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test: add NOTEEVENTS demo data and enable multimodal mortality test #967

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test: add NOTEEVENTS demo data and enable multimodal mortality test #967

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Binary file added test-resources/core/mimic3demo/NOTEEVENTS.csv.gz
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70 changes: 40 additions & 30 deletions tests/core/test_mimic3_mortality_prediction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,6 @@ def test_mortality_prediction_mimic3_set_task(self):
traceback.print_exc()
self.fail(f"Failed to use set_task with MortalityPredictionMIMIC3: {e}")

@unittest.skip("Skipping multimodal test - noteevents not included in test resources")
def test_multimodal_mortality_prediction_mimic3_set_task(self):
"""Test MultimodalMortalityPredictionMIMIC3 task with set_task() method."""
task = MultimodalMortalityPredictionMIMIC3()
Expand All @@ -144,44 +143,55 @@ def test_multimodal_mortality_prediction_mimic3_set_task(self):
self.assertIn("clinical_notes", task.input_schema)
self.assertIn("mortality", task.output_schema)

# Load dataset with noteevents for multimodal testing
multimodal_dataset = MIMIC3Dataset(
root=self.demo_dataset_path,
tables=["diagnoses_icd", "procedures_icd", "prescriptions", "noteevents"],
)

# Test using set_task method
try:
sample_dataset = self.dataset.set_task(task)
sample_dataset = multimodal_dataset.set_task(task)
self.assertIsNotNone(sample_dataset, "set_task should return a dataset")
self.assertTrue(
hasattr(sample_dataset, "samples"), "Sample dataset should have samples"
)

# Verify we got some samples
self.assertGreater(
len(sample_dataset.samples), 0, "Should generate at least one sample"
)
num_samples = len(sample_dataset)
self.assertGreater(num_samples, 0, "Should generate at least one sample")

# Test sample structure
if len(sample_dataset.samples) > 0:
sample = sample_dataset.samples[0]
required_keys = [
"hadm_id",
"patient_id",
"conditions",
"procedures",
"drugs",
"clinical_notes",
"mortality",
]
for key in required_keys:
self.assertIn(key, sample, f"Sample should contain key: {key}")
sample = sample_dataset[0]
required_keys = [
"hadm_id",
"patient_id",
"conditions",
"procedures",
"drugs",
"clinical_notes",
"mortality",
]
for key in required_keys:
self.assertIn(key, sample, f"Sample should contain key: {key}")

# Verify data types
self.assertIsInstance(
sample["clinical_notes"], str, "clinical_notes should be a string"
)
self.assertIn(
int(sample["mortality"]), [0, 1], "Mortality label should be 0 or 1"
)

# Verify data types
self.assertIsInstance(
sample["clinical_notes"], str, "clinical_notes should be a string"
)
self.assertIn(
sample["mortality"], [0, 1], "Mortality label should be 0 or 1"
)
# Verify that at least one sample has non-empty clinical notes,
# proving that NOTEEVENTS data was actually loaded
has_notes = any(
len(sample_dataset[i]["clinical_notes"]) > 0
for i in range(num_samples)
)
self.assertTrue(
has_notes, "At least one sample should have non-empty clinical notes"
)

print(f"Generated {len(sample_dataset.samples)} multimodal samples")
print(f"Clinical notes length: {len(sample['clinical_notes'])}")
print(f"Generated {num_samples} multimodal samples")
print(f"Clinical notes length: {len(sample['clinical_notes'])}")

except Exception as e:
self.fail(
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