Develop

.github/workflows/test.yml

@@ -0,0 +1,75 @@
+name: Test Neotoma API
+
+on:
+  workflow_run:
+    workflows: ["Deploy Neotoma API"]
+    types: [completed]
+    branches: [develop]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
+    timeout-minutes: 25
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: dev
+            flag: '-d'
+            host: https://api-dev.neotomadb.org
+          - name: production
+            flag: '-p'
+            host: https://api.neotomadb.org
+
+    name: test (${{ matrix.name }})
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+          cache: 'yarn'
+
+      - name: Install dependencies
+        run: yarn install --frozen-lockfile
+
+      # genoatt.sh and runmochabatch.sh invoke `oatts` and `mocha` bare. Those resolve
+      # under `yarn run` but not under `run: bash …`, so put the bin dir on PATH.
+      - name: Put node_modules/.bin on PATH
+        run: echo "$PWD/node_modules/.bin" >> "$GITHUB_PATH"
+
+      - name: Build the OpenAPI spec
+        run: yarn build:openapi
+
+      - name: Wait for ${{ matrix.host }} to be ready
+        run: |
+          MAX_ATTEMPTS=10
+          ATTEMPT=1
+          until curl -sf ${{ matrix.host }}/healthcheck > /dev/null; do
+            echo "Attempt $ATTEMPT/$MAX_ATTEMPTS..."
+            [ $ATTEMPT -eq $MAX_ATTEMPTS ] && echo "${{ matrix.host }} not ready" && exit 1
+            ATTEMPT=$((ATTEMPT + 1))
+            sleep 15
+          done
+          echo "${{ matrix.host }} is ready"
+
+      # The oatts-generated suites hardcode their target host, so they must be
+      # regenerated per target — APIPATH alone only redirects the hand-written suites.
+      - name: Generate tests targeting ${{ matrix.host }}
+        run: bash genoatt.sh ${{ matrix.flag }}
+
+      - name: Run tests against ${{ matrix.host }}
+        run: bash runmochabatch.sh ${{ matrix.flag }}
+
+      - name: Upload test report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-report-${{ matrix.name }}
+          path: public/tests.html

genoatt.sh

@@ -25,7 +25,7 @@ HELP
 run_oatt() {
 
     rm ./test/v*.js
-    oatts generate --host $remote -s ./openapi.yaml -w test
+    oatts generate --host $remote -m $scheme -s ./openapi.yaml -w test
     yarn dlx eslint --quiet --fix ./test > genoatt.log
 
     # oatts is a bit silly in picking its variables.  We need to make sure that we're
@@ -53,6 +53,9 @@ run_oatt() {
 
 test=0
 remote=localhost:3001
+# The remote hosts 301-redirect http -> https, so generated tests must use the right
+# scheme. oatts defaults to http when the flag is absent.
+scheme=http
 
  while getopts "htldpa" opt; do
      case $opt in
@@ -68,12 +71,15 @@ remote=localhost:3001
              ;;
          d)
              remote=api-dev.neotomadb.org
+             scheme=https
              ;;
          p)
              remote=api.neotomadb.org
+             scheme=https
              ;;
          a)
              remote=neotomaapi-env.eba-wd29jtvf.us-east-2.elasticbeanstalk.com
+             scheme=https
              ;;
          *)
              echo You didn\'t use the correct flag.

openapi.yaml

@@ -2345,6 +2345,8 @@ components:
           type: array
         geography:
           $ref: '#/components/schemas/geography'
+        recdatecreated:
+          $ref: '#/components/schemas/recdatecreated'
         sitedescription:
           $ref: '#/components/schemas/sitedescription'
         siteid:
@@ -3345,6 +3347,38 @@ paths:
       tags:
         - Lithology metadata
         - v2.0
+  /v2.0/data/datasets/{datasetid}/assays:
+    get:
+      description: Returns the aeDNA assays (and their sequencing libraries) linked to a dataset.
+      parameters:
+        - $ref: '#/components/parameters/datasetidPath'
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                type: object
+          description: Assays
+      summary: aeDNA assay and library metadata for a dataset.
+      tags:
+        - Assay metadata
+        - v2.0
+  /v2.0/data/datasets/{datasetid}/projects:
+    get:
+      description: Returns the research projects (and their participants) linked to a dataset.
+      parameters:
+        - $ref: '#/components/parameters/datasetidPath'
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                type: object
+          description: Projects
+      summary: Project and participant metadata for a dataset.
+      tags:
+        - Project metadata
+        - v2.0
   /v2.0/data/datasets/{datasetid}/publications:
     get:
       description: Returns publications data associated with specific datasets.

openapi/components/schemas/schemas.yml

@@ -1556,6 +1556,8 @@ sitesv2:
       type: array
     geography:
       $ref: '#/components/schemas/geography'
+    recdatecreated:
+      $ref: '#/components/schemas/recdatecreated'
     sitedescription:
       $ref: '#/components/schemas/sitedescription'
     siteid:

openapi/paths/v20/data.yml

@@ -333,6 +333,38 @@
     tags:
       - Lithology metadata
       - v2.0
+/v2.0/data/datasets/{datasetid}/assays:
+  get:
+    description: Returns the aeDNA assays (and their sequencing libraries) linked to a dataset.
+    parameters:
+      - $ref: '#/components/parameters/datasetidPath'
+    responses:
+      '200':
+        content:
+          application/json:
+            schema:
+              type: object
+        description: Assays
+    summary: aeDNA assay and library metadata for a dataset.
+    tags:
+      - Assay metadata
+      - v2.0
+/v2.0/data/datasets/{datasetid}/projects:
+  get:
+    description: Returns the research projects (and their participants) linked to a dataset.
+    parameters:
+      - $ref: '#/components/parameters/datasetidPath'
+    responses:
+      '200':
+        content:
+          application/json:
+            schema:
+              type: object
+        description: Projects
+    summary: Project and participant metadata for a dataset.
+    tags:
+      - Project metadata
+      - v2.0
 /v2.0/data/datasets/{datasetid}/publications:
   get:
     description: Returns publications data associated with specific datasets.

package.json

@@ -13,7 +13,7 @@
   "scripts": {
     "start": "NODE_ENV=production nodemon --legacy-watch app.js",
     "dev": "NODE_ENV=development nodemon --legacy-watch app.js",
-    "test": "node ./node_modules/mocha/bin/mocha --config=test/.mocharc.yml --reporter-options reportDir=public,reportFilename=tests",
+    "test": "APIPATH=${APIPATH:-http://localhost:3001/} node ./node_modules/mocha/bin/mocha --config=test/.mocharc.yml --reporter-options reportDir=public,reportFilename=tests",
     "build:openapi": "(cd ./openapi && node ./scripts/build-openapi.js)",
     "validate:openapi": "yarn build:openapi && bash genoatt.sh && sleep 4 && bash runmochabatch.sh"
   },