inst/unitTests/test_FileCacheAddFile.R

In Sage-Bionetworks/rSynapseClientRewrite: Synapse R Client from Sage Bionetworks

## Unit tests for adding files to entities
## 
## Author: Matthew D. Furia <matt.furia@sagebase.org>
###############################################################################

unitTestOverwriteFile <-
  function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  path <- "/foo/bar/"
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  
  d <- diag(x = 2, nrow=10, ncol=10)
  save(d, file=file)
  checksum2 <- as.character(tools::md5sum(file))
  addFile(fc, file, path)
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(checksum2, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkTrue(checksum2 != checksum)
  
  file2 <- tempfile()
  d <- diag(x = 2, nrow=10, ncol=10)
  save(d, file=file2)
  checksum3 <- as.character(tools::md5sum(file2))
  addFile(fc, file2, path)
  checkEquals(length(fc$getFileMetaData()), 2L)
  checkEquals(checksum3, as.character(tools::md5sum(names(fc$getFileMetaData())[2])))
  
  ## overwrite again
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  
  addFile(fc, file, path)
  checkEquals(length(fc$getFileMetaData()), 2L)
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkEquals(checksum3, as.character(tools::md5sum(names(fc$getFileMetaData())[2])))
}

unitTestAddFileToRoot <-
  function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  path <- "/"
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  
  file <- tempfile()
  d <- diag(x = 2, nrow=10, ncol=10)
  save(d, file=file)
  path <- ""
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  
  file <- tempfile()
  d <- diag(x = 2, nrow=10, ncol=10)
  save(d, file=file)
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  fc <- addFile(fc, file)
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(checksum, as.character(tools::md5sum( names(fc$getFileMetaData())[1])))
}

unitTestMultipleSlashes <-
  function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  path <- "////foo//bar/"
  
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  checkEquals(relPaths[1], sprintf("%s/%s", "foo/bar", gsub("^.+[\\\\//]","",file)))
  
  path <- "////foo\\\\bar/"
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  checkEquals(relPaths[1], sprintf("%s/%s", "foo/bar", gsub("^.+[\\\\//]","",file)))
  
  path <- "\\\\\\\\foo\\\\bar/"
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  checkEquals(relPaths[1], sprintf("%s/%s", "foo/bar", gsub("^.+[\\\\//]","",file)))
  
}

unitTestAddDirNoPathTwoFiles <-
  function()
{
  dir <- tempfile()
  dir.create(file.path(dir,"/subdir"), recursive=T)
  file <- file.path(dir, "/subdir/myFile.rbin")
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  
  file2 <- file.path(dir, "myFile2.rbin")
  d <- diag(x=2,nrow=10, ncol=10)
  save(d, file=file2)
  
  fc <- new(Class="FileCache")
  addFile(fc, dir)
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  checkTrue(all(file.path(gsub("^.+[\\\\/]+", "", dir), c("subdir/myFile.rbin", "myFile2.rbin")) %in% relPaths))
  
}

unitTestAddDirNoPath <-
  function()
{
  dir <- tempfile()
  file <- file.path(dir, "/subdir/myFile.rbin")
  dir.create(file.path(dir, "/subdir"), recursive = TRUE)
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  
  fc <- new(Class="FileCache")
  addFile(fc, dir)
  checkEquals(fc$getFileMetaData()[[1]]$relativePath, sprintf("%s/%s", gsub("^.+[\\\\/]", "", dir), "subdir/myFile.rbin"))
}

unitTestAddDirAndFileTwoPaths <-
  function()
{
  fc <- new(Class="FileCache")
  file <- tempfile()
  file <- normalizePath(file, mustWork=F)
  d <- diag(nrow=10,ncol=10)
  save(d, file=file)
  
  adir <- normalizePath(tempfile(), mustWork=F)
  dir.create(adir, recursive=T)
  afile1 <- normalizePath(tempfile(tmpdir=adir), mustWork=F)
  d1 <- diag(nrow=100,ncol=100)
  save(d1, file=afile1)
  
  afile2 <- normalizePath(tempfile(tmpdir=adir), mustWork=F)
  d2 <- diag(nrow=1000,ncol=1000)
  save(d2, file=afile2)
  
  addFile(fc, c(adir,file), c("foo/", "bar/"))
  
  checkEquals(length(fc$metaData), 3L)
  
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  expectedPaths <- gsub("[\\/]+", "/", file.path(c("bar", "foo", "foo"), gsub(tempdir(), "", c(file, list.files(adir, recursive=T, full.names=T)), fixed = TRUE)))
  checkTrue(all(relPaths %in% expectedPaths))
  
  addFile(fc, c(adir,file), c("foo/", "bar/"))
  
  checkEquals(length(fc$metaData), 3L)
  
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  expectedPaths <- gsub("[\\/]+", "/", file.path(c("bar", "foo", "foo"), gsub(tempdir(), "", c(file, list.files(adir, recursive=T, full.names=T)), fixed = TRUE)))
  checkTrue(all(relPaths %in% expectedPaths))
}

unitTestTwoFilesOnePath <-
  function()
{
  fc <- new(Class="FileCache")
  file1 <- tempfile()
  d <- diag(nrow=10,ncol=10)
  save(d, file=file1)
  
  file2 <- tempfile()
  d <- diag(x=2,nrow=10,ncol=10)
  save(d, file=file2)
  path <- "aPath/"
  addFile(fc, c(file1, file2), path)
  checkEquals(length(names(fc$getFileMetaData())), 2L)
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  checkTrue(all(gsub("/+", "/", file.path(path, gsub("^.+[\\\\/]+", "", c(file1, file2)))) %in% relPaths))
}

unitTestTwoFilesThreePaths <-
  function()
{
  fc <- new(Class="FileCache")
  file <- tempfile()
  file.create(file)
  
  checkException(addFile(fc, c(file, file), c("one", "two", "three")))
}

unitTestAddToSubDirKeepName <-
    function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  path <- "/foo/"
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  
  relPaths <- as.character(unlist(lapply(fc$metaData, function(m) m$relativePath)))
  checkEquals(length(relPaths), 1L)
  checkEquals(relPaths, gsub("^/", "", gsub("[\\/]+","/", gsub(tempdir(), "", file.path(path, file), fixed = TRUE))))
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  
}

unitTestReturnValue <-
  function()
{
    file <- tempfile()
    d <- diag(nrow=10, ncol=10)
    save(d, file=file)
    path <- "/foo/bar"
    checksum <- as.character(tools::md5sum(file))
    
    fc <- new(Class="FileCache")
    copy <- addFile(fc, file, path)
    checkEquals(length(fc$getFileMetaData()), 1L)
    checkEquals(length(copy$getFileMetaData()), 1L)
    checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
    checkEquals(checksum, as.character(tools::md5sum(names(copy$getFileMetaData())[1])))
}

unitTestAddFileToSubdir <-
  function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  path <- "/foo/"
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, path)
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  
  file2 <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file2)
  path <- "foo/"
  checksum2 <- as.character(tools::md5sum(file))
  addFile(fc, file2, path)
  checkEquals(length(fc$files()), 2L)
  checkTrue(all(grepl("^foo/", fc$files())))
  
}

unitTestAddFileRename <-
  function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, "blah.txt")
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(fc$files(), "blah.txt")
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkTrue(file.exists(file.path(fc$getCacheDir(), fc$files())))
  checkEquals(checksum, as.character(tools::md5sum(file.path(fc$getCacheDir(), fc$files()))))
  
}


unitTestAddFileToSubDirRename <-
  function()
{
  file <- tempfile()
  d <- diag(nrow=10, ncol=10)
  save(d, file=file)
  checksum <- as.character(tools::md5sum(file))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, "/foo/blah.txt")
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(fc$files(), "foo/blah.txt")
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkTrue(file.exists(file.path(fc$getCacheDir(), fc$files())))
  checkEquals(checksum, as.character(tools::md5sum(file.path(fc$getCacheDir(), fc$files()))))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, "foo/blah.txt")
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(fc$files(), "foo/blah.txt")
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkTrue(file.exists(file.path(fc$getCacheDir(), fc$files())))
  checkEquals(checksum, as.character(tools::md5sum(file.path(fc$getCacheDir(), fc$files()))))
  
  fc <- new(Class="FileCache")
  addFile(fc, file, "\\foo\\blah.txt")
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(fc$files(), "foo/blah.txt")
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkTrue(file.exists(file.path(fc$getCacheDir(), fc$files())))
  checkEquals(checksum, as.character(tools::md5sum(file.path(fc$getCacheDir(), fc$files()))))
  
  
  fc <- new(Class="FileCache")
  addFile(fc, file, "/foo/bar")
  checkEquals(length(fc$getFileMetaData()), 1L)
  checkEquals(fc$files(), "foo/bar")
  checkEquals(checksum, as.character(tools::md5sum(names(fc$getFileMetaData())[1])))
  checkTrue(file.exists(file.path(fc$getCacheDir(), fc$files())))
  checkEquals(checksum, as.character(tools::md5sum(file.path(fc$getCacheDir(), fc$files()))))
  
}

unitTestNoZip <-
  function()
{
  ## need to verify behavior of file cache when zip is not present:
  ##
  ## 1) if a single file is already being managed, fileCache should generate
  ## an informative error message when a second file is added. and reject
  ## the change
  ##
  ## 2) the archive file name should be the same as the single file currently
  ## being managed by the FileCache and the archive name should change each time
  ## the filename being managed changes
  ##
  ## 3) the cacheDir name should be equal to file.path(fc$getCacheRoot(), sprintf("%s_unpacked", fc$archiveFile))
  ## so if there is no zip and a single file named foo.txt is being managed, the
  ## file should be located in <cacheRoot>/foo.txt_unpacked/foo.txt. there should
  ## be another copy of the file located in <cacheRoot>/foo.txt, which is the "archive file"
  ##
  ## 4) calling fc$createArchive() should copy <cacheRoot>/foo.txt_unpacked/foo.txt
  ## to <cacheRoot>/foo.txt_unpacked/foo.txt
  ##
  ## 5) calling fc$unpackArchive() should copy <cacheRoot>/foo.txt to
  ## <cacheRoot>/foo.txt_unpacked/foo.txt
  ##
  ## 6) when the single file is deleted via a call to deleteFile(), the cacheDir
  ## foo.txt_unpacked/ should also be deleted, but <cacheRoot> should be left in
  ## place.
  ##
  ## 7) in the event that a user tries to add a file to a subdirectory of the
  ## cacheRoot, that file should instead be placed directly in the cache root
  ## and an informative warning message should be printed.
  ##
  
  stop("not yet implemented: Bruce?")
}