.gitlab-ci.yml

@@ -49,6 +49,6 @@ update_datasets:
   script:
     - source docker/datasets_utils.sh
     - import_datasets_by_keyword iseedata || true
-    - renku dataset ls --format tabular > release/renku_dataset_ls.tab
-    - renku dataset ls-files --format tabular > release/renku_dataset_ls_files.tab
+    - renku dataset ls --format tabular > release/datasets.tab
+    - renku dataset ls-files --format tabular > release/files.tab
     - date +%Y-%m-%d > release/RELEASE_DATE

notebooks/app-release.R

+library(iSEE)
+# library(jsonlite)
+library(shinyjs)
+
+# JSON approach ----
+
+# x <- jsonlite::read_json("release/renku_ls.json")
+# length(x)
+# We have 2 datasets, let's check out the first one
+# x1 <- x[[1]]
+# keep <- vapply(x1[["http://schema.org/keywords"]], function(x) tolower("iSEEdata") %in% tolower(x[["@value"]]), logical(1))
+# x1[keep,]
+
+# Tabular approach ----
+
+input_file <- "release/datasets.tab"
+datasets_table <- readLines(input_file)
+column_dashes <- strsplit(datasets_table[2], "  ")[[1]]
+column_widths <- nchar(column_dashes) + 2
+datasets_table <- read.fwf(file = input_file, widths = column_widths,
+                           skip = 2, strip.white = TRUE,
+                           col.names = c("id", "name", "title", "version"))
+
+input_file <- "release/files.tab"
+files_table <- readLines(input_file)
+column_dashes <- strsplit(files_table[2], "  ")[[1]]
+column_widths <- nchar(column_dashes) + 2
+files_table <- read.fwf(file = input_file, widths = column_widths,
+                        skip = 2, strip.white = TRUE,
+                        col.names = c("dataset_name", "added", "size", "path", "lfs"))
+
+merge_table <- merge(datasets_table, files_table, by.x = "name", by.y = "dataset_name")
+
+dataset_rds_files <- subset(merge_table, grepl("\\.rds$", path, ignore.case = TRUE), c("name", "title", "added", "size", "path"))
+configuration_scripts <- subset(merge_table, grepl("\\.R$", path, ignore.case = TRUE), c("name", "added", "size", "path"))
+
+# Release info ----
+
+release_date <- scan("release/RELEASE_DATE", "character")
+
+# Initialise the landing page ----
+
+seLoad <- function(x) {
+    dataset_rds <- as.character(dataset_rds_files[x, "path"])
+    readRDS(dataset_rds)
+}
+
+initLoad <- function(x) {
+    list(FeatureAssayPlot())
+}
+
+renku_landing_page <- function(FUN, input, output, session) {
+    .initializeLaunch <- "iSEE_INTERNAL_launch_init"
+    .initializeSE <- "se"
+    .initializeInitial <- "initial"
+    .initializeSE_row_selected <- paste0(.initializeSE, "_rows_selected")
+    .initializeInitial_row_selected <- paste0(.initializeInitial, "_rows_selected")
+    
+    output$allPanels <- renderUI({
+        useShinyjs()
+        tagList(
+            h1("Select a data set"),
+            DT::dataTableOutput(.initializeSE),
+            h1("Select a configuration"),
+            HTML("<blockquote>Unselect the default option (if any) to use the <code>iSEE</code> default settings.</blockquote>"),
+            DT::dataTableOutput(.initializeInitial),
+            actionButton(.initializeLaunch, label = "Launch", style = iSEE:::.actionbutton_biocstyle)
+        )
+    })
+    
+    output[[.initializeSE]] <- DT::renderDataTable({
+        DT::datatable(
+            dataset_rds_files[, c("name", "title", "added", "size")], filter="top", rownames=FALSE,
+            options=list(
+                search=list(smart=FALSE, regex=TRUE, caseInsensitive=FALSE),
+                scrollX=TRUE),
+            selection=list(mode="single", selected = 1)
+        )
+    })
+    
+    output[[.initializeInitial]] <- DT::renderDataTable({
+        selected_dataset_index <- input[[.initializeSE_row_selected]]
+        selected_dataset_name <- dataset_rds_files$name[selected_dataset_index]
+        configurations_subset_table <- subset(configuration_scripts, name == selected_dataset_name, c("name", "added", "size", "path"))
+        DT::datatable(
+            configurations_subset_table, filter="top", rownames=FALSE,
+            options=list(
+                search=list(smart=FALSE, regex=TRUE, caseInsensitive=FALSE),
+                scrollX=TRUE),
+            selection=list(mode="single", selected = 1)
+        )
+    })
+    
+    observeEvent(input[[.initializeSE_row_selected]], {
+        if (is.null(input[[.initializeSE_row_selected]])) {
+            disable(.initializeLaunch)
+            updateActionButton(inputId = .initializeLaunch, label = "Select a dataset")
+        } else {
+            enable(.initializeLaunch)
+            updateActionButton(inputId = .initializeLaunch, label = "Launch")
+        }
+    }, ignoreNULL=FALSE, ignoreInit=TRUE)
+    
+    observeEvent(input[[.initializeLaunch]], {
+        print(input[[.initializeSE_row_selected]])
+        se2 <- try(seLoad(input[[.initializeSE_row_selected]]))
+        if (is(se2, "try-error")) {
+            showNotification("invalid SummarizedExperiment supplied", 
+                             type = "error")
+        }
+        else {
+            print(input[[.initializeInitial_row_selected]])
+            init <- try(initLoad(input[[.initializeInitial_row_selected]]))
+            if (is(init, "try-error")) {
+                showNotification("invalid initial state supplied", 
+                                 type = "warning")
+                init <- NULL
+            }
+            FUN(SE = se2, INITIAL = init)
+        }
+    }, ignoreNULL = TRUE, ignoreInit = TRUE)
+    
+    invisible(NULL)
+}
+
+app <- iSEE(
+    landingPage = renku_landing_page,
+    appTitle = sprintf("iSEE dashboard @ Renku (updated %s)", release_date))
+if (interactive()) {
+    shiny::runApp(app, port=1234)
+}
+

release/RELEASE_DATE

+2021-04-23