# configure logging and create module logger logging.config.fileConfig(file_utils.get_logging_config_file_name(__file__)) logger = logging.getLogger(file_utils.get_logger_name(__file__)) # module constants DNM = "---" # Does Not Matter NA = "N/A" # Not Available DATE_FORMAT = '%Y-%m-%d %H:%M:%S' if __name__ == '__main__': # get list of subjects to check 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') # open complete and incomplete files for writing complete_file = open('complete.status', 'w') incomplete_file = open('incomplete.status', 'w') # create archive access object archive = hcp3t_archive.Hcp3T_Archive() # create on subject completion checker completion_checker = one_subject_completion_checker.OneSubjectCompletionChecker( ) # create and output the header line header_line = "\t".join([ "Project", "Subject ID", "Output Resource Exists",
if __name__ == '__main__': # Get environment variables packages_root = os.getenv('PACKAGES_ROOT') if not packages_root: log.info("Environment variable PACKAGES_ROOT must be set!") sys.exit(1) # Create archive access object archive = hcp3t_archive.Hcp3T_Archive() # Get list of subjects subject_file_name = file_utils.get_subjects_file_name(__file__) log.info("Retrieving subject list from: " + subject_file_name) subject_list = hcp3t_subject.read_subject_info_list(subject_file_name) print("Project", end="\t") print("Subject ID", end="\t") print("Preproc Resource Date", end="\t") print("Package Path", end="\t") print("Package Exists", end="\t") print("Package Date", end="\t") print("Package Size", end="\t") print("Package Newer Than Resource", end="\t") print("Checksum Exists", end="\t") print("Checksum Date", end="\t") print("Checksum Newer Than Package") for subject in subject_list:
if __name__ == '__main__': # Get environment variables packages_root = os.getenv('PACKAGES_ROOT') if not packages_root: log.info("Environment variable PACKAGES_ROOT must be set!") sys.exit(1) # Create archive access object archive = hcp3t_archive.Hcp3T_Archive() # Get list of subjects subject_file_name = file_utils.get_subjects_file_name(__file__) log.info("Retrieving subject list from: " + subject_file_name) subject_list = hcp3t_subject.read_subject_info_list(subject_file_name) # Print header row print("Project", end="\t") print("Subject ID", end="\t") print("FIX Processed Exists", end="\t") print("Last FIX Resource Date", end="\t") print("Package Path", end="\t") print("Package Exists", end="\t") print("Package Date", end="\t") print("Package Size", end="\t") print("Package Newer Than Last FIX Resource", end="\t") print("Checksum Exists", end="\t") print("Checksum Date", end="\t") print("Checksum Newer Than Package")
# 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)