R/setCellContents.R

In AmundsenJunior/pfsrsdk: Functions for interacting with Platform for Science APIs

#' setCellContents -  Puts a sample lot in a container Cell.
#'
#' \code{setCellContents} Puts a sample lot in a container cell.
#' @param coreApi coreApi object with valid jsessionid
#' @param containerType container type
#' @param containerBarcode barcode of a container that IS NOT assigned to an experiment.
#' @param containerCellId container cell id. (In PFS 5.3.8 (semVer 2.7.1) if multi-wells are used, cell A1 has to be filled or filled first in order to setCellContents in other cells.)
#' @param sampleLotType sample lot type
#' @param sampleLotBarcode barcode of lot to add to cell
#' @param amount amount to add (numeric)
#' @param amountUnit units
#' @param concentration (numeric)
#' @param concentrationUnit concentration units
#' @param ... additional arguments passed to \code{apiPOST}
#' @export
#' @return List of length 2, containing \code{content} and \code{response} objects:
#' \itemize{
#'  \item{\code{content}} is the HTTP response content of updated cell information.
#'  \item{\code{response}} is the entire HTTP response.
#' }
#' @examples
#' \dontrun{
#' api <- coreAPI("PATH TO JSON FILE")
#' login <- authBasic(api)
#' cell <- setCellContents(login$coreAPI, containerType, containerBarcode, containerCellId,
#'   sampleLotType, sampleLotBarcode, amount, amountUnit, concentration,
#'   concentrationUnit,
#'   useVerbose = FALSE
#' )
#' logOut(login$coreApi)
#' }
#' @author Craig Parman info@ngsanalytics.com
#' @author Natasha Mora natasha.mora@thermofisher.com
#' @author Scott Russell scott.russell@thermofisher.com
#' @description \code{setCellContents} - Puts a cell lot in a container cell.

setCellContents <-
  function(coreApi,
             containerType,
             containerBarcode,
             containerCellId,
             sampleLotType,
             sampleLotBarcode,
             amount,
             amountUnit,
             concentration,
             concentrationUnit,
             ...) {
    # clean the name for ODATA
    containerType <- odataCleanName(containerType)

    containerCellId <- as.numeric(containerCellId)
    amount <- as.numeric(amount)
    concentration <- as.numeric(concentration)

    if ((grepl("[0-2]+\\.[0-9]+\\.[0-9]+", coreApi$semVer) & (!(amount %% 1 == 0) | !(concentration %% 1 == 0)))) {
      stop(paste0("Amount: ", amount, " and Concentration: ", concentration, " values have to be of type numeric with no decimal places."))
    }

    # get ID for lot number
    lotID <-
      getEntityByBarcode(
        coreApi,
        entityType = sampleLotType,
        barcode = sampleLotBarcode,
        fullMetadata = FALSE,
        useVerbose = TRUE
      )$entity$Id

    body <- list()

    cells <-
      list(c(
        list(
          cellId = jsonlite::unbox(containerCellId),
          amount = jsonlite::unbox(amount),
          amountUnit = jsonlite::unbox(amountUnit),

          contents = list(c(
            list(
              lotId = jsonlite::unbox(lotID),
              concentration = jsonlite::unbox(concentration),
              concentrationUnit = jsonlite::unbox(concentrationUnit)
            )
          ))
        )
      ))

    body[["cells"]] <- cells

    query <-
      paste0(
        "CONTAINER('",
        containerBarcode,
        "')/pfs.Container.SetCellContents"
      )

    response <-
      apiPOST(
        coreApi,
        resource = query,
        body = body,
        encode = "json",
        ...
      )

    list(entity = response$content, response = response$response)
  }