tests/testthat/test_globalVariables.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

context("Checks EZ_GLOBAL_VARIABLES for valid file paths.")

globalVarsFile = system.file("extdata/EZ_GLOBAL_VARIABLES.txt", package="ezRun", mustWork=TRUE)
globalVars = read.table(globalVarsFile, sep="=", row.names=1)
varNames = rownames(globalVars)
globalVars = sapply(globalVars, trimWhiteSpace)

containsWhiteSpace = sapply(globalVars, grepl, pattern=" ")
isPythonPath = sapply(globalVars, grepl, pattern="PYTHONPATH")
isJavaCall = sapply(globalVars, grepl, pattern="java")
isInternetAddress = sapply(globalVars, grepl, pattern="http")
hasSlash = sapply(globalVars, grepl, pattern="/")

test_that("Test file paths", {
  globalPaths = globalVars[-which(containsWhiteSpace | isInternetAddress | !hasSlash),]
  names(globalPaths) = varNames[!(containsWhiteSpace | isInternetAddress | !hasSlash)]
  exception = globalPaths["REFSEQ_mRNA_REF"]
  expect_true(file.exists(sub("/transcriptome", "", exception)))
  globalPaths = globalPaths[-which(globalPaths==exception)]
  fileExists = sapply(globalPaths, file.exists)
  if (any(!fileExists)){
    print("Some paths do not exist:")
    print(globalPaths[which(!fileExists)])
  }
  #expect_true(sum(fileExists) == length(fileExists))
})