362 lines
8.8 KiB
SQL
362 lines
8.8 KiB
SQL
/*********************************************************************************
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# Copyright 2017 Observational Health Data Sciences and Informatics
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#
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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********************************************************************************/
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/*******************************************************************************
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PURPOSE: Generate Era table (based on conversion script from V4 V5).
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last revised: Jun 2017
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authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
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*********************************************************************************/
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/* SCRIPT PARAMETERS */
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-- The target CDMv5 database name
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-- the target CDMv5 database plus schema
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SET search_path TO [CDM];
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/****
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DRUG ERA
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Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
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****/
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DROP TABLE IF EXISTS cteDrugTarget;
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/* / */
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-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
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CREATE TEMP TABLE cteDrugTarget
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AS
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SELECT
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d.DRUG_EXPOSURE_ID
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,d.PERSON_ID
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,c.CONCEPT_ID
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,d.DRUG_TYPE_CONCEPT_ID
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,DRUG_EXPOSURE_START_DATE
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,COALESCE(DRUG_EXPOSURE_END_DATE, (DRUG_EXPOSURE_START_DATE + DAYS_SUPPLY*INTERVAL'1 day'), (DRUG_EXPOSURE_START_DATE + 1*INTERVAL'1 day')) AS DRUG_EXPOSURE_END_DATE
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,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
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FROM
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[CDM].[CDMSCHEMA].DRUG_EXPOSURE d
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INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
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INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
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WHERE c.VOCABULARY_ID = 'RxNorm'
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AND c.CONCEPT_CLASS_ID = 'Ingredient';
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/* / */
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DROP TABLE IF EXISTS cteEndDates;
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/* / */
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CREATE TEMP TABLE cteEndDates
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AS
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SELECT
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PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,(EVENT_DATE + - 30*INTERVAL'1 day') AS END_DATE -- unpad the end date
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FROM
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(
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SELECT E1.PERSON_ID
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,E1.INGREDIENT_CONCEPT_ID
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,E1.EVENT_DATE
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,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
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,E1.OVERALL_ORD
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FROM (
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,EVENT_DATE
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,EVENT_TYPE
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,START_ORDINAL
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE
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,EVENT_TYPE
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) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
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FROM (
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-- select the start dates, assigning a row number to each
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
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,0 AS EVENT_TYPE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
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) AS START_ORDINAL
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FROM cteDrugTarget
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UNION ALL
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-- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges.
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,(DRUG_EXPOSURE_END_DATE + 30*INTERVAL'1 day')
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,1 AS EVENT_TYPE
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,NULL
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FROM cteDrugTarget
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) RAWDATA
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) E1
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INNER JOIN (
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SELECT PERSON_ID
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,INGREDIENT_CONCEPT_ID
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,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
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) AS START_ORDINAL
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FROM cteDrugTarget
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) E2 ON E1.PERSON_ID = E2.PERSON_ID
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AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
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AND E2.EVENT_DATE <= E1.EVENT_DATE
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GROUP BY E1.PERSON_ID
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,E1.INGREDIENT_CONCEPT_ID
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,E1.EVENT_DATE
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,E1.START_ORDINAL
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,E1.OVERALL_ORD
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) E
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WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
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/* / */
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DROP TABLE IF EXISTS cteDrugExpEnds;
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/* / */
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CREATE TEMP TABLE cteDrugExpEnds
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AS
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SELECT
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d.PERSON_ID
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,d.INGREDIENT_CONCEPT_ID
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,d.DRUG_TYPE_CONCEPT_ID
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,d.DRUG_EXPOSURE_START_DATE
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,MIN(e.END_DATE) AS ERA_END_DATE
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FROM
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cteDrugTarget d
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INNER JOIN cteEndDates e ON d.PERSON_ID = e.PERSON_ID
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AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
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AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
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GROUP BY d.PERSON_ID
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,d.INGREDIENT_CONCEPT_ID
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,d.DRUG_TYPE_CONCEPT_ID
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,d.DRUG_EXPOSURE_START_DATE;
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/* / */
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INSERT INTO [CDM].[CDMSCHEMA].drug_era
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SELECT row_number() OVER (
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ORDER BY person_id
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) AS drug_era_id
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,person_id
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,INGREDIENT_CONCEPT_ID
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,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date
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,ERA_END_DATE
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,COUNT(*) AS DRUG_EXPOSURE_COUNT
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,30 AS gap_days
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FROM cteDrugExpEnds
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GROUP BY person_id
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,INGREDIENT_CONCEPT_ID
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,drug_type_concept_id
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,ERA_END_DATE;
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/****
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CONDITION ERA
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Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
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****/
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DROP TABLE IF EXISTS condition_era_phase_1;
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/* / */
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DROP TABLE IF EXISTS cteConditionTarget;
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/* / */
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-- create base eras from the concepts found in condition_occurrence
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CREATE TEMP TABLE cteConditionTarget
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AS
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SELECT
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co.PERSON_ID
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,co.condition_concept_id
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,co.CONDITION_START_DATE
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,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1*INTERVAL'1 day')) AS CONDITION_END_DATE
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FROM
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[CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
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/* / */
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DROP TABLE IF EXISTS cteCondEndDates;
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/* / */
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CREATE TEMP TABLE cteCondEndDates
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AS
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SELECT
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PERSON_ID
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,CONDITION_CONCEPT_ID
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,(EVENT_DATE + - 30*INTERVAL'1 day') AS END_DATE -- unpad the end date
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FROM
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(
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SELECT E1.PERSON_ID
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,E1.CONDITION_CONCEPT_ID
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,E1.EVENT_DATE
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,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
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,E1.OVERALL_ORD
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FROM (
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,EVENT_DATE
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,EVENT_TYPE
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,START_ORDINAL
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,CONDITION_CONCEPT_ID ORDER BY EVENT_DATE
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,EVENT_TYPE
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) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
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FROM (
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-- select the start dates, assigning a row number to each
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,CONDITION_START_DATE AS EVENT_DATE
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,- 1 AS EVENT_TYPE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
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) AS START_ORDINAL
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FROM cteConditionTarget
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UNION ALL
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-- pad the end dates by 30 to allow a grace period for overlapping ranges.
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,(CONDITION_END_DATE + 30*INTERVAL'1 day')
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,1 AS EVENT_TYPE
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,NULL
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FROM cteConditionTarget
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) RAWDATA
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) E1
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INNER JOIN (
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SELECT PERSON_ID
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,CONDITION_CONCEPT_ID
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,CONDITION_START_DATE AS EVENT_DATE
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,ROW_NUMBER() OVER (
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PARTITION BY PERSON_ID
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,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
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) AS START_ORDINAL
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FROM cteConditionTarget
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) E2 ON E1.PERSON_ID = E2.PERSON_ID
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AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID
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AND E2.EVENT_DATE <= E1.EVENT_DATE
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GROUP BY E1.PERSON_ID
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,E1.CONDITION_CONCEPT_ID
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,E1.EVENT_DATE
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,E1.START_ORDINAL
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,E1.OVERALL_ORD
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) E
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WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0;
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/* / */
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DROP TABLE IF EXISTS cteConditionEnds;
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/* / */
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CREATE TEMP TABLE cteConditionEnds
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AS
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SELECT
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c.PERSON_ID
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,c.CONDITION_CONCEPT_ID
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,c.CONDITION_START_DATE
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,MIN(e.END_DATE) AS ERA_END_DATE
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FROM
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cteConditionTarget c
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INNER JOIN cteCondEndDates e ON c.PERSON_ID = e.PERSON_ID
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AND c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID
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AND e.END_DATE >= c.CONDITION_START_DATE
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GROUP BY c.PERSON_ID
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,c.CONDITION_CONCEPT_ID
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,c.CONDITION_START_DATE;
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/* / */
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INSERT INTO [CDM].[CDMSCHEMA].condition_era (
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condition_era_id
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,person_id
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,condition_concept_id
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,condition_era_start_date
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,condition_era_end_date
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,condition_occurrence_count
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)
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SELECT row_number() OVER (
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ORDER BY person_id
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) AS condition_era_id
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,person_id
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,CONDITION_CONCEPT_ID
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,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE
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,ERA_END_DATE AS CONDITION_ERA_END_DATE
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,COUNT(*) AS CONDITION_OCCURRENCE_COUNT
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FROM cteConditionEnds
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GROUP BY person_id
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,CONDITION_CONCEPT_ID
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,ERA_END_DATE;
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