Update of CMS Place of Service

CMS Place of Service/load_stage.sql

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+/**************************************************************************
+* Copyright 2016 Observational Health Data Sciences and Informatics (OHDSI)
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*
+* Authors: Medical team
+* Date: 2021
+**************************************************************************/
+
+--1. Update latest_update field to new date
+DO $_$
+BEGIN
+	PERFORM VOCABULARY_PACK.SetLatestUpdate(
+	pVocabularyName			=>'CMS Place of Service',
+	pVocabularyDate			=> TO_DATE('20190101','YYYYMMDD'),
+	pVocabularyVersion		=> 'CMS Place of Service v2019',
+	pVocabularyDevSchema	=> 'DEV_CMSPOS'
+);
+END $_$;
+
+--2. Truncate all working tables
+TRUNCATE TABLE concept_stage;
+TRUNCATE TABLE concept_relationship_stage;
+TRUNCATE TABLE concept_synonym_stage;
+TRUNCATE TABLE pack_content_stage;
+TRUNCATE TABLE drug_strength_stage;
+
+--3. Add all existing concepts
+INSERT INTO concept_stage
+SELECT *
+FROM concept
+WHERE vocabulary_id = 'CMS Place of Service';
+
+--4. Apply the manual changes
+DO $_$
+BEGIN
+	PERFORM VOCABULARY_PACK.ProcessManualConcepts();
+END $_$;
+
+-- At the end, the three tables concept_stage, concept_relationship_stage and concept_synonym_stage should be ready to be fed into the generic_update.sql script

CMS Place of Service/manual_work/preparing_the_source.sql

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+/**************************************************************************
+* Copyright 2016 Observational Health Data Sciences and Informatics (OHDSI)
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+* 
+* Authors: Medical team
+* Date: 2021
+**************************************************************************/
+
+--1. Create a local source table inside dev_cmspos schema
+DROP TABLE IF EXISTS dev_cmspos.cmspos_source;
+CREATE TABLE dev_cmspos.cmspos_source (
+	action_mode TEXT,
+	concept_code TEXT,
+	concept_name TEXT,
+	valid_start_date DATE,
+	valid_end_date DATE
+);
+
+--2. Load csv file
+--for example:
+DO $$
+BEGIN
+	TRUNCATE dev_cmspos.cmspos_source;
+	SET LOCAL DATESTYLE=DMY;
+	COPY dev_cmspos.cmspos_source FROM '/home/vocab_import/manual/CMS_POS-2019.csv' DELIMITER ';' CSV QUOTE '"' HEADER;
+END $$;
+
+--3. Fill the manual tables (truncate if necessary)
+--concepts for update
+INSERT INTO concept_manual (
+	concept_name,
+	vocabulary_id,
+	standard_concept,
+	concept_code,
+	valid_start_date
+	)
+SELECT concept_name,
+	'CMS Place of Service' AS vocabulary_id,
+	'S' AS standard_concept,
+	concept_code,
+	valid_start_date
+FROM dev_cmspos.cmspos_source
+WHERE action_mode IN (
+		'U',
+		'R'
+		);
+
+--concepts for deprecate
+INSERT INTO concept_manual (
+	vocabulary_id,
+	standard_concept,
+	concept_code,
+	valid_end_date,
+	invalid_reason
+	)
+SELECT 'CMS Place of Service' AS vocabulary_id,
+	NULL AS standard_concept,
+	concept_code,
+	valid_end_date,
+	'D' AS invalid_reason
+FROM dev_cmspos.cmspos_source
+WHERE action_mode = 'D';
+
+--new concepts
+INSERT INTO concept_manual
+SELECT concept_name,
+	'Visit' AS domain_id,
+	'CMS Place of Service' AS vocabulary_id,
+	'Visit' AS concept_class_id,
+	'S' AS standard_concept,
+	concept_code,
+	TO_DATE('19700101', 'YYYYMMDD') AS valid_start_date,
+	TO_DATE('20991231', 'YYYYMMDD') AS valid_end_date,
+	NULL AS invalid_reason
+FROM dev_cmspos.cmspos_source
+WHERE action_mode = 'I';

CMS Place of Service/readme.md

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+Update of CMS Place of Service
+
+Prerequisites:
+- Schema DevV5 with copies of tables concept, concept_relationship and concept_synonym from ProdV5, fully indexed.
+- Working directory CMS Place of Service.
+
+1. Get new source from https://drive.google.com/drive/u/1/folders/1MG_XoVCylyiUs0zV6IqtEpCiEdmT0wWc
+2. Run manual_work/preparing_the_source.sql
+3. Run load_stage.sql
+4. Run generic_update: devv5.GenericUpdate();