last fixes

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.0
+Version: 4.3.1
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
@@ -60,7 +60,7 @@ Imports:
     S4Vectors,
     IRanges,
     SummarizedExperiment,
-    MsCoreUtils (>= 1.15.5),
+    MsCoreUtils (>= 1.16.0),
     MsFeatures,
     MsExperiment (>= 1.5.4),
     Spectra (>= 1.13.7),

NAMESPACE

@@ -33,7 +33,7 @@ importFrom("SummarizedExperiment", "rowData")
 importFrom("SummarizedExperiment", "rowData<-")
 importFrom("SummarizedExperiment", "assay")
 importFrom("MsCoreUtils", "rbindFill", "closest", "i2index", "sumi", "between",
-           "maxi", "breaks_ppm", "force_sorted")
+           "maxi", "breaks_ppm", "force_sorted", "common_path")
 importFrom("RColorBrewer", "brewer.pal")
 
 importFrom("graphics", "image", "boxplot", "matplot", "rect", "axis",

NEWS.md

@@ -1,4 +1,9 @@
-# xcms 4.1
+# xcms 4.3
+
+## Changes in version 4.3.1
+
+- Addition of generic function `loadResults()`and method for import using 
+  `RDataParam` and `PlaintTextParam`.
 
 ## Changes in version 4.1.14
 

R/AllGenerics.R

@@ -1523,7 +1523,7 @@ setGeneric("levelplot", function(x, data, ...) standardGeneric("levelplot"))
 #'
 #' ## Save as a collection of plain text files
 #' pth = file.path(tempdir(), "test")
-#' param <- PlainTextParam(path = pth)
+#' param <- PlainTextParam(path = pth, spectraExport = TRUE)
 #' storeResults(object = faahko_sub, param = param)
 #'
 #' ## Load this saved dataset

R/PlainTextParam.R

@@ -56,6 +56,14 @@
 #' `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()`.
@@ -109,7 +117,7 @@
 #'
 #' ## Define param
 #' pth = file.path(tempdir(), "test")
-#' param <- PlainTextParam(path = pth)
+#' param <- PlainTextParam(path = pth, spectraExport = TRUE)
 #'
 #' ## Save as a collection of plain text files
 #' storeResults(object = faahko_sub, param = param)

tests/testthat/test_PlainTextParam.R

@@ -45,7 +45,7 @@ test_that("loadResults, PlainTextParam works", {
     storeResults(mse, param = param)
     load_mse <- loadResults(param)
     expect_true(inherits(load_mse, "MsExperiment"))
-    expect_equal(mse, load_mse) # does nto work but make sense because no spectra data. other checks ?
+    expect_equal(mse, load_mse) # does nto work but make sense because no spectra data. ideas for other checks ?
     expect_equal(sampleData(mse), sampleData(load_mse))
     #with spectra ?
     param <- PlainTextParam(path = pth, spectraExport = TRUE)
@@ -61,12 +61,15 @@ test_that("loadResults, PlainTextParam works", {
     storeResults(xmse_full, param = param)
     load_xmse <- loadResults(param)
     expect_true(inherits(load_xmse, "XcmsExperiment"))
-    expect_equal(xmse_full, load_xmse)
-    expect_equal(processHistory(xmse_full), processHistory(load_xmse))
+    expect_equal(xmse_full, load_xmse) # also fail probably because of spectra missing
+    expect_equal(processHistory(xmse_full), processHistory(load_xmse)) #fail why ?
     expect_equal(xmse_full@featureDefinitions,
                  load_xmse@featureDefinitions)
     expect_equal(adjustedRtime(xmse_full), adjustedRtime(load_xmse))
     param <- PlainTextParam(path = pth, spectraExport = TRUE)
     storeResults(xmse_full, param = param)
+    load_xmse <- loadResults(param)
+    expect_equal(xmse_full, load_xmse)
+    # not sure how to check  for `spectraFilePath`
     })