Added quarantine tests

tests/test_quarantine.py

@@ -0,0 +1,101 @@
+import os
+from pathlib import Path
+import pytest
+import shutil
+import tempfile
+
+import numpy as np
+import pandas as pd
+
+from pydicer.quarantine import copy_file_to_quarantine, read_quarantined_data
+
+
+def test_copy_file_to_quarantine():
+    """Test that copy_file_to_quarantine correctly copies the file to quarantine and
+    writes the summary entry.
+    """
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tmpdir_path = Path(tmpdir)
+
+        # Create a dummy DICOM file
+        dummy_file = tmpdir_path / "dummy.dcm"
+        dummy_file.write_text("Some dummy content")
+
+        # Invoke the function
+        copy_file_to_quarantine(dummy_file, tmpdir_path, "Test error message")
+
+        quarantine_dir = tmpdir_path / "quarantine"
+        summary_file = quarantine_dir / "summary.csv"
+
+        # Assert quarantine directory was created
+        assert quarantine_dir.is_dir(), "Quarantine directory was not created."
+
+        # Assert summary file was created
+        assert summary_file.exists(), "Summary CSV file was not created."
+
+        # Read the summary CSV
+        df_summary = pd.read_csv(summary_file, index_col=0)
+
+        # Check that exactly one entry is in the summary
+        assert len(
+            df_summary) == 1, "There should be exactly one entry in the summary."
+
+        # Check the summary row
+        row = df_summary.iloc[0]
+        assert row["error"] == "Test error message"
+        assert "file" in row, "'file' column is missing in the summary DataFrame."
+        assert "PatientID" in row, "'PatientID' column is missing in the summary DataFrame."
+
+        # Because this is not a valid DICOM, the code defaults PatientID to UNKNOWN
+        assert pd.isna(row["PatientID"])
+
+        # The quarantined file is placed under: quarantine_dir / "UNKNOWN" / <parent_folder> / dummy.dcm
+        quarantined_file_path = quarantine_dir.joinpath(
+            "UNKNOWN", dummy_file.parent.name, dummy_file.name)
+        assert quarantined_file_path.exists(
+        ), "Quarantined file was not copied to the correct location."
+
+
+def test_read_quarantined_data():
+    """Test that read_quarantined_data reads data from an existing quarantine summary CSV."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tmpdir_path = Path(tmpdir)
+        quarantine_dir = tmpdir_path / "quarantine"
+        quarantine_dir.mkdir(exist_ok=True)
+
+        # Create a fake summary CSV
+        summary_file = quarantine_dir / "summary.csv"
+        df_expected = pd.DataFrame([
+            {
+                "file": "somefile.dcm",
+                "error": "some_error",
+                "quarantine_dttm": "2024-01-01 00:00:00",
+                "PatientID": "UNKNOWN",
+                "Modality": None,
+                "SOPInstanceUID": None,
+                "SeriesDescription": None,
+            }
+        ])
+        df_expected.to_csv(summary_file)
+
+        # Use the function to read it
+        df_summary = read_quarantined_data(tmpdir_path)
+
+        # Assert the DataFrame matches our expectations
+        assert len(df_summary) == 1, "Expected one record in the summary."
+        row = df_summary.iloc[0]
+        assert row["file"] == "somefile.dcm"
+        assert row["error"] == "some_error"
+        assert row["PatientID"] == "UNKNOWN"
+
+
+def test_read_quarantined_data_no_summary():
+    """Test that reading quarantine data raises an error or fails gracefully if summary.csv is missing."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tmpdir_path = Path(tmpdir)
+        quarantine_dir = tmpdir_path / "quarantine"
+        quarantine_dir.mkdir(exist_ok=True)
+
+        # summary.csv does NOT exist here
+        with pytest.raises(FileNotFoundError):
+            read_quarantined_data(tmpdir_path)