def test_config_validates_transfer_log():
config = transfer_log.Config({
'query': [{'session.label': 'Label'}, {'project.label': 'Project'}],
'join': 'session'
})
rows = [{'Label': 'ses-01', 'Project': 'My Project'}]
errors = transfer_log.check_config_and_log_match(config, rows)
assert not errors
def test_transfer_log_missing_column():
config = transfer_log.Config({
'query': [{'session.label': 'Label'}, {'project.label': 'Project'}],
'join': 'session'
})
rows = [{'Label': 'ses-01'}]
errors = transfer_log.check_config_and_log_match(config, rows)
assert len(errors) == 1
assert errors[0]['column'] == 'Project'
assert errors[0]['error'] == 'Transfer log missing column Project'
def test_config_mappings():
config = transfer_log.Config({
'query': [{'session.label': 'Label'}, {'project.label': 'Project'}],
'join': 'session',
'mappings': {
'Week 4': ['w04', 'wk4', 'Week_4']
}
})
assert config.mappings == {
'w04': 'Week 4',
'wk4': 'Week 4',
'Week_4': 'Week 4'
}
def test_transfer_log_invalid_value():
config = transfer_log.Config({
'query': [
{'session.label': 'Label', 'validate': '^[0-9]+$'},
{'project.label': 'Project'}
],
'join': 'session'
})
rows = [{'Label': 'ses-01', 'Project': 'My Project'}]
errors = transfer_log.check_config_and_log_match(config, rows)
print(errors)
assert len(errors) == 1
assert errors[0]['row'] == 2
assert errors[0]['column'] == 'Label'
def test_metadata_row():
config = transfer_log.Config(
{'query': [
{'subject.info.ClinicalTrialSiteID': 'SITE'},
{'subject.label': 'SUBJECT'},
{'session.label': 'VISIT'},
{'session.timestamp': 'SCAN DATE', 'timeformat': '%m/%d/%Y'}],
'join': 'session'}
)
test_meta_dict = {'SITE': '266099', 'SUBJECT': '1129', 'VISIT': 'screening', 'SCAN DATE': '8/1/2014'}
test_meta_row = transfer_log.MetadataRow(config=config, row_dict=test_meta_dict, index=2, case_insensitive=False)
expected_match_dict = {'subject.info.ClinicalTrialSiteID': '266099', 'subject.label': '1129',
'session.label': 'screening', 'session.timestamp': '08/01/2014'}
assert test_meta_row.match_dict == expected_match_dict
def test_flywheel_row():
config = transfer_log.Config(
{'query': [
{'subject.info.ClinicalTrialSiteID': 'SITE'},
{'subject.label': 'SUBJECT'},
{'session.label': 'VISIT'},
{'session.timestamp': 'SCAN DATE', 'timeformat': '%m/%d/%Y'}],
'join': 'session'}
)
test_fw_dict = {'subject.info.ClinicalTrialSiteID': '266099', 'subject.label': '1129',
'session.label': 'screening',
'session.timestamp': str(datetime.datetime(2014, 8, 1, tzinfo=datetime.timezone.utc))}
test_fw_index = 'test_id'
test_fw_row = transfer_log.FlywheelRow(config=config, row_dict=test_fw_dict.copy(), index=test_fw_index,
case_insensitive=False)
test_fw_dict['session.timestamp'] = '08/01/2014'
assert test_fw_row.spreadsheet_index == 'test_id'
assert test_fw_row.match_dict == test_fw_dict