From 7157198fd50fcca76c54c5203f90951a4f899da8 Mon Sep 17 00:00:00 2001
From: jorainer <johannes.rainer@gmail.com>
Date: Thu, 30 May 2024 10:04:32 +0200
Subject: [PATCH] refactor: add storeResults/loadResults for Spectra etc
---
R/PlainTextParam.R | 36 ++++++++++++++++++++++++++++
tests/testthat/test_PlainTextParam.R | 33 +++++++++++++++----------
2 files changed, 57 insertions(+), 12 deletions(-)
diff --git a/R/PlainTextParam.R b/R/PlainTextParam.R
index 74ce977c..b024f41e 100644
--- a/R/PlainTextParam.R
+++ b/R/PlainTextParam.R
@@ -152,6 +152,8 @@ setMethod("storeResults",
recursive = TRUE,
showWarnings = TRUE)
.store_msexperiment(x = object, path = param@path)
+ ## call export of individual other objects (not MsExperiment data)
+ storeResults(spectra(object), param)
}
)
@@ -189,6 +191,40 @@ setMethod("loadResults",
}
)
+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.
+ 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.
+ })
+
+setMethod("storeResults", signature(object = "MsBackendMzR",
+ param = "PlainTextParam"),
+ function(object, param) {
+ ## save the @spectraData -> text file (tab delimited table).
+})
+
+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.
+})
+
+
#' @noRd
.store_msexperiment <- function(x, path = tempdir()) {
.export_sample_data(as.data.frame(sampleData(x)),
diff --git a/tests/testthat/test_PlainTextParam.R b/tests/testthat/test_PlainTextParam.R
index 3d5bc7cb..0d0bc9ee 100644
--- a/tests/testthat/test_PlainTextParam.R
+++ b/tests/testthat/test_PlainTextParam.R
@@ -1,20 +1,37 @@
xmse_full <- loadXcmsData("xmse")
-test_that("storeResults,PlainTextParam,MsExperiment works", {
+test_that("storeResults,loadResults,PlainTextParam,MsExperiment works", {
pth <- file.path(tempdir(), "test")
param <- PlainTextParam(path = pth)
param2 <- PlainTextParam()
expect_false(is.null(param2))
expect_error(new("PlainTextParam", path = c(tempdir(), tempdir())))
- mse <- filterMzRange(mse, c(200, 500))
- storeResults(mse, param = param)
+ tmp <- filterMzRange(mse, c(200, 500))
+ storeResults(tmp, param = param)
expect_true(dir.exists(pth))
expect_true(file.exists(file.path(param@path, "sample_data.txt")))
expect_true(file.exists(file.path(param@path, "spectra_files.txt")))
expect_true(file.exists(file.path(param@path, "spectra_processing_queue.json")))
+ ## Loading data again
+ load_mse <- loadResults(object = MsExperiment(), param)
+ expect_true(inherits(load_mse, "MsExperiment"))
+ expect_equal(sampleData(tmp), sampleData(load_mse))
+ a <- spectra(tmp)
+ b <- spectra(load_mse)
+ ## processingQueue can not be identical because of FUN, which is a function
+ ## expect_equal(a@processingQueue, b@processingQueue)
+ expect_equal(a@processingQueue[[1L]]@ARGS, b@processingQueue[[1L]]@ARGS)
+ expect_equal(rtime(a), rtime(b))
+ expect_equal(intensity(a), intensity(b))
+ expect_equal(mz(a), mz(b))
+ ## NOTE: if we in addition filter or subset the Spectra we can't store
+ ## properly to a txt file! Would need to store information on the data
+ ## subset too.
+ tmp <- filterRt(tmp, c(3000, 3500))
+
})
-test_that("storeResults,PlainTextParam,XcmsExperiment works", {
+test_that("storeResults,loadResults,PlainTextParam,XcmsExperiment works", {
pth = file.path(tempdir(), "test")
param <- PlainTextParam(path = pth)
param2 <- PlainTextParam()
@@ -38,12 +55,6 @@ test_that("storeResults,PlainTextParam,XcmsExperiment works", {
test_that("loadResults, PlainTextParam works", {
## test for MsExperiment object only
- pth = file.path(tempdir(), "test3")
- param <- PlainTextParam(path = pth)
- storeResults(mse, param = param)
- load_mse <- loadResults(object = MsExperiment(), param)
- expect_true(inherits(load_mse, "MsExperiment"))
- expect_equal(mse, load_mse)
## test for XcmsExperiment object
pth = file.path(tempdir(), "test4")
@@ -59,5 +70,3 @@ test_that("loadResults, PlainTextParam works", {
expect_equal(xmse_full, load_xmse)
# not sure how to check for `spectraFilePath`
})
-
-