genMetadataFile

#!/usr/bin/env python3

import argparse
import flywheel
import fwgearutils
import json
import os
import pyjq
import subprocess
import sys

from flywheel_gear_toolkit import GearToolkitContext  # GearToolkitContext object allows metadata method

CmdName = os.path.basename(sys.argv[0])

ap = argparse.ArgumentParser()

ap.add_argument('-a', '--atlas', default=None, action='store', help='Atlas name')
ap.add_argument('-c', '--config-file', default=None, action='store', help='Config json file to use instead of default config.json')
ap.add_argument('-i', '--id-string', default=None, action='store', help='IdString: 7_anat_T1w-trimmed')
ap.add_argument('-n', '--no-op', default=False,  action='store_true', help='no-op')
ap.add_argument('-o', '--output-dir', default=None,  action='store', help='Directory to copy the Ashs output file to')
ap.add_argument('-t', '--tags', default=None,  action='store', help='comma separated list of tags to add to the files')
ap.add_argument('-v', '--verbose', default=False,  action='store_true', help='verbose')

ap.add_argument('ashsoutput', nargs='+', type=str, default=None, help='Files copy to output and add to .metadata.json')

args = ap.parse_args()

fw = fwgearutils.getFW(args, Root=True)
if (not fw):
    print("{} : unable to initialize flywheel object".format(CmdName), file=sys.stderr)
    sys.exit(1)

if (args.config_file):
   ConfigJsonFile = args.config_file
else:
   ConfigJsonFile='config.json'

#Modality = pyjq.all('first(..|.modality?|select(.!=null))', ConfigJson)
#Classification = pyjq.all('first(..|.classification?|select(.!=null))', ConfigJson)

IdString=args.id_string
Atlas=args.atlas

if (args.output_dir):
    OutputDir=args.output_dir
else:
    OutputDir="/flywheel/v0/output"

if (args.tags):
    TagArgs="-t {}".format(args.tags)
else:
    TagArgs=""

with GearToolkitContext(config_path=ConfigJsonFile) as context:    
    for File in args.ashsoutput:
        SubProcessCmd = "./copyFile2Output -a {} -c {} -i {} -o {} {} {}".format(
              Atlas
            , ConfigJsonFile
            , IdString
            , OutputDir
            , TagArgs
            , File
        )            
        if (args.verbose):
            print(CmdName + ": " + SubProcessCmd, file=sys.stderr)
            
        OutputJsonString = subprocess.getoutput(SubProcessCmd)

        if (args.verbose):
            print(OutputJsonString, file=sys.stderr)

        OutputJson = json.loads(OutputJsonString)

        OutputFilename = pyjq.all('.OutputFilename', OutputJson)[0]
        Metadata = pyjq.all('.Metadata', OutputJson)[0]

        if (Metadata):
            if (args.verbose):
                print("Filename = '{}', Metadata = '{}'".format(OutputFilename, Metadata), file=sys.stderr)

            if (not args.no_op):
                context.update_file_metadata(OutputFilename, **Metadata)