Fix api healthchecks

.github/workflows/PR-validation.yml

@@ -802,6 +802,11 @@ jobs:
           tags: agr_pavi/webui:latest
           outputs: type=docker,dest=/tmp/pavi_webui_docker_image.tar
   commit-deps-lock-updates:
+    #TODO: Moving the commit from before to after merge to prevent need for repetitive forced reruns of PR-validation.
+    #       * Convert this job into job that tars up all updated dependency files and uploads them as a single artifact.
+    #       * The new artifact should then be downloaded, unpacked and committed in the main-build-and-deploy workflow.
+    #       * PR validation should get an additional job that reports in the open PR if dependency files have been updated,
+    #         with a link to the updated files or summary report to enable inspection before merge (download and report git diff?).
     runs-on: ubuntu-22.04
     #Only commit updated lock files on successfull validation (to prevent PR cluttering)
     needs:

api/Makefile

@@ -80,13 +80,13 @@ run-tests: test-deps nextflow.sh protein-msa.nf nextflow.config
 	python -m pytest --cov --cov-fail-under=80
 
 run-tests-dev: test-deps nextflow.sh protein-msa.nf nextflow.config
-	python -m pytest --cov --cov-fail-under=80 --cov-report html
+	python -m pytest --cov --cov-fail-under=80 --cov-report html -v
 
 run-integration-test-container: test-deps
 	export API_PIPELINE_IMAGE_TAG=${TAG_NAME} && \
 	  docker-compose -f docker-compose-dev.yml --env-file dev.env up -d agr.pavi.dev-local.api
 	sleep 30 # Allow container some startup time before attempting to connect
 	export EXTERNAL_API_BASE_URL="http://localhost:8080" && \
-	  python -m pytest tests/integration \
+	  python -m pytest tests/b_integration \
 	  || (echo "Container logs:" && docker logs agr.pavi.dev-local.api.server && exit 1)
 	docker-compose -f docker-compose-dev.yml down

api/aws_infra/.ebextensions/loadbalancer.yml.config

@@ -31,7 +31,7 @@ option_settings:
   aws:elasticbeanstalk:environment:process:api:
     Port: '8080'
     Protocol: HTTP
-    HealthCheckPath: /api/health/
+    HealthCheckPath: /api/health
     MatcherHTTPCode: 200
   aws:elbv2:loadbalancer:
     IdleTimeout: 600

api/tests/unit/test_main.py → api/tests/a_unit/test_main.py

@@ -3,7 +3,7 @@
 from main import app
 from uuid import UUID
 
-client = TestClient(app)
+client = TestClient(app, follow_redirects=False)
 
 NOT_FOUND_UUID: UUID = UUID('00000000-0000-0000-0000-000000000000')
 
@@ -12,7 +12,7 @@
 # If path or response status-code changes then .ebextensions/loadbalancer.yml.config
 # needs to be updated (HealthCheckPath)
 def test_health_reporting() -> None:
-    response = client.get("/api/health/")
+    response = client.get("/api/health")
 
     assert response.status_code == 200
 

api/tests/integration/test_main.py → api/tests/b_integration/test_main.py

@@ -15,9 +15,9 @@
 
 client: TestClient | Client
 if external_api_base_url:
-    client = Client(base_url=external_api_base_url)
+    client = Client(base_url=external_api_base_url, follow_redirects=False)
 else:
-    client = TestClient(app)
+    client = TestClient(app, follow_redirects=False)
     environ["API_RESULTS_PATH_PREFIX"] = f'{getcwd()}/'
     environ["API_EXECUTION_ENV"] = 'local'
 

pipeline/seq_retrieval/Makefile

@@ -63,7 +63,7 @@ run-unit-tests: test-deps
 	python -m pytest --cov --cov-fail-under=80
 
 run-unit-tests-dev: test-deps
-	python -m pytest --cov --cov-fail-under=80 --cov-report html
+	python -m pytest --cov --cov-fail-under=80 --cov-report html -v
 
 run-code-checks: run-type-checks run-style-checks run-unit-tests