Unverified Commit 9b43bf58 authored by Björn Grüning's avatar Björn Grüning Committed by GitHub
Browse files

Merge pull request #19301 from mvdbeek/implicit_dataset_as_input 

[24.1] Record implicitly converted dataset as input dataset
parents 058d2377 a75bca59

lib/galaxy/datatypes/data.py

+4 −0
Original line number Diff line number Diff line
@@ -847,7 +847,11 @@ class Data(metaclass=DataMeta): 
        job, converted_datasets, *_ = converter.execute(

            trans, incoming=params, set_output_hid=visible, history=history, flush_job=False

        )

        # We should only have a single converted output, but let's be defensive here

        n_converted_datasets = len(converted_datasets)

        for converted_dataset in converted_datasets.values():

            if converted_dataset.extension == "auto" and n_converted_datasets == 1:

                converted_dataset.extension = target_type

            original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)

        trans.app.job_manager.enqueue(job, tool=converter)

        if len(params) > 0:

lib/galaxy_test/api/test_tools.py

+18 −0
Original line number Diff line number Diff line
@@ -2511,6 +2511,24 @@ class TestToolsApi(ApiTestCase, TestsTools): 
                exception_raised = e

            assert exception_raised, "Expected invalid column selection to fail job"



    @skip_without_tool("implicit_conversion_format_input")

    def test_implicit_conversion_input_dataset_tracking(self):

        with self.dataset_populator.test_history() as history_id:

            compressed_path = self.test_data_resolver.get_filename("1.fastqsanger.gz")

            with open(compressed_path, "rb") as fh:

                dataset = self.dataset_populator.new_dataset(

                    history_id, content=fh, file_type="fastqsanger.gz", wait=True

                )

            outputs = self._run(

                "Grep1", history_id=history_id, inputs={"data": {"src": "hda", "id": dataset["id"]}}, assert_ok=True

            )

            job_details = self.dataset_populator.get_job_details(outputs["jobs"][0]["id"], full=True).json()

            assert job_details["inputs"]["input"]["id"] != dataset["id"]

            converted_input = self.dataset_populator.get_history_dataset_details(

                history_id=history_id, content_id=job_details["inputs"]["input"]["id"]

            )

            assert converted_input["extension"] == "fastqsanger"



    @skip_without_tool("column_multi_param")

    def test_implicit_conversion_and_reduce(self):

        with self.dataset_populator.test_history() as history_id: