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DT-940 adding config for person
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@freemabd
freemabd committed Dec 19, 2024
1 parent 52fb269 commit 14de5dc
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Showing 3 changed files with 71 additions and 60 deletions.
28 changes: 19 additions & 9 deletions underlay/src/main/resources/config/datamapping/aouCT/entity/person/all.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -20,14 +20,14 @@ SELECT p.person_id,
WHEN rc.concept_name = 'PMI: Skip' THEN 'Skip'
ELSE rc.concept_name
END AS race_concept_name,
p.ethnicity_concept_id,
CASE
WHEN ec.concept_name = 'No matching concept' THEN 'Unknown'
WHEN ec.concept_name = 'PMI: Skip' THEN 'Skip'
WHEN ec.concept_name = 'PMI: Prefer Not To Answer' THEN 'Prefer Not To Answer'
WHEN ec.concept_name = 'What Race Ethnicity: Race Ethnicity None Of These' THEN 'None Of These'
ELSE ec.concept_name
END AS ethnicity_concept_name,
p.ethnicity_concept_id,
CASE
WHEN ec.concept_name = 'No matching concept' THEN 'Unknown'
WHEN ec.concept_name = 'PMI: Skip' THEN 'Skip'
WHEN ec.concept_name = 'PMI: Prefer Not To Answer' THEN 'Prefer Not To Answer'
WHEN ec.concept_name = 'What Race Ethnicity: Race Ethnicity None Of These' THEN 'None Of These'
ELSE ec.concept_name
END AS ethnicity_concept_name,
p.sex_at_birth_concept_id,
CASE
WHEN sc.concept_name = 'No matching concept' THEN 'Unknown'
Expand Down Expand Up @@ -69,6 +69,8 @@ SELECT p.person_id,
WHEN ws.person_id IS NULL THEN FALSE ELSE TRUE END has_wear_consent,
CASE
WHEN ehr.person_id IS NULL THEN FALSE ELSE TRUE END has_ehr_data,
CASE
WHEN pm.person_id IS NULL THEN FALSE ELSE TRUE END has_pm_data,
CASE
WHEN d.death_date is null THEN FALSE ELSE TRUE END is_deceased
FROM `${omopDataset}.person` p
Expand Down Expand Up @@ -116,5 +118,13 @@ LEFT JOIN (SELECT DISTINCT person_id FROM`${omopDataset}.measurement` as a
LEFT JOIN`${omopDataset}.visit_occurrence_ext` as b on a.visit_occurrence_id = b.visit_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
) ehr ON (p.person_id = ehr.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
WHERE measurement_source_concept_id in (
SELECT concept_id FROM `${omopDataset}.concept`
WHERE vocabulary_id = 'PPI'
AND concept_class_id = 'Clinical Observation'
AND domain_id = 'Measurement'
)
) pm ON (p.person_id = pm.person_id)
LEFT JOIN (SELECT person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
ON (p.person_id = d.person_id)
ON (p.person_id = d.person_id)
3 changes: 2 additions & 1 deletion underlay/src/main/resources/config/datamapping/aouCT/entity/person/entity.json
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@
{ "name": "age", "dataType": "TIMESTAMP", "valueFieldName": "birth_datetime_not_deceased",
"runtimeSqlFunctionWrapper": "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)",
"runtimeDataType": "INT64", "isComputeDisplayHint": true, "isSuppressedForExport": true,
"displayHintRangeMin": 18, "displayHintRangeMax": 125 },
"displayHintRangeMin": 18, "displayHintRangeMax": 120 },
{ "name": "has_fitbit_activity_summary", "dataType": "BOOLEAN", "isSuppressedForExport": true },
{ "name": "has_fitbit_heart_rate_level", "dataType": "BOOLEAN", "isSuppressedForExport": true },
{ "name": "has_fitbit_heart_rate_summary", "dataType": "BOOLEAN", "isSuppressedForExport": true },
Expand All @@ -63,6 +63,7 @@
{ "name": "has_structural_variant_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
{ "name": "has_wear_consent", "dataType": "BOOLEAN", "isSuppressedForExport": true },
{ "name": "has_ehr_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
{ "name": "has_pm_data", "dataType": "BOOLEAN", "isSuppressedForExport": true },
{ "name": "is_deceased", "dataType": "BOOLEAN", "isSuppressedForExport": true }
],
"idAttribute": "id",
Expand Down
100 changes: 50 additions & 50 deletions underlay/src/main/resources/config/datamapping/aouRT/entity/person/all.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ SELECT p.person_id,
WHEN sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit_sleep_level,
CASE
WHEN asum.person_id IS NULL AND hrml.person_id IS NULL AND hrs.person_id IS NULL
AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit,
AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL THEN FALSE ELSE TRUE END has_fitbit,
CASE
WHEN ws.person_id IS NULL THEN FALSE ELSE TRUE END has_wear_consent,
CASE
Expand All @@ -62,53 +62,53 @@ SELECT p.person_id,
CASE
WHEN d.death_date is null THEN FALSE ELSE TRUE END is_deceased
FROM `${omopDataset}.person` p
LEFT JOIN `${omopDataset}.concept` gc ON gc.concept_id = p.gender_concept_id
LEFT JOIN `${omopDataset}.concept` rc ON rc.concept_id = p.race_concept_id
LEFT JOIN `${omopDataset}.concept` ec ON ec.concept_id = p.ethnicity_concept_id
LEFT JOIN `${omopDataset}.concept` sc ON sc.concept_id = p.sex_at_birth_concept_id
LEFT JOIN `${omopDataset}.concept` sr ON sr.concept_id = p.self_reported_category_concept_id
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.activity_summary`) asum ON (p.person_id = asum.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.heart_rate_minute_level`) hrml ON (p.person_id = hrml.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.heart_rate_summary`) hrs ON (p.person_id = hrs.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.steps_intraday`) si ON (p.person_id = si.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_daily_summary`) sds ON (p.person_id = sds.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_level`) sl ON (p.person_id = sl.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.wear_study`) ws ON (p.person_id = ws.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM`${omopDataset}.measurement` as a
LEFT JOIN`${omopDataset}.measurement_ext` as b on a.measurement_id = b.measurement_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.condition_occurrence` as a
LEFT JOIN`${omopDataset}.condition_occurrence_ext` as b on a.condition_occurrence_id = b.condition_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.device_exposure` as a
LEFT JOIN`${omopDataset}.device_exposure_ext` as b on a.device_exposure_id = b.device_exposure_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.drug_exposure` as a
LEFT JOIN`${omopDataset}.drug_exposure_ext` as b on a.drug_exposure_id = b.drug_exposure_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.observation` as a
LEFT JOIN`${omopDataset}.observation_ext` as b on a.observation_id = b.observation_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.procedure_occurrence` as a
LEFT JOIN`${omopDataset}.procedure_occurrence_ext` as b on a.procedure_occurrence_id = b.procedure_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.visit_occurrence` as a
LEFT JOIN`${omopDataset}.visit_occurrence_ext` as b on a.visit_occurrence_id = b.visit_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
) ehr ON (p.person_id = ehr.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
WHERE measurement_source_concept_id in (
SELECT concept_id FROM `${omopDataset}.concept`
WHERE vocabulary_id = 'PPI'
AND concept_class_id = 'Clinical Observation'
AND domain_id = 'Measurement'
)
LEFT JOIN `${omopDataset}.concept` gc ON gc.concept_id = p.gender_concept_id
LEFT JOIN `${omopDataset}.concept` rc ON rc.concept_id = p.race_concept_id
LEFT JOIN `${omopDataset}.concept` ec ON ec.concept_id = p.ethnicity_concept_id
LEFT JOIN `${omopDataset}.concept` sc ON sc.concept_id = p.sex_at_birth_concept_id
LEFT JOIN `${omopDataset}.concept` sr ON sr.concept_id = p.self_reported_category_concept_id
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.activity_summary`) asum ON (p.person_id = asum.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.heart_rate_minute_level`) hrml ON (p.person_id = hrml.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.heart_rate_summary`) hrs ON (p.person_id = hrs.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.steps_intraday`) si ON (p.person_id = si.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_daily_summary`) sds ON (p.person_id = sds.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.sleep_level`) sl ON (p.person_id = sl.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.wear_study`) ws ON (p.person_id = ws.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM`${omopDataset}.measurement` as a
LEFT JOIN`${omopDataset}.measurement_ext` as b on a.measurement_id = b.measurement_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.condition_occurrence` as a
LEFT JOIN`${omopDataset}.condition_occurrence_ext` as b on a.condition_occurrence_id = b.condition_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.device_exposure` as a
LEFT JOIN`${omopDataset}.device_exposure_ext` as b on a.device_exposure_id = b.device_exposure_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.drug_exposure` as a
LEFT JOIN`${omopDataset}.drug_exposure_ext` as b on a.drug_exposure_id = b.drug_exposure_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.observation` as a
LEFT JOIN`${omopDataset}.observation_ext` as b on a.observation_id = b.observation_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.procedure_occurrence` as a
LEFT JOIN`${omopDataset}.procedure_occurrence_ext` as b on a.procedure_occurrence_id = b.procedure_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
UNION DISTINCT
SELECT DISTINCT person_id FROM`${omopDataset}.visit_occurrence` as a
LEFT JOIN`${omopDataset}.visit_occurrence_ext` as b on a.visit_occurrence_id = b.visit_occurrence_id
WHERE lower(b.src_id) like 'ehr site%'
) ehr ON (p.person_id = ehr.person_id)
LEFT JOIN (SELECT DISTINCT person_id FROM `${omopDataset}.measurement`
WHERE measurement_source_concept_id in (
SELECT concept_id FROM `${omopDataset}.concept`
WHERE vocabulary_id = 'PPI'
AND concept_class_id = 'Clinical Observation'
AND domain_id = 'Measurement'
)
) pm ON (p.person_id = pm.person_id)
LEFT JOIN (SELECT person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
ON (p.person_id = d.person_id)
LEFT JOIN (SELECT person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
ON (p.person_id = d.person_id)

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