comparison data_manager/bigg_model_sbml_fetcher.py @ 0:262b8d79bc08 draft

"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"

0:262b8d79bc08

import argparse
import json
import os
import sys
try:
    # For Python 3.0 and later
    from urllib.request import Request, urlopen
except ImportError:
    # Fall back to Python 2 imports
    from urllib2 import Request, urlopen


def url_download(url, workdir):
    file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
    src = None
    dst = None
    try:
        req = Request(url)
        src = urlopen(req)
        with open(file_path, 'wb') as dst:
            while True:
                chunk = src.read(2**10)
                if chunk:
                    dst.write(chunk)
                else:
                    break
    except Exception as e:
        sys.exit(str(e))
    finally:
        if src:
            src.close()
    return file_path


def download(model_id, out_file):

    with open(out_file) as fh:
        params = json.load(fh)

    workdir = params['output_data'][0]['extra_files_path']
    os.makedirs(workdir)
    file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml' % (model_id,), workdir)
    entry_name = os.path.basename(file_path)

    data_manager_json = {"data_tables": {}}
    data_manager_entry = {}
    data_manager_entry['value'] = model_id
    data_manager_entry['name'] = entry_name
    data_manager_entry['path'] = file_path

    with open(out_file, 'w') as fh:
        json.dump(data_manager_json, fh, sort_keys=True)


parser = argparse.ArgumentParser()

parser.add_argument('--model-id', help='Model id')
parser.add_argument('--out-file', help='JSON output file')

args = parser.parse_args()

download(args.model_id, args.out_file)