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revised prefixes

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vojtechhuser 2017-06-21 16:16:53 -04:00
parent 4171cb6d27
commit 6b0197af31
8 changed files with 89 additions and 436 deletions
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63
CodeExcerpts/DerivedTables/GenerateEra.sql
View File

@ -16,71 +16,18 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
(@TARGET_CDMV5, @TARGET_CDMV5_SCHEMA)
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
{DEFAULT @SOURCE_CDMV4 = '[SOURCE_CDMV4]' } -- The CDMv4 database name
{DEFAULT @SOURCE_CDMV4_SCHEMA = '[SOURCE_CDMV4].[SCHEMA]' } -- The CDMv4 database plus schema
{DEFAULT @TARGET_CDMV5 = '[TARGET_CDMV5]' } -- The target CDMv5 database name {DEFAULT @TARGET_CDMV5 = '[CDM]' } -- The target CDMv5 database name
{DEFAULT @TARGET_CDMV5_SCHEMA = '[TARGET_CDMV5].[SCHEMA]' } -- the target CDMv5 database plus schema {DEFAULT @TARGET_CDMV5_SCHEMA = '[CDM].[CDMSCHEMA]' } -- the target CDMv5 database plus schema
USE @TARGET_CDMV5; USE @TARGET_CDMV5;

24
CodeExcerpts/DerivedTables/TranslateSnippet.R
View File

@ -30,5 +30,29 @@ ttb<-SqlRender::translateSql(tta$sql,targetDialect = 'postgresql')
cat(ttb$sql,file='c:/temp/drug_era_2017.sql') cat(ttb$sql,file='c:/temp/drug_era_2017.sql')
sql<-ttb$sql sql<-ttb$sql
fname<-'GenerateEra.sql'
flavors<-c(
'oracle'
,'postgresql'
,'pdw'
,'redshift'
,'impala'
,'netezza'
,'bigquery')
#,'sql server')
for (flavor in flavors){
print(flavor)
sql<-readChar(fname, file.info(fname)$size)
tta<-SqlRender::renderSql(sql,results_database_schema='results',vocab_database_schema='vocab')
ttb<-SqlRender::translateSql(tta$sql,targetDialect = flavor)
dir.create(flavor)
cat(ttb$sql,file=file.path(flavor,paste0(fname)))
# sql<-ttb$sql
}

73
CodeExcerpts/DerivedTables/impala/GenerateEra.sql
View File

@ -16,73 +16,20 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA])
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
-- The CDMv4 database name
-- The CDMv4 database plus schema
-- The target CDMv5 database name -- The target CDMv5 database name
-- the target CDMv5 database plus schema -- the target CDMv5 database plus schema
USE [TARGET_CDMV5]; USE [CDM];
@ -109,9 +56,9 @@ d.DRUG_EXPOSURE_ID
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM FROM
[TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d [CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient'; AND c.CONCEPT_CLASS_ID = 'Ingredient';
@ -216,7 +163,7 @@ GROUP BY d.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
ORDER BY person_id ORDER BY person_id
) AS drug_era_id ) AS drug_era_id
@ -284,7 +231,7 @@ co.PERSON_ID
,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 ,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 FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
/* / */ /* / */
@ -385,7 +332,7 @@ GROUP BY c.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id condition_era_id
,person_id ,person_id
,condition_concept_id ,condition_concept_id

73
CodeExcerpts/DerivedTables/netezza/GenerateEra.sql
View File

@ -16,73 +16,20 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA])
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
-- The CDMv4 database name
-- The CDMv4 database plus schema
-- The target CDMv5 database name -- The target CDMv5 database name
-- the target CDMv5 database plus schema -- the target CDMv5 database plus schema
SET search_path TO [TARGET_CDMV5]; SET search_path TO [CDM];
@ -110,9 +57,9 @@ d.DRUG_EXPOSURE_ID
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM FROM
[TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d [CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient'; AND c.CONCEPT_CLASS_ID = 'Ingredient';
@ -219,7 +166,7 @@ GROUP BY d.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
ORDER BY person_id ORDER BY person_id
) AS drug_era_id ) AS drug_era_id
@ -288,7 +235,7 @@ co.PERSON_ID
,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1)) AS CONDITION_END_DATE ,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1)) AS CONDITION_END_DATE
FROM FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
/* / */ /* / */
@ -391,7 +338,7 @@ GROUP BY c.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id condition_era_id
,person_id ,person_id
,condition_concept_id ,condition_concept_id

73
CodeExcerpts/DerivedTables/oracle/GenerateEra.sql
View File

@ -16,73 +16,20 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA])
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
-- The CDMv4 database name
-- The CDMv4 database plus schema
-- The target CDMv5 database name -- The target CDMv5 database name
-- the target CDMv5 database plus schema -- the target CDMv5 database plus schema
ALTER SESSION SET current_schema = [TARGET_CDMV5]; ALTER SESSION SET current_schema = [CDM];
@ -117,9 +64,9 @@ d.DRUG_EXPOSURE_ID
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM FROM
[TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d [CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient' ; AND c.CONCEPT_CLASS_ID = 'Ingredient' ;
@ -235,7 +182,7 @@ GROUP BY d.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
ORDER BY person_id ORDER BY person_id
) AS drug_era_id ) AS drug_era_id
@ -319,7 +266,7 @@ co.PERSON_ID
,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + NUMTODSINTERVAL(1, 'day'))) AS CONDITION_END_DATE ,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + NUMTODSINTERVAL(1, 'day'))) AS CONDITION_END_DATE
FROM FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co ; [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co ;
/* / */ /* / */
@ -431,7 +378,7 @@ GROUP BY c.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id condition_era_id
,person_id ,person_id
,condition_concept_id ,condition_concept_id

73
CodeExcerpts/DerivedTables/pdw/GenerateEra.sql
View File

@ -16,73 +16,20 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA])
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
-- The CDMv4 database name
-- The CDMv4 database plus schema
-- The target CDMv5 database name -- The target CDMv5 database name
-- the target CDMv5 database plus schema -- the target CDMv5 database plus schema
USE [TARGET_CDMV5]; USE [CDM];
@ -108,9 +55,9 @@ d.DRUG_EXPOSURE_ID
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM FROM
[TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d [CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient'; AND c.CONCEPT_CLASS_ID = 'Ingredient';
@ -213,7 +160,7 @@ GROUP BY d.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
ORDER BY person_id ORDER BY person_id
) AS drug_era_id ) AS drug_era_id
@ -280,7 +227,7 @@ co. person_id, co.condition_concept_id
,COALESCE(co.CONDITION_END_DATE, DATEADD(day, 1, CONDITION_START_DATE)) AS CONDITION_END_DATE ,COALESCE(co.CONDITION_END_DATE, DATEADD(day, 1, CONDITION_START_DATE)) AS CONDITION_END_DATE
FROM FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
/* / */ /* / */
@ -379,7 +326,7 @@ GROUP BY c.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id condition_era_id
,person_id ,person_id
,condition_concept_id ,condition_concept_id

73
CodeExcerpts/DerivedTables/postgresql/GenerateEra.sql
View File

@ -16,73 +16,20 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA])
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
-- The CDMv4 database name
-- The CDMv4 database plus schema
-- The target CDMv5 database name -- The target CDMv5 database name
-- the target CDMv5 database plus schema -- the target CDMv5 database plus schema
SET search_path TO [TARGET_CDMV5]; SET search_path TO [CDM];
@ -110,9 +57,9 @@ d.DRUG_EXPOSURE_ID
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM FROM
[TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d [CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient'; AND c.CONCEPT_CLASS_ID = 'Ingredient';
@ -219,7 +166,7 @@ GROUP BY d.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
ORDER BY person_id ORDER BY person_id
) AS drug_era_id ) AS drug_era_id
@ -288,7 +235,7 @@ co.PERSON_ID
,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1*INTERVAL'1 day')) AS CONDITION_END_DATE ,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1*INTERVAL'1 day')) AS CONDITION_END_DATE
FROM FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
/* / */ /* / */
@ -391,7 +338,7 @@ GROUP BY c.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id condition_era_id
,person_id ,person_id
,condition_concept_id ,condition_concept_id

73
CodeExcerpts/DerivedTables/redshift/GenerateEra.sql
View File

@ -16,73 +16,20 @@
********************************************************************************/ ********************************************************************************/
/******************************************************************************* /*******************************************************************************
PURPOSE: Use this script to convert your OMOP V4 common data model to CDM V5. PURPOSE: Generate Era table (based on conversion script from V4 V5).
last revised: Jun 2017 last revised: Jun 2017
authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser authors: Patrick Ryan, Chris Knoll, Anthony Sena, Vojtech Huser
!!!!!!!!!!!!!!!!!!!!! PLEASE READ THESE INSTRUCTIONS !!!!!!!!!!!!!!!!!!!!!!!!!!!
This script was authored using OHDSI-SQL which will require you to run this
script through SqlRender to creat a version that is compatible with your target
RDBMS. We have pre-generated these scripts using SQL Render and have placed
them in folders for each RDBMS. Depending on which script you are viewing, your
instructions will be slightly different.
General Assumptions
-------------------
This script assumes that your V4 and V5 database are located on the same
RDBMS server. It also assumes that the V4 and V5 databases were created
using the standard data definition scripts for these databases. If you
altered your V4 database in any way, this script will likely require
some mo
Getting Started
---------------
Before you can use this script, there are some prerequisites:
1. Create a target CDMv5 database on your database server using the
appropriate script from https://github.com/OHDSI/CommonDataModel
2. Load VocabV5 into the target database/schema that will contain CDMv5 using
Athena: http://ohdsi.org/web/ATHENA
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
([TARGET_CDMV5], [TARGET_CDMV5].[SCHEMA])
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:
a. [SOURCE_CDMV4]
b. [SOURCE_CDMV4].[SCHEMA]
c. [TARGET_CDMV5]
d. [TARGET_CDMV5].[SCHEMA]
2. Run the resulting script on your target RDBDMS.
*********************************************************************************/ *********************************************************************************/
/* SCRIPT PARAMETERS */ /* SCRIPT PARAMETERS */
-- The CDMv4 database name
-- The CDMv4 database plus schema
-- The target CDMv5 database name -- The target CDMv5 database name
-- the target CDMv5 database plus schema -- the target CDMv5 database plus schema
SET search_path TO [TARGET_CDMV5]; SET search_path TO [CDM];
@ -110,9 +57,9 @@ d.DRUG_EXPOSURE_ID
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID ,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
FROM FROM
[TARGET_CDMV5].[SCHEMA].DRUG_EXPOSURE d [CDM].[CDMSCHEMA].DRUG_EXPOSURE d
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN [TARGET_CDMV5].[SCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID INNER JOIN [CDM].[CDMSCHEMA].CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = 'RxNorm' WHERE c.VOCABULARY_ID = 'RxNorm'
AND c.CONCEPT_CLASS_ID = 'Ingredient'; AND c.CONCEPT_CLASS_ID = 'Ingredient';
@ -219,7 +166,7 @@ GROUP BY d.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].drug_era INSERT INTO [CDM].[CDMSCHEMA].drug_era
SELECT row_number() OVER ( SELECT row_number() OVER (
ORDER BY person_id ORDER BY person_id
) AS drug_era_id ) AS drug_era_id
@ -288,7 +235,7 @@ co.PERSON_ID
,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1*INTERVAL'1 day')) AS CONDITION_END_DATE ,COALESCE(co.CONDITION_END_DATE, (CONDITION_START_DATE + 1*INTERVAL'1 day')) AS CONDITION_END_DATE
FROM FROM
[TARGET_CDMV5].[SCHEMA].CONDITION_OCCURRENCE co; [CDM].[CDMSCHEMA].CONDITION_OCCURRENCE co;
/* / */ /* / */
@ -391,7 +338,7 @@ GROUP BY c.PERSON_ID
/* / */ /* / */
INSERT INTO [TARGET_CDMV5].[SCHEMA].condition_era ( INSERT INTO [CDM].[CDMSCHEMA].condition_era (
condition_era_id condition_era_id
,person_id ,person_id
,condition_concept_id ,condition_concept_id