Merge pull request #18249 from mvdbeek/fix_no_elements_exception_extr…

…act_dataset [24.0] Raise exception when extracting dataset from collection without datasets
galaxyproject · May 30, 2024 · 4c8b4bf · 4c8b4bf
2 parents 1dd31f0 + 455a851
commit 4c8b4bf
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -6507,7 +6507,7 @@ def dataset_elements_and_identifiers(self, identifiers=None):
         return elements
 
     @property
-    def first_dataset_element(self):
+    def first_dataset_element(self) -> Optional[HistoryDatasetAssociation]:
         for element in self.elements:
             if element.is_collection:
                 first_element = element.child_collection.first_dataset_element

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -3355,18 +3355,20 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
         how = incoming["which"]["which_dataset"]
         if how == "first":
             extracted_element = collection.first_dataset_element
+            if not extracted_element:
+                raise exceptions.RequestParameterInvalidException("Input collection has no dataset elements.")
         elif how == "by_identifier":
             try:
                 extracted_element = collection[incoming["which"]["identifier"]]
             except KeyError as e:
-                raise exceptions.MessageException(e.args[0])
+                raise exceptions.RequestParameterInvalidException(e.args[0])
         elif how == "by_index":
             try:
                 extracted_element = collection[int(incoming["which"]["index"])]
             except KeyError as e:
-                raise exceptions.MessageException(e.args[0])
+                raise exceptions.RequestParameterInvalidException(e.args[0])
         else:
-            raise exceptions.MessageException("Invalid tool parameters.")
+            raise exceptions.RequestParameterInvalidException("Invalid tool parameters.")
         extracted = extracted_element.element_object
         extracted_o = extracted.copy(
             copy_tags=extracted.tags, new_name=extracted_element.element_identifier, flush=False