tests/testthat/test_file_attach.R

In ceparman/Core5.3: Core API fucntions

context("Tests for create and attach a file to the entity")

 

rm(list=ls())

verbose <- FALSE   

#setup to work with environment

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



     test_that(paste("create a sample and attach a file", 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(con$coreApi,"PATIENT_SAMPLE",body=body)
              
              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)
              
              #create a text file
              
              filepath <- tempfile()
              write.csv(x =runif(n = 1000),file = filepath )
              filename <- paste0("testfile",as.character(floor(runif(1, 1,101))),".txt")
              
      #Attach to the entity        
              
              
            r<-CoreAPIV2::attachFile(con$coreApi,b$Barcode,filename,
                                     filepath,targetAttributeName="",useVerbose=verbose)
             
             
              
              
              expect_equal(grep(pattern = paste0(filename,".[0-9]"),r$entity$name),1)
              
              expect_equal( httr::status_code(r$response),200)
              
    #attach a binary to an atribute          
          
              filepath <- tempfile()
              filename <- paste0("testfile",as.character(floor(runif(1, 1,101))),".jpg")
              
              jpeg(filepath)
              image(matrix(runif(100),10,10))
              dev.off()
              
            
              
              r<-CoreAPIV2::attachFile(con$coreApi,b$Barcode,filename,filepath,targetAttributeName="CI_FILE",useVerbose=verbose)   
              
              expect_equal(grep(pattern = paste0(filename,".[0-9]"),r$entity$name),1)
              
              expect_equal( httr::status_code(r$response),200)
              
              
              logout<-CoreAPIV2::logOut(con$coreApi,useVerbose = verbose)
              expect_match(logout$success,"Success")
              
             
              })
     
     
     test_that(paste("get a file attached as assay data", instance),
               {
                 
                 verbose <- FALSE
                 api <- CoreAPIV2::coreAPI(instance)
                 
                 
                 con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
                 
                 
                 
                 
                 assayType<-"SIMPLE_ASSAY"
                 experimentSamplebarcode<-"XPX85"
                 attributeName <-"ci_file"
                 
                 response<-   CoreAPIV2::getExperimentSamplesAssayFileData(con$coreApi,assayType,
                                          experimentSamplebarcode, attributeName,useVerbose = verbose)
                
                 
                  expect_equal( httr::status_code(response$response),200)
                 
                 filename<-paste0(tempdir(),"/myfile.png")
                 writeBin(response$entity, filename)
                 
                 expect_true(file.exists(filename))
                 CoreAPIV2::logOut(con$coreApi)
                 
                 
                 
               })
     
    
     test_that(paste("attach file  as assay data", instance),
               {
                 
                 verbose <- FALSE
                 api <- CoreAPIV2::coreAPI(instance)
                 
                 
                 con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
                 
                 
                 
                 
                 assayType<-"SIMPLE_ASSAY"
                 experimentSamplebarcode<-"XPX85"
                 attributeName <-"ci_file"
                 
                 
                 
                 filepath <-"test_files/stocks.txt"
                 response<-CoreAPIV2::setExperimentSamplesAssayFileData(con$coreApi,assayType,
                                                                        "XPX85","CI_FILE",filepath,useVerbose = verbose)
        
                 expect_equal( httr::status_code(response$response),204)
                 
                 CoreAPIV2::logOut(con$coreApi)
                 
                 
                 
               })
     
     
     
     
     test_that(paste("reteive a attached file", instance),
               {
                 
                 verbose <- FALSE
                 api <- CoreAPIV2::coreAPI(instance)
                 
                 
                 con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
                 
                 entityType <- "PATIENT SAMPLE"
                 barcode <- "PS2"
                 attribute <- "CI_FILE"
                 useVerbose <- TRUE
                 
                 t<- getAttachedFile(con$coreApi,entityType,barcode,attribute,useVerbose = verbose)
                 expect_equal(rawToChar(t$entity), "Text File")
                 
      
                 CoreAPIV2::logOut(con$coreApi)
                 
                 
                 
               })