annotate env/lib/python3.9/site-packages/galaxy/tool_util/linters/command.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""This module contains a linting function for a tool's command description.

A command description describes how to build the command-line to execute
from supplied inputs.
"""


def lint_command(tool_xml, lint_ctx):
    """Ensure tool contains exactly one command and check attributes."""
    root = tool_xml.getroot()
    commands = root.findall("command")
    if len(commands) > 1:
        lint_ctx.error("More than one command tag found, behavior undefined.")
        return

    if len(commands) == 0:
        lint_ctx.error("No command tag found, must specify a command template to execute.")
        return

    command = get_command(tool_xml)
    if "TODO" in command:
        lint_ctx.warn("Command template contains TODO text.")

    command_attrib = command.attrib
    interpreter_type = None
    for key, value in command_attrib.items():
        if key == "interpreter":
            interpreter_type = value
        elif key == "detect_errors":
            detect_errors = value
            if detect_errors not in ["default", "exit_code", "aggressive"]:
                lint_ctx.warn("Unknown detect_errors attribute [%s]" % detect_errors)

    interpreter_info = ""
    if interpreter_type:
        interpreter_info = " with interpreter of type [%s]" % interpreter_type
    if interpreter_type:
        lint_ctx.info("Command uses deprecated 'interpreter' attribute.")
    lint_ctx.info("Tool contains a command%s." % interpreter_info)


def get_command(tool_xml):
    """Get command XML element from supplied XML root."""
    root = tool_xml.getroot()
    commands = root.findall("command")
    command = None
    if len(commands) == 1:
        command = commands[0]
    return command