Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/tool_lint.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 from __future__ import absolute_import
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2
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3 from os.path import basename
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4
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5 from galaxy.tool_util.lint import lint_tool_source
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6
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7 from planemo.exit_codes import (
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8 EXIT_CODE_GENERIC_FAILURE,
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9 EXIT_CODE_OK,
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10 )
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11 from planemo.io import (
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12 coalesce_return_codes,
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13 error,
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14 info,
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15 )
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16 from planemo.tools import (
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17 is_tool_load_error,
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18 yield_tool_sources_on_paths,
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19 )
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20
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21 LINTING_TOOL_MESSAGE = "Linting tool %s"
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22
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23
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24 def lint_tools_on_path(ctx, paths, lint_args, **kwds):
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25 assert_tools = kwds.get("assert_tools", True)
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26 recursive = kwds.get("recursive", False)
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27 exit_codes = []
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28 for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
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29 if handle_tool_load_error(tool_path, tool_xml):
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30 exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
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31 continue
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32 info("Linting tool %s" % tool_path)
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33 if not lint_tool_source(tool_xml, name=basename(tool_path), **lint_args):
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34 error("Failed linting")
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35 exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
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36 else:
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37 exit_codes.append(EXIT_CODE_OK)
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38 return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
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39
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40
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41 def handle_tool_load_error(tool_path, tool_xml):
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42 """ Return True if tool_xml is tool load error (invalid XML), and
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43 print a helpful error message.
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44 """
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45 is_error = False
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46 if is_tool_load_error(tool_xml):
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47 info("Could not lint %s due to malformed xml." % tool_path)
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48 is_error = True
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49 return is_error