Profiling UltraESB with YourKit Java Profiler

YourKit Java Profiler is a rich Java profiling tool that can be used to easily identify CPU usage, memory usage, thread utilisation, garbage collections and possible dead locks of your  Java applications. In this post I'll briefly go through how to profile an UltraESB instance hosted on a EC2 instance using YourKit Java Profiler.

Before move into further details, you have to download YourKit Java profiler from their site. If you don't have a distribution of UltraESB, you can download a binary distribution of UltraESB from here.

EC2 Setup

Because this is a remote profiling between a EC2 hosted UltraESB instance and your local YourKit application, at the setup of ESC2 instance, ports 10001 - 10010 should be opened for external access.

Figure 1

Both UltraESB distribution and YourKit has to be on EC2 instance. To configure UltraESB with YourKit, JVM_OPTS line of ultraesb.sh in <UltraESB Home>/bin directory should be changed as figure 2.

Figure 2

Path of the libyjpagnet.so file should be changed according to the platform. Once those configurations are done, now you can start UltraESB from

<UltraESB Home>/bin/ultaesb.sh

If configuration is correct, you can see a line like following at the top of ultraesb log.

[YourKit Java Profiler 2015 build 15070] Log file: /home/ubuntu/.yjp/log/java-

1445.log

You can put a load on UltraESB using jb-run tool that is shipped with UltraESB distribution.

cd <UltraESB Home>/bin

./uterm.sh

jbrun -c 100 -d 1 -k -m POST -n 1000 -p /home/ubuntu/payload.txt -s 100 -t 150000 http://localhost:8280/service/echo-back 

YourKit (local machine) setup

Start YourKit by running <YourKit Home>/bin/yjp.sh

Click "Connect to remote application". Fill EC2 machine username and domain. (Figure 3)

Figure 3

Add security credentials that you used to log into EC2 instance over ssh (Figure 4)

Figure 4

Then you can see the dashboard of YourKit that describes memory usage statistics, thread utilisation and etc,

To do a CPU profiling, click start CPU profiling button

Launching simple echo experiment in Apache Airavata

Apache Airavata is a science gateway application that enables managing different scientific computational tasks among computational resources. Here I describe how to register a simple echo application in Airavata and launch it using Airavata API

1. Clone Airavata source https://github.com/apache/airavata/tree/0.14_release and build

2. Start Airavata server as given in https://cwiki.apache.org/confluence/display/AIRAVATA/XBAYA+Quick-Start+Tutorial

3. Run Sample class to register echo application
https://github.com/apache/airavata/blob/0.14_release/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/RegisterSampleData.java

4. Run following command to create and run the experiment

Airavata.Client airavataClient = AiravataClientFactory.createAiravataClient("127.0.0.1", 8930);

String appId = "Echo_e82aa96b-66ea-4f31-97e7-1182a32e55d2";

List exInputs = new ArrayList();
InputDataObjectType input = new InputDataObjectType();
input.setName("Input_to_Echo");
input.setType(DataType.STRING);
input.setValue("Echoed_Output=Hello World");
exInputs.add(input);

List exOut = new ArrayList();
OutputDataObjectType output = new OutputDataObjectType();
output.setName("Echoed_Output");
output.setType(DataType.STRING);
output.setValue("");
exOut.add(output);

Experiment simpleExperiment = ExperimentModelUtil.createSimpleExperiment("default", "admin", "echoExperiment", "Echo Exp", appId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);

Map computeResources = getClient().getAvailableAppInterfaceComputeResources(appId);
String id = computeResources.keySet().iterator().next();
String resourceName = computeResources.get(id);
System.out.println(computeResources.size());
System.out.println(id);
System.out.println(resourceName);
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1, "sds128");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);

String exp = airavataClient.createExperiment(simpleExperiment);
airavataClient.launchExperiment(exp,"sample");

SinMin - Sinhala Corpus Project

We (Dimuthu Upeksha, Chamila Wijayarathna, Maduranga Siriwardan, Lahiru Lasadun) started SinMin - Sinhala Corpus Project as final year undergraduates for our final year project under the supervision of Dr. Chinthana Wimalasuriya, Mr. N. H. N. D. de Silva and Prof Gihan Dias.

A rich language corpus enables a wide area of research topics for a language. Most of them include

1. Statistical analysis of the language usage pattens
2. Translators
3. Spell and Grammar Tools
4. Backend support to third party applications like OCR tools

Usually a corpus contains a collection of authentic texts of the language. However rather than storing them as raw text files, Sinmin further stores them in different databases with different schemas. This enables Sinmin to easily process language data in realtime.  In addition to that SinMin Corpus contains a REST API that enable querying and finding data through third party applications.

SinMin web interface provides ability to illustrate and find patterns that occur in Sinhala Language over different time periods and different categories.

Useful Links

• SinMin Web : http://sinhala-corpus.projects.uom.lk/sinmin-web
• Crawled raw data files in XML format : http://sinhala-corpus.projects.uom.lk/sinmin-web/data
• Documentation : http://sinhala-corpus.projects.uom.lk/docs
• API documentation : http://sinhala-corpus.projects.uom.lk/docs/display/ds/REST+API
• Source Code : https://github.com/sinmin/core
• Additional Resources
• http://www.slideshare.net/cdwijayarathna/sinmin-literature-review-presentation
• http://www.slideshare.net/cdwijayarathna/implementing-a-corpus-for-sinhala-language
• http://www.slideshare.net/cdwijayarathna/sinmin-final-presentation
• Chamila's blog post : http://cdwijayarathna.blogspot.com/2015/04/sinmin-corpus-for-sinhala-language.html

SinMin Sinhala Corpus currently crawl data from following sources

• Sinhala Online Newspapers
• Lankadeepa - http://lankadeepa.lk/
• Divaina - http://www.divaina.com/
• Dinamina - http://www.dinamina.lk/2014/06/26/
• Lakbima - http://www.lakbima.lk/
• Mawbima - http://www.mawbima.lk/
• Rawaya - http://ravaya.lk/
• Silumina - http://www.silumina.lk/
• Sinhala News Sites
• Ada Derana - http://sinhala.adaderana.lk/
• Sinhala Religious and Educational Magazines
• Aloka Udapadi - http://www.lakehouse.lk/alokoudapadi/
• Budusarana - http://www.lakehouse.lk/budusarana/
• Namaskara - http://namaskara.lk/
• Sarasawiya - http://sarasaviya.lk/
• Vidusara - http://www.vidusara.com/
• Wijeya - http://www.wijeya.lk/
• Sri Lanka Gazette in Sinhala - http://documents.gov.lk/gazette/
• Online Mahawansaya - http://mahamegha.lk/mahawansa/
• Sinhala Movie Subtitles - http://www.baiscopelk.com/category/සිංහල-උපසිරැස/
• Sinhala Wikipedia - http://si.wikipedia.org/
• Sinhala Blogs 

Java Wrapper for Tesseract OCR Library

Tesseract is a very popular OCR library written in C++. It can be simply used to identify characters in a given image that contains text. In addition to that it can be used to get positions of each word/ character. Tesseract provides a command line tool and a C++ api to give services to users. However there is not a implementation for Java users that can directly use Tesseract for their applications.

As a part of my GSoC project in Apache PDFBox  I implemented a Java wrapper for Tesseract C++ api that can be used by Java users to directly use Tesseract in their applications. Code repository can be found from here.

To use Java API simply import Tesseract-JNI-Wrapper-1.0.0.jar to your project. If you are using maven, add this to your pom

<dependency>
  <groupId>org.apache.pdfbox.ocr</groupId>
  <artifactId>Tesseract-JNI-Wrapper</artifactId>
  <name>Tesseract Jni Wrapper</name>
  <version>1.0.0</version>
</dependency>

Here is a sample code that can use Java API invoke Tesseract.

public String getOCRText(BufferedImage image){ //You need to send BufferedImage (RGB) of scanned image
  TessBaseAPI api = new TessBaseAPI();
  boolean init = api.init("src/main/resources/data", "eng"); // position of Training data files
  api.setBufferedImage(image);
  String text = api.getUTF8Text();
  System.out.println(text);
  api.end();
  return text;
}

Getting positions of each OCRed word

public void printOCRTextPositions(BufferedImage image){
  TessBaseAPI api = new TessBaseAPI();
  boolean init = api.init("src/main/resources/data", "eng");
  api.setBufferedImage(image);
  api.getResultIterator();
  if (api.isResultIteratorAvailable()) {
    do {
      System.out.println(api.getWord().trim());
      String result = api.getBoundingBox();
      System.out.println(result);
    } while (api.resultIteratorNext());
  }
  api.end();
}

P.S.
This wrapper currently is working in MacOS and Linux environments. It wasn't tested in Windows environments. If anyone is willing to develop or improve functionalities of this wrapper please let me know.

Continuous Integration for GitHub - Travis CI

Travis CI is a very impressive and cool CI tool that can directly fetch and automatically build your GitHub projects. Following few steps you can easily integrate your GitHub projects with Travis CI

1. Got to https://travis-ci.org/ and log in using your GitHub account

2. click + button and add your project to Travis CI

3. Add .travis.yml file to the root folder of the project and push it to GitHub
This is the file that contains configuration details to Travis CI about your project details like language and build instructions
If your project is a java maven project, you can simply add

language: java

install: mvn install -Dmaven.compiler.target=1.6 -Dmaven.compiler.source=1.6 -DskipTests=true

script: mvn test -Dmaven.compiler.target=1.6 -Dmaven.compiler.source=1.6

For more configuration details refer to the documentation of Travis CI

4. Do some change to your project and push it to GitHub. Commit will be reflected in Travis Console same time and it will start to build project automatically and send build details to your mail.

LDAP connector for WSO2 ESB

As we were working on our intern project : "Infra portal", we had to connect to WSO2 user store LDAP (Lightweight Directory Access Protocol) directory in several ways like authenticating users, getting user list in a particular group, adding new entries (users in our case), editing entries and deleting them. Currently these operations can be done using javax.naming.* packages in java. However because most of our developments are done in jaggery, we had to write a java client for each property and integrate it with jaggery server. Then we could invoke its methods inside jaggery. But when time goes on, it was really painful to write methods to each operation that is required in the application in a single java class. It became too large and most of them were repetitions of previous methods with small changes, which is not suitable. 

So we decided to search for a better solution and finally we decided it is better to write a LDAP connector for WSO2 ESB. Main reasons for writing a LDAP connector were

1. Connecting through an ESB connector makes most of the integrations with external LDAP directories become easy
2. Loosely coupled interface between LDAP and client
3. Others who are willing to use LDAP in their products can re-use this easily
4. Language independent (Data exchange is done using REST or SOAP)

In our connector there are basic four functions implemented and one special function

Basic functions

• Add new entry
• Delete an entry
• Update an entry
• Search for an entry

Special Functions

• Authenticate user

Before using any operation it is required to provide admin authenticate details to ESB. For that there is an Init operation.

<ldap.init xmlns="http://ws.apache.org/ns/synapse">

      <providerUrl>ldap://192.168.1.164:389/</providerUrl>

      <securityPrincipal>cn=admin,dc=wso2,dc=com</securityPrincipal>

      <securityCredentials>comadmin</securityCredentials>

   </ldap.init>

   

This signs in as the admin of LDAP directory which can perform any operation on LDAP Directory.

It is better to put this in a local entry and refer it in other operations with configKey

Add new entry

<ldap.addEntry configKey="LdapConfig">

    <objectClass>inetOrgPerson</objectClass>

    <dn>uid=dimuthuu2,ou=staff,dc=wso2,dc=com</dn>

    <attributes>cn=Dimuthu2Upeksha,mail=dimuthuu2wso2.com,userPassword=123,sn=Dimuthu2</attributes>

</ldap.addEntry

To add a new entry there are 3 parameters. 

1. Object class - This is a mandatory parameter. This defines the objectClass of the new entry

2. dn - Distinguished name of the new entry

3. attributes - Other attributes you need to add in to the entry

Delete an entry

<ldap.deleteEntry configKey="LdapConfig">

    <dn>uid=dimuthuu2,ou=staff,dc=wso2,dc=com</dn>

</ldap.deleteEntry>

Update an entry

<ldap.addEntry configKey="LdapConfig">

    <dn>uid=dimuthuu2,ou=staff,dc=wso2,dc=com</dn>

    <attributes>cn=Dimuthu2Upeksha,mail=dimuthuu2wso2.com,userPassword=123,sn=Dimuthu2</attributes>

</ldap.addEntry

1. dn - Distinguished name of the entry that is needed to update attributes

2. attributes- Key value pairs of attributes that are needed to be changed

Search for an entry

This searches a particular entry of a set of entries for given keywords.

<ldap.searchEntry configKey="LdapConfig">

            <objectClass>inetOrgPerson</objectClass>

            <filters>uid=dimuthuu</filters>

            <dn>ou=staff,dc=wso2,dc=com</dn>

            <attributes>uid,mail</attributes>

</ldap.searchEntry>

1. objectClass - type of entry that is needed to be searched

2. filters - keywords to search. Above case: search entries with uid with "dimuthuu"

3. dn - Distinguished name of the scope which searching should be applied.

4. attributes -  Attributes of the entry that should be included in the search result.

Authenticate

LDAP authentication is one of the major requirement in most LDAP based applications. To simplify this authentication mechanism, there is a special operation. For your given username and password it tells whether authentication succeeded or not.

<ldap.authenticate configKey="LdapConfig">

            <dn>uid=dimuthuu,ou=staff,dc=wso2,dc=com</dn>

            <password>1234</password>

</ldap.authenticate>

1. dn : Distinguished name of user

2. password: password of the user

-----------------------------------------
Special thanks should go to WSO2 ESB team including Dushan ayya and Isuru ayya for giving us a great help when we were in trouble.

If you think that this should be improved or I'm missing something here, please do comment below. Thanks

Adding Google Maps to your Java Standalone applications

Google maps is a very impressive tool to present details of particular location in any part of world. It is very common to see google maps integration in web applications using java scripts. However it can be included in to Java SE applications also. It can be simply done using google static maps api and java swing components. Here is my code.

public class Main {

     JFrame frame = new JFrame();

     JPanel panel;

     BufferedImage image;

     public void show(String gps) {

            panel = new JPanel();

            try {

                   image = ImageIO.read(new URL("http://maps.google.com/staticmapcenter="+gps+"&zoom=14&size=600x300&maptype=roadmap&markers="+gps+"&sensor=false&key=ABQIAAAAgb5KEVTm54vkPcAkU9xOvBR30EG5jFWfUzfYJTWEkWk2p04CHxTGDNV791-cU95kOnweeZ0SsURYSA&format=jpg"));

                   JLabel label = new JLabel(new ImageIcon(image));

                   panel.add(label);

                   frame.add(panel);

                   frame.pack();

                   frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

                   frame.setLocationRelativeTo(null);

                   frame.setVisible(true);

            } catch (MalformedURLException e) {

                   e.printStackTrace();

            } catch (Exception e) {

                  e.printStackTrace();

            }

     }

     public Main(){

             show("6.423601,79.996755");

     }

     public static void main(String[] args){

           new Main();

     }

}

More details can be added to map by referring to google static maps api.