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
