Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/general.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 functions for general aspects of the tool."""
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2 import re
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3
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4 import packaging.version
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5
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6 ERROR_VERSION_MSG = "Tool version is missing or empty."
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7 WARN_VERSION_MSG = "Tool version [%s] is not compliant with PEP 440."
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8 VALID_VERSION_MSG = "Tool defines a version [%s]."
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9
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10 ERROR_NAME_MSG = "Tool name is missing or empty."
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11 VALID_NAME_MSG = "Tool defines a name [%s]."
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12
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13 ERROR_ID_MSG = "Tool does not define an id attribute."
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14 VALID_ID_MSG = "Tool defines an id [%s]."
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16 PROFILE_PATTERN = re.compile(r"^[1,2]\d\.[0,1]\d$")
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17 PROFILE_INFO_DEFAULT_MSG = "Tool targets 16.01 Galaxy profile."
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18 PROFILE_INFO_SPECIFIED_MSG = "Tool specifies profile version [%s]."
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19 PROFILE_INVALID_MSG = "Tool specifies an invalid profile version [%s]."
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20
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21 lint_tool_types = ["*"]
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24 def lint_general(tool_source, lint_ctx):
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25 """Check tool version, name, and id."""
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26 version = tool_source.parse_version() or ''
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27 parsed_version = packaging.version.parse(version)
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28 if not version:
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29 lint_ctx.error(ERROR_VERSION_MSG)
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30 elif isinstance(parsed_version, packaging.version.LegacyVersion):
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31 lint_ctx.warn(WARN_VERSION_MSG % version)
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32 else:
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33 lint_ctx.valid(VALID_VERSION_MSG % version)
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34
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35 name = tool_source.parse_name()
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36 if not name:
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37 lint_ctx.error(ERROR_NAME_MSG)
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38 else:
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39 lint_ctx.valid(VALID_NAME_MSG % name)
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40
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41 tool_id = tool_source.parse_id()
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42 if not tool_id:
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43 lint_ctx.error(ERROR_ID_MSG)
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44 else:
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45 lint_ctx.valid(VALID_ID_MSG % tool_id)
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46
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47 profile = tool_source.parse_profile()
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48 profile_valid = PROFILE_PATTERN.match(profile) is not None
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49 if not profile_valid:
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50 lint_ctx.warn(PROFILE_INVALID_MSG)
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51 elif profile == "16.01":
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52 lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG)
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53 else:
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54 lint_ctx.valid(PROFILE_INFO_SPECIFIED_MSG % profile)
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55
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56 if re.search(r"\s", tool_id):
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57 lint_ctx.warn("Tool id contains a space - this is discouraged.")