Mercurial > repos > guerler > springsuite
diff planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/command.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/command.py Fri Jul 31 00:32:28 2020 -0400 @@ -0,0 +1,49 @@ +"""This module contains a linting function for a tool's command description. + +A command description describes how to build the command-line to execute +from supplied inputs. +""" + + +def lint_command(tool_xml, lint_ctx): + """Ensure tool contains exactly one command and check attributes.""" + root = tool_xml.getroot() + commands = root.findall("command") + if len(commands) > 1: + lint_ctx.error("More than one command tag found, behavior undefined.") + return + + if len(commands) == 0: + lint_ctx.error("No command tag found, must specify a command template to execute.") + return + + command = get_command(tool_xml) + if "TODO" in command: + lint_ctx.warn("Command template contains TODO text.") + + command_attrib = command.attrib + interpreter_type = None + for key, value in command_attrib.items(): + if key == "interpreter": + interpreter_type = value + elif key == "detect_errors": + detect_errors = value + if detect_errors not in ["default", "exit_code", "aggressive"]: + lint_ctx.warn("Unknown detect_errors attribute [%s]" % detect_errors) + + interpreter_info = "" + if interpreter_type: + interpreter_info = " with interpreter of type [%s]" % interpreter_type + if interpreter_type: + lint_ctx.info("Command uses deprecated 'interpreter' attribute.") + lint_ctx.info("Tool contains a command%s." % interpreter_info) + + +def get_command(tool_xml): + """Get command XML element from supplied XML root.""" + root = tool_xml.getroot() + commands = root.findall("command") + command = None + if len(commands) == 1: + command = commands[0] + return command