Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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)