R/exportCohortDefinitionSet.R

In OHDSI/ROhdsiWebApi: Interacting With an OHDSI WebApi Instance

#' Export cohort definition set from WebAPI
#'
#' @param baseUrl                 The base URL for the WebApi instance, for example:
#'                                "http://server.org:80/WebAPI".
#' @param cohortIds               A set of cohortIds to fetch from WebApi.
#' @param generateStats           Should cohort inclusion rule statistics be generated?
#'
#' @details
#' Constructs a CohortDefinition set containing the following fields: \describe{
#' \item{atlasId}{The cohort ID in
#' ATLAS.} \item{cohortId}{a copy of the value in atlasId.} \item{cohortName}{The name of the cohort.}
#' \item{sql}{The cohort generation sql.} \item{json}{The cohort definition JSON.}
#' \item{logicDescription}{The cohort description.}}
#'
#' @export
exportCohortDefinitionSet <-
  function(baseUrl, cohortIds, generateStats = FALSE) {
    if (length(cohortIds) == 0) {
      stop("Must provide a non-zero length cohortIds vector.")
    }
    cohortDefinitionSet <- dplyr::tibble(
      atlasId = integer(),
      cohortId = integer(),
      cohortName = character(),
      sql = character(),
      json = character(),
      logicDescription = character(),
      generateStats = logical()
    )
    
    for (i in (1:length(cohortIds))) {
      cohortId <- cohortIds[i]
      message(paste("Fetching cohortId:", cohortId))
      object <-
        getCohortDefinition(cohortId = cohortId, baseUrl = baseUrl)
      json <- .toJSON(object$expression, pretty = TRUE)
      sql <-
        getCohortSql(
          baseUrl = baseUrl,
          cohortDefinition = object,
          generateStats = generateStats
        )
      cohortDefinitionSet <- dplyr::bind_rows(
        cohortDefinitionSet,
        dplyr::tibble(
          atlasId = cohortId,
          cohortId = cohortId,
          cohortName = object$name,
          sql = sql,
          json = json,
          logicDescription = ifelse(is.null(object$description), NA, object$description),
          generateStats=as.logical(generateStats)
        )
      )
    }
    return(cohortDefinitionSet)
  }