Merge pull request #857 from UW-GAC/main

Deploy to stage

.github/release-drafter.yml

@@ -0,0 +1,13 @@
+sort-direction: ascending
+
+categories:
+  - title: "⬆️ Dependencies"
+    labels:
+      - "dependencies"
+      - "update-requirements-files"
+      - "combined-pr"
+
+template: |
+  ## What’s Changed
+
+  $CHANGES

.github/workflows/ci.yml

@@ -140,6 +140,6 @@ jobs:
           python -m coverage report
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release-drafter.yml

@@ -0,0 +1,114 @@
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - deploy/production
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: read
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Get current date
+      id: get-date
+      run: |
+          export CURRENT_DATE=$(TZ=":America/Los_Angeles" date "+%Y-%m-%d")
+          echo "current_date=${CURRENT_DATE}" >> $GITHUB_OUTPUT
+          echo "Current date set to ${CURRENT_DATE}"
+
+    - name: Get number of releases for the current date
+      id: get-release-count
+      run: |
+        export RELEASE_COUNT=$(gh release list \
+          --repo ${{ github.repository }} \
+          --json tagName \
+          --exclude-drafts \
+          --jq "map(select(.tagName | startswith(\"${CURRENT_DATE}\")))|length" \
+          )
+        echo "release_count=${RELEASE_COUNT}" >> $GITHUB_OUTPUT
+        echo "Found ${RELEASE_COUNT} releases"
+      env:
+        CURRENT_DATE: ${{ steps.get-date.outputs.current_date }}
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Prepare release version
+      id: get-version
+      run: |
+          export VERSION="${CURRENT_DATE}"
+
+          if [ $RELEASE_COUNT -gt 0 ]; then
+            echo "Release already exists for version ${VERSION}"
+            echo "Appending release count to version"
+            export VERSION="${CURRENT_DATE}-${RELEASE_COUNT}"
+          fi
+
+          echo "version=${VERSION}" >> $GITHUB_OUTPUT
+          echo "Version set to ${VERSION}"
+      env:
+        CURRENT_DATE: ${{ steps.get-date.outputs.current_date }}
+        RELEASE_COUNT: ${{ steps.get-release-count.outputs.release_count }}
+
+
+    - name: Check that version doesn't exist
+      id: check-release
+      run: |
+        echo "Checking version ${VERSION}"
+
+        export CHECK=$(gh release list \
+          --repo ${{ github.repository }} \
+          --json tagName \
+          --exclude-drafts \
+          --jq "map(select(.tagName == \"${VERSION}\"))|length" \
+          )
+        echo "Found ${CHECK} releases"
+
+        if [ $CHECK -gt 0 ]; then
+          echo "Release already exists for version ${VERSION}"
+          exit 1
+        fi
+      env:
+        VERSION: ${{ steps.get-version.outputs.version }}
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Check that tag doesn't exist
+      id: check-tag
+      run: |
+        echo "Checking tag for version ${VERSION}"
+
+        # Query the API for this tag.
+        export CHECK=$(gh api \
+          -H "Accept: application/vnd.github+json" \
+          -H "X-GitHub-Api-Version: 2022-11-28" \
+          /repos/${{ github.repository }}/tags \
+          --jq "map(select(.name  == \"${VERSION}\"))|length" \
+        )
+        echo "Found ${CHECK} tags"
+
+        if [ $CHECK -gt 0 ]; then
+          echo "Tag already exists for version ${VERSION}"
+          exit 1
+        fi
+      env:
+        VERSION: ${{ steps.get-version.outputs.version }}
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+
+    - uses: release-drafter/release-drafter@v6
+      with:
+        commitish: deploy/production
+        tag: ${{ steps.get-version.outputs.version }}
+        name: ${{ steps.get-version.outputs.version }}
+        version: ${{ steps.get-version.outputs.version }}
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.0
+    rev: v0.8.1
     hooks:
       # Run the linter.
       - id: ruff
@@ -21,7 +21,7 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.21.1
+    rev: v8.21.2
     hooks:
       - id: gitleaks
 

config/settings/base.py

@@ -298,6 +298,7 @@
     "socialaccount_signup",
     "admin:index",
     "admin:login",
+    "favicon",
 ]
 
 # django-dbbackup
@@ -345,6 +346,11 @@
                 "request_scope": True,
                 "django_group_name": "Approved by PI for AnVIL access",
             },
+            {
+                "drupal_machine_name": "authenticated",
+                "request_scope": True,
+                "django_group_name": "Authenticated",
+            },
         ],
     }
 }
@@ -375,25 +381,19 @@
 # django-anvil-consortium-manager
 # ------------------------------------------------------------------------------
 ANVIL_WORKSPACE_ADAPTERS = [
-    "gregor_django.gregor_anvil.adapters.ResourceWorkspaceAdapter",
-    "gregor_django.gregor_anvil.adapters.TemplateWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.CombinedConsortiumDataWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.UploadWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.ResourceWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.ExchangeWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.PartnerUploadWorkspaceAdapter",
-    "gregor_django.gregor_anvil.adapters.CombinedConsortiumDataWorkspaceAdapter",
-    "gregor_django.gregor_anvil.adapters.ReleaseWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.DCCProcessingWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.DCCProcessedDataWorkspaceAdapter",
-    "gregor_django.gregor_anvil.adapters.ExchangeWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.ReleaseWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.TemplateWorkspaceAdapter",
 ]
 ANVIL_ACCOUNT_ADAPTER = "gregor_django.gregor_anvil.adapters.AccountAdapter"
 ANVIL_MANAGED_GROUP_ADAPTER = "gregor_django.gregor_anvil.adapters.ManagedGroupAdapter"
 
-# Specify the URL name that AccountLink and AccountLinkVerify redirect to.
-ANVIL_ACCOUNT_LINK_REDIRECT = "users:redirect"
-# Specify the subject for AnVIL account verification emails.
-ANVIL_ACCOUNT_LINK_EMAIL_SUBJECT = "Verify your AnVIL account email"
-ANVIL_ACCOUNT_VERIFY_NOTIFICATION_EMAIL = "[email protected]"
-
 DRUPAL_API_CLIENT_ID = env("DRUPAL_API_CLIENT_ID", default="")
 DRUPAL_API_CLIENT_SECRET = env("DRUPAL_API_CLIENT_SECRET", default="")
 DRUPAL_API_REL_PATH = env("DRUPAL_API_REL_PATH", default="mockapi")

config/urls.py

@@ -1,9 +1,11 @@
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
+from django.templatetags.static import static as static_url_tag
 from django.urls import include, path
 from django.views import defaults as default_views
 from django.views.generic import TemplateView
+from django.views.generic.base import RedirectView
 
 urlpatterns = [
     path("", TemplateView.as_view(template_name="pages/home.html"), name="home"),
@@ -22,6 +24,11 @@
         "gregor_anvil/",
         include("gregor_django.gregor_anvil.urls", namespace="gregor_anvil"),
     ),
+    path(
+        "favicon.ico",
+        RedirectView.as_view(url=static_url_tag("images/favicons/favicon_1.jpg"), permanent=True),
+        name="favicon",
+    ),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 

gregor_django/drupal_oauth_provider/tests.py

@@ -116,7 +116,7 @@ def get_mocked_response(self):
             "name": "testmaster",
             "email": "[email protected]",
             "email_verified": "True",
-            "sub": 20122
+            "sub": "20122"
         }""",
             ),
         ]
@@ -184,7 +184,7 @@ def get_id_token(self):
                 "iat": self.setup_time,
                 "aud": allowed_audience,
                 "scope": ["authenticated", "oauth_client_user"],
-                "sub": 20122,
+                "sub": "20122",
             }
         )
 

gregor_django/gregor_anvil/adapters.py

@@ -67,6 +67,9 @@ class AccountAdapter(BaseAccountAdapter):
 
     list_table_class = tables.AccountTable
     list_filterset_class = filters.AccountListFilter
+    account_link_verify_redirect = "users:redirect"
+    account_link_email_subject = "Verify your AnVIL account email"
+    account_verify_notification_email = "[email protected]"
 
     def get_autocomplete_queryset(self, queryset, q):
         """Filter to Accounts where the email or the associated user name matches the query `q`."""
@@ -115,6 +118,7 @@ class UploadWorkspaceAdapter(WorkspaceAdminSharingAdapterMixin, BaseWorkspaceAda
     workspace_data_form_class = forms.UploadWorkspaceForm
     workspace_form_class = WorkspaceForm
     workspace_detail_template_name = "gregor_anvil/uploadworkspace_detail.html"
+    workspace_list_template_name = "gregor_anvil/uploadworkspace_list.html"
 
     def get_autocomplete_queryset(self, queryset, q, forwarded={}):
         """Filter to Accounts where the email or the associated user name matches the query `q`."""
@@ -139,7 +143,7 @@ class PartnerUploadWorkspaceAdapter(WorkspaceAdminSharingAdapterMixin, BaseWorks
     name = "Partner upload workspace"
     description = "Workspaces that contain data uploaded by a Partner Group "
     list_table_class_view = tables.PartnerUploadWorkspaceTable
-    list_table_class_staff_view = tables.PartnerUploadWorkspaceTable
+    list_table_class_staff_view = tables.PartnerUploadWorkspaceStaffTable
 
     workspace_data_model = models.PartnerUploadWorkspace
     workspace_data_form_class = forms.PartnerUploadWorkspaceForm
@@ -156,7 +160,7 @@ class ResourceWorkspaceAdapter(WorkspaceAdminSharingAdapterMixin, BaseWorkspaceA
         "Workspaces that contain general Consortium resources (e.g., examples of using AnVIL, working with data, etc.)"  # noqa: E501
     )
     list_table_class_view = tables.DefaultWorkspaceTable
-    list_table_class_staff_view = tables.DefaultWorkspaceTable
+    list_table_class_staff_view = tables.DefaultWorkspaceStaffTable
     workspace_data_model = models.ResourceWorkspace
     workspace_data_form_class = forms.ResourceWorkspaceForm
     workspace_detail_template_name = "gregor_anvil/resourceworkspace_detail.html"
@@ -189,6 +193,7 @@ class CombinedConsortiumDataWorkspaceAdapter(WorkspaceAdminSharingAdapterMixin,
     workspace_data_form_class = forms.CombinedConsortiumDataWorkspaceForm
     workspace_detail_template_name = "gregor_anvil/combinedconsortiumdataworkspace_detail.html"
     workspace_form_class = WorkspaceForm
+    workspace_list_template_name = "gregor_anvil/combinedconsortiumdataworkspace_list.html"
 
 
 class ReleaseWorkspaceAdapter(WorkspaceAdminSharingAdapterMixin, BaseWorkspaceAdapter):
@@ -240,8 +245,9 @@ class ExchangeWorkspaceAdapter(WorkspaceAdminSharingAdapterMixin, BaseWorkspaceA
     name = "Exchange workspace"
     description = "Workspaces for exchanging data with a Research Center outside of an upload cycle"
     list_table_class_view = tables.ExchangeWorkspaceTable
-    list_table_class_staff_view = tables.ExchangeWorkspaceTable
+    list_table_class_staff_view = tables.ExchangeWorkspaceStaffTable
     workspace_data_model = models.ExchangeWorkspace
     workspace_data_form_class = forms.ExchangeWorkspaceForm
     workspace_form_class = WorkspaceForm
     workspace_detail_template_name = "gregor_anvil/exchangeworkspace_detail.html"
+    workspace_list_template_name = "gregor_anvil/exchangeworkspace_list.html"