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[DT-683-684] Use death table for is deceased attribute and group dempgraphic #652

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Jan 3, 2024
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[DT-683-684] Use death table for is deceased attribute and group dempgraphic #652

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a3a7db8
Updated with is_deceased attribute for person table from death table …
chenchals Jan 2, 2024
f49dd7f
cleaned up SQLs
chenchals Jan 2, 2024
725b19e
changed deceased to Demographics category
chenchals Jan 2, 2024
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127 changes: 47 additions & 80 deletions underlay/src/main/resources/config/datamapping/aouCT/entity/person/all.sql
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Expand Up @@ -33,84 +33,51 @@ SELECT p.person_id,
CASE
WHEN svd.sample_name IS NULL THEN 0 ELSE 1 END has_structural_variant_data,
CASE
WHEN ehr.person_id IS NULL THEN 0 ELSE 1 END has_ehr_data
WHEN ehr.person_id IS NULL THEN 0 ELSE 1 END has_ehr_data,
CASE
WHEN d.death_date is null THEN 0 ELSE 1 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
(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 sample_name
FROM `${omopDataset}.prep_wgs_metadata`) wgv ON (CAST(p.person_id AS STRING) = wgv.sample_name)
LEFT JOIN
(SELECT DISTINCT sample_name
FROM `${omopDataset}.prep_microarray_metadata`) mad ON (CAST(p.person_id AS STRING) = mad.sample_name)
LEFT JOIN
(SELECT DISTINCT sample_name
FROM `${omopDataset}.prep_longreads_metadata`) lrwgv ON (CAST(p.person_id AS STRING) = lrwgv.sample_name)
LEFT JOIN
(SELECT DISTINCT sample_name
FROM `${omopDataset}.prep_structural_variants_metadata`) svd ON (CAST(p.person_id AS STRING) = svd.sample_name)
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 `${omopDataset}.concept` gc ON gc.concept_id = p.gender_concept_id
LEFT JOIN `${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 (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 sample_name FROM `${omopDataset}.prep_wgs_metadata`) wgv ON (CAST(p.person_id AS STRING) = wgv.sample_name)
LEFT JOIN (SELECT DISTINCT sample_name FROM `${omopDataset}.prep_microarray_metadata`) mad ON (CAST(p.person_id AS STRING) = mad.sample_name)
LEFT JOIN (SELECT DISTINCT sample_name FROM `${omopDataset}.prep_longreads_metadata`) lrwgv ON (CAST(p.person_id AS STRING) = lrwgv.sample_name)
LEFT JOIN (SELECT DISTINCT sample_name FROM `${omopDataset}.prep_structural_variants_metadata`) svd ON (CAST(p.person_id AS STRING) = svd.sample_name)
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 person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
ON (p.person_id = d.person_id)
5 changes: 3 additions & 2 deletions underlay/src/main/resources/config/datamapping/aouCT/entity/person/entity.json
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Expand Up @@ -20,8 +20,9 @@
{ "name": "has_whole_genome_variant", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "has_lr_whole_genome_variant", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "has_structural_variant_data", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "has_ehr_data", "dataType": "INT64", "isComputeDisplayHint": true }
{ "name": "has_ehr_data", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "is_deceased", "dataType": "INT64", "isComputeDisplayHint": true }
],
"idAttribute": "id",
"optimizeGroupByAttributes": [ "gender", "race", "age" ]
"optimizeGroupByAttributes": [ "gender", "race", "age", "ethnicity" ]
}
111 changes: 43 additions & 68 deletions underlay/src/main/resources/config/datamapping/aouRT/entity/person/all.sql
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Expand Up @@ -25,72 +25,47 @@ SELECT p.person_id,
WHEN asum.person_id IS NULL AND hrml.person_id IS NULL AND hrs.person_id IS NULL
AND si.person_id IS NULL AND sds.person_id IS NULL AND sl.person_id IS NULL THEN 0 ELSE 1 END has_fitbit,
CASE
WHEN ehr.person_id IS NULL THEN 0 ELSE 1 END has_ehr_data
WHEN ehr.person_id IS NULL THEN 0 ELSE 1 END has_ehr_data,
CASE
WHEN d.death_date is null THEN 0 ELSE 1 END is_deceased
FROM `${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
(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`${omopDataset}.measurement` as a
LEFT JOIN`${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 `${omopDataset}.concept` gc ON gc.concept_id = p.gender_concept_id
LEFT JOIN `${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 (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`${omopDataset}.measurement` as a
LEFT JOIN`${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 person_id, max(death_date) as death_date FROM `${omopDataset}.death` GROUP BY person_id) d
ON (p.person_id = d.person_id)
5 changes: 3 additions & 2 deletions underlay/src/main/resources/config/datamapping/aouRT/entity/person/entity.json
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,9 @@
{ "name": "has_fitbit_sleep_daily_summary", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "has_fitbit_sleep_level", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "has_fitbit", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "has_ehr_data", "dataType": "INT64", "isComputeDisplayHint": true }
{ "name": "has_ehr_data", "dataType": "INT64", "isComputeDisplayHint": true },
{ "name": "is_deceased", "dataType": "INT64", "isComputeDisplayHint": true }
],
"idAttribute": "id",
"optimizeGroupByAttributes": [ "gender", "race", "age" ]
"optimizeGroupByAttributes": [ "gender", "race", "age", "ethnicity" ]
}
44 changes: 26 additions & 18 deletions underlay/src/main/resources/config/underlay/aouSC2023Q3R1/ui.json
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Expand Up @@ -601,6 +601,13 @@
"start_date_group_by_count"
]
},
{
"type": "attribute",
"id": "tanagra-has-ehr-data",
"title": "Has EHR Data",
"category": "Domains",
"attribute": "has_ehr_data"
},
{
"type": "classification",
"id": "tanagra-cpt4",
Expand Down Expand Up @@ -785,45 +792,46 @@
},
{
"type": "attribute",
"id": "tanagra-has-ehr-data",
"title": "Has EHR Data",
"category": "Program data",
"attribute": "has_ehr_data"
"id": "tanagra-age",
"title": "Age",
"category": "Demographics",
"attribute": "age"
},
{
"type": "attribute",
"id": "tanagra-is-deceased",
"title": "Deceased",
"category": "Demographics",
"attribute": "is_deceased"
},
{

"type": "attribute",
"id": "tanagra-ethnicity",
"title": "Ethnicity",
"category": "Program data",
"category": "Demographics",
"attribute": "ethnicity"
},
{
"type": "attribute",
"id": "tanagra-gender",
"title": "Gender identity",
"category": "Program data",
"category": "Demographics",
"attribute": "gender"
},
{
"type": "attribute",
"id": "tanagra-sex-at-birth",
"title": "Sex At Birth",
"category": "Program data",
"attribute": "sex_at_birth"
},
{
"type": "attribute",
"id": "tanagra-race",
"title": "Race",
"category": "Program data",
"category": "Demographics",
"attribute": "race"
},
{
"type": "attribute",
"id": "tanagra-age",
"title": "Age",
"category": "Program data",
"attribute": "age"
"id": "tanagra-sex-at-birth",
"title": "Sex At Birth",
"category": "Demographics",
"attribute": "sex_at_birth"
},
{
"type": "attribute",
Expand Down
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