add ProjectIrodsFileListAPIView checksum field (#2039)

Author: mikkonie

CHANGELOG.rst

@@ -23,6 +23,7 @@ Added
     - ``cleanup_file_prohibit()`` utility method (#2064)
 - **Samplesheets**
     - Site read-only mode support (#2051)
+    - ``checksum`` field in ``ProjectIrodsFileListAPIView`` return data (#2039)
 - **Taskflowbackend**
     - Project deletion support (#2051)
     - Zone validation and moving progress indicators (#2024)

docs_manual/source/api_samplesheets.rst

@@ -12,9 +12,9 @@ Versioning
 Media Type
     ``application/vnd.bihealth.sodar.samplesheets+json``
 Current Version
-    ``1.0``
+    ``1.1``
 Accepted Versions
-    ``1.0``
+    ``1.0``, ``1.1``
 Header Example
     ``Accept: application/vnd.bihealth.sodar.samplesheets+json; version=x.y``
 
@@ -71,3 +71,13 @@ iRODS Data Requests
 .. autoclass:: IrodsDataRequestAcceptAPIView
 
 .. autoclass:: IrodsDataRequestRejectAPIView
+
+
+Version Changes
+===============
+
+v1.1
+----
+
+- ``ProjectIrodsFileListAPIView``
+    * Add ``checksum`` field to return data

docs_manual/source/sodar_release_notes.rst

@@ -15,6 +15,7 @@ Release for SODAR Core 1.1 upgrade and feature updates.
 
 - Add landing zone validation and moving progress indicators
 - Add landing zone file type prohibiting
+- Upgrade Sample Sheets REST API version to v1.1
 - Upgrade to python-irodsclient v3.0
 - Upgrade to SODAR Core v1.1.2
 - Replace SODAR_SUPPORT_* settings with PROJECTROLES_SUPPORT_CONTACT
@@ -24,6 +25,15 @@ Release for SODAR Core 1.1 upgrade and feature updates.
 
 :ref:`Administrator upgrade guide for v1.1 <admin_upgrade_v1.1>`
 
+REST API Updates
+----------------
+
+- Sample Sheets API
+    * Current version: ``1.1`` (non-breaking changes)
+    * Allowed versions: ``1.0``, ``1.1``
+    * ``ProjectIrodsFileListAPIView``
+        + Add ``checksum`` field to return data
+
 
 v1.0.1 (2025-03-12)
 ===================

samplesheets/tests/test_views_api_taskflow.py

@@ -1258,8 +1258,7 @@ def setUp(self):
 
     def test_get_no_collection(self):
         """Test ProjectIrodsFileListAPIView GET without collection"""
-        with self.login(self.user):
-            response = self.client.get(self.url)
+        response = self.request_knox(self.url)
         self.assertEqual(response.status_code, 404)
         self.assertEqual(
             response.data['detail'],
@@ -1272,27 +1271,45 @@ def test_get_empty_collection(self):
         """Test GET with empty collection"""
         # Set up iRODS collections
         self.make_irods_colls(self.investigation)
-        with self.login(self.user):
-            response = self.client.get(self.url)
+        response = self.request_knox(self.url)
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response.data, [])
 
     def test_get_files(self):
         """Test GET with files"""
-        # Set up iRODS collections
         self.make_irods_colls(self.investigation)
         coll_path = self.irods_backend.get_sample_path(self.project) + '/'
         self.irods.data_objects.put(
             IRODS_FILE_PATH, coll_path, **{REG_CHKSUM_KW: ''}
         )
-        with self.login(self.user):
-            response = self.client.get(self.url)
+        data_obj = self.irods.data_objects.get(coll_path + '/' + 'test1.txt')
+        response = self.request_knox(self.url)
         self.assertEqual(response.status_code, 200)
         self.assertEqual(len(response.data), 1)
         self.assertEqual(response.data[0]['name'], IRODS_FILE_NAME)
         self.assertEqual(response.data[0]['type'], 'obj')
+        self.assertEqual(
+            response.data[0]['modify_time'],
+            self.get_drf_datetime(data_obj.modify_time),
+        )
+        self.assertEqual(response.data[0]['checksum'], data_obj.checksum)
+        self.assertIsNotNone(response.data[0]['checksum'])
+
+    def test_get_files_v1_0(self):
+        """Test GET with files and API version 1.0"""
+        self.make_irods_colls(self.investigation)
+        coll_path = self.irods_backend.get_sample_path(self.project) + '/'
+        self.irods.data_objects.put(
+            IRODS_FILE_PATH, coll_path, **{REG_CHKSUM_KW: ''}
+        )
         data_obj = self.irods.data_objects.get(coll_path + '/' + 'test1.txt')
+        response = self.request_knox(self.url, version='1.0')
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.data), 1)
+        self.assertEqual(response.data[0]['name'], IRODS_FILE_NAME)
+        self.assertEqual(response.data[0]['type'], 'obj')
         self.assertEqual(
             response.data[0]['modify_time'],
             self.get_drf_datetime(data_obj.modify_time),
         )
+        self.assertNotIn('checksum', response.data[0])  # Should not be included

samplesheets/views_api.py

@@ -6,6 +6,7 @@
 
 from irods.exception import CAT_NO_ROWS_FOUND
 from irods.models import DataObject
+from packaging.version import parse as parse_version
 
 from django.conf import settings
 from django.urls import reverse
@@ -85,8 +86,8 @@
 
 # Local constants
 SAMPLESHEETS_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar.samplesheets+json'
-SAMPLESHEETS_API_ALLOWED_VERSIONS = ['1.0']
-SAMPLESHEETS_API_DEFAULT_VERSION = '1.0'
+SAMPLESHEETS_API_ALLOWED_VERSIONS = ['1.0', '1.1']
+SAMPLESHEETS_API_DEFAULT_VERSION = '1.1'
 MD5_RE = re.compile(r'([a-fA-F\d]{32})')
 APP_NAME = 'samplesheets'
 IRODS_QUERY_ERROR_MSG = 'Exception querying iRODS objects'
@@ -993,6 +994,7 @@ def get(self, request, *args, **kwargs):
                 'path': serializers.CharField(),
                 'size': serializers.IntegerField(),
                 'modify_time': serializers.DateTimeField(),
+                'checksum': serializers.CharField(),
             },
         ),
     }
@@ -1016,6 +1018,11 @@ class ProjectIrodsFileListAPIView(
     - ``path``: Full path to file
     - ``size``: Size in bytes
     - ``modify_time``: Datetime of last modification (YYYY-MM-DDThh:mm:ssZ)
+    - ``checksum``: Checksum of data object
+
+    **Version Changes**:
+
+    - ``1.1``: Add ``checksum`` field to return data
     """
 
     http_method_names = ['get']
@@ -1027,10 +1034,12 @@ def get(self, request, *args, **kwargs):
         irods_backend = get_backend_api('omics_irods')
         project = self.get_project()
         path = irods_backend.get_sample_path(project)
+        version = parse_version(self.request.version)
+        checksum = True if version >= parse_version('1.1') else False
         try:
             with irods_backend.get_session() as irods:
                 obj_list = irods_backend.get_objects(
-                    irods, path, api_format=True
+                    irods, path, api_format=True, checksum=checksum
                 )
         except Exception as ex:
             return Response(