tests/testthat/test-backend-functions.R

In jmbuhr/ShinyLipids: ShinyLipids

context("Full data processing pipeline until main plot")

input <- defaultInput()

path <- system.file("extdata/exampleDatabase.db", package = "ShinyLipids")
databaseConnection <- DBI::dbConnect(RSQLite::SQLite(), path)


test_that("Example database exists", {
  DBI::dbListTables(databaseConnection) %>% 
    expect_length(2)
})

test_that("collectLipidClassOrder default return value exists", {
  collectLipidClassOrder(databaseConnection) %>% 
    expect_length(48)
})

test_that("Example meta data exists", {
    metaData <- collectMetaData(databaseConnection)
    expect_equal(metaData$sample_from[[1]], "Harry Potter")
})

test_that("Example meta data exists", {
  rawData <- collectRawData(con = databaseConnection, id = 1)
  expect_is(rawData, "tbl")
})


test_that(
  "Default data processing steps run until visualisation", {
    metaData <- collectMetaData(databaseConnection)
    rawData <- collectRawData(con = databaseConnection, id = 1)
    
    plotData <- rawData %>%
      imputeMissingIf(input) %>% 
      addLipidProperties() %>% 
      standardizeWithinTechnicalReplicatesIf(input) %>%
      filterRawDataFor(input) %>%
      standardizeWithin(input) %>%
      createPlotData(input)
    
    meanPlotData <- summarisePlotData(plotData, input)
    
    plt <- createMainPlot(plotData            = plotData,
                          meanPlotData        = meanPlotData,
                          pairwiseComparisons = NULL,
                          input = input)
    expect_is(plt, "ggplot")
  }
)