comparison data_manager_fetch_mapseq_db.py @ 3:a0d77af1d226 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit b6798b5213eca0d4b176ad3aeef81127dac6dcab

2:23511530b8fd

    filename = wget.download(url, out=tmp_path)
    tarfile_path = os.path.join(tmp_path, filename)
    tar = tarfile.open(tarfile_path)
    tar.extractall(extract_path)

    if len(list(os.listdir(extract_path))) > 1:
        print("More then one folder in zipped file, aborting !")
    else:
        for folder in os.listdir(extract_path):
            folder_path = os.path.join(extract_path, folder)

            print(f"Copy data to {dest_path}")
            shutil.copytree(folder_path, dest_path)

def main():
    # Parse Command Line
    parser = argparse.ArgumentParser(description="Create data manager JSON.")
    parser.add_argument("--out", dest="output", action="store", help="JSON filename")
    parser.add_argument("--version", dest="version", action="store", help="Version of the DB")
    parser.add_argument("--database-type", dest="db_type", action="store", help="Db type")
    parser.add_argument(
        "--test",
        action="store_true",
        help="option to test the script with an lighted database",
    )

    # the output file of a DM is a json containing args that can be used by the DM
    # most tools mainly use these args to find the extra_files_path for the DM, which can be used
    # to store the DB data
    with open(args.output) as fh:
        params = json.load(fh)

    print(params)

    workdir = params["output_data"][0]["extra_files_path"]
    os.mkdir(workdir)

    time = datetime.utcnow().strftime("%Y-%m-%d")

3:a0d77af1d226

    filename = wget.download(url, out=tmp_path)
    tarfile_path = os.path.join(tmp_path, filename)
    tar = tarfile.open(tarfile_path)
    tar.extractall(extract_path)

    print(f"Content of folder: {extract_path}", os.listdir(extract_path))

    # case for mapseq v6: all DB files are directly in the tar.gz file
    # remove the VERSION.txt file since the tool can only handle on .txt file in the DB
    if len(list(os.listdir(extract_path))) > 1:
        print(f"Found multiple files in {extract_path}. Copy the content.")
        print(f"Copy data to {dest_path}")
        version_file_path = os.path.join(extract_path, "VERSION.txt")
        os.remove(version_file_path)
        shutil.copytree(extract_path, dest_path)
        print("Done !")

    # case for mapseq v5: all files are in a subfolder in the tar.gz file
    else:
        print(f"Found a folder in {extract_path}. Copy the content of the folder.")
        for folder in os.listdir(extract_path):
            folder_path = os.path.join(extract_path, folder)

            print(f"Copy data to {dest_path}")
            shutil.copytree(folder_path, dest_path)

def main():
    # Parse Command Line
    parser = argparse.ArgumentParser(description="Create data manager JSON.")
    parser.add_argument("--out", dest="output", action="store", help="JSON filename")
    parser.add_argument(
        "--version", dest="version", action="store", help="Version of the DB"
    )
    parser.add_argument(
        "--database-type", dest="db_type", action="store", help="Db type"
    )
    parser.add_argument(
        "--test",
        action="store_true",
        help="option to test the script with an lighted database",
    )

    # the output file of a DM is a json containing args that can be used by the DM
    # most tools mainly use these args to find the extra_files_path for the DM, which can be used
    # to store the DB data
    with open(args.output) as fh:
        params = json.load(fh)

    workdir = params["output_data"][0]["extra_files_path"]
    os.mkdir(workdir)

    time = datetime.utcnow().strftime("%Y-%m-%d")