def test_md5_updater_newmd5(update_ffmeta_event_data_newmd5):
event = update_ffmeta_event_data_newmd5
tibanna_settings = event.get('_tibanna', {})
tibanna = pony_utils.Tibanna(**tibanna_settings)
awsem = Awsem(update_ffmeta_event_data_newmd5)
ouf = awsem.output_files()['report']
md5_updater('uploaded', ouf, None, tibanna)
def test_register_to_higlass2(used_env):
bucket = 'elasticbeanstalk-fourfront-webdev-wfoutput'
bigwig_key = 'a940cf00-6001-473e-80d1-1e4a43866863/4DNFI75GAT6T.bw'
tibanna = pony_utils.Tibanna(used_env)
with mock.patch('requests.post') as mock_request:
res = register_to_higlass(tibanna, bucket, bigwig_key, 'bigwig', 'vector')
mock_request.assert_called_once()
LOG.info(res)
assert res
def real_handler(event, context):
# check the status and other details of import
'''
this is to check if the task run is done:
http://docs.sevenbridges.com/reference#get-task-execution-details
'''
# get data
# used to automatically determine the environment
tibanna_settings = event.get('_tibanna', {})
tibanna = pony_utils.Tibanna(tibanna_settings['env'],
settings=tibanna_settings)
ff_meta = pony_utils.create_ffmeta_awsem(
app_name=event.get('ff_meta').get('awsem_app_name'),
**event.get('ff_meta'))
pf_meta = [
pony_utils.ProcessedFileMetadata(**pf) for pf in event.get('pf_meta')
]
# ensure this bad boy is always initialized
patch_meta = False
awsem = pony_utils.Awsem(event)
# go through this and replace awsemfile_report with awsf format
# actually interface should be look through ff_meta files and call
# give me the status of this thing from the runner, and runner.output_files.length
# so we just build a runner with interface to sbg and awsem
# runner.output_files.length()
# runner.output_files.file.status
# runner.output_files.file.loc
# runner.output_files.file.get
if event.get('error', False):
ff_meta.run_status = 'error'
ff_meta.description = event.get('error')
ff_meta.patch(key=tibanna.ff_keys)
raise Exception(event.get('error'))
awsem_output = awsem.output_files()
awsem_output_extra = awsem.secondary_output_files()
ff_output = len(ff_meta.output_files)
if len(awsem_output) != ff_output:
ff_meta.run_status = 'error'
ff_meta.description = "%d files output expected %s" % (
ff_output, len(awsem_output))
ff_meta.patch(key=tibanna.ff_keys)
raise Exception(
"Failing the workflow because outputed files = %d and ffmeta = %d"
% (awsem_output, ff_output))
for _, awsemfile in awsem_output.iteritems():
upload_key = awsemfile.key
status = awsemfile.status
print("awsemfile res is %s", status)
if status == 'COMPLETED':
patch_meta = OUTFILE_UPDATERS[awsemfile.argument_type]('uploaded',
awsemfile,
ff_meta,
tibanna)
if pf_meta:
for pf in pf_meta:
if pf.accession == awsemfile.accession:
try:
add_higlass_to_pf(pf, tibanna, awsemfile)
except Exception as e:
raise Exception("failed to regiter to higlass %s" %
e)
try:
add_md5_filesize_to_pf(pf, awsemfile)
except Exception as e:
raise Exception(
"failed to update processed file metadata %s" %
e)
elif status in ['FAILED']:
patch_meta = OUTFILE_UPDATERS[awsemfile.argument_type](
'upload failed', awsemfile, ff_meta, tibanna)
ff_meta.run_status = 'error'
ff_meta.patch(key=tibanna.ff_keys)
raise Exception("Failed to export file %s" % (upload_key))
for _, awsemfile in awsem_output_extra.iteritems():
upload_key = awsemfile.key
status = awsemfile.status
print("awsemfile res is %s", status)
if status == 'COMPLETED':
if pf_meta:
for pf in pf_meta:
if pf.accession == awsemfile.accession:
try:
add_md5_filesize_to_pf_extra(pf, awsemfile)
except Exception as e:
raise Exception(
"failed to update processed file metadata %s" %
e)
elif status in ['FAILED']:
ff_meta.run_status = 'error'
ff_meta.patch(key=tibanna.ff_keys)
raise Exception("Failed to export file %s" % (upload_key))
# if we got all the awsemfiles let's go ahead and update our ff_metadata object
ff_meta.run_status = "complete"
# allow for a simple way for updater to add appropriate meta_data
if patch_meta:
ff_meta.__dict__.update(patch_meta)
# add postrunjson log file to ff_meta as a url
ff_meta.awsem_postrun_json = get_postrunjson_url(event)
# make all the file awsemfile meta-data stuff here
# TODO: fix bugs with ff_meta mapping for output and input file
try:
ff_meta.patch(key=tibanna.ff_keys)
except Exception as e:
raise Exception("Failed to update run_status %s" % str(e))
# patch processed files - update only status, extra_files, md5sum and file_size
if pf_meta:
patch_fields = ['uuid', 'status', 'extra_files', 'md5sum', 'file_size']
try:
for pf in pf_meta:
print(pf.as_dict())
pf.patch(key=tibanna.ff_keys, fields=patch_fields)
except Exception as e:
raise Exception("Failed to update processed metadata %s" % str(e))
event['ff_meta'] = ff_meta.as_dict()
event['pf_meta'] = [_.as_dict() for _ in pf_meta]
return event