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- method for spectra and MsBackend
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@philouail
philouail committed Jun 4, 2024
1 parent 170e6fd commit 36ab4c1
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Showing 6 changed files with 204 additions and 159 deletions.
214 changes: 107 additions & 107 deletions R/PlainTextParam.R
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Original file line number Diff line number Diff line change
Expand Up @@ -23,15 +23,22 @@
#'
#' - The [sampleData()] stored as a text file named *sample_data.txt*.
#'
#' - The [fileNames()] of the *Spectra* object stored in a tabular format in a
#' text file named *spectra_files.txt*.The file names will only be exported if
#' the `Spectra` object uses a [MsBackendMzR()] backend. For other backends no
#' information on raw spectra data is currently exported with `PlainTextParam`.
#' For a `Spectra` object, the exported files include:
#'
#' - The [spectraData()] stored in a tabular format in a text file named
#' *backend_data.txt*.
#'
#' - The `processingQueueVariables`, `processing`, [processingChunkSize()] and
#' `backend` class information of the object stored in a text file named
#' *spectra_slots.txt*.
#'
#' - Processing queue of the `Spectra` object, ensuring that any spectra data
#' modifications are retained. It is stored in a `json` file named
#' *spectra_processing_queue.json*.
#'
#' Note : The Spectra object will only be exported if it uses a
#' [MsBackendMzR()] backend. Other backends are no supported as of now.
#'
#' For an `XcmsExperiment` object, the exported files are the same as those
#' for an `MsExperiment` object, with the addition of the following:
#'
Expand All @@ -56,19 +63,11 @@
#' `storeResults`. If the folder already exists, previous exports in that
#' folder might get overwritten.
#'
#' If the `spectraExport` parameter is set to `TRUE`, the spectra data will be
#' exported/imported. The import should be done in a file system similar to the
#' one used for the export. The `spectraFilePath` parameter can be used to
#' define the absolute path where the spectra files should be imported from
#' when loading the object. The default will be set using the common file path
#' of all the spectra files when exporting. If the `spectraExport` parameter is
#' set to `FALSE`, the spectra data will not be exported/imported.
#'
#' @param path for `PlainTextParam` `character(1)`, defining where the files
#' are going to be stored/ should be loaded from. The default will be
#' `tempdir()`.
#'
#' @param spectraFilePath for `loadResults` `character(1)`, defining the
#' @param spectraPath for `loadResults` `character(1)`, defining the
#' absolute path where the spectra files should be imported from when loading
#' the object. The default will be set using the common file path of all the
#' spectra files when exporting.
Expand Down Expand Up @@ -151,9 +150,12 @@ setMethod("storeResults",
dir.create(path = param@path,
recursive = TRUE,
showWarnings = TRUE)
.store_msexperiment(x = object, path = param@path)
write.table(as.data.frame(sampleData(object)),
file = file.path(param@path,
"sample_data.txt"))
## call export of individual other objects (not MsExperiment data)
storeResults(spectra(object), param)
## at some point also chromatograms, etc.
}
)

Expand All @@ -171,9 +173,14 @@ setMethod("storeResults",
setMethod("loadResults",
signature(object = "MsExperiment",
param = "PlainTextParam"),
function(object, param, spectraFilePath = character()){
res <- .load_msexperiment(path = param@path,
spectraFilePath = spectraFilePath)
function(object, param, spectraPath = character()){
fl <- file.path(param@path, "sample_data.txt")
if (file.exists(fl)){ # should i have a error if does not exist ?
sd <- read.table(fl)
rownames(sd) <- NULL #read.table force numbering of rownames
}
s <- loadResults(Spectra(), param)
res <- MsExperiment(sampleData = sd, spectra = s)
validObject(res)
res
}
Expand All @@ -183,123 +190,117 @@ setMethod("loadResults",
setMethod("loadResults",
signature(object = "XcmsExperiment",
param = "PlainTextParam"),
function(object, param, spectraFilePath){
res <- callNextMethod()
function(object, param, spectraPath){
res <- callNextMethod() #check if need to add spectraPath = spectraPath
res <- .load_xcmsexperiment(res, path = param@path)
validObject(res)
res
}
)

#' @rdname PlainTextParam
setMethod("storeResults", signature(object = "Spectra",
param = "PlainTextParam"),
function(object, param) {
## Check if there is a method to store the backend. Throw an
## error if not.
dir.create(path = param@path,
recursive = TRUE,
showWarnings = TRUE)
if (!existsMethod("storeResults", c(class(object@backend)[1L],
"PlainTextParam")))
stop("Can not store a 'Spectra' object with backend '",
class(object@backend)[1L], "'")
## - Call storeResults on @backend.
## - save @processingQueue -> json (use previously implemented
## function).
## Save the rest of the slots to a txt file, spectra_slots.txt
## - save @processingQueueVariables, separated by "|"
## - save @processingChunkSize.
## - save the class of the backend (to allow calling import on
## the specific class.
storeResults(object@backend, param = param)
.export_spectra_processing_queue(object, path = param@path)
.export_spectra_slots(object, path = param@path)
})

#' @rdname PlainTextParam
setMethod("loadResults", signature(object = "Spectra",
param = "PlainTextParam"),
function(object, param, spectraPath = character()) {
## here i am NOT making a separate function for the slots
fl <- file.path(param@path, "spectra_slots.txt")
if (!file.exists(fl))
stop("No 'spectra_slots.txt' file found in ", param@path)
fls <- readLines(fl)
var_names <- sub(" =.*", "", fls)
var_values <- sub(".* = ", "", fls)
variables <- setNames(var_values, var_names)
if (!existsMethod("loadResults", c(variables[["backend"]],
"PlainTextParam")))
stop("Can not store a 'Spectra' object with backend '",
variables["backend"], "'")
b <- loadResults(object= do.call(what = variables[["backend"]],
args = list()),
param = param, spectraPath = spectraPath) ##better way to do this ?
s <- Spectra(b)
s@processingQueueVariables <- unlist(strsplit(variables[["processingQueueVariables"]],
"|", fixed = TRUE))
s@processing <- unlist(strsplit(variables[["processing"]], "|" ,
fixed = TRUE))
s@processingChunkSize <- as.numeric(variables[["processingChunkSize"]])
fl <- file.path(param@path, "spectra_processing_queue.json")
if (file.exists(fl))
s <- .import_spectra_processing_queue(s, file = fl)
s
})



# Notes: This and the Spectra method will be moved to it's respective package
#' @rdname PlainTextParam
setMethod("storeResults", signature(object = "MsBackendMzR",
param = "PlainTextParam"),
function(object, param) {
## save the @spectraData -> text file (tab delimited table).
dir.create(path = param@path,
recursive = TRUE,
showWarnings = TRUE)
object <- dropNaSpectraVariables(object)
write.table(object@spectraData,
file = file.path(param@path, "backend_data.txt"),
sep = "\t", quote = FALSE)
})

#' @rdname PlainTextParam
setMethod("loadResults", signature(object = "MsBackendMzR",
param = "PlainTextParam"),
function(object, param, spectraPath = character()) {
## load spectraData data.frame
## replace the absolute paths in "dataStorage" with
## spectraPath if that is defined.
b <- MsBackendMzR()
data <- read.table(file = file.path(param@path,
"backend_data.txt"),
sep = "\t", header = TRUE)
rownames(data) <- NULL
data <- DataFrame(data)
b@spectraData <- data
if (length(spectraPath) > 0){
old <- MsCoreUtils::common_path(dataStorage(b))
if (nchar(old) > 0)
old <- paste0(old, "/")
dataStorage(b) <- sub(old, spectraPath, dataStorage(b))
}
b
})


#' @noRd
.store_msexperiment <- function(x, path = tempdir()) {
.export_sample_data(as.data.frame(sampleData(x)),
file.path(path, "sample_data.txt"))
.export_spectra_files(x, path = path)
.export_spectra_processing_queue(spectra(x), path = path)
}

#' @noRd
.load_msexperiment <- function(path = character(),
spectraFilePath = character()) {
fl <- file.path(path, "sample_data.txt")
if (file.exists(fl))
sd <- .import_sample_data(fl)
else stop("No \"sample_data.txt\" file found in ", path)
fl <- file.path(path, "spectra_files.txt")
if (file.exists(fl)){
sf <- .import_spectra_files(fl, spectraFilePath = spectraFilePath)
res <- readMsExperiment(spectraFiles = sf, sampleData = sd)
fl <- file.path(path, "spectra_processing_queue.json")
if (file.exists(fl))
res <- .import_spectra_processing_queue(res, fl)
} else {
res <- MsExperiment(sampleData = sd)
warning("Spectra data will not be restored")
}
res
}

#' Sample data
#' @noRd
.export_sample_data <- function(x, file = tempfile()) {
write.table(x, file = file)
}

#' @noRd
.import_sample_data <- function(file = character()) {
x <- read.table(file)
rownames(x) <- NULL #read.table force numbering of rownames
x
}

#' Spectra file
#' Spectra slots
#' @param x `Spectra`
#'
#' @noRd
.export_spectra_files <- function(x, path = character()) {
s <- spectra(x)
if (!inherits(s@backend, "MsBackendMzR"))
warning("Spectra data will not be exported, backend need to be of ",
"class 'MsBackendMzR'")
else {
pth <- MsCoreUtils::common_path(fileNames(x))
if (nchar(pth) > 0)
pth <- paste0(pth, "/")
fnames <- gsub("\\\\", "/", fileNames(x))
fnames <- sub(pth, "", fixed = TRUE, fnames)
con <- file(file.path(path, "spectra_files.txt"), open = "wt")
on.exit(close(con))
writeLines(paste0("spectraFilePath = ", pth), con = con)
writeLines(fnames, con = con)
}
.export_spectra_slots <-function(x, path = character()){
con <- file(file.path(path, "spectra_slots.txt"), open = "wt")
on.exit(close(con))
pq <- x@processingQueueVariables
writeLines(paste0("processingQueueVariables = ", paste(pq, collapse = "|")),
con = con)
p <- x@processing
writeLines(paste0("processing = ", paste(p,collapse = "|")), con = con)
writeLines(paste0("processingChunkSize = ", processingChunkSize(x)),
con = con)
writeLines(paste0("backend = ", class(x@backend)[1L]), con = con)
}

#' @noRd
.import_spectra_files <- function(file = character(),
spectraFilePath = character()) {
if (!length(spectraFilePath) > 0){
spectraFilePath <- readLines(file, n = 1L)
spectraFilePath <- sub("spectraFilePath = ", "", spectraFilePath)
}
fls <- readLines(file, n = -1L)[-1]
fls <- paste0(spectraFilePath, fls)
}

#' Processing queue
#' @param x `Spectra` (for export) `MsExperiment` (for import)
#' @param x `Spectra`
#'
#' @noRd
.export_spectra_processing_queue <- function(x, path = character()) {
Expand All @@ -311,13 +312,12 @@ setMethod("loadResults", signature(object = "MsBackendMzR",

#' @noRd
.import_spectra_processing_queue <- function(x, file = character()) {
x@spectra@processingQueue <- unserializeJSON(read_json(file)[[1L]])
x@processingQueue <- unserializeJSON(read_json(file)[[1L]])
x
}

#' @noRd
.store_xcmsexperiment <- function(x, path = tempdir(),
spectraExport = logical()) {
.store_xcmsexperiment <- function(x, path = tempdir()) {
.export_process_history(x, path = path)
if (hasChromPeaks(x))
.export_chrom_peaks(x, path)
Expand Down
8 changes: 4 additions & 4 deletions R/RDataParam.R
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
#' @param fileName for `RDataParam` `character(1)`, defining the file name. The
#' default will be `tempfile()`.
#'
#' @param spectraFilePath for `loadResults` `character(1)`, defining the
#' @param spectraPath for `loadResults` `character(1)`, defining the
#' absolute path where the spectra files should be imported from when loading
#' the object. The default will be set using the common file path of all the
#' spectra files when exporting. This is only supported if the backend of the
Expand Down Expand Up @@ -84,13 +84,13 @@ setMethod("storeResults",
setMethod("loadResults",
signature(object = "XcmsExperiment",
param = "RDataParam"),
function(object, param, spectraFilePath = character()){
function(object, param, spectraPath = character()){
env <- new.env()
load(file = param@fileName, envir = env)
res <- get(ls(env)[1], envir = env)
if (!length(spectraFilePath) == 0 &&
if (!length(spectraPath) == 0 &&
inherits(spectra(res)@backend, "MsBackendMzR")) {
dataStorageBasePath(spectra(res)) <- spectraFilePath
dataStorageBasePath(spectra(res)) <- spectraPath
}

res
Expand Down
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