def create_site_bundle(syn: Synapse, question: int, site: str):
"""Creates workflow and entity bundles for the internal site submissions
Args:
syn: Synapse connection
question: Question number
site: Site
"""
shutil.copyfile(
os.path.join(SCRIPT_DIR, "../infrastructure/internal_workflow.cwl"),
os.path.join(SCRIPT_DIR,
f"../infrastructure/{question}_internal_workflow.cwl"))
internal = create_evaluation_queue(
syn, f"COVID-19 DREAM {site} - Question {question}")
syn.setPermissions(internal,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
internal_test = create_evaluation_queue(
syn, f"COVID-19 DREAM {site} - Question {question} TEST")
syn.setPermissions(internal_test,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
prod_wf = os.path.join("covid19-challenge-master/infrastructure",
f"{question}_internal_workflow.cwl")
test_wf = os.path.join("covid19-challenge-develop/infrastructure",
f"{question}_internal_workflow.cwl")
ent = create_entity(syn,
name=f"COVID-19 {site} Q{question}",
link=MASTER,
annotations={'ROOT_TEMPLATE': prod_wf})
test_ent = create_entity(syn,
name=f"COVID-19 {site} Q{question} TEST",
link=DEV,
annotations={'ROOT_TEMPLATE': test_wf})
print(f"Add to {site}'s docker-compose .env")
print({internal.id: ent.id, internal_test.id: test_ent.id})
return {
"internal_queueid": internal.id,
"internal_queue_testid": internal_test.id
}
def _set_acl(syn: Synapse, entity: Union[File, Folder, Project],
acl_config: dict):
"""Sets ACLs to Synapse entity
Args:
syn: Synapse connection
entity: Synapse Folder or Project
acl_config: ACL template json configuration
"""
for acl in acl_config:
syn.setPermissions(entity=entity,
principalId=acl['principal_id'],
accessType=acl['access_type'])
def create_main_bundle(syn: Synapse, question: int):
"""Creates workflow and entity bundles for the main submission
Args:
syn: Synapse connection
question: Question number
"""
shutil.copyfile(
os.path.join(SCRIPT_DIR, "../infrastructure/main_workflow.cwl"),
os.path.join(SCRIPT_DIR, f"../infrastructure/{question}_workflow.cwl"))
main_queue = create_evaluation_queue(
syn, f"COVID-19 DREAM Challenge - Question {question}")
# Global view
syn.setPermissions(main_queue, accessType=['READ'])
# Participant team
syn.setPermissions(main_queue, accessType=['READ'], principalId=3407543)
# Admin team
syn.setPermissions(main_queue,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
main_queue_test = create_evaluation_queue(
syn, f"COVID-19 DREAM Challenge - Question {question} TEST")
syn.setPermissions(main_queue_test,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
prof_wf = os.path.join("covid19-challenge-master/infrastructure",
f"{question}_workflow.cwl")
test_wf = os.path.join("covid19-challenge-develop/infrastructure",
f"{question}_workflow.cwl")
main_ent = create_entity(syn,
name=f"COVID-19 Q{question}",
link=MASTER,
annotations={'ROOT_TEMPLATE': prof_wf})
main_test_ent = create_entity(syn,
name=f"COVID-19 Q{question} TEST",
link=DEV,
annotations={'ROOT_TEMPLATE': test_wf})
print("Add to NCAT's docker-compose .env")
print({main_queue.id: main_ent.id, main_queue_test.id: main_test_ent.id})
return {
"main_queueid": main_queue.id,
"main_queue_testid": main_queue_test.id
}
def main():
# Parse command-line arguments
args = parse_arguments()
# Set up Synapse
syn = Synapse()
syn.login(args.username, args.password, rememberMe=args.remember)
# Retrieve Synapse entity (e.g., project, folder)
entity = syn.get(args.synid, downloadFile=False)
log("Entity", entity)
# Retrieve team
team = syn.getTeam(args.team) # TODO: Handle users with try-catch
log("Team", team)
# Assign specified permissions for given entity and team
permissions = syn.setPermissions(entity,
team.id,
accessType=args.permissions)
log("Permissions", permissions)
# Celebrate
print("Success!")