def test_observation_period(self):
cohort_definition = {
'demographic_criteria': {
'min_year_of_birth': None,
'max_year_of_birth': None,
'gender_concept_id': None
},
'criteria_list': [{
'concept_type': 'condition_occurrence',
'concept_id': [44831230],
'is_excluded': 0,
'get_descendants': 0,
'occurrence_start_date': None,
'occurrence_end_date': None,
'min_occurrence': None,
'min_duration': None,
'is_before_previous_criteria': None,
'is_after_previous_criteria': None
}],
'observation_period_criteria': {
'before_index': 365,
'after_index': None
}
}
output = CohortBuilder(cohort_definition, omop_tables)()
output = output.reset_index(drop=True)
expected = pd.DataFrame({
'person_id': [1],
'index_date': [pd.to_datetime('2017-12-10')]
})
pd.testing.assert_frame_equal(output, expected)
def test_attributes_min_length(self):
drug_exposure = pd.DataFrame({
'person_id': [1, 1, 1, 1, 2, 2],
'drug_concept_id': [10, 10, 30, 40, 10, 20],
'drug_exposure_start_datetime': [
pd.to_datetime('2018-12-10'),
pd.to_datetime('2017-12-10'),
pd.to_datetime('2017-12-10'),
pd.to_datetime('2017-12-10'),
pd.to_datetime('2017-12-10'),
pd.to_datetime('2017-12-10'),
]
})
drug_exposure = dd.from_pandas(drug_exposure,
npartitions=1).set_index('person_id')
cohort_definition = {
'demographic_criteria': {
'min_year_of_birth': None,
'max_year_of_birth': None,
'gender_concept_id': None
},
'criteria_list': [{
'concept_type': 'drug_exposure',
'concept_id': [10],
'is_excluded': 0,
'get_descendants': 0,
'occurrence_start_date': None,
'occurrence_end_date': None,
'min_occurrence': None,
'min_duration': 100,
'is_before_previous_criteria': None,
'is_after_previous_criteria': None
}],
'observation_period_criteria': {
'before_index': None,
'after_index': None
}
}
omop_tables = {
'person': person,
'condition_occurrence': condition_occurrence,
'procedure_occurrence': procedure,
'drug_exposure': drug_exposure,
'visit_occurrence': visit_occurrence,
'observation_period': observation_period,
'measurement': measurement
}
output = CohortBuilder(cohort_definition, omop_tables)()
expected = pd.DataFrame({
'person_id': [1],
'index_date': [pd.to_datetime('2017-12-10')]
})
pd.testing.assert_frame_equal(output, expected)
def test_year_of_birth(self):
cohort_definition = {
'demographic_criteria': {
'min_year_of_birth': 1970,
'max_year_of_birth': 2000,
'gender_concept_id': None
},
'criteria_list': []
}
output = CohortBuilder(cohort_definition, omop_tables)()
output = output.reset_index(drop=True)
expected = pd.DataFrame({
'person_id': [1, 2, 4],
'index_date': [
pd.to_datetime('1970-01-01'),
pd.to_datetime('1970-01-01'),
pd.to_datetime('1970-01-01')
]
})
pd.testing.assert_frame_equal(output, expected)
def test_condition(self):
cohort_definition = {
'criteria_list': [{
'concept_type': 'condition_occurrence',
'concept_id': [3]
}],
'observation_period_criteria': {
'before_index': None,
'after_index': None
}
}
output = CohortBuilder(cohort_definition, omop_tables)()
expected = pd.DataFrame({
'person_id': [1],
'index_date': [pd.to_datetime('2017-12-10')]
})
pd.testing.assert_frame_equal(output, expected)