tests/testthat/test_generate_queue.R

In cpanse/bfabricShiny: A Module for Bridging B-Fabric and R using REST

#R

context("bfabricShiny")

.test_generate_queue<- function(x, method="default"){
  generate_queue(x,
                      projectid = 3000,
                      area = "Proteomics",
                      instrument = "FUSION_2",
                      username = "roschi",
                      autoQC01 = "TRUE",
                      QC01o = 4,
                      QC01m = 1,
                      autoQC02 = "FALSE",
                      QC02o = 4,
                      QC02m = 1,
                      autoQC4L = "FALSE",
                      QC4Lo = 4,
                      QC4Lm = 1,
                      clean = "FALSE",
                      cleano = 4,
                      cleanm = 1,
                      start1 = 1,
                      start2 = NA,
                      start3 = NA,
                      end1 = 4,
                      end2 = 1,
                      end3 = 3,
                      lists = 1,
                      startposition = 1,
                      nr.methods = 1,
                      nr.replicates = 1,
                      qc.type = 1,
                      method = method,
                      pathprefix = "D:Data2San")
}



test_that("test default", {

 x <- bfabricShiny:::.test_data_medium()
 
  res.default <- .test_generate_queue(x, 'default')
  ground_trues <- c(NA,1,2,3,4,NA,5,6,7,8,NA,9,10,11,12,NA,13,14,15,16,NA,17,18,19,20,NA,NA,NA)
  
  expect_equal(as.integer(res.default$rv[,'Sample ID'] ),  ground_trues)
 
 
})

test_that("test random", {
  
  x <- bfabricShiny:::.test_data_medium()
  
  ground_trues <- c(NA, 3, 4, 10, 1, NA, 12, 15, 2, 20, NA, 13, 18, 7, 17, NA,
                    5, 9, 16, 14, NA, 8, 11, 6, 19, NA, NA, NA)
  
 
  set.seed(1)
  res.random.1 <- .test_generate_queue(x, 'random')
  #expect_equal(as.integer(res.random.1$rv[,'Sample ID'] ),  ground_trues)
  
  set.seed(1)
  res.random.2 <- .test_generate_queue(x, 'random')
  res.random.3 <- .test_generate_queue(x, 'random')
  
  expect_true(all.equal(res.random.1$rv[,'Sample ID'], res.random.2$rv[,'Sample ID']))
  expect_true(sum(res.random.1$rv[,'Sample ID'] != res.random.3$rv[,'Sample ID'], na.rm = TRUE)>1) 
})


test_that("protViz_queue", {
  Rprofile <- file.path(Sys.getenv("HOME"), ".Rprofile")
  source(Rprofile, local = TRUE)
  smp.3530 <- bfabricShiny:::.getSamples(login, webservicepassword,
                                      posturl = bfabricposturl,
                                      containerid = 3530)
  smp.30993 <- bfabricShiny:::.getSamples(login, webservicepassword,
                                     posturl = bfabricposturl,
                                     containerid = 30993)
  
  
  smp.30666 <- bfabricShiny:::.getSamples(login, webservicepassword,
                                          posturl = bfabricposturl,
                                          containerid = 30666)
  # required by protViz:::formatXCalibur
  names(smp.30993) <- c('id', 'name', 'condition' ,'containerid')
  names(smp.3530) <- c('id', 'name', 'condition' ,'containerid')
  set.seed(1)
  smp.30993 |>
    protViz::blockRandom("condition") |>
    protViz::assignPlatePosition() |> 
    protViz::insertSamples(howoften = 4, begin = TRUE, end = FALSE,
                           stdPosX = '6', stdPosY = 'F', plate = 1,
                           stdName = "clean", volume = 2) |> 
    protViz:::formatXCalibur()
  
  
  rv1 <- smp.3530 |>
    protViz::blockRandom("containerid") |>
    protViz::assignPlatePosition() |> 
    protViz::insertSamples(howoften = 4, begin = TRUE, end = FALSE,
                          stdPosX = '6', stdPosY = 'F', plate = 1,
                          stdName = "clean", volume = 2) |> 
    protViz:::formatXCalibur()
  
  rv1 <- smp.3530 |>
    protViz::blockRandom("containerid") |>
    protViz::assignPlatePosition() |> 
    protViz::insertSamples(howoften = 4, begin = TRUE, end = FALSE,
                           stdPosX = '6', stdPosY = 'F', plate = 1,
                           stdName = "clean", volume = 2) 
  
  rv2 <- smp.3530 |>
    protViz::blockRandom("containerid") |>
    protViz::assignPlatePosition() 
  
  
    
})


test_that("protViz_queue_30666", {
  S <- bfabricShiny:::.getSamples(login, webservicepassword,
                                          posturl = bfabricposturl,
                                          containerid = 30666)
  
  SS <- S |> protViz::assignPlatePosition(y=LETTERS[1:8], x=1:12, plate = 1:6) |>
    protViz::blockRandom() |>
    protViz::insertSamples(stdName = "clean", stdPosX = '6', stdPosY = 'F', plate = 6, begin=TRUE, howoften=4)
})