R/CreateVocabTables.R

In OHDSI/ETL-HealthVerityBuilder: A Builder for Converting the HealthVerity Data Model to the OMOP CDM

# Copyright 2017 Observational Health Data Sciences and Informatics
#
# This file is part of healthVerityBuildr
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

#' Run the vocab queries to create the vocab mapping tables.
#' @param connectionDetails  An R object of type\cr\code{connectionDetails} created using the
#'                                     function \code{createConnectionDetails} in the
#'                                     \code{DatabaseConnector} package.
#' @param cdmDatabaseSchema  The name of the database schema that contains the OMOP CDM
#'                                     instance.  Requires read permissions to this database. On SQL
#'                                     Server, this should specifiy both the database and the schema,
#'                                     so for example 'cdm_instance.dbo'.
#' @param vocabDatabaseSchema  The name of the database schema that contains the OMOP CDM Vocabulary
#'                                     instance.  Requires read permissions to this database. On SQL
#'                                     Server, this should specifiy both the database and the schema,
#'                                     so for example 'vocab_instance.dbo'.
#' @param oracleTempSchema             For Oracle only: the name of the database schema where you want
#'                                     all temporary tables to be managed. Requires create/insert
#'                                     permissions to this database.
#'
#' @export
createVocabTables <- function(connectionDetails,
                              cdmDatabaseSchema,
                              vocabDatabaseSchema,
                              oracleTempSchema = NULL){

  conn <- DatabaseConnector::connect(connectionDetails)
  writeLines("Running vocab queries and creating mapping tables")
  sqlFile <- "VocabTables.sql"

  writeLines(paste("-Running", sqlFile))
  sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFile,
                                           packageName = "healthVerityBuildr",
                                           dbms = connectionDetails$dbms,
                                           oracleTempSchema = oracleTempSchema,
                                           cdm_schema = cdmDatabaseSchema,
                                           vocab_schema = vocabDatabaseSchema)
  DatabaseConnector::executeSql(conn, sql, progressBar = TRUE, reportOverallTime = TRUE)
  dbDisconnect(conn)
}