Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/linters/general.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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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15 |
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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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22 |
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23 |
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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.") |