Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/citations.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 citation lint function.
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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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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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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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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)