tests/testthat/test_Database.R

In dmenne/d13cbreath: Reads and Evaluates Gastric Emptying 13C Breath Test Data

context("Database write test")

test_that("Writing sample BreathID database returns valid set of fit parameters ",{
  if (exists("con")) suppressWarnings(try(dbDisconnect(con)))
  sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  unlink(sqlitePath)
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  filename = system.file("extdata", "350_20043_0_GER.txt", package = "D13CBreath")
  # Check Debug output
  options(D13CBreath.sqldebug = TRUE)
  expect_output(AddBreathTestRecord(filename,con),"SELECT.*")
  options(D13CBreath.sqldebug = FALSE)
  # Check Patient record
  pat = dbGetQuery(con,"SELECT * from Patient")
  expect_equal(pat$PatientID,"0")
  expect_equal(pat$Gender,"m")
  rec = dbGetQuery(con,"SELECT * from BreathTestRecord")
  expect_equal(nrow(rec),1)
  expect_equal(rec$TestNo,20043)
  expect_equal(rec$FileName,"350_20043_0_GER.txt")
  expect_equal(rec$PatientID,"0")
  # Check parameter record
  nParameters = dbGetQuery(con,"SELECT Parameter, Method from BreathTestParameter")
  
  dbDisconnect(con)
  unlink(sqlitePath)
  # BreathID, ExpBeta, BluckCoward, Maes, MaesScint,WN
  expect_equal(length(unique(nParameters$Method)),6,
               info = paste(unique(nParameters$Method),collapse = ", "))    
  # t50 tlag GEC beta deviance k m       
  expect_equal(length(unique(nParameters$Parameter)),7,
               info = paste(unique(nParameters$Parameter),collapse = ", "))
})

test_that("Update Cascade and Delete Cascade must be effective for BreathTestRecord",{
  countSQL = function(PatientID){
    sprintf(
      "SELECT Count(*) from BreathTestRecord where  patientID='%s'",PatientID)
  }
  sqlitePath = CreateSimulatedBreathTestDatabase()
  con = OpenSqliteConnection(sqlitePath)
  patID = dbGetQuery(con,"SELECT PatientID from Patient")$PatientID
  # Test Delete
  expect_equal(dbGetQuery(con, countSQL(patID[1]))[1,1] ,4)
  DBI::dbExecute(con, sprintf("DELETE from Patient where patientID='%s'",patID[1]))
  expect_equal(dbGetQuery(con, countSQL(patID[1]))[1,1] ,0)
  # Test Update
  expect_equal(dbGetQuery(con, countSQL(patID[3]))[1,1] ,5)
  DBI::dbExecute(con, 
    sprintf("UPDATE Patient SET patientID='blub' where PatientID='%s'", patID[3]))
  expect_equal(dbGetQuery(con, countSQL(patID[3]))[1,1] ,0)
  expect_equal(dbGetQuery(con, countSQL('blub'))[1,1] ,5)  
  dbDisconnect(con)
})  

test_that("Summary returns list of Record and Parameters",{
 sqlitePath = CreateSimulatedBreathTestDatabase()
 con = OpenSqliteConnection(sqlitePath)
 breathTestRecordID = 1
 sum = Summary13CRecord(con,breathTestRecordID)
 dbDisconnect(con)
 expect_equal(length(sum),2)
 expect_equal(class(sum[[1]]),"data.frame")
 expect_equal(class(sum[[2]]),"data.frame")
 expect_equal(length(sum$Record),23)
 expect_true( nrow(sum$Parameters) > 5)
})

test_that("Reading of multiple files returns dataframe with status",{
  # Setup
  if (exists("con")) suppressWarnings(dbDisconnect(con))
  sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  unlink(sqlitePath)
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  path = dirname(
    system.file("extdata", "350_20043_0_GER.txt", package = "D13CBreath"))
  # Test
  res = AddAllBreathTestRecords(path, con)
  res1 = AddAllBreathTestRecords(path, con) # Try again, same records
  pars = dbGetQuery(con,"SELECT DISTINCT Parameter from BreathTestTimeSeries order by Parameter") 
  dbDisconnect(con)
  unlink(sqlitePath)
  expectParams = c("CPDR","CPDRfit","DOB","PDR","PDRfit","WN")
  expect_equal(pars[,1],expectParams)
})


test_that("Reading all good files in a directory", {
  if (exists("con")) suppressWarnings(dbDisconnect(con))
  sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  unlink(sqlitePath)
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  path = dirname(
    system.file("extdata/good", "IrisCSV.TXT", package = "D13CBreath"))
  res = AddAllBreathTestRecords(path, con)
  dbDisconnect(con)
  unlink(sqlitePath)
  expect_true(all(res$status == "saved"))
})


test_that("Data columns with NaN are not stored",{
  # Setup
  if (exists("con")) suppressWarnings(dbDisconnect(con))
  sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  unlink(sqlitePath)
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  filename = system.file("extdata", "350_20023_0_GERWithNan.txt", 
                         package = "D13CBreath")
  AddBreathTestRecord(filename,con)
  pars = dbGetQuery(con,"SELECT DISTINCT Parameter from BreathTestTimeSeries order by Parameter") 
  ### Change this when new method has been added
  expectParams = c("CPDR","DOB","PDR","PDRfit","WN")
  expect_equal(pars[,1],expectParams)
  dbDisconnect(con)
  unlink(sqlitePath)
})

test_that("Duplicate Time values raise",{
  # Setup
  if (exists("con")) suppressWarnings(dbDisconnect(con))
  sqlitePath = tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  unlink(sqlitePath)
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  filename = system.file("extdata", "350_20043_0_GERDuplicateTime.txt", 
                         package = "D13CBreath")
  expect_error(AddBreathTestRecord(filename,con), "raw time series")
  dbDisconnect(con)
  unlink(sqlitePath)
})


test_that("Wagner-Nelson creates a valid predicted time series",{
   sqliteFile = CreateSimulatedBreathTestDatabase()
   con = OpenSqliteConnection(sqliteFile)
   BreathTestRecordID = 1
   wn = dbGetQuery(con,"SELECT * from BreathTestParameter where Method = 'WN'")
   expect_equal(nrow(wn),10)
   expect_true(max(wn$Value) < 50)
   expect_true(min(wn$Value) > 10)
   ts = dbGetQuery(con,"SELECT * from BreathTestTimeSeries where Parameter = 'WN'")
   expect_equal(range(ts$Time),c(0,225))
   expect_true(max(ts$Value) <= 1)
   expect_true(min(ts$Value) >= -0.2)
   dbDisconnect(con)
})


test_that("ReadBreathID on difficult file does not throw",{
  if (exists("con")) suppressWarnings(dbDisconnect(con))
  sqlitePath = 
    tempfile(pattern = "Gastrobase", tmpdir = tempdir(), fileext = ".sqlite")
  unlink(sqlitePath)
  # This file fails in WN t50
  breathfilename = d13File("badCurve.txt")
  f = ReadBreathId(breathfilename)
  expect_is(f,"BreathTestData")
  CreateEmptyBreathTestDatabase(sqlitePath)
  con = OpenSqliteConnection(sqlitePath)
  filename = system.file("extdata", "350_20023_0_GERWithNan.txt", 
                         package = "D13CBreath")
  AddBreathTestRecord(filename,con)
  dbDisconnect(con)
  unlink(sqlitePath)
})

test_that("Rebuild database must recreate parameters", {
  sqlitePath = CreateSimulatedBreathTestDatabase()
  con = OpenSqliteConnection(sqlitePath)
  expect_count = 210
  expect_equal(DBI::dbExecute(con,"DELETE FROM BreathTestParameter"), expect_count)
  expect_equal(dbGetQuery(con, "SELECT count(*) from BreathTestParameter")[1,1], 0)
  RebuildFitDatabase(con)
  # Currently, population fits are not recomputed
  expect_gte(dbGetQuery(con, "SELECT count(*) from BreathTestParameter")[1,1], 
            100)
  dbDisconnect(con)
  unlink(sqlitePath)
})