From a7a91a137634a869c9080b3fd8145fdeb1395f08 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Fri, 22 Mar 2024 13:23:34 -0400 Subject: [PATCH] debugging --- tests/docker_yaml_conversion_specification_cli.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/tests/docker_yaml_conversion_specification_cli.py b/tests/docker_yaml_conversion_specification_cli.py index bd2739b66..03cad8838 100644 --- a/tests/docker_yaml_conversion_specification_cli.py +++ b/tests/docker_yaml_conversion_specification_cli.py @@ -31,9 +31,10 @@ def test_run_conversion_from_yaml_cli(self): command=( "docker run -t " f"--volume {self.source_volume}:{self.source_volume} " + f"--volume {self.test_folder}:{self.test_folder} " "ghcr.io/catalystneuro/neuroconv:{self.tag} " f"neuroconv {yaml_file_path} " - f"--data-folder-path /neuroconv/{DATA_PATH} --output-folder-path {self.test_folder} --overwrite" + f"--data-folder-path {self.source_volume}/{DATA_PATH} --output-folder-path {self.test_folder} --overwrite" ), catch_output=True, ) @@ -80,16 +81,17 @@ def test_run_conversion_from_yaml_variable(self): yaml_string = "".join(yaml_lines) os.environ["NEUROCONV_YAML"] = yaml_string - os.environ["NEUROCONV_DATA_PATH"] = str(DATA_PATH) + os.environ["NEUROCONV_DATA_PATH"] = self.source_volume + str(DATA_PATH) os.environ["NEUROCONV_OUTPUT_PATH"] = str(self.test_folder) output = deploy_process( command=( "docker run -t " - f"--volume {self.source_volume}:/neuroconv " - "--env NEUROCONV_YAML=$NEUROCONV_YAML " - "--env NEUROCONV_DATA_PATH=$NEUROCONV_DATA_PATH " - "--env NEUROCONV_OUTPUT_PATH=$NEUROCONV_OUTPUT_PATH " + f"--volume {self.source_volume}:{self.source_volume} " + f"--volume {self.test_folder}:{self.test_folder} " + "-e NEUROCONV_YAML=$NEUROCONV_YAML " + "-e NEUROCONV_DATA_PATH=$NEUROCONV_DATA_PATH " + "-e NEUROCONV_OUTPUT_PATH=$NEUROCONV_OUTPUT_PATH " "ghcr.io/catalystneuro/neuroconv:yaml_variable" ), catch_output=True,