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)