param already_se_object is not required anymore, replaced by the he…

…uristics
iSEE · Oct 2, 2024 · 7aecda4 · 7aecda4
1 parent dab973b
commit 7aecda4
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Showing 6 changed files with 13 additions and 26 deletions.
diff --git a/R/iSEEindex.R b/R/iSEEindex.R
@@ -96,7 +96,6 @@
 #' info on the versions of the `iSEEindex` and `iSEE` packages.
 #' @param body.header UI element to display \emph{above} the main landing page body.
 #' @param body.footer UI element to display \emph{below} the main landing page body.
-#' @param already_se_object TODO
 #'
 #' @return An [iSEE::iSEE()] app with a custom landing page using a [BiocFileCache()] to cache a selection of data sets.
 #'
@@ -168,8 +167,7 @@
 #'     default.position = "last",
 #'     app.title = "iSEE ❤️ Tonsil Data Atlas",
 #'     body.header = header_tonsils,
-#'     body.footer = footer_tonsils,
-#'     already_se_object = TRUE)
+#'     body.footer = footer_tonsils)
 #'
 #' if (interactive()) {
 #'     shiny::runApp(app_tonsils, port = 5678)
@@ -181,8 +179,7 @@ iSEEindex <- function(bfc,
                       default.position = c("first", "last"),
                       app.title = NULL,
                       body.header = NULL,
-                      body.footer = NULL,
-                      already_se_object = FALSE) {
+                      body.footer = NULL) {
     stopifnot(is(bfc, "BiocFileCache"))
     if (is.null(FUN.initial)) {
         FUN.initial <- function() NULL
@@ -201,8 +198,7 @@ iSEEindex <- function(bfc,
                                     default.add,
                                     default.position,
                                     body.header,
-                                    body.footer,
-                                    already_se_object = already_se_object
+                                    body.footer
         ),
         appTitle = app.title
     )
@@ -319,7 +315,6 @@ iSEEindex <- function(bfc,
 #' @param session The Shiny session object from the server function.
 #' @param pObjects An environment containing global parameters generated in the
 #' landing page.
-#' @param already_se_object TODO propagated
 #'
 #' @return A `NULL` value is invisibly returned.
 #'
@@ -331,7 +326,7 @@ iSEEindex <- function(bfc,
 #' @importFrom shinyjs enable
 #'
 #' @rdname INTERNAL_launch_isee
-.launch_isee <- function(FUN, bfc, session, pObjects, already_se_object) {
+.launch_isee <- function(FUN, bfc, session, pObjects) {
     # nocov start
     dataset_id <- pObjects[[.dataset_selected_id]]
     which_dataset <- which(pObjects$datasets_table[[.datasets_id]] == dataset_id)
@@ -342,8 +337,7 @@ iSEEindex <- function(bfc,
     withProgress(message = sprintf("Loading '%s'", dataset_title),
         value = 0, max = 2, {
         incProgress(1, detail = "(Down)loading object")
-        se2 <- try(.load_sce(bfc, dataset_id, dataset_metadata,
-                             already_se_object = already_se_object))
+        se2 <- try(.load_sce(bfc, dataset_id, dataset_metadata))
         incProgress(1, detail = "Launching iSEE app")
         if (is(se2, "try-error")) {
             showNotification("Invalid SummarizedExperiment supplied.", type="error")

diff --git a/R/landing_page.R b/R/landing_page.R
@@ -11,7 +11,6 @@
 #' in the Shiny `selectizeInput()`.
 #' @param body.header UI element to display \emph{above} the main landing page body.
 #' @param body.footer UI element to display \emph{below} the main landing page body.
-#' @param already_se_object TODO to be propagated
 #'
 #' @return A `function` that defines UI elements and observers for the
 #' landing page of the app.
@@ -31,8 +30,7 @@
                           default.add = TRUE,
                           default.position = c("first", "last"),
                           body.header = NULL,
-                          body.footer = NULL,
-                          already_se_object) {
+                          body.footer = NULL) {
     default.position <- match.arg(default.position)
     # datasets
     datasets_available_list <- FUN.datasets()
@@ -103,7 +101,7 @@
 
         .create_observers(input, session, pObjects, rObjects, FUN.initial, default.add, default.position)
 
-        .create_launch_observers(FUN, bfc, input, session, pObjects, already_se_object = already_se_object)
+        .create_launch_observers(FUN, bfc, input, session, pObjects)
 
         .render_datasets_table(output, pObjects, rObjects)
 

diff --git a/R/observers.R b/R/observers.R
@@ -71,16 +71,15 @@
 #' @param input TODO
 #' @param session TODO
 #' @param pObjects TODO
-#' @param already_se_object TODO
 #'
 #' @importFrom shiny observeEvent
 #'
 #' @rdname INTERNAL_create_observers
-.create_launch_observers <- function(FUN, bfc, input, session, pObjects, already_se_object) {
+.create_launch_observers <- function(FUN, bfc, input, session, pObjects) {
 
     # nocov start
     observeEvent(input[[.ui_launch_button]], {
-        .launch_isee(FUN, bfc, session, pObjects, already_se_object = already_se_object)
+        .launch_isee(FUN, bfc, session, pObjects)
     }, ignoreNULL=TRUE, ignoreInit=TRUE)
     # nocov end
 

diff --git a/man/iSEEindex.Rd b/man/iSEEindex.Rd
diff --git a/tests/testthat/test-observers.R b/tests/testthat/test-observers.R
@@ -19,7 +19,7 @@ test_that(".create_launch_observers works", {
     pObjects <- new.env()
     FUN <- function(SE, INITIAL) invisible(NULL)
 
-    out <- iSEEindex:::.create_launch_observers(FUN, bfc, input, session = NULL, pObjects, already_se_object = FALSE)
+    out <- iSEEindex:::.create_launch_observers(FUN, bfc, input, session = NULL, pObjects)
     expect_null(out)
 
 })
diff --git a/tests/testthat/test-utils-datasets.R b/tests/testthat/test-utils-datasets.R
@@ -10,7 +10,7 @@ test_that(".load_sce works", {
 
     ## Usage ---
 
-    out <- iSEEindex:::.load_sce(bfc, id, metadata, already_se_object = FALSE)
+    out <- iSEEindex:::.load_sce(bfc, id, metadata)
 
     expect_s4_class(out, "SummarizedExperiment")
 })