EVA-3681 Fix last updated (#227)

* Last_updated_by needs to be a characteristics * update test
EBIvariation · Oct 25, 2024 · ab17370 · ab17370
1 parent 1a4bd35
commit ab17370
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Showing 2 changed files with 16 additions and 14 deletions.
diff --git a/eva_submission/biosample_submission/biosamples_submitters.py b/eva_submission/biosample_submission/biosamples_submitters.py
@@ -29,7 +29,8 @@
 class BioSamplesSubmitter(AppLogger):
 
     valid_actions = ('create', 'overwrite', 'override', 'curate', 'derive')
-    characteristics_allowed_to_override = ('collection_date', 'geographic location (country and/or sea)')
+    characteristics_allowed_to_override = ('collection_date', 'geographic location (country and/or sea)',
+                                           'last_updated_by')
 
     def __init__(self, communicators, submit_type=('create',), allow_removal=False):
         assert len(communicators) > 0, 'Specify at least one communicator object to BioSamplesSubmitter'
@@ -467,7 +468,8 @@ def map_metadata_to_bsd_data(self):
             self.apply_mapping(bsd_sample_entry, 'organization', organisations)
 
             bsd_sample_entry['release'] = _now
-            bsd_sample_entry['last_updated_by'] = 'EVA'
+            # Custom attributes added to all the BioSample we create/modify
+            bsd_sample_entry['characteristics']['last_updated_by'] = [{'text': 'EVA'}]
             payloads.append(bsd_sample_entry)
 
         return payloads

diff --git a/tests/test_biosamples_submission.py b/tests/test_biosamples_submission.py
@@ -208,7 +208,6 @@ def test_map_metadata_to_bsd_data(self):
 
         expected_payload = [
             {'name': 'S%s' % (i + 1), 'taxId': 9606, 'release': now,
-             'last_updated_by': 'EVA',
              'contact': [{'LastName': 'John', 'FirstName': 'Doe', 'E-mail': 'john.doe@example.com'},
                          {'LastName': 'Jane', 'FirstName': 'Doe', 'E-mail': 'jane.doe@example.com'}],
              'organization': [{'Name': 'GPE', 'Address': 'The place to be'},
@@ -218,7 +217,8 @@ def test_map_metadata_to_bsd_data(self):
                 'description': [{'text': 'Sample %s' % (i+1)}],
                 'scientific name': [{'text': 'Homo sapiens'}],
                 'collection_date': [{'text': '2020-01-15'}],
-                'geographic location (country and/or sea)': [{'text': 'not provided'}]
+                'geographic location (country and/or sea)': [{'text': 'not provided'}],
+                'last_updated_by': [{'text': 'EVA'}]
             }}
             for i in range(100)
         ]
@@ -239,29 +239,29 @@ def test_map_partial_metadata_to_bsd_data(self):
         ]
         organizations = [{'Name': 'GPE', 'Address': 'The place to be'}, {'Name': 'GPE', 'Address': 'The place to be'}]
         updated_samples = [{
-            'last_updated_by': 'EVA',
             'accession': 'SAMD1234' + str(567 + i),
             'name': 'S%s' % (i + 1), 'taxId': 9606, 'release': now,
             'contact': contacts, 'organization': organizations,
             'characteristics': {
                 'Organism': [{'text': 'Homo sapiens'}],
                 'description': [{'text': 'Sample %s' % (i + 1)}],
-                'scientific name': [{'text': 'Homo sapiens'}]
+                'scientific name': [{'text': 'Homo sapiens'}],
+                'last_updated_by': [{'text': 'EVA'}]
             }
         } for i in range(10)]
         existing_samples = [{
-            'last_updated_by': 'EVA',
             'accession': 'SAMD1234' + str(567 + i),
             'contact': contacts, 'organization': organizations,
-            'characteristics': {},
+            'characteristics': {'last_updated_by': [{'text': 'EVA'}]},
             'release': now
         } for i in range(10, 20)]
-        new_samples = [{'last_updated_by': 'EVA', 'name': 'S%s' % (i + 1), 'taxId': 9606, 'release': now,
+        new_samples = [{'name': 'S%s' % (i + 1), 'taxId': 9606, 'release': now,
                         'contact': contacts, 'organization': organizations,
                         'characteristics': {
                             'Organism': [{'text': 'Homo sapiens'}],
                             'description': [{'text': 'Sample %s' % (i + 1)}],
-                            'scientific name': [{'text': 'Homo sapiens'}]
+                            'scientific name': [{'text': 'Homo sapiens'}],
+                            'last_updated_by': [{'text': 'EVA'}]
                         }} for i in range(20, 100)]
 
         expected_payload = updated_samples + existing_samples + new_samples
@@ -343,16 +343,16 @@ def test_override_samples(self):
         with patch.object(BioSamplesSubmitter, '_get_existing_sample', side_effect=self._get_fake_sample), \
                 patch.object(HALCommunicator, 'follows_link') as m_follows_link:
 
-            sample_submitter = SampleMetadataSubmitter(self.metadata_file_ncbi, submit_type=('override',))
-            sample_submitter.submit_to_bioSamples()
-
             sample1 = copy.deepcopy(self.samples.get('SAMN1234567'))
             sample1['characteristics']['collection_date'] = [{'text': '2020-12-24'}]
             sample1['characteristics']['geographic location (country and/or sea)'] = [{'text': 'United Kingdom'}]
+            sample1['characteristics']['last_updated_by'] = [{'text': 'EVA'}]
             sample2 = copy.deepcopy(self.samples.get('SAMN1234568'))
             sample2['characteristics']['collection_date'] = [{'text': '1920-12-24'}]
             sample2['characteristics']['geographic location (country and/or sea)'] = [{'text': 'USA'}]
-
+            sample2['characteristics']['last_updated_by'] = [{'text': 'EVA'}]
+            sample_submitter = SampleMetadataSubmitter(self.metadata_file_ncbi, submit_type=('override',))
+            sample_submitter.submit_to_bioSamples()
             m_follows_link.assert_any_call('samples', method='PUT', join_url='SAMN1234567', json=sample1)
             m_follows_link.assert_any_call('samples', method='PUT', join_url='SAMN1234568', json=sample2)