Unverified Commit 206fe020 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #17952 from mvdbeek/fix_implicit_conversion_mapped_over 

[23.2] Fix missing implicit conversion for mapped over jobs
parents e35ea08c ec6a8e72

lib/galaxy/tools/evaluation.py

+1 −0
Original line number Diff line number Diff line
@@ -355,6 +355,7 @@ class ToolEvaluator: 
                element_identifier = element_identifier_mapper.identifier(dataset, param_dict)

                if element_identifier:

                    wrapper_kwds["identifier"] = element_identifier

                wrapper_kwds["formats"] = input.formats

                input_values[input.name] = DatasetFilenameWrapper(dataset, **wrapper_kwds)

            elif isinstance(input, DataCollectionToolParameter):

                dataset_collection = value

lib/galaxy_test/api/test_workflows.py

+25 −0
Original line number Diff line number Diff line
@@ -3828,6 +3828,31 @@ test_data: 
                assert_ok=True,

            )



    @skip_without_tool("implicit_conversion_format_input")

    def test_run_with_implicit_collection_map_over(self):

        with self.dataset_populator.test_history() as history_id:

            self._run_workflow(

                """

class: GalaxyWorkflow

inputs:

  collection: collection

steps:

  map_over:

    tool_id: implicit_conversion_format_input

    in:

      input1: collection

test_data:

  collection:

    collection_type: list

    elements:

      - identifier: 1

        value: 1.fasta.gz

        type: File

""",

                history_id=history_id,

                assert_ok=True,

            )



    @skip_without_tool("random_lines1")

    def test_change_datatype_collection_map_over(self):

        with self.dataset_populator.test_history() as history_id:

lib/galaxy_test/base/populators.py

+12 −6
Original line number Diff line number Diff line
@@ -2857,6 +2857,8 @@ class BaseDatasetCollectionPopulator: 
            history_id=history_id,

            targets=targets,

        )

        if "__files" in kwds:

            payload["__files"] = kwds.pop("__files")

        return payload



    def wait_for_fetched_collection(self, fetch_response: Union[Dict[str, Any], Response]):
@@ -2992,7 +2994,8 @@ def load_data_dict( 
        if is_dict and ("elements" in value or value.get("collection_type")):

            elements_data = value.get("elements", [])

            elements = []

            for element_data in elements_data:

            new_collection_kwds: Dict[str, Any] = {}

            for i, element_data in enumerate(elements_data):

                # Adapt differences between test_data dict and fetch API description.

                if "name" not in element_data:

                    identifier = element_data.pop("identifier")
@@ -3000,14 +3003,17 @@ def load_data_dict( 
                input_type = element_data.pop("type", "raw")

                content = None

                if input_type == "File":

                    content = read_test_data(element_data)

                    content = open_test_data(element_data)

                    element_data["src"] = "files"

                    if "__files" not in new_collection_kwds:

                        new_collection_kwds["__files"] = {}

                    new_collection_kwds["__files"][f"file_{i}|file_data"] = content

                else:

                    content = element_data.pop("content")

                    if content is not None:

                        element_data["src"] = "pasted"

                        element_data["paste_content"] = content

                elements.append(element_data)

            new_collection_kwds = {}

            if "name" in value:

                new_collection_kwds["name"] = value["name"]

            collection_type = value.get("collection_type", "")