update design figure and Dockerfile

Author: Miachol

Dockerfile

@@ -19,4 +19,4 @@ Run apt update && apt install -y lmodern \
     && rm -rf /var/lib/apt/lists/* \
     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
-CMD service cron start && runuser -l opencpu -c 'Rscript -e "BioInstaller::set_shiny_workers(3)" &>/log/BioInstaller_worker_main.log &' && runuser -l opencpu -c 'sh /usr/bin/start_shiny_server' && /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND
+CMD service cron start && runuser -l opencpu -c 'export AUTO_CREATE_BIOINSTALLER_DIR="TRUE";Rscript -e "BioInstaller::set_shiny_workers(3, auto_create = TRUE)" &' && runuser -l opencpu -c 'sh /usr/bin/start_shiny_server' && /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND

R/conda.R

@@ -12,7 +12,7 @@
 #' }
 conda <- function(suffix_params = "", prefix_params = "", conda = Sys.which('conda'), ...) {
   conda <- unname(conda)
-  if (conda == "") stop("Executable 'conda' Not Found.")
+  if (conda == "") {warning("Executable 'conda' Not Found."); return(FALSE)}
   objs <- system(sprintf("%s%s %s", prefix_params, conda, suffix_params), intern = TRUE, ...)
   x <- paste0(objs, collapse = "\n")
   return(x) 
@@ -32,6 +32,7 @@ conda <- function(suffix_params = "", prefix_params = "", conda = Sys.which('con
 conda.list <- function(env_name = "base", ...) {
   if (!is.null(env_name) && env_name != "") objs <- conda("list", prefix_params = sprintf("source activate %s;", env_name), ...)
   if (is.null (env_name) || env_name == "") objs <- conda("list", ...)
+  if (is.logical(objs) && !objs) {return(FALSE)}
   text <- paste0(objs, collapse = "\n")
   x <- tryCatch(read.table(text=text), error = function(e) {
     data.frame()
@@ -53,6 +54,7 @@ conda.list <- function(env_name = "base", ...) {
 #' }
 conda.env.list <- function(...) {
   objs <- conda("env list", ...)
+  if (is.logical(objs) && !objs) {return(FALSE)}
   text <- paste0(objs, collapse = "\n")
   x <- read.table(text=str_replace(text, " [*] ", ""), skip=2)
   colnames(x) <- c("env_name", "env_path")

R/spack.R

@@ -12,7 +12,7 @@
 #' }
 spack <- function(suffix_params = "", prefix_params = "", spack = Sys.which('spack'), ...) {
   spack <- unname(spack)
-  if (spack == "") stop("Executable 'spack' Not Found.")
+  if (spack == "") {warning("Executable 'spack' Not Found."); return(FALSE)}
   objs <- system(sprintf("%s%s %s", prefix_params, spack, suffix_params), intern = TRUE, ...)
   paste0(objs, collapse = "\n")
 }
@@ -28,6 +28,7 @@ spack <- function(suffix_params = "", prefix_params = "", spack = Sys.which('spa
 #' }
 spack.list <- function(...) {
   objs <- spack("list", ...)
+  if (is.logical(objs) && !objs) {return(FALSE)}
   text <- paste0(objs, collapse = "\n")
   x <- read.table(text=text)
   colnames(x) <- c("Name")

inst/extdata/config/shiny/shiny.conda.parameters.toml

@@ -27,7 +27,7 @@ label = ["Conda subcommands", "Conda environment", "Conda parameters"]
 conda_sub_cmd = ["clean", "config", "create", "info", "install",
                  "list", "package", "remove", "uninstall",
                  "search", "update", "upgrade"]
-conda_env_name = "!!glue {BioInstaller::conda.env.list()[,1]}"
+conda_env_name = "!!glue {conda_envs <- BioInstaller::conda.env.list(); if (is.data.frame(conda_envs)) conda_envs <- conda_envs[,1]}"
 [conda.paramters.conda_input_box.input.single_input.selected]
 conda_sub_cmd = "list"
 conda_env_name = "base"

inst/extdata/shiny/server_dashbord.R

@@ -274,15 +274,16 @@ dashbord_section_server <- function(input, output) {
   output <- custom_render_DT(input, output, "bioinstaller_items_monitor",
                              "get_bioinstaller_installed()")
   output <- custom_render_DT(input, output, "conda_envlist_monitor",
-                             "BioInstaller::conda.env.list()")
+                             "tryCatch(BioInstaller::conda.env.list(), warning=function(w){data.frame()})")
   output$conda_env_name_ui <- renderUI({
-    conda_envs <- BioInstaller::conda.env.list()[,1]
+    conda_envs <- BioInstaller::conda.env.list()
+    if (is.data.frame(conda_envs)) conda_envs <- conda_envs[,1]
     selectInput("conda_env_name", "Environment name",
                 choices = conda_envs,
                 selected = conda_envs[1])
   })
   output <- custom_render_DT(input, output, "conda_items_monitor",
-                             "BioInstaller::conda.list(env_name = input$conda_env_name)")
+                             "tryCatch(BioInstaller::conda.list(env_name = input$conda_env_name), warning = function(w){data.frame()})")
 
   output$spack_items_monitor <- renderPrint({
     cat(BioInstaller::spack("find"))

inst/extdata/shiny/server_download.R

@@ -68,7 +68,8 @@ download_section_server <- function(input, output) {
 
 
   output$conda_installer_ui <- renderUI({
-    conda_envs <- BioInstaller::conda.env.list()[,1]
+    conda_envs <- BioInstaller::conda.env.list()
+    if (is.data.frame(conda_envs)) conda_envs <- conda_envs[,1]
     HTML(
     paste0(shiny::selectInput("installer_conda_sub_command", "Conda subcommands",
                        c("clean", "config", "create",
@@ -86,7 +87,8 @@ download_section_server <- function(input, output) {
   })
 
   output$spack_installer_ui <- renderUI({
-    conda_envs <- BioInstaller::conda.env.list()[,1]
+    conda_envs <- BioInstaller::conda.env.list()
+    if (is.data.frame(conda_envs)) conda_envs <- conda_envs[,1]
     HTML(
       paste0(shiny::selectInput("installer_spack_sub_command", "Sub command of spack",
                                 c("list", "info", "find",