R/createExperimentSample.R

In ceparman/Core5.3: Core API fucntions

#' createExperimentSample - Create a new experiment sample from a sample lot.
#' 
#' \code{createExperimentSample} Creates a new instance of an entity.
#' @param coreApi coreApi object with valid jsessionid
#' @param experimentType experiment type to get as character string
#' @param experimentBarcode experiment barcode
#' @param sampleLotBarcode barcode of sample to add to experiment 
#' @param body values for sample 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, $response contains the entire http response
#' @examples
#'\dontrun{
#' api<-CoreAPIV2::coreApi("PATH TO JSON FILE")
#' login<- CoreAPIV2::authBasic(api)
#' item<-CoreAPIV2::createExperimentSample(login$coreApi,"Experiment_Type",
#'        "Assaybarcode","ProtocolBarcode")
#' CoreAPIV2::logOut(login$coreApi )
#' }
#'@author Craig Parman ngsAnalytics, ngsanalytics.com
#'@description \code{createExperimentSample} Creates a new experiment sample fomr a sample lot.

createExperimentSample <-
  function (coreApi,
            experimentType,
            experimentBarcode,
            sampleLotBarcode,
            body = NULL,
            useVerbose = FALSE)
    
  {
    #clean the names for ODATA
    
    experimentType <- CoreAPIV2::ODATAcleanName(experimentType)
    
    experimentSampleType <- paste0(experimentType, "_SAMPLE")
    
    exptRef <-
      list('EXPERIMENT@odata.bind' = paste0("/", experimentType, "('", experimentBarcode, "')"))
    
    entityRef <-
      list('ENTITY@odata.bind' = paste0("/ENTITY('", sampleLotBarcode, "')"))
    
    fullBody <-
      jsonlite::toJSON(c(body, exptRef, entityRef), auto_unbox = TRUE)
    
    
    
    headers <-
      c('Content-Type' = "application/json;odata.metadata=full")
    
    response <-
      CoreAPIV2::apiPOST(
        coreApi,
        resource = experimentSampleType,
        body = fullBody,
        encode = "json",
        headers = headers ,
        special = NULL,
        useVerbose = useVerbose
      )
    
    
    
    list(entity = httr::content(response), response = response)
    
  }