tests/testthat/test_build.R

In annovarR: Integrated Framework to Annotate Genetic Variants

test_that("sqlite.build", {
  test.sqlite <- tempfile()
  test.dat <- system.file("extdata", "demo/sqlite.dat.txt", package = "annovarR")
  x <- sqlite.build(test.dat, list(dbname = test.sqlite, table.name = "snp_test"))
  expect_that(x, equals(TRUE))
  unlink(test.sqlite)
})

test_that("sqlite.index", {
  test.sqlite <- tempfile()
  test.dat <- system.file("extdata", "demo/sqlite.dat.txt", package = "annovarR")
  x <- sqlite.build(test.dat, list(dbname = test.sqlite, table.name = "snp_test"))
  x <- sqlite.index(list(dbname = test.sqlite, table.name = "snp_test"), "index4", 
    c("V1", "V2"))
  expect_that(is.logical(x), equals(FALSE))
  x <- sqlite.index(list(dbname = test.sqlite, table.name = "snp_test"), "index")
  expect_that(x, equals(FALSE))
  unlink(test.sqlite)
})

test_that("drop.sqlite.index", {
  test.sqlite <- tempfile()
  test.dat <- system.file("extdata", "demo/sqlite.dat.txt", package = "annovarR")
  x <- sqlite.build(test.dat, list(dbname = test.sqlite, table.name = "snp_test"))
  x <- sqlite.index(list(dbname = test.sqlite, table.name = "snp_test"), "index4", 
    c("V1", "V2"))
  x <- drop.sqlite.index(list(dbname = test.sqlite), "index4")
  expect_that(is.logical(x), equals(FALSE))
  unlink(test.sqlite)
})

test_that("del", {
  db <- tempfile()
  db <- normalizePath(db, "/", mustWork = FALSE)
  file.create(db)
  x <- del(db, del.type = "file")
  expect_that(file.exists(db), equals(FALSE))
  test.dat <- system.file("extdata", "demo/sqlite.dat.txt", package = "annovarR")
  test.sqlite <- tempfile()
  test.sqlite <- normalizePath(test.sqlite, "/", mustWork = FALSE)
  x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, table.name = "snp_test"))
  expect_that(file.exists(test.sqlite), equals(TRUE))
  params <- list(sqlite.connect.params = list(dbname = test.sqlite, table.name = "snp_test"), 
    del.type = "table")
  result <- do.call(del, params)
  x <- del(sqlite.connect.params = list(dbname = test.sqlite, table.name = "snp_test"), 
    del.type = "file")
  expect_that(x, equals(TRUE))
  expect_that(file.exists(test.sqlite), equals(FALSE))
  x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, table.name = "snp_test"))
  x <- del(sqlite.connect.params = list(dbname = test.sqlite, table.name = "snp_test"), 
    del.type = "database")
  expect_that(x, equals(TRUE))
})

sqlite <- Sys.which(c("sqlite3", "sqlite"))
sqlite <- sqlite[sqlite != ""][1]
sqlite <- unname(sqlite)
if (!is.na(sqlite)) {
  test_that("sql2sqlite-file", {
    sql.file <- system.file("extdata", "demo/hg19_avsnp147.sqlite.sql", package = "annovarR")
    out.sqlite <- tempfile()
    sql2sqlite(sql.file = sql.file, dbname = out.sqlite, verbose = FALSE)
    con <- dbConnect(SQLite(), out.sqlite)
    tables <- dbListTables(con)
    dbDisconnect(con)
    x <- "hg19_avsnp147" %in% tables
    expect_that(x, equals(TRUE))
    unlink(out.sqlite)
  })
}
test_that("sql2sqlite-statements", {
  sql.file <- system.file("extdata", "demo/hg19_avsnp147.sqlite.sql", package = "annovarR")
  out.sqlite <- tempfile()
  statements <- paste0(readLines(sql.file), collapse = "\n")
  sql2sqlite(statements = statements, dbname = out.sqlite, verbose = FALSE)
  con <- dbConnect(SQLite(), out.sqlite)
  tables <- dbListTables(con)
  dbDisconnect(con)
  x <- "hg19_avsnp147" %in% tables
  expect_that(x, equals(TRUE))
  unlink(out.sqlite)
})