Add serialisation tests

src/python/tests/test_serialization.py

@@ -0,0 +1,84 @@
+import gzip
+import json
+import tempfile
+import pytest
+
+from oxli import KmerCountTable
+from os import remove
+from test_attr import get_version_from_cargo_toml
+
+CURRENT_VERSION = get_version_from_cargo_toml()
+
+@pytest.fixture
+def sample_kmer_table():
+    """Fixture that provides a sample KmerCountTable object."""
+    table = KmerCountTable(ksize=4)
+    table.count("AAAA")
+    table.count("TTTT")
+    return table
+
+@pytest.fixture
+def temp_file():
+    """Fixture that provides a temporary file path for testing."""
+    with tempfile.NamedTemporaryFile(delete=False, suffix='.json.gz') as temp:
+        yield temp.name
+    # Remove the file after the test is done
+    remove(temp.name)
+
+def test_serialize_json(sample_kmer_table):
+    """
+    Test case for the `serialize_json` function.
+    
+    This test verifies that the `serialize_json` function correctly serializes a
+    KmerCountTable object into a JSON string.
+    """
+    # Serialize the KmerCountTable object to JSON
+    json_data = sample_kmer_table.serialize_json()
+
+    # Convert back to dict to verify correctness
+    json_dict = json.loads(json_data)
+
+    # Check that essential attributes exist
+    assert "counts" in json_dict, "Counts should be serialized."
+    assert json_dict["ksize"] == 4, "Ksize should be correctly serialized."
+    assert sample_kmer_table.version == json_dict["version"], "Version should be serialized."
+
+def test_save_load_roundtrip(sample_kmer_table, temp_file):
+    """
+    Test the save and load functionality.
+
+    This test saves a KmerCountTable object to a file, then loads it back and
+    verifies that the data in the loaded object matches the original.
+    """
+    # Save the sample KmerCountTable to a Gzip file
+    sample_kmer_table.save(temp_file)
+
+    # Load the KmerCountTable from the file
+    loaded_table = KmerCountTable.load(temp_file)
+
+    # Verify that the loaded data matches the original
+    assert loaded_table.get("AAAA") == sample_kmer_table.get("AAAA"), "Counts should be preserved after loading."
+    assert loaded_table.get("TTTT") == sample_kmer_table.get("TTTT"), "Counts for reverse complement should be preserved."
+    assert list(loaded_table) == list(sample_kmer_table), "All records in same order."
+
+def test_version_warning_on_load_stderr(sample_kmer_table, temp_file, capfd):
+    """
+    Test that a warning is issued if the loaded object's version is different from the current Oxli version.
+
+    Uses pytest's capsys fixture to capture stderr output.
+    """
+    # Save the table to a file
+    sample_kmer_table.save(temp_file)
+
+    # Mock the current version to simulate a version mismatch
+    mock_json = sample_kmer_table.serialize_json().replace(CURRENT_VERSION, "0.0.1")
+    with gzip.open(temp_file, 'wt') as f:
+        json.dump(json.loads(mock_json), f)
+
+    # Capture stderr output
+    loaded_table = KmerCountTable.load(temp_file)
+    captured = capfd.readouterr()
+
+    # Check stderr for the version mismatch warning
+    assert "Version mismatch" in captured.err
+    assert f"loaded version is 0.0.1, but current version is {CURRENT_VERSION}" in captured.err