tests/testthat/test-ResourcesPage-sdyMetaData.R

In RGLab/ImmuneSpaceLabKeyAPI: ImmuneSpace Internal API for use in visualizations and reports

context("Process Study Meta-Data")

assays <- c(
  "elisa", "elispot", "fcs", "gene_expression",
  "hai", "mbaa", "neut_ab_titer", "pcr"
)
sdyMetaData <- readRDS("datasets/2019-12-09_sdyMetaData.rds")

test_that("ensureAllIntegerValues", {
  tmp <- c(".00", ">30", "20", "8.00")
  newMinAge <- ImmuneSpaceAPI:::ensureAllIntegerValues(tmp)
  expect_true(all(is.double(newMinAge)))
  expect_true(all.equal(newMinAge, c(0, 30, 20, 8)))
})

test_that("addConditionData", {
  conditions <- c(
    "Dengue", "Dermatomyositis", "Ebola", "Healthy", "Hepatitis",
    "HIV", "Influenza", "Malaria", "Meningitis", "Smallpox", "Tuberculosis",
    "Unknown", "Varicella_Zoster", "West_Nile", "Yellow_Fever", "Zika", "CMV"
  )
  res <- ImmuneSpaceAPI:::addConditionData(sdyMetaData)
  expect_true(all(conditions %in% colnames(res)))
  res <- res[, colnames(res) %in% conditions]
  expect_true(sum(res$Influenza) == 38)
  expect_equivalent(range(res), c(0, 1))
})

test_that("addAssayData", {
  res <- ImmuneSpaceAPI:::addAssayData(sdyMetaData, assays)
  expectedColnames <- paste0("has_", assays)
  expect_true(all(expectedColnames %in% colnames(res)))
  res <- res[, colnames(res) %in% expectedColnames]
  expect_true(sum(res$has_hai) == 41)
  expect_equivalent(range(res), c(0, 1))
})

test_that("calculateDistanceMatrix", {
  sdyMetaData$newMinAge <- ImmuneSpaceAPI:::ensureAllIntegerValues(sdyMetaData$minimum_age)
  euclideanCols <- c("actual_enrollment", "newMinAge")
  categoricalCols <- c("elisa_0_Days", "gene_expression_files_0_Days")
  res <- sdyMetaData[, colnames(sdyMetaData) %in% c(euclideanCols, categoricalCols)]
  distMx <- ImmuneSpaceAPI:::calculateDistanceMatrix(res)
  expect_equivalent(dim(distMx), c(nrow(res), nrow(res)))
  expect_equivalent(colnames(distMx), rownames(res))
  expect_equivalent(rownames(distMx), rownames(res))
  expect_equivalent(range(distMx), c(0, 0.5811834))
})

test_that("calculateDistanceMatrix", {
  studyAccessions <- rownames(sdyMetaData)
  res <- ImmuneSpaceAPI:::prepareSdyMetaDataForService(
    sdyMetaData,
    assays,
    studyAccessions
  )
  assaysGrep <- paste(paste0("^", assays), collapse = "|")
  remainingAssayCols <- grep(assaysGrep, colnames(res), value = TRUE)
  expect_true(length(remainingAssayCols) == 0)
  expect_true("study" %in% colnames(res))
})