Create 4c_ncrascr_map_tbl_simple.sql

Author: adelmestri

sql_scripts/4c_ncrascr_map_tbl_simple.sql

@@ -0,0 +1,93 @@
+--------------------------------
+-- PERSON
+--------------------------------
+INSERT INTO {TARGET_SCHEMA}.person (
+  person_id					,
+  gender_concept_id			,
+  year_of_birth				,
+  month_of_birth			,
+  day_of_birth				,
+  birth_datetime			,
+  race_concept_id			,
+  ethnicity_concept_id		,
+  location_id				,
+  provider_id				,
+  care_site_id				,
+  person_source_value		,
+  gender_source_value		,
+  gender_source_concept_id	,
+  race_source_value			,
+  race_source_concept_id	,
+  ethnicity_source_value	,
+  ethnicity_source_concept_id
+)
+WITH cte1 as (
+	SELECT DISTINCT e_patid, ethnicityname
+	FROM {SOURCE_SCHEMA}.tumour
+)
+SELECT 
+	t1.e_patid AS person_id,
+	0 AS gender_concept_id,
+	0 AS year_of_birth,
+	NULL::int AS month_of_birth,
+	NULL::int AS day_of_birth,
+	NULL::timestamp AS birth_datetime,
+	CASE WHEN t2.target_concept_id IS NOT NULL THEN t2.target_concept_id ELSE 0 END AS race_concept_id,
+	0 AS ethnicity_concept_id,
+	NULL::int AS location_id,
+	NULL::int AS provider_id,
+	NULL::int AS care_site_id,
+	t1.e_patid::varchar AS person_source_value,
+	NULL AS gender_source_value,
+	NULL::int AS gender_source_concept_id,
+	t2.source_code_description AS race_source_value,
+	NULL::int AS race_source_concept_id, 
+	NULL AS ethnicity_source_value,
+	0 AS ethnicity_source_concept_id
+FROM cte1 as t1
+LEFT JOIN {VOCABULARY_SCHEMA}.source_to_standard_vocab_map as t2 on t1.ethnicityname = t2.source_code 
+	and t2.source_vocabulary_id = 'NCRAS_ETHNIC_STCM';
+
+ALTER TABLE {TARGET_SCHEMA}.person ADD CONSTRAINT xpk_person PRIMARY KEY (person_id) USING INDEX TABLESPACE pg_default;
+
+CREATE UNIQUE INDEX idx_person_id ON {TARGET_SCHEMA}.person (person_id ASC) TABLESPACE pg_default;
+CLUSTER {TARGET_SCHEMA}.person USING xpk_person;
+
+--------------------------------
+-- OBSERVATION_PERIOD --
+--------------------------------
+DROP SEQUENCE IF EXISTS {TARGET_SCHEMA}.observation_period_seq;
+
+CREATE SEQUENCE {TARGET_SCHEMA}.observation_period_seq;
+
+with cte2 as ( 
+	select t1.e_patid as person_id, 
+	LEAST(MIN(t1.diagnosisdatebest), MIN(t2.eventdate)) as min_date, 
+	GREATEST(MAX(t1.diagnosisdatebest), MAX(t2.eventdate)) as max_date 
+	from {SOURCE_SCHEMA}.tumour as t1 
+	inner join {SOURCE_SCHEMA}.treatment as t2 on t2.e_patid = t1.e_patid 
+	inner join {TARGET_SCHEMA}.person as t3 on t3.person_id = t1.e_patid 
+	group by t1.e_patid 
+) 
+INSERT INTO {TARGET_SCHEMA}.OBSERVATION_PERIOD
+ (
+	observation_period_id,
+	person_id,
+	observation_period_start_date,
+	observation_period_end_date,
+	period_type_concept_id
+ )
+select
+	nextval('{TARGET_SCHEMA}.observation_period_seq'),
+	cte2.person_id,  
+	GREATEST(cte2.min_date, t3.start) as observation_period_start_date,  
+	LEAST(cte2.max_date,t3.end) as observation_period_end_date,
+	32880
+from cte2, {SOURCE_SCHEMA}.linkage_coverage as t3 
+where t3.data_source = 'ncras_cr'; 
+
+DROP SEQUENCE IF EXISTS {TARGET_SCHEMA}.observation_period_seq;
+
+ALTER TABLE {TARGET_SCHEMA}.observation_period ADD CONSTRAINT xpk_observation_period PRIMARY KEY (observation_period_id) USING INDEX TABLESPACE pg_default;
+CREATE INDEX idx_observation_period_id ON {TARGET_SCHEMA}.observation_period (person_id ASC) TABLESPACE pg_default;
+CLUSTER {TARGET_SCHEMA}.observation_period USING idx_observation_period_id;