R/updateExperimentSampleRawData.R

In ceparman/Core5.3: Core API fucntions

#' 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 cellNum cell (well) number of container
#' @param values assay attributes as a list of key-values pairs
#' @param useVerbose Use verbose communication for debugging
#' @export
#' @return RETURN returns a list $entity contains entity information,
#'        $response contains the entire http response
#' @examples
#'\dontrun{
#' api<-CoreAPI("PATH TO JSON FILE")
#' login<- CoreAPIV2::authBasic(api)
#' response<-updateExperimentSampleRawData(login$coreApi,"contBarcode",cellNum=1,
#'                    values = list(DATA_VALUE = 100 ,CI_ACCEPT = FALSE)
#'
#' updatedEntity <- response$entity
#' CoreAPIV2::logOut(login$coreApi ) response<- CoreAPI::authBasic(coreApi)
#' }
#'@author Craig Parman ngsAnalytics, ngsanalytics.com
#'@description \code{updateExperimentSampleRawData} Update experiment sample assay raw data.



updateExperimentSampleRawData <-
  function (coreApi,
            experimentContainerBarcode,
            cellNum,
            values,
            useVerbose = FALSE)
    
  {
    
  #get the current values  
    
    resource <- "RAW_DATA"
    
    
    query   <- paste0(
      
      "?$filter=CI_CELL%20eq%20",
      as.integer(cellNum),
      "%20and%20EXPERIMENT_CONTAINER/Name%20eq%20'",
      experimentContainerBarcode,
      "'"
    )
    
    
    header <- c(Accept = "application/json")
    
    
    
    
    response <-
      CoreAPIV2::apiGET(
        coreApi,
        resource = resource,
        query = query,
        headers = header,
        useVerbose = useVerbose
      )
    
    
    body <- response$content[[1]]
    
    
    for (i in 1:length(values))
    {
      
      eval(parse(text=
                   paste0("body$",names(values)[i],
                          "<-",values[i])
                 ))
    }
   
    
  
    resource <- paste0("RAW_DATA")
    query <- paste0("(", body$Id, ")")
    
    header <- c("Content-Type" = "application/json", "If-Match" = "*")
    
    response <-
      CoreAPIV2::apiPUT(
        coreApi,
        resource = resource,
        query = query,
        body = body,
        encode = "raw",
        headers = header,
        useVerbose = useVerbose
      )
    
    
    list(entity = httr::content(response), response = response)
    
  }