add samplesheets api pagination (#1994)

config/settings/base.py

@@ -345,6 +345,9 @@
         'knox.auth.TokenAuthentication',
     ),
     'EXCEPTION_HANDLER': 'rest_framework.views.exception_handler',
+    'DEFAULT_PAGINATION_CLASS': (
+        'rest_framework.pagination.PageNumberPagination'
+    ),
     'PAGE_SIZE': env.int('SODAR_API_PAGE_SIZE', 100),
 }
 

samplesheets/tests/test_views_api.py

@@ -739,17 +739,14 @@ def test_get(self):
         with self.login(self.user_contributor):
             response = self.client.get(self.url)
         self.assertEqual(response.status_code, 200)
-        local_date_created = self.ticket.date_created.astimezone(
-            timezone.get_current_timezone()
-        )
         expected = {
             'sodar_uuid': str(self.ticket.sodar_uuid),
             'label': self.ticket.label,
             'ticket': self.ticket.ticket,
             'study': str(self.study.sodar_uuid),
             'assay': str(self.assay.sodar_uuid),
             'path': self.ticket.path,
-            'date_created': local_date_created.isoformat(),
+            'date_created': self.get_drf_datetime(self.ticket.date_created),
             'date_expires': self.ticket.date_expires,
             'user': self.get_serialized_user(self.user),
             'is_active': self.ticket.is_active(),
@@ -771,23 +768,49 @@ def test_get_active(self):
         with self.login(self.user_contributor):
             response = self.client.get(self.url + '?active=1')
         self.assertEqual(response.status_code, 200)
-        local_date_created = self.ticket.date_created.astimezone(
-            timezone.get_current_timezone()
-        )
         expected = {
             'sodar_uuid': str(self.ticket.sodar_uuid),
             'label': self.ticket.label,
             'ticket': self.ticket.ticket,
             'study': str(self.study.sodar_uuid),
             'assay': str(self.assay.sodar_uuid),
             'path': self.ticket.path,
-            'date_created': local_date_created.isoformat(),
+            'date_created': self.get_drf_datetime(self.ticket.date_created),
             'date_expires': self.ticket.date_expires,
             'user': self.get_serialized_user(self.user),
             'is_active': self.ticket.is_active(),
         }
         self.assertEqual(json.loads(response.content), [expected])
 
+    def test_get_pagination(self):
+        """Test GET with pagination"""
+        url = self.url + '?page=1'
+        with self.login(self.user_contributor):
+            response = self.client.get(url)
+        self.assertEqual(response.status_code, 200)
+        expected = {
+            'count': 1,
+            'next': None,
+            'previous': None,
+            'results': [
+                {
+                    'sodar_uuid': str(self.ticket.sodar_uuid),
+                    'label': self.ticket.label,
+                    'ticket': self.ticket.ticket,
+                    'study': str(self.study.sodar_uuid),
+                    'assay': str(self.assay.sodar_uuid),
+                    'path': self.ticket.path,
+                    'date_created': self.get_drf_datetime(
+                        self.ticket.date_created
+                    ),
+                    'date_expires': self.ticket.date_expires,
+                    'user': self.get_serialized_user(self.user),
+                    'is_active': self.ticket.is_active(),
+                }
+            ],
+        }
+        self.assertEqual(json.loads(response.content), expected)
+
 
 class TestIrodsDataRequestRetrieveAPIView(
     IrodsDataRequestMixin, SampleSheetAPIViewTestBase
@@ -868,7 +891,7 @@ def setUp(self):
         )
 
     def test_get(self):
-        """Test retrieving iRODS data request list"""
+        """Test IrodsDataRequestListAPIView GET"""
         response = self.request_knox(self.url)
         self.assertEqual(response.status_code, 200)
         self.assertEqual(len(response.data), 1)
@@ -887,24 +910,53 @@ def test_get(self):
         }
         self.assertEqual(response_data[0], expected)
 
+    def test_get_pagination(self):
+        """Test GET with pagination"""
+        url = self.url + '?page=1'
+        response = self.request_knox(url)
+        self.assertEqual(response.status_code, 200)
+        response_data = json.loads(response.content)
+        expected = {
+            'count': 1,
+            'next': None,
+            'previous': None,
+            'results': [
+                {
+                    'project': str(self.project.sodar_uuid),
+                    'action': IRODS_REQUEST_ACTION_DELETE,
+                    'path': self.request.path,
+                    'target_path': '',
+                    'user': self.get_serialized_user(self.user_contributor),
+                    'status': IRODS_REQUEST_STATUS_ACTIVE,
+                    'status_info': '',
+                    'description': self.request.description,
+                    'date_created': self.get_drf_datetime(
+                        self.request.date_created
+                    ),
+                    'sodar_uuid': str(self.request.sodar_uuid),
+                }
+            ],
+        }
+        self.assertEqual(response_data, expected)
+
     def test_get_failed_as_superuser(self):
-        """Test retrieving list as superuser with failed request"""
+        """Test GET as superuser with failed request"""
         self.request.status = IRODS_REQUEST_STATUS_FAILED
         self.request.save()
         response = self.request_knox(self.url)
         self.assertEqual(response.status_code, 200)
         self.assertEqual(len(response.data), 1)
 
     def test_get_accepted_as_superuser(self):
-        """Test retrieving list as superuser with accepted request"""
+        """Test GET as superuser with accepted request"""
         self.request.status = IRODS_REQUEST_STATUS_ACCEPTED
         self.request.save()
         response = self.request_knox(self.url)
         self.assertEqual(response.status_code, 200)
         self.assertEqual(len(response.data), 0)
 
     def test_get_accepted_as_owner(self):
-        """Test retrieving list as owner with accepted request"""
+        """Test GET as owner with accepted request"""
         self.request.status = IRODS_REQUEST_STATUS_ACCEPTED
         self.request.save()
         response = self.request_knox(
@@ -914,7 +966,7 @@ def test_get_accepted_as_owner(self):
         self.assertEqual(len(response.data), 0)
 
     def test_get_accepted_as_request_creator(self):
-        """Test retrieving list as request creator with accepted request"""
+        """Test GET as request creator with accepted request"""
         self.request.status = IRODS_REQUEST_STATUS_ACCEPTED
         self.request.save()
         response = self.request_knox(

samplesheets/views_api.py

@@ -38,6 +38,7 @@
     SODARAPIBaseMixin,
     SODARAPIBaseProjectMixin,
     SODARAPIGenericProjectMixin,
+    SODARPageNumberPagination,
 )
 from projectroles.utils import build_secret
 
@@ -388,17 +389,23 @@ class IrodsAccessTicketListAPIView(
     """
     List iRODS access tickets for a project.
 
+    Supports optional pagination for listing by providing the ``page`` query
+    string. This will return results in the Django Rest Framework
+    ``PageNumberPagination`` format.
+
     **URL:** ``/samplesheets/api/irods/ticket/list/{Project.sodar_uuid}``
 
     **Methods:** ``GET``
 
     **Query parameters:**
 
     - ``active`` (boolean, optional, default=false)
+    - ``page``: Page number for paginated results (int, optional)
 
     **Returns:** List of ticket dicts, see ``IrodsAccessTicketRetrieveAPIView``
     """
 
+    pagination_class = SODARPageNumberPagination
     permission_required = 'samplesheets.edit_sheet'
     serializer_class = IrodsAccessTicketSerializer
 
@@ -584,13 +591,22 @@ class IrodsDataRequestListAPIView(
     all requests with the status of ACTIVE or FAILED. If called as a
     contributor, returns the user's own requests regardless of the state.
 
+    Supports optional pagination for listing by providing the ``page`` query
+    string. This will return results in the Django Rest Framework
+    ``PageNumberPagination`` format.
+
     **URL:** ``/samplesheets/api/irods/requests/{Project.sodar_uuid}``
 
     **Methods:** ``GET``
 
+    **Query parameters:**
+
+    - ``page``: Page number for paginated results (int, optional)
+
     **Returns:** List of iRODS data requests (list of dicts)
     """
 
+    pagination_class = SODARPageNumberPagination
     permission_required = 'samplesheets.edit_sheet'
     serializer_class = IrodsDataRequestSerializer
 
@@ -879,6 +895,7 @@ def get(self, request, *args, **kwargs):
         return Response(ret, status=status.HTTP_200_OK)
 
 
+# TODO: Standardize output and add pagination
 class ProjectIrodsFileListAPIView(
     SamplesheetsAPIVersioningMixin, SODARAPIBaseProjectMixin, APIView
 ):