diff --git a/tests/docker_yaml_conversion_specification_cli.py b/tests/docker_yaml_conversion_specification_cli.py index 4145a6888..fb2405758 100644 --- a/tests/docker_yaml_conversion_specification_cli.py +++ b/tests/docker_yaml_conversion_specification_cli.py @@ -28,7 +28,7 @@ def test_run_conversion_from_yaml_cli(self): yaml_file_path = path_to_test_yml_files / "GIN_conversion_specification.yml" deploy_process( command=( - "docker run -it " + "docker run -t " f"--volume {self.source_volume}:/neuroconv ghcr.io/catalystneuro/neuroconv:{self.tag}" f"neuroconv /neuroconv/tests/test_on_data/conversion_specifications/{yaml_file_path} " f"--data-folder-path /neuroconv/{DATA_PATH} --output-folder-path {self.test_folder} --overwrite" @@ -74,7 +74,7 @@ def test_run_conversion_from_yaml_default_nwbfile_name(self): yaml_file_path = path_to_test_yml_files / "GIN_conversion_specification_missing_nwbfile_names.yml" deploy_process( command=( - "docker run -it " + "docker run -t " f"--volume {self.source_volume}:/neuroconv ghcr.io/catalystneuro/neuroconv:{self.tag}" f"neuroconv {yaml_file_path} " f"--data-folder-path {DATA_PATH} --output-folder-path {self.test_folder} --overwrite" @@ -123,3 +123,54 @@ def test_run_conversion_from_yaml_default_nwbfile_name(self): assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-11T21:19:09+00:00") assert nwbfile.subject.subject_id == "Subject Name" assert "spike_times" in nwbfile.units + +def test_run_conversion_from_yaml_variable(self): + path_to_test_yml_files = Path(__file__).parent / "conversion_specifications" + yaml_file_path = path_to_test_yml_files / "GIN_conversion_specification.yml" + + with open(file=yaml_file_path, mode="r") as io: + yaml_lines = io.readlines() + + yaml_string = "".join(yaml_lines) + os.environ["NEUROCONV_YAML"] = yaml_string + os.environ["NEUROCONV_DATA_PATH"] = DATA_PATH + os.environ["NEUROCONV_OUTPUT_PATH"] = OUTPUT_PATH + + deploy_process( + command=( + "docker run -t " + f"--volume {self.source_volume}:/neuroconv ghcr.io/catalystneuro/neuroconv:yaml_variable" + ) + ) + + nwbfile_path = self.test_folder / "example_converter_spec_1.nwb" + assert nwbfile_path.exists(), f"`run_conversion_from_yaml` failed to create the file at '{nwbfile_path}'! " + with NWBHDF5IO(path=nwbfile_path, mode="r") as io: + nwbfile = io.read() + assert nwbfile.session_description == "Subject navigating a Y-shaped maze." + assert nwbfile.lab == "My Lab" + assert nwbfile.institution == "My Institution" + assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-09T21:19:09+00:00") + assert nwbfile.subject.subject_id == "1" + assert "ElectricalSeriesAP" in nwbfile.acquisition + + nwbfile_path = self.test_folder / "example_converter_spec_2.nwb" + assert nwbfile_path.exists(), f"`run_conversion_from_yaml` failed to create the file at '{nwbfile_path}'! " + with NWBHDF5IO(path=nwbfile_path, mode="r") as io: + nwbfile = io.read() + assert nwbfile.session_description == "Subject navigating a Y-shaped maze." + assert nwbfile.lab == "My Lab" + assert nwbfile.institution == "My Institution" + assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-10T21:19:09+00:00") + assert nwbfile.subject.subject_id == "002" + + nwbfile_path = self.test_folder / "example_converter_spec_3.nwb" + assert nwbfile_path.exists(), f"`run_conversion_from_yaml` failed to create the file at '{nwbfile_path}'! " + with NWBHDF5IO(path=nwbfile_path, mode="r") as io: + nwbfile = io.read() + assert nwbfile.session_description == "Auto-generated by neuroconv" + assert nwbfile.lab == "My Lab" + assert nwbfile.institution == "My Institution" + assert nwbfile.session_start_time == datetime.fromisoformat("2020-10-11T21:19:09+00:00") + assert nwbfile.subject.subject_id == "Subject Name" + assert "spike_times" in nwbfile.units