Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/linters/citations.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """This module contains a citation lint function. |
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2 |
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3 Citations describe references that should be used when consumers |
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4 of the tool publish results. |
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5 """ |
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6 |
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7 |
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8 def lint_citations(tool_xml, lint_ctx): |
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9 """Ensure tool contains at least one valid citation.""" |
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10 root = tool_xml.getroot() |
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11 citations = root.findall("citations") |
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12 if len(citations) > 1: |
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13 lint_ctx.error("More than one citation section found, behavior undefined.") |
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14 return |
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15 |
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16 if len(citations) == 0: |
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17 lint_ctx.warn("No citations found, consider adding citations to your tool.") |
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18 return |
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19 |
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20 valid_citations = 0 |
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21 for citation in citations[0]: |
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22 if citation.tag != "citation": |
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23 lint_ctx.warn("Unknown tag discovered in citations block [%s], will be ignored." % citation.tag) |
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24 continue |
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25 citation_type = citation.attrib.get("type") |
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26 if citation_type not in ('bibtex', 'doi'): |
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27 lint_ctx.warn("Unknown citation type discovered [%s], will be ignored.", citation_type) |
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28 continue |
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29 if citation.text is None or not citation.text.strip(): |
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30 lint_ctx.error('Empty %s citation.' % citation_type) |
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31 continue |
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32 valid_citations += 1 |
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33 |
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34 if valid_citations > 0: |
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35 lint_ctx.valid("Found %d likely valid citations.", valid_citations) |