chore(deps): upgrade Graphon to 0.9.0 and adapt runtime contracts by WH-2099 · Pull Request #45356 · langgenius/dify

WH-2099 · 2026-11-02T19:14:08Z

Summary

Upgrade the API and standalone Agent package to Graphon 0.9.0 and adapt the host to its segment and engine contracts.
Both manifests, lockfiles, and installed environments use the reviewed commit 454cd1c1d9707fbd04634841c746c6487f97c791.

Accept secret variables in knowledge retrieval and dynamic Human Input email recipients, preserving secret tags and variable metadata during truncation.
Preserve ordinary JSON resembling files and existing fields in mixed arrays, draft values, pipeline outputs, and streaming responses; complete typed runtime snapshots retain actual File identity.
Refresh URLs for validated file variables and keep single node debugging within the admitted account's tenant through loading, execution, and persistence.
Bind pipeline worker file access to the admitted tenant and user, restoring the caller's scope afterward.
Extend failure cleanup to all started draft nodes and terminal persistence errors, preserving the original exception.
Disable unused frame observations in WorkflowEntry while retaining execution, container output commits, and pause/resume.
Update variable contracts and regression fixtures, and install Git in the Agent image's build stage for its frozen source dependency.

Dependencies

This draft depends on langgenius/graphon#382 and langgenius/graphon#383.
The integration fix covers JSON/File identity, nested serialization, templates over object arrays, cumulative tool call snapshots, unused stream retention, and frame observation copying.
Replace both temporary Git sources with the published package when it includes these fixes.
Historical mixed-array snapshots without file type metadata retain dictionaries as JSON.

Validation

All 12 changed API unit test files: 907 passed against the installed final Graphon pin.
Full Agent suite: 1,069 passed, 5 skipped against that pin.
API make lint and make type-check; Agent Ruff and pyrefly checks passed.
Both frozen dependency installs succeeded; independent verification matched all source references, installed commit metadata, and imported source bytes.
Graphon: 1,185 tests passed, just check, wheel/source distribution builds, and 29 documentation checks passed.
Independent reviews covered file permissions and serialization, execution lifecycle, persistence, runtime and model adapter contracts, packaging, tests, documentation, and naming; findings were fixed and rechecked.
Regression coverage exercises a real website crawl pipeline through engine execution, SQL output conversion, and response conversion after the execution scope exits.

Local tests used a valid NO_PROXY list and an ephemeral socksio dependency for the Agent test environment.
Live provider calls, complete Docker builds, database integration tests, and production concurrency were not run.

Screenshots

Not applicable: backend dependency and runtime integration changes.

Checklist

This change requires a documentation update, included: Dify Document — no public documentation change required.
I understand that this PR may be closed in case there was no previous discussion or issues. (This doesn't apply to typos!)
I've verified the change and added or updated tests where meaningful regression risk justifies coverage.
I've updated the documentation accordingly; affected local contracts and upstream Graphon documentation are current.
I ran make lint && make type-check (backend); frontend checks do not apply.

From Codex

github-actions · 2026-11-02T19:16:28Z

Pyrefly Type Coverage

Metric	Base	PR	Delta
Type coverage	83.13%	83.14%	+0.01%
Strict coverage	82.79%	82.79%	+0.01%
Typed symbols	85,756	85,789	+33
Untyped symbols	17,471	17,471	0
Modules	4373	4373	0

github-actions · 2026-11-02T19:17:53Z

Pyrefly Diff

base → PR

--- /tmp/pyrefly_base.txt	2026-11-03 08:15:58.589846616 +0000
+++ /tmp/pyrefly_pr.txt	2026-11-03 08:15:45.209703065 +0000
@@ -3629,7 +3629,7 @@
 ERROR Cannot index into `str` [bad-index]
    --> tests/unit_tests/core/app/apps/completion/test_generate_response_converter.py:175:16
 ERROR Class `PipelineRunner` has no class attribute `call_args` [missing-attribute]
-   --> tests/unit_tests/core/app/apps/pipeline/test_pipeline_generator.py:444:21
+   --> tests/unit_tests/core/app/apps/pipeline/test_pipeline_generator.py:450:21
 ERROR Object of class `Account` has no attribute `tenant_id` [missing-attribute]
    --> tests/unit_tests/core/app/apps/test_base_app_generator.py:609:9
 ERROR `list[str]` is not assignable to attribute `allowed_file_types` with type `Sequence[FileType] | None` [bad-assignment]
@@ -5375,13 +5375,13 @@
 ERROR Argument `dict[str, bool]` is not assignable to parameter `summary_index_setting` with type `SummaryIndexSettingDict | None` in function `core.workflow.nodes.knowledge_index.knowledge_index_node.KnowledgeIndexNode._invoke_knowledge_index` [bad-argument-type]
    --> tests/unit_tests/core/workflow/nodes/knowledge_index/test_knowledge_index_node.py:638:35
 ERROR `None` is not subscriptable [unsupported-operation]
-   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:615:16
+   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:641:16
 ERROR `None` is not subscriptable [unsupported-operation]
-   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:616:27
+   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:642:27
 ERROR `None` is not subscriptable [unsupported-operation]
-   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:617:16
+   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:643:16
 ERROR `None` is not subscriptable [unsupported-operation]
-   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:618:16
+   --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_knowledge_retrieval_node.py:644:16
 ERROR Object of class `Span` has no attribute `events` [missing-attribute]
    --> tests/unit_tests/core/workflow/nodes/knowledge_retrieval/test_retrieval.py:174:42
 ERROR Missing argument `name` in function `core.workflow.nodes.trigger_webhook.entities.WebhookParameter.__init__` [missing-argument]
@@ -5549,39 +5549,39 @@
 ERROR Object of class `object` has no attribute `tool` [missing-attribute]
     --> tests/unit_tests/core/workflow/test_node_runtime.py:2252:16
 WARN Cannot instantiate `BaseNodeData` because it directly extends `ABC` or uses `ABCMeta` [direct-abstract-base-instantiation]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1010:50
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1061:50
 ERROR `in` is not supported between `Literal['Maximum execution steps exceeded: 3 > 2']` and `None` [not-iterable]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1067:20
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1118:20
 WARN Cannot instantiate `BaseNodeData` because it directly extends `ABC` or uses `ABCMeta` [direct-abstract-base-instantiation]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1200:37
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1251:37
 ERROR Class member `EmptySplitKey.split` overrides parent class `UserString` in an inconsistent manner [bad-override]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1632:21
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1683:21
 ERROR Class member `EmptySplitKey.split` overrides a member in a parent class but is missing an `@override` decorator [missing-override-decorator]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1632:21
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1683:21
 ERROR `TestWorkflowEntryHelpersCases.TestMappingUserInputsBranches.test_rejects_invalid_node_variable_key.EmptySplitKey` is not assignable to dict key type `str` [bad-assignment]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1637:39
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1688:39
 ERROR Argument `TestWorkflowEntryHelpersCases.TestWorkflowEntryNodeLayers.test_run_node_with_layers_reports_success.FakeNode` is not assignable to parameter `node` with type `Node[Unknown]` in function `core.workflow.workflow_entry.WorkflowEntry._run_node_with_layers` [bad-argument-type]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1740:82
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1791:82
 ERROR Object of class `FunctionType` has no attribute `assert_called_once_with` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1745:17
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1796:17
 ERROR Object of class `FunctionType` has no attribute `assert_called_once_with` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1746:17
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1797:17
 ERROR Object of class `FunctionType` has no attribute `assert_called_once_with` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1747:17
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1798:17
 ERROR Object of class `FunctionType` has no attribute `assert_called_once_with` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1748:17
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1799:17
 ERROR Object of class `FunctionType` has no attribute `assert_called_once_with` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1749:17
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1800:17
 ERROR Argument `TestWorkflowEntryHelpersCases.TestWorkflowEntryNodeLayers.test_run_node_with_layers_reports_errors.FakeNode` is not assignable to parameter `node` with type `Node[Unknown]` in function `core.workflow.workflow_entry.WorkflowEntry._run_node_with_layers` [bad-argument-type]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1776:77
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1827:77
 ERROR Object of class `FunctionType` has no attribute `call_args` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1779:24
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1830:24
 ERROR Object of class `FunctionType` has no attribute `call_args` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1780:35
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1831:35
 ERROR Object of class `FunctionType` has no attribute `call_args` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1781:24
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1832:24
 ERROR Object of class `FunctionType` has no attribute `call_args` [missing-attribute]
-    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1782:35
+    --> tests/unit_tests/core/workflow/test_workflow_entry.py:1833:35
 ERROR Object of class `object` has no attribute `append` [missing-attribute]
    --> tests/unit_tests/dev/test_generate_knowledge_fs_contract.py:121:13
 ERROR Cannot set item in `object` [unsupported-operation]
@@ -5655,7 +5655,7 @@
 ERROR Argument `str` is not assignable to parameter `indexing_status` with type `IndexingStatus | SQLCoreOperations[IndexingStatus]` in function `models.dataset.Document.__init__` [bad-argument-type]
    --> tests/unit_tests/fields/test_dataset_fields.py:299:25
 ERROR Cannot set item in `OrderedDict[str, bool | list[str] | str]` [unsupported-operation]
-   --> tests/unit_tests/fields/test_workflow_draft_variable_fields.py:142:47
+   --> tests/unit_tests/fields/test_workflow_draft_variable_fields.py:144:47
 ERROR Object of class `Subscription` has no attribute `_start_if_needed` [missing-attribute]
    --> tests/unit_tests/libs/broadcast_channel/redis/test_pubsub_channel.py:152:13
 ERROR Object of class `Subscription` has no attribute `_start_if_needed` [missing-attribute]
@@ -5941,19 +5941,19 @@
 ERROR Object of class `FromClause` has no attribute `create` [missing-attribute]
   --> tests/unit_tests/services/plugin/test_plugin_parameter_service.py:47:9
 ERROR Object of class `NoneType` has no attribute `marked_name` [missing-attribute]
-   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:552:16
+   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:618:16
 ERROR Object of class `NoneType` has no attribute `marked_comment` [missing-attribute]
-   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:553:16
+   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:619:16
 ERROR Object of class `NoneType` has no attribute `updated_by` [missing-attribute]
-   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:555:16
+   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:621:16
 ERROR Argument `dict[str, list[dict[str, dict[str, str | dict[str, str] | dict[str, int | str]]]]]` is not assignable to parameter `graph` with type `dict[str, object] | None` in function `_make_workflow` [bad-argument-type]
-   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:669:71
+   --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:735:71
 ERROR Argument `() -> tuple[StartNode, Generator[object, Unknown]]` is not assignable to parameter `getter` with type `() -> tuple[Node[Unknown], Generator[CustomContainerRequest | IterationFrameRequest | LoopFrameRequest | NodeEvent]]` in function `services.rag_pipeline.rag_pipeline.RagPipelineService._handle_node_run_result` [bad-argument-type]
-    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:1909:24
+    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:1975:24
 ERROR Argument `() -> tuple[StartNode, Iterator[NodeRunFailedEvent]]` is not assignable to parameter `getter` with type `() -> tuple[Node[Unknown], Generator[CustomContainerRequest | IterationFrameRequest | LoopFrameRequest | NodeEvent]]` in function `services.rag_pipeline.rag_pipeline.RagPipelineService._handle_node_run_result` [bad-argument-type]
-    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:1929:20
+    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:1995:20
 ERROR Argument `() -> tuple[StartNode, Iterator[NodeRunFailedEvent]]` is not assignable to parameter `getter` with type `() -> tuple[Node[Unknown], Generator[CustomContainerRequest | IterationFrameRequest | LoopFrameRequest | NodeEvent]]` in function `services.rag_pipeline.rag_pipeline.RagPipelineService._handle_node_run_result` [bad-argument-type]
-    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:1949:20
+    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline.py:2015:20
 ERROR Argument `Literal['']` is not assignable to parameter `plan` with type `CloudPlan` in function `RagPipelineTaskProxyTestDataFactory.create_mock_features` [bad-argument-type]
    --> tests/unit_tests/services/rag_pipeline/test_rag_pipeline_task_proxy.py:590:91
 ERROR Argument `None` is not assignable to parameter `plan` with type `CloudPlan` in function `RagPipelineTaskProxyTestDataFactory.create_mock_features` [bad-argument-type]
@@ -6259,11 +6259,13 @@
 ERROR `None` is not subscriptable [unsupported-operation]
     --> tests/unit_tests/services/test_workflow_persistence.py:1422:20
 ERROR `dict[str, str]` is not assignable to dict value type `list[Unknown] | str` [bad-assignment]
-   --> tests/unit_tests/services/test_workflow_service.py:239:30
+   --> tests/unit_tests/services/test_workflow_service.py:248:30
+ERROR Argument `Literal['array[any]']` is not assignable to parameter `value_type` with type `SQLCoreOperations[SegmentType] | SegmentType` in function `models.workflow.WorkflowDraftVariable.__init__` [bad-argument-type]
+    --> tests/unit_tests/services/test_workflow_service.py:3391:36
 ERROR Argument `Literal['invalid']` is not assignable to parameter `value` with type `AppMode | SQLCoreOperations[AppMode]` in function `sqlalchemy.orm.base.Mapped.__set__` [bad-argument-type]
-    --> tests/unit_tests/services/test_workflow_service.py:3945:24
+    --> tests/unit_tests/services/test_workflow_service.py:4034:24
 ERROR Argument `dict[str, str | dict[str, str]]` is not assignable to parameter `node_config` with type `NodeConfigDict` in function `services.workflow_service.WorkflowService._build_human_input_node_for_debugging` [bad-argument-type]
-    --> tests/unit_tests/services/test_workflow_service.py:3976:69
+    --> tests/unit_tests/services/test_workflow_service.py:4065:69
 ERROR Object of class `MCPToolProvider` has no attribute `provider_icon` [missing-attribute]
   --> tests/unit_tests/services/tools/test_tools_transform_service.py:82:9
 ERROR Object of class `MCPToolProvider` has no attribute `masked_server_url` [missing-attribute]

codecov · 2026-11-02T19:23:29Z

Codecov Report

❌ Patch coverage is 93.42105% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.88%. Comparing base (a8631e5) to head (4799bd2).
⚠️ Report is 36 commits behind head on main.

Files with missing lines	Patch %	Lines
api/services/workflow_service.py	89.74%	4 Missing and 4 partials ⚠️
api/services/rag_pipeline/rag_pipeline.py	96.07%	1 Missing and 1 partial ⚠️

❌ Your project check has failed because the head coverage (85.88%) is below the adjusted base coverage (88.77%). You can increase the head coverage or adjust the Removed Code Behavior.

Additional details and impacted files

@@            Coverage Diff             @@
##             main   #45356      +/-   ##
==========================================
- Coverage   89.77%   85.88%   -3.90%     
==========================================
  Files        6239     6240       +1     
  Lines      390902   390955      +53     
  Branches    79285    79174     -111     
==========================================
- Hits       350934   335756   -15178     
- Misses      33870    49106   +15236     
+ Partials     6098     6093       -5

Flag	Coverage Δ
api	`89.65% <93.42%> (+0.01%)`	⬆️
cli	`94.26% <ø> (ø)`
dify-ui	`92.54% <ø> (+0.15%)`	⬆️
web	`80.03% <ø> (-9.73%)`	⬇️

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WH-2099 added 2 commits November 2, 2026 19:02

chore(deps): upgrade Graphon to 0.9.0 and adapt runtime contracts

7b07341

chore(deps): include Graphon nested model serialization fix

58db770

WH-2099 self-assigned this Nov 2, 2026

github-actions Bot added the size:XL This PR changes 500-999 lines, ignoring generated files. label Nov 2, 2026

[autofix.ci] apply automated fixes

80ddffa

github-actions Bot added the web This relates to changes on the web. label Nov 2, 2026

WH-2099 mentioned this pull request Nov 2, 2026

fix(agent): preserve complete model messages #44502

Draft

fix(workflow): scope file access during node debugging

79c230d

github-actions Bot added size:XXL This PR changes 1000+ lines, ignoring generated files. and removed size:XL This PR changes 500-999 lines, ignoring generated files. labels Nov 3, 2026

fix(workflow): preserve file JSON and finalize failed drafts

4799bd2

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chore(deps): upgrade Graphon to 0.9.0 and adapt runtime contracts - #45356

chore(deps): upgrade Graphon to 0.9.0 and adapt runtime contracts#45356
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