Mercurial > repos > guerler > springsuite
diff planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/stdio.py @ 1:56ad4e20f292 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author | guerler |
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date | Fri, 31 Jul 2020 00:32:28 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/stdio.py Fri Jul 31 00:32:28 2020 -0400 @@ -0,0 +1,43 @@ +"""This module contains a linting functions for tool error detection.""" +from .command import get_command + + +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)