Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.linters.stdio

"""This module contains a linting functions for tool error detection."""
import re

from galaxy.util import etree
from .command import get_command


[docs]def lint_stdio(tool_source, lint_ctx): tool_xml = getattr(tool_source, "xml_tree", None) if not tool_xml: # Can only lint XML tools at this point. # Should probably use tool_source.parse_stdio() to abstract away XML details return stdios = tool_xml.findall("./stdio") if tool_xml else [] # determine node to report for general problems with stdio tool_node = tool_xml.find("./stdio") if tool_node is None: tool_node = tool_xml.getroot() if not stdios: command = get_command(tool_xml) if tool_xml else None if command is None or not command.get("detect_errors"): if tool_source.parse_profile() <= "16.01": lint_ctx.info( "No stdio definition found, tool indicates error conditions with output written to stderr.", node=tool_node, ) else: lint_ctx.info( "No stdio definition found, tool indicates error conditions with non-zero exit codes.", node=tool_node, ) return if len(stdios) > 1: lint_ctx.error("More than one stdio tag found, behavior undefined.", node=stdios[1]) return stdio = stdios[0] for child in list(stdio): if child.tag is etree.Comment: continue if child.tag == "regex": _lint_regex(tool_xml, child, lint_ctx) elif child.tag == "exit_code": _lint_exit_code(tool_xml, child, lint_ctx) else: message = "Unknown stdio child tag discovered [%s]. " message += "Valid options are exit_code and regex." lint_ctx.warn(message % child.tag, node=child)
def _lint_exit_code(tool_xml, child, lint_ctx): for key in child.attrib.keys(): if key not in ["description", "level", "range"]: lint_ctx.warn(f"Unknown attribute [{key}] encountered on exit_code tag.", node=child) def _lint_regex(tool_xml, child, lint_ctx): for key in child.attrib.keys(): if key not in ["description", "level", "match", "source"]: lint_ctx.warn(f"Unknown attribute [{key}] encountered on regex tag.", node=child) match = child.attrib.get("match") if match: try: re.compile(match) except Exception as e: lint_ctx.error(f"Match '{match}' is no valid regular expression: {str(e)}", node=child)