def submit_jobs(self,
username,
password,
subject_list,
config,
force_job_submission=False):
# submit jobs for the listed subjects
for subject in subject_list:
if not force_job_submission:
run_status_checker = one_subject_run_status_checker.OneSubjectRunStatusChecker(
)
if run_status_checker.get_queued_or_running(subject):
print("-----")
print("\t NOT SUBMITTING JOBS FOR")
print("\t project: " + subject.project)
print("\t subject: " + subject.subject_id)
print("\t session classifier: " + subject.classifier)
print("\t JOBS ARE ALREADY QUEUED OR RUNNING")
continue
submitter = one_subject_job_submitter.OneSubjectJobSubmitter(
self._archive, self._archive.build_home)
put_server_name = os.environ.get(
"XNAT_PBS_JOBS_PUT_SERVER_LIST").split(" ")
put_server = random.choice(put_server_name)
# get information for the subject from the configuration
clean_output_first = config.get_bool_value(subject.subject_id,
'CleanOutputFirst')
processing_stage_str = config.get_value(subject.subject_id,
'ProcessingStage')
processing_stage = submitter.processing_stage_from_string(
processing_stage_str)
walltime_limit_hrs = config.get_value(subject.subject_id,
'WalltimeLimitHours')
vmem_limit_gbs = config.get_value(subject.subject_id,
'VmemLimitGbs')
output_resource_suffix = config.get_value(subject.subject_id,
'OutputResourceSuffix')
brain_size = config.get_value(subject.subject_id, 'BrainSize')
use_prescan_normalized = config.get_bool_value(
subject.subject_id, 'UsePrescanNormalized')
print("-----")
print("\tSubmitting", submitter.PIPELINE_NAME, "jobs for:")
print("\t project:", subject.project)
print("\t subject:", subject.subject_id)
print("\t session classifier:", subject.classifier)
print("\t put_server:", put_server)
print("\t clean_output_first:", clean_output_first)
print("\t processing_stage:", processing_stage)
print("\t walltime_limit_hrs:", walltime_limit_hrs)
print("\t vmem_limit_gbs:", vmem_limit_gbs)
print("\toutput_resource_suffix:", output_resource_suffix)
print("\t brain_size:", brain_size)
print("\tuse_prescan_normalized:", use_prescan_normalized)
# configure one subject submitter
# user and server information
submitter.username = username
submitter.password = password
submitter.server = 'https://' + os_utils.getenv_required(
'XNAT_PBS_JOBS_XNAT_SERVER')
# subject and project information
submitter.project = subject.project
submitter.subject = subject.subject_id
submitter.session = subject.subject_id + '_' + subject.classifier
submitter.classifier = subject.classifier
submitter.brain_size = brain_size
submitter.use_prescan_normalized = use_prescan_normalized
# job parameters
submitter.clean_output_resource_first = clean_output_first
submitter.put_server = put_server
submitter.walltime_limit_hours = walltime_limit_hrs
submitter.vmem_limit_gbs = vmem_limit_gbs
submitter.output_resource_suffix = output_resource_suffix
# submit jobs
submitted_job_list = submitter.submit_jobs(processing_stage)
for job in submitted_job_list:
print("\tsubmitted jobs:", job)
print("-----")
print(completed_mark_cmd_process.stdout)
return
if __name__ == "__main__":
import ccf.structural_preprocessing.one_subject_run_status_checker as one_subject_run_status_checker
xnat_server = os_utils.getenv_required('XNAT_PBS_JOBS_XNAT_SERVER')
username, password = user_utils.get_credentials(xnat_server)
archive = ccf_archive.CcfArchive()
subject = ccf_subject.SubjectInfo(sys.argv[1], sys.argv[2], sys.argv[3])
submitter = OneSubjectJobSubmitter(archive, archive.build_home)
run_status_checker = one_subject_run_status_checker.OneSubjectRunStatusChecker(
)
if run_status_checker.get_queued_or_running(subject):
print("-----")
print("NOT SUBMITTING JOBS FOR")
print("project: " + subject.project)
print("subject: " + subject.subject_id)
print("session classifier: " + subject.classifier)
print("JOBS ARE ALREADY QUEUED OR RUNNING")
print('Process terminated')
sys.exit()
job_submitter = OneSubjectJobSubmitter(archive, archive.build_home)
put_server_name = os.environ.get("XNAT_PBS_JOBS_PUT_SERVER_LIST").split(
" ")
put_server = random.choice(put_server_name)