Stopping new Icon when I launch a java appication from Gnome or Unity

So I had successfully created a .desktop file to launch Eclipse from Gnome.  I also found it no problem  making it a favorite.  The problem I was having was every time I launched Eclipse I ended up with 2 icons.  The Favorite and one for the running process.  The trick to making not getting this is to make sure the .desktop name matches the xwindows WM_CLASS property. You can get this value by running:

 xprop WM_CLASS 

Next click on the window of the Java application you are interested in.  In the case of Eclipse the value is "Eclipse" so the file needs to be named Eclipse.desktop.

Java Base64 OutputStream cutting off characters

This took me a while to figure out. I am using a Outputstream to write create a piece of XML.  One of the elements needed to be Base64 encoded.  I wrapped my outputstring using java.util.Base64.wrap.  I did not close the Base64 OutputStream.  It is not really clear but the close of this stream is when it takes care of padding,

Bad Code

// out is a FileOutputStream 
final Base64.Encoder encoder = Base64.getMimeEncoder(); 
final OutputStream clob = encoder.wrap(out); 
IOUtils.copy(in, clob, Charset.forName("UTF-8")); 
// No close of clob Just went and kept writing to out 

Good Code

// out is a FileOutputStream 
final Base64.Encoder encoder = Base64.getMimeEncoder(); 
final OutputStream clob = encoder.wrap(
      new CloseShieldOutputStream(out)); // Use nice Apache IO Wrapper that does                        // not chain close 
IOUtils.copy(in, clob, Charset.forName("UTF-8")); 
clob.close(); // this forces out the padding

Java Epoch to TIMESTAMP function

One of the timestamps in one tables I work with is stored as a java epoch.  Here is a function I wrote to convert it to a timestamp.

This is done in DB2 on a iSeries so some you may need to edit it some.  In particular ant line that *SomeWord is probably a iSeries thing.

CREATE FUNCTION YFUALFA.TIMESTAMP_EPOCH ( 
 EPOCH BIGINT ) 
 RETURNS TIMESTAMP   
 LANGUAGE SQL 
 SPECIFIC YFUALFA.TIMESTAMP_EPOCH 
 DETERMINISTIC 
 READS SQL DATA 
 RETURNS NULL ON NULL INPUT 
 NO EXTERNAL ACTION 
 SET OPTION  ALWBLK = *ALLREAD , 
 ALWCPYDTA = *OPTIMIZE , 
 COMMIT = *NONE , 
 DECRESULT = (31, 31, 00) , 
 DFTRDBCOL = *NONE , 
 DYNDFTCOL = *NO , 
 DYNUSRPRF = *USER , 
 SRTSEQ = *HEX   
 RETURN TIMESTAMP ( '1970-01-01' , '00:00:00' ) + EPOCH SECONDS  ; 
  
COMMENT ON SPECIFIC FUNCTION YFUALFA.TIMESTAMP_EPOCH 
 IS 'Timestamp from a Java epoch' ;

How to create a Hibernate UserType for a Boolean that really works

So I am working with a legacy database using JPA/Hibernate.  Our booleans are stored as a VARCHAR(5) with the values of either 'true' or 'false',  This does not lend its self to using the built in Hibernate type or either yes_no or true_false.

I tried using Hibernates org.hibernate.usertype.UserType interface to create a user type.  This almost worked.  I was able to successfully read and write data.  The problem was that if I had a query in which  I want to statically use true or false I had to singe quote the true or false.  See below for what did and did not work.

What I wanted

Select ss from StudentSupportSurvey ss where ss.stopNags = true 

What I had to do

Select ss from StudentSupportSurvey ss where ss.stopNags = 'true' 

UserType that worked

Notice that I did not implement UserType I instead extended AbstractSingleColumnStandardBasicType.  In my opinion it is probably always better to override one of the abstract classes found in org.hibernate.type then to implement UserType.

package org.yfu.util.hibernate;

import java.io.Serializable;

import org.hibernate.dialect.Dialect;
import org.hibernate.type.AbstractSingleColumnStandardBasicType;
import org.hibernate.type.DiscriminatorType;
import org.hibernate.type.PrimitiveType;
import org.hibernate.type.StringType;
import org.hibernate.type.descriptor.java.BooleanTypeDescriptor;
import org.hibernate.type.descriptor.sql.VarcharTypeDescriptor;

public class TrueFalseBooleanUserType extends AbstractSingleColumnStandardBasicType<Boolean>
 implements PrimitiveType<Boolean>, DiscriminatorType<Boolean>{

 private static final long serialVersionUID = -2794554001044861116L;
 
 public TrueFalseBooleanUserType() {
  super(VarcharTypeDescriptor.INSTANCE, BooleanTypeDescriptor.INSTANCE);
 }

 @Override
 public String getName() {
  return "yfu_boolean";
 }
 
 public Class getPrimitiveClass() {
  return boolean.class;
 }

 public Boolean stringToObject(String xml) throws Exception {
  return fromString( xml );
 }

 public Serializable getDefaultValue() {
  return Boolean.FALSE;
 }

 public String objectToSQLString(Boolean value, Dialect dialect) throws Exception {
  return StringType.INSTANCE.objectToSQLString( value.booleanValue() ? "true" : "false", dialect );
 }
}

This allowed me to right my query like this:

Select ss from StudentSupportSurvey ss where ss.stopNags = true 

CAS Single Sign On Server Seam 3 Security Integration

Where I work at we use the CAS Single Signon Server so that our users only have to sign into one of our Web applications. They are then signed into all of our applications. This makes integration between them very easy. For my newest application We decided to use JSF and Seam Security.

Holder for CAS Returned Information

The following class is used to hold the information returned in the CAS Assertion. I have pulled out the getters, setters, equals and toString.

package org.yfu.util.cas;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Map;

import javax.inject.Inject;

import org.apache.commons.lang.StringUtils;
import org.jasig.cas.client.validation.Assertion;
import org.jboss.solder.logging.Logger;
import org.picketlink.idm.api.User;

public class CASUserBean implements Serializable, User 
{
 
 private static final long serialVersionUID = 401263788421715826L;
 
 @Inject
 private Logger log;
 
 
 private static final String STUDENT = "student";
// private static final String HOST_FAMILY = "hostfamily";
// private static final String PARTNER = "partner";
 private static final String VOLUNTEER = "volunteer";
 private static final String STAFF = "staff";
 private static final String REWARDS = "Rewards";
 private static final String TELEPHONE_NUMBER = "telephoneNumber";
 private static final String DEPARTMENT = "department";
 private static final String MAIL = "mail";
 private static final String TITLE = "title";
 private static final String ELECTRONIC_SIGNATURE = "electronicSignature";
 private static final String USER_LEVEL = "userLevel";
 private static final String POSTAL_CODE = "postalCode";
 private static final String SECURITY_QUESTION_ANSWER = "securityQuestionAnswer";
 private static final String SECURITY_QUESTION = "securityQuestion";
 private static final String PFO = "pfo";
 private static final String DISTINGUISHED_NAME = "distinguishedName";
 private static final String USER_PRINCIPAL_NAME = "userPrincipalName";
 private static final String NAME = "Name";


 private Integer pfoId;
 private String username;
 private String name;
 private List<String> groups = new ArrayList<String>();;
 private String email;
 private String securityQuestion;
 private String securityQuestionAnswer;
 private String postalCode;
 private String electronicSignature;
 private String title;
 private String studentID;
 private String department;
 private String telephone;
 private String userLevel;
 private Date validUntilDate; 
 private Date validFromDate;
 private String distinguishedName;
 private boolean loggedIn;
 private boolean staff;
 private boolean volunteer;
 
 
 public CASUserBean() {

 }
 
 public void init(Assertion assertion) {
  if (assertion != null && assertion.getPrincipal() != null) {
   this.validFromDate = assertion.getValidFromDate(); 
   this.validUntilDate = assertion.getValidUntilDate();
   Map<String, Object> attribs = assertion.getPrincipal().getAttributes();
   this.department = (String) attribs.get(DEPARTMENT);
   this.distinguishedName = (String) attribs.get(DISTINGUISHED_NAME);
   this.electronicSignature = (String) attribs.get(ELECTRONIC_SIGNATURE);
   this.email = (String) attribs.get(MAIL);
   this.name = (String) attribs.get(NAME);
   this.postalCode = (String) attribs.get(POSTAL_CODE);
   this.securityQuestion = (String) attribs.get(SECURITY_QUESTION);
   this.securityQuestionAnswer = (String) attribs.get(SECURITY_QUESTION_ANSWER);
   this.studentID = (String) attribs.get(STUDENT);
   this.telephone = (String) attribs.get(TELEPHONE_NUMBER);
   this.title = (String) attribs.get(TITLE);
   this.userLevel = (String) attribs.get(USER_LEVEL);
   this.username = (String) attribs.get(USER_PRINCIPAL_NAME);
   this.setLoggedIn(true);
   
   String value = (String) attribs.get(PFO);
   
   if (org.apache.commons.lang.StringUtils.isNotBlank(value)
     && org.apache.commons.lang.StringUtils.isNumeric(value)) {
    this.pfoId = Integer.valueOf(value);
   }
   
      
   groups = new ArrayList<String>();
   Object ldapGroups = attribs.get("group");
   
   if (ldapGroups instanceof List) {
    List<?> list = (List<?>) ldapGroups;
       for (Object obj : list ) {
        String group = (String) obj;
        addRole(group);
    }
   } else {
    addRole((String) ldapGroups);
   }
   
      
      value =  getDistinguishedName();
      
      if (StringUtils.contains(value, "DC=YFUUSA,DC=Local")) {
       groups.add(STAFF);
      }
      
      setStaff(getGroups().contains(STAFF));
      setVolunteer(getGroups().contains(VOLUNTEER));
  }
 }

 private void addRole(String group) {
  log.trace(group);
  group = StringUtils.substringAfter(group, "CN=");
  log.trace(group);
  group = StringUtils.substringBefore(group, ",");
  log.trace(group);
  if (StringUtils.isNotBlank(group)) {
   groups.add(group);
  }
 }

 @Override
 public String getKey() {
  return getDistinguishedName();
 }

 @Override
 public String getId() {
  return "" + getPfoId();
 }
}

Producer For CASUserBean

Nothing much interesting here.  Just a simple producer.  You could get away with out this I have it since I started not using Seam Security.

package org.yfu.util.cas;

import javax.enterprise.context.RequestScoped;
import javax.enterprise.context.SessionScoped;
import javax.enterprise.inject.Alternative;
import javax.enterprise.inject.New;
import javax.enterprise.inject.Produces;
import javax.inject.Inject;
import javax.inject.Named;
import javax.servlet.http.HttpSession;

import org.jasig.cas.client.util.AbstractCasFilter;
import org.jasig.cas.client.validation.Assertion;
import org.jboss.solder.servlet.http.HttpSessionStatus;

@RequestScoped @Alternative 
public class CASUserProducer {

 
 @Inject private HttpSessionStatus sessionStatus;
 
 public CASUserProducer() {
  
 }
 
 @Produces
 @Named("casUser")
 @SessionScoped
 public CASUserBean getCasUser(@New CASUserBean user) {
  CASUserBean ret = user;
  
  ret.setName("Not Logged in");
  
  if (sessionStatus.isActive()) {
   HttpSession session = sessionStatus.get();
   Assertion assertion = (Assertion) session.getAttribute(AbstractCasFilter.CONST_CAS_ASSERTION);
   if (assertion != null && assertion.getPrincipal() != null) {
    user.init(assertion);
    ret = user;
   }
  } 
  return ret;
 }

}

Seam Security Authenticator

The need this little class so that we can tell Seam Security we are logged in.  We also set the CASUserBean as our User.

package org.yfu.util.cas;

import javax.inject.Inject;
import javax.inject.Named;

import org.jboss.seam.security.BaseAuthenticator;
import org.jboss.seam.security.Identity;

public class CASSeamAuthenticator extends BaseAuthenticator
{

 
 @Inject  @Named("casUser")  private CASUserBean casUser;
 
 public CASSeamAuthenticator() {
 }

 @Override
 public void authenticate() {
  if (casUser != null && casUser.isLoggedIn()) {
   setStatus(AuthenticationStatus.SUCCESS);
   setUser(casUser);   
  }  

 }

 @Override
 public void postAuthenticate() {

 }


}

A Servlet Filter

We now create a Servlet filter that will be placed after our CAS Servlet Filters.  This is where we actually do the login (see line 38).

package org.jasig.cas.client.seam3.authentication;

import java.io.IOException;

import javax.inject.Inject;
import javax.servlet.Filter;
import javax.servlet.FilterChain;
import javax.servlet.FilterConfig;
import javax.servlet.ServletException;
import javax.servlet.ServletRequest;
import javax.servlet.ServletResponse;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;

import org.jasig.cas.client.util.AbstractCasFilter;
import org.jasig.cas.client.validation.Assertion;
import org.jboss.seam.security.Identity;
import org.yfu.util.cas.CASUserBean;


public class Seam3SecurityAuthenticationFilter implements Filter {


 @Inject private Identity identity;
 
 
 @Override
 public void doFilter(ServletRequest servletRequest, ServletResponse servletResponse,
   FilterChain chain) throws IOException, ServletException {

        final HttpServletRequest request = (HttpServletRequest) servletRequest;
        final HttpServletResponse response = (HttpServletResponse) servletResponse;
        final HttpSession session = request.getSession(false);
        final Assertion assertion = session != null ? (Assertion) session.getAttribute(AbstractCasFilter.CONST_CAS_ASSERTION) : null;

        if (!identity.isLoggedIn() && assertion != null) {
         identity.login();  // this is alway successful
         
         CASUserBean user = (CASUserBean) identity.getUser();
         
         // Now we will add LDAP Groups as Groups with a group type of group.  
         
         for (String group : user.getGroups()) {
    identity.addGroup(group, "group");
   }
         
         
         
        }
         
        
        chain.doFilter(request, response);
  
 }


 @Override
 public void init(FilterConfig filterConfig) throws ServletException {
  
 }


 @Override
 public void destroy() {
  
 }

 
}

Include the filter in the web.xml

I included the CAS filters so that you can see them in order. The order of the filter mappings is vitally important.

 
  CASWebAuthenticationFilter
  org.jasig.cas.client.jboss.authentication.WebAuthenticationFilter7
  
   casServerLoginUrl
   https://login.yfu.org/cas/login
  
  
   serverName
   ${cas.serverName}
  
 
 
  CASAuthenticationFilter
  org.jasig.cas.client.authentication.AuthenticationFilter
  
   casServerLoginUrl
   https://login.yfu.org/cas/login
  
  
   serverName
   ${cas.serverName}
  
 
 
  CASSeam3SecurityFilter
  org.jasig.cas.client.seam3.authentication.Seam3SecurityAuthenticationFilter
 
 
 
 
  CASWebAuthenticationFilter
  /secured/*
 
 
  CASAuthenticationFilter
  /secured/*
 
 
  CASSeam3SecurityFilter
  /secured/*
 

Death to a Deadlock

One of the systems I have been working on has has had a deadlock that happens intermittently for the last 6 years.  Well today I finally found it.  We have a thread that runs in our application that times how long a web request takes.  If the request takes more then 30 minuets it assumes a deadlock and kills the application.  The thread also send an email to the programmers.  Below is the code I inserted in the monitoring thread code that allowed me to find the deadlock.

public static StringBuffer getDeadTraces(StringBuffer errorStringBuff) {
        StringBuffer deadtraces = new StringBuffer();
	try {
	    long[] ids = ManagementFactory.getThreadMXBean().findDeadlockedThreads();
	    if(null != ids && ids.length > 0) {
	         Map map = Thread.getAllStackTraces();
		 Set set = map.entrySet();
		 for (long id : ids) {
		    for (Entry entry : set) {
			 Thread thread = entry.getKey();
			if (thread.getId() == id) {
				deadtraces.append("\n===================  ");
				deadtraces.append(thread.getName());
				StringBufferUtils.append(deadtraces, "  ===================","\n");
							
				for (StackTraceElement el : entry.getValue()) {
					StringBufferUtils.append(deadtraces, el.toString(),"\n");                    						
				}												
			}
		    }				 
	         }
	    }
	} catch (Exception e) {
		errorStringBuff.append("Error trying to create a snapshot: " + 
		e.getMessage() + org.apache.commons.lang.exception.ExceptionUtils.getFullStackTrace(e));
	}
	return deadtraces;
}

FindBugs

I just found the FindBugs project.  It is a great way of finding possible bugs in Java programs.  I spend some of my time taking care of a cranky old WebObjects + Java website.  I run the program against its code base and it found 368 possible errors.   Some were the relatively benign "Repeated conditional test" while others where the more serious "Incorrect lazy initialization and update of static field ".