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Source code for galaxy.tool_util.linters.command
"""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.
"""
[docs]def lint_command(tool_xml, lint_ctx):
"""Ensure tool contains exactly one command and check attributes."""
root = tool_xml.find("./command")
if root is None:
root = tool_xml.getroot()
commands = tool_xml.findall("./command")
if len(commands) > 1:
lint_ctx.error("More than one command tag found, behavior undefined.", node=commands[1])
return
if len(commands) == 0:
lint_ctx.error("No command tag found, must specify a command template to execute.", node=root)
return
command = get_command(tool_xml)
if command.text is None:
lint_ctx.error("Command is empty.", node=root)
elif "TODO" in command.text:
lint_ctx.warn("Command template contains TODO text.", node=command)
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(f"Unknown detect_errors attribute [{detect_errors}]", node=command)
interpreter_info = ""
if interpreter_type:
interpreter_info = f" with interpreter of type [{interpreter_type}]"
if interpreter_type:
lint_ctx.warn("Command uses deprecated 'interpreter' attribute.", node=command)
lint_ctx.info(f"Tool contains a command{interpreter_info}.", node=command)
[docs]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