R/getExperimentSamples.R

In ceparman/Core5.3: Core API fucntions

#' getExperimentSamples - Gets experiment sample barcodes from experiment identified by barcode.
#'
#'\code{getExperimentSamples}  Gets experiment samples from experiment identified by barcode.
#'
#'@param coreApi coreApi object with valid jsessionid
#'@param experimentType experiment entity type to get
#'@param barcode barcode of entity to get
#'@param useVerbose TRUE or FALSE to indicate if verbose options should be used in http POST
#'@return returns a list $entity contains entity information, $response contains the entire http response
#'@export
#'@examples
#'\dontrun{
#' api<-CoreAPIV2::CoreAPI("PATH TO JSON FILE")
#' login<- CoreAPIV2::authBasic(api)
#' response<-  CoreAPIV2::getExperimentSamples(login$coreApi,"entityType","barcode")
#' experimentsampleBarcodes <- response$entity
#' CoreAPIV2:logOut(login$coreApi)
#' }
#'@author Craig Parman ngsAnalytics, ngsanalytics.com
#'@description \code{ getExperimentSamples}  Gets experiment sample barcodes from experiment identified by experiment barcode. 





getExperimentSamples <-
  function (coreApi,
            experimentType,
            barcode,
            useVerbose = FALSE)
    
  {
    #clean the name for ODATA
    
    resource <- CoreAPIV2::ODATAcleanName(experimentType)
    
    
    query   <-
      paste0("('", barcode, "')/EXPERIMENT_SAMPLES")
    
    
    header <-
      c('Content-Type' = "application/json;odata.metadata=full", Accept = "application/json")
    
    
    
    response <-
      CoreAPIV2::apiGET(
        coreApi,
        resource = resource,
        query = query,
        headers = header,
        useVerbose = useVerbose
      )
    
    
    
    
    list(entity = unlist((
      lapply(
        response$content,
        FUN = function(x)
          x$Barcode
      )
    )), response = response)
    
  }