def handler(event, context):
'''
this is to check if the task run is done:
http://docs.sevenbridges.com/reference#get-task-execution-details
'''
# used to automatically determine the environment
tibanna_settings = event.get('_tibanna', {})
tibanna = Tibanna(**tibanna_settings)
sbg = sbg_utils.create_sbg_workflow(token=tibanna.sbg_keys, **event.get('workflow'))
ff_meta = ff_utils.create_ffmeta(sbg, **event.get('ff_meta'))
# check status of workflow, error if not done
status = sbg.check_task()
LOG.info("status of sbg task is %s" % status)
if not status['status'] in ['DONE', 'COMPLETED', 'FAILED']:
data = {'workflow': sbg.as_dict(),
'status': status}
raise sbg_utils.SBGStillRunningException('Task not finished => %s' % data)
if status['status'] == 'FAILED':
ff_meta.run_status = 'error'
ff_meta.description = 'SBG task %s reported FAILED status' % sbg.task_id
ff_meta.post(key=tibanna.ff_keys)
# TODO: handle only specific errors so this can terminate the rest of the workflow
return {'workflow': sbg.as_dict(),
'run_response': status,
'ff_meta': ff_meta.as_dict(),
'pf_meta': event.get('pf_meta'),
'_tibanna': tibanna.as_dict(),
}
def test_proc_file_for_arg_name(run_awsem_event_data_processed_files,
proc_file_in_webdev):
of = [{
"workflow_argument_name": "output_file1",
"uuid": proc_file_in_webdev['uuid']
}, {
"workflow_argument_name": "output_file2",
"uuid": "f4864029-a8ad-4bb8-93e7-5108f46bbbbb"
}]
tibanna_settings = run_awsem_event_data_processed_files.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(
env,
ff_keys=run_awsem_event_data_processed_files.get('ff_keys'),
settings=tibanna_settings)
file_with_type = proc_file_in_webdev.copy()
file_with_type['@type'] = ['FileProcessed', 'Item', 'whatever']
with mock.patch('core.utils.get_metadata', return_value=file_with_type):
pf, resp = proc_file_for_arg_name(of, 'output_file1', tibanna)
assert type(pf) == ProcessedFileMetadata
assert pf.__dict__ == proc_file_in_webdev
def test_handle_processed_files(run_awsf_event_data_secondary_files):
data = run_awsf_event_data_secondary_files
tibanna_settings = data.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env,
s3_keys=data.get('s3_keys'),
ff_keys=data.get('ff_keys'),
settings=tibanna_settings)
workflow_uuid = data['workflow_uuid']
workflow_info = ff_utils.get_metadata(workflow_uuid, key=tibanna.ff_keys)
output_files, pf_meta = handle_processed_files(workflow_info, tibanna)
assert (output_files)
assert len(output_files) == 3
for of in output_files:
if of['extension'] == '.pairs.gz':
assert of['secondary_file_extensions'] == ['.pairs.gz.px2']
assert of['secondary_file_formats'] == ['pairs_px2']
assert of['extra_files']
else:
assert 'secondary_files_extension' not in of
assert 'secondary_files_formats' not in of
assert (pf_meta)
assert len(pf_meta) == 3
for pf in pf_meta:
pdict = pf.__dict__
if pdict['file_format'] == 'pairs':
assert pdict['extra_files'] == [{'file_format': 'pairs_px2'}]
else:
assert 'extra_files' not in pdict
def test_add_secondary_files_to_args(run_awsem_event_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"]
}
args = {
'input_files': {
'input_pairs': {
'bucket':
'elasticbeanstalk-fourfront-webdev-wfoutput',
'object_key': [
'd2c897ec-bdb2-47ce-b1b1-845daccaa571/4DNFI25JXLLI.pairs.gz',
'd2c897ec-bdb2-47ce-b1b1-845daccaa571/4DNFI25JXLLI.pairs.gz'
]
}
}
}
data = run_awsem_event_data
tibanna_settings = data.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env,
ff_keys=data.get('ff_keys'),
settings=tibanna_settings)
add_secondary_files_to_args(input_file, tibanna.ff_keys, tibanna.env, args)
def run_md5(ctx, env, accession, uuid):
tibanna = Tibanna(env=env)
meta_data = get_metadata(accession, key=tibanna.ff_keys)
file_name = meta_data['upload_key'].split('/')[-1]
input_json = make_input(env=env,
workflow='md5',
object_key=file_name,
uuid=uuid)
return _run_workflow(input_json, accession)
def test_get_format_extension_map(run_awsem_event_data):
tibanna_settings = run_awsem_event_data.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env, ff_keys=run_awsem_event_data.get('ff_keys'),
settings=tibanna_settings)
fe_map = get_format_extension_map(tibanna.ff_keys)
assert(fe_map)
assert 'pairs' in fe_map.keys()
def handler(event, context):
'''
export output files from sbg to our s3
'''
# get data
# used to automatically determine the environment
tibanna_settings = event.get('_tibanna', {})
tibanna = Tibanna(**tibanna_settings)
sbg = sbg_utils.create_sbg_workflow(token=tibanna.sbg_keys,
**event.get('workflow'))
run_response = event.get('run_response')
ff_meta = event.get('ff_meta')
uuid = ff_meta['uuid']
pf_meta = event.get('pf_meta')
if run_response in ['FAILED', 'ABORTED']:
raise Exception("workflow run failed or aborted")
sbg.export_all_output_files(run_response, ff_meta, base_dir=uuid)
# creating after we export will add output file info to ff_meta
ff_meta = ff_utils.create_ffmeta(sbg, **event.get('ff_meta'))
ff_meta.run_status = "output_files_transferring"
ff_meta.post(key=tibanna.ff_keys)
for pf in pf_meta:
pf['status'] = "uploading"
# we still need a code for patching.
return {
'workflow': sbg.as_dict(),
'ff_meta': ff_meta.as_dict(),
# 'pf_meta': [pf.as_dict() for pf in pf_meta]
'pf_meta': pf_meta,
'_tibanna': tibanna.as_dict()
}
def batch_fastqc(ctx, env, batch_size=20):
'''
try to run fastqc on everythign that needs it ran
'''
files_processed = 0
files_skipped = 0
# handle ctrl-c
import signal
def report(signum, frame):
print("Processed %s files, skipped %s files" %
(files_processed, files_skipped))
sys.exit(-1)
signal.signal(signal.SIGINT, report)
tibanna = Tibanna(env=env)
uploaded_files = get_files_to_match(
tibanna,
"search/?type=File&status=uploaded&limit=%s" % batch_size,
frame="embedded")
# TODO: need to change submit 4dn to not overwrite my limit
if len(uploaded_files['@graph']) > batch_size:
limited_files = uploaded_files['@graph'][:batch_size]
else:
limited_files = uploaded_files['@graph']
for ufile in limited_files:
fastqc_run = False
for wfrun in ufile.get('workflow_run_inputs', []):
if 'fastqc' in wfrun:
fastqc_run = True
if not fastqc_run:
print("running fastqc for %s" % ufile.get('accession'))
run_fastqc(ctx, env, ufile.get('accession'), ufile.get('uuid'))
files_processed += 1
else:
print("******** fastqc already run for %s skipping" %
ufile.get('accession'))
files_skipped += 1
sleep(5)
if files_processed % 10 == 0:
sleep(60)
print("Processed %s files, skipped %s files" %
(files_processed, files_skipped))
def test_merge_source_experiment(run_awsem_event_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 = run_awsem_event_data
tibanna_settings = data.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env, ff_keys=data.get('ff_keys'),
settings=tibanna_settings)
res = merge_source_experiments(input_file['uuid'], tibanna.ff_keys, tibanna.env)
LOG.info(res)
assert 'fake_source_experiment' in res
def test_handle_processed_files2(run_awsem_event_data_processed_files2):
data = run_awsem_event_data_processed_files2
tibanna_settings = data.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env,
ff_keys=data.get('ff_keys'),
settings=tibanna_settings)
workflow_uuid = data['workflow_uuid']
workflow_info = ff_utils.get_metadata(workflow_uuid, key=tibanna.ff_keys)
output_files, pf_meta = handle_processed_files(
workflow_info, tibanna, custom_fields=data.get('custom_pf_fields'))
assert (pf_meta)
assert (output_files)
for pf in pf_meta:
pdict = pf.__dict__
assert 'genome_assembly' in pdict
assert pdict['genome_assembly'] == 'GRCh38'
def is_status_uploading(event):
print("is status uploading: %s" % event)
upload_key = event['Records'][0]['s3']['object']['key']
if upload_key.endswith('html'):
return False
uuid, object_key = upload_key.split('/')
accession = object_key.split('.')[0]
# guess env from bucket name
bucket = event['Records'][0]['s3']['bucket']['name']
env = '-'.join(bucket.split('-')[1:3])
tibanna = Tibanna(env=env)
meta = get_metadata(accession,
key=tibanna.ff_keys,
ff_env=env,
add_on='frame=object',
check_queue=True)
if meta:
return meta.get('status', '') == 'uploading'
else:
return False
def test_process_input_file_info(run_awsem_event_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"]
}
args = {'input_files': {"some_input": {}, "some_other_input": {}}}
data = run_awsem_event_data
tibanna_settings = data.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env')
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env,
ff_keys=data.get('ff_keys'),
settings=tibanna_settings)
process_input_file_info(input_file, tibanna.ff_keys, tibanna.env, args)
assert len(args['input_files']) == 3
assert 'secondary_files' in args
def batch_md5(ctx, env, batch_size=20):
'''
try to run fastqc on everythign that needs it ran
'''
tibanna = Tibanna(env=env)
file_bucket = tibanna.s3.outfile_bucket.replace('wfoutput', 'files')
tibanna.s3.outfile_bucket = file_bucket
uploaded_files = get_files_to_match(tibanna,
"search/?type=File&status=uploading",
frame="embedded")
limited_files = uploaded_files['@graph']
files_processed = 0
total_files = len(limited_files)
skipped_files = 0
for ufile in limited_files:
if files_processed >= batch_size:
print("we have done enough here")
sys.exit(0)
if not tibanna.s3.does_key_exist(ufile.get('upload_key')):
print("******** no file for %s on s3, can't run md5, skipping" %
ufile.get('accession'))
skipped_files += 1
continue
else:
print("running md5 for %s" % ufile.get('accession'))
run_md5(ctx, env, ufile.get('accession'), ufile.get('uuid'))
files_processed += 1
sleep(10)
if files_processed % 10 == 0:
sleep(60)
print("Total Files: %s, Processed Files: %s, Skipped Files: %s" %
(total_files, files_processed, skipped_files))
def real_handler(event, context):
'''
this is generic function to run awsem workflow
based on the data passed in
workflow_uuid : for now, pass this on. Later we can add a code to automatically retrieve this from app_name.
Note multiple workflow_uuids can be available for an app_name
(different versions of the same app could have a different uuid)
'''
# get incomming data
input_file_list = event.get('input_files')
for infile in input_file_list:
if not infile:
raise ("malformed input, check your input_files")
app_name = event.get('app_name')
print(app_name)
workflow_uuid = event.get('workflow_uuid')
output_bucket = event.get('output_bucket')
parameters = ff_utils.convert_param(event.get('parameters'), True)
tibanna_settings = event.get('_tibanna', {})
tag = event.get('tag')
# if they don't pass in env guess it from output_bucket
try:
env = tibanna_settings.get('env',
'-'.join(output_bucket.split('-')[1:-1]))
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env,
ff_keys=event.get('ff_keys'),
settings=tibanna_settings)
except Exception as e:
raise TibannaStartException("%s" % e)
args = dict()
# get argument format & type info from workflow
workflow_info = ff_utils.get_metadata(workflow_uuid,
key=tibanna.ff_keys,
ff_env=tibanna.env,
add_on='frame=object')
print("workflow info %s" % workflow_info)
LOG.info("workflow info %s" % workflow_info)
if 'error' in workflow_info.get('@type', []):
raise Exception("FATAL, can't lookup workflow info for %s fourfront" %
workflow_uuid)
# get cwl info from workflow_info
for k in [
'app_name', 'app_version', 'cwl_directory_url',
'cwl_main_filename', 'cwl_child_filenames'
]:
print(workflow_info.get(k))
LOG.info(workflow_info.get(k))
args[k] = workflow_info.get(k)
if not args['cwl_child_filenames']:
args['cwl_child_filenames'] = []
# switch to v1 if available
if 'cwl_directory_url_v1' in workflow_info: # use CWL v1
args['cwl_directory_url'] = workflow_info['cwl_directory_url_v1']
args['cwl_version'] = 'v1'
else:
args['cwl_version'] = 'draft3'
# create the ff_meta output info
input_files = []
for input_file in input_file_list:
for idx, uuid in enumerate(ensure_list(input_file['uuid'])):
input_files.append({
'workflow_argument_name':
input_file['workflow_argument_name'],
'value':
uuid,
'ordinal':
idx + 1
})
print("input_files is %s" % input_files)
LOG.info("input_files is %s" % input_files)
# input file args for awsem
for input_file in input_file_list:
process_input_file_info(input_file, tibanna.ff_keys, tibanna.env, args)
# source experiments
input_file_uuids = [_['uuid'] for _ in input_file_list]
pf_source_experiments = merge_source_experiments(input_file_uuids,
tibanna.ff_keys,
tibanna.env)
# processed file metadata
output_files, pf_meta = handle_processed_files(
workflow_info,
tibanna,
pf_source_experiments,
custom_fields=event.get('custom_pf_fields'),
user_supplied_output_files=event.get('output_files'))
print("output files= %s" % str(output_files))
# 4DN dcic award and lab are used here, unless provided in wfr_meta
ff_meta = create_ffmeta_awsem(
workflow_uuid,
app_name,
input_files,
tag=tag,
run_url=tibanna.settings.get('url', ''),
output_files=output_files,
parameters=parameters,
extra_meta=event.get('wfr_meta'),
)
print("ff_meta is %s" % ff_meta.__dict__)
LOG.info("ff_meta is %s" % ff_meta.__dict__)
# store metadata so we know the run has started
ff_meta.post(key=tibanna.ff_keys)
# parameters
args['input_parameters'] = event.get('parameters')
# output target
args['output_target'] = dict()
args['secondary_output_target'] = dict()
for of in ff_meta.output_files:
arg_name = of.get('workflow_argument_name')
if of.get('type') == 'Output processed file':
args['output_target'][arg_name] = of.get('upload_key')
else:
args['output_target'][arg_name] = ff_meta.uuid + '/' + arg_name
if 'secondary_file_formats' in of:
# takes only the first secondary file.
args['secondary_output_target'][arg_name] \
= [_.get('upload_key') for _ in of.get('extra_files', [{}, ])]
# output bucket
args['output_S3_bucket'] = event.get('output_bucket')
# initialize config parameters as null for benchmarking
config = event['config']
if 'instance_type' not in config:
config['instance_type'] = ''
if 'EBS_optimized' not in config:
config['EBS_optimized'] = ''
if 'ebs_size' not in config:
config['ebs_size'] = 0
event.update({
"ff_meta": ff_meta.as_dict(),
'pf_meta': [meta.as_dict() for meta in pf_meta],
"_tibanna": tibanna.as_dict(),
"args": args
})
return (event)
def handler(event, context):
'''
this is generic function to run sbg workflow
based on the data passed in
workflow_uuid : for now, pass this on. Later we can add a code to automatically retrieve this from app_name.
Note multiple workflow_uuids can be available for an app_name
(different versions of the same app could have a different uuid)
'''
# get incomming data
input_file_list = event.get('input_files')
app_name = event.get('app_name')
parameter_dict = event.get('parameters')
workflow_uuid = event.get('workflow_uuid')
output_bucket = event.get('output_bucket')
tibanna_settings = event.get('_tibanna', {})
# if they don't pass in env guess it from output_bucket
env = tibanna_settings.get('env', '-'.join(output_bucket.split('-')[1:-1]))
# tibanna provides access to keys based on env and stuff like that
tibanna = Tibanna(env,
s3_keys=event.get('s3_keys'),
ff_keys=event.get('ff_keys'),
settings=tibanna_settings)
LOG.info("input data is %s" % event)
# represents the SBG info we need
sbg = sbg_utils.create_sbg_workflow(app_name, tibanna.sbg_keys)
LOG.info("sbg is %s" % sbg.__dict__)
# represents the workflow metadata to be stored in fourfront
parameters, _ = sbg_utils.to_sbg_workflow_args(parameter_dict,
vals_as_string=True)
# get argument format & type info from workflow
workflow_info = ff_utils.get_metadata(workflow_uuid, key=tibanna.ff_keys)
LOG.info("workflow info %s" % workflow_info)
if 'error' in workflow_info.get('@type', []):
raise Exception("FATAL, can't lookupt workflow info for % fourfront" %
workflow_uuid)
# This dictionary has a key 'arguments' with a value
# { 'workflow_argument_name': ..., 'argument_type': ..., 'argument_format': ... }
# get format-extension map
try:
fp_schema = ff_utils.get_metadata("profiles/file_processed.json",
key=tibanna.ff_keys)
fe_map = fp_schema.get('file_format_file_extension')
except Exception as e:
LOG.error(
"Can't get format-extension map from file_processed schema. %s\n" %
e)
# processed file metadata
output_files = []
try:
if 'arguments' in workflow_info:
pf_meta = []
for arg in workflow_info.get('arguments'):
if (arg.get('argument_type') in [
'Output processed file', 'Output report file',
'Output QC file'
]):
of = dict()
of['workflow_argument_name'] = arg.get(
'workflow_argument_name')
of['type'] = arg.get('argument_type')
if 'argument_format' in arg:
# These are not processed files but report or QC files.
pf = ff_utils.ProcessedFileMetadata(
file_format=arg.get('argument_format'))
try:
resp = pf.post(
key=tibanna.ff_keys
) # actually post processed file metadata here
resp = resp.get('@graph')[0]
of['upload_key'] = resp.get('upload_key')
of['value'] = resp.get('uuid')
except Exception as e:
LOG.error(
"Failed to post Processed file metadata. %s\n"
% e)
LOG.error("resp" + str(resp) + "\n")
raise e
of['format'] = arg.get('argument_format')
of['extension'] = fe_map.get(
arg.get('argument_format'))
pf_meta.append(pf)
output_files.append(of)
except Exception as e:
LOG.error("output_files = " + str(output_files) + "\n")
LOG.error("Can't prepare output_files information. %s\n" % e)
raise e
# create the ff_meta output info
input_files = []
for input_file in input_file_list:
for idx, uuid in enumerate(ensure_list(input_file['uuid'])):
input_files.append({
'workflow_argument_name':
input_file['workflow_argument_name'],
'value':
uuid,
'ordinal':
idx + 1
})
LOG.info("input_files is %s" % input_files)
ff_meta = ff_utils.create_ffmeta(sbg,
workflow_uuid,
input_files,
parameters,
run_url=tibanna.settings.get('url', ''),
output_files=output_files)
LOG.info("ff_meta is %s" % ff_meta.__dict__)
# store metadata so we know the run has started
ff_meta.post(key=tibanna.ff_keys)
# mount all input files to sbg this will also update sbg to store the import_ids
for infile in input_file_list:
imps = mount_on_sbg(infile, tibanna.s3_keys, sbg)
infile['import_ids'] = imps
# create a link to the output directory as well
if output_bucket:
sbg_volume = sbg_utils.create_sbg_volume_details()
res = sbg.create_volumes(sbg_volume,
output_bucket,
public_key=tibanna.s3_keys['key'],
secret_key=tibanna.s3_keys['secret'])
vol_id = res.get('id')
if not vol_id:
# we got an error
raise Exception("Unable to mount output volume, error is %s " %
res)
sbg.output_volume_id = vol_id
# let's not pass keys in plain text parameters
return {
"input_file_args": input_file_list,
"workflow": sbg.as_dict(),
"ff_meta": ff_meta.as_dict(),
'pf_meta': [meta.as_dict() for meta in pf_meta],
"_tibanna": tibanna.as_dict(),
"parameter_dict": parameter_dict
}
def test_tibanna():
data = {'env': 'fourfront-webdev', 'settings': {'1': '1'}}
tibanna = Tibanna(**data)
assert tibanna
assert tibanna.as_dict() == data
