wip

samplesheets/forms.py

@@ -456,8 +456,7 @@ def clean(self):
             irods_backend, self.project, self.instance, cleaned_data
         )
         if errors:
-            field, error = errors
-            self.add_error(field, error)
+            self.add_error(*errors)
         return self.cleaned_data
 
 

samplesheets/serializers.py

@@ -200,6 +200,5 @@ def validate(self, attrs):
             irods_backend, self.context['project'], self.instance, attrs
         )
         if errors:
-            field, error = errors
-            raise serializers.ValidationError('{}: {}'.format(field, error))
+            raise serializers.ValidationError('{}: {}'.format(*errors))
         return attrs

samplesheets/tests/test_permissions_api_taskflow.py

@@ -35,6 +35,11 @@
 )
 
 
+# Local constants
+LABEL_CREATE = 'label'
+LABEL_UPDATE = 'label_update'
+
+
 # Base Classes and Mixins ------------------------------------------------------
 
 
@@ -157,7 +162,6 @@ class TestIrodsAccessTicketListAPIView(IrodsAccessTicketAPIViewTestBase):
 
     def setUp(self):
         super().setUp()
-        # Set up URLs
         self.url = (
             reverse(
                 'samplesheets:api_irods_ticket_list',
@@ -171,7 +175,7 @@ def setUp(self):
             path=self.coll.path + '/ticket1',
             user=self.user_owner,
             ticket='ticket',
-            label='label',
+            label=LABEL_CREATE,
             date_expires=(timezone.localtime() + timedelta(days=1)).isoformat(),
         )
 
@@ -227,14 +231,13 @@ class TestIrodsAccessTicketRetrieveAPIView(IrodsAccessTicketAPIViewTestBase):
 
     def setUp(self):
         super().setUp()
-        # Set up URLs
         self.ticket = self.make_irods_ticket(
             study=self.study,
             assay=self.assay,
             path=self.coll.path + '/ticket1',
             user=self.user_owner,
             ticket='ticket',
-            label='label',
+            label=LABEL_CREATE,
             date_expires=(timezone.localtime() + timedelta(days=1)).isoformat(),
         )
         self.url = reverse(
@@ -292,33 +295,31 @@ def test_get_archive(self):
 class TestIrodsAccessTicketCreateAPIView(IrodsAccessTicketAPIViewTestBase):
     """Test permissions for IrodsAccessTicketCreateAPIView"""
 
+    def _delete_ticket(self):
+        """Delete ticket created in test case"""
+        access_ticket = IrodsAccessTicket.objects.all().first()
+        ticket_str = access_ticket.ticket
+        self.irods_backend.delete_ticket(self.irods, ticket_str)
+        access_ticket.delete()
+
     def setUp(self):
         super().setUp()
-        # Set up URLs
         self.url = reverse(
             'samplesheets:api_irods_ticket_create',
             kwargs={'project': self.project.sodar_uuid},
         )
         self.path = self.coll.path
-        self.label = 'label'
         self.date_expires = (
             timezone.localtime() + timedelta(days=1)
         ).isoformat()
         # Set up post data
         self.post_data = {
             'assay': self.assay.pk,
             'path': self.path,
-            'label': self.label,
+            'label': LABEL_CREATE,
             'date_expires': self.date_expires,
         }
 
-    def _delete_ticket(self):
-        """Delete ticket created in test case"""
-        access_ticket = IrodsAccessTicket.objects.all().first()
-        ticket_str = access_ticket.ticket
-        self.irods_backend.delete_ticket(self.irods, ticket_str)
-        access_ticket.delete()
-
     def test_create(self):
         """Test IrodsAccessTicketCreateAPIView POST"""
         good_users = [
@@ -395,23 +396,21 @@ class TestIrodsAccessTicketUpdateAPIView(IrodsAccessTicketAPIViewTestBase):
 
     def setUp(self):
         super().setUp()
-        # Set up URLs
         self.ticket = self.make_irods_ticket(
             study=self.study,
             assay=self.assay,
             path=self.coll.path + '/ticket1',
             user=self.user_owner,
             ticket='ticket',
-            label='label',
+            label=LABEL_CREATE,
             date_expires=(timezone.localtime() + timedelta(days=1)).isoformat(),
         )
         self.url = reverse(
             'samplesheets:api_irods_ticket_update',
             kwargs={'irodsaccessticket': self.ticket.sodar_uuid},
         )
         # Set up post data
-        self.label_update = 'label_update'
-        self.post_data = {'label': self.label_update}
+        self.post_data = {'label': LABEL_UPDATE}
 
     def test_update(self):
         """Test IrodsAccessTicketUpdateAPIView PATCH"""
@@ -480,15 +479,14 @@ class TestIrodsAccessTicketDestroyAPIView(IrodsAccessTicketAPIViewTestBase):
     def _create_irods_ticket(self):
         # Create ticket in database and iRODS
         ticket_str = 'ticket'
-        label = 'label'
         # Create ticket in database and iRODS
         self.ticket = self.make_irods_ticket(
             study=self.study,
             assay=self.assay,
             path=self.coll.path,
             user=self.user_owner,
             ticket=ticket_str,
-            label=label,
+            label=LABEL_CREATE,
             date_expires=timezone.localtime() + timedelta(days=1),
         )
         self.irods_backend.issue_ticket(

samplesheets/tests/test_views_api_taskflow.py

@@ -43,7 +43,6 @@
 )
 from samplesheets.views_api import (
     IRODS_QUERY_ERROR_MSG,
-    IRODS_TICKETS_NOT_FOUND_MSG,
 )
 
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
@@ -392,9 +391,8 @@ def test_get_no_tickets(self):
         self.assertEqual(IrodsAccessTicket.objects.count(), 0)
         with self.login(self.user_contrib):
             response = self.client.get(self.url)
-        self.assertEqual(response.status_code, 404)
-        expected = {'detail': IRODS_TICKETS_NOT_FOUND_MSG}
-        self.assertEqual(json.loads(response.content), expected)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(json.loads(response.content), [])
 
     def test_get_active(self):
         """Test GET IrodsAccessTicketListAPIView with active = True"""
@@ -761,10 +759,7 @@ def test_patch(self):
         with self.login(self.user_contrib):
             response = self.client.patch(
                 self.url,
-                {
-                    'label': LABEL_UPDATE,
-                    'date_expires': self.date_expires_update,
-                },
+                {'date_expires': self.date_expires_update},
             )
 
         self.assertEqual(response.status_code, 200)
@@ -773,7 +768,7 @@ def test_patch(self):
         )
         expected = {
             'sodar_uuid': str(self.ticket.sodar_uuid),
-            'label': LABEL_UPDATE,
+            'label': self.label,
             'ticket': self.ticket.ticket,
             'assay': self.ticket.assay.pk,
             'study': self.ticket.study.pk,

samplesheets/views_api.py

@@ -327,11 +327,9 @@ class IrodsAccessTicketListAPIView(
 
     **Methods:** ``GET``
 
-    **Query parameters:** ``active`` (boolean, default ``0``)
+    **Query parameters:**
 
-    **Returns:**
-
-    - ``tickets``: List of iRODS access tickets
+    - ``active`` (boolean, default ``0``)
     """
 
     permission_required = 'samplesheets.edit_sheet'
@@ -346,24 +344,18 @@ def get_queryset(self):
         active = bool(int(active))
         if active:
             tickets = [t for t in tickets if t.is_active()]
-        if not tickets:
-            raise NotFound(IRODS_TICKETS_NOT_FOUND_MSG)
         return tickets
 
 
 class IrodsAccessTicketRetrieveAPIView(
-    IrodsAccessTicketModifyMixin, SODARAPIBaseProjectMixin, RetrieveAPIView
+    IrodsAccessTicketModifyMixin, SODARAPIGenericProjectMixin, RetrieveAPIView
 ):
     """
     Retrieve an iRODS access ticket for a project.
 
     **URL:** ``/samplesheets/api/irods/ticket/retrieve/{IrodsAccessTicket.sodar_uuid}``
 
     **Methods:** ``GET``
-
-    **Returns:**
-
-    - ``ticket``: iRODS access ticket
     """
 
     lookup_field = 'sodar_uuid'
@@ -379,7 +371,7 @@ def get_object(self):
 
 
 class IrodsAccessTicketCreateAPIView(
-    IrodsAccessTicketModifyMixin, SODARAPIBaseProjectMixin, CreateAPIView
+    IrodsAccessTicketModifyMixin, SODARAPIGenericProjectMixin, CreateAPIView
 ):
     """
     Create an iRODS access ticket for a project.
@@ -393,10 +385,6 @@ class IrodsAccessTicketCreateAPIView(
     - ``path``: iRODS path
     - ``label``: Label (string)
     - ``date_expires``: Expiration date (YYYY-MM-DDThh:mm:ssZ, optional)
-
-    **Returns:**
-
-    - ``ticket``: iRODS access ticket
     """
 
     permission_required = 'samplesheets.edit_sheet'
@@ -411,22 +399,19 @@ def get_serializer_context(self):
     def perform_create(self, serializer):
         """Override perform_create() to create IrodsAccessTicket"""
         irods_backend = get_backend_api('omics_irods')
-        if serializer.is_valid():
-            try:
-                with irods_backend.get_session() as irods:
-                    ticket = irods_backend.issue_ticket(
-                        irods,
-                        'read',
-                        serializer.validated_data.get('path'),
-                        ticket_str=build_secret(16),
-                        expiry_date=serializer.validated_data.get(
-                            'date_expires'
-                        ),
-                    )
-            except Exception as ex:
-                raise ValidationError(
-                    '{} {}'.format('Creating ' + IRODS_TICKET_EX_MSG + ':', ex)
+        try:
+            with irods_backend.get_session() as irods:
+                ticket = irods_backend.issue_ticket(
+                    irods,
+                    'read',
+                    serializer.validated_data.get('path'),
+                    ticket_str=build_secret(16),
+                    expiry_date=serializer.validated_data.get('date_expires'),
                 )
+        except Exception as ex:
+            raise ValidationError(
+                '{} {}'.format('Creating ' + IRODS_TICKET_EX_MSG + ':', ex)
+            )
 
         serializer.validated_data['ticket'] = ticket.ticket
         serializer.save()
@@ -468,9 +453,9 @@ def get_object(self):
 
     def perform_update(self, serializer):
         """Override perform_update() to update IrodsAccessTicket"""
-        serializer.save()
         if not set(serializer.initial_data) & {'label', 'date_expires'}:
             raise ValidationError(IRODS_TICKET_NO_UPDATE_FIELDS_MSG)
+        serializer.save()
         # Create timeline event
         self.create_timeline_event(serializer.instance, 'update')
         # Add app alerts to owners/delegates