tests/testthat/test-api_genes_queries.R

In CRI-iAtlas/iatlas-graphql-client: iatlas API Client

test_that("query_genes", {
  expected_columns <- c(
    "hgnc",
    "entrez",
    "description",
    "friendly_name",
    "io_landscape_name",
    "gene_family",
    "gene_function",
    "immune_checkpoint",
    "pathway",
    "super_category"
  )
  result1 <- query_genes(entrez = 1, query_dir = query_dir)
  result2 <- query_genes(entrez = -1, query_dir = query_dir)
  expect_named(result1, expected_columns)
  expect_named(result2, expected_columns)
  expect_equal(nrow(result1), 1)
  expect_equal(nrow(result2), 0)
})

test_that("query_immunomodulators", {
  expected_columns <-  c(
    "entrez",
    "hgnc",
    "friendly_name",
    "description",
    "gene_family",
    "gene_function",
    "immune_checkpoint",
    "super_category",
    "publications"
  )
  result1 <- query_immunomodulators(query_dir = query_dir)
  result2 <- query_immunomodulators(entrez = -1, query_dir = query_dir)

  expect_named(result1, expected_columns)
  expect_named(result2, expected_columns)
  expect_true(nrow(result1) > 0)
  expect_equal(nrow(result2), 0)

})

test_that("query_io_targets", {
  result1 <- query_io_targets(query_dir = query_dir)
  expect_named(
    result1,
    c(
      "entrez",
      "hgnc",
      "description",
      "io_landscape_name" ,
      "pathway",
      "therapy_type"
    )
  )
})

test_that("query_gene_expression", {
  expected_columns <- c(
    "sample",
    "entrez",
    "hgnc",
    "rna_seq_expr"
  )
  result1 <- query_gene_expression(
    entrez = c(135L, 136L),
    samples = c("TCGA-XF-A9T8", "TCGA-2G-AAFN"),
    query_dir = query_dir
  )
  expect_named(result1, expected_columns)
  expect_equal(nrow(result1), 4L)

  result2 <- query_gene_expression(
    "entrez" = 0L, samples = "TCGA-XF-A9T8", query_dir = query_dir
  )
  expect_named(result2, expected_columns)
  expect_equal(nrow(result2), 0L)
})