diff env/lib/python3.9/site-packages/galaxy/tool_util/linters/citations.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/linters/citations.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,35 @@
+"""This module contains a citation lint function.
+
+Citations describe references that should be used when consumers
+of the tool publish results.
+"""
+
+
+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)