/*********************************************************************************
# Copyright 2017 Observational Health Data Sciences and Informatics
#
#
# 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.
********************************************************************************/
/*******************************************************************************
PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
OHDSI-SQL File Instructions
-----------------------------
1. Set parameter name of schema that contains CDMv4 instance
(@SOURCE_CDMV4, @SOURCE_CDMV4_SCHEMA)
2. Set parameter name of schema that contains CDMv5 instance
([CDM], [CDM].[CDMSCHEMA])
3. Run this script through SqlRender to produce a script that will work in your
source dialect. SqlRender can be found here: https://github.com/OHDSI/SqlRender
4. Run the script produced by SQL Render on your target RDBDMS.
<RDBMS> File Instructions
-------------------------
1. This script will hold a number of placeholders for your CDM V4 and CDMV5
database/schema. In order to make this file work in your environment, you
should plan to do a global "FIND AND REPLACE" on this file to fill in the
file with values that pertain to your environment. The following are the
tokens you should use when doing your "FIND AND REPLACE" operation:
[CMD]
[CDM].[CDMSCHEMA]
*********************************************************************************/
/* SCRIPT PARAMETERS */
-- The target CDMv5 database name
-- the target CDMv5 database plus schema
USE [CDM];
/****
DRUG ERA
Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
****/
DROP TABLE IF EXISTS iob2wlgwcteDrugTarget;
/* / */
-- 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
CREATE TABLE iob2wlgwcteDrugTarget
AS
SELECT
d.DRUG_EXPOSURE_ID
,d.PERSON_ID
,c.CONCEPT_ID
,d.DRUG_TYPE_CONCEPT_ID
,DRUG_EXPOSURE_START_DATE
,COALESCE(DRUG_EXPOSURE_END_DATE, DATE_ADD(CASE TYPEOF(DRUG_EXPOSURE_START_DATE ) WHEN 'TIMESTAMP' THEN CAST(DRUG_EXPOSURE_START_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(DRUG_EXPOSURE_START_DATE AS STRING), 1, 4), SUBSTR(CAST(DRUG_EXPOSURE_START_DATE AS STRING), 5, 2), SUBSTR(CAST(DRUG_EXPOSURE_START_DATE AS STRING), 7, 2)), 'UTC') END, DAYS_SUPPLY), DATE_ADD(CASE TYPEOF(DRUG_EXPOSURE_START_DATE ) WHEN 'TIMESTAMP' THEN CAST(DRUG_EXPOSURE_START_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(DRUG_EXPOSURE_START_DATE AS STRING), 1, 4), SUBSTR(CAST(DRUG_EXPOSURE_START_DATE AS STRING), 5, 2), SUBSTR(CAST(DRUG_EXPOSURE_START_DATE AS STRING), 7, 2)), 'UTC') END, 1)) AS DRUG_EXPOSURE_END_DATE
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM
[CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient';
/* / */
DROP TABLE IF EXISTS iob2wlgwcteEndDates;
/* / */
CREATE TABLE iob2wlgwcteEndDates
AS
SELECT
PERSON_ID
,INGREDIENT_CONCEPT_ID
,DATE_ADD(CASE TYPEOF(EVENT_DATE ) WHEN 'TIMESTAMP' THEN CAST(EVENT_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(EVENT_DATE AS STRING), 1, 4), SUBSTR(CAST(EVENT_DATE AS STRING), 5, 2), SUBSTR(CAST(EVENT_DATE AS STRING), 7, 2)), 'UTC') END, - 30) AS END_DATE -- unpad the end date
FROM
(
SELECT E1.PERSON_ID
,E1.INGREDIENT_CONCEPT_ID
,E1.EVENT_DATE
,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
,E1.OVERALL_ORD
FROM (
SELECT PERSON_ID
,INGREDIENT_CONCEPT_ID
,EVENT_DATE
,EVENT_TYPE
,START_ORDINAL
,ROW_NUMBER() OVER (
PARTITION BY PERSON_ID
,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE
,EVENT_TYPE
) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
FROM (
-- select the start dates, assigning a row number to each
SELECT PERSON_ID
,INGREDIENT_CONCEPT_ID
,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
,0 AS EVENT_TYPE
,ROW_NUMBER() OVER (
PARTITION BY PERSON_ID
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
) AS START_ORDINAL
FROM iob2wlgwcteDrugTarget
UNION ALL
-- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges.
SELECT PERSON_ID
,INGREDIENT_CONCEPT_ID
,DATE_ADD(CASE TYPEOF(DRUG_EXPOSURE_END_DATE ) WHEN 'TIMESTAMP' THEN CAST(DRUG_EXPOSURE_END_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(DRUG_EXPOSURE_END_DATE AS STRING), 1, 4), SUBSTR(CAST(DRUG_EXPOSURE_END_DATE AS STRING), 5, 2), SUBSTR(CAST(DRUG_EXPOSURE_END_DATE AS STRING), 7, 2)), 'UTC') END, 30)
,1 AS EVENT_TYPE
,NULL
FROM iob2wlgwcteDrugTarget
) RAWDATA
) E1
INNER JOIN (
SELECT PERSON_ID
,INGREDIENT_CONCEPT_ID
,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
,ROW_NUMBER() OVER (
PARTITION BY PERSON_ID
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
) AS START_ORDINAL
FROM iob2wlgwcteDrugTarget
) E2 ON E1.PERSON_ID = E2.PERSON_ID
AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
AND E2.EVENT_DATE <= E1.EVENT_DATE
GROUP BY E1.PERSON_ID
,E1.INGREDIENT_CONCEPT_ID
,E1.EVENT_DATE
,E1.START_ORDINAL
,E1.OVERALL_ORD
) E
WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
/* / */
DROP TABLE IF EXISTS iob2wlgwcteDrugExpEnds;
/* / */
CREATE TABLE iob2wlgwcteDrugExpEnds
AS
SELECT
d.PERSON_ID
,d.INGREDIENT_CONCEPT_ID
,d.DRUG_TYPE_CONCEPT_ID
,d.DRUG_EXPOSURE_START_DATE
,MIN(e.END_DATE) AS ERA_END_DATE
FROM
iob2wlgwcteDrugTarget d
INNER JOIN iob2wlgwcteEndDates e ON d.PERSON_ID = e.PERSON_ID
AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
GROUP BY d.PERSON_ID
,d.INGREDIENT_CONCEPT_ID
,d.DRUG_TYPE_CONCEPT_ID
,d.DRUG_EXPOSURE_START_DATE;
/* / */
INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER (
ORDER BY person_id
) AS drug_era_id
,person_id
,INGREDIENT_CONCEPT_ID
,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date
,ERA_END_DATE
,COUNT(*) AS DRUG_EXPOSURE_COUNT
,30 AS gap_days
FROM iob2wlgwcteDrugExpEnds
GROUP BY person_id
,INGREDIENT_CONCEPT_ID
,drug_type_concept_id
,ERA_END_DATE;
/****
CONDITION ERA
Note: Eras derived from CONDITION_OCCURRENCE table, using 30d gap
****/
DROP TABLE IF EXISTS iob2wlgwcondition_era_phase_1;
/* / */
DROP TABLE IF EXISTS iob2wlgwcteConditionTarget;
/* / */
-- create base eras from the concepts found in condition_occurrence
CREATE TABLE iob2wlgwcteConditionTarget
AS
SELECT
co.PERSON_ID
,co.condition_concept_id
,co.CONDITION_START_DATE
,COALESCE(co.CONDITION_END_DATE, DATE_ADD(CASE TYPEOF(CONDITION_START_DATE ) WHEN 'TIMESTAMP' THEN CAST(CONDITION_START_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(CONDITION_START_DATE AS STRING), 1, 4), SUBSTR(CAST(CONDITION_START_DATE AS STRING), 5, 2), SUBSTR(CAST(CONDITION_START_DATE AS STRING), 7, 2)), 'UTC') END, 1)) AS CONDITION_END_DATE
FROM
[CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
/* / */
DROP TABLE IF EXISTS iob2wlgwcteCondEndDates;
/* / */
CREATE TABLE iob2wlgwcteCondEndDates
AS
SELECT
PERSON_ID
,CONDITION_CONCEPT_ID
,DATE_ADD(CASE TYPEOF(EVENT_DATE ) WHEN 'TIMESTAMP' THEN CAST(EVENT_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(EVENT_DATE AS STRING), 1, 4), SUBSTR(CAST(EVENT_DATE AS STRING), 5, 2), SUBSTR(CAST(EVENT_DATE AS STRING), 7, 2)), 'UTC') END, - 30) AS END_DATE -- unpad the end date
FROM
(
SELECT E1.PERSON_ID
,E1.CONDITION_CONCEPT_ID
,E1.EVENT_DATE
,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
,E1.OVERALL_ORD
FROM (
SELECT PERSON_ID
,CONDITION_CONCEPT_ID
,EVENT_DATE
,EVENT_TYPE
,START_ORDINAL
,ROW_NUMBER() OVER (
PARTITION BY PERSON_ID
,CONDITION_CONCEPT_ID ORDER BY EVENT_DATE
,EVENT_TYPE
) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
FROM (
-- select the start dates, assigning a row number to each
SELECT PERSON_ID
,CONDITION_CONCEPT_ID
,CONDITION_START_DATE AS EVENT_DATE
,- 1 AS EVENT_TYPE
,ROW_NUMBER() OVER (
PARTITION BY PERSON_ID
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
) AS START_ORDINAL
FROM iob2wlgwcteConditionTarget
UNION ALL
-- pad the end dates by 30 to allow a grace period for overlapping ranges.
SELECT PERSON_ID
,CONDITION_CONCEPT_ID
,DATE_ADD(CASE TYPEOF(CONDITION_END_DATE ) WHEN 'TIMESTAMP' THEN CAST(CONDITION_END_DATE AS TIMESTAMP) ELSE TO_UTC_TIMESTAMP(CONCAT_WS('-', SUBSTR(CAST(CONDITION_END_DATE AS STRING), 1, 4), SUBSTR(CAST(CONDITION_END_DATE AS STRING), 5, 2), SUBSTR(CAST(CONDITION_END_DATE AS STRING), 7, 2)), 'UTC') END, 30)
,1 AS EVENT_TYPE
,NULL
FROM iob2wlgwcteConditionTarget
) RAWDATA
) E1
INNER JOIN (
SELECT PERSON_ID
,CONDITION_CONCEPT_ID
,CONDITION_START_DATE AS EVENT_DATE
,ROW_NUMBER() OVER (
PARTITION BY PERSON_ID
,CONDITION_CONCEPT_ID ORDER BY CONDITION_START_DATE
) AS START_ORDINAL
FROM iob2wlgwcteConditionTarget
) E2 ON E1.PERSON_ID = E2.PERSON_ID
AND E1.CONDITION_CONCEPT_ID = E2.CONDITION_CONCEPT_ID
AND E2.EVENT_DATE <= E1.EVENT_DATE
GROUP BY E1.PERSON_ID
,E1.CONDITION_CONCEPT_ID
,E1.EVENT_DATE
,E1.START_ORDINAL
,E1.OVERALL_ORD
) E
WHERE (2 * E.START_ORDINAL) - E.OVERALL_ORD = 0;
/* / */
DROP TABLE IF EXISTS iob2wlgwcteConditionEnds;
/* / */
CREATE TABLE iob2wlgwcteConditionEnds
AS
SELECT
c.PERSON_ID
,c.CONDITION_CONCEPT_ID
,c.CONDITION_START_DATE
,MIN(e.END_DATE) AS ERA_END_DATE
FROM
iob2wlgwcteConditionTarget c
INNER JOIN iob2wlgwcteCondEndDates e ON c.PERSON_ID = e.PERSON_ID
AND c.CONDITION_CONCEPT_ID = e.CONDITION_CONCEPT_ID
AND e.END_DATE >= c.CONDITION_START_DATE
GROUP BY c.PERSON_ID
,c.CONDITION_CONCEPT_ID
,c.CONDITION_START_DATE;
/* / */
INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id
,person_id
,condition_concept_id
,condition_era_start_date
,condition_era_end_date
,condition_occurrence_count
)
SELECT row_number() OVER (
ORDER BY person_id
) AS condition_era_id
,person_id
,CONDITION_CONCEPT_ID
,min(CONDITION_START_DATE) AS CONDITION_ERA_START_DATE
,ERA_END_DATE AS CONDITION_ERA_END_DATE
,COUNT(*) AS CONDITION_OCCURRENCE_COUNT
FROM iob2wlgwcteConditionEnds
GROUP BY person_id
,CONDITION_CONCEPT_ID
,ERA_END_DATE;