subject_list = ccf_subject.read_subject_info_list(subject_file_name,
separator=":")
# open output file
output_file = open('FunctionalPreprocessing.status', 'w')
_write_header(output_file)
# create archive
archive = ccf_archive.CcfArchive()
# create one subject checkers
completion_checker = one_subject_completion_checker.OneSubjectCompletionChecker(
)
prereq_checker = one_subject_prereq_checker.OneSubjectPrereqChecker()
running_checker = one_subject_run_status_checker.OneSubjectRunStatusChecker(
)
for subject in subject_list:
project = subject.project
subject_id = subject.subject_id
classifier = subject.classifier
scan = subject.extra
prereqs_met = prereq_checker.are_prereqs_met(archive, subject)
queued_or_running = running_checker.get_queued_or_running(subject)
if completion_checker.does_processed_resource_exist(archive, subject):
resource_exists = True
fullpath = archive.functional_preproc_dir_full_path(subject)
resource = archive.functional_preproc_dir_name(subject)
def submit_jobs(self, username, password, subject_list, config):
# submit jobs for the listed subject scans
for subject in subject_list:
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 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 = 'http://intradb-shadow'
# ####put_server += str(self.get_and_inc_shadow_number())
# ####put_server += '.nrg.mir:8080'
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/scan 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')
print("-----")
print("\tSubmitting", submitter.PIPELINE_NAME, "jobs for:")
print("\t project:", subject.project)
print("\t subject:", subject.subject_id)
print("\t scan:", subject.extra)
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)
# 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.classifier = subject.classifier
submitter.session = subject.subject_id + '_' + subject.classifier
submitter.scan = subject.extra
# 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("-----")