Warning
This document is for an in-development version 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)