Merge pull request #21 from rformassspectrometry/jomain

feat: add extractByIndex method.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendSql
 Title: SQL-based Mass Spectrometry Data Backend
-Version: 1.5.0
+Version: 1.5.1
 Authors@R:
     c(person(given = "Johannes", family = "Rainer",
              email = "Johannes.Rainer@eurac.edu",
@@ -21,7 +21,7 @@ Description: SQL-based mass spectrometry (MS) data backend supporting also
 	     representation for very large or remote MS data sets.
 Depends:
     R (>= 4.2.0),
-    Spectra (>= 1.9.12)
+    Spectra (>= 1.15.10)
 Imports:
     BiocParallel,
     S4Vectors,
@@ -50,7 +50,7 @@ BugReports: https://github.com/RforMassSpectrometry/MsBackendSql/issues
 URL: https://github.com/RforMassSpectrometry/MsBackendSql
 biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport, Proteomics
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'MsBackendSql-functions.R'
     'MsBackendSql.R'

NAMESPACE

@@ -14,6 +14,7 @@ exportMethods(backendInitialize)
 exportMethods(backendMerge)
 exportMethods(centroided)
 exportMethods(dataStorage)
+exportMethods(extractByIndex)
 exportMethods(filterDataOrigin)
 exportMethods(filterMsLevel)
 exportMethods(filterPrecursorMzRange)
@@ -93,6 +94,7 @@ importMethodsFrom(ProtGenerics,spectraNames)
 importMethodsFrom(ProtGenerics,tic)
 importMethodsFrom(ProtGenerics,uniqueMsLevels)
 importMethodsFrom(Spectra,backendBpparam)
+importMethodsFrom(Spectra,extractByIndex)
 importMethodsFrom(Spectra,reset)
 importMethodsFrom(Spectra,show)
 importMethodsFrom(Spectra,spectraData)

NEWS.md

@@ -1,3 +1,9 @@
+# MsBackendSql 1.5
+
+## Changes in 1.5.1
+
+- Implement the new `extractByIndex()` methods.
+
 # MsBackendSql 1.3
 
 ## Changes in 1.3.5

R/MsBackendSql-functions.R

@@ -545,7 +545,7 @@ createMsBackendSqlDatabase <- function(dbcon, x = character(),
 
 .subset_query <- function(object, qry) {
             ids <- dbGetQuery(.dbcon(object), qry)[, "spectrum_id_"]
-            object[object@spectraIds %in% ids]
+            extractByIndex(object, which(object@spectraIds %in% ids))
 }
 
 .precursor_mz_query <- function(mz, ppm = 20, tolerance = 0) {

R/MsBackendSql.R

@@ -136,12 +136,12 @@
 #'
 #' @section Subsetting, merging and filtering data:
 #'
-#' `MsBackendSql` objects can be subsetted using the `[` function. Internally,
-#' this will simply subset the `integer` vector of the primary keys and
-#' eventually cached data. The original data in the database **is not**
-#' affected by any subsetting operation. Any subsetting operation can be
-#' *undone* by resetting the object with the `reset()` function. Subsetting
-#' in arbitrary order as well as index replication is supported.
+#' `MsBackendSql` objects can be subsetted using the `[` or `extractByIndex()`
+#' functions. Internally, this will simply subset the `integer` vector of the
+#' primary keys and eventually cached data. The original data in the database
+#' **is not** affected by any subsetting operation. Any subsetting operation
+#' can be *undone* by resetting the object with the `reset()` function.
+#' Subsetting in arbitrary order as well as index replication is supported.
 #'
 #' Multiple `MsBackendSql` objects can also be merged (combined) with the
 #' `backendMerge()` function. Note that this requires that all `MsBackendSql`
@@ -527,9 +527,17 @@ setMethod("[", "MsBackendSql", function(x, i, j, ..., drop = FALSE) {
     if (missing(i))
         return(x)
     i <- i2index(i, length(x), x@spectraIds)
-    slot(x, "spectraIds", check = FALSE) <- x@spectraIds[i]
-    x <- callNextMethod(x, i = i)
-    x
+    extractByIndex(x, i)
+})
+
+#' @rdname MsBackendSql
+#'
+#' @importMethodsFrom Spectra extractByIndex
+#'
+#' @export
+setMethod("extractByIndex", c("MsBackendSql", "ANY"), function(object, i) {
+    slot(object, "spectraIds", check = FALSE) <- object@spectraIds[i]
+    callNextMethod(object, i = i)
 })
 
 #' @importMethodsFrom ProtGenerics peaksData
@@ -707,7 +715,8 @@ setMethod(
             object <- .subset_query(object, qry)
             ## Need to ensure the order is correct.
             if (length(dataOrigin) > 1L)
-                object <- object[order(match(dataOrigin(object), dataOrigin))]
+                object <- extractByIndex(
+                    object, order(match(dataOrigin(object), dataOrigin)))
             object
         }
     })

tests/testthat/test_MsBackendSql.R

@@ -32,7 +32,16 @@ test_that("dataStorage works", {
     expect_identical(length(res), length(mm8_be))
 })
 
+test_that("extractByIndex,MsBackendSql works", {
+    idx <- c(4L, 12L, 100L, 14L)
+    res <- extractByIndex(mm8_be, idx)
+    expect_identical(res@spectraIds, idx)
+})
+
 test_that("[,MsBackendSql works", {
+    res <- mm8_be[]
+    expect_equal(res, mm8_be)
+
     idx <- c(4L, 12L, 100L, 14L)
     res <- mm8_be[idx]
     expect_identical(res@spectraIds, idx)