def setup(self):
api = TransmartRestClient(self.mocked_config)
constraint = {'type': 'true'}
test_query_result = QueryResults(api.get_observations(constraint),
api.get_tree_nodes(),
api.get_dimensions(),
api.get_studies(),
api.get_relation_types(),
api.get_relations())
mapper = TransmartLoaderMapper()
self.qr_collection = mapper.map_query_results(test_query_result)
def copy_slice(self, constraint: Dict, output_dir: Path) -> None:
"""
Reads data from a TranSMART instance using the input constraint
and writes transmart-copy staging files to the output directory.
:param constraint the constraint to use when reading data
:param output_dir the directory to write staging files to
"""
Console.info('Reading data from tranSMART...')
transmart_client = TransmartRestClient(self.config)
query_results = QueryResults(
transmart_client.get_observations(constraint),
transmart_client.get_tree_nodes(depth=0, tags=True),
transmart_client.get_dimensions(), transmart_client.get_studies(),
transmart_client.get_relation_types(),
transmart_client.get_relations())
collection: DataCollection = TransmartLoaderMapper().map_query_results(
query_results)
Console.info('Writing files to {}'.format(output_dir))
copy_writer = TransmartCopyWriter(str(output_dir))
copy_writer.write_collection(collection)
Console.info('Done.')
def test_get_dimensions(mocked_config, mocked_responses):
api = TransmartRestClient(mocked_config)
response: Dimensions = api.get_dimensions()
assert len(response.dimensions) == 10