Merge pull request #154 from UW-GAC/feature/dbgap-workspace-table-upd…

…ates

Feature/dbgap workspace table updates

primed/dbgap/tables.py

@@ -33,24 +33,63 @@ def render_dbgap_phs(self, value):
 class dbGaPWorkspaceTable(tables.Table):
     """Class to render a table of Workspace objects with dbGaPWorkspace workspace data."""
 
-    name = tables.columns.Column(linkify=True)
-
-    class Meta:
-        model = Workspace
-        fields = (
-            "name",
-            "dbgapworkspace__dbgap_study_accession__studies",
+    workspace = tables.columns.Column(
+        linkify=True, accessor="pk", order_by=("billing_project__name", "name")
+    )
+    dbgap_accession = tables.columns.Column(
+        verbose_name="dbGaP accession",
+        accessor="pk",
+        order_by=(
             "dbgapworkspace__dbgap_study_accession__dbgap_phs",
             "dbgapworkspace__dbgap_version",
             "dbgapworkspace__dbgap_participant_set",
-            "dbgapworkspace__dbgap_consent_abbreviation",
-        )
+        ),
+    )
+    dbgapworkspace__dbgap_consent_abbreviation = tables.columns.Column(
+        verbose_name="Consent"
+    )
+    number_approved_dars = tables.columns.Column(
+        accessor="pk",
+        verbose_name="Approved DARs",
+        orderable=False,
+    )
+    is_shared = tables.columns.Column(
+        accessor="pk",
+        verbose_name="Shared with PRIMED?",
+        orderable=False,
+    )
 
-    def render_dbgapworkspace__dbgap_phs(self, value):
-        return "phs{0:06d}".format(value)
+    class Meta:
+        model = Workspace
+        fields = ()
+
+    def render_workspace(self, record):
+        return str(record)
 
-    def render_dbgapworkspace__version(self, value):
-        return "v{}".format(value)
+    def render_dbgap_accession(self, record):
+        return record.dbgapworkspace.get_dbgap_accession()
+
+    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
+
+    def render_is_shared(self, record):
+        is_shared = record.workspacegroupsharing_set.filter(
+            group__name="PRIMED_ALL"
+        ).exists()
+        if is_shared:
+            icon = "check-circle-fill"
+            color = "green"
+            value = format_html(
+                """<i class="bi bi-{}" style="color: {};"></i>""".format(icon, color)
+            )
+        else:
+            value = ""
+        return value
 
 
 class ManyToManyDateTimeColumn(tables.columns.ManyToManyColumn):

primed/dbgap/tests/test_tables.py

@@ -70,6 +70,99 @@ def test_row_count_with_two_objects(self):
         table = self.table_class(self.model.objects.all())
         self.assertEqual(len(table.rows), 2)
 
+    def test_render_workspace(self):
+        """render_workspace returns the correct value."""
+        instance = self.model_factory.create(
+            workspace__billing_project__name="bp", workspace__name="ws"
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_workspace(instance.workspace), "bp/ws")
+        self.assertEqual(table.rows[0].get_cell_value("workspace"), "bp/ws")
+
+    def test_render_dbgap_accession(self):
+        """render_workspace returns the correct value."""
+        instance = self.model_factory.create(
+            dbgap_study_accession__dbgap_phs=1,
+            dbgap_version=2,
+            dbgap_participant_set=3,
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(
+            table.render_dbgap_accession(instance.workspace), "phs000001.v2.p3"
+        )
+        self.assertEqual(
+            table.rows[0].get_cell_value("dbgap_accession"), "phs000001.v2.p3"
+        )
+
+    def test_render_number_approved_dars_no_dars(self):
+        instance = self.model_factory.create()
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_number_approved_dars(instance.workspace), 0)
+
+    def test_render_number_approved_dars_one_dar(self):
+        instance = self.model_factory.create()
+        factories.dbGaPDataAccessRequestForWorkspaceFactory(dbgap_workspace=instance)
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_number_approved_dars(instance.workspace), 1)
+
+    def test_render_number_approved_dars_one_dar_does_not_match(self):
+        instance = self.model_factory.create()
+        factories.dbGaPDataAccessRequestFactory()
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_number_approved_dars(instance.workspace), 0)
+
+    def test_render_number_approved_dars_two_dars(self):
+        instance = self.model_factory.create()
+        factories.dbGaPDataAccessRequestForWorkspaceFactory(dbgap_workspace=instance)
+        factories.dbGaPDataAccessRequestForWorkspaceFactory(dbgap_workspace=instance)
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_number_approved_dars(instance.workspace), 2)
+
+    def test_render_number_approved_dars_not_approved(self):
+        instance = self.model_factory.create()
+        factories.dbGaPDataAccessRequestForWorkspaceFactory(
+            dbgap_workspace=instance,
+            dbgap_current_status=models.dbGaPDataAccessRequest.REJECTED,
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_number_approved_dars(instance.workspace), 0)
+
+    def test_render_number_approved_dars_only_most_recent(self):
+        instance = self.model_factory.create()
+        factories.dbGaPDataAccessRequestForWorkspaceFactory(
+            dbgap_workspace=instance, dbgap_data_access_snapshot__is_most_recent=False
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual(table.render_number_approved_dars(instance.workspace), 0)
+
+    def test_render_is_shared_not_shared(self):
+        """render_is_shared works correctly when the workspace is not shared with anyone."""
+        factories.ManagedGroupFactory.create(name="PRIMED_ALL")
+        factories.dbGaPWorkspaceFactory.create()
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual("", table.rows[0].get_cell_value("is_shared"))
+
+    def test_render_is_shared_true(self):
+        """render_is_shared works correctly when the workspace is shared with PRIMED_ALL."""
+        group = factories.ManagedGroupFactory.create(name="PRIMED_ALL")
+        dbgap_workspace = factories.dbGaPWorkspaceFactory.create()
+        WorkspaceGroupSharingFactory.create(
+            group=group, workspace=dbgap_workspace.workspace
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertIn("circle-fill", table.rows[0].get_cell_value("is_shared"))
+
+    def test_render_is_shared_shared_with_different_group(self):
+        """render_is_shared works correctly when the workspace is shared with a group other PRIMED_ALL."""
+        factories.ManagedGroupFactory.create(name="PRIMED_ALL")
+        group = factories.ManagedGroupFactory.create()
+        dbgap_workspace = factories.dbGaPWorkspaceFactory.create()
+        WorkspaceGroupSharingFactory.create(
+            group=group, workspace=dbgap_workspace.workspace
+        )
+        table = self.table_class(self.model.objects.all())
+        self.assertEqual("", table.rows[0].get_cell_value("is_shared"))
+
 
 class dbGaPApplicationTableTest(TestCase):
     model = models.dbGaPApplication