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)
 

test/unit/tool_util/invalid_citation.xml

@@ -0,0 +1,17 @@
+<tool id="invalid_citation" name="invalid_citation" version="1.0.0">
+    <command>
+        cat $input1 > $out_file1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <!-- https://github.com/workflow4metabolomics/anova/blob/4bd408440b71359eac2c373917f5daff2ec9f69f/galaxy/stat_anova/abims_anova.xml -->
+    <citations>
+        <citation>Ronald A. Fisher in the 1930s</citation>
+    </citations>
+    <help>
+    </help>
+</tool>

test/unit/tool_util/invalid_citation_24.2.xml

@@ -0,0 +1,17 @@
+<tool id="invalid_citation" name="invalid_citation" version="1.0.0" profile="24.2">
+    <command>
+        cat $input1 > $out_file1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <!-- https://github.com/workflow4metabolomics/anova/blob/4bd408440b71359eac2c373917f5daff2ec9f69f/galaxy/stat_anova/abims_anova.xml -->
+    <citations>
+        <citation>Ronald A. Fisher in the 1930s</citation>
+    </citations>
+    <help>
+    </help>
+</tool>

test/unit/tool_util/test_parsing.py

@@ -20,6 +20,10 @@ from galaxy.tool_util.parser.output_models import (
 )
 from galaxy.tool_util.unittest_utils import functional_test_tool_path
 from galaxy.util import galaxy_directory
+from galaxy.util.resources import (
+    as_file,
+    resource_path,
+)
 from galaxy.util.unittest import TestCase
 
 TOOL_XML_1 = """
@@ -948,6 +952,23 @@ class TestCollectionCatGroupTag(FunctionalTestToolTestCase):
         assert output_dataset_model.metadata_source == "input1"
 
 
+def test_old_invalid_citation_dont_cause_failure_to_load():
+    with as_file(resource_path(__name__, "invalid_citation.xml")) as tool_path:
+        tool_source = get_tool_source(tool_path)
+    assert tool_source.parse_citations() == []
+
+
+def test_invalid_citation_not_allowed_in_modern_tools():
+    with as_file(resource_path(__name__, "invalid_citation_24.2.xml")) as tool_path:
+        tool_source = get_tool_source(tool_path)
+    exc = None
+    try:
+        tool_source.parse_citations()
+    except Exception as e:
+        exc = e
+    assert exc is not None
+
+
 class TestToolProvidedMetadata2(FunctionalTestToolTestCase):
     test_path = "tool_provided_metadata_2.xml"