R/updateExperimentSampleData.R

In ceparman/Core5.3: Core API fucntions

#' updateExperimentSampleData - Update experiment sample assay data.
#'
#' \code{updateExperimentSampleData} Update experiment sample assay data.
#'
#' @param coreApi coreApi object with valid jsessionid
#' @param assayType entity type to get as character string
#' @param experimentSamplebarcode User provided barcode as a character string
#' @param assayAttributeValues 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,
#'        $response contains the entire http response
#' @examples
#'\dontrun{
#' api<-CoreAPI("PATH TO JSON FILE")
#' login<- CoreAPIV2::authBasic(api)
#' response<-CoreAPIV2::updateExperimentSampleData(login$coreApi,assayType,
#'                   experimentSampleBarcode,assayAtributeValues)
#' updatedEntity <- response$entity
#' CoreAPIV2::logOut(login$coreApi ) response<- CoreAPI::authBasic(coreApi)
#' }
#'@author Craig Parman ngsAnalytics, ngsanalytics.com
#'@description \code{updateExperimentSampleData} Update experiment sample assay data.



updateExperimentSampleData <-
  function (coreApi,
            assayType,
            experimentSamplebarcode,
            assayAttributeValues,
            useVerbose = FALSE)
    
  {
    #Clean Names of assay
    
    assayType <- CoreAPIV2::ODATAcleanName(assayType)
    
    
    #Clean Names of attributes
    
    
    for (i in 1:length(names(assayAttributeValues)))
    {
      names(assayAttributeValues)[i] <-
        CoreAPIV2::attributeCleanName(names(assayAttributeValues)[i])
      
    }
    
    
    
    body <- assayAttributeValues   #needs to be unboxed
    
    resource <- paste0(assayType, "_DATA")
    query <- paste0("('", experimentSamplebarcode, "')")
    
    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)
    
  }