Merge dependabot/pip/mypy-1.10.1 into combined-prs-branch

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.9
+    rev: v0.4.10
     hooks:
       # Run the linter.
       - id: ruff

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)
@@ -147,52 +164,69 @@
 
 
 # Add some users to the CDSA groups.
-accounts = AccountFactory.create_batch(10, verified=True)
-GroupAccountMembershipFactory.create(
-    group=cdsa_1001.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
-)
+users = UserFactory.create_batch(12)
+cdsa_1001.signed_agreement.accessors.add(users[0])
 GroupAccountMembershipFactory.create(
     group=cdsa_1001.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[0],
 )
+# # Do not add as an accessor so we can check auditing.
+# cdsa_1001.signed_agreement.accessors.add(users[1])
 GroupAccountMembershipFactory.create(
     group=cdsa_1001.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
-)
+    account__user=users[1],
+)
+cdsa_1001.signed_agreement.accessors.add(users[2])
+AccountFactory.create(user=users[2])
+# # Do not create the GroupAccountMembership so we can check auditing.
+# GroupAccountMembershipFactory.create(
+#     group=cdsa_1001.signed_agreement.anvil_access_group,
+#     account__user=users[2],
+# )
+cdsa_1002.signed_agreement.accessors.add(users[3])
 GroupAccountMembershipFactory.create(
     group=cdsa_1002.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[3],
 )
+cdsa_1002.signed_agreement.accessors.add(users[4])
 GroupAccountMembershipFactory.create(
     group=cdsa_1002.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[4],
 )
+cdsa_1003.signed_agreement.accessors.add(users[5])
 GroupAccountMembershipFactory.create(
     group=cdsa_1003.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[5],
 )
+cdsa_1005.signed_agreement.accessors.add(users[6])
 GroupAccountMembershipFactory.create(
     group=cdsa_1005.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[6],
 )
+cdsa_1005.signed_agreement.accessors.add(users[7])
 GroupAccountMembershipFactory.create(
     group=cdsa_1005.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[7],
 )
+cdsa_1006.signed_agreement.accessors.add(users[8])
 GroupAccountMembershipFactory.create(
     group=cdsa_1006.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[8],
 )
+cdsa_1006.signed_agreement.accessors.add(users[9])
 GroupAccountMembershipFactory.create(
     group=cdsa_1006.signed_agreement.anvil_access_group,
-    account__user=UserFactory.create(),
+    account__user=users[9],
 )
+# Add uploaders.
+cdsa_1006.uploaders.add(users[10])
+AccountFactory.create(user=users[10])
+cdsa_1006.uploaders.add(users[11])
 
 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(
@@ -205,7 +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.",
 )
@@ -216,6 +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)