def test_get_observations(mocked_config, mocked_responses):
constraint = {'type': 'true'}
api = TransmartRestClient(mocked_config)
response: Hypercube = api.get_observations(constraint)
dimension_declaration = response.dimensionDeclarations
cells = response.cells
dimension_elements = response.dimensionElements
assert len(dimension_declaration) == 12
assert len(cells) == 3
assert len(dimension_elements) == 9
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.')