Merge pull request #597 from UW-GAC/deploy/stage

Deploy to prod

.github/workflows/ci.yml

@@ -28,9 +28,15 @@ jobs:
         backend: ["sqlite", "mariadb"]
         mariadb-version: ["10.4"]
         include:
-          - python-version: 3.8  # Possible future version.
+          - python-version: 3.12  # Possible future version.
             backend: "mariadb"
             mariadb-version: "10.5"
+            pip-recompile: true
+          - python-version: 3.12  # Possible future version.
+            backend: "mariadb"
+            mariadb-version: "10.11"
+            pip-recompile: true
+
     name: "py${{ matrix.python-version }}-${{ matrix.backend }}-${{ matrix.mariadb-version }}"
 
     services:
@@ -63,23 +69,44 @@ jobs:
             requirements/requirements.txt
             requirements/test-requirements.txt
 
-      - name: Install Dependencies
+      - name: Ensure pip is installed
         run: |
+          python -m ensurepip --upgrade
           python -m pip install --upgrade pip
-          pip install pip-tools
+          # Upgrade setup tools
+          python -m pip install --upgrade setuptools
+
+      - name: Install piptools
+        run: python -m pip install pip-tools
+
+      - name: Recompile pip files if requested
+        if: matrix.pip-recompile
+        run: |
+          pip-compile requirements/requirements.in
+          pip-compile requirements/test-requirements.in
+          # Print out changes.
+          git diff
+
+      - name: Install Dependencies
+        run: |
           pip-sync requirements/requirements.txt requirements/test-requirements.txt
 
       - name: Collect staticfiles
         run: python manage.py collectstatic --noinput --settings=config.settings.test
 
       - name: Run tests
-        run:  coverage run -p -m pytest
+        run:  |
+          pytest --cov=primed -n auto
+          mv .coverage .coverage-${{ strategy.job-index }}
+
+      - name: List files for debugging purposes
+        run: ls -lhta
 
       - name: Upload coverage data
         uses: actions/upload-artifact@v4
         with:
           name: coverage-data-${{ strategy.job-index }}
-          path: .coverage.*
+          path: .coverage-${{ strategy.job-index }}
 
   coverage:
     needs:
@@ -106,13 +133,14 @@ jobs:
 
       - name: Merge coverage files
         run: |
-          mv ./artifacts/coverage-data*/.coverage* .
+          python -m coverage combine ./artifacts/coverage-data*/.coverage-*
+          python -m coverage xml
           ls -la .coverage*
 
-      - name: Combine coverage data
+      - name: Report coverage
         run: |
-          python -m coverage combine
-          python -m coverage xml
+          python -m coverage report
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:

.github/workflows/pip-compile.yml

@@ -0,0 +1,30 @@
+name: Update pip-tools requirements files
+on:
+  pull_request:
+    branches: [ "main" ]
+
+
+jobs:
+  update-requirements-files:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code Repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.8
+
+      - name: Update requirements files
+        uses: UW-GAC/pip-tools-actions/[email protected]
+        with:
+          requirements_files:  |-
+            requirements/requirements.in
+            requirements/test-requirements.in
+            requirements/dev-requirements.in
+          pr-title: Update requirements file for ${{ github.head_ref }}
+          pr-branch-suffix: "${{ github.event.number}}"

.pre-commit-config.yaml

@@ -4,15 +4,15 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.2
+    rev: v0.4.7
     hooks:
       # Run the linter.
       - id: ruff
@@ -21,7 +21,7 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.16.1
+    rev: v8.18.3
     hooks:
       - id: gitleaks
 

add_dbgap_example_data.py

@@ -94,6 +94,10 @@
     dbgap_dac="NHLBI",
     dbgap_current_status=models.dbGaPDataAccessRequest.REJECTED,
 )
+dar_1_5 = factories.dbGaPDataAccessRequestFactory(
+    dbgap_data_access_snapshot=dar_snapshot_1,
+    dbgap_current_status=models.dbGaPDataAccessRequest.APPROVED,
+)
 
 dbgap_application_2 = factories.dbGaPApplicationFactory.create(
     principal_investigator=UserFactory.create(name="Alisa", username="Alisa"),

primed/dbgap/models.py

@@ -473,3 +473,9 @@ def get_dbgap_workspaces(self):
             dbgap_consent_code=self.dbgap_consent_code,
         ).order_by("dbgap_version")
         return dbgap_workspaces
+
+    def get_matching_studies(self):
+        """Get the list of studies matching dbGaP study accession phs associated with this data access request."""
+
+        study_list = Study.objects.filter(dbgapstudyaccession__dbgap_phs=self.dbgap_phs)
+        return study_list

primed/dbgap/tables.py

@@ -261,6 +261,11 @@ class dbGaPDataAccessRequestBySnapshotTable(dbGaPDataAccessRequestTable):
     dbgap_data_access_snapshot__dbgap_application__dbgap_project_id = None
     dbgap_data_access_snapshot__created = None
     matching_workspaces = tables.columns.Column(accessor="get_dbgap_workspaces", orderable=False, default=" ")
+    matching_studies = tables.columns.ManyToManyColumn(
+        accessor="get_matching_studies",
+        verbose_name="Studies",
+        linkify_item=True,
+    )
 
     class Meta:
         model = models.dbGaPDataAccessRequest
@@ -273,6 +278,11 @@ class Meta:
         )
         order_by = ("dbgap_dar_id",)
         attrs = {"class": "table table-sm"}
+        sequence = (
+            "dbgap_dar_id",
+            "dbgap_dac",
+            "matching_studies",
+        )
 
     def render_matching_workspaces(self, value, record):
         template_code = """

primed/dbgap/tests/factories.py

@@ -151,18 +151,14 @@ class Meta:
         model = models.dbGaPDataAccessRequest
 
 
-class dbGaPDataAccessRequestForWorkspaceFactory(DjangoModelFactory):
+class dbGaPDataAccessRequestForWorkspaceFactory(dbGaPDataAccessRequestFactory):
     """A factory for the dbGaPApplication model to match a workspace."""
 
-    dbgap_data_access_snapshot = SubFactory(dbGaPDataAccessSnapshotFactory)
     dbgap_phs = LazyAttribute(lambda o: o.dbgap_workspace.dbgap_study_accession.dbgap_phs)
-    dbgap_dar_id = Sequence(lambda n: n + 1)
     original_version = LazyAttribute(lambda o: o.dbgap_workspace.dbgap_version)
     original_participant_set = LazyAttribute(lambda o: o.dbgap_workspace.dbgap_participant_set)
     dbgap_consent_code = LazyAttribute(lambda o: o.dbgap_workspace.dbgap_consent_code)
     dbgap_consent_abbreviation = LazyAttribute(lambda o: o.dbgap_workspace.dbgap_consent_abbreviation)
-    dbgap_current_status = models.dbGaPDataAccessRequest.APPROVED
-    dbgap_dac = Faker("word")
 
     class Params:
         dbgap_workspace = None

primed/dbgap/tests/test_models.py

@@ -1525,3 +1525,31 @@ def test_get_dbgap_link(self):
         """`get_dbgab_link` returns a link."""
         instance = factories.dbGaPDataAccessRequestFactory.create()
         self.assertIsInstance(instance.get_dbgap_link(), str)
+
+    def test_get_studies_no_matches(self):
+        """Returns an empty queryset when there is no matching studies."""
+        factories.dbGaPStudyAccessionFactory.create()
+        dar = factories.dbGaPDataAccessRequestFactory.create()
+        self.assertEqual(dar.get_matching_studies().count(), 0)
+
+    def test_get_studies_one_match(self):
+        """Returns the correct study when there is one match."""
+        test_study = StudyFactory.create(short_name="Test", full_name="Test Study")
+        dbgap_study_accession = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=1, studies=[test_study])
+        dar = factories.dbGaPDataAccessRequestFactory.create(dbgap_phs=dbgap_study_accession.dbgap_phs)
+        qs = dar.get_matching_studies()
+        self.assertEqual(qs.count(), 1)
+        self.assertEqual(qs[0], test_study)
+
+    def test_get_studies_two_match(self):
+        """Returns the correct studies when there are 2 match."""
+        test_study_1 = StudyFactory.create(short_name="Test 1", full_name="Test Study 1")
+        test_study_2 = StudyFactory.create(short_name="Test 2", full_name="Test Study 2")
+        dbgap_study_accession = factories.dbGaPStudyAccessionFactory.create(
+            dbgap_phs=1, studies=[test_study_1, test_study_2]
+        )
+        dar = factories.dbGaPDataAccessRequestFactory.create(dbgap_phs=dbgap_study_accession.dbgap_phs)
+        qs = dar.get_matching_studies()
+        self.assertEqual(qs.count(), 2)
+        self.assertEqual(qs[0], test_study_1)
+        self.assertEqual(qs[1], test_study_2)

primed/dbgap/tests/test_tables.py

@@ -694,6 +694,26 @@ def test_ordering(self):
         self.assertEqual(table.data[0], instance_2)
         self.assertEqual(table.data[1], instance_1)
 
+    def test_one_matching_study(self):
+        """Table works if there is a matching study"""
+        test_study = factories.StudyFactory.create(short_name="Test", full_name="Test Study")
+        dbgap_study_accession = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=1, studies=[test_study])
+        dar = factories.dbGaPDataAccessRequestFactory.create(dbgap_phs=dbgap_study_accession.dbgap_phs)
+        table = self.table_class([dar])
+        self.assertIn(test_study.short_name, table.rows[0].get_cell("matching_studies"))
+
+    def test_two_matching_studies(self):
+        """Table works if there is are two matching studies"""
+        test_study_1 = factories.StudyFactory.create(short_name="Test 1", full_name="Test Study 1")
+        test_study_2 = factories.StudyFactory.create(short_name="Test 2", full_name="Test Study 2")
+        dbgap_study_accession = factories.dbGaPStudyAccessionFactory.create(
+            dbgap_phs=1, studies=[test_study_1, test_study_2]
+        )
+        dar = factories.dbGaPDataAccessRequestFactory.create(dbgap_phs=dbgap_study_accession.dbgap_phs)
+        table = self.table_class([dar])
+        self.assertIn(test_study_1.short_name, table.rows[0].get_cell("matching_studies"))
+        self.assertIn(test_study_2.short_name, table.rows[0].get_cell("matching_studies"))
+
 
 class dbGaPDataAccessRequestSummaryTable(TestCase):
     model = models.dbGaPDataAccessRequest

primed/dbgap/tests/test_views.py

@@ -2141,17 +2141,17 @@ def test_error_missing_json(self):
 
     def test_get_dbgap_application_pk_does_not_exist(self):
         """Raises a 404 error with an invalid object dbgap_application_pk."""
-        request = self.factory.get(self.get_url(self.dbgap_application.pk + 1))
+        request = self.factory.get(self.get_url(self.dbgap_application.pk + 999))
         request.user = self.user
         with self.assertRaises(Http404):
-            self.get_view()(request, dbgap_project_id=self.dbgap_application.pk + 1)
+            self.get_view()(request, dbgap_project_id=self.dbgap_application.pk + 999)
 
     def test_post_dbgap_application_pk_does_not_exist(self):
         """Raises a 404 error with an invalid object dbgap_application_pk."""
-        request = self.factory.post(self.get_url(self.dbgap_application.pk + 1), {})
+        request = self.factory.post(self.get_url(self.dbgap_application.pk + 999), {})
         request.user = self.user
         with self.assertRaises(Http404):
-            self.get_view()(request, dbgap_project_id=self.dbgap_application.pk + 1)
+            self.get_view()(request, dbgap_project_id=self.dbgap_application.pk + 999)
 
     def test_has_form_when_one_snapshot_exists(self):
         phs_int = fake.random_int()

primed/drupal_oauth_provider/tests.py

@@ -104,7 +104,7 @@ def get_mocked_response(self):
     # This login response mimics drupals in that it contains a set of scopes
     # and the uid which has the name sub
     def get_login_response_json(self, with_refresh_token=True):
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         app = get_adapter().get_app(request=None, provider=self.provider_id)
         allowed_audience = app.client_id
         id_token = sign_id_token(

pytest.ini

@@ -1,5 +1,5 @@
 [pytest]
-addopts = --ds=config.settings.test --reuse-db
+addopts = --ds=config.settings.test --reuse-db -n auto
 python_files = tests.py test_*.py
 filterwarnings =
     # Convert all warnings to errors.
@@ -8,3 +8,4 @@ filterwarnings =
     ignore:pkg_resources is deprecated as an API.:DeprecationWarning:model_utils
     # Warning raised by pkg_resources via model_utils. ??
     ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning:pkg_resources
+    ignore:'pkgutil.find_loader' is deprecated and slated for removal in Python 3.14:DeprecationWarning

requirements/dev-requirements.in

@@ -7,7 +7,7 @@ ipdb  # https://github.com/gotcha/ipdb
 # Type checking
 # ------------------------------------------------------------------------------
 mypy  # https://github.com/python/mypy
-django-stubs  # https://github.com/typeddjango/django-stubs
+django-stubs>=4.2,<5.0  # https://github.com/typeddjango/django-stubs
 types-requests
 
 # Documentation

requirements/dev-requirements.txt

@@ -40,13 +40,13 @@ decorator==5.1.1
     #   ipython
 distlib==0.3.8
     # via virtualenv
-django==4.2.11
+django==4.2.13
     # via
     #   -c requirements/requirements.txt
     #   django-debug-toolbar
     #   django-stubs
     #   django-stubs-ext
-django-debug-toolbar==4.3.0
+django-debug-toolbar==4.4.2
     # via -r requirements/dev-requirements.in
 django-stubs==4.2.7
     # via -r requirements/dev-requirements.in
@@ -77,7 +77,7 @@ ipython==8.12.3
     # via ipdb
 jedi==0.19.1
     # via ipython
-jinja2==3.1.3
+jinja2==3.1.4
     # via sphinx
 livereload==2.6.3
     # via sphinx-autobuild
@@ -136,7 +136,7 @@ requests==2.31.0
     #   -c requirements/requirements.txt
     #   -c requirements/test-requirements.txt
     #   sphinx
-ruff==0.4.2
+ruff==0.4.7
     # via -r requirements/dev-requirements.in
 six==1.16.0
     # via
@@ -188,7 +188,7 @@ types-pytz==2024.1.0.20240203
     # via django-stubs
 types-pyyaml==6.0.12.12
     # via django-stubs
-types-requests==2.31.0.20240406
+types-requests==2.32.0.20240602
     # via -r requirements/dev-requirements.in
 typing-extensions==4.8.0
     # via
@@ -209,7 +209,7 @@ virtualenv==20.25.1
     # via pre-commit
 wcwidth==0.2.13
     # via prompt-toolkit
-werkzeug==3.0.2
+werkzeug==3.0.3
     # via -r requirements/dev-requirements.in
 zipp==3.17.0
     # via

requirements/requirements.in

@@ -33,7 +33,7 @@ django-dbbackup # https://github.com/jazzband/django-dbbackup
 django-extensions  # https://github.com/django-extensions/django-extensions
 
 # anvil_consortium_manager
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.22
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.23
 
 # Simple history - model history tracking
 django-simple-history