if (!dir.exists(tempdir())) {
dir.create(tempdir())
}
test_that("db.check", {
db <- sprintf('%s/config.db', tempdir())
db <- normalizePath(db, "/", FALSE)
x <- db.check(db)
expect_that(x, equals(TRUE))
unlink(db)
})
test_that("config.and.name.initial", {
config.cfg <- system.file("extdata", "config/github/github.toml", package = "BioInstaller")
x <- config.and.name.initial(config.cfg, "bwa")
expect_that(x, equals(TRUE))
x <- check.configfile.validate(config.cfg)
expect_that(x, equals(TRUE))
config.cfg <- system.file("extdata", "config.error.toml", package = "configr")
x <- tryCatch({
x <- check.configfile.validate(config.cfg)
}, warning = function(w) {
return(FALSE)
})
expect_that(x, equals(FALSE))
})
test_that("initial",{
config.cfg <- system.file("extdata", "config/github/github.toml", package = "BioInstaller")
x <- NULL
tryCatch({
x <- check.install.name(NULL, config.cfg)
}, warning = function(w) {
x <- FALSE
})
expect_that(x, equals(NULL))
config.cfg <- system.file("extdata", "config/github/github.toml", package = "BioInstaller")
x <- config.and.name.initial(config.cfg, "bwa")
config <- eval.config(config = "bwa", file = config.cfg)
versions <- tryCatch(show.avaliable.versions(config),
error = function(e) {message("Featch bwa version failed."); NULL})
if (!is.null(versions)) {
params <- list(name = "bwa", version = "v0.7.15", versions = versions, config = config)
x <- do.call(version.initial, params)
expect_that(x, equals("v0.7.15"))
}
x <- tryCatch({
x <- check.configfile.validate(config.cfg)
}, warning = function(w) {}, error = function(e){
x <- TRUE
return(x)
})
expect_that(x, equals(TRUE))
})
test_that("set.makedir", {
old.workdir <- getwd()
tmp.dir <- normalizePath(tempdir(), "/")
makedir.1 <- sprintf("%s/setmakedir/test_makedir1", tmp.dir)
makedir.2 <- sprintf("%s/setmakedir/test_makedir2", tmp.dir)
destdir <- sprintf("%s/setmakedir", tmp.dir)
destdir <- normalizePath(destdir, "/", FALSE)
makedir.1 <- normalizePath(makedir.1, "/", FALSE)
makedir.2 <- normalizePath(makedir.2, "/", FALSE)
params <- list(make.dir = makedir.1, destdir = destdir)
do.call(set.makedir, params)
expect_that(getwd(), equals(destdir))
dir.create(makedir.1)
params <- list(make.dir = makedir.1, destdir = destdir)
do.call(set.makedir, params)
expect_that(getwd(), equals(makedir.1))
params <- list(make.dir = makedir.2, destdir = destdir)
do.call(set.makedir, params)
expect_that(getwd(), equals(destdir))
setwd(old.workdir)
unlink(destdir, recursive = T, TRUE)
})
test_that("dependence",{
db <- sprintf('%s/.BioInstaller', tempdir())
unlink(db)
set.biosoftwares.db(db)
x <- change.info(name = "demo", installed = "yes", debug = TRUE, verbose = F, version = '1.0')
x <- check.need.install('demo', '1.0', db)
expect_that(x, equals(TRUE))
config.cfg <- system.file("extdata", "config/github/github.toml", package = "BioInstaller")
x <- get.need.install(eval.config(config = "bcftools", file = config.cfg), db)
expect_that(is.list(x), equals(TRUE))
expect_that(x[[1]][1], equals('htslib'))
destdir <- sprintf('%s/', tempdir())
destdir <- normalizePath(destdir, "/", FALSE)
x <- tryCatch(install.dependence('github_demo', 'master', destdir, destdir, F),
error = function(e) {message("Connecting Github website failed."); NULL})
if (!is.null(x)) {
expect_that(x, equals(TRUE))
unlink(destdir, recursive=TRUE, TRUE)
x <- process.dependence(eval.config(config = "github_demo", file = config.cfg), db, destdir, destdir, FALSE)
expect_that(x, equals(TRUE))
unlink(destdir, recursive=TRUE, TRUE)
}
})
test_that("git.download",{
destdir <- sprintf('%s/denpendence1', tempdir())
destdir <- normalizePath(destdir, "/", FALSE)
unlink(destdir, recursive = TRUE, TRUE)
url <- "https://github.com/Miachol/github_demo"
x <- tryCatch(git.download("github_demo", destdir, "master",
url, TRUE, FALSE, FALSE),
error = function(e) {NULL})
expect_that(is.null(x) || x, equals(TRUE))
unlink(destdir, recursive=TRUE, TRUE)
})
temps <- list.files(tempdir(), ".*")
unlink(sprintf("%s/%s", tempdir(), temps), recursive = TRUE, TRUE)
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