Source code for galaxy.tool_util.linters.xml_order

"""This module contains a linting functions for tool XML block order.

For more information on the IUC standard for XML block order see -
https://github.com/galaxy-iuc/standards.
"""

# https://github.com/galaxy-iuc/standards
# https://github.com/galaxy-iuc/standards/pull/7/files
TAG_ORDER = [
    "description",
    "macros",
    "edam_topics",
    "edam_operations",
    "xrefs",
    "parallelism",
    "requirements",
    "required_files",
    "code",
    "stdio",
    "version_command",
    "command",
    "environment_variables",
    "configfiles",
    "inputs",
    "outputs",
    "tests",
    "help",
    "citations",
]

DATASOURCE_TAG_ORDER = [
    "description",
    "macros",
    "command",
    "configfiles",
    "inputs",
    "request_param_translation",
    "uihints",
    "outputs",
    "options",
    "help",
    "citations",
]


# Ensure the XML blocks appear in the correct order prescribed
# by the tool author best practices.
[docs]def lint_xml_order(tool_xml, lint_ctx):
    tool_root = tool_xml.getroot()

    if tool_root.attrib.get("tool_type", "") == "data_source":
        tag_ordering = DATASOURCE_TAG_ORDER
    else:
        tag_ordering = TAG_ORDER

    last_tag = None
    last_key = None
    for elem in tool_root:
        tag = elem.tag
        if tag in tag_ordering:
            key = tag_ordering.index(tag)
            if last_key:
                if last_key > key:
                    lint_ctx.warn(
                        f"Best practice violation [{tag}] elements should come before [{last_tag}]", node=elem
                    )
            last_tag = tag
            last_key = key
        else:
            lint_ctx.info(f"Unknown tag [{tag}] encountered, this may result in a warning in the future.", node=elem)