buildCdmSource: buildCdmSource

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

Description

buildCdmSource

Usage

buildCdmSource(sourceKey, sourceName = NULL, dbms = NULL,
  cdmDatabaseSchema = NULL, resultsDatabaseSchema = NULL,
  vocabDatabaseSchema = cdmDatabaseSchema, connectionString = NULL,
  sourceId = NULL, priority = 0, user = NULL, password = NULL,
  connectionDetails = NULL)

Arguments

sourceKey	A unique string identifier for the data source
sourceName	The name of the CDM source
dbms	The dbms of the CDM source
cdmDatabaseSchema	The name of the schema where CDM data sits
resultsDatabaseSchema	The name of the schema where results data sits
vocabDatabaseSchema	The name of the schema where the vocabulary sits
connectionString	The JDBC connection string to the CDM source; REQUIRED if trying to insert a CDM source (insertCdmSources), unnecessary when trying to remove a CDM source (removeCdmSources)
sourceId	An optional value to pre-specify the database index identifier for the data source. If left NULL, this is either auto-generated by the Repo database, or the next available source_id is obtained.
priority	1 = the source become the one Atlas uses by default (e.g. to show record counts) 0 = the source will not become the one Atlas uses by default (e.g. to show record counts)
user	(OPTIONAL) The user name for the connection to the CDM. Only used if encryption of source credentials is enabled.
password	(OPTIONAL) The password for the connection to the CDM. Only used if encryption of source credentials is enabled.
connectionDetails	A connectionDetails object created using DatabaseConnector of this source

Details

Creates a CDM source object for use in the package with necessary connection information. If using insertCdmSources then connectionString will need to be defined.

Value

A CDM source object with the necessary parameters to fulfill SOURCE and SOURCE_DAIMON

Author(s)

Ajit Londhe

Examples

## When building a CDM source to insert, and to make it top priority:

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")

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