Unverified Commit 27991b95 authored by mvdbeek's avatar mvdbeek
Browse files

Fix writing data bundle manifest to object store

parent 3c4e1195

lib/galaxy/tool_util/data/__init__.py

+5 −1
Original line number Diff line number Diff line
@@ -1174,8 +1174,10 @@ class ToolDataTableManager(Dictifiable): 
        out_data: Dict[str, OutputDataset],

        bundle_description: DataTableBundleProcessorDescription,

        repo_info: Optional[RepoInfo],

    ) -> None:

    ) -> Dict[str, OutputDataset]:

        """Writes bundle and returns bundle path."""

        data_manager_dict = _data_manager_dict(out_data, ensure_single_output=True)

        bundle_datasets: Dict[str, OutputDataset] = {}

        for output_name, dataset in out_data.items():

            if dataset.ext != "data_manager_json":

                continue
@@ -1190,6 +1192,8 @@ class ToolDataTableManager(Dictifiable): 
            bundle_path = os.path.join(extra_files_path, BUNDLE_INDEX_FILE_NAME)

            with open(bundle_path, "w") as fw:

                json.dump(bundle.dict(), fw)

            bundle_datasets[bundle_path] = dataset

        return bundle_datasets





SUPPORTED_DATA_TABLE_TYPES = TabularToolDataTable

lib/galaxy/tools/__init__.py

+11 −1
Original line number Diff line number Diff line
@@ -3064,7 +3064,17 @@ class DataManagerTool(OutputParameterJSONTool): 
        elif data_manager_mode == "dry_run":

            pass

        elif data_manager_mode == "bundle":

            data_manager.write_bundle(out_data)

            for bundle_path, dataset in data_manager.write_bundle(out_data).items():

                dataset = cast(model.HistoryDatasetAssociation, dataset)

                dataset.dataset.object_store.update_from_file(

                    dataset.dataset,

                    extra_dir=dataset.dataset.extra_files_path_name,

                    file_name=bundle_path,

                    alt_name=os.path.basename(bundle_path),

                    create=True,

                    preserve_symlinks=True,

                )



        else:

            raise Exception("Unknown data manager mode encountered type...")

lib/galaxy/tools/data_manager/manager.py

+2 −2
Original line number Diff line number Diff line
@@ -236,9 +236,9 @@ class DataManager: 
    def write_bundle(

        self,

        out_data: Dict[str, OutputDataset],

    ) -> None:

    ):

        tool_data_tables = self.data_managers.app.tool_data_tables

        tool_data_tables.write_bundle(

        return tool_data_tables.write_bundle(

            out_data,

            self.processor_description,

            self.repo_info,