view data_manager/bigg_model_sbml_fetcher.py @ 5:5e6f76507721 draft

"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"

import argparse
import ast
import json
import os
import sys
import time
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


MODEL_URL = 'http://bigg.ucsd.edu/static/models/'
MODEL_DETAIL_URL = 'http://bigg.ucsd.edu/api/v2/models/'


def url_download(url, path):
    try:
        with urlopen(Request(url)) as fod:
            with open(path, 'wb') as dst:
                while True:
                    chunk = fod.read(2**10)
                    if chunk:
                        dst.write(chunk)
                    else:
                        break
    except Exception as e:
        sys.exit(str(e))


def url_json(url):
    data = {}
    try:
        with urlopen(Request(url)) as fod:
            data = fod.read().encode('utf-8')
        data = ast.literal_evals(data)
    except Exception as e:
        sys.exit(str(e))
    return data


def get_model_organism(model_id):
    data = url_json(MODEL_DETAIL_URL + model_id)
    org = data.get('organism', 'undefined')
    res = "(%s) %s" (model_id, org)
    return res


def download_entries(model_ids, workdir):
    for model_id in model_ids:
        model_filename = model_id + '.xml'
        path = os.path.abspath(os.path.join(workdir, model_filename))

        url_download(MODEL_DETAIL_URL + model_filename, path)
        data_manager_entry = {}
        data_manager_entry['value'] = model_id
        data_manager_entry['name'] = get_model_organism(model_id)
        data_manager_entry['path'] = path

        # Make sure that less than 10 requests per second, as required by host (http://bigg.ucsd.edu/data_access)
        time.sleep(1)
        yield data_manager_entry


if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    pinput = parser.add_mutually_exclusive_group(required=True)
    pinput.add_argument('--model-id', help='Model BIGG id')
    pinput.add_argument('--model-all', action='store_true', help='Download all models')
    parser.add_argument('--out-file', help='JSON output file')
    args = parser.parse_args()

    # Init.
    data_manager_json = {'data_tables': {}}
    with open(args.out_file) as fh:
        params = json.load(fh)

    workdir = params['output_data'][0]['extra_files_path']
    os.makedirs(workdir)

    model_ids = []
    if args.model_id:
        model_ids.append(args.model_id)
    else:
        data = url_json(MODEL_DETAIL_URL)
        for result in data.get("results", []):
            model_ids.append(result.get("bigg_id"))

    entries = list(download_entries(model_ids, workdir))

    # Write data.
    data_manager_json['data_tables']['bigg_model_sbml'] = entries
    with open(args.out_file, 'w') as fh:
        json.dump(data_manager_json, fh, sort_keys=True)