Set up deploy/stage branch for ubuntu 22.04 upgrade

.github/workflows/ci.yml

@@ -24,14 +24,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.10"]
         backend: ["sqlite", "mariadb"]
-        mariadb-version: ["10.4"]
+        mariadb-version: ["10.6"]
         include:
-          - python-version: "3.10"  # Future ubuntu 22.04 upgrade.
-            backend: "mariadb"
-            mariadb-version: "10.6"
-            pip-recompile: true
           - python-version: 3.12  # Future ubuntu 24.04.01 upgrade.
             backend: "mariadb"
             mariadb-version: "10.11"

.github/workflows/combine-prs.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
       - name: combine-prs
         id: combine-prs
-        uses: github/combine-prs@v5.0.0
+        uses: github/combine-prs@v5.1.0
         with:
           labels: combined-pr # Optional: add a label to the combined PR
           ci_required: true # require all checks to pass before combining

.github/workflows/pip-compile.yml

@@ -6,8 +6,6 @@ on:
 
 jobs:
   update-requirements-files:
-    permissions:
-      pull-requests: write
     runs-on: ubuntu-latest
 
     steps:
@@ -16,10 +14,10 @@ jobs:
         with:
           ref: ${{ github.head_ref }}
 
-      - name: Set up Python 3.8
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.10"
 
       - name: Update requirements files
         uses: UW-GAC/pip-tools-actions/[email protected]

add_phenotype_inventory_input_example_data.py → add_inventory_input_example_data.py

@@ -1,5 +1,5 @@
 # Temporary script to create some test data.
-# Run with: python manage.py shell < add_phenotype_inventory_input_example_data.py
+# Run with: python manage.py shell < add_inventory_input_example_data.py
 
 from anvil_consortium_manager.tests.factories import (
     ManagedGroupFactory,

primed-apps-activate.sh

@@ -2,6 +2,7 @@ export DJANGO_SITE_DIR=/var/www/django/primed_apps/
 export DJANGO_SITE_USER=primedweb
 export DJANGO_SETTINGS_MODULE=config.settings.apps
 export DJANGO_WSGI_FILE=config/primed_apps_wsgi.py
+export DJANGO_CRONTAB=primed_apps.cron
 export GAC_ENV=primed_apps
 cd $DJANGO_SITE_DIR
 . venv/bin/activate

primed-apps-dev-activate.sh

@@ -6,6 +6,7 @@ export DJANGO_SITE_DIR=/var/www/django/primed_apps_dev/
 export DJANGO_SITE_USER=primedweb
 export DJANGO_SETTINGS_MODULE=config.settings.apps_dev
 export DJANGO_WSGI_FILE=config/primed_apps_dev_wsgi.py
+export DJANGO_CRONTAB=primed_apps_dev.cron
 export GAC_ENV=primed_apps_dev
 cd $DJANGO_SITE_DIR
 . venv/bin/activate

primed/dbgap/tests/test_forms.py

@@ -857,7 +857,9 @@ def test_dbgap_dar_data_missing_DAC_abbrev(self):
     def test_dbgap_project_id_does_not_match(self):
         """Form is not valid when the dbgap_project_id does not match."""
         form_data = {
-            "dbgap_dar_data": json.dumps([factories.dbGaPJSONProjectFactory(Project_id=2)]),
+            "dbgap_dar_data": json.dumps(
+                [factories.dbGaPJSONProjectFactory(Project_id=self.dbgap_application.dbgap_project_id + 1)]
+            ),
             "dbgap_application": self.dbgap_application,
         }
         form = self.form_class(data=form_data)

primed/primed_anvil/helpers.py

@@ -130,12 +130,12 @@ def get_summary_table_data():
     return data
 
 
-def get_workspaces_for_phenotype_inventory():
+def get_workspaces_for_inventory():
     """Get input to the primed-phenotype-inventory workflow.
 
     This function generates the input for the "workspaces" field of the primed-phenotype-inventory workflow. Only
     workspaces that have been shared with the consortium are included.
-    See dockstore link: https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_phenotype_inventory:main?tab=info
+    See dockstore link: https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_inventory:main?tab=info
 
     The "workspaces" field has the format:
     {
@@ -212,7 +212,8 @@ def get_workspaces_for_phenotype_inventory():
 
     # Combine all querysets and process into the expected output for the AnVIL workflow.
     workspaces = dbgap_workspaces.union(cdsa_workspaces).union(open_access_workspaces)
-
+    # Sort by workspace_name so that itertools.groupby works as expected.
+    workspaces = sorted(workspaces, key=lambda x: x["workspace_name"])
     json = {}
     for key, group in groupby(workspaces, lambda x: x["workspace_name"]):
         study_names = [x["study_names"] if x["study_names"] else "" for x in group]

primed/primed_anvil/tests/test_views.py

@@ -910,6 +910,19 @@ def test_site_user_table_when_member_group_is_set(self):
         self.assertIsInstance(table, tables.UserAccountSingleGroupMembershipTable)
         self.assertEqual(table.managed_group, member_group)
 
+    def test_site_user_table_does_not_include_inactive_users(self):
+        """Site user table does not include inactive users."""
+        obj = self.model_factory.create()
+        inactive_site_user = UserFactory.create()
+        inactive_site_user.study_sites.set([obj])
+        inactive_site_user.is_active = False
+        inactive_site_user.save()
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(obj.pk))
+        table = response.context_data["tables"][0]
+        self.assertEqual(len(table.rows), 0)
+        self.assertNotIn(inactive_site_user, table.data)
+
     def test_member_group_table(self):
         member_group = ManagedGroupFactory.create()
         obj = self.model_factory.create(member_group=member_group)
@@ -1234,8 +1247,8 @@ def test_includes_cdsa_workspaces(self):
         self.assertEqual(len(response.context_data["summary_table"].rows), 1)
 
 
-class PhenotypeInventoryInputsViewTest(TestCase):
-    """Tests for the PhenotypeInventoryInputsView view."""
+class InventoryInputsViewTest(TestCase):
+    """Tests for the InventoryInputsView view."""
 
     def setUp(self):
         """Set up test class."""
@@ -1249,11 +1262,11 @@ def setUp(self):
 
     def get_url(self, *args):
         """Get the url for the view being tested."""
-        return reverse("primed_anvil:utilities:phenotype_inventory_inputs", args=args)
+        return reverse("primed_anvil:utilities:inventory_inputs", args=args)
 
     def get_view(self):
         """Return the view being tested."""
-        return views.PhenotypeInventoryInputsView.as_view()
+        return views.InventoryInputsView.as_view()
 
     def test_view_redirect_not_logged_in(self):
         "View redirects to login view when user is not logged in."

primed/primed_anvil/urls.py

@@ -40,9 +40,9 @@
 utilities_patterns = (
     [
         path(
-            "phenotype_inventory_inputs/",
-            views.PhenotypeInventoryInputsView.as_view(),
-            name="phenotype_inventory_inputs",
+            "inventory_inputs/",
+            views.InventoryInputsView.as_view(),
+            name="inventory_inputs",
         ),
     ],
     "utilities",

primed/primed_anvil/views.py

@@ -125,7 +125,7 @@ class StudySiteDetail(AnVILConsortiumManagerStaffViewRequired, MultiTableMixin,
     model = models.StudySite
 
     def get_tables(self):
-        user_qs = User.objects.filter(study_sites=self.object)
+        user_qs = User.objects.filter(is_active=True, study_sites=self.object)
         if self.object.member_group:
             user_table = tables.UserAccountSingleGroupMembershipTable(user_qs, managed_group=self.object.member_group)
         else:
@@ -180,10 +180,10 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class PhenotypeInventoryInputsView(AnVILConsortiumManagerStaffViewRequired, TemplateView):
-    template_name = "primed_anvil/phenotype_inventory_inputs.html"
+class InventoryInputsView(AnVILConsortiumManagerStaffViewRequired, TemplateView):
+    template_name = "primed_anvil/inventory_inputs.html"
 
     def get_context_data(self, **kwargs):
         context = super().get_context_data(**kwargs)
-        context["workspaces_input"] = json.dumps(helpers.get_workspaces_for_phenotype_inventory(), indent=2)
+        context["workspaces_input"] = json.dumps(helpers.get_workspaces_for_inventory(), indent=2)
         return context

primed/templates/anvil_consortium_manager/navbar.html

@@ -36,7 +36,7 @@
 
       <li><hr class="dropdown-divider"></li>
       <li>
-        <a class="dropdown-item" href="{% url 'primed_anvil:utilities:phenotype_inventory_inputs' %}">Phenotype inventory</a>
+        <a class="dropdown-item" href="{% url 'primed_anvil:utilities:inventory_inputs' %}">Inventory inputs</a>
       </li>
 
       <li><hr class="dropdown-divider"></li>

primed/templates/base.html

@@ -28,8 +28,8 @@
     {# Placed at the top of the document so pages load faster with defer #}
     {% block javascript %}
       <!-- Bootstrap JS and its dependencies-->
-      <script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
       <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p" crossorigin="anonymous"></script>
+      <script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
       <script src="https://unpkg.com/[email protected]" integrity="sha384-D1Kt99CQMDuVetoL1lrYwg5t+9QdHe7NLX/SoJYkXDFfX37iInKRy5xLSi8nO7UC" crossorigin="anonymous"></script>
 
       <!-- Your stuff: Third-party javascript libraries go here -->
@@ -119,9 +119,10 @@
       {% endif %}
 
       {% if request.user.is_authenticated and not request.user.account %}
-      <div class="alert alert-warning" role="alert">
+      <div class="alert alert-warning alert-dismissible fade show" role="alert">
         <i class="bi bi-exclamation-triangle-fill me-1"></i>
         You must <a href="{% url 'anvil_consortium_manager:accounts:link' %}">link your AnVIL account</a> before you can access any data on AnVIL.
+        <button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>
       </div>
     {% endif %}
 

primed/templates/primed_anvil/phenotype_inventory_inputs.html → primed/templates/primed_anvil/inventory_inputs.html

@@ -11,7 +11,7 @@ <h2>Phenotype inventory workflow</h2>
 
 <p>
   This page creates the input for the "workspaces" field in the
-  <a href="https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_phenotype_inventory:main?tab=info">PRIMED phenotype inventory workflow</a>.
+  <a href="https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_inventory:main?tab=info">PRIMED phenotype inventory workflow</a>.
   Copy the text in the box below and paste it into the "workspaces" field when running the workflow on AnVIL.
 </p>
 

primed/templates/primed_anvil/studysite_detail.html

@@ -60,7 +60,7 @@ <h2 class="accordion-header" id="headingMembersOne">
         <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseMembersOne" aria-expanded="false" aria-controls="collapseMembersOne">
           <span class="fa-solid fa-cloud-arrow-down mx-2"></span>
           View consortium members with data access
-          <span class="badge mx-2 bg-secondary pill"> {{ tables.1.rows|length }}</span>
+          <span class="badge mx-2 bg-secondary pill"> {{ tables.3.rows|length }}</span>
         </button>
       </h2>
       <div id="collapseMembersOne" class="accordion-collapse collapse" aria-labelledby="headingMembersOne" data-bs-parent="#accordionMembers">

primed/templates/users/user_detail.html

@@ -6,6 +6,15 @@
 {% block content %}
 <div class="container">
 
+  {% if not object.is_active %}
+
+    <p class='alert alert-danger mt-3'>
+      <i class="bi bi-exclamation-triangle-fill"></i>
+      This user is inactive.
+    </p>
+
+    {% endif %}
+
   <div class="row row-cols-1 rows-cols-sm-2 row-cols-md-2 g-2 mt-3">
     <div class="col">
       <div class='card card-shadow-sm'>
@@ -57,6 +66,14 @@ <h3><i class="bi bi-link-45deg"></i> {% if object == request.user %}My{% else %}
         <div class='card-body'>
           {% if object.account %}
             <p><i class="bi bi-check-circle-fill text-success"></i> Profile has a linked AnVIL account established</p>
+
+            {% if not object.account.status %}
+              <p class='alert alert-danger mt-3'>
+                <i class="bi bi-exclamation-triangle-fill"></i>
+                This account is inactive.
+              </p>
+              {% endif %}
+
             <ul class='list-group'>
               <li class='list-group-item'>
                 <h5>Account Email</h5>

primed/users/forms.py

@@ -24,7 +24,7 @@ class UserLookupForm(Bootstrap5MediaFormMixin, forms.Form):
     """Form for the user lookup"""
 
     user = forms.ModelChoiceField(
-        queryset=User.objects.all(),
+        queryset=User.objects.filter(is_active=True),
         widget=autocomplete.ModelSelect2(
             url="users:autocomplete",
             attrs={"data-theme": "bootstrap-5"},

primed/users/tests/test_forms.py

@@ -63,3 +63,16 @@ def test_invalid_missing_name(self):
         self.assertIn("user", form.errors)
         self.assertEqual(len(form.errors["user"]), 1)
         self.assertIn("required", form.errors["user"][0])
+
+    def test_inactive_user(self):
+        """Form is invalid when user is inactive."""
+        user_obj = UserFactory.create(is_active=False)
+        form_data = {
+            "user": user_obj,
+        }
+        form = self.form_class(data=form_data)
+        self.assertFalse(form.is_valid())
+        self.assertEqual(len(form.errors), 1)
+        self.assertIn("user", form.errors)
+        self.assertEqual(len(form.errors["user"]), 1)
+        self.assertIn("valid choice", form.errors["user"][0])

primed/users/tests/test_views.py

@@ -574,6 +574,39 @@ def test_acm_staff_view(self):
         self.assertIn(agreement_1.signed_agreement, response.context["signed_agreements"])
         self.assertIn(agreement_2.signed_agreement, response.context["signed_agreements"])
 
+    def test_inactive_user_inactive_message(self):
+        """Inactive user alert is shown for an inactive user."""
+        user = UserFactory.create(is_active=False)
+        self.client.force_login(self.user)
+        response = self.client.get(user.get_absolute_url())
+        self.assertEqual(response.status_code, 200)
+        self.assertContains(response, "This user is inactive.")
+
+    def test_active_user_no_inactive_message(self):
+        """Inactive user alert is not shown for an active user."""
+        self.client.force_login(self.user)
+        response = self.client.get(self.user.get_absolute_url())
+        self.assertEqual(response.status_code, 200)
+        self.assertNotContains(response, "This user is inactive.")
+
+    def test_inactive_anvil_account_alert_is_inactive(self):
+        """Alert is shown when AnVIL account is inactive."""
+        account = AccountFactory.create(email="[email protected]", user=self.user, verified=True)
+        account.status = account.INACTIVE_STATUS
+        account.save()
+        self.client.force_login(self.user)
+        response = self.client.get(self.user.get_absolute_url())
+        self.assertEqual(response.status_code, 200)
+        self.assertContains(response, "This account is inactive.")
+
+    def test_inactive_anvil_account_alert_is_active(self):
+        """Alert is not shown when AnVIL account is active."""
+        AccountFactory.create(email="[email protected]", user=self.user, verified=True)
+        self.client.force_login(self.user)
+        response = self.client.get(self.user.get_absolute_url())
+        self.assertEqual(response.status_code, 200)
+        self.assertNotContains(response, "This account is inactive.")
+
 
 class UserAutocompleteTest(TestCase):
     def setUp(self):
@@ -723,6 +756,17 @@ def test_get_selected_result_label(self):
         view.setup(request)
         self.assertEqual(view.get_selected_result_label(instance), "First Last ([email protected])")
 
+    def test_excludes_inactive_users(self):
+        """Queryset excludes excludes inactive users."""
+        UserFactory.create(is_active=False)
+        request = self.factory.get(self.get_url())
+        request.user = self.user
+        response = self.get_view()(request)
+        returned_ids = [int(x["id"]) for x in json.loads(response.content.decode("utf-8"))["results"]]
+        # Only test user.
+        self.assertEqual(len(returned_ids), 1)
+        self.assertEqual(returned_ids, [self.user.pk])
+
 
 class UserLookup(TestCase):
     """Test for UserLookup view"""
@@ -799,3 +843,21 @@ def test_blank_user(self):
         self.assertIn("user", form.errors.keys())
         self.assertEqual(len(form.errors["user"]), 1)
         self.assertIn("required", form.errors["user"][0])
+
+    def test_invalid_inactive_user(self):
+        """Form is invalid with an inactive user."""
+        object = UserFactory.create(
+            username="user1",
+            password="passwd",
+            email="[email protected]",
+            is_active=False,
+        )
+        self.client.force_login(self.user)
+        response = self.client.post(self.get_url(), {"user": object.pk})
+        self.assertEqual(response.status_code, 200)
+        form = response.context_data["form"]
+        self.assertFalse(form.is_valid())
+        self.assertEqual(len(form.errors), 1)
+        self.assertIn("user", form.errors)
+        self.assertEqual(len(form.errors["user"]), 1)
+        self.assertIn("valid choice", form.errors["user"][0])

primed/users/views.py

@@ -67,7 +67,9 @@ def get_result_label(self, result):
 
     def get_queryset(self):
         """Filter to users matching the query."""
-        qs = User.objects.all().order_by("username")
+        qs = User.objects.filter(
+            is_active=True,
+        ).order_by("username")
 
         if self.q:
             # Filter to users whose name or email matches the query.