def test_load_table_pickle_list(self):
table_list = ['admissions', 'patients']
pre_store = PrepareData('test1', '../../data/demo_data/all')
pre_store.read_tables(table_list, True)
pre_load = PrepareData('test2', '../../data/demo_data/all')
pre_load.load_table_pickle_list(table_list)
self.assertEqual(pre_load.admissions['DIAGNOSIS'][2], 'SEPSIS',
'Not loaded multipe tables from pickle files.')
self.assertEqual(pre_load.patients['SUBJECT_ID'][3], int(10017),
'Not loaded multipe tables from pickle files.')
def test_read_tables(self):
pre = PrepareData('test', '../../data/demo_data/all')
table_list = ['admissions', 'patients']
pre.read_tables(table_list)
# Check if the two tables are loaded
self.assertEqual(pre.admissions['DIAGNOSIS'][2], 'SEPSIS',
'Not read multiple tables correctly.')
self.assertEqual(pre.patients['SUBJECT_ID'][3], int(10017),
'Not read multiple tables correctly.')
def test_transform(self):
pre = PrepareData('test', '../../data/demo_data/all')
pre.read_tables(['prescriptions', 'admissions'])
drug_enc = DrugEncoderV2(48, 10)
drug_enc.fit(pre.prescriptions)
hadm_drug_matrix, hadm_id_mapping = drug_enc.transform(
pre.prescriptions, pre.admissions)
self.assertTrue(
((hadm_drug_matrix[7, :] == [0, 1, 1, 1, 0, 1, 1, 1, 1, 0]) *
1).sum(),
'Error in DrugEncoder.transform(); hadm_drug_matrix wrong')
self.assertEqual(
hadm_drug_matrix.shape, (len(pre.admissions), 10),
'Error in DrugEncoder.transform(); hadm_drug_matrix has wrong shape;'
)
self.assertEqual(len(hadm_id_mapping),
pre.admissions['HADM_ID'].unique().shape[0],
'Error in DrugEncoder.transform(); wrong shape;')
self.assertEqual(
drug_enc.drug_mapping, {
'FURO40I': 0,
'NS500': 1,
'NS1000': 2,
'NACLFLUSH': 3,
'INSULIN': 4,
'D5W250': 5,
'VANC1F': 6,
'VANCOBASE': 7,
'HEPA5I': 8,
'KCL20PM': 9
}, 'Error in DrugEncoder.transform(); drug_mapping is wrong')