Refactor

NAMESPACE

@@ -21,8 +21,8 @@ S3method(init_filter_states,MultiAssayExperiment)
 S3method(init_filter_states,SummarizedExperiment)
 S3method(init_filter_states,data.frame)
 S3method(init_filter_states,matrix)
-S3method(init_filtered_data,TealData)
 S3method(init_filtered_data,default)
+S3method(init_filtered_data,teal_data)
 S3method(init_filtered_dataset,MultiAssayExperiment)
 S3method(init_filtered_dataset,data.frame)
 S3method(print,teal_slice)

R/FilteredData-utils.R

@@ -26,36 +26,26 @@ init_filtered_data <- function(x, join_keys, code, check) {
 
 #' @keywords internal
 #' @export
-init_filtered_data.TealData <- function(x, # nolint
-                                        join_keys = x$get_join_keys(),
-                                        code = x$get_code_class(),
-                                        check = x$get_check()) {
-  data_objects <- lapply(
-    x$get_datanames(),
-    function(dataname) {
-      dataset <- x$get_dataset(dataname)
-      list(
-        dataset = dataset$get_raw_data(),
-        metadata = dataset$get_metadata(),
-        label = dataset$get_dataset_label()
-      )
-    }
-  )
-  names(data_objects) <- x$get_datanames()
-
-  init_filtered_data(
-    x = data_objects,
-    join_keys = join_keys,
-    code = code,
+init_filtered_data.teal_data <- function(x, join_keys = teal.data::join_keys(), code = NULL, check = FALSE) { # nolint
+  checkmate::assert_class(code, "CodeClass", null.ok = TRUE)
+  checkmate::assert_class(join_keys, "JoinKeys")
+  checkmate::assert_flag(check)
+  FilteredData$new(
+    as.list(x@env),
+    join_keys = x@join_keys,
+    code = teal.data:::CodeClass$new(
+      code = paste(teal.code::get_code(x), collapse = "\n"),
+      dataname = teal.data::get_dataname(x)
+    ),
     check = check
   )
 }
 
+
 #' @keywords internal
 #' @export
 init_filtered_data.default <- function(x, join_keys = teal.data::join_keys(), code = NULL, check = FALSE) { # nolint
   checkmate::assert_list(x, any.missing = FALSE, names = "unique")
-  mapply(validate_dataset_args, x, names(x))
   checkmate::assert_class(code, "CodeClass", null.ok = TRUE)
   checkmate::assert_class(join_keys, "JoinKeys")
   checkmate::assert_flag(check)

R/FilteredData.R

@@ -95,7 +95,6 @@ FilteredData <- R6::R6Class( # nolint
 
       for (dataname in ordered_datanames) {
         ds_object <- data_objects[[dataname]]
-        validate_dataset_args(ds_object, dataname)
         if (inherits(ds_object, c("data.frame", "MultiAssayExperiment"))) {
           self$set_dataset(
             data = ds_object,
@@ -104,6 +103,7 @@ FilteredData <- R6::R6Class( # nolint
         } else {
           # custom support for TealData object which pass metadata and label also
           # see init_filtered_data.TealData
+          validate_dataset_args(ds_object, dataname)
           self$set_dataset(
             data = ds_object$dataset,
             dataname = dataname,
@@ -327,7 +327,7 @@ FilteredData <- R6::R6Class( # nolint
     #'   Label to describe the dataset
     #' @return (`self`) invisibly this `FilteredData`
     #'
-    set_dataset = function(data, dataname, metadata, label) {
+    set_dataset = function(data, dataname, metadata = attr(data, "metadata"), label = attr(data, "label")) {
       logger::log_trace("FilteredData$set_dataset setting dataset, name: { dataname }")
       # to include it nicely in the Show R Code;
       # the UI also uses `datanames` in ids, so no whitespaces allowed