# Skip these tests on CRAN

skip_on_cran()

context("test-basic-workflow")

data("XenaData", package = "UCSCXenaTools")

head(XenaData)

test_that("Load XenaData works", {

  expect_is(XenaData, "data.frame")

})

xe <- XenaGenerate(subset = XenaHostNames == "tcgaHub")

test_that("XenaGenerate works", {

  expect_is(xe, "XenaHub")

})

test_that("Xena Scan works", {

  XenaScan()

  XenaScan(pattern = "zzzzzzzzzzz")

  x1 <- XenaScan(pattern = "Blood")

  x2 <- XenaScan(pattern = "LUNG", ignore.case = FALSE)

  x1 %>%

    XenaGenerate()

  x2 %>%

    XenaGenerate()

})

xe2 <- XenaFilter(xe, filterDatasets = "clinical")

xe2 <- XenaFilter(xe2, filterDatasets = "LUAD|LUSC")

test_that("XenaFilter works", {

  expect_is(xe2, "XenaHub")

})

xe2_query <- XenaQuery(xe2)

test_that("XenaQuery works", {

  expect_is(xe2_query, "data.frame")

})

xe2_download <- XenaDownload(xe2_query, trans_slash = FALSE, download_probeMap = TRUE)

xe2_download <- XenaDownload(xe2_query,

  trans_slash = TRUE,

  destdir = file.path(tempdir(), "test_ucscxenatools")

)

# 4 ways to prepare data

dt1 <- XenaPrepare(file.path(tempdir(), "test_ucscxenatools"))

dt1 <- XenaPrepare(file.path(tempdir(), "test_ucscxenatools"), use_chunk = TRUE)

dt2 <- XenaPrepare(xe2_download$destfiles[1])

dt2 <- XenaPrepare(xe2_download$destfiles[1], use_chunk = TRUE)

dt3 <- XenaPrepare(xe2_download$url[1])

dt3 <- XenaPrepare(xe2_download$url[1], use_chunk = TRUE)

dt3 <- XenaPrepare(xe2_download$url, use_chunk = TRUE)

dt4 <- XenaPrepare(xe2_download)

dt4 <- XenaPrepare(xe2_download, use_chunk = TRUE)

### Simplified functions

expect_error(getTCGAdata("xxx"))

expect_error(getTCGAdata(c("UVM", "LUAD"), mRNASeq = TRUE, mRNASeqType = "xxx"))

expect_error(getTCGAdata(c("UVM", "LUAD"),

  Methylation = TRUE, MethylationType = "xxx",

  RPPAArray = TRUE, ReplicateBaseNormalization = FALSE

))

getTCGAdata(c("UVM", "LUAD"),

  GisticCopyNumber = TRUE, Gistic2Threshold = FALSE,

  CopyNumberSegment = TRUE, RemoveGermlineCNV = FALSE

)

getTCGAdata("LUNG", download = TRUE)

getTCGAdata("LUAD",

  clinical = FALSE, mRNASeq = TRUE,

  mRNAArray = TRUE, miRNASeq = TRUE, exonRNASeq = TRUE,

  RPPAArray = TRUE, ReplicateBaseNormalization = TRUE,

  Methylation = TRUE, GeneMutation = TRUE, SomaticMutation = TRUE,

  GisticCopyNumber = TRUE, Gistic2Threshold = TRUE, CopyNumberSegment = TRUE, RemoveGermlineCNV = TRUE

)

downloadTCGA(

  project = "UVM",

  data_type = "Phenotype",

  file_type = "Clinical Information"

)

downloadTCGA("xxx",

  data_type = "Phenotype",

  file_type = "Clinical Information"

)

availTCGA()

availTCGA(which = "ProjectID")

availTCGA(which = "DataType")

availTCGA(which = "FileType")

showTCGA()

showTCGA("LUAD")

# clean all

rm(list = ls())