def test_fourfront_starter2(start_run_nestedarray_data):
starter = FourfrontStarter(**start_run_nestedarray_data)
assert starter
starter.run()
assert len(starter.inp.args.input_files['input_file']['object_key']) == 2
assert len(
starter.inp.args.input_files['input_file']['object_key'][0]) == 2
def test_merge_source_experiment(start_run_md5_mount_data):
starter = FourfrontStarter(**start_run_md5_mount_data)
starter.create_ff()
starter.inp.add_args(starter.ff)
assert 'input_file' in starter.inp.args.input_files
assert 'mount' in starter.inp.args.input_files['input_file']
assert starter.inp.args.input_files['input_file']['mount']
def test_processed_extra_file_use_for(start_run_repliseq_data):
starter = FourfrontStarter(**start_run_repliseq_data)
exf = starter.pf_extra_files(['bg_px2', 'bw'], {
'file_format': 'bw',
'use_for': 'visualization'
})
assert len(exf) == 2
assert exf[1]['file_format'] == 'bw' and 'use_for' in exf[1]
assert exf[1]['use_for'] == 'visualization'
def test_fourfront_starter(start_run_md5_data):
starter = FourfrontStarter(**start_run_md5_data)
assert starter
assert 'arguments' in starter.inp.wf_meta
assert len(starter.inp.wf_meta['arguments']) == 2
assert starter.inp.wf_meta['arguments'][1][
'argument_type'] == 'Output report file'
starter.run()
assert len(starter.output_argnames) == 1
def test_fourfront_starter7(start_run_hicprocessingbam_customfield_wALL_data):
"""testing a case where input_bam is a list with two elements
and without an extra file. It should not add any null secondary files."""
starter = FourfrontStarter(
**start_run_hicprocessingbam_customfield_wALL_data)
assert starter
starter.run()
outjson = starter.inp.as_dict()
assert 'secondary_files' in outjson['args']
assert len(outjson['args']['secondary_files']) == 0
def test_fourfront_starter7c(start_run_hicprocessingbam_customfield_wALL_data):
"""testing a case where input_bam is a list with three elements,
two without an extra file and one with an extra file.
It should not add one element to the secondary files."""
data = start_run_hicprocessingbam_customfield_wALL_data
data['input_files'][0]['uuid'].append(
'8a64c5e9-b669-425c-a78a-3177abc9ebd5')
starter = FourfrontStarter(
**start_run_hicprocessingbam_customfield_wALL_data)
assert starter
starter.run()
outjson = starter.inp.as_dict()
assert 'secondary_files' in outjson['args']
assert len(outjson['args']['secondary_files']) == 1
def test_merge_source_experiment(start_run_md5_data):
input_file = {
"bucket_name":
"elasticbeanstalk-fourfront-webdev-wfoutput",
"workflow_argument_name":
"input_pairs",
"uuid": [
"d2c897ec-bdb2-47ce-b1b1-845daccaa571",
"d2c897ec-bdb2-47ce-b1b1-845daccaa571"
],
"object_key": ["4DNFI25JXLLI.pairs.gz", "4DNFI25JXLLI.pairs.gz"]
}
data = start_run_md5_data
starter = FourfrontStarter(**data)
starter.inp.input_files = [input_file]
res = starter.merge_source_experiments()
logger.debug("response from merge_source_experiment=" + str(res))
assert 'fake_source_experiment' in res
def test_add_meta_to_dynamodb(start_run_md5_data):
jobid = 'randomtestjobid-' + str(uuid.uuid4())
Job.add_to_dd(jobid, 'someexecname', 'somesfn', 'somelogbucket')
starter = FourfrontStarter(**start_run_md5_data)
starter.inp.jobid = jobid
starter.create_ff()
starter.add_meta_to_dynamodb()
logger.debug("jobid=%s" % jobid)
time.sleep(10)
dd_info = Job.info(jobid)
assert dd_info
print(dd_info)
assert 'WorkflowRun uuid' in dd_info
assert dd_info['WorkflowRun uuid'] == starter.ff.uuid
assert 'env' in dd_info
assert dd_info['env'] == starter.tbn.env
# cleanup
dd = boto3.client('dynamodb')
dd.delete_item(TableName=DYNAMODB_TABLE,
Key={DYNAMODB_KEYNAME: {
'S': jobid
}})
def test_fourfront_starter6(start_run_fixedname_data):
starter = FourfrontStarter(**start_run_fixedname_data)
assert starter
starter.run()
assert starter.inp.as_dict().get('_tibanna').get('run_name') == 'md5_test'
def test_fourfront_starter5(start_run_fail_data):
starter = FourfrontStarter(**start_run_fail_data)
assert starter
starter.run()
def test_fourfront_starter4(start_run_dependency_fail_data):
starter = FourfrontStarter(**start_run_dependency_fail_data)
assert starter
starter.run()
assert starter.inp.dependency
def test_fourfront_starter8(
start_run_hicprocessingbam_customfield_wArgname_data):
starter = FourfrontStarter(
**start_run_hicprocessingbam_customfield_wArgname_data)
assert starter
starter.run()