# skip()
skip_on_cran()
# skip_on_ci()
library(dplyr)
a <- try(api_status())
if (inherits(a, c("try-error", "response"))) skip("Server issues")
test_that("get_query_content", {
a <- try(api_query("FALSE_ENDPOINT"))
if (inherits(a, c("try-error", "response"))) skip("Server issues")
expect_true(inherits(a, "response"))
})
test_that("gwasinfo",
{
skip_on_ci()
expect_true(
nrow(api_query('gwasinfo/ieu-a-2') %>% get_query_content()) == 1
)
expect_equal(
nrow(api_query('gwasinfo', query=list(id=c("ieu-a-2","ieu-a-1001"))) %>% get_query_content()),
2
)
expect_gt(
nrow(gwasinfo()),
100
)
})
test_that("gwasinfo without token", {
skip_on_ci()
a1 <- gwasinfo("ieu-a-2", opengwas_jwt="")
a2 <- gwasinfo("ieu-a-2")
expect_true(all(a1 == a2, na.rm=TRUE))
})
test_that("associations",
{
skip_on_ci()
expect_true(
nrow(associations(c("rs9662760", "rs12759473"), "ieu-a-2")) == 2
)
expect_true(
nrow(associations(c("rs9662760", "rs12759473"), "ieu-a-2", proxies=0)) == 1
)
expect_true(
nrow(associations(c("1:1000000-10002000", "2:1000000-10002000"), "ieu-a-2")) > 10000
)
})
test_that("fill_n",
{
skip_on_ci()
x <- associations(c("rs12759473"), "bbj-a-10") %>% fill_n
expect_true(
is.numeric(x$n) & !is.na(x$n)
)
})
test_that("phewas",
{
a <- try(phewas("rs977747", 0.01))
if (inherits(a, c("try-error", "response"))) skip("Server issues")
expect_true(nrow(a)>100)
b <- try(phewas("rs977747", 0.01, batch=c("ieu-a")))
if (inherits(b, c("try-error", "response"))) skip("Server issues")
expect_true(nrow(b) < nrow(a))
expect_true(nrow(b) > 0)
})
# test_that("phewas",
# {
# a <- phewas("1:1000000-10000100", 0.1)
# expect_true(nrow(a)>100)
# })
test_that("phewas",
{
a <- try(phewas("1:1850428", 0.001))
if (inherits(a, c("try-error", "response"))) skip("Server issues")
expect_true(nrow(a)>10)
})
test_that("tophits",
{
a <- try(tophits("ieu-a-2"))
if (inherits(a, c("try-error", "response"))) skip("Server issues")
expect_equal(nrow(a), 79)
b <- try(tophits("ieu-a-2", clump=0))
if (inherits(b, c("try-error", "response"))) skip("Server issues")
expect_true(nrow(b)>79)
})
test_that("batch", {
b <- try(batch_from_id(c("ieu-a-1", "ukb-b-100-10")))
if (inherits(b, c("try-error", "response"))) skip("Server issues")
expect_true(all(b == c("ieu-a", "ukb-b")))
})
test_that("user", {
# with no key
# u1 <- user(opengwas_jwt="")
# expect_true(inherits(u1, "response"))
skip_on_cran()
skip_on_ci()
skip_if(Sys.getenv('OPENGWAS_X_TEST_MODE_KEY') != "")
# make sure valid jwt is in .Renviron
key <- get_opengwas_jwt()
expect_true(nchar(key) > 0)
u2 <- user()
expect_false(inherits(u2, "response"))
})
test_that("gwasinfo/files", {
skip_on_cran()
skip_on_ci()
test <- try(api_query('gwasinfo/files', query = list(id='ieu-a-2'), opengwas_jwt = get_opengwas_jwt()) %>% get_query_content())
if (inherits(test, c("try-error", "response"))) skip("Server issues")
expect_equal(test %>% length(), 1)
expect_equal(test$`ieu-a-2` %>% length(), 3)
})
test_that("Test gwasinfo_files()", {
skip_on_cran()
skip_on_ci()
urls <- try(gwasinfo_files(id = 'ieu-a-2'))
if (inherits(urls, c("try-error", "response"))) skip("Server issues")
expect_equal(urls %>% ncol(), 1)
expect_equal(urls %>% nrow(), 3)
expect_is(urls, "data.frame")
expect_equal(urls %>% colnames(), "ieu-a-2")
})
test_that("Test gwasinfo_files()", {
skip_on_cran()
skip_on_ci()
urls2 <- try(gwasinfo_files(id = c('ieu-a-2', 'ieu-a-31')))
if (inherits(urls2, c("try-error", "response"))) skip("Server issues")
expect_equal(urls2 %>% ncol(), 2)
expect_equal(urls2 %>% nrow(), 3)
expect_is(urls2, "data.frame")
expect_equal(urls2 %>% colnames(), c("ieu-a-2", "ieu-a-31"))
})
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