R/LoadVocabFromSchema.r

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

#' @title Load Vocabulary Tables From a Preexisting Schema.
#'
#' @description This function populates all Vocabulary tables with data from Vocabulary tables in a specified schema.
#'
#' @details This function assumes \cr\code{createCDMTables()} has already been run and \cr\code{cdmSourceSchema} has all required Vocabulary tables.
#'
#' @param connectionDetails  An R object of type\cr\code{connectionDetails} created using the
#'                                     function \code{createConnectionDetails} in the
#'                                     \code{DatabaseConnector} package.
#' @param cdmSourceSchema  The name of the database schema that already contains the Vocabulary
#'                                     tables to copy.  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 cdmTargetSchema  The name of the database schema into which to copy the Vocabulary
#'                                     tables.  Requires read and write permissions to this database. On SQL
#'                                     Server, this should specifiy both the database and the schema,
#'                                     so for example 'cdm_instance.dbo'.
#'
#'@export

LoadVocabFromSchema <-
  function(connectionDetails,
           cdmSourceSchema,
           cdmTargetSchema)
  {
    vocabTableList <-
      c(
        "concept",
        "concept_ancestor",
        "concept_class",
        "concept_relationship",
        "concept_synonym",
        "domain",
        "drug_strength",
        "relationship",
        "source_to_concept_map",
        "vocabulary"
      )

    conn <- DatabaseConnector::connect(connectionDetails)

    for (tableName in vocabTableList) {
      sql <-
        paste0(
          "INSERT INTO ",
          cdmTargetSchema,
          ".",
          tableName,
          " SELECT * FROM ",
          cdmSourceSchema,
          ".",
          tableName
        )
      writeLines(paste0("Copying: ", tableName))
      DatabaseConnector::executeSql(
        conn,
        sql,
        profile = FALSE,
        progressBar = TRUE,
        reportOverallTime = TRUE
      )
    }
    on.exit(DatabaseConnector::disconnect(conn))
  }