Merge pull request #606 from Sage-Bionetworks/FDS-2212-test-coverage

Fds 2212 test coverage

.Rbuildignore

@@ -2,4 +2,5 @@
 ^renv$
 ^renv\.lock$
 ^.venv
-^schematic$
+^schematic$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      SYNAPSE_PAT: ${{ secrets.SYNAPSE_PAT }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2, any::testthat
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -7,6 +7,6 @@ License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Imports: httr, dplyr, jsonlite, shinyjs, yaml, promises, readr
+Imports: httr, dplyr, jsonlite, shinyjs, yaml, promises, readr, httr2
 Suggests: 
     covr

NAMESPACE

@@ -12,6 +12,7 @@ export(manifest_populate)
 export(manifest_validate)
 export(model_component_requirements)
 export(model_submit)
+export(parse_env_var)
 export(storage_dataset_files)
 export(storage_project_datasets)
 export(storage_projects)

R/datacurator_package.R

@@ -0,0 +1 @@
+#' @importFrom httr GET POST content

R/schematic_rest_api.R

@@ -414,7 +414,7 @@ get_asset_view_table <- function(url="http://localhost:3001/v1/storage/assets/ta
 
   check_success(req)
   if (return_type=="json") {
-    return(list2DF(fromJSON(httr::content(req))))
+    return(list2DF(jsonlite::fromJSON(httr::content(req))))
   } else {
   csv <- readr::read_csv(httr::content(req), show_col_types = FALSE)
   return(csv)

R/utils.R

@@ -0,0 +1,14 @@
+#' @title parse environment variables for configuration
+#' @param x string
+#' @param el_delim delimeter of list elements
+#' @param kv_delim delimeter of key-value pairs
+#' @export
+parse_env_var <- function(x, el_delim=",", kv_delim=":"){
+  if (!grepl(kv_delim, x)) stop(sprintf("%s delimiter not in %s", kv_delim, x))
+  # assume string of key-value pairs
+  elements <- stringr::str_split(x, el_delim, simplify = TRUE)
+  unlist(lapply(elements, function(y){
+    kv <- stringr::str_split(y, kv_delim, n=2)
+    setNames(kv[[1]][[2]], kv[[1]][[1]])
+  }))
+}

tests/testthat/test_schematic_rest_api.R

@@ -20,35 +20,42 @@ test_that("manifest_generate returns a URL if sucessful", {
   skip_it()
 
   url <- manifest_generate(url=file.path(schematic_url, "v1/manifest/generate"),
-    schema_url = schema_url, access_token = Sys.getenv("SNYAPSE_PAT"),
+    schema_url = schema_url, access_token = Sys.getenv("SYNAPSE_PAT"),
     title="Test biospecimen", data_type="Biospecimen",
     use_annotations = FALSE,
     dataset_id="syn33715357", asset_view="syn33715412",
     output_format = "google_sheet")
   expect_true(grepl("^https://docs.google", url))
 })
 
-test_that("manifest_generate returns an xlsx", {
-  skip_it()
-
-  xlsx <- manifest_generate(title="Test biospecimen", data_type="Biospecimen",
-                    asset_view="syn33715412", output_format="excel")
-
-})
+# test_that("manifest_generate returns an xlsx", {
+#   skip_it()
+#   
+#   xlsx <- manifest_generate(url=file.path(schematic_url, "v1/manifest/generate"),
+#                     title="Test biospecimen", data_type="Biospecimen",
+#                     asset_view="syn33715412", output_format="excel")
+#   
+# })
 
-test_that("manifest_populate returns a google sheet link with records filled", {
-  skip_it()
-  req <- manifest_populate(data_type="Biospecimen", title="Example",
-                           csv_file = pass_csv)
-})
+# test_that("manifest_populate returns a google sheet link with records filled", {
+#   skip_it()
+#   req <- manifest_populate(data_type="Biospecimen", title="Example",
+#                            csv_file = pass_csv)
+# })
 
 test_that("manifest_validate passes and fails correctly", {
   skip_it()
 
-  pass <- manifest_validate(data_type="Biospecimen", csv_file=pass_csv)
-  expect_identical(pass, list())
+  pass <- manifest_validate(url=file.path(schematic_url, "v1/model/validate"),
+                            data_type="Biospecimen", file_name=fail_csv,
+                            access_token = Sys.getenv("SYNAPSE_PAT"),
+                            schema_url = schema_url)
+  expect_identical(pass, list(errors = list(), warnings = list()))
 
-  fail <- manifest_validate(data_type="Biospecimen", csv_file=fail_csv)
+  fail <- manifest_validate(url=file.path(schematic_url, "v1/model/validate"),
+                            data_type="Biospecimen", file_name=pass_csv,
+                            access_token = Sys.getenv("SYNAPSE_PAT"),
+                            schema_url = schema_url)
   expect_true(length(unlist(fail)) > 0L)
 })
 
@@ -57,64 +64,67 @@ test_that("model_submit successfully uploads to synapse", {
 
   submit <- model_submit(url=file.path(schematic_url,"v1/model/submit"),
                          schema_url = schema_url,
-                         data_type="Biospecimen", dataset_id="syn20977135",
-                         restrict_rules = FALSE, input_token=Sys.getenv("SYNAPSE_PAT"),
+                         data_type=NULL, dataset_id="syn20977135",
+                         restrict_rules = FALSE, access_token=Sys.getenv("SYNAPSE_PAT"),
                          asset_view="syn33715412", file_name=pass_csv,
-                         use_schema_label = TRUE, manifest_record_type="table",
+                         manifest_record_type="file_only",
                          table_manipulation="replace"
                       )
-  expect_true(submit)
+  expect_true(grepl("^syn", submit))
 })
 
 test_that("storage_project_datasets returns available datasets", {
   skip_it()
-  storage_project_datasets(asset_view="syn23643253",
+  storage_project_datasets(url=file.path(schematic_url, "v1/storage/project/datasets"),
+                           asset_view="syn23643253",
                            project_id="syn26251192",
-                           input_token=Sys.getenv("SYNAPSE_PAT"))
+                           access_token=Sys.getenv("SYNAPSE_PAT"))
 })
 
 test_that("storage_projects returns available projects", {
   skip_it()
-  storage_projects(url=file.path(schematic_url, "v1/storage/project/datasets"),
+  storage_projects(url=file.path(schematic_url, "v1/storage/projects"),
                    asset_view="syn23643253",
-                   input_token=Sys.getenv("SYNAPSE_PAT"))
+                   access_token=Sys.getenv("SYNAPSE_PAT"))
 })
 
 test_that("storage_dataset_files returns files", {
   skip_it()
-  storage_dataset_files(asset_view = "syn23643253",
+  storage_dataset_files(url=file.path(schematic_url, "v1/storage/dataset/files"),
+                        asset_view = "syn23643253",
                         dataset_id = "syn23643250",
-                        input_token=Sys.getenv("SYNAPSE_PAT"))
+                        access_token=Sys.getenv("SYNAPSE_PAT"))
 })
 
 test_that("model_component_requirements returns list of required components", {
   skip_it()
-  good <- model_component_requirements(url="http://localhost:3001/v1/model/component-requirements",
+  good <- model_component_requirements(url=file.path(schematic_url, "v1/model/component-requirements"),
                                            schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld",
                                            source_component="Patient",
                                            as_graph = FALSE)
   expect_equal(length(good), 8L)
 
-  expect_error(model_component_requirements(url="http://localhost:3001/v1/model/component-requirements",
+  expect_error(model_component_requirements(url=file.path(schematic_url, "v1/model/component-requirements"),
                                        schema_url="https://aaaabad.url.jsonld",
                                        source_component="Patient",
                                        as_graph = FALSE))
 
 })
 
-test_that("manifest_download returns a csv.", {
-  skip_it()
-  csv <- manifest_download(input_token=Sys.getenv("SYNAPSE_PAT"),
-                           asset_view="syn28559058",
-                           dataset_id="syn28268700")
-  exp <- setNames(c("BulkRNA-seqAssay", "CSV/TSV", "Sample_A", "GRCm38", NA, 2022L, "syn28278954"),
-    c("Component", "File Format", "Filename", "Genome Build", "Genome FASTA", "Sample ID", "entityId"))
-  expect_equal(unlist(csv), exp)
-})
+# test_that("manifest_download returns a csv.", {
+#   skip_it()
+#  csv <- manifest_download(url=file.path(schematic_url, "v1/manifest/download"),
+#                           manifest_id="syn51078535",
+#                           access_token=Sys.getenv("SYNAPSE_PAT"))
+#   exp <- setNames(c("BulkRNA-seqAssay", "CSV/TSV", "Sample_A", "GRCm38", NA, 2022L, "syn28278954"),
+#     c("Component", "File Format", "Filename", "Genome Build", "Genome FASTA", "Sample ID", "entityId"))
+#   expect_equal(unlist(csv), exp)
+# })
 
 test_that("get_asset_view_table returns asset view table", {
   skip_it()
-  av <- get_asset_view_table(input_token = Sys.getenv("SYNAPSE_PAT"),
+  av <- get_asset_view_table(url=file.path(schematic_url, "v1/storage/assets/tables"),
+                             access_token = Sys.getenv("SYNAPSE_PAT"),
                        asset_view="syn23643253")
   storage_tbl <- subset(av, av$name == "synapse_storage_manifest.csv")
   expect_true(inherits(av, "data.frame"), "name" %in% names(av))
@@ -124,13 +134,13 @@ test_that("asset_tables returns a data.frame", {
   skip_it()
   tst <- get_asset_view_table(url=file.path(schematic_url, "v1/storage/assets/tables"),
                        asset_view = "syn28559058",
-                       input_token = Sys.getenv("SYNAPSE_TOKEN"),
-                       as_json=TRUE)
-  expect_identical(nrow(tst), 3L)
+                       access_token = Sys.getenv("SYNAPSE_PAT"),
+                       return_type="json")
+  expect_identical(nrow(tst), 4L)
 
-  tst2 <- get_asset_view_table(url=file.path(schematic_url, "v1/storage/assets/tables"),
+  expect_error(get_asset_view_table(url=file.path(schematic_url, "v1/storage/assets/tables"),
                                   asset_view = "syn28559058",
-                                  input_token = Sys.getenv("SYNAPSE_TOKEN"),
-                                  as_json=FALSE)
-  expect_identical(nrow(tst2), 3L)
+                                  access_token = Sys.getenv("SYNAPSE_PAT"),
+                                  return_type = "csv")
+               )
 })