R/CreateSyntheaTables.r

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

#' @title Create Synthea Tables.
#'
#' @description This function creates all Synthea tables.
#'
#' @param connectionDetails  An R object of type\cr\code{connectionDetails} created using the
#'                                     function \code{createConnectionDetails} in the
#'                                     \code{DatabaseConnector} package.
#' @param syntheaSchema  The name of the database schema that will contain the Synthea
#'                                     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 syntheaVersion The version of Synthea used to generate the csv files.
#'                       Currently "2.7.0", "3.0.0", "3.1.0", and "3.2.0" are is supported.
#'
#'@export



CreateSyntheaTables <-
  function(connectionDetails,
           syntheaSchema,
           syntheaVersion = "2.7.0")
  {
    if (syntheaVersion == "2.7.0")
      sqlFilePath <- "synthea_version/v270"
    else if (syntheaVersion == "3.0.0")
      sqlFilePath <- "synthea_version/v300"
    else if (syntheaVersion == "3.1.0")
      sqlFilePath <- "synthea_version/v310"
    else if (syntheaVersion == "3.2.0")
      sqlFilePath <- "synthea_version/v320"
    else
      stop(
        "Invalid synthea version specified. Currently \"2.7.0\", \"3.0.0\", \"3.1.0\" and \"3.2.0\" are supported."
      )

    sqlFilename <-
      paste0(sqlFilePath, "/", "create_synthea_tables.sql")

    translatedSql <- SqlRender::loadRenderTranslateSql(
      sqlFilename     = sqlFilename,
      packageName     = "ETLSyntheaBuilder",
      dbms            = connectionDetails$dbms,
      synthea_schema  = syntheaSchema
    )

    writeLines(paste0("Running ", sqlFilename))

    conn <- DatabaseConnector::connect(connectionDetails)

    DatabaseConnector::executeSql(conn, translatedSql)

    on.exit(DatabaseConnector::disconnect(conn))

  }