add api_format in get_objects(), update modify_time field (#2045)

CHANGELOG.rst

@@ -17,6 +17,8 @@ Added
 - **Irodsbackend**
     - Token auth support in ``BasicAuthView`` (#1999)
     - Django checks for enabled authentication methods (#1999)
+    - ``api_format`` arg in ``get_objects()`` and ``get_objs_recursively()`` (#2045)
+    - REST API compatible date format support in ``get_objects()`` (#2045)
 - **Irodsinfo**
     - Alert on token usage for OIDC users (#1999)
 - **Landingzones**

docs_manual/source/sodar_release_notes.rst

@@ -78,6 +78,7 @@ REST API Updates
         + Return ``503`` if project is locked
     * ``ProjectIrodsFileListAPIView``
         + Return results as list without ``irods_data`` object
+        + Return ``modify_time`` field in standard REST API format
 - Landing Zones API
     * ``ZoneCreateAPIView``
         + Return ``503`` if Taskflow is not enabled

irodsbackend/api.py

@@ -115,13 +115,18 @@ def _init_irods(self):
             raise ex
 
     @classmethod
-    def _get_datetime(cls, naive_dt):
+    def _get_datetime(cls, naive_dt, api_format=False):
         """
         Return a printable datetime in the system timezone from a naive
         datetime object.
+
+        :param naive_dt: Naive DateTime object
+        :param api_format: Return in REST API format (bool, default=False)
         """
         dt = naive_dt.replace(tzinfo=pytz.timezone('GMT'))
         dt = dt.astimezone(timezone.get_default_timezone())
+        if api_format:
+            return dt.isoformat()
         return dt.strftime('%Y-%m-%d %H:%M')
 
     @classmethod
@@ -581,7 +586,13 @@ def get_colls_recursively(cls, coll):
         return [iRODSCollection(coll.manager, row) for row in query]
 
     def get_objs_recursively(
-        self, irods, coll, include_md5=False, name_like=None, limit=None
+        self,
+        irods,
+        coll,
+        include_md5=False,
+        name_like=None,
+        limit=None,
+        api_format=False,
     ):
         """
         Return objects below a coll recursively. Replacement for the
@@ -593,6 +604,7 @@ def get_objs_recursively(
         :param include_md5: if True, include .md5 files
         :param name_like: Filtering of file names (string or list of strings)
         :param limit: Limit retrieval to n rows (int)
+        :param api_format: Format data for REST API (bool, default=False)
         :return: List
         """
         ret = []
@@ -645,7 +657,7 @@ def _do_query(irods, nl=None):
                             'path': obj_path,
                             'size': row[DataObject.size],
                             'modify_time': self._get_datetime(
-                                row[DataObject.modify_time]
+                                row[DataObject.modify_time], api_format
                             ),
                         }
                     )
@@ -683,6 +695,7 @@ def get_objects(
         include_colls=False,
         name_like=None,
         limit=None,
+        api_format=False,
     ):
         """
         Return a flat iRODS object list recursively under a given path.
@@ -693,6 +706,7 @@ def get_objects(
         :param include_colls: Include collections (bool)
         :param name_like: Filtering of file names (string or list of strings)
         :param limit: Limit search to n rows (int)
+        :param api_format: Format data for REST API (bool, default=False)
         :return: List
         :raise: FileNotFoundError if collection is not found
         """
@@ -711,6 +725,7 @@ def get_objects(
             include_md5=include_md5,
             name_like=name_like,
             limit=limit,
+            api_format=api_format,
         )
 
         # Add collections if enabled

irodsbackend/tests/test_api_taskflow.py

@@ -1,5 +1,6 @@
 """Tests for the API in the irodsbackend app with Taskflow and iRODS"""
 
+import pytz
 import random
 import string
 
@@ -108,15 +109,20 @@ def test_get_objects(self):
         self.assertIsNotNone(obj_list)
         self.assertEqual(len(obj_list), 2)
 
-        obj = obj_list[0]
+        data_obj = self.irods.data_objects.get(path + '/' + TEST_FILE_NAME)
+        modify_time = (
+            data_obj.modify_time.replace(tzinfo=pytz.timezone('GMT'))
+            .astimezone(pytz.timezone(settings.TIME_ZONE))
+            .strftime('%Y-%m-%d %H:%M')
+        )
         expected = {
             'name': TEST_FILE_NAME,
             'type': 'obj',
             'path': path + '/' + TEST_FILE_NAME,
             'size': 0,
-            'modify_time': obj['modify_time'],
+            'modify_time': modify_time,
         }
-        self.assertEqual(obj, expected)
+        self.assertEqual(obj_list[0], expected)
 
     def test_get_objects_with_colls(self):
         """Test get_objects() with collections included"""
@@ -228,6 +234,30 @@ def test_get_objects_limit(self):
         self.assertIsNotNone(obj_list)
         self.assertEqual(len(obj_list), 1)  # Limited to 1
 
+    def test_get_objects_api_format(self):
+        """Test get_objects() with api_format=True"""
+        self.make_irods_colls(self.investigation)
+        path = self.irods_backend.get_path(self.assay)
+        self.irods.data_objects.create(path + '/' + TEST_FILE_NAME)
+        obj_list = self.irods_backend.get_objects(
+            self.irods, path, api_format=True
+        )
+        self.assertEqual(len(obj_list), 1)
+        data_obj = self.irods.data_objects.get(path + '/' + TEST_FILE_NAME)
+        modify_time = (
+            data_obj.modify_time.replace(tzinfo=pytz.timezone('GMT'))
+            .astimezone(pytz.timezone(settings.TIME_ZONE))
+            .isoformat()
+        )
+        expected = {
+            'name': TEST_FILE_NAME,
+            'type': 'obj',
+            'path': path + '/' + TEST_FILE_NAME,
+            'size': 0,
+            'modify_time': modify_time,
+        }
+        self.assertEqual(obj_list[0], expected)
+
     def test_issue_ticket(self):
         """Test issue_ticket()"""
         self.make_irods_colls(self.investigation)

samplesheets/tests/test_views_api_taskflow.py

@@ -4,6 +4,7 @@
 
 import json
 import os
+import pytz
 
 from datetime import timedelta, datetime
 
@@ -1249,7 +1250,7 @@ def test_get_empty_collection(self):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response.data, [])
 
-    def test_get_collection_with_files(self):
+    def test_get_files(self):
         """Test GET with files"""
         # Set up iRODS collections
         self.make_irods_colls(self.investigation)
@@ -1263,3 +1264,10 @@ def test_get_collection_with_files(self):
         self.assertEqual(len(response.data), 1)
         self.assertEqual(response.data[0]['name'], IRODS_FILE_NAME)
         self.assertEqual(response.data[0]['type'], 'obj')
+        data_obj = self.irods.data_objects.get(coll_path + '/' + 'test1.txt')
+        aware_dt = timezone.make_aware(
+            data_obj.modify_time, pytz.timezone('GMT')
+        )
+        self.assertEqual(
+            response.data[0]['modify_time'], self.get_drf_datetime(aware_dt)
+        )

samplesheets/views_api.py

@@ -937,7 +937,7 @@ class ProjectIrodsFileListAPIView(
     - ``type``: iRODS item type type (``obj`` for file)
     - ``path``: Full path to file
     - ``size``: Size in bytes
-    - ``modify_time``: Datetime of last modification (YYYY-MM-DD HH:MM)
+    - ``modify_time``: Datetime of last modification (YYYY-MM-DDThh:mm:ssZ)
     """
 
     http_method_names = ['get']
@@ -951,7 +951,9 @@ def get(self, request, *args, **kwargs):
         path = irods_backend.get_sample_path(project)
         try:
             with irods_backend.get_session() as irods:
-                obj_list = irods_backend.get_objects(irods, path)
+                obj_list = irods_backend.get_objects(
+                    irods, path, api_format=True
+                )
         except Exception as ex:
             return Response(
                 {'detail': '{}: {}'.format(IRODS_QUERY_ERROR_MSG, ex)},