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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)