"""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
)