R/TruncateEventTables.r

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

#' @title Truncate Event Tables.
#'
#' @description This function truncates CDM tables, excluding Vocabulary tables.
#'
#' @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 OMOP CDM
#'                   instance.  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


TruncateEventTables <- function(connectionDetails, cdmSchema)
{
  eventTables <- c(
    "CARE_SITE",
    "CDM_SOURCE",
    "COHORT",
    "COHORT_ATTRIBUTE",
    "CONDITION_ERA",
    "CONDITION_OCCURRENCE",
    "COST",
    "DEATH",
    "DEVICE_EXPOSURE",
    "DOSE_ERA",
    "DRUG_ERA",
    "DRUG_EXPOSURE",
    "FACT_RELATIONSHIP",
    "LOCATION",
    "MEASUREMENT",
    "METADATA",
    "NOTE",
    "NOTE_NLP",
    "OBSERVATION",
    "OBSERVATION_PERIOD",
    "PAYER_PLAN_PERIOD",
    "PERSON",
    "PROCEDURE_OCCURRENCE",
    "PROVIDER",
    "SPECIMEN",
    "VISIT_DETAIL",
    "VISIT_OCCURRENCE"
  )

  conn <- DatabaseConnector::connect(connectionDetails)
  allTables <- DatabaseConnector::getTableNames(conn, cdmSchema)
  tablesToTruncate <- allTables[which(allTables %in% eventTables)]
  sql <-
    paste(
      "truncate table @cdm_schema.",
      tablesToTruncate,
      ";",
      collapse = "\n",
      sep = ""
    )
  sql <- SqlRender::render(sql, cdm_schema = cdmSchema)
  sql <-
    SqlRender::translate(sql, targetDialect = connectionDetails$dbms)
  DatabaseConnector::executeSql(conn, sql)
  on.exit(DatabaseConnector::disconnect(conn))
}