Scripts to convert Taverna output files into a single CSV

workflow2csv.js

/* 
 * This script reads all files inside a given directory. The filenames are in the following format:
 *  1 ... n --> sub workflow n returned a value
 *  n.error --> sub workflow n threw an error and was not successful
 *
 */

var io = require("io");
var fs = require("fs");
var term = require("ringo/term");
var sytem = require("system");


if (system.args.length !== 2) {
   term.writeln(term.RED, "Missing parameter: path to directory with input file.");
}

var count = 0;
do {

   // Read the next file from the automated workflow
   var fileName = system.args[1] + "/" + (++count);

   if (fs.exists(fileName)) {
      var stream = fs.open(fileName, "r");
      term.writeln(count + "," + stream.read());
   } else if (fs.exists(fileName + ".error")) {
      term.writeln(count + ",-1");
   } else {
      // Abort. Last file read
      count = -1;
   }
} while (count > 0);