Merge pull request #63 from iSEE/runr_flexible_handling

Runr flexible handling of the behavior for the different resource classes
iSEE · Oct 2, 2024 · 247814e · 247814e
2 parents 193d0b6 + 34080f9
commit 247814e
Show file tree

Hide file tree

Showing 21 changed files with 480 additions and 538 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -48,6 +48,7 @@ Suggests:
     knitr,
     RefManageR,
     rmarkdown,
+    scRNAseq,
     sessioninfo,
     testthat (>= 3.0.0),
     yaml

diff --git a/R/iSEEindex.R b/R/iSEEindex.R
@@ -6,56 +6,74 @@
 #' states prepared by the app maintainer.
 #'
 #' @section Data Sets:
-#' The function passed to the argument `FUN.datasets` must return a `list` that contains metadata about the available data sets.
+#' The function passed to the argument `FUN.datasets` must return a `list` that
+#' contains metadata about the available data sets.
 #'
 #' For each data set, required metadata are:
 #'
 #' \describe{
 #' \item{id}{A unique identifier for the data set.}
-#' \item{title}{A short human-readable title for the data set, displayed in the 'Info' panel when the data set is selected.}
-#' \item{uri}{A Uniform Resource Identifier (URI) that indicates the location of the data file that contains the data set.}
-#' \item{description}{A more detailed description of the data set, displayed in the 'Info' panel when the data set is selected.}
+#' \item{title}{A short human-readable title for the data set, displayed in the
+#' 'Info' panel when the data set is selected.}
+#' \item{uri}{A Uniform Resource Identifier (URI) that indicates the location of
+#' the data file that contains the data set.}
+#' \item{description}{A more detailed description of the data set, displayed in
+#' the 'Info' panel when the data set is selected.}
 #' }
 #'
 #' Example:
 #'
 #' ```
 #' list(
 #'   list(
-#'      id = "dataset01",
-#'      title = "Dataset 01",
-#'      uri = "https://example.com/1.rds",
-#'      description = "My first data set."
+#'     id = "dataset01",
+#'     title = "Dataset 01",
+#'     uri = "https://example.com/1.rds",
+#'     description = "My first data set."
 #'   ),
 #'   list(
-#'      id = "dataset02",
-#'      title = "Dataset 02",
-#'      uri = "https://example.com/1.rds",
-#'      description = "My second data set."
+#'     id = "dataset02",
+#'     title = "Dataset 02",
+#'     uri = "https://example.com/1.rds",
+#'     description = "My second data set."
 #'   )
 #' )
 #' ```
 #'
-#' The individual sub-lists may also contain optional named metadata specific to individual [`iSEEindexResource-class`] classes (refer to the help page of those classes for details).
+#' The individual sub-lists may also contain optional named metadata specific to
+#' individual [`iSEEindexResource-class`] classes (refer to the help page of
+#' those classes for details).
 #'
-#' **Important**: The `id` value is used to identify the data set file in the \pkg{BiocFileCache}.
-#' Thus, we recommend using a dedicated `BiocFileCache()` for the app, using the `BiocFileCache(cache)` argument to specify an on-disk location (directory path) for the dedicated cache.
+#' **Important**: The `id` value is used to identify the data set file in the
+#' \pkg{BiocFileCache}.
+#' Thus, we recommend using a dedicated `BiocFileCache()` for the app, using the
+#' `BiocFileCache(cache)` argument to specify an on-disk location (directory
+#' path) for the dedicated cache.
 #'
 #' @section Initial Configurations:
-#' The function passed to the argument `FUN.initial` must return a `list` that contains metadata about the available initial configurations, or `NULL` in the absence of any custom initial configuration (default settings will be applied to all data sets.).
+#' The function passed to the argument `FUN.initial` must return a `list` that
+#' contains metadata about the available initial configurations, or `NULL` in
+#' the absence of any custom initial configuration (default settings will be
+#' applied to all data sets.).
 #'
 #' For each initial configuration, required metadata are:
 #'
 #' \describe{
 #' \item{id}{A unique identifier for the initial configuration.}
-#' \item{title}{A short human-readable title for the initial configuration, representing the initial configuration in the 'Initial settings' dropdown menu.}
-#' \item{uri}{A Uniform Resource Identifier (URI) that indicates the location of the R script that contains the initial configuration.}
-#' \item{description}{A more detailed description of the initial configuration, displayed in the 'Configure and launch' panel when the initial configuration is selected.}
+#' \item{title}{A short human-readable title for the initial configuration,
+#' representing the initial configuration in the 'Initial settings' dropdown menu.}
+#' \item{uri}{A Uniform Resource Identifier (URI) that indicates the location of
+#' the R script that contains the initial configuration.}
+#' \item{description}{A more detailed description of the initial configuration,
+#' displayed in the 'Configure and launch' panel when the initial configuration
+#' is selected.}
 #' }
 #'
 #' For each initial configuration, optional metadata are:
 #' \describe{
-#' \item{datasets}{A series of data set identifiers for which the configuration should be made available. If missing, the configuration will be available for all data sets.}
+#' \item{datasets}{A series of data set identifiers for which the configuration
+#' should be made available. If missing, the configuration will be available for
+#' all data sets.}
 #' }
 #'
 #' Example:
@@ -78,7 +96,9 @@
 #' )
 #' ```
 #'
-#' The individual sub-lists may also contain additional optional named metadata specific to individual [`iSEEindexResource-class`] classes (refer to the help page of those classes for details).
+#' The individual sub-lists may also contain additional optional named metadata
+#' specific to individual [`iSEEindexResource-class`] classes (refer to the help
+#' page of those classes for details).
 #'
 #' @param bfc An [BiocFileCache()] object.
 #' @param FUN.datasets A function that returns a `list` of metadata for
@@ -96,9 +116,9 @@
 #' 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.
+#' @return An [iSEE::iSEE()] app with a custom landing page using a
+#' [BiocFileCache()] to cache a selection of data sets.
 #'
 #' @author Kevin Rue-Albrecht
 #'
@@ -168,8 +188,7 @@
 #'     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 +200,7 @@ 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
@@ -195,108 +213,19 @@ iSEEindex <- function(bfc,
     }
 
     iSEE(
-        landingPage = .landing_page(bfc,
-                                    FUN.datasets,
-                                    FUN.initial,
-                                    default.add,
-                                    default.position,
-                                    body.header,
-                                    body.footer,
-                                    already_se_object = already_se_object
+        landingPage = .landing_page(
+            bfc,
+            FUN.datasets,
+            FUN.initial,
+            default.add,
+            default.position,
+            body.header,
+            body.footer
         ),
         appTitle = app.title
     )
 }
 
-#### #' @examples
-#### #' ##
-#### #' ##
-#### #'
-#### #' library(BiocFileCache)
-#### #' bfc <- BiocFileCache(cache = tempdir())
-#### #'
-#### #' ##
-#### #' ##
-#### #'
-#### #' dataset_fun <- function() {
-#### #'     x <- yaml::read_yaml(
-#### #'       system.file("tonsils_example", "tonsil_package.yml", package = "iSEEindex")
-#### #'     )
-#### #'     x$datasets
-#### #' }
-#### #'
-#### #' initial_fun <- function() {
-#### #'     x <- yaml::read_yaml(
-#### #'       system.file("tonsils_example", "tonsil_package.yml", package = "iSEEindex")
-#### #'     )
-#### #'     x$initial
-#### #' }
-#### #'
-#### #' library("shiny")
-#### #' header_tonsils <- fluidRow(
-#### #'   shinydashboard::box(
-#### #'     width = 12,
-#### #'     collapsible = TRUE,
-#### #'     collapsed = TRUE,
-#### #'     title = "How to explore the Tonsil Atlas datasets",
-#### #'     includeMarkdown(
-#### #'       system.file("tonsils_example", "header_tonsils.md", package = "iSEEindex")
-#### #'     )
-#### #'   )
-#### #' )
-#### #'
-#### #' footer_tonsils <- fluidRow(
-#### #'   shinydashboard::box(
-#### #'     width = 12,
-#### #'     includeMarkdown(
-#### #'       system.file("tonsils_example", "footer_tonsils.md", package = "iSEEindex")
-#### #'     )
-#### #'   )
-#### #' )
-#### #'
-#### #' app <- iSEEindex_runr(bfc, dataset_fun, initial_fun,
-#### #'                       default.add = TRUE,
-#### #'                       default.position = "last",
-#### #'                       app.title = "iSEE ❤️ Tonsil Data Atlas",
-#### #'                       body.header = header_tonsils,
-#### #'                       body.footer = footer_tonsils)
-#### #'
-#### #' if (interactive()) {
-#### #'     shiny::runApp(app, port = 1234)
-#### #' }
-#### # iSEEindex_runr <- function(bfc,
-#### #                            FUN.datasets,
-#### #                            FUN.initial = NULL,
-#### #                            default.add = TRUE,
-#### #                            default.position = c("first", "last"),
-#### #                            app.title = NULL,
-#### #                            body.header = NULL,
-#### #                            body.footer = NULL) {
-#### #   stopifnot(is(bfc, "BiocFileCache"))
-#### #   if (is.null(FUN.initial)) {
-#### #     FUN.initial <- function() NULL
-#### #   }
-#### #
-#### #   if (is.null(app.title)) {
-#### #     app.title <- sprintf("iSEEindex - v%s",
-#### #                          packageVersion("iSEEindex"))
-#### #   } else {
-#### #     app.title <- app.title
-#### #   }
-#### #
-#### #   iSEE(
-#### #     landingPage=.landing_page(bfc,
-#### #                               FUN.datasets,
-#### #                               FUN.initial,
-#### #                               default.add, default.position,
-#### #                               body.header,
-#### #                               body.footer,
-#### #                               already_se_object = TRUE),
-#### #     appTitle = app.title
-#### #   )
-#### # }
-
-
 
 #' Prepare and Launch the Main App.
 #'
@@ -319,7 +248,6 @@ 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 +259,7 @@ 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 +270,7 @@ 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")
@@ -392,67 +319,3 @@ iSEEindex <- function(bfc,
     # nocov end
 }
 
-
-
-
-
-
-# .launch_isee_runr <- function(FUN, bfc, session, pObjects) {
-#   # nocov start
-#   dataset_id <- pObjects[[.dataset_selected_id]]
-#   which_dataset <- which(pObjects$datasets_table[[.datasets_id]] == dataset_id)
-#   # TODO: refactor as function that takes data set identifier and returns uri
-#   dataset_metadata <- as.list(pObjects$datasets_table[which_dataset, , drop=FALSE])
-#   # TODO: refactor as function that takes data set identifier and returns title
-#   dataset_title <- pObjects$datasets_table[which_dataset, .datasets_title, drop=TRUE]
-#   withProgress(message = sprintf("Loading '%s'", dataset_title),
-#                value = 0, max = 2, {
-#                  incProgress(1, detail = "(Down)loading object")
-#                  se2 <- try(.load_sce(bfc, dataset_id, dataset_metadata, already_se_object = TRUE))
-#                  incProgress(1, detail = "Launching iSEE app")
-#                  if (is(se2, "try-error")) {
-#                    showNotification("Invalid SummarizedExperiment supplied.", type="error")
-#                  } else {
-#                    if (is.null(pObjects$initial_table)) {
-#                      initial <- NULL
-#                      tour <- NULL
-#                    } else {
-#                      initial_id <- pObjects[[.ui_initial]]
-#                      which_initial <- which(
-#                        pObjects$initial_table[[.initial_config_id]] == initial_id &
-#                          pObjects$initial_table[[.initial_datasets_id]] == dataset_id
-#                      )
-#                      initial_metadata <- as.list(pObjects$initial_table[which_initial, , drop = FALSE])
-#                      initial_message <- capture.output(
-#                        init <- try(.parse_initial(bfc, dataset_id, initial_id, initial_metadata)),
-#                        type = "message")
-#                      initial <- init$initial
-#                      tour <- init$tour
-#                    }
-#                    if (is(init, "try-error")) {
-#                      showModal(modalDialog(
-#                        title = "Invalid initial state",
-#                        p("An error occured while evaluating the script:"),
-#                        markdown(paste0(c("```", initial_message, "```"), collapse = "\n")),
-#                        p("Contact the app maintainer for further help."),
-#                        footer = NULL,
-#                        size = "l",
-#                        easyClose = TRUE
-#                      ))
-#                      return(NULL)
-#                    }
-#                    FUN(SE=se2, INITIAL=initial, TOUR=tour)
-#                    shinyjs::enable(iSEE:::.generalOrganizePanels) # organize panels
-#                    shinyjs::enable(iSEE:::.generalLinkGraph) # link graph
-#                    shinyjs::enable(iSEE:::.generalExportOutput) # export content
-#                    shinyjs::enable(iSEE:::.generalCodeTracker) # tracked code
-#                    shinyjs::enable(iSEE:::.generalPanelSettings) # panel settings
-#                    shinyjs::enable(iSEE:::.generalVignetteOpen) # open vignette
-#                    shinyjs::enable(iSEE:::.generalSessionInfo) # session info
-#                    shinyjs::enable(iSEE:::.generalCitationInfo) # citation info
-#                  }
-#                }, session = session)
-#
-#   invisible(NULL)
-#   # nocov end
-# }