def rename_db_wf(workflow_id, new_name):
try:
d_wf = Workflows.query.filter(Workflows.id == workflow_id).first()
d_wf.name = new_name
db_session.commit()
return True
except:
return False
def delete_whole_db():
try:
db_session.query(WorkflowMessages).delete()
db_session.query(WorkflowJobs).delete()
db_session.query(Workflows).delete()
db_session.commit()
return True
except:
return False
def rename_db_job(workflow_id, job_id, new_name):
try:
job = WorkflowJobs.query.filter(WorkflowJobs.wf_id == workflow_id)\
.filter(WorkflowJobs.jobid == job_id).first()
job.name = new_name
db_session.commit()
return True
except:
return False
def create_workflow():
try:
w = Workflows(str(uuid.uuid4()), "Running")
db_session.add(w)
db_session.commit()
return w.get_workflow()
except:
traceback.print_exc()
return render_template('404.html')
def job_garbage_collector():
result = db_session.query(Workflows.id).all()
notin_list_tuple = tuple([r[0] for r in result])
result = db_session.query(WorkflowJobs.id).filter(
~WorkflowJobs.wf_id.in_(notin_list_tuple)).distinct()
in_list_tuple = tuple([r[0] for r in result])
if in_list_tuple:
delete_q = WorkflowJobs.__table__.delete().where(
WorkflowJobs.id.in_(in_list_tuple))
db_session.execute(delete_q)
db_session.commit()
return True
def delete_db_wf(workflow_id):
try:
db_session.query(WorkflowMessages).filter(
WorkflowMessages.wf_id == workflow_id).delete()
db_session.query(WorkflowJobs).filter(
WorkflowJobs.wf_id == workflow_id).delete()
d_wf = Workflows.query.filter(Workflows.id == workflow_id).first()
db_session.delete(d_wf)
db_session.commit()
msg_garbage_collector()
job_garbage_collector()
return True
except:
return False
def maintain_jobs(msg, wf_id):
# The message should be a json dump
msg_json = json.loads(msg)
if "jobid" in msg_json.keys():
if msg_json["level"] == 'job_info':
job = WorkflowJobs(
msg_json['jobid'],
wf_id,
msg_json['msg'],
msg_json['name'],
repr(msg_json['input']),
repr(msg_json['output']),
repr(msg_json['log']),
repr(msg_json['wildcards']),
msg_json['is_checkpoint'],
)
db_session.add(job)
db_session.commit()
return True
if msg_json["level"] == 'job_finished':
job = WorkflowJobs.query.filter(WorkflowJobs.wf_id == wf_id)\
.filter(WorkflowJobs.jobid == msg_json["jobid"]).first()
job.job_done()
db_session.commit()
return True
if msg_json["level"] == 'job_error':
job = WorkflowJobs.query.filter(WorkflowJobs.wf_id == wf_id)\
.filter(WorkflowJobs.jobid == msg_json["jobid"]).first()
job.job_error()
db_session.commit()
wf = Workflows.query.filter(Workflows.id == wf_id).first()
wf.set_error()
db_session.commit()
return True
if msg_json["level"] == 'info':
if msg_json['msg'] == 'Nothing to be done.':
wf = Workflows.query.filter(Workflows.id == wf_id).first()
wf.set_not_executed()
db_session.commit()
return True
if msg_json["level"] == 'progress':
wf = Workflows.query.filter(Workflows.id == wf_id).first()
wf.edit_workflow(msg_json['done'], msg_json['total'])
db_session.commit()
return True
if msg_json["level"] == 'error':
wf = Workflows.query.filter(Workflows.id == wf_id).first()
wf.set_error()
db_session.commit()
return True
if msg_json["level"] in ['shellcmd', '']:
w = WorkflowMessages(msg, wf_id=wf_id)
db_session.add(w)
db_session.commit()
return True
return False