Mercurial > repos > guerler > springsuite
comparison planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/command.py @ 1:56ad4e20f292 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 00:32:28 -0400 |
| parents | |
| children |
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| 0:d30785e31577 | 1:56ad4e20f292 |
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| 1 """This module contains a linting function for a tool's command description. | |
| 2 | |
| 3 A command description describes how to build the command-line to execute | |
| 4 from supplied inputs. | |
| 5 """ | |
| 6 | |
| 7 | |
| 8 def lint_command(tool_xml, lint_ctx): | |
| 9 """Ensure tool contains exactly one command and check attributes.""" | |
| 10 root = tool_xml.getroot() | |
| 11 commands = root.findall("command") | |
| 12 if len(commands) > 1: | |
| 13 lint_ctx.error("More than one command tag found, behavior undefined.") | |
| 14 return | |
| 15 | |
| 16 if len(commands) == 0: | |
| 17 lint_ctx.error("No command tag found, must specify a command template to execute.") | |
| 18 return | |
| 19 | |
| 20 command = get_command(tool_xml) | |
| 21 if "TODO" in command: | |
| 22 lint_ctx.warn("Command template contains TODO text.") | |
| 23 | |
| 24 command_attrib = command.attrib | |
| 25 interpreter_type = None | |
| 26 for key, value in command_attrib.items(): | |
| 27 if key == "interpreter": | |
| 28 interpreter_type = value | |
| 29 elif key == "detect_errors": | |
| 30 detect_errors = value | |
| 31 if detect_errors not in ["default", "exit_code", "aggressive"]: | |
| 32 lint_ctx.warn("Unknown detect_errors attribute [%s]" % detect_errors) | |
| 33 | |
| 34 interpreter_info = "" | |
| 35 if interpreter_type: | |
| 36 interpreter_info = " with interpreter of type [%s]" % interpreter_type | |
| 37 if interpreter_type: | |
| 38 lint_ctx.info("Command uses deprecated 'interpreter' attribute.") | |
| 39 lint_ctx.info("Tool contains a command%s." % interpreter_info) | |
| 40 | |
| 41 | |
| 42 def get_command(tool_xml): | |
| 43 """Get command XML element from supplied XML root.""" | |
| 44 root = tool_xml.getroot() | |
| 45 commands = root.findall("command") | |
| 46 command = None | |
| 47 if len(commands) == 1: | |
| 48 command = commands[0] | |
| 49 return command |