Update to ACM v0.21 and open more views to logged in users

config/settings/base.py

@@ -370,14 +370,14 @@
 ANVIL_API_SERVICE_ACCOUNT_FILE = env("ANVIL_API_SERVICE_ACCOUNT_FILE")
 # Specify workspace adapters.
 ANVIL_WORKSPACE_ADAPTERS = [
-    "primed.miscellaneous_workspaces.adapters.TemplateWorkspaceAdapter",
     "primed.dbgap.adapters.dbGaPWorkspaceAdapter",
     "primed.cdsa.adapters.CDSAWorkspaceAdapter",
+    "primed.miscellaneous_workspaces.adapters.OpenAccessWorkspaceAdapter",
+    "primed.miscellaneous_workspaces.adapters.SimulatedDataWorkspaceAdapter",
+    "primed.miscellaneous_workspaces.adapters.ResourceWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.ConsortiumDevelWorkspaceAdapter",
+    "primed.miscellaneous_workspaces.adapters.TemplateWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.DataPrepWorkspaceAdapter",
-    "primed.miscellaneous_workspaces.adapters.ResourceWorkspaceAdapter",
-    "primed.miscellaneous_workspaces.adapters.SimulatedDataWorkspaceAdapter",
-    "primed.miscellaneous_workspaces.adapters.OpenAccessWorkspaceAdapter",
 ]
 ANVIL_ACCOUNT_ADAPTER = "primed.primed_anvil.adapters.AccountAdapter"
 

primed/cdsa/adapters.py

@@ -10,9 +10,10 @@ class CDSAWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "cdsa"
     name = "CDSA workspace"
     description = (
-        "Workspaces containing data from the Consortium Data Sharing Agreement."
+        "Workspaces containing data from the Consortium Data Sharing Agreement"
     )
-    list_table_class = tables.CDSAWorkspaceTable
+    list_table_class_staff_view = tables.CDSAWorkspaceStaffTable
+    list_table_class_view = tables.CDSAWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.CDSAWorkspace
     workspace_data_form_class = forms.CDSAWorkspaceForm

primed/cdsa/tables.py

@@ -295,7 +295,7 @@ def render_date_shared(self, record):
             return "—"
 
 
-class CDSAWorkspaceTable(tables.Table):
+class CDSAWorkspaceStaffTable(tables.Table):
     """A table for the CDSAWorkspace model."""
 
     name = tables.Column(linkify=True)
@@ -324,10 +324,10 @@ class Meta:
         order_by = ("name",)
 
 
-class CDSAWorkspaceLimitedViewTable(tables.Table):
+class CDSAWorkspaceUserTable(tables.Table):
     """A table for the CDSAWorkspace model."""
 
-    name = tables.Column()
+    name = tables.Column(linkify=True)
     billing_project = tables.Column()
     cdsaworkspace__data_use_permission__abbreviation = tables.Column(
         verbose_name="DUO permission",

primed/cdsa/tests/test_tables.py

@@ -447,12 +447,12 @@ def test_ordering(self):
         self.assertEqual(table.data[1], instance_1)
 
 
-class CDSAWorkspaceTableTest(TestCase):
-    """Tests for the CDSAWorkspaceTable class."""
+class CDSAWorkspaceStaffTableTest(TestCase):
+    """Tests for the CDSAWorkspaceStaffTable class."""
 
     model = Workspace
     model_factory = factories.CDSAWorkspaceFactory
-    table_class = tables.CDSAWorkspaceTable
+    table_class = tables.CDSAWorkspaceStaffTable
 
     def test_row_count_with_no_objects(self):
         table = self.table_class(self.model.objects.all())
@@ -477,12 +477,12 @@ def test_ordering(self):
         self.assertEqual(table.data[1], instance_1.workspace)
 
 
-class CDSAWorkspaceLimitedViewTableTest(TestCase):
-    """Tests for the CDSAWorkspaceLimitedViewTable class."""
+class CDSAWorkspaceUserTableTest(TestCase):
+    """Tests for the CDSAWorkspaceUserTable class."""
 
     model = Workspace
     model_factory = factories.CDSAWorkspaceFactory
-    table_class = tables.CDSAWorkspaceLimitedViewTable
+    table_class = tables.CDSAWorkspaceUserTable
 
     def test_row_count_with_no_objects(self):
         table = self.table_class(self.model.objects.all())

primed/dbgap/adapters.py

@@ -10,7 +10,8 @@ class dbGaPWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "dbgap"
     name = "dbGaP workspace"
     description = "Workspaces containing data from released dbGaP accessions"
-    list_table_class = tables.dbGaPWorkspaceTable
+    list_table_class_staff_view = tables.dbGaPWorkspaceStaffTable
+    list_table_class_view = tables.dbGaPWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.dbGaPWorkspace
     workspace_data_form_class = forms.dbGaPWorkspaceForm

primed/dbgap/tables.py

@@ -71,7 +71,7 @@ def render_dbgap_phs(self, value):
         return "phs{0:06d}".format(value)
 
 
-class dbGaPWorkspaceTable(tables.Table):
+class dbGaPWorkspaceStaffTable(tables.Table):
     """Class to render a table of Workspace objects with dbGaPWorkspace workspace data."""
 
     name = tables.columns.Column(linkify=True)
@@ -116,10 +116,10 @@ def render_number_approved_dars(self, record):
         return n
 
 
-class dbGaPWorkspaceLimitedViewTable(tables.Table):
+class dbGaPWorkspaceUserTable(tables.Table):
     """Class to render a table of Workspace objects with dbGaPWorkspace workspace data."""
 
-    name = tables.columns.Column()
+    name = tables.columns.Column(linkify=True)
     billing_project = tables.Column()
     dbgap_accession = dbGaPAccessionColumn(
         accessor="dbgapworkspace__get_dbgap_accession",

primed/dbgap/tests/test_tables.py

@@ -116,10 +116,10 @@ def test_ordering(self):
         self.assertEqual(table.data[1], instance_1)
 
 
-class dbGaPWorkspaceTableTest(TestCase):
+class dbGaPWorkspaceStaffTableTest(TestCase):
     model = acm_models.Workspace
     model_factory = factories.dbGaPWorkspaceFactory
-    table_class = tables.dbGaPWorkspaceTable
+    table_class = tables.dbGaPWorkspaceStaffTable
 
     def test_row_count_with_no_objects(self):
         table = self.table_class(self.model.objects.all())
@@ -206,10 +206,10 @@ def test_render_number_approved_dars_only_most_recent(self):
     #     self.assertEqual("", table.rows[0].get_cell_value("is_shared"))
 
 
-class dbGaPWorkspaceLimitedViewTableTest(TestCase):
+class dbGaPWorkspaceUserTableTest(TestCase):
     model = acm_models.Workspace
     model_factory = factories.dbGaPWorkspaceFactory
-    table_class = tables.dbGaPWorkspaceTable
+    table_class = tables.dbGaPWorkspaceStaffTable
 
     def test_row_count_with_no_objects(self):
         table = self.table_class(self.model.objects.all())

primed/dbgap/tests/test_views.py

@@ -267,7 +267,7 @@ def test_workspace_table(self):
         response = self.get_view()(request, dbgap_phs=self.obj.dbgap_phs)
         self.assertIn("workspace_table", response.context_data)
         self.assertIsInstance(
-            response.context_data["workspace_table"], tables.dbGaPWorkspaceTable
+            response.context_data["workspace_table"], tables.dbGaPWorkspaceStaffTable
         )
 
     def test_workspace_table_none(self):
@@ -856,7 +856,7 @@ def test_view_has_correct_table_class(self):
         response = self.get_view()(request, workspace_type=self.workspace_type)
         self.assertIn("table", response.context_data)
         self.assertIsInstance(
-            response.context_data["table"], tables.dbGaPWorkspaceTable
+            response.context_data["table"], tables.dbGaPWorkspaceStaffTable
         )
 
 

primed/dbgap/views.py

@@ -57,7 +57,7 @@ def get_object(self, queryset=None):
         return obj
 
     def get_table(self):
-        return tables.dbGaPWorkspaceTable(
+        return tables.dbGaPWorkspaceStaffTable(
             Workspace.objects.filter(dbgapworkspace__dbgap_study_accession=self.object),
             exclude=(
                 "dbgapworkspace__dbgap_study_accession__study",

primed/duo/tests/test_views.py

@@ -19,7 +19,7 @@ class DataUsePermissionListTest(TestCase):
     def setUp(self):
         """Set up test class."""
         self.factory = RequestFactory()
-        # Create a user with both view and edit permission.
+        # Create a user with staff view permission.
         self.user = UserFactory.create(username="test", password="test")
         self.user.user_permissions.add(
             Permission.objects.get(
@@ -122,11 +122,11 @@ class DataUsePermissionDetailTest(TestCase):
     def setUp(self):
         """Set up test class."""
         self.factory = RequestFactory()
-        # Create a user with both view and edit permission.
+        # Create a user with view permission.
         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
             )
         )
 
@@ -282,7 +282,7 @@ 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

@@ -1,4 +1,7 @@
-from anvil_consortium_manager.auth import AnVILConsortiumManagerStaffViewRequired
+from anvil_consortium_manager.auth import (
+    AnVILConsortiumManagerStaffViewRequired,
+    AnVILConsortiumManagerViewRequired,
+)
 from django.http import Http404
 from django.views.generic import DetailView, ListView
 
@@ -18,7 +21,7 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class DataUsePermissionDetail(AnVILConsortiumManagerStaffViewRequired, DetailView):
+class DataUsePermissionDetail(AnVILConsortiumManagerViewRequired, DetailView):
 
     model = models.DataUsePermission
 
@@ -51,7 +54,7 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class DataUseModifierDetail(AnVILConsortiumManagerStaffViewRequired, DetailView):
+class DataUseModifierDetail(AnVILConsortiumManagerViewRequired, DetailView):
 
     model = models.DataUseModifier
 

primed/miscellaneous_workspaces/adapters.py

@@ -3,7 +3,10 @@
 from anvil_consortium_manager.adapters.workspace import BaseWorkspaceAdapter
 from anvil_consortium_manager.forms import WorkspaceForm
 
-from primed.primed_anvil.tables import DefaultWorkspaceTable
+from primed.primed_anvil.tables import (
+    DefaultWorkspaceStaffTable,
+    DefaultWorkspaceUserTable,
+)
 
 from . import forms, models, tables
 
@@ -14,7 +17,8 @@ class SimulatedDataWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "simulated_data"
     name = "Simulated Data workspace"
     description = "Workspaces containing simulated data"
-    list_table_class = DefaultWorkspaceTable
+    list_table_class_staff_view = DefaultWorkspaceStaffTable
+    list_table_class_view = DefaultWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.SimulatedDataWorkspace
     workspace_data_form_class = forms.SimulatedDataWorkspaceForm
@@ -29,7 +33,8 @@ class ConsortiumDevelWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "devel"
     name = "Consortium development workspace"
     description = "Workspaces intended for consortium development of methods"
-    list_table_class = DefaultWorkspaceTable
+    list_table_class_staff_view = DefaultWorkspaceStaffTable
+    list_table_class_view = DefaultWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.ConsortiumDevelWorkspace
     workspace_data_form_class = forms.ConsortiumDevelWorkspaceForm
@@ -42,7 +47,8 @@ class ResourceWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "resource"
     name = "Resource workspace"
     description = "Workspaces containing consortium resources (e.g., examples of using AnVIL, data inventories)"
-    list_table_class = DefaultWorkspaceTable
+    list_table_class_staff_view = DefaultWorkspaceStaffTable
+    list_table_class_view = DefaultWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.ResourceWorkspace
     workspace_data_form_class = forms.ResourceWorkspaceForm
@@ -54,8 +60,11 @@ class TemplateWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "template"
     name = "Template workspace"
-    description = "Template workspaces that can be cloned to create other workspaces"
-    list_table_class = DefaultWorkspaceTable
+    description = (
+        "Template workspaces that will be cloned by the CC to create other workspaces"
+    )
+    list_table_class_staff_view = DefaultWorkspaceStaffTable
+    list_table_class_view = DefaultWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.TemplateWorkspace
     workspace_data_form_class = forms.TemplateWorkspaceForm
@@ -68,7 +77,8 @@ class OpenAccessWorkspaceAdapter(BaseWorkspaceAdapter):
     type = "open_access"
     name = "Open access workspace"
     description = "Workspaces containing open access data"
-    list_table_class = tables.OpenAccessWorkspaceTable
+    list_table_class_staff_view = tables.OpenAccessWorkspaceStaffTable
+    list_table_class_view = tables.OpenAccessWorkspaceUserTable
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.OpenAccessWorkspace
     workspace_data_form_class = forms.OpenAccessWorkspaceForm
@@ -82,8 +92,9 @@ class DataPrepWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "data_prep"
     name = "Data prep workspace"
-    description = "Workspaces used to prepare data."
-    list_table_class = tables.DataPrepWorkspaceTable
+    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
     workspace_form_class = WorkspaceForm
     workspace_data_model = models.DataPrepWorkspace
     workspace_data_form_class = forms.DataPrepWorkspaceForm

primed/miscellaneous_workspaces/tables.py

@@ -9,7 +9,7 @@
 )
 
 
-class OpenAccessWorkspaceTable(tables.Table):
+class OpenAccessWorkspaceStaffTable(tables.Table):
     """Class to render a table of Workspace objects with OpenAccessWorkspace workspace data."""
 
     name = tables.columns.Column(linkify=True)
@@ -27,10 +27,10 @@ class Meta:
         order_by = ("name",)
 
 
-class OpenAccessWorkspaceLimitedViewTable(tables.Table):
+class OpenAccessWorkspaceUserTable(tables.Table):
     """Class to render a table of Workspace objects with OpenAccessWorkspace workspace data."""
 
-    name = tables.columns.Column()
+    name = tables.columns.Column(linkify=True)
     billing_project = tables.Column()
     is_shared = WorkspaceSharedWithConsortiumColumn()
 

primed/miscellaneous_workspaces/tests/test_tables.py

@@ -7,11 +7,11 @@
 from . import factories
 
 
-class OpenAccessWorkspaceTableTest(TestCase):
-    """Tests for the OpenAccessWorkspaceTable table."""
+class OpenAccessWorkspaceStaffTableTest(TestCase):
+    """Tests for the OpenAccessWorkspaceStaffTable table."""
 
     model_factory = factories.OpenAccessWorkspaceFactory
-    table_class = tables.OpenAccessWorkspaceTable
+    table_class = tables.OpenAccessWorkspaceStaffTable
 
     def test_row_count_with_no_objects(self):
         table = self.table_class(Workspace.objects.all())
@@ -28,11 +28,11 @@ def test_row_count_with_two_objects(self):
         self.assertEqual(len(table.rows), 2)
 
 
-class OpenAccessWorkspaceLimitedViewTableTest(TestCase):
-    """Tests for the OpenAccessWorkspaceTable table."""
+class OpenAccessWorkspaceUserTableTest(TestCase):
+    """Tests for the OpenAccessWorkspaceStaffTable table."""
 
     model_factory = factories.OpenAccessWorkspaceFactory
-    table_class = tables.OpenAccessWorkspaceLimitedViewTable
+    table_class = tables.OpenAccessWorkspaceUserTable
 
     def test_row_count_with_no_objects(self):
         table = self.table_class(Workspace.objects.all())