R/createPrunedTables.r

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

#' @title Create pruned CDM and Vocab tables.
#'
#' @description This function creates the pruned cdm and vocab tables by keeping only those rows from
#'              the original tables for given concept_ids. (Eunomia support)
#'
#' @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.
#'                           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 eventConceptId      A vector of concept_ids returned from \code{getEventConceptId}.
#' @param cdmVersion The version of your CDM.  Currently "5.3.1" and "5.4.0".
#'
#'@export


createPrunedTables <-
  function(connectionDetails,
           cdmSchema,
           eventConceptId,
           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, "/create_pruned_tables.sql"),
      packageName = "ETLSyntheaBuilder",
      dbms        = connectionDetails$dbms,
      cdm_schema = cdmSchema,
      event_concept_id = eventConceptId
    )

    conn <- DatabaseConnector::connect(connectionDetails)

    DatabaseConnector::executeSql(conn, sql)

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