save-to-workspaces.py

#!/usr/bin/env python
#
#   Usage:
#       ./save-to-workspaces.py -h
#
#   Example:
#        ./save-to-workspaces.py --include-only .png --dir ../some/dir/ --ws /username/models/ecoli/
#

import io
import json
import sys
import os
import base64
import argparse
from api.patric import workspace as wsclient
from api.kbase import workspace as kbwsclient


parser = argparse.ArgumentParser()
parser.add_argument('-s', '--skip', help="skip any file with substring match")
parser.add_argument('-i', '--include-only', help="only include files with this substring match")
parser.add_argument('-f', '--file', help="file to upload")
parser.add_argument('-d', '--dir', help="directory to upload")
parser.add_argument('-w', '--ws', help="workspace path where files will be saved", required=True)
parser.add_argument('-k', '--kbase', help="save to kbase workspace", action='store_true')
args = parser.parse_args()


with open(os.environ['HOME'] + '/.rastauth') as file:
    token = file.read()


ws = wsclient.Workspace(token=token);           #patric
kbws = kbwsclient.Workspace(url="https://ci.kbase.us/services/ws");          #kbase (uses .authrc file in home)

def save_all():
    print '\n\n*** Saving all files  ***\n'

    os.chdir(args.dir)

    for name in os.listdir(os.getcwd()):

        # skip any names that don't have substring for --include-only option
        if (args.include_only and args.include_only not in name):
            continue

        # skip any substring matches for --skip option
        if (args.skip and any(sub in name for sub in args.skip.split(',') ) ):
            print 'skipping:', name
            continue

        with open(name, "rb") as f:
            encoded_string = base64.b64encode(f.read())

        print 'saving:', args.ws+name

        if (args.kbase):
            kbws.save_objects({'workspace': args.ws,
                               'objects': [
                                   {'type': 'KBaseBiochem.MetabolicMap',
                                    'data':  {'id': encoded_string,
                                              'name': name,
                                              'source_id': '',
                                              'source': '',
                                              'reaction_ids': [],
                                              'compound_ids': [],
                                              'groups': [],
                                              'compounds': [],
                                              'reactions': [],
                                              'linkedmaps': []},   # , name, source_id, source, reaction_ids, compound_ids, groups, reactions, compounds, linkedmaps
                                    'name': name,
                                    'meta': {} }]
                              })
        else:
            ws.create({'objects': [[args.ws+name, 'png', {}, encoded_string]], 'overwrite': True})



        print


if __name__ == "__main__":

    if (args.file):
        pass
    if (args.dir):
        save_all()

    print 'Done.'