diff --git a/src/mednet/scripts/upload.py b/src/mednet/scripts/upload.py index 8d0b14d98bb5439359831c7d127fd89904cab5a1..f233865cc20282744591f09684f6df4086b39446 100644 --- a/src/mednet/scripts/upload.py +++ b/src/mednet/scripts/upload.py @@ -72,24 +72,24 @@ def _create_temp_copy(source, target): .. code:: sh - mednet upload --output-folder=path/to/results + mednet upload --experiment-folder=/path/to/results 2. Upload an existing experiment result with an experiment name: .. code:: sh - mednet upload--output-folder=path/to/results --experiment-name=exp-pasa_mc + mednet upload --experiment-folder=/path/to/results --experiment-name=exp-pasa_mc 3. Upload an existing experiment result with a run name: .. code:: sh - mednet upload--output-folder=path/to/results --run-name=run-1 + mednet upload --experiment-folder=/path/to/results --run-name=run-1 """, ) @click.option( - "--output-folder", - "-o", + "--experiment-folder", + "-f", help="Directory in which to upload results from", required=True, type=click.Path( @@ -114,12 +114,12 @@ def _create_temp_copy(source, target): ) @verbosity_option(logger=logger, cls=ResourceOption, expose_value=False) def upload( - output_folder: pathlib.Path, + experiment_folder: pathlib.Path, experiment_name: str, run_name: str, **_, # ignored ) -> None: # numpydoc ignore=PR01 - """Upload results from an experiment output folder.""" + """Upload results from an experiment folder.""" logger.info("Getting Gitlab credentials for accessing to MLFlow server...") gitlab, config = _get_gitlab_config() @@ -130,10 +130,10 @@ def upload( ) # prepare train files - train_output_folder = output_folder / "model" - train_meta_file = train_output_folder / "meta.json" - train_log_file = train_output_folder / "trainlog.pdf" - train_model_file = [f for f in train_output_folder.glob("*lowest*")][0] + train_folder = experiment_folder / "model" + train_meta_file = train_folder / "meta.json" + train_log_file = train_folder / "trainlog.pdf" + train_model_file = [f for f in train_folder.glob("*lowest*")][0] train_model_temp_file = train_model_file.parts[-1].replace("=", "_") train_model_temp_file = _create_temp_copy( train_model_file, train_model_temp_file @@ -142,9 +142,9 @@ def upload( meta_data = json.load(f) # prepare evaluation files - evaluation_file = output_folder / "evaluation.json" - evaluation_meta_file = output_folder / "evaluation.meta.json" - evaluation_log_file = output_folder / "evaluation.pdf" + evaluation_file = experiment_folder / "evaluation.json" + evaluation_meta_file = experiment_folder / "evaluation.meta.json" + evaluation_log_file = experiment_folder / "evaluation.pdf" with evaluation_file.open("r") as f: evaluation_data = json.load(f) test_data = evaluation_data["test"]