dbGaP application views for PIs

primed/collaborative_analysis/audit.py

@@ -8,6 +8,7 @@
     GroupGroupMembership,
     ManagedGroup,
 )
+from django.conf import settings
 from django.urls import reverse
 
 from primed.primed_anvil.audit import PRIMEDAudit, PRIMEDAuditResult
@@ -176,7 +177,7 @@ def _audit_workspace(self, workspace):
             )
             .exclude(
                 # Ignore cc admins group - it is handled differently because it should have admin privileges.
-                child_group__name="PRIMED_CC_ADMINS",
+                child_group__name=settings.ANVIL_CC_ADMINS_GROUP_NAME,
             )
             .exclude(
                 # Ignore allowed groups - they will be checked separately later.

primed/collaborative_analysis/management/commands/run_collaborative_analysis_audit.py

@@ -25,7 +25,7 @@ def handle(self, *args, **options):
         # Report errors and needs access.
         audit_ok = data_access_audit.ok()
         # Construct the url for handling errors.
-        url = "https://" + Site.objects.get_current().domain + reverse("dbgap:audit:all")
+        url = "https://" + Site.objects.get_current().domain + reverse("collaborative_analysis:audit:all")
         if audit_ok:
             self.stdout.write(self.style.SUCCESS("ok!"))
         else:

primed/collaborative_analysis/tests/test_audit.py

@@ -6,7 +6,7 @@
     WorkspaceAuthorizationDomainFactory,
     WorkspaceFactory,
 )
-from django.test import TestCase
+from django.test import TestCase, override_settings
 from django.urls import reverse
 
 from primed.cdsa.tests.factories import CDSAWorkspaceFactory
@@ -845,7 +845,22 @@ def test_unexpected_group_in_auth_domain(self):
     def test_ignores_primed_admins_group(self):
         workspace = factories.CollaborativeAnalysisWorkspaceFactory.create()
         # Add a group to the auth domain.
-        group = ManagedGroupFactory.create(name="PRIMED_CC_ADMINS")
+        group = ManagedGroupFactory.create(name="TEST_PRIMED_CC_ADMINS")
+        GroupGroupMembershipFactory.create(
+            parent_group=workspace.workspace.authorization_domains.first(),
+            child_group=group,
+        )
+        collab_audit = audit.CollaborativeAnalysisWorkspaceAccessAudit()
+        collab_audit._audit_workspace(workspace)
+        self.assertEqual(len(collab_audit.verified), 0)
+        self.assertEqual(len(collab_audit.needs_action), 0)
+        self.assertEqual(len(collab_audit.errors), 0)
+
+    @override_settings(ANVIL_CC_ADMINS_GROUP_NAME="FOOBAR")
+    def test_ignores_primed_admins_group_different_setting(self):
+        workspace = factories.CollaborativeAnalysisWorkspaceFactory.create()
+        # Add a group to the auth domain.
+        group = ManagedGroupFactory.create(name="FOOBAR")
         GroupGroupMembershipFactory.create(
             parent_group=workspace.workspace.authorization_domains.first(),
             child_group=group,

primed/collaborative_analysis/tests/test_commands.py

@@ -1,4 +1,4 @@
-"""Tests for management commands in the `dbgap` app."""
+"""Tests for management commands in the `collaborative_analysis` app."""
 
 from io import StringIO
 

primed/dbgap/audit.py → primed/dbgap/audit/access_audit.py

@@ -7,7 +7,7 @@
 from primed.primed_anvil.audit import PRIMEDAudit, PRIMEDAuditResult
 from primed.primed_anvil.tables import BooleanIconColumn
 
-from .models import (
+from ..models import (
     dbGaPApplication,
     dbGaPDataAccessRequest,
     dbGaPDataAccessSnapshot,
@@ -17,7 +17,7 @@
 
 # Dataclasses for storing audit results?
 @dataclass
-class AuditResult(PRIMEDAuditResult):
+class AccessAuditResult(PRIMEDAuditResult):
     """Base class to hold results for auditing dbGaP workspace access for a dbGaPDataAccessSnapshot."""
 
     workspace: dbGaPWorkspace
@@ -36,7 +36,7 @@ def __post_init__(self):
     def get_action_url(self):
         """The URL that handles the action needed."""
         return reverse(
-            "dbgap:audit:resolve",
+            "dbgap:audit:access:resolve",
             args=[
                 self.dbgap_application.dbgap_project_id,
                 self.workspace.workspace.billing_project.name,
@@ -67,7 +67,7 @@ def get_table_dictionary(self):
 
 
 @dataclass
-class VerifiedAccess(AuditResult):
+class VerifiedAccess(AccessAuditResult):
     """Audit results class for when access has been verified."""
 
     has_access: bool = True
@@ -77,7 +77,7 @@ def __str__(self):
 
 
 @dataclass
-class VerifiedNoAccess(AuditResult):
+class VerifiedNoAccess(AccessAuditResult):
     """Audit results class for when no access has been verified."""
 
     has_access: bool = False
@@ -87,7 +87,7 @@ def __str__(self):
 
 
 @dataclass
-class GrantAccess(AuditResult):
+class GrantAccess(AccessAuditResult):
     """Audit results class for when access should be granted."""
 
     has_access: bool = False
@@ -98,7 +98,7 @@ def __str__(self):
 
 
 @dataclass
-class RemoveAccess(AuditResult):
+class RemoveAccess(AccessAuditResult):
     """Audit results class for when access should be removed for a known reason."""
 
     has_access: bool = True
@@ -109,7 +109,7 @@ def __str__(self):
 
 
 @dataclass
-class Error(AuditResult):
+class Error(AccessAuditResult):
     """Audit results class for when an error has been detected (e.g., has access and never should have)."""
 
     pass
@@ -125,7 +125,7 @@ class dbGaPAccessAuditTable(tables.Table):
     dar_consent = tables.Column(verbose_name="DAR consent")
     has_access = BooleanIconColumn(show_false_icon=True)
     note = tables.Column()
-    action = tables.TemplateColumn(template_name="dbgap/snippets/dbgap_audit_action_button.html")
+    action = tables.TemplateColumn(template_name="dbgap/snippets/dbgap_access_audit_action_button.html")
 
     class Meta:
         attrs = {"class": "table align-middle"}