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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 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)