README.md

In OHDSI/CdmAtlasCutover: A package to prepare CDM databases for usage in Atlas/WebAPI

CdmAtlasCutover

Introduction

This R package is designed to support the management of multiple CDM sources in Atlas. CDM sources can be removed, prepared for release, and released using this package.

Features

• Remove CDM sources from Ohdsi Repository Schema
• Remove records in Ohdsi Repository's SOURCE and SOURCE_DAIMON tables
• Clear Atlas cohort assets for the sources to be remvoed
• Prepare CDM sources for release
• Create tables in results database schema that Atlas requires
  • Cohort inclusion tables
  • Cohort feature tables
  • Heracles tables
  • Feasibility tables
  • IR tables
• Add sources to Ohdsi Repository Schema
• Add records to SOURCE and SOURCE_DAIMON tables
• Specify if source is to be set at high priority
• Refresh sources in WebAPI to reflect changes in SOURCE and SOURCE_DAIMON
• Code can be executed through the package or written to SQL files for manual execution
• Written using OHDSql, so should work in all dialects supported by SqlRender.

Examples

oldCdmSources <- list(
  buildCdmSource(sourceKey = "TestDb_V123", sourceName = "Test Database v123", dbms = "redshift", cdmDatabaseSchema = "cdm",
    resultsDatabaseSchema = "ohdsi_results", vocabDatabaseSchema = "cdm", priority = 1,
    connectionString = "jdbc:redshift://some-redshift-cluster:5439/testdb_v123?user=some-user&password=some-password")
  )

## if not using encrypted credentials in WebAPI  
newCdmSources <- list(
  buildCdmSource(sourceKey = "TestDb_V456", sourceName = "Test Database v456", dbms = "redshift", cdmDatabaseSchema = "cdm",
    resultsDatabaseSchema = "ohdsi_results", vocabDatabaseSchema = "cdm", priority = 1,
    connectionString = "jdbc:redshift://some-redshift-cluster:5439/testdb_v456?user=some-user&password=some-password")
  )

## if using encrypted credentials in WebAPI
newCdmSources <- list(
  buildCdmSource(sourceKey = "TestDb_V456", sourceName = "Test Database v456", dbms = "redshift", cdmDatabaseSchema = "cdm",
    resultsDatabaseSchema = "ohdsi_results", vocabDatabaseSchema = "cdm", priority = 1,
    connectionString = "jdbc:redshift://some-redshift-cluster:5439/testdb_v456"),
    user = some-user, password = some-password
  )

## remove old version of a CDM data source  
removeCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = oldCdmSources, sqlOnly = TRUE)

## prepare new CDM data source by ensuring all necessary tables are available
createOhdsiResultsTables(cdmSources = newCdmSources, sqlOnly = TRUE)

## add new CDM data source
insertCdmSources(repoConnectionDetails = repoConnectionDetails, cdmSources = newCdmSources, sourceIdx = TRUE, 
                 daimonIdx = TRUE, sqlOnly = TRUE)

## refresh WebAPI / Atlas sources
refreshAtlasSources(baseUrl = "http://api.ohdsi.org:80/WebAPI")

Technology

CdmAtlasCutover is an R package

System Requirements

Requires R.

Dependencies

CdmAtlasCutover depends on the OHDSI DatabaseConnector and SqlRender packages as well as the StringR and HTTR packages from CRAN.

Getting Started

Use the following commands in R to install the DatabaseConnector package:

r install.packages("devtools") devtools::install_github("OHDSI/CdmAtlasCutover")

Getting Involved

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

CdmAtlasCutover is licensed under Apache License 2.0.

Development

CdmAtlasCutover is being developed in RStudio.

OHDSI/CdmAtlasCutover documentation built on Sept. 28, 2019, 11:14 a.m.