Fixes.

galaxyproject · Jul 2, 2024 · 2457f97 · 2457f97
1 parent 3b693e9
commit 2457f97
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Showing 3 changed files with 14 additions and 10 deletions.
diff --git a/lib/galaxy/tools/stock.py b/lib/galaxy/tools/stock.py
@@ -1,18 +1,20 @@
 """Reason about stock tools based on ToolSource abstractions."""
 
+from pathlib import Path
+
 from lxml.etree import XMLSyntaxError
 
 # Set GALAXY_INCLUDES_ROOT from tool shed to point this at a Galaxy root
 # (once we are running the tool shed from packages not rooted with Galaxy).
 import galaxy.tools
 from galaxy.tool_util.parser import get_tool_source
-from galaxy.util import galaxy_root_path
+from galaxy.util import galaxy_directory
 from galaxy.util.resources import files
 
 
 def stock_tool_paths():
     yield from _walk_directory_for_tools(files(galaxy.tools))
-    yield from _walk_directory_for_tools(galaxy_root_path / "test" / "functional" / "tools")
+    yield from _walk_directory_for_tools(Path(galaxy_directory()) / "test" / "functional" / "tools")
 
 
 def stock_tool_sources():
@@ -23,7 +25,6 @@ def stock_tool_sources():
             continue
 
 
-
 def _walk_directory_for_tools(path):
     if path.is_file() and path.name.endswith(".xml"):
         yield path

diff --git a/lib/tool_shed/managers/tools.py b/lib/tool_shed/managers/tools.py
@@ -24,11 +24,11 @@
     tool_parameter_bundle_from_json,
     ToolParameterBundleModel,
 )
-from galaxy.tools.stock import stock_tool_sources
 from galaxy.tool_util.parser import (
     get_tool_source,
     ToolSource,
 )
+from galaxy.tools.stock import stock_tool_sources
 from tool_shed.context import (
     ProvidesRepositoriesContext,
     SessionRequestContext,
@@ -38,7 +38,6 @@
 from tool_shed.webapp.search.tool_search import ToolSearch
 from .trs import trs_tool_id_to_repository_metadata
 
-
 STOCK_TOOL_SOURCES: Optional[Dict[str, Dict[str, ToolSource]]] = None
 
 
@@ -123,7 +122,10 @@ def tool_source_for(
     if "~" in trs_tool_id:
         return _shed_tool_source_for(trans, trs_tool_id, tool_version, repository_clone_url)
     else:
-        return _stock_tool_source_for(trs_tool_id, tool_version)
+        tool_source = _stock_tool_source_for(trs_tool_id, tool_version)
+        if tool_source is None:
+            raise ObjectNotFound()
+        return tool_source
 
 
 def _shed_tool_source_for(
@@ -151,9 +153,10 @@ def _shed_tool_source_for(
 
 def _stock_tool_source_for(tool_id: str, tool_version: str) -> Optional[ToolSource]:
     _init_stock_tool_sources()
+    assert STOCK_TOOL_SOURCES
     tool_version_sources = STOCK_TOOL_SOURCES.get(tool_id)
     if tool_version_sources is None:
-        return
+        return None
     return tool_version_sources.get(tool_version)
 
 

diff --git a/test/functional/tools/parameters/gx_select_multiple_optional.xml b/test/functional/tools/parameters/gx_select_multiple_optional.xml
@@ -1,4 +1,4 @@
-<tool id="gx_select_multiple" name="gx_select_multiple" version="1.0.0">
+<tool id="gx_select_multiple_optional" name="gx_select_multiple_optional" version="1.0.0">
     <command><![CDATA[
 echo '$parameter' >> '$output'
     ]]></command>
@@ -16,10 +16,10 @@ echo '$parameter' >> '$output'
     </outputs>
     <tests>
         <test>
-            <param name="parameter" value="12456" />
+            <param name="parameter" value="ex2" />
             <output name="output">
                 <assert_contents>
-                    <has_line line="12456" />
+                    <has_line line="ex2" />
                 </assert_contents>
             </output>
         </test>