Source code for padmet_utils.connection.wikiGenerator

#!/usr/bin/env python
# -*- coding: utf-8 -*-
    Contains all necessary functions to generate wikiPages from a padmet file and update 
    a wiki online. Require WikiManager module (with wikiMate,Vendor)


    usage: --padmet=FILE/DIR --output=DIR --wiki_id=STR [--database=STR] [--padmetRef=FILE] [--log_file=FILE] [-v] --aureme_run=DIR --padmetSpec=ID -v
        -h --help     Show help.
        --padmet=FILE    path to padmet file.
        --output=DIR    path to folder to create with all wikipages in subdir.
        --wiki_id=STR    id of the wiki.
        --padmetRef=FILE    path to padmet of reference, ex: metacyc_xx.padmet, if given, able to calcul pathway rate completion.
        --log_file=FILE    log file from an aureme run, use this file to create a wikipage with all the command used during the aureme run.
        --aureme_run=DIR    can use an aureme run as input, will use from config file information for model_id and log_file and padmetRef.
        -v    print info.
from padmet.classes import PadmetRef
from padmet.utils.connection import wikiGenerator
import docopt

[docs]def main(): #files to upload: folder genomic_data, all sbml in output ortho, annot, external, seeds, targets args = docopt.docopt(__doc__) padmet = args["--padmet"] verbose = args["-v"] if args["--padmetRef"]: padmetRef = PadmetRef(args["--padmetRef"]) else: padmetRef = None wiki_id = args["--wiki_id"] output = args["--output"] log_file = args["--log_file"] database = args["--database"] wikiGenerator.wikiGenerator(padmet, output, wiki_id, padmetRef, database, log_file, verbose)
if __name__ == "__main__": main()