def test_convert_miniml_control(): geo_id = 'GSE99650' gsm_id = 'GSM2649283' test_data_dir = f'docs/example_data/{geo_id}' # created by this in test environment testargs = ["__program__", '-i', geo_id, '-d', test_data_dir, '-k', 'SKTR'] with patch.object(sys, 'argv', testargs): convert_miniml( geo_id, data_dir=test_data_dir, merge=True, download_it=True, extract_controls=True, require_keyword=None, sync_idats=True, remove_tgz=True, verbose=True) files_found = list(Path(test_data_dir).rglob('*')) if len(files_found) != 3: raise AssertionError("Did not download all the files.") samplesheet = pd.read_csv(Path(test_data_dir,f'{geo_id}_GPL13534_samplesheet.csv')) if samplesheet['GSM_ID'][0] != gsm_id: raise AssertionError("Samplesheet did not contain the right data.") if len(samplesheet['GSM_ID']) != 1: raise AssertionError("Control filtering failed") for file in Path(test_data_dir).rglob('*.xml'): file.unlink() for file in Path(test_data_dir).rglob('*.pkl'): file.unlink() for file in Path(test_data_dir).rglob('*.csv'): file.unlink() for file in Path(test_data_dir).rglob('*.tgz'): file.unlink() Path(test_data_dir).rmdir()
def test_convert_miniml(): geo_id = 'GSE17769' test_data_dir = f'docs/example_data/{geo_id}' # created by this in test environment testargs = ["__program__", '-i', geo_id, '-d', test_data_dir] with patch.object(sys, 'argv', testargs): convert_miniml(geo_id, data_dir=test_data_dir, merge=True, download_it=True, extract_controls=False, require_keyword=None, sync_idats=True, remove_tgz=True, verbose=True) #for file in Path(test_data_dir).rglob('*.xml'): # file.unlink() shutil.rmtree(test_data_dir)