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Source code for galaxy.tool_util.linters.citations
"""This module contains a citation lint function.
Citations describe references that should be used when consumers
of the tool publish results.
"""
[docs]def lint_citations(tool_xml, lint_ctx):
"""Ensure tool contains at least one valid citation."""
root = tool_xml.getroot()
citations = root.findall("citations")
if len(citations) > 1:
lint_ctx.error("More than one citation section found, behavior undefined.")
return
if len(citations) == 0:
lint_ctx.warn("No citations found, consider adding citations to your tool.")
return
valid_citations = 0
for citation in citations[0]:
if citation.tag != "citation":
lint_ctx.warn("Unknown tag discovered in citations block [%s], will be ignored." % citation.tag)
continue
citation_type = citation.attrib.get("type")
if citation_type not in ('bibtex', 'doi'):
lint_ctx.warn("Unknown citation type discovered [%s], will be ignored.", citation_type)
continue
if citation.text is None or not citation.text.strip():
lint_ctx.error('Empty %s citation.' % citation_type)
continue
valid_citations += 1
if valid_citations > 0:
lint_ctx.valid("Found %d likely valid citations.", valid_citations)