diff helper.R @ 6:7c54fd452b8e draft

add kableExtra package

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/helper.R	Wed Apr 18 15:59:38 2018 -0400
@@ -0,0 +1,72 @@
+#' \code{getopt_specification_matrix} returns a getopt specification matrix.
+#'
+#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
+#' 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)
+  # check if there are duplicated short flags
+  short_flags = df[, 1]
+  if (length(unique(short_flags)) < length(short_flags)) {
+    cat('----Duplicated short flags found ----\n')
+    cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
+    stop('Duplicated short flags are not allowed.')
+  }
+  
+  # use short flags to generate long flags
+  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])
+  
+  as.matrix(df2)
+}
+
+
+
+#' \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
+        })
+      }
+    }
+  )
+}