comparison data_manager/data_manager_qiime_download.py @ 3:cc18f0f3514c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

2:cbe065fbd038

    NB the directory pointed to by 'extra_files_path'
    doesn't exist initially, it is the job of the script
    to create it if necessary.

    """
    params = json.loads(open(jsonfile).read())
    return (params['param_dict'],
            params['output_data'][0]['extra_files_path'])


# Utility functions for creating data table dictionaries

# Example usage:
# >>> d = create_data_tables_dict()
# >>> add_data_table(d,'my_data')
# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
# >>> print str(json.dumps(d))
def create_data_tables_dict():
    """Return a dictionary for storing data table information

    Returns a dictionary that can be used with 'add_data_table'
    and 'add_data_table_entry' to store information about a

def get_ftp_file(ftp, filename):
    """
    """
    try:
        ftp.retrbinary("RETR " + filename, open(filename, 'wb').write)
    except Exception:
        print("Error")


def download_archive(db, version, ext):

def extract_archive(filepath, ext, db):
    """
    """
    archive_content_path = "tmp"
    if ext == "tar.gz" or ext == "tgz":
        tar = tarfile.open(filepath)
        tar.extractall(path=archive_content_path)
        tar.close()
        archive_content_path = find_archive_content_path(archive_content_path)
    elif ext == "zip":
        zip_ref = zipfile.ZipFile(filepath, 'r')
        zip_ref.extractall(archive_content_path)
        zip_ref.close()
        archive_content_path = find_archive_content_path(archive_content_path)
    return archive_content_path


def move_unite_files(archive_content_path, filename_prefix, name_prefix, data_tables, target_dir):

        args.version,
        target_dir)

    # Write output JSON
    print("Outputting JSON")
    print(str(json.dumps(data_tables)))
    with open(jsonfile, 'w') as out:
        json.dump(data_tables, out)
    print("Done.")

3:cc18f0f3514c

    NB the directory pointed to by 'extra_files_path'
    doesn't exist initially, it is the job of the script
    to create it if necessary.

    """
    with open(jsonfile) as fh:
        params = json.load(fh)
    return (params['param_dict'],
            params['output_data'][0]['extra_files_path'])


# Utility functions for creating data table dictionaries

# Example usage:
# >>> d = create_data_tables_dict()
# >>> add_data_table(d,'my_data')
# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
# >>> print(json.dumps(d))
def create_data_tables_dict():
    """Return a dictionary for storing data table information

    Returns a dictionary that can be used with 'add_data_table'
    and 'add_data_table_entry' to store information about a

def get_ftp_file(ftp, filename):
    """
    """
    try:
        with open(filename, 'wb') as fh:
            ftp.retrbinary("RETR " + filename, fh.write)
    except Exception:
        print("Error")


def download_archive(db, version, ext):

def extract_archive(filepath, ext, db):
    """
    """
    archive_content_path = "tmp"
    if ext == "tar.gz" or ext == "tgz":
        with tarfile.open(filepath) as tar:
            tar.extractall(path=archive_content_path)
        archive_content_path = find_archive_content_path(archive_content_path)
    elif ext == "zip":
        with zipfile.ZipFile(filepath, 'r') as zip_ref:
            zip_ref.extractall(archive_content_path)
        archive_content_path = find_archive_content_path(archive_content_path)
    return archive_content_path


def move_unite_files(archive_content_path, filename_prefix, name_prefix, data_tables, target_dir):

        args.version,
        target_dir)

    # Write output JSON
    print("Outputting JSON")
    with open(jsonfile, 'w') as out:
        json.dump(data_tables, out, sort_keys=True)
    print("Done.")