comparison xena_import.py @ 38:1ef1886dae04

data import sucess/unsuccess message more informative

37:97325a1202d2

    # with zero status.
    xenaLoadCmd = "java -jar %s -l --force %s/%s -p %s" % (xena.jarPath(),
                                                           xenaFileDir,
                                                           genomicDataFile, 
                                                           xena.port())
    loadInToXena (xenaLoadCmd, genomicDataFile, fp2)
    if args.probeMap is not None:
        xenaLoadCmd = "java -jar %s -l --force %s/%s -p %s" % (xena.jarPath(),
                                                               xenaFileDir,
                                                               probeMapDataFile,
                                                               xena.port())
        loadInToXena (xenaLoadCmd, probeMapDataFile, fp2)
    fp2.close()

def loadInToXena (xenaLoadCmd, name, fp2):
    print xenaLoadCmd
    try:

        lines = traceback.format_exception(exc_type, exc_value, exc_traceback)
        allLines = ''.join('!! ' + line for line in lines)
        fp2.write("Unsuccessful: Import %s\n" % (name))
        fp2.write("Unsuccessful: error %s\n" % allLines)
    else:
        fp2.write( "Import %s is successful\n" % (name))

if __name__ == "__main__":
    main()

38:1ef1886dae04

    # with zero status.
    xenaLoadCmd = "java -jar %s -l --force %s/%s -p %s" % (xena.jarPath(),
                                                           xenaFileDir,
                                                           genomicDataFile, 
                                                           xena.port())
    if args.label is not None:
        name = args.label
    else:
        name = genomicDataFile
    loadInToXena (xenaLoadCmd, name, fp2)

    if args.probeMap is not None:
        xenaLoadCmd = "java -jar %s -l --force %s/%s -p %s" % (xena.jarPath(),
                                                               xenaFileDir,
                                                               probeMapDataFile,
                                                               xena.port())
        loadInToXena (xenaLoadCmd, "id to gene mapping file for %s" % (name), fp2)
    fp2.close()

def loadInToXena (xenaLoadCmd, name, fp2):
    print xenaLoadCmd
    try:

        lines = traceback.format_exception(exc_type, exc_value, exc_traceback)
        allLines = ''.join('!! ' + line for line in lines)
        fp2.write("Unsuccessful: Import %s\n" % (name))
        fp2.write("Unsuccessful: error %s\n" % allLines)
    else:
        fp2.write( "Importing %s is successful\n" % (name))

if __name__ == "__main__":
    main()