def upload_to_bioSamples(self, force=False):
metadata_spreadsheet = self.eload_cfg['validation']['valid'][
'metadata_spreadsheet']
sample_tab_submitter = SampleMetadataSubmitter(metadata_spreadsheet)
if sample_tab_submitter.check_submit_done() and not force:
self.info(
'Biosamples accession already provided in the metadata, Skip!')
self.eload_cfg.set('brokering', 'Biosamples', 'pass', value=True)
elif self.eload_cfg.query('brokering', 'Biosamples',
'Samples') and not force:
self.info('BioSamples brokering is already done, Skip!')
else:
sample_name_to_accession = sample_tab_submitter.submit_to_bioSamples(
)
self.eload_cfg.set('brokering',
'Biosamples',
'date',
value=self.now)
self.eload_cfg.set('brokering',
'Biosamples',
'Samples',
value=sample_name_to_accession)
self.eload_cfg.set('brokering',
'Biosamples',
'pass',
value=bool(sample_name_to_accession))
def upload_to_bioSamples(self, force=False):
metadata_spreadsheet = self.eload_cfg['validation']['valid']['metadata_spreadsheet']
sample_metadata_submitter = SampleMetadataSubmitter(metadata_spreadsheet)
if sample_metadata_submitter.check_submit_done() and not force:
self.info('Biosamples accession already provided in the metadata, Skip!')
self.eload_cfg.set('brokering', 'Biosamples', 'pass', value=True)
# Retrieve the sample names to accession from the metadata
sample_name_to_accession = sample_metadata_submitter.already_submitted_sample_names_to_accessions()
self.eload_cfg.set('brokering', 'Biosamples', 'Samples', value=sample_name_to_accession)
elif (
self.eload_cfg.query('brokering', 'Biosamples', 'Samples')
and self.eload_cfg.query('brokering', 'Biosamples', 'pass')
and not force
):
self.info('BioSamples brokering is already done, Skip!')
else:
sample_name_to_accession = sample_metadata_submitter.submit_to_bioSamples()
# Check whether all samples have been accessioned
passed = (
bool(sample_name_to_accession)
and all(sample_name in sample_name_to_accession for sample_name in sample_metadata_submitter.all_sample_names())
)
self.eload_cfg.set('brokering', 'Biosamples', 'date', value=self.now)
self.eload_cfg.set('brokering', 'Biosamples', 'Samples', value=sample_name_to_accession)
self.eload_cfg.set('brokering', 'Biosamples', 'pass', value=passed)
# Make sure we crash if we haven't brokered everything
if not passed:
raise ValueError('Brokering to BioSamples failed!')
def setUp(self) -> None:
brokering_folder = os.path.join(ROOT_DIR, 'tests', 'resources', 'brokering')
metadata_file1 = os.path.join(brokering_folder, 'metadata_sheet.xlsx')
metadata_file2 = os.path.join(brokering_folder, 'metadata_sheet2.xlsx')
metadata_partial_file = os.path.join(brokering_folder, 'metadata_sheet_partial.xlsx')
self.submitter_no_biosample_ids = SampleMetadataSubmitter(metadata_file1)
self.submitter = SampleMetadataSubmitter(metadata_file2)
self.submitter_partial_biosample_ids = SampleMetadataSubmitter(metadata_partial_file)
class TestSampleMetadataSubmitter(BSDTestCase):
top_dir = os.path.dirname(os.path.dirname(__file__))
resources_folder = os.path.join(os.path.dirname(__file__), 'resources')
def setUp(self) -> None:
brokering_folder = os.path.join(ROOT_DIR, 'tests', 'resources', 'brokering')
metadata_file1 = os.path.join(brokering_folder, 'metadata_sheet.xlsx')
metadata_file2 = os.path.join(brokering_folder, 'metadata_sheet2.xlsx')
self.submitter_no_biosample_ids = SampleMetadataSubmitter(metadata_file1)
self.submitter = SampleMetadataSubmitter(metadata_file2)
def test_map_metadata_to_bsd_data(self):
now = '2020-07-06T19:09:29.090Z'
biosamples_submission._now = now
expected_payload = [
{'name': 'S%s' % (i + 1), 'taxId': 9606, 'release': now,
'contact': [{'LastName': 'John', 'FirstName': 'Doe', 'E-mail': '*****@*****.**'},
{'LastName': 'Jane', 'FirstName': 'Doe', 'E-mail': '*****@*****.**'}],
'organization': [{'Name': 'GPE', 'Address': 'The place to be'},
{'Name': 'GPE', 'Address': 'The place to be'}],
'characteristics': {
'Organism': [{'text': 'H**o sapiens'}],
'description': [{'text': 'Sample %s' % (i+1)}],
'scientific name': [{'text': 'H**o sapiens'}]
}}
for i in range(100)
]
payload = self.submitter.map_metadata_to_bsd_data()
self.assertEqual(payload, expected_payload)
def test_check_submit_done(self):
# This data has already been brokered to BioSamples
self.assertTrue(self.submitter_no_biosample_ids.check_submit_done())
def test_check_submit_not_done(self):
# This submitter contains data to broker to BioSamples
self.assertFalse(self.submitter.check_submit_done())