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Source code for galaxy.tools.linters.stdio

"""This module contains a linting functions for tool error detection."""
from .command import get_command


[docs]def lint_stdio(tool_source, lint_ctx): tool_xml = getattr(tool_source, "xml_tree", None) stdios = tool_xml.findall("./stdio") if tool_xml else [] 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.") else: lint_ctx.info("No stdio definition found, tool indicates error conditions with non-zero exit codes.") return if len(stdios) > 1: lint_ctx.error("More than one stdio tag found, behavior undefined.") return stdio = stdios[0] for child in list(stdio): if child.tag == "regex": _lint_regex(child, lint_ctx) elif child.tag == "exit_code": _lint_exit_code(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)
def _lint_exit_code(child, lint_ctx): for key in child.attrib.keys(): if key not in ["description", "level", "range"]: lint_ctx.warn("Unknown attribute [%s] encountered on exit_code tag." % key) def _lint_regex(child, lint_ctx): for key in child.attrib.keys(): if key not in ["description", "level", "match", "source"]: lint_ctx.warn("Unknown attribute [%s] encountered on regex tag." % key)