Warp2D - 2D Time Alignment Workflow

Wsdl

Wsdl Operation

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Wsdl

Wsdl Operation

Script

Thread.sleep(60000);
out = in;

Script

import java.io.*;

int BUFF_SIZE = 100000;
byte[] buffer = new byte[BUFF_SIZE];
String base_url="";
String session_id="";
URL postURL;
HttpURLConnection con = null;
String BASE_URL = "http://www.nbpp.nl/warp2d/";
String AUTH_URL = "tavernaProfile.php";
String resultsZipFile = ""+ pathToFile(".") + "/myResults.zip" ;
String contents = "";
        PrintWriter out = null;
        try {
	    postURL = new URL(BASE_URL.concat(AUTH_URL));
            con = (HttpURLConnection) postURL.openConnection();
            con.setUseCaches(false); // do not use cache
            con.setDoOutput(true); // use for output
            con.setDoInput(true); // use the POST method to submit the form
            con.setRequestMethod("POST"); // use the POST method to submit the form

            out = new PrintWriter(con.getOutputStream());
            String postStr = "Email="+AuthKey;           
            out.println(postStr); // send to server
            out.close(); // close outputstream
            String inputLine = ""; //Stores the line of text returned by the server
            BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
            while ((inputLine = in.readLine()) != null) {
                session_id += inputLine;
            }
            in.close();
            System.out.println(session_id);
	} catch (MalformedURLException ex) {
            //Logger.getLogger("warp2d workflow").log(Level.SEVERE, null, ex);
        } catch (IOException ex) {
           // Logger.getLogger("warp2d workflow").log(Level.SEVERE, null, ex);
        } finally {
            out.close();
        }

if (session_id == null || session_id.trim().isEmpty() ) {
	contents = "Error";
	exit(1);
}
	String downloadURL="warp2d/tavernaDownloadFile.php?SessionID="+session_id+"&jobId="+jobId;

        try {
	    postURL = new URL(BASE_URL.concat(downloadURL));
            con = (HttpURLConnection) postURL.openConnection();
            con.setUseCaches(false);
            con.setDoOutput(true); 
            con.setDoInput(true);
            con.setRequestMethod("GET");

/**
 Copy
*/
	fileIn_strm = con.getInputStream();	
        FileOutputStream fileOut_strm = new FileOutputStream(new File(resultsZipFile));
	try {            
            while (true) {
                synchronized (buffer) {
                    int amountRead = fileIn_strm.read(buffer);
                    if (amountRead == -1) {
                        break;
                    }
                    fileOut_strm.write(buffer, 0, amountRead);
                }
            }
	} finally {
            if (fileIn_strm != null) {
                fileIn_strm.close();
            }
            if (fileOut_strm != null) {
                fileOut_strm.close();
            }
        }

        } catch (IOException ex) {
		contents +="\r\n Error Downloading";
		exit(1);
        } finally {
            out.close();
        }

contents = contents + "\r\n Warped Result files has been download at: "+ resultsZipFile ;

Script

/************* functions ******************/

File validateInputFile(String optName) {
        File inputFile =  new File(optName);
            if (inputFile.exists()) {
                if (inputFile.isFile() && inputFile.canRead() && inputFile.length() > 0) {
                    return inputFile;
                } else {
                    System.err.println("Either supplied input file is a Directory or can not reade it");
                    return null;
                }
            } else {
                System.err.println("No input file or not correct argument!");
                return null;
            }
}
String getSession() {
	String ssid="";
	HttpURLConnection con = null;       
        PrintWriter out = null;
	try {
        	URL postURL = new URL(BASE_URL.concat(AUTH_URL));
	        con = (HttpURLConnection) postURL.openConnection();
		con.setUseCaches(false); // do not use cache
		con.setDoOutput(true); // use for output
		con.setDoInput(true); // use the POST method to submit the form
		con.setRequestMethod("POST"); // use the POST method to submit the form
		out = new PrintWriter(con.getOutputStream());
		String postStr = "Email="+API_Key;
		out.println(postStr); // send to server
		out.close(); // close outputstream
		String inputLine = ""; //Stores the line of text returned by the server
		BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
		while ((inputLine = in.readLine()) != null) {
                	ssid += inputLine;
            	}
		in.close();
	} catch (MalformedURLException ex) {
		message += "\r\n Authentication fail:"+ ex;
        } catch (IOException ex) {
		message += "\r\n Authentication fail:"+ ex;
        } finally {
		out.close();
        }
	return ssid;
}

String uploadFile(File uploadedfile) {
        String resultsPage = ""; // Stores the complete HTML results page
        PrintWriter out = null;
        String lineEnd = "\r\n";
        String twoHyphens = "--";
        String boundary = "*****";

        try {
            URL postURL = new URL(BASE_URL.concat(UPLOAD_SUBURL));
            HttpURLConnection con = (HttpURLConnection) postURL.openConnection();
            con.setUseCaches(false); // do not use cache
            con.setDoOutput(true); // use for output
            con.setDoInput(true); // use the POST method to submit the form
            con.setRequestMethod("POST"); // use the POST method to submit the form
            con.setRequestProperty("Connection", "Keep-Alive");
            con.setRequestProperty("Content-Type", "multipart/form-data; boundary=" + boundary);
            out = new PrintWriter(con.getOutputStream());            
            out.print(twoHyphens + boundary + lineEnd);
            out.print("Content-Disposition: form-data; name=\"SessionID\";" + lineEnd);
            out.print(lineEnd);
            out.print(session_id);
            out.print(lineEnd);
            out.print(twoHyphens + boundary + lineEnd);
            out.print("Content-Disposition: form-data; name=\"uploadedfile\"; filename=\"" + uploadedfile.getName() + "\"");
            out.print(lineEnd);
            out.print(lineEnd);
            pipe(uploadedfile, out);
            out.print(lineEnd);
            out.print(twoHyphens + boundary + twoHyphens + lineEnd);
            out.flush();
            out.close(); // close outputstream
            String inputLine = ""; //Stores the line of text returned by the server
            BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
            while ((inputLine = in.readLine()) != null) {
                resultsPage += inputLine;
            }
            in.close();
		message += "\r\n uploadFile Return Result: "+ resultsPage;
        } catch (MalformedURLException ex) {
		message += "\r\n File upload fail:"+ ex;
        } catch (IOException ex) {		
		message += "\r\n File upload fail:"+ ex;
        } finally {
            out.close();
        }
        return resultsPage;
    }

void pipe(File aFile, PrintWriter out) throws IOException {
        StringBuilder contents = new StringBuilder();
        BufferedReader input = new BufferedReader(new FileReader(aFile));
        try {
            String line = null; //not declared within while loop

            /*
             * readLine is a bit quirky :
             * it returns the content of a line MINUS the newline.
             * it returns null only for the END of the stream.
             * it returns an empty String if two newlines appear in a row.
             */
            while ((line = input.readLine()) != null) {
                out.println(line);
                contents.append(line);
                contents.append(System.getProperty("line.separator"));
            }
        } finally {
            input.close();
            out.flush();
        }
    }

String BASE_URL = "http://www.nbpp.nl/warp2d/";
String AUTH_URL = "tavernaProfile.php";
String UPLOAD_SUBURL = "warp2d/tavernaUploadFile.php";
String message ="";
File refFile = validateInputFile(ref_peaklistFile);
File sampFile = validateInputFile(samp_peaklistFile);
	if (refFile == null || sampFile == null || !refFile.exists() || !sampFile.exists()) {
		message += "\r\nEither refrence or sampl. Peaklist not specified. exiting...";
        	print("Either refrence or sampl. Peaklist not specified. exiting...");
                exit(1);
        }

String session_id = getSession();

if (session_id == null || session_id.trim().isEmpty() ) {
	message += "\r\n Error";
	exit(1);
}
message += "\r\n Uploading refPeaklist file";
String refPeaklist_fileRef = uploadFile(refFile);
message += "\r\n Uploading sampPeaklist file";
String sampPeaklist_fileRef = uploadFile(sampFile);
System.out.println(message);