Merge pull request #39 from microbiomedata/issue-32-ci-mongo-service

CI: spin up MongoDB service so live-DB tests actually run (closes #32)

Author: sierra-moxon

.github/workflows/main.yaml

@@ -37,6 +37,27 @@ jobs:
       matrix:
         python-version: [ '3.9', '3.10', '3.11', '3.12' ]
 
+    services:
+      # Spin up a MongoDB the live-DB tests can connect to. The host port is
+      # 27022 to match the value hardcoded in
+      # tests/test_linkml_store_client_connections.py (which on `main` still
+      # reads `MONGO_PORT = 27022` as a module-level constant); the env-reading
+      # tests also pick up port 27022 via the MONGO_PORT env on the test step.
+      # After #22's port-from-env change lands on `main`, this port choice
+      # becomes arbitrary and can move to 27017.
+      mongo:
+        image: mongo:7
+        ports:
+          - 27022:27017
+        env:
+          MONGO_INITDB_ROOT_USERNAME: admin
+          MONGO_INITDB_ROOT_PASSWORD: testpass
+        options: >-
+          --health-cmd "mongosh -u admin -p testpass --authenticationDatabase admin --eval 'db.adminCommand({ping:1})' --quiet"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 10
+
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
@@ -54,4 +75,12 @@ jobs:
         run: poetry install --all-extras
 
       - name: Run test suite
+        env:
+          MONGO_HOST: localhost
+          MONGO_PORT: '27022'
+          MONGO_USERNAME: admin
+          MONGO_PASSWORD: testpass
+          MONGO_DBNAME: nmdc
+          MONGO_DB: nmdc
+          ENABLE_DB_TESTS: 'true'
         run: make test