R/createExperiment.R

In ceparman/Core5.3: Core API fucntions

#' createExperiment - Create a new instance of an experiment.
#' 
#' \code{createExperiment} Creates a new instance of an entity.
#' @param coreApi coreApi object with valid jsessionid
#' @param experimentType experiment type to get as character string
#' @param assayType assay type
#' @param assayBarcode assay barcode
#' @param protocolType protocol type
#' @param protocolBarcode protocol barcode
#' @param body values for experiment attributes and associations as a  list of key-values pairs
#' @param useVerbose Use verbose communication for debugging
#' @export
#' @return RETURN returns a list $entity contains entity information, $response contains the entire http response
#' @examples
#'\dontrun{
#' api<-CoreAPIV2::coreApi("PATH TO JSON FILE")
#' login<- CoreAPIV2::authBasic(api)
#' experiment<-CoreAPIV2::createExperiment(login$coreApi,"Experiment_Type","Assaybarcode","Protocolbarcode")
#' CoreAPIV2::logOut(login$coreApi )
#' }
#'@author Craig Parman ngsAnalytics, ngsanalytics.com
#'@description \code{createExperiment} Creates a new experiment.

createExperiment <-
  function (coreApi,
            experimentType,
            assayType,
            assayBarcode,
            protocolType,
            protocolBarcode,
            body = NULL,
            useVerbose = FALSE)
    
  {
    #clean the names for ODATA
    
    experimentType <- CoreAPIV2::ODATAcleanName(experimentType)
    assayType <- CoreAPIV2::ODATAcleanName(assayType)
    protocolType <- CoreAPIV2::ODATAcleanName(protocolType)
    
    assayRef <-
      list('EXPERIMENT_ASSAY@odata.bind' = paste0("/", assayType, "('", assayBarcode, "')"))
    
    protocolRef <-
      list(
        'EXPERIMENT_PROTOCOL@odata.bind' = paste0("/", protocolType, "('", protocolBarcode, "')")
      )
    
    fullBody <-
      jsonlite::toJSON(c(body, assayRef, protocolRef), auto_unbox = TRUE)
    
    
    
    
    headers <- c('Content-Type' = "application/json")
    
    response <-
      CoreAPIV2::apiPOST(
        coreApi,
        resource = experimentType,
        body = fullBody,
        encode = "json",
        headers = headers ,
        special = NULL,
        useVerbose = useVerbose
      )
    
    
    
    list(entity = httr::content(response), response = response)
    
  }