unit tests for setup steps (WIP)

brainglobe · Dec 4, 2023 · c162460 · c162460
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diff --git a/tests/data/input_data_GIN.json b/tests/data/input_data_GIN.json
@@ -0,0 +1,39 @@
+{
+  "install_path": ".cellfinder_workflows",
+  "data_url": "https://gin.g-node.org/BrainGlobe/test-data/raw/master/cellfinder/cellfinder-test-data.zip",
+  "data_hash": "b0ef53b1530e4fa3128fcc0a752d0751909eab129d701f384fc0ea5f138c5914",
+  "extract_dir_relative": "cellfinder_test_data",
+  "signal_subdir": "signal",
+  "background_subdir": "background",
+  "output_path_basename_relative": "cellfinder_output_",
+  "detected_cells_filename": "detected_cells.xml",
+  "voxel_sizes": [
+    5,
+    2,
+    2
+  ],
+  "start_plane": 0,
+  "end_plane": -1,
+  "trained_model": null,
+  "model_weights": null,
+  "model": "resnet50_tv",
+  "batch_size": 32,
+  "n_free_cpus": 2,
+  "network_voxel_sizes": [
+    5,
+    1,
+    1
+  ],
+  "soma_diameter": 16,
+  "ball_xy_size": 6,
+  "ball_z_size": 15,
+  "ball_overlap_fraction": 0.6,
+  "log_sigma_size": 0.2,
+  "n_sds_above_mean_thresh": 10,
+  "soma_spread_factor": 1.4,
+  "max_cluster_size": 100000,
+  "cube_width": 50,
+  "cube_height": 50,
+  "cube_depth": 20,
+  "network_depth": "50"
+}
diff --git a/tests/data/input_data_locally.json b/tests/data/input_data_locally.json
@@ -0,0 +1,39 @@
+{
+  "install_path": ".cellfinder_workflows",
+  "data_url": "https://gin.g-node.org/BrainGlobe/test-data/raw/master/cellfinder/cellfinder-test-data.zip",
+  "data_hash": "b0ef53b1530e4fa3128fcc0a752d0751909eab129d701f384fc0ea5f138c5914",
+  "extract_dir_relative": "cellfinder_test_data",
+  "signal_subdir": "signal",
+  "background_subdir": "background",
+  "output_path_basename_relative": "cellfinder_output_",
+  "detected_cells_filename": "detected_cells.xml",
+  "voxel_sizes": [
+    5,
+    2,
+    2
+  ],
+  "start_plane": 0,
+  "end_plane": -1,
+  "trained_model": null,
+  "model_weights": null,
+  "model": "resnet50_tv",
+  "batch_size": 32,
+  "n_free_cpus": 2,
+  "network_voxel_sizes": [
+    5,
+    1,
+    1
+  ],
+  "soma_diameter": 16,
+  "ball_xy_size": 6,
+  "ball_z_size": 15,
+  "ball_overlap_fraction": 0.6,
+  "log_sigma_size": 0.2,
+  "n_sds_above_mean_thresh": 10,
+  "soma_spread_factor": 1.4,
+  "max_cluster_size": 100000,
+  "cube_width": 50,
+  "cube_height": 50,
+  "cube_depth": 20,
+  "network_depth": "50"
+}
diff --git a/tests/data/input_data_missing_background.json b/tests/data/input_data_missing_background.json
@@ -0,0 +1,39 @@
+{
+  "install_path": ".cellfinder_workflows",
+  "data_url": "https://gin.g-node.org/BrainGlobe/test-data/raw/master/cellfinder/cellfinder-test-data.zip",
+  "data_hash": "b0ef53b1530e4fa3128fcc0a752d0751909eab129d701f384fc0ea5f138c5914",
+  "extract_dir_relative": "cellfinder_test_data",
+  "signal_subdir": "signal",
+  "background_subdir": "__",
+  "output_path_basename_relative": "cellfinder_output_",
+  "detected_cells_filename": "detected_cells.xml",
+  "voxel_sizes": [
+    5,
+    2,
+    2
+  ],
+  "start_plane": 0,
+  "end_plane": -1,
+  "trained_model": null,
+  "model_weights": null,
+  "model": "resnet50_tv",
+  "batch_size": 32,
+  "n_free_cpus": 2,
+  "network_voxel_sizes": [
+    5,
+    1,
+    1
+  ],
+  "soma_diameter": 16,
+  "ball_xy_size": 6,
+  "ball_z_size": 15,
+  "ball_overlap_fraction": 0.6,
+  "log_sigma_size": 0.2,
+  "n_sds_above_mean_thresh": 10,
+  "soma_spread_factor": 1.4,
+  "max_cluster_size": 100000,
+  "cube_width": 50,
+  "cube_height": 50,
+  "cube_depth": 20,
+  "network_depth": "50"
+}
diff --git a/tests/data/input_data_missing_signal.json b/tests/data/input_data_missing_signal.json
@@ -0,0 +1,39 @@
+{
+  "install_path": ".cellfinder_workflows",
+  "data_url": "https://gin.g-node.org/BrainGlobe/test-data/raw/master/cellfinder/cellfinder-test-data.zip",
+  "data_hash": "b0ef53b1530e4fa3128fcc0a752d0751909eab129d701f384fc0ea5f138c5914",
+  "extract_dir_relative": "cellfinder_test_data",
+  "signal_subdir": "__",
+  "background_subdir": "background",
+  "output_path_basename_relative": "cellfinder_output_",
+  "detected_cells_filename": "detected_cells.xml",
+  "voxel_sizes": [
+    5,
+    2,
+    2
+  ],
+  "start_plane": 0,
+  "end_plane": -1,
+  "trained_model": null,
+  "model_weights": null,
+  "model": "resnet50_tv",
+  "batch_size": 32,
+  "n_free_cpus": 2,
+  "network_voxel_sizes": [
+    5,
+    1,
+    1
+  ],
+  "soma_diameter": 16,
+  "ball_xy_size": 6,
+  "ball_z_size": 15,
+  "ball_overlap_fraction": 0.6,
+  "log_sigma_size": 0.2,
+  "n_sds_above_mean_thresh": 10,
+  "soma_spread_factor": 1.4,
+  "max_cluster_size": 100000,
+  "cube_width": 50,
+  "cube_height": 50,
+  "cube_depth": 20,
+  "network_depth": "50"
+}
diff --git a/tests/data/input_data_not_locally_or_GIN.json b/tests/data/input_data_not_locally_or_GIN.json
@@ -0,0 +1,37 @@
+{
+  "install_path": ".cellfinder_workflows",
+  "extract_dir_relative": "cellfinder_test_data",
+  "signal_subdir": "signal",
+  "background_subdir": "background",
+  "output_path_basename_relative": "cellfinder_output_",
+  "detected_cells_filename": "detected_cells.xml",
+  "voxel_sizes": [
+    5,
+    2,
+    2
+  ],
+  "start_plane": 0,
+  "end_plane": -1,
+  "trained_model": null,
+  "model_weights": null,
+  "model": "resnet50_tv",
+  "batch_size": 32,
+  "n_free_cpus": 2,
+  "network_voxel_sizes": [
+    5,
+    1,
+    1
+  ],
+  "soma_diameter": 16,
+  "ball_xy_size": 6,
+  "ball_z_size": 15,
+  "ball_overlap_fraction": 0.6,
+  "log_sigma_size": 0.2,
+  "n_sds_above_mean_thresh": 10,
+  "soma_spread_factor": 1.4,
+  "max_cluster_size": 100000,
+  "cube_width": 50,
+  "cube_height": 50,
+  "cube_depth": 20,
+  "network_depth": "50"
+}
diff --git a/tests/test_integration/test_cellfinder_workflow.py b/tests/test_integration/test_cellfinder_workflow.py
@@ -34,7 +34,7 @@ def test_run_with_default_config(tmp_path, default_json_config_path):
             / "workflows"
             / "cellfinder.py",
         ],
-        cwd=tmp_path,
+        cwd=tmp_path,  # -------------------
         stdout=subprocess.PIPE,
         stderr=subprocess.STDOUT,
         text=True,

diff --git a/tests/test_unit/test_cellfinder.py b/tests/test_unit/test_cellfinder.py
@@ -1 +1,75 @@
-# cellfinder-specific unit tests
+import json
+import logging
+
+from workflows.cellfinder import read_cellfinder_config, retrieve_input_data
+from workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
+
+# @pytest.fixture() --- for where configs are
+# def
+
+
+def test_read_cellfinder_config(
+    input_config_path=DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
+):
+    # read json as Cellfinder config
+    config = read_cellfinder_config(input_config_path)
+
+    # read json as dict
+    with open(input_config_path) as cfg:
+        config_dict = json.load(cfg)
+
+    # check keys of dict are a subset of Cellfinder config attributes
+    assert all(
+        [ky in config.__dataclass_fields__.keys() for ky in config_dict.keys()]
+    )
+
+
+# define different configs
+# @pytest.mark.parametrize(
+#     "input_config_path, message",
+#     [
+#         (DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
+# "Fetching input data from the local directories"),
+#         (, "The directory does not exist"),
+#         (, "The directory does not exist"),
+#         (,"Input data not found locally,
+# and URL/hash to GIN repository not provided"),
+#         (,"Fetching input data from the provided GIN repository")
+#     ]
+# )
+def test_retrieve_input_data(caplog, input_config_path, message):
+    # set logger to capture
+    caplog.set_level(
+        logging.DEBUG, logger="root"
+    )  # --- why root? :( "workflows.utils")
+
+    # read json as Cellfinder config
+    config = read_cellfinder_config(input_config_path)
+
+    # retrieve data
+    retrieve_input_data(config)
+
+    assert message in caplog.messages
+
+    # if (
+    #     Path(config.signal_dir_path).exists()
+    #     and Path(config.background_dir_path).exists()
+    # ):
+
+    #     # with caplog.at_level(
+    #     #     logging.DEBUG,
+    #     #     logger="root" # why root?
+    #     # ):
+    #     updated_config = retrieve_input_data(config)
+
+    #     assert message in caplog.messages
+
+    # # If exactly one of the input data directories is missing, print error
+    # elif (
+    #     Path(config.signal_dir_path).resolve().exists()
+    #     or Path(config.background_dir_path).resolve().exists()
+    # ):
+
+
+# def test_setup_workflow():
+#     pass
diff --git a/workflows/cellfinder.py b/workflows/cellfinder.py
@@ -98,6 +98,7 @@ def read_cellfinder_config(input_config_path):
     """Instantiate a CellfinderConfig from the input json file
     (assumes config is json serializable)
 
+
     Parameters
     ----------
     input_config_path : _type_
@@ -142,7 +143,7 @@ def retrieve_input_data(config: CellfinderConfig) -> CellfinderConfig:
         for running cellfinder.
     """
     # Fetch logger
-    logger = logging.getLogger("root")
+    logger = logging.getLogger("workflow.utils")
 
     # Check if input data (signal and background) exist locally.
     # If both directories exist, get list of signal and background files
@@ -250,7 +251,7 @@ def setup_workflow(input_config_path: Path) -> CellfinderConfig:
     """
 
     # Fetch logger
-    logger = logging.getLogger("root")
+    logger = logging.getLogger("workflow.utils")
 
     # Check config file exists
     assert input_config_path.exists()