self.increment_shadow_number()
time.sleep(60)
if __name__ == "__main__":
# Get environment variables
scripts_home = os.getenv('SCRIPTS_HOME')
if scripts_home is None:
_inform("Environment variable SCRIPTS_HOME must be set!")
sys.exit(1)
home = os.getenv('HOME')
if home is None:
_inform("Environment variable HOME must be set!")
sys.exit(1)
# Get Connectome DB credentials
userid = input("Connectome DB Username: "******"Connectome DB Password: ")
# Get list of subjects to process
subject_file_name = file_utils.get_subjects_file_name(__file__)
_inform('Retrieving subject list from: ' + subject_file_name)
subject_list = hcp7t_subject.read_subject_info_list(subject_file_name)
# Process subjects in list
batch_submitter = DeDriftAndResampleHcp7T_HighResBatchSubmitter()
batch_submitter.submit_jobs(subject_list)
logger.info(" server: " + server)
logger.info(" packaging_stage: " + str(packaging_stage))
logger.info("-----")
submitter = one_subject_package_job_submitter.OneSubjectPackageJobSubmitter(self._archive, self._archive.build_home)
submitter.project = subject.project
submitter.subject = subject.subject_id
submitter.session = subject.subject_id + '_3T'
submitter.server = server
submitter.submit_jobs(packaging_stage)
if __name__ == '__main__':
# read the configuration file
config_file_name = file_utils.get_config_file_name(__file__)
logger.info("Reading configuration from file: " + config_file_name)
config = my_configparser.MyConfigParser()
config.read(config_file_name)
# get list of subjects to process
subject_file_name = file_utils.get_subjects_file_name(__file__)
logger.info("Retrieving subject list from: " + subject_file_name)
subject_list = hcp3t_subject.read_subject_info_list(subject_file_name, separator='\t')
# process the subjects in the list
batch_submitter = BatchPackagingSubmitter()
batch_submitter.submit_jobs(subject_list, config)
# submitter.vmem_limit_gbs = vmem_limit_gbs
submitter.clean_output_resource_first = clean_output_first
submitter.put_server = put_server
submitter.submit_jobs(processing_stage)
if __name__ == '__main__':
# get ConnectomeDB credentials
userid = input("Connectome DB Username: "******"Connectome DB Password: "******"Reading configuration from file: " + config_file_name)
config = my_configparser.MyConfigParser()
config.read(config_file_name)
# get list of subjects to process
subject_file_name = file_utils.get_subjects_file_name(__file__)
logger.info("Retrieving subject list from: " + subject_file_name)
subject_list = hcp3t_subject.read_subject_info_list(subject_file_name, separator='\t')
# process the subjects in the list
batch_submitter = BatchSubmitter()
batch_submitter.submit_jobs(subject_list, config)
submitter.put_server = put_server
submitter.submit_jobs()
if __name__ == "__main__":
# Get Environment varialbles
xnat_pbs_jobs_home = os.getenv('XNAT_PBS_JOBS')
if not xnat_pbs_jobs_home:
_inform("Environment variable XNAT_PBS_JOBS must be set!")
sys.exit(1)
# home = os.getenv('HOME')
# if home == None:
# _inform("Environment variable HOME must be set!")
# sys.exit(1)
# Get Connectome DB credentials
userid = input("Connectome DB Username: "******"Connectome DB Password: ")
# Get list of subjects to process
subject_file_name = 'SubmitDiffusionPreprocessingHCP7TBatch.subjects'
_inform('Retrieving subject list from: ' + subject_file_name)
subject_list = hcp7t_subject.read_subject_info_list(subject_file_name)
# Process the subjects in the list
batch_submitter = BatchSubmitter()
batch_submitter.submit_jobs(subject_list)
submitter.setup_script = setup_file
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.submit_jobs(processing_stage)
if __name__ == '__main__':
# get ConnectomeDB credentials
userid = input("Connectome DB Username: "******"Connectome DB Password: "******"Reading configuration from file: " + config_file_name)
config = my_configparser.MyConfigParser()
config.read(config_file_name)
# get list of subjects to process
subject_file_name = file_utils.get_subjects_file_name(__file__)
logger.info("Retrieving subject list from: " + subject_file_name)
subject_list = hcp3t_subject.read_subject_info_list(subject_file_name, separator=':')
# process the subjects in the list
batch_submitter = BatchSubmitter()
batch_submitter.submit_jobs(userid, password, subject_list, config)