R/restoreCDMTables.r

In OHDSI/ETL-Synthea: A Builder for Converting the Synthea Data to the OMOP CDM

#' @title Restore the CDM (undo the pruning).
#'
#' @description This function undoes the pruning by renaming (the *_orig tables are given their names back).
#'
#' @param connectionDetails  An R object of type\cr\code{connectionDetails} created using the
#'                                     function \code{createConnectionDetails} in the
#'                                     \code{DatabaseConnector} package.
#' @param cdmSchema  The name of the database schema that contains the CDM
#'                                     instance.  Requires read and write permissions to this database. On SQL
#'                                     Server, this should specify both the database and the schema,
#'                                     so for example 'cdm_instance.dbo'.
#' @param cdmVersion The version of your CDM.  Currently "5.3.1" and "5.4.0" are supported.
#'@export


restoreCDMTables <-
  function(connectionDetails, cdmSchema, cdmVersion)
  {
    if (cdmVersion == "5.3.1")
      sqlFilePath <- "cdm_version/v531"
    else if (cdmVersion == "5.4.0")
      sqlFilePath <- "cdm_version/v540"
    else
      stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"5.4.0\"")

    sql <- SqlRender::loadRenderTranslateSql(
      sqlFileName = paste0(sqlFilePath, "/restore_cdm_tables.sql"),
      packageName = "ETLSyntheaBuilder",
      dbms        = connectionDetails$dbms,
      cdm_schema  = cdmSchema
    )
    writeLines("Running restore_cdm_tables.sql")
    conn <- DatabaseConnector::connect(connectionDetails)
    DatabaseConnector::executeSql(conn, sql)
    on.exit(DatabaseConnector::disconnect(conn))
  }