Merge pull request #821 from UW-GAC/main

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UW-GAC · Nov 8, 2024 · 3d2e189 · 3d2e189
2 parents 8ea488f + 349bb88
commit 3d2e189
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -54,10 +54,10 @@ jobs:
     steps:
 
       - name: Checkout Code Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
@@ -78,8 +78,8 @@ jobs:
       - name: Recompile pip files if requested
         if: matrix.pip-recompile
         run: |
-          pip-compile requirements/requirements.in
-          pip-compile requirements/test-requirements.in
+          pip-compile -v requirements/requirements.in
+          pip-compile -v requirements/test-requirements.in
           # Print out changes.
           git diff
 
@@ -93,27 +93,28 @@ jobs:
       - name: Run tests
         run:  |
           pytest --cov=gregor_django -n auto
-          mv .coverage .coverage-${{ strategy.job-index }}
+          mv .coverage coverage-${{ strategy.job-index }}
 
       - name: List files for debugging purposes
         run: ls -lhta
 
       - name: Upload coverage data
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.3
         with:
           name: coverage-data-${{ strategy.job-index }}
-          path: .coverage-${{ strategy.job-index }}
+          path: coverage-${{ strategy.job-index }}
+          if-no-files-found: error
 
   coverage:
     needs:
       - test
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: '3.10'
 
@@ -123,13 +124,14 @@ jobs:
           pip install --upgrade coverage "django<4" django-coverage-plugin
 
       - name: Download coverage data
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.8
         with:
           path: ./artifacts/
 
       - name: Merge coverage files
         run: |
-          python -m coverage combine ./artifacts/coverage-data*/.coverage-*
+          ls -la ./artifacts/coverage-data*
+          python -m coverage combine ./artifacts/coverage-data*/coverage-*
           python -m coverage xml
           ls -la .coverage*
 
@@ -138,6 +140,6 @@ jobs:
           python -m coverage report
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v4.6.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/combine-prs.yml b/.github/workflows/combine-prs.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
       - name: combine-prs
         id: combine-prs
-        uses: github/combine-prs@v5.1.0
+        uses: github/combine-prs@v5.2.0
         with:
           labels: combined-pr # Optional: add a label to the combined PR
           ci_required: true # require all checks to pass before combining

diff --git a/.github/workflows/gitleaks.yml b/.github/workflows/gitleaks.yml
@@ -10,10 +10,10 @@ jobs:
     name: gitleaks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.2.2
         with:
           fetch-depth: 0
-      - uses: gitleaks/gitleaks-action@v2
+      - uses: gitleaks/gitleaks-action@v2.3.7
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITLEAKS_LICENSE: ${{ secrets.GITLEAKS_LICENSE}} # Only required for Organizations, not personal accounts.
diff --git a/.github/workflows/pip-compile.yml b/.github/workflows/pip-compile.yml
@@ -13,17 +13,17 @@ jobs:
 
     steps:
       - name: Checkout Code Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
         with:
           ref: ${{ github.head_ref }}
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: "3.10"
 
       - name: Update requirements files
-        uses: UW-GAC/pip-tools-actions/update-requirements-files@v0.1
+        uses: UW-GAC/pip-tools-actions/update-requirements-files@v0.2
         with:
           requirements_files:  |-
             requirements/requirements.in

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,18 +1,18 @@
 exclude: 'docs|node_modules|migrations|.git|.tox'
-default_stages: [commit]
+default_stages: [pre-commit]
 fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.2
+    rev: v0.7.0
     hooks:
       # Run the linter.
       - id: ruff
@@ -21,7 +21,7 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.18.4
+    rev: v8.21.1
     hooks:
       - id: gitleaks
 

diff --git a/add_upload_workspace_audit_test_data.py → add_upload_cycle_audit_test_data.py b/add_upload_workspace_audit_test_data.py → add_upload_cycle_audit_test_data.py
@@ -17,6 +17,7 @@
 rc_1_uploader_group = ManagedGroupFactory(name="DEMO_RC1_UPLOADERS")
 rc_1_nonmember_group = ManagedGroupFactory(name="DEMO_RC1_NONMEMBERS")
 gregor_all_group = ManagedGroupFactory(name="GREGOR_ALL")
+combined_auth_domain = ManagedGroupFactory(name="AUTH_GREGOR_COMBINED")
 
 # Create an RC
 rc = factories.ResearchCenterFactory.create(
@@ -27,8 +28,20 @@
     non_member_group=rc_1_nonmember_group,
 )
 
+# Add GREGOR_ALL and DCC_ADMINS to the combined auth domain.
+GroupGroupMembershipFactory.create(
+    parent_group=combined_auth_domain,
+    child_group=gregor_all_group,
+    role=GroupGroupMembership.MEMBER,
+)
+GroupGroupMembershipFactory.create(
+    parent_group=combined_auth_domain,
+    child_group=dcc_admin_group,
+    role=GroupGroupMembership.ADMIN,
+)
 
-# Create a future upload cycle.
+
+## Future upload cycle.
 upload_cycle = factories.UploadCycleFactory.create(
     cycle=1,
     is_future=True,
@@ -39,7 +52,7 @@
     workspace__name="TEST_U01_RC1",
 )
 
-# Create a current upload cycle before compute.
+## Current upload cycle before compute.
 upload_cycle = factories.UploadCycleFactory.create(
     cycle=2,
     is_current=True,
@@ -111,7 +124,7 @@
 )
 
 
-# Create a current upload cycle after compute.
+## Current upload cycle after compute.
 upload_cycle = factories.UploadCycleFactory.create(
     cycle=3,
     is_current=True,
@@ -256,7 +269,7 @@
     role=GroupGroupMembership.ADMIN,
 )
 
-# Create a past upload cycle after QC is completed.
+## Past upload cycle after QC is completed; combined workspace is not complete.
 upload_cycle = factories.UploadCycleFactory.create(
     cycle=5,
     is_past=True,
@@ -320,8 +333,18 @@
     child_group=dcc_admin_group,
     role=GroupGroupMembership.ADMIN,
 )
+# Create the combined workspace and its records.
+combined_workspace = factories.CombinedConsortiumDataWorkspaceFactory.create(
+    upload_cycle=upload_cycle,
+    workspace__name="TEST_U05_COMBINED",
+)
+# Delete the auth domain created by the factory and add the shared auth domain.
+combined_workspace.workspace.authorization_domains.clear()
+combined_workspace.workspace.authorization_domains.add(combined_auth_domain)
+# No sharing records yet.
+
 
-# Create a past upload cycle with a combined workspace.
+## Past upload cycle with a combined workspace.
 upload_cycle = factories.UploadCycleFactory.create(
     cycle=6,
     is_past=True,
@@ -332,11 +355,6 @@
     workspace__name="TEST_U06_RC1",
     date_qc_completed=timezone.now(),
 )
-factories.CombinedConsortiumDataWorkspaceFactory.create(
-    upload_cycle=upload_cycle,
-    date_completed=timezone.now(),
-    workspace__name="TEST_U06_COMBINED",
-)
 # Create records as appropriate for the previous point in the cycle - past cycle before QC complete.
 # Auth domain.
 WorkspaceGroupSharingFactory.create(
@@ -383,3 +401,31 @@
     child_group=dcc_admin_group,
     role=GroupGroupMembership.ADMIN,
 )
+# Create the combined workspace and its records.
+combined_workspace = factories.CombinedConsortiumDataWorkspaceFactory.create(
+    upload_cycle=upload_cycle,
+    date_completed=timezone.now(),
+    workspace__name="TEST_U06_COMBINED",
+)
+# Delete the auth domain created by the factory and add the shared auth domain.
+combined_workspace.workspace.authorization_domains.clear()
+combined_workspace.workspace.authorization_domains.add(combined_auth_domain)
+# Add sharing records from previous step - DCC admins, writers, and members.
+WorkspaceGroupSharingFactory.create(
+    workspace=combined_workspace.workspace,
+    group=dcc_admin_group,
+    access=WorkspaceGroupSharing.OWNER,
+    can_compute=True,
+)
+WorkspaceGroupSharingFactory.create(
+    workspace=combined_workspace.workspace,
+    group=dcc_writer_group,
+    access=WorkspaceGroupSharing.WRITER,
+    can_compute=True,
+)
+WorkspaceGroupSharingFactory.create(
+    workspace=combined_workspace.workspace,
+    group=dcc_member_group,
+    access=WorkspaceGroupSharing.READER,
+    can_compute=False,
+)
diff --git a/config/settings/base.py b/config/settings/base.py
@@ -155,6 +155,7 @@
     "maintenance_mode.middleware.MaintenanceModeMiddleware",
     "simple_history.middleware.HistoryRequestMiddleware",
     "django_htmx.middleware.HtmxMiddleware",
+    "allauth.account.middleware.AccountMiddleware",
 ]
 
 # STATIC

diff --git a/gregor_apps.cron b/gregor_apps.cron
@@ -10,3 +10,9 @@ MAILTO="[email protected]"
 
 # Nightly user data audit
 0 3 * * * . /var/www/django/gregor_apps/gregor-apps-activate.sh; python manage.py sync-drupal-data --update --email [email protected] >> cron.log
+
+# Nightly upload workspace audit
+0 3 * * * . /var/www/django/gregor_apps/gregor-apps-activate.sh; python manage.py run_upload_workspace_audit --email [email protected] >> cron.log
+
+# Nightly combined workspace audit
+0 3 * * * . /var/www/django/gregor_apps/gregor-apps-activate.sh; python manage.py run_combined_workspace_audit --email [email protected] >> cron.log
diff --git a/gregor_django/drupal_oauth_provider/provider.py b/gregor_django/drupal_oauth_provider/provider.py
@@ -2,11 +2,14 @@
 
 from allauth.account.models import EmailAddress
 from allauth.socialaccount import app_settings, providers
+from allauth.socialaccount.adapter import get_adapter
 from allauth.socialaccount.providers.base import ProviderAccount
 from allauth.socialaccount.providers.oauth2.provider import OAuth2Provider
 from django.conf import settings
 from django.core.exceptions import ImproperlyConfigured
 
+from .views import CustomAdapter
+
 logger = logging.getLogger(__name__)
 
 DRUPAL_PROVIDER_ID = "drupal_oauth_provider"
@@ -27,6 +30,13 @@ class CustomProvider(OAuth2Provider):
     id = DRUPAL_PROVIDER_ID
     name = OVERRIDE_NAME
     account_class = CustomAccount
+    oauth2_adapter_class = CustomAdapter
+    supports_token_authentication = True
+
+    def __init__(self, request, app=None):
+        if app is None:
+            app = get_adapter().get_app(request, self.id)
+        super().__init__(request, app=app)
 
     def extract_uid(self, data):
         return str(data["sub"])