feat: add backendRequiredSpectraVariables method

NAMESPACE

@@ -9,6 +9,7 @@ export(mtbls_sync_data_files)
 exportClasses(MsBackendMetaboLights)
 exportMethods(backendInitialize)
 exportMethods(backendMerge)
+exportMethods(backendRequiredSpectraVariables)
 importClassesFrom(Spectra,MsBackendDataFrame)
 importClassesFrom(Spectra,MsBackendMzR)
 importFrom(BiocFileCache,BiocFileCache)
@@ -31,3 +32,4 @@ importMethodsFrom(ProtGenerics,backendInitialize)
 importMethodsFrom(ProtGenerics,dataOrigin)
 importMethodsFrom(Spectra,"[")
 importMethodsFrom(Spectra,backendInitialize)
+importMethodsFrom(Spectra,backendRequiredSpectraVariables)

R/MsBackendMetaboLights.R

@@ -37,6 +37,9 @@
 #' and eventually synchronizes changes/updates. This can be skipped with
 #' `offline = TRUE` in which case only locally cached content is queried.
 #'
+#' The `backendRequiredSpectraVariables()` function returns the names of the
+#' spectra variables required for the backend to provide the MS data.
+#'
 #' The `mtbls_sync()` function can be used to *synchronize* the local data
 #' cache and ensure that all data files are locally available. The function
 #' will check the local cache and eventually download missing data files from
@@ -71,6 +74,8 @@
 #' - For `MsBackendMetaboLights()`: an instance of `MsBackendMetaboLights`.
 #' - For `backendInitialize()`: an instance of `MsBackendMetaboLights` with
 #' the MS data of the specified MetaboLights data set.
+#' - For `backendRequiredSpectraVariables()`: `character` with spectra
+#' variables that are needed for the backend to provide the MS data.
 #' - For `mtbls_sync()`: the input `MsBackendMetaboLights` with the paths to
 #' the locally cached data files being eventually updated.
 #'
@@ -202,6 +207,18 @@ setMethod(
  "supports merging, such as the 'MsBackendMemory'.")
  })
 
+#' @rdname MsBackendMetaboLights
+#'
+#' @importMethodsFrom Spectra backendRequiredSpectraVariables
+#'
+#' @exportMethod backendRequiredSpectraVariables
+setMethod(
+ "backendRequiredSpectraVariables", "MsBackendMetaboLights",
+ function(object, ...) {
+ c(callNextMethod(), "mtbls_id", "mtbls_assay_name",
+ "derived_spectral_data_file")
+ })
+
 .valid_mtbls_required_columns <- function(object) {
  if (nrow(object@spectraData)) {
  if (!all(c("mtbls_id", "mtbls_assay_name",

tests/testthat/test_MsBackendMetaboLights.R

@@ -41,6 +41,12 @@ test_that("backendInitialize,MsBackendMetaboLights works", {
  expect_equal(Spectra::rtime(res), Spectra::rtime(res_o))
 })
 
+test_that("backendRequiredSpectraVariables,MsBackendMetaboLights works", {
+ expect_equal(backendRequiredSpectraVariables(MsBackendMetaboLights()),
+ c("dataStorage", "scanIndex", "mtbls_id", "mtbls_assay_name",
+ "derived_spectral_data_file"))
+})
+
 test_that("mtbls_sync works", {
  expect_error(mtbls_sync(3, offline = TRUE), "'x' is expected to be")