Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/linters/xml_order.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 tool XML block order. |
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2 |
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3 For more information on the IUC standard for XML block order see - |
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4 https://github.com/galaxy-iuc/standards. |
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5 """ |
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6 # https://github.com/galaxy-iuc/standards |
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7 # https://github.com/galaxy-iuc/standards/pull/7/files |
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8 TAG_ORDER = [ |
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9 'description', |
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10 'macros', |
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11 'parallelism', |
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12 'requirements', |
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13 'code', |
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14 'stdio', |
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15 'version_command', |
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16 'command', |
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17 'environment_variables', |
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18 'configfiles', |
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19 'inputs', |
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20 'outputs', |
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21 'tests', |
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22 'help', |
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23 'citations', |
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24 ] |
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25 |
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26 DATASOURCE_TAG_ORDER = [ |
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27 'description', |
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28 'macros', |
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29 'command', |
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30 'configfiles', |
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31 'inputs', |
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32 'request_param_translation', |
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33 'uihints', |
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34 'outputs', |
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35 'options', |
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36 'help', |
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37 'citations', |
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38 ] |
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39 |
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40 |
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41 # Ensure the XML blocks appear in the correct order prescribed |
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42 # by the tool author best practices. |
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43 def lint_xml_order(tool_xml, lint_ctx): |
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44 tool_root = tool_xml.getroot() |
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45 |
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46 if tool_root.attrib.get('tool_type', '') == 'data_source': |
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47 _validate_for_tags(tool_root, lint_ctx, DATASOURCE_TAG_ORDER) |
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48 else: |
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49 _validate_for_tags(tool_root, lint_ctx, TAG_ORDER) |
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50 |
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51 |
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52 def _validate_for_tags(root, lint_ctx, tag_ordering): |
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53 last_tag = None |
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54 last_key = None |
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55 for elem in root: |
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56 tag = elem.tag |
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57 if tag in tag_ordering: |
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58 key = tag_ordering.index(tag) |
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59 if last_key: |
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60 if last_key > key: |
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61 lint_ctx.warn(f"Best practice violation [{tag}] elements should come before [{last_tag}]") |
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62 last_tag = tag |
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63 last_key = key |
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64 else: |
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65 lint_ctx.info("Unknown tag [%s] encountered, this may result in a warning in the future." % tag) |