tests/testthat/test_create.R

In ceparman/Core5.3: Core API fucntions

context("Tests for create")



rm(list=ls())

verbose <- FALSE

#setup to work with environment

instance <- "test_environments/5-2-2.json"


     test_that(paste("test login,create sample and lot", instance),
            {

              verbose <- FALSE
              api <- CoreAPIV2::coreAPI(instance)


              con<- CoreAPIV2::authBasic(api,useVerbose=verbose)

              expect_match(api$coreUrl,con$coreApi$coreUrl,all=verbose)
              expect_that(is.null(con$coreApi$jsessionId),equals(FALSE))


              out<-CoreAPIV2::getEntityMetadata(con$coreApi,"PATIENT_SAMPLE",useVerbose = FALSE)


              body<-out$template


              body[["SOURCE_LAB"]] <- "ACME"

              body[["NUMBER"]] <- 3

              body[["REQUESTOR"]] <- "Dr Strange"


             body[["CI_FILE"]] <- NULL
              body[["IMAGE_FILE"]] <- NULL

              body[["SAMPLE_ENZYME@odata.bind"]] <- "/ENZYME('ENZ1')"
              
  

              return<-CoreAPIV2::createEntity(coreApi = con$coreApi,entityType = "PATIENT_SAMPLE",body=body,useVerbose = TRUE)

              barcode<-return$entity$Barcode


              b<-CoreAPIV2::getEntityByBarcode(con$coreApi,"PATIENT_SAMPLE",barcode,useVerbose=verbose)$entity

              expect_match(b$Barcode,barcode,all=verbose)

              expect_match(b$SOURCE_LAB,"ACME",all=verbose)


          #test update attributes
          
              #you don't include file attribute names in updates

              updateValues<-list(SOURCE_LAB = "My Lab",REQUESTOR = "you") #,CI_FILE <- NULL, IMAGE_FILE  <- NULL)
              

              ue<-CoreAPIV2::updateEntityAttributes(con$coreApi,"PATIENT_SAMPLE",barcode,updateValues,useVerbose=FALSE)

              expect_match(ue$entity$SOURCE_LAB,"My Lab",all=verbose)


        #test update associations    
              
              context <- "SAMPLE_ENZYME"
              
              updateValues<-list(SAMPLE_ENZYME = c("ENZYME", "ENZ2"))
              
              us<- CoreAPIV2::updateEntityAssociations(con$coreApi,"PATIENT_SAMPLE",barcode,updateValues,useVerbose=FALSE)
              

              
              as<-CoreAPIV2::getEntityAssociations(con$coreApi,"PATIENT_SAMPLE",barcode,context,fullMetadata = TRUE, useVerbose=FALSE)
              
              expect_match(as$entity[[1]]$Barcode,"ENZ2")
              
            #Change it back
              
              updateValues<-list(SAMPLE_ENZYME = c("ENZYME", "ENZ1"))
              
              us<- CoreAPIV2::updateEntityAssociations(con$coreApi,"PATIENT_SAMPLE",barcode,updateValues,useVerbose=FALSE)
              
              as<-CoreAPIV2::getEntityAssociations(con$coreApi,"PATIENT_SAMPLE",barcode,context,fullMetadata = TRUE, useVerbose=FALSE)
              
              expect_match(as$entity[[1]]$Barcode,"ENZ1")
              
              

          #create sample lot

              sl<-CoreAPIV2::createSampleLot(con$coreApi,sampleType="PATIENT_SAMPLE",sampleBarcode=b$Barcode,body=NULL,
                                         useVerbose=TRUE)

              expect_equal(is.numeric(sl$entity$Sequence),TRUE,all=verbose)

              expect_equal( httr::status_code(sl$response),201,all=verbose)


              logout<-CoreAPIV2::logOut(api,useVerbose = verbose)
              expect_match(logout$success,"Success")

              })

     test_that(paste("create object that requires cleaned name for ODATA", instance),
               {

                 verbose <- FALSE
                 api <- CoreAPIV2::coreAPI(instance)

                 con<- CoreAPIV2::authBasic(api,useVerbose=verbose)

                 expect_match(api$coreUrl,con$coreApi$coreUrl,all=verbose)
                 expect_that(is.null(con$coreApi$jsessionId),equals(FALSE))


                 out<-CoreAPIV2::getEntityMetadata(con$coreApi,"384 WELL PLATE",useVerbose = FALSE)


                 body<-out$template
                 return<-CoreAPIV2::createEntity(con$coreApi,"384 WELL PLATE",body=body)

                 barcode<-return$entity$Barcode


                 b<-CoreAPIV2::getEntityByBarcode(con$coreApi,"384 WELL PLATE",barcode,useVerbose=verbose)$entity

                 expect_match(b$Barcode,barcode,all=verbose)


                 logout<-CoreAPIV2::logOut(api,useVerbose = verbose)
                 expect_match(logout$success,"Success")

               })