# 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())