comparison data_manager/data_manager.py @ 2:ae5ddc5a6511 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit b63133897598f2881de7bad1f18fcd69d7d7e9df-dirty"

1:7548eaf95697

    # Fall back to Python 2 imports
    from urllib2 import Request, urlopen

ZENODO = {
    "mitos": "2683856",
    "mitos2": "3685310"
}
NAMES = {
    "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
    "refseq39": "RefSeq39 (equivalent to MITOS1 data)",
    "refseq63m": "RefSeq63 Metazoa",

                    break
    finally:
        if src:
            src.close()
    with tarfile.open(tarfname, "r:bz2") as tar:
        tar.extractall(workdir)
    os.remove(tarfname)
    unzipped = os.listdir(workdir)
    assert len(unzipped) == 1
    return unzipped[0]


def main(tpe, db, outjson):
    workdir = os.getcwd()

    data_manager_entry['name'] = NAMES[db]
    data_manager_entry['type'] = tpe
    data_manager_entry['path'] = path
    data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))

    params = json.loads(open(outjson).read())
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
    shutil.move(os.path.join(workdir, path), target_directory)
    with open(outjson, 'w') as fh:
        fh.write(json.dumps(data_manager_json))


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create data manager json.')
    parser.add_argument('--out', action='store', help='JSON filename')

2:ae5ddc5a6511

    # Fall back to Python 2 imports
    from urllib2 import Request, urlopen

ZENODO = {
    "mitos": "2683856",
    "mitos2": "4284483"
}
NAMES = {
    "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
    "refseq39": "RefSeq39 (equivalent to MITOS1 data)",
    "refseq63m": "RefSeq63 Metazoa",

                    break
    finally:
        if src:
            src.close()
    with tarfile.open(tarfname, "r:bz2") as tar:
        dirname = tar.getnames()[0]
        tar.extractall(workdir)
    os.remove(tarfname)
    return dirname


def main(tpe, db, outjson):
    workdir = os.getcwd()

    data_manager_entry['name'] = NAMES[db]
    data_manager_entry['type'] = tpe
    data_manager_entry['path'] = path
    data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))

    with open(outjson) as fh:
        params = json.load(fh)
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
    shutil.move(os.path.join(workdir, path), target_directory)
    with open(outjson, 'w') as fh:
        json.dump(data_manager_json, fh, sort_keys=True)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create data manager json.')
    parser.add_argument('--out', action='store', help='JSON filename')