context("Load GEO and its utils") library(jsonlite) library(Biobase) library(data.table) test_that("loadGEO finishes with result", { options(phantasusMirrorPath = "https://genome.ifmo.ru/files/software/phantasus") x <- loadGEO("GSE27112") expect_is(x, "json") ess <- protolite::unserialize_pb(readBin(fromJSON(x), what="raw", n=100000000)) expect_equal(length(ess), 2) x <- loadGEO("GSE27112-GPL6885") expect_is(x, "json") ess <- protolite::unserialize_pb(readBin(fromJSON(x), what="raw", n=100000000)) expect_equal(length(ess), 1) expect_is(loadGEO("GSE14308"), "json") expect_is(loadGEO("GDS4885"), "json") expect_error(loadGEO("WRONGNAME")) options(phantasusMirrorPath = NULL) }) test_that("reparseCachedGSEs works", { cacheDir <- tempdir() getES("GSE14308", destdir = cacheDir) expect_true("GSE14308" %in% reparseCachedESs(destdir = cacheDir)) }) test_that("checkGPLs counts gpls correctly", { options(phantasusMirrorPath = "https://genome.ifmo.ru/files/software/phantasus") expect_equal(fromJSON(checkGPLs("GSE14308")), c("GSE14308")) expect_equal(fromJSON(checkGPLs("GDS4885")), c("GDS4885")) expect_length(fromJSON(checkGPLs("GSE27112")), 2) expect_length(fromJSON(checkGPLs("GSE10000")), 2) expect_warning(checkGPLs("GSE101")) expect_warning(checkGPLs("GSE201")) options(phantasusMirrorPath = NULL) }) test_that("checkGPLs counts existing files correctly without connection", { options(phantasusMirrorPath = "https://notworkingdomain", phantasusCacheDir = system.file("testdata", package="phantasus")) expect_message(checkGPLs("GSE27112"), regexp = "Problems establishing connection") expect_length(fromJSON(checkGPLs("GSE27112")), 1) expect_warning(checkGPLs("GSE14308")) options(phantasusCacheDir = NULL, phantasusMirrorPath = NULL) }) test_that("getGSE works with ARCHS4", { ess <- getGSE("GSE99709", destdir=system.file("testdata", package="phantasus")) expect_gt(nrow(ess[[1]]), 0) expect_gt(ncol(ess[[1]]), 0) }) test_that("InferConditionImpl works correctly", { tests <- fread(system.file("testdata/dts.tsv", package="phantasus")) test_ds <- data.table(title=tests$Title, series=tests$Series, accession=tests$Accession, rep=tests$Replicate, inferCondition=tests$InferCondition) cond <- split(test_ds$title, test_ds$series) inf_cond_test <- split(test_ds$inferCondition, test_ds$series) rep_test <- split(test_ds$rep, test_ds$series) new_cond <- lapply(cond, inferConditionImpl) expect_equal(new_cond$GSE100221, list()) # text in all titles is unique expect_equal(new_cond$GSE10380, list()) # long dataset expect_equal(new_cond$GSE10382, list()) # number-only titles expect_equal(new_cond$GSE10383, list()) # two-color datasets expect_equal(new_cond$GSE10385, list()) # the same text and replicate number in all titles expect_equal(new_cond$GSE10039, list()) # ambiguous replicate number "High_Mo_seg_pool_Ler_col_F2" "Low_Mo_seg_pool_Ler_col_F2" "Col-0 3" expect_equal(new_cond$GSE101508$condition, inf_cond_test$GSE101508) #"IFNγ+LPS rep2" -> "IFNγ+LPS" + "2" expect_equal(new_cond$GSE101508$replicate, as.character(rep_test$GSE101508)) expect_equal(new_cond$GSE10392$condition, inf_cond_test$GSE10392) # "MPA 1" - > "MPA" + "1" expect_equal(new_cond$GSE10392$replicate, as.character(rep_test$GSE10392)) expect_equal(new_cond$GSE10123$condition, inf_cond_test$GSE10123) # "WT-GFP-lamin A Induction: Day 0 Replicate A" -> "WT-GFP-lamin A Induction: Day 0" + "A" expect_equal(new_cond$GSE10123$replicate, as.character(rep_test$GSE10123)) })