def test_start_awsem_handler_secondary_files( run_awsem_event_data_secondary_files): try: handler(run_awsem_event_data_secondary_files, '') except Exception as e: print(e) pytest.skip("seems data is not in place")
def test_pseudo_run_add_extra_meta(run_task_awsem_pseudo_workflow_event_data): wfr_meta = { 'description': 'test-descrip', 'awsem_job_id': 'test-pseudo-run', } run_task_awsem_pseudo_workflow_event_data['wfr_meta'] = wfr_meta res = handler(run_task_awsem_pseudo_workflow_event_data, '') assert (res) # did we set additional fields correctly for k, v in wfr_meta.iteritems(): assert res['ff_meta'][k] == v # just to be extra safe, also check pfmeta user_supplied_of = [ of['uuid'] for of in run_task_awsem_pseudo_workflow_event_data['output_files'] ] for pf in res['pf_meta']: assert pf['uuid'] in user_supplied_of for of in res['ff_meta']['output_files']: assert of['value'] in user_supplied_of
def test_start_awsem_handler(run_awsem_event_data): res = handler(run_awsem_event_data, '') assert(res) assert 'ff_meta' in res assert 'notes' in res['ff_meta'] assert 'award' in res['ff_meta'] assert res['ff_meta']['award'] == '/awards/1U01DA040582-01/'
def test_start_awsem_handler_processed_files( run_awsem_event_data_processed_files): res = handler(run_awsem_event_data_processed_files, '') assert (res) assert ('pf_meta' in res) assert ('source_experiments' in res['pf_meta'][0]) assert ('genome_assembly' in res['pf_meta'][0]) assert (res['pf_meta'][0]['genome_assembly'] == 'GRCh38')
def test_start_awsem_handler_processed_files(run_awsem_event_data_processed_files): with mock.patch('core.pony_utils.post_metadata') as mock_request: res = handler(run_awsem_event_data_processed_files, '') assert mock_request.call_count == 2 # one for wfr, two pfs. assert(res) assert('pf_meta' in res) assert('genome_assembly' in res['pf_meta'][0]) assert(res['pf_meta'][0]['genome_assembly'] == 'GRCh38')
def test_start_awsem_handler(run_awsem_event_data): with mock.patch('core.pony_utils.post_metadata') as mock_request: res = handler(run_awsem_event_data, '') assert mock_request.call_count == 1 # one for wfr, no pf assert (res) assert 'ff_meta' in res assert 'notes' in res['ff_meta'] assert 'award' in res['ff_meta'] assert res['ff_meta']['award'] == '/awards/1U01DA040582-01/'
def test_pseudo_run(run_task_awsem_pseudo_workflow_event_data): res = handler(run_task_awsem_pseudo_workflow_event_data, '') assert (res) # check pf_meta user_supplied_of = [ of['uuid'] for of in run_task_awsem_pseudo_workflow_event_data['output_files'] ] for pf in res['pf_meta']: assert pf['uuid'] in user_supplied_of for of in res['ff_meta']['output_files']: assert of['value'] in user_supplied_of
def test_pseudo_run(run_task_awsem_pseudo_workflow_event_data): with mock.patch('core.pony_utils.post_metadata') as mock_request: res = handler(run_task_awsem_pseudo_workflow_event_data, '') mock_request.assert_called_once() assert(res) # check pf_meta user_supplied_of = [of['uuid'] for of in run_task_awsem_pseudo_workflow_event_data['output_files']] for pf in res['pf_meta']: assert pf['uuid'] in user_supplied_of for of in res['ff_meta']['output_files']: assert of['value'] in user_supplied_of
def test_start_awsem_handler(run_awsem_event_data): res = handler(run_awsem_event_data, '') assert (res)
def test_start_awsem_handler_processed_files_pf(run_awsem_event_data_processed_files): with mock.patch('core.pony_utils.ProcessedFileMetadata.post') as mock_request: res = handler(run_awsem_event_data_processed_files, '') assert mock_request.call_count == 1 # one pf (bam). assert(res)