Merge pull request #181 from umccr/improve-srm-testing-regime

Fixed sequence_run_manager endpoint unit test

.gitignore

@@ -56,3 +56,6 @@ Brewfile.lock.json
 *.xml
 
 target/
+
+.coverage
+htmlcov/

lib/workload/stateless/sequence_run_manager/.coveragerc

@@ -0,0 +1,5 @@
+[run]
+omit = */tests/*,*tests*,sequence_run_manager/management/*,sequence_run_manager/migrations/*,sequence_run_manager/wsgi.py,migrate.py,manage.py
+
+[report]
+omit = */tests/*,*tests*,sequence_run_manager/management/*,sequence_run_manager/migrations/*,sequence_run_manager/wsgi.py,migrate.py,manage.py

lib/workload/stateless/sequence_run_manager/Makefile

@@ -1,3 +1,6 @@
+.EXPORT_ALL_VARIABLES:
+DJANGO_SETTINGS_MODULE = sequence_run_manager.settings.local
+
 .PHONY: test suite
 
 install:
@@ -17,6 +20,26 @@ test: install up suite down
 suite:
 	@python manage.py test
 
+migrate:
+	@python manage.py migrate
+
+start: migrate
+	@python manage.py runserver_plus
+
+openapi:
+	@python manage.py generateschema > orcabus.srm.openapi.yaml
+
+validate: openapi
+	@python -m openapi_spec_validator orcabus.srm.openapi.yaml
+
+coverage: install up migrate
+	@echo $$DJANGO_SETTINGS_MODULE
+	@coverage run --source='.' manage.py test
+
+report:
+	@coverage report -m
+	@coverage html
+
 up:
 	@docker compose up --wait -d
 

lib/workload/stateless/sequence_run_manager/README.md

@@ -134,6 +134,14 @@ python manage.py generateschema > orcabus.srm.openapi.yaml
 
 ## Testing
 
+### Coverage report
+
+```
+make coverage report
+```
+
+_The html report is in `htmlcov/index.html`._
+
 ### Run test suite
 
 ```

lib/workload/stateless/sequence_run_manager/deps/requirements-dev.txt

@@ -1,3 +1,4 @@
 -r requirements-test.txt
 django_extensions==3.2.3
 drf_yasg==1.21.7
+openapi-spec-validator

lib/workload/stateless/sequence_run_manager/deps/requirements-test.txt

@@ -5,3 +5,4 @@ pytz==2024.1
 mockito==1.5.0
 # Intentionally leave out the boto3 version here. They bump like daily and latest is always fine.
 boto3
+coverage==7.4.4

lib/workload/stateless/sequence_run_manager/sequence_run_manager/tests/test_viewsets.py

@@ -4,12 +4,15 @@
 from django.utils.timezone import now
 
 from sequence_run_manager.models.sequence import Sequence
+from sequence_run_manager.urls.base import api_base
 
 logger = logging.getLogger()
 logger.setLevel(logging.INFO)
 
 
 class SequenceViewSetTestCase(TestCase):
+    endpoint = f"/{api_base}sequence"
+
     def setUp(self):
         Sequence.objects.create(
             instrument_run_id="190101_A01052_0001_BH5LY7ACGT",
@@ -29,22 +32,41 @@ def test_get_api(self):
         """
         # Get sequence list
         logger.info("Get sequence API")
-        response = self.client.get("/sequence/")
+        response = self.client.get(self.endpoint)
         self.assertEqual(response.status_code, 200, "Ok status response is expected")
 
         logger.info("Check if API return result")
         result_response = response.data["results"]
         self.assertGreater(len(result_response), 0, "A result is expected")
 
+    def test_get_by_uk_surrogate_key(self):
+        """
+        python manage.py test sequence_run_manager.tests.test_viewsets.SequenceViewSetTestCase.test_get_by_uk_surrogate_key
+        """
         logger.info("Check if unique data has a single entry")
-        response = self.client.get("/sequence/?sequence_run_id=r.AAAAAA")
+        response = self.client.get(f"{self.endpoint}/?instrument_run_id=190101_A01052_0001_BH5LY7ACGT")
         results_response = response.data["results"]
         self.assertEqual(
             len(results_response), 1, "Single result is expected for unique data"
         )
 
+    def test_get_by_sequence_run_id(self):
+        """
+        python manage.py test sequence_run_manager.tests.test_viewsets.SequenceViewSetTestCase.test_get_by_sequence_run_id
+        """
+        logger.info("Check if unique data has a single entry")
+        response = self.client.get(f"{self.endpoint}/?sequence_run_id=r.AAAAAA")
+        results_response = response.data["results"]
+        self.assertEqual(
+            len(results_response), 1, "Single result is expected for unique data"
+        )
+
+    def test_get_by_invalid_parameter(self):
+        """
+        python manage.py test sequence_run_manager.tests.test_viewsets.SequenceViewSetTestCase.test_get_by_invalid_parameter
+        """
         logger.info("Check if wrong parameter")
-        response = self.client.get("/sequence/?lib_id=LBR0001")
+        response = self.client.get(f"{self.endpoint}/?lib_id=LBR0001")
         results_response = response.data["results"]
         self.assertEqual(
             len(results_response),