comparison ms_data_converter.py @ 1:a36e9f847308 default tip

Fixes for running on Windows via pulsar

0:dfafbfd7983d

        stop_err("Number(s) of supplied input names and input files do not match")
    if not options.output:
        stop_err("Must specify output location")
    input_files = []
    for i, input in enumerate(options.inputs):
        input_base = None
        if len(options.input_names) > i:
            input_base = options.input_names[i]
            input_base = input_base.replace("'", "").replace("\"", "")
            print("1- input_base: %s" % input_base)

        if input not in options.implicits:
            input_files.append(input_file)
    ## AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
    inputs_as_str = " ".join(['%s' % shellquote(input) for input in input_files])
    output_file = re.sub('(%s)?$' % options.fromextension.lower(), options.toextension, input_files[0].lower())
    cmd = "AB_SCIEX_MS_Converter %s %s %s %s %s" % (options.fromextension.upper(), inputs_as_str, options.content_type, options.toextension.upper(), output_file )
    if str_to_bool(options.zlib):
        cmd = "%s %s" % (cmd, "/zlib")
    if options.binaryencoding:
        cmd = "%s %s" % (cmd, "/singleprecision" if options.binaryencoding == '32' else "/doubleprecision")
    if str_to_bool(options.zlib):
        cmd = "%s %s" % (cmd, "/index")
    if options.debug:
        print(cmd)
    execute(cmd)

1:a36e9f847308

        stop_err("Number(s) of supplied input names and input files do not match")
    if not options.output:
        stop_err("Must specify output location")
    input_files = []
    for i, input in enumerate(options.inputs):
        # the commnadline template cannot determine if optional files exists, so do it here
        if not os.path.exists(input):  
            continue
        input_base = None
        if len(options.input_names) > i:
            input_base = options.input_names[i]
            input_base = input_base.replace("'", "").replace("\"", "")
            print("1- input_base: %s" % input_base)

        if input not in options.implicits:
            input_files.append(input_file)
    ## AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
    inputs_as_str = " ".join(['%s' % shellquote(input) for input in input_files])
    output_file = re.sub('(%s)?$' % options.fromextension.lower(), options.toextension, input_files[0].lower())
    cmd = "AB_SCIEX_MS_Converter %s %s -%s %s %s" % (options.fromextension.upper(), inputs_as_str, options.content_type, options.toextension.upper(), output_file )
    if str_to_bool(options.zlib):
        cmd = "%s %s" % (cmd, "/zlib")
    if options.binaryencoding:
        cmd = "%s %s" % (cmd, "/singleprecision" if options.binaryencoding == '32' else "")
    if str_to_bool(options.zlib):
        cmd = "%s %s" % (cmd, "/index")
    if options.debug:
        print(cmd)
    execute(cmd)