# 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)
