Revision 2bf4b7346eb13ff77a90b84e177d83f94f2377d9 authored by petrovich on 29 January 2019, 16:29:30 UTC, committed by Vladislav Kamenev on 04 February 2019, 16:04:05 UTC
1 parent 34b4118
loadPreloaded.R
#' Load GEO Dataset.
#'
#' \code{loadPreloaded} returns the file with serialized ExpressionSets using
#' ProtoBuf, that were preloaded on server.
#'
#' @param name String, containing filename. Assuming
#' that in the directory with preloaded files \code{preloadedDir}
#' exists file \code{filename.rda} with list of ExpressionSets \code{ess}.
#'
#' @param exactName If you know, that inside file is object with name
#' \code{exactName}, you can specify it to load only this object.
#' Otherwise, whole file will be loaded.
#'
#' @return File with ProtoBuf-serialized ExpressionSet-s
#' that were loaded from specified file.
#'
#' @import Biobase
loadPreloaded <- function(name, exactName = NULL) {
preloadedDir <- getOption("phantasusPreloadedDir")
if (is.null(preloadedDir)) {
stop("Specify the directory with presaved files")
} else if (!dir.exists(preloadedDir)) {
stop("No such directory")
}
fileToLoad <- file.path(preloadedDir, paste0(name, '.rda'))
if (file.exists(fileToLoad)) {
x <- load(fileToLoad) # must return the object ess
loaded <- get(x)
wrongFormat <- paste("Wrong format.",
"File must contain either ExpressionSet",
"or list of ExpressionSets")
ess <- NULL
if (class(loaded) == "ExpressionSet") {
ess <- list()
ess[[x]] <- loaded
} else if (class(loaded) != "list") {
stop(wrongFormat)
} else {
ess <- loaded
}
files <- list()
seriesNames <- names(ess)
if (is.null(seriesNames)) {
seriesNames <- paste0(name, "_", 1:length(ess))
}
if (!is.null(exactName) && exactName == name) {
exactName <- NULL
}
if (!is.null(exactName) && !(exactName %in% seriesNames)) {
stop("There is not such object in this file")
}
if (!is.null(exactName)) {
ess <- list(ess[[exactName]])
}
for (i in 1:length(ess)) {
if (class(ess[[i]]) != "ExpressionSet") {
stop(wrongFormat)
}
assign("es", ess[[i]], envir = parent.frame())
files[[seriesNames[[i]]]] <- writeToList(ess[[i]])
}
f <- tempfile(pattern = "gse", tmpdir = getwd(), fileext = ".bin")
writeBin(protolite::serialize_pb(files), f)
jsonlite::toJSON(basename(f))
} else {
stop("No such file")
}
}
#' Check existence of phantasusPreloadedDir
#'
#' \code{preloadedDirExists} checks if there is specified
#' directory with preloaded files.
#'
#' @return Boolean value.
preloadedDirExists <- function() {
preloadedDir <- getOption("phantasusPreloadedDir")
jsonlite::toJSON(!is.null(preloadedDir) && dir.exists(preloadedDir))
}
#' Check names inside preloaded file
#'
#' \code{checkPreloadedNames} checks names of ExpressionSets that
#' are included in file \code{name}
#'
#' @param name String, containing filename. Assuming
#' that in the directory with preloaded files \code{preloadedDir}
#' exists file \code{filename.rda} with list of ExpressionSets \code{ess}.
#'
#' @return Vector of names serialized in JSON format.
#'
checkPreloadedNames <- function(name) {
if (!jsonlite::fromJSON(preloadedDirExists())) {
stop("No such directory")
}
preloadedDir <- getOption("phantasusPreloadedDir")
fileToLoad <- file.path(preloadedDir, paste0(name, '.rda'))
if (!file.exists(fileToLoad)) {
fileToLoadGct <- file.path(preloadedDir, paste0(name, '.gct'))
if (!file.exists(fileToLoadGct)) {
stop("No such file")
}
es <- read.gct(fileToLoadGct)
ess <- list(es=es)
names(ess) <- name
save(ess, file=fileToLoad, compress = TRUE)
}
x <- load(fileToLoad) # must return the object ess
loaded <- get(x)
answer <- c()
if (class(loaded) == "ExpressionSet") {
answer <- c(x)
} else if (class(loaded) == "list") {
if (!is.null(names(loaded))) {
answer <- names(loaded)
}
else {
if (length(loaded) > 1) {
answer <- paste0(name, "_", 1:length(loaded))
} else {
answer <- c(name)
}
}
} else {
wrongFormat <- paste("Wrong format.",
"File must contain either ExpressionSet",
"or list of ExpressionSets")
stop(wrongFormat)
}
jsonlite::toJSON(answer)
}
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