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Source code for galaxy.tool_util.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)