From d7911c3ec10d3632cdba92d8b99264aeaef85890 Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Mon, 14 Oct 2019 13:02:08 +0200
Subject: [PATCH] Add possibility to remove example; bump version

---
 wilson-basic/.Renviron.j2 |  3 +++
 wilson-basic/app.R        | 15 ++++++++++++---
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/wilson-basic/.Renviron.j2 b/wilson-basic/.Renviron.j2
index 8740f67..0bb19a6 100644
--- a/wilson-basic/.Renviron.j2
+++ b/wilson-basic/.Renviron.j2
@@ -6,3 +6,6 @@ WILSON_SIDEPANELWIDTH={{ "WILSON_SIDEPANELWIDTH"|env("2") }}
 
 # Define with of the main panel
 WILSON_MAINPANELWIDTH={{ "WILSON_MAINPANELWIDTH"|env("10") }}
+
+# Remove examples from data source
+WILSON_BLACKLIST_EXAMPLES={{ "WILSON_BLACKLIST_EXAMPLES"|env("false") }}
diff --git a/wilson-basic/app.R b/wilson-basic/app.R
index ba37a02..18b56d6 100755
--- a/wilson-basic/app.R
+++ b/wilson-basic/app.R
@@ -11,7 +11,7 @@ if(!requireNamespace("shinyBS", quietly = TRUE)) { stop("The package shinyBS nee
 if(!requireNamespace("htmltools", quietly = TRUE)) { stop("The package htmltools needs to be installed in order to use this app.")}
 
 # Set versions
-wilson_app_version <- "WIlsON basic 2.1.0"
+wilson_app_version <- "WIlsON basic 2.1.1"
 wilson_package_version <- as.character(packageVersion("wilson"))
 
 #
@@ -52,12 +52,16 @@ wilson_auto_reload_pattern <- ".*\\.(r|se|R|clarion)$"
 wilson_auto_reload_interval <- 3000
 
 # Sets the max file upload size in mb
-# This value only changes upload size of the shiny-server preceeding services (e.g. reverse proxy) must be altered aswell.
+# This value only changes upload size of the shiny-server. Other services (e.g. a reverse proxy) must be configured properly as well.
 wilson_max_upload_size <- 100
 
 # Allow logging of uploaded files for debugging purposes
 wilson_log_upload <- TRUE
 
+# Remove example files from data selection
+example_files <- c("A_RNAseq_Zhang_2015.se", "B_Methylation_Hautefort_Oncot_2017.se", "C_Proteomics_Worzfeld_MCP_2017.se")
+wilson_blacklist_examples <- as.logical(Sys.getenv("WILSON_BLACKLIST_EXAMPLES", unset = FALSE))
+
 #
 # WIlsON application logic
 #
@@ -142,7 +146,7 @@ ui <- dashboardPage(header = dashboardHeader(disable = TRUE), sidebar = dashboar
                                                          tags$h6("Highlighted Features"),
                                                          verbatimTextOutput("filter_h1"),
                                                          tags$h3("Global Parameters"),
-                                                         radioButtons(inputId = "data_origin", label = "Choose data origin:", choices = c("Examples", "Upload")),
+                                                         radioButtons(inputId = "data_origin", label = "Choose data source:", choices = c("Select from list", "Upload file")),
                                                          uiOutput(outputId = "fileLoader"),
                                                          bsButton("filter_log_b", label = "Toggle log", style = "default", size = "small"),
                                                          hidden(verbatimTextOutput("filter_log"))
@@ -536,6 +540,11 @@ server <- function(session, input, output) {
   # Use all .se and .clarion files specified in data
   load <- sapply(list.files(path = "data", pattern = "\\.se$|\\.clarion$"), function(x){ file.path("data", x)})
 
+  # Remove example files if requested
+  if (wilson_blacklist_examples) {
+    load <- load[setdiff(names(load), example_files)]
+  }
+
   # check for additional data
   if (dir.exists("external_data")) {
     # use all .se and .clarion files specified in external_data