Merge pull request #634 from UW-GAC/main

Deploy to stage

.github/workflows/ci.yml

@@ -28,11 +28,11 @@ jobs:
         backend: ["sqlite", "mariadb"]
         mariadb-version: ["10.4"]
         include:
-          - python-version: 3.12  # Possible future version.
+          - python-version: "3.10"  # Future ubuntu 22.04 upgrade.
             backend: "mariadb"
-            mariadb-version: "10.5"
+            mariadb-version: "10.6"
             pip-recompile: true
-          - python-version: 3.12  # Possible future version.
+          - python-version: 3.12  # Future ubuntu 24.04.01 upgrade.
             backend: "mariadb"
             mariadb-version: "10.11"
             pip-recompile: true

add_cdsa_example_data.py

@@ -37,11 +37,28 @@
 dum = DataUseModifier.objects.get(abbreviation="NPU")
 
 # Create some study sites.
-StudySiteFactory.create(short_name="CC", full_name="Coordinating Center")
-StudySiteFactory.create(short_name="CARDINAL", full_name="CARDINAL")
+try:
+    cc = StudySite.objects.get(short_name="CC")
+except StudySite.DoesNotExist:
+    cc = StudySiteFactory.create(short_name="CC", full_name="Coordinating Center")
+try:
+    cardinal = StudySite.objects.get(short_name="CARDINAL")
+except StudySite.DoesNotExist:
+    cardinal = StudySiteFactory.create(short_name="CARDINAL", full_name="CARDINAL")
+
 # Create some studies.
-StudyFactory.create(short_name="Amish", full_name="Amish")
-StudyFactory.create(short_name="MESA", full_name="MESA")
+try:
+    amish = Study.objects.get(short_name="Amish")
+except Study.DoesNotExist:
+    amish = StudyFactory.create(short_name="Amish", full_name="Amish")
+try:
+    mesa = Study.objects.get(short_name="MESA")
+except Study.DoesNotExist:
+    mesa = StudyFactory.create(short_name="MESA", full_name="MESA")
+try:
+    aric = Study.objects.get(short_name="ARIC")
+except Study.DoesNotExist:
+    aric = Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities")
 
 # Create some CDSAs
 cdsa_1001 = factories.MemberAgreementFactory.create(
@@ -51,7 +68,7 @@
     signed_agreement__representative_role="Contact PI",
     is_primary=True,
     signed_agreement__version=v10,
-    study_site=StudySite.objects.get(short_name="CC"),
+    study_site=cc,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group)
 
@@ -62,7 +79,7 @@
     signed_agreement__representative_role="Contact PI",
     is_primary=True,
     signed_agreement__version=v10,
-    study_site=StudySite.objects.get(short_name="CARDINAL"),
+    study_site=cardinal,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group)
 
@@ -73,7 +90,7 @@
     signed_agreement__representative_role="Co-PI",
     is_primary=False,
     signed_agreement__version=v10,
-    study_site=StudySite.objects.get(short_name="CARDINAL"),
+    study_site=cardinal,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group)
 
@@ -84,7 +101,7 @@
     signed_agreement__representative_role="Co-I",
     is_primary=False,
     signed_agreement__version=v11,
-    study_site=StudySite.objects.get(short_name="CARDINAL"),
+    study_site=cardinal,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group)
 
@@ -93,7 +110,7 @@
     signed_agreement__representative=User.objects.get(name="Brackie Mitchell"),
     signed_agreement__signing_institution="UMaryland",
     signed_agreement__representative_role="Study PI",
-    study=Study.objects.get(short_name="Amish"),
+    study=amish,
     signed_agreement__version=v10,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group)
@@ -103,7 +120,7 @@
     signed_agreement__representative=UserFactory.create(name="Robyn"),
     signed_agreement__representative_role="DCC PI",
     signed_agreement__signing_institution="UW",
-    study=Study.objects.get(short_name="MESA"),
+    study=mesa,
     signed_agreement__version=v10,
     additional_limitations="This data can only be used for testing the app.",
     requires_study_review=True,
@@ -116,7 +133,7 @@
     signed_agreement__signing_institution="JHU",
     signed_agreement__representative_role="Field Center PI",
     is_primary=False,
-    study=Study.objects.get(short_name="MESA"),
+    study=mesa,
     signed_agreement__version=v10,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group)
@@ -127,7 +144,7 @@
     signed_agreement__signing_institution="Lundquist",
     signed_agreement__representative_role="Analysis Center PI",
     is_primary=False,
-    study=Study.objects.get(short_name="MESA"),
+    study=mesa,
     signed_agreement__version=v10,
 )
 GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group)
@@ -209,7 +226,7 @@
 cdsa_workspace_1 = factories.CDSAWorkspaceFactory.create(
     workspace__billing_project__name="demo-primed-cdsa",
     workspace__name="DEMO_PRIMED_CDSA_MESA_1",
-    study=Study.objects.get(short_name="MESA"),
+    study=mesa,
     data_use_permission=dup,
 )
 GroupGroupMembershipFactory.create(
@@ -222,7 +239,7 @@
 cdsa_workspace_2 = factories.CDSAWorkspaceFactory.create(
     workspace__billing_project__name="demo-primed-cdsa",
     workspace__name="DEMO_PRIMED_CDSA_MESA_2",
-    study=Study.objects.get(short_name="MESA"),
+    study=mesa,
     data_use_permission=dup,
     additional_limitations="Additional limitations for workspace.",
 )
@@ -233,6 +250,6 @@
 cdsa_workspace_3 = factories.CDSAWorkspaceFactory.create(
     workspace__billing_project__name="demo-primed-cdsa",
     workspace__name="DEMO_PRIMED_CDSA_ARIC_1",
-    study=Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities"),
+    study=aric,
     data_use_permission=dup,
 )

add_dbgap_example_data.py

@@ -1,17 +1,30 @@
 # Temporary script to create some test data.
 # Run with: python manage.py shell < add_cdsa_example_data.py
 
-from anvil_consortium_manager.tests.factories import GroupGroupMembershipFactory
+from anvil_consortium_manager.tests.factories import (
+    AccountFactory,
+    GroupAccountMembershipFactory,
+    GroupGroupMembershipFactory,
+)
 
 from primed.dbgap import models
 from primed.dbgap.tests import factories
 from primed.primed_anvil.tests.factories import StudyFactory
 from primed.users.tests.factories import UserFactory
 
 # Studies
-fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
-mesa = StudyFactory.create(short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis")
-aric = StudyFactory.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities")
+try:
+    fhs = models.Study.objects.get(short_name="FHS")
+except models.Study.DoesNotExist:
+    fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
+try:
+    mesa = models.Study.objects.get(short_name="MESA")
+except models.Study.DoesNotExist:
+    mesa = StudyFactory.create(short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis")
+try:
+    aric = models.Study.objects.get(short_name="ARIC")
+except models.Study.DoesNotExist:
+    aric = StudyFactory.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities")
 
 # dbGaP study accessions
 dbgap_study_accession_fhs = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=7, studies=[fhs])
@@ -124,3 +137,24 @@
     parent_group=workspace_fhs_1.workspace.authorization_domains.first(),
     child_group=dbgap_application_1.anvil_access_group,
 )
+
+# Add the PI to the access group for the first application.
+GroupAccountMembershipFactory.create(
+    group=dbgap_application_1.anvil_access_group,
+    account__user=dbgap_application_1.principal_investigator,
+)
+# Add some collaborators for the first application.
+users = UserFactory.create_batch(3)
+dbgap_application_1.collaborators.add(users[0])
+GroupAccountMembershipFactory.create(
+    group=dbgap_application_1.anvil_access_group,
+    account__user=users[0],
+)
+# # Do not add as an collaborator so we can check auditing.
+# dbgap_application_1.collaborators.add(users[1])
+GroupAccountMembershipFactory.create(
+    group=dbgap_application_1.anvil_access_group,
+    account__user=users[1],
+)
+dbgap_application_1.collaborators.add(users[2])
+AccountFactory.create(user=users[2], verified=True)

primed/cdsa/tests/test_views.py

@@ -2879,7 +2879,7 @@ def test_response_is_primary(self):
         self.assertContains(response, "Primary?")
         self.assertContains(
             response,
-            """<dt class="col-sm-2">Primary?</dt><dd class="col-sm-9">Yes <i class="bi bi-check-circle-fill px-2" style="color: green;"></i></dd>""",  # noqa: E501
+            """<dt class="col-sm-3">Primary?</dt><dd class="col-sm-9">Yes <i class="bi bi-check-circle-fill px-2" style="color: green;"></i></dd>""",  # noqa: E501
             html=True,
         )
         instance.is_primary = False
@@ -2888,7 +2888,7 @@ def test_response_is_primary(self):
         self.assertContains(response, "Primary?")
         self.assertContains(
             response,
-            """<dt class="col-sm-2">Primary?</dt><dd class="col-sm-9">No <i class="bi bi-x-circle-fill px-2" style="color: red;"></i></dd>""",  # noqa: E501
+            """<dt class="col-sm-3">Primary?</dt><dd class="col-sm-9">No <i class="bi bi-x-circle-fill px-2" style="color: red;"></i></dd>""",  # noqa: E501
             html=True,
         )
 
@@ -4698,7 +4698,7 @@ def test_response_is_primary(self):
         self.assertContains(response, "Primary?")
         self.assertContains(
             response,
-            """<dt class="col-sm-2">Primary?</dt><dd class="col-sm-9">Yes <i class="bi bi-check-circle-fill px-2" style="color: green;"></i></dd>""",  # noqa: E501
+            """<dt class="col-sm-3">Primary?</dt><dd class="col-sm-9">Yes <i class="bi bi-check-circle-fill px-2" style="color: green;"></i></dd>""",  # noqa: E501
             html=True,
         )
         instance.is_primary = False
@@ -4707,7 +4707,7 @@ def test_response_is_primary(self):
         self.assertContains(response, "Primary?")
         self.assertContains(
             response,
-            """<dt class="col-sm-2">Primary?</dt><dd class="col-sm-9">No <i class="bi bi-x-circle-fill px-2" style="color: red;"></i></dd>""",  # noqa: E501
+            """<dt class="col-sm-3">Primary?</dt><dd class="col-sm-9">No <i class="bi bi-x-circle-fill px-2" style="color: red;"></i></dd>""",  # noqa: E501
             html=True,
         )
 
@@ -4720,7 +4720,7 @@ def test_response_requires_study_review(self):
         # import ipdb; ipdb.set_trace()
         self.assertContains(
             response,
-            """<dt class="col-sm-2">Study review required?</dt> <dd class="col-sm-9">Yes <i class="bi bi-check-circle-fill px-2" style="color: green;"></i></dd>""",  # noqa: E501
+            """<dt class="col-sm-3">Study review required?</dt> <dd class="col-sm-9">Yes <i class="bi bi-check-circle-fill px-2" style="color: green;"></i></dd>""",  # noqa: E501
             html=True,
         )
         instance.requires_study_review = False
@@ -4729,7 +4729,7 @@ def test_response_requires_study_review(self):
         self.assertContains(response, "Study review required?")
         self.assertContains(
             response,
-            """<dt class="col-sm-2">Study review required?</dt> <dd class="col-sm-9">No <i class="bi bi-x-circle-fill px-2" style="color: red;"></i></dd>""",  # noqa: E501
+            """<dt class="col-sm-3">Study review required?</dt> <dd class="col-sm-9">No <i class="bi bi-x-circle-fill px-2" style="color: red;"></i></dd>""",  # noqa: E501
             html=True,
         )
 

primed/dbgap/tests/test_views.py

@@ -1452,6 +1452,7 @@ def test_staff_edit_links(self):
         self.assertContains(
             response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name])
         )
+        self.assertContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id]))
 
     def test_staff_view_links(self):
         """No edit links if staff user only has view permission."""
@@ -1475,6 +1476,7 @@ def test_staff_view_links(self):
         self.assertContains(
             response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name])
         )
+        self.assertNotContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id]))
 
     def test_links_pi(self):
         """Links seen by PI are correct."""
@@ -1500,6 +1502,7 @@ def test_links_pi(self):
         self.assertNotContains(
             response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name])
         )
+        self.assertNotContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id]))
 
     def test_links_collaborators(self):
         """Links seen by collaborators are correct."""
@@ -1526,6 +1529,7 @@ def test_links_collaborators(self):
         self.assertNotContains(
             response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name])
         )
+        self.assertNotContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id]))
 
     def test_table_classes(self):
         """The table classes are correct."""

primed/dbgap/views.py

@@ -246,7 +246,8 @@ class dbGaPApplicationUpdate(AnVILConsortiumManagerStaffEditRequired, SuccessMes
 
     model = models.dbGaPApplication
     form_class = forms.dbGaPApplicationUpdateForm
-    success_message = "dbGaP application successfully updated."
+    success_message = "dbGaP collaborators successfully updated."
+    template_name = "dbgap/dbgapapplication_update_collaborators.html"
 
     def get_object(self, queryset=None):
         queryset = self.get_queryset()

primed/primed_anvil/filters.py

@@ -2,9 +2,18 @@
 from anvil_consortium_manager.models import Account
 from django_filters import FilterSet
 
+from .models import Study
+
 
 class AccountListFilter(FilterSet):
     class Meta:
         model = Account
         fields = {"email": ["icontains"], "user__name": ["icontains"]}
         form = FilterForm
+
+
+class StudyListFilter(FilterSet):
+    class Meta:
+        model = Study
+        fields = {"short_name": ["icontains"], "full_name": ["icontains"]}
+        form = FilterForm

primed/primed_anvil/tests/test_views.py

@@ -37,7 +37,7 @@
 from primed.primed_anvil.tests.factories import AvailableDataFactory, StudyFactory
 from primed.users.tests.factories import UserFactory
 
-from .. import models, tables, views
+from .. import filters, models, tables, views
 from . import factories
 
 # from .utils import AnVILAPIMockTestMixin
@@ -724,6 +724,66 @@ def test_view_with_two_objects(self):
         self.assertIn("table", response.context_data)
         self.assertEqual(len(response.context_data["table"].rows), 2)
 
+    def test_filterset_class(self):
+        self.model_factory.create()
+        request = self.factory.get(self.get_url())
+        request.user = self.user
+        response = self.get_view()(request)
+        self.assertIn("filter", response.context_data)
+        self.assertIsInstance(response.context_data["filter"], filters.StudyListFilter)
+
+    def test_view_with_filter_return_no_object(self):
+        self.model_factory.create(short_name="TEST", full_name="Test study")
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(), {"short_name__icontains": "abc"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 0)
+        response = self.client.get(self.get_url(), {"full_name__icontains": "abc"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 0)
+
+    def test_view_with_filter_returns_one_object_exact(self):
+        self.model_factory.create(short_name="TEST", full_name="Test Study")
+        self.model_factory.create(short_name="ABC", full_name="ABC Study")
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(), {"short_name__icontains": "TEST"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+        response = self.client.get(self.get_url(), {"full_name__icontains": "Test Study"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+
+    def test_view_with_filter_returns_one_object_case_insensitive(self):
+        self.model_factory.create(short_name="TEST", full_name="TEST Study")
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(), {"short_name__icontains": "test"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+        response = self.client.get(self.get_url(), {"full_name__icontains": "test study"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+
+    def test_view_with_filter_returns_one_object_contains(self):
+        self.model_factory.create(short_name="TEST", full_name="TEST Study")
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(), {"short_name__icontains": "TES"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+        response = self.client.get(self.get_url(), {"full_name__icontains": "TES"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 1)
+
+    def test_view_with_filter_returns_all_objects(self):
+        self.model_factory.create(short_name="Test 1", full_name="Test 1 Study")
+        self.model_factory.create(short_name="Test 2", full_name="Test 2 Study")
+        self.client.force_login(self.user)
+        response = self.client.get(self.get_url(), {"short_name__icontains": "Test"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 2)
+        response = self.client.get(self.get_url(), {"full_name__icontains": "Test"})
+        self.assertIn("table", response.context_data)
+        self.assertEqual(len(response.context_data["table"].rows), 2)
+
 
 class StudySiteDetailTest(TestCase):
     """Tests for the StudySiteDetail view."""