cdm_data_loaders.parsers.uniprot.metalink ¶

def parse_metalink(metalink_xml_path: Path | str) -> Element | None:
    """Parse the metalink file and return the root node."""
    document = parse(str(metalink_xml_path))
    root = document.getroot()
    if root is not None:
        return root
    msg = f"Could not find root in metalink file: {metalink_xml_path!s}"
    logger.error(msg)
    raise RuntimeError(msg)

def generate_data_source_table(metalink_xml_path: Path | str) -> dict[str, Any]:
    """Generate the data source information for the ID Mapping data."""
    root = parse_metalink(metalink_xml_path)
    if root is None:
        return {}

    data_source = {
        "license": root.findtext("./license/name", namespaces=NS),
        "publisher": root.findtext("./publisher/name", namespaces=NS),
        "resource_type": "dataset",
        "version": root.findtext("./version", namespaces=NS),
    }
    missing = [k for k in data_source if not data_source[k]]
    if missing:
        msg = f"Missing required elements from metalink file: {', '.join(missing)}"
        logger.error(msg)
        raise RuntimeError(msg)

    return data_source

def get_files(metalink_xml_path: Path | str, files_to_find: list[str] | None = None) -> dict[str, Any]:
    """Generate the data source information for the ID Mapping data."""
    root = parse_metalink(metalink_xml_path)
    assert root is not None

    if files_to_find is not None and files_to_find == []:
        logger.warning("Empty file list supplied to get_files: aborting.")
        return {}

    files = {}
    for f in root.findall("./files/file", NS):
        # get the name, size, any verification info
        name = f.get("name")
        # skip now if the file is not of interest
        if files_to_find and name not in files_to_find:
            continue

        size = f.findtext("./size", namespaces=NS)
        checksum = f.find("./verification/hash", NS)
        if checksum is not None:
            checksum_fn = checksum.get("type")
            checksum_value = checksum.text
        else:
            checksum_fn = checksum_value = None
        dl_url = f.findtext("./resources/url[@location='us']", namespaces=NS)
        files[name] = {
            "name": name,
            "size": size,
            "checksum": checksum_value,
            "checksum_fn": checksum_fn,
            "url": dl_url,
        }

    # report on unfound files
    if files_to_find:
        not_found = {f for f in files_to_find if f not in files}
        if not_found:
            msg = "The following files were not found: " + ", ".join(sorted(not_found))
            logger.warning(msg)

    return files