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Source code for galaxy.tool_util.linters.stdio

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

import re
from typing import TYPE_CHECKING

from packaging.version import Version

from galaxy.tool_util.lint import Linter

if TYPE_CHECKING:
    from galaxy.tool_util.lint import LintContext
    from galaxy.tool_util.parser.interface import ToolSource


[docs]class StdIOAbsenceLegacy(Linter):
[docs] @classmethod def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"): 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 [] if stdios: return tool_node = tool_xml.getroot() command = tool_xml.find("./command") if command is None or not command.get("detect_errors"): if Version(tool_source.parse_profile()) <= Version("16.01"): lint_ctx.info( "No stdio definition found, tool indicates error conditions with output written to stderr.", linter=cls.name(), node=tool_node, )
[docs]class StdIOAbsence(Linter):
[docs] @classmethod def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"): 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 [] if stdios: return tool_node = tool_xml.getroot() command = tool_xml.find("./command") if command is None or not command.get("detect_errors"): if Version(tool_source.parse_profile()) > Version("16.01"): lint_ctx.info( "No stdio definition found, tool indicates error conditions with non-zero exit codes.", linter=cls.name(), node=tool_node, )
[docs]class StdIORegex(Linter):
[docs] @classmethod def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"): 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 [] if len(stdios) != 1: return stdio = stdios[0] for child in list(stdio): if child.tag == "regex": 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)}", linter=cls.name(), node=child )