Accommodate OMOP 5.4

Renamed file (5.3) and created new one (5.4) to accommodate OMOP version

Author: adelmestri

sql_scripts/4d_aurum_map_tbl_tmp.sql sql_scripts/4d3_aurum_map_tbl_tmp.sql

@@ -0,0 +1,107 @@
+--------------------------------
+-- TEMP_DRUG_CONCEPT_MAP
+--------------------------------
+drop table if exists {SOURCE_SCHEMA}.temp_drug_concept_map CASCADE;
+
+create table if not exists {SOURCE_SCHEMA}.temp_drug_concept_map as
+select d.prodcodeid,
+	d.termfromemis,
+	d.dmdid,
+	st1.target_concept_id as dmd_source_concept_id
+from {SOURCE_SCHEMA}.productdictionary d
+left join {TARGET_SCHEMA}.source_to_source_vocab_map st1 on d.dmdid::varchar = st1.source_code and st1.source_vocabulary_id = 'dm+d';
+
+alter table {SOURCE_SCHEMA}.temp_drug_concept_map add constraint pk_temp_drug_concept_map primary key (prodcodeid);
+
+--------------------------------
+-- TEMP_CONCEPT_MAP
+--------------------------------
+drop table if exists {SOURCE_SCHEMA}.temp_concept_map CASCADE;
+
+create table if not exists {SOURCE_SCHEMA}.temp_concept_map as
+with cte1 as (
+	SELECT source_code, target_concept_id as Read_source_concept_id
+		FROM {TARGET_SCHEMA}.source_to_source_vocab_map
+		WHERE source_vocabulary_id = 'Read'
+	),
+	cte2 as (
+	SELECT source_code, target_concept_id as SNOMED_source_concept_id
+		FROM {TARGET_SCHEMA}.source_to_source_vocab_map
+		WHERE source_vocabulary_id = 'SNOMED'
+	)
+SELECT m.medcodeid,
+	m.term,
+	m.cleansedreadcode,
+	m.snomedctconceptid,
+	cte1.Read_source_concept_id,
+	cte2.SNOMED_source_concept_id
+from {SOURCE_SCHEMA}.medicaldictionary m
+left join cte1 on m.cleansedreadcode = cte1.source_code
+left join cte2 on m.snomedctconceptid = cte2.source_code;
+
+alter table {SOURCE_SCHEMA}.temp_concept_map add constraint pk_temp_concept_map primary key (medcodeid);
+
+--------------------------------
+-- TEMP_VISIT_DETAIL
+--------------------------------
+drop table if exists {SOURCE_SCHEMA}.temp_visit_detail CASCADE;
+
+CREATE TABLE {SOURCE_SCHEMA}.temp_visit_detail 
+(
+	visit_detail_id bigint NOT NULL,
+	visit_detail_source_id bigint NOT NULL,
+	person_id bigint NOT NULL,
+	visit_detail_start_date date NOT NULL,
+	visit_detail_end_date date NOT NULL,
+	provider_id bigint NULL,
+	care_site_id bigint NULL,
+	parent_visit_detail_id bigint NULL,
+	source_table varchar(20) NULL
+);
+
+WITH cte3 as (
+	select o.obsid as visit_detail_source_id,
+		o.patid as person_id,
+		case
+			when c.consdate is NULL then o.obsdate
+			else c.consdate
+			end as visit_detail_start_date,
+		case
+			when c.consdate is NULL then o.obsdate
+			else c.consdate
+			end as visit_detail_end_date,
+		c.staffid as provider_id,
+		o.pracid as care_site_id,
+		o.parentobsid as parent_visit_detail_id,
+		'Observation' as source_table
+	from {SOURCE_SCHEMA}.observation o
+	left join {SOURCE_SCHEMA}.consultation c on o.consid = c.consid
+--	where c.consdate is not null or o.obsdate is not null -- not necessary as obsdate is always not NULL, filtered in check_source_data.sql
+),
+cte4 as (
+	select c.consid	as visit_detail_source_id,
+		c.patid		as person_id,
+		c.consdate	as visit_detail_start_date,
+		c.consdate	as visit_detail_end_date,
+		c.staffid	as provider_id,
+		c.pracid	as care_site_id,
+		NULL::bigint	as parent_visit_detail_id,
+		'Consultation' as source_table
+	from {SOURCE_SCHEMA}.consultation c
+	where c.consdate is not null
+),
+cte5 as (
+	select * 
+	from cte3
+	UNION
+	select * 
+	from cte4
+)
+INSERT INTO {SOURCE_SCHEMA}.temp_visit_detail
+SELECT row_number() over (order by visit_detail_source_id) as visit_detail_id, *
+FROM cte5;
+
+
+alter table {SOURCE_SCHEMA}.temp_visit_detail add constraint pk_temp_visit_d primary key (visit_detail_id); --added 31/10/2022
+create index idx_temp_visit_det1 on {SOURCE_SCHEMA}.temp_visit_detail (visit_detail_source_id, source_table); --modified 27/10/2022
+create index idx_temp_visit_det2 on {SOURCE_SCHEMA}.temp_visit_detail (person_id, visit_detail_start_date, care_site_id);