Fix and add tests

tests/unit/test_slurm_client.py

@@ -201,9 +201,6 @@ def test_get_workflow_command(slurm_client,
         "IMAGE_PATH": "/path/to/slurm_images/workflow_path",
         "IMAGE_VERSION": "1.0",
         "SINGULARITY_IMAGE": "image_1.0.sif",
-        "CONVERSION_PATH": "/path/to/slurm_converters",
-        "CONVERTER_IMAGE": "convert_zarr_to_tiff.sif",
-        "DO_CONVERT": "true",
         "SCRIPT_PATH": "/path/to/slurm_script",
         "PARAM1": "value1",
         "PARAM2": "value2"
@@ -218,6 +215,55 @@ def test_get_workflow_command(slurm_client,
     assert env == expected_env
 
 
+@pytest.mark.parametrize("source_format, target_format", [("zarr", "tiff"), ("xyz", "abc")])
+@patch('biomero.slurm_client.SlurmClient.run_commands')
+@patch('fabric.Result')
+def test_run_conversion_workflow_job(mock_result, mock_run_commands, slurm_client, source_format, target_format):
+    # GIVEN
+    folder_name = "example_folder"
+
+    slurm_client.slurm_data_path = "/path/to/slurm_data"
+    slurm_client.slurm_converters_path = "/path/to/slurm_converters"
+    slurm_client.slurm_script_path = "/path/to/slurm_script"
+
+    expected_config_file = f"config_{folder_name}.txt"
+    expected_data_path = f"{slurm_client.slurm_data_path}/{folder_name}"
+    expected_conversion_cmd, expected_sbatch_env = (
+        "sbatch --job-name=conversion --export=ALL,CONFIG_PATH=\"$PWD/$CONFIG_FILE\" --array=1-$N $SCRIPT_PATH/convert_job_array.sh",
+        {
+            "DATA_PATH": f"{expected_data_path}",
+            "CONVERSION_PATH": f"{slurm_client.slurm_converters_path}",
+            "CONVERTER_IMAGE": f"convert_{source_format}_to_{target_format}.sif",
+            "SCRIPT_PATH": f"{slurm_client.slurm_script_path}",
+            "CONFIG_FILE": f"{expected_config_file}"
+        }
+    )
+    expected_commands = [
+        f"find {expected_data_path}/data/in -name '*.{source_format}' | awk '{{print NR, $0}}' > {expected_config_file}",
+        f"N=$(wc -l < \"{expected_config_file}\")",
+        f"echo \"Number of .{source_format} files: $N\"",
+        expected_conversion_cmd
+    ]
+
+    # Mocking the run_commands method to avoid actual execution
+    mock_run_commands.return_value = mock_result
+
+    # WHEN
+    slurm_job = slurm_client.run_conversion_workflow_job(
+        folder_name, source_format, target_format)
+
+    # THEN
+    assert slurm_job is not None
+
+    assert mock_run_commands.call_args[0][0] == expected_commands
+    assert mock_run_commands.call_args[0][1] == expected_sbatch_env
+
+    # Check properties of slurm_job
+    assert slurm_job.job_id == -1
+    assert slurm_job.submit_result.ok
+    assert slurm_job.job_state is None
+
+
 def test_pull_descriptor_from_github(slurm_client):
     # GIVEN
     workflow = "example_workflow"