diff helper.R @ 5:2c663ddb8488 draft

planemo upload commit f0ae5255b6c75f69c85319bba8da742be83f27d2-dirty

--- a/helper.R	Wed Apr 18 10:03:56 2018 -0400
+++ b/helper.R	Wed Apr 25 16:47:59 2018 -0400
@@ -4,9 +4,14 @@
 #' 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_DIR')) {
-  df = read.csv(paste0(tool_dir, '/', specification_file),
-                header = TRUE, stringsAsFactors = FALSE)
+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]
   if (length(unique(short_flags)) < length(short_flags)) {
@@ -19,10 +24,12 @@
   long_flags = paste0('X_', df[, 1])
   
   # specification matrix
-  df2 = data.frame(long_flags = long_flags,
-                   short_flags = df[, 1],
-                   argument_mask = df[, 2],
-                   data_type = df[, 3])
+  df2 = data.frame(
+    long_flags = long_flags,
+    short_flags = df[, 1],
+    argument_mask = df[, 2],
+    data_type = df[, 3]
+  )
   
   as.matrix(df2)
 }
@@ -30,43 +37,46 @@
 
 
 #' \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 = '.'){
+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 = 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"}')
+  dirs = list.dirs(path = dir,
+                   recursive = FALSE,
+                   full.names = TRUE)
+  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) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        # hide vakata-jstree-3.3.5 folder
+        if (path_end != 'vakata-jstree-3.3.5') {
+          # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+          li_item = tags$li(path_end, file_tree(x))
+          li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
           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
-        })
-      }
+        }
+      })
     }
-  )
+  })
 }