def main(argsv):
parser = argparse.ArgumentParser(
description='Add one or more methods to Broad Methods Repository')
parser.add_argument('-n',
'--namespace',
dest='namespace',
action='store',
required=True,
help='Methods namespace')
parser.add_argument('-p',
'--public',
dest='public',
action='store_true',
help='Make methods publicly readable')
parser.add_argument(dest='wdl', help='Path to WDL file.', nargs='+')
args = parser.parse_args(argsv)
namespace = args.namespace
public = args.public
for wdl in args.wdl:
method_name = os.path.basename(wdl)
suffix = method_name.lower().rfind('.wdl')
if suffix != -1:
method_name = method_name[0:suffix]
method_acl = []
try:
existing_method = alto.get_method(namespace, method_name)
method_acl = fapi.get_repository_method_acl(
namespace=existing_method['namespace'],
method=existing_method['name'],
snapshot_id=existing_method['snapshotId']).json()
except ValueError:
pass
if public:
existing_public_user = False
for i in range(len(method_acl)):
if method_acl[i]['user'] == 'public':
existing_public_user = True
method_acl[i] = dict(user="******", role="READER")
break
if not existing_public_user:
method_acl.append(dict(user="******", role="READER"))
result = fapi.update_repository_method(namespace=namespace,
method=method_name,
wdl=wdl,
synopsis='')
if result.status_code == 201:
result = result.json()
if len(method_acl) > 0:
fapi.update_repository_method_acl(
namespace=result['namespace'],
method=result['name'],
snapshot_id=result['snapshotId'],
acl_updates=method_acl)
print(
'import "https://api.firecloud.org/ga4gh/v1/tools/{}:{}/versions/{}/plain-WDL/descriptor"'
.format(result['namespace'], result['name'],
result['snapshotId']))
else:
print('Unable to add {}'.format(method_name))
print(result.json())
def main(argv):
parser = argparse.ArgumentParser(description='Add one or more methods to Broad Methods Repository.')
parser.add_argument('-n', '--namespace', dest='namespace', action='store', required=True, help='Methods namespace')
parser.add_argument('-p', '--public', dest='public', action='store_true', help='Make methods publicly readable')
parser.add_argument(dest='wdl', help='Path to WDL file.', nargs='+')
args = parser.parse_args(argv)
namespace = args.namespace
public = args.public
n_success = 0
for wdl in args.wdl:
method_name = os.path.basename(wdl)
suffix = method_name.lower().rfind('.wdl')
if suffix != -1:
method_name = method_name[0:suffix]
method_acl = []
try:
existing_method = get_firecloud_workflow(namespace, method_name)
method_acl = fapi.get_repository_method_acl(namespace=existing_method['namespace'], method=existing_method['name'], snapshot_id=existing_method['snapshotId']).json()
except ValueError:
pass
if public:
existing_public_user = False
for i in range(len(method_acl)):
if method_acl[i]['user'] == 'public':
existing_public_user = True
method_acl[i] = dict(user='******', role='READER')
break
if not existing_public_user:
method_acl.append(dict(user='******', role='READER'))
result = fapi.update_repository_method(namespace=namespace, method=method_name, wdl=wdl, synopsis='')
if result.status_code == 201:
result = result.json()
if len(method_acl) > 0:
fapi.update_repository_method_acl(namespace=result['namespace'], method=result['name'], snapshot_id=result['snapshotId'], acl_updates=method_acl)
print(f'Workflow {method_name} is imported! See https://api.firecloud.org/ga4gh/v1/tools/{result["namespace"]}:{result["name"]}/versions/{result["snapshotId"]}/plain-WDL/descriptor')
n_success += 1
else:
print(f'Unable to add workflow {method_name} - {result.json()}')
print(f'Successfully added {n_success} workflows.')
execute(f'git remote add origin-staging "https://{GH_TOKEN}@github.com/{STAGING_TRAVIS_REPO_SLUG}.git"')
execute(f'git push --set-upstream origin-staging {STAGING_BRANCH}')
#dir(fapi)
#help(fapi)
#z = fapi.list_workspace_configs(namespace=SEL_NAMESPACE, workspace=SEL_WORKSPACE, allRepos=True).json()
#print('LIST_WORKSPACE_CONFIGS result is', z)
#z = fapi.get_workspace_config(workspace=SEL_WORKSPACE, namespace=SEL_NAMESPACE,
# config=TERRA_CONFIG_NAME, cnamespace=SEL_NAMESPACE)
#print('CONFIG_IS', z, z.json())
#z = fapi.list_repository_methods(namespace=SEL_NAMESPACE, name=TERRA_METHOD_NAME).json()
#print('METHODS LIST BEF', z)
z = fapi.update_repository_method(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, synopsis='run sims and compute component stats',
wdl=os.path.abspath(f'./Dockstore.wdl'))
#print('UPDATE IS', z, z.json())
new_method = z.json()
print('NEW_METHOD IS', new_method)
#z = fapi.list_repository_methods(namespace=SEL_NAMESPACE, name=TERRA_METHOD_NAME).json()
#print('METHODS LIST AFT', z)
snapshot_id = new_method['snapshotId']
z = fapi.get_repository_method_acl(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, snapshot_id=snapshot_id)
print('ACL:', z, z.json())
z = fapi.update_repository_method_acl(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, snapshot_id=snapshot_id,
acl_updates=[{'role': 'OWNER', 'user': '******'},
{'role': 'OWNER', 'user': '******'}])
def main():
if len(sys.argv) < 2:
return
global billing_project
global template_workspace_name
parser = argparse.ArgumentParser(prog="python " + sys.argv[0],
add_help=False)
subparser = parser.add_subparsers(dest="cmd")
delete_workspace = subparser.add_parser('delete_workspace',
help='delete workspace')
delete_workspace.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
clone_workspace = subparser.add_parser(
'clone_workspace', help='clone from existing workspace')
clone_workspace.add_argument('--source-work-space',
dest='src_work_space',
help="name of source workspace")
clone_workspace.add_argument('--destination-work-space',
dest='dest_work_space',
help="name of destination workspace")
get_data_info = subparser.add_parser('get_participant_table',
help='get participant.tsv')
get_data_info.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
get_data_info.add_argument('--participant-table-name',
dest="participant_table_name",
help="name of sample table")
get_data_info.add_argument('--output-name',
dest="output_table_name",
required=False,
default="participant.tsv",
help="name of output tsv")
create_participant_lane = subparser.add_parser(
'create_participant_lane',
help='create participant_lane/lane_set_id tables')
create_participant_lane.add_argument('--input-name',
dest="input_participant_table_name",
required=False,
default="participant.tsv",
help="input participant table name")
create_participant_lane.add_argument(
'--output-prefix',
dest="output_prefix",
required=False,
help="name of output prefix for the lanes")
upload_participant_lane = subparser.add_parser(
'upload_participant',
help=
'uploads the participant_lane_set, _lane_membership and _lane_entity files'
)
upload_participant_lane.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
upload_participant_lane.add_argument('--input-prefix',
dest="input_prefix",
help="name of the input prefix")
upload_workflow = subparser.add_parser(
'upload_workflow', help='uploads wdl to --workspace-name')
upload_workflow.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
upload_workflow.add_argument('--method',
dest="method",
help="name of the input prefix")
upload_workflow.add_argument('--wdl',
dest="wdl",
help="name of the input prefix")
upload_config = subparser.add_parser('upload_config',
help='upload config information')
upload_config.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
upload_config.add_argument('--chemistry',
dest="chemistry",
choices=["V2", "V3"],
help="chemistry")
upload_config.add_argument(
'--counting-mode',
dest="counting_mode",
choices=["sc_rna", "sn_rna"],
help="counting mode: whether to count intronic alignments")
upload_config.add_argument('--species',
dest="species",
choices=["human", "mouse"],
help="species")
submit_workflow = subparser.add_parser('submit_workflow',
help='submit a workflow run')
submit_workflow.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
submit_workflow.add_argument('--workflow-repo',
dest="workflow_repo",
help="workflow repo name")
submit_workflow.add_argument('--workflow-name',
dest="workflow_name",
help="workflow name")
submit_workflow.add_argument('--entity-id',
dest="entity_id",
help="entity id")
get_status = subparser.add_parser('get_status',
help='get status of a submission')
get_status.add_argument('--workspace-name',
dest="workspace_name",
help="name of the workspace")
get_status.add_argument('--submission-id',
dest="submission_id",
help="submission_id")
# show help when no arguments supplied
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
args = parser.parse_args()
# new_workspace_name = "DCP2_Optimus_template_KMK_v1"
if args.cmd == 'delete_workspace':
print("Delete existing workspace ", args.workspace_name)
delete_status = fapi.delete_workspace(billing_project,
args.workspace_name)
elif args.cmd == 'clone_workspace':
print("Cloning a new workspace from template", args.src_work_space)
status = create_newworkspace(billing_project, args.src_work_space,
args.dest_work_space)
elif args.cmd == 'get_participant_table':
print("Get information from workspace", args.workspace_name)
r = fapi.get_entities_tsv(billing_project, args.workspace_name,
args.participant_table_name)
with open(args.output_table_name, 'w') as fout:
fout.write(r.content.decode())
elif args.cmd == 'create_participant_lane':
parse_terra.create_output_files(args.input_participant_table_name,
args.output_prefix)
elif args.cmd == 'upload_participant':
upload_tables(args.input_prefix + ".tsv", billing_project,
args.workspace_name)
upload_tables(args.input_prefix + "_membership.tsv", billing_project,
args.workspace_name)
upload_tables(args.input_prefix + "_entity.tsv", billing_project,
args.workspace_name)
elif args.cmd == 'upload_workflow':
r = fapi.update_repository_method(args.workspace_name, args.method,
"args.synopsis", args.wdl,
"comment.txt", "args.comment")
with open("response.txt", 'w') as fout:
fout.write(r.content.decode())
elif args.cmd == 'upload_config':
work_space_config = fapi.get_workspace_config(billing_project,
args.workspace_name,
args.workspace_name,
"Optimus")
work_space_json = work_space_config.json()
work_space_json['inputs'] = json_templates.optimus_inputs
work_space_json['outputs'] = json_templates.optimus_outputs
if args.chemistry == "V2":
work_space_json['inputs']['Optimus.chemistry'] = '\"tenX_v2\"'
work_space_json['inputs'][
'Optimus.whitelist'] = 'workspace.whitelist_v2'
if args.chemistry == "V3":
work_space_json['inputs']['Optimus.chemistry'] = '\"tenX_v3\"'
work_space_json['inputs'][
'Optimus.whitelist'] = 'workspace.whitelist_v3'
if args.chemistry == "sn_rna":
work_space_json['inputs']['Optimus.counting_mode'] = "\"sn_rna\""
if args.chemistry == "sc_rna":
work_space_json['inputs']['Optimus.counting_mode'] = "\"sc_rna\""
if args.species == "human":
work_space_json['inputs'][
'Optimus.annotations_gtf'] = 'workspace.human_annotations_gtf'
work_space_json['inputs'][
'Optimus.ref_genome_fasta'] = 'workspace.human_ref_genome_fasta'
work_space_json['inputs'][
'Optimus.tar_star_reference'] = 'workspace.human_tar_star_reference'
if args.species == "mouse":
work_space_json['inputs'][
'Optimus.annotations_gtf'] = 'workspace.mouse_annotations_gtf'
work_space_json['inputs'][
'Optimus.ref_genome_fasta'] = 'workspace.mouse_ref_genome_fasta'
work_space_json['inputs'][
'Optimus.tar_star_reference'] = 'workspace.mouse_tar_star_reference'
updated_workflow = fapi.update_workspace_config(
billing_project, args.workspace_name, args.workspace_name,
"Optimus", work_space_json)
if updated_workflow.status_code != 200:
print("ERROR :" + updated_workflow.content)
sys.exit(1)
else:
print("updated successfully")
elif args.cmd == 'submit_workflow':
# Launching the Updated Monitor Submission Workflow
response = fapi.get_entities_with_type(billing_project,
args.workspace_name)
entities = response.json()
for ent in entities:
ent_name = ent['name']
ent_type = ent['entityType']
ent_attrs = ent['attributes']
submisson_response = fapi.create_submission(
billing_project,
args.workspace_name,
args.workflow_repo,
args.workflow_name,
entity=args.entity_id,
etype="participant_lane_set",
expression=None,
use_callcache=True)
if submisson_response.status_code != 201:
print(submisson_response.content)
sys.exit(1)
else:
print("Successfully Created Submisson")
with open('response.txt', 'w') as fout:
# json.dump(submisson_response.json(), fout)
fout.write(submisson_response.json()['submissionId'] + '\n')
# r = create_workspace_config("broadgdac", args.workspace_name, body):
# print(r.content.decode())
elif args.cmd == 'get_status':
res = fapi.get_submission(billing_project, args.workspace_name,
args.submission_id)
print(res.content.decode())
allRepos=True).json()
print(z)
z = fapi.get_workspace_config(workspace=SEL_WORKSPACE,
namespace=SEL_NAMESPACE,
config='dockstore-tool-cosi2',
cnamespace=SEL_NAMESPACE)
print('CONFIG_IS', z, z.json())
z = fapi.list_repository_methods(namespace=SEL_NAMESPACE,
name='test-cosi2-method-01').json()
print('METHODS LIST BEF', z)
z = fapi.update_repository_method(
namespace=SEL_NAMESPACE,
method='test-cosi2-method-01',
synopsis='run cosi2',
wdl='/data/ilya-work/proj/dockstore-tool-cosi2/Dockstore.wdl')
print('UPDATE IS', z, z.json())
new_method = z.json()
z = fapi.list_repository_methods(namespace=SEL_NAMESPACE,
name='test-cosi2-method-01').json()
print('METHODS LIST AFT', z)
z = fapi.get_config_template(namespace=SEL_NAMESPACE,
method='test-cosi2-method-01',
version=new_method['snapshotId'])
print('CONFIG TEMPLATE AFT IS', z, z.json())
config_template = z.json()