tests/testthat/test.Samples.Clinical.R

In mariodeng/FirebrowseR: An 'API' Client for Broads 'Firehose' Pipeline

#library(FirebrowseR)
context("Samples.Clinical")

test_that("Samples.Clinical", {

  format = "json"
  cohort = ""
  tcga_participant_barcode = ""
  cde_name = ""
  page = 1
  page_size = ""
  sort_by = "cohort"
  expect_error(Samples.Clinical(format = format,
                                cohort = cohort,
                                tcga_participant_barcode = tcga_participant_barcode,
                                cde_name = cde_name,
                                page = page,
                                page_size = page_size,
                                sort_by = sort_by))

  format = "csv"
  cohort = "COAD"
  obj = Samples.Clinical(format = format,
                        cohort = cohort,
                        tcga_participant_barcode = tcga_participant_barcode,
                        cde_name = cde_name,
                        page = page,
                        page_size = page_size,
                        sort_by = sort_by)
  test.q = "http://firebrowse.org/api/v1/Samples/Clinical?format=tsv&cohort=COAD&page=1&page_size=150&sort_by=cohort"
  test.obj = read.table(test.q, header = T, sep = "\t", quote = "\"")
  expect_equal(nrow(obj), nrow(test.obj))
  expect_equal(ncol(obj), ncol(test.obj))
  

  tcga_participant_barcode = "TCGA-GF-A4EO"
  expect_error(Samples.Clinical(format = "tsv",
                                cohort = cohort,
                                tcga_participant_barcode = tcga_participant_barcode,
                                cde_name = cde_name,
                                page = page,
                                page_size = page_size,
                                sort_by = sort_by))
})