Merge branch 'main' into feature/audit-drupal-data

primed/cdsa/adapters.py

@@ -2,7 +2,7 @@
 from anvil_consortium_manager.forms import WorkspaceForm
 from anvil_consortium_manager.models import Workspace
 
-from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceTable
+from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceUserTable
 
 from . import forms, models, tables
 
@@ -27,7 +27,7 @@ def get_extra_detail_context_data(self, workspace, request):
         associated_data_prep = Workspace.objects.filter(
             dataprepworkspace__target_workspace=workspace
         )
-        extra_context["associated_data_prep_workspaces"] = DataPrepWorkspaceTable(
+        extra_context["associated_data_prep_workspaces"] = DataPrepWorkspaceUserTable(
             associated_data_prep
         )
         extra_context["data_prep_active"] = associated_data_prep.filter(

primed/cdsa/tables.py

@@ -299,11 +299,10 @@ def render_date_shared(self, record):
             return "—"
 
 
-class CDSAWorkspaceStaffTable(tables.Table):
+class CDSAWorkspaceUserTable(tables.Table):
     """A table for the CDSAWorkspace model."""
 
     name = tables.Column(linkify=True)
-    billing_project = tables.Column(linkify=True)
     cdsaworkspace__data_use_permission__abbreviation = tables.Column(
         verbose_name="DUO permission",
         linkify=lambda record: record.cdsaworkspace.data_use_permission.get_absolute_url(),
@@ -329,7 +328,6 @@ class Meta:
         model = Workspace
         fields = (
             "name",
-            "billing_project",
             "cdsaworkspace__study",
             "cdsaworkspace__data_use_permission__abbreviation",
             "cdsaworkspace__data_use_modifiers",
@@ -351,27 +349,10 @@ def render_cdsaworkspace__requires_study_review(self, record):
         return mark_safe(f'<i class="bi bi-{icon}" style="color: {color}"></i>')
 
 
-class CDSAWorkspaceUserTable(tables.Table):
+class CDSAWorkspaceStaffTable(CDSAWorkspaceUserTable):
     """A table for the CDSAWorkspace model."""
 
-    name = tables.Column(linkify=True)
-    billing_project = tables.Column()
-    cdsaworkspace__data_use_permission__abbreviation = tables.Column(
-        verbose_name="DUO permission",
-    )
-    cdsaworkspace__study = tables.Column()
-    cdsaworkspace__data_use_modifiers = tables.ManyToManyColumn(
-        transform=lambda x: x.abbreviation,
-        verbose_name="DUO modifiers",
-    )
-    cdsaworkspace__requires_study_review = BooleanIconColumn(
-        verbose_name="Study review required?",
-        orderable=False,
-        true_icon="dash-circle-fill",
-        true_color="#ffc107",
-    )
-    cdsaworkspace__gsr_restricted = BooleanIconColumn(orderable=False)
-    is_shared = WorkspaceSharedWithConsortiumColumn()
+    billing_project = tables.Column(linkify=True)
 
     class Meta:
         model = Workspace
@@ -385,15 +366,3 @@ class Meta:
             "cdsaworkspace__gsr_restricted",
         )
         order_by = ("name",)
-
-    def render_cdsaworkspace__requires_study_review(self, record):
-        try:
-            if record.cdsaworkspace.get_primary_cdsa().requires_study_review:
-                icon = "dash-circle-fill"
-                color = "#ffc107"
-            else:
-                return ""
-        except models.DataAffiliateAgreement.DoesNotExist:
-            icon = "question-circle-fill"
-            color = "red"
-        return mark_safe(f'<i class="bi bi-{icon}" style="color: {color}"></i>')

primed/cdsa/tests/test_views.py

@@ -30,7 +30,7 @@
 from freezegun import freeze_time
 
 from primed.duo.tests.factories import DataUseModifierFactory, DataUsePermissionFactory
-from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceTable
+from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceUserTable
 from primed.miscellaneous_workspaces.tests.factories import DataPrepWorkspaceFactory
 from primed.primed_anvil.tests.factories import (
     AvailableDataFactory,
@@ -7436,14 +7436,37 @@ def test_render_duo_modifiers(self):
         self.assertContains(response, modifiers[0].abbreviation)
         self.assertContains(response, modifiers[1].abbreviation)
 
+    def test_associated_data_prep_view_user(self):
+        """View users do not see the associated data prep section"""
+        user = User.objects.create_user(username="test-view", password="test-view")
+        user.user_permissions.add(
+            Permission.objects.get(
+                codename=AnVILProjectManagerAccess.VIEW_PERMISSION_CODENAME
+            )
+        )
+
+        obj = factories.CDSAWorkspaceFactory.create()
+        DataPrepWorkspaceFactory.create(target_workspace=obj.workspace)
+        self.client.force_login(user)
+        response = self.client.get(obj.get_absolute_url())
+        self.assertNotContains(response, "Associated data prep workspaces")
+
+    def test_associated_data_prep_staff_view_user(self):
+        """Staff view users do see the associated data prep section."""
+        obj = factories.CDSAWorkspaceFactory.create()
+        DataPrepWorkspaceFactory.create(target_workspace=obj.workspace)
+        self.client.force_login(self.user)
+        response = self.client.get(obj.get_absolute_url())
+        self.assertContains(response, "Associated data prep workspaces")
+
     def test_associated_data_prep_workspaces_context_exists(self):
         obj = factories.CDSAWorkspaceFactory.create()
         self.client.force_login(self.user)
         response = self.client.get(obj.get_absolute_url())
         self.assertIn("associated_data_prep_workspaces", response.context_data)
         self.assertIsInstance(
             response.context_data["associated_data_prep_workspaces"],
-            DataPrepWorkspaceTable,
+            DataPrepWorkspaceUserTable,
         )
 
     def test_only_show_one_associated_data_prep_workspace(self):

primed/collaborative_analysis/tables.py

@@ -2,12 +2,10 @@
 from anvil_consortium_manager.models import Workspace
 
 
-class CollaborativeAnalysisWorkspaceStaffTable(tables.Table):
+class CollaborativeAnalysisWorkspaceUserTable(tables.Table):
     """Class to render a table of Workspace objects with CollaborativeAnalysisWorkspace data."""
 
     name = tables.columns.Column(linkify=True)
-    billing_project = tables.Column(linkify=True)
-    collaborativeanalysisworkspace__custodian = tables.Column(linkify=True)
     number_source_workspaces = tables.columns.Column(
         accessor="pk",
         verbose_name="Number of source workspaces",
@@ -18,7 +16,6 @@ class Meta:
         model = Workspace
         fields = (
             "name",
-            "billing_project",
             "collaborativeanalysisworkspace__custodian",
             "number_source_workspaces",
         )
@@ -29,16 +26,12 @@ def render_number_source_workspaces(self, record):
         return record.collaborativeanalysisworkspace.source_workspaces.count()
 
 
-class CollaborativeAnalysisWorkspaceUserTable(tables.Table):
+class CollaborativeAnalysisWorkspaceStaffTable(CollaborativeAnalysisWorkspaceUserTable):
     """Class to render a table of Workspace objects with CollaborativeAnalysisWorkspace data."""
 
     name = tables.columns.Column(linkify=True)
-    billing_project = tables.Column()
-    number_source_workspaces = tables.columns.Column(
-        accessor="pk",
-        verbose_name="Number of source workspaces",
-        orderable=False,
-    )
+    billing_project = tables.Column(linkify=True)
+    collaborativeanalysisworkspace__custodian = tables.Column(linkify=True)
 
     class Meta:
         model = Workspace
@@ -49,7 +42,3 @@ class Meta:
             "number_source_workspaces",
         )
         order_by = ("name",)
-
-    def render_number_source_workspaces(self, record):
-        """Render the number of source workspaces."""
-        return record.collaborativeanalysisworkspace.source_workspaces.count()

primed/dbgap/adapters.py

@@ -2,7 +2,7 @@
 from anvil_consortium_manager.forms import WorkspaceForm
 from anvil_consortium_manager.models import Workspace
 
-from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceTable
+from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceUserTable
 
 from . import forms, models, tables
 
@@ -25,7 +25,7 @@ def get_extra_detail_context_data(self, workspace, request):
         associated_data_prep = Workspace.objects.filter(
             dataprepworkspace__target_workspace=workspace
         )
-        extra_context["associated_data_prep_workspaces"] = DataPrepWorkspaceTable(
+        extra_context["associated_data_prep_workspaces"] = DataPrepWorkspaceUserTable(
             associated_data_prep
         )
         extra_context["data_prep_active"] = associated_data_prep.filter(

primed/dbgap/tables.py

@@ -74,11 +74,10 @@ def render_dbgap_phs(self, value):
         return "phs{0:06d}".format(value)
 
 
-class dbGaPWorkspaceStaffTable(tables.Table):
+class dbGaPWorkspaceUserTable(tables.Table):
     """Class to render a table of Workspace objects with dbGaPWorkspace workspace data."""
 
     name = tables.columns.Column(linkify=True)
-    billing_project = tables.Column(linkify=True)
     dbgap_accession = dbGaPAccessionColumn(
         accessor="dbgapworkspace__get_dbgap_accession",
         dbgap_link_accessor="dbgapworkspace__get_dbgap_link",
@@ -91,11 +90,6 @@ class dbGaPWorkspaceStaffTable(tables.Table):
     dbgapworkspace__dbgap_consent_abbreviation = tables.columns.Column(
         verbose_name="Consent"
     )
-    number_approved_dars = tables.columns.Column(
-        accessor="pk",
-        verbose_name="Approved DARs",
-        orderable=False,
-    )
     dbgapworkspace__gsr_restricted = BooleanIconColumn(
         orderable=False, true_icon="dash-circle-fill", true_color="#ffc107"
     )
@@ -105,43 +99,23 @@ class Meta:
         model = Workspace
         fields = (
             "name",
-            "billing_project",
             "dbgap_accession",
             "dbgapworkspace__dbgap_consent_abbreviation",
-            "number_approved_dars",
             "dbgapworkspace__gsr_restricted",
             "is_shared",
         )
         order_by = ("name",)
 
-    def render_number_approved_dars(self, record):
-        n = (
-            record.dbgapworkspace.get_data_access_requests(most_recent=True)
-            .filter(dbgap_current_status=models.dbGaPDataAccessRequest.APPROVED)
-            .count()
-        )
-        return n
-
 
-class dbGaPWorkspaceUserTable(tables.Table):
+class dbGaPWorkspaceStaffTable(dbGaPWorkspaceUserTable):
     """Class to render a table of Workspace objects with dbGaPWorkspace workspace data."""
 
-    name = tables.columns.Column(linkify=True)
-    billing_project = tables.Column()
-    dbgap_accession = dbGaPAccessionColumn(
-        accessor="dbgapworkspace__get_dbgap_accession",
-        dbgap_link_accessor="dbgapworkspace__get_dbgap_link",
-        order_by=(
-            "dbgapworkspace__dbgap_study_accession__dbgap_phs",
-            "dbgapworkspace__dbgap_version",
-            "dbgapworkspace__dbgap_participant_set",
-        ),
-    )
-    dbgapworkspace__dbgap_consent_abbreviation = tables.columns.Column(
-        verbose_name="Consent"
+    billing_project = tables.Column(linkify=True)
+    number_approved_dars = tables.columns.Column(
+        accessor="pk",
+        verbose_name="Approved DARs",
+        orderable=False,
     )
-    dbgapworkspace__gsr_restricted = BooleanIconColumn(orderable=False)
-    is_shared = WorkspaceSharedWithConsortiumColumn()
 
     class Meta:
         model = Workspace
@@ -150,11 +124,20 @@ class Meta:
             "billing_project",
             "dbgap_accession",
             "dbgapworkspace__dbgap_consent_abbreviation",
+            "number_approved_dars",
             "dbgapworkspace__gsr_restricted",
             "is_shared",
         )
         order_by = ("name",)
 
+    def render_number_approved_dars(self, record):
+        n = (
+            record.dbgapworkspace.get_data_access_requests(most_recent=True)
+            .filter(dbgap_current_status=models.dbGaPDataAccessRequest.APPROVED)
+            .count()
+        )
+        return n
+
 
 class dbGaPApplicationTable(tables.Table):
     """Class to render a table of dbGaPApplication objects."""

primed/dbgap/tests/test_views.py

@@ -32,7 +32,7 @@
 from freezegun import freeze_time
 
 from primed.duo.tests.factories import DataUseModifierFactory, DataUsePermissionFactory
-from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceTable
+from primed.miscellaneous_workspaces.tables import DataPrepWorkspaceUserTable
 from primed.miscellaneous_workspaces.tests.factories import DataPrepWorkspaceFactory
 from primed.primed_anvil.tests.factories import (  # DataUseModifierFactory,; DataUsePermissionFactory,
     StudyFactory,
@@ -953,14 +953,37 @@ def test_links_audit_access_view_permission(self):
             ),
         )
 
+    def test_associated_data_prep_view_user(self):
+        """View users do not see the associated data prep section"""
+        user = User.objects.create_user(username="test-view", password="test-view")
+        user.user_permissions.add(
+            Permission.objects.get(
+                codename=AnVILProjectManagerAccess.VIEW_PERMISSION_CODENAME
+            )
+        )
+
+        obj = factories.dbGaPWorkspaceFactory.create()
+        DataPrepWorkspaceFactory.create(target_workspace=obj.workspace)
+        self.client.force_login(user)
+        response = self.client.get(obj.get_absolute_url())
+        self.assertNotContains(response, "Associated data prep workspaces")
+
+    def test_associated_data_prep_staff_view_user(self):
+        """Staff view users do see the associated data prep section."""
+        obj = factories.dbGaPWorkspaceFactory.create()
+        DataPrepWorkspaceFactory.create(target_workspace=obj.workspace)
+        self.client.force_login(self.user)
+        response = self.client.get(obj.get_absolute_url())
+        self.assertContains(response, "Associated data prep workspaces")
+
     def test_associated_data_prep_workspaces_context_exists(self):
         obj = factories.dbGaPWorkspaceFactory.create()
         self.client.force_login(self.user)
         response = self.client.get(obj.get_absolute_url())
         self.assertIn("associated_data_prep_workspaces", response.context_data)
         self.assertIsInstance(
             response.context_data["associated_data_prep_workspaces"],
-            DataPrepWorkspaceTable,
+            DataPrepWorkspaceUserTable,
         )
 
     def test_only_show_one_associated_data_prep_workspace(self):

primed/duo/tests/test_views.py

@@ -23,7 +23,7 @@ def setUp(self):
         self.user = UserFactory.create(username="test", password="test")
         self.user.user_permissions.add(
             Permission.objects.get(
-                codename=AnVILProjectManagerAccess.STAFF_VIEW_PERMISSION_CODENAME
+                codename=AnVILProjectManagerAccess.VIEW_PERMISSION_CODENAME
             )
         )
 
@@ -180,7 +180,7 @@ def setUp(self):
         self.user = UserFactory.create(username="test", password="test")
         self.user.user_permissions.add(
             Permission.objects.get(
-                codename=AnVILProjectManagerAccess.STAFF_VIEW_PERMISSION_CODENAME
+                codename=AnVILProjectManagerAccess.VIEW_PERMISSION_CODENAME
             )
         )
 

primed/duo/views.py

@@ -1,14 +1,11 @@
-from anvil_consortium_manager.auth import (
-    AnVILConsortiumManagerStaffViewRequired,
-    AnVILConsortiumManagerViewRequired,
-)
+from anvil_consortium_manager.auth import AnVILConsortiumManagerViewRequired
 from django.http import Http404
 from django.views.generic import DetailView, ListView
 
 from . import models
 
 
-class DataUsePermissionList(AnVILConsortiumManagerStaffViewRequired, ListView):
+class DataUsePermissionList(AnVILConsortiumManagerViewRequired, ListView):
 
     model = models.DataUsePermission
 
@@ -41,7 +38,7 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class DataUseModifierList(AnVILConsortiumManagerStaffViewRequired, ListView):
+class DataUseModifierList(AnVILConsortiumManagerViewRequired, ListView):
 
     model = models.DataUseModifier
 

primed/miscellaneous_workspaces/adapters.py

@@ -93,8 +93,8 @@ class DataPrepWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "data_prep"
     name = "Data prep workspace"
     description = "Workspaces used to prepare data for sharing or update data that is already shared"
-    list_table_class_staff_view = tables.DataPrepWorkspaceTable
-    list_table_class_view = tables.DataPrepWorkspaceTable
+    list_table_class_staff_view = tables.DataPrepWorkspaceStaffTable
+    list_table_class_view = tables.DataPrepWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.DataPrepWorkspace
     workspace_data_form_class = forms.DataPrepWorkspaceForm