Unverified Commit 4c8b4bf2 authored by John Chilton's avatar John Chilton Committed by GitHub
Browse files

Merge pull request #18249 from mvdbeek/fix_no_elements_exception_extract_dataset 

[24.0] Raise exception when extracting dataset from collection without datasets
parents 1dd31f08 455a851e

lib/galaxy/model/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -6507,7 +6507,7 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable): 
        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

lib/galaxy/tools/__init__.py

+5 −3
Original line number Diff line number Diff line
@@ -3355,18 +3355,20 @@ class ExtractDatasetCollectionTool(DatabaseOperationTool): 
        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