Merge pull request #19716 from jmchilton/fix_citation_handling

[24.2] Fix #19515 - invalid citation handling changed with 24.2.

lib/galaxy/tool_util/fetcher.py

@@ -1,3 +1,4 @@
+import os
 from typing import (
     Dict,
     Type,
@@ -8,6 +9,7 @@ from galaxy.util import plugin_config
 
 if TYPE_CHECKING:
     from galaxy.tool_util.locations import ToolLocationResolver
+    from galaxy.util.path import StrPath
 
 
 class ToolLocationFetcher:
@@ -19,8 +21,8 @@ class ToolLocationFetcher:
 
         return plugin_config.plugins_dict(galaxy.tool_util.locations, "scheme")
 
-    def to_tool_path(self, path_or_uri_like: str, **kwds) -> str:
-        if "://" not in path_or_uri_like:
+    def to_tool_path(self, path_or_uri_like: "StrPath", **kwds) -> "StrPath":
+        if isinstance(path_or_uri_like, os.PathLike) or "://" not in path_or_uri_like:
             path = path_or_uri_like
         else:
             uri_like = path_or_uri_like

lib/galaxy/tool_util/parser/factory.py

@@ -86,9 +86,8 @@ def get_tool_source(
         tool_location_fetcher = ToolLocationFetcher()
 
     assert config_file
-    config_file = str(config_file)
 
-    config_file = tool_location_fetcher.to_tool_path(config_file)
+    config_file = str(tool_location_fetcher.to_tool_path(config_file))
     if not enable_beta_formats:
         tree, macro_paths = load_tool_with_refereces(config_file)
         return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths)

lib/galaxy/tool_util/parser/xml.py

@@ -708,7 +708,13 @@ class XmlToolSource(ToolSource):
             return citations
 
         for citation_elem in citations_elem:
-            citation = parse_citation_elem(citation_elem)
+            try:
+                citation = parse_citation_elem(citation_elem)
+            except Exception:
+                if Version(self.parse_profile()) < Version("24.2"):
+                    continue
+                else:
+                    raise
             if citation:
                 citations.append(citation)