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[DC-3779] Add aou_death to EhrSubmissionDataCutoff #1859

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Apr 22, 2024
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[DC-3779] Add aou_death to EhrSubmissionDataCutoff #1859

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4 changes: 2 additions & 2 deletions data_steward/cdr_cleaner/cleaning_rules/ehr_submission_data_cutoff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

# Project imports
from cdr_cleaner.cleaning_rules.base_cleaning_rule import BaseCleaningRule
from common import JINJA_ENV, AOU_REQUIRED
from common import JINJA_ENV, AOU_REQUIRED, AOU_DEATH
from constants import bq_utils as bq_consts
from utils import pipeline_logging
from resources import fields_for, validate_date_string
Expand Down Expand Up @@ -86,7 +86,7 @@ def get_affected_tables(self):
:return: list of affected tables
"""
tables = []
for table in AOU_REQUIRED:
for table in AOU_REQUIRED + [AOU_DEATH]:

# skips the person table
if table == 'person':
Expand Down
33 changes: 30 additions & 3 deletions ...egration_tests/data_steward/cdr_cleaner/cleaning_rules/ehr_submission_data_cutoff_test.py
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Expand Up @@ -46,13 +46,15 @@ def setUpClass(cls):
cls.rule_instance = EhrSubmissionDataCutoff(project_id, dataset_id,
sandbox_id)

for table_name in common.VISIT_OCCURRENCE:
for table_name in [common.VISIT_OCCURRENCE, common.AOU_DEATH]:
sandbox_table_name = cls.rule_instance.sandbox_table_for(table_name)
cls.fq_sandbox_table_names.append(
f'{cls.project_id}.{cls.sandbox_id}.{sandbox_table_name}')

cls.fq_table_names.append(
f'{cls.project_id}.{cls.dataset_id}.{common.VISIT_OCCURRENCE}')
cls.fq_table_names.append(
f'{cls.project_id}.{cls.dataset_id}.{common.AOU_DEATH}')

# call super to set up the client, create datasets, and create
# empty test tables
Expand Down Expand Up @@ -82,8 +84,10 @@ def test_ehr_submission_data_cutoff(self, mock_get_affected_tables):
statements and the tables_and_counts variable.
"""
# mocks the return value of get_affected_tables as we only want to loop through the
# visit_occurrence not all of the CDM tables
mock_get_affected_tables.return_value = [common.VISIT_OCCURRENCE]
# visit_occurrence and aou_death, not all of the CDM tables
mock_get_affected_tables.return_value = [
common.VISIT_OCCURRENCE, common.AOU_DEATH
]

queries = []
visit_occurrence_tmpl = self.jinja_env.from_string("""
Expand All @@ -105,6 +109,19 @@ def test_ehr_submission_data_cutoff(self, mock_get_affected_tables):
cdm_table=common.VISIT_OCCURRENCE)
queries.append(visit_occurrence_tmpl)

aou_death_tmpl = self.jinja_env.from_string("""
INSERT INTO `{{project}}.{{dataset}}.aou_death`
(aou_death_id, person_id, death_date, death_datetime, death_type_concept_id,
src_id, primary_death_record)
VALUES
('a1', 1, '2020-01-01', NULL, 0, 'hpo_a', False),
('h1', 1, '2010-01-01', '2010-01-01 00:00:00', 0, 'healthpro', True),
('a2', 2, '2020-01-01', '2020-01-01 00:00:00', 0, 'hpo_a', False),
('b2', 2, '2024-01-01', '2024-01-01 00:00:00', 0, 'hpo_b', True),
('h3', 3, NULL, NULL, 0, 'Staff Portal: HealthPro', False)
""").render(project=self.project_id, dataset=self.dataset_id)
queries.append(aou_death_tmpl)

self.load_test_data(queries)

table_and_counts = [{
Expand All @@ -130,6 +147,16 @@ def test_ehr_submission_data_cutoff(self, mock_get_affected_tables):
parse('2020-03-06 11:00:00 UTC'), parse('2020-03-07').date(),
parse('2020-03-07 11:00:00 UTC'), 4)
]
}, {
'fq_table_name':
'.'.join([self.fq_dataset_name, 'aou_death']),
'fq_sandbox_table_name':
f'{self.fq_sandbox_name}.{self.rule_instance.sandbox_table_for(common.AOU_DEATH)}',
'loaded_ids': ['a1', 'h1', 'a2', 'b2', 'h3'],
'sandboxed_ids': ['b2'],
'fields': ['aou_death_id', 'person_id', 'primary_death_record'],
'cleaned_values': [('a1', 1, False), ('h1', 1, True),
('a2', 2, False), ('h3', 3, False)]
}]

self.default_test(table_and_counts)