Update transform for birth measurements

#532
PEDSnet · Sep 7, 2021 · 31b7b27 · 31b7b27
1 parent 1b79131
commit 31b7b27
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Showing 3 changed files with 25 additions and 13 deletions.
diff --git a/v4.3_to_v6.0/sql_etl/data/concept_map.csv b/v4.3_to_v6.0/sql_etl/data/concept_map.csv
@@ -6786,3 +6786,5 @@ result_qual_source,TRACE,Trace,,Trace,
 result_qual_source,TRACE,Trace,,TRACE,
 result_qual_source,URINE,Urine,,Urine,
 result_qual_source,URINE,Urine,,URINE, 
+Birth Measures,'8339-4','Birth weight Measured',3013762,'Birth weight Measured',
+Birth Measures,'89269-5','Birth height Measured',3023540,'Birth height Measured',  
diff --git a/v4.3_to_v6.0/sql_etl/scripts/etl_scripts/l_vitals.sql b/v4.3_to_v6.0/sql_etl/scripts/etl_scripts/l_vitals.sql
@@ -11,7 +11,7 @@ create table SITE_pcornet.ms_ht as
 (
     select  distinct person_id, 'SITE' as site, measurement_id,visit_occurrence_id, measurement_date, measurement_datetime, value_as_number
 	,  measurement_concept_id,measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value, value_as_concept_id,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pedsnet.measurement
 	where measurement_concept_id = '3023540'
 );
@@ -33,7 +33,7 @@ create table SITE_pcornet.ms_wt as
 (
    select person_id, 'SITE' as site, measurement_id,visit_occurrence_id, measurement_date, measurement_datetime, value_as_number
 	,  measurement_concept_id,measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value, value_as_concept_id,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pedsnet.measurement
 	where measurement_concept_id = '3013762'
 );
@@ -55,7 +55,7 @@ create table SITE_pcornet.ms_bmi as
 (
     select distinct person_id, 'SITE' as site, measurement_id,visit_occurrence_id, provider_id, value_as_concept_id,
 	measurement_date, measurement_datetime, value_as_number,  measurement_concept_id,measurement_source_value,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
     from SITE_pedsnet.measurement
     where measurement_concept_id = '3038553'
 );
@@ -76,7 +76,7 @@ create table SITE_pcornet.ms_sys as
 (
    select distinct person_id, 'SITE' as site, measurement_id, visit_occurrence_id, provider_id, value_as_concept_id,
 		measurement_date, measurement_datetime, value_as_number,  measurement_concept_id,measurement_source_value,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
    from SITE_pedsnet.measurement
    where measurement_concept_id in ('3018586','3035856','3009395','3004249')
 );
@@ -98,7 +98,7 @@ create table SITE_pcornet.ms_dia as
     select distinct person_id, 'SITE' as site, measurement_id, provider_id, value_as_concept_id,
 		visit_occurrence_id, measurement_date, measurement_datetime, value_as_number, 
 			 measurement_concept_id,measurement_source_value,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pedsnet.measurement
 	where measurement_concept_id in ('3034703','3019962','3013940','3012888')
 );
@@ -118,23 +118,23 @@ commit;
 begin;
 create table SITE_pcornet.ms as
 	select person_id, site, measurement_id, visit_occurrence_id, value_as_concept_id, measurement_date, measurement_datetime, value_as_number, measurement_concept_id, measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pcornet.ms_ht
 	UNION
 	select person_id, site, measurement_id, visit_occurrence_id, value_as_concept_id, measurement_date, measurement_datetime, value_as_number, measurement_concept_id, measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pcornet.ms_wt
 	UNION
 	select person_id, site, measurement_id, visit_occurrence_id, value_as_concept_id, measurement_date, measurement_datetime, value_as_number, measurement_concept_id, measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pcornet.ms_bmi
 	UNION
 	select person_id, site, measurement_id, visit_occurrence_id, value_as_concept_id, measurement_date, measurement_datetime, value_as_number, measurement_concept_id, measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pcornet.ms_sys
 	UNION
 	select person_id, site, measurement_id, visit_occurrence_id, value_as_concept_id, measurement_date, measurement_datetime, value_as_number, measurement_concept_id, measurement_source_value, provider_id,operator_concept_id, unit_concept_id, unit_source_value,
-	value_source_value
+	value_source_value,measurement_type_concept_id
 	from SITE_pcornet.ms_dia;
 commit;
 
@@ -240,7 +240,8 @@ and ms.measurement_datetime = ms_ht.measurement_datetime
 left join SITE_pcornet.ms_wt on ms.visit_occurrence_id = ms_wt.visit_occurrence_id
 and ms.measurement_datetime = ms_wt.measurement_datetime 
 left join SITE_pcornet.ms_bmi on ms.visit_occurrence_id = ms_bmi.visit_occurrence_id
-and ms.measurement_datetime = ms_bmi.measurement_datetime;
+and ms.measurement_datetime = ms_bmi.measurement_datetime
+;
 commit;
 
 begin;

diff --git a/v4.3_to_v6.0/sql_etl/scripts/etl_scripts/n_obs_clin.sql b/v4.3_to_v6.0/sql_etl/scripts/etl_scripts/n_obs_clin.sql
@@ -20,7 +20,11 @@ INSERT INTO SITE_pcornet.obs_clin(encounterid, obsclin_code, obsclin_abn_ind, ob
 	obsclin_result_unit, obsclin_source, obsclin_start_time, obsclin_type, obsclinid, patid, raw_obsclin_code, raw_obsclin_modifier, raw_obsclin_name, raw_obsclin_result, raw_obsclin_type, 
 	raw_obsclin_unit, obsclin_stop_date, obsclin_stop_time,site)
 select distinct on (obsclinid) ms.visit_occurrence_id::int as encounterid, 
-coalesce(code.concept_code, null) as obsclin_code, 
+case
+	when measurement_type_concept_id = 44818704 
+	then birth_meas.target_concept 
+	else coalesce(code.concept_code, null) 
+end as obsclin_code, 
 coalesce(abn.target_concept, 'NI') as obsclin_abn_ind,
 ms.measurement_date as obsclin_start_date, 
 ms.provider_id as obsclin_providerid, 
@@ -36,7 +40,11 @@ LPAD(date_part('hour',ms.measurement_datetime)::text,2,'0')||':'||LPAD(date_part
 person_id::text as patid, 
 coalesce(code.concept_code,'NI')  as raw_obsclin_code, 
 null as raw_obsclin_modifier, 
-code.concept_name as raw_obsclin_name, 
+case 
+	when measurement_type_concept_id = 44818704 
+	then birth_meas.concept_description 
+	else code.concept_name 
+end as raw_obsclin_name, 
 ms.value_as_number::text as raw_obsclin_result, 
 code.vocabulary_id as raw_obsclin_type, 
 ms.unit_source_value as raw_obsclin_unit, 
@@ -45,6 +53,7 @@ null as obsclin_stop_time,
 ms.site as site
 from SITE_pcornet.ms
 left join vocabulary.concept code on code.concept_id = ms.measurement_concept_id and code.vocabulary_id = 'LOINC'
+left join pcornet_maps.pedsnet_pcornet_valueset_map birth_meas on birth_meas.source_concept_id=ms.measurement_concept_id and birth_meas.source_concept_class = 'Birth Measures'
 left join pcornet_maps.pedsnet_pcornet_valueset_map modif on modif.source_concept_id = ms.operator_concept_id::text and modif.source_concept_class = 'Result modifier'
 left join pcornet_maps.pedsnet_pcornet_valueset_map unit on unit.source_concept_id = ms.unit_concept_id::text and unit.source_concept_class in ('Dose unit','Result unit')
 Left join pcornet_maps.pedsnet_pcornet_valueset_map abn on abn.source_concept_id::int = ms.value_as_concept_id and abn.source_concept_class = 'abnormal_indicator'