R/updateExperimentSampleRawData.R

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

#' updateExperimentSampleRawData - Update experiment sample raw data.
#'
#' \code{updateExperimentSampleRawData} Update experiment sample raw data.
#'
#' @param coreApi coreApi object with valid jsessionid
#' @param experimentContainerBarcode User provided barcode as a character string
#' @param rawDataCellNum cell (well) number of container
#' @param rawDataValues assay attributes as a list of key-values pairs
#' @param ... additional arguments passed to \code{apiPUT}
#' @export
#' @return List of length 2, containing \code{entity} and \code{response} objects:
#' \itemize{
#'  \item{\code{entity}} is the HTTP response content of updated sample raw data.
#'  \item{\code{response}} is the entire HTTP response.
#' }
#' @examples
#' \dontrun{
#' api <- coreAPI("PATH TO JSON FILE")
#' login <- authBasic(api)
#' response <- updateExperimentSampleRawData(login$coreApi,
#'   experimentContainerBarcode = "BTCR1", rawDataCellNum = 1,
#'   rawDataValues = list(DATA_VALUE = 100, CI_ACCEPT = FALSE)
#' )
#'
#' updatedEntity <- response$entity
#' logOut(login$coreApi)
#' response <- authBasic(coreApi)
#' }
#' @author Craig Parman info@ngsanalytics.com
#' @author Natasha Mora natasha.mora@thermofisher.com
#' @author Scott Russell scott.russell@thermofisher.com
#' @description \code{updateExperimentSampleRawData} Update experiment sample assay raw data.

updateExperimentSampleRawData <-
  function(coreApi,
             experimentContainerBarcode,
             rawDataCellNum,
             rawDataValues,
             ...) {
    # get the current values
    resource <- "RAW_DATA"

    query <- paste0(
      "?$filter=CI_CELL%20eq%20",
      as.integer(rawDataCellNum),
      "%20and%20EXPERIMENT_CONTAINER/Name%20eq%20'",
      experimentContainerBarcode,
      "'"
    )

    experiment <-
      apiGET(
        coreApi,
        resource = resource,
        query = query,
        useVerbose = TRUE
      )

    body <- experiment$content[[1]]

    for (i in 1:length(rawDataValues))
    {
      eval(parse(
        text =
          paste0(
            "body$", names(rawDataValues)[i],
            "<-", rawDataValues[i]
          )
      ))
    }

    resource <- paste0("RAW_DATA")
    query <- paste0("(", body$Id, ")")
    header <- c("Content-Type" = "application/json", "If-Match" = "*")

    response <-
      apiPUT(
        coreApi,
        resource = resource,
        query = query,
        body = body,
        encode = "raw",
        headers = header,
        ...
      )


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