Merge pull request #15 from suzannejin/docstring-add-test-csv-loader

add test csv loader

tests/test_csv_loader.py

@@ -0,0 +1,201 @@
+import os
+from typing import Any
+
+import numpy as np
+import pytest
+
+from src.stimulus.data.csv import CsvLoader
+from src.stimulus.data.experiments import DnaToFloatExperiment, ProtDnaToFloatExperiment
+
+
+class DataCsvLoader:
+    """Helper class to store CsvLoader objects and expected values for testing.
+
+    This class initializes CsvLoader objects with given csv data and stores expected
+    values for testing purposes.
+
+    Attributes:
+        experiment: An experiment instance to process the data.
+        csv_path (str): Absolute path to the CSV file.
+        csv_loader (CsvLoader): Initialized CsvLoader object.
+        data_length (int, optional): Expected length of the data.
+        shape_splits (dict, optional): Expected split indices and their lengths.
+    """
+
+    def __init__(self, filename: str, experiment: Any):
+        """Initialize DataCsvLoader with a CSV file and experiment type.
+
+        Args:
+            filename (str): Path to the CSV file.
+            experiment (Any): Experiment class to be instantiated.
+        """
+        self.experiment = experiment()
+        self.csv_path = os.path.abspath(filename)
+        self.csv_loader = CsvLoader(self.experiment, self.csv_path)
+        self.data_length = None
+        self.shape_splits = None
+
+
+@pytest.fixture
+def dna_test_data():
+    """This stores the basic dna test csv"""
+    data = DataCsvLoader("tests/test_data/dna_experiment/test.csv", DnaToFloatExperiment)
+    data.data_length = 2
+    return data
+
+
+@pytest.fixture
+def dna_test_data_with_split():
+    """This stores the basic dna test csv with split"""
+    data = DataCsvLoader("tests/test_data/dna_experiment/test_with_split.csv", DnaToFloatExperiment)
+    data.data_length = 48
+    data.shape_splits = {0: 16, 1: 16, 2: 16}
+    return data
+
+
+@pytest.fixture
+def prot_dna_test_data():
+    """This stores the basic prot-dna test csv"""
+    data = DataCsvLoader("tests/test_data/prot_dna_experiment/test.csv", ProtDnaToFloatExperiment)
+    data.data_length = 2
+    return data
+
+
+@pytest.fixture
+def prot_dna_test_data_with_split():
+    """This stores the basic prot-dna test csv with split"""
+    data = DataCsvLoader("tests/test_data/prot_dna_experiment/test_with_split.csv", ProtDnaToFloatExperiment)
+    data.data_length = 3
+    data.shape_splits = {0: 1, 1: 1, 2: 1}
+    return data
+
+
+@pytest.mark.parametrize(
+    "fixture_name",
+    [
+        ("dna_test_data"),
+        ("dna_test_data_with_split"),
+        ("prot_dna_test_data"),
+        ("prot_dna_test_data_with_split"),
+    ],
+)
+def test_data_length(request, fixture_name: str):
+    """Verify data is loaded with correct length.
+
+    Args:
+        request: Pytest fixture request object.
+        fixture_name (str): Name of the fixture to test.
+    """
+    data = request.getfixturevalue(fixture_name)
+    assert len(data.csv_loader) == data.data_length
+
+
+@pytest.mark.parametrize(
+    "fixture_name",
+    [
+        ("dna_test_data"),
+        ("prot_dna_test_data"),
+    ],
+)
+def test_parse_csv_to_input_label_meta(request, fixture_name: str):
+    """Test parsing of CSV to input, label, and meta.
+
+    Args:
+        request: Pytest fixture request object.
+        fixture_name (str): Name of the fixture to test.
+
+    Verifies:
+        - Input data is a dictionary
+        - Label data is a dictionary
+        - Meta data is a dictionary
+    """
+    data = request.getfixturevalue(fixture_name)
+    assert isinstance(data.csv_loader.input, dict)
+    assert isinstance(data.csv_loader.label, dict)
+    assert isinstance(data.csv_loader.meta, dict)
+
+
+@pytest.mark.parametrize(
+    "fixture_name",
+    [
+        ("dna_test_data"),
+        ("prot_dna_test_data"),
+    ],
+)
+def test_get_all_items(request, fixture_name: str):
+    """Test retrieval of all items from the CSV loader.
+
+    Args:
+        request: Pytest fixture request object.
+        fixture_name (str): Name of the fixture to test.
+
+    Verifies:
+        - All returned data (input, label, meta) are dictionaries
+    """
+    data = request.getfixturevalue(fixture_name)
+    input_data, label_data, meta_data = data.csv_loader.get_all_items()
+    assert isinstance(input_data, dict)
+    assert isinstance(label_data, dict)
+    assert isinstance(meta_data, dict)
+
+
+@pytest.mark.parametrize(
+    "fixture_name,slice,expected_length",
+    [
+        ("dna_test_data", 0, 1),
+        ("dna_test_data", slice(0, 2), 2),
+        ("prot_dna_test_data", 0, 1),
+        ("prot_dna_test_data", slice(0, 2), 2),
+    ],
+)
+def test_get_encoded_item(request, fixture_name: str, slice: Any, expected_length: int):
+    """Test retrieval of encoded items through slicing.
+
+    Args:
+        request: Pytest fixture request object.
+        fixture_name (str): Name of the fixture to test.
+        slice (int or slice): Index or slice object for data access.
+        expected_length (int): Expected length of the retrieved data.
+
+    Verifies:
+        - Returns 3 dictionaries (input, label, meta)
+        - All items are encoded as numpy arrays
+        - Arrays have the expected length
+    """
+    data = request.getfixturevalue(fixture_name)
+    encoded_items = data.csv_loader[slice]
+
+    assert len(encoded_items) == 3
+    for i in range(3):
+        assert isinstance(encoded_items[i], dict)
+        for item in encoded_items[i].values():
+            assert isinstance(item, np.ndarray)
+            if expected_length > 1:
+                assert len(item) == expected_length
+
+
+@pytest.mark.parametrize(
+    "fixture_name",
+    [
+        ("dna_test_data_with_split"),
+        ("prot_dna_test_data_with_split"),
+    ],
+)
+def test_splitting(request, fixture_name):
+    """Test data splitting functionality.
+
+    Args:
+        request: Pytest fixture request object.
+        fixture_name (str): Name of the fixture to test.
+
+    Verifies:
+        - Data can be loaded with different split indices
+        - Splits have correct lengths
+        - Invalid split index raises ValueError
+    """
+    data = request.getfixturevalue(fixture_name)
+    for i in [0, 1, 2]:
+        data_i = CsvLoader(data.experiment, data.csv_path, split=i)
+        assert len(data_i) == data.shape_splits[i]
+    with pytest.raises(ValueError):
+        CsvLoader(data.experiment, data.csv_path, split=3)

tests/test_csv_processing.py

@@ -35,6 +35,7 @@ def __init__(self, filename: str, experiment: Any):
         self.expected_split = None
         self.expected_transformed_values = None
 
+
 @pytest.fixture
 def dna_test_data():
     """This stores the basic dna test csv"""
@@ -49,26 +50,32 @@ def dna_test_data():
     }
     return data
 
+
 @pytest.fixture
 def dna_test_data_long():
     """This stores the long dna test csv"""
     data = DataCsvProcessing("tests/test_data/dna_experiment/test_shuffling_long.csv", DnaToFloatExperiment)
     data.data_length = 1000
     return data
 
+
 @pytest.fixture
 def dna_test_data_long_shuffled():
     """This stores the shuffled long dna test csv"""
-    data = DataCsvProcessing("tests/test_data/dna_experiment/test_shuffling_long_shuffled.csv", ProtDnaToFloatExperiment)
+    data = DataCsvProcessing(
+        "tests/test_data/dna_experiment/test_shuffling_long_shuffled.csv", ProtDnaToFloatExperiment
+    )
     data.data_length = 1000
     return data
 
+
 @pytest.fixture
 def dna_config():
     """This is the config file for the dna experiment"""
     with open("tests/test_data/dna_experiment/test_config.json") as f:
         return json.load(f)
-
+
+
 @pytest.fixture
 def prot_dna_test_data():
     """This stores the basic prot-dna test csv"""
@@ -84,21 +91,26 @@ def prot_dna_test_data():
     }
     return data
 
+
 @pytest.fixture
 def prot_dna_config():
     """This is the config file for the prot experiment"""
     with open("tests/test_data/prot_dna_experiment/test_config.json") as f:
         return json.load(f)
 
-@pytest.mark.parametrize("fixture_name", [
+
+@pytest.mark.parametrize(
+    "fixture_name",
+    [
         ("dna_test_data"),
         ("dna_test_data_long"),
         ("dna_test_data_long_shuffled"),
-        ("prot_dna_test_data")
-    ])
+        ("prot_dna_test_data"),
+    ],
+)
 def test_data_length(request, fixture_name):
     """Test that data is loaded with the correct length.
-    
+
     Args:
         request: Pytest fixture request object.
         fixture_name (str): Name of the fixture to test.
@@ -108,13 +120,17 @@ def test_data_length(request, fixture_name):
     data = request.getfixturevalue(fixture_name)
     assert len(data.csv_processing.data) == data.data_length
 
-@pytest.mark.parametrize("fixture_data_name,fixture_config_name", [
+
+@pytest.mark.parametrize(
+    "fixture_data_name,fixture_config_name",
+    [
         ("dna_test_data", "dna_config"),
-        ("prot_dna_test_data", "prot_dna_config")
-    ])
+        ("prot_dna_test_data", "prot_dna_config"),
+    ],
+)
 def test_add_split(request, fixture_data_name, fixture_config_name):
     """Test that the add_split function properly adds the split column.
-    
+
     Args:
         request: Pytest fixture request object.
         fixture_data_name (str): Name of the data fixture to test.
@@ -128,13 +144,17 @@ def test_add_split(request, fixture_data_name, fixture_config_name):
     data.csv_processing.add_split(config["split"])
     assert data.csv_processing.data["split:split:int"].to_list() == data.expected_split
 
-@pytest.mark.parametrize("fixture_data_name,fixture_config_name", [
+
+@pytest.mark.parametrize(
+    "fixture_data_name,fixture_config_name",
+    [
         ("dna_test_data", "dna_config"),
-        ("prot_dna_test_data", "prot_dna_config")
-    ])
+        ("prot_dna_test_data", "prot_dna_config"),
+    ],
+)
 def test_transform_data(request, fixture_data_name, fixture_config_name):
     """Test that transformation functionalities properly transform the data.
-    
+
     Args:
         request: Pytest fixture request object.
         fixture_data_name (str): Name of the data fixture to test.
@@ -144,7 +164,7 @@ def test_transform_data(request, fixture_data_name, fixture_config_name):
     """
     data = request.getfixturevalue(fixture_data_name)
     config = request.getfixturevalue(fixture_config_name)
-    
+
     data.csv_processing.add_split(config["split"])
     data.csv_processing.transform(config["transform"])
 
@@ -153,13 +173,14 @@ def test_transform_data(request, fixture_data_name, fixture_config_name):
         observed_values = [round(v, 6) if isinstance(v, float) else v for v in observed_values]
         assert observed_values == expected_values
 
+
 def test_shuffle_labels(dna_test_data_long, dna_test_data_long_shuffled):
     """Test that shuffling of labels works correctly.
-    
+
     This test verifies that when labels are shuffled with a fixed seed,
     they match the expected shuffled values from a pre-computed dataset.
     Currently only tests the long DNA test data.
-    
+
     Args:
         dna_test_data_long: Fixture containing the original unshuffled DNA test data.
         dna_test_data_long_shuffled: Fixture containing the expected shuffled DNA test data.
@@ -169,4 +190,3 @@ def test_shuffle_labels(dna_test_data_long, dna_test_data_long_shuffled):
         dna_test_data_long.csv_processing.data["hola:label:float"],
         dna_test_data_long_shuffled.csv_processing.data["hola:label:float"],
     )
-