def test_get_object_from_json(self): client = DatasetClient() dataset = client.get_dataset_details("pride", "PXD000210") # dataset = Dataset.get_object_from_json(object_json) assert dataset.accession == "PXD000210" assert dataset.title == "Proteome analysis by charge state-selective separation of peptides: a multidimensional approach" assert len(dataset.dates) > 0 assert len(dataset.scores) > 0 assert len(dataset.cross_references) > 0 assert len(dataset.keywords) > 0 assert len(dataset.organisms) > 0 assert len(dataset.get_posttranslational_modifications()) == 7 assert len(dataset.get_diseases()) == 0 assert len(dataset.get_tissues()) == 0 dataset_transcriptomics = client.get_dataset_details("arrayexpress-repository", "E-TABM-555") # dataset_transcriptomics = Dataset.get_object_from_json(object_json) assert dataset_transcriptomics.accession == "E-TABM-555" assert dataset_transcriptomics.title == "Transcription profiling of rat to investigate technical and biological variability on the Agilent platform" assert len(dataset_transcriptomics.dates) > 0 assert len(dataset_transcriptomics.scores) > 0 assert len(dataset_transcriptomics.cross_references) > 0 assert len(dataset_transcriptomics.keywords) > 0 assert len(dataset_transcriptomics.organisms) > 0 assert len(dataset_transcriptomics.get_posttranslational_modifications()) == 0 assert len(dataset_transcriptomics.get_diseases()) == 0 assert len(dataset_transcriptomics.get_tissues()) == 4
def test_get_dataset_details(self): """ check the details for one dataset. :return: """ client = DatasetClient() dataset = client.get_dataset_details("pride", "PXD000210", False) assert dataset['accession'] == "PXD000210" assert len(dataset['description']) == 2227 try: dataset = client.get_dataset_details("PXD@£", "pride") except BadRequest as err: assert err.status == 500 try: dataset = client.get_dataset_details(None, "pride") except BadRequest as err: assert err.status == MISSING_PARAMETER
def file_links(source, acc): client = DatasetClient() api_output = client.get_dataset_details(source, acc) file_links = {} if api_output.files: files = api_output.files[0]['files'] else: click.echo('INFO') click.echo( f'The accession {acc} is found in the {source} database, but contains no files.' ) sys.exit() return files