Initial commit for the CDM v4 to v5 conversion scripts.
This commit is contained in:
Anthony Sena
parent
d23321a00b
commit
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/*********************************************************************************
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# Copyright 2015 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: Use this script is used to help perform Quality Assurance activities
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after you convert your OMOP V4 common data model to CDM V5.
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last revised: 01 July 2015
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author: Anthony Sena
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This script was authored against SQL Server and will require conversion to other
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dialects. Please keep this in mind if you plan to use this against another RDBMS.
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General Notes
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---------------
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The V4 to V5 conversion script utilizes the standard vocabularies to map data
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from the V4 source tables to the V5 target tables. As a result, comparing the
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rowcounts for the following tables is not adviseable since we are expecting
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certain entries to move from their source table to a different target:
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Condition_Occurrence
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Drug_Exposure
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Observation
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Measurement
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Procedure_Occurrence
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This script will produce 2 tables:
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Table 1: This will contain the source table name (i.e. Condition_Occurrence),
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the target domain_id from the V5 vocabulary and the expected rowcount
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from the conversion. When there is no target defined in the V5 vocabulary,
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the source data is carried over to the same target table in V5 with
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a concept_id of 0. For example:
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TableName Domain RowCount
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--------- ------ --------
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Condition_Occurrence condition 464849
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Condition_Occurrence measurement 8416
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Condition_Occurrence observation 31522
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Condition_Occurrence procedure 24298
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Table 2: This will contain a summary of the V5 Target Domains and Rowcounts.
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I found this helpful to tie out the expected rowcounts and what actually
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happened during the conversion.
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INSTRUCTIONS
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------------
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1. This script has placeholders for your CDM V4 and CDMV5 database/schema.
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In order to make this file work in your environment, you
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should plan to do a global "FIND AND REPLACE" on this file to fill in the
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file with values that pertain to your environment. The following are the
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tokens you should use when doing your "FIND AND REPLACE" operation:
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a. [SOURCE_CDMV4]
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b. [TARGET_CDMV5]
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2. Run the resulting script on your target RDBDMS.
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*********************************************************************************/
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USE [TARGET_CDMV5]
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GO
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/*
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* CONCEPT MAP
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*/
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IF OBJECT_ID('tempdb..#concept_map', 'U') IS NOT NULL
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DROP TABLE #concept_map;
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--standard concepts
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SELECT concept_id AS source_concept_id
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,concept_id AS target_concept_id
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,domain_id
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,NULL AS source_concept_mapping_occurrence
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INTO #concept_map
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FROM dbo.concept
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WHERE standard_concept = 'S'
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AND invalid_reason IS NULL
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UNION
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--concepts with 'map to' standard
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SELECT DISTINCT c1.concept_id AS source_concept_id
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,c2.concept_id AS target_concept_id
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,c2.domain_id
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,NULL
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FROM (
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SELECT concept_id
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FROM dbo.concept
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WHERE (
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(
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standard_concept <> 'S'
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OR standard_concept IS NULL
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)
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OR invalid_reason IS NOT NULL
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)
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) c1
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INNER JOIN dbo.concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1
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INNER JOIN dbo.concept c2 ON cr1.concept_id_2 = c2.concept_id
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WHERE c2.standard_concept = 'S'
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AND c2.invalid_reason IS NULL
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AND cr1.relationship_id IN ('Maps to')
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AND cr1.invalid_reason IS NULL
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UNION
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--concepts without 'map to' standard with another non 'is a' relation to standard
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SELECT DISTINCT c1.concept_id AS source_concept_id
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,c2.concept_id AS target_concept_id
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,c2.domain_id
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,NULL
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FROM (
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SELECT concept_id
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FROM dbo.concept
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WHERE (
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(
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standard_concept <> 'S'
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OR standard_concept IS NULL
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)
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OR invalid_reason IS NOT NULL
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)
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AND concept_id NOT IN (
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SELECT DISTINCT c1.concept_id
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FROM (
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SELECT concept_id
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FROM dbo.concept
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WHERE (
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(
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standard_concept <> 'S'
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OR standard_concept IS NULL
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)
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OR invalid_reason IS NOT NULL
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)
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) c1
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INNER JOIN dbo.concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1
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INNER JOIN dbo.concept c2 ON cr1.concept_id_2 = c2.concept_id
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WHERE c2.standard_concept = 'S'
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AND c2.invalid_reason IS NULL
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AND cr1.relationship_id IN ('Maps to')
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AND cr1.invalid_reason IS NULL
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)
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) c1
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INNER JOIN dbo.concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1
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INNER JOIN dbo.concept c2 ON cr1.concept_id_2 = c2.concept_id
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WHERE c2.standard_concept = 'S'
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AND c2.invalid_reason IS NULL
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AND cr1.relationship_id IN (
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'RxNorm replaced by'
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,'SNOMED replaced by'
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,'UCUM replaced by'
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,'Concept replaced by'
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,'ICD9P replaced by'
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,'LOINC replaced by'
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,'Concept same_as to'
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,'Concept was_a to'
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,'Concept alt_to to'
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)
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AND cr1.invalid_reason IS NULL
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UNION
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--concepts without 'map to' standard with 'is a' relation to standard
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SELECT DISTINCT c1.concept_id AS source_concept_id
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,c2.concept_id AS target_concept_id
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,c2.domain_id
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,NULL
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FROM (
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SELECT concept_id
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FROM dbo.concept
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WHERE (
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(
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standard_concept <> 'S'
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OR standard_concept IS NULL
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)
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OR invalid_reason IS NOT NULL
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)
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AND concept_id NOT IN (
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SELECT DISTINCT c1.concept_id
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FROM (
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SELECT concept_id
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FROM dbo.concept
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WHERE (
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(
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standard_concept <> 'S'
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OR standard_concept IS NULL
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)
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OR invalid_reason IS NOT NULL
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)
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) c1
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INNER JOIN dbo.concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1
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INNER JOIN dbo.concept c2 ON cr1.concept_id_2 = c2.concept_id
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WHERE c2.standard_concept = 'S'
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AND c2.invalid_reason IS NULL
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AND cr1.relationship_id IN (
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'Maps to'
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,'RxNorm replaced by'
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,'SNOMED replaced by'
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,'UCUM replaced by'
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,'Concept replaced by'
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,'ICD9P replaced by'
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,'LOINC replaced by'
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,'Concept same_as to'
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,'Concept was_a to'
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,'Concept alt_to to'
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)
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AND cr1.invalid_reason IS NULL
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)
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) c1
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INNER JOIN dbo.concept_relationship cr1 ON c1.concept_id = cr1.concept_id_1
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INNER JOIN dbo.concept c2 ON cr1.concept_id_2 = c2.concept_id
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WHERE c2.standard_concept = 'S'
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AND c2.invalid_reason IS NULL
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AND cr1.relationship_id IN ('Is a')
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AND cr1.invalid_reason IS NULL;
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GO
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-- Update the source_concept_mapping_occurrence column
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-- to contain a count to indicate the number of target_concept_ids
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-- map to that source_concept_id. This will be used elsewhere in
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-- the script to ensure that we generate new primary keys
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-- for the target tables when applicable
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UPDATE #concept_map
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SET #concept_map.source_concept_mapping_occurrence = A.[Rowcount]
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FROM #concept_map
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,(
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SELECT source_concept_id
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,domain_id
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,count(*) AS "rowcount"
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FROM #concept_map
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GROUP BY source_concept_id
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,domain_id
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) AS A
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WHERE #concept_map.source_concept_id = A.source_concept_id
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AND #concept_map.domain_id = A.domain_id
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IF OBJECT_ID('tempdb..#concept_map_distinct', 'U') IS NOT NULL
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DROP TABLE #concept_map_distinct;
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SELECT DISTINCT source_concept_id
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,domain_id
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,COUNT(*) AS "rowcount"
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INTO #concept_map_distinct
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FROM #concept_map
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GROUP BY source_concept_id
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,domain_id
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/*
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* V4 - Condition_Occurrence summary and mapping to #concept_map
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*/
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IF OBJECT_ID('tempdb..#classification_map', 'U') IS NOT NULL
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DROP TABLE #classification_map;
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SELECT *
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INTO #classification_map
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FROM
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(
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SELECT 'Condition_Occurrence' as TableName, ISNULL(LOWER(cm.domain_id), 'condition') AS "Domain", COUNT(*) AS "RowCount"
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FROM [SOURCE_CDMV4].[dbo].[Condition_Occurrence] as CO
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LEFT JOIN #concept_map as CM ON co.condition_concept_id = cm.source_concept_id
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GROUP BY ISNULL(LOWER(cm.domain_id), 'condition')
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UNION
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SELECT 'Drug_Exposure' as TableName, ISNULL(LOWER(cm.domain_id), 'drug') AS "Domain", COUNT(*) AS "RowCount"
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FROM [SOURCE_CDMV4].[dbo].[Drug_Exposure] as de
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LEFT JOIN #concept_map as CM ON de.drug_concept_id = cm.source_concept_id
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GROUP BY ISNULL(LOWER(cm.domain_id), 'drug')
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UNION
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SELECT 'Observation' as TableName, ISNULL(LOWER(cm.domain_id), 'observation') AS "Domain", COUNT(*) AS "RowCount"
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FROM [SOURCE_CDMV4].[dbo].[Observation] as o
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LEFT JOIN #concept_map as CM ON o.observation_concept_id = cm.source_concept_id
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GROUP BY ISNULL(LOWER(cm.domain_id), 'observation')
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UNION
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SELECT 'Procedure_Occurrence' as TableName, ISNULL(LOWER(cm.domain_id), 'procedure') AS "Domain", COUNT(*) AS "RowCount"
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FROM [SOURCE_CDMV4].[dbo].[Procedure_Occurrence] as po
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LEFT JOIN #concept_map as CM ON po.PROCEDURE_CONCEPT_ID = cm.source_concept_id
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GROUP BY ISNULL(LOWER(cm.domain_id), 'procedure')
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) AS A
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ORDER by A.[TableName], A.[Domain]
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select *
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from #classification_map
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order by [TableName], [Domain]
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select domain, SUM([RowCount])
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from #classification_map
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group by domain
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order by domain
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@ -0,0 +1,150 @@
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/*********************************************************************************
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# Copyright 2015 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: Use this script is used to help perform Quality Assurance activities
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||||
after you convert your OMOP V4 common data model to CDM V5.
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||||
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||||
last revised: 01 July 2015
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||||
author: Anthony Sena
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||||
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||||
This script was authored against SQL Server and will require conversion to other
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dialects. Please keep this in mind if you plan to use this against another RDBMS.
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||||
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||||
General Notes
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||||
---------------
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This script will use the metadata tables from the V4 and V5 tables to get a list
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of all of the tables from each database and the rowcounts for each table in an
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effort to help you see how your data has changed through the conversion process.
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In the results, we include a column to identify the tables that were part of
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the migration process in an effort to hone in on the key tables.
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There is a Part 2 of this QA script which will also show you how data moved
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amongst some specific tables.
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INSTRUCTIONS
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------------
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||||
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1. This script has placeholders for your CDM V4 and CDMV5 database/schema.
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||||
In order to make this file work in your environment, you
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||||
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
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||||
tokens you should use when doing your "FIND AND REPLACE" operation:
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||||
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||||
a. [SOURCE_CDMV4]
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b. [TARGET_CDMV5]
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||||
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2. Run the resulting script on your target RDBDMS.
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||||
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||||
*********************************************************************************/
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USE [TARGET_CDMV5]
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GO
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IF OBJECT_ID('tempdb..#v5_stats', 'U') IS NOT NULL
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DROP TABLE #v5_stats;
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SELECT
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DB_NAME() as DBName,
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t.NAME AS TableName,
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p.[Rows]
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INTO #v5_stats
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FROM
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sys.tables t
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INNER JOIN
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sys.indexes i ON t.OBJECT_ID = i.object_id
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INNER JOIN
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sys.partitions p ON i.object_id = p.OBJECT_ID AND i.index_id = p.index_id
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INNER JOIN
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sys.allocation_units a ON p.partition_id = a.container_id
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WHERE
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t.NAME NOT LIKE 'dt%' AND
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i.OBJECT_ID > 255 AND
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i.index_id <= 1
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GROUP BY
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t.NAME, i.object_id, i.index_id, i.name, p.[Rows]
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ORDER BY
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object_name(i.object_id)
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USE [SOURCE_CDMV4]
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GO
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IF OBJECT_ID('tempdb..#v4_stats', 'U') IS NOT NULL
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DROP TABLE #v4_stats;
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SELECT
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DB_NAME() as DBName,
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t.NAME AS TableName,
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p.[Rows]
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INTO #v4_stats
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FROM
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sys.tables t
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INNER JOIN
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sys.indexes i ON t.OBJECT_ID = i.object_id
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INNER JOIN
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sys.partitions p ON i.object_id = p.OBJECT_ID AND i.index_id = p.index_id
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INNER JOIN
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sys.allocation_units a ON p.partition_id = a.container_id
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WHERE
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t.NAME NOT LIKE 'dt%' AND
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i.OBJECT_ID > 255 AND
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i.index_id <= 1
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GROUP BY
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t.NAME, i.object_id, i.index_id, i.name, p.[Rows]
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ORDER BY
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object_name(i.object_id)
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DECLARE @MigrationTarget TABLE (TableName varchar(100))
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INSERT INTO @MigrationTarget SELECT 'care_site'
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INSERT INTO @MigrationTarget SELECT 'condition_era'
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INSERT INTO @MigrationTarget SELECT 'condition_occurrence'
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INSERT INTO @MigrationTarget SELECT 'death'
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INSERT INTO @MigrationTarget SELECT 'device_exposure'
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INSERT INTO @MigrationTarget SELECT 'drug_cost'
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INSERT INTO @MigrationTarget SELECT 'drug_era'
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INSERT INTO @MigrationTarget SELECT 'drug_exposure'
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INSERT INTO @MigrationTarget SELECT 'location'
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INSERT INTO @MigrationTarget SELECT 'measurement'
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INSERT INTO @MigrationTarget SELECT 'observation'
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INSERT INTO @MigrationTarget SELECT 'observation_period'
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INSERT INTO @MigrationTarget SELECT 'payer_plan_period'
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INSERT INTO @MigrationTarget SELECT 'person'
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INSERT INTO @MigrationTarget SELECT 'procedure_cost'
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INSERT INTO @MigrationTarget SELECT 'procedure_occurrence'
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INSERT INTO @MigrationTarget SELECT 'provider'
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INSERT INTO @MigrationTarget SELECT 'visit_occurrence'
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select
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ISNULL(V4.DBName, 'No V4 Table Equivalent') as "Database Name",
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v4.TableName,
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v4.rows,
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ISNULL(V5.DBName, 'No V5 Table Equivalent') as "Database Name",
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v5.TableName,
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v5.rows,
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CASE WHEN mt.TableName IS NULL THEN 'N' ELSE 'Y' END AS "Migration Target",
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ISNULL(v5.Rows, 0) - ISNULL(v4.Rows, 0) AS "Row Count Change"
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from #v4_stats as v4
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full outer join #v5_stats as v5 ON v4.TableName = v5.TableName
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left join @MigrationTarget mt on v5.TableName = mt.TableName
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order by v5.TableName
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,4 @@
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Common-Data-Model - Conversion from CDM v4 to CDM v5
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====================================================
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Scrips for converting data from the Common Data Model V4 to V5.
|
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File diff suppressed because it is too large
Load Diff
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