tests/testthat/test_pubchem_view.R

In bhklab/AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data

library(AnnotationGx)
library(testthat)
library(checkmate)




test_that("AnnotationGx:::.get_all_heading_types", {
  res <- AnnotationGx:::.get_all_heading_types()
  checkmate::expect_data_table(res, min.rows = 1, min.cols = 2, any.missing = FALSE)
  checkmate::expect_names(names(res), must.include = c("Heading", "Type"))
})


test_that("AnnotationGx::getPubchemAnnotationHeadings", {
  query <- getPubchemAnnotationHeadings("compound", "ChEMBL ID")
  expect_data_table(query, ncols = 2, nrows = 1)
  expect_equal(names(query), c("Heading", "Type"))

  dt <- capture.output(
    query <- capture.output(getPubchemAnnotationHeadings("compound", "fake_placeholder"), type = c("message"))
  )
  assert(any(grepl("WARNING", query)))
  expect_equal(dt, "Empty data.table (0 rows and 2 cols): Heading,Type")
})

test_that("AnnotationGx::getAnotationHeadings Failure", {
  expect_error(getPubchemAnnotationHeadings("substance", "ChEMBL ID"))
})

test_that("AnnotationGx::annotatePubchemCompound", {
  CID <- 176870 # Erlotonib
  expected <- "CHEMBL553"
  expect_equal(annotatePubchemCompound(CID, "ChEMBL ID"), expected)

  expected <- "183321-74-6"
  expect_equal(annotatePubchemCompound(CID, "CAS"), expected)

  query <- annotatePubchemCompound(CID, "ChEMBL ID", query_only=T)
  expect_class(query[[1]], "httr2_request")

  response <- annotatePubchemCompound(CID, "ChEMBL ID", raw=T)
  expect_class(response[[1]], "httr2_response")

  expected <- NA_character_
  expect_equal(annotatePubchemCompound(CID, "NSC Number"), expected)

  expected <- "L01EB02"
  expect_equal(annotatePubchemCompound(CID, "ATC Code"), expected)

  expected <- "LT01214"
  expect_equal(annotatePubchemCompound(CID, "Drug Induced Liver Injury"), expected)


  # CID <- 3672 # Ibuprofen
  # expected <- "CHEMBL521"
  # expect_equal(annotatePubchemCompound(CID, "ChEMBL ID"), expected)

  # expected <- "15687-27-1"
  # expect_equal(annotatePubchemCompound(CID, "CAS"), expected)

  # expected <- "M02AA13; C01EB16; R02AX02; G02CC01; M01AE01"
  # expect_equal(annotatePubchemCompound(CID, "ATC Code"), expected)

  # expected <- "LT00199"
  # expect_equal(annotatePubchemCompound(CID, "Drug Induced Liver Injury"), expected)

  expect_error(annotatePubchemCompound(CID, heading = "fake_placeholder"))

  expect_error(annotatePubchemCompound(CID, heading = "fake_placeholder", parse_function = fake_parser))
  
  fake_parser <- function(x) {
    return(data.table::data.table(Heading = "CAS", Value = "fake_value"))
  }
  annotatePubchemCompound(CID, heading = "CAS", parse_function = fake_parser)
})

test_that("AnnotationGx:::.build_pubchem_view_query", {
  # Test case 1: Test with default parameters
  query <- AnnotationGx:::.build_pubchem_view_query(id = "12345")
  expected_url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/12345/JSON"
  expect_equal(query$url, expected_url)

  # Test case 2: Test with custom parameters
  query <- AnnotationGx:::.build_pubchem_view_query(
    id = "67890", record = "substance", page = 2
  )
  expected_url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/substance/67890/JSON?page=2"
  expect_equal(query$url, expected_url)

  query <- AnnotationGx:::.build_pubchem_view_query(
    id = "176870", heading = "ChEMBL ID", output = "XML"
  )
  expected_url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/176870/XML?heading=ChEMBL%20ID"
  expect_equal(query$url, expected_url)

  query <- AnnotationGx:::.build_pubchem_view_query(
    id = "176870", output = "JSON", source = "DrugBank"
  )
  expected_url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/176870/JSON?source=DrugBank"
  expect_equal(query$url, expected_url)

  query <- AnnotationGx:::.build_pubchem_view_query(
    id = "176870", record = "substance", version = "1.2"
  )
  expected_url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/substance/176870/JSON?version=1.2"
  expect_equal(query$url, expected_url)

  query <- AnnotationGx:::.build_pubchem_view_query(
    id = "176870", version = 1
  )
  expected_url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/176870/JSON?version=1"
  expect_equal(query$url, expected_url)
})


test_that("AnnotationGx:::.build_pubchem_view_query Failure", {
  # Test case 1: Test with invalid annotation
  expect_error(AnnotationGx:::.build_pubchem_view_query(
    id = "67890", record = "substance",
    page = 2, version = 1, heading = "Heading1", source = "Source1", output = "XML"
  ))
  expect_error(AnnotationGx:::.build_pubchem_view_query(id = "67890", record = "substance", version = 1.5))
  expect_error(AnnotationGx:::.build_pubchem_view_query(
    id = "176870", record = "substance", version = 1
  ))

  expect_error(AnnotationGx:::.build_pubchem_view_query(
    id = "176870", output = "JSON", source = ""
  ))

  expect_error(AnnotationGx:::.build_pubchem_view_query(
    id = "176870", record = "compound", heading = "fale"
  ))
})