MIMIC3 Initialize Test Case for Tests/Core

tests/core/test_mimic3.py

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+import unittest
+import tempfile
+import shutil
+import subprocess
+import os
+from pathlib import Path
+
+from pyhealth.datasets import MIMIC3Dataset
+
+
+class TestMIMIC3Demo(unittest.TestCase):
+    """Test MIMIC3 dataset with demo data downloaded from PhysioNet."""
+
+    def setUp(self):
+        """Download and set up demo dataset for each test."""
+        self.temp_dir = tempfile.mkdtemp()
+        self._download_demo_dataset()
+        self._load_dataset()
+
+    def tearDown(self):
+        """Clean up downloaded dataset after each test."""
+        if self.temp_dir and os.path.exists(self.temp_dir):
+            shutil.rmtree(self.temp_dir)
+
+    def _download_demo_dataset(self):
+        """Download MIMIC-III demo dataset using wget."""
+        download_url = "https://physionet.org/files/mimiciii-demo/1.4/"
+
+        # Use wget to download the demo dataset recursively
+        cmd = [
+            "wget",
+            "-r",
+            "-N",
+            "-c",
+            "-np",
+            "--directory-prefix",
+            self.temp_dir,
+            download_url,
+        ]
+
+        try:
+            subprocess.run(cmd, check=True, capture_output=True, text=True)
+        except subprocess.CalledProcessError as e:
+            raise unittest.SkipTest(f"Failed to download MIMIC-III demo dataset: {e}")
+        except FileNotFoundError:
+            raise unittest.SkipTest("wget not available - skipping download test")
+
+        # Find the downloaded dataset path
+        physionet_dir = (
+            Path(self.temp_dir) / "physionet.org" / "files" / "mimiciii-demo" / "1.4"
+        )
+        if physionet_dir.exists():
+            self.demo_dataset_path = str(physionet_dir)
+        else:
+            raise unittest.SkipTest("Downloaded dataset not found in expected location")
+
+    def _load_dataset(self):
+        """Load the dataset for testing."""
+        tables = ["diagnoses_icd", "procedures_icd", "prescriptions", "noteevents"]
+        self.dataset = MIMIC3Dataset(root=self.demo_dataset_path, tables=tables)
+
+    def test_stats(self):
+        """Test .stats() method execution."""
+        try:
+            self.dataset.stats()
+        except Exception as e:
+            self.fail(f"dataset.stats() failed: {e}")
+
+    def test_get_events(self):
+        """Test get_patient and get_events methods with patient 10006."""
+        # Test get_patient method
+        patient = self.dataset.get_patient("10006")
+        self.assertIsNotNone(patient, msg="Patient 10006 should exist in demo dataset")
+
+        # Test get_events method
+        events = patient.get_events()
+        self.assertIsNotNone(events, msg="get_events() should not return None")
+        self.assertIsInstance(events, list, msg="get_events() should return a list")
+        self.assertGreater(
+            len(events), 0, msg="get_events() should not return an empty list"
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()