Unverified Commit 81781787 authored by mvdbeek's avatar mvdbeek
Browse files

Test deferred data with extended metadata and metadata files 

And also test that option filters work correctly.
parent f8721ccb

lib/galaxy_test/api/test_tools.py

+16 −0
Original line number Diff line number Diff line
@@ -2729,6 +2729,22 @@ class ToolsTestCase(ApiTestCase, TestsTools): 
        output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)

        assert output_content.startswith("chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-")



    @skip_without_tool("metadata_bam")

    @uses_test_history(require_new=False)

    def test_run_deferred_dataset_with_metadata_options_filter(self, history_id):

        details = self.dataset_populator.create_deferred_hda(

            history_id, "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bam", ext="bam"

        )

        inputs = {"input_bam": dataset_to_param(details), "ref_names": "chrM"}

        run_response = self.dataset_populator.run_tool(tool_id="metadata_bam", inputs=inputs, history_id=history_id)

        output = run_response["outputs"][0]

        details = self.dataset_populator.get_history_dataset_details(

            history_id, dataset=output, wait=True, assert_ok=True

        )

        assert details["state"] == "ok"

        output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)

        assert output_content.startswith("chrM")



    @skip_without_tool("cat1")

    @uses_test_history(require_new=False)

    def test_run_deferred_mapping(self, history_id: str):

test/integration/test_extended_metadata.py

+31 −0
Original line number Diff line number Diff line
@@ -91,6 +91,37 @@ class ExtendedMetadataIntegrationTestCase(integration_util.IntegrationTestCase): 
        assert dataset["created_from_basename"] == "4.bed"





class ExtendedMetadataDeferredIntegrationTestCase(integration_util.IntegrationTestCase):

    def setUp(self):

        super().setUp()

        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)



    @classmethod

    def handle_galaxy_config_kwds(cls, config):

        config["metadata_strategy"] = "extended"

        config["object_store_store_by"] = "uuid"

        config["retry_metadata_internally"] = False



    def test_deferred_upload_with_metadata_files(self):

        history_id = self.dataset_populator.new_history()

        deferred_dataset = self.dataset_populator.create_deferred_hda(

            history_id=history_id,

            uri="https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bam",

            ext="bam",

        )

        inputs = {"input1": {"src": "hda", "id": deferred_dataset["id"]}}

        run_response = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=history_id)

        self.dataset_populator.wait_for_job(run_response["jobs"][0]["id"], assert_ok=True)

        bam_dataset = self.dataset_populator.get_history_dataset_details(

            history_id=history_id, content_id=run_response["outputs"][0]["id"]

        )

        assert bam_dataset["state"] == "ok"

        assert bam_dataset["extension"] == "bam"

        metadata_response = self._get(f"datasets/{bam_dataset['id']}/metadata_file?metadata_file=bam_index")

        metadata_response.raise_for_status()

        assert metadata_response.content.startswith(b"BAI")





class ExtendedMetadataIntegrationInstance(integration_util.IntegrationInstance):

    """Describe a Galaxy test instance with embedded pulsar configured."""