Nothing
# TODO: Add comments
#
# Author: rweeks
###############################################################################
test.getVarDescription <- function()
{
varDescription <- RNMImport:::getVarDescription
testFrameOne <- data.frame(Variable = c("ID", "SEX"), Label = c("Subject Number", "Gender"),
Format = c("", "0=male, 1=female"), VarType = c("Undefined", "Covariate"), stringsAsFactors = FALSE)
testFrameTwo <- data.frame(Variable = "BILT", Label = paste0("Total Bilirubin (", intToUtf8(181), "mol/L)"), Format = "", VarType = "Lab Covariate", stringsAsFactors = FALSE)
x <- varDescription(c("ID", "SEX"))
rownames(x) <- NULL
checkEquals(x, testFrameOne, check.attributes = FALSE)
checkEquals(names(varDescription(c("ID", "SEX"))), names(testFrameOne))
checkEquals(varDescription("BILT"), testFrameTwo, check.attributes = FALSE)
checkEquals(names(varDescription(c("BILT"))), names(testFrameTwo))
# TODO: add test for when there are missing variable descriptions
}
test.setVarDescription <- function()
{
df <- RNMImport:::.RNMImportEnv$variables
getVar <- RNMImport:::getVarDescription
setVar <- RNMImport:::setVarDescription
checkException(setVar("NONSENSE"))
testFrame <- data.frame(Variable = "SEX", Label = "M/F", Format = "0=male,1=female",
VarType = "Unknown", stringsAsFactors = FALSE)
setVar(varName = "SEX", varLabel = "M/F", varFormat = "0=male,1=female", varType = "Unknown")
checkEquals(getVar("SEX"), testFrame, check.attributes = FALSE)
checkEquals(names(getVar("SEX")), names(testFrame))
assign("variables", df, envir = RNMImport:::.RNMImportEnv)
}
test.addVarDescription <- function()
{
df <- RNMImport:::.RNMImportEnv$variables
addVar <- RNMImport:::addVarDescription
getVar <- RNMImport:::getVarDescription
checkException(addVar(varName = "ID", varLabel = "Sequence ID", varType = "Unknown"))
testFrame <- data.frame(Variable = "XXX", Label = "RUNIT Test", Format = "", VarType = "Undefined", stringsAsFactors = FALSE)
addVar(varName = "XXX", varLabel = "RUNIT Test", varType = "Undefined")
checkEquals(getVar("XXX"), testFrame, check.attributes = FALSE)
checkEquals(names(getVar("SEX")), names(testFrame))
assign("variables", df, envir = RNMImport:::.RNMImportEnv)
}
test.getNmFileExtensions <- function()
{
fileExtension <- RNMImport:::getNmFileExtensions
checkException(fileExtension("NONSENSE"))
checkEquals(fileExtension("control"), c("mod", "ctl", "con"))
checkEquals(fileExtension("report"), c("lst", "out", "sep"))
checkEquals(fileExtension("table"), c("fit", "tab"))
checkEquals(fileExtension("input"), c("", "txt", "dat"))
}
test.setNmFileExtensions <- function()
{
original <- RNMImport:::.RNMImportEnv$fileExtensions
setFileExts <- RNMImport:::setNmFileExtensions
getFileExts <- RNMImport:::getNmFileExtensions
checkException(setFileExts("NONSENSE", c("blah", "blah")))
setFileExts("control", "testc1")
setFileExts("report", c("testl1", "testl2"))
setFileExts("table", c("testt1", "testt2", "testt3"))
setFileExts("input", c("testi1", "testi2", "testi3", "testi4"))
checkEquals(getFileExts("control"), "testc1")
checkEquals(getFileExts("report"), c("testl1", "testl2"))
checkEquals(getFileExts("table"), c("testt1", "testt2", "testt3"))
checkEquals(getFileExts("input"), c("testi1", "testi2", "testi3", "testi4"))
assign("fileExtensions", original, envir = RNMImport:::.RNMImportEnv)
}
test.getNmPath <- function()
{
tmp <- original <-RNMImport:::.RNMImportEnv$dataPath
getPath <- RNMImport:::getNmPath
tmp[["Dummy"]] <- "X:\\Program Files\\Dummy Data"
assign("dataPath", tmp, envir = RNMImport:::.RNMImportEnv)
checkEquals(getPath("Dummy"), "X:\\Program Files\\Dummy Data")
assign("dataPath", original, envir = RNMImport:::.RNMImportEnv)
}
test.setNmPath <- function()
{
original <-RNMImport:::.RNMImportEnv$dataPath
getPath <- RNMImport:::getNmPath
setPath <- RNMImport:::setNmPath
setPath("Dummy", "X:\\Program Files\\Dummy Data")
checkEquals(getPath("Dummy"), "X:\\Program Files\\Dummy Data")
assign("dataPath", original, envir = RNMImport:::.RNMImportEnv)
}
test.removeNmPath <- function()
{
original <-RNMImport:::.RNMImportEnv$dataPath
setPath <- RNMImport:::setNmPath
getPath <- RNMImport:::getNmPath
removePath <- RNMImport:::removeNmPath
assign("dataPath", character(0), envir = RNMImport:::.RNMImportEnv)
testVectorOne <- c("X:\\Program Files\\Dummy Data 1", "X:\\Program Files\\Dummy Data 2")
names(testVectorOne) <- c("Dummy1", "Dummy2")
testVectorTwo <- "X:\\Program Files\\Dummy Data 1"
names(testVectorTwo) <- "Dummy1"
setPath("Dummy1", "X:\\Program Files\\Dummy Data 1")
setPath("Dummy2", "X:\\Program Files\\Dummy Data 2")
setPath("Dummy3", "X:\\Program Files\\Dummy Data 3")
removePath("Dummy3")
checkEquals(get("dataPath", envir = RNMImport:::.RNMImportEnv), testVectorOne)
removePath("Dummy2")
checkEquals(get("dataPath", envir = RNMImport:::.RNMImportEnv), testVectorTwo)
removePath("Dummy1")
checkEquals(get("dataPath", envir = RNMImport:::.RNMImportEnv), character(0))
assign("dataPath", envir = RNMImport:::.RNMImportEnv, original)
}
# Tests whether or not the subset configuration functions work correctly
test.configSubsets <- function()
{
STANDARDSUBSET <- c("MDV != 1", "EVID == 0", "AMT <= 0")
# by default, should attach subsets
checkTrue( RNMImport:::applySubsetOnLoad(), msg = " |By default, data subset should be applied|" )
# check default is loaded correctly.
checkEquals(defaultDataSubset(), STANDARDSUBSET,
msg = " |Default data subset as expected|")
# check that the subset can be modified
setDefaultDataSubset("MDV != 1", TRUE)
checkEquals(defaultDataSubset(),"MDV != 1", " |Default data subset changed as expected|")
# check that it can be augmented
augmentDefaultDataSubset("EVID == 0")
checkEquals(defaultDataSubset(),c("MDV != 1", "EVID == 0"), " |Default data subset augmented as expected|")
# check that duplicates eliminated when augmenting
augmentDefaultDataSubset("EVID == 0")
checkEquals(defaultDataSubset(),c("MDV != 1", "EVID == 0"), " |Default data subset augmented as expected, no duplicates|")
# check that when loaded, subset is attached to object
# set internal unit path from runRNMImportTests?
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testRun <- importNm(conFile = "testdata1notab.ctl", reportFile = "testdata1notab.lst",
path = file.path(unitTestPath, "testdata/TestRunNoTab"))
checkEquals(dataSubset(getProblem(testRun)), c("MDV != 1", "EVID == 0"), " |Subset loaded correctly|")
# disable subsetting
setDefaultDataSubset(STANDARDSUBSET, FALSE)
# TODO: remove use of the global unitTestPath!!
testRun <- importNm(conFile = "testdata1notab.ctl", reportFile = "testdata1notab.lst",
path = file.path(unitTestPath, "testdata/TestRunNoTab"))
checkTrue(is.null(dataSubset(testRun)), " |No default data subset attached|")
# reset configuration
RNMImport:::applySubsetOnLoad(TRUE)
checkTrue(RNMImport:::applySubsetOnLoad())
}
# Tests whether or not the subset configuration functions handle errors as expected.
test.configSubsetsErrorHandling <- function()
{
checkException(setDefaultDataSubset(1:10, TRUE), " |Non-character subset not allowed|")
checkException(setDefaultDataSubset("MDV != 1", 1), " |Non-logical toggle not allowed|" )
checkException(augmentDefaultDataSubset(1:10)," |Non-character subset not allowed|" )
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.