context("Feature search")
test_that("Query format for local search", {
# Query can be vector or a list
loc.vec <- local.features(query["DNase"], path = test.dir)
loc.lst <- local.features(query[["DNase"]], path = test.dir)
expect_identical(loc.vec[[1]], loc.lst[[1]])
})
test_that("Query format for online search", {
# Query can be vector or a list
hub.vec <- hub.features(query["DNase"], path = test.dir, online = FALSE)
hub.lst <- hub.features(query[["DNase"]], path = test.dir, online = FALSE)
expect_identical(hub.vec[[1]], hub.lst[[1]])
})
test_that("Online AnnotationHub feature search", {
# Modify query to be more general
query <- lapply(query, Filter, f = function(x) x != "narrowPeak")
# Online search identifies previously cached features
offline <- hub.features(query, path = test.dir, online = FALSE)
online <- hub.features(query, path = test.dir, online = TRUE)
online.cached <- IRanges::endoapply(online, function(x)
x[x$Cached, names(offline[[1]])])
expect_equivalent(online.cached, offline)
# Offline features are a subset of online features
offline.hits <- unlist(lapply(offline, function(x) x$LocalPath))
online.hits <- unlist(lapply(online, function(x) x$LocalPath))
expect_true(all(offline.hits %in% online.hits))
})
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