def is_in_gallery(id_job, mode="webserver"):
if mode == "webserver":
from dgenies.database import Gallery, Job
from peewee import DoesNotExist
try:
return len(Gallery.select().where(Gallery.job == Job.get(id_job=id_job))) > 0
except DoesNotExist:
return False
return False
def prepare_job(id_job):
_printer("Prepare data for job:", id_job)
with Job.connect():
job = Job.get(Job.id_job == id_job)
job.status = "preparing"
job.save()
job_mng = JobManager(id_job=id_job, email=job.email, tool=job.tool)
job_mng.set_inputs_from_res_dir()
job_mng.prepare_data_in_thread()
def start_job(id_job, batch_system_type="local"):
_printer("Start job", id_job)
with Job.connect():
job = Job.get(Job.id_job == id_job)
job.status = "starting"
job.save()
job_mng = JobManager(id_job=id_job, email=job.email, tool=job.tool)
job_mng.set_inputs_from_res_dir()
job_mng.run_job_in_thread(batch_system_type)
def move_job_to_cluster(id_job):
"""
Change local job to be run on the cluster
:param id_job:
:return:
"""
with Job.connect():
job = Job.get(Job.id_job == id_job)
job.batch_type = config_reader.batch_system_type
job.save()
def get_mail_for_job(id_job):
"""
Retrieve associated mail for a job
:param id_job: job id
:type id_job: int
:return: associated mail address
:rtype: str
"""
from dgenies.database import Job
with Job.connect():
j1 = Job.get(Job.id_job == id_job)
return j1.email
def prepare_job(id_job):
"""
Launch job preparation of data
:param id_job: job id
:type id_job: str
"""
_printer("Prepare data for job:", id_job)
with Job.connect():
job = Job.get(Job.id_job == id_job)
job.status = "preparing"
job.save()
job_mng = JobManager(id_job=id_job, email=job.email, tool=job.tool)
job_mng.set_inputs_from_res_dir()
job_mng.prepare_data_in_thread()
def start_job(id_job, batch_system_type="local"):
"""
Start a job (mapping step)
:param id_job: job id
:type id_job: str
:param batch_system_type: local, slurm or sge
:type batch_system_type: str
"""
_printer("Start job", id_job)
with Job.connect():
job = Job.get(Job.id_job == id_job)
job.status = "starting"
job.save()
job_mng = JobManager(id_job=id_job, email=job.email, tool=job.tool)
job_mng.set_inputs_from_res_dir()
job_mng.run_job_in_thread(batch_system_type)
def is_in_gallery(id_job, mode="webserver"):
"""
Check whether a job is in the gallery
:param id_job: job id
:type id_job: str
:param mode: webserver or standalone
:type mode: str
:return: True if job is in the gallery, else False
:rtype: bool
"""
if mode == "webserver":
from dgenies.database import Gallery, Job
from peewee import DoesNotExist
try:
return len(Gallery.select().where(Gallery.job == Job.get(
id_job=id_job))) > 0
except DoesNotExist:
return False
return False
def get_mail_for_job(id_job):
from dgenies.database import Job
with Job.connect():
j1 = Job.get(Job.id_job == id_job)
return j1.email
def move_job_to_cluster(id_job):
with Job.connect():
job = Job.get(Job.id_job == id_job)
job.batch_type = config_reader.batch_system_type
job.save()