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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.find("./citations") if root is None: root = tool_xml.getroot() citations = tool_xml.findall("citations") if len(citations) > 1: lint_ctx.error("More than one citation section found, behavior undefined.", node=citations[1]) return if len(citations) == 0: lint_ctx.warn("No citations found, consider adding citations to your tool.", node=root) return valid_citations = 0 for citation in citations[0]: if citation.tag != "citation": lint_ctx.warn( f"Unknown tag discovered in citations block [{citation.tag}], will be ignored.", node=citation ) continue citation_type = citation.attrib.get("type") if citation_type not in ("bibtex", "doi"): lint_ctx.warn(f"Unknown citation type discovered [{citation_type}], will be ignored.", node=citation) continue if citation.text is None or not citation.text.strip(): lint_ctx.error(f"Empty {citation_type} citation.", node=citation) continue valid_citations += 1 if valid_citations > 0: lint_ctx.valid(f"Found {valid_citations} likely valid citations.", node=root) else: lint_ctx.warn("Found no valid citations.", node=root)