Merge pull request #111 from OHDSI/health-verity-upd

Health verity upd
OHDSI · Aug 29, 2024 · 7306191 · 7306191
2 parents 23111cc + 6d58bdb
commit 7306191
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Showing 17 changed files with 151 additions and 68 deletions.
diff --git a/sources/Framework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Batch.sql b/sources/Framework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Batch.sql
@@ -1,10 +1,10 @@
 SELECT DISTINCT {0} row_number() over (order by hvid) person_id, hvid
 from 
 (
-SELECT DISTINCT hvid FROM cdm_health_verity_cc_ehr_cce_v2776.enrollment 
+SELECT DISTINCT hvid FROM {sc}.enrollment 
 where lower(benefit_type) = 'medical'
 union
-SELECT DISTINCT hvid FROM cdm_health_verity_cc_ehr_cce_v2776.enrollment 
+SELECT DISTINCT hvid FROM {sc}.enrollment 
 where lower(benefit_type) = 'pharmacy' or benefit_type is null
 ) a 
 where hvid != '' and hvid is not null

diff --git a/...mework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/L_PROVIDER.xml b/...mework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/L_PROVIDER.xml
@@ -1,9 +1,9 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		select distinct enc_prov_taxnmy_id as specialty_source_value,
 		enc_prov_id provider_source_value,
 		coalesce(enc_prov_id, '') || ';' || coalesce(enc_prov_taxnmy_id, '') ProviderIdKey
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_enc
+		from {sc}.emr_enc
 	</Query>
 	<Providers>
 		<ProviderDefinition>

diff --git a/...ramework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/cdm_diag.xml b/...ramework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/cdm_diag.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-  <Query>
+  <Query database="none">
     SELECT
     ch.person_id as PersonId,
     hvid,
@@ -17,7 +17,7 @@
     when enc_start_dt &lt; '10/1/2015' then '9'
     when enc_start_dt &gt;= '10/1/2015' then '10'
 		end as icd_ver
-		FROM cdm_health_verity_cc_ehr_cce_v2776.cdm_diag
+		FROM {sc}.cdm_diag
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where enc_start_dt is not null
 		order by ch.person_id

diff --git a/...ework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/cdm_enc_dtl.xml b/...ework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/cdm_enc_dtl.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT distinct
 		ch.person_id as PersonId,
 		d.hvid,
@@ -15,9 +15,9 @@
 		when enc_grp_txt LIKE '%ENCOUNTER_VISIT_TYPE: Inpatient%' and los_day_cnt > 1 then 9201
 		else 9202
 		end defaultConceptId
-		FROM cdm_health_verity_cc_ehr_cce_v2776.cdm_enc_dtl d
+		FROM {sc}.cdm_enc_dtl d
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND d.hvid = ch.PERSON_SOURCE_VALUE
-		JOIN cdm_health_verity_cc_ehr_cce_v2776.cdm_enc e ON d.hvid = e.hvid and d.hv_enc_id = e.hv_enc_id
+		JOIN {sc}.cdm_enc e ON d.hvid = e.hvid and d.hv_enc_id = e.hv_enc_id
 		where d.proc_dt is not null
 		order by ch.person_id
 	</Query>

diff --git a/...ork/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_clin_obsn.xml b/...ork/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_clin_obsn.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT
 		ch.person_id as PersonId,
 		hvid,
@@ -11,7 +11,7 @@
 		clin_obsn_uom,
 		32827 type_concept_id,
 		coalesce(clin_obsn_prov_id, '') || ';' || coalesce(clin_obsn_prov_taxnmy_id, '') ProviderIdKey
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_clin_obsn
+		from {sc}.emr_clin_obsn
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		order by ch.person_id
 	</Query>

diff --git a/...ramework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_diag.xml b/...ramework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_diag.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT
 		ch.person_id as PersonId,
 		hvid,
@@ -28,7 +28,7 @@
 		END as condition_status_concept_id,
 		32827 type_concept_id,
 		coalesce(diag_prov_id, '') || ';' || coalesce(diag_prov_taxnmy_id, '') ProviderIdKey
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_diag
+		from {sc}.emr_diag
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where upper(coalesce(diag_stat_desc, '')) not in
 		(

diff --git a/...Framework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_enc.xml b/...Framework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_enc.xml
@@ -1,12 +1,12 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT distinct
 		ch.person_id as PersonId,
 		hvid,
 		hv_enc_dt,
 		hv_enc_id,
 		coalesce(enc_prov_id, '') || ';' || coalesce(enc_prov_taxnmy_id, '') ProviderIdKey
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_enc
+		from {sc}.emr_enc
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where hv_enc_dt is not null
 		order by ch.person_id

diff --git a/...work/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_lab_test.xml b/...work/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_lab_test.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT
 		ch.person_id as PersonId,
 		hvid,
@@ -11,7 +11,7 @@
 		lab_result_uom,
 		lab_result_msrmt,
 		coalesce(lab_test_prov_id, '') || ';' || coalesce(lab_test_prov_taxnmy_id, '') ProviderIdKey
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_lab_test
+		from {sc}.emr_lab_test
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where upper(prmy_src_tbl_nm) in
 		(

diff --git a/...mework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_medctn.xml b/...mework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_medctn.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT
 		ch.person_id as PersonId,
 		hvid,
@@ -19,7 +19,7 @@
 		else '4'
 		end as type,
 		32833 type_concept_id
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_medctn
+		from {sc}.emr_medctn
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where coalesce(hv_medctn_dt, medctn_start_dt, medctn_admin_dt, medctn_ord_dt) is not null
 		order by 1

diff --git a/...ramework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_proc.xml b/...ramework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/emr_proc.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT
 		ch.person_id as PersonId,
 		hvid,
@@ -17,7 +17,7 @@
 		end proc,
 		32827 type_concept_id,
 		coalesce(proc_prov_id, '') || ';' || coalesce(proc_prov_taxnmy_id, '') ProviderIdKey
-		from cdm_health_verity_cc_ehr_cce_v2776.emr_proc
+		from {sc}.emr_proc
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where coalesce(upper(proc_stat_cd), '') not in
 		(

diff --git a/...mework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/enrollment.xml b/...mework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/enrollment.xml
@@ -11,7 +11,7 @@
 		date_end,
 		1 as benefit_type,
 		data_vendor
-		FROM cdm_health_verity_cc_ehr_cce_v2776.enrollment
+		FROM {sc}.enrollment
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where lower(benefit_type) = 'medical'
 
@@ -26,7 +26,7 @@
 		date_end,
 		2 as benefit_type,
 		data_vendor
-		FROM cdm_health_verity_cc_ehr_cce_v2776.enrollment
+		FROM {sc}.enrollment
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where lower(benefit_type) = 'pharmacy' or benefit_type is null
 		)

diff --git a/...amework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/lab_tests.xml b/...amework/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/lab_tests.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT
 		ch.person_id as PersonId,
 		coalesce(date_service, date_specimen) as date_service,
@@ -10,7 +10,7 @@
 		result_unit_of_measure,
 		replace(result, chr(9), ' ') as result,
 		data_vendor
-		from cdm_health_verity_cc_ehr_cce_v2776.lab_tests
+		from {sc}.lab_tests
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where loinc_code is not null and test_ordered_name is not null and result_name is not null and coalesce(date_service, date_specimen) is not null
 		order by ch.person_id

diff --git a/...rk/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/medical_claims.xml b/...rk/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/medical_claims.xml
@@ -4,7 +4,7 @@
 		ch.person_id as PersonId,
 		hvid,
 		date_service,
-		diagnosis_code,
+		trim(replace(replace(replace(diagnosis_code, chr(9), ' '), chr(10), ' '), chr(13), ' ')) diagnosis_code,
 		procedure_code,
 		ndc_code,
 		claim_type,
@@ -36,7 +36,7 @@
 		end as icd_ver,
 		hv_enc_id,
 		1 as fake
-		FROM cdm_health_verity_cc_ehr_cce_v2776.medical_claims
+		FROM {sc}.medical_claims
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where  date_service is not null and date_part('year', date_service) &gt;= 2009 and
 		(logical_delete_reason is null or logical_delete_reason = '' or logical_delete_reason = 'null' or lower(logical_delete_reason) not in ('denied claims', 'reversal to original claim'))

diff --git a/...k/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/pharmacy_claims.xml b/...k/org.ohdsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/pharmacy_claims.xml
@@ -23,7 +23,7 @@
 		when date_service &gt;= '10/1/2015' then '10'
 		end as icd_ver
 
-		FROM cdm_health_verity_cc_ehr_cce_v2776.pharmacy_claims
+		FROM {sc}.pharmacy_claims
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where date_service is not null and date_part('year', date_service) &gt;= 2009 and
 		(logical_delete_reason is null or logical_delete_reason = '' or logical_delete_reason = 'null')

diff --git a/...dsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/pharmacy_claims_vaccine.xml b/...dsi.cdm.framework.etl/Transformation/HealthVerity/Definitions/pharmacy_claims_vaccine.xml
@@ -1,5 +1,5 @@
 <QueryDefinition>
-	<Query>
+	<Query database="none">
 		SELECT distinct
 		ch.person_id as PersonId,
 		hvid,
@@ -23,7 +23,7 @@
 		when date_service &gt;= '10/1/2015' then '10'
 		end as icd_ver
 
-		FROM cdm_health_verity_cc_ehr_cce_v2776.pharmacy_claims_vaccine
+		FROM {sc}.pharmacy_claims_vaccine
 		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND hvid = ch.PERSON_SOURCE_VALUE
 		where date_service is not null and date_part('year', date_service) &gt;= 2009 and
 		(logical_delete_reason is null or logical_delete_reason = '' or logical_delete_reason = 'null')