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Hack to remove the null values in external reference #169

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Sep 18, 2023
Merged

Hack to remove the null values in external reference #169

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bff2ba3
Hack to remove the null values in external reference when pushing a c…
tcezard Sep 12, 2023
64d0716
Add test
tcezard Sep 12, 2023
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18 changes: 18 additions & 0 deletions eva_submission/biosamples_submission.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,6 +196,15 @@ def validate_in_bsd(self, samples_data):
def convert_sample_data_to_curation_object(self, future_sample):
"""Curation object can only change 3 attributes characteristics, externalReferences and relationships"""
current_sample = self.communicator.follows_link('samples', method='GET', join_url=future_sample.get('accession'))

#FIXME: Remove this hack when this i fixed on BioSample's side
# remove null values in externalReferences that causes crash when POSTing the curation object
if 'externalReferences' in current_sample:
current_sample['externalReferences'] = [
dict([(k, v) for k, v in external_ref.items() if v is not None])
for external_ref in current_sample['externalReferences']
]

curation_object = {}
attributes_pre = []
attributes_post = []
Expand Down Expand Up @@ -481,5 +490,14 @@ def retrieve_biosamples(self):
if 'externalReferences' not in sample_json:
sample_json['externalReferences'] = []
sample_json['externalReferences'].append({'url': eva_study_url})

# FIXME: Remove this hack when this i fixed on BioSample's side
# remove null values in externalReferences that causes crash when POSTing the curation object
if 'externalReferences' in sample_json:
sample_json['externalReferences'] = [
dict([(k, v) for k, v in external_ref.items() if v is not None])
for external_ref in sample_json['externalReferences']
]
biosample_objects.append(sample_json)

return biosample_objects
4 changes: 2 additions & 2 deletions tests/test_submit_to_bsd.py
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Expand Up @@ -352,12 +352,12 @@ class TestSampleReferenceSubmitter(BSDTestCase):
def test_retrieve_biosamples(self):
sample_accessions = ['SAME001', 'SAME002']
project_accession = 'PRJEB001'
sample_1 = {"name": "FakeSample1", "accession": "SAME001", "domain": "self.ExampleDomain", "_links": {}}
sample_1 = {"name": "FakeSample1", "accession": "SAME001", "domain": "self.ExampleDomain", "_links": {}, 'externalReferences': [{'url': 'test_url', 'duo': None}]}
sample_2 = {"name": "FakeSample2", "accession": "SAME002", "domain": "self.ExampleDomain", "_links": {}}
with patch.object(HALCommunicator, 'follows_link', side_effect=[sample_1, sample_2]):
self.submitter = SampleReferenceSubmitter(sample_accessions, project_accession)
assert self.submitter.sample_data == [
{'name': 'FakeSample1', 'accession': 'SAME001', 'domain': 'self.ExampleDomain', 'externalReferences': [{'url': 'https://www.ebi.ac.uk/eva/?eva-study=PRJEB001'}]},
{'name': 'FakeSample1', 'accession': 'SAME001', 'domain': 'self.ExampleDomain', 'externalReferences': [{'url': 'test_url'}, {'url': 'https://www.ebi.ac.uk/eva/?eva-study=PRJEB001'}]},
{'name': 'FakeSample2', 'accession': 'SAME002', 'domain': 'self.ExampleDomain', 'externalReferences': [{'url': 'https://www.ebi.ac.uk/eva/?eva-study=PRJEB001'}]}
]

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