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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/command.py @ 1:56ad4e20f292 draft

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