fix: support spectraData<- on Spectra of length 1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SpectriPy
 Title: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
-Version: 1.1.4
+Version: 1.1.5
 Description: The SpectriPy package allows integration of Python-based MS
     analysis code with the Spectra package. Spectra objects can be converted
     into Python MS data structures. In addition, SpectriPy integrates

NEWS.md

@@ -1,5 +1,10 @@
 # SpectriPy 1.1
 
+## Changes in 1.1.5
+
+- Fix `$<-`, `spectraData()<-` and related replacement methods for
+  `Spectra`/`MsBackendPy` of length 1.
+
 ## Changes in 1.1.4
 
 - Implement a `setBackend()` method for `MsBackendPy` with a parameter

R/MsBackendPython.R

@@ -29,6 +29,20 @@
 #' between R and Python. See the description for `backendInitialize()` and the
 #' package vignette for details and examples.
 #'
+#' @section Python metadata names *vs* spectra variables:
+#'
+#' The *matchms* library in Python supports arbitrary metadata assigned to
+#' a spectrum, similar to *Spectra*'s spectra variables concept. However,
+#' *matchms* and *Spectra* use different names for the same metadata/variables.
+#' To support this, *MsBackendPy* implements `spectraVariableMapping` which
+#' allows to link spectra variable names to *matchms* metadata names. This
+#' mapping can be provided with the `spectraVariableMapping` to the
+#' `backendInitialize()` function. Also, be aware that *matchms* automatically
+#' **renames** certain metadata fields: a metadata `"NAME"` will be
+#' automatically renamed to `"compound_name"`. Also, *matchms* generally
+#' supports only lower-case metadata names.
+#' See also [setSpectraVariableMapping()] for more information.
+#'
 #' @details
 #'
 #' The `MsBackendPy` keeps only a reference to the MS data in Python (i.e. the
@@ -633,7 +647,7 @@ setMethod("$", "MsBackendPy", function(x, name) {
 #' @importMethodsFrom Spectra peaksVariables
 setReplaceMethod("$", "MsBackendPy", function(x, name, value) {
     spd <- spectraData(
-        x, union(names(spectraVariableMapping(x)), peaksVariables(x)))
+        x, union(spectraVariables(x), peaksVariables(x)))
     spd[[name]] <- value
     spectraData(x) <- spd
     x
@@ -678,7 +692,7 @@ setMethod("intensity", "MsBackendPy", function(object) {
 #' @rdname MsBackendPy
 setReplaceMethod("intensity", "MsBackendPy", function(object, value) {
     .check_mz_intensity(value, length(object), lengths(object))
-    spd <- spectraData(object, union(names(spectraVariableMapping(object)),
+    spd <- spectraData(object, union(spectraVariables(object),
                                      peaksVariables(object)))
     spd[["intensity"]] <- value
     spectraData(object) <- spd

R/conversion.R

@@ -245,7 +245,8 @@ NULL
     collisionEnergy = "collision_energy",
     isolationWindowTargetMz = "isolation_window_target_mz",
     ## polarity = "ionmode", # Disabling since matchms does not support int.
-    msLevel = "ms_level"
+    msLevel = "ms_level",
+    dataStorage = "data_storage"
 )
 
 .SPECTRA_2_SPECTRUM_UTILS <- c(
@@ -408,7 +409,8 @@ rspec_to_pyspec <- function(x, mapping = spectraVariableMapping(),
 .rspec_to_matchms_pyspec <- function(x, mapping = spectraVariableMapping()) {
     if (is(x, "Spectra"))
         pks <- peaksData(x, c("mz", "intensity"), return.type = "list")
-    else pks <- mapply(mz = x$mz, intensity = x$intensity, FUN = cbind)
+    else pks <- mapply(mz = x$mz, intensity = x$intensity, FUN = cbind,
+                       SIMPLIFY = FALSE, USE.NAMES = FALSE)
     sv <- mapping[!mapping %in% c("mz", "intensity")]
     if (length(sv)) {
         if (is(x, "Spectra"))
@@ -447,7 +449,8 @@ rspec_to_pyspec <- function(x, mapping = spectraVariableMapping(),
     function(x, mapping = spectraVariableMapping()) {
         if (is(x, "Spectra"))
             pks <- peaksData(x, c("mz", "intensity"))
-        else pks <- mapply(mz = x$mz, intensity = x$intensity, FUN = cbind)
+        else pks <- mapply(mz = x$mz, intensity = x$intensity, FUN = cbind,
+                           SIMPLIFY = FALSE, USE.NAMES = FALSE)
         l <- length(pks)
         sv <- mapping[!mapping %in% c("mz", "intensity")]
         svm <- sv[sv %in% .SPECTRA_2_SPECTRUM_UTILS]

tests/testthat.R

@@ -13,9 +13,9 @@ test_check("SpectriPy")
 
 ## TODO: add tests from the Spectra unit test suite!
 
-## ## Run the MsBackend spectra variable test suite
-## test_suite <- system.file("test_backends", "test_MsBackend",
-##                           package = "Spectra")
+## Run the MsBackend spectra variable test suite
+test_suite <- system.file("test_backends", "test_MsBackend",
+                          package = "Spectra")
 
-## ## Run single test file.
+## Run single test file.
 ## res <- test_dir(test_suite, stop_on_failure = TRUE)

tests/testthat/test_MsBackendPython.R

@@ -124,7 +124,8 @@ test_that("backendInitialize,MsBackendPy works with providing data", {
     expect_true(all(is.na(res$precursorMz)))
     ## Only non-NA variables have a mapping
     expect_equal(res@spectraVariableMapping,
-                 c(precursorCharge = "charge", msLevel = "ms_level"))
+                 c(precursorCharge = "charge", msLevel = "ms_level",
+                   dataStorage = "data_storage"))
 
     ## Repeat with spectrum_utils
     py_del_attr(py, "ttt")
@@ -788,6 +789,46 @@ test_that("setBackend,Spectra,MsBackendPy works", {
     expect_equal(smod_1$compound_name, smod$NAME)
 })
 
+test_that("$<- does not change any other spectra variables", {
+    map <- c(spectraVariableMapping(), INCHI = "inchi", NAME = "NAME",
+             SMILES = "smiles", spectrum_index = "spectrum_index")
+    a <- setBackend(s, MsBackendPy(), pythonVariableName = "tmp",
+                    spectraVariableMapping = map)@backend
+    sd <- spectraData(a)
+    a$other_variable <- "a"
+    res <- spectraData(a)
+    expect_true(all(colnames(sd) %in% colnames(res)))
+    expect_equal(sd[, intersect(colnames(sd), colnames(res))],
+                 res[, intersect(colnames(sd), colnames(res))])
+    expect_true(all(res$other_col == "a"))
+})
+
+test_that("MsBackendPy of length 1 works", {
+    map <- c(spectraVariableMapping(), INCHI = "inchi", NAME = "NAME",
+             SMILES = "smiles")
+    a <- setBackend(s, MsBackendPy(), pythonVariableName = "tmp",
+                    spectraVariableMapping = map)@backend
+    ## Subset
+    a_3 <- a[c(3L, 1L, 5L)]
+    sd <- spectraData(a_3)
+    expect_equal(sd$SMILES, a$SMILES[c(3L, 1L, 5L)])
+    a_3$other_var <- "a"
+    res <- spectraData(a_3)
+    expect_true(all(colnames(sd) %in% colnames(res)))
+    expect_equal(sd[, intersect(colnames(sd), colnames(res))],
+                 res[, intersect(colnames(sd), colnames(res))])
+    expect_true(all(res$other_var == "a"))
+
+    a_1 <- a[3L]
+    sd <- spectraData(a_1)
+    a_1$other_var_2 <- "a"
+    res <- spectraData(a_1)
+    expect_true(all(colnames(sd) %in% colnames(res)))
+    expect_equal(sd[, intersect(colnames(sd), colnames(res))],
+                 res[, intersect(colnames(sd), colnames(res))])
+    expect_equal(res$other_var_2, "a")
+})
+
 ## Comments, thoughts TODO
 ## DONE spectraData()<-: replaces the full data and allows adding/removing
 ##      spectra variables. number of spectra has to match.