Release v1.0.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AzimuthAPI
 Title: Pan-Azimuth Web API Interface
-Version: 0.9.0
+Version: 1.0.0
 Authors@R: 
     person("Satija", "Lab", email = "satijalabnygc@gmail.com", role = c("aut", "cre"))
 Description: An R package providing an interface to the Pan-Azimuth Web API for single-cell RNA sequencing analysis.

R/annotation.R

@@ -28,7 +28,7 @@
 #' @param process_obj Whether to process the object
 #' @param cutoff_abs Absolute cutoff for label filtering
 #' @param cutoff_frac Fractional cutoff for label filtering
-#' @param model_version Version of the model to use
+#' @param model_version Version of the model to use (default: 'v1')
 #' @param assay Assay to use for annotation
 #' 
 #' @importFrom SeuratObject Idents<-
@@ -61,7 +61,7 @@ ANNotate <- function(
   spread = 1.0,
   verbose = TRUE,
   init = "spectral",
-  model_version = "v0",
+  model_version = "v1",
   process_obj = TRUE,
   cutoff_abs = 5,
   cutoff_frac = 0.001,

R/argument_parser.R

@@ -161,8 +161,8 @@ parse_annotate_args <- function() {
 
   parser$add_argument(
     "--model_version",
-    default = "v0",
-    help = "Version of the model to use (default: 'v0')",
+    default = "v1",
+    help = "Version of the model to use (default: 'v1')",
     type = "character"
   )
 

R/cloud.R

@@ -2,21 +2,59 @@
 #'
 #' @param object Seurat object to annotate
 #' @param assay Name of the assay to use (default: 'RNA')
-#' @param ip Hostname or IP address of the cloud server (default: 'azimuthapi.satijalab.org')
-#' @param port Port number for the API (default: 5000)
+#' @param ip Server hostname (default: 'azimuthapi.satijalab.org')
+#' @param port Server port (default: NULL)
+#' @param scheme Server URL scheme (default: 'https').
 #' @param ... Additional arguments for the API to pass to the model (see ANNotate function for details)
 #' @return Annotated Seurat object
+#' @details
+#' Use `CloudAzimuth(object)` for the public cloud service. The `ip`, `port`, and `scheme`
+#' arguments should not be set manually by users; the default values follow standard use.
 #' @importFrom httr POST GET upload_file content status_code
 #' @importFrom RCurl url.exists
 #' @importFrom SeuratObject LayerData Idents IsMatrixEmpty CreateAssay5Object CreateSeuratObject Cells Idents<-
 #' @concept annotation
 #' @export
 CloudAzimuth <- function(object = object, assay = 'RNA', ip = 'azimuthapi.satijalab.org', 
-                         port = 5000, ...) {
+                         port = NULL, scheme = NULL, ...) {
 
   cli::cli_h1("Running Pan-human Azimuth on the cloud")
 
-  api_base_url <- paste0('http://', ip, ":", port)
+  if (grepl("^https?://", ip)) {
+    stop("`ip` should not include 'http://' or 'https://'. Use `scheme` to choose HTTP or HTTPS.")
+  }
+
+  # the default scheme and port depend on whether the user is connecting to the production server or a custom host
+  # defaults preserve the official HTTPS path and the temporary legacy HTTP path
+  if (identical(ip, "azimuthapi.satijalab.org")) {
+    if (is.null(scheme) && is.null(port)) {
+      scheme <- "https"
+    } else if (is.null(scheme) && isTRUE(port == 5000)) {
+      scheme <- "http"
+    }
+  } else {
+    if (is.null(scheme)) {
+      scheme <- "http"
+    }
+    if (is.null(port) && identical(scheme, "http")) {
+      port <- 5000
+    }
+  }
+
+  # restrict the official host to supported public entrypoints
+  if (identical(ip, "azimuthapi.satijalab.org")) {
+    https <- identical(scheme, "https") && is.null(port)
+    http_5000 <- identical(scheme, "http") && isTRUE(port == 5000)
+    allowed_official_access <- https || http_5000
+    if (isTRUE(http_5000)) {
+      cli::cli_alert_warning("Using HTTP connection to the AzimuthAPI server. This is not recommended for security reasons and will be deprecated in the future. Please use HTTPS instead.")
+    } else if (isFALSE(allowed_official_access)) {
+      stop("For the AzimuthAPI server, use either (default) HTTPS with no port or (legacy) HTTP on port 5000.")
+    }
+  }
+
+  api_base_url <- build_cloud_api_base_url(ip = ip, port = port, scheme = scheme)
+
   update <- check_api_version(api_base_url)
 
   if (isTRUE(update)) {
@@ -134,3 +172,21 @@ process_rds_file <- function(api_base_url, file_path, ...) {
   cli::cli_alert_success("Annotation complete. Output saved to: {save_path}")
 } 
 
+#' Build base URL for the cloud API
+#'
+#' @param ip Hostname or IP address of the cloud server
+#' @param port Port number for the API, or `NULL` to omit it
+#' @param scheme URL scheme to use
+#' @return Character containing the base API URL to connect to
+#' @noRd
+build_cloud_api_base_url <- function(ip, port = NULL, scheme = "https") {
+  if (!is.character(scheme) || length(scheme) != 1 || is.na(scheme) || !scheme %in% c("http", "https")) {
+    stop("`scheme` must be either 'http' or 'https'.")
+  }
+
+  if (is.null(port) || identical(port, "")) {
+    return(paste0(scheme, "://", ip))
+  }
+
+  paste0(scheme, "://", ip, ":", port)
+}

README.md

@@ -1,6 +1,6 @@
 # AzimuthAPI
 
-## Version 0.9.0
+## Version 1.0.0
 
 An R package providing an interface to the Pan-human Azimuth neural network, enabling users to run cell type annotation on single-cell and spatial transcriptomics data.
 
@@ -15,7 +15,7 @@ Two options for annotation are available:
 ## Installation
 
 ```r
-# Install devtools if not already installed
+# Install remotes if not already installed
 install.packages("remotes")
 
 # Install AzimuthAPI from GitHub

tests/testthat/test_interface.R

@@ -23,13 +23,117 @@ test_that("CloudAzimuth returns an annotated Seurat object", {
     .package = "AzimuthAPI"
   )
 
-  annotated <- CloudAzimuth(query, ip = "azimuthapi.satijalab.org", port = 5000)
+  annotated <- CloudAzimuth(query, ip = "azimuthapi.satijalab.org")
 
   expect_s4_class(annotated, "Seurat")
   expect_true(all(c("final_level_labels", "azimuth_label") %in% colnames(annotated@meta.data)))
   expect_identical(unname(annotated@meta.data$azimuth_label), rep(c("T cell", "B cell"), length.out = ncol(query)))
 })
 
+test_that("CloudAzimuth builds HTTPS and legacy URLs correctly", {
+  expect_identical(
+    build_cloud_api_base_url("azimuthapi.satijalab.org"),
+    "https://azimuthapi.satijalab.org"
+  )
+
+  expect_identical(
+    build_cloud_api_base_url("localhost", port = 5000, scheme = "http"),
+    "http://localhost:5000"
+  )
+
+  expect_identical(
+    build_cloud_api_base_url("azimuthapi.satijalab.org", scheme = "http", port = 5000),
+    "http://azimuthapi.satijalab.org:5000"
+  )
+
+  expect_error(
+    build_cloud_api_base_url("azimuthapi.satijalab.org", scheme = "ftp"),
+    "`scheme` must be either 'http' or 'https'.",
+    fixed = TRUE
+  )
+
+})
+
+test_that("CloudAzimuth requires ip without scheme prefix", {
+  expect_error(
+    CloudAzimuth(object = NULL, ip = "https://example.org"),
+    "`ip` should not include 'http://' or 'https://'.",
+    fixed = TRUE
+  )
+})
+
+test_that("CloudAzimuth defaults to official HTTPS endpoint", {
+  query <- make_test_object()
+  expected <- query
+  expected@meta.data$final_level_labels <- rep(c("T cell", "B cell"), length.out = ncol(expected))
+  expected@meta.data$azimuth_label <- expected@meta.data$final_level_labels
+  api_base_urls <- character()
+
+  testthat::local_mocked_bindings(
+    check_api_version = function(url) {
+      api_base_urls <<- c(api_base_urls, url)
+      invisible(url)
+    },
+    process_rds_file = function(url, file_path, ...) {
+      api_base_urls <<- c(api_base_urls, url)
+      saveRDS(expected, file = sub("\\.rds$", "_ANN.rds", file_path))
+      invisible(NULL)
+    },
+    .package = "AzimuthAPI"
+  )
+
+  CloudAzimuth(query, ip = "azimuthapi.satijalab.org")
+  expect_true(all(api_base_urls[1:2] == "https://azimuthapi.satijalab.org"))
+})
+
+test_that("CloudAzimuth preserves alternate-host HTTP defaults", {
+  query <- make_test_object()
+  expected <- query
+  expected@meta.data$final_level_labels <- rep(c("T cell", "B cell"), length.out = ncol(expected))
+  expected@meta.data$azimuth_label <- expected@meta.data$final_level_labels
+  api_base_urls <- character()
+
+  testthat::local_mocked_bindings(
+    check_api_version = function(url) {
+      api_base_urls <<- c(api_base_urls, url)
+      invisible(url)
+    },
+    process_rds_file = function(url, file_path, ...) {
+      api_base_urls <<- c(api_base_urls, url)
+      saveRDS(expected, file = sub("\\.rds$", "_ANN.rds", file_path))
+      invisible(NULL)
+    },
+    .package = "AzimuthAPI"
+  )
+
+  CloudAzimuth(query, ip = "localhost")
+  expect_true(all(api_base_urls[1:2] == "http://localhost:5000"))
+})
+
+test_that("CloudAzimuth preserves legacy official HTTP when port 5000 is explicit", {
+  query <- make_test_object()
+  expected <- query
+  expected@meta.data$final_level_labels <- rep(c("T cell", "B cell"), length.out = ncol(expected))
+  expected@meta.data$azimuth_label <- expected@meta.data$final_level_labels
+  api_base_urls <- character()
+
+  testthat::local_mocked_bindings(
+    check_api_version = function(url) {
+      api_base_urls <<- c(api_base_urls, url)
+      invisible(url)
+    },
+    process_rds_file = function(url, file_path, ...) {
+      api_base_urls <<- c(api_base_urls, url)
+      saveRDS(expected, file = sub("\\.rds$", "_ANN.rds", file_path))
+      invisible(NULL)
+    },
+    .package = "AzimuthAPI"
+  )
+
+  CloudAzimuth(query, ip = "azimuthapi.satijalab.org", port = 5000)
+  expect_true(all(api_base_urls[1:2] == "http://azimuthapi.satijalab.org:5000"))
+})
+
 test_that("ANNotate returns an annotated Seurat object", {
   skip_if_not_installed("Seurat")
   skip_if_not_installed("reticulate")