Commit eaacbd48 authored by davelopez's avatar davelopez
Browse files

Add test for metadata generation

parent 8a057d10

lib/galaxy/model/store/__init__.py

+5 −2
Original line number Diff line number Diff line
@@ -590,8 +590,11 @@ class ModelImportStore(metaclass=abc.ABCMeta): 
                                )

                            else:

                                # Try to set metadata directly. TODO: check efficiency of this?

                                try:

                                    if dataset_instance.has_metadata_files:

                                        dataset_instance.datatype.set_meta(dataset_instance)

                                except Exception:

                                    dataset_instance.dataset.state = dataset_instance.dataset.states.FAILED_METADATA



                if model_class == "HistoryDatasetAssociation":

                    if object_key in dataset_attrs:

test/integration/test_history_import_export.py

+13 −1
Original line number Diff line number Diff line
@@ -60,6 +60,10 @@ class ImportExportHistoryViaTasksIntegrationTestCase( 
    def test_import_model_store_from_file_source_async_with_format(self):

        history_name = f"for_export_format_async_{uuid4()}"

        history_id = self.dataset_populator.setup_history_for_export_testing(history_name)

        # Add bam dataset to test metadata generation on import

        self.dataset_populator.new_dataset(

            history_id, content=open(self.test_data_resolver.get_filename("1.bam"), "rb"), file_type="bam", wait=True

        )

        model_store_format = "rocrate.zip"

        target_uri = f"gxfiles://posix_test/history.{model_store_format}"
@@ -72,14 +76,22 @@ class ImportExportHistoryViaTasksIntegrationTestCase( 
        imported_history_id = imported_history["id"]

        assert imported_history_id != history_id

        assert imported_history["name"] == history_name

        self.dataset_populator.wait_for_history(imported_history_id)

        history_contents = self.dataset_populator.get_history_contents(imported_history_id)

        assert len(history_contents) == 2

        assert len(history_contents) == 3

        # Only deleted datasets should appear as "discarded"

        for dataset in history_contents:

            if dataset["deleted"] is True:

                assert dataset["state"] == "discarded"

            else:

                assert dataset["state"] == "ok"

                # Check metadata generation

            if dataset["extension"] == "bam":

                imported_bam_details = self.dataset_populator.get_history_dataset_details(

                    imported_history_id, dataset_id=dataset["id"]

                )

                bai_metadata = imported_bam_details["meta_files"][0]

                assert bai_metadata["file_type"] == "bam_index"





class ImportExportHistoryContentsViaTasksIntegrationTestCase(IntegrationTestCase, UsesCeleryTasks):