view xena_import.py @ 14:55c1451f92b2

Determined that the tool installation works if the toolshed and changeset repository are both provided for the complex dependency. Testing with just the toolshed now.

#!/usr/bin/env python

"""
  xena_import.py: import a dataset into Xena

  Given a cmdline-specified genomic data file and a cmdline-specified Xena 
  directory, import the genomic data fle into Xena.  This requires assembling
  the necessary json file, based on cmdline input.
"""

import argparse
import json
import os
import shutil

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("genomicDataPathname", type=str)
    parser.add_argument("cohort", type=str)
    parser.add_argument("type", type=str)
    args = parser.parse_args()

    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
    xenaFileDir = xenaBaseDir + "/files"

    # Assemble the metadata in JSON format
    metadata = { 'cohort': args.cohort, 'type': args.type }
    jsonMetadata = json.dumps(metadata, indent=2) 
    
    # Write the metadata to a file in the Xena directory.  Use the filename
    # of the genomic data file, with an added .json extension.
    genomicDataFilename = args.genomicDataPathname.split("/")[-1]
    jsonMetadataPathname = "%s/%s.json" % (xenaFileDir, 
                                           genomicDataFilename)
    #fp = open("/inside/home/cline/tmp/xena_import.out", "w")
    #fp.write("xena file dir %s\n" % (xenaFileDir))
    #fp.write("copying metadata to %s and data to %s" % (jsonMetadataPathname, 
    #                                                    xenaFileDir))
    #fp.close()

    fp = open(jsonMetadataPathname, "w")
    fp.write("%s\n" % (jsonMetadata))
    fp.close()

    # Finally, copy the genomic data into the Xena directory
    shutil.copy(args.genomicDataPathname, xenaFileDir)

if __name__ == "__main__":
    main()