Unverified Commit 4c7ab9f8 authored by mvdbeek's avatar mvdbeek
Browse files

Support directory uploads in workflow framework tests

parent 6d1d03e1

lib/galaxy_test/base/populators.py

+47 −1
Original line number Diff line number Diff line
@@ -483,6 +483,45 @@ class BaseDatasetPopulator(BasePopulator): 
            history_id, content=open(test_data_resolver.get_filename("1.bam"), "rb"), file_type="bam", wait=True

        )



    def new_directory_dataset(

        self, test_data_resolver: TestDataResolver, history_id: str, directory: str, format: str = "directory"

    ):

        directory_path = test_data_resolver.get_filename(directory)

        assert os.path.isdir(directory_path)



        tmp = tempfile.NamedTemporaryFile(delete=False)

        tf = tarfile.open(fileobj=tmp, mode="w:")

        tf.add(directory_path, ".")

        tf.close()



        with open(tmp.name, "rb") as tar_f:

            destination = {"type": "hdas"}

            targets = [

                {

                    "destination": destination,

                    "items": [

                        {

                            "src": "pasted",

                            "paste_content": "",

                            "ext": format,

                            "extra_files": {

                                "items_from": "archive",

                                "src": "files",

                                # Prevent Galaxy from checking for a single file in

                                # a directory and re-interpreting the archive

                                "fuzzy_root": False,

                            },

                        }

                    ],

                }

            ]

            payload = {"history_id": history_id, "targets": targets, "__files": {"files_0|file_data": tar_f}}

            fetch_response = self.fetch(payload)

        assert fetch_response.status_code == 200, fetch_response.content

        outputs = fetch_response.json()["outputs"]

        assert len(outputs) == 1

        return outputs[0]



    def fetch(

        self,

        payload: dict,
@@ -3273,8 +3312,9 @@ def load_data_dict( 
) -> LoadDataDictResponseT:

    """Load a dictionary as inputs to a workflow (test data focused)."""



    def open_test_data(test_dict, mode="rb"):

    test_data_resolver = TestDataResolver()



    def open_test_data(test_dict, mode="rb"):

        filename = test_data_resolver.get_filename(test_dict.pop("value"))

        return open(filename, mode)
@@ -3356,6 +3396,12 @@ def load_data_dict( 
                hda = dataset_populator.new_dataset(history_id, wait=True, **new_dataset_kwds)

                label_map[key] = dataset_populator.ds_entry(hda)

                has_uploads = True

            elif input_type == "Directory":

                hda = dataset_populator.new_directory_dataset(

                    test_data_resolver, history_id, directory=value["value"], format=value.get("file_type", "directory")

                )

                label_map[key] = dataset_populator.ds_entry(hda)

                has_uploads = True

            elif input_type == "raw":

                label_map[key] = value["value"]

                inputs[key] = value["value"]

lib/galaxy_test/workflow/test_framework_workflows.py

+1 −3
Original line number Diff line number Diff line
@@ -93,9 +93,7 @@ class TestWorkflow(ApiTestCase): 
        item_label = f"Output named {output_name}"



        def get_filename(name: str) -> str:

            return tempfile.NamedTemporaryFile(

                prefix=f"gx_workflow_framework_test_file_{output_name}", delete=False

            ).name

            return self.test_data_resolver.get_filename(name)



        def verify_dataset(dataset: dict, test_properties: OutputChecks):

            output_content = self.dataset_populator.get_history_dataset_content(