diff helper.R @ 4:c7de860e5be7 draft

add jstree

--- a/helper.R	Sun Mar 18 12:29:18 2018 -0400
+++ b/helper.R	Wed Apr 18 10:03:56 2018 -0400
@@ -4,8 +4,8 @@
 #' The first column are short flags, the second column are argument masks, the third column
 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
 #' @param gtg_name the name of a running GTG.
-getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIRECTORY')) {
-  df = read.csv(paste0(tool_dir, specification_file),
+getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
+  df = read.csv(paste0(tool_dir, '/', specification_file),
                 header = TRUE, stringsAsFactors = FALSE)
   # check if there are duplicated short flags
   short_flags = df[, 1]
@@ -25,4 +25,48 @@
                    data_type = df[, 3])
   
   as.matrix(df2)
-}
\ No newline at end of file
+}
+
+
+
+#' \code{file_tree} generate file tree of a directory in the format of HTML lists.
+#' 
+#' @param dir the path to the directory for generating the file tree.
+#' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
+# define a recursive function to build html string of the file tree
+file_tree = function(dir = '.'){
+  # get the OUTPUT_DIR folder data: dataset_NUMBER_files
+  report_files_path = Sys.getenv('REPORT_FILES_PATH')
+  output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
+  
+  files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
+  # files also include directorys, need to remove directorys
+  files = files[!dir.exists(files)]
+  dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
+  # hide vakata-jstree-3.3.5 folder
+  #jstree_index = grep(pattern = 'vakata-jstree-3.3.5', x = dirs)
+  #dirs = dirs[-jstree_index]
+  tags$ul(
+    {
+      if (length(files) > 0) {
+        lapply(files, function(x){
+          path_end = tail(strsplit(x, '/')[[1]],1)
+          href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+          li_item = tags$li(tags$a(path_end, href=href_path))
+          li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
+          li_item
+        })
+      }
+    },
+    {
+      if (length(dirs) > 0) {
+        lapply(dirs, function(x){
+          x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+          li_item = tags$li(x_path, file_tree(x))
+          li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
+          li_item
+        })
+      }
+    }
+  )
+}