public String executeQuery(String queryString) {
    /*
    //System.out.println(queryString);
    Query query = QueryFactory.create(queryString);

    QueryExecution qe = QueryExecutionFactory.create(query, model);
    ResultSet results = qe.execSelect();

    ByteArrayOutputStream ostream = new ByteArrayOutputStream();

    ResultSetFormatter.out(ostream, results, query);
    //ResultSetFormatter.out(System.out, results, query);
    String r = "";
    try{
        r = new String(ostream.toByteArray(), "UTF-8");
        //System.out.println(r);
    }
    catch(Exception e){
        System.out.println(e.getMessage());
    }
    qe.close();
    return r;
    */

    //// new added for test JSON output
    try {
      Query query = QueryFactory.create(queryString);

      QueryExecution qe = QueryExecutionFactory.create(query, model);
      ResultSet results = qe.execSelect();

      ByteArrayOutputStream ostream = new ByteArrayOutputStream();
      ResultSetFormatter.outputAsJSON(ostream, results);
      // ResultSetFormatter.out(ostream, results, query);
      // ResultSetFormatter.out(System.out, results, query);
      String r = "";
      try {
        r = new String(ostream.toByteArray(), "UTF-8");
        // System.out.println(r);
      } catch (Exception e) {
        System.out.println(e.getMessage());
      }
      qe.close();
      return r;
    } catch (Exception e) {
      System.out.println(e.toString());
      return "";
    }
  }
  public ArrayList<QuerySolution> executeQueryRaw(String queryString) {
    // System.out.println(queryString);
    try {
      Query query = QueryFactory.create(queryString);

      QueryExecution qe = QueryExecutionFactory.create(query, model);
      ResultSet results = qe.execSelect();
      /*
      ByteArrayOutputStream ostream = new ByteArrayOutputStream();
      ResultSetFormatter.out(ostream, results, query);
      //ResultSetFormatter.out(System.out, results, query);
      String r = "";
      try{
          r = new String(ostream.toByteArray(), "UTF-8");
          System.out.println(r);
      }
      catch(Exception e){
          System.out.println(e.getMessage());
      }
      */

      /*
      ArrayList<QuerySolution> resList = new ArrayList<QuerySolution>();
      if(results.hasNext()) {

          QuerySolution qs = results.next();
          resList.add(qs);
          //double x = qs.getLiteral("x").getFloat();
          //Literal y = qs.getLiteral("y");
          //Literal theta = qs.getLiteral("theta");
      }
      */
      ArrayList<QuerySolution> resList = (ArrayList) ResultSetFormatter.toList(results);
      qe.close();
      return resList; // results;
    } catch (Exception e) {
      System.out.println(e.toString());
      return new ArrayList<QuerySolution>();
    }
  }
  /**
   * agINFRA Social visualization components aux. tool
   *
   * @param args
   * @throws FileNotFoundException
   */
  public static void main(String[] args) throws FileNotFoundException {

    System.out.println("Hello");

    // PARAMS
    if (args.length != 5) {
      System.out.println(
          "Proper Arguments are: [Dataset files full path] [URL store] [URI graph base] [Destination directory] [commit to 4store]");
      System.out.println(
          "Example: java -jar xxxxx.jar /home/carlos/Desktop/agINFRA-workflow/workflow/loms/bioe/ http://localhost:81 http://laclo.laflor /home/carlos/Desktop/agINFRA-workflow/workflow/loms/bioerdf/ false");
      System.exit(0);
    }

    String dspath = args[0];
    String urlStore = args[1];
    String uriGraph = args[2];
    String destination = args[3];
    String commit4store_arg = args[4];

    /*String dspath = "/home/carlos/workspace/WebAPI/ds/";
    String urlStore = "http://4store.ipb.ac.rs:81";
    String uriGraph = "http://aginfra.eu";
    String localCouchdbProxy = "localhost";
    String commit4store_arg = "no";*/

    boolean commit4store = false;
    if (commit4store_arg.equals("commit")) commit4store = true;

    String output = "0"; // valor de retorno
    String status = "ERROR";
    String errorDescription = "";
    String tmpMetadataFile = "";
    // check if type is valid
    boolean bContinuar = true;
    // StorageService service;
    ArrayList<KeyValue> keyValues = new ArrayList<KeyValue>();
    HashMap fileDatasetMap = new HashMap();

    /*
    //Fetch and download IPB metadata sets.
    //CouchDB via PHP local proxy
    //http://agro.ipb.ac.rs/agcouchdb/_design/datasets/_view/list?limit=10
    //http://localhost/ag_couch_proxy/proxy-IPB-datasets.php
    try{
    	System.out.println("Connecting IPB CouchDB...");

    	String url = "http://"+localCouchdbProxy+"/ag_couch_proxy/proxy-IPB-datasets.php?dspath="+dspath;
    	WebResource webResource = Client.create().resource(url);
    	//System.out.println(url);
    	ClientResponse response = webResource.accept(MediaType.APPLICATION_JSON,MediaType.TEXT_HTML,MediaType.WILDCARD).get(ClientResponse.class);
    	if (response.getStatus() != 200) {
    	   throw new RuntimeException("Failed : HTTP error code : " + response.getStatus());
    	}


    	//String response_str = response.getEntity(String.class);	//I don't know why this does not work when running in shell
    	String response_str = getStringFromInputStream(response.getEntityInputStream());
    	//System.out.println(response_str);	//debug

    	System.out.println("Finished IPB call");



    	System.out.println("Reading Dataset Map...");

    	//READ CSV
    	//create BufferedReader to read csv file
              StringTokenizer st = null;
              int lineNumber = 0, tokenNumber = 0;

              //read comma separated file line by line
              Scanner scanner = new Scanner(response_str);
              while (scanner.hasNextLine())
              {
                      lineNumber++;
                      String strLine = scanner.nextLine();

                      //break comma separated line using ","
                      st = new StringTokenizer(strLine, ",");

                      String datasetFile = "";
                      String datasetName = "";

                      while(st.hasMoreTokens())
                      {
                              //display csv values
                              tokenNumber++;
                              //System.out.println("Line # " + lineNumber +", Token # " + tokenNumber + ", Token : "+ st.nextToken());
                              if(tokenNumber == 1)
                              	datasetFile = st.nextToken();
                              if(tokenNumber == 2)
                              	datasetName = st.nextToken();
                      }

                      fileDatasetMap.put(datasetFile,datasetName);

                      //reset token number
                      tokenNumber = 0;

              }

              System.out.println("Finished Map reading");

    } catch (Exception e) {
    	e.printStackTrace();
    }
    */

    /*
    //foreach dataset.tar.gz **
    //Iterate
    File root = new File("ds/");
    Collection files = FileUtils.listFiles(root, null, false);

    //mini db processed files
    ArrayList processed = new ArrayList();
          try {
          	BufferedReader br = new BufferedReader(new FileReader("processed.txt"));
              String line;
          	while((line = br.readLine()) != null) {
          		processed.add(line);
    	}
    } catch (IOException e) {
    	e.printStackTrace();
    }

    System.out.println("Iterating all downloaded datasets tgz files...");
    int dsCount = 0;

    for (Iterator iterator = files.iterator(); iterator.hasNext();) {
    	File dsFile = (File) iterator.next();
    	String inputDataset = dsFile.getAbsolutePath();

    	dsCount = dsCount + 1;
    	System.out.println("  Processing "+dsCount+":"+inputDataset);	//debug

    	//po5i: mini db processed files
    	if(processed.contains(inputDataset)){
    		System.out.println("    >>Already processed... skipping... ");
    		continue;
    	}
    	else
    	{
    		processed.add(inputDataset);
    		try {
    			FileWriter fileWritter = new FileWriter("processed.txt",true);
    			BufferedWriter bufferWritter = new BufferedWriter(fileWritter);
       	        bufferWritter.write(inputDataset+"\n");
       	        bufferWritter.close();
    		} catch (IOException e) {
    			e.printStackTrace();
    		}
    	}

    	//Set the GraphID
    	String graphID = (String) fileDatasetMap.get(dsFile.getName());
    	System.out.println("    Graph:: "+graphID);



    	//Uncompress the dataset and iterate throughout the files
    	try {
    		FileInputStream fin = new FileInputStream(inputDataset);
    		BufferedInputStream in = new BufferedInputStream(fin);
    		FileOutputStream out = new FileOutputStream("ds/archive.tar");
    		GzipCompressorInputStream gzIn;
    		gzIn = new GzipCompressorInputStream(in);
    		final byte[] buffer = new byte[1024];
    		int n = 0;
    		while (-1 != (n = gzIn.read(buffer))) {
    		    out.write(buffer, 0, n);
    		}
    		out.close();
    		gzIn.close();

    		//read the tar
    		File input = new File("ds/archive.tar"); //getFile("ds/archive.tar");
            InputStream is = new FileInputStream(input);
            ArchiveInputStream in1 = new ArchiveStreamFactory().createArchiveInputStream("tar", is);
            TarArchiveEntry entry = (TarArchiveEntry)in1.getNextEntry();

            while (entry != null) {// create a file with the same name as the tarEntry
                File destPath = new File("ds/extract/" + entry.getName());
                if (entry.isDirectory()) {
                    destPath.mkdirs();
                } else {
                    destPath.createNewFile();
                    OutputStream out1 = new FileOutputStream(destPath);
                    IOUtils.copy(in1, out1);
                    out1.close();
                }
                entry = (TarArchiveEntry)in1.getNextEntry();
            }

            in1.close();
    	} catch (Exception e) {
    		e.printStackTrace();
    	}*/

    // Iterate on extracted files
    try {
      File root1 = new File(dspath);
      Collection files1 = FileUtils.listFiles(root1, null, true);
      // new File(dspath+"../rdf").mkdir();

      for (Iterator iterator1 = files1.iterator(); iterator1.hasNext(); ) {
        File lomFile = (File) iterator1.next();
        String inputFile = lomFile.getAbsolutePath();

        // System.out.println("      Processing:"+inputFile);	//debug

        if (bContinuar) {
          // save metadata stream in a local file
          tmpMetadataFile = inputFile;
          String valid = "1";
          // valid = XMLValidator.validate(tmpMetadataFile,
          //		StorageService.getXSDFile(storageType));
          boolean hasSource = false;
          if (tmpMetadataFile.length() > 0) {
            // TODO: metadata validation
            // valid = "1";
            if (valid.equalsIgnoreCase("1")) {
              // generate id for the new material

              // output = graphID;
              // save metatada in rdf
              // obtain key-value pairs
              try {
                LOMParser.parseToKeyValue(tmpMetadataFile);
                if (!LOMParser.keyValues.isEmpty()) {
                  keyValues = LOMParser.keyValues;
                }
              } catch (MalformedURLException e1) {
                e1.printStackTrace();
              } catch (IOException e1) {
                e1.printStackTrace();
              }

              if (!keyValues.isEmpty()) {

                int canSave = 1;

                if (canSave > 0) {

                  // 4store
                  // save to rdf this triple (slow)
                  // HandleGraph graph = new HandleGraph(urlStore,uriGraph);
                  // result = graph.AppendTriple(graphID, keyValues);

                  // 4store
                  // prepare RDF file (better)
                  try {
                    // HELP: http://www.roseindia.net/tutorials/rdf/generateRDF.shtml

                    Model model = ModelFactory.createDefaultModel();

                    for (KeyValue kv : keyValues) {
                      String s = uriGraph + "/" + lomFile.getName();
                      // String p = URLEncoder.encode(kv.getKey(),"UTF-8");
                      String p = kv.getKey().replaceAll("[^\\w\\s\\.]", "_");
                      String v = kv.getValue();

                      // obtener el autor del CDATA en variable v
                      if (v.contains("CDATA")) {
                        v = v.replace("<![CDATA[", "");
                        v = v.replace("]]>", "");

                        VCardEngine vcardEngine = new VCardEngine();
                        VCard vcard = vcardEngine.parse(v);
                        if (vcard.hasFN()) v = vcard.getFN().getFormattedName();
                        else if (vcard.hasN()) v = vcard.getN().getFamilyName();
                        else {
                          // format string it can be parsed.

                          StringBuffer sb;
                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("VERSION:"), "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf(" FN:") + 1, "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf(" N:") + 1, "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("ORG:"), "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("EMAIL:"), "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("END:"), "\n");
                          v = sb.toString();

                          vcard = vcardEngine.parse(v);
                          if (vcard.hasFN()) v = vcard.getFN().getFormattedName();
                          else if (vcard.hasN()) v = vcard.getN().getFamilyName();
                          else {
                            System.out.println(" ~ ~ Problem with:::" + v);
                            System.out.println(" ~ ~ When Processing:" + inputFile); // debug
                          }

                          // System.out.println(" ~ author is: "+v);
                        }
                      }

                      // System.out.println("p: "+p+"\t\t\t v: "+v);

                      Property lom_prop = model.createProperty("http://ltsc.ieee.org/xsd/LOM#" + p);
                      Resource node = model.createResource(s).addProperty(lom_prop, v);
                    }

                    FileOutputStream fop = null;
                    File rdfFile =
                        new File(destination + lomFile.getName().replace(".xml", ".rdf"));
                    fop = new FileOutputStream(rdfFile);

                    // model.write(System.out);
                    model.write(fop);

                    // 4store
                    if (commit4store) {
                      HandleGraph graph = new HandleGraph(urlStore, uriGraph);
                      int result = graph.AppendGraph(rdfFile.getAbsolutePath()); // returns 0-1
                    }

                  } catch (Exception e) {
                    e.printStackTrace();
                  }
                  // break;	//debug

                }
                output = "1";
              } else {
                output = "0";
                errorDescription = "Could not handle metadata to key-value";
              }

            } else {
              errorDescription = "XML Validation:" + valid;
            }
          } else {
            errorDescription = "Could not handle metadata file";
          }
        }
      }
    } catch (Exception e) {
      e.printStackTrace();
    }

    /*//break;	//debug

    			//Borrar todo lo de ds/extract/, rdf y el archive.tar para liberar espacio
    			try {
    				FileUtils.deleteDirectory(new File("ds/extract/"));
    				FileUtils.deleteDirectory(new File("ds/rdf/"));
    				FileUtils.deleteQuietly(new File("ds/archive.tar"));

    			} catch (IOException e) {
    				e.printStackTrace();
    			}

    		}
    */

    // prepare response
    if (output.contentEquals("0")) status = "ERROR: " + errorDescription;
    else status = "OK";

    System.out.println(status);
  }