view data_manager/recetox_metabolite_fetcher.py @ 0:953dd78a34d3 draft default tip

"planemo upload commit be4b24b2dacc3f23538068d5a6082bca246f6887"

import os
import errno

from argparse import ArgumentParser
from datetime import datetime
from json import dumps, loads
from urllib.parse import urlparse
from shutil import copy


def main(args):
    with open(args.data_manager_json, 'r') as json_in:
        data_manager_input = loads(json_in.read())
    target_directory = data_manager_input['output_data'][0]['extra_files_path']

    try:
        os.mkdir(target_directory)
    except OSError as exc:
        if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
            pass
        else:
            raise

    date = str(datetime.now())
    base = urlparse(args.database_url).hostname.split('.')[-2]
    name = f'{base}_{date}'.replace(' ', '_')

    if base not in ['hmdb', 't3db']:
        raise NameError('Unknown database')
    
    src = os.path.join(args.tool_data_dir, f'{base}.h5')
    dst = os.path.join(target_directory, f'{name}.h5')
    copy(src, dst)
        
    data_table_entry = {
        'data_tables': {
            'recetox_metabolite_databases' : [
                {
                    "value": name,
                    "name": name,
                    "date": date,
                    "path": f'{name}.h5',
                }
            ]
        }
    }

    with open(args.data_manager_json, 'w') as json_out:
        json_out.write(dumps(data_table_entry))


if __name__ == "__main__":
    parser = ArgumentParser()
    parser.add_argument('--tool_data_dir')
    parser.add_argument('--database_url')
    parser.add_argument('--data_manager_json')
    main(parser.parse_args())