parameters import apply_request_parameters from beacon.connections.mongo.filters.filters import apply_filters from beacon.connections.mongo.utils import get_docs_by_response_type, query_id @@ -25,13 +24,13 @@ def get_phenotypic_endpoint(self, dataset: SingleDatasetResponse): query_parameters = {} query={} # Process the filters - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, query_parameters, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, query_parameters, dataset.dataset) if query == {} and query_parameters != {} and parameters_as_filters == False: # If the filters and the parameters didn't build any query, just return the dataset. return dataset # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -42,8 +41,8 @@ def get_phenotypic_endpoint(self, dataset: SingleDatasetResponse): def get_phenotypic_endpoint_with_id(self, dataset: SingleDatasetResponse): genomicVariant_confile=import_genomicVariant_confile() # If the entry type records to return are variants, apply request parameters checking if they come by query string or not. Otherwise, just process the parameters as usual. - if RequestAttributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: - query = {"$and": [{"_id": RequestAttributes.entry_id}]} + if self.request_attributes.entry_type == genomicVariant_confile["genomicVariant"]["endpoint_name"]: + query = {"$and": [{"_id": self.request_attributes.entry_id}]} query_parameters, parameters_as_filters = apply_request_parameters(self, query, dataset.dataset) if parameters_as_filters == True: query, parameters_as_filters = apply_request_parameters(self, {}, dataset.dataset) @@ -53,14 +52,14 @@ def get_phenotypic_endpoint_with_id(self, dataset: SingleDatasetResponse): else: query, parameters_as_filters = apply_request_parameters(self, {}, dataset.dataset) # Process filters - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # If the entry type records are not variants, include the id queried in the query. - if RequestAttributes.entry_type != genomicVariant_confile["genomicVariant"]["endpoint_name"]: - query = query_id(self, query, RequestAttributes.entry_id) + if self.request_attributes.entry_type != genomicVariant_confile["genomicVariant"]["endpoint_name"]: + query = query_id(self, query, self.request_attributes.entry_id) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -76,12 +75,12 @@ def get_variants_of_phenotypic_endpoint(self, dataset: SingleDatasetResponse): caseLevelData=client['beacon'].caseLevelData analysis_confile=import_analysis_confile() run_confile=import_run_confile() - new_entry_id = RequestAttributes.entry_id + new_entry_id = self.request_attributes.entry_id # Check which is the queried initial entry type of the cross query and process and get the ids to convert to the final entry type response. - if RequestAttributes.pre_entry_type == analysis_confile["analysis"]["endpoint_name"] or RequestAttributes.pre_entry_type == run_confile["run"]["endpoint_name"]: - query = {"$and": [{"id": RequestAttributes.entry_id}]} - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) - if RequestAttributes.pre_entry_type == analysis_confile["analysis"]["endpoint_name"]: + if self.request_attributes.pre_entry_type == analysis_confile["analysis"]["endpoint_name"] or self.request_attributes.pre_entry_type == run_confile["run"]["endpoint_name"]: + query = {"$and": [{"id": self.request_attributes.entry_id}]} + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) + if self.request_attributes.pre_entry_type == analysis_confile["analysis"]["endpoint_name"]: initial_ids = analyses \ .find_one(query, {"biosampleId": 1, "_id": 0}) else: @@ -110,7 +109,7 @@ def get_variants_of_phenotypic_endpoint(self, dataset: SingleDatasetResponse): # Query the caseLevelData to get the variants that are related to these ids. query_cl={"$or": [{ position: "10", "datasetId": dataset.dataset},{ position: "11", "datasetId": dataset.dataset}, { position: "01", "datasetId": dataset.dataset}, { position: "y", "datasetId": dataset.dataset}]} string_of_ids = caseLevelData \ - .find(query_cl, {"id": 1, "_id": 0}).limit(RequestAttributes.qparams.query.pagination.limit).skip(RequestAttributes.qparams.query.pagination.skip) + .find(query_cl, {"id": 1, "_id": 0}).limit(self.request_attributes.qparams.query.pagination.limit).skip(self.request_attributes.qparams.query.pagination.skip) HGVSIds=list(string_of_ids) # Build the query using the identifiers.genomicHGVSId query={} @@ -124,11 +123,11 @@ def get_variants_of_phenotypic_endpoint(self, dataset: SingleDatasetResponse): # Apply request parameters query, parameters_as_filters = apply_request_parameters(self, query, dataset.dataset) # Process filters - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -143,7 +142,7 @@ def get_phenotypic_endpoint_of_variants(self, dataset: SingleDatasetResponse): caseLevelData=client['beacon'].caseLevelData biosamples=client['beacon'].biosamples # Add the variantInternalId of the variant to the query constructor. - query = {"$and": [{"_id": RequestAttributes.entry_id}]} + query = {"$and": [{"_id": self.request_attributes.entry_id}]} # Handle the request parameters and create the first built of the query. query_parameters, parameters_as_filters = apply_request_parameters(self, query, dataset.dataset) if parameters_as_filters == True and query_parameters != {'$and': []}: # If there are request parameters that come from query string, reprocess the request parameters @@ -184,7 +183,7 @@ def get_phenotypic_endpoint_of_variants(self, dataset: SingleDatasetResponse): # Initialize the biosampleIds array obtained from variants. biosampleIds=[] biosampleIds_restricted=[] - filters=RequestAttributes.qparams.query.filters + filters=self.request_attributes.qparams.query.filters new_filters=[] if filters != []: # If there are filters, check if there are zygosity filters. for filter in filters: @@ -192,12 +191,12 @@ def get_phenotypic_endpoint_of_variants(self, dataset: SingleDatasetResponse): for key, value in list_of_positions_strings.items(): if key != 'datasetId' and key != 'id' and key != '_id' and value != '11': biosampleIds_restricted.append(list_of_targets[int(key)]) - RequestAttributes.qparams.query.filters.remove(filter) + self.request_attributes.qparams.query.filters.remove(filter) elif filter['id']=='GENO:0000136': # If there is any filter of heterozygosity, collect only those ids. for key, value in list_of_positions_strings.items(): if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01' and value != 'y': biosampleIds_restricted.append(list_of_targets[int(key)]) - RequestAttributes.qparams.query.filters.remove(filter) + self.request_attributes.qparams.query.filters.remove(filter) else: # Otherwise, collect all the ids. new_filters.append(filter) for key, value in list_of_positions_strings.items(): @@ -217,11 +216,11 @@ def get_phenotypic_endpoint_of_variants(self, dataset: SingleDatasetResponse): individual_confile=import_individual_confile() biosample_confile=import_biosample_confile() # Build the query translating the biosampleIds to individualIds in case the entry type needed is individuals. - if RequestAttributes.entry_type != individual_confile["individual"]["endpoint_name"]: + if self.request_attributes.entry_type != individual_confile["individual"]["endpoint_name"]: finalids=biosampleIds try: finalids=[] - if RequestAttributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: + if self.request_attributes.entry_type == biosample_confile["biosample"]["endpoint_name"]: idq = 'id' else: idq = 'biosampleId' @@ -259,9 +258,9 @@ def get_phenotypic_endpoint_of_variants(self, dataset: SingleDatasetResponse): # Process filters query = apply_filters(self, superfinalquery, new_filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -274,7 +273,7 @@ def get_variants_of_dataset(self, dataset: SingleDatasetResponse): query_count={} query_count["$or"]=[] # If the entry_id belongs to any dataset, build the query, otherwise, dataset is not found. - if dataset.dataset == RequestAttributes.entry_id: + if dataset.dataset == self.request_attributes.entry_id: queryid={} queryid["datasetId"]=dataset.dataset query_count["$or"].append(queryid) @@ -283,11 +282,11 @@ def get_variants_of_dataset(self, dataset: SingleDatasetResponse): dataset.exists=False return dataset # Process filters - query = apply_filters(self, query_count, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query_count, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -297,23 +296,23 @@ def get_variants_of_dataset(self, dataset: SingleDatasetResponse): @log_with_args(config.level) def get_phenotypic_endpoint_of_dataset(self, dataset: SingleDatasetResponse): # Process filters - query = apply_filters(self, {}, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, {}, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Add the dataset id requested in the query syntax. - query = query_id(self, query, RequestAttributes.entry_id) + query = query_id(self, query, self.request_attributes.entry_id) # If the entry_id belongs to any dataset, build the query, otherwise, dataset is not found. dict_in={} - if dataset.dataset == RequestAttributes.entry_id: - dict_in['datasetId']=RequestAttributes.entry_id + if dataset.dataset == self.request_attributes.entry_id: + dict_in['datasetId']=self.request_attributes.entry_id else: dataset.dataset_count=0 dataset.exists=False return dataset # Process filters - query = apply_filters(self, dict_in, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, dict_in, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -326,7 +325,7 @@ def get_phenotypic_endpoint_of_cohort(self, dataset: SingleDatasetResponse): cohorts=client['beacon'].cohorts # Make an initial query to translate the datasetId into cohort id. dataset_found = cohorts \ - .find({"id": RequestAttributes.entry_id}, {"datasetId": 1, "_id": 0}) + .find({"id": self.request_attributes.entry_id}, {"datasetId": 1, "_id": 0}) dataset_found=list(dataset_found) # If the entry_id belongs to any dataset, build the query, otherwise, dataset is not found. dict_in={} @@ -338,11 +337,11 @@ def get_phenotypic_endpoint_of_cohort(self, dataset: SingleDatasetResponse): dataset.exists=False return dataset # Process filters - query = apply_filters(self, dict_in, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, dict_in, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - limit = RequestAttributes.qparams.query.pagination.limit - include = RequestAttributes.qparams.query.includeResultsetResponses - skip = RequestAttributes.qparams.query.pagination.skip + limit = self.request_attributes.qparams.query.pagination.limit + include = self.request_attributes.qparams.query.includeResultsetResponses + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -354,12 +353,12 @@ def get_variants_of_cohort(self, dataset: SingleDatasetResponse): client=get_client() cohorts=client['beacon'].cohorts # Save the include, limit and skip parameters so they are used later. - limit = RequestAttributes.qparams.query.pagination.limit - include = RequestAttributes.qparams.query.includeResultsetResponses - skip = RequestAttributes.qparams.query.pagination.skip + limit = self.request_attributes.qparams.query.pagination.limit + include = self.request_attributes.qparams.query.includeResultsetResponses + skip = self.request_attributes.qparams.query.pagination.skip # Make an initial query to translate the datasetId into cohort id. dataset_found = cohorts \ - .find({"id": RequestAttributes.entry_id}, {"datasetId": 1, "_id": 0}) + .find({"id": self.request_attributes.entry_id}, {"datasetId": 1, "_id": 0}) dataset_found=list(dataset_found) # If the entry_id belongs to any dataset, build the query, otherwise, dataset is not found. dict_in={} @@ -371,20 +370,20 @@ def get_variants_of_cohort(self, dataset: SingleDatasetResponse): dataset.exists=False return dataset # Process filters - query = apply_filters(self, dict_in, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, dict_in, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Get the datasets ids found in the cohorts, otherwise, dataset for the cohort is not found. query_count={} query_count["$or"]=[] docs = get_documents_for_cohorts(self, cohorts, query, - RequestAttributes.qparams.query.pagination.skip, - RequestAttributes.qparams.query.pagination.skip*limit + self.request_attributes.qparams.query.pagination.skip, + self.request_attributes.qparams.query.pagination.skip*limit ) for doc in docs: if doc["datasetId"] == dataset.dataset: - RequestAttributes.entry_id = dataset.dataset - if dataset.dataset == RequestAttributes.entry_id: + self.request_attributes.entry_id = dataset.dataset + if dataset.dataset == self.request_attributes.entry_id: queryid={} queryid["datasetId"]=dataset.dataset query_count["$or"].append(queryid) @@ -393,7 +392,7 @@ def get_variants_of_cohort(self, dataset: SingleDatasetResponse): dataset.exists=False return dataset # Process filters. - query = apply_filters(self, query_count, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query_count, self.request_attributes.qparams.query.filters, {}, dataset.dataset) if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. @@ -403,21 +402,21 @@ def get_variants_of_cohort(self, dataset: SingleDatasetResponse): @log_with_args(config.level) def get_phenotypic_cross_query(self, dataset: SingleDatasetResponse): # Get the translation of ids for the entry types lookup for the cross query. - mapping = get_phenotypic_cross_query_attributes(self, RequestAttributes.entry_type, RequestAttributes.pre_entry_type) + mapping = get_phenotypic_cross_query_attributes(self, self.request_attributes.entry_type, self.request_attributes.pre_entry_type) # Get the ids found for the initial entry type query. items_found = mapping["secondary_collection"] \ - .find({"id": RequestAttributes.entry_id, "datasetId": dataset.dataset}, {mapping["idq2"]: 1, "_id": 0}) + .find({"id": self.request_attributes.entry_id, "datasetId": dataset.dataset}, {mapping["idq2"]: 1, "_id": 0}) # Translate the ids. list_of_itemsfound=[] for itemfound in items_found: list_of_itemsfound.append(itemfound[mapping["idq2"]]) query = {mapping["idq"]: {"$in": list_of_itemsfound}} # Process filters. - query = apply_filters(self, query, RequestAttributes.qparams.query.filters, {}, dataset.dataset) + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) # Save the include, limit and skip parameters so they are used later. - include = RequestAttributes.qparams.query.includeResultsetResponses - limit = RequestAttributes.qparams.query.pagination.limit - skip = RequestAttributes.qparams.query.pagination.skip + include = self.request_attributes.qparams.query.includeResultsetResponses + limit = self.request_attributes.qparams.query.pagination.limit + skip = self.request_attributes.qparams.query.pagination.skip if limit > 100 or limit == 0: limit = config.max_limit_of_records_per_dataset_in_a_page # Get the docs with the query syntax built. diff --git a/beacon/permissions/__main__.py b/beacon/permissions/__main__.py index 608cee98..15767130 100644 --- a/beacon/permissions/__main__.py +++ b/beacon/permissions/__main__.py @@ -8,14 +8,13 @@ from beacon.budget.__main__ import check_budget from beacon.utils.modules import get_all_modules_datasets from beacon.response.classes import SingleDatasetResponse -from beacon.request.classes import RequestAttributes from beacon.exceptions.exceptions import InvalidRequest, NoPermissionsAvailable @log_with_args(config.level) async def authorization(self): try: # Get the token from the header Authorization - auth = RequestAttributes.headers.get('Authorization') + auth = self.request_attributes.headers.get('Authorization') if not auth or not auth.lower().startswith('bearer '): raise NoPermissionsAvailable('request received did not add a token or token did not start with bearer') # Initialize the list that will contain the datasets permissions that come from a visa. @@ -40,11 +39,11 @@ async def authorization(self): async def get_datasets_list(self, authorized_datasets): try: # Get the requested datasets and save them in a list. - specific_datasets = RequestAttributes.qparams.query.requestParameters['datasets'] + specific_datasets = self.request_attributes.qparams.query.requestParameters['datasets'] except Exception as e: specific_datasets = [] # Get the datasets from all the databases. - list_of_datasets_confs = get_all_modules_datasets(RequestAttributes.source) + list_of_datasets_confs = get_all_modules_datasets(self.request_attributes.source) beacon_datasets=[] for dataset_conf in list_of_datasets_confs: try: @@ -68,13 +67,13 @@ async def permission(self): username = 'public' try: # Get the requested datasets and save them in a list. - requested_datasets = RequestAttributes.qparams.query.requestParameters["datasets"] + requested_datasets = self.request_attributes.qparams.query.requestParameters["datasets"] except Exception: requested_datasets = [] # Get the usernq, and the list of datasets that the user has permissions for from visas. username, list_visa_datasets = await authorization(self) # Get the datasets that the user has permissions for from the datasets permissions conf file in a list of classes for the datasets. - datasets_permissions = await PermissionsProxy.get_permissions(self, username=username, requested_datasets=requested_datasets, testMode=RequestAttributes.qparams.query.testMode) + datasets_permissions = await PermissionsProxy.get_permissions(self, username=username, requested_datasets=requested_datasets, testMode=self.request_attributes.qparams.query.testMode) # Return the time to be inserted in the budget in case the budget doesn't return an exception for the query. time_now = check_budget(self, username) # Add as well in the list of dataset classes, the dataset classes that have permissions for the query coming from visas. diff --git a/beacon/permissions/utils.py b/beacon/permissions/utils.py index dd5a2277..9caefd71 100644 --- a/beacon/permissions/utils.py +++ b/beacon/permissions/utils.py @@ -1,11 +1,11 @@ -from beacon.request.classes import RequestAttributes + def return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity): """Method to get the granularity needed to be returned for a specific permissions case""" for granularity_exception in granularity_exceptions: # Loop over all the exceptions that are handed in and take the one that belongs to the entry type that is being requested for entry_type_id, entry_type_granularity in granularity_exception.items(): - if entry_type_id == RequestAttributes.entry_type_id: + if entry_type_id == self.request_attributes.entry_type_id: # Assign the entry type granularity and return it back default_granularity = entry_type_granularity return default_granularity diff --git a/beacon/response/includeResultsetResponses.py b/beacon/response/includeResultsetResponses.py index 6e0c257b..eafb29fd 100644 --- a/beacon/response/includeResultsetResponses.py +++ b/beacon/response/includeResultsetResponses.py @@ -1,4 +1,3 @@ -from beacon.request.classes import RequestAttributes from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config from beacon.response.classes import MultipleDatasetsResponse @@ -13,7 +12,7 @@ def gather_final_datasets_to_return(self, responseClass, finalMultiDatasetsClass @log_with_args(config.level) def include_resultSet_responses(self, multipleDatasetsClass): # Load the include resultSet response from the request attributes. - include = RequestAttributes.qparams.query.includeResultsetResponses + include = self.request_attributes.qparams.query.includeResultsetResponses # Start a multiple datasets class that is empty. finalMultiDatasetsClass = MultipleDatasetsResponse(total_count=0, datasets_responses=[]) for dataset in multipleDatasetsClass.datasets_responses: diff --git a/beacon/tests/test_concurrency.py b/beacon/tests/test_concurrency.py new file mode 100644 index 00000000..d4e7eb58 --- /dev/null +++ b/beacon/tests/test_concurrency.py @@ -0,0 +1,728 @@ +#!/usr/bin/env python3 + +import json +import os +import time +from concurrent.futures import ThreadPoolExecutor, as_completed + +import requests + + +# ============================================================ +# CONFIGURACIÓN +# ============================================================ + +BASE_URL = "http://localhost:5050/api/individuals" + +# Número total de peticiones +TOTAL_REQUESTS = 30 + +# Número máximo de workers simultáneos +MAX_WORKERS = 30 + +# Timeout de cada petición +TIMEOUT = 60 + +# limit=0 => pedir todos los documentos +LIMIT = 0 + +# Directorio donde se guardarán las respuestas +OUTPUT_DIR = "beacon_test_results" + +# Margen entre el inicio de una petición y la siguiente +# Las peticiones siguen siendo concurrentes. +REQUEST_START_MARGIN = 0 + + +# ============================================================ +# FILTROS +# ============================================================ + +FILTERS = [ + "NCIT:C16576", + "ECO:0006017", + "BTO:0004718", +] + + +# ============================================================ +# PREPARACIÓN +# ============================================================ + +os.makedirs(OUTPUT_DIR, exist_ok=True) + + +def safe_filename(value): + """ + Convierte un filtro en un nombre de fichero seguro. + """ + return value.replace(":", "_").replace("/", "_").replace("\\", "_") + + +def find_all_ids(obj): + """ + Recorre recursivamente todo el JSON y devuelve todos los valores + encontrados en campos llamados 'id'. + + Sirve para comprobar si el filtro aparece en cualquier parte + del documento. + """ + ids = [] + + if isinstance(obj, dict): + for key, value in obj.items(): + if key == "id" and isinstance(value, str): + ids.append(value) + + ids.extend(find_all_ids(value)) + + elif isinstance(obj, list): + for item in obj: + ids.extend(find_all_ids(item)) + + return ids + + +def extract_documents(data): + """ + Extrae los documentos de: + + response.resultSets[*].results + """ + + documents = [] + + try: + result_sets = ( + data + .get("response", {}) + .get("resultSets", []) + ) + + for result_set in result_sets: + results = result_set.get("results", []) + + if isinstance(results, list): + documents.extend(results) + + except Exception: + pass + + return documents + + +def get_received_filters(data): + """ + Extrae el filtro que Beacon dice haber recibido: + + meta.receivedRequestSummary.filters + """ + + try: + filters = ( + data + .get("meta", {}) + .get("receivedRequestSummary", {}) + .get("filters", []) + ) + + if isinstance(filters, list): + return filters + + except Exception: + pass + + return [] + + +def get_response_count(data): + """ + Obtiene responseSummary.numTotalResults. + """ + + try: + return ( + data + .get("responseSummary", {}) + .get("numTotalResults") + ) + except Exception: + return None + + +# ============================================================ +# UNA PETICIÓN +# ============================================================ + +def execute_request(request_number, filter_value): + """ + Ejecuta UNA petición. + + Es importante que filter_value sea un argumento local de esta + función. De esta forma cada thread conserva su propio filtro. + """ + + request_id = f"REQ-{request_number:03d}" + + start_time = time.perf_counter() + + # -------------------------------------------------------- + # IMPORTANTE: + # + # Cada request construye sus propios parámetros. + # No se utiliza ninguna variable global para el filtro. + # -------------------------------------------------------- + + params = { + "filters": filter_value, + "limit": LIMIT, + } + + result = { + "request_id": request_id, + "expected_filter": filter_value, + "url": BASE_URL, + "params": params, + "http_status": None, + "elapsed_seconds": None, + "status": None, + "received_filters": [], + "documents_count": 0, + "expected_filter_found_in_documents": 0, + "documents_missing_filter": [], + "response_file": None, + "error": None, + } + + try: + + response = requests.get( + BASE_URL, + params=params, + timeout=TIMEOUT, + ) + + elapsed = time.perf_counter() - start_time + + result["http_status"] = response.status_code + result["elapsed_seconds"] = round(elapsed, 3) + + # ---------------------------------------------------- + # ERROR HTTP + # ---------------------------------------------------- + + if response.status_code != 200: + + result["status"] = "HTTP_ERROR" + + # Guardamos también el cuerpo aunque sea un error + try: + data = response.json() + except Exception: + data = { + "raw_response": response.text + } + + else: + + # ------------------------------------------------ + # PARSE JSON + # ------------------------------------------------ + + try: + data = response.json() + + except Exception as exc: + + result["status"] = "INVALID_JSON" + result["error"] = str(exc) + + return result + + # ------------------------------------------------ + # FILTROS QUE BEACON DICE HABER RECIBIDO + # ------------------------------------------------ + + received_filters = get_received_filters(data) + + result["received_filters"] = received_filters + + # ------------------------------------------------ + # DOCUMENTOS + # ------------------------------------------------ + + documents = extract_documents(data) + + result["documents_count"] = len(documents) + + # ------------------------------------------------ + # COMPROBAR QUE BEACON RECIBIÓ EL FILTRO CORRECTO + # ------------------------------------------------ + + received_filter_ok = ( + filter_value in received_filters + ) + + # ------------------------------------------------ + # COMPROBAR CADA DOCUMENTO + # + # El filtro debe aparecer en algún campo "id" + # del documento. + # ------------------------------------------------ + + documents_missing = [] + documents_with_filter = 0 + + for document in documents: + + document_id = document.get( + "id", + "" + ) + + ids = find_all_ids(document) + + if filter_value in ids: + documents_with_filter += 1 + + else: + documents_missing.append( + document_id + ) + + result["expected_filter_found_in_documents"] = ( + documents_with_filter + ) + + result["documents_missing_filter"] = ( + documents_missing + ) + + # ------------------------------------------------ + # DETERMINAR RESULTADO + # ------------------------------------------------ + + if not received_filter_ok: + + result["status"] = ( + "REQUEST_FILTER_MISMATCH" + ) + + elif documents_missing: + + result["status"] = ( + "FILTER_MISSING_IN_DOCUMENT" + ) + + else: + + result["status"] = "OK" + + # ---------------------------------------------------- + # GUARDAR RESPUESTA + # + # El nombre usa filter_value LOCAL de esta petición. + # No se obtiene de otra request. + # ---------------------------------------------------- + + filename = ( + f"{request_id}_" + f"{safe_filename(filter_value)}.json" + ) + + filepath = os.path.join( + OUTPUT_DIR, + filename + ) + + with open( + filepath, + "w", + encoding="utf-8" + ) as f: + + json.dump( + { + "test": result, + "response": data, + }, + f, + indent=2, + ensure_ascii=False, + ) + + result["response_file"] = filepath + + except requests.exceptions.Timeout: + + result["status"] = "TIMEOUT" + result["elapsed_seconds"] = round( + time.perf_counter() - start_time, + 3 + ) + result["error"] = ( + f"Timeout after {TIMEOUT} seconds" + ) + + except requests.exceptions.RequestException as exc: + + result["status"] = "REQUEST_ERROR" + result["elapsed_seconds"] = round( + time.perf_counter() - start_time, + 3 + ) + result["error"] = str(exc) + + except Exception as exc: + + result["status"] = "SCRIPT_ERROR" + result["elapsed_seconds"] = round( + time.perf_counter() - start_time, + 3 + ) + result["error"] = str(exc) + + return result + + +# ============================================================ +# CREAR PETICIONES +# ============================================================ + +def build_requests(): + + requests_to_run = [] + + for i in range(1, TOTAL_REQUESTS + 1): + + # Repetimos los filtros en orden: + # + # REQ-001 -> NCIT:C16576 + # REQ-002 -> ECO:0006017 + # REQ-003 -> BTO:0004718 + # REQ-004 -> NCIT:C16576 + # ... + + filter_value = FILTERS[ + (i - 1) % len(FILTERS) + ] + + requests_to_run.append( + (i, filter_value) + ) + + return requests_to_run + + +# ============================================================ +# MAIN +# ============================================================ + +def main(): + + print("=" * 78) + print("BEACON - CONCURRENT RESPONSE ISOLATION TEST") + print("=" * 78) + print(f"URL: {BASE_URL}") + print(f"Total requests: {TOTAL_REQUESTS}") + print(f"Concurrent: {MAX_WORKERS}") + print(f"limit: {LIMIT}") + print( + f"Request start margin: " + f"{REQUEST_START_MARGIN}s" + ) + print(f"Output directory: {OUTPUT_DIR}") + print() + + requests_to_run = build_requests() + + all_results = [] + + start_total = time.perf_counter() + + # -------------------------------------------------------- + # EJECUCIÓN CONCURRENTE + # -------------------------------------------------------- + + with ThreadPoolExecutor( + max_workers=MAX_WORKERS + ) as executor: + + futures = [] + + for index, ( + request_number, + filter_value + ) in enumerate(requests_to_run): + + # ------------------------------------------------ + # IMPORTANTE: + # + # Cada petición se somete al executor y esperamos + # 0.5 segundos ANTES de iniciar/someter la siguiente. + # + # Esto significa: + # + # REQ-001 -> t=0.0s + # REQ-002 -> t=0.5s + # REQ-003 -> t=1.0s + # REQ-004 -> t=1.5s + # + # Las peticiones continúan ejecutándose en paralelo. + # ------------------------------------------------ + + future = executor.submit( + execute_request, + request_number, + filter_value, + ) + + futures.append(future) + + if index < len(requests_to_run) - 1: + time.sleep(REQUEST_START_MARGIN) + + # ---------------------------------------------------- + # RECIBIR RESULTADOS A MEDIDA QUE TERMINAN + # ---------------------------------------------------- + + for future in as_completed(futures): + + result = future.result() + + all_results.append(result) + + # ------------------------------------------------ + # Mostrar inmediatamente el resultado + # ------------------------------------------------ + + request_id = result["request_id"] + expected = result["expected_filter"] + status = result["status"] + http = result["http_status"] + elapsed = result["elapsed_seconds"] + + docs = result["documents_count"] + + print( + f"{request_id} | " + f"{expected:<15} | " + f"HTTP {str(http):<3} | " + f"{status:<32} | " + f"Docs: {docs:<3} | " + f"{elapsed}s" + ) + + if result["documents_missing_filter"]: + + missing = ",".join( + result["documents_missing_filter"] + ) + + print( + f" Documents failing: " + f"{missing}" + ) + + total_elapsed = ( + time.perf_counter() - start_total + ) + + # ======================================================== + # ORDENAR RESULTADOS + # ======================================================== + + all_results.sort( + key=lambda x: x["request_id"] + ) + + # ======================================================== + # GUARDAR RESUMEN + # ======================================================== + + summary_file = os.path.join( + OUTPUT_DIR, + "summary.json" + ) + + with open( + summary_file, + "w", + encoding="utf-8" + ) as f: + + json.dump( + { + "configuration": { + "url": BASE_URL, + "total_requests": TOTAL_REQUESTS, + "max_workers": MAX_WORKERS, + "limit": LIMIT, + "request_start_margin": REQUEST_START_MARGIN, + "filters": FILTERS, + }, + "total_elapsed_seconds": round( + total_elapsed, + 3 + ), + "results": all_results, + }, + f, + indent=2, + ensure_ascii=False, + ) + + # ======================================================== + # RESUMEN FINAL + # ======================================================== + + ok = sum( + 1 for r in all_results + if r["status"] == "OK" + ) + + filter_missing = sum( + 1 for r in all_results + if r["status"] + == "FILTER_MISSING_IN_DOCUMENT" + ) + + request_mismatch = sum( + 1 for r in all_results + if r["status"] + == "REQUEST_FILTER_MISMATCH" + ) + + http_errors = sum( + 1 for r in all_results + if r["status"] == "HTTP_ERROR" + ) + + other_errors = len(all_results) - ( + ok + + filter_missing + + request_mismatch + + http_errors + ) + + # ======================================================== + # DETECCIÓN ESPECÍFICA DE RESPUESTAS CRUZADAS + # ======================================================== + + cross_response_candidates = [] + + for result in all_results: + + expected = result["expected_filter"] + received = result["received_filters"] + + if received and expected not in received: + + cross_response_candidates.append( + { + "request_id": result["request_id"], + "expected_filter": expected, + "received_filters": received, + } + ) + + print() + print("=" * 78) + print("FINAL SUMMARY") + print("=" * 78) + + print(f"Total requests: {len(all_results)}") + print(f"OK: {ok}") + print(f"Filter missing in document: {filter_missing}") + print(f"Request filter mismatch: {request_mismatch}") + print(f"HTTP errors: {http_errors}") + print(f"Other errors: {other_errors}") + print( + f"Cross-response candidates: " + f"{len(cross_response_candidates)}" + ) + print( + f"Total elapsed: " + f"{round(total_elapsed, 3)}s" + ) + + print() + print(f"Responses saved in: {OUTPUT_DIR}/") + print(f"Summary: {summary_file}") + + # ======================================================== + # DETALLE DE POSIBLES RESPUESTAS CRUZADAS + # ======================================================== + + if cross_response_candidates: + + print() + print("=" * 78) + print("POSSIBLE CROSS-RESPONSE DETECTED") + print("=" * 78) + + for item in cross_response_candidates: + + print( + f"{item['request_id']} | " + f"Expected: {item['expected_filter']} | " + f"Received: {item['received_filters']}" + ) + + # ======================================================== + # DETALLE DE DOCUMENTOS INCORRECTOS + # ======================================================== + + failing_documents = [] + + for result in all_results: + + if result["documents_missing_filter"]: + + failing_documents.append( + result + ) + + if failing_documents: + + print() + print("=" * 78) + print("DOCUMENT VALIDATION FAILURES") + print("=" * 78) + + for result in failing_documents: + + print( + f"{result['request_id']} | " + f"Filter: {result['expected_filter']} | " + f"Missing from: " + f"{','.join(result['documents_missing_filter'])}" + ) + + print() + print("=" * 78) + + # ======================================================== + # CÓDIGO DE SALIDA + # ======================================================== + + if ( + filter_missing > 0 + or request_mismatch > 0 + or http_errors > 0 + or other_errors > 0 + ): + + print("TEST RESULT: FAIL") + + return 1 + + else: + + print("TEST RESULT: PASS") + + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/beacon/utils/checks.py b/beacon/utils/checks.py index 744a4379..b6a781f0 100644 --- a/beacon/utils/checks.py +++ b/beacon/utils/checks.py @@ -1,5 +1,4 @@ from beacon.utils.modules import check_database_connections -from beacon.request.classes import RequestAttributes from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config @@ -7,6 +6,6 @@ def state_check(func): @log_with_args(config.level) async def state_check(self, *args, **kwargs): """Function that will check the status of the database connections""" - await check_database_connections(LOG=self.LOG, entry_type=RequestAttributes.entry_type, pre_entry_type=RequestAttributes.pre_entry_type) + await check_database_connections(LOG=self.LOG, entry_type=self.request_attributes.entry_type, pre_entry_type=self.request_attributes.pre_entry_type) return await func(self, *args, **kwargs) return state_check \ No newline at end of file diff --git a/beacon/utils/modules.py b/beacon/utils/modules.py index 8fe84b6f..0980b14d 100644 --- a/beacon/utils/modules.py +++ b/beacon/utils/modules.py @@ -1,4 +1,4 @@ -from beacon.request.classes import RequestAttributes + import os from typing import Union import re @@ -12,7 +12,7 @@ def load_framework_module(self, script_name): """Choose what is the validator object class that will be loaded depending on the API version to return""" - module='beacon.framework.validator.'+RequestAttributes.returned_apiVersion.replace(".","_")+'.'+script_name + module='beacon.framework.validator.'+self.request_attributes.returned_apiVersion.replace(".","_")+'.'+script_name import importlib loaded_module = importlib.import_module(module, package=None) return loaded_module @@ -20,7 +20,7 @@ def load_framework_module(self, script_name): @log_with_args(config.level) def load_source_module(self, script_name): """Choose on the fly what is the database that is going to be used for the current request""" - complete_module='beacon.connections.'+RequestAttributes.source+'.' + script_name + complete_module='beacon.connections.'+self.request_attributes.source+'.' + script_name import importlib module = importlib.import_module(complete_module, package=None) return module @@ -30,9 +30,9 @@ async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=N """Choose on the fly what is the database that is going to be used for the current request""" try: # Store the value for the entry type requested - entry_type=RequestAttributes.entry_type + entry_type=self.request_attributes.entry_type # In case of a cross query, store the value for the entry type that will serve the requested id - pre_entry_type=RequestAttributes.pre_entry_type + pre_entry_type=self.request_attributes.pre_entry_type except Exception: # In case there is an exception, load the variables to be added to the error response entry_type=None @@ -151,15 +151,15 @@ def load_client(folder): module = importlib.import_module(complete_client_module, package=None) client_from_module = getattr(module, 'get_client') -def load_class(script_name, className): +def load_class(self, script_name, className): """Method to get the classes for the validators that match the API version to return""" - module='beacon.framework.validator.'+RequestAttributes.returned_apiVersion.replace(".","_")+'.'+script_name + module='beacon.framework.validator.'+self.request_attributes.returned_apiVersion.replace(".","_")+'.'+script_name import importlib loaded_module = importlib.import_module(module, package=None) klass = getattr(loaded_module, className) return klass -def load_types_of_results(response_type): +def load_types_of_results(self, response_type): """Method to get the type of schema that are accepted (for validation) in case of a model and entry type match""" # Load the configuration file for the models that are enabled with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: @@ -168,7 +168,7 @@ def load_types_of_results(response_type): # Initialize the array to collect all the entry types objects to be accepted for validation list_of_results_classes_accepted=[] # Generate a search of the version getting rid of the characters that join the string to the version number in conf - version_catch = re.search(r"(v\d+(\.\d+)*)", RequestAttributes.returned_schema[0]["schema"]) + version_catch = re.search(r"(v\d+(\.\d+)*)", self.request_attributes.returned_schema[0]["schema"]) # Keep the version number if version_catch: version = version_catch.group(1) diff --git a/beacon/utils/requests.py b/beacon/utils/requests.py index 650ab1f7..6776953f 100644 --- a/beacon/utils/requests.py +++ b/beacon/utils/requests.py @@ -5,7 +5,6 @@ import logging from beacon.logs.logs import log_with_args from beacon.conf.conf_override import config -from beacon.request.classes import RequestAttributes from beacon.exceptions.exceptions import IncoherenceInRequestError, InvalidRequest, WrongURIPath, NoFiltersAllowed import html from beacon.conf import filtering_terms @@ -151,7 +150,7 @@ async def get_qparams(self, request): elif post_data[k][k1]!=v1: raise IncoherenceInRequestError('two parameters conflict from string: {} and from json body query: {}'.format(v1, post_data[k][k1])) qparams = RequestParams(**final_body).from_request(final_body) - RequestAttributes.qparams = qparams + self.request_attributes.qparams = qparams except ValidationError: raise InvalidRequest('set of meta/query parameters: {} not allowed'.format(post_data)) @@ -159,68 +158,68 @@ async def get_qparams(self, request): def set_entry_type_configuration(self): ''' On the action of checking if there is a match between the endpoint queried an entry type in configuration, we then grab the database (source), max_granularity (allowed_granularity) - and id name of the records of the entry type to keep them in the RequestAttributes object for later. + and id name of the records of the entry type to keep them in the self.request_attributes object for later. ''' - if RequestAttributes.entry_type == 'filtering_terms': - RequestAttributes.source = filtering_terms.database - RequestAttributes.allowed_granularity = 'record' - elif RequestAttributes.entry_type == 'map': - RequestAttributes.allowed_granularity = 'record' - elif RequestAttributes.entry_type == 'configuration': - RequestAttributes.allowed_granularity = 'record' - elif RequestAttributes.entry_type == 'info': - RequestAttributes.allowed_granularity = 'record' - elif RequestAttributes.entry_type == 'service-info': - RequestAttributes.allowed_granularity = 'record' - elif RequestAttributes.entry_type == 'entry_types': - RequestAttributes.allowed_granularity = 'record' + if self.request_attributes.entry_type == 'filtering_terms': + self.request_attributes.source = filtering_terms.database + self.request_attributes.allowed_granularity = 'record' + elif self.request_attributes.entry_type == 'map': + self.request_attributes.allowed_granularity = 'record' + elif self.request_attributes.entry_type == 'configuration': + self.request_attributes.allowed_granularity = 'record' + elif self.request_attributes.entry_type == 'info': + self.request_attributes.allowed_granularity = 'record' + elif self.request_attributes.entry_type == 'service-info': + self.request_attributes.allowed_granularity = 'record' + elif self.request_attributes.entry_type == 'entry_types': + self.request_attributes.allowed_granularity = 'record' else: - endpoint_module = get_one_module_conf(RequestAttributes.entry_type) + endpoint_module = get_one_module_conf(self.request_attributes.entry_type) for entry_typeid, params in endpoint_module.items(): - RequestAttributes.entry_type_id = entry_typeid + self.request_attributes.entry_type_id = entry_typeid for param_key, param_value in params.items(): if param_key == 'max_granularity': - RequestAttributes.allowed_granularity = param_value + self.request_attributes.allowed_granularity = param_value elif param_key == 'connection': - RequestAttributes.source = param_value["name"] - if RequestAttributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: + self.request_attributes.source = param_value["name"] + if self.request_attributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: client_module=load_source_module(self, 'client') client_function_from_module = getattr(client_module, 'get_client') client = client_function_from_module() - RequestAttributes.client = client - RequestAttributes.table = param_value["table"] - if RequestAttributes.source == 'mongo': - connection = client[mongo_conf.database_name][RequestAttributes.table] - RequestAttributes.mongo_collection = connection - if RequestAttributes.entry_id != None: - if RequestAttributes.pre_entry_type == None: - RequestAttributes.function = param_value["functions"]["id_query_function_name_assigned"] + self.request_attributes.client = client + self.request_attributes.table = param_value["table"] + if self.request_attributes.source == 'mongo': + connection = client[mongo_conf.database_name][self.request_attributes.table] + self.request_attributes.mongo_collection = connection + if self.request_attributes.entry_id != None: + if self.request_attributes.pre_entry_type == None: + self.request_attributes.function = param_value["functions"]["id_query_function_name_assigned"] else: - pre_endpoint_module = get_one_module_conf(RequestAttributes.pre_entry_type) + pre_endpoint_module = get_one_module_conf(self.request_attributes.pre_entry_type) for pre_entry_typeid, preparams in pre_endpoint_module.items(): for pre_param_key, pre_param_value in preparams.items(): - if pre_param_key == 'lookups' and RequestAttributes.pre_entry_type != None: + if pre_param_key == 'lookups' and self.request_attributes.pre_entry_type != None: for lookup_param_entry_id, lookup_param_value in pre_param_value.items(): endpoint_splitted = lookup_param_value["endpoint_name"].split('/') - if endpoint_splitted[0] == RequestAttributes.pre_entry_type and endpoint_splitted[2] == RequestAttributes.entry_type: - RequestAttributes.function = lookup_param_value["connection"]["functions"]["function_name_assigned"] + if endpoint_splitted[0] == self.request_attributes.pre_entry_type and endpoint_splitted[2] == self.request_attributes.entry_type: + self.request_attributes.function = lookup_param_value["connection"]["functions"]["function_name_assigned"] else: - RequestAttributes.function = param_value["functions"]["function_name_assigned"] + self.request_attributes.function = param_value["functions"]["function_name_assigned"] elif param_key == 'allow_queries_without_filters': - if RequestAttributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: - if param_value == False and RequestAttributes.qparams.query.filters == [] and RequestAttributes.qparams.query.requestParameters == {}: - raise NoFiltersAllowed("{} endpoint doesn't allow query without filters".format(RequestAttributes.entry_type)) + if self.request_attributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: + if param_value == False and self.request_attributes.qparams.query.filters == [] and self.request_attributes.qparams.query.requestParameters == {}: + raise NoFiltersAllowed("{} endpoint doesn't allow query without filters".format(self.request_attributes.entry_type)) elif param_key == 'schema': - if RequestAttributes.qparams.meta.requestedSchemas != []: - for schema in RequestAttributes.qparams.meta.requestedSchemas: + if self.request_attributes.qparams.meta.requestedSchemas != []: + for schema in self.request_attributes.qparams.meta.requestedSchemas: if schema["schema"] == param_value["default_schema_id"]: - RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema["schema"]).model_dump()] + self.request_attributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema["schema"]).model_dump()] elif schema["schema"] in param_value["supported_schemas"]: - RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema["schema"]).model_dump()] + self.request_attributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=schema["schema"]).model_dump()] else: - RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=param_value["default_schema_id"]).model_dump()] - elif RequestAttributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: - RequestAttributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=param_value["default_schema_id"]).model_dump()] + self.request_attributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=param_value["default_schema_id"]).model_dump()] + elif self.request_attributes.entry_type not in ['filtering_terms', 'map', 'configuration', 'info', 'service-info', 'entry_types']: + self.request_attributes.returned_schema = [SchemasPerEntity(entityType=entry_typeid,schema=param_value["default_schema_id"]).model_dump()] @@ -242,7 +241,7 @@ def set_entry_type(self, request): if abs_url[:starting_endpoint] != def_uri : self.LOG.warning('configuration variable uri: {} not the same as where the beacon is hosted'.format(config.uri)) if abs_url_with_query_string.endswith('/api'): - RequestAttributes.entry_type='info' + self.request_attributes.entry_type='info' set_entry_type_configuration(self) else: path_list = abs_url[starting_endpoint:].split('/') @@ -251,19 +250,19 @@ def set_entry_type(self, request): raise WrongURIPath('the {} parameter from conf.py is not the same as the root one received in request: {}. Configure you uri accordingly.'.format(config.uri, abs_url)) if len(path_list) > 2: try: - RequestAttributes.pre_entry_type=path_list[0] - RequestAttributes.entry_type=path_list[2] + self.request_attributes.pre_entry_type=path_list[0] + self.request_attributes.entry_type=path_list[2] except Exception: raise WrongURIPath('path received is wrong, check your uri: {} from conf file to make sure is correct'.format(config.uri)) - RequestAttributes.entry_id=request.match_info.get('id', None) + self.request_attributes.entry_id=request.match_info.get('id', None) set_entry_type_configuration(self) else: try: - RequestAttributes.entry_type=path_list[0] + self.request_attributes.entry_type=path_list[0] except Exception: raise WrongURIPath('path received is wrong, check your uri: {} from conf file to make sure is correct'.format(config.uri)) - RequestAttributes.entry_id=request.match_info.get('id', None) + self.request_attributes.entry_id=request.match_info.get('id', None) set_entry_type_configuration(self) @@ -273,45 +272,45 @@ def set_response_type(self): We receive an absolute url with a host and a port, the endpoint queried and the query string. We check that the url and host match with the beacon uri in conf and then we keep the name of the endpoint checking if it matches an entry type in configuration and the internal id queried, if there is one. ''' - if RequestAttributes.qparams.query.includeResultsetResponses != 'NONE': - RequestAttributes.response_type = 'resultSet' - elif RequestAttributes.qparams.query.includeResultsetResponses == 'NONE' and RequestAttributes.allowed_granularity in ['count','record'] and RequestAttributes.qparams.query.requestedGranularity in ['count', 'record']: - RequestAttributes.response_type = 'count' + if self.request_attributes.qparams.query.includeResultsetResponses != 'NONE': + self.request_attributes.response_type = 'resultSet' + elif self.request_attributes.qparams.query.includeResultsetResponses == 'NONE' and self.request_attributes.allowed_granularity in ['count','record'] and self.request_attributes.qparams.query.requestedGranularity in ['count', 'record']: + self.request_attributes.response_type = 'count' else: - RequestAttributes.response_type = 'boolean' - if RequestAttributes.allowed_granularity == 'boolean': - RequestAttributes.returned_granularity = 'boolean' - elif RequestAttributes.allowed_granularity in ['count', 'record'] and RequestAttributes.qparams.query.requestedGranularity == 'boolean': - RequestAttributes.returned_granularity = 'boolean' - elif RequestAttributes.allowed_granularity == 'record' and RequestAttributes.qparams.query.requestedGranularity == 'record' and RequestAttributes.response_type == 'resultSet': - RequestAttributes.returned_granularity = 'record' + self.request_attributes.response_type = 'boolean' + if self.request_attributes.allowed_granularity == 'boolean': + self.request_attributes.returned_granularity = 'boolean' + elif self.request_attributes.allowed_granularity in ['count', 'record'] and self.request_attributes.qparams.query.requestedGranularity == 'boolean': + self.request_attributes.returned_granularity = 'boolean' + elif self.request_attributes.allowed_granularity == 'record' and self.request_attributes.qparams.query.requestedGranularity == 'record' and self.request_attributes.response_type == 'resultSet': + self.request_attributes.returned_granularity = 'record' else: - RequestAttributes.returned_granularity = 'count' - if RequestAttributes.qparams.meta.apiVersion in os.listdir("/beacon/framework"): - RequestAttributes.returned_apiVersion = RequestAttributes.qparams.meta.apiVersion + self.request_attributes.returned_granularity = 'count' + if self.request_attributes.qparams.meta.apiVersion in os.listdir("/beacon/framework"): + self.request_attributes.returned_apiVersion = self.request_attributes.qparams.meta.apiVersion else: - RequestAttributes.returned_apiVersion = config.api_version + self.request_attributes.returned_apiVersion = config.api_version - if RequestAttributes.entry_type == 'filtering_terms': - RequestAttributes.returned_schema = {"schema": "filtering_terms-{}".format(RequestAttributes.returned_apiVersion)} - elif RequestAttributes.entry_type == 'map': - RequestAttributes.returned_schema = {"schema": "map-{}".format(RequestAttributes.returned_apiVersion)} - elif RequestAttributes.entry_type == 'configuration': - RequestAttributes.returned_schema = {"schema": "configuration-{}".format(RequestAttributes.returned_apiVersion)} - elif RequestAttributes.entry_type == 'info': - RequestAttributes.returned_schema = {"schema": "info-{}".format(RequestAttributes.returned_apiVersion)} - elif RequestAttributes.entry_type == 'service-info': - RequestAttributes.returned_schema = {"schema": "service-info-{}".format(RequestAttributes.returned_apiVersion)} - elif RequestAttributes.entry_type == 'entry_types': - RequestAttributes.returned_schema = {"schema": "entry_types-{}".format(RequestAttributes.returned_apiVersion)} + if self.request_attributes.entry_type == 'filtering_terms': + self.request_attributes.returned_schema = {"schema": "filtering_terms-{}".format(self.request_attributes.returned_apiVersion)} + elif self.request_attributes.entry_type == 'map': + self.request_attributes.returned_schema = {"schema": "map-{}".format(self.request_attributes.returned_apiVersion)} + elif self.request_attributes.entry_type == 'configuration': + self.request_attributes.returned_schema = {"schema": "configuration-{}".format(self.request_attributes.returned_apiVersion)} + elif self.request_attributes.entry_type == 'info': + self.request_attributes.returned_schema = {"schema": "info-{}".format(self.request_attributes.returned_apiVersion)} + elif self.request_attributes.entry_type == 'service-info': + self.request_attributes.returned_schema = {"schema": "service-info-{}".format(self.request_attributes.returned_apiVersion)} + elif self.request_attributes.entry_type == 'entry_types': + self.request_attributes.returned_schema = {"schema": "entry_types-{}".format(self.request_attributes.returned_apiVersion)} @log_with_args(config.level) def set_ip(self, request): - RequestAttributes.ip=request.remote + self.request_attributes.ip=request.remote @log_with_args(config.level) def set_headers(self, request): - RequestAttributes.headers=request.headers + self.request_attributes.headers=request.headers @log_with_args(config.level) async def deconstruct_request(self, request): diff --git a/beacon/views/collection.py b/beacon/views/collection.py index 3bd35fce..b36cbae8 100644 --- a/beacon/views/collection.py +++ b/beacon/views/collection.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView @@ -33,19 +32,19 @@ async def handler(self): module_common = load_framework_module(self, "common") module_collection = load_framework_module(self, "collection") # Generate the dynamic class to be instantiated for the response that depend on the request and the collection entry types available - Collections = module_collection.make_Collections() - CollectionResponse = module_collection.make_CollectionResponse(Collections) + Collections = module_collection.make_Collections(self) + CollectionResponse = module_collection.make_CollectionResponse(self, Collections) try: # Instantiate the meta class with the attributes collected in the request - meta = module_meta.Meta(receivedRequestSummary=RequestAttributes.qparams.summary(),returnedGranularity=RequestAttributes.returned_granularity,returnedSchemas=RequestAttributes.returned_schema,testMode=RequestAttributes.qparams.query.testMode) - if RequestAttributes.qparams.query.requestedGranularity == 'record' and RequestAttributes.allowed_granularity == 'record': + meta = module_meta.Meta(receivedRequestSummary=self.request_attributes.qparams.summary(),returnedGranularity=self.request_attributes.returned_granularity,returnedSchemas=self.request_attributes.returned_schema,testMode=self.request_attributes.qparams.query.testMode) + if self.request_attributes.qparams.query.requestedGranularity == 'record' and self.request_attributes.allowed_granularity == 'record': # Instantiate the responseSummary class with the counts and yes/no found to be in the response responseSummary = module_common.ResponseSummary(exists=collectionsResponseClass.count>0,numTotalResults=collectionsResponseClass.count) # Instantiate the final response class with the meta, responseSumary end collections classes generated previously self.classResponse = CollectionResponse(meta=meta.model_dump(exclude_none=True),response=Collections(collections=collectionsResponseClass.docs).model_dump(exclude_none=True),responseSummary=responseSummary.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response response_obj = self.create_response() - elif RequestAttributes.qparams.query.requestedGranularity == 'count' and RequestAttributes.allowed_granularity in ['count', 'record']: + elif self.request_attributes.qparams.query.requestedGranularity == 'count' and self.request_attributes.allowed_granularity in ['count', 'record']: # Load the module that have the class that will serve as the count part of the response module_count = load_framework_module(self, "count") # Instantiate the responseSummary with the class CountResponseSummary filled in with the counts found for the query @@ -67,7 +66,7 @@ async def handler(self): except ValidationError as v: self.LOG.error(str(v)) # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Collection object class collected return web.Response( text=json.dumps(response_obj, default=json_default), diff --git a/beacon/views/configuration.py b/beacon/views/configuration.py index 673aeedd..a89a0341 100644 --- a/beacon/views/configuration.py +++ b/beacon/views/configuration.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView @@ -18,7 +17,7 @@ async def handler(self): # Generate the configuration class for the configuration part of the response and populate it with data from the configuration configuration = module_configuration.ConfigurationSchema.return_schema(module_configuration.ConfigurationSchema) # Generate the Meta class for the meta part of the response and populate it with data from the configuration - meta = module_meta.InformationalMeta(returnedSchemas=[RequestAttributes.returned_schema]) + meta = module_meta.InformationalMeta(returnedSchemas=[self.request_attributes.returned_schema]) # Create the response class that will allocate both Meta and Configuration parts of the response self.classResponse = module_configuration.ConfigurationResponse(meta=meta.model_dump(exclude_none=True),response=configuration.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response @@ -26,6 +25,6 @@ async def handler(self): # Catch the cases where the Configuration response is not valid against the reference schema except ValidationError as v: # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Configuration object class collected return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file diff --git a/beacon/views/endpoint.py b/beacon/views/endpoint.py index b6e7a5c6..d9ff4480 100644 --- a/beacon/views/endpoint.py +++ b/beacon/views/endpoint.py @@ -14,25 +14,27 @@ class EndpointView(web.View, CorsViewMixin): def __init__(self, request: Request): # Initialize dhe endpoint with some of the attributes that will need to be collected later on self._request = request - RequestAttributes.ip = None - RequestAttributes.headers=None - RequestAttributes.entry_type=None - RequestAttributes.entry_id=None - RequestAttributes.pre_entry_type=None - RequestAttributes.returned_schema=None - RequestAttributes.returned_apiVersion="v2.2.0" - RequestAttributes.qparams=RequestParams() - RequestAttributes.returned_granularity="boolean" + self.request_attributes = RequestAttributes() + self.request_attributes.ip = None + self.request_attributes.headers=None + self.request_attributes.entry_type=None + self.request_attributes.entry_id=None + self.request_attributes.pre_entry_type=None + self.request_attributes.returned_schema=None + self.request_attributes.returned_apiVersion="v2.2.0" + self.request_attributes.qparams=RequestParams() + self.request_attributes.returned_granularity="boolean" self.LOG=self.request.app['logger'] self._id=None self._id = generate_txid(self) async def get(self): - try: - # Decompound/validate the request and store the attributes needed in the class RequestAttributes - await deconstruct_request(self, self.request) - # Call the handler function for the view assigned to the queried endpoint - return await self.handler() + #try: + # Decompound/validate the request and store the attributes needed in the class RequestAttributes + await deconstruct_request(self, self.request) + # Call the handler function for the view assigned to the queried endpoint + return await self.handler() + """ except AppError as e: # In case a handled error occurs, return the error message and status for it response_obj = self.error_builder(e.status, e.message) @@ -41,6 +43,7 @@ async def get(self): # In case an unhandled error occurs, return a 500 and the generic error message below response_obj = self.error_builder(500, "Unexpected internal error: {}".format(e)) return web.Response(text=json_util.dumps(response_obj), status=500, content_type='application/json') + """ async def post(self): try: @@ -70,7 +73,7 @@ def error_builder(self, status, message): # Instantiate the error class with the status and the message collected during the error handling error = module_error.BeaconError(errorCode=status,errorMessage=message) # Instantiat the meta class with the attributes collected in the request - meta = module_meta.Meta(receivedRequestSummary=RequestAttributes.qparams.summary(),returnedGranularity=RequestAttributes.returned_granularity,returnedSchemas=[{"schema": "error-v2.2.0"}],testMode=RequestAttributes.qparams.query.testMode) + meta = module_meta.Meta(receivedRequestSummary=self.request_attributes.qparams.summary(),returnedGranularity=self.request_attributes.returned_granularity,returnedSchemas=[{"schema": "error-v2.2.0"}],testMode=self.request_attributes.qparams.query.testMode) # Create the response class that will allocate the Meta and error parts of the response self.classResponse = module_error.ErrorResponse(meta=meta.model_dump(exclude_none=True),error=error.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response diff --git a/beacon/views/entry_types.py b/beacon/views/entry_types.py index 50b47249..bf566937 100644 --- a/beacon/views/entry_types.py +++ b/beacon/views/entry_types.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView @@ -18,7 +17,7 @@ async def handler(self): # Generate the Entry Types class for the entry types part of the response and populate it with data from the configuration entry_types = module_entry_types.EntryTypesSchema.return_schema(module_entry_types.EntryTypesSchema) # Generate the Meta class for the meta part of the response and populate it with data from the configuration - meta = module_meta.InformationalMeta(returnedSchemas=[RequestAttributes.returned_schema]) + meta = module_meta.InformationalMeta(returnedSchemas=[self.request_attributes.returned_schema]) # Create the response class that will allocate both Meta and Entry Types parts of the response self.classResponse = module_entry_types.EntryTypesResponse(meta=meta.model_dump(exclude_none=True),response=entry_types.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response @@ -26,6 +25,6 @@ async def handler(self): # Catch the cases where the Entry Types response is not valid against the reference schema except ValidationError as v: # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Entry Types object class collected return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file diff --git a/beacon/views/filtering_terms.py b/beacon/views/filtering_terms.py index 3fffbbd7..813f76e7 100644 --- a/beacon/views/filtering_terms.py +++ b/beacon/views/filtering_terms.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView @@ -21,7 +20,7 @@ async def handler(self): # Generate the class for the filtering terms results and load it with the docs returned from the filtering terms source filteringterms = module_filtering_terms.FilteringTermsResults(filteringTerms=ftResponseClass.docs) # Generate the Meta class for the meta part of the response and populate it with data from the configuration - meta = module_meta.InformationalMeta(returnedSchemas=[RequestAttributes.returned_schema]) + meta = module_meta.InformationalMeta(returnedSchemas=[self.request_attributes.returned_schema]) # Create the response class that will allocate both Meta and Filtering Terms parts of the response self.classResponse = module_filtering_terms.FilteringTermsResponse(meta=meta.model_dump(exclude_none=True),response=filteringterms.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response @@ -29,6 +28,6 @@ async def handler(self): # Catch the cases where the Filtering Terms response is not valid against the reference schema except ValidationError as v: # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Filtering Terms object class collected return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file diff --git a/beacon/views/health.py b/beacon/views/health.py index d60e23fa..3eac6fe3 100644 --- a/beacon/views/health.py +++ b/beacon/views/health.py @@ -15,8 +15,9 @@ class HealthView(web.View, CorsViewMixin): def __init__(self, request: Request): # Initialize dhe endpoint with some of the attributes that will need to be collected later on self._request = request - RequestAttributes.ip = None - RequestAttributes.headers=None + self.request_attributes = RequestAttributes() + self.request_attributes.ip = None + self.request_attributes.headers=None self.LOG=self.request.app['logger'] self._id=None self._id = generate_txid(self) diff --git a/beacon/views/info.py b/beacon/views/info.py index a02c43ba..156d089d 100644 --- a/beacon/views/info.py +++ b/beacon/views/info.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView from pydantic import ValidationError @@ -18,7 +17,7 @@ async def handler(self): # Generate the Info class for the info part of the response and populate it with data from the configuration info = module_info.InfoBody() # Generate the Meta class for the meta part of the response and populate it with data from the configuration - meta = module_meta.InformationalMeta(returnedSchemas=[RequestAttributes.returned_schema]) + meta = module_meta.InformationalMeta(returnedSchemas=[self.request_attributes.returned_schema]) # Create the response class that will allocate both Meta and Info parts of the response self.classResponse = module_info.InfoResponse(meta=meta.model_dump(exclude_none=True),response=info.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response @@ -26,6 +25,6 @@ async def handler(self): # Catch the cases where the Info response is not valid against the reference schema except ValidationError as v: # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Info object class collected return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file diff --git a/beacon/views/map.py b/beacon/views/map.py index 9858dde8..78407af0 100644 --- a/beacon/views/map.py +++ b/beacon/views/map.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView @@ -18,7 +17,7 @@ async def handler(self): # Generate the Map class for the map part of the response and populate it with data from the configuration map = module_map.MapSchema.populate_endpoints(module_map.MapSchema) # Generate the Meta class for the meta part of the response and populate it with data from the configuration - meta = module_meta.InformationalMeta(returnedSchemas=[RequestAttributes.returned_schema]) + meta = module_meta.InformationalMeta(returnedSchemas=[self.request_attributes.returned_schema]) # Create the response class that will allocate both Meta and Map parts of the response self.classResponse = module_map.MapResponse(meta=meta.model_dump(exclude_none=True),response=map.model_dump(exclude_none=True)) # Convert the class to JSON to return it in the final stream response @@ -26,6 +25,6 @@ async def handler(self): # Catch the cases where the Map response is not valid against the reference schema except ValidationError as v: # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the Map object class collected return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file diff --git a/beacon/views/non_collection.py b/beacon/views/non_collection.py index 4e62e2ad..536941ef 100644 --- a/beacon/views/non_collection.py +++ b/beacon/views/non_collection.py @@ -3,7 +3,6 @@ import aiohttp.web as web from beacon.permissions.__main__ import query_permissions import json -from beacon.request.classes import RequestAttributes from beacon.budget.__main__ import load_module_to_insert_budget from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData @@ -38,8 +37,8 @@ async def handler(self, datasets, username, time_now): module_meta = load_framework_module(self, "meta") try: # Instantiat the meta class with the attributes collected in the request - meta = module_meta.Meta(receivedRequestSummary=RequestAttributes.qparams.summary(),returnedGranularity=RequestAttributes.returned_granularity,returnedSchemas=RequestAttributes.returned_schema,testMode=RequestAttributes.qparams.query.testMode) - if RequestAttributes.response_type == 'resultSet': + meta = module_meta.Meta(receivedRequestSummary=self.request_attributes.qparams.summary(),returnedGranularity=self.request_attributes.returned_granularity,returnedSchemas=self.request_attributes.returned_schema,testMode=self.request_attributes.qparams.query.testMode) + if self.request_attributes.response_type == 'resultSet': # Load the modules that have the classes that will serve as the resultSet and responseSummary part of the response module_resultSet = load_framework_module(self, "resultSet") module_common = load_framework_module(self, "common") @@ -47,12 +46,12 @@ async def handler(self, datasets, username, time_now): list_of_resultSets=[] new_datasets=[] # Generate the dynamic classes to be instantiated for the response that depend on the request and the entry types available - ResultsetInstance, Resultsets, ResultsetsResponse = module_resultSet.build_full_dynamic_response() + ResultsetInstance, Resultsets, ResultsetsResponse = module_resultSet.build_full_dynamic_response(self) # Instantiate the different datasets found using the ResultSetInstance class created and store them in the arrays for dataset in multipleDatasetsResponseClass.datasets_responses: try: # Create each of the ResultInstance object fed by the incoming dataset and its granularity depending on permissions and restrictions for the entry type - resultSet = ResultsetInstance.build_response_by_dataset(dataset, RequestAttributes.allowed_granularity,RequestAttributes.qparams.query.requestedGranularity) + resultSet = ResultsetInstance.build_response_by_dataset(dataset, self.request_attributes.allowed_granularity,self.request_attributes.qparams.query.requestedGranularity) # Accumulate the datasets instance of results in a list list_of_resultSets.append(resultSet) # Accumulate the dataset object class in a list @@ -62,13 +61,13 @@ async def handler(self, datasets, username, time_now): # Format the output dataset with the name of the dataset and the exception caught and log it out self.LOG.error('{} dataset is invalid: {}'.format(dataset.dataset, str(v))) # Instantiate the responseSummary and the resultSets with the datasets to be in the response - responseSummary = module_common.ResponseSummary.build_response_summary_by_dataset(module_common.ResponseSummary, new_datasets) + responseSummary = module_common.ResponseSummary.build_response_summary_by_dataset(self, new_datasets) resultSets = Resultsets.return_resultSets(list_of_resultSets) # Create the response class that will allocate the Meta, responseSumary and resultSet parts of the response self.classResponse = ResultsetsResponse.return_response(meta, resultSets, responseSummary) # Convert the class to JSON to return it in the final stream response response_obj = self.create_response() - elif RequestAttributes.response_type == 'count': + elif self.request_attributes.response_type == 'count': # Load the module that have the class that will serve as the count part of the response module_count = load_framework_module(self, "count") # Instantiate the responseSummary with the class CountResponseSummary filled in with the counts found for the query @@ -88,7 +87,7 @@ async def handler(self, datasets, username, time_now): response_obj = self.create_response() # Catch the cases where the NonCollection response is not valid against the reference schema except ValidationError as v: - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # If a time could be obtained for the moment of the query, register it for the budget count if time_now is not None: load_module_to_insert_budget(self, username, time_now) diff --git a/beacon/views/service_info.py b/beacon/views/service_info.py index cd276bd6..f2f8f4ed 100644 --- a/beacon/views/service_info.py +++ b/beacon/views/service_info.py @@ -2,7 +2,6 @@ from beacon.conf.conf_override import config import aiohttp.web as web from bson import json_util -from beacon.request.classes import RequestAttributes from pydantic import ValidationError from beacon.exceptions.exceptions import InvalidData from beacon.views.endpoint import EndpointView @@ -21,6 +20,6 @@ async def handler(self): # Catch the cases where the ServiceInfo response is not valid against the reference schema except ValidationError as v: # Stdout the information about what entry type failed about it not being according to the spec - raise InvalidData('{} templates or data are not correct'.format(RequestAttributes.entry_type)) + raise InvalidData('{} templates or data are not correct'.format(self.request_attributes.entry_type)) # Give a HTTP response with json data application and a 200 status, and the ServiceInfo object class collected return web.Response(text=json_util.dumps(response_obj), status=200, content_type='application/json') \ No newline at end of file From 6e0d0097ccde92453fec13cca2aacca51241f3a2 Mon Sep 17 00:00:00 2001 From: costero-e Date: Sat, 12 Sep 2026 13:51:26 +0200 Subject: [PATCH 33/56] fixing residual changes --- beacon/framework/validator/v2_0_0/boolean.py | 2 +- beacon/framework/validator/v2_0_0/configuration.py | 2 +- beacon/framework/validator/v2_0_0/count.py | 2 +- beacon/framework/validator/v2_0_0/entry_types.py | 2 +- beacon/views/endpoint.py | 12 +++++------- 5 files changed, 9 insertions(+), 11 deletions(-) diff --git a/beacon/framework/validator/v2_0_0/boolean.py b/beacon/framework/validator/v2_0_0/boolean.py index 83872614..b403a3ab 100644 --- a/beacon/framework/validator/v2_0_0/boolean.py +++ b/beacon/framework/validator/v2_0_0/boolean.py @@ -3,7 +3,7 @@ ) from typing import List, Optional, Dict from beacon.framework.validator.v2_0_0.meta import Meta -from common import Handover +from beacon.framework.validator.v2_0_0.common import Handover class BooleanResponseSummary(BaseModel): exists: bool diff --git a/beacon/framework/validator/v2_0_0/configuration.py b/beacon/framework/validator/v2_0_0/configuration.py index 39a45813..ee18ad09 100644 --- a/beacon/framework/validator/v2_0_0/configuration.py +++ b/beacon/framework/validator/v2_0_0/configuration.py @@ -6,7 +6,7 @@ ) from beacon.conf.conf_override import config from beacon.framework.validator.v2_0_0.meta import InformationalMeta -from entry_types import EntryTypesSchema +from beacon.framework.validator.v2_0_0.entry_types import EntryTypesSchema class SecurityAttributes(BaseModel): # Default granularity level used by the Beacon when none is explicitly requested. diff --git a/beacon/framework/validator/v2_0_0/count.py b/beacon/framework/validator/v2_0_0/count.py index 2ff5055d..d2993ba2 100644 --- a/beacon/framework/validator/v2_0_0/count.py +++ b/beacon/framework/validator/v2_0_0/count.py @@ -6,7 +6,7 @@ import math from beacon.conf import conf_override from beacon.framework.validator.v2_0_0.meta import Meta -from common import Handover +from beacon.framework.validator.v2_0_0.common import Handover class CountResponseSummary(BaseModel): """ diff --git a/beacon/framework/validator/v2_0_0/entry_types.py b/beacon/framework/validator/v2_0_0/entry_types.py index ca978080..8f6dda86 100644 --- a/beacon/framework/validator/v2_0_0/entry_types.py +++ b/beacon/framework/validator/v2_0_0/entry_types.py @@ -7,7 +7,7 @@ import re from typing import List, Optional from beacon.utils.modules import get_modules_confiles -from common import ReferenceToAnSchema +from beacon.framework.validator.v2_0_0.common import ReferenceToAnSchema from beacon.framework.validator.v2_0_0.meta import InformationalMeta class OntologyTerm(BaseModel): diff --git a/beacon/views/endpoint.py b/beacon/views/endpoint.py index d9ff4480..337bf64b 100644 --- a/beacon/views/endpoint.py +++ b/beacon/views/endpoint.py @@ -29,12 +29,11 @@ def __init__(self, request: Request): self._id = generate_txid(self) async def get(self): - #try: - # Decompound/validate the request and store the attributes needed in the class RequestAttributes - await deconstruct_request(self, self.request) - # Call the handler function for the view assigned to the queried endpoint - return await self.handler() - """ + try: + # Decompound/validate the request and store the attributes needed in the class RequestAttributes + await deconstruct_request(self, self.request) + # Call the handler function for the view assigned to the queried endpoint + return await self.handler() except AppError as e: # In case a handled error occurs, return the error message and status for it response_obj = self.error_builder(e.status, e.message) @@ -43,7 +42,6 @@ async def get(self): # In case an unhandled error occurs, return a 500 and the generic error message below response_obj = self.error_builder(500, "Unexpected internal error: {}".format(e)) return web.Response(text=json_util.dumps(response_obj), status=500, content_type='application/json') - """ async def post(self): try: From 9b85af9499db1d87127c627d029a372c6c0306e0 Mon Sep 17 00:00:00 2001 From: costero-e Date: Sat, 12 Sep 2026 14:42:44 +0200 Subject: [PATCH 34/56] fixing permissions with request_attributes from unit tests --- beacon/auth/tests.py | 2 +- beacon/permissions/__main__.py | 2 +- beacon/permissions/plugins.py | 4 ++-- beacon/permissions/tests.py | 32 ++++++++++++++++++-------------- beacon/permissions/utils.py | 4 ++-- 5 files changed, 24 insertions(+), 20 deletions(-) diff --git a/beacon/auth/tests.py b/beacon/auth/tests.py index 90b67017..8f33604b 100644 --- a/beacon/auth/tests.py +++ b/beacon/auth/tests.py @@ -13,7 +13,7 @@ import beacon.conf.conf_override as conf_override # for keycloak, create aud in mappers, with custom, aud and beacon for audience -mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.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.U_5ukvmexZBQOVczz3B-NFsPzhpuVpkrNve7RYgns3L7rCVbkvDScX7sf3zcLoYfT8ndY-fwlrIjz5e_P0MpCbT9IkkSZlDgZJWFfJ706CKkyHil0X2cwKLTNlhTeGeBeP5YsgHByl7rqzfsBcfj-pIWBDXJ0LmaqlcOZapjKcKroKx4dZ-bKxdO3anZ3ejW9GcWwooaKsSRdJ0DvMGDk1jCd2a9jzbYG1OvQ-eReQNREkM0FubM4wL2sZyzB71wpRT5pEIqOOju8ZGjpU0WaCTMsiiyk8nCK7VtfkSxNLF-CUeshfJbl84MXNQ6pOJQ5JxalU_ear9PyfILZyDuig' +mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.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.ognNPMqZYlQCXmj0ZXu_IodasLHCWJtBHX3ElWEFyakbAkHsOzLxGwrFkRyrmwB1jyg_lXcXt7E9z2mB7FzNfCpzdhIXBqBQf_v9OFjZv0-maVIItjRzmHLF5jnbPwBj6jQVzwkvCHOAqFYx0wBTviDWsVYSgNOuPmZcCj3KKrzDrJzUUSZ82DoyGjc9aTfMJQFFb0Sw-d2-ubN4XlFjwvGreJB3OG0n_eUkbvmFDwxWnR5OKcb7r0IYr15RigaKaqFiurNWC9vsttDZPL2LC5LuesMj6QMA3xkCMVReazj28-bFkOsGIgr9QSGx-OpJ4pKqubP4X7MtIx3TN7xpFw' mock_access_token_false = 'public' #audit --> TODO: get very specific information that we are interested in saving and keeping it (example: what individuals were returned in response) diff --git a/beacon/permissions/__main__.py b/beacon/permissions/__main__.py index 15767130..32890605 100644 --- a/beacon/permissions/__main__.py +++ b/beacon/permissions/__main__.py @@ -73,7 +73,7 @@ async def permission(self): # Get the usernq, and the list of datasets that the user has permissions for from visas. username, list_visa_datasets = await authorization(self) # Get the datasets that the user has permissions for from the datasets permissions conf file in a list of classes for the datasets. - datasets_permissions = await PermissionsProxy.get_permissions(self, username=username, requested_datasets=requested_datasets, testMode=self.request_attributes.qparams.query.testMode) + datasets_permissions = await PermissionsProxy.get_permissions(self, username=username, requested_datasets=requested_datasets, testMode=self.request_attributes.qparams.query.testMode, entry_type_id=self.request_attributes.entry_type_id) # Return the time to be inserted in the budget in case the budget doesn't return an exception for the query. time_now = check_budget(self, username) # Add as well in the list of dataset classes, the dataset classes that have permissions for the query coming from visas. diff --git a/beacon/permissions/plugins.py b/beacon/permissions/plugins.py index 7b71e055..a971dd90 100644 --- a/beacon/permissions/plugins.py +++ b/beacon/permissions/plugins.py @@ -25,7 +25,7 @@ class DummyPermissions(Permissions): async def initialize(self): pass - async def get_permissions(self, username, requested_datasets=None, testMode=False): + async def get_permissions(self, username, requested_datasets=None, testMode=False, entry_type_id=None): # Initialize the list of datasets that will be returned depending on the permissions. datasets = [] try: @@ -59,7 +59,7 @@ async def get_permissions(self, username, requested_datasets=None, testMode=Fals default_granularity, granularity_exceptions = return_granularity_and_exceptions(self, security_level_dict, username, default_granularity, granularity_exceptions) # If there is any restriction apply it to the max granularity to return. if granularity_exceptions != None: - default_granularity=return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity) + default_granularity=return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity, entry_type_id) # If there is a default granularity, return it instantiating initially the datasets with their name and the default granularity. if default_granularity != None: datasetInstance = SingleDatasetResponse(dataset=dataset, granularity=default_granularity) diff --git a/beacon/permissions/tests.py b/beacon/permissions/tests.py index cbca5c3e..f861087e 100644 --- a/beacon/permissions/tests.py +++ b/beacon/permissions/tests.py @@ -191,13 +191,14 @@ def test_authZ_authorization(self): loop.run_until_complete(client.start_server()) - MagicClass = MagicMock(_id='hohoho') + async def test_authorization(): # Attach Authorization header with mocked access token headers = {'Authorization': 'Bearer ' + mock_access_token} - RequestAttributes.headers = headers - + request_attributes = RequestAttributes() + request_attributes.headers=headers + MagicClass = MagicMock(_id='hohoho', request_attributes=request_attributes) # Resolve username and visa dataset context username, list_visa_datasets = await authorization( self=MagicClass @@ -221,7 +222,6 @@ def check_granularity_returned_is_correct(self): async def test_granularity_returned(): # Individual-level granularity - RequestAttributes.entry_type_id = 'individual' returned_granularity = return_found_granularity_in_exceptions( self=MagicClass, granularity_exceptions=[ @@ -229,12 +229,13 @@ async def test_granularity_returned(): {"biosample": "count"}, {"analysis": "boolean"} ], - default_granularity=None + default_granularity=None, + entry_type_id='individual' ) assert returned_granularity == 'record' # Biosample-level granularity - RequestAttributes.entry_type_id = 'biosample' + returned_granularity = return_found_granularity_in_exceptions( self=MagicClass, granularity_exceptions=[ @@ -242,12 +243,12 @@ async def test_granularity_returned(): {"biosample": "count"}, {"analysis": "boolean"} ], - default_granularity=None + default_granularity=None, + entry_type_id='biosample' ) assert returned_granularity == 'count' # Analysis-level granularity - RequestAttributes.entry_type_id = 'analysis' returned_granularity = return_found_granularity_in_exceptions( self=MagicClass, granularity_exceptions=[ @@ -255,7 +256,8 @@ async def test_granularity_returned(): {"biosample": "count"}, {"analysis": "boolean"} ], - default_granularity=None + default_granularity=None, + entry_type_id='analysis' ) assert returned_granularity == 'boolean' @@ -283,7 +285,7 @@ async def test_controlled_granularity_returned(): if dataset == 'test2': # --- Individual level --- - RequestAttributes.entry_type_id = 'individual' + returned_granularity, exceptions = return_granularity_and_exceptions( self=MagicClass, security_level_dict=security_level_dict, @@ -295,12 +297,12 @@ async def test_controlled_granularity_returned(): returned_granularity = return_found_granularity_in_exceptions( self=MagicClass, granularity_exceptions=exceptions, - default_granularity=returned_granularity + default_granularity=returned_granularity, + entry_type_id='individual' ) assert returned_granularity == 'record' # --- Biosample level --- - RequestAttributes.entry_type_id = 'biosample' returned_granularity, exceptions = return_granularity_and_exceptions( self=MagicClass, security_level_dict=security_level_dict, @@ -312,7 +314,8 @@ async def test_controlled_granularity_returned(): returned_granularity = return_found_granularity_in_exceptions( self=MagicClass, granularity_exceptions=exceptions, - default_granularity=returned_granularity + default_granularity=returned_granularity, + entry_type_id='biosample' ) assert returned_granularity == 'count' @@ -329,7 +332,8 @@ async def test_controlled_granularity_returned(): returned_granularity = return_found_granularity_in_exceptions( self=MagicClass, granularity_exceptions=exceptions, - default_granularity=returned_granularity + default_granularity=returned_granularity, + entry_type_id='analysis' ) assert returned_granularity == 'boolean' diff --git a/beacon/permissions/utils.py b/beacon/permissions/utils.py index 9caefd71..0bf1db58 100644 --- a/beacon/permissions/utils.py +++ b/beacon/permissions/utils.py @@ -1,11 +1,11 @@ -def return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity): +def return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity, request_attr_entry_type_id,): """Method to get the granularity needed to be returned for a specific permissions case""" for granularity_exception in granularity_exceptions: # Loop over all the exceptions that are handed in and take the one that belongs to the entry type that is being requested for entry_type_id, entry_type_granularity in granularity_exception.items(): - if entry_type_id == self.request_attributes.entry_type_id: + if entry_type_id == request_attr_entry_type_id: # Assign the entry type granularity and return it back default_granularity = entry_type_granularity return default_granularity From d8cba09e841b39c714e65923fc93b37a9698a93b Mon Sep 17 00:00:00 2001 From: github-actions Date: Sat, 12 Sep 2026 12:45:41 +0000 Subject: [PATCH 35/56] Update API version to v2.3.1 --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index 492eabc9..93518aa7 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.3.0 +api_version: v2.3.1 From 466476d4287ef721468fa4763b577f7e54b9cd5f Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 14 Sep 2026 16:43:20 +0200 Subject: [PATCH 36/56] adding logs config to have rotating files --- beacon/conf/conf_default.py | 7 +- beacon/logs/logs.log | 915 ------------------------------------ beacon/logs/logs.py | 13 +- docker-compose.yml | 2 +- 4 files changed, 18 insertions(+), 919 deletions(-) delete mode 100644 beacon/logs/logs.log diff --git a/beacon/conf/conf_default.py b/beacon/conf/conf_default.py index 1cdfe33c..3bb6c118 100644 --- a/beacon/conf/conf_default.py +++ b/beacon/conf/conf_default.py @@ -8,8 +8,13 @@ except Exception as e: raise FileNotFound('There are issues with the api_version.yml file. Check if it can be opened or if has any content') +# logs level=logging.DEBUG -log_file=None +log_file='/beacon/logs/log_files/logs.log' # path needs to be pointing to a file inside a volumed dir, preferably /beacon/logs/log_files, e.g. /beacon/logs/log_files/logs.log +log_retention_days = 7 # days which the file will be kept until it is destroyed +log_rotating_interval = 'midnight' # S, M, H, D, W0, W1, W2, W3, W4, W5, W6, midnight + +# Beacon generic conf beacon_id = 'org.ega-archive.beacon-ri-demo' # ID of the Beacon beacon_name = 'Beacon Production Implementation demo' # Name of the Beacon service api_version = 'v2.2.0' # Version of the Beacon implementation diff --git a/beacon/logs/logs.log b/beacon/logs/logs.log deleted file mode 100644 index d161770b..00000000 --- a/beacon/logs/logs.log +++ /dev/null @@ -1,915 +0,0 @@ -DEBUG - 2024-07-24 13:43:03,224 - 808a47e8 - permission((,),{}) - initial call -DEBUG - 2024-07-24 13:43:03,224 - 808a47e8 - permission((,),{}) - 0.0010287761688232422 - returned .permission at 0xffff8ecd46d0> -DEBUG - 2024-07-24 13:43:03,225 - 808a47e8 - authorization((,),{}) - initial call -DEBUG - 2024-07-24 13:43:03,225 - 808a47e8 - authorization((,),{}) - 0.00032806396484375 - returned -DEBUG - 2024-07-24 13:43:03,227 - 808a47e8 - genomicVariations((, {'username': 'public', 'datasets': ['CINECA_dataset', 'coadread_tcga_pan_can_atlas_2018', 'rd-connect_dataset', 'CINECA_synthetic_cohort_EUROPE_UK1', 'AV_Dataset']}),{}) - initial call -DEBUG - 2024-07-24 13:43:03,227 - 808a47e8 - genomicVariations((, {'username': 'public', 'datasets': ['CINECA_dataset', 'coadread_tcga_pan_can_atlas_2018', 'rd-connect_dataset', 'CINECA_synthetic_cohort_EUROPE_UK1', 'AV_Dataset']}),{}) - 0.00038743019104003906 - returned -DEBUG - 2024-07-24 13:43:05,271 - [{'_id': ObjectId('669fcb1ad4ff9b9c09af20c1'), 'createDateTime': '2021-12-29T20:33:40Z', 'dataUseConditions': {'duoDataUse': [{'id': 'DUO:0000019,DUO:00000020', 'label': 'publication required,publication required', 'version': '7-1-19,7-1-19'}]}, 'description': 'Please note: This synthetic data set (with cohort participants / subjects marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk This dataset (CINECA_synthetic_cohort_EUROPE_UK1) consists of 2521 samples which have genetic data based on 1000 Genomes data (https://www.nature.com/articles/nature15393), and synthetic subject attributes and phenotypic data derived from UKBiobank (https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001779). These data were initially derived using the TOFU tool (https://github.com/spiros/tofu), which generates randomly generated values based on the UKBiobank data dictionary. Categorical values were randomly generated based on the data dictionary, continuous variables generated based on the distribution of values reported by the UK Biobank showcase, and date / time values were random. Additionally we split the phenotypes and attributes into 4 main classes - general, cancer, diabetes mellitus, and cardiac. We assigned the general attributes to all the samples, and the cardiac / diabetes mellitus / cancer attributes to a proportion of the total samples. Once the initial set of phenotypes and attributes were generated, the data data was checked for consistency and where possible dependent attributes were calculated from the independent variables generated by TOFU. For example, BMI was calculated from height and weight data, and age at death generated by date of death and date of birth. These data were then loaded to the development instance of Biosamples (https://www.ebi.ac.uk/biosamples/) which accessioned each of the samples. The genetic data are derived from the 1000 Genomes Phase 3 release (https://www.internationalgenome.org/category/phase-3/). The genotype data consists of a single joint call vcf files with call genotypes for all 2504 samples, plus bed, bim, fam, and nosex files generated via plink for these samples and genotypes. The genotype data has had a variety of errors introduced to mimic real data and as a test for quality control pipelines. These include gender mismatches, ethnic background mislabelling and low call rates for a randomly chosen subset of sample data as well as deviations from Hardy Weinberg equilibrium and low call rates for a random selection of variants. Additionally 40 samples have raw genetic data available in the form of both bam and cram files, including unmapped data. The gender of the samples in the 1000 genomes data has been matched to the synthetic phenotypic data generated for these samples. The genetic data was then linked to the synthetic data in BioSamples, and submitted to EGA.","externalUrl":\xa0"https://ega-archive.org/datasets/EGAD00001006673/', 'externalUrl': 'https://ega-archive.org/datasets/EGAD00001006673/', 'id': 'CINECA_synthetic_cohort_EUROPE_UK1', 'info': {'beacon': {'contact': 'manuel.rueda@crg.eu', 'mapping': 'ManuelRueda', 'version': 'v2.0'}, 'dataset': {'derived': [{'EGA': {'contact': 'helpdesk@ega-archive.org', 'externalUrl': 'https://ega-archive.org/datasets/EGAD00001006673', 'license': {'$ref': '#/dataUseConditions/duoDataUse'}}}, {'BioSamples': {'contact': 'biosamples@ebi.ac.uk', 'externalUrl': 'https://www.ebi.ac.uk/biosamples', 'license': 'CreativeCommonsLicence(CC-BY)'}}], 'origin': [{'CINECAprojectEU': {'contact': 'cthomas@ebi.ac.uk', 'externalUrl': 'https://www.cineca-project.eu/cineca-synthetic-dataset', 'license': 'CreativeCommonsLicence(CC-BY)', 'managers': 'ColineThomas,IsuruLiyanageandDylanSpalding'}}, {'1000Genomes': {'externalUrl': 'https://www.internationalgenome.org/category/phase-3', 'license': 'CCBY-NC-SA3.0', 'version': 'v5aphase3VCF'}}]}}, 'name': 'CINECA_synthetic_cohort_EUROPE_UK1', 'updateDateTime': '2021-12-29T20:33:40Z', 'version': 'v1.0'}] -DEBUG - 2024-07-24 13:43:05,272 - -DEBUG - 2024-07-24 15:33:32,671 - 13af8ad6 - permission((,),{}) - initial call -DEBUG - 2024-07-24 15:33:32,672 - 13af8ad6 - permission((,),{}) - 0.0011172294616699219 - returned .permission at 0xffffa3e34350> -DEBUG - 2024-07-24 15:33:32,672 - 13af8ad6 - authorization((,),{}) - initial call -DEBUG - 2024-07-24 15:33:32,673 - 13af8ad6 - authorization((,),{}) - 0.0006797313690185547 - returned -DEBUG - 2024-07-24 15:33:32,687 - [{'_id': ObjectId('669fcb1ad4ff9b9c09af20c1'), 'createDateTime': '2021-12-29T20:33:40Z', 'dataUseConditions': {'duoDataUse': [{'id': 'DUO:0000019,DUO:00000020', 'label': 'publication required,publication required', 'version': '7-1-19,7-1-19'}]}, 'description': 'Please note: This synthetic data set (with cohort participants / subjects marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk This dataset (CINECA_synthetic_cohort_EUROPE_UK1) consists of 2521 samples which have genetic data based on 1000 Genomes data (https://www.nature.com/articles/nature15393), and synthetic subject attributes and phenotypic data derived from UKBiobank (https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001779). These data were initially derived using the TOFU tool (https://github.com/spiros/tofu), which generates randomly generated values based on the UKBiobank data dictionary. Categorical values were randomly generated based on the data dictionary, continuous variables generated based on the distribution of values reported by the UK Biobank showcase, and date / time values were random. Additionally we split the phenotypes and attributes into 4 main classes - general, cancer, diabetes mellitus, and cardiac. We assigned the general attributes to all the samples, and the cardiac / diabetes mellitus / cancer attributes to a proportion of the total samples. Once the initial set of phenotypes and attributes were generated, the data data was checked for consistency and where possible dependent attributes were calculated from the independent variables generated by TOFU. For example, BMI was calculated from height and weight data, and age at death generated by date of death and date of birth. These data were then loaded to the development instance of Biosamples (https://www.ebi.ac.uk/biosamples/) which accessioned each of the samples. The genetic data are derived from the 1000 Genomes Phase 3 release (https://www.internationalgenome.org/category/phase-3/). The genotype data consists of a single joint call vcf files with call genotypes for all 2504 samples, plus bed, bim, fam, and nosex files generated via plink for these samples and genotypes. The genotype data has had a variety of errors introduced to mimic real data and as a test for quality control pipelines. These include gender mismatches, ethnic background mislabelling and low call rates for a randomly chosen subset of sample data as well as deviations from Hardy Weinberg equilibrium and low call rates for a random selection of variants. Additionally 40 samples have raw genetic data available in the form of both bam and cram files, including unmapped data. The gender of the samples in the 1000 genomes data has been matched to the synthetic phenotypic data generated for these samples. The genetic data was then linked to the synthetic data in BioSamples, and submitted to EGA.","externalUrl":\xa0"https://ega-archive.org/datasets/EGAD00001006673/', 'externalUrl': 'https://ega-archive.org/datasets/EGAD00001006673/', 'id': 'CINECA_synthetic_cohort_EUROPE_UK1', 'info': {'beacon': {'contact': 'manuel.rueda@crg.eu', 'mapping': 'ManuelRueda', 'version': 'v2.0'}, 'dataset': {'derived': [{'EGA': {'contact': 'helpdesk@ega-archive.org', 'externalUrl': 'https://ega-archive.org/datasets/EGAD00001006673', 'license': {'$ref': '#/dataUseConditions/duoDataUse'}}}, {'BioSamples': {'contact': 'biosamples@ebi.ac.uk', 'externalUrl': 'https://www.ebi.ac.uk/biosamples', 'license': 'CreativeCommonsLicence(CC-BY)'}}], 'origin': [{'CINECAprojectEU': {'contact': 'cthomas@ebi.ac.uk', 'externalUrl': 'https://www.cineca-project.eu/cineca-synthetic-dataset', 'license': 'CreativeCommonsLicence(CC-BY)', 'managers': 'ColineThomas,IsuruLiyanageandDylanSpalding'}}, {'1000Genomes': {'externalUrl': 'https://www.internationalgenome.org/category/phase-3', 'license': 'CCBY-NC-SA3.0', 'version': 'v5aphase3VCF'}}]}}, 'name': 'CINECA_synthetic_cohort_EUROPE_UK1', 'updateDateTime': '2021-12-29T20:33:40Z', 'version': 'v1.0'}] -DEBUG - 2024-07-24 15:33:32,688 - -DEBUG - 2024-07-24 15:33:32,689 - 13af8ad6 - genomicVariations((, ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - initial call -DEBUG - 2024-07-24 15:33:32,690 - 13af8ad6 - genomicVariations((, ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - 0.000965118408203125 - returned -DEBUG - 2024-09-18 08:53:18,496 - db693ee2 - generate_txid((),{}) - initial call -DEBUG - 2024-09-18 08:53:18,497 - db693ee2 - generate_txid((),{}) - 0.0011801719665527344 - returned db693ee2 -DEBUG - 2024-09-18 08:53:18,497 - db693ee2 - info((,),{}) - initial call -DEBUG - 2024-09-18 08:53:18,497 - db693ee2 - info((,),{}) - 0.00029015541076660156 - returned -DEBUG - 2024-09-18 08:53:18,498 - db693ee2 - info_builder((),{}) - initial call -DEBUG - 2024-09-18 08:53:18,498 - db693ee2 - info_builder((),{}) - 0.0002923011779785156 - returned -DEBUG - 2024-09-18 08:53:18,498 - db693ee2 - build_beacon_info_response((),{}) - initial call -DEBUG - 2024-09-18 08:53:18,498 - db693ee2 - build_info_meta((None,),{}) - initial call -DEBUG - 2024-09-18 08:53:18,499 - db693ee2 - build_info_meta((None,),{}) - 0.0002288818359375 - returned {'beaconId': 'org.ega-archive.beacon-ri-demo', 'apiVersion': 'v2.0.0', 'returnedSchemas': []} -DEBUG - 2024-09-18 08:53:18,499 - db693ee2 - build_beacon_info_response((),{}) - 0.0006921291351318359 - returned {'meta': {'beaconId': 'org.ega-archive.beacon-ri-demo', 'apiVersion': 'v2.0.0', 'returnedSchemas': []}, 'response': {'id': 'org.ega-archive.beacon-ri-demo', 'name': 'Beacon Reference Implementation demo', 'apiVersion': 'v2.0.0', 'environment': 'test', 'organization': {'id': 'EGA', 'name': 'European Genome-Phenome Archive (EGA)', 'description': 'The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.', 'address': 'C/ Dr. Aiguader, 88PRBB Building08003 Barcelona, Spain', 'welcomeUrl': 'https://ega-archive.org/', 'contactUrl': 'mailto:beacon.ega@crg.eu', 'logoUrl': 'https://legacy.ega-archive.org/images/logo.png'}, 'description': "This Beacon is based on synthetic data hosted at the EGA. The dataset contains 2504 samples including genetic data based on 1K Genomes data, and 76 individual attributes and phenotypic data derived from UKBiobank.", 'version': 'v2.0.0', 'welcomeUrl': 'https://beacon.ega-archive.org/', 'alternativeUrl': 'https://beacon.ega-archive.org/api', 'createDateTime': '2021-11-29T12:00:00.000000', 'updateDateTime': ''}} -DEBUG - 2024-09-27 10:31:17,730 - d31c32b8 - generate_txid((),{}) - initial call -DEBUG - 2024-09-27 10:31:17,731 - d31c32b8 - generate_txid((),{}) - 0.0010521411895751953 - returned d31c32b8 -DEBUG - 2024-09-27 10:31:17,732 - d31c32b8 - permission((,),{}) - initial call -DEBUG - 2024-09-27 10:31:17,733 - d31c32b8 - permission((,),{}) - 0.0004911422729492188 - returned .permission at 0xffff83734040> -DEBUG - 2024-09-27 10:31:17,733 - d31c32b8 - check_request_content_type((,),{}) - initial call -DEBUG - 2024-09-27 10:31:17,733 - d31c32b8 - check_request_content_type((,),{}) - 0.00034999847412109375 - returned -DEBUG - 2024-09-27 10:31:17,734 - d31c32b8 - authorization((,),{}) - initial call -DEBUG - 2024-09-27 10:31:17,734 - d31c32b8 - authorization((,),{}) - 0.0005855560302734375 - returned -DEBUG - 2024-09-27 10:31:17,737 - d31c32b8 - get_datasets_list((, ['rd-connect_dataset', 'coadread_tcga_pan_can_atlas_2018', 'CINECA_synthetic_cohort_EUROPE_UK1', 'CINECA_dataset']),{}) - initial call -DEBUG - 2024-09-27 10:31:17,737 - d31c32b8 - get_datasets_list((, ['rd-connect_dataset', 'coadread_tcga_pan_can_atlas_2018', 'CINECA_synthetic_cohort_EUROPE_UK1', 'CINECA_dataset']),{}) - 0.0004987716674804688 - returned -DEBUG - 2024-09-27 10:31:17,738 - d31c32b8 - get_qparams((,),{}) - initial call -DEBUG - 2024-09-27 10:31:17,738 - d31c32b8 - get_qparams((,),{}) - 0.000274658203125 - returned -DEBUG - 2024-09-27 10:31:17,739 - d31c32b8 - get_list_of_datasets - initial call -DEBUG - 2024-09-27 10:31:17,739 - d31c32b8 - get_datasets - initial call -DEBUG - 2024-09-27 10:31:17,739 - d31c32b8 - get_datasets - 0.00044274330139160156 - returned -DEBUG - 2024-09-27 10:31:17,753 - d31c32b8 - get_list_of_datasets - 0.014242887496948242 - returned [{'_id': ObjectId('66f405cbd209459029c09db7'), 'createDateTime': '2021-12-29T20:33:40Z', 'dataUseConditions': {'duoDataUse': [{'id': 'DUO:0000019,DUO:00000020', 'label': 'publication required,publication required', 'version': '7-1-19,7-1-19'}]}, 'description': 'Please note: This synthetic data set (with cohort participants / subjects marked with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or results. The purpose of this dataset is to aid development of technical implementations for cohort data discovery, harmonization, access, and federated analysis. In support of FAIRness in data sharing, this dataset is made freely available under the Creative Commons Licence (CC-BY). Please ensure this preamble is included with this dataset and that the CINECA project (funding: EC H2020 grant 825775) is acknowledged. For any questions please contact isuru@ebi.ac.uk or cthomas@ebi.ac.uk This dataset (CINECA_synthetic_cohort_EUROPE_UK1) consists of 2521 samples which have genetic data based on 1000 Genomes data (https://www.nature.com/articles/nature15393), and synthetic subject attributes and phenotypic data derived from UKBiobank (https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001779). These data were initially derived using the TOFU tool (https://github.com/spiros/tofu), which generates randomly generated values based on the UKBiobank data dictionary. Categorical values were randomly generated based on the data dictionary, continuous variables generated based on the distribution of values reported by the UK Biobank showcase, and date / time values were random. Additionally we split the phenotypes and attributes into 4 main classes - general, cancer, diabetes mellitus, and cardiac. We assigned the general attributes to all the samples, and the cardiac / diabetes mellitus / cancer attributes to a proportion of the total samples. Once the initial set of phenotypes and attributes were generated, the data data was checked for consistency and where possible dependent attributes were calculated from the independent variables generated by TOFU. For example, BMI was calculated from height and weight data, and age at death generated by date of death and date of birth. These data were then loaded to the development instance of Biosamples (https://www.ebi.ac.uk/biosamples/) which accessioned each of the samples. The genetic data are derived from the 1000 Genomes Phase 3 release (https://www.internationalgenome.org/category/phase-3/). The genotype data consists of a single joint call vcf files with call genotypes for all 2504 samples, plus bed, bim, fam, and nosex files generated via plink for these samples and genotypes. The genotype data has had a variety of errors introduced to mimic real data and as a test for quality control pipelines. These include gender mismatches, ethnic background mislabelling and low call rates for a randomly chosen subset of sample data as well as deviations from Hardy Weinberg equilibrium and low call rates for a random selection of variants. Additionally 40 samples have raw genetic data available in the form of both bam and cram files, including unmapped data. The gender of the samples in the 1000 genomes data has been matched to the synthetic phenotypic data generated for these samples. The genetic data was then linked to the synthetic data in BioSamples, and submitted to EGA.","externalUrl":\xa0"https://ega-archive.org/datasets/EGAD00001006673/', 'externalUrl': 'https://ega-archive.org/datasets/EGAD00001006673/', 'id': 'CINECA_synthetic_cohort_EUROPE_UK1', 'info': {'beacon': {'contact': 'manuel.rueda@crg.eu', 'mapping': 'ManuelRueda', 'version': 'v2.0'}, 'dataset': {'derived': [{'EGA': {'contact': 'helpdesk@ega-archive.org', 'externalUrl': 'https://ega-archive.org/datasets/EGAD00001006673', 'license': {'$ref': '#/dataUseConditions/duoDataUse'}}}, {'BioSamples': {'contact': 'biosamples@ebi.ac.uk', 'externalUrl': 'https://www.ebi.ac.uk/biosamples', 'license': 'CreativeCommonsLicence(CC-BY)'}}], 'origin': [{'CINECAprojectEU': {'contact': 'cthomas@ebi.ac.uk', 'externalUrl': 'https://www.cineca-project.eu/cineca-synthetic-dataset', 'license': 'CreativeCommonsLicence(CC-BY)', 'managers': 'ColineThomas,IsuruLiyanageandDylanSpalding'}}, {'1000Genomes': {'externalUrl': 'https://www.internationalgenome.org/category/phase-3', 'license': 'CCBY-NC-SA3.0', 'version': 'v5aphase3VCF'}}]}}, 'name': 'CINECA_synthetic_cohort_EUROPE_UK1', 'updateDateTime': '2021-12-29T20:33:40Z', 'version': 'v1.0'}] -DEBUG - 2024-09-27 10:31:17,754 - d31c32b8 - resultset((, ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - initial call -DEBUG - 2024-09-27 10:31:17,754 - d31c32b8 - resultset((, ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - 0.0005125999450683594 - returned -DEBUG - 2024-09-27 10:31:17,755 - d31c32b8 - builder((, ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), 'individuals'),{}) - initial call -DEBUG - 2024-09-27 10:31:17,755 - d31c32b8 - builder((, ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), 'individuals'),{}) - 0.0005052089691162109 - returned -DEBUG - 2024-09-27 10:31:17,756 - d31c32b8 - execute_function(('individuals', ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), None),{}) - initial call -DEBUG - 2024-09-27 10:31:17,756 - d31c32b8 - execute_function(('individuals', ['CINECA_synthetic_cohort_EUROPE_UK1'], RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), None),{}) - 0.0003287792205810547 - returned -DEBUG - 2024-09-27 10:31:17,757 - d31c32b8 - get_individuals((None, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), 'CINECA_synthetic_cohort_EUROPE_UK1'),{}) - initial call -DEBUG - 2024-09-27 10:31:17,757 - d31c32b8 - apply_request_parameters(({}, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - initial call -DEBUG - 2024-09-27 10:31:17,757 - d31c32b8 - apply_request_parameters(({}, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - 0.0003056526184082031 - returned ({}, False) -DEBUG - 2024-09-27 10:31:17,758 - d31c32b8 - apply_filters(({}, [], 'individuals', {}),{}) - initial call -DEBUG - 2024-09-27 10:31:17,758 - d31c32b8 - apply_filters(({}, [], 'individuals', {}),{}) - 0.0002892017364501953 - returned {} -DEBUG - 2024-09-27 10:31:17,853 - d31c32b8 - get_docs_by_response_type - initial call -DEBUG - 2024-09-27 10:31:17,853 - d31c32b8 - get_count - initial call -DEBUG - 2024-09-27 10:31:17,863 - d31c32b8 - get_count - 0.009831905364990234 - returned 2504 -DEBUG - 2024-09-27 10:31:17,863 - d31c32b8 - get_documents - initial call -DEBUG - 2024-09-27 10:31:17,864 - d31c32b8 - get_documents - 0.00024008750915527344 - returned -DEBUG - 2024-09-27 10:31:17,864 - d31c32b8 - get_docs_by_response_type - 0.011170625686645508 - returned (0, 2504, ) -DEBUG - 2024-09-27 10:31:17,864 - d31c32b8 - get_individuals((None, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), 'CINECA_synthetic_cohort_EUROPE_UK1'),{}) - 0.10755515098571777 - returned (, 0, 2504, , 'CINECA_synthetic_cohort_EUROPE_UK1') -DEBUG - 2024-09-27 10:31:17,865 - d31c32b8 - build_beacon_boolean_response_by_dataset(({'CINECA_synthetic_cohort_EUROPE_UK1': }, {'CINECA_synthetic_cohort_EUROPE_UK1': 2504}, 2504, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), ),{}) - initial call -DEBUG - 2024-09-27 10:31:17,865 - d31c32b8 - build_meta((RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), , ),{}) - initial call -DEBUG - 2024-09-27 10:31:17,865 - d31c32b8 - build_meta((RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), , ),{}) - 0.0002624988555908203 - returned {'beaconId': 'org.ega-archive.beacon-ri-demo', 'apiVersion': 'v2.0.0', 'returnedGranularity': , 'receivedRequestSummary': {'apiVersion': 'v2.0.0', 'requestedSchemas': [], 'filters': [], 'requestParameters': {}, 'includeResultsetResponses': , 'pagination': {'skip': 0, 'limit': 10}, 'requestedGranularity': , 'testMode': False}, 'returnedSchemas': [{'entityType': 'individual', 'schema': 'beacon-individual-v2.0.0'}]} -DEBUG - 2024-09-27 10:31:17,865 - d31c32b8 - build_response_summary_by_dataset((True, 2504, {'CINECA_synthetic_cohort_EUROPE_UK1': }),{}) - initial call -DEBUG - 2024-09-27 10:31:17,865 - d31c32b8 - build_response_summary_by_dataset((True, 2504, {'CINECA_synthetic_cohort_EUROPE_UK1': }),{}) - 0.0001480579376220703 - returned {'exists': True, 'numTotalResults': 2504} -DEBUG - 2024-09-27 10:31:17,866 - d31c32b8 - build_response_by_dataset(({'CINECA_synthetic_cohort_EUROPE_UK1': }, {'CINECA_synthetic_cohort_EUROPE_UK1': 2504}, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - initial call -DEBUG - 2024-09-27 10:31:17,866 - d31c32b8 - build_response_by_dataset(({'CINECA_synthetic_cohort_EUROPE_UK1': }, {'CINECA_synthetic_cohort_EUROPE_UK1': 2504}, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None))),{}) - 0.00016069412231445312 - returned [{'id': 'CINECA_synthetic_cohort_EUROPE_UK1', 'setType': 'dataset', 'exists': True, 'resultsCount': 2504, 'results': }] -DEBUG - 2024-09-27 10:31:17,866 - d31c32b8 - build_beacon_boolean_response_by_dataset(({'CINECA_synthetic_cohort_EUROPE_UK1': }, {'CINECA_synthetic_cohort_EUROPE_UK1': 2504}, 2504, RequestParams(meta=RequestMeta(requested_schemas=[], api_version='v2.0.0'), query=RequestQuery(filters=[], include_resultset_responses=, pagination=Pagination(skip=0, limit=10), request_parameters={}, test_mode=False, requested_granularity=, scope=None)), ),{}) - 0.001344442367553711 - returned {'meta': {'beaconId': 'org.ega-archive.beacon-ri-demo', 'apiVersion': 'v2.0.0', 'returnedGranularity': , 'receivedRequestSummary': {'apiVersion': 'v2.0.0', 'requestedSchemas': [], 'filters': [], 'requestParameters': {}, 'includeResultsetResponses': , 'pagination': {'skip': 0, 'limit': 10}, 'requestedGranularity': , 'testMode': False}, 'returnedSchemas': [{'entityType': 'individual', 'schema': 'beacon-individual-v2.0.0'}]}, 'responseSummary': {'exists': True, 'numTotalResults': 2504}, 'response': {'resultSets': [{'id': 'CINECA_synthetic_cohort_EUROPE_UK1', 'setType': 'dataset', 'exists': True, 'resultsCount': 2504, 'results': }]}, 'beaconHandovers': [{'note': 'Description of the handover', 'url': 'Link for the handover', 'handoverType': {'id': 'NCIT:C189151', 'label': 'Study Data Repository'}}]} -ERROR - 2024-10-04 07:49:39,917 - test - There was an exception in fetch_idp -DEBUG - 2024-10-04 15:26:35,845 - fbae90fa - generate_txid - initial call -DEBUG - 2024-10-04 15:26:35,845 - fbae90fa - generate_txid- 0.000667572021484375 - returned OK -DEBUG - 2024-10-04 15:26:35,846 - fbae90fa - get_qparams - initial call -DEBUG - 2024-10-04 15:26:35,846 - fbae90fa - get_qparams - 0.0003006458282470703 - returned OK -DEBUG - 2024-10-04 15:26:35,846 - fbae90fa - permission - initial call -DEBUG - 2024-10-04 15:26:35,847 - fbae90fa - permission - 0.00017881393432617188 - returned OK -DEBUG - 2024-10-04 15:26:35,847 - fbae90fa - authorization - initial call -DEBUG - 2024-10-04 15:26:35,847 - fbae90fa - authorization - 0.00018596649169921875 - returned OK -DEBUG - 2024-10-04 15:26:35,849 - fbae90fa - get_datasets_list - initial call -DEBUG - 2024-10-04 15:26:35,849 - fbae90fa - get_datasets_list - 0.00024771690368652344 - returned OK -DEBUG - 2024-10-04 15:26:35,849 - fbae90fa - get_list_of_datasets - initial call -DEBUG - 2024-10-04 15:26:35,850 - fbae90fa - get_datasets - initial call -DEBUG - 2024-10-04 15:26:35,850 - fbae90fa - get_datasets - 0.0006628036499023438 - returned OK -DEBUG - 2024-10-04 15:26:35,864 - fbae90fa - get_list_of_datasets - 0.015046119689941406 - returned OK -DEBUG - 2024-10-04 15:26:35,865 - fbae90fa - resultset - initial call -DEBUG - 2024-10-04 15:26:35,865 - fbae90fa - resultset - 0.00011610984802246094 - returned OK -DEBUG - 2024-10-04 15:26:35,865 - fbae90fa - builder - initial call -DEBUG - 2024-10-04 15:26:35,865 - fbae90fa - builder - 7.390975952148438e-05 - returned OK -DEBUG - 2024-10-04 15:26:35,872 - fbae90fa - execute_function - initial call -DEBUG - 2024-10-04 15:26:35,872 - fbae90fa - execute_function - 0.000171661376953125 - returned OK -DEBUG - 2024-10-04 15:26:35,872 - fbae90fa - get_individuals - initial call -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - apply_request_parameters - initial call -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - get_individuals - initial call -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - apply_request_parameters - 0.00016927719116210938 - returned OK -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - apply_request_parameters - initial call -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - apply_filters - initial call -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - apply_request_parameters - 0.0001456737518310547 - returned OK -DEBUG - 2024-10-04 15:26:35,873 - fbae90fa - apply_filters - 0.0001671314239501953 - returned OK -DEBUG - 2024-10-04 15:26:35,874 - fbae90fa - apply_filters - initial call -DEBUG - 2024-10-04 15:26:35,874 - fbae90fa - get_docs_by_response_type - initial call -DEBUG - 2024-10-04 15:26:35,874 - fbae90fa - apply_filters - 0.0002751350402832031 - returned OK -DEBUG - 2024-10-04 15:26:35,874 - fbae90fa - get_count - initial call -DEBUG - 2024-10-04 15:26:35,874 - fbae90fa - get_docs_by_response_type - initial call -DEBUG - 2024-10-04 15:26:35,875 - fbae90fa - get_count - initial call -DEBUG - 2024-10-04 15:26:35,876 - fbae90fa - get_count - 0.001621246337890625 - returned OK -DEBUG - 2024-10-04 15:26:35,876 - fbae90fa - get_documents - initial call -DEBUG - 2024-10-04 15:26:35,876 - fbae90fa - get_documents - 0.0003542900085449219 - returned OK -DEBUG - 2024-10-04 15:26:35,878 - fbae90fa - get_docs_by_response_type - 0.0038993358612060547 - returned OK -DEBUG - 2024-10-04 15:26:35,878 - fbae90fa - get_individuals - 0.005435466766357422 - returned OK -DEBUG - 2024-10-04 15:26:35,880 - fbae90fa - get_count - 0.005815267562866211 - returned OK -DEBUG - 2024-10-04 15:26:35,881 - fbae90fa - get_documents - initial call -DEBUG - 2024-10-04 15:26:35,882 - fbae90fa - get_documents - 0.0017001628875732422 - returned OK -DEBUG - 2024-10-04 15:26:35,884 - fbae90fa - get_docs_by_response_type - 0.010338783264160156 - returned OK -DEBUG - 2024-10-04 15:26:35,885 - fbae90fa - get_individuals - 0.012140750885009766 - returned OK -DEBUG - 2024-10-04 15:26:35,885 - fbae90fa - build_beacon_boolean_response_by_dataset - initial call -DEBUG - 2024-10-04 15:26:35,886 - fbae90fa - build_meta - initial call -DEBUG - 2024-10-04 15:26:35,886 - fbae90fa - build_meta - 0.0002834796905517578 - returned OK -DEBUG - 2024-10-04 15:26:35,886 - fbae90fa - build_response_summary_by_dataset - initial call -DEBUG - 2024-10-04 15:26:35,886 - fbae90fa - build_response_summary_by_dataset - 0.0001690387725830078 - returned OK -DEBUG - 2024-10-04 15:26:35,887 - fbae90fa - build_response_by_dataset - initial call -DEBUG - 2024-10-04 15:26:35,887 - fbae90fa - build_response_by_dataset - 0.00020813941955566406 - returned OK -DEBUG - 2024-10-04 15:26:35,887 - fbae90fa - build_beacon_boolean_response_by_dataset - 0.0014164447784423828 - returned OK -DEBUG - 2024-10-09 16:13:57,992 - a9abb5f7 - generate_txid - initial call -DEBUG - 2024-10-09 16:13:57,992 - a9abb5f7 - generate_txid- 0.0005514621734619141 - returned OK -DEBUG - 2024-10-09 16:13:57,993 - a9abb5f7 - get_qparams - initial call -DEBUG - 2024-10-09 16:13:57,993 - a9abb5f7 - get_qparams - 0.00019621849060058594 - returned OK -DEBUG - 2024-10-09 16:13:57,993 - a9abb5f7 - permission - initial call -DEBUG - 2024-10-09 16:13:57,993 - a9abb5f7 - permission - 0.0002510547637939453 - returned OK -DEBUG - 2024-10-09 16:13:57,994 - a9abb5f7 - authorization - initial call -DEBUG - 2024-10-09 16:13:57,994 - a9abb5f7 - authorization - 0.00017333030700683594 - returned OK -DEBUG - 2024-10-09 16:13:57,997 - a9abb5f7 - get_datasets_list - initial call -DEBUG - 2024-10-09 16:13:57,997 - a9abb5f7 - get_datasets_list - 0.00023484230041503906 - returned OK -DEBUG - 2024-10-09 16:13:57,997 - a9abb5f7 - get_list_of_datasets - initial call -DEBUG - 2024-10-09 16:13:57,997 - a9abb5f7 - get_datasets - initial call -DEBUG - 2024-10-09 16:13:57,998 - a9abb5f7 - get_datasets - 0.0004937648773193359 - returned OK -DEBUG - 2024-10-09 16:14:05,411 - a9abb5f7 - get_list_of_datasets - 7.413520812988281 - returned OK -DEBUG - 2024-10-09 16:14:05,411 - a9abb5f7 - resultset - initial call -DEBUG - 2024-10-09 16:14:05,411 - a9abb5f7 - resultset - 0.00023365020751953125 - returned OK -DEBUG - 2024-10-09 16:14:05,412 - a9abb5f7 - builder - initial call -DEBUG - 2024-10-09 16:14:05,412 - a9abb5f7 - builder - 0.000141143798828125 - returned OK -DEBUG - 2024-10-09 16:14:05,425 - a9abb5f7 - execute_function - initial call -DEBUG - 2024-10-09 16:14:05,425 - a9abb5f7 - execute_function - 0.0002124309539794922 - returned OK -DEBUG - 2024-10-09 16:14:05,426 - a9abb5f7 - get_variants - initial call -DEBUG - 2024-10-09 16:14:05,426 - a9abb5f7 - apply_request_parameters - initial call -DEBUG - 2024-10-09 16:14:05,426 - a9abb5f7 - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:05,426 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_value - 0.00013446807861328125 - returned OK -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_operator - 0.00016164779663085938 - returned OK -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_value - 0.00015091896057128906 - returned OK -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,427 - a9abb5f7 - format_operator - 0.00012946128845214844 - returned OK -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - apply_alphanumeric_filter - 0.0012536048889160156 - returned OK -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - format_value - 0.00013136863708496094 - returned OK -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - format_operator - 0.0001270771026611328 - returned OK -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,428 - a9abb5f7 - format_value - 0.0001304149627685547 - returned OK -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - format_operator - 0.0001239776611328125 - returned OK -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - apply_alphanumeric_filter - 0.001239776611328125 - returned OK -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - generate_position_filter_start - initial call -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - generate_position_filter_start - 0.00012040138244628906 - returned OK -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:05,429 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_value - 0.00014853477478027344 - returned OK -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_operator - 0.00013184547424316406 - returned OK -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_value - 0.0001266002655029297 - returned OK -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - format_operator - 0.00011968612670898438 - returned OK -DEBUG - 2024-10-09 16:14:05,430 - a9abb5f7 - apply_alphanumeric_filter - 0.0011301040649414062 - returned OK -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - format_value - initial call -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - format_value - 0.00014090538024902344 - returned OK -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - format_operator - initial call -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - format_operator - 0.00011968612670898438 - returned OK -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - apply_alphanumeric_filter - 0.0006256103515625 - returned OK -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - apply_request_parameters - 0.005240440368652344 - returned OK -DEBUG - 2024-10-09 16:14:05,431 - a9abb5f7 - apply_filters - initial call -DEBUG - 2024-10-09 16:14:05,432 - a9abb5f7 - apply_filters - 0.000133514404296875 - returned OK -DEBUG - 2024-10-09 16:14:05,432 - a9abb5f7 - get_docs_by_response_type - initial call -DEBUG - 2024-10-09 16:14:05,432 - a9abb5f7 - get_count - initial call -DEBUG - 2024-10-09 16:14:05,433 - a9abb5f7 - get_count - 0.0010590553283691406 - returned OK -DEBUG - 2024-10-09 16:14:05,433 - a9abb5f7 - get_documents - initial call -DEBUG - 2024-10-09 16:14:05,433 - a9abb5f7 - get_documents - 0.0001666545867919922 - returned OK -DEBUG - 2024-10-09 16:14:05,439 - a9abb5f7 - get_docs_by_response_type - 0.007301807403564453 - returned OK -DEBUG - 2024-10-09 16:14:05,439 - a9abb5f7 - get_variants - 0.013436555862426758 - returned OK -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_beacon_boolean_response_by_dataset - initial call -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_meta - initial call -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_meta - 0.00018215179443359375 - returned OK -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_response_summary_by_dataset - initial call -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_response_summary_by_dataset - 0.00011491775512695312 - returned OK -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_response_by_dataset - initial call -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_response_by_dataset - 0.0001277923583984375 - returned OK -DEBUG - 2024-10-09 16:14:05,440 - a9abb5f7 - build_beacon_boolean_response_by_dataset - 0.0009200572967529297 - returned OK -DEBUG - 2024-10-09 16:14:14,850 - b567038c - generate_txid - initial call -DEBUG - 2024-10-09 16:14:14,850 - b567038c - generate_txid- 0.00041604042053222656 - returned OK -DEBUG - 2024-10-09 16:14:14,850 - b567038c - get_qparams - initial call -DEBUG - 2024-10-09 16:14:14,851 - b567038c - get_qparams - 0.0001952648162841797 - returned OK -DEBUG - 2024-10-09 16:14:14,851 - b567038c - permission - initial call -DEBUG - 2024-10-09 16:14:14,851 - b567038c - permission - 0.00020694732666015625 - returned OK -DEBUG - 2024-10-09 16:14:14,851 - b567038c - authorization - initial call -DEBUG - 2024-10-09 16:14:14,852 - b567038c - authorization - 0.00025844573974609375 - returned OK -DEBUG - 2024-10-09 16:14:14,853 - b567038c - get_datasets_list - initial call -DEBUG - 2024-10-09 16:14:14,854 - b567038c - get_datasets_list - 0.0003006458282470703 - returned OK -DEBUG - 2024-10-09 16:14:14,854 - b567038c - get_list_of_datasets - initial call -DEBUG - 2024-10-09 16:14:14,854 - b567038c - get_datasets - initial call -DEBUG - 2024-10-09 16:14:14,854 - b567038c - get_datasets - 0.00028204917907714844 - returned OK -DEBUG - 2024-10-09 16:14:14,856 - b567038c - get_list_of_datasets - 0.0019156932830810547 - returned OK -DEBUG - 2024-10-09 16:14:14,856 - b567038c - resultset - initial call -DEBUG - 2024-10-09 16:14:14,856 - b567038c - resultset - 0.00018477439880371094 - returned OK -DEBUG - 2024-10-09 16:14:14,857 - b567038c - builder - initial call -DEBUG - 2024-10-09 16:14:14,857 - b567038c - builder - 0.00023627281188964844 - returned OK -DEBUG - 2024-10-09 16:14:14,857 - b567038c - execute_function - initial call -DEBUG - 2024-10-09 16:14:14,857 - b567038c - execute_function - 0.0001857280731201172 - returned OK -DEBUG - 2024-10-09 16:14:14,858 - b567038c - get_variants - initial call -DEBUG - 2024-10-09 16:14:14,858 - b567038c - apply_request_parameters - initial call -DEBUG - 2024-10-09 16:14:14,858 - b567038c - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:14,859 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,859 - b567038c - format_value - 0.00035071372985839844 - returned OK -DEBUG - 2024-10-09 16:14:14,859 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,859 - b567038c - format_operator - 0.00020885467529296875 - returned OK -DEBUG - 2024-10-09 16:14:14,860 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,860 - b567038c - format_value - 0.0001957416534423828 - returned OK -DEBUG - 2024-10-09 16:14:14,860 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,860 - b567038c - format_operator - 0.0001850128173828125 - returned OK -DEBUG - 2024-10-09 16:14:14,860 - b567038c - apply_alphanumeric_filter - 0.002054929733276367 - returned OK -DEBUG - 2024-10-09 16:14:14,861 - b567038c - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:14,861 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,861 - b567038c - format_value - 0.00017833709716796875 - returned OK -DEBUG - 2024-10-09 16:14:14,861 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,862 - b567038c - format_operator - 0.00019407272338867188 - returned OK -DEBUG - 2024-10-09 16:14:14,862 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,862 - b567038c - format_value - 0.00016641616821289062 - returned OK -DEBUG - 2024-10-09 16:14:14,862 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,862 - b567038c - format_operator - 0.0001609325408935547 - returned OK -DEBUG - 2024-10-09 16:14:14,862 - b567038c - apply_alphanumeric_filter - 0.001749277114868164 - returned OK -DEBUG - 2024-10-09 16:14:14,863 - b567038c - generate_position_filter_start - initial call -DEBUG - 2024-10-09 16:14:14,863 - b567038c - generate_position_filter_start - 0.00020122528076171875 - returned OK -DEBUG - 2024-10-09 16:14:14,863 - b567038c - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:14,863 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,864 - b567038c - format_value - 0.0003139972686767578 - returned OK -DEBUG - 2024-10-09 16:14:14,864 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,864 - b567038c - format_operator - 0.0003972053527832031 - returned OK -DEBUG - 2024-10-09 16:14:14,865 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,865 - b567038c - format_value - 0.0003142356872558594 - returned OK -DEBUG - 2024-10-09 16:14:14,865 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,866 - b567038c - format_operator - 0.00025200843811035156 - returned OK -DEBUG - 2024-10-09 16:14:14,866 - b567038c - apply_alphanumeric_filter - 0.0028488636016845703 - returned OK -DEBUG - 2024-10-09 16:14:14,866 - b567038c - apply_alphanumeric_filter - initial call -DEBUG - 2024-10-09 16:14:14,866 - b567038c - format_value - initial call -DEBUG - 2024-10-09 16:14:14,866 - b567038c - format_value - 0.0001666545867919922 - returned OK -DEBUG - 2024-10-09 16:14:14,867 - b567038c - format_operator - initial call -DEBUG - 2024-10-09 16:14:14,867 - b567038c - format_operator - 0.000202178955078125 - returned OK -DEBUG - 2024-10-09 16:14:14,867 - b567038c - apply_alphanumeric_filter - 0.0009324550628662109 - returned OK -DEBUG - 2024-10-09 16:14:14,867 - b567038c - apply_request_parameters - 0.009212493896484375 - returned OK -DEBUG - 2024-10-09 16:14:14,867 - b567038c - apply_filters - initial call -DEBUG - 2024-10-09 16:14:14,868 - b567038c - apply_filters - 0.000179290771484375 - returned OK -DEBUG - 2024-10-09 16:14:14,868 - b567038c - get_docs_by_response_type - initial call -DEBUG - 2024-10-09 16:14:14,868 - b567038c - get_count - initial call -DEBUG - 2024-10-09 16:14:14,869 - b567038c - get_count - 0.0012814998626708984 - returned OK -DEBUG - 2024-10-09 16:14:14,869 - b567038c - get_documents - initial call -DEBUG - 2024-10-09 16:14:14,870 - b567038c - get_documents - 0.00022363662719726562 - returned OK -DEBUG - 2024-10-09 16:14:14,876 - b567038c - get_docs_by_response_type - 0.008071184158325195 - returned OK -DEBUG - 2024-10-09 16:14:14,876 - b567038c - get_variants - 0.018425464630126953 - returned OK -DEBUG - 2024-10-09 16:14:14,877 - b567038c - build_beacon_boolean_response_by_dataset - initial call -DEBUG - 2024-10-09 16:14:14,877 - b567038c - build_meta - initial call -DEBUG - 2024-10-09 16:14:14,878 - b567038c - build_meta - 0.0004093647003173828 - returned OK -DEBUG - 2024-10-09 16:14:14,878 - b567038c - build_response_summary_by_dataset - initial call -DEBUG - 2024-10-09 16:14:14,878 - b567038c - build_response_summary_by_dataset - 0.00017523765563964844 - returned OK -DEBUG - 2024-10-09 16:14:14,879 - b567038c - build_response_by_dataset - initial call -DEBUG - 2024-10-09 16:14:14,879 - b567038c - build_response_by_dataset - 0.0003180503845214844 - returned OK -DEBUG - 2024-10-09 16:14:14,879 - b567038c - build_beacon_boolean_response_by_dataset - 0.002157926559448242 - returned OK -DEBUG - 2024-10-11 14:12:08,602 - a82e92f7 - generate_txid - initial call -DEBUG - 2024-10-11 14:12:08,603 - a82e92f7 - generate_txid- 0.0009777545928955078 - returned OK -DEBUG - 2024-10-11 14:12:08,603 - a82e92f7 - map - initial call -DEBUG - 2024-10-11 14:12:08,603 - a82e92f7 - map - 0.0001957416534423828 - returned OK -DEBUG - 2024-10-11 14:12:08,603 - a82e92f7 - map_builder - initial call -DEBUG - 2024-10-11 14:12:08,603 - a82e92f7 - map_builder - 0.00014638900756835938 - returned OK -DEBUG - 2024-10-11 14:12:08,604 - a82e92f7 - build_map - initial call -DEBUG - 2024-10-11 14:12:08,604 - a82e92f7 - build_map - 0.00019860267639160156 - returned OK -DEBUG - 2024-11-02 23:14:10,350 - 2b5711a4 - generate_txid - initial call -DEBUG - 2024-11-02 23:14:10,351 - 2b5711a4 - generate_txid- 0.0008347034454345703 - returned OK -DEBUG - 2024-11-02 23:14:10,351 - 2b5711a4 - get_qparams - initial call -DEBUG - 2024-11-02 23:14:10,352 - 2b5711a4 - get_qparams - 0.00016951560974121094 - returned OK -DEBUG - 2024-11-02 23:14:10,352 - 2b5711a4 - collection - initial call -DEBUG - 2024-11-02 23:14:10,352 - 2b5711a4 - collection - 0.00015807151794433594 - returned OK -DEBUG - 2024-11-02 23:14:10,352 - 2b5711a4 - collection_builder - initial call -DEBUG - 2024-11-02 23:14:10,352 - 2b5711a4 - collection_builder - 0.0001533031463623047 - returned OK -DEBUG - 2024-11-02 23:14:10,368 - 2b5711a4 - execute_collection_function - initial call -DEBUG - 2024-11-02 23:14:10,369 - 2b5711a4 - execute_collection_function - 0.0003871917724609375 - returned OK -DEBUG - 2024-11-02 23:14:10,369 - 2b5711a4 - get_dataset_with_id - initial call -DEBUG - 2024-11-02 23:14:10,369 - 2b5711a4 - apply_request_parameters - initial call -DEBUG - 2024-11-02 23:14:10,369 - 2b5711a4 - apply_request_parameters - 0.00019049644470214844 - returned OK -DEBUG - 2024-11-02 23:14:10,370 - 2b5711a4 - query_id - initial call -DEBUG - 2024-11-02 23:14:10,370 - 2b5711a4 - query_id - 0.0002315044403076172 - returned OK -DEBUG - 2024-11-02 23:14:10,370 - 2b5711a4 - get_count - initial call -DEBUG - 2024-11-02 23:14:15,393 - 2b5711a4 - get_count - 5.023151397705078 - returned OK -DEBUG - 2024-11-02 23:14:15,394 - 2b5711a4 - get_documents - initial call -DEBUG - 2024-11-02 23:14:15,394 - 2b5711a4 - get_documents - 0.00032806396484375 - returned OK -DEBUG - 2024-11-02 23:14:15,395 - 2b5711a4 - get_dataset_with_id - 5.026194334030151 - returned OK -DEBUG - 2024-11-02 23:14:15,395 - 2b5711a4 - build_beacon_collection_response - initial call -DEBUG - 2024-11-02 23:14:15,396 - 2b5711a4 - build_meta - initial call -DEBUG - 2024-11-02 23:14:15,396 - 2b5711a4 - build_meta - 0.0003445148468017578 - returned OK -DEBUG - 2024-11-02 23:14:15,396 - 2b5711a4 - build_response_summary - initial call -DEBUG - 2024-11-02 23:14:15,396 - 2b5711a4 - build_response_summary - 0.0002200603485107422 - returned OK -DEBUG - 2024-11-02 23:14:15,397 - 2b5711a4 - build_beacon_collection_response - 0.0012629032135009766 - returned OK -DEBUG - 2024-11-02 23:15:07,134 - e6c89a2a - generate_txid - initial call -DEBUG - 2024-11-02 23:15:07,135 - e6c89a2a - generate_txid- 0.0005137920379638672 - returned OK -DEBUG - 2024-11-02 23:15:07,135 - e6c89a2a - get_qparams - initial call -DEBUG - 2024-11-02 23:15:07,135 - e6c89a2a - get_qparams - 0.0001609325408935547 - returned OK -DEBUG - 2024-11-02 23:15:07,136 - e6c89a2a - permission - initial call -DEBUG - 2024-11-02 23:15:07,136 - e6c89a2a - permission - 0.0001704692840576172 - returned OK -DEBUG - 2024-11-02 23:15:07,136 - e6c89a2a - authorization - initial call -DEBUG - 2024-11-02 23:15:07,136 - e6c89a2a - authorization - 0.00014257431030273438 - returned OK -DEBUG - 2024-11-02 23:15:07,138 - e6c89a2a - get_datasets_list - initial call -DEBUG - 2024-11-02 23:15:07,138 - e6c89a2a - get_datasets_list - 0.00029540061950683594 - returned OK -DEBUG - 2024-11-02 23:15:07,139 - e6c89a2a - get_list_of_datasets - initial call -DEBUG - 2024-11-02 23:15:07,139 - e6c89a2a - get_datasets - initial call -DEBUG - 2024-11-02 23:15:07,139 - e6c89a2a - get_datasets - 0.0002617835998535156 - returned OK -DEBUG - 2024-11-02 23:15:07,140 - e6c89a2a - get_list_of_datasets - 0.001798391342163086 - returned OK -DEBUG - 2024-11-02 23:15:07,141 - e6c89a2a - resultset - initial call -DEBUG - 2024-11-02 23:15:07,141 - e6c89a2a - resultset - 0.0003333091735839844 - returned OK -DEBUG - 2024-11-02 23:15:07,141 - e6c89a2a - builder - initial call -DEBUG - 2024-11-02 23:15:07,142 - e6c89a2a - builder - 0.0002307891845703125 - returned OK -DEBUG - 2024-11-02 23:15:07,142 - e6c89a2a - execute_function - initial call -DEBUG - 2024-11-02 23:15:07,142 - e6c89a2a - execute_function - 0.00015211105346679688 - returned OK -DEBUG - 2024-11-02 23:15:07,143 - e6c89a2a - get_variants - initial call -DEBUG - 2024-11-02 23:15:07,143 - e6c89a2a - apply_request_parameters - initial call -DEBUG - 2024-11-02 23:15:07,143 - e6c89a2a - apply_request_parameters - 0.0002009868621826172 - returned OK -DEBUG - 2024-11-02 23:15:07,143 - e6c89a2a - apply_filters - initial call -DEBUG - 2024-11-02 23:15:07,143 - e6c89a2a - apply_filters - 0.00023317337036132812 - returned OK -DEBUG - 2024-11-02 23:15:07,144 - e6c89a2a - get_docs_by_response_type - initial call -DEBUG - 2024-11-02 23:15:07,144 - e6c89a2a - get_count - initial call -DEBUG - 2024-11-02 23:15:07,145 - e6c89a2a - get_count - 0.0009770393371582031 - returned OK -DEBUG - 2024-11-02 23:15:07,145 - e6c89a2a - get_documents - initial call -DEBUG - 2024-11-02 23:15:07,145 - e6c89a2a - get_documents - 0.00020503997802734375 - returned OK -DEBUG - 2024-11-02 23:15:07,147 - e6c89a2a - get_docs_by_response_type - 0.0037505626678466797 - returned OK -DEBUG - 2024-11-02 23:15:07,148 - e6c89a2a - get_variants - 0.005189418792724609 - returned OK -DEBUG - 2024-11-02 23:15:07,148 - e6c89a2a - build_beacon_record_response_by_dataset - initial call -DEBUG - 2024-11-02 23:15:07,148 - e6c89a2a - build_meta - initial call -DEBUG - 2024-11-02 23:15:07,149 - e6c89a2a - build_meta - 0.00018310546875 - returned OK -DEBUG - 2024-11-02 23:15:07,149 - e6c89a2a - build_response_summary_by_dataset - initial call -DEBUG - 2024-11-02 23:15:07,149 - e6c89a2a - build_response_summary_by_dataset - 0.0001399517059326172 - returned OK -DEBUG - 2024-11-02 23:15:07,149 - e6c89a2a - build_response_by_dataset - initial call -DEBUG - 2024-11-02 23:15:07,149 - e6c89a2a - build_response_by_dataset - 0.00012993812561035156 - returned OK -DEBUG - 2024-11-02 23:15:07,149 - e6c89a2a - build_beacon_record_response_by_dataset - 0.0010402202606201172 - returned OK -DEBUG - 2024-11-02 23:15:34,033 - c1614990 - generate_txid - initial call -DEBUG - 2024-11-02 23:15:34,033 - c1614990 - generate_txid- 0.0003554821014404297 - returned OK -DEBUG - 2024-11-02 23:15:34,034 - c1614990 - get_qparams - initial call -DEBUG - 2024-11-02 23:15:34,034 - c1614990 - get_qparams - 0.0004374980926513672 - returned OK -DEBUG - 2024-11-02 23:15:34,034 - c1614990 - collection - initial call -DEBUG - 2024-11-02 23:15:34,035 - c1614990 - collection - 0.00019288063049316406 - returned OK -DEBUG - 2024-11-02 23:15:34,035 - c1614990 - collection_builder - initial call -DEBUG - 2024-11-02 23:15:34,035 - c1614990 - collection_builder - 0.0002868175506591797 - returned OK -DEBUG - 2024-11-02 23:15:34,036 - c1614990 - execute_collection_function - initial call -DEBUG - 2024-11-02 23:15:34,036 - c1614990 - execute_collection_function - 0.000225067138671875 - returned OK -DEBUG - 2024-11-02 23:15:34,036 - c1614990 - get_full_datasets - initial call -DEBUG - 2024-11-02 23:15:34,037 - c1614990 - get_count - initial call -DEBUG - 2024-11-02 23:15:34,038 - c1614990 - get_count - 0.0013496875762939453 - returned OK -DEBUG - 2024-11-02 23:15:34,039 - c1614990 - get_full_datasets - 0.0029144287109375 - returned OK -DEBUG - 2024-11-02 23:15:34,039 - c1614990 - build_beacon_collection_response - initial call -DEBUG - 2024-11-02 23:15:34,039 - c1614990 - build_meta - initial call -DEBUG - 2024-11-02 23:15:34,040 - c1614990 - build_meta - 0.00023055076599121094 - returned OK -DEBUG - 2024-11-02 23:15:34,040 - c1614990 - build_response_summary - initial call -DEBUG - 2024-11-02 23:15:34,040 - c1614990 - build_response_summary - 0.00021505355834960938 - returned OK -DEBUG - 2024-11-02 23:15:34,040 - c1614990 - build_beacon_collection_response - 0.0011241436004638672 - returned OK -DEBUG - 2024-11-02 23:15:37,148 - 7cb819a9 - generate_txid - initial call -DEBUG - 2024-11-02 23:15:37,149 - 7cb819a9 - generate_txid- 0.00046563148498535156 - returned OK -DEBUG - 2024-11-02 23:15:37,149 - 7cb819a9 - get_qparams - initial call -DEBUG - 2024-11-02 23:15:37,149 - 7cb819a9 - get_qparams - 0.00018095970153808594 - returned OK -DEBUG - 2024-11-02 23:15:37,149 - 7cb819a9 - collection - initial call -DEBUG - 2024-11-02 23:15:37,150 - 7cb819a9 - collection - 0.00020360946655273438 - returned OK -DEBUG - 2024-11-02 23:15:37,150 - 7cb819a9 - collection_builder - initial call -DEBUG - 2024-11-02 23:15:37,150 - 7cb819a9 - collection_builder - 0.0001499652862548828 - returned OK -DEBUG - 2024-11-02 23:15:37,150 - 7cb819a9 - execute_collection_function - initial call -DEBUG - 2024-11-02 23:15:37,151 - 7cb819a9 - execute_collection_function - 0.0002968311309814453 - returned OK -DEBUG - 2024-11-02 23:15:37,151 - 7cb819a9 - get_dataset_with_id - initial call -DEBUG - 2024-11-02 23:15:37,151 - 7cb819a9 - apply_request_parameters - initial call -DEBUG - 2024-11-02 23:15:37,151 - 7cb819a9 - apply_request_parameters - 0.0001742839813232422 - returned OK -DEBUG - 2024-11-02 23:15:37,152 - 7cb819a9 - query_id - initial call -DEBUG - 2024-11-02 23:15:37,152 - 7cb819a9 - query_id - 0.00016260147094726562 - returned OK -DEBUG - 2024-11-02 23:15:37,152 - 7cb819a9 - get_count - initial call -DEBUG - 2024-11-02 23:15:37,154 - 7cb819a9 - get_count - 0.0016632080078125 - returned OK -DEBUG - 2024-11-02 23:15:37,154 - 7cb819a9 - get_documents - initial call -DEBUG - 2024-11-02 23:15:37,154 - 7cb819a9 - get_documents - 0.00020766258239746094 - returned OK -DEBUG - 2024-11-02 23:15:37,156 - 7cb819a9 - get_dataset_with_id - 0.004978656768798828 - returned OK -DEBUG - 2024-11-02 23:15:37,156 - 7cb819a9 - build_beacon_collection_response - initial call -DEBUG - 2024-11-02 23:15:37,156 - 7cb819a9 - build_meta - initial call -DEBUG - 2024-11-02 23:15:37,157 - 7cb819a9 - build_meta - 0.0002796649932861328 - returned OK -DEBUG - 2024-11-02 23:15:37,157 - 7cb819a9 - build_response_summary - initial call -DEBUG - 2024-11-02 23:15:37,157 - 7cb819a9 - build_response_summary - 0.0002930164337158203 - returned OK -DEBUG - 2024-11-02 23:15:37,158 - 7cb819a9 - build_beacon_collection_response - 0.0012044906616210938 - returned OK -DEBUG - 2024-11-02 23:15:38,954 - 2a4d8471 - generate_txid - initial call -DEBUG - 2024-11-02 23:15:38,954 - 2a4d8471 - generate_txid- 0.0004572868347167969 - returned OK -DEBUG - 2024-11-02 23:15:38,955 - 2a4d8471 - get_qparams - initial call -DEBUG - 2024-11-02 23:15:38,955 - 2a4d8471 - get_qparams - 0.0001971721649169922 - returned OK -DEBUG - 2024-11-02 23:15:38,955 - 2a4d8471 - collection - initial call -DEBUG - 2024-11-02 23:15:38,955 - 2a4d8471 - collection - 0.00017333030700683594 - returned OK -DEBUG - 2024-11-02 23:15:38,956 - 2a4d8471 - collection_builder - initial call -DEBUG - 2024-11-02 23:15:38,956 - 2a4d8471 - collection_builder - 0.00017762184143066406 - returned OK -DEBUG - 2024-11-02 23:15:38,956 - 2a4d8471 - execute_collection_function - initial call -DEBUG - 2024-11-02 23:15:38,956 - 2a4d8471 - execute_collection_function - 0.00013828277587890625 - returned OK -DEBUG - 2024-11-02 23:15:38,956 - 2a4d8471 - get_dataset_with_id - initial call -DEBUG - 2024-11-02 23:15:38,956 - 2a4d8471 - apply_request_parameters - initial call -DEBUG - 2024-11-02 23:15:38,957 - 2a4d8471 - apply_request_parameters - 0.00018310546875 - returned OK -DEBUG - 2024-11-02 23:15:38,957 - 2a4d8471 - query_id - initial call -DEBUG - 2024-11-02 23:15:38,957 - 2a4d8471 - query_id - 0.00013566017150878906 - returned OK -DEBUG - 2024-11-02 23:15:38,957 - 2a4d8471 - get_count - initial call -DEBUG - 2024-11-02 23:15:38,960 - 2a4d8471 - get_count - 0.003238201141357422 - returned OK -DEBUG - 2024-11-02 23:15:38,961 - 2a4d8471 - get_documents - initial call -DEBUG - 2024-11-02 23:15:38,961 - 2a4d8471 - get_documents - 0.0003116130828857422 - returned OK -DEBUG - 2024-11-02 23:15:38,963 - 2a4d8471 - get_dataset_with_id - 0.006453275680541992 - returned OK -DEBUG - 2024-11-02 23:15:38,963 - 2a4d8471 - build_beacon_collection_response - initial call -DEBUG - 2024-11-02 23:15:38,963 - 2a4d8471 - build_meta - initial call -DEBUG - 2024-11-02 23:15:38,964 - 2a4d8471 - build_meta - 0.0002875328063964844 - returned OK -DEBUG - 2024-11-02 23:15:38,964 - 2a4d8471 - build_response_summary - initial call -DEBUG - 2024-11-02 23:15:38,964 - 2a4d8471 - build_response_summary - 0.00015854835510253906 - returned OK -DEBUG - 2024-11-02 23:15:38,964 - 2a4d8471 - build_beacon_collection_response - 0.0010828971862792969 - returned OK -DEBUG - 2024-11-13 10:31:37,843 - 8501c358 - generate_txid - initial call -DEBUG - 2024-11-13 10:31:37,844 - 8501c358 - generate_txid- 0.0008754730224609375 - returned OK -DEBUG - 2024-11-13 10:31:37,844 - 8501c358 - get_qparams - initial call -DEBUG - 2024-11-13 10:31:37,844 - 8501c358 - get_qparams - 0.00019669532775878906 - returned OK -DEBUG - 2024-11-13 10:31:37,846 - 8501c358 - permission - initial call -DEBUG - 2024-11-13 10:31:37,846 - 8501c358 - permission - 0.0002624988555908203 - returned OK -DEBUG - 2024-11-13 10:31:37,846 - 8501c358 - authorization - initial call -DEBUG - 2024-11-13 10:31:37,846 - 8501c358 - authorization - 0.00018668174743652344 - returned OK -DEBUG - 2024-11-13 10:31:37,849 - 8501c358 - get_datasets_list - initial call -DEBUG - 2024-11-13 10:31:37,849 - 8501c358 - get_datasets_list - 0.00026702880859375 - returned OK -DEBUG - 2024-11-13 10:31:37,849 - 8501c358 - get_list_of_datasets - initial call -DEBUG - 2024-11-13 10:31:37,849 - 8501c358 - get_datasets - initial call -DEBUG - 2024-11-13 10:31:37,849 - 8501c358 - get_datasets - 0.00019431114196777344 - returned OK -DEBUG - 2024-11-13 10:31:38,875 - 8501c358 - get_list_of_datasets - 1.0261871814727783 - returned OK -DEBUG - 2024-11-13 10:31:38,876 - 8501c358 - resultset - initial call -DEBUG - 2024-11-13 10:31:38,876 - 8501c358 - resultset - 0.0002627372741699219 - returned OK -DEBUG - 2024-11-13 10:31:38,876 - 8501c358 - builder - initial call -DEBUG - 2024-11-13 10:31:38,876 - 8501c358 - builder - 0.00015664100646972656 - returned OK -DEBUG - 2024-11-13 10:31:38,889 - 8501c358 - execute_function - initial call -DEBUG - 2024-11-13 10:31:38,890 - 8501c358 - execute_function - 0.00021910667419433594 - returned OK -DEBUG - 2024-11-13 10:31:38,890 - 8501c358 - get_variants - initial call -DEBUG - 2024-11-13 10:31:38,890 - 8501c358 - apply_request_parameters - initial call -DEBUG - 2024-11-13 10:31:38,891 - 8501c358 - get_variants - initial call -DEBUG - 2024-11-13 10:31:38,891 - 8501c358 - generate_position_filter_start - initial call -DEBUG - 2024-11-13 10:31:38,891 - 8501c358 - apply_request_parameters - initial call -DEBUG - 2024-11-13 10:31:38,891 - 8501c358 - generate_position_filter_start - 0.0003800392150878906 - returned OK -DEBUG - 2024-11-13 10:31:38,891 - 8501c358 - generate_position_filter_start - initial call -DEBUG - 2024-11-13 10:31:38,892 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,892 - 8501c358 - generate_position_filter_start - 0.0003209114074707031 - returned OK -DEBUG - 2024-11-13 10:31:38,892 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,892 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,892 - 8501c358 - format_value - 0.00027680397033691406 - returned OK -DEBUG - 2024-11-13 10:31:38,892 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,893 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,893 - 8501c358 - format_value - 0.0003910064697265625 - returned OK -DEBUG - 2024-11-13 10:31:38,893 - 8501c358 - format_operator - 0.00029850006103515625 - returned OK -DEBUG - 2024-11-13 10:31:38,893 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,893 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,893 - 8501c358 - format_operator - 0.0003216266632080078 - returned OK -DEBUG - 2024-11-13 10:31:38,894 - 8501c358 - format_value - 0.00030612945556640625 - returned OK -DEBUG - 2024-11-13 10:31:38,894 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,894 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,894 - 8501c358 - format_value - 0.0003573894500732422 - returned OK -DEBUG - 2024-11-13 10:31:38,894 - 8501c358 - format_operator - 0.00046539306640625 - returned OK -DEBUG - 2024-11-13 10:31:38,894 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,895 - 8501c358 - apply_alphanumeric_filter - 0.002965211868286133 - returned OK -DEBUG - 2024-11-13 10:31:38,895 - 8501c358 - format_operator - 0.00032401084899902344 - returned OK -DEBUG - 2024-11-13 10:31:38,895 - 8501c358 - generate_position_filter_end - initial call -DEBUG - 2024-11-13 10:31:38,895 - 8501c358 - apply_alphanumeric_filter - 0.0030527114868164062 - returned OK -DEBUG - 2024-11-13 10:31:38,895 - 8501c358 - generate_position_filter_end - 0.0003783702850341797 - returned OK -DEBUG - 2024-11-13 10:31:38,895 - 8501c358 - generate_position_filter_end - initial call -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - generate_position_filter_end - 0.0002613067626953125 - returned OK -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - format_value - 0.0004432201385498047 - returned OK -DEBUG - 2024-11-13 10:31:38,896 - 8501c358 - format_value - 0.0003345012664794922 - returned OK -DEBUG - 2024-11-13 10:31:38,897 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,897 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,897 - 8501c358 - format_operator - 0.0003154277801513672 - returned OK -DEBUG - 2024-11-13 10:31:38,897 - 8501c358 - format_operator - 0.00030040740966796875 - returned OK -DEBUG - 2024-11-13 10:31:38,897 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,897 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,898 - 8501c358 - format_value - 0.00022101402282714844 - returned OK -DEBUG - 2024-11-13 10:31:38,898 - 8501c358 - format_value - 0.00029206275939941406 - returned OK -DEBUG - 2024-11-13 10:31:38,898 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,898 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,898 - 8501c358 - format_operator - 0.0003192424774169922 - returned OK -DEBUG - 2024-11-13 10:31:38,898 - 8501c358 - format_operator - 0.0003631114959716797 - returned OK -DEBUG - 2024-11-13 10:31:38,899 - 8501c358 - apply_alphanumeric_filter - 0.002984762191772461 - returned OK -DEBUG - 2024-11-13 10:31:38,899 - 8501c358 - apply_alphanumeric_filter - 0.002838134765625 - returned OK -DEBUG - 2024-11-13 10:31:38,899 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,899 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,899 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,899 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_value - 0.00030350685119628906 - returned OK -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_value - 0.00030493736267089844 - returned OK -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_operator - 0.0003139972686767578 - returned OK -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_operator - 0.000362396240234375 - returned OK -DEBUG - 2024-11-13 10:31:38,900 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_value - 0.0003743171691894531 - returned OK -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_value - 0.00023889541625976562 - returned OK -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_operator - 0.00030803680419921875 - returned OK -DEBUG - 2024-11-13 10:31:38,901 - 8501c358 - format_operator - 0.00025582313537597656 - returned OK -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - apply_alphanumeric_filter - 0.0027930736541748047 - returned OK -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - apply_alphanumeric_filter - 0.0026748180389404297 - returned OK -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,902 - 8501c358 - format_value - 0.0002663135528564453 - returned OK -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_value - 0.0002582073211669922 - returned OK -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_operator - 0.0002751350402832031 - returned OK -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_operator - 0.00031065940856933594 - returned OK -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,903 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - format_value - 0.0003020763397216797 - returned OK -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - format_value - 0.0002548694610595703 - returned OK -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - format_operator - 0.0002307891845703125 - returned OK -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - format_operator - 0.00028228759765625 - returned OK -DEBUG - 2024-11-13 10:31:38,904 - 8501c358 - apply_alphanumeric_filter - 0.0025010108947753906 - returned OK -DEBUG - 2024-11-13 10:31:38,905 - 8501c358 - apply_alphanumeric_filter - 0.002530336380004883 - returned OK -DEBUG - 2024-11-13 10:31:38,905 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,905 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,905 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,905 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,905 - 8501c358 - format_value - 0.00029277801513671875 - returned OK -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - format_value - 0.0002880096435546875 - returned OK -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - format_operator - 0.00027489662170410156 - returned OK -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - apply_alphanumeric_filter - 0.0013477802276611328 - returned OK -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - format_operator - 0.0003578662872314453 - returned OK -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,906 - 8501c358 - apply_alphanumeric_filter - 0.0015239715576171875 - returned OK -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_value - 0.0002689361572265625 - returned OK -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_value - initial call -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_value - 0.00024080276489257812 - returned OK -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_operator - 0.0002429485321044922 - returned OK -DEBUG - 2024-11-13 10:31:38,907 - 8501c358 - format_operator - initial call -DEBUG - 2024-11-13 10:31:38,908 - 8501c358 - apply_alphanumeric_filter - 0.0012671947479248047 - returned OK -DEBUG - 2024-11-13 10:31:38,908 - 8501c358 - format_operator - 0.00038123130798339844 - returned OK -DEBUG - 2024-11-13 10:31:38,908 - 8501c358 - apply_request_parameters - 0.017613649368286133 - returned OK -DEBUG - 2024-11-13 10:31:38,908 - 8501c358 - apply_alphanumeric_filter - 0.0014040470123291016 - returned OK -DEBUG - 2024-11-13 10:31:38,908 - 8501c358 - apply_filters - initial call -DEBUG - 2024-11-13 10:31:38,908 - 8501c358 - apply_request_parameters - 0.017423629760742188 - returned OK -DEBUG - 2024-11-13 10:31:38,909 - 8501c358 - apply_filters - 0.00019669532775878906 - returned OK -DEBUG - 2024-11-13 10:31:38,909 - 8501c358 - apply_filters - initial call -DEBUG - 2024-11-13 10:31:38,909 - 8501c358 - get_docs_by_response_type - initial call -DEBUG - 2024-11-13 10:31:38,909 - 8501c358 - apply_filters - 0.00029087066650390625 - returned OK -DEBUG - 2024-11-13 10:31:38,909 - 8501c358 - get_count - initial call -DEBUG - 2024-11-13 10:31:38,909 - 8501c358 - get_docs_by_response_type - initial call -DEBUG - 2024-11-13 10:31:38,910 - 8501c358 - get_count - initial call -DEBUG - 2024-11-13 10:31:38,915 - 8501c358 - get_count - 0.005980968475341797 - returned OK -DEBUG - 2024-11-13 10:31:38,915 - 8501c358 - get_documents - initial call -DEBUG - 2024-11-13 10:31:38,916 - 8501c358 - get_documents - 0.0001392364501953125 - returned OK -DEBUG - 2024-11-13 10:31:38,916 - 8501c358 - get_count - 0.005973100662231445 - returned OK -DEBUG - 2024-11-13 10:31:38,916 - 8501c358 - get_documents - initial call -DEBUG - 2024-11-13 10:31:38,916 - 8501c358 - get_documents - 0.00011801719665527344 - returned OK -DEBUG - 2024-11-13 10:31:38,917 - 8501c358 - get_docs_by_response_type - 0.008407831192016602 - returned OK -DEBUG - 2024-11-13 10:31:38,917 - 8501c358 - get_docs_by_response_type - 0.008048772811889648 - returned OK -DEBUG - 2024-11-13 10:31:38,917 - 8501c358 - get_variants - 0.027384042739868164 - returned OK -DEBUG - 2024-11-13 10:31:38,918 - 8501c358 - get_variants - 0.027053117752075195 - returned OK -DEBUG - 2024-11-13 10:31:38,918 - 8501c358 - build_beacon_record_response_by_dataset - initial call -DEBUG - 2024-11-13 10:31:38,918 - 8501c358 - build_meta - initial call -DEBUG - 2024-11-13 10:31:38,918 - 8501c358 - build_meta - 0.00015497207641601562 - returned OK -DEBUG - 2024-11-13 10:31:38,918 - 8501c358 - build_response_summary_by_dataset - initial call -DEBUG - 2024-11-13 10:31:38,919 - 8501c358 - build_response_summary_by_dataset - 8.58306884765625e-05 - returned OK -DEBUG - 2024-11-13 10:31:38,919 - 8501c358 - build_response_by_dataset - initial call -DEBUG - 2024-11-13 10:31:38,919 - 8501c358 - build_response_by_dataset - 0.0001087188720703125 - returned OK -DEBUG - 2024-11-13 10:31:38,919 - 8501c358 - build_beacon_record_response_by_dataset - 0.0007033348083496094 - returned OK -DEBUG - 2024-11-13 10:31:43,250 - de54cb92 - generate_txid - initial call -DEBUG - 2024-11-13 10:31:43,251 - de54cb92 - generate_txid- 0.0006208419799804688 - returned OK -DEBUG - 2024-11-13 10:31:43,251 - de54cb92 - get_qparams - initial call -DEBUG - 2024-11-13 10:31:43,252 - de54cb92 - get_qparams - 0.00025463104248046875 - returned OK -DEBUG - 2024-11-13 10:31:43,252 - de54cb92 - permission - initial call -DEBUG - 2024-11-13 10:31:43,252 - de54cb92 - permission - 0.0002110004425048828 - returned OK -DEBUG - 2024-11-13 10:31:43,253 - de54cb92 - authorization - initial call -DEBUG - 2024-11-13 10:31:43,253 - de54cb92 - authorization - 0.00018906593322753906 - returned OK -DEBUG - 2024-11-13 10:31:43,255 - de54cb92 - get_datasets_list - initial call -DEBUG - 2024-11-13 10:31:43,256 - de54cb92 - get_datasets_list - 0.0006017684936523438 - returned OK -DEBUG - 2024-11-13 10:31:43,256 - de54cb92 - get_list_of_datasets - initial call -DEBUG - 2024-11-13 10:31:43,256 - de54cb92 - get_datasets - initial call -DEBUG - 2024-11-13 10:31:43,257 - de54cb92 - get_datasets - 0.00038814544677734375 - returned OK -DEBUG - 2024-11-13 10:31:43,259 - de54cb92 - get_list_of_datasets - 0.0023872852325439453 - returned OK -DEBUG - 2024-11-13 10:31:43,259 - de54cb92 - resultset - initial call -DEBUG - 2024-11-13 10:31:43,259 - de54cb92 - resultset - 0.0002536773681640625 - returned OK -DEBUG - 2024-11-13 10:31:43,260 - de54cb92 - builder - initial call -DEBUG - 2024-11-13 10:31:43,260 - de54cb92 - builder - 0.000244140625 - returned OK -DEBUG - 2024-11-13 10:31:43,260 - de54cb92 - execute_function - initial call -DEBUG - 2024-11-13 10:31:43,260 - de54cb92 - execute_function - 0.00022792816162109375 - returned OK -DEBUG - 2024-11-13 10:31:43,261 - de54cb92 - get_variants - initial call -DEBUG - 2024-11-13 10:31:43,261 - de54cb92 - apply_request_parameters - initial call -DEBUG - 2024-11-13 10:31:43,261 - de54cb92 - get_variants - initial call -DEBUG - 2024-11-13 10:31:43,262 - de54cb92 - generate_position_filter_start - initial call -DEBUG - 2024-11-13 10:31:43,262 - de54cb92 - apply_request_parameters - initial call -DEBUG - 2024-11-13 10:31:43,263 - de54cb92 - generate_position_filter_start - 0.0008149147033691406 - returned OK -DEBUG - 2024-11-13 10:31:43,263 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,263 - de54cb92 - generate_position_filter_start - initial call -DEBUG - 2024-11-13 10:31:43,263 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,264 - de54cb92 - generate_position_filter_start - 0.0008065700531005859 - returned OK -DEBUG - 2024-11-13 10:31:43,264 - de54cb92 - format_value - 0.0006527900695800781 - returned OK -DEBUG - 2024-11-13 10:31:43,264 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,265 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,265 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,265 - de54cb92 - format_operator - 0.0005273818969726562 - returned OK -DEBUG - 2024-11-13 10:31:43,265 - de54cb92 - format_value - 0.0007123947143554688 - returned OK -DEBUG - 2024-11-13 10:31:43,266 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,266 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,267 - de54cb92 - format_value - 0.000997304916381836 - returned OK -DEBUG - 2024-11-13 10:31:43,267 - de54cb92 - format_operator - 0.0007688999176025391 - returned OK -DEBUG - 2024-11-13 10:31:43,267 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,267 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,268 - de54cb92 - format_operator - 0.00058746337890625 - returned OK -DEBUG - 2024-11-13 10:31:43,268 - de54cb92 - format_value - 0.0005733966827392578 - returned OK -DEBUG - 2024-11-13 10:31:43,268 - de54cb92 - apply_alphanumeric_filter - 0.005095958709716797 - returned OK -DEBUG - 2024-11-13 10:31:43,268 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,269 - de54cb92 - generate_position_filter_end - initial call -DEBUG - 2024-11-13 10:31:43,269 - de54cb92 - format_operator - 0.000469207763671875 - returned OK -DEBUG - 2024-11-13 10:31:43,269 - de54cb92 - generate_position_filter_end - 0.0005092620849609375 - returned OK -DEBUG - 2024-11-13 10:31:43,269 - de54cb92 - apply_alphanumeric_filter - 0.00528407096862793 - returned OK -DEBUG - 2024-11-13 10:31:43,270 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,270 - de54cb92 - generate_position_filter_end - initial call -DEBUG - 2024-11-13 10:31:43,270 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,270 - de54cb92 - generate_position_filter_end - 0.0005192756652832031 - returned OK -DEBUG - 2024-11-13 10:31:43,271 - de54cb92 - format_value - 0.000492095947265625 - returned OK -DEBUG - 2024-11-13 10:31:43,271 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,271 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,271 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,272 - de54cb92 - format_operator - 0.0005116462707519531 - returned OK -DEBUG - 2024-11-13 10:31:43,272 - de54cb92 - format_value - 0.0004260540008544922 - returned OK -DEBUG - 2024-11-13 10:31:43,272 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,272 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,272 - de54cb92 - format_value - 0.0003974437713623047 - returned OK -DEBUG - 2024-11-13 10:31:43,273 - de54cb92 - format_operator - 0.00041937828063964844 - returned OK -DEBUG - 2024-11-13 10:31:43,273 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,273 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,273 - de54cb92 - format_operator - 0.00043845176696777344 - returned OK -DEBUG - 2024-11-13 10:31:43,274 - de54cb92 - format_value - 0.0004322528839111328 - returned OK -DEBUG - 2024-11-13 10:31:43,274 - de54cb92 - apply_alphanumeric_filter - 0.0041506290435791016 - returned OK -DEBUG - 2024-11-13 10:31:43,274 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,274 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,274 - de54cb92 - format_operator - 0.0003886222839355469 - returned OK -DEBUG - 2024-11-13 10:31:43,274 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,275 - de54cb92 - apply_alphanumeric_filter - 0.004028797149658203 - returned OK -DEBUG - 2024-11-13 10:31:43,275 - de54cb92 - format_value - 0.0004355907440185547 - returned OK -DEBUG - 2024-11-13 10:31:43,275 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,275 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,276 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,276 - de54cb92 - format_operator - 0.0006439685821533203 - returned OK -DEBUG - 2024-11-13 10:31:43,276 - de54cb92 - format_value - 0.0004017353057861328 - returned OK -DEBUG - 2024-11-13 10:31:43,276 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,277 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,277 - de54cb92 - format_value - 0.00033974647521972656 - returned OK -DEBUG - 2024-11-13 10:31:43,277 - de54cb92 - format_operator - 0.0003628730773925781 - returned OK -DEBUG - 2024-11-13 10:31:43,277 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,278 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,278 - de54cb92 - format_operator - 0.0003902912139892578 - returned OK -DEBUG - 2024-11-13 10:31:43,278 - de54cb92 - format_value - 0.00028586387634277344 - returned OK -DEBUG - 2024-11-13 10:31:43,278 - de54cb92 - apply_alphanumeric_filter - 0.0038995742797851562 - returned OK -DEBUG - 2024-11-13 10:31:43,278 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,279 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,279 - de54cb92 - format_operator - 0.00044989585876464844 - returned OK -DEBUG - 2024-11-13 10:31:43,279 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,279 - de54cb92 - apply_alphanumeric_filter - 0.003912448883056641 - returned OK -DEBUG - 2024-11-13 10:31:43,279 - de54cb92 - format_value - 0.0003998279571533203 - returned OK -DEBUG - 2024-11-13 10:31:43,280 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,280 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,280 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,280 - de54cb92 - format_operator - 0.0003592967987060547 - returned OK -DEBUG - 2024-11-13 10:31:43,280 - de54cb92 - format_value - 0.0003001689910888672 - returned OK -DEBUG - 2024-11-13 10:31:43,281 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,281 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,281 - de54cb92 - format_value - 0.0003495216369628906 - returned OK -DEBUG - 2024-11-13 10:31:43,281 - de54cb92 - format_operator - 0.00042724609375 - returned OK -DEBUG - 2024-11-13 10:31:43,281 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,281 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,282 - de54cb92 - format_operator - 0.0004658699035644531 - returned OK -DEBUG - 2024-11-13 10:31:43,282 - de54cb92 - format_value - 0.00037097930908203125 - returned OK -DEBUG - 2024-11-13 10:31:43,282 - de54cb92 - apply_alphanumeric_filter - 0.003411531448364258 - returned OK -DEBUG - 2024-11-13 10:31:43,282 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,282 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,283 - de54cb92 - format_operator - 0.00039958953857421875 - returned OK -DEBUG - 2024-11-13 10:31:43,283 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,283 - de54cb92 - apply_alphanumeric_filter - 0.0032842159271240234 - returned OK -DEBUG - 2024-11-13 10:31:43,283 - de54cb92 - format_value - 0.0004897117614746094 - returned OK -DEBUG - 2024-11-13 10:31:43,283 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,284 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,284 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,284 - de54cb92 - format_operator - 0.00040411949157714844 - returned OK -DEBUG - 2024-11-13 10:31:43,284 - de54cb92 - format_value - 0.0003180503845214844 - returned OK -DEBUG - 2024-11-13 10:31:43,284 - de54cb92 - apply_alphanumeric_filter - 0.0018079280853271484 - returned OK -DEBUG - 2024-11-13 10:31:43,284 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,285 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,285 - de54cb92 - format_operator - 0.0002503395080566406 - returned OK -DEBUG - 2024-11-13 10:31:43,285 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,285 - de54cb92 - apply_alphanumeric_filter - 0.00177764892578125 - returned OK -DEBUG - 2024-11-13 10:31:43,285 - de54cb92 - format_value - 0.0002636909484863281 - returned OK -DEBUG - 2024-11-13 10:31:43,285 - de54cb92 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:31:43,286 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,286 - de54cb92 - format_value - initial call -DEBUG - 2024-11-13 10:31:43,286 - de54cb92 - format_operator - 0.0004000663757324219 - returned OK -DEBUG - 2024-11-13 10:31:43,286 - de54cb92 - format_value - 0.0004086494445800781 - returned OK -DEBUG - 2024-11-13 10:31:43,287 - de54cb92 - apply_alphanumeric_filter - 0.0019676685333251953 - returned OK -DEBUG - 2024-11-13 10:31:43,287 - de54cb92 - format_operator - initial call -DEBUG - 2024-11-13 10:31:43,287 - de54cb92 - apply_request_parameters - 0.025641679763793945 - returned OK -DEBUG - 2024-11-13 10:31:43,287 - de54cb92 - format_operator - 0.00030517578125 - returned OK -DEBUG - 2024-11-13 10:31:43,287 - de54cb92 - apply_filters - initial call -DEBUG - 2024-11-13 10:31:43,287 - de54cb92 - apply_alphanumeric_filter - 0.0018329620361328125 - returned OK -DEBUG - 2024-11-13 10:31:43,288 - de54cb92 - apply_filters - 0.0004372596740722656 - returned OK -DEBUG - 2024-11-13 10:31:43,288 - de54cb92 - apply_request_parameters - 0.025821924209594727 - returned OK -DEBUG - 2024-11-13 10:31:43,288 - de54cb92 - get_docs_by_response_type - initial call -DEBUG - 2024-11-13 10:31:43,288 - de54cb92 - apply_filters - initial call -DEBUG - 2024-11-13 10:31:43,288 - de54cb92 - get_count - initial call -DEBUG - 2024-11-13 10:31:43,289 - de54cb92 - apply_filters - 0.00038123130798339844 - returned OK -DEBUG - 2024-11-13 10:31:43,290 - de54cb92 - get_docs_by_response_type - initial call -DEBUG - 2024-11-13 10:31:43,290 - de54cb92 - get_count - initial call -DEBUG - 2024-11-13 10:31:43,290 - de54cb92 - get_count - 0.0017466545104980469 - returned OK -DEBUG - 2024-11-13 10:31:43,291 - de54cb92 - get_documents - initial call -DEBUG - 2024-11-13 10:31:43,291 - de54cb92 - get_documents - 0.00015473365783691406 - returned OK -DEBUG - 2024-11-13 10:31:43,291 - de54cb92 - get_count - 0.0010280609130859375 - returned OK -DEBUG - 2024-11-13 10:31:43,291 - de54cb92 - get_documents - initial call -DEBUG - 2024-11-13 10:31:43,291 - de54cb92 - get_documents - 0.0001766681671142578 - returned OK -DEBUG - 2024-11-13 10:31:43,292 - de54cb92 - get_docs_by_response_type - 0.0036737918853759766 - returned OK -DEBUG - 2024-11-13 10:31:43,292 - de54cb92 - get_variants - 0.03127408027648926 - returned OK -DEBUG - 2024-11-13 10:31:43,292 - de54cb92 - get_docs_by_response_type - 0.0029845237731933594 - returned OK -DEBUG - 2024-11-13 10:31:43,293 - de54cb92 - get_variants - 0.03127288818359375 - returned OK -DEBUG - 2024-11-13 10:31:43,293 - de54cb92 - build_beacon_record_response_by_dataset - initial call -DEBUG - 2024-11-13 10:31:43,293 - de54cb92 - build_meta - initial call -DEBUG - 2024-11-13 10:31:43,293 - de54cb92 - build_meta - 0.0001842975616455078 - returned OK -DEBUG - 2024-11-13 10:31:43,294 - de54cb92 - build_response_summary_by_dataset - initial call -DEBUG - 2024-11-13 10:31:43,294 - de54cb92 - build_response_summary_by_dataset - 0.00015592575073242188 - returned OK -DEBUG - 2024-11-13 10:31:43,294 - de54cb92 - build_response_by_dataset - initial call -DEBUG - 2024-11-13 10:31:43,294 - de54cb92 - build_response_by_dataset - 0.0001285076141357422 - returned OK -DEBUG - 2024-11-13 10:31:43,294 - de54cb92 - build_beacon_record_response_by_dataset - 0.0009944438934326172 - returned OK -DEBUG - 2024-11-13 10:32:47,619 - 71053e71 - generate_txid - initial call -DEBUG - 2024-11-13 10:32:47,620 - 71053e71 - generate_txid- 0.0007691383361816406 - returned OK -DEBUG - 2024-11-13 10:32:47,620 - 71053e71 - get_qparams - initial call -DEBUG - 2024-11-13 10:32:47,620 - 71053e71 - get_qparams - 0.00023174285888671875 - returned OK -DEBUG - 2024-11-13 10:32:47,621 - 71053e71 - permission - initial call -DEBUG - 2024-11-13 10:32:47,621 - 71053e71 - permission - 0.00018835067749023438 - returned OK -DEBUG - 2024-11-13 10:32:47,621 - 71053e71 - authorization - initial call -DEBUG - 2024-11-13 10:32:47,622 - 71053e71 - authorization - 0.00019860267639160156 - returned OK -DEBUG - 2024-11-13 10:32:47,624 - 71053e71 - get_datasets_list - initial call -DEBUG - 2024-11-13 10:32:47,624 - 71053e71 - get_datasets_list - 0.00042819976806640625 - returned OK -DEBUG - 2024-11-13 10:32:47,625 - 71053e71 - get_list_of_datasets - initial call -DEBUG - 2024-11-13 10:32:47,625 - 71053e71 - get_datasets - initial call -DEBUG - 2024-11-13 10:32:47,625 - 71053e71 - get_datasets - 0.0002906322479248047 - returned OK -DEBUG - 2024-11-13 10:32:47,627 - 71053e71 - get_list_of_datasets - 0.0019307136535644531 - returned OK -DEBUG - 2024-11-13 10:32:47,627 - 71053e71 - resultset - initial call -DEBUG - 2024-11-13 10:32:47,627 - 71053e71 - resultset - 0.0003209114074707031 - returned OK -DEBUG - 2024-11-13 10:32:47,628 - 71053e71 - builder - initial call -DEBUG - 2024-11-13 10:32:47,628 - 71053e71 - builder - 0.00024580955505371094 - returned OK -DEBUG - 2024-11-13 10:32:47,628 - 71053e71 - execute_function - initial call -DEBUG - 2024-11-13 10:32:47,628 - 71053e71 - execute_function - 0.00020384788513183594 - returned OK -DEBUG - 2024-11-13 10:32:47,629 - 71053e71 - get_variants - initial call -DEBUG - 2024-11-13 10:32:47,630 - 71053e71 - apply_request_parameters - initial call -DEBUG - 2024-11-13 10:32:47,630 - 71053e71 - get_variants - initial call -DEBUG - 2024-11-13 10:32:47,630 - 71053e71 - generate_position_filter_start - initial call -DEBUG - 2024-11-13 10:32:47,630 - 71053e71 - apply_request_parameters - initial call -DEBUG - 2024-11-13 10:32:47,631 - 71053e71 - generate_position_filter_start - 0.0006263256072998047 - returned OK -DEBUG - 2024-11-13 10:32:47,631 - 71053e71 - generate_position_filter_start - initial call -DEBUG - 2024-11-13 10:32:47,631 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,632 - 71053e71 - generate_position_filter_start - 0.0005238056182861328 - returned OK -DEBUG - 2024-11-13 10:32:47,632 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,632 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,632 - 71053e71 - format_value - 0.000457763671875 - returned OK -DEBUG - 2024-11-13 10:32:47,633 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,633 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,633 - 71053e71 - format_value - 0.0003342628479003906 - returned OK -DEBUG - 2024-11-13 10:32:47,633 - 71053e71 - format_operator - 0.0005669593811035156 - returned OK -DEBUG - 2024-11-13 10:32:47,633 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,634 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,634 - 71053e71 - format_operator - 0.0004360675811767578 - returned OK -DEBUG - 2024-11-13 10:32:47,634 - 71053e71 - format_value - 0.00036907196044921875 - returned OK -DEBUG - 2024-11-13 10:32:47,634 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,634 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,635 - 71053e71 - format_value - 0.00047969818115234375 - returned OK -DEBUG - 2024-11-13 10:32:47,635 - 71053e71 - format_operator - 0.0004930496215820312 - returned OK -DEBUG - 2024-11-13 10:32:47,635 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,635 - 71053e71 - apply_alphanumeric_filter - 0.003927707672119141 - returned OK -DEBUG - 2024-11-13 10:32:47,636 - 71053e71 - format_operator - 0.00044989585876464844 - returned OK -DEBUG - 2024-11-13 10:32:47,636 - 71053e71 - generate_position_filter_end - initial call -DEBUG - 2024-11-13 10:32:47,636 - 71053e71 - apply_alphanumeric_filter - 0.0038306713104248047 - returned OK -DEBUG - 2024-11-13 10:32:47,636 - 71053e71 - generate_position_filter_end - 0.0004267692565917969 - returned OK -DEBUG - 2024-11-13 10:32:47,636 - 71053e71 - generate_position_filter_end - initial call -DEBUG - 2024-11-13 10:32:47,637 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,637 - 71053e71 - generate_position_filter_end - 0.0004260540008544922 - returned OK -DEBUG - 2024-11-13 10:32:47,637 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,637 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,637 - 71053e71 - format_value - 0.0003993511199951172 - returned OK -DEBUG - 2024-11-13 10:32:47,638 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,638 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,638 - 71053e71 - format_value - 0.0002987384796142578 - returned OK -DEBUG - 2024-11-13 10:32:47,638 - 71053e71 - format_operator - 0.00044274330139160156 - returned OK -DEBUG - 2024-11-13 10:32:47,638 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,638 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,639 - 71053e71 - format_operator - 0.00043463706970214844 - returned OK -DEBUG - 2024-11-13 10:32:47,639 - 71053e71 - format_value - 0.00044155120849609375 - returned OK -DEBUG - 2024-11-13 10:32:47,639 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,639 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,640 - 71053e71 - format_value - 0.00033736228942871094 - returned OK -DEBUG - 2024-11-13 10:32:47,640 - 71053e71 - format_operator - 0.00047707557678222656 - returned OK -DEBUG - 2024-11-13 10:32:47,640 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,640 - 71053e71 - apply_alphanumeric_filter - 0.0037643909454345703 - returned OK -DEBUG - 2024-11-13 10:32:47,641 - 71053e71 - format_operator - 0.0005831718444824219 - returned OK -DEBUG - 2024-11-13 10:32:47,641 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,641 - 71053e71 - apply_alphanumeric_filter - 0.004152059555053711 - returned OK -DEBUG - 2024-11-13 10:32:47,641 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,642 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,642 - 71053e71 - format_value - 0.0004279613494873047 - returned OK -DEBUG - 2024-11-13 10:32:47,642 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,642 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,642 - 71053e71 - format_value - 0.00040340423583984375 - returned OK -DEBUG - 2024-11-13 10:32:47,643 - 71053e71 - format_operator - 0.00039649009704589844 - returned OK -DEBUG - 2024-11-13 10:32:47,643 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,643 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,643 - 71053e71 - format_operator - 0.0004737377166748047 - returned OK -DEBUG - 2024-11-13 10:32:47,644 - 71053e71 - format_value - 0.00040531158447265625 - returned OK -DEBUG - 2024-11-13 10:32:47,644 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,644 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,644 - 71053e71 - format_value - 0.00037789344787597656 - returned OK -DEBUG - 2024-11-13 10:32:47,644 - 71053e71 - format_operator - 0.0003902912139892578 - returned OK -DEBUG - 2024-11-13 10:32:47,644 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,645 - 71053e71 - apply_alphanumeric_filter - 0.003803253173828125 - returned OK -DEBUG - 2024-11-13 10:32:47,645 - 71053e71 - format_operator - 0.0004966259002685547 - returned OK -DEBUG - 2024-11-13 10:32:47,645 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,645 - 71053e71 - apply_alphanumeric_filter - 0.0037186145782470703 - returned OK -DEBUG - 2024-11-13 10:32:47,645 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,646 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,646 - 71053e71 - format_value - 0.0004887580871582031 - returned OK -DEBUG - 2024-11-13 10:32:47,646 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,646 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,646 - 71053e71 - format_value - 0.00032806396484375 - returned OK -DEBUG - 2024-11-13 10:32:47,647 - 71053e71 - format_operator - 0.00045013427734375 - returned OK -DEBUG - 2024-11-13 10:32:47,647 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,647 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,647 - 71053e71 - format_operator - 0.00038814544677734375 - returned OK -DEBUG - 2024-11-13 10:32:47,647 - 71053e71 - format_value - 0.00031828880310058594 - returned OK -DEBUG - 2024-11-13 10:32:47,648 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,648 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,648 - 71053e71 - format_value - 0.00026345252990722656 - returned OK -DEBUG - 2024-11-13 10:32:47,648 - 71053e71 - format_operator - 0.0003528594970703125 - returned OK -DEBUG - 2024-11-13 10:32:47,648 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,649 - 71053e71 - apply_alphanumeric_filter - 0.0034189224243164062 - returned OK -DEBUG - 2024-11-13 10:32:47,649 - 71053e71 - format_operator - 0.00036144256591796875 - returned OK -DEBUG - 2024-11-13 10:32:47,649 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,649 - 71053e71 - apply_alphanumeric_filter - 0.00344085693359375 - returned OK -DEBUG - 2024-11-13 10:32:47,649 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,650 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,650 - 71053e71 - format_value - 0.0003726482391357422 - returned OK -DEBUG - 2024-11-13 10:32:47,650 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,650 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,650 - 71053e71 - format_value - 0.0003654956817626953 - returned OK -DEBUG - 2024-11-13 10:32:47,650 - 71053e71 - format_operator - 0.0003750324249267578 - returned OK -DEBUG - 2024-11-13 10:32:47,651 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,651 - 71053e71 - apply_alphanumeric_filter - 0.0019068717956542969 - returned OK -DEBUG - 2024-11-13 10:32:47,651 - 71053e71 - format_operator - 0.00036144256591796875 - returned OK -DEBUG - 2024-11-13 10:32:47,651 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,651 - 71053e71 - apply_alphanumeric_filter - 0.0018277168273925781 - returned OK -DEBUG - 2024-11-13 10:32:47,651 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,652 - 71053e71 - apply_alphanumeric_filter - initial call -DEBUG - 2024-11-13 10:32:47,652 - 71053e71 - format_value - 0.0005180835723876953 - returned OK -DEBUG - 2024-11-13 10:32:47,652 - 71053e71 - format_value - initial call -DEBUG - 2024-11-13 10:32:47,652 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,653 - 71053e71 - format_value - 0.00047087669372558594 - returned OK -DEBUG - 2024-11-13 10:32:47,653 - 71053e71 - format_operator - 0.0005283355712890625 - returned OK -DEBUG - 2024-11-13 10:32:47,653 - 71053e71 - format_operator - initial call -DEBUG - 2024-11-13 10:32:47,653 - 71053e71 - apply_alphanumeric_filter - 0.002093076705932617 - returned OK -DEBUG - 2024-11-13 10:32:47,654 - 71053e71 - format_operator - 0.0006232261657714844 - returned OK -DEBUG - 2024-11-13 10:32:47,654 - 71053e71 - apply_request_parameters - 0.024219036102294922 - returned OK -DEBUG - 2024-11-13 10:32:47,654 - 71053e71 - apply_alphanumeric_filter - 0.002368927001953125 - returned OK -DEBUG - 2024-11-13 10:32:47,654 - 71053e71 - apply_filters - initial call -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - apply_request_parameters - 0.024049043655395508 - returned OK -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - apply_filters - 0.0003895759582519531 - returned OK -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - apply_filters - initial call -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - get_docs_by_response_type - initial call -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - apply_filters - 0.0003437995910644531 - returned OK -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - get_count - initial call -DEBUG - 2024-11-13 10:32:47,655 - 71053e71 - get_docs_by_response_type - initial call -DEBUG - 2024-11-13 10:32:47,656 - 71053e71 - get_count - initial call -DEBUG - 2024-11-13 10:32:47,659 - 71053e71 - get_count - 0.0034601688385009766 - returned OK -DEBUG - 2024-11-13 10:32:47,659 - 71053e71 - get_count - 0.0026917457580566406 - returned OK -DEBUG - 2024-11-13 10:32:47,659 - 71053e71 - get_documents - initial call -DEBUG - 2024-11-13 10:32:47,659 - 71053e71 - get_documents - initial call -DEBUG - 2024-11-13 10:32:47,659 - 71053e71 - get_documents - 0.0002989768981933594 - returned OK -DEBUG - 2024-11-13 10:32:47,660 - 71053e71 - get_documents - 0.0004105567932128906 - returned OK -DEBUG - 2024-11-13 10:32:47,660 - 71053e71 - get_docs_by_response_type - 0.005432605743408203 - returned OK -DEBUG - 2024-11-13 10:32:47,661 - 71053e71 - get_variants - 0.031337738037109375 - returned OK -DEBUG - 2024-11-13 10:32:47,661 - 71053e71 - get_docs_by_response_type - 0.0052716732025146484 - returned OK -DEBUG - 2024-11-13 10:32:47,661 - 71053e71 - get_variants - 0.03131699562072754 - returned OK -DEBUG - 2024-11-13 10:32:47,661 - 71053e71 - build_beacon_record_response_by_dataset - initial call -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_meta - initial call -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_meta - 0.0001919269561767578 - returned OK -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_response_summary_by_dataset - initial call -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_response_summary_by_dataset - 0.00012254714965820312 - returned OK -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_response_by_dataset - initial call -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_response_by_dataset - 9.465217590332031e-05 - returned OK -DEBUG - 2024-11-13 10:32:47,662 - 71053e71 - build_beacon_record_response_by_dataset - 0.0008749961853027344 - returned OK diff --git a/beacon/logs/logs.py b/beacon/logs/logs.py index e7761d5f..860a03ab 100644 --- a/beacon/logs/logs.py +++ b/beacon/logs/logs.py @@ -2,6 +2,7 @@ import time from beacon.conf.conf_override import config import datetime +from logging import handlers def initialize_logger(level): try: @@ -20,9 +21,17 @@ def initialize_logger(level): datefmt='%Y-%m-%dT%H:%M:%S' ) formatter.converter = time.gmtime - # Choose which type of logs you want (in a file or in stream) + # Choose which type of logs you want (in a file or in stream). If file option is chosen, also remember to set how many days you + # want the file to be kept for before rotating, so the file is not grown too big. if config.log_file is not None: - handler = logging.FileHandler(config.log_file) + handler = handlers.TimedRotatingFileHandler( + filename=config.log_file, + when=config.log_rotating_interval, + interval=1, + backupCount=config.log_retention_days, + encoding="utf-8", + delay=True, + ) else: handler = logging.StreamHandler() # Set the same lavel and format to the handlers diff --git a/docker-compose.yml b/docker-compose.yml index 07366fe6..505f994a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -14,7 +14,7 @@ services: - "5050:5050" entrypoint: ['python','-m','beacon'] volumes: - - ./beacon/logs/logs.log:/beacon/logs/logs.log + - ./beacon/logs/log_files:/beacon/logs/log_files - ./beacon/conf/conf.py:/beacon/conf/conf.py - ./beacon/conf/conf_default.py:/beacon/conf/conf_default.py - ./beacon/connections/mongo/conf.py:/beacon/connections/mongo/conf.py From a7421e7a9d3790fedc92608ca085de8c8e05a387 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 15 Sep 2026 09:35:10 +0200 Subject: [PATCH 37/56] created unit test for checking logs conf --- beacon/conf/conf_default.py | 2 +- beacon/tests/dif_conf_test.py | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 35 insertions(+), 1 deletion(-) diff --git a/beacon/conf/conf_default.py b/beacon/conf/conf_default.py index 3bb6c118..c47bc7c0 100644 --- a/beacon/conf/conf_default.py +++ b/beacon/conf/conf_default.py @@ -10,7 +10,7 @@ # logs level=logging.DEBUG -log_file='/beacon/logs/log_files/logs.log' # path needs to be pointing to a file inside a volumed dir, preferably /beacon/logs/log_files, e.g. /beacon/logs/log_files/logs.log +log_file=None # path needs to be pointing to a file inside a volumed dir, preferably /beacon/logs/log_files, e.g. /beacon/logs/log_files/logs.log log_retention_days = 7 # days which the file will be kept until it is destroyed log_rotating_interval = 'midnight' # S, M, H, D, W0, W1, W2, W3, W4, W5, W6, midnight diff --git a/beacon/tests/dif_conf_test.py b/beacon/tests/dif_conf_test.py index 9d68921c..471b4917 100644 --- a/beacon/tests/dif_conf_test.py +++ b/beacon/tests/dif_conf_test.py @@ -1281,6 +1281,40 @@ def test_conf_override_takes_user_param(self): # Confirm override differs from framework defaults assert conf_override.config.uri != conf_default.uri + + + def test_main_check_logs_configuration(self): + with loop_context() as loop: + from beacon.conf import conf_override + + # Configure unsupported default granularity + conf_override.config.log_file='/beacon/logs/log_files/logs_test.log' + app = create_app() + client = TestClient(TestServer(app), loop=loop) + loop.run_until_complete(client.start_server()) + + async def test_check_logs_files_is_saved(): + from pathlib import Path + + log_file = Path("/beacon/logs/log_files/logs_test.log") + + + resp = await client.get( + conf_override.config.uri_subpath + "/" + + biosample["biosample"]["endpoint_name"] + ) + + if log_file.is_file(): + pass + else: + raise Exception + + + loop.run_until_complete(test_check_logs_files_is_saved()) + loop.run_until_complete(client.close()) + + # Restore valid default granularity + conf_override.config.log_file=None From f5f1f2d5a11d861e0c779217e03eb08f2cd56160 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 15 Sep 2026 11:00:15 +0200 Subject: [PATCH 38/56] additional unit test to check logs conf work --- beacon/conf/conf_default.py | 2 +- beacon/logs/logs.py | 2 +- beacon/tests/dif_conf_test.py | 45 +++++++++++++++++++++++++++++++++++ 3 files changed, 47 insertions(+), 2 deletions(-) diff --git a/beacon/conf/conf_default.py b/beacon/conf/conf_default.py index c47bc7c0..4235930f 100644 --- a/beacon/conf/conf_default.py +++ b/beacon/conf/conf_default.py @@ -11,7 +11,7 @@ # logs level=logging.DEBUG log_file=None # path needs to be pointing to a file inside a volumed dir, preferably /beacon/logs/log_files, e.g. /beacon/logs/log_files/logs.log -log_retention_days = 7 # days which the file will be kept until it is destroyed +log_num_of_files_to_keep = 7 # number of files that will be kept for backup, the most recent ones, the oldest will get deleted log_rotating_interval = 'midnight' # S, M, H, D, W0, W1, W2, W3, W4, W5, W6, midnight # Beacon generic conf diff --git a/beacon/logs/logs.py b/beacon/logs/logs.py index 860a03ab..bece132b 100644 --- a/beacon/logs/logs.py +++ b/beacon/logs/logs.py @@ -28,7 +28,7 @@ def initialize_logger(level): filename=config.log_file, when=config.log_rotating_interval, interval=1, - backupCount=config.log_retention_days, + backupCount=config.log_num_of_files_to_keep, encoding="utf-8", delay=True, ) diff --git a/beacon/tests/dif_conf_test.py b/beacon/tests/dif_conf_test.py index 471b4917..02ed56a4 100644 --- a/beacon/tests/dif_conf_test.py +++ b/beacon/tests/dif_conf_test.py @@ -7,6 +7,7 @@ import yaml from beacon.logs.logs import initialize_logger from beacon.conf.conf_override import config +import asyncio def import_genomicVariant_confile(): """Get the information about the genomic variant entry type gor ga4gh model""" @@ -1315,6 +1316,50 @@ async def test_check_logs_files_is_saved(): # Restore valid default granularity conf_override.config.log_file=None + + def test_main_check_logs_files_are_deleted(self): + with loop_context() as loop: + from beacon.conf import conf_override + + # Configure unsupported default granularity + conf_override.config.log_file='/beacon/logs/log_files/logs_test.log' + conf_override.config.num_of_files_to_keep=1 + conf_override.config.log_rotating_interval='S' + app = create_app() + client = TestClient(TestServer(app), loop=loop) + loop.run_until_complete(client.start_server()) + + async def test_check_logs_files_are_deleted(): + from pathlib import Path + + directory = Path("/beacon/logs/log_files") + + + resp = await client.get( + conf_override.config.uri_subpath + "/" + + biosample["biosample"]["endpoint_name"] + ) + await asyncio.sleep(5) + + resp = await client.get( + conf_override.config.uri_subpath + "/" + + biosample["biosample"]["endpoint_name"] + ) + num_logs = sum( + 1 for p in Path(directory).glob("logs_test.log*") + if p.is_file() + ) + + assert num_logs == 3 + + + loop.run_until_complete(test_check_logs_files_are_deleted()) + loop.run_until_complete(client.close()) + + # Restore valid default granularity + conf_override.config.log_file=None + conf_override.config.num_of_files_to_keep=7 + conf_override.config.log_rotating_interval='midnight' From 71e58197fe83ac1a3df9a563cbf5e870389bc4e4 Mon Sep 17 00:00:00 2001 From: costero-e Date: Fri, 18 Sep 2026 12:39:31 +0200 Subject: [PATCH 39/56] removing limit for individuals to variants query --- .../connections/mongo/non_collections.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py index c87270ab..0ae91335 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/non_collections.py @@ -73,8 +73,10 @@ def get_variants_of_phenotypic_endpoint(self, dataset: SingleDatasetResponse): runs=client['beacon'].runs targets_=client['beacon'].targets caseLevelData=client['beacon'].caseLevelData + biosamples=client['beacon'].biosamples analysis_confile=import_analysis_confile() run_confile=import_run_confile() + individual_confile=import_individual_confile() new_entry_id = self.request_attributes.entry_id # Check which is the queried initial entry type of the cross query and process and get the ids to convert to the final entry type response. if self.request_attributes.pre_entry_type == analysis_confile["analysis"]["endpoint_name"] or self.request_attributes.pre_entry_type == run_confile["run"]["endpoint_name"]: @@ -90,6 +92,15 @@ def get_variants_of_phenotypic_endpoint(self, dataset: SingleDatasetResponse): new_entry_id = initial_ids["biosampleId"] except Exception as e: return dataset + elif self.request_attributes.pre_entry_type == individual_confile["individual"]["endpoint_name"]: + query = {"$and": [{"individualId": self.request_attributes.entry_id}]} + query = apply_filters(self, query, self.request_attributes.qparams.query.filters, {}, dataset.dataset) + initial_ids = biosamples \ + .find_one(query, {"id": 1, "_id": 0}) + try: + new_entry_id = initial_ids["id"] + except Exception as e: + return dataset try: # Retrieve the ids per dataset. targets = targets_ \ @@ -109,7 +120,7 @@ def get_variants_of_phenotypic_endpoint(self, dataset: SingleDatasetResponse): # Query the caseLevelData to get the variants that are related to these ids. query_cl={"$or": [{ position: "10", "datasetId": dataset.dataset},{ position: "11", "datasetId": dataset.dataset}, { position: "01", "datasetId": dataset.dataset}, { position: "y", "datasetId": dataset.dataset}]} string_of_ids = caseLevelData \ - .find(query_cl, {"id": 1, "_id": 0}).limit(self.request_attributes.qparams.query.pagination.limit).skip(self.request_attributes.qparams.query.pagination.skip) + .find(query_cl, {"id": 1, "_id": 0}) HGVSIds=list(string_of_ids) # Build the query using the identifiers.genomicHGVSId query={} From 96ff9a5b83a2080daeb0cfee66807a3b55e8658a Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 21 Sep 2026 11:06:17 +0200 Subject: [PATCH 40/56] added alternative uris when checking the request uri paths --- beacon/conf/conf_default.py | 3 ++- beacon/utils/requests.py | 16 ++++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/beacon/conf/conf_default.py b/beacon/conf/conf_default.py index 4235930f..61362885 100644 --- a/beacon/conf/conf_default.py +++ b/beacon/conf/conf_default.py @@ -18,9 +18,10 @@ beacon_id = 'org.ega-archive.beacon-ri-demo' # ID of the Beacon beacon_name = 'Beacon Production Implementation demo' # Name of the Beacon service api_version = 'v2.2.0' # Version of the Beacon implementation -uri = 'http://localhost:5050' +uri = 'http://localhost:50510' uri_subpath = '/api' complete_url = uri + uri_subpath +allowed_uris = ["http://localhost:5050"] environment = 'test' description = r"This Beacon is based on synthetic data hosted at the EGA. The dataset contains 2504 samples including genetic data based on 1K Genomes data, and 76 individual attributes and phenotypic data derived from UKBiobank." version = api_version_yaml['api_version'] diff --git a/beacon/utils/requests.py b/beacon/utils/requests.py index 6776953f..4838a37b 100644 --- a/beacon/utils/requests.py +++ b/beacon/utils/requests.py @@ -235,18 +235,34 @@ def set_entry_type(self, request): abs_url=abs_url_with_query_string.split('?') abs_url=abs_url[0] starting_endpoint = len(config.uri) + len(config.uri_subpath) + new_starting_endpoints = [] def_uri = config.uri + config.uri_subpath if 'https' not in abs_url and 'https' in def_uri: abs_url = abs_url.replace('http', 'https') if abs_url[:starting_endpoint] != def_uri : self.LOG.warning('configuration variable uri: {} not the same as where the beacon is hosted'.format(config.uri)) + for alternative_uri in config.allowed_uris: + new_starting_endpoint=len(alternative_uri) + new_starting_endpoints.append(new_starting_endpoint) + if abs_url[:new_starting_endpoint] != alternative_uri: + self.LOG.warning('configuration variable allowed uri: {} not the same as where the beacon is hosted'.format(alternative_uri)) if abs_url_with_query_string.endswith('/api'): self.request_attributes.entry_type='info' set_entry_type_configuration(self) else: path_list = abs_url[starting_endpoint:].split('/') path_list = list(filter(None, path_list)) + is_uri_path_correct=False if path_list == []: + for startingendpoint in new_starting_endpoints: + path_list = abs_url[startingendpoint:].split('/') + path_list = list(filter(None, path_list)) + if path_list!=[]: + is_uri_path_correct=True + break + else: + is_uri_path_correct=True + if is_uri_path_correct == False: raise WrongURIPath('the {} parameter from conf.py is not the same as the root one received in request: {}. Configure you uri accordingly.'.format(config.uri, abs_url)) if len(path_list) > 2: try: From f99eb60ee0af756d8e7540141b9fc73f4ec6df5d Mon Sep 17 00:00:00 2001 From: costero-e Date: Mon, 21 Sep 2026 17:49:12 +0200 Subject: [PATCH 41/56] finished implementing allowed uris --- beacon/conf/conf_default.py | 4 ++-- beacon/tests/dif_conf_test.py | 35 ++++++++++++++++++++++++++++++- beacon/utils/requests.py | 32 +++++++++++++++++----------- beacon/validator/configuration.py | 19 +++++++++++++++++ 4 files changed, 75 insertions(+), 15 deletions(-) diff --git a/beacon/conf/conf_default.py b/beacon/conf/conf_default.py index 61362885..65669e5c 100644 --- a/beacon/conf/conf_default.py +++ b/beacon/conf/conf_default.py @@ -18,10 +18,10 @@ beacon_id = 'org.ega-archive.beacon-ri-demo' # ID of the Beacon beacon_name = 'Beacon Production Implementation demo' # Name of the Beacon service api_version = 'v2.2.0' # Version of the Beacon implementation -uri = 'http://localhost:50510' +uri = 'http://localhost:5050' uri_subpath = '/api' complete_url = uri + uri_subpath -allowed_uris = ["http://localhost:5050"] +allowed_uris = ["*"] # example: ["http://localhost:5054/api"] or if you want to enable all: ["*"] environment = 'test' description = r"This Beacon is based on synthetic data hosted at the EGA. The dataset contains 2504 samples including genetic data based on 1K Genomes data, and 76 individual attributes and phenotypic data derived from UKBiobank." version = api_version_yaml['api_version'] diff --git a/beacon/tests/dif_conf_test.py b/beacon/tests/dif_conf_test.py index 02ed56a4..96803fc9 100644 --- a/beacon/tests/dif_conf_test.py +++ b/beacon/tests/dif_conf_test.py @@ -322,7 +322,6 @@ async def test_check_configuration_enable_run(): run["run"]["entry_type_enabled"]=True with open("/beacon/tests/mock_conf_files/conf/entry_types/ga4gh/beacon_v2_default_model/run.yml", 'w') as outfile: yaml.dump(run, outfile, default_flow_style=False) - def test_configuration_endpoint_response_with_disabled_endpoint(self): with loop_context() as loop: # Disable analysis entry type in configuration @@ -358,6 +357,7 @@ async def test_check_configuration_endpoint_response_with_disabled_endpoint(): analysis["analysis"]["entry_type_enabled"] = True with open("/beacon/tests/mock_conf_files/conf/entry_types/ga4gh/beacon_v2_default_model/analysis.yml", 'w') as outfile: yaml.dump(analysis, outfile, default_flow_style=False) + def test_main_check_configuration_with_wrong_analysis_enable_endpoint(self): with loop_context() as loop: # Inject an invalid value where a boolean is expected @@ -1280,8 +1280,10 @@ def test_conf_override_takes_user_param(self): # User configuration should override default configuration values assert conf_override.config.uri == conf.uri + conf_default.uri = 'invent' # Confirm override differs from framework defaults assert conf_override.config.uri != conf_default.uri + conf_default.uri = 'http://localhost:5050/api' def test_main_check_logs_configuration(self): @@ -1360,6 +1362,37 @@ async def test_check_logs_files_are_deleted(): conf_override.config.log_file=None conf_override.config.num_of_files_to_keep=7 conf_override.config.log_rotating_interval='midnight' + + def test_main_allowed_uris_fails(self): + with loop_context() as loop: + from beacon.conf import conf_override + + # Configure unsupported default granularity + conf_override.config.allowed_uris=[] + app = create_app() + client = TestClient(TestServer(app), loop=loop) + loop.run_until_complete(client.start_server()) + + async def test_check_allowed_uris_fails(): + from pathlib import Path + + directory = Path("/beacon/logs/log_files") + + try: + resp = await client.get( + conf_override.config.uri_subpath + "/" + + biosample["biosample"]["endpoint_name"] + ) + raise('Allowed uris must fail and it is not') + except Exception: + pass + + + loop.run_until_complete(test_check_allowed_uris_fails()) + loop.run_until_complete(client.close()) + + # Restore valid default granularity + conf_override.config.allowed_uris=['*'] diff --git a/beacon/utils/requests.py b/beacon/utils/requests.py index 4838a37b..8a0ed74e 100644 --- a/beacon/utils/requests.py +++ b/beacon/utils/requests.py @@ -239,30 +239,38 @@ def set_entry_type(self, request): def_uri = config.uri + config.uri_subpath if 'https' not in abs_url and 'https' in def_uri: abs_url = abs_url.replace('http', 'https') + used_uri=None if abs_url[:starting_endpoint] != def_uri : self.LOG.warning('configuration variable uri: {} not the same as where the beacon is hosted'.format(config.uri)) for alternative_uri in config.allowed_uris: + if alternative_uri == '*': + used_uri='*' + break new_starting_endpoint=len(alternative_uri) new_starting_endpoints.append(new_starting_endpoint) if abs_url[:new_starting_endpoint] != alternative_uri: self.LOG.warning('configuration variable allowed uri: {} not the same as where the beacon is hosted'.format(alternative_uri)) + else: + used_uri=alternative_uri + starting_endpoint=new_starting_endpoint + else: + used_uri = def_uri + if used_uri is None: + raise WrongURIPath('the {} parameter from conf.py is not the same as the root one received in request: {}. Configure you uri accordingly.'.format(config.uri, abs_url)) if abs_url_with_query_string.endswith('/api'): self.request_attributes.entry_type='info' set_entry_type_configuration(self) else: - path_list = abs_url[starting_endpoint:].split('/') - path_list = list(filter(None, path_list)) - is_uri_path_correct=False - if path_list == []: - for startingendpoint in new_starting_endpoints: - path_list = abs_url[startingendpoint:].split('/') - path_list = list(filter(None, path_list)) - if path_list!=[]: - is_uri_path_correct=True - break + if used_uri != '*': + path_list = abs_url[starting_endpoint:].split('/') + path_list = list(filter(None, path_list)) else: - is_uri_path_correct=True - if is_uri_path_correct == False: + used_uri_splitted = abs_url.split('/') + if '.' not in used_uri_splitted[-3]: + path_list=used_uri_splitted[-3:] + else: + path_list=[used_uri_splitted[-1]] + if path_list == []: raise WrongURIPath('the {} parameter from conf.py is not the same as the root one received in request: {}. Configure you uri accordingly.'.format(config.uri, abs_url)) if len(path_list) > 2: try: diff --git a/beacon/validator/configuration.py b/beacon/validator/configuration.py index 0f979163..844d6426 100644 --- a/beacon/validator/configuration.py +++ b/beacon/validator/configuration.py @@ -407,6 +407,25 @@ def check_configuration( ) ) + # Validate allowed uris are an array + if not isinstance(conf_override.config.allowed_uris, list): + raise Exception("The conf parameter allowed_uris must be an array") + + # Validate elements in allowed_uris are uris or * + for uri in conf_override.config.allowed_uris: + if uri.startswith('http://'): + LOG.warning( + 'The alternative uri: {} for your beacon is not https. Please change to https as soon as you can.'.format(uri) + ) + elif uri.startswith('https://'): + pass + elif uri == '*': + pass + else: + raise Exception( + "The alternative uri: {} for your beacon must start with https protocol.".format(uri) + ) + # Validate dataset permissions configuration file try: with open("/beacon/permissions/datasets/datasets_permissions.yml", 'r') as pfile: From 3c843a91f6138436ca8a9a4e2f43b83025069d78 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 22 Sep 2026 10:33:39 +0200 Subject: [PATCH 42/56] making empty the allowed uris array by default --- beacon/conf/conf_default.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/conf_default.py b/beacon/conf/conf_default.py index 65669e5c..3efe9787 100644 --- a/beacon/conf/conf_default.py +++ b/beacon/conf/conf_default.py @@ -21,7 +21,7 @@ uri = 'http://localhost:5050' uri_subpath = '/api' complete_url = uri + uri_subpath -allowed_uris = ["*"] # example: ["http://localhost:5054/api"] or if you want to enable all: ["*"] +allowed_uris = [] # example: ["http://localhost:5054/api"] or if you want to enable all: ["*"] environment = 'test' description = r"This Beacon is based on synthetic data hosted at the EGA. The dataset contains 2504 samples including genetic data based on 1K Genomes data, and 76 individual attributes and phenotypic data derived from UKBiobank." version = api_version_yaml['api_version'] From 67f2b5b0b798e5fceecf0b42144841e5a3430df5 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 29 Sep 2026 10:17:55 +0200 Subject: [PATCH 43/56] fixing allele frequency subproperties not showing up --- .../data/test/v2_2_0/genomicVariations.json | 17 ++++++++++++ .../beacon_genomicVariant_v2_2_0.py | 23 ++++++++-------- beacon/tests/__main__.py | 27 +++++++++++++++++++ 3 files changed, 56 insertions(+), 11 deletions(-) diff --git a/beacon/connections/mongo/data/test/v2_2_0/genomicVariations.json b/beacon/connections/mongo/data/test/v2_2_0/genomicVariations.json index 5764256c..5dffdd82 100644 --- a/beacon/connections/mongo/data/test/v2_2_0/genomicVariations.json +++ b/beacon/connections/mongo/data/test/v2_2_0/genomicVariations.json @@ -1,6 +1,23 @@ [ { "_id": "5e8df629d9ce607c1c56354eb012cbea32cf0f7744973db740724ad9578d667b", + "frequencyInPopulations": [ + { + "frequencies": [ + { + "alleleFrequency": 0, + "population": "Total", + "alleleCount": 0, + "alleleCountHomozygous": 0, + "alleleCountHeterozygous": 0, + "alleleCountHemizygous": 0, + "alleleNumber": 17906 + } + ], + "source": "Federated EGA Spain", + "sourceReference": "https://metadata.ega-archive.org/datasets/EGAD50000000955" + } + ], "identifiers": { "genomicHGVSId": "NC_000001.10:g.1234567_1234866del" }, diff --git a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py index 04646248..e9051474 100644 --- a/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py +++ b/beacon/models/ga4gh/beacon_v2_default_model/validator/non_collections/genomicVariant/beacon_genomicVariant_v2_2_0.py @@ -9,6 +9,10 @@ from pydantic import AnyUrl, BaseModel, ConfigDict, Field, RootModel, conint, constr +class CamelModel(BaseModel): + model_config = ConfigDict( + extra='allow', + ) class Info(BaseModel): pass @@ -291,7 +295,7 @@ class ClinicalRelevance(Enum): pathogenic = 'pathogenic' -class PopulationFrequency(BaseModel): +class PopulationFrequency(CamelModel): alleleFrequency: float = Field( ..., description='Allele frequency between 0 and 1.', examples=[3.186e-05] ) @@ -307,7 +311,7 @@ class PopulationFrequency(BaseModel): ) -class SoftwareTool(BaseModel): +class SoftwareTool(CamelModel): toolName: str = Field( ..., description='Name of the tool.', @@ -437,7 +441,7 @@ class Pagination(BaseModel): skip: Skip | None = Field(0, validate_default=True) -class FrequencyInPopulations(BaseModel): +class FrequencyInPopulations(CamelModel): frequencies: list[PopulationFrequency] = Field(..., min_length=1) source: str = Field( ..., @@ -470,7 +474,7 @@ class GenomicFeature(BaseModel): ) -class Identifiers(BaseModel): +class Identifiers(CamelModel): clinvarVariantId: constr(pattern=r'^(clinvar:)?\d+$') | None = Field( None, description='ClinVar variant id. Other id values used by ClinVar can be added to `variantAlternativeIds`', @@ -543,7 +547,7 @@ class MolecularAttributes(BaseModel): ) -class PhenoClinicEffect(BaseModel): +class PhenoClinicEffect(CamelModel): annotatedWith: SoftwareTool | None = None category: OntologyTerm | None = Field( None, @@ -584,7 +588,7 @@ class PhenoClinicEffect(BaseModel): ) -class VariantLevelData(BaseModel): +class VariantLevelData(CamelModel): clinicalInterpretations: list[PhenoClinicEffect] | None = None phenotypicEffects: list[PhenoClinicEffect] | None = None @@ -687,7 +691,7 @@ class Feature(RootModel[Gene]): ) -class CaseLevelVariant(BaseModel): +class CaseLevelVariant(CamelModel): alleleOrigin: OntologyTerm | None = Field( None, description='Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762). Categories are `somatic variant`, `germline variant`, `maternal variant`, `paternal variant`, `de novo variant`, `pedigree specific variant`, `population specific variant`. Corresponds to Variant Inheritance in FHIR.', @@ -880,7 +884,7 @@ class GenotypeMember(BaseModel): ) -class LegacyVariation(BaseModel): +class LegacyVariation(CamelModel): alternateBases: constr(pattern=r'^([ACGTUNRYSWKMBDHV\-\.]*)$') = Field( ..., description='Alternate bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used as\n a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of deletions with the maximally\n trimmed, deleted sequence being indicated in `ReferenceBases`', @@ -956,9 +960,6 @@ class VariationSet(BaseModel): class Genomicvariant(BaseModel): - model_config = ConfigDict( - extra='allow', - ) caseLevelData: list[CaseLevelVariant] | None = Field( None, description='caseLevelData reports about the variation instances observed in individual analyses.', diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index dd214e26..54c5b9db 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -7066,6 +7066,33 @@ async def test_check_post_alternative_schema_works(): loop.run_until_complete(test_check_post_alternative_schema_works()) loop.run_until_complete(client.close()) + def test_main_check_allele_frequency_per_zygosity_shows_up(self): + with loop_context() as loop: + # Specific genomic variant lookup by hash-like identifier + app = create_app() + client = TestClient(TestServer(app), loop=loop) + + loop.run_until_complete(client.start_server()) + + async def test_check_allele_frequency_per_zygosity_shows_up(): + # Query single genomic variant by unique ID (hash) + resp = await client.get( + conf_override.config.uri_subpath + "/" + + genomicVariant["genomicVariant"]["endpoint_name"] + + "/5e8df629d9ce607c1c56354eb012cbea32cf0f7744973db740724ad9578d667b" + ) + + responsetext = await resp.text() + responsedict = json.loads(responsetext) + + # Ensure only one result is returned for unique variant + assert responsedict["responseSummary"]["numTotalResults"] == 1 + assert responsedict["response"]["resultSets"][0]["results"][0]["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHomozygous"] == 0 + assert responsedict["response"]["resultSets"][0]["results"][0]["frequencyInPopulations"][0]["frequencies"][0]["alleleNumber"] == 17906 + assert resp.status == 200 + + loop.run_until_complete(test_check_allele_frequency_per_zygosity_shows_up()) + loop.run_until_complete(client.close()) class AsyncTest(unittest.IsolatedAsyncioTestCase): From ec18ff51999431c121d3de5f2adf7aedb7544fa7 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 29 Sep 2026 15:03:57 +0200 Subject: [PATCH 44/56] caching modules --- beacon/conf/models/models_conf.yml | 2 +- beacon/utils/modules.py | 1004 ++++++++++++++++------------ 2 files changed, 574 insertions(+), 432 deletions(-) diff --git a/beacon/conf/models/models_conf.yml b/beacon/conf/models/models_conf.yml index 5453d1a1..07c06037 100644 --- a/beacon/conf/models/models_conf.yml +++ b/beacon/conf/models/models_conf.yml @@ -2,4 +2,4 @@ ga4gh/beacon_v2_default_model: model_enabled: True EUCAIM: - model_enabled: True \ No newline at end of file + model_enabled: False \ No newline at end of file diff --git a/beacon/utils/modules.py b/beacon/utils/modules.py index 0980b14d..1419c6d1 100644 --- a/beacon/utils/modules.py +++ b/beacon/utils/modules.py @@ -7,468 +7,610 @@ from beacon.conf.conf_override import config from beacon.exceptions.exceptions import DatabaseIsDown import asyncio +import time +from functools import lru_cache +from pathlib import Path +import importlib -#TODO: get_client() passing one variable with the database name. +MODELS_CONFIG_PATH = Path("/beacon/conf/models/models_conf.yml") +CONNECTIONS_CONFIG_PATH = Path( + "/beacon/conf/connections/connections_conf.yml" +) +MODELS_PATH = Path("/beacon/models") + +# Increment this whenever configuration or model files change. +_CACHE_VERSION = 0 + + +def clear_configuration_caches(): + """ + Clear all caches that depend on filesystem/configuration state. + Call this after changing models_conf.yml, connections_conf.yml, + adding/removing models, or adding/removing validator modules. + """ + global _CACHE_VERSION + _CACHE_VERSION += 1 + + _load_models_config.cache_clear() + _load_connections_config.cache_clear() + _get_model_directories.cache_clear() + _get_directory_entries.cache_clear() + _load_entry_type_config.cache_clear() + _discover_result_classes.cache_clear() + _get_one_module_conf_cached.cache_clear() + _get_modules_confiles_cached.cache_clear() + _get_all_modules_connections_script_cached.cache_clear() + _get_all_modules_datasets_cached.cache_clear() + +@lru_cache(maxsize=1) +def _load_models_config(): + with MODELS_CONFIG_PATH.open("r") as pfile: + return yaml.safe_load(pfile) or {} + + +@lru_cache(maxsize=1) +def _load_connections_config(): + with CONNECTIONS_CONFIG_PATH.open("r") as infile: + return yaml.safe_load(infile) or {} + + +@lru_cache(maxsize=1) +def _get_model_directories(): + """ + Return a tuple because cached return values should not be mutated. + """ + return tuple( + entry.name + for entry in MODELS_PATH.iterdir() + if entry.is_dir() + ) + + +@lru_cache(maxsize=None) +def _get_directory_entries(path_string): + """ + Cached equivalent of os.listdir(path). + """ + path = Path(path_string) + + return tuple( + entry.name + for entry in path.iterdir() + ) + + +@lru_cache(maxsize=None) +def _load_entry_type_config(path_string): + path = Path(path_string) + + with path.open("r") as pfile: + return yaml.safe_load(pfile) or {} + +@lru_cache(maxsize=None) +def _load_module(module_name): + return importlib.import_module(module_name) + + +@lru_cache(maxsize=None) +def _load_class(module_name, class_name): + module = _load_module(module_name) + return getattr(module, class_name) + +@log_with_args(config.level) def load_framework_module(self, script_name): - """Choose what is the validator object class that will be loaded depending on the API version to return""" - module='beacon.framework.validator.'+self.request_attributes.returned_apiVersion.replace(".","_")+'.'+script_name - import importlib - loaded_module = importlib.import_module(module, package=None) - return loaded_module + module_name = ( + "beacon.framework.validator." + f"{self.request_attributes.returned_apiVersion.replace('.', '_')}." + f"{script_name}" + ) + return _load_module(module_name) + @log_with_args(config.level) def load_source_module(self, script_name): - """Choose on the fly what is the database that is going to be used for the current request""" - complete_module='beacon.connections.'+self.request_attributes.source+'.' + script_name - import importlib - module = importlib.import_module(complete_module, package=None) - return module + module_name = ( + f"beacon.connections." + f"{self.request_attributes.source}." + f"{script_name}" + ) + return _load_module(module_name) + -@log_with_args_check_configuration(config.level) -async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=None): - """Choose on the fly what is the database that is going to be used for the current request""" - try: - # Store the value for the entry type requested - entry_type=self.request_attributes.entry_type - # In case of a cross query, store the value for the entry type that will serve the requested id - pre_entry_type=self.request_attributes.pre_entry_type - except Exception: - # In case there is an exception, load the variables to be added to the error response - entry_type=None - pre_entry_type=None - # Load the configuration file for the models that are enabled - with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: - models_confile= yaml.safe_load(pfile) - pfile.close() - # Check all the model folders that are found in the beacon/models path - dirs = os.listdir("/beacon/models") - # Load conf file for connection to check which are enabled - with open('/beacon/conf/connections/connections_conf.yml') as infile: - connections_conf=yaml.safe_load(infile) - # Get array of enabled connections - connections_enabled=[] - for k, v in connections_conf.items(): - if v['connection_enabled']==True: - connections_enabled.append(k) - # Initialize an array to keep what database connections are performed (and needed to have checks) - database_connections_to_check=[] - # Loop over the folders found in the mentioned path and save the ones that are active (enabled) - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - if folder in models_confile: - if models_confile[folder]["model_enabled"] == False: - continue - # Go over the conf for the entry types of the models enabled - if "conf" in subdirs: - confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") - for confile in confiles: - # Check that the files are not pycache files - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - # Map over the different conf files attributes and look for the name of the connections - for entry_type_id, conf_entry_type_param in entry_type_confile.items(): - if entry_type == None or conf_entry_type_param['endpoint_name'] == entry_type and pre_entry_type == None or conf_entry_type_param['endpoint_name'] == pre_entry_type: - if conf_entry_type_param['entry_type_enabled'] == True: - if conf_entry_type_param['connection']['name'] not in database_connections_to_check: - if conf_entry_type_param['connection']['name'] in connections_enabled: - database_connections_to_check.append(conf_entry_type_param['connection']['name']) - # Do the same for the lookups inside the entry types - for conf_param, value_param in conf_entry_type_param.items(): - if conf_param == 'lookups': - for lookup_id, lookup_value in value_param.items(): - if isinstance(lookup_value, dict): - if pre_entry_type != None and entry_type != None: - if lookup_value['endpoint_name'] == pre_entry_type+'/{id}/'+entry_type: - if lookup_value['connection']['name'] not in database_connections_to_check: - if lookup_value['connection']['name'] in connections_enabled: - database_connections_to_check.append(lookup_value['connection']['name']) - else: - if lookup_value['connection']['name'] in connections_enabled: - database_connections_to_check.append(lookup_value['connection']['name']) - # Loop over the subfolders found in the targeted path and save the ones that are active (enabled) - else: - for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - if folder+'/'+subfolder in models_confile: - if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: - continue - # Go over the conf for the entry types of the models enabled - if "conf" in underdirs: - confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") - for confile in confiles: - # Check that the files are not pycache files - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - # Map over the different conf files attributes and look for the name of the connections - for entry_type_id, conf_entry_type_param in entry_type_confile.items(): - if entry_type == None or conf_entry_type_param['endpoint_name'] == entry_type and pre_entry_type == None or conf_entry_type_param['endpoint_name'] == pre_entry_type: - if conf_entry_type_param['entry_type_enabled'] == True: - if conf_entry_type_param['connection']['name'] not in database_connections_to_check: - if conf_entry_type_param['connection']['name'] in connections_enabled: - database_connections_to_check.append(conf_entry_type_param['connection']['name']) - # Do the same for the lookups inside the entry types - for conf_param, value_param in conf_entry_type_param.items(): - if conf_param == 'lookups': - for lookup_id, lookup_value in value_param.items(): - if isinstance(lookup_value, dict): - if pre_entry_type != None and entry_type != None: - if lookup_value['endpoint_name'] == pre_entry_type+'/{id}/'+entry_type: - if lookup_value['connection']['name'] not in database_connections_to_check: - if lookup_value['connection']['name'] in connections_enabled: - database_connections_to_check.append(lookup_value['connection']['name']) - else: - if lookup_value['connection']['name'] in connections_enabled: - database_connections_to_check.append(lookup_value['connection']['name']) - # Loop over the database connections collected - for folder in database_connections_to_check: - # Dynamically load all the modules to ping each of the databases - complete_module='beacon.connections.'+folder+'.ping' - import importlib - module = importlib.import_module(complete_module, package=None) - ping_from_module = getattr(module, 'ping_database') - # And dynamically load all the modules to get the connections strings for each of the databases - complete_client_module='beacon.connections.'+folder+'.client' - import importlib - module = importlib.import_module(complete_client_module, package=None) - client_from_module = getattr(module, 'get_client') - # Perform the ping of each of the connections with a timeout - try: - await asyncio.wait_for(ping_from_module(client_from_module()), timeout=config.pending_requests_timeout_in_seconds) - # In case of timeout or ping not successful, raise an error of the database being down - except Exception: - LOG.error('{} database is down'.format(folder)) - raise DatabaseIsDown(folder) - def load_client(folder): - """Method to get the modules of the connection strings for the databases dynamically""" - complete_client_module='beacon.connections.'+folder+'.client' - import importlib - module = importlib.import_module(complete_client_module, package=None) - client_from_module = getattr(module, 'get_client') + module_name = f"beacon.connections.{folder}.client" + return getattr(_load_module(module_name), "get_client") + def load_class(self, script_name, className): - """Method to get the classes for the validators that match the API version to return""" - module='beacon.framework.validator.'+self.request_attributes.returned_apiVersion.replace(".","_")+'.'+script_name - import importlib - loaded_module = importlib.import_module(module, package=None) - klass = getattr(loaded_module, className) - return klass + module_name = ( + "beacon.framework.validator." + f"{self.request_attributes.returned_apiVersion.replace('.', '_')}." + f"{script_name}" + ) + return _load_class(module_name, className) -def load_types_of_results(self, response_type): - """Method to get the type of schema that are accepted (for validation) in case of a model and entry type match""" - # Load the configuration file for the models that are enabled - with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: - models_confile= yaml.safe_load(pfile) - pfile.close() - # Initialize the array to collect all the entry types objects to be accepted for validation - list_of_results_classes_accepted=[] - # Generate a search of the version getting rid of the characters that join the string to the version number in conf - version_catch = re.search(r"(v\d+(\.\d+)*)", self.request_attributes.returned_schema[0]["schema"]) - # Keep the version number - if version_catch: - version = version_catch.group(1) - - # Replace dot for underscores of the version number as dots are not allowed for file names - underscored_version = version.replace(".","_") - dirs = os.listdir("/beacon/models") - - # Loop over the folders found in the mentioned path and save the ones that are active (enabled) - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - if folder in models_confile: - if models_confile[folder]["model_enabled"] == False: +@lru_cache(maxsize=None) +def _discover_result_classes(response_type, underscored_version): + models_config = _load_models_config() + result_classes = [] + + def add_validator_classes( + model_parts, + validator_base_path + ): + try: + validator_dirs = _get_directory_entries( + str(validator_base_path) + ) + except FileNotFoundError: + return + + for validator_folder in validator_dirs: + validator_path = validator_base_path / validator_folder + + try: + validator_files = _get_directory_entries( + str(validator_path) + ) + except FileNotFoundError: continue - # Go over the validator folders for the entry types of the models enabled + + for validator_file in validator_files: + if not validator_file.endswith(".py"): + continue + + if underscored_version not in validator_file: + continue + + module_name = ".".join( + [ + "beacon", + "models", + *model_parts, + "validator", + response_type, + validator_folder, + validator_file[:-3], + ] + ) + + class_name = validator_folder.capitalize() + result_classes.append( + _load_class(module_name, class_name) + ) + + for folder in _get_model_directories(): + folder_path = MODELS_PATH / folder + subdirs = _get_directory_entries(str(folder_path)) + + if ( + folder in models_config + and models_config[folder]["model_enabled"] is False + ): + continue + + # Model layout: + # + # /beacon/models//validator/... + # if "validator" in subdirs: - validatordirs = os.listdir("/beacon/models/"+folder+"/validator/"+response_type) - for validatorfolder in validatordirs: - validatorfiles = os.listdir("/beacon/models/"+folder+"/validator/"+response_type+"/"+validatorfolder) - # In case a validator folder is found, load the modules dynamically - for validatorfile in validatorfiles: - if underscored_version in validatorfile: - complete_module='beacon.models.'+folder+'.validator.'+response_type+'.'+validatorfolder+'.'+validatorfile - # Replace the python extension of the file in case there's any to avoid name not matching module - complete_module=complete_module.replace('.py', '') - import importlib - module = importlib.import_module(complete_module, package=None) - # Extract the module class matching the module name - klass = getattr(module, validatorfolder.capitalize()) - list_of_results_classes_accepted.append(klass) - # Loop over the subfolders found in the targeted path and save the ones that are active (enabled) + add_validator_classes( + [folder], + folder_path / "validator" / response_type + ) + + # Nested model layout: + # + # /beacon/models///validator/... + # for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - if folder+'/'+subfolder in models_confile: - if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: - continue - # Go over the validator for the entry types of the models enabled - if "validator" in underdirs: - try: - validatordirs = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/validator/"+response_type) - except Exception: - return None - # In case a validator folder is found, load the modules dynamically - for validatorfolder in validatordirs: - validatorfiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/validator/"+response_type+"/"+validatorfolder) - for validatorfile in validatorfiles: - if underscored_version in validatorfile: - complete_module='beacon.models.'+folder+'.'+subfolder+'.validator.'+response_type+'.'+validatorfolder+'.'+validatorfile - # Replace the python extension of the file in case there's any to avoid name not matching module - complete_module=complete_module.replace('.py', '') - import importlib - module = importlib.import_module(complete_module, package=None) - # Extract the module class matching the module name - klass = getattr(module, validatorfolder.capitalize()) - list_of_results_classes_accepted.append(klass) - # Return a pydantinc Union type of response having all the possible entry types to be returned in response as validators of the response - union_type = Union[tuple(list_of_results_classes_accepted)] - return union_type + model_key = f"{folder}/{subfolder}" -def load_routes(): - """Method to add all the needed routes when initializing or restarting the API""" - #TODO: add only the enabled lookups - # Load the configuration file for the models that are enabled - with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: - models_confile= yaml.safe_load(pfile) - pfile.close() - dirs = os.listdir("/beacon/models") - routes_to_add={} - # Loop over the folders found in the mentioned path and save the ones that are active (enabled) - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - if folder in models_confile: - if models_confile[folder]["model_enabled"] == False: + if ( + model_key in models_config + and models_config[model_key]["model_enabled"] is False + ): + continue + + model_path = folder_path / subfolder + underdirs = _get_directory_entries(str(model_path)) + + if "validator" not in underdirs: continue - # Go over the conf for the entry types of the models enabled + + add_validator_classes( + [folder, subfolder], + model_path / "validator" / response_type + ) + + return tuple(result_classes) + + +def load_types_of_results(self, response_type): + schema = self.request_attributes.returned_schema[0]["schema"] + + version_match = re.search(r"(v\d+(?:\.\d+)*)", schema) + + if not version_match: + raise ValueError( + "Could not determine schema version from returned_schema" + ) + + version = version_match.group(1) + underscored_version = version.replace(".", "_") + + classes = _discover_result_classes( + response_type, + underscored_version + ) + + if not classes: + raise ValueError( + f"No result validator classes found for " + f"response_type={response_type!r}, " + f"version={version!r}" + ) + + return Union[classes] + +def _iter_enabled_entry_type_configs(): + models_config = _load_models_config() + + for folder in _get_model_directories(): + folder_path = MODELS_PATH / folder + subdirs = _get_directory_entries(str(folder_path)) + + if ( + folder in models_config + and models_config[folder]["model_enabled"] is False + ): + continue + + model_paths = [] + if "conf" in subdirs: - confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") - for confile in confiles: - # Check that the files are not pycache files - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - # Get the routes names for each of the entry types - for entry_type_id, conf_entry_type_param in entry_type_confile.items(): - if conf_entry_type_param['entry_type_enabled'] == True: - routes_to_add[conf_entry_type_param['endpoint_name']]=[conf_entry_type_param['response_type']] - routes_to_add[conf_entry_type_param['endpoint_name']+'/{id}']=[conf_entry_type_param['response_type']] - for conf_param, value_param in conf_entry_type_param.items(): - # Get the routes names for each of the entry types lookups - if conf_param == 'lookups': - for lookup_id, lookup_value in value_param.items(): - if isinstance(lookup_value, dict): - routes_to_add[lookup_value['endpoint_name']]=[lookup_value['response_type']] + model_paths.append((folder, folder_path)) else: - # Loop over the subfolders found in the targeted path and save the ones that are active (enabled) for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - if folder+'/'+subfolder in models_confile: - if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: - continue - # Go over the conf for the entry types of the models enabled - if "conf" in underdirs: - confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") - for confile in confiles: - # Check that the files are not pycache files - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - # Get the routes names for each of the entry types - for entry_type_id, conf_entry_type_param in entry_type_confile.items(): - if conf_entry_type_param['entry_type_enabled'] == True: - routes_to_add[conf_entry_type_param['endpoint_name']]=[conf_entry_type_param['response_type']] - routes_to_add[conf_entry_type_param['endpoint_name']+'/{id}']=[conf_entry_type_param['response_type']] - for conf_param, value_param in conf_entry_type_param.items(): - # Get the routes names for each of the entry types lookups - if conf_param == 'lookups': - for lookup_id, lookup_value in value_param.items(): - if isinstance(lookup_value, dict): - routes_to_add[lookup_value['endpoint_name']]=[lookup_value['response_type']] + model_key = f"{folder}/{subfolder}" + + if ( + model_key in models_config + and models_config[model_key]["model_enabled"] is False + ): + continue + + model_paths.append( + ( + model_key, + folder_path / subfolder + ) + ) + + for model_key, model_path in model_paths: + entry_types_path = ( + model_path / "conf" / "entry_types" + ) + + try: + config_files = _get_directory_entries( + str(entry_types_path) + ) + except FileNotFoundError: + continue + + for config_file in config_files: + if config_file == "__pycache__": + continue + + if not config_file.endswith((".yml", ".yaml")): + continue + + config_path = entry_types_path / config_file + yield _load_entry_type_config(str(config_path)) + +@lru_cache(maxsize=1) +def _load_routes_cached(): + routes_to_add = {} + + for entry_type_config in _iter_enabled_entry_type_configs(): + for _, entry_type_params in entry_type_config.items(): + if not entry_type_params.get("entry_type_enabled", False): + continue + + endpoint = entry_type_params["endpoint_name"] + response_type = entry_type_params["response_type"] + + routes_to_add[endpoint] = [response_type] + routes_to_add[f"{endpoint}/{{id}}"] = [response_type] + + for lookup in entry_type_params.get("lookups", {}).values(): + if isinstance(lookup, dict): + routes_to_add[lookup["endpoint_name"]] = [ + lookup["response_type"] + ] + return routes_to_add -def _model_is_enabled(models_confile, folder, subfolder=None): - """Methot tho get the models enabled dynamically""" - if folder in models_confile and models_confile[folder]["model_enabled"] == False: - return False - if subfolder is not None: - model_key = folder + '/' + subfolder - if model_key in models_confile and models_confile[model_key]["model_enabled"] == False: - return False - return True -def get_all_modules_connections_script(script, connection): - """Method to get all the submodules of connections per model loaded dynamically""" - list_of_modules=[] - # Load the configuration file for the models that are enabled - with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: - models_confile= yaml.safe_load(pfile) - pfile.close() - dirs = os.listdir("/beacon/models") - # Loop over the folders found in the mentioned path and save the ones that are active (enabled) - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - # Get the models that are specifically enabled - if not _model_is_enabled(models_confile, folder): +def load_routes(): + """ + Return a copy so callers cannot mutate the cached dictionary. + """ + return dict(_load_routes_cached()) + +@lru_cache(maxsize=None) +def _get_one_module_conf_cached(entry_type): + for entry_type_config in _iter_enabled_entry_type_configs(): + for _, entry_type_params in entry_type_config.items(): + if entry_type_params["endpoint_name"] == entry_type: + return entry_type_config + + return None + + +def get_one_module_conf(entry_type): + result = _get_one_module_conf_cached(entry_type) + + if result is None: + return None + + return dict(result) + +@lru_cache(maxsize=1) +def _get_modules_confiles_cached(): + return tuple( + _iter_enabled_entry_type_configs() + ) + + +def get_modules_confiles(): + """ + Return a tuple of configuration dictionaries. + """ + return _get_modules_confiles_cached() + +@lru_cache(maxsize=None) +def _get_all_modules_connections_script_cached(script, connection): + modules = [] + + for folder in _get_model_directories(): + folder_path = MODELS_PATH / folder + subdirs = _get_directory_entries(str(folder_path)) + + # Direct model layout + if "connections" in subdirs: + connection_path = ( + folder_path / "connections" / connection + ) + + if connection_path.is_dir(): + module_name = ( + f"beacon.models.{folder}." + f"connections.{connection}.{script}" + ) + + try: + modules.append(_load_module(module_name)) + except ModuleNotFoundError: + pass + continue - # Go over the connections for the entry types of the models enabled + # Nested model layout + for subfolder in subdirs: + model_path = folder_path / subfolder + underdirs = _get_directory_entries(str(model_path)) + + if "connections" not in underdirs: + continue + + connection_path = ( + model_path / "connections" / connection + ) + + if not connection_path.is_dir(): + continue + + module_name = ( + f"beacon.models.{folder}.{subfolder}." + f"connections.{connection}.{script}" + ) + + try: + modules.append(_load_module(module_name)) + except ModuleNotFoundError: + pass + + return tuple(modules) + + +def get_all_modules_connections_script(script, connection): + return list( + _get_all_modules_connections_script_cached( + script, + connection + ) + ) + +@lru_cache(maxsize=None) +def _get_all_modules_datasets_cached(connection): + modules = [] + + for folder in _get_model_directories(): + folder_path = MODELS_PATH / folder + subdirs = _get_directory_entries(str(folder_path)) + if "connections" in subdirs: - connections = os.listdir("/beacon/models/"+folder+"/connections") - for dir in connections: - if dir == connection: - # Get the modules names in an array - complete_module='beacon.models.'+folder+'.connections.'+connection+'.'+script - import importlib - try: - module = importlib.import_module(complete_module, package=None) - list_of_modules.append(module) - except Exception as e: - continue - else: - # Loop over the subfolders found in the mentioned path and save the ones that are active (enabled) - for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - # Get the models that are specifically enabled - if not _model_is_enabled(models_confile, folder, subfolder): - continue - # Go over the connections for the entry types of the models enabled - if "connections" in underdirs: - connections = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/connections") - for dir in connections: - if dir == connection: - # Get the modules names in an array - complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.'+connection+'.'+script - import importlib - module = importlib.import_module(complete_module, package=None) - list_of_modules.append(module) - return list_of_modules + module_name = ( + f"beacon.models.{folder}." + f"connections.{connection}.collections" + ) + + try: + modules.append(_load_module(module_name)) + except ModuleNotFoundError: + pass + + for subfolder in subdirs: + model_path = folder_path / subfolder + underdirs = _get_directory_entries(str(model_path)) + + if "connections" not in underdirs: + continue + + module_name = ( + f"beacon.models.{folder}.{subfolder}." + f"connections.{connection}.collections" + ) + + try: + modules.append(_load_module(module_name)) + except ModuleNotFoundError: + pass + + return tuple(modules) + def get_all_modules_datasets(connection): - """Method to get the datasets collections for each of the models to be returned""" - list_of_modules=[] - # Load the configuration file for the models that are enabled - with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: - models_confile= yaml.safe_load(pfile) - pfile.close() - dirs = os.listdir("/beacon/models") - # Loop over the folders found in the mentioned path and save the ones that are active (enabled) - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - # Get the models that are specifically enabled - if not _model_is_enabled(models_confile, folder): - continue - # Go over the collections of the models enabled in the connections folder + return list( + _get_all_modules_datasets_cached(connection) + ) + +@lru_cache(maxsize=None) +def _get_all_modules_datasets_cached(connection): + modules = [] + + for folder in _get_model_directories(): + folder_path = MODELS_PATH / folder + subdirs = _get_directory_entries(str(folder_path)) + if "connections" in subdirs: + module_name = ( + f"beacon.models.{folder}." + f"connections.{connection}.collections" + ) + try: - # Get the names of the collections validators to be validated and accepted - complete_module='beacon.models.'+folder+'.connections.'+connection+'.collections' - import importlib - module = importlib.import_module(complete_module, package=None) - list_of_modules.append(module) - except Exception: + modules.append(_load_module(module_name)) + except ModuleNotFoundError: pass - # Loop over the subfolders found in the mentioned path and save the ones that are active (enabled) + for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - # Get the models that are specifically enabled - if not _model_is_enabled(models_confile, folder, subfolder): + model_path = folder_path / subfolder + underdirs = _get_directory_entries(str(model_path)) + + if "connections" not in underdirs: continue - # Go over the collections of the models enabled in the connections folder - if "connections" in underdirs: - try: - # Get the names of the collections validators to be validated and accepted - complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.'+connection+'.collections' - import importlib - module = importlib.import_module(complete_module, package=None) - list_of_modules.append(module) - except Exception: - pass - return list_of_modules - -def get_one_module_conf(entry_type): - """Method to get the configuration of the desired entry types""" - # TODO: Cache the module conf loading to only execute it once. - dirs = os.listdir("/beacon/models") - # Loop over the folders found in the models and get the entry types configuration - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - # Go over the entry types files in the conf folder - if "conf" in subdirs: - confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") - for confile in confiles: - # Skip the files that are of pycache type - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - # Get the configuration file for the entry type that matches the one requested - for entry_type_id, entry_type_params in entry_type_confile.items(): - if entry_type_params["endpoint_name"] == entry_type: - return entry_type_confile - else: - # Loop over the subfolders found in the models and get the entry types configuration - for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - # Go over the entry types files in the conf folder - if "conf" in underdirs: - confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") - for confile in confiles: - # Skip the files that are of pycache type - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - # Get the configuration file for the entry type that matches the one requested - for entry_type_id, entry_type_params in entry_type_confile.items(): - if entry_type_params["endpoint_name"] == entry_type: - return entry_type_confile -def get_modules_confiles(): - """Method to get all the entry types configuration files""" - # Load the configuration file for the models that are enabled - with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: - models_confile= yaml.safe_load(pfile) - pfile.close() - dirs = os.listdir("/beacon/models") - list_of_confiles=[] - # Loop over the folders found in the models and get the entry types configuration - for folder in dirs: - subdirs = os.listdir("/beacon/models/"+folder) - # Go over the entry types files in the conf folder - if "conf" in subdirs: - confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") - if folder in models_confile: - if models_confile[folder]["model_enabled"] == False: + module_name = ( + f"beacon.models.{folder}.{subfolder}." + f"connections.{connection}.collections" + ) + + try: + modules.append(_load_module(module_name)) + except ModuleNotFoundError: + pass + + return tuple(modules) + + +def get_all_modules_datasets(connection): + return list( + _get_all_modules_datasets_cached(connection) + ) + +@lru_cache(maxsize=None) +def _get_database_connections_to_check( + entry_type=None, + pre_entry_type=None +): + connections_config = _load_connections_config() + + connections_enabled = { + name + for name, value in connections_config.items() + if value.get("connection_enabled") is True + } + + connections_to_check = set() + + for entry_type_config in _iter_enabled_entry_type_configs(): + for _, params in entry_type_config.items(): + endpoint = params.get("endpoint_name") + + matches = ( + entry_type is None + or endpoint == entry_type + or pre_entry_type is None + or endpoint == pre_entry_type + ) + + if not matches: + continue + + if not params.get("entry_type_enabled", False): + continue + + connection_name = params["connection"]["name"] + + if connection_name in connections_enabled: + connections_to_check.add(connection_name) + + for lookup in params.get("lookups", {}).values(): + if not isinstance(lookup, dict): continue - for confile in confiles: - # Skip the files that are of pycache type - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - list_of_confiles.append(entry_type_confile) - else: - # Loop over the subfolders found in the models and get the entry types configuration - for subfolder in subdirs: - underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) - if folder+'/'+subfolder in models_confile: - if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: - continue - # Go over the entry types files in the conf folder - if "conf" in underdirs: - confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") - for confile in confiles: - # Skip the files that are of pycache type - if confile != '__pycache__': - with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: - entry_type_confile = yaml.safe_load(pfile) - pfile.close() - list_of_confiles.append(entry_type_confile) - return list_of_confiles - + + lookup_endpoint = lookup.get("endpoint_name") + + if ( + entry_type is not None + and pre_entry_type is not None + and lookup_endpoint + == f"{pre_entry_type}/{{id}}/{entry_type}" + ): + lookup_connection = lookup["connection"]["name"] + + if lookup_connection in connections_enabled: + connections_to_check.add(lookup_connection) + + return tuple(sorted(connections_to_check)) + +@log_with_args_check_configuration(config.level) +async def check_database_connections( + LOG=None, + entry_type=None, + pre_entry_type=None +): + connections = _get_database_connections_to_check( + entry_type, + pre_entry_type + ) + + for folder in connections: + ping_module = _load_module( + f"beacon.connections.{folder}.ping" + ) + client_module = _load_module( + f"beacon.connections.{folder}.client" + ) + + ping_database = getattr( + ping_module, + "ping_database" + ) + get_client = getattr( + client_module, + "get_client" + ) + + try: + await asyncio.wait_for( + ping_database(get_client()), + timeout=config.pending_requests_timeout_in_seconds + ) + except Exception: + LOG.error(f"{folder} database is down") + raise DatabaseIsDown(folder) \ No newline at end of file From 57d3a127acefab8fc382b178a6f34cab46becd0a Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 29 Sep 2026 15:14:13 +0200 Subject: [PATCH 45/56] updating load types of results --- beacon/utils/modules.py | 1253 ++++++++++++++++++++++++--------------- 1 file changed, 779 insertions(+), 474 deletions(-) diff --git a/beacon/utils/modules.py b/beacon/utils/modules.py index 1419c6d1..e172aeec 100644 --- a/beacon/utils/modules.py +++ b/beacon/utils/modules.py @@ -8,609 +8,914 @@ from beacon.exceptions.exceptions import DatabaseIsDown import asyncio import time -from functools import lru_cache -from pathlib import Path -import importlib -MODELS_CONFIG_PATH = Path("/beacon/conf/models/models_conf.yml") -CONNECTIONS_CONFIG_PATH = Path( - "/beacon/conf/connections/connections_conf.yml" -) -MODELS_PATH = Path("/beacon/models") +#TODO: get_client() passing one variable with the database name. +@log_with_args(config.level) +def load_framework_module(self, script_name): + """Choose what is the validator object class that will be loaded depending on the API version to return""" + module='beacon.framework.validator.'+self.request_attributes.returned_apiVersion.replace(".","_")+'.'+script_name + import importlib + loaded_module = importlib.import_module(module, package=None) + return loaded_module +@log_with_args(config.level) +def load_source_module(self, script_name): + """Choose on the fly what is the database that is going to be used for the current request""" + complete_module='beacon.connections.'+self.request_attributes.source+'.' + script_name + import importlib + module = importlib.import_module(complete_module, package=None) + return module -# Increment this whenever configuration or model files change. -_CACHE_VERSION = 0 +@log_with_args_check_configuration(config.level) +async def check_database_connections(LOG=None, entry_type=None, pre_entry_type=None): + """Choose on the fly what is the database that is going to be used for the current request""" + # Load the configuration file for the models that are enabled + with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: + models_confile= yaml.safe_load(pfile) + pfile.close() + # Check all the model folders that are found in the beacon/models path + dirs = os.listdir("/beacon/models") + # Load conf file for connection to check which are enabled + with open('/beacon/conf/connections/connections_conf.yml') as infile: + connections_conf=yaml.safe_load(infile) + # Get array of enabled connections + connections_enabled=[] + for k, v in connections_conf.items(): + if v['connection_enabled']==True: + connections_enabled.append(k) + # Initialize an array to keep what database connections are performed (and needed to have checks) + database_connections_to_check=[] + # Loop over the folders found in the mentioned path and save the ones that are active (enabled) + for folder in dirs: + subdirs = os.listdir("/beacon/models/"+folder) + if folder in models_confile: + if models_confile[folder]["model_enabled"] == False: + continue + # Go over the conf for the entry types of the models enabled + if "conf" in subdirs: + confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") + for confile in confiles: + # Check that the files are not pycache files + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + # Map over the different conf files attributes and look for the name of the connections + for entry_type_id, conf_entry_type_param in entry_type_confile.items(): + if entry_type == None or conf_entry_type_param['endpoint_name'] == entry_type and pre_entry_type == None or conf_entry_type_param['endpoint_name'] == pre_entry_type: + if conf_entry_type_param['entry_type_enabled'] == True: + if conf_entry_type_param['connection']['name'] not in database_connections_to_check: + if conf_entry_type_param['connection']['name'] in connections_enabled: + database_connections_to_check.append(conf_entry_type_param['connection']['name']) + # Do the same for the lookups inside the entry types + for conf_param, value_param in conf_entry_type_param.items(): + if conf_param == 'lookups': + for lookup_id, lookup_value in value_param.items(): + if isinstance(lookup_value, dict): + if pre_entry_type != None and entry_type != None: + if lookup_value['endpoint_name'] == pre_entry_type+'/{id}/'+entry_type: + if lookup_value['connection']['name'] not in database_connections_to_check: + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) + else: + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) + # Loop over the subfolders found in the targeted path and save the ones that are active (enabled) + else: + for subfolder in subdirs: + underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) + if folder+'/'+subfolder in models_confile: + if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: + continue + # Go over the conf for the entry types of the models enabled + if "conf" in underdirs: + confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") + for confile in confiles: + # Check that the files are not pycache files + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + # Map over the different conf files attributes and look for the name of the connections + for entry_type_id, conf_entry_type_param in entry_type_confile.items(): + if entry_type == None or conf_entry_type_param['endpoint_name'] == entry_type and pre_entry_type == None or conf_entry_type_param['endpoint_name'] == pre_entry_type: + if conf_entry_type_param['entry_type_enabled'] == True: + if conf_entry_type_param['connection']['name'] not in database_connections_to_check: + if conf_entry_type_param['connection']['name'] in connections_enabled: + database_connections_to_check.append(conf_entry_type_param['connection']['name']) + # Do the same for the lookups inside the entry types + for conf_param, value_param in conf_entry_type_param.items(): + if conf_param == 'lookups': + for lookup_id, lookup_value in value_param.items(): + if isinstance(lookup_value, dict): + if pre_entry_type != None and entry_type != None: + if lookup_value['endpoint_name'] == pre_entry_type+'/{id}/'+entry_type: + if lookup_value['connection']['name'] not in database_connections_to_check: + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) + else: + if lookup_value['connection']['name'] in connections_enabled: + database_connections_to_check.append(lookup_value['connection']['name']) + # Loop over the database connections collected + for folder in database_connections_to_check: + # Dynamically load all the modules to ping each of the databases + complete_module='beacon.connections.'+folder+'.ping' + import importlib + module = importlib.import_module(complete_module, package=None) + ping_from_module = getattr(module, 'ping_database') + # And dynamically load all the modules to get the connections strings for each of the databases + complete_client_module='beacon.connections.'+folder+'.client' + import importlib + module = importlib.import_module(complete_client_module, package=None) + client_from_module = getattr(module, 'get_client') + # Perform the ping of each of the connections with a timeout + try: + await asyncio.wait_for(ping_from_module(client_from_module()), timeout=config.pending_requests_timeout_in_seconds) + # In case of timeout or ping not successful, raise an error of the database being down + except Exception: + LOG.error('{} database is down'.format(folder)) + raise DatabaseIsDown(folder) + +def load_client(folder): + """Method to get the modules of the connection strings for the databases dynamically""" + complete_client_module='beacon.connections.'+folder+'.client' + import importlib + module = importlib.import_module(complete_client_module, package=None) + client_from_module = getattr(module, 'get_client') +def load_class(self, script_name, className): + """Method to get the classes for the validators that match the API version to return""" + module='beacon.framework.validator.'+self.request_attributes.returned_apiVersion.replace(".","_")+'.'+script_name + import importlib + loaded_module = importlib.import_module(module, package=None) + klass = getattr(loaded_module, className) + return klass -def clear_configuration_caches(): - """ - Clear all caches that depend on filesystem/configuration state. - Call this after changing models_conf.yml, connections_conf.yml, - adding/removing models, or adding/removing validator modules. - """ - global _CACHE_VERSION - _CACHE_VERSION += 1 - - _load_models_config.cache_clear() - _load_connections_config.cache_clear() - _get_model_directories.cache_clear() - _get_directory_entries.cache_clear() - _load_entry_type_config.cache_clear() - _discover_result_classes.cache_clear() - _get_one_module_conf_cached.cache_clear() - _get_modules_confiles_cached.cache_clear() - _get_all_modules_connections_script_cached.cache_clear() - _get_all_modules_datasets_cached.cache_clear() - -@lru_cache(maxsize=1) -def _load_models_config(): - with MODELS_CONFIG_PATH.open("r") as pfile: - return yaml.safe_load(pfile) or {} - - -@lru_cache(maxsize=1) -def _load_connections_config(): - with CONNECTIONS_CONFIG_PATH.open("r") as infile: - return yaml.safe_load(infile) or {} - - -@lru_cache(maxsize=1) -def _get_model_directories(): - """ - Return a tuple because cached return values should not be mutated. - """ - return tuple( - entry.name - for entry in MODELS_PATH.iterdir() - if entry.is_dir() - ) +# Module-level cache. +# Put these OUTSIDE load_types_of_results(), near the top of the module. +_RESULT_TYPES_CACHE = {} +_RESULT_TYPES_CONFIG_MTIME = None -@lru_cache(maxsize=None) -def _get_directory_entries(path_string): - """ - Cached equivalent of os.listdir(path). - """ - path = Path(path_string) +_MODELS_CONF_PATH = "/beacon/conf/models/models_conf.yml" +_MODELS_BASE_PATH = "/beacon/models" - return tuple( - entry.name - for entry in path.iterdir() - ) +def load_types_of_results(self, response_type): + """ + Load the result validator types for the requested response type/version. -@lru_cache(maxsize=None) -def _load_entry_type_config(path_string): - path = Path(path_string) + The discovered Union type is cached so that filesystem scanning, + YAML parsing and dynamic imports do not happen on every request. - with path.open("r") as pfile: - return yaml.safe_load(pfile) or {} + The cache is automatically invalidated when models_conf.yml changes. + """ -@lru_cache(maxsize=None) -def _load_module(module_name): - return importlib.import_module(module_name) + import importlib + import sys + import time + global _RESULT_TYPES_CONFIG_MTIME -@lru_cache(maxsize=None) -def _load_class(module_name, class_name): - module = _load_module(module_name) - return getattr(module, class_name) + total_start = time.perf_counter() -@log_with_args(config.level) -def load_framework_module(self, script_name): - module_name = ( - "beacon.framework.validator." - f"{self.request_attributes.returned_apiVersion.replace('.', '_')}." - f"{script_name}" - ) - return _load_module(module_name) + # --------------------------------------------------------- + # Get schema version + # --------------------------------------------------------- + start = time.perf_counter() - -@log_with_args(config.level) -def load_source_module(self, script_name): - module_name = ( - f"beacon.connections." - f"{self.request_attributes.source}." - f"{script_name}" + version_catch = re.search( + r"(v\d+(\.\d+)*)", + self.request_attributes.returned_schema[0]["schema"] ) - return _load_module(module_name) - -def load_client(folder): - module_name = f"beacon.connections.{folder}.client" - return getattr(_load_module(module_name), "get_client") + if not version_catch: + raise ValueError( + "Could not determine schema version from returned_schema" + ) + version = version_catch.group(1) + underscored_version = version.replace(".", "_") -def load_class(self, script_name, className): - module_name = ( - "beacon.framework.validator." - f"{self.request_attributes.returned_apiVersion.replace('.', '_')}." - f"{script_name}" + print( + f"[TIMING] version processing: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, ) - return _load_class(module_name, className) -@lru_cache(maxsize=None) -def _discover_result_classes(response_type, underscored_version): - models_config = _load_models_config() - result_classes = [] - - def add_validator_classes( - model_parts, - validator_base_path - ): - try: - validator_dirs = _get_directory_entries( - str(validator_base_path) - ) - except FileNotFoundError: - return + # --------------------------------------------------------- + # Check models_conf.yml modification time + # --------------------------------------------------------- + start = time.perf_counter() - for validator_folder in validator_dirs: - validator_path = validator_base_path / validator_folder + config_mtime = os.stat( + _MODELS_CONF_PATH + ).st_mtime_ns - try: - validator_files = _get_directory_entries( - str(validator_path) - ) - except FileNotFoundError: - continue + print( + f"[TIMING] config mtime check: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) - for validator_file in validator_files: - if not validator_file.endswith(".py"): - continue + # --------------------------------------------------------- + # Invalidate entire cache if configuration changed + # --------------------------------------------------------- + if _RESULT_TYPES_CONFIG_MTIME != config_mtime: - if underscored_version not in validator_file: - continue + if _RESULT_TYPES_CONFIG_MTIME is not None: + print( + "[TIMING] models_conf.yml changed - " + "clearing result types cache", + flush=True, + ) - module_name = ".".join( - [ - "beacon", - "models", - *model_parts, - "validator", - response_type, - validator_folder, - validator_file[:-3], - ] - ) + _RESULT_TYPES_CACHE.clear() - class_name = validator_folder.capitalize() - result_classes.append( - _load_class(module_name, class_name) - ) + _RESULT_TYPES_CONFIG_MTIME = config_mtime - for folder in _get_model_directories(): - folder_path = MODELS_PATH / folder - subdirs = _get_directory_entries(str(folder_path)) + # --------------------------------------------------------- + # Cache lookup + # --------------------------------------------------------- + cache_key = ( + response_type, + underscored_version, + ) - if ( - folder in models_config - and models_config[folder]["model_enabled"] is False - ): - continue + if cache_key in _RESULT_TYPES_CACHE: - # Model layout: - # - # /beacon/models//validator/... - # - if "validator" in subdirs: - add_validator_classes( - [folder], - folder_path / "validator" / response_type - ) + print( + f"[TIMING] load_types_of_results CACHE HIT: " + f"{cache_key}", + flush=True, + ) - # Nested model layout: - # - # /beacon/models///validator/... - # - for subfolder in subdirs: - model_key = f"{folder}/{subfolder}" + print( + f"[TIMING] load_types_of_results TOTAL: " + f"{(time.perf_counter() - total_start) * 1000:.2f} ms", + flush=True, + ) - if ( - model_key in models_config - and models_config[model_key]["model_enabled"] is False - ): - continue + return _RESULT_TYPES_CACHE[cache_key] - model_path = folder_path / subfolder - underdirs = _get_directory_entries(str(model_path)) + print( + f"[TIMING] load_types_of_results CACHE MISS: " + f"{cache_key}", + flush=True, + ) - if "validator" not in underdirs: - continue + # --------------------------------------------------------- + # Load configuration + # --------------------------------------------------------- + start = time.perf_counter() + + with open( + _MODELS_CONF_PATH, + "r" + ) as pfile: + models_confile = yaml.safe_load(pfile) + + print( + f"[TIMING] load_types YAML: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) - add_validator_classes( - [folder, subfolder], - model_path / "validator" / response_type - ) + # --------------------------------------------------------- + # Initialize + # --------------------------------------------------------- + list_of_results_classes_accepted = [] - return tuple(result_classes) + import_count = 0 + cached_import_count = 0 + # --------------------------------------------------------- + # Helper for imports + # --------------------------------------------------------- + def timed_import(module_name): -def load_types_of_results(self, response_type): - schema = self.request_attributes.returned_schema[0]["schema"] + nonlocal import_count + nonlocal cached_import_count - version_match = re.search(r"(v\d+(?:\.\d+)*)", schema) + already_cached = module_name in sys.modules - if not version_match: - raise ValueError( - "Could not determine schema version from returned_schema" + print( + f"[TIMING] IMPORT START: {module_name} " + f"(cached={already_cached})", + flush=True, ) - version = version_match.group(1) - underscored_version = version.replace(".", "_") + start_import = time.perf_counter() - classes = _discover_result_classes( - response_type, - underscored_version - ) + module = importlib.import_module( + module_name, + package=None + ) - if not classes: - raise ValueError( - f"No result validator classes found for " - f"response_type={response_type!r}, " - f"version={version!r}" + elapsed_import = ( + time.perf_counter() - start_import ) - return Union[classes] + import_count += 1 -def _iter_enabled_entry_type_configs(): - models_config = _load_models_config() + if already_cached: + cached_import_count += 1 - for folder in _get_model_directories(): - folder_path = MODELS_PATH / folder - subdirs = _get_directory_entries(str(folder_path)) + print( + f"[TIMING] IMPORT END: {module_name} " + f"{elapsed_import * 1000:.2f} ms " + f"(cached={already_cached})", + flush=True, + ) - if ( - folder in models_config - and models_config[folder]["model_enabled"] is False - ): - continue + return module - model_paths = [] + # --------------------------------------------------------- + # Get model directories + # --------------------------------------------------------- + start = time.perf_counter() - if "conf" in subdirs: - model_paths.append((folder, folder_path)) - else: - for subfolder in subdirs: - model_key = f"{folder}/{subfolder}" + dirs = os.listdir( + _MODELS_BASE_PATH + ) - if ( - model_key in models_config - and models_config[model_key]["model_enabled"] is False - ): - continue + print( + f"[TIMING] initial os.listdir: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) - model_paths.append( - ( - model_key, - folder_path / subfolder - ) - ) + # --------------------------------------------------------- + # Search models + # --------------------------------------------------------- + filesystem_start = time.perf_counter() - for model_key, model_path in model_paths: - entry_types_path = ( - model_path / "conf" / "entry_types" - ) + for folder in dirs: - try: - config_files = _get_directory_entries( - str(entry_types_path) - ) - except FileNotFoundError: - continue + start = time.perf_counter() - for config_file in config_files: - if config_file == "__pycache__": - continue + subdirs = os.listdir( + _MODELS_BASE_PATH + "/" + folder + ) - if not config_file.endswith((".yml", ".yaml")): - continue + elapsed = time.perf_counter() - start - config_path = entry_types_path / config_file - yield _load_entry_type_config(str(config_path)) + if elapsed > 0.5 / 1000: + print( + f"[TIMING] os.listdir folder={folder}: " + f"{elapsed * 1000:.2f} ms", + flush=True, + ) -@lru_cache(maxsize=1) -def _load_routes_cached(): - routes_to_add = {} + # ----------------------------------------------------- + # Check if top-level model is enabled + # ----------------------------------------------------- + if folder in models_confile: - for entry_type_config in _iter_enabled_entry_type_configs(): - for _, entry_type_params in entry_type_config.items(): - if not entry_type_params.get("entry_type_enabled", False): + if models_confile[ + folder + ]["model_enabled"] is False: continue - endpoint = entry_type_params["endpoint_name"] - response_type = entry_type_params["response_type"] - - routes_to_add[endpoint] = [response_type] - routes_to_add[f"{endpoint}/{{id}}"] = [response_type] + # ===================================================== + # Direct validator directory + # ===================================================== + if "validator" in subdirs: - for lookup in entry_type_params.get("lookups", {}).values(): - if isinstance(lookup, dict): - routes_to_add[lookup["endpoint_name"]] = [ - lookup["response_type"] - ] + validator_base_path = ( + _MODELS_BASE_PATH + + "/" + + folder + + "/validator/" + + response_type + ) - return routes_to_add + start = time.perf_counter() + validatordirs = os.listdir( + validator_base_path + ) -def load_routes(): - """ - Return a copy so callers cannot mutate the cached dictionary. - """ - return dict(_load_routes_cached()) + print( + f"[TIMING] os.listdir validators " + f"{validator_base_path}: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) -@lru_cache(maxsize=None) -def _get_one_module_conf_cached(entry_type): - for entry_type_config in _iter_enabled_entry_type_configs(): - for _, entry_type_params in entry_type_config.items(): - if entry_type_params["endpoint_name"] == entry_type: - return entry_type_config + for validatorfolder in validatordirs: - return None + validator_path = ( + validator_base_path + + "/" + + validatorfolder + ) + start = time.perf_counter() -def get_one_module_conf(entry_type): - result = _get_one_module_conf_cached(entry_type) + validatorfiles = os.listdir( + validator_path + ) - if result is None: - return None + elapsed = time.perf_counter() - start - return dict(result) + if elapsed > 0.5 / 1000: + print( + f"[TIMING] os.listdir validator " + f"{validatorfolder}: " + f"{elapsed * 1000:.2f} ms", + flush=True, + ) -@lru_cache(maxsize=1) -def _get_modules_confiles_cached(): - return tuple( - _iter_enabled_entry_type_configs() - ) + for validatorfile in validatorfiles: + if underscored_version not in validatorfile: + continue -def get_modules_confiles(): - """ - Return a tuple of configuration dictionaries. - """ - return _get_modules_confiles_cached() + complete_module = ( + "beacon.models." + + folder + + ".validator." + + response_type + + "." + + validatorfolder + + "." + + validatorfile + ) -@lru_cache(maxsize=None) -def _get_all_modules_connections_script_cached(script, connection): - modules = [] + complete_module = complete_module.replace( + ".py", + "" + ) - for folder in _get_model_directories(): - folder_path = MODELS_PATH / folder - subdirs = _get_directory_entries(str(folder_path)) + module = timed_import( + complete_module + ) - # Direct model layout - if "connections" in subdirs: - connection_path = ( - folder_path / "connections" / connection - ) + start = time.perf_counter() - if connection_path.is_dir(): - module_name = ( - f"beacon.models.{folder}." - f"connections.{connection}.{script}" - ) + klass = getattr( + module, + validatorfolder.capitalize() + ) - try: - modules.append(_load_module(module_name)) - except ModuleNotFoundError: - pass + print( + f"[TIMING] getattr " + f"{complete_module}: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) - continue + list_of_results_classes_accepted.append( + klass + ) - # Nested model layout + # ===================================================== + # Nested model directories + # ===================================================== for subfolder in subdirs: - model_path = folder_path / subfolder - underdirs = _get_directory_entries(str(model_path)) - - if "connections" not in underdirs: - continue - connection_path = ( - model_path / "connections" / connection + model_path = ( + _MODELS_BASE_PATH + + "/" + + folder + + "/" + + subfolder ) - if not connection_path.is_dir(): - continue + start = time.perf_counter() - module_name = ( - f"beacon.models.{folder}.{subfolder}." - f"connections.{connection}.{script}" + underdirs = os.listdir( + model_path ) - try: - modules.append(_load_module(module_name)) - except ModuleNotFoundError: - pass + elapsed = time.perf_counter() - start - return tuple(modules) + if elapsed > 0.5 / 1000: + print( + f"[TIMING] os.listdir model " + f"{folder}/{subfolder}: " + f"{elapsed * 1000:.2f} ms", + flush=True, + ) + model_config_key = ( + folder + "/" + subfolder + ) -def get_all_modules_connections_script(script, connection): - return list( - _get_all_modules_connections_script_cached( - script, - connection - ) - ) + if model_config_key in models_confile: -@lru_cache(maxsize=None) -def _get_all_modules_datasets_cached(connection): - modules = [] + if models_confile[ + model_config_key + ]["model_enabled"] is False: + continue - for folder in _get_model_directories(): - folder_path = MODELS_PATH / folder - subdirs = _get_directory_entries(str(folder_path)) + if "validator" not in underdirs: + continue - if "connections" in subdirs: - module_name = ( - f"beacon.models.{folder}." - f"connections.{connection}.collections" + validator_base_path = ( + _MODELS_BASE_PATH + + "/" + + folder + + "/" + + subfolder + + "/validator/" + + response_type ) try: - modules.append(_load_module(module_name)) - except ModuleNotFoundError: - pass - for subfolder in subdirs: - model_path = folder_path / subfolder - underdirs = _get_directory_entries(str(model_path)) + start = time.perf_counter() - if "connections" not in underdirs: - continue + validatordirs = os.listdir( + validator_base_path + ) - module_name = ( - f"beacon.models.{folder}.{subfolder}." - f"connections.{connection}.collections" - ) + print( + f"[TIMING] os.listdir nested validators " + f"{folder}/{subfolder}: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) - try: - modules.append(_load_module(module_name)) - except ModuleNotFoundError: - pass + except Exception: + return None - return tuple(modules) + for validatorfolder in validatordirs: + validator_path = ( + validator_base_path + + "/" + + validatorfolder + ) -def get_all_modules_datasets(connection): - return list( - _get_all_modules_datasets_cached(connection) - ) + start = time.perf_counter() -@lru_cache(maxsize=None) -def _get_all_modules_datasets_cached(connection): - modules = [] + validatorfiles = os.listdir( + validator_path + ) - for folder in _get_model_directories(): - folder_path = MODELS_PATH / folder - subdirs = _get_directory_entries(str(folder_path)) + elapsed = time.perf_counter() - start - if "connections" in subdirs: - module_name = ( - f"beacon.models.{folder}." - f"connections.{connection}.collections" - ) + if elapsed > 0.5 / 1000: + print( + f"[TIMING] os.listdir nested validator " + f"{validatorfolder}: " + f"{elapsed * 1000:.2f} ms", + flush=True, + ) - try: - modules.append(_load_module(module_name)) - except ModuleNotFoundError: - pass + for validatorfile in validatorfiles: + + if underscored_version not in validatorfile: + continue + + complete_module = ( + "beacon.models." + + folder + + "." + + subfolder + + ".validator." + + response_type + + "." + + validatorfolder + + "." + + validatorfile + ) - for subfolder in subdirs: - model_path = folder_path / subfolder - underdirs = _get_directory_entries(str(model_path)) + complete_module = complete_module.replace( + ".py", + "" + ) - if "connections" not in underdirs: - continue + module = timed_import( + complete_module + ) - module_name = ( - f"beacon.models.{folder}.{subfolder}." - f"connections.{connection}.collections" - ) + start = time.perf_counter() - try: - modules.append(_load_module(module_name)) - except ModuleNotFoundError: - pass + klass = getattr( + module, + validatorfolder.capitalize() + ) - return tuple(modules) + print( + f"[TIMING] getattr " + f"{complete_module}: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) + list_of_results_classes_accepted.append( + klass + ) -def get_all_modules_datasets(connection): - return list( - _get_all_modules_datasets_cached(connection) + # --------------------------------------------------------- + # Filesystem + imports timing + # --------------------------------------------------------- + print( + f"[TIMING] filesystem + imports: " + f"{(time.perf_counter() - filesystem_start) * 1000:.2f} ms " + f"({import_count} imports, " + f"{cached_import_count} already cached)", + flush=True, ) -@lru_cache(maxsize=None) -def _get_database_connections_to_check( - entry_type=None, - pre_entry_type=None -): - connections_config = _load_connections_config() - - connections_enabled = { - name - for name, value in connections_config.items() - if value.get("connection_enabled") is True - } - - connections_to_check = set() - - for entry_type_config in _iter_enabled_entry_type_configs(): - for _, params in entry_type_config.items(): - endpoint = params.get("endpoint_name") - - matches = ( - entry_type is None - or endpoint == entry_type - or pre_entry_type is None - or endpoint == pre_entry_type - ) + # --------------------------------------------------------- + # Show discovered classes + # --------------------------------------------------------- + print( + f"[TIMING] result classes found: " + f"{len(list_of_results_classes_accepted)}", + flush=True, + ) - if not matches: - continue + for klass in list_of_results_classes_accepted: - if not params.get("entry_type_enabled", False): - continue + print( + f"[TIMING] result class: " + f"{klass.__module__}.{klass.__name__}", + flush=True, + ) - connection_name = params["connection"]["name"] + # --------------------------------------------------------- + # Build Union + # --------------------------------------------------------- + start = time.perf_counter() - if connection_name in connections_enabled: - connections_to_check.add(connection_name) + union_type = Union[ + tuple(list_of_results_classes_accepted) + ] - for lookup in params.get("lookups", {}).values(): - if not isinstance(lookup, dict): - continue + print( + f"[TIMING] Union construction: " + f"{(time.perf_counter() - start) * 1000:.2f} ms", + flush=True, + ) - lookup_endpoint = lookup.get("endpoint_name") + # --------------------------------------------------------- + # Store in cache + # --------------------------------------------------------- + _RESULT_TYPES_CACHE[cache_key] = union_type - if ( - entry_type is not None - and pre_entry_type is not None - and lookup_endpoint - == f"{pre_entry_type}/{{id}}/{entry_type}" - ): - lookup_connection = lookup["connection"]["name"] + print( + f"[TIMING] load_types_of_results cached: " + f"{cache_key}", + flush=True, + ) - if lookup_connection in connections_enabled: - connections_to_check.add(lookup_connection) + # --------------------------------------------------------- + # Total + # --------------------------------------------------------- + print( + f"[TIMING] load_types_of_results TOTAL: " + f"{(time.perf_counter() - total_start) * 1000:.2f} ms", + flush=True, + ) - return tuple(sorted(connections_to_check)) + return union_type -@log_with_args_check_configuration(config.level) -async def check_database_connections( - LOG=None, - entry_type=None, - pre_entry_type=None -): - connections = _get_database_connections_to_check( - entry_type, - pre_entry_type - ) +def load_routes(): + """Method to add all the needed routes when initializing or restarting the API""" + #TODO: add only the enabled lookups + # Load the configuration file for the models that are enabled + with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: + models_confile= yaml.safe_load(pfile) + pfile.close() + dirs = os.listdir("/beacon/models") + routes_to_add={} + # Loop over the folders found in the mentioned path and save the ones that are active (enabled) + for folder in dirs: + subdirs = os.listdir("/beacon/models/"+folder) + if folder in models_confile: + if models_confile[folder]["model_enabled"] == False: + continue + # Go over the conf for the entry types of the models enabled + if "conf" in subdirs: + confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") + for confile in confiles: + # Check that the files are not pycache files + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + # Get the routes names for each of the entry types + for entry_type_id, conf_entry_type_param in entry_type_confile.items(): + if conf_entry_type_param['entry_type_enabled'] == True: + routes_to_add[conf_entry_type_param['endpoint_name']]=[conf_entry_type_param['response_type']] + routes_to_add[conf_entry_type_param['endpoint_name']+'/{id}']=[conf_entry_type_param['response_type']] + for conf_param, value_param in conf_entry_type_param.items(): + # Get the routes names for each of the entry types lookups + if conf_param == 'lookups': + for lookup_id, lookup_value in value_param.items(): + if isinstance(lookup_value, dict): + routes_to_add[lookup_value['endpoint_name']]=[lookup_value['response_type']] + else: + # Loop over the subfolders found in the targeted path and save the ones that are active (enabled) + for subfolder in subdirs: + underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) + if folder+'/'+subfolder in models_confile: + if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: + continue + # Go over the conf for the entry types of the models enabled + if "conf" in underdirs: + confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") + for confile in confiles: + # Check that the files are not pycache files + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + # Get the routes names for each of the entry types + for entry_type_id, conf_entry_type_param in entry_type_confile.items(): + if conf_entry_type_param['entry_type_enabled'] == True: + routes_to_add[conf_entry_type_param['endpoint_name']]=[conf_entry_type_param['response_type']] + routes_to_add[conf_entry_type_param['endpoint_name']+'/{id}']=[conf_entry_type_param['response_type']] + for conf_param, value_param in conf_entry_type_param.items(): + # Get the routes names for each of the entry types lookups + if conf_param == 'lookups': + for lookup_id, lookup_value in value_param.items(): + if isinstance(lookup_value, dict): + routes_to_add[lookup_value['endpoint_name']]=[lookup_value['response_type']] + return routes_to_add - for folder in connections: - ping_module = _load_module( - f"beacon.connections.{folder}.ping" - ) - client_module = _load_module( - f"beacon.connections.{folder}.client" - ) +def _model_is_enabled(models_confile, folder, subfolder=None): + """Methot tho get the models enabled dynamically""" + if folder in models_confile and models_confile[folder]["model_enabled"] == False: + return False + if subfolder is not None: + model_key = folder + '/' + subfolder + if model_key in models_confile and models_confile[model_key]["model_enabled"] == False: + return False + return True - ping_database = getattr( - ping_module, - "ping_database" - ) - get_client = getattr( - client_module, - "get_client" - ) +def get_all_modules_connections_script(script, connection): + """Method to get all the submodules of connections per model loaded dynamically""" + list_of_modules=[] + # Load the configuration file for the models that are enabled + with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: + models_confile= yaml.safe_load(pfile) + pfile.close() + dirs = os.listdir("/beacon/models") + # Loop over the folders found in the mentioned path and save the ones that are active (enabled) + for folder in dirs: + subdirs = os.listdir("/beacon/models/"+folder) + # Get the models that are specifically enabled + if not _model_is_enabled(models_confile, folder): + continue - try: - await asyncio.wait_for( - ping_database(get_client()), - timeout=config.pending_requests_timeout_in_seconds - ) - except Exception: - LOG.error(f"{folder} database is down") - raise DatabaseIsDown(folder) \ No newline at end of file + # Go over the connections for the entry types of the models enabled + if "connections" in subdirs: + connections = os.listdir("/beacon/models/"+folder+"/connections") + for dir in connections: + if dir == connection: + # Get the modules names in an array + complete_module='beacon.models.'+folder+'.connections.'+connection+'.'+script + import importlib + try: + module = importlib.import_module(complete_module, package=None) + list_of_modules.append(module) + except Exception as e: + continue + else: + # Loop over the subfolders found in the mentioned path and save the ones that are active (enabled) + for subfolder in subdirs: + underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) + # Get the models that are specifically enabled + if not _model_is_enabled(models_confile, folder, subfolder): + continue + # Go over the connections for the entry types of the models enabled + if "connections" in underdirs: + connections = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/connections") + for dir in connections: + if dir == connection: + # Get the modules names in an array + complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.'+connection+'.'+script + import importlib + module = importlib.import_module(complete_module, package=None) + list_of_modules.append(module) + return list_of_modules + +def get_all_modules_datasets(connection): + """Method to get the datasets collections for each of the models to be returned""" + list_of_modules=[] + # Load the configuration file for the models that are enabled + with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: + models_confile= yaml.safe_load(pfile) + pfile.close() + dirs = os.listdir("/beacon/models") + # Loop over the folders found in the mentioned path and save the ones that are active (enabled) + for folder in dirs: + subdirs = os.listdir("/beacon/models/"+folder) + # Get the models that are specifically enabled + if not _model_is_enabled(models_confile, folder): + continue + # Go over the collections of the models enabled in the connections folder + if "connections" in subdirs: + try: + # Get the names of the collections validators to be validated and accepted + complete_module='beacon.models.'+folder+'.connections.'+connection+'.collections' + import importlib + module = importlib.import_module(complete_module, package=None) + list_of_modules.append(module) + except Exception: + pass + # Loop over the subfolders found in the mentioned path and save the ones that are active (enabled) + for subfolder in subdirs: + underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) + # Get the models that are specifically enabled + if not _model_is_enabled(models_confile, folder, subfolder): + continue + # Go over the collections of the models enabled in the connections folder + if "connections" in underdirs: + try: + # Get the names of the collections validators to be validated and accepted + complete_module='beacon.models.'+folder+'.'+subfolder+'.connections.'+connection+'.collections' + import importlib + module = importlib.import_module(complete_module, package=None) + list_of_modules.append(module) + except Exception: + pass + return list_of_modules + +def get_one_module_conf(entry_type): + """Method to get the configuration of the desired entry types""" + # TODO: Cache the module conf loading to only execute it once. + dirs = os.listdir("/beacon/models") + # Loop over the folders found in the models and get the entry types configuration + for folder in dirs: + subdirs = os.listdir("/beacon/models/"+folder) + # Go over the entry types files in the conf folder + if "conf" in subdirs: + confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") + for confile in confiles: + # Skip the files that are of pycache type + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + # Get the configuration file for the entry type that matches the one requested + for entry_type_id, entry_type_params in entry_type_confile.items(): + if entry_type_params["endpoint_name"] == entry_type: + return entry_type_confile + else: + # Loop over the subfolders found in the models and get the entry types configuration + for subfolder in subdirs: + underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) + # Go over the entry types files in the conf folder + if "conf" in underdirs: + confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") + for confile in confiles: + # Skip the files that are of pycache type + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + # Get the configuration file for the entry type that matches the one requested + for entry_type_id, entry_type_params in entry_type_confile.items(): + if entry_type_params["endpoint_name"] == entry_type: + return entry_type_confile + +def get_modules_confiles(): + """Method to get all the entry types configuration files""" + # Load the configuration file for the models that are enabled + with open("/beacon/conf/models/models_conf.yml", 'r') as pfile: + models_confile= yaml.safe_load(pfile) + pfile.close() + dirs = os.listdir("/beacon/models") + list_of_confiles=[] + # Loop over the folders found in the models and get the entry types configuration + for folder in dirs: + subdirs = os.listdir("/beacon/models/"+folder) + # Go over the entry types files in the conf folder + if "conf" in subdirs: + confiles = os.listdir("/beacon/models/"+folder+"/conf/entry_types/") + if folder in models_confile: + if models_confile[folder]["model_enabled"] == False: + continue + for confile in confiles: + # Skip the files that are of pycache type + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + list_of_confiles.append(entry_type_confile) + else: + # Loop over the subfolders found in the models and get the entry types configuration + for subfolder in subdirs: + underdirs = os.listdir("/beacon/models/"+folder+"/"+subfolder) + if folder+'/'+subfolder in models_confile: + if models_confile[folder+'/'+subfolder ]["model_enabled"] == False: + continue + # Go over the entry types files in the conf folder + if "conf" in underdirs: + confiles = os.listdir("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/") + for confile in confiles: + # Skip the files that are of pycache type + if confile != '__pycache__': + with open("/beacon/models/"+folder+"/"+subfolder+"/conf/entry_types/" + confile, 'r') as pfile: + entry_type_confile = yaml.safe_load(pfile) + pfile.close() + list_of_confiles.append(entry_type_confile) + return list_of_confiles + From 3fb34ad393bf4f62bf4ab6eb441fc4ba3ece9d6d Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 29 Sep 2026 15:24:55 +0200 Subject: [PATCH 46/56] updating load types of results --- beacon/utils/modules.py | 301 +--------------------------------------- 1 file changed, 1 insertion(+), 300 deletions(-) diff --git a/beacon/utils/modules.py b/beacon/utils/modules.py index e172aeec..d4cf22b7 100644 --- a/beacon/utils/modules.py +++ b/beacon/utils/modules.py @@ -7,7 +7,6 @@ from beacon.conf.conf_override import config from beacon.exceptions.exceptions import DatabaseIsDown import asyncio -import time #TODO: get_client() passing one variable with the database name. @log_with_args(config.level) @@ -173,215 +172,79 @@ def load_types_of_results(self, response_type): import importlib import sys - import time global _RESULT_TYPES_CONFIG_MTIME - - total_start = time.perf_counter() - - # --------------------------------------------------------- - # Get schema version - # --------------------------------------------------------- - start = time.perf_counter() - version_catch = re.search( r"(v\d+(\.\d+)*)", self.request_attributes.returned_schema[0]["schema"] ) - if not version_catch: raise ValueError( "Could not determine schema version from returned_schema" ) - version = version_catch.group(1) underscored_version = version.replace(".", "_") - - print( - f"[TIMING] version processing: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - - # --------------------------------------------------------- # Check models_conf.yml modification time - # --------------------------------------------------------- - start = time.perf_counter() - config_mtime = os.stat( _MODELS_CONF_PATH ).st_mtime_ns - - print( - f"[TIMING] config mtime check: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - - # --------------------------------------------------------- # Invalidate entire cache if configuration changed - # --------------------------------------------------------- if _RESULT_TYPES_CONFIG_MTIME != config_mtime: - if _RESULT_TYPES_CONFIG_MTIME is not None: print( "[TIMING] models_conf.yml changed - " "clearing result types cache", flush=True, ) - _RESULT_TYPES_CACHE.clear() - _RESULT_TYPES_CONFIG_MTIME = config_mtime - - # --------------------------------------------------------- # Cache lookup - # --------------------------------------------------------- cache_key = ( response_type, underscored_version, ) - if cache_key in _RESULT_TYPES_CACHE: - - print( - f"[TIMING] load_types_of_results CACHE HIT: " - f"{cache_key}", - flush=True, - ) - - print( - f"[TIMING] load_types_of_results TOTAL: " - f"{(time.perf_counter() - total_start) * 1000:.2f} ms", - flush=True, - ) - return _RESULT_TYPES_CACHE[cache_key] - - print( - f"[TIMING] load_types_of_results CACHE MISS: " - f"{cache_key}", - flush=True, - ) - - # --------------------------------------------------------- # Load configuration - # --------------------------------------------------------- - start = time.perf_counter() - with open( _MODELS_CONF_PATH, "r" ) as pfile: models_confile = yaml.safe_load(pfile) - - print( - f"[TIMING] load_types YAML: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - - # --------------------------------------------------------- # Initialize - # --------------------------------------------------------- list_of_results_classes_accepted = [] - import_count = 0 cached_import_count = 0 - - # --------------------------------------------------------- # Helper for imports - # --------------------------------------------------------- def timed_import(module_name): - nonlocal import_count nonlocal cached_import_count - already_cached = module_name in sys.modules - - print( - f"[TIMING] IMPORT START: {module_name} " - f"(cached={already_cached})", - flush=True, - ) - - start_import = time.perf_counter() - module = importlib.import_module( module_name, package=None ) - - elapsed_import = ( - time.perf_counter() - start_import - ) - import_count += 1 - if already_cached: cached_import_count += 1 - - print( - f"[TIMING] IMPORT END: {module_name} " - f"{elapsed_import * 1000:.2f} ms " - f"(cached={already_cached})", - flush=True, - ) - return module - - # --------------------------------------------------------- # Get model directories - # --------------------------------------------------------- - start = time.perf_counter() - dirs = os.listdir( _MODELS_BASE_PATH ) - - print( - f"[TIMING] initial os.listdir: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - - # --------------------------------------------------------- # Search models - # --------------------------------------------------------- - filesystem_start = time.perf_counter() - for folder in dirs: - - start = time.perf_counter() - subdirs = os.listdir( _MODELS_BASE_PATH + "/" + folder ) - - elapsed = time.perf_counter() - start - - if elapsed > 0.5 / 1000: - print( - f"[TIMING] os.listdir folder={folder}: " - f"{elapsed * 1000:.2f} ms", - flush=True, - ) - - # ----------------------------------------------------- # Check if top-level model is enabled - # ----------------------------------------------------- if folder in models_confile: - if models_confile[ folder ]["model_enabled"] is False: continue - - # ===================================================== # Direct validator directory - # ===================================================== if "validator" in subdirs: - validator_base_path = ( _MODELS_BASE_PATH + "/" @@ -389,49 +252,22 @@ def timed_import(module_name): + "/validator/" + response_type ) - - start = time.perf_counter() - validatordirs = os.listdir( validator_base_path ) - - print( - f"[TIMING] os.listdir validators " - f"{validator_base_path}: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - for validatorfolder in validatordirs: - validator_path = ( validator_base_path + "/" + validatorfolder ) - - start = time.perf_counter() - validatorfiles = os.listdir( validator_path ) - - elapsed = time.perf_counter() - start - - if elapsed > 0.5 / 1000: - print( - f"[TIMING] os.listdir validator " - f"{validatorfolder}: " - f"{elapsed * 1000:.2f} ms", - flush=True, - ) - for validatorfile in validatorfiles: if underscored_version not in validatorfile: continue - complete_module = ( "beacon.models." + folder @@ -442,39 +278,23 @@ def timed_import(module_name): + "." + validatorfile ) - complete_module = complete_module.replace( ".py", "" ) - module = timed_import( complete_module ) - - start = time.perf_counter() - klass = getattr( module, validatorfolder.capitalize() ) - - print( - f"[TIMING] getattr " - f"{complete_module}: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - list_of_results_classes_accepted.append( klass ) - # ===================================================== # Nested model directories - # ===================================================== for subfolder in subdirs: - model_path = ( _MODELS_BASE_PATH + "/" @@ -482,37 +302,19 @@ def timed_import(module_name): + "/" + subfolder ) - - start = time.perf_counter() - underdirs = os.listdir( model_path ) - - elapsed = time.perf_counter() - start - - if elapsed > 0.5 / 1000: - print( - f"[TIMING] os.listdir model " - f"{folder}/{subfolder}: " - f"{elapsed * 1000:.2f} ms", - flush=True, - ) - model_config_key = ( folder + "/" + subfolder ) - if model_config_key in models_confile: - if models_confile[ model_config_key ]["model_enabled"] is False: continue - if "validator" not in underdirs: continue - validator_base_path = ( _MODELS_BASE_PATH + "/" @@ -522,54 +324,24 @@ def timed_import(module_name): + "/validator/" + response_type ) - try: - - start = time.perf_counter() - validatordirs = os.listdir( validator_base_path ) - - print( - f"[TIMING] os.listdir nested validators " - f"{folder}/{subfolder}: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - except Exception: return None - for validatorfolder in validatordirs: - validator_path = ( validator_base_path + "/" + validatorfolder ) - - start = time.perf_counter() - validatorfiles = os.listdir( validator_path ) - - elapsed = time.perf_counter() - start - - if elapsed > 0.5 / 1000: - print( - f"[TIMING] os.listdir nested validator " - f"{validatorfolder}: " - f"{elapsed * 1000:.2f} ms", - flush=True, - ) - for validatorfile in validatorfiles: - if underscored_version not in validatorfile: continue - complete_module = ( "beacon.models." + folder @@ -582,97 +354,26 @@ def timed_import(module_name): + "." + validatorfile ) - complete_module = complete_module.replace( ".py", "" ) - module = timed_import( complete_module ) - - start = time.perf_counter() - klass = getattr( module, validatorfolder.capitalize() ) - - print( - f"[TIMING] getattr " - f"{complete_module}: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - list_of_results_classes_accepted.append( klass ) - - # --------------------------------------------------------- - # Filesystem + imports timing - # --------------------------------------------------------- - print( - f"[TIMING] filesystem + imports: " - f"{(time.perf_counter() - filesystem_start) * 1000:.2f} ms " - f"({import_count} imports, " - f"{cached_import_count} already cached)", - flush=True, - ) - - # --------------------------------------------------------- - # Show discovered classes - # --------------------------------------------------------- - print( - f"[TIMING] result classes found: " - f"{len(list_of_results_classes_accepted)}", - flush=True, - ) - - for klass in list_of_results_classes_accepted: - - print( - f"[TIMING] result class: " - f"{klass.__module__}.{klass.__name__}", - flush=True, - ) - - # --------------------------------------------------------- # Build Union - # --------------------------------------------------------- - start = time.perf_counter() - union_type = Union[ tuple(list_of_results_classes_accepted) ] - - print( - f"[TIMING] Union construction: " - f"{(time.perf_counter() - start) * 1000:.2f} ms", - flush=True, - ) - - # --------------------------------------------------------- # Store in cache - # --------------------------------------------------------- _RESULT_TYPES_CACHE[cache_key] = union_type - - print( - f"[TIMING] load_types_of_results cached: " - f"{cache_key}", - flush=True, - ) - - # --------------------------------------------------------- - # Total - # --------------------------------------------------------- - print( - f"[TIMING] load_types_of_results TOTAL: " - f"{(time.perf_counter() - total_start) * 1000:.2f} ms", - flush=True, - ) - return union_type def load_routes(): @@ -837,7 +538,7 @@ def get_all_modules_datasets(connection): except Exception: pass return list_of_modules - + def get_one_module_conf(entry_type): """Method to get the configuration of the desired entry types""" # TODO: Cache the module conf loading to only execute it once. From 47be0b432f9785f2f06d100c7f4d0b9c876897a6 Mon Sep 17 00:00:00 2001 From: costero-e Date: Wed, 30 Sep 2026 10:52:49 +0200 Subject: [PATCH 47/56] addressing unit testing problematics --- .../collections/EUCAIM_collections_v0_0_1.py | 74 +-- .../patients/EUCAIM-patients_v0_0_1.py | 553 ++++++++++++------ beacon/tests/__main__.py | 10 +- beacon/utils/requests.py | 4 +- docker-compose.yml | 23 +- template-ui/{src => }/config/config.json | 269 ++++++--- 6 files changed, 643 insertions(+), 290 deletions(-) rename template-ui/{src => }/config/config.json (60%) diff --git a/beacon/models/EUCAIM/validator/collections/collections/EUCAIM_collections_v0_0_1.py b/beacon/models/EUCAIM/validator/collections/collections/EUCAIM_collections_v0_0_1.py index 6b882bc8..0f1302db 100644 --- a/beacon/models/EUCAIM/validator/collections/collections/EUCAIM_collections_v0_0_1.py +++ b/beacon/models/EUCAIM/validator/collections/collections/EUCAIM_collections_v0_0_1.py @@ -1,33 +1,41 @@ -from pydantic import ( - BaseModel, - PrivateAttr -) - -from typing import Optional, List - -# This is the class to validate a property value that requires an object like AgeRange -class AgeRange(BaseModel, extra='forbid'): - min: float - max: float - -# This is the generic class to validate a record for a collection -class Collections(BaseModel, extra='forbid'): - def __init__(self, **data) -> None: - for private_key in self.__class__.__private_attributes__.keys(): - try: - value = data.pop(private_key) - except KeyError: - pass - - super().__init__(**data) - _id: Optional[str] = PrivateAttr() - name: str - id: str - description: str - ageRange:AgeRange - modalities: List[str] - bodyParts: List[str] - gender: List[str] - subjectsCount: int - studiesCount: int - datasetId: Optional[str] = None \ No newline at end of file +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/EGA-archive/EUCAIM-Schema/refs/heads/main/CollectionsMetadata.json +# timestamp: 2026-07-30T20:48:15+00:00 + +from __future__ import annotations + +from typing import Any + +from pydantic import BaseModel, Field, RootModel, conint + + + +class Age(RootModel[Any]): + root: Any + + +class AgeRange(BaseModel): + min: Age + max: Age + + +class Collections(BaseModel): + name: str = Field( + ..., description='Name of the dataset', examples=['Dataset with synthetic data'] + ) + id: str = Field( + ..., description='Unique identifier of the dataset', examples=['ds01010101'] + ) + description: str = Field( + ..., + description='Description of the dataset', + examples=[ + 'This dataset provides examples of the actual data in this Beacon instance.' + ], + ) + subjectsCount: conint(ge=0) + studiesCount: conint(ge=0) + ageRange: AgeRange + modalities: list[str] + bodyParts: list[str] + gender: list[str] diff --git a/beacon/models/EUCAIM/validator/non_collections/patients/EUCAIM-patients_v0_0_1.py b/beacon/models/EUCAIM/validator/non_collections/patients/EUCAIM-patients_v0_0_1.py index ef232551..42f71a7e 100644 --- a/beacon/models/EUCAIM/validator/non_collections/patients/EUCAIM-patients_v0_0_1.py +++ b/beacon/models/EUCAIM/validator/non_collections/patients/EUCAIM-patients_v0_0_1.py @@ -1,172 +1,399 @@ -import re -from rfc3339_validator import validate_rfc3339 +# generated by datamodel-codegen: +# filename: https://raw.githubusercontent.com/EGA-archive/EUCAIM-Schema/refs/heads/main/PatientsMetadata.json +# timestamp: 2026-07-30T16:55:25+00:00 -from pydantic import ( - BaseModel, - field_validator, - PrivateAttr -) -from typing import Optional, List +from __future__ import annotations -class OntologyTerm(BaseModel): - # Generic ontology reference structure used across the schema - id: str # CURIE-style identifier (e.g. EUCAIM:COM1001288) - label: Optional[str] = None # Human-readable label (optional) - - @field_validator('id') - @classmethod - def id_must_be_CURIE(cls, v: str) -> str: - # Ensure identifier follows CURIE pattern: prefix:local_id - if re.match("[A-Za-z0-9]+:[A-Za-z0-9]", v): - pass - else: - # Reject malformed ontology identifiers early - raise ValueError('id must be CURIE, e.g. EUCAIM:COM1001288') - - # Normalize formatting (title-casing the identifier) - return v.title() - - -class Tumors(BaseModel, extra="forbid"): - # Tumor-specific biomarker and staging metadata container - - def __init__(self, **data) -> None: - # Remove private attributes before validation (internal bookkeeping) - for private_key in self.__class__.__private_attributes__.keys(): - try: - value = data.pop(private_key) - except KeyError: - pass - - super().__init__(**data) - - _id: Optional[str] = PrivateAttr() # Internal DB identifier (not exposed externally) - - tumorId: str # Primary tumor identifier - - # Hormone receptor / biomarker annotations - ER: Optional[OntologyTerm] = None - PR: Optional[OntologyTerm] = None - PSA: Optional[float] = None # Numeric biomarker - HER2: Optional[OntologyTerm] = None - KI67: Optional[float] = None # Proliferation index - - # Cancer staging fields (various clinical classification systems) - cancerStageCMCategory: Optional[OntologyTerm] = None - cancerStagePMCategory: Optional[OntologyTerm] = None - - # Histopathology grading systems - histologicGraceGleasonScore: Optional[OntologyTerm] = None - histologicGradeISUP: Optional[OntologyTerm] = None - - # Imaging-based tumor assessments - tumorBIRADSAssesment: Optional[OntologyTerm] = None - tumorPIRADSAssesment: Optional[OntologyTerm] = None - - -class Diseases(BaseModel, extra='forbid'): - # Disease record linked to a patient or cohort entity - - def __init__(self, **data) -> None: - # Strip private fields before Pydantic validation - for private_key in self.__class__.__private_attributes__.keys(): - try: - value = data.pop(private_key) - except KeyError: - pass - - super().__init__(**data) - - _id: Optional[str] = PrivateAttr() # Internal persistence ID - - diseaseId: str # Unique disease record identifier - ageAtDiagnosis: float # Age in years (or standardized unit) - diagnosis: OntologyTerm # Primary diagnosis term - - yearOfDiagnosis: Optional[int] = None # Year-only representation - dateOfFirstTreatment: Optional[str] = None # ISO/RFC3339 timestamp - - pathologyConfirmation: Optional[OntologyTerm] = None # Confirmatory test - pathology: Optional[list] = None # List of pathology descriptors - imagingProcedureProtocol: Optional[OntologyTerm] = None +from typing import Any - treatment: Optional[List] = None # Treatment records (untyped list for flexibility) - tumorMetadata: Optional[Tumors] = None # Nested tumor characterization +from pydantic import AwareDatetime, BaseModel, ConfigDict, Field, RootModel, constr - @field_validator('dateOfFirstTreatment') - @classmethod - def validate_datetime(cls, v): - # Validate RFC3339-compliant timestamp for interoperability - if not validate_rfc3339(v): - raise ValueError("Must be a valid RFC3339 date-time (JSON Schema format=date-time)") - return v - @field_validator('pathology') - @classmethod - def check_pathology(cls, v): - # Ensure each pathology entry conforms to OntologyTerm structure - for pathology in v: - OntologyTerm(**pathology) +class Sex(RootModel[Any]): + root: Any - @field_validator('treatment') - @classmethod - def check_treatment(cls, v): - # Validate each treatment entry as ontology-based object - for treatment in v: - OntologyTerm(**treatment) +class Age(RootModel[Any]): + root: Any -class ImageStudies(BaseModel, extra='forbid'): - # Imaging study metadata linked to disease context - def __init__(self, **data) -> None: - # Clean private attributes before model initialization - for private_key in self.__class__.__private_attributes__.keys(): - try: - value = data.pop(private_key) - except KeyError: - pass - - super().__init__(**data) - - _id: Optional[str] = PrivateAttr() # Internal identifier - - imageStudyId: str # Unique imaging study ID - disease: Diseases # Linked disease object - - # Imaging acquisition metadata - imageModality: OntologyTerm - imageBodyPart: OntologyTerm - imageManufacturer: OntologyTerm - - dateOfImageAcquisition: str # Timestamp of imaging session - - @field_validator('dateOfImageAcquisition') - @classmethod - def validate_datetime(cls, v): - # Ensure imaging date follows RFC3339 standard format - if not validate_rfc3339(v): - raise ValueError("Must be a valid RFC3339 date-time (JSON Schema format=date-time)") - return v - - -class Patients(BaseModel, extra='forbid'): - # Top-level patient entity aggregating clinical and imaging data - - def __init__(self, **data) -> None: - # Remove internal/private fields before schema validation - for private_key in self.__class__.__private_attributes__.keys(): - try: - value = data.pop(private_key) - except KeyError: - pass - - super().__init__(**data) - - _id: Optional[str] = PrivateAttr() # Internal DB reference - - patientId: str # Primary patient identifier - sex: OntologyTerm # Biological sex encoded as ontology term - - diseases: Optional[List[Diseases]] = None # Associated disease records - imageStudy: Optional[List[ImageStudies]] = None # Linked imaging studies \ No newline at end of file +class OntologyTerm(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HER2(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HistologicGraceGleasonScore(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class HistologicGradeISUP(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class TumorBIRADSAssesment(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class TumorPIRADSAssesment(BaseModel): + model_config = ConfigDict( + extra='allow', + ) + id: constr(pattern=r'^\w[^:]+:.+$') = Field( + ..., + description='Definition of an identifier in the CURIE `prefix:local-part` format which is the default type of e.g. ontology term `id` values (used e.g. for filters or external identifiers).', + examples=[ + 'ga4gh:GA.01234abcde', + 'DUO:0000004', + 'orcid:0000-0003-3463-0775', + 'PMID:15254584', + ], + ) + label: str | None = Field( + None, + description='The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.', + ) + + +class TumorsMetadata(BaseModel): + tumorId: str = Field( + ..., + description='A unique identifier for the Tumor. This field was not in the original EUCAIM Federated Query metadata.', + examples=['X123456-T01'], + ) + ER: OntologyTerm | None = Field( + None, + description='Estrogen receptor Ag [Presence] in Breast cancer specimen by Immune stain', + examples=[ + {'id': 'EUCAIM:COM1001310', 'label': 'Positive'}, + {'id': 'EUCAIM:COM1001332', 'label': 'Negative'}, + ], + ) + PR: OntologyTerm | None = Field( + None, + description='Progesterone receptor Ag [Presence] in Breast cancer specimen by Immune stain', + examples=[ + {'id': 'EUCAIM:COM1001310', 'label': 'Positive'}, + {'id': 'EUCAIM:COM1001332', 'label': 'Negative'}, + ], + ) + PSA: float | None = Field( + None, + description='Prostate specific Ag [Mass/Volume] in Serum or Plasma', + examples=[4.5], + ) + HER2_1: HER2 | None = Field( + None, + alias='HER2', + description='HER2 [Presence] in Breast cancer specimen by Immune stain', + examples=[ + {'id': 'EUCAIM:COM1002257', 'label': '0'}, + {'id': 'EUCAIM:COM1001877', 'label': '1+'}, + {'id': 'EUCAIM:COM1001879', 'label': '2+'}, + {'id': 'EUCAIM:COM1001882', 'label': '3+'}, + ], + title='Ontology Term', + ) + KI67: float | None = Field( + None, + description='Cells.Ki-67 nuclear Ag/100 cells in Breast cancer specimen by Immune stain', + examples=[2.4], + ) + cancerStageCMCategory: OntologyTerm | None = Field( + None, + description='The cancer stage according to the cM category system.', + examples=[ + {'id': 'EUCAIM:COM1001860', 'label': 'cM0'}, + {'id': 'EUCAIM:COM1000246', 'label': 'cM1'}, + {'id': 'EUCAIM:COM1000258', 'label': 'cM1a'}, + {'id': 'EUCAIM:COM1000271', 'label': 'cM1b'}, + {'id': 'EUCAIM:COM1001876', 'label': 'cM1c'}, + ], + ) + cancerStagePMCategory: OntologyTerm | None = Field( + None, + description='The cancer stage according to the pM category system.', + examples=[ + {'id': 'EUCAIM:COM1001845', 'label': 'pM0'}, + {'id': 'EUCAIM:COM1000531', 'label': 'pM1'}, + {'id': 'EUCAIM:COM1000558', 'label': 'pM1a'}, + {'id': 'EUCAIM:COM1000586', 'label': 'pM1b'}, + {'id': 'EUCAIM:COM1000615', 'label': 'pM1c'}, + ], + ) + histologicGraceGleasonScore: HistologicGraceGleasonScore | None = Field( + None, + description='The Gleason scoring system for malignant neoplasm of prostate', + examples=[ + {'id': 'EUCAIM:CLIN1025818', 'label': 'Gleason grade score 2 out of 10'}, + {'id': 'EUCAIM:CLIN1025912', 'label': 'Gleason score 3 out of 10'}, + {'id': 'EUCAIM:CLIN1026007', 'label': 'Gleason score 4 out of 10'}, + ], + title='Ontology Term', + ) + histologicGradeISUP: HistologicGradeISUP | None = Field( + None, + description='The International Society of Urological Pathology (ISUP) grading system for malignant neoplasm of prostate', + examples=[ + { + 'id': 'EUCAIM:COM1001362', + 'label': 'International Society of Pathology histologic group 1', + }, + { + 'id': 'EUCAIM:COM1001365', + 'label': 'International Society of Pathology histologic group 2', + }, + { + 'id': 'EUCAIM:COM1001367', + 'label': 'International Society of Pathology histologic group 3', + }, + ], + title='Ontology Term', + ) + tumorBIRADSAssesment: TumorBIRADSAssesment | None = Field( + None, + description='Breast Imaging-Reporting and Data System (BI-RADS) assessment categories for breast tumors', + examples=[ + {'id': 'EUCAIM:IMG1005470', 'label': 'BI-RADS 0'}, + {'id': 'EUCAIM:IMG1005469', 'label': 'BI-RADS 1'}, + {'id': 'EUCAIM:IMG1005468', 'label': 'BI-RADS 2'}, + {'id': 'EUCAIM:IMG1005466', 'label': 'BI-RADS 3'}, + ], + title='Ontology Term', + ) + tumorPIRADSAssesment: TumorPIRADSAssesment | None = Field( + None, + description='Prostate Imaging-Reporting and Data System (PI-RADS) assessment categories for prostate tumors', + examples=[ + {'id': 'EUCAIM:IMG1005487', 'label': 'PI-RADS 1'}, + {'id': 'EUCAIM:IMG1005486', 'label': 'PI-RADS 2'}, + {'id': 'EUCAIM:IMG1005485', 'label': 'PI-RADS 3'}, + {'id': 'EUCAIM:IMG1005484', 'label': 'PI-RADS 4'}, + ], + title='Ontology Term', + ) + + +class ImageModality(RootModel[Any]): + root: Any + + +class BodyPart(RootModel[Any]): + root: Any + + +class DiseasesMetadata(BaseModel): + diseaseId: str = Field( + ..., + description='Unique identifier for the diagnostic/disease. This field was not in the original EUCAIM Federated Query metadata.', + examples=['X123456-D01'], + ) + ageAtDiagnosis: Age = Field( + ..., + description='Age of the patient at the time the tumor or lesion was confirmed.', + examples=[45.6], + ) + diagnosis: OntologyTerm = Field( + ..., + description='Diagnosis of the disease.', + examples=[ + {'id': 'EUCAIM:CLIN1000075', 'label': 'Malignant neoplasm of prostate'}, + {'id': 'EUCAIM:CLIN1000060', 'label': 'Malignant neoplasm of breast'}, + {'id': 'EUCAIM:CLIN1000057', 'label': 'Malignant neoplasm of colon'}, + {'id': 'EUCAIM:CLIN1000185', 'label': 'Malignant neoplasm of rectum'}, + ], + ) + yearOfDiagnosis: int | None = Field( + None, + description='Date when the tumor was histologically confirmed or confirmed by imaging.', + examples=['2022'], + ) + dateOfFirstTreatment: AwareDatetime | None = Field( + None, + description='Date and time when the first treatment occurred, in ISO 8601 date-time format.', + examples=['2024-03-01T10:30:00Z'], + ) + pathologyConfirmation: OntologyTerm | None = Field( + None, + description='Method used to confirm pathology (e.g., histological biopsy or imaging for specific cases).', + examples=[ + {'id': 'EUCAIM:CLIN1001712', 'label': 'Biopsy'}, + {'id': 'EUCAIM:CLIN1004598', 'label': 'Excision'}, + ], + ) + pathology: list[OntologyTerm] | None = Field( + None, + description='Histology and histological subtype of the lesion (ICD-O-3 if available).', + examples=[ + [ + {'id': 'EUCAIM:CLIN1047138', 'label': 'Adenocarcinoma'}, + {'id': 'EUCAIM:CLIN1063544', 'label': 'Papillary carcinoma'}, + ] + ], + ) + imagingProcedureProtocol: OntologyTerm | None = Field( + None, + description='Specific protocol applied to obtain the radiology diagnostic image.', + examples=[ + [ + {'id': 'EUCAIM:IMG1000076', 'label': 'CT of thorax with contrast'}, + {'id': 'EUCAIM:IMG1000078', 'label': 'CT of breast'}, + ] + ], + ) + treatment: list[OntologyTerm] | None = Field( + None, + description='Type of treatment received by the patient.', + examples=[ + [ + {'id': 'EUCAIM:CLIN1024528', 'label': 'Chemotherapy'}, + {'id': 'EUCAIM:COM1001099', 'label': 'Surgery'}, + ] + ], + ) + tumorMetadata: TumorsMetadata | None = Field( + None, description='Additional metadata related to the tumor or lesion.' + ) + + +class ImageStudiesMetadata(BaseModel): + imageStudyId: str = Field( + ..., + description='Unique identifier for the image. This field was not in the original EUCAIM Federated Query metadata.', + examples=['X123456-IMG01'], + ) + disease: DiseasesMetadata = Field( + ..., description='Disease information associated with the image.' + ) + imageModality: ImageModality = Field( + ..., + description='Modality of the imaging study (DICOM tag 0008,0060), controlled vocabulary', + examples=[ + {'id': 'EUCAIM:IMG1000026', 'label': 'Computed tomography'}, + {'id': 'EUCAIM:IMG1000030', 'label': 'Mammography'}, + ], + ) + imageBodyPart: BodyPart = Field( + ..., + description='Anatomical area imaged (DICOM tag 0018,0015), controlled vocabulary', + examples=[ + {'id': 'EUCAIM:BP1000067', 'label': 'Chest'}, + {'id': 'EUCAIM:BP1000220', 'label': 'Arm'}, + ], + ) + imageManufacturer: OntologyTerm = Field( + ..., + description='Device manufacturer (DICOM tag 0008,0070), controlled vocabulary', + examples=[ + {'id': 'EUCAIM:IMG1000047', 'label': 'General Electric'}, + {'id': 'EUCAIM:IMG1000044', 'label': 'Siemens'}, + ], + ) + dateOfImageAcquisition: AwareDatetime = Field( + ..., + description='Acquisition date of the image (DICOM tag 0008,0022), in ISO 8601 date-time format (e.g. YYYY-MM-DDThh:mm:ssZ).', + examples=['2000-01-01T00:00:00Z'], + ) + + +class Patients(BaseModel): + patientId: str = Field( + ..., + description='A unique identifier for the patient. Should match the Patient ID DICOM tag (0010,0020) and anonymization processes.', + examples=['X123456'], + ) + sex: Sex = Field( + ..., + description='Biological sex at birth.', + examples=[ + {'id': 'EUCAIM:COM1001370', 'label': 'Female'}, + {'id': 'EUCAIM:COM1001366', 'label': 'Male'}, + {'id': 'EUCAIM:COM1001288', 'label': 'Unspecified'}, + ], + ) + + imageStudy: list[ImageStudiesMetadata] = Field( + ..., description='Imaging study information associated with the patient.' + ) diff --git a/beacon/tests/__main__.py b/beacon/tests/__main__.py index 54c5b9db..c3ab46a8 100644 --- a/beacon/tests/__main__.py +++ b/beacon/tests/__main__.py @@ -784,7 +784,7 @@ async def test_check_analyses_g_variants_endpoint_is_working(): # Expect multiple matches for variant-linked analyses assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 10 + assert responsedict["responseSummary"]["numTotalResults"] == 21 loop.run_until_complete(test_check_analyses_g_variants_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -1042,7 +1042,7 @@ async def test_check_biosamples_g_variants_endpoint_is_working(): # Verify existence of matching records and expected cardinality assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 10 + assert responsedict["responseSummary"]["numTotalResults"] == 22 loop.run_until_complete(test_check_biosamples_g_variants_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -1273,7 +1273,7 @@ async def test_check_individuals_g_variants_endpoint_is_working(): # Expect multiple matches for variant association assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 10 + assert responsedict["responseSummary"]["numTotalResults"] == 23 loop.run_until_complete(test_check_individuals_g_variants_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -1490,7 +1490,7 @@ async def test_check_runs_g_variants_endpoint_is_working(): # Expect multiple linked results for variant association assert responsedict["responseSummary"]["exists"] is True - assert responsedict["responseSummary"]["numTotalResults"] == 10 + assert responsedict["responseSummary"]["numTotalResults"] == 21 loop.run_until_complete(test_check_runs_g_variants_endpoint_is_working()) loop.run_until_complete(client.close()) @@ -7093,7 +7093,6 @@ async def test_check_allele_frequency_per_zygosity_shows_up(): loop.run_until_complete(test_check_allele_frequency_per_zygosity_shows_up()) loop.run_until_complete(client.close()) - class AsyncTest(unittest.IsolatedAsyncioTestCase): # Starts a background API server using asyncio and waits briefly for it to initialize. @@ -7279,6 +7278,5 @@ def test_risky_function_raises(self, mock_risky): - if __name__ == '__main__': unittest.main() \ No newline at end of file diff --git a/beacon/utils/requests.py b/beacon/utils/requests.py index 8a0ed74e..55d51c1a 100644 --- a/beacon/utils/requests.py +++ b/beacon/utils/requests.py @@ -266,8 +266,10 @@ def set_entry_type(self, request): path_list = list(filter(None, path_list)) else: used_uri_splitted = abs_url.split('/') - if '.' not in used_uri_splitted[-3]: + if '.' not in used_uri_splitted[-3] and '/'+used_uri_splitted[-3] != config.uri_subpath: path_list=used_uri_splitted[-3:] + elif '.' not in used_uri_splitted[-3]: + path_list=used_uri_splitted[-2:] else: path_list=[used_uri_splitted[-1]] if path_list == []: diff --git a/docker-compose.yml b/docker-compose.yml index 505f994a..4d761c0b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -125,7 +125,7 @@ services: - pub beacon-ri-tools: - image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.3.0 + image: ghcr.io/ega-archive/beacon2-ri-tools-v2:2.3.1 hostname: beacon-ri-tools container_name: ri-tools networks: @@ -150,22 +150,15 @@ services: - pub templateUI: - image: ghcr.io/ega-archive/beacon-template-ui:main - restart: always - hostname: template-ui - container_name: template-ui - command: node /opt/yarn-v1.22.22/bin/yarn.js start - ports: - - 3000:3000 - volumes: - - ./template-ui/src/config/config.json:/client/src/config/config.json - - ./template-ui/.env:/client/.env + image: ghcr.io/ega-archive/beacon-template-ui:egadev + hostname: frontend + container_name: "template-ui" networks: - pub - environment: - - CHOKIDAR_USEPOLLING=true - - WATCHPACK_POLLING=true - + ports: + - '3000:80' + volumes: + - ./template-ui/config:/usr/share/nginx/html/config:ro postgres: image: postgres:16 diff --git a/template-ui/src/config/config.json b/template-ui/config/config.json similarity index 60% rename from template-ui/src/config/config.json rename to template-ui/config/config.json index 5fd095b1..f722a217 100644 --- a/template-ui/src/config/config.json +++ b/template-ui/config/config.json @@ -11,40 +11,46 @@ { "jsonName": "CNV", "displayName": "CNV" }, { "jsonName": "BND", "displayName": "BND" } ], + "queryCoordinatesAre0Based": true, + "ui": { - "title": "EGA Beacon Browser", + "title": "EGA Beacon Template UI - Main main", "favicon": "/assets/logos/favicon.ico", + "colors": { "primary": "#3176B1", "darkPrimary": "#173D5D", "secondary": "#FFE4D4" }, + "logos": { "main": "/assets/logos/main.svg", - "founders": [ - "/assets/logos/founder1.svg", - "/assets/logos/founder2.svg", - "/assets/logos/founder3.svg" - ] + "founders": [] }, + "showExternalNavBarLink": true, + "externalNavBarLink": [ { "label": "AF Browser", "url": "https://af-beacon.ega-archive.org/" } ], + "showAboutPage": true, + "about": { "logos": [ "/assets/logos/about1.svg", "/assets/logos/about2.svg", "/assets/logos/about3.svg" ], + "descriptions": [ "The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated by biomedical research projects or in the context of research-focused healthcare systems. With expertise in data management and technical infrastructure, EGA promotes FAIR data reuse and enables researchers to share their data securely. The EGA is jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona, and provides a free service for permanent data storage, data discovery, and secure data access.", "The EGA is part of the ELIXIR Infrastructure and one of the ELIXIR Core Data Resources, a collection of data resources considered of fundamental importance to the wider life-science community and the long-term preservation of biological data. Additionally, the EGA has played a central role in driving the development of the Beacon data discovery tool and coordinating its implementation by ELIXIR Nodes." ], + "fundingOrgs": [ { "title": "Funding Organizations", @@ -58,19 +64,40 @@ ] }, + "download": { + "enabled": true, + "maxRecordsDownloadableLimit": 10000 + }, + + "cookies": { + "enabled": true, + "message": "This website requires cookies, and the limited processing of your personal data in order to function. By using the site you agree to this as outlined in our Privacy Notice and Terms of Use.", + "buttonText": "I understand", + "links": [ + { + "label": "Privacy Notice", + "url": "https://ega-archive.org/data-protection/privacy-notice/ega-website/" + }, + { + "label": "Terms of Use", + "url": "https://ega-archive.org/legal-notice/" + } + ] + }, + "showLogin": false, + "auth": { - "providerType": "private", "oidc": { + "clientId": "a5e08da0-9e30-45c4-b4c4-4c45ab8262c6", "authority": "https://login.aai.lifescience-ri.eu/oidc", + "redirectUri": "http://localhost:3000", "autoSignIn": false, - "responseType": "code", "automaticSilentRenew": true, - "redirectUri": "http://localhost:3000/", - "scope": "openid profile email ga4gh_passport_v1 offline_access", - "revokeAccessTokenOnSignout": true + "scope": "openid profile email ga4gh_passport_v1 offline_access" } }, + "entryTypesOrder": [ "g_variants", "individuals", @@ -78,7 +105,9 @@ "analyses", "cohorts", "datasets", - "runs" + "runs", + "patients", + "collections" ], "commonFilters": { @@ -87,6 +116,7 @@ "Metabolic Diseases", "Mental Diseases" ], + "filterLabels": { "Demographics": [ { @@ -116,7 +146,6 @@ "type": "alphanumeric", "scopes": ["individual"] }, - { "key": "Asian or Asian British", "id": "NCIT:C41260", @@ -125,6 +154,7 @@ "scopes": ["individual"] } ], + "Metabolic Diseases": [ { "key": "obesity", @@ -162,6 +192,7 @@ "scopes": ["individual"] } ], + "Mental Diseases": [ { "key": "schizophrenia", @@ -187,16 +218,156 @@ ] } }, + "genomicAnnotations": { - "visibleGenomicCategories": [ + "annotationCategories": [ "SNP Examples", "Genomic Variant Examples", "Protein Examples", - "Molecular Effect" - ] + "Molecular Effects" + ], + + "annotationLabels": { + "SNP Examples": [ + { + "queryType": "Gene ID", + "queryParams": { + "geneId": "CHR_START-DUXAP8" + } + }, + { + "queryType": "Sequence Query", + "queryParams": { + "assemblyId": "GRCh37", + "referenceName": "11", + "start": [87202], + "referenceBases": "G", + "alternateBases": "T" + } + }, + { + "queryType": "Genomic Allele Query (HGVS)", + "queryParams": { + "genomicAlleleShortForm": "NC_000017.11:g.43057063G>A" + } + } + ], + + "Genomic Variant Examples": [ + { + "queryType": "Gene ID", + "queryParams": { + "geneId": "BRCA1", + "refAa": "Pro", + "aaPosition": "1856", + "altAa": "Ser" + } + }, + { + "queryType": "Genomic Allele Query (HGVS)", + "queryParams": { + "genomicAlleleShortForm": "NC_000008.10:g.467881_467885delinsA" + } + }, + { + "queryType": "Bracket Query", + "queryParams": { + "assemblyId": "GRCh37", + "referenceName": "17", + "start": [43045703, 43045704], + "end": [43045704, 43045705] + } + }, + { + "queryType": "Range Query", + "queryParams": { + "assemblyId": "GRCh37", + "referenceName": "2", + "start": [343675], + "end": [345681] + } + } + ], + + "Protein Examples": [ + { + "queryType": "Gene ID", + "queryParams": { + "geneId": "BRCA1", + "refAa": "Glu", + "aaPosition": "1817", + "altAa": "Ter" + } + }, + { + "queryType": "Gene ID", + "queryParams": { + "geneId": "BRCA2", + "refAa": "Val", + "aaPosition": "25", + "altAa": "Gly" + } + } + ] + } }, "genomicQueries": { + "chromosomeLibrary": [ + "1", + "2", + "3", + "4", + "5", + "6", + "7", + "8", + "9", + "10", + "11", + "12", + "13", + "14", + "15", + "16", + "17", + "18", + "19", + "20", + "21", + "22", + "23", + "24", + "X", + "Y", + "MT" + ], + "showAminoacidChange": true, + "aminoAcidNotation": [ + "Ala", + "Arg", + "Asn", + "Asp", + "Cys", + "Gln", + "Glu", + "Gly", + "His", + "Ile", + "Leu", + "Lys", + "Met", + "Phe", + "Pro", + "Ser", + "Ter", + "Thr", + "Trp", + "Tyr", + "Val", + "Xaa" + ], + "genomicQueryTypes": { "sequenceQuery": true, "geneId": true, @@ -204,63 +375,17 @@ "bracketQuery": true, "hgvsQuery": true }, + + "searchInputExample": { + "referenceName": "22", + "position": 16050527, + "referenceBases": "C", + "alternateBases": "A" + }, + "genomicQueryBuilder": { - "showAlternateBases": true, - "showAminoacidChange": true, - "aminoAcidNotation": [ - "Ala", - "Arg", - "Asn", - "Asp", - "Cys", - "Gln", - "Glu", - "Gly", - "His", - "Ile", - "Leu", - "Lys", - "Met", - "Phe", - "Pro", - "Ser", - "Ter", - "Thr", - "Trp", - "Tyr", - "Val", - "Xaa" - ], - "chromosomeLibrary": [ - "1", - "2", - "3", - "4", - "5", - "6", - "7", - "8", - "9", - "10", - "11", - "12", - "13", - "14", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "23", - "24", - "X", - "Y", - "MT" - ] + "showAlternateBases": true } } } -} +} \ No newline at end of file From 44e02615613217583eca3f112f774f6c7f67e3ae Mon Sep 17 00:00:00 2001 From: costero-e Date: Wed, 30 Sep 2026 12:25:03 +0200 Subject: [PATCH 48/56] adapting ri tools to new 2.3.1 version --- .dockerignore | 4 +- .gitignore | 4 +- docker-compose.yml | 3 + ri-tools/csv/examples/test/biosamples.csv | 42 +- ri-tools/csv/examples/test/cohorts.csv | 4 +- ri-tools/csv/examples/test/datasets.csv | 4 +- .../csv/examples/test/genomicVariations.csv | 6 +- ri-tools/csv/examples/test/individuals.csv | 42 +- ri-tools/csv/examples/test/runs.csv | 2 +- ri-tools/csv/templates/biosamples.csv | 2 +- ri-tools/csv/templates/cohorts.csv | 2 +- ri-tools/csv/templates/datasets.csv | 2 +- ri-tools/csv/templates/genomicVariations.csv | 2 +- ri-tools/csv/templates/individuals.csv | 2 +- .../deref_schemas/EUCAIM/collections.json | 17 + .../deref_schemas/EUCAIM/imageStudies.json | 85 + .../files/deref_schemas/EUCAIM/patients.json | 151 ++ ri-tools/files/deref_schemas/analyses.json | 13 +- ri-tools/files/deref_schemas/biosamples.json | 297 ++- ri-tools/files/deref_schemas/cohorts.json | 43 +- ri-tools/files/deref_schemas/datasets.json | 26 +- .../deref_schemas/genomicVariations.json | 1819 ++++++++++++++++- ri-tools/files/deref_schemas/individuals.json | 99 +- ri-tools/files/deref_schemas/runs.json | 20 +- ri-tools/files/headers/EUCAIM/collections.txt | 10 + .../files/headers/EUCAIM/imageStudies.txt | 42 + ri-tools/files/headers/EUCAIM/patients.txt | 81 + ri-tools/files/headers/biosamples.txt | 29 +- ri-tools/files/headers/cohorts.txt | 96 +- ri-tools/files/headers/datasets.txt | 5 +- ri-tools/files/headers/genomicVariations.txt | 392 +++- ri-tools/files/headers/individuals.txt | 117 +- ri-tools/files/updated_json/update.json | 40 + 33 files changed, 3309 insertions(+), 194 deletions(-) create mode 100644 ri-tools/files/deref_schemas/EUCAIM/collections.json create mode 100644 ri-tools/files/deref_schemas/EUCAIM/imageStudies.json create mode 100644 ri-tools/files/deref_schemas/EUCAIM/patients.json create mode 100644 ri-tools/files/headers/EUCAIM/collections.txt create mode 100644 ri-tools/files/headers/EUCAIM/imageStudies.txt create mode 100644 ri-tools/files/headers/EUCAIM/patients.txt create mode 100644 ri-tools/files/updated_json/update.json diff --git a/.dockerignore b/.dockerignore index 3611f7f1..269b83f3 100644 --- a/.dockerignore +++ b/.dockerignore @@ -5,4 +5,6 @@ beacon/connections/mongo/data/db/* *.json.gz adminui/node_modules *.vcf.bgz -ri-tools/files/vcf/files_to_read/* \ No newline at end of file +ri-tools/files/vcf/files_to_read/* +*.msgpack +*.initialized \ No newline at end of file diff --git a/.gitignore b/.gitignore index 08bc2973..7fb946f6 100644 --- a/.gitignore +++ b/.gitignore @@ -14,4 +14,6 @@ adminui/adminclient/migrations/* adminui/node_modules *.vcf.bgz beacon/conf/conf.py -beacon/models/prova \ No newline at end of file +beacon/models/prova +*.msgpack +*.initialized \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 4d761c0b..805d4690 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -138,6 +138,9 @@ services: - ./ri-tools/csv:/usr/src/app/csv - ./ri-tools/files/updated_json:/usr/src/app/files/updated_json - ./ri-tools/pipelines/default/templates:/usr/src/app/pipelines/default/templates + - ./ri-tools/refgen-data:/opt/refgen-data + - ./ri-tools/files/headers:/usr/src/app/files/headers + - ./ri-tools/files/deref_schemas:/usr/src/app/files/deref_schemas phenopackets-to-BFF: image: ghcr.io/ega-archive/phenopackets-to-bff:latest diff --git a/ri-tools/csv/examples/test/biosamples.csv b/ri-tools/csv/examples/test/biosamples.csv index e97622ec..8787d547 100644 --- a/ri-tools/csv/examples/test/biosamples.csv +++ b/ri-tools/csv/examples/test/biosamples.csv @@ -1,21 +1,21 @@ -biosampleStatus|id,biosampleStatus|label,collectionDate,collectionMoment,diagnosticMarkers|id,diagnosticMarkers|label,histologicalDiagnosis|id,histologicalDiagnosis|label,id,individualId,info,measurements|assayCode|id,measurements|assayCode|label,measurements|date,measurements|measurementValue|id,measurements|measurementValue|label,measurements|measurementValue|referenceRange|high,measurements|measurementValue|referenceRange|low,measurements|measurementValue|referenceRange|unit|id,measurements|measurementValue|referenceRange|unit|label,measurements|measurementValue|typedQuantities|quantity|referenceRange|high,measurements|measurementValue|typedQuantities|quantity|referenceRange|low,measurements|measurementValue|typedQuantities|quantity|referenceRange|unit,measurements|measurementValue|typedQuantities|quantity|unit|id,measurements|measurementValue|typedQuantities|quantity|unit|label,measurements|measurementValue|typedQuantities|quantity|value,measurements|measurementValue|unit|id,measurements|measurementValue|unit|label,measurements|measurementValue|value,measurements|notes,measurements|observationMoment,measurements|observationMoment|days,measurements|observationMoment|end,measurements|observationMoment|end|iso8601duration,measurements|observationMoment|id,measurements|observationMoment|iso8601duration,measurements|observationMoment|label,measurements|observationMoment|start,measurements|observationMoment|start|iso8601duration,measurements|observationMoment|weeks,measurements|procedure|ageAtProcedure,measurements|procedure|bodySite|id,measurements|procedure|bodySite|label,measurements|procedure|dateOfProcedure,measurements|procedure|procedureCode|id,measurements|procedure|procedureCode|label,notes,pathologicalStage|id,pathologicalStage|label,pathologicalTnmFinding|id,pathologicalTnmFinding|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset,phenotypicFeatures|onset|days,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|onset|weeks,phenotypicFeatures|resolution,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|end,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sampleOriginDetail|id,sampleOriginDetail|label,sampleOriginType|id,sampleOriginType|label,sampleProcessing|id,sampleProcessing|label,sampleStorage|id,sampleStorage|label,tumorGrade|id,tumorGrade|label,tumorProgression|id,tumorProgression|label -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE1,SAMPLE1,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE2,SAMPLE2,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE3,SAMPLE3,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE4,SAMPLE4,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE5,SAMPLE5,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE6,SAMPLE6,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE7,SAMPLE7,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE8,SAMPLE8,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE9,SAMPLE9,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE10,SAMPLE10,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE11,SAMPLE11,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE12,SAMPLE12,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE13,SAMPLE13,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE14,SAMPLE14,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE15,SAMPLE15,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE16,SAMPLE16,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE17,SAMPLE17,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE18,SAMPLE18,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE19,SAMPLE19,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm -EFO:0009655,abnormal sample,2020-09-11,P32Y6M1D,RO:0000085,has_function,NCIT:C3778,Serous Cystadenocarcinoma,SAMPLE20,SAMPLE20,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,,10,NCIT:C28253,Milligram,,,,,,,,,,Bear in mind that all this information is synthetic,,,,,,P53Y8M,,,,,P1Y1,FMAID:7195,lung,2020-08-19,OBI:0002657,surgical biopsy,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T2a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,5,,,,,,,,,5,8,,,,,,,,8,HP:0012828,Severe,UBERON:0000474,female reproductive system,UBERON:0000992,ovary,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +biosampleStatus|id,biosampleStatus|label,collectionDate,collectionMoment,diagnosticMarkers|id,diagnosticMarkers|label,histologicalDiagnosis|id,histologicalDiagnosis|label,id,individualId,info,measurements|assayCode|id,measurements|assayCode|label,measurements|date,measurements|measurementValue|unit|id,measurements|measurementValue|unit|label,measurements|measurementValue|referenceRange|high,measurements|measurementValue|referenceRange|low,measurements|measurementValue|referenceRange|unit|id,measurements|measurementValue|referenceRange|unit|label,measurements|measurementValue|typedQuantities|quantity|referenceRange|high,measurements|measurementValue|typedQuantities|quantity|referenceRange|low,measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|id,measurements|measurementValue|typedQuantities|quantity|unit|id,measurements|measurementValue|typedQuantities|quantity|unit|label,measurements|measurementValue|typedQuantities|quantity|value,measurements|measurementValue|id,measurements|measurementValue|label,measurements|measurementValue|value,measurements|notes,measurements|observationMoment|days,measurements|observationMoment|end,measurements|observationMoment|end|iso8601duration,measurements|observationMoment|id,measurements|observationMoment|iso8601duration,measurements|observationMoment|label,measurements|observationMoment|start,measurements|observationMoment|start|iso8601duration,measurements|observationMoment|weeks,measurements|procedure|ageAtProcedure|iso8601duration,measurements|procedure|bodySite|id,measurements|procedure|bodySite|label,measurements|procedure|dateOfProcedure,measurements|procedure|procedureCode|id,measurements|procedure|procedureCode|label,notes,pathologicalStage|id,pathologicalStage|label,pathologicalTnmFinding|id,pathologicalTnmFinding|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset|days,phenotypicFeatures|onset|weeks,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|weeks,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sampleOriginDetail|id,sampleOriginDetail|label,sampleOriginType|id,sampleOriginType|label,sampleProcessing|id,sampleProcessing|label,sampleStorage|id,sampleStorage|label,tumorGrade|id,tumorGrade|label,tumorProgression|id,tumorProgression|label +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE1,SAMPLE1,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,5,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0004718,breast lobe,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE2,SAMPLE2,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,6,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0004718,breast lobe,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28078,Grade 2,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE3,SAMPLE3,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,7,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0004718,breast lobe,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE4,SAMPLE4,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,8,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0004718,breast lobe,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE5,SAMPLE5,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,9,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0004718,breast lobe,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28078,Grade 2,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE6,SAMPLE6,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,10,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0004718,breast lobe,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE7,SAMPLE7,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,11,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000912,nasal mucosa,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE8,SAMPLE8,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,12,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000912,nasal mucosa,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4194,Invasive Breast Carcinoma of No Special Type,SAMPLE9,SAMPLE9,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,13,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000912,nasal mucosa,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28078,Grade 2,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE10,SAMPLE10,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,14,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000671,kidney,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE11,SAMPLE11,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,15,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000671,kidney,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE12,SAMPLE12,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,16,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000671,kidney,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE13,SAMPLE13,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,17,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000671,kidney,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28078,Grade 2,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE14,SAMPLE14,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,18,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000199,cardiac muscle,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE15,SAMPLE15,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,19,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000199,cardiac muscle,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE16,SAMPLE16,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,20,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000199,cardiac muscle,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28078,Grade 2,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE17,SAMPLE17,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,21,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0000199,cardiac muscle,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE18,SAMPLE18,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,22,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0001806,visceral mass,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE19,SAMPLE19,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,23,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0001806,visceral mass,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28078,Grade 2,NCIT:C84509,Primary Malignant Neoplasm +EFO:0009655,abnormal sample,2020-09-11,P53Y4M,RO:0000085,has_function,NCIT:C4126,Intestinal-Type Adenocarcinoma,SAMPLE20,SAMPLE20,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",UBERON:0001062,anatomical entity,2019-04-23,LOINC:26515-7,Platelets [#/volume] in Blood,12,10,NCIT:C28253,Milligram,,,,,,,,,24,Bear in mind that all this information is synthetic,,,,,P53Y8M,,,,,P53Y8M,BTO:0000089,blood,2020-08-19,OBI:0002651,venipuncture,Bear in mind that all this information is synthetic,NCIT:C27977,Stage IIIA,NCIT:C48725,T3a Stage Finding,ECO:0006017,author statement from published clinical study used in manual assertion,ECO:0006017,author statement from published clinical study used in manual assertion,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,6,1,,,,,,,,5,8,,,,,,,HP:0012828,Severe,BTO:0004718,breast cancer cell,BTO:0001806,visceral mass,EFO:0009129,mechanical dissociation,OBI:0000915,freezing storage,NCIT:C28080,Grade 3a,NCIT:C84509,Primary Malignant Neoplasm diff --git a/ri-tools/csv/examples/test/cohorts.csv b/ri-tools/csv/examples/test/cohorts.csv index 37c6c8b5..c47b81d8 100644 --- a/ri-tools/csv/examples/test/cohorts.csv +++ b/ri-tools/csv/examples/test/cohorts.csv @@ -1,2 +1,2 @@ -cohortDataTypes|id,cohortDataTypes|label,cohortDesign|id,cohortDesign|label,cohortSize,cohortType,collectionEvents|eventAgeRange|availability,collectionEvents|eventAgeRange|availabilityCount,collectionEvents|eventAgeRange|distribution,collectionEvents|eventDataTypes|availability,collectionEvents|eventDataTypes|availabilityCount,collectionEvents|eventDataTypes|distribution,collectionEvents|eventDiseases|availability,collectionEvents|eventDiseases|availabilityCount,collectionEvents|eventDiseases|distribution,collectionEvents|eventEthnicities|availability,collectionEvents|eventEthnicities|availabilityCount,collectionEvents|eventEthnicities|distribution,collectionEvents|eventGenders|availability,collectionEvents|eventGenders|availabilityCount,collectionEvents|eventGenders|distribution,collectionEvents|eventLocations|availability,collectionEvents|eventLocations|availabilityCount,collectionEvents|eventLocations|distribution,collectionEvents|eventPhenotypes|availability,collectionEvents|eventPhenotypes|availabilityCount,collectionEvents|eventPhenotypes|distribution,exclusionCriteria|ageRange|end|iso8601duration,exclusionCriteria|ageRange|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset,exclusionCriteria|diseaseConditions|diseaseCode|id,exclusionCriteria|diseaseConditions|diseaseCode|label,exclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|diseaseConditions|notes,exclusionCriteria|diseaseConditions|severity|id,exclusionCriteria|diseaseConditions|severity|label,exclusionCriteria|diseaseConditions|stage|id,exclusionCriteria|diseaseConditions|stage|label,exclusionCriteria|ethnicities|id,exclusionCriteria|ethnicities|label,exclusionCriteria|genders|id,exclusionCriteria|genders|label,exclusionCriteria|locations|id,exclusionCriteria|locations|label,exclusionCriteria|phenotypicConditions|evidence|evidenceCode,exclusionCriteria|phenotypicConditions|evidence|reference,exclusionCriteria|phenotypicConditions|excluded,exclusionCriteria|phenotypicConditions|featureType|id,exclusionCriteria|phenotypicConditions|featureType|label,exclusionCriteria|phenotypicConditions|modifiers,exclusionCriteria|phenotypicConditions|notes,exclusionCriteria|phenotypicConditions|onset,exclusionCriteria|phenotypicConditions|resolution,exclusionCriteria|phenotypicConditions|severity|id,exclusionCriteria|phenotypicConditions|severity|label,id,inclusionCriteria|ageRange|end|iso8601duration,inclusionCriteria|ageRange|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset,inclusionCriteria|diseaseConditions|diseaseCode|id,inclusionCriteria|diseaseConditions|diseaseCode|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|diseaseConditions|notes,inclusionCriteria|diseaseConditions|severity|id,inclusionCriteria|diseaseConditions|severity|label,inclusionCriteria|diseaseConditions|stage|id,inclusionCriteria|diseaseConditions|stage|label,inclusionCriteria|ethnicities|id,inclusionCriteria|ethnicities|label,inclusionCriteria|genders|id,inclusionCriteria|genders|label,inclusionCriteria|locations|id,inclusionCriteria|locations|label,inclusionCriteria|phenotypicConditions|evidence|evidenceCode,inclusionCriteria|phenotypicConditions|evidence|reference,inclusionCriteria|phenotypicConditions|excluded,inclusionCriteria|phenotypicConditions|featureType|id,inclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|phenotypicConditions|modifiers,inclusionCriteria|phenotypicConditions|notes,inclusionCriteria|phenotypicConditions|onset,inclusionCriteria|phenotypicConditions|resolution,inclusionCriteria|phenotypicConditions|severity|id,inclusionCriteria|phenotypicConditions|severity|label,name -OGMS:0000015,clinical history,OMIABIS:0001019,longitudinal study design,20000,study-defined,TRUE,101,"{""ranges"": {""20-40"": 51,""50-60"": 50}}",TRUE,29,"{""datatypes"": {""OGMS:0000015"": 5,""OBI:0000070"": 8,""OMIABIS:0000060"": 16}}",TRUE,100,"{""diseases"":{""HP:0001645"": 50}}",TRUE,101,"{""ethnicities"": {""African"": 3,""European"": 90,""Latin American"": 8}}",TRUE,101,"{""genders"": {""female"": 51,""male"": 50}}",TRUE,101,"{""ethnicities"": {""GAZ:00004501"":101}}",TRUE,101,"{""Phenotype"": {""GAZ:00004501"":101}}",P58Y,P18Y,"{""id"": ""NCIT:C49685"",""label"": ""Adult 18-65 Years Old""}",HP:0004789,lactose intolerance,FALSE,All this information is synthetic.,HP:0012828,Severe,OGMS:0000119,acute onset,NCIT:C43851,European,NCIT:C16576|NCIT:C20197|NCIT:C1799,Female|male|uknown,GAZ:00000460,Eurasia,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0000002,Abnormality of body height,"{""id"": ""HP:0032500"",""label"": ""Exacerbated by tobacco use""}",Bear in mind that all this information is synthetic,"{""iso8601duration"": ""P58Y""}","{""iso8601duration"": ""P98Y""}",HP:0012828,Severe,EGA-testing,P59Y,P18Y,"{""id"": ""NCIT:C49685"",""label"": ""Adult 18-65 Years Old""}",HP:0004789,lactose intolerance,FALSE,All this information is synthetic.,HP:0012828,Severe,OGMS:0000119,acute onset,NCIT:C43851,European,NCIT:C16576|NCIT:C20197|NCIT:C1799,Female|male|uknown,GAZ:00000460,Eurasia,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0000002,Abnormality of body height,"{""id"": ""HP:0032500"",""label"": ""Exacerbated by tobacco use""}",Bear in mind that all this information is synthetic,"{""iso8601duration"": ""P59Y""}","{""iso8601duration"": ""P98Y""}",HP:0012828,Severe,syntheticCohort +cohortDataTypes|id,cohortDataTypes|label,cohortDesign|id,cohortDesign|label,cohortSize,cohortType,collectionEvents|eventAgeRange|availability,collectionEvents|eventAgeRange|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,collectionEvents|eventDataTypes|availability,collectionEvents|eventDataTypes|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,collectionEvents|eventDiseases|availability,collectionEvents|eventDiseases|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,collectionEvents|eventEthnicities|availability,collectionEvents|eventEthnicities|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,collectionEvents|eventGenders|availability,collectionEvents|eventGenders|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,collectionEvents|eventLocations|availability,collectionEvents|eventLocations|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,collectionEvents|eventPhenotypes|availability,collectionEvents|eventPhenotypes|availabilityCount,inclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|ageRange|end|iso8601duration,exclusionCriteria|ageRange|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset|id,exclusionCriteria|diseaseConditions|ageOfOnset|label,exclusionCriteria|diseaseConditions|diseaseCode|id,exclusionCriteria|diseaseConditions|diseaseCode|label,exclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|diseaseConditions|notes,exclusionCriteria|diseaseConditions|severity|id,exclusionCriteria|diseaseConditions|severity|label,exclusionCriteria|diseaseConditions|stage|id,exclusionCriteria|diseaseConditions|stage|label,exclusionCriteria|ethnicities|id,exclusionCriteria|ethnicities|label,exclusionCriteria|genders|id,exclusionCriteria|genders|label,exclusionCriteria|locations|id,exclusionCriteria|locations|label,exclusionCriteria|phenotypicConditions|evidence|evidenceCode|id,exclusionCriteria|phenotypicConditions|evidence|reference|id,exclusionCriteria|phenotypicConditions|excluded,exclusionCriteria|phenotypicConditions|featureType|id,exclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|phenotypicConditions|notes,exclusionCriteria|phenotypicConditions|onset|iso8601duration,exclusionCriteria|phenotypicConditions|severity|id,exclusionCriteria|phenotypicConditions|severity|label,id,inclusionCriteria|ageRange|end|iso8601duration,inclusionCriteria|ageRange|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset|id,inclusionCriteria|diseaseConditions|ageOfOnset|label,inclusionCriteria|diseaseConditions|diseaseCode|id,inclusionCriteria|diseaseConditions|diseaseCode|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|diseaseConditions|notes,inclusionCriteria|diseaseConditions|severity|id,inclusionCriteria|diseaseConditions|severity|label,inclusionCriteria|diseaseConditions|stage|id,inclusionCriteria|diseaseConditions|stage|label,inclusionCriteria|ethnicities|id,inclusionCriteria|ethnicities|label,inclusionCriteria|genders|id,inclusionCriteria|genders|label,inclusionCriteria|locations|id,inclusionCriteria|locations|label,inclusionCriteria|phenotypicConditions|evidence|evidenceCode|id,inclusionCriteria|phenotypicConditions|evidence|reference|id,inclusionCriteria|phenotypicConditions|excluded,inclusionCriteria|phenotypicConditions|featureType|id,inclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|phenotypicConditions|notes,inclusionCriteria|phenotypicConditions|onset|iso8601duration,inclusionCriteria|phenotypicConditions|severity|id,inclusionCriteria|phenotypicConditions|severity|label,name +OGMS:0000015,clinical history,OMIABIS:0001019,longitudinal study design,20,study-defined,TRUE,20,"{""ranges"": {""20-40"": 10,""50-60"": 10}}",TRUE,20,"{""datatypes"": {""OGMS:0000015"": 20, ""OMIABIS:0001032"": 20, ""OGMS:0000073"":20}}",TRUE,20,"{""diseases"":{""MONDO:0004989"": 3, ""MONDO:0003661"": 3, ""MONDO:0005138"": 3, ""MONDO:0006181"": 4, ""MONDO:0003354"": 4, ""MONDO:0005060"": 3}}",TRUE,20,"{""ethnicities"": {""European"": 13, ""African"": 3, ""Asian"": 4}}",TRUE,20,"{""genders"": {""female"": 16, ""male"": 4}}",TRUE,20,"{""ethnicities"": {""GAZ:00002960"":20}}",TRUE,20,"{""Phenotype"": {""GAZ:00004501"":20}}",P58Y,P18Y,NCIT:C49685,Adult 18-65 Years Old,HP:0000002,Abnormality of body height,TRUE,All this information is synthetic.,HP:0012828,Severe,OGMS:0000119,acute onset,NCIT:C43851,European,NCIT:C16576|NCIT:C20197|NCIT:C1799,Female|male|uknown,GAZ:00000460,Eurasia,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0000002,Abnormality of body height,"{""id"": ""HP:0032500"",""label"": ""Exacerbated by tobacco use""}",This information is synthetic,P58Y,HP:0012828,Severe,EGA-testing,P59Y,P18Y,NCIT:C49685,Adult 18-65 Years Old,MONDO:0005002,breast carcinoma,FALSE,All this information is synthetic.,HP:0012828,Severe,OGMS:0000119,acute onset,NCIT:C43851,European,NCIT:C16576,Female,GAZ:00000460,Eurasia,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,MONDO:0004994,breast carcinoma,,Bear in mind that all this information is synthetic,P20Y,HP:0012828,Severe,syntheticCohort diff --git a/ri-tools/csv/examples/test/datasets.csv b/ri-tools/csv/examples/test/datasets.csv index e92e7496..73fc96c0 100644 --- a/ri-tools/csv/examples/test/datasets.csv +++ b/ri-tools/csv/examples/test/datasets.csv @@ -1,2 +1,2 @@ -createDateTime,dataUseConditions|duoDataUse|description,dataUseConditions|duoDataUse|id,dataUseConditions|duoDataUse|label,dataUseConditions|duoDataUse|modifiers,dataUseConditions|duoDataUse|version,description,externalUrl,id,info,name,updateDateTime,version -2021-12-29T20:33:40Z,,"DUO:0000019,DUO:00000020","publication required,publication required","{""id"": ""EFO:0001645"",""label"": ""coronary artery disease""}","7-1-19,7-1-19",Bear in mind that both genomic and metadata information is synthetic ,https://ega-archive.org/datasets/EGAD00001006673/,synthetic_usecases_4beacon_testingV3,"{""info"": ""Both metadata and genomic variations information are synthetic.""}",Dataset with synthetic data for beacon testing,2021-12-29T20:33:40Z,v1.0 +createDateTime,dataUseConditions|duoDataUse|id,dataUseConditions|duoDataUse|label,dataUseConditions|duoDataUse|version,description,externalUrl,id,info,name,updateDateTime,version +2021-12-29T20:33:40Z,DUO:0000019,publication required,7-1-19,Bear in mind that both genomic and metadata information is synthetic,http://synthetic_usecases_4beacon_testingV4.com,test,,Dataset with synthetic data for beacon testing,2021-12-29T20:33:40Z,v1.0 diff --git a/ri-tools/csv/examples/test/genomicVariations.csv b/ri-tools/csv/examples/test/genomicVariations.csv index 3eb4d03c..61f26658 100644 --- a/ri-tools/csv/examples/test/genomicVariations.csv +++ b/ri-tools/csv/examples/test/genomicVariations.csv @@ -1,4 +1,4 @@ caseLevelData|biosampleId,caseLevelData|phenotypicEffects|conditionId,caseLevelData|phenotypicEffects|effect|id,caseLevelData|phenotypicEffects|effect|label,variantInternalId,variation|alternateBases,variation|location|_id,variation|location|interval|end|type,variation|location|interval|end|value,variation|location|interval|start|type,variation|location|interval|start|value,variation|location|interval|type,variation|location|sequence_id,variation|location|type,variation|referenceBases,variation|variantType -SAMPLE2|SAMPLE3|SAMPLE14|SAMPLE15|SAMPLE18|SAMPLE19,Alzheimer|||||,DOID:10652|||||,Alzheimer's disease|||||,Chr19_44908684_T_C,C,Var:00001,Number,44908684,Number,44908683,SequenceInterval,HGVSid:19:g.44908683T>C,SequenceLocation,T,SNP -SAMPLE9|SAMPLE17,Thrombophilia|,DOID:0111902|,thrombophilia due to activated protein C resistance|,chr1_169549811_C_T,T,Var:00002,Number,169549811,Number,169549810,SequenceInterval,HGVSid:1:g.169549810C>T,SequenceLocation ,C,SNP -SAMPLE5|SAMPLE18,Thiopurine Drug Toxicity|,NCIT:C4389|,Thiopurine Methyltransferase Deficiency|,chr6_18138997_C_T,T,Var:00003,Number,18138997,Number,18138996,SequenceInterval,HGVSid:6:g.18138996C>T,SequenceLocation,C,SNP +SAMPLE2|SAMPLE3|SAMPLE14|SAMPLE15|SAMPLE18|SAMPLE19,colorectal cancer,DOID:9256,colorectal cancer,ed823050df2291f304dfa097de2bcdafd22bbe771609339a8c0b915f0319d874,T,Var:00001,Number,7232464,Number,7232463,SequenceInterval,HGVSID:N,SequenceLocation,C,SNP +SAMPLE9|SAMPLE17,Melanoma,DOID:1909,melanoma,4dbae68746e521da4d8fe4da3b61f56e579e001400b4410f9b5f1316fdb24bbb,T,Var:00002,Number,7232464,Number,7232463,SequenceInterval,HGVSID:N,SequenceLocation,A,SNP +SAMPLE5|SAMPLE18,pancreatic cancer,DOID:1793,pancreatic cancer,fa27ec7bb2726ccad3a9429bcb728e65c13205a613c5496162be75bd5c2594c5,T,Var:00003,Number,7232464,Number,7232463,SequenceInterval,HGVSID:N,SequenceLocation,C,SNP diff --git a/ri-tools/csv/examples/test/individuals.csv b/ri-tools/csv/examples/test/individuals.csv index a1bb2116..569b2bea 100644 --- a/ri-tools/csv/examples/test/individuals.csv +++ b/ri-tools/csv/examples/test/individuals.csv @@ -1,21 +1,21 @@ -diseases|ageOfOnset,diseases|ageOfOnset|days,diseases|ageOfOnset|end,diseases|ageOfOnset|end|iso8601duration,diseases|ageOfOnset|id,diseases|ageOfOnset|iso8601duration,diseases|ageOfOnset|label,diseases|ageOfOnset|start,diseases|ageOfOnset|start|iso8601duration,diseases|ageOfOnset|weeks,diseases|diseaseCode|id,diseases|diseaseCode|label,diseases|familyHistory,diseases|notes,diseases|severity|id,diseases|severity|label,diseases|stage|id,diseases|stage|label,ethnicity|id,ethnicity|label,exposures|ageAtExposure|iso8601duration,exposures|date,exposures|duration,exposures|exposureCode|id,exposures|exposureCode|label,exposures|unit|id,exposures|unit|label,geographicOrigin|id,geographicOrigin|label,id,info,interventionsOrProcedures|ageAtProcedure,interventionsOrProcedures|ageAtProcedure|days,interventionsOrProcedures|ageAtProcedure|end,interventionsOrProcedures|ageAtProcedure|end|iso8601duration,interventionsOrProcedures|ageAtProcedure|id,interventionsOrProcedures|ageAtProcedure|iso8601duration,interventionsOrProcedures|ageAtProcedure|label,interventionsOrProcedures|ageAtProcedure|start,interventionsOrProcedures|ageAtProcedure|start|iso8601duration,interventionsOrProcedures|ageAtProcedure|weeks,interventionsOrProcedures|bodySite|id,interventionsOrProcedures|bodySite|label,interventionsOrProcedures|dateOfProcedure,interventionsOrProcedures|procedureCode|id,interventionsOrProcedures|procedureCode|label,karyotypicSex,measures|assayCode|id,measures|assayCode|label,measures|date,measures|measurementValue|id,measures|measurementValue|label,measures|measurementValue|referenceRange|high,measures|measurementValue|referenceRange|low,measures|measurementValue|referenceRange|unit|id,measures|measurementValue|referenceRange|unit|label,measures|measurementValue|typedQuantities|quantity|referenceRange|high,measures|measurementValue|typedQuantities|quantity|referenceRange|low,measures|measurementValue|typedQuantities|quantity|referenceRange|unit,measures|measurementValue|typedQuantities|quantity|unit|id,measures|measurementValue|typedQuantities|quantity|unit|label,measures|measurementValue|typedQuantities|quantity|value,measures|measurementValue|unit|id,measures|measurementValue|unit|label,measures|measurementValue|value,measures|notes,measures|observationMoment,measures|observationMoment|days,measures|observationMoment|end,measures|observationMoment|end|iso8601duration,measures|observationMoment|id,measures|observationMoment|iso8601duration,measures|observationMoment|label,measures|observationMoment|start,measures|observationMoment|start|iso8601duration,measures|observationMoment|weeks,measures|procedure|ageAtProcedure,measures|procedure|bodySite|id,measures|procedure|bodySite|label,measures|procedure|dateOfProcedure,measures|procedure|procedureCode|id,measures|procedure|procedureCode|label,pedigrees|disease|ageOfOnset,pedigrees|disease|diseaseCode|id,pedigrees|disease|diseaseCode|label,pedigrees|disease|familyHistory,pedigrees|disease|notes,pedigrees|disease|severity|id,pedigrees|disease|severity|label,pedigrees|disease|stage|id,pedigrees|disease|stage|label,pedigrees|id,pedigrees|members|affected,pedigrees|members|memberId,pedigrees|members|role|id,pedigrees|members|role|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset,phenotypicFeatures|onset|days,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|onset|weeks,phenotypicFeatures|resolution,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|end,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sex|id,sex|label,treatments|ageAtOnset|iso8601duration,treatments|treatmentCode|id,treatments|treatmentCode|label,treatments|routeOfAdministration|id,treatments|routeOfAdministration|label,treatments|treatmentCode|id,treatments|treatmentCode|label -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE1,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE2,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE3,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE4,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE5,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE6,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE7,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE8,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE9,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE10,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE11,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE12,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE13,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE14,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE15,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE16,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE17,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE18,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE19,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure -,,,,NCIT:C16731,,Neonate,,,,MONDO:0004975,Cystic fibrosis,FALSE,Bear in mind that all information is synthetic,HP:0012828,Severe,,,NCIT:C43851,European,P32Y6M1D,2024-09-25,P2Y6M1D,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002586,State of Wisconsin,SAMPLE20,Bear in mind that all this information is synthetic,1999-08-05T17:21:00+01:00,,,,,,,,,,FMAID:7195,lung,2024-12-24,OBI:0002657,surgical biopsy,"XX,XY",UBERON:0001062,anatomical entity,2024-11-08,,,50,20,NCIT:C28253,Milligram,10,5,,,,,NCIT:C28253,Milligram,50,Bear in mind that all this information is synthetic,P1Y1,,,,,P32Y6M1D,,,,,1999-08-05T17:21:00+01:00,FMAID:7195,lung,2024-08-15,OBI:0002657,surgical biopsy,,HP:0001645,Sudden cardiac death,TRUE,Bear in mind that all this information is synthetic ,HP:0012828,Severe,OGMS:0000103,Disease stage,SCD-Pedigree001,TRUE|TRUE|TRUE,Ind001|Ind002|Ind003,NCIT:C64435|NCIT:C96572|NCIT:C111201,Proband|Father|Full Brother,ECO:0006017,author statement from published clinical study used in manual assertion,,,,TRUE,HP:0000002,Abnormality of body height,HP:0032500,Exacerbated by tobacco use,Please note that all this information is synthetic,,,,,HP:0011463,,Infantile onset,,,,5,8,,,,,,,,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration,OGMS:0000113,chemotherapy procedure +diseases|ageOfOnset|id,diseases|ageOfOnset|label,diseases|diseaseCode|id,diseases|diseaseCode|label,diseases|familyHistory,diseases|notes,diseases|severity|id,diseases|severity|label,ethnicity|id,ethnicity|label,exposures|ageAtExposure|iso8601duration,exposures|date,exposures|duration,exposures|exposureCode|id,exposures|exposureCode|label,exposures|unit|id,exposures|unit|label,geographicOrigin|id,geographicOrigin|label,id,info,interventionsOrProcedures|ageAtProcedure|iso8601duration,interventionsOrProcedures|ageAtProcedure|weeks,interventionsOrProcedures|bodySite|id,interventionsOrProcedures|bodySite|label,interventionsOrProcedures|dateOfProcedure,interventionsOrProcedures|procedureCode|id,interventionsOrProcedures|procedureCode|label,karyotypicSex,measurements|assayCode|id,measurements|assayCode|label,measurements|date,measurements|measurementValue|referenceRange|high,measurements|measurementValue|referenceRange|low,measurements|measurementValue|referenceRange|unit|id,measurements|measurementValue|referenceRange|unit|label,measurements|measurementValue|typedQuantities|quantity|referenceRange|high,measurements|measurementValue|typedQuantities|quantity|referenceRange|low,pedigrees|disease|ageOfOnset|start,measurements|measurementValue|typedQuantities|quantity|unit|id,measurements|measurementValue|typedQuantities|quantity|unit|label,measurements|observationMoment|iso8601duration,measurements|measurementValue|unit|id,measurements|measurementValue|unit|label,measurements|measurementValue|value,measurements|procedure|ageAtProcedure|iso8601duration,measurements|procedure|bodySite|id,measurements|procedure|bodySite|label,measurements|procedure|dateOfProcedure,measurements|procedure|procedureCode|id,measurements|procedure|procedureCode|label,pedigrees|disease|ageOfOnset,pedigrees|disease|diseaseCode|id,pedigrees|disease|diseaseCode|label,pedigrees|disease|familyHistory,pedigrees|disease|notes,pedigrees|disease|severity|id,pedigrees|disease|severity|label,pedigrees|disease|stage|id,pedigrees|disease|stage|label,pedigrees|id,pedigrees|members|affected,pedigrees|members|memberId,pedigrees|members|role|id,pedigrees|members|role|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset|id,phenotypicFeatures|onset|label,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sex|id,sex|label,treatments|ageAtOnset|iso8601duration,treatments|treatmentCode|id,treatments|treatmentCode|label,treatments|routeOfAdministration|id,treatments|routeOfAdministration|label +NCIT:C49685,Adult 18-65 Years Old,MONDO:0004989,breast carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C41260,Asian,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002949,Iberian Peninsula,SAMPLE1,Bear in mind that all this information is synthetic,P16Y,,BTO:0004718,breast lobe,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,26.63838307|85.6358|179.2973,P26Y,BTO:0004718,breast lobe,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91108,Middle Adult,MONDO:0004989,breast carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012826,Moderate,NCIT:C43851,European,P31Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002950,Iberian Peninsula,SAMPLE2,Bear in mind that all this information is synthetic,P16Y,,BTO:0004718,breast lobe,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,20.02935755|61.5485|175.2973,P19Y,BTO:0004718,breast lobe,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000116,radiation therapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25289,Brother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C20197,male,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38675,Cutaneous Route of Administration +NCIT:C91107,Young Adult,MONDO:0004989,breast carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012826,Moderate,NCIT:C43851,European,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002951,Iberian Peninsula,SAMPLE3,Bear in mind that all this information is synthetic,P16Y,,BTO:0004718,breast lobe,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,23.25781428|72.5702|176.6423,P2Y,BTO:0004718,breast lobe,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25289,Brother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C20197,male,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C49685,Adult 18-65 Years Old,MONDO:0003661,breast lymphoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P44Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002952,Iberian Peninsula,SAMPLE4,Bear in mind that all this information is synthetic,P16Y,,BTO:0004718,breast lobe,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,28.25888232|84.5764|173.0004,P16Y,BTO:0004718,breast lobe,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91108,Middle Adult,MONDO:0003661,breast lymphoma,TRUE,Bear in mind that all information is synthetic,HP:0012826,Moderate,NCIT:C41260,Asian,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002953,Iberian Peninsula,SAMPLE5,Bear in mind that all this information is synthetic,P16Y,,BTO:0004718,breast lobe,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,21.15225593|57.9888|165.5746,P5Y,BTO:0004718,breast lobe,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C49685,Adult 18-65 Years Old,MONDO:0003661,breast lymphoma,TRUE,Bear in mind that all information is synthetic,HP:0012825,Mild,NCIT:C42331,African,P55Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002954,Iberian Peninsula,SAMPLE6,Bear in mind that all this information is synthetic,P16Y,,BTO:0004718,breast lobe,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,22.43565228|60.1796|163.7779,P8Y,BTO:0004718,breast lobe,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38675,Cutaneous Route of Administration +NCIT:C91107,Young Adult,MONDO:0005138,lung carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002955,Iberian Peninsula,SAMPLE7,Bear in mind that all this information is synthetic,P16Y,,BTO:0000912,nasal mucosa,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,22.4686257|62.253|166.4531,P7Y,BTO:0000912,nasal mucosa,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91108,Middle Adult,MONDO:0005138,lung carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012826,Moderate,NCIT:C43851,European,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002956,Iberian Peninsula,SAMPLE8,Bear in mind that all this information is synthetic,P16Y,,BTO:0000912,nasal mucosa,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,24.70926291|76.1434|175.5441,P3Y,BTO:0000912,nasal mucosa,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C49685,Adult 18-65 Years Old,MONDO:0005138,lung carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P67Y,2024-09-25,14 months,NCIT:C29853,Silicon Dioxide,NCIT:C28253,Milligram,GAZ:00002957,Iberian Peninsula,SAMPLE9,Bear in mind that all this information is synthetic,P16Y,,BTO:0000912,nasal mucosa,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,24.73002079|89.9811|190.7495,P16Y,BTO:0000912,nasal mucosa,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91107,Young Adult,MONDO:0006181,digestive system carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P21Y,2024-09-25,14 months,NCIT:C29853,Silicon Dioxide,NCIT:C28253,Milligram,GAZ:00002958,Iberian Peninsula,SAMPLE10,Bear in mind that all this information is synthetic,P16Y,,BTO:0000671,kidney,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,25.14125758|58.8324|152.973,P16Y,BTO:0000671,kidney,2024-08-15,OBI:0002657,surgical biopsy,,HP:0005959,Impaired gluconeogenesis,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91108,Middle Adult,MONDO:0006181,digestive system carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C41260,Asian,P29Y,2024-09-25,14 months,NCIT:C29853,Silicon Dioxide,NCIT:C28253,Milligram,GAZ:00002959,Iberian Peninsula,SAMPLE11,Bear in mind that all this information is synthetic,P16Y,,BTO:0000671,kidney,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,28.45056882|82.6649|170.4571,P36Y,BTO:0000671,kidney,2024-08-15,OBI:0002657,surgical biopsy,,HP:0005959,Impaired gluconeogenesis,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000116,radiation therapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C49685,Adult 18-65 Years Old,MONDO:0006181,digestive system carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C42331,African,P21Y,2024-09-25,14 months,NCIT:C29853,Silicon Dioxide,NCIT:C28253,Milligram,GAZ:00002960,Iberian Peninsula,SAMPLE12,Bear in mind that all this information is synthetic,P16Y,,BTO:0000671,kidney,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,25.71804789|97.2114|194.4194,P16Y,BTO:0000671,kidney,2024-08-15,OBI:0002657,surgical biopsy,,HP:0005959,Impaired gluconeogenesis,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91107,Young Adult,MONDO:0006181,digestive system carcinoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P40Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002961,Iberian Peninsula,SAMPLE13,Bear in mind that all this information is synthetic,P16Y,,BTO:0000671,kidney,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,28.87940028|74.3618|160.4652,P16Y,BTO:0000671,kidney,2024-08-15,OBI:0002657,surgical biopsy,,HP:0005959,Impaired gluconeogenesis,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38675,Cutaneous Route of Administration +NCIT:C91108,Middle Adult,MONDO:0003354,heart sarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012826,Moderate,NCIT:C43851,European,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002962,Iberian Peninsula,SAMPLE14,Bear in mind that all this information is synthetic,P16Y,,BTO:0000199,cardiac muscle,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,35.72130281|98.5093|166.0638,P16Y,BTO:0000199,cardiac muscle,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C49685,Adult 18-65 Years Old,MONDO:0003354,heart sarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P71Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002963,Iberian Peninsula,SAMPLE15,Bear in mind that all this information is synthetic,P16Y,,BTO:0000199,cardiac muscle,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,24.60430212|65.9034|163.6622,P16Y,BTO:0000199,cardiac muscle,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38675,Cutaneous Route of Administration +NCIT:C91107,Young Adult,MONDO:0003354,heart sarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C43851,European,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002964,Iberian Peninsula,SAMPLE16,Bear in mind that all this information is synthetic,P16Y,,BTO:0000199,cardiac muscle,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,21.98192586|52.4475|154.4648,P46Y,BTO:0000199,cardiac muscle,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91108,Middle Adult,MONDO:0003354,heart sarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012825,Mild,NCIT:C43851,European,P21Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002965,Iberian Peninsula,SAMPLE17,Bear in mind that all this information is synthetic,P16Y,,BTO:0000199,cardiac muscle,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,24.96495618|64.5542|160.804,P15Y,BTO:0000199,cardiac muscle,2024-08-15,OBI:0002657,surgical biopsy,,HP:0030079,Cervix cancer,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25680,Sister,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P2Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C49685,Adult 18-65 Years Old,MONDO:0005060,liposarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012825,Mild,NCIT:C43851,European,P33Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002966,Iberian Peninsula,SAMPLE18,Bear in mind that all this information is synthetic,P16Y,,BTO:0001806,visceral mass,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,20.81439531|48.4287|152.535,P56Y,BTO:0001806,visceral mass,2024-08-15,OBI:0002657,surgical biopsy,,HP:0000819,Diabetes mellitus,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000116,radiation therapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C71386,Grandmother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C16576,female,P1Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration +NCIT:C91107,Young Adult,MONDO:0005060,liposarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C42331,African,P27Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002967,Iberian Peninsula,SAMPLE19,Bear in mind that all this information is synthetic,P16Y,,BTO:0001806,visceral mass,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,22.50451404|77.1479|185.1515,P26Y,BTO:0001806,visceral mass,2024-08-15,OBI:0002657,surgical biopsy,,HP:0000819,Diabetes mellitus,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C25289,Brother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C20197,male,P3Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38675,Cutaneous Route of Administration +NCIT:C91108,Middle Adult,MONDO:0005060,liposarcoma,TRUE,Bear in mind that all information is synthetic,HP:0012828,Severe,NCIT:C41260,Asian,P51Y,2024-09-25,14 months,CHEBI:46661,asbestos,NCIT:C28253,Milligram,GAZ:00002968,Iberian Peninsula,SAMPLE20,Bear in mind that all this information is synthetic,P16Y,,BTO:0001806,visceral mass,2024-12-24,OBI:0002657,surgical biopsy,XX,LOINC:35925-4|LOINC:3141-9|LOINC:8308-9,BMI|Weight|Height-standing,2021-09-24|2021-09-24|2021-09-24,,,,,,,,,,,NCIT:C49671|NCIT:C28252|NCIT:C49668,Kilogram per Square Meter|Kilogram|Centimeter,34.57457359|96.1068|166.7242,P16Y,BTO:0001806,visceral mass,2024-08-15,OBI:0002657,surgical biopsy,,HP:0000819,Diabetes mellitus,TRUE,Bear in mind that all this information is synthetic,HP:0012828,Severe,OGMS:0000113,chemotherapy procedure,SCD-Pedigree001,TRUE,Ind005,NCIT:C252896,Brother,ECO:0006017,author statement from published clinical study used in manual assertion,TRUE,HP:0012245,Sex reversal,HP:0000061,Ambiguous genitalia,Please note that all this information is synthetic,HP:0003587,Insidious onset,8,8,HP:0012828,Severe,NCIT:C20197,male,P4Y1,OGMS:0000113,chemotherapy procedure,NCIT:C38288,Oral Route of Administration \ No newline at end of file diff --git a/ri-tools/csv/examples/test/runs.csv b/ri-tools/csv/examples/test/runs.csv index 38bc6299..2429e558 100644 --- a/ri-tools/csv/examples/test/runs.csv +++ b/ri-tools/csv/examples/test/runs.csv @@ -1,2 +1,2 @@ biosampleId,id,individualId,info,libraryLayout,librarySelection,librarySource|id,librarySource|label,libraryStrategy,platform,platformModel|id,platformModel|label,runDate -008dafdd-a3d1-4801-8c0a-8714e2b58e48,EGA-testing,EGA,"{""info"": {""info"": ""Both metadata and genomic variations information are synthetic.""}}",PAIRED,RANDOM,GENEPIO:0001966,genomic source,WGS,Illumina,OBI:0002048,Illumina HiSeq 3000,2021-10-18 +SAMPLE1|SAMPLE2|SAMPLE3|SAMPLE4|SAMPLE5|SAMPLE6|SAMPLE7|SAMPLE8|SAMPLE9|SAMPLE10|SAMPLE11|SAMPLE12|SAMPLE13|SAMPLE14|SAMPLE15|SAMPLE16|SAMPLE17|SAMPLE18|SAMPLE19|SAMPLE20,EGA-testing,SAMPLE1|SAMPLE2|SAMPLE3|SAMPLE4|SAMPLE5|SAMPLE6|SAMPLE7|SAMPLE8|SAMPLE9|SAMPLE10|SAMPLE11|SAMPLE12|SAMPLE13|SAMPLE14|SAMPLE15|SAMPLE16|SAMPLE17|SAMPLE18|SAMPLE19|SAMPLE20,"{""info"": {""info"": ""Both metadata and genomic variations information are synthetic.""}}",PAIRED,RANDOM,GENEPIO:0001966,genomic source,WGS,Illumina,OBI:0002048,Illumina HiSeq 3000,2021-10-18 diff --git a/ri-tools/csv/templates/biosamples.csv b/ri-tools/csv/templates/biosamples.csv index 475a68b7..547ac5a3 100644 --- a/ri-tools/csv/templates/biosamples.csv +++ b/ri-tools/csv/templates/biosamples.csv @@ -1 +1 @@ -biosampleStatus|id,biosampleStatus|label,collectionDate,collectionMoment,diagnosticMarkers|id,diagnosticMarkers|label,histologicalDiagnosis|id,histologicalDiagnosis|label,id,individualId,info,measurements|assayCode|id,measurements|assayCode|label,measurements|date,measurements|measurementValue|id,measurements|measurementValue|label,measurements|measurementValue|referenceRange|high,measurements|measurementValue|referenceRange|low,measurements|measurementValue|referenceRange|unit|id,measurements|measurementValue|referenceRange|unit|label,measurements|measurementValue|typedQuantities|quantity|referenceRange|high,measurements|measurementValue|typedQuantities|quantity|referenceRange|low,measurements|measurementValue|typedQuantities|quantity|referenceRange|unit,measurements|measurementValue|typedQuantities|quantity|unit|id,measurements|measurementValue|typedQuantities|quantity|unit|label,measurements|measurementValue|typedQuantities|quantity|value,measurements|measurementValue|unit|id,measurements|measurementValue|unit|label,measurements|measurementValue|value,measurements|notes,measurements|observationMoment,measurements|observationMoment|days,measurements|observationMoment|end,measurements|observationMoment|end|iso8601duration,measurements|observationMoment|id,measurements|observationMoment|iso8601duration,measurements|observationMoment|label,measurements|observationMoment|start,measurements|observationMoment|start|iso8601duration,measurements|observationMoment|weeks,measurements|procedure|ageAtProcedure,measurements|procedure|bodySite|id,measurements|procedure|bodySite|label,measurements|procedure|dateOfProcedure,measurements|procedure|procedureCode|id,measurements|procedure|procedureCode|label,notes,pathologicalStage|id,pathologicalStage|label,pathologicalTnmFinding|id,pathologicalTnmFinding|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset,phenotypicFeatures|onset|days,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|onset|weeks,phenotypicFeatures|resolution,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|end,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sampleOriginDetail|id,sampleOriginDetail|label,sampleOriginType|id,sampleOriginType|label,sampleProcessing|id,sampleProcessing|label,sampleStorage|id,sampleStorage|label,tumorGrade|id,tumorGrade|label,tumorProgression|id,tumorProgression|label +biosampleStatus|id,biosampleStatus|label,collectionDate,collectionMoment,diagnosticMarkers|id,diagnosticMarkers|label,histologicalDiagnosis|id,histologicalDiagnosis|label,id,individualId,info,measurements|assayCode|id,measurements|assayCode|label,measurements|date,measurements|measurementValue|id,measurements|measurementValue|label,measurements|measurementValue|referenceRange|high,measurements|measurementValue|referenceRange|low,measurements|measurementValue|referenceRange|unit|id,measurements|measurementValue|referenceRange|unit|label,measurements|measurementValue|typedQuantities|quantityType|id,measurements|measurementValue|typedQuantities|quantityType|label,measurements|measurementValue|typedQuantities|quantity|referenceRange|high,measurements|measurementValue|typedQuantities|quantity|referenceRange|low,measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|id,measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|label,measurements|measurementValue|typedQuantities|quantity|unit|id,measurements|measurementValue|typedQuantities|quantity|unit|label,measurements|measurementValue|typedQuantities|quantity|value,measurements|measurementValue|unit|id,measurements|measurementValue|unit|label,measurements|measurementValue|value,measurements|notes,measurements|observationMoment,measurements|observationMoment|days,measurements|observationMoment|end,measurements|observationMoment|end|iso8601duration,measurements|observationMoment|id,measurements|observationMoment|iso8601duration,measurements|observationMoment|label,measurements|observationMoment|start,measurements|observationMoment|start|iso8601duration,measurements|observationMoment|weeks,measurements|procedure|ageAtProcedure,measurements|procedure|ageAtProcedure|days,measurements|procedure|ageAtProcedure|end,measurements|procedure|ageAtProcedure|end|iso8601duration,measurements|procedure|ageAtProcedure|id,measurements|procedure|ageAtProcedure|iso8601duration,measurements|procedure|ageAtProcedure|label,measurements|procedure|ageAtProcedure|start,measurements|procedure|ageAtProcedure|start|iso8601duration,measurements|procedure|ageAtProcedure|weeks,measurements|procedure|bodySite|id,measurements|procedure|bodySite|label,measurements|procedure|dateOfProcedure,measurements|procedure|procedureCode|id,measurements|procedure|procedureCode|label,notes,obtentionProcedure|ageAtProcedure,obtentionProcedure|ageAtProcedure|days,obtentionProcedure|ageAtProcedure|end,obtentionProcedure|ageAtProcedure|end|iso8601duration,obtentionProcedure|ageAtProcedure|id,obtentionProcedure|ageAtProcedure|iso8601duration,obtentionProcedure|ageAtProcedure|label,obtentionProcedure|ageAtProcedure|start,obtentionProcedure|ageAtProcedure|start|iso8601duration,obtentionProcedure|ageAtProcedure|weeks,obtentionProcedure|bodySite|id,obtentionProcedure|bodySite|label,obtentionProcedure|dateOfProcedure,obtentionProcedure|procedureCode|id,obtentionProcedure|procedureCode|label,pathologicalStage|id,pathologicalStage|label,pathologicalTnmFinding|id,pathologicalTnmFinding|label,phenotypicFeatures|evidence|evidenceCode|id,phenotypicFeatures|evidence|evidenceCode|label,phenotypicFeatures|evidence|reference|id,phenotypicFeatures|evidence|reference|notes,phenotypicFeatures|evidence|reference|reference,phenotypicFeatures|excluded,phenotypicFeatures|featureType|id,phenotypicFeatures|featureType|label,phenotypicFeatures|modifiers|id,phenotypicFeatures|modifiers|label,phenotypicFeatures|notes,phenotypicFeatures|onset,phenotypicFeatures|onset|days,phenotypicFeatures|onset|end,phenotypicFeatures|onset|end|iso8601duration,phenotypicFeatures|onset|id,phenotypicFeatures|onset|iso8601duration,phenotypicFeatures|onset|label,phenotypicFeatures|onset|start,phenotypicFeatures|onset|start|iso8601duration,phenotypicFeatures|onset|weeks,phenotypicFeatures|resolution,phenotypicFeatures|resolution|days,phenotypicFeatures|resolution|end,phenotypicFeatures|resolution|end|iso8601duration,phenotypicFeatures|resolution|id,phenotypicFeatures|resolution|iso8601duration,phenotypicFeatures|resolution|label,phenotypicFeatures|resolution|start,phenotypicFeatures|resolution|start|iso8601duration,phenotypicFeatures|resolution|weeks,phenotypicFeatures|severity|id,phenotypicFeatures|severity|label,sampleOriginDetail|id,sampleOriginDetail|label,sampleOriginType|id,sampleOriginType|label,sampleProcessing|id,sampleProcessing|label,sampleStorage|id,sampleStorage|label,tumorGrade|id,tumorGrade|label,tumorProgression|id,tumorProgression|label diff --git a/ri-tools/csv/templates/cohorts.csv b/ri-tools/csv/templates/cohorts.csv index a5d034b9..02505387 100644 --- a/ri-tools/csv/templates/cohorts.csv +++ b/ri-tools/csv/templates/cohorts.csv @@ -1 +1 @@ -cohortDataTypes|id,cohortDataTypes|label,cohortDesign|id,cohortDesign|label,cohortSize,cohortType,collectionEvents|eventAgeRange|availability,collectionEvents|eventAgeRange|availabilityCount,collectionEvents|eventAgeRange|distribution,collectionEvents|eventDataTypes|availability,collectionEvents|eventDataTypes|availabilityCount,collectionEvents|eventDataTypes|distribution,collectionEvents|eventDiseases|availability,collectionEvents|eventDiseases|availabilityCount,collectionEvents|eventDiseases|distribution,collectionEvents|eventEthnicities|availability,collectionEvents|eventEthnicities|availabilityCount,collectionEvents|eventEthnicities|distribution,collectionEvents|eventGenders|availability,collectionEvents|eventGenders|availabilityCount,collectionEvents|eventGenders|distribution,collectionEvents|eventLocations|availability,collectionEvents|eventLocations|availabilityCount,collectionEvents|eventLocations|distribution,collectionEvents|eventPhenotypes|availability,collectionEvents|eventPhenotypes|availabilityCount,collectionEvents|eventPhenotypes|distribution,collectionEvents|eventTimeline|availability,collectionEvents|eventTimeline|availabilityCount,collectionEvents|eventTimeline|distribution,exclusionCriteria|ageRange,exclusionCriteria|ageRange|end|iso8601duration,exclusionCriteria|ageRange|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset,exclusionCriteria|diseaseConditions|diseaseCode|id,exclusionCriteria|diseaseConditions|diseaseCode|label,exclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|diseaseConditions|notes,exclusionCriteria|diseaseConditions|severity|id,exclusionCriteria|diseaseConditions|severity|label,exclusionCriteria|diseaseConditions|stage|id,exclusionCriteria|diseaseConditions|stage|label,exclusionCriteria|ethnicities|id,exclusionCriteria|ethnicities|label,exclusionCriteria|genders|id,exclusionCriteria|genders|label,exclusionCriteria|locations|id,exclusionCriteria|locations|label,exclusionCriteria|phenotypicConditions|evidence|evidenceCode,exclusionCriteria|phenotypicConditions|evidence|reference,exclusionCriteria|phenotypicConditions|excluded,exclusionCriteria|phenotypicConditions|featureType|id,exclusionCriteria|phenotypicConditions|featureType|label,exclusionCriteria|phenotypicConditions|modifiers,exclusionCriteria|phenotypicConditions|notes,exclusionCriteria|phenotypicConditions|onset,exclusionCriteria|phenotypicConditions|resolution,exclusionCriteria|phenotypicConditions|severity|id,exclusionCriteria|phenotypicConditions|severity|label,exclusionCriteria|type|availability,exclusionCriteria|type|availabilityCount,id,inclusionCriteria|ageRange,inclusionCriteria|ageRange|end|iso8601duration,inclusionCriteria|ageRange|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset,inclusionCriteria|diseaseConditions|diseaseCode|id,inclusionCriteria|diseaseConditions|diseaseCode|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|diseaseConditions|notes,inclusionCriteria|diseaseConditions|severity|id,inclusionCriteria|diseaseConditions|severity|label,inclusionCriteria|diseaseConditions|stage|id,inclusionCriteria|diseaseConditions|stage|label,inclusionCriteria|ethnicities|id,inclusionCriteria|ethnicities|label,inclusionCriteria|genders|id,inclusionCriteria|genders|label,inclusionCriteria|locations|id,inclusionCriteria|locations|label,inclusionCriteria|phenotypicConditions|evidence|evidenceCode,inclusionCriteria|phenotypicConditions|evidence|reference,inclusionCriteria|phenotypicConditions|excluded,inclusionCriteria|phenotypicConditions|featureType|id,inclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|phenotypicConditions|modifiers,inclusionCriteria|phenotypicConditions|notes,inclusionCriteria|phenotypicConditions|onset,inclusionCriteria|phenotypicConditions|resolution,inclusionCriteria|phenotypicConditions|severity|id,inclusionCriteria|phenotypicConditions|severity|label,inclusionCriteria|type|availability,inclusionCriteria|type|availabilityCount,name +cohortDataTypes|id,cohortDataTypes|label,cohortDesign|id,cohortDesign|label,cohortSize,cohortType,collectionEvents|eventAgeRange|availability,collectionEvents|eventAgeRange|availabilityCount,collectionEvents|eventCases,collectionEvents|eventControls,collectionEvents|eventDataTypes|availability,collectionEvents|eventDataTypes|availabilityCount,collectionEvents|eventDate,collectionEvents|eventDiseases|availability,collectionEvents|eventDiseases|availabilityCount,collectionEvents|eventEthnicities|availability,collectionEvents|eventEthnicities|availabilityCount,collectionEvents|eventGenders|availability,collectionEvents|eventGenders|availabilityCount,collectionEvents|eventLocations|availability,collectionEvents|eventLocations|availabilityCount,collectionEvents|eventNum,collectionEvents|eventPhenotypes|availability,collectionEvents|eventPhenotypes|availabilityCount,collectionEvents|eventSize,collectionEvents|eventTimeline|end,collectionEvents|eventTimeline|start,exclusionCriteria|ageRange|end|iso8601duration,exclusionCriteria|ageRange|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset,exclusionCriteria|diseaseConditions|ageOfOnset|days,exclusionCriteria|diseaseConditions|ageOfOnset|end,exclusionCriteria|diseaseConditions|ageOfOnset|end|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset|id,exclusionCriteria|diseaseConditions|ageOfOnset|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset|label,exclusionCriteria|diseaseConditions|ageOfOnset|start,exclusionCriteria|diseaseConditions|ageOfOnset|start|iso8601duration,exclusionCriteria|diseaseConditions|ageOfOnset|weeks,exclusionCriteria|diseaseConditions|diseaseCode|id,exclusionCriteria|diseaseConditions|diseaseCode|label,exclusionCriteria|diseaseConditions|familyHistory,exclusionCriteria|diseaseConditions|notes,exclusionCriteria|diseaseConditions|severity|id,exclusionCriteria|diseaseConditions|severity|label,exclusionCriteria|diseaseConditions|stage|id,exclusionCriteria|diseaseConditions|stage|label,exclusionCriteria|ethnicities|id,exclusionCriteria|ethnicities|label,exclusionCriteria|genders|id,exclusionCriteria|genders|label,exclusionCriteria|locations|id,exclusionCriteria|locations|label,exclusionCriteria|phenotypicConditions|evidence|evidenceCode|id,exclusionCriteria|phenotypicConditions|evidence|evidenceCode|label,exclusionCriteria|phenotypicConditions|evidence|reference|id,exclusionCriteria|phenotypicConditions|evidence|reference|notes,exclusionCriteria|phenotypicConditions|evidence|reference|reference,exclusionCriteria|phenotypicConditions|excluded,exclusionCriteria|phenotypicConditions|featureType|id,exclusionCriteria|phenotypicConditions|featureType|label,exclusionCriteria|phenotypicConditions|modifiers|id,exclusionCriteria|phenotypicConditions|modifiers|label,exclusionCriteria|phenotypicConditions|notes,exclusionCriteria|phenotypicConditions|onset,exclusionCriteria|phenotypicConditions|onset|days,exclusionCriteria|phenotypicConditions|onset|end,exclusionCriteria|phenotypicConditions|onset|end|iso8601duration,exclusionCriteria|phenotypicConditions|onset|id,exclusionCriteria|phenotypicConditions|onset|iso8601duration,exclusionCriteria|phenotypicConditions|onset|label,exclusionCriteria|phenotypicConditions|onset|start,exclusionCriteria|phenotypicConditions|onset|start|iso8601duration,exclusionCriteria|phenotypicConditions|onset|weeks,exclusionCriteria|phenotypicConditions|resolution,exclusionCriteria|phenotypicConditions|resolution|days,exclusionCriteria|phenotypicConditions|resolution|end,exclusionCriteria|phenotypicConditions|resolution|end|iso8601duration,exclusionCriteria|phenotypicConditions|resolution|id,exclusionCriteria|phenotypicConditions|resolution|iso8601duration,exclusionCriteria|phenotypicConditions|resolution|label,exclusionCriteria|phenotypicConditions|resolution|start,exclusionCriteria|phenotypicConditions|resolution|start|iso8601duration,exclusionCriteria|phenotypicConditions|resolution|weeks,exclusionCriteria|phenotypicConditions|severity|id,exclusionCriteria|phenotypicConditions|severity|label,id,inclusionCriteria|ageRange|end|iso8601duration,inclusionCriteria|ageRange|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset,inclusionCriteria|diseaseConditions|ageOfOnset|days,inclusionCriteria|diseaseConditions|ageOfOnset|end,inclusionCriteria|diseaseConditions|ageOfOnset|end|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset|id,inclusionCriteria|diseaseConditions|ageOfOnset|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset|label,inclusionCriteria|diseaseConditions|ageOfOnset|start,inclusionCriteria|diseaseConditions|ageOfOnset|start|iso8601duration,inclusionCriteria|diseaseConditions|ageOfOnset|weeks,inclusionCriteria|diseaseConditions|diseaseCode|id,inclusionCriteria|diseaseConditions|diseaseCode|label,inclusionCriteria|diseaseConditions|familyHistory,inclusionCriteria|diseaseConditions|notes,inclusionCriteria|diseaseConditions|severity|id,inclusionCriteria|diseaseConditions|severity|label,inclusionCriteria|diseaseConditions|stage|id,inclusionCriteria|diseaseConditions|stage|label,inclusionCriteria|ethnicities|id,inclusionCriteria|ethnicities|label,inclusionCriteria|genders|id,inclusionCriteria|genders|label,inclusionCriteria|locations|id,inclusionCriteria|locations|label,inclusionCriteria|phenotypicConditions|evidence|evidenceCode|id,inclusionCriteria|phenotypicConditions|evidence|evidenceCode|label,inclusionCriteria|phenotypicConditions|evidence|reference|id,inclusionCriteria|phenotypicConditions|evidence|reference|notes,inclusionCriteria|phenotypicConditions|evidence|reference|reference,inclusionCriteria|phenotypicConditions|excluded,inclusionCriteria|phenotypicConditions|featureType|id,inclusionCriteria|phenotypicConditions|featureType|label,inclusionCriteria|phenotypicConditions|modifiers|id,inclusionCriteria|phenotypicConditions|modifiers|label,inclusionCriteria|phenotypicConditions|notes,inclusionCriteria|phenotypicConditions|onset,inclusionCriteria|phenotypicConditions|onset|days,inclusionCriteria|phenotypicConditions|onset|end,inclusionCriteria|phenotypicConditions|onset|end|iso8601duration,inclusionCriteria|phenotypicConditions|onset|id,inclusionCriteria|phenotypicConditions|onset|iso8601duration,inclusionCriteria|phenotypicConditions|onset|label,inclusionCriteria|phenotypicConditions|onset|start,inclusionCriteria|phenotypicConditions|onset|start|iso8601duration,inclusionCriteria|phenotypicConditions|onset|weeks,inclusionCriteria|phenotypicConditions|resolution,inclusionCriteria|phenotypicConditions|resolution|days,inclusionCriteria|phenotypicConditions|resolution|end,inclusionCriteria|phenotypicConditions|resolution|end|iso8601duration,inclusionCriteria|phenotypicConditions|resolution|id,inclusionCriteria|phenotypicConditions|resolution|iso8601duration,inclusionCriteria|phenotypicConditions|resolution|label,inclusionCriteria|phenotypicConditions|resolution|start,inclusionCriteria|phenotypicConditions|resolution|start|iso8601duration,inclusionCriteria|phenotypicConditions|resolution|weeks,inclusionCriteria|phenotypicConditions|severity|id,inclusionCriteria|phenotypicConditions|severity|label,info,name diff --git a/ri-tools/csv/templates/datasets.csv b/ri-tools/csv/templates/datasets.csv index f8384693..9293332d 100644 --- a/ri-tools/csv/templates/datasets.csv +++ b/ri-tools/csv/templates/datasets.csv @@ -1 +1 @@ -createDateTime,dataUseConditions|duoDataUse|description,dataUseConditions|duoDataUse|id,dataUseConditions|duoDataUse|label,dataUseConditions|duoDataUse|modifiers,dataUseConditions|duoDataUse|version,description,externalUrl,id,info,name,updateDateTime,version +createDateTime,dataUseConditions|duoDataUse,dataUseConditions|duoDataUse|id,dataUseConditions|duoDataUse|label,dataUseConditions|duoDataUse|modifiers|id,dataUseConditions|duoDataUse|modifiers|label,dataUseConditions|duoDataUse|version,description,externalUrl,id,info,name,updateDateTime,version diff --git a/ri-tools/csv/templates/genomicVariations.csv b/ri-tools/csv/templates/genomicVariations.csv index f809e4ae..e28812f7 100644 --- a/ri-tools/csv/templates/genomicVariations.csv +++ b/ri-tools/csv/templates/genomicVariations.csv @@ -1 +1 @@ -caseLevelData|alleleOrigin|id,caseLevelData|alleleOrigin|label,caseLevelData|analysisId,caseLevelData|biosampleId,caseLevelData|clinicalInterpretations|annotatedWith|toolName,caseLevelData|clinicalInterpretations|annotatedWith|version,caseLevelData|clinicalInterpretations|category|id,caseLevelData|clinicalInterpretations|category|label,caseLevelData|clinicalInterpretations|clinicalRelevance,caseLevelData|clinicalInterpretations|conditionId,caseLevelData|clinicalInterpretations|effect|id,caseLevelData|clinicalInterpretations|effect|label,caseLevelData|clinicalInterpretations|evidenceType|id,caseLevelData|clinicalInterpretations|evidenceType|label,caseLevelData|id,caseLevelData|individualId,caseLevelData|phenotypicEffects|annotatedWith|toolName,caseLevelData|phenotypicEffects|annotatedWith|version,caseLevelData|phenotypicEffects|category|id,caseLevelData|phenotypicEffects|category|label,caseLevelData|phenotypicEffects|clinicalRelevance,caseLevelData|phenotypicEffects|conditionId,caseLevelData|phenotypicEffects|effect|id,caseLevelData|phenotypicEffects|effect|label,caseLevelData|phenotypicEffects|evidenceType|id,caseLevelData|phenotypicEffects|evidenceType|label,caseLevelData|runId,caseLevelData|zygosity|id,caseLevelData|zygosity|label,frequencyInPopulations|frequencies|alleleFrequency,frequencyInPopulations|frequencies|population,frequencyInPopulations|source,frequencyInPopulations|sourceReference,frequencyInPopulations|version,identifiers|clinvarVariantId,identifiers|genomicHGVSId,identifiers|proteinHGVSIds,identifiers|transcriptHGVSIds,identifiers|variantAlternativeIds|id,identifiers|variantAlternativeIds|notes,identifiers|variantAlternativeIds|reference,identifiers|variantAlternativeIds|type,molecularAttributes|aminoacidChanges,molecularAttributes|geneIds,molecularAttributes|genomicFeatures|featureClass|id,molecularAttributes|genomicFeatures|featureClass|label,molecularAttributes|genomicFeatures|featureID|id,molecularAttributes|genomicFeatures|featureID|label,molecularAttributes|molecularEffects|id,molecularAttributes|molecularEffects|label,variantInternalId,variantLevelData|clinicalInterpretations|annotatedWith|toolName,variantLevelData|clinicalInterpretations|annotatedWith|toolReferences,variantLevelData|clinicalInterpretations|annotatedWith|version,variantLevelData|clinicalInterpretations|category|id,variantLevelData|clinicalInterpretations|category|label,variantLevelData|clinicalInterpretations|clinicalRelevance,variantLevelData|clinicalInterpretations|conditionId,variantLevelData|clinicalInterpretations|effect|id,variantLevelData|clinicalInterpretations|effect|label,variantLevelData|clinicalInterpretations|evidenceType|id,variantLevelData|clinicalInterpretations|evidenceType|label,variantLevelData|phenotypicEffects|annotatedWith|toolName,variantLevelData|phenotypicEffects|annotatedWith|toolReferences,variantLevelData|phenotypicEffects|annotatedWith|version,variantLevelData|phenotypicEffects|category|id,variantLevelData|phenotypicEffects|category|label,variantLevelData|phenotypicEffects|clinicalRelevance,variantLevelData|phenotypicEffects|conditionId,variantLevelData|phenotypicEffects|effect|id,variantLevelData|phenotypicEffects|effect|label,variantLevelData|phenotypicEffects|evidenceType|id,variantLevelData|phenotypicEffects|evidenceType|label,variation|_id,variation|alternateBases,variation|copies,variation|copy_change,variation|count|_id,variation|count|chr,variation|count|gene_id,variation|count|interval,variation|count|sequence_id,variation|count|species_id,variation|count|type,variation|location|_id,variation|location|chr,variation|location|interval,variation|location|interval|end,variation|location|interval|end|comparator,variation|location|interval|end|max,variation|location|interval|end|min,variation|location|interval|end|type,variation|location|interval|end|value,variation|location|interval|start,variation|location|interval|start|comparator,variation|location|interval|start|max,variation|location|interval|start|min,variation|location|interval|start|type,variation|location|interval|start|value,variation|location|interval|type,variation|location|sequence_id,variation|location|species_id,variation|location|type,variation|members,variation|members|count|comparator,variation|members|count|max,variation|members|count|min,variation|members|count|type,variation|members|count|value,variation|members|type,variation|members|variation,variation|referenceBases,variation|state|components|location|_id,variation|state|components|location|chr,variation|state|components|location|interval,variation|state|components|location|interval|end,variation|state|components|location|interval|end|comparator,variation|state|components|location|interval|end|max,variation|state|components|location|interval|end|min,variation|state|components|location|interval|end|type,variation|state|components|location|interval|end|value,variation|state|components|location|interval|start,variation|state|components|location|interval|start|com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a/ri-tools/files/deref_schemas/individuals.json +++ b/ri-tools/files/deref_schemas/individuals.json @@ -31,7 +31,7 @@ "id": "", "label": "" }, - "familyHistory": true, + "familyHistory": false, "notes": "", "severity": { "id": "", @@ -61,7 +61,8 @@ "unit": { "id": "", "label": "" - } + }, + "value": 0 } ], "geographicOrigin": { @@ -109,8 +110,8 @@ } } ], - "karyotypicSex": "", - "measures": [ + "karyotypicSex": "UNKNOWN_KARYOTYPE", + "measurements": [ { "assayCode": { "id": "", @@ -126,35 +127,41 @@ "id": "", "label": "" } - } - }, - { + }, "unit": { "id": "", "label": "" }, - "value": 0, + "value": 0 + }, + { "id": "", "label": "" }, { - "typedQuantities": { - "quantity": { - "referenceRange": { - "high": 0, - "low": 0, + "typedQuantities": [ + { + "quantity": { + "referenceRange": { + "high": 0, + "low": 0, + "unit": { + "id": "", + "label": "" + } + }, "unit": { "id": "", "label": "" - } + }, + "value": 0 }, - "unit": { + "quantityType": { "id": "", "label": "" - }, - "value": 0 + } } - } + ] } ], "notes": "", @@ -256,7 +263,7 @@ "id": "", "label": "" }, - "familyHistory": true, + "familyHistory": false, "notes": "", "severity": { "id": "", @@ -268,14 +275,17 @@ } }, "id": "", - "members": { - "affected": true, - "memberId": "", - "role": { - "id": "", - "label": "" + "members": [ + { + "affected": false, + "memberId": "", + "role": { + "id": "", + "label": "" + } } - } + ], + "numSubjects": 0 } ], "phenotypicFeatures": [ @@ -291,7 +301,7 @@ "reference": "" } }, - "excluded": true, + "excluded": false, "featureType": { "id": "", "label": "" @@ -372,15 +382,44 @@ }, "cumulativeDose": { "referenceRange": { + "high": 0, + "low": 0, + "unit": { + "id": "", + "label": "" + } + }, + "unit": { "id": "", "label": "" }, - "unit": {} + "value": 0 }, "doseIntervals": [ { - "id": "", - "label": "" + "interval": { + "end": "", + "start": "" + }, + "quantity": { + "referenceRange": { + "high": 0, + "low": 0, + "unit": { + "id": "", + "label": "" + } + }, + "unit": { + "id": "", + "label": "" + }, + "value": 0 + }, + "scheduleFrequency": { + "id": "", + "label": "" + } } ], "routeOfAdministration": { diff --git a/ri-tools/files/deref_schemas/runs.json b/ri-tools/files/deref_schemas/runs.json index e7025444..eaf90fcb 100644 --- a/ri-tools/files/deref_schemas/runs.json +++ b/ri-tools/files/deref_schemas/runs.json @@ -1 +1,19 @@ -{"biosampleId": "", "id": "", "individualId": "", "info": {}, "libraryLayout": "", "librarySelection": "", "librarySource": {"id": "", "label": ""}, "libraryStrategy": "", "platform": "", "platformModel": {"id": "", "label": ""}, "runDate": ""} \ No newline at end of file +{ + "biosampleId": "", + "id": "", + "individualId": "", + "info": {}, + "libraryLayout": "", + "librarySelection": "", + "librarySource": { + "id": "", + "label": "" + }, + "libraryStrategy": "", + "platform": "", + "platformModel": { + "id": "", + "label": "" + }, + "runDate": "" +} \ No newline at end of file diff --git a/ri-tools/files/headers/EUCAIM/collections.txt b/ri-tools/files/headers/EUCAIM/collections.txt new file mode 100644 index 00000000..b4816b9d --- /dev/null +++ b/ri-tools/files/headers/EUCAIM/collections.txt @@ -0,0 +1,10 @@ +ageRange|min +ageRange|max +description +id +name +studiesCount +subjectsCount +modalities +bodyParts +gender \ No newline at end of file diff --git a/ri-tools/files/headers/EUCAIM/imageStudies.txt b/ri-tools/files/headers/EUCAIM/imageStudies.txt new file mode 100644 index 00000000..9bff4655 --- /dev/null +++ b/ri-tools/files/headers/EUCAIM/imageStudies.txt @@ -0,0 +1,42 @@ +dateOfImageAcquisition +disease|dateOfFirstTreatment +disease|diagnosis|id +disease|diagnosis|label +disease|diseaseId +disease|imagingProcedureProtocol|id +disease|imagingProcedureProtocol|label +disease|pathologyConfirmation|id +disease|pathologyConfirmation|label +disease|pathology|id +disease|pathology|label +disease|treatment|id +disease|treatment|label +disease|yearOfDiagnosis +imageModality|id +imageModality|label +imageBodyPart|id +imageBodyPart|label +imageManufacturer|id +imageManufacturer|label +imageStudyId +tumorMetadata|cancerStageCMCategory|id +tumorMetadata|cancerStageCMCategory|label +tumorMetadata|cancerStagePMCategory|id +tumorMetadata|cancerStagePMCategory|label +tumorMetadata|histologicGraceGleasonScore|id +tumorMetadata|histologicGraceGleasonScore|label +tumorMetadata|histologicGradeISUP|id +tumorMetadata|histologicGradeISUP|label +tumorMetadata|tumorBIRADSAssesment|id +tumorMetadata|tumorBIRADSAssesment|label +tumorMetadata|tumorId +tumorMetadata|ER|id +tumorMetadata|ER|label +tumorMetadata|PR|id +tumorMetadata|PR|label +tumorMetadata|PSA +tumorMetadata|HER2|id +tumorMetadata|HER2|label +tumorMetadata|KI67 +tumorMetadata|tumorPIRADSAssesment|id +tumorMetadata|tumorPIRADSAssesment|label \ No newline at end of file diff --git a/ri-tools/files/headers/EUCAIM/patients.txt b/ri-tools/files/headers/EUCAIM/patients.txt new file mode 100644 index 00000000..13902223 --- /dev/null +++ b/ri-tools/files/headers/EUCAIM/patients.txt @@ -0,0 +1,81 @@ +patientId +sex|id +sex|label +disease|diseaseId +disease|ageAtDiagnosis +disease|dateOfFirstTreatment +disease|diagnosis|id +disease|diagnosis|label +disease|imagingProcedureProtocol|id +disease|imagingProcedureProtocol|label +disease|pathologyConfirmation|id +disease|pathologyConfirmation|label +disease|pathology|id +disease|pathology|label +disease|treatment|id +disease|treatment|label +disease|yearOfDiagnosis +disease|tumorMetadata|cancerStageCMCategory|id +disease|tumorMetadata|cancerStageCMCategory|label +disease|tumorMetadata|cancerStagePMCategory|id +disease|tumorMetadata|cancerStagePMCategory|label +disease|tumorMetadata|histologicGraceGleasonScore|id +disease|tumorMetadata|histologicGraceGleasonScore|label +disease|tumorMetadata|histologicGradeISUP|id +disease|tumorMetadata|histologicGradeISUP|label +disease|tumorMetadata|tumorBIRADSAssesment|id +disease|tumorMetadata|tumorBIRADSAssesment|label +disease|tumorMetadata|tumorId +disease|tumorMetadata|ER|id +disease|tumorMetadata|ER|label +disease|tumorMetadata|PR|id +disease|tumorMetadata|PR|label +disease|tumorMetadata|PSA +disease|tumorMetadata|HER2|id +disease|tumorMetadata|HER2|label +disease|tumorMetadata|KI67 +disease|tumorMetadata|tumorPIRADSAssesment|id +disease|tumorMetadata|tumorPIRADSAssesment|label +imageStudy|imageStudyId +imageStudy|disease|diseaseId +imageStudy|disease|ageAtDiagnosis +imageStudy|disease|dateOfFirstTreatment +imageStudy|disease|diagnosis|id +imageStudy|disease|diagnosis|label +imageStudy|disease|imagingProcedureProtocol|id +imageStudy|disease|imagingProcedureProtocol|label +imageStudy|disease|pathologyConfirmation|id +imageStudy|disease|pathologyConfirmation|label +imageStudy|disease|pathology|id +imageStudy|disease|pathology|label +imageStudy|disease|treatment|id +imageStudy|disease|treatment|label +imageStudy|disease|yearOfDiagnosis +imageStudy|disease|tumorMetadata|cancerStageCMCategory|id +imageStudy|disease|tumorMetadata|cancerStageCMCategory|label +imageStudy|disease|tumorMetadata|cancerStagePMCategory|id +imageStudy|disease|tumorMetadata|cancerStagePMCategory|label +imageStudy|disease|tumorMetadata|histologicGraceGleasonScore|id +imageStudy|disease|tumorMetadata|histologicGraceGleasonScore|label +imageStudy|disease|tumorMetadata|histologicGradeISUP|id +imageStudy|disease|tumorMetadata|histologicGradeISUP|label +imageStudy|disease|tumorMetadata|tumorBIRADSAssesment|id +imageStudy|disease|tumorMetadata|tumorBIRADSAssesment|label +imageStudy|disease|tumorMetadata|tumorId +imageStudy|disease|tumorMetadata|ER|id +imageStudy|disease|tumorMetadata|ER|label +imageStudy|disease|tumorMetadata|PR|id +imageStudy|disease|tumorMetadata|PR|label +imageStudy|disease|tumorMetadata|PSA +imageStudy|disease|tumorMetadata|HER2|id +imageStudy|disease|tumorMetadata|HER2|label +imageStudy|disease|tumorMetadata|KI67 +imageStudy|disease|tumorMetadata|tumorPIRADSAssesment|id +imageStudy|disease|tumorMetadata|tumorPIRADSAssesment|label +imageStudy|imageModality|id +imageStudy|imageModality|label +imageStudy|imageBodyPart|id +imageStudy|imageBodyPart|label +imageStudy|imageManufacturer|id +imageStudy|imageManufacturer|label +imageStudy|dateOfImageAcquisition \ No newline at end of file diff --git a/ri-tools/files/headers/biosamples.txt b/ri-tools/files/headers/biosamples.txt index 87bd71bc..ee19ee98 100644 --- a/ri-tools/files/headers/biosamples.txt +++ b/ri-tools/files/headers/biosamples.txt @@ -18,9 +18,12 @@ measurements|measurementValue|referenceRange|high measurements|measurementValue|referenceRange|low measurements|measurementValue|referenceRange|unit|id measurements|measurementValue|referenceRange|unit|label +measurements|measurementValue|typedQuantities|quantityType|id +measurements|measurementValue|typedQuantities|quantityType|label measurements|measurementValue|typedQuantities|quantity|referenceRange|high measurements|measurementValue|typedQuantities|quantity|referenceRange|low -measurements|measurementValue|typedQuantities|quantity|referenceRange|unit +measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|id +measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|label measurements|measurementValue|typedQuantities|quantity|unit|id measurements|measurementValue|typedQuantities|quantity|unit|label measurements|measurementValue|typedQuantities|quantity|value @@ -39,12 +42,36 @@ measurements|observationMoment|start measurements|observationMoment|start|iso8601duration measurements|observationMoment|weeks measurements|procedure|ageAtProcedure +measurements|procedure|ageAtProcedure|days +measurements|procedure|ageAtProcedure|end +measurements|procedure|ageAtProcedure|end|iso8601duration +measurements|procedure|ageAtProcedure|id +measurements|procedure|ageAtProcedure|iso8601duration +measurements|procedure|ageAtProcedure|label +measurements|procedure|ageAtProcedure|start +measurements|procedure|ageAtProcedure|start|iso8601duration +measurements|procedure|ageAtProcedure|weeks measurements|procedure|bodySite|id measurements|procedure|bodySite|label measurements|procedure|dateOfProcedure measurements|procedure|procedureCode|id measurements|procedure|procedureCode|label notes +obtentionProcedure|ageAtProcedure +obtentionProcedure|ageAtProcedure|days +obtentionProcedure|ageAtProcedure|end +obtentionProcedure|ageAtProcedure|end|iso8601duration +obtentionProcedure|ageAtProcedure|id +obtentionProcedure|ageAtProcedure|iso8601duration +obtentionProcedure|ageAtProcedure|label +obtentionProcedure|ageAtProcedure|start +obtentionProcedure|ageAtProcedure|start|iso8601duration +obtentionProcedure|ageAtProcedure|weeks +obtentionProcedure|bodySite|id +obtentionProcedure|bodySite|label +obtentionProcedure|dateOfProcedure +obtentionProcedure|procedureCode|id +obtentionProcedure|procedureCode|label pathologicalStage|id pathologicalStage|label pathologicalTnmFinding|id diff --git a/ri-tools/files/headers/cohorts.txt b/ri-tools/files/headers/cohorts.txt index ad3b1fd2..8b9b244b 100644 --- a/ri-tools/files/headers/cohorts.txt +++ b/ri-tools/files/headers/cohorts.txt @@ -6,32 +6,37 @@ cohortSize cohortType collectionEvents|eventAgeRange|availability collectionEvents|eventAgeRange|availabilityCount -collectionEvents|eventAgeRange|distribution +collectionEvents|eventCases +collectionEvents|eventControls collectionEvents|eventDataTypes|availability collectionEvents|eventDataTypes|availabilityCount -collectionEvents|eventDataTypes|distribution +collectionEvents|eventDate collectionEvents|eventDiseases|availability collectionEvents|eventDiseases|availabilityCount -collectionEvents|eventDiseases|distribution collectionEvents|eventEthnicities|availability collectionEvents|eventEthnicities|availabilityCount -collectionEvents|eventEthnicities|distribution collectionEvents|eventGenders|availability collectionEvents|eventGenders|availabilityCount -collectionEvents|eventGenders|distribution collectionEvents|eventLocations|availability collectionEvents|eventLocations|availabilityCount -collectionEvents|eventLocations|distribution +collectionEvents|eventNum collectionEvents|eventPhenotypes|availability collectionEvents|eventPhenotypes|availabilityCount -collectionEvents|eventPhenotypes|distribution -collectionEvents|eventTimeline|availability -collectionEvents|eventTimeline|availabilityCount -collectionEvents|eventTimeline|distribution -exclusionCriteria|ageRange +collectionEvents|eventSize +collectionEvents|eventTimeline|end +collectionEvents|eventTimeline|start exclusionCriteria|ageRange|end|iso8601duration exclusionCriteria|ageRange|start|iso8601duration exclusionCriteria|diseaseConditions|ageOfOnset +exclusionCriteria|diseaseConditions|ageOfOnset|days +exclusionCriteria|diseaseConditions|ageOfOnset|end +exclusionCriteria|diseaseConditions|ageOfOnset|end|iso8601duration +exclusionCriteria|diseaseConditions|ageOfOnset|id +exclusionCriteria|diseaseConditions|ageOfOnset|iso8601duration +exclusionCriteria|diseaseConditions|ageOfOnset|label +exclusionCriteria|diseaseConditions|ageOfOnset|start +exclusionCriteria|diseaseConditions|ageOfOnset|start|iso8601duration +exclusionCriteria|diseaseConditions|ageOfOnset|weeks exclusionCriteria|diseaseConditions|diseaseCode|id exclusionCriteria|diseaseConditions|diseaseCode|label exclusionCriteria|diseaseConditions|familyHistory @@ -46,22 +51,52 @@ exclusionCriteria|genders|id exclusionCriteria|genders|label exclusionCriteria|locations|id exclusionCriteria|locations|label -exclusionCriteria|phenotypicConditions|evidence|evidenceCode -exclusionCriteria|phenotypicConditions|evidence|reference +exclusionCriteria|phenotypicConditions|evidence|evidenceCode|id +exclusionCriteria|phenotypicConditions|evidence|evidenceCode|label +exclusionCriteria|phenotypicConditions|evidence|reference|id +exclusionCriteria|phenotypicConditions|evidence|reference|notes +exclusionCriteria|phenotypicConditions|evidence|reference|reference exclusionCriteria|phenotypicConditions|excluded exclusionCriteria|phenotypicConditions|featureType|id exclusionCriteria|phenotypicConditions|featureType|label -exclusionCriteria|phenotypicConditions|modifiers +exclusionCriteria|phenotypicConditions|modifiers|id +exclusionCriteria|phenotypicConditions|modifiers|label exclusionCriteria|phenotypicConditions|notes exclusionCriteria|phenotypicConditions|onset +exclusionCriteria|phenotypicConditions|onset|days +exclusionCriteria|phenotypicConditions|onset|end +exclusionCriteria|phenotypicConditions|onset|end|iso8601duration +exclusionCriteria|phenotypicConditions|onset|id +exclusionCriteria|phenotypicConditions|onset|iso8601duration +exclusionCriteria|phenotypicConditions|onset|label +exclusionCriteria|phenotypicConditions|onset|start +exclusionCriteria|phenotypicConditions|onset|start|iso8601duration +exclusionCriteria|phenotypicConditions|onset|weeks exclusionCriteria|phenotypicConditions|resolution +exclusionCriteria|phenotypicConditions|resolution|days +exclusionCriteria|phenotypicConditions|resolution|end +exclusionCriteria|phenotypicConditions|resolution|end|iso8601duration +exclusionCriteria|phenotypicConditions|resolution|id +exclusionCriteria|phenotypicConditions|resolution|iso8601duration +exclusionCriteria|phenotypicConditions|resolution|label +exclusionCriteria|phenotypicConditions|resolution|start +exclusionCriteria|phenotypicConditions|resolution|start|iso8601duration +exclusionCriteria|phenotypicConditions|resolution|weeks exclusionCriteria|phenotypicConditions|severity|id exclusionCriteria|phenotypicConditions|severity|label id -inclusionCriteria|ageRange inclusionCriteria|ageRange|end|iso8601duration inclusionCriteria|ageRange|start|iso8601duration inclusionCriteria|diseaseConditions|ageOfOnset +inclusionCriteria|diseaseConditions|ageOfOnset|days +inclusionCriteria|diseaseConditions|ageOfOnset|end +inclusionCriteria|diseaseConditions|ageOfOnset|end|iso8601duration +inclusionCriteria|diseaseConditions|ageOfOnset|id +inclusionCriteria|diseaseConditions|ageOfOnset|iso8601duration +inclusionCriteria|diseaseConditions|ageOfOnset|label +inclusionCriteria|diseaseConditions|ageOfOnset|start +inclusionCriteria|diseaseConditions|ageOfOnset|start|iso8601duration +inclusionCriteria|diseaseConditions|ageOfOnset|weeks inclusionCriteria|diseaseConditions|diseaseCode|id inclusionCriteria|diseaseConditions|diseaseCode|label inclusionCriteria|diseaseConditions|familyHistory @@ -76,15 +111,38 @@ inclusionCriteria|genders|id inclusionCriteria|genders|label inclusionCriteria|locations|id inclusionCriteria|locations|label -inclusionCriteria|phenotypicConditions|evidence|evidenceCode -inclusionCriteria|phenotypicConditions|evidence|reference +inclusionCriteria|phenotypicConditions|evidence|evidenceCode|id +inclusionCriteria|phenotypicConditions|evidence|evidenceCode|label +inclusionCriteria|phenotypicConditions|evidence|reference|id +inclusionCriteria|phenotypicConditions|evidence|reference|notes +inclusionCriteria|phenotypicConditions|evidence|reference|reference inclusionCriteria|phenotypicConditions|excluded inclusionCriteria|phenotypicConditions|featureType|id inclusionCriteria|phenotypicConditions|featureType|label -inclusionCriteria|phenotypicConditions|modifiers +inclusionCriteria|phenotypicConditions|modifiers|id +inclusionCriteria|phenotypicConditions|modifiers|label inclusionCriteria|phenotypicConditions|notes inclusionCriteria|phenotypicConditions|onset +inclusionCriteria|phenotypicConditions|onset|days +inclusionCriteria|phenotypicConditions|onset|end +inclusionCriteria|phenotypicConditions|onset|end|iso8601duration +inclusionCriteria|phenotypicConditions|onset|id +inclusionCriteria|phenotypicConditions|onset|iso8601duration +inclusionCriteria|phenotypicConditions|onset|label +inclusionCriteria|phenotypicConditions|onset|start +inclusionCriteria|phenotypicConditions|onset|start|iso8601duration +inclusionCriteria|phenotypicConditions|onset|weeks inclusionCriteria|phenotypicConditions|resolution +inclusionCriteria|phenotypicConditions|resolution|days +inclusionCriteria|phenotypicConditions|resolution|end +inclusionCriteria|phenotypicConditions|resolution|end|iso8601duration +inclusionCriteria|phenotypicConditions|resolution|id +inclusionCriteria|phenotypicConditions|resolution|iso8601duration +inclusionCriteria|phenotypicConditions|resolution|label +inclusionCriteria|phenotypicConditions|resolution|start +inclusionCriteria|phenotypicConditions|resolution|start|iso8601duration +inclusionCriteria|phenotypicConditions|resolution|weeks inclusionCriteria|phenotypicConditions|severity|id inclusionCriteria|phenotypicConditions|severity|label -name \ No newline at end of file +info +name diff --git a/ri-tools/files/headers/datasets.txt b/ri-tools/files/headers/datasets.txt index 5153ce5d..761cf382 100644 --- a/ri-tools/files/headers/datasets.txt +++ b/ri-tools/files/headers/datasets.txt @@ -1,8 +1,9 @@ createDateTime -dataUseConditions|duoDataUse|description +dataUseConditions|duoDataUse dataUseConditions|duoDataUse|id dataUseConditions|duoDataUse|label -dataUseConditions|duoDataUse|modifiers +dataUseConditions|duoDataUse|modifiers|id +dataUseConditions|duoDataUse|modifiers|label dataUseConditions|duoDataUse|version description externalUrl diff --git a/ri-tools/files/headers/genomicVariations.txt b/ri-tools/files/headers/genomicVariations.txt index 2fcc0b2b..04b82fa8 100644 --- a/ri-tools/files/headers/genomicVariations.txt +++ b/ri-tools/files/headers/genomicVariations.txt @@ -39,7 +39,7 @@ identifiers|transcriptHGVSIds identifiers|variantAlternativeIds|id identifiers|variantAlternativeIds|notes identifiers|variantAlternativeIds|reference -identifiers|variantAlternativeIds|type +info molecularAttributes|aminoacidChanges molecularAttributes|geneIds molecularAttributes|genomicFeatures|featureClass|id @@ -50,7 +50,6 @@ molecularAttributes|molecularEffects|id molecularAttributes|molecularEffects|label variantInternalId variantLevelData|clinicalInterpretations|annotatedWith|toolName -variantLevelData|clinicalInterpretations|annotatedWith|toolReferences variantLevelData|clinicalInterpretations|annotatedWith|version variantLevelData|clinicalInterpretations|category|id variantLevelData|clinicalInterpretations|category|label @@ -61,7 +60,6 @@ variantLevelData|clinicalInterpretations|effect|label variantLevelData|clinicalInterpretations|evidenceType|id variantLevelData|clinicalInterpretations|evidenceType|label variantLevelData|phenotypicEffects|annotatedWith|toolName -variantLevelData|phenotypicEffects|annotatedWith|toolReferences variantLevelData|phenotypicEffects|annotatedWith|version variantLevelData|phenotypicEffects|category|id variantLevelData|phenotypicEffects|category|label @@ -73,18 +71,20 @@ variantLevelData|phenotypicEffects|evidenceType|id variantLevelData|phenotypicEffects|evidenceType|label variation|_id variation|alternateBases -variation|copies +variation|copies|comparator +variation|copies|max +variation|copies|min +variation|copies|type +variation|copies|value variation|copy_change -variation|count|_id -variation|count|chr -variation|count|gene_id -variation|count|interval -variation|count|sequence_id -variation|count|species_id +variation|count|comparator +variation|count|max +variation|count|min variation|count|type +variation|count|value +variation|location variation|location|_id variation|location|chr -variation|location|interval variation|location|interval|end variation|location|interval|end|comparator variation|location|interval|end|max @@ -102,17 +102,340 @@ variation|location|sequence_id variation|location|species_id variation|location|type variation|members +variation|members|_id variation|members|count|comparator variation|members|count|max variation|members|count|min variation|members|count|type variation|members|count|value +variation|members|location +variation|members|location|_id +variation|members|location|chr +variation|members|location|interval|end +variation|members|location|interval|end|comparator +variation|members|location|interval|end|max +variation|members|location|interval|end|min +variation|members|location|interval|end|type +variation|members|location|interval|end|value +variation|members|location|interval|start +variation|members|location|interval|start|comparator +variation|members|location|interval|start|max +variation|members|location|interval|start|min +variation|members|location|interval|start|type +variation|members|location|interval|start|value +variation|members|location|interval|type +variation|members|location|sequence_id +variation|members|location|species_id +variation|members|location|type +variation|members|state|components|count|comparator +variation|members|state|components|count|max +variation|members|state|components|count|min +variation|members|state|components|count|type +variation|members|state|components|count|value +variation|members|state|components|location|_id +variation|members|state|components|location|interval|end +variation|members|state|components|location|interval|end|comparator +variation|members|state|components|location|interval|end|max +variation|members|state|components|location|interval|end|min +variation|members|state|components|location|interval|end|type +variation|members|state|components|location|interval|end|value +variation|members|state|components|location|interval|start +variation|members|state|components|location|interval|start|comparator 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+variation|members|variation|state|type +variation|members|variation|type variation|referenceBases +variation|state|components|count|comparator +variation|state|components|count|max +variation|state|components|count|min +variation|state|components|count|type +variation|state|components|count|value variation|state|components|location|_id -variation|state|components|location|chr -variation|state|components|location|interval variation|state|components|location|interval|end variation|state|components|location|interval|end|comparator variation|state|components|location|interval|end|max @@ -127,9 +450,27 @@ variation|state|components|location|interval|start|type variation|state|components|location|interval|start|value variation|state|components|location|interval|type variation|state|components|location|sequence_id -variation|state|components|location|species_id variation|state|components|location|type variation|state|components|reverse_complement +variation|state|components|seq_expr|location|_id +variation|state|components|seq_expr|location|interval|end +variation|state|components|seq_expr|location|interval|end|comparator +variation|state|components|seq_expr|location|interval|end|max +variation|state|components|seq_expr|location|interval|end|min +variation|state|components|seq_expr|location|interval|end|type +variation|state|components|seq_expr|location|interval|end|value +variation|state|components|seq_expr|location|interval|start +variation|state|components|seq_expr|location|interval|start|comparator +variation|state|components|seq_expr|location|interval|start|max +variation|state|components|seq_expr|location|interval|start|min +variation|state|components|seq_expr|location|interval|start|type +variation|state|components|seq_expr|location|interval|start|value +variation|state|components|seq_expr|location|interval|type +variation|state|components|seq_expr|location|sequence_id +variation|state|components|seq_expr|location|type +variation|state|components|seq_expr|reverse_complement +variation|state|components|seq_expr|sequence +variation|state|components|seq_expr|type variation|state|components|sequence variation|state|components|type variation|state|count|comparator @@ -138,8 +479,6 @@ variation|state|count|min variation|state|count|type variation|state|count|value variation|state|location|_id -variation|state|location|chr -variation|state|location|interval variation|state|location|interval|end variation|state|location|interval|end|comparator variation|state|location|interval|end|max @@ -154,12 +493,9 @@ variation|state|location|interval|start|type variation|state|location|interval|start|value variation|state|location|interval|type variation|state|location|sequence_id -variation|state|location|species_id variation|state|location|type variation|state|reverse_complement variation|state|seq_expr|location|_id -variation|state|seq_expr|location|chr -variation|state|seq_expr|location|interval variation|state|seq_expr|location|interval|end variation|state|seq_expr|location|interval|end|comparator variation|state|seq_expr|location|interval|end|max @@ -174,17 +510,29 @@ variation|state|seq_expr|location|interval|start|type variation|state|seq_expr|location|interval|start|value variation|state|seq_expr|location|interval|type variation|state|seq_expr|location|sequence_id -variation|state|seq_expr|location|species_id variation|state|seq_expr|location|type variation|state|seq_expr|reverse_complement variation|state|seq_expr|sequence variation|state|seq_expr|type variation|state|sequence variation|state|type +variation|subject variation|subject|_id variation|subject|chr variation|subject|gene_id -variation|subject|interval +variation|subject|interval|end +variation|subject|interval|end|comparator +variation|subject|interval|end|max +variation|subject|interval|end|min +variation|subject|interval|end|type +variation|subject|interval|end|value +variation|subject|interval|start +variation|subject|interval|start|comparator +variation|subject|interval|start|max +variation|subject|interval|start|min +variation|subject|interval|start|type +variation|subject|interval|start|value +variation|subject|interval|type variation|subject|sequence_id variation|subject|species_id variation|subject|type diff --git a/ri-tools/files/headers/individuals.txt b/ri-tools/files/headers/individuals.txt index 6c8a4e7c..c9377b60 100644 --- a/ri-tools/files/headers/individuals.txt +++ b/ri-tools/files/headers/individuals.txt @@ -25,6 +25,7 @@ exposures|exposureCode|id exposures|exposureCode|label exposures|unit|id exposures|unit|label +exposures|value geographicOrigin|id geographicOrigin|label id @@ -45,42 +46,63 @@ interventionsOrProcedures|dateOfProcedure interventionsOrProcedures|procedureCode|id interventionsOrProcedures|procedureCode|label karyotypicSex -measures|assayCode|id -measures|assayCode|label -measures|date -measures|measurementValue|id -measures|measurementValue|label -measures|measurementValue|referenceRange|high -measures|measurementValue|referenceRange|low -measures|measurementValue|referenceRange|unit|id -measures|measurementValue|referenceRange|unit|label -measures|measurementValue|typedQuantities|quantity|referenceRange|high -measures|measurementValue|typedQuantities|quantity|referenceRange|low -measures|measurementValue|typedQuantities|quantity|referenceRange|unit -measures|measurementValue|typedQuantities|quantity|unit|id -measures|measurementValue|typedQuantities|quantity|unit|label -measures|measurementValue|typedQuantities|quantity|value -measures|measurementValue|unit|id -measures|measurementValue|unit|label -measures|measurementValue|value -measures|notes -measures|observationMoment -measures|observationMoment|days -measures|observationMoment|end -measures|observationMoment|end|iso8601duration -measures|observationMoment|id -measures|observationMoment|iso8601duration -measures|observationMoment|label -measures|observationMoment|start -measures|observationMoment|start|iso8601duration -measures|observationMoment|weeks -measures|procedure|ageAtProcedure -measures|procedure|bodySite|id -measures|procedure|bodySite|label -measures|procedure|dateOfProcedure -measures|procedure|procedureCode|id -measures|procedure|procedureCode|label +measurements|assayCode|id +measurements|assayCode|label +measurements|date +measurements|measurementValue|id +measurements|measurementValue|label +measurements|measurementValue|referenceRange|high +measurements|measurementValue|referenceRange|low +measurements|measurementValue|referenceRange|unit|id +measurements|measurementValue|referenceRange|unit|label +measurements|measurementValue|typedQuantities|quantityType|id +measurements|measurementValue|typedQuantities|quantityType|label +measurements|measurementValue|typedQuantities|quantity|referenceRange|high +measurements|measurementValue|typedQuantities|quantity|referenceRange|low +measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|id +measurements|measurementValue|typedQuantities|quantity|referenceRange|unit|label +measurements|measurementValue|typedQuantities|quantity|unit|id +measurements|measurementValue|typedQuantities|quantity|unit|label +measurements|measurementValue|typedQuantities|quantity|value +measurements|measurementValue|unit|id +measurements|measurementValue|unit|label +measurements|measurementValue|value +measurements|notes +measurements|observationMoment +measurements|observationMoment|days +measurements|observationMoment|end +measurements|observationMoment|end|iso8601duration +measurements|observationMoment|id +measurements|observationMoment|iso8601duration +measurements|observationMoment|label +measurements|observationMoment|start +measurements|observationMoment|start|iso8601duration +measurements|observationMoment|weeks +measurements|procedure|ageAtProcedure +measurements|procedure|ageAtProcedure|days +measurements|procedure|ageAtProcedure|end +measurements|procedure|ageAtProcedure|end|iso8601duration +measurements|procedure|ageAtProcedure|id +measurements|procedure|ageAtProcedure|iso8601duration +measurements|procedure|ageAtProcedure|label +measurements|procedure|ageAtProcedure|start +measurements|procedure|ageAtProcedure|start|iso8601duration +measurements|procedure|ageAtProcedure|weeks +measurements|procedure|bodySite|id +measurements|procedure|bodySite|label +measurements|procedure|dateOfProcedure +measurements|procedure|procedureCode|id +measurements|procedure|procedureCode|label pedigrees|disease|ageOfOnset +pedigrees|disease|ageOfOnset|days +pedigrees|disease|ageOfOnset|end +pedigrees|disease|ageOfOnset|end|iso8601duration +pedigrees|disease|ageOfOnset|id +pedigrees|disease|ageOfOnset|iso8601duration +pedigrees|disease|ageOfOnset|label +pedigrees|disease|ageOfOnset|start +pedigrees|disease|ageOfOnset|start|iso8601duration +pedigrees|disease|ageOfOnset|weeks pedigrees|disease|diseaseCode|id pedigrees|disease|diseaseCode|label pedigrees|disease|familyHistory @@ -94,6 +116,7 @@ pedigrees|members|affected pedigrees|members|memberId pedigrees|members|role|id pedigrees|members|role|label +pedigrees|numSubjects phenotypicFeatures|evidence|evidenceCode|id phenotypicFeatures|evidence|evidenceCode|label phenotypicFeatures|evidence|reference|id @@ -130,11 +153,25 @@ phenotypicFeatures|severity|label sex|id sex|label treatments|ageAtOnset|iso8601duration -treatments|cumulativeDose|referenceRange|id -treatments|cumulativeDose|referenceRange|label -treatments|doseIntervals|id -treatments|doseIntervals|label +treatments|cumulativeDose|referenceRange|high +treatments|cumulativeDose|referenceRange|low +treatments|cumulativeDose|referenceRange|unit|id +treatments|cumulativeDose|referenceRange|unit|label +treatments|cumulativeDose|unit|id +treatments|cumulativeDose|unit|label +treatments|cumulativeDose|value +treatments|doseIntervals|interval|end +treatments|doseIntervals|interval|start +treatments|doseIntervals|quantity|referenceRange|high +treatments|doseIntervals|quantity|referenceRange|low +treatments|doseIntervals|quantity|referenceRange|unit|id +treatments|doseIntervals|quantity|referenceRange|unit|label +treatments|doseIntervals|quantity|unit|id +treatments|doseIntervals|quantity|unit|label +treatments|doseIntervals|quantity|value +treatments|doseIntervals|scheduleFrequency|id +treatments|doseIntervals|scheduleFrequency|label treatments|routeOfAdministration|id treatments|routeOfAdministration|label treatments|treatmentCode|id -treatments|treatmentCode|label \ No newline at end of file +treatments|treatmentCode|label diff --git a/ri-tools/files/updated_json/update.json b/ri-tools/files/updated_json/update.json new file mode 100644 index 00000000..59d09dfc --- /dev/null +++ b/ri-tools/files/updated_json/update.json @@ -0,0 +1,40 @@ +{ + "_id": "e4099e2aab49581017751a6c310775818d4146845e13f12811643684041ab801", + "caseLevelData": [ + { + "biosampleId": "SAMPLE17", + "phenotypicEffects": [ + { + "conditionId": "Melanoma", + "effect": { + "id": "DOID:1909", + "label": "melanoma" + } + } + ] + } + ], + "variantInternalId": "4dbae68746e521da4d8fe4da3b61f56e579e001400b4410f9b5f1316fdb24bbb", + "variation": { + "alternateBases": "T", + "location": { + "_id:": "Var:00002", + "type": "SequenceLocation", + "sequence_id": "ga4gh:SQ.-BOZ8Esn8J88qDwNiSEwUr5425UXdiGX", + "interval": { + "type": "SequenceInterval", + "start": { + "type": "Number", + "value": 7232463 + }, + "end": { + "type": "Number", + "value": 7232464 + } + } + }, + "referenceBases": "A", + "variantType": "SNP " + }, + "datasetId": "test" +} \ No newline at end of file From 658d9d6a3178351744defc2dcd1635c6c3f3f33a Mon Sep 17 00:00:00 2001 From: github-actions Date: Wed, 30 Sep 2026 10:35:34 +0000 Subject: [PATCH 49/56] Update API version to v2.3.2 --- beacon/conf/api_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml index 93518aa7..3aa55ad4 100644 --- a/beacon/conf/api_version.yml +++ b/beacon/conf/api_version.yml @@ -1 +1 @@ -api_version: v2.3.1 +api_version: v2.3.2 From 0fe9c1e54ebb5a872c6a5e7efae64f576fe37ecf Mon Sep 17 00:00:00 2001 From: costero-e Date: Wed, 30 Sep 2026 12:46:41 +0200 Subject: [PATCH 50/56] adding refgen-data to ignored docker files --- .dockerignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.dockerignore b/.dockerignore index 269b83f3..4742abfb 100644 --- a/.dockerignore +++ b/.dockerignore @@ -7,4 +7,5 @@ adminui/node_modules *.vcf.bgz ri-tools/files/vcf/files_to_read/* *.msgpack -*.initialized \ No newline at end of file +*.initialized +ri-tools/refgen-data/* \ No newline at end of file From 1de46afb9050bc8fdbee354cb2c57ceb4e0ad351 Mon Sep 17 00:00:00 2001 From: mmatito Date: Wed, 14 Oct 2026 15:46:52 +0200 Subject: [PATCH 51/56] Run version-update workflow only on EGA-archive repo --- .github/workflows/update_beacon_pi_version.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml index f9d381be..1ae0ed9d 100644 --- a/.github/workflows/update_beacon_pi_version.yml +++ b/.github/workflows/update_beacon_pi_version.yml @@ -15,6 +15,7 @@ permissions: jobs: update-version: + if: github.repository == 'EGA-archive/beacon2-pi-api' runs-on: ubuntu-latest steps: @@ -72,4 +73,4 @@ jobs: - name: Create tag run: | git tag ${{ steps.version.outputs.version }} - git push origin ${{ steps.version.outputs.version }} \ No newline at end of file + git push origin ${{ steps.version.outputs.version }} From f3ed8aded67c19f58b221052d6c7cbcc4d11a458 Mon Sep 17 00:00:00 2001 From: mmatito Date: Wed, 14 Oct 2026 16:22:51 +0200 Subject: [PATCH 52/56] Adapt MongoPermissions to upstream get_permissions signature (entry_type_id) --- beacon/permissions/plugins.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/beacon/permissions/plugins.py b/beacon/permissions/plugins.py index a320adb4..da13d22a 100644 --- a/beacon/permissions/plugins.py +++ b/beacon/permissions/plugins.py @@ -77,7 +77,7 @@ class MongoPermissions(Permissions): async def initialize(self): pass - async def get_permissions(self, username, requested_datasets=None, testMode=False): + async def get_permissions(self, username, requested_datasets=None, testMode=False, entry_type_id=None): datasets = [] try: datasets_permissions = { @@ -99,7 +99,7 @@ async def get_permissions(self, username, requested_datasets=None, testMode=Fals granularity_exceptions = None default_granularity, granularity_exceptions = return_granularity_and_exceptions(self, security_level_dict, username, default_granularity, granularity_exceptions) if granularity_exceptions != None: - default_granularity = return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity) + default_granularity = return_found_granularity_in_exceptions(self, granularity_exceptions, default_granularity, entry_type_id) if default_granularity != None: datasetInstance = SingleDatasetResponse(dataset=dataset, granularity=default_granularity) datasets.append(datasetInstance) From f2c377f67826f8c952e8800a3c1754ce9cefb686 Mon Sep 17 00:00:00 2001 From: mmatito Date: Wed, 14 Oct 2026 16:36:20 +0200 Subject: [PATCH 53/56] Update deploy/fix_permissions.sh and LEAME.md --- deploy/fix_permissions.sh | 24 ++++++++++++------------ docs/LEAME.md | 10 +++------- 2 files changed, 15 insertions(+), 19 deletions(-) diff --git a/deploy/fix_permissions.sh b/deploy/fix_permissions.sh index 7885ceed..d5d2b050 100755 --- a/deploy/fix_permissions.sh +++ b/deploy/fix_permissions.sh @@ -141,11 +141,9 @@ if want admin-ui; then fi if want beaconprod; then - mkdir -p \ - "${CERTS_DIR}" \ - "${APP_LOG_DIR}" - - podman unshare touch "${APP_LOG_DIR}/beacon/beacon.log" + # La API rota su propio log (log_rotating_interval en conf_default.py), + # por eso necesita el directorio completo, no un fichero montado. + mkdir -p "${APP_LOG_DIR}/beacon" fi if want apache-beacon; then @@ -219,12 +217,14 @@ fi echo "Ajustando logs..." if want beaconprod; then - podman unshare chown \ + # El directorio debe ser del usuario de beacon para crear y renombrar + # los ficheros rotados (beacon.log, beacon.log.YYYY-MM-DD, ...). + podman unshare chown -R \ "${BEACON_UID}:${BEACON_GID}" \ - "${APP_LOG_DIR}/beacon/beacon.log" + "${APP_LOG_DIR}/beacon" - podman unshare chmod 0644 \ - "${APP_LOG_DIR}/beacon/beacon.log" + podman unshare chmod 0755 \ + "${APP_LOG_DIR}/beacon" fi if want db; then @@ -313,7 +313,7 @@ if command -v getenforce >/dev/null 2>&1 && want beaconprod && selinux_paths+=( "${APP_ROOT}/beacon" - "${APP_LOG_DIR}/beacon/beacon.log" + "${APP_LOG_DIR}/beacon" "${CERTS_DIR}" ) @@ -359,7 +359,7 @@ if [[ "${SERVICE}" == "all" ]]; then "${POSTGRES_DATA}" "${ADMIN_UI_DATA}" "${ADMIN_UI_DATA}/db.sqlite3" - "${APP_LOG_DIR}/beacon/beacon.log" + "${APP_LOG_DIR}/beacon" "${APP_LOG_DIR}/mongodb/mongod.log" "${APP_LOG_DIR}/postgres" "${APP_LOG_DIR}/apache" @@ -386,7 +386,7 @@ else ) want beaconprod && status_paths+=( - "${APP_LOG_DIR}/beacon/beacon.log" + "${APP_LOG_DIR}/beacon" "${CERTS_DIR}/beacon_server.crt" "${CERTS_DIR}/beacon_server.key" ) diff --git a/docs/LEAME.md b/docs/LEAME.md index b08d208f..8833c445 100644 --- a/docs/LEAME.md +++ b/docs/LEAME.md @@ -108,7 +108,8 @@ Los logs se almacenan en: ```text ${APP_LOG_DIR}/ -├── beacon.log +├── beacon/ +│ └── beacon.log # la API lo rota a medianoche y conserva 7 ficheros ├── mongo/ │ └── mongod.log ├── postgres/ @@ -244,12 +245,7 @@ uri = 'http://beaconprod:5050' Esto es obligatorio: aiohttp construye `request.url` a partir de la conexión TCP y la compara con `config.uri`. Si ambos no coinciden, la API rechaza las peticiones. -Los ficheros siguientes se siguen montando por compatibilidad, pero actualmente no se utilizan: - -```text -${BIND_ROOT}/etc/certs/beacon_server.crt -${BIND_ROOT}/etc/certs/beacon_server.key -``` +Por eso `beaconprod` ya no monta `${BIND_ROOT}/etc/certs/beacon_server.crt` ni `beacon_server.key`. **Pendiente:** certificados institucionales y terminación TLS en Apache para acceso exterior. From 10d07ad1573db95532f7286486311cd3689b4435 Mon Sep 17 00:00:00 2001 From: mmatito Date: Thu, 15 Oct 2026 13:20:21 +0200 Subject: [PATCH 54/56] Update template-ui, LEAME.md and beacon conf.py --- .env.example | 2 +- beacon/conf/conf.py | 3 +- conf/beacon_apache_reverse_proxy.conf | 4 +-- docker-compose.yml | 8 ++---- docs/LEAME.md | 41 ++++++++++++++++----------- 5 files changed, 31 insertions(+), 27 deletions(-) diff --git a/.env.example b/.env.example index cfadf66f..e0db391b 100644 --- a/.env.example +++ b/.env.example @@ -26,7 +26,7 @@ MONGO_PORT=8085 MONGO_EXPRESS_PORT=8081 # Container images -TEMPLATE_UI_IMAGE=ghcr.io/ega-archive/beacon-template-ui:main +TEMPLATE_UI_IMAGE=ghcr.io/ega-archive/beacon-template-ui:1.1.1 MONGO_IMAGE=docker.io/library/mongo:8.2.3 POSTGRES_IMAGE=docker.io/library/postgres:15 KEYCLOAK_IMAGE=quay.io/keycloak/keycloak:18.0.0 diff --git a/beacon/conf/conf.py b/beacon/conf/conf.py index 3675ea2b..4766a23f 100644 --- a/beacon/conf/conf.py +++ b/beacon/conf/conf.py @@ -16,6 +16,7 @@ uri = 'http://beaconprod:5050' uri_subpath = '/api' complete_url = uri + uri_subpath +allowed_uris = ['http://beaconaf-isciiiciber.isciiides.es:8443/api', 'http://apibeacon-isciiiciber.isciiides.es:8443/api'] # public hosts behind Apache (ProxyPreserveHost On) environment = 'TEST' description = r"This Beacon is based on synthetic data hosted at the EGA. The dataset contains 2504 samples including genetic data based on 1K Genomes data, and 76 individual attributes and phenotypic data derived from UKBiobank." version = api_version_yaml['api_version'] @@ -42,7 +43,7 @@ org_adress = 'C/ Monforte de Lemos, 5, 28029 Madrid, Spain' org_welcome_url = 'https://www.isciii.es/' org_contact_url = 'mailto:bioinformatica@isciii.es' -org_logo_url = 'https://www.isciii.es/images/logo.png' +org_logo_url = 'https://sirena.isciii.es/wp-content/uploads/2022/10/horizontal.jpg' org_info = '' # Certificates diff --git a/conf/beacon_apache_reverse_proxy.conf b/conf/beacon_apache_reverse_proxy.conf index adc37254..09fc1bcd 100644 --- a/conf/beacon_apache_reverse_proxy.conf +++ b/conf/beacon_apache_reverse_proxy.conf @@ -24,8 +24,8 @@ ServerName beaconaf-isciiiciber.isciiides.es ProxyPassReverse /auth/ http://idp:8082/auth/ ProxyPass /mongo-express/ http://mongo-express:8081/mongo-express/ ProxyPassReverse /mongo-express/ http://mongo-express:8081/mongo-express/ - ProxyPass / http://template-ui:3000/ - ProxyPassReverse / http://template-ui:3000/ + ProxyPass / http://template-ui:80/ + ProxyPassReverse / http://template-ui:80/ ErrorLog /var/log/httpd/beacon-af.error.log CustomLog /var/log/httpd/beacon-af.access.log combined diff --git a/docker-compose.yml b/docker-compose.yml index da54466c..a680f885 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -159,16 +159,12 @@ services: restart: always hostname: template-ui container_name: ${TEMPLATE_UI_CONTAINER} - command: node /opt/yarn-v1.22.22/bin/yarn.js start ports: - - "${TEMPLATE_UI_PORT}:3000" + - "${TEMPLATE_UI_PORT}:80" volumes: - - ${APP_ROOT}/template-ui/src/config/config.json:/client/src/config/config.json:ro + - ${APP_ROOT}/template-ui/config:/usr/share/nginx/html/config:ro networks: - pub - environment: - - CHOKIDAR_USEPOLLING=true - - WATCHPACK_POLLING=true apache-beacon: image: ${APACHE_IMAGE} diff --git a/docs/LEAME.md b/docs/LEAME.md index 8833c445..e161415a 100644 --- a/docs/LEAME.md +++ b/docs/LEAME.md @@ -237,15 +237,21 @@ En este despliegue **el tráfico interno entre contenedores va en claro**: - MongoDB no utiliza TLS. La sección `net.tls` de `mongod.conf` está comentada. - Apache habla con Beacon mediante `ProxyPass http://beaconprod:5050/api`. -`beacon/conf/conf.py` debe declarar el `uri` con el mismo esquema: +Por eso `beaconprod` ya no monta `${BIND_ROOT}/etc/certs/beacon_server.crt` ni `beacon_server.key`. + +### `uri` y `allowed_uris` + +La API compara la URL de cada petición con `uri` + `uri_subpath` de `beacon/conf/conf.py`. Apache usa `ProxyPreserveHost On`, así que la API recibe las peticiones con el nombre público (`beaconaf-isciiiciber.isciiides.es:8443` o `apibeacon-isciiiciber.isciiides.es:8443`), no con `beaconprod:5050`. + +Desde la v2.3.x, si la URL no coincide con `uri`, la API solo la acepta si está en `allowed_uris`; si no, responde **HTTP 400** (antes solo dejaba un warning en el log). Por eso `conf.py` debe tener las dos URLs públicas, con el `/api` final: ```python uri = 'http://beaconprod:5050' +uri_subpath = '/api' +allowed_uris = ['http://beaconaf-isciiiciber.isciiides.es:8443/api', 'http://apibeacon-isciiiciber.isciiides.es:8443/api'] ``` -Esto es obligatorio: aiohttp construye `request.url` a partir de la conexión TCP y la compara con `config.uri`. Si ambos no coinciden, la API rechaza las peticiones. - -Por eso `beaconprod` ya no monta `${BIND_ROOT}/etc/certs/beacon_server.crt` ni `beacon_server.key`. +- Si se añade otro nombre público o se pasa a HTTPS, hay que añadirlo aquí con el esquema y el puerto exactos. **Pendiente:** certificados institucionales y terminación TLS en Apache para acceso exterior. @@ -288,32 +294,32 @@ beacon/models/ga4gh/beacon_v2_default_model/conf/entry_types/ El ownership del código se mantiene en el usuario del host. El acceso del UID interno de Admin UI se concede mediante ACL. -**Importante:** las ACL se pierden al reemplazar un fichero. `sed -i`, `git checkout`, `git switch` y la mayoría de editores no modifican el fichero en su sitio: escriben uno nuevo y lo renombran encima, y la ACL se va con el original. Tras editar a mano cualquiera de las rutas anteriores, reejecuta el script o restaura la ACL del fichero concreto: +Ejecuta, con el stack bajado (`podman compose down`): ```bash set -a source .env set +a -podman unshare setfacl -m "u:${ADMIN_UI_UID}:rw" \ - "${APP_ROOT}/beacon/conf/conf.py" +chmod +x deploy/fix_permissions.sh +./deploy/fix_permissions.sh ``` -Ejecuta, con el stack bajado (`podman compose down`): +El script se detendrá si detecta algún contenedor del stack activo. + +Al finalizar muestra los modos y propietarios efectivos de las rutas principales. + +**Importante:** las ACL se pierden al reemplazar un fichero. `sed -i`, `git checkout`, `git switch` y la mayoría de editores no modifican el fichero en su sitio: escriben uno nuevo y lo renombran encima, y la ACL se va con el original. Tras editar a mano cualquiera de las rutas anteriores, reejecuta el script o restaura la ACL del fichero concreto: ```bash set -a source .env set +a -chmod +x deploy/fix_permissions.sh -./deploy/fix_permissions.sh +podman unshare setfacl -m "u:${ADMIN_UI_UID}:rw" \ + "${APP_ROOT}/beacon/conf/conf.py" ``` -El script se detendrá si detecta algún contenedor del stack activo. - -Al finalizar muestra los modos y propietarios efectivos de las rutas principales. - ## Construir y arrancar el stack Valida primero la configuración de Compose: @@ -483,9 +489,9 @@ use admin db.changeUserPassword("root", passwordPrompt()) ``` -`passwordPrompt()` pide la nueva contraseña de forma interactiva. Así no queda escrita en el historial de `mongosh`, que se guarda dentro del contenedor. +`passwordPrompt()` pide la nueva contraseña de forma interactiva. Así no queda escrita en el historial de `mongosh`, que se guarda dentro del contenedor. -El cambio se aplica automáticamente sin reiniciar el contenedor. +El cambio se aplica automáticamente sin reiniciar el contenedor. ### Mongo Express @@ -504,7 +510,7 @@ curl -s -u "${MONGO_EXPRESS_USERNAME}:${MONGO_EXPRESS_PASSWORD}" \ "${PUBLIC_SCHEME}://${PUBLIC_HOST}:${PUBLIC_PORT}/mongo-express/" ``` -No deben utilizarse las credenciales predeterminadas. +No deben utilizarse las credenciales predeterminadas. ## Comprobaciones posteriores @@ -1076,6 +1082,7 @@ Servicios admitidos: - `template-ui` Para reparar todo el despliegue: + ```bash podman compose down ./deploy/fix_permissions.sh From 1468558c0650b97e41a60de7afec59712a60b67c Mon Sep 17 00:00:00 2001 From: mmatito Date: Thu, 15 Oct 2026 14:02:12 +0200 Subject: [PATCH 55/56] Remove unsupported elements from template-ui config --- template-ui/config/config.json | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/template-ui/config/config.json b/template-ui/config/config.json index edf3a20b..2c934b63 100644 --- a/template-ui/config/config.json +++ b/template-ui/config/config.json @@ -94,14 +94,11 @@ "auth": { "oidc": { "clientId": "beacon-ui", - "authority": "http://beaconaf-isciiiciber.isciiides.es:8443/auth/realms/Beacon", "redirectUri": "http://beaconaf-isciiiciber.isciiides.es:8443/", "autoSignIn": false, "automaticSilentRenew": true, - "scope": "openid profile email", - "revokeAccessTokenOnSignout": true + "scope": "openid profile email" } - }, "entryTypesOrder": [ From dbf1df55895423a742639102cb7bc502b7e2f0f0 Mon Sep 17 00:00:00 2001 From: mmatito Date: Thu, 15 Oct 2026 16:41:00 +0200 Subject: [PATCH 56/56] Restore upstream version-update workflow --- .github/workflows/update_beacon_pi_version.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/update_beacon_pi_version.yml b/.github/workflows/update_beacon_pi_version.yml index 1ae0ed9d..f9d381be 100644 --- a/.github/workflows/update_beacon_pi_version.yml +++ b/.github/workflows/update_beacon_pi_version.yml @@ -15,7 +15,6 @@ permissions: jobs: update-version: - if: github.repository == 'EGA-archive/beacon2-pi-api' runs-on: ubuntu-latest steps: @@ -73,4 +72,4 @@ jobs: - name: Create tag run: | git tag ${{ steps.version.outputs.version }} - git push origin ${{ steps.version.outputs.version }} + git push origin ${{ steps.version.outputs.version }} \ No newline at end of file