add list support for comment fields (#1789, #2033)

bihealth · Nov 18, 2024 · 5116290 · 5116290
1 parent 37ecfc1
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Showing 5 changed files with 65 additions and 8 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -31,7 +31,7 @@ Added
     - Study plugin override via ISA-Tab comments (#1885)
     - Token auth support in study plugin IGV XML serving views (#1999, #2021)
     - Support for newlines in altamISA error messages (#2033)
-    - Support for performer and contact field values as list (#1789, #2033)
+    - Support for comment, performer and contact field values as list (#1789, #2033)
 - **Taskflowbackend**
     - ``TaskflowAPI.raise_submit_api_exception()`` helper (#1847)
 

diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
@@ -19,7 +19,7 @@ Release for SODAR Core v1.0 upgrade, iRODS v4.3 upgrade and feature updates.
 - Add study plugin override via ISA-Tab comments
 - Add session control in Django settings and environment variables
 - Add token-based iRODS/IGV basic auth support for OIDC users
-- Add support for performer and contact field values as list
+- Add support for comment, performer and contact field values as list
 - Update minimum supported iRODS version to v4.3.3
 - Update REST API versioning
 - Update REST API views for OpenAPI support

diff --git a/samplesheets/rendering.py b/samplesheets/rendering.py
@@ -398,6 +398,9 @@ def _add_annotation(self, ann, header, header_type, obj):
         # TODO: TBD: Should these be added in this function at all?
         if isinstance(ann, str):
             val = ann
+        # Comment as a list
+        elif isinstance(ann, list):
+            val = ann
         # Ontology reference(s) (altamISA v0.1+, SODAR v0.5.2+)
         elif isinstance(ann['value'], dict) or (
             isinstance(ann['value'], list)

diff --git a/samplesheets/tests/test_views_ajax.py b/samplesheets/tests/test_views_ajax.py
@@ -1315,6 +1315,10 @@ def setUp(self):
         )
         self.study = self.investigation.studies.first()
         self.values = {'updated_cells': []}
+        self.url = reverse(
+            'samplesheets:ajax_edit_cell',
+            kwargs={'project': self.project.sodar_uuid},
+        )
 
     def test_post_extract_label_string(self):
         """Test SheetCellEditAjaxView POST with extract label and string value"""
@@ -1337,17 +1341,68 @@ def test_post_extract_label_string(self):
         )
         with self.login(self.user):
             response = self.client.post(
-                reverse(
-                    'samplesheets:ajax_edit_cell',
-                    kwargs={'project': self.project.sodar_uuid},
-                ),
+                self.url,
                 json.dumps(self.values),
                 content_type='application/json',
             )
         self.assertEqual(response.status_code, 200)
         obj.refresh_from_db()
         self.assertEqual(obj.extract_label, label)
 
+    def test_post_comment_single(self):
+        """Test POST with comment and single value"""
+        name = 'Replicate'
+        obj = GenericMaterial.objects.get(
+            study=self.study, name='0815-N1-Pro1-A-114'
+        )
+        self.assertEqual(obj.comments, {name: 'A'})
+        self.values['updated_cells'].append(
+            {
+                'uuid': str(obj.sodar_uuid),
+                'header_name': name,
+                'header_type': 'comments',
+                'obj_cls': 'GenericMaterial',
+                'value': 'B',
+                'uuid_ref': str(obj.sodar_uuid),
+            }
+        )
+        with self.login(self.user):
+            response = self.client.post(
+                self.url,
+                json.dumps(self.values),
+                content_type='application/json',
+            )
+        self.assertEqual(response.status_code, 200)
+        obj.refresh_from_db()
+        self.assertEqual(obj.comments, {name: 'B'})
+
+    def test_post_comment_list(self):
+        """Test POST with comment and list value"""
+        name = 'Replicate'
+        obj = GenericMaterial.objects.get(
+            study=self.study, name='0815-N1-Pro1-A-114'
+        )
+        self.assertEqual(obj.comments, {name: 'A'})
+        self.values['updated_cells'].append(
+            {
+                'uuid': str(obj.sodar_uuid),
+                'header_name': name,
+                'header_type': 'comments',
+                'obj_cls': 'GenericMaterial',
+                'value': ['A', 'B'],
+                'uuid_ref': str(obj.sodar_uuid),
+            }
+        )
+        with self.login(self.user):
+            response = self.client.post(
+                self.url,
+                json.dumps(self.values),
+                content_type='application/json',
+            )
+        self.assertEqual(response.status_code, 200)
+        obj.refresh_from_db()
+        self.assertEqual(obj.comments, {name: ['A', 'B']})
+
 
 class TestSheetRowInsertAjaxView(
     RowEditMixin, SheetConfigMixin, SamplesheetsViewTestBase

diff --git a/samplesheets/vueapp/src/components/editors/DataCellEditor.vue b/samplesheets/vueapp/src/components/editors/DataCellEditor.vue
@@ -350,8 +350,7 @@ export default Vue.extend({
     if (!this.destroyCalled) {
       this.destroyCalled = true // HACK for issue #869
       // Convert to list value if applicable
-      if (this.editValue.includes(';') &&
-        this.headerInfo.header_type !== 'comments' && (
+      if (this.editValue.includes(';') && (
         this.isValueArray || (
           !['integer', 'double'].includes(this.editConfig.format) &&
           !this.value.unit))) {