Commit d713037a authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Return bytes for content and automatically set type if available

parent ce0d46b6

src/nova/galaxy/dataset.py

+1 −3
Original line number Diff line number Diff line
@@ -129,9 +129,7 @@ class Dataset(AbstractData): 
        try:

            if self.store and self.id:

                dataset_client = DatasetClient(self.store.nova_connection.galaxy_instance)

                self._content = dataset_client.download_dataset(

                    self.id, use_default_filename=False, file_path=None

                ).decode("utf-8")

                self._content = dataset_client.download_dataset(self.id, use_default_filename=False, file_path=None)

            else:

                with open(self.path, "r") as file:

                    self._content = file.read()

src/nova/galaxy/job.py

+1 −0
Original line number Diff line number Diff line
@@ -155,6 +155,7 @@ class Job: 
                for dataset in self.datasets:

                    d = Dataset(dataset["output_name"])

                    d.id = dataset["id"]

                    d.file_type = dataset["file_ext"]

                    d.store = self.store

                    outputs.add_output(d)

            if self.collections:

tests/test_run_tool.py

+1 −1
Original line number Diff line number Diff line
@@ -23,7 +23,7 @@ def test_run_tool(nova_instance: Connection) -> None: 
        outputs = test_tool.run(data_store=store, params=Parameters())

        assert outputs is not None

        data = outputs.get_dataset("output1")

        assert "hostname:" in data.get_content()

        assert "hostname:" in data.get_content().decode("utf-8")





def test_run_tool_interactive(nova_instance: Connection, galaxy_instance: GalaxyInstance) -> None: