--- a
+++ b/tests/testthat/test-full-tests.R
@@ -0,0 +1,169 @@
+# This extends tests in test-basic-workflow.R
+# Skip these tests on CRAN
+skip_on_cran()
+
+xe <- XenaGenerate(subset = grepl("BRCA", XenaCohorts))
+xe2 <- XenaHub(hostName = "tcgaHub")
+xe3 <- XenaHub(
+  hosts = "https://tcga.xenahubs.net",
+  cohorts = "TCGA Breast Cancer (BRCA)",
+  datasets = "TCGA.BRCA.sampleMap/HiSeqV2"
+)
+
+
+all_hosts <- c(
+    "https://ucscpublic.xenahubs.net",
+    "https://tcga.xenahubs.net",
+    "https://gdc.xenahubs.net",
+    "https://gdcV18.xenahubs.net",
+    "https://icgc.xenahubs.net",
+    "https://toil.xenahubs.net",
+    "https://pancanatlas.xenahubs.net",
+    "https://xena.treehouse.gi.ucsc.edu:443",
+    "https://pcawg.xenahubs.net",
+    "https://atacseq.xenahubs.net",
+    "https://singlecellnew.xenahubs.net",
+    "https://kidsfirst.xenahubs.net",
+    "https://tdi.xenahubs.net"
+)
+
+
+# XenaHub-class.R ---------------------------------------------------------
+
+test_that("show method for XenaHub object works", {
+  expect_output(show(xe), "class: XenaHub")
+})
+
+test_that("fun xena_default_hosts works", {
+  expect_identical(xena_default_hosts(), all_hosts)
+})
+
+test_that("fun XenaHub works", {
+  expect_output(show(xe2), "class: XenaHub")
+  expect_error(XenaHub(hostName = "xxx"))
+  expect_output(show(xe3), "class: XenaHub")
+})
+
+test_that("fun .collapse_list works", {
+  expect_identical(.collapse_list(c("a", "b")), "a,b")
+})
+
+
+# api-higher --------------------------------------------------------------
+
+test_that("funs to get hosts, cohorts, datasets and samples work", {
+  expect_identical("https://tcga.xenahubs.net", hosts(xe3))
+  expect_identical("TCGA Breast Cancer (BRCA)", cohorts(xe3))
+  expect_identical("TCGA.BRCA.sampleMap/HiSeqV2", datasets(xe3))
+  samples <- samples(xe3)[[1]]
+  expect_true("TCGA-GI-A2C8-01" %in% samples)
+})
+
+
+# Fetch -------------------------------------------------------------------
+
+host <- "https://toil.xenahubs.net"
+dataset <- "tcga_RSEM_gene_tpm"
+samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
+probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
+genes <- c("TP53", "RB1", "PIK3CA")
+
+
+fetch()
+# Fetch samples
+fetch_dataset_samples(host, dataset, 2)
+# Fetch identifiers
+tryCatch({
+  fetch_dataset_identifiers(host, dataset)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+
+# Fetch expression value by probes
+tryCatch({
+  fetch_dense_values(host, dataset, probes, samples, check = FALSE)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+tryCatch({
+  fetch_dense_values(host, dataset, probes, samples[1], check = TRUE)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+tryCatch({
+  fetch_dense_values(host, dataset, probes[1], samples[1], check = TRUE)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+tryCatch({
+  fetch_dense_values(host, dataset, probes[1], samples[1], check = TRUE)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+tryCatch({
+  expect_error(fetch_dense_values(host, dataset, probes[1], 33, check = TRUE))
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+tryCatch({
+  fetch_dense_values(host, dataset, c(probes[1], "xxx"), c(samples[1], "xxx"), check = TRUE)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+# The following two are two time consuming
+# fetch_dense_values(host, dataset, probes[1], check = TRUE)
+# fetch_dense_values(host, dataset, samples = samples[1], check = TRUE)
+
+# Fetch expression value by gene symbol (if the dataset has probeMap)
+tryCatch({
+  fetch_dense_values(host, dataset, genes, samples, check = TRUE, use_probeMap = TRUE)
+}, error = function(e) {
+  if (grepl("500", e$message)) {
+    message("Bad network, skipping check")
+  } else {
+    stop(e$message)
+  }
+})
+
+# Workflow ----------------------------------------------------------------
+expect_warning(XenaFilter(xe))
+expect_warning(XenaFilter(xe2, filterCohorts = "TCGA Breast Cancer (BRCA)"))
+XenaQueryProbeMap(xe3)
+
+# clean all
+rm(list = ls())