Switched to a JSON-formatted OBJECT, as per alabaster.base's updates.

Also bumped the version and date for BioC-devel.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: alabaster.se
 Title: Load and Save SummarizedExperiments from File
-Version: 1.3.2
-Date: 2023-11-30
+Version: 1.3.3
+Date: 2023-12-12
 Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="[email protected]")
 License: MIT + file LICENSE
 Description: 

R/readRangedSummarizedExperiment.R

@@ -1,8 +1,10 @@
 #' Read a RangedSummarizedExperiment from disk
 #'
 #' Read a \linkS4class{RangedSummarizedExperiment} from its on-disk representation.
+#' This is usually not directly called by users, but is instead called by dispatch in \code{\link{readObject}}.
 #'
 #' @param path String containing a path to a directory, itself created using the \code{\link{stageObject}} method for \linkS4class{RangedSummarizedExperiment} objects.
+#' @param metadata Named list of metadata for this object, see \code{\link{readObjectFile}} for details.
 #' @param ... Further arguments passed to \code{\link{readSummarizedExperiment}} and internal \code{\link{altReadObject}} calls.
 #' 
 #' @return A \linkS4class{RangedSummarizedExperiment} object.
@@ -25,13 +27,14 @@
 #' 
 #' tmp <- tempfile()
 #' saveObject(se, tmp)
-#' readRangedSummarizedExperiment(tmp)
+#' readObject(tmp)
 #'
 #' @export
 #' @importFrom SummarizedExperiment SummarizedExperiment rowData rowData<- rowRanges<-
 #' @import alabaster.base
-readRangedSummarizedExperiment <- function(path, ...) {
-    se <- altReadObject(path, type="summarized_experiment", ...)
+readRangedSummarizedExperiment <- function(path, metadata, ...) {
+    metadata$type <- "summarized_experiment"
+    se <- altReadObject(path, metadata=metadata, ...)
 
     rrdir <- file.path(path, "row_ranges")
     if (file.exists(rrdir)) {

R/readSummarizedExperiment.R

@@ -1,8 +1,10 @@
 #' Read a SummarizedExperiment from disk
 #'
 #' Read a \linkS4class{SummarizedExperiment} from its on-disk representation.
+#' This is usually not directly called by users, but is instead called by dispatch in \code{\link{readObject}}.
 #'
 #' @param path String containing a path to a directory, itself created using the \code{\link{stageObject}} method for \linkS4class{SummarizedExperiment} objects.
+#' @param metadata Named list of metadata for this object, see \code{\link{readObjectFile}} for details.
 #' @param ... Further arguments passed to internal \code{\link{altReadObject}} calls.
 #' 
 #' @return A \linkS4class{SummarizedExperiment} object.
@@ -24,7 +26,7 @@
 #' 
 #' tmp <- tempfile()
 #' saveObject(se, tmp)
-#' readSummarizedExperiment(tmp)
+#' readObject(tmp)
 #'
 #' @export
 #' @aliases loadSummarizedExperiment
@@ -33,8 +35,8 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom S4Vectors make_zero_col_DFrame
 #' @import alabaster.base
-readSummarizedExperiment <- function(path, ...) {
-    info <- fromJSON(file.path(path, "summarized_experiment.json"))
+readSummarizedExperiment <- function(path, metadata, ...) {
+    info <- metadata$summarized_experiment
 
     all.assays <- list()
     names(all.assays) <- character(0)
@@ -49,14 +51,14 @@ readSummarizedExperiment <- function(path, ...) {
     if (file.exists(cd.path)) {
         cd <- altReadObject(cd.path, ...)
     } else {
-        cd <- make_zero_col_DFrame(info$dimensions[2])
+        cd <- make_zero_col_DFrame(info$dimensions[[2]])
     }
 
     rd.path <- file.path(path, "row_data")
     if (file.exists(rd.path)) {
         rd <- altReadObject(rd.path, ...)
     } else {
-        rd <- make_zero_col_DFrame(info$dimensions[1])
+        rd <- make_zero_col_DFrame(info$dimensions[[1]])
     }
 
     se <- SummarizedExperiment(all.assays, colData=cd, rowData=rd, checkDimnames=FALSE)

R/saveRangedSummarizedExperiment.R

@@ -52,8 +52,10 @@ setMethod("saveObject", "RangedSummarizedExperiment", function(x, path, ...) {
         })
     }
 
-    write(toJSON(list(dimensions=dim(x), version="1.0"), auto_unbox=TRUE), file=file.path(path, "ranged_summarized_experiment.json"))
-    write(file=file.path(path, "OBJECT"), "ranged_summarized_experiment")
+    info <- readObjectFile(path)
+    info$ranged_summarized_experiment <- list(version="1.0")
+    saveObjectFile(path, "ranged_summarized_experiment", info)
+
     invisible(NULL)
 })
 

R/saveSummarizedExperiment.R

@@ -46,8 +46,12 @@ NULL
 #' @import methods
 setMethod("saveObject", "SummarizedExperiment", function(x, path, summarizedexperiment.allow.dataframe.assay=FALSE, ...) {
     dir.create(path)
-    write(file=file.path(path, "OBJECT"), "summarized_experiment")
-    write(toJSON(list(dimensions=dim(x), version="1.0"), auto_unbox=TRUE), file=file.path(path, "summarized_experiment.json"))
+    saveObjectFile(
+        path, 
+        "summarized_experiment", 
+        list(summarized_experiment=list(version="1.0", dimensions=dim(x)))
+    )
+
     args <- list(summarizedexperiment.allow.dataframe.assay=summarizedexperiment.allow.dataframe.assay, ...)
 
     cd <- colData(x)