Payara/GlassFish DataSource JNDI Lookup Reference

Introduction

This article is more of a reference than a how-to.  Setting up a JDBC Connection Pool and JDBC Resource in Payara/GlassFish is easy. However remembering how to do the JNDI lookups from your application is a little harder because, let's face it, we don't have to do it that often so its easy to forget.  So here is a reference.

Create "JDBC Connection Pool"

The first thing you'll need to do is create a "JDBC Connection Pool". As shown in Figure 1, Payara/GlassFish have a simple wizard for this. 

Figure 1: Wizard to start a new "JDBC Connection Pool"

PostgreSQL is my database of choice.  So during the setup I choose "Postgresql" and add the following configuration:

Datasource classname: org.postgresql.ds.PGSimpleDataSource
 

Property	Value
user	elephant
password	jafj2r@#Rhh
serverName	localhost
portNumber	5432
databaseName	email

Remember, after creating a "JDBC Connection Pool", your application cannot use it because the pool has yet to be bound to JNDI.  To do the binding, let's look at the next step, which is to create a JDBC Resource.

Create "JDBC Resource"

This steps creates a JNDI binding for the "JDBC Connection Pool" so your application is able to perform a lookup and find it.  Payara/GlassFish again provides a nice simple wizard for you, and you start the wizard as shown in figure 2.

Figure 2: Wizard to start a new "JDBC Resource"

The Wizard can't get any simpler.  You need to supply a "JNDI Name"for the "JDBC Resource" and select a "JDBC Connection Pool" from the dropdown box.  That's it!  Well not quite.  Let's look at the "JNDI Name" value in a bit more detail.

JNDI can get really confusing.  In general, JNDI is a tree-like structure with a number of special contexts (java:global, java:app, java:module, java:comp) and some special paths (java:comp/env).  It gets even more confusing because in some cases a context - like java:comp/env - is assumed and prepended for you but in other cases it's not. So let's consider what "JNDI Name" really means for a "JDBC Resource" by looking at some examples.
 

JNDI Name	@Resource(lookup = "%s") OR InitialContext.lookup("%s")	Result	Comments
"EmailDS"	"EmailDS"	SUCCESS	Lookup and "JNDI Name" match!
"EmailDS"	"/EmailDS"	FAILS	Lookup does not match "JNDI Name"!  Lookup name has a leading "/" character!
"EmailDS"	"java:global/EmailDS"	FAILS	Lookup does not match "JNDI Name"! Payara/Glassfish does not prepend the global context when binding to JNDI.
"EmailDS"	"java:comp/env/EmailDS"	FAILS	Lookup does not match "JNDI Name"! The "java:comp/env" context and path is application specific.  We'll cover how to do this application specific configuration below.
"jdbc/app/EmailDS"	"jdbc/app/EmailDS"	SUCCESS	Lookup and JNDI Name match!
"jdbc/app/EmailDS"	"/jdbc/app/EmailDS"	FAILS	Lookup does not match "JNDI Name"!  Lookup name has a leading "/" character!
"jdbc/app/EmailDS"	"java:global/jdbc/app/EmailDS"	FAILS	Lookup does not match "JNDI Name". Payara/Glassfish does not pre-pend the global context when binding to JNDI.
"jdbc/app/EmailDS"	"java:comp/env/jdbc/app/EmailDS"	FAILS	Lookup does not match "JNDI Name". The "java:comp/env" context and path is application specific.  We'll cover how to do this application specific configuration below.

So, if your application has a Payara/GlassFish "JDBC Resource" and your code is performing a direct JNDI lookup, the above table should give you enough information to figure out what will succeed and what will fail.  When you create the "JDBC Resource", Payara/GlassFish will use the "JNDI Name" you give as the exact path in the JNDI tree to make the binding.  Payara/GlassFish does not prepend any contexts or paths onto the name you give.  So your code needs to do a lookup on the exact "JNDI Name" value.

Now you may be asking yourself, what about JNDI redirection?  It's always good practice to have your application JNDI lookup names to be decoupled from the real JNDI locations of the resources.  In other words, I want my application to lookup "java:module/env/jdbc/MyDS" but I want that lookup to be redirected/mapped to the real JNDI location - "EmailDS" - which in Payara/GlassFish is the "JNDI Name" value of the "JNDI Resource".  We'll take a look at how to do this next.


Redirection with web.xml and glassfish-web.xml

The web.xml and glassfish-web.xml files are used to accomplish JNDI redirection.  In general, inside of web.xml you specify what JNDI lookup your application will use to lookup a resource and then inside of glassfish-web.xml you map your application's lookup with the "JNDI Name" of the "JDBC Resource".  But with multiple context rules and automatic prepending of contexts, this too can get confusing so let's take a look at some examples.

Listing 1 shows a fully-qualified example.  In this example, the web.xml says the JNDI lookup used in your application is fully-qualified to "java:comp/email/database".  The glassfish-web.xml says "java:comp/email/database" is mapped to the real JNDI resource "EmailDS".

Listing 1: Fully-qualified redirect example

web.xml

  java:comp/email/database
  javax.sql.DataSource
    

glassfish-web.xml

  java:comp/email/database 
  EmailDS
    

For this example, let's consider some application lookups and see what happens.
 

@Resource(lookup = "%s") OR InitialContext.lookup("%s")	Result	Comments
"java:comp/email/database"	SUCCESS	Lookup matches what's in web.xml.  Successful redirection to real JNDI resource "EmailDS"
"java:comp/env/email/database"	FAILS	Lookup does not match what's in web.xml!  Lookup has an "/env/" path which is not in web.xml.  Redirection fails.
"java:module/email/database"	SUCCESS	Lookup does not match what's in web.xml, however, lookup succeeds because in a WAR the "java:comp" and "java:module" contexts are treated as the same thing for backward compatibility with previous EE versions. Successful redirection to real JNDI resource "EmailDS"
"EmailDS"	SUCCESS	Redirection avoided altogether, this is a direct lookup of the real JNDI resource.

Listing 2 shows a relative example.  In this example, the web.xml says the JNDI lookup used in your application is the relative name "Puppy".  The glassfish-web.xml says the relative name "Puppy" is mapped to the real JNDI resource "EmailDS".

Listing 2: Relative redirect example

web.xml

  Puppy
  javax.sql.DataSource

glassfish-web.xml

  Puppy 
  EmailDS

Now the big question is, this JNDI lookup name is relative to what?  Well, in this case it is relative to "java:module/env" or "java:comp/env" because remember in a WAR file the "java:comp" and "java:module" contexts are treated as the same thing for backward compatibility with previous EE versions.  These contexts are automatically prepended onto your relative name "Puppy".  Let's consider some application lookups and see what happens.
 

@Resource(lookup = "%s") OR InitialContext.lookup("%s")	Result	Comments
"java:comp/env/Puppy"	SUCCESS	The web.xml says "Puppy" which get's automatically prepended with "java:comp/env/".  Successful redirection to real JNDI resource "EmailDS"
"Puppy"	FAILS	Lookup matchs what's in web.xml, but lookup forgot about the automatic context prepending.  Redirection fails.
"java:module/env/Puppy"	SUCCESS	The web.xml says "Puppy" which get's automatically prepended with "java:comp/env/".  But remember, in a WAR the "java:comp" and "java:module" contexts are treated as the same thing for backward compatibility with previous EE versions. Successful redirection to real JNDI resource "EmailDS"
"EmailDS"	SUCCESS	Redirection avoided altogether, this is a direct lookup of the real JNDI resource.

So far, all these examples assume your application doing JNDI resource lookups itself.  However what if you are using a framework like JPA and the lookup of the JNDI resource is done for you?  What do you do then?  We'll look at this next.

A note about JPA persistence.xml
If you are using JPA, you specify the JNDI lookup using one of the "jta-data-source" tags like this:

EmailDS

However, the big question is what JNDI lookup string to use for this tag's value?  Well as far as I can make out, JPA does not use any of the redirection configured in web.xml and glassfish-web.xml.  Which means the value for <jta-data-source> must be the exact Payara/GlassFish "JNDI Name" value of the "JDBC Resource".  This of course couples the JPA configuration to the Payara/GlassFish EE server which may not be desirable.  Hopefully, this will be something the JPA expert group addresses in the next JPA spec update.

A note about @DataSourceDefinition
Java EE has the @DataSourceDefinition annotation which allows your application to create a data source by itself instead of relying on an EE server administrator to create the data source prior to your application's deployment.  This cuts down on some administration steps.  It has its advantages and disadvantages which I won't go into.  But what I do want to look at is how JNDI lookups work with a data source created by the @DataSourceDefinition annotation.

Redirection with web.xml and glassfish-web.xml

The @DataSourceDefinition annotation does not support redirection by web.xml and glassfish-web.xml.  If you think about it, this makes sense.  The @DataSourceDefinition is hard-coded in your source code so you know exactly what JNDI Name you used to create it so there is no need to redirect since the value is already in your code.

JPA data source 

There seemed to be a debate on whether or not @DataSourceDefinition support the JPA persistence.xml file.  The last word of the debate states it should be supported, that the JSR specification will be updated to make it more clear, and that a test will be added to the TCK to verify it. 

At this time (03 Nov 2015), in Payara/GlassFish, the @DataSourceDefinition annotation does not support the JPA persistence.xml file.  In other words, you cannot use the JNDI Name you used for the @DataSourceDefinition annotation in the JPA persistence.xml file.  I will continue to monitor this and will make an update to this article if anything changes.

Listing 3 shows a fully-qualified example.  In this example, the @DataSourceDefinition annotation has a JNDI Name which is fully qualified.  This exact, fully-qualified name, needs to be used in lookups in order for the lookup to succeed.

Listing 3: Fully-qualified @DataSourceDefinition example 

@DataSourceDefinition(
    name="java:global/jdbc/MyApplicationDS",
    className = "org.postgresql.ds.PGPoolingDataSource",
    url = "jdbc:postgresql://localhost:5432/email",
    user = "elephant",
    password = "jafj2r@#Rhh"
)

For this example, let's consider some application lookups and see what happens.
 

@Resource(lookup = "%s") OR InitialContext.lookup("%s")	Result	Comments
"java:global/jdbc/MyApplicationDS"	SUCCESS	Lookup matches what's in the @DataSourceDefinition#name annotation.
"java:global/env/jdbc/MyApplicationDS"	FAILS	Lookup does not exactly match what's in the @DataSourceDefinition#name annotation.  The lookup has an "/env/" path which is not in the annotation

Listing 4 shows a relative example.  In this example, the @DataSourceDefinition annotation has a JNDI Name which is relative path.

Listing 4: Relative @DataSourceDefinition example

@DataSourceDefinition(
    name="MyApplicationDS",
    className = "org.postgresql.ds.PGPoolingDataSource",
    url = "jdbc:postgresql://localhost:5432/email",
    user = "elephant",
    password = "jafj2r@#Rhh"
)

Now the big question is, this JNDI lookup name is relative to what?  Well, in this case it is relative to "java:module/env" or "java:comp/env" because remember in a WAR file the "java:comp" and "java:module" contexts are treated as the same thing for backward compatibility with previous EE versions.  These contexts are automatically prepended onto your relative name "MyApplicationDS".  Let's consider some application lookups and see what happens.
 

@Resource(lookup = "%s") OR InitialContext.lookup("%s")	Result	Comments
"java:comp/env/MyApplicationDS"	SUCCESS	The @DataSourceDefinition says "MyApplicationDS" which get's automatically prepended with "java:comp/env/".  "
"MyApplicationDS"	FAILS	Lookup matches what's in @DataSourceDefinition, but lookup forgot about the automatic context prepending.  So the lookup fails.
"java:module/env/MyApplicationDS"	SUCCESS	The @DataSourceDefinition says "MyApplicationDS" which get's automatically prepended with "java:comp/env/".  But remember, in a WAR the "java:comp" and "java:module" contexts are treated as the same thing for backward compatibility with previous EE versions.

Finaly, listing 5 shows a special condition of a fully-qualified example.  In this example, the @DataSourceDefinition annotation has a JNDI Name which is fully qualified, but to special "java:comp/env/" context and path.

Listing 5: Special case fully-qualified @DataSourceDefinition example 

@DataSourceDefinition(
    name="java:comp/env/jdbc/WebAppDS",
    className = "org.postgresql.ds.PGPoolingDataSource",
    url = "jdbc:postgresql://localhost:5432/email",
    user = "elephant",
    password = "jafj2r@#Rhh"
)

For this example, let's consider some application lookups and see what happens.
 

@Resource(lookup = "%s") OR InitialContext.lookup("%s")	Result	Comments
"java:comp/env/jdbc/WebAppDS"	SUCCESS	Lookup matches what's in the @DataSourceDefinition#name annotation.
"java:module/env/jdbc/WebAppDS"	SUCCESS	Lookup does not exactly match what's in the @DataSourceDefinition#name annotation.  The lookup uses the "module" context which is not in the annotation.  But remember, in a WAR the "java:comp" and "java:module" contexts are treated as the same thing for backward compatibility with previous EE versions.

That's it,
Enjoy!

Begin and end index of a regular expression pattern matched string

This is a quick tip on regular expressions.  Nothing too exciting, but something I use often enough but can never remember so I always have to look it up.

The String.indexOf("match me") method is handy for finding the beginning index of some pattern within a String you want to match.  Combine this beginning index with "match me".length() and you can get the ending index as well.  This works for finding simple substrings, but what if the pattern is more complicated and needs a regular expression?  Let's take a look at the code in listing 1.

Listing 1: Simple pattern matching.

package pattern.matching;

import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class PatternMatching {

    public static void main(String[] args) throws Exception {
        StringBuilder searchMe = new StringBuilder();
        searchMe.append("hello").append("\n");
        searchMe.append(" package doctor;  ").append("\n");
        searchMe.append("name // comment").append("\n");
        searchMe.append("/* continue */").append("\n");
        searchMe.append("int yesterday = 9;").append("\n");
        searchMe.append("tomorrow!").append("\n");
        
        System.out.printf("BEFORE\n------\n%s", searchMe.toString());
        
        final Pattern pattern = Pattern.compile("^ *package .*; *$", Pattern.MULTILINE);
        final Matcher matcher = pattern.matcher(searchMe.toString());

        if (matcher.find()) {
            System.out.println();
            System.out.printf("Start index: %d\n", matcher.start());
            System.out.printf("End index:   %d\n", matcher.end());
            System.out.printf("Match found: [%s]\n", matcher.group());            
            searchMe.replace(6, 24, "I've been replaced...so sad :(");
        } else {
            System.out.println("Matcher matched nothing! ");
        }
        
        System.out.println();
        System.out.printf("AFTER\n-----\n%s\n", searchMe.toString());       
    }
}

Listing 2: Output

BEFORE
------
hello
 package doctor;  
name // comment
/* continue */
int yesterday = 9;
tomorrow!

Start index: 6
End index:   24
Match found: [ package doctor;  ]

AFTER
-----
hello
I've been replaced...so sad :(
name // comment
/* continue */
int yesterday = 9;
tomorrow!

Listing 1 shows the code for a simple regular expression pattern matching of a String.  The Matcher is looking for a simple pattern.  If found, the Matcher.start and Matcher.end methods are used to get the beginning and ending indices within the String.  The StringBuilder.replace method is then used to replace the matched pattern with another String.  As you can see in Listing 2, the output of the application shows the before state, the matcher information, and the after state.

So pretty simple :)
Enjoy!

Bamboo, maven-release-plugin, public/private key SSH access to SVN, password access to Nexus

Introduction

Bamboo is great for performing builds.  The maven-release-plugin is great at releasing new versions of your software. SVN is a great source code repository. SSL public/private keys are great for keeping everything secure, and Nexus is great for Maven artifacts.  What's not so great is trying to get all these things working together!  What we'll look at in this blog is how to configure Bamboo build steps for both the repository host and the Maven configuration. Also, we'll look at how to configure your project's pom. Let's start with the Bamboo repository host build step.

Bamboo repository host build step

First, you need to configure the Bamboo repository host build step so Bamboo can checkout your source code:

Figure 1: Repository host build step

Looking at figure 1, the repository host setup is pretty easy: 

(A)
The URL.  It will need to be in the form "svn+ssh" instead of "https". 

(B)
The username.  It's a good idea to create an account specifically for bamboo to use. 

(C)
The authentication type...no big deal. 

(D)
A variable reference to the fully-qualified location of the SSL key.

Next let's take a look at the Maven configuration build step.

Maven configuration build step

Figure 2: Maven configuration build step

Let's take a look at this configuration one field at a time.

(A)
The version of Maven to use for this build. I did this research using 3.0.5.  No guarantees other versions of Maven will work.

(B)
The Maven goal to perform along with some additional attributes.

--batch-mode release:clean release:prepare release:perform
This runs the release plugin in batch mode so there is no user interaction and all defaults are used.

-s /home/bamboo_builder/.m2/bamboo_builder-settings.xml
This configures Maven to use a specific settings file.  In most cases the same Maven settings will be used for all builds in your organization. But, if you have builds which require unique settings, this is how to configure which settings file to use.  The main purpose of this file is to contain the username and encrypted password to access Nexus  (Maven Encryption, 2015, June 21), which will look something like listing 1.

Listing 1: Nexus username & password in settings.xml

  
    nexus
    bamboo_builder
    {lAHiuyjiu4387y5jKLHE29kjlkahyr/=}
  

(C)
The version of Java to use.

(D)
The environment varibles for the build. This is most important field.  After much research, I found these values MUST BE CONFIGURED HERE (not in goals) otherwise the build will fail.

SVN_SSH="ssh -v -l bamboo_builder -i /home/bamboo_builder/.ssh/id_rsa"
This environment variable configures ssh to use the bamboo_builder user and the id_rsa private key when establishing an SSL connection with SVN.  Now, Maven itself has a number of different ways to configure a username and private key both within a settings.xml file and within the pom.xml for a project.  I tried them all and they all failed.  This was the only way I got it to work.

MAVEN_OPTS="-Dsettings.security=/home/bamboo_builder/.m2/bamboo_builder-security-settings.xml"
This configures Maven with a master password used to encrypt the other passwords in the settings.xml file (Maven Encryption, 2015, June 21).  Though not strictly necessary, it's good to have this file.  If you do have it, this is where you put the configuration for the build. Listing 2 shows what this looks like

Listing 2: Maven master password

    {jj498POHIU4HRUhj2rjpu2ajkshdfur/YI=}

(E)
If your project does not have unit tests, uncheck this box so the build won't fail.

Finally, your project's pom.xml needs a bit of special configuration so let's take a look at that next.

Project pom.xml

The project's pom.xml needs a couple configurations: The <scm> tag and the maven-release-plugin version.

First the <scm> tag needs to be configured so Maven knows where the project is located in SVN.  Listing 3 shows what this tag will look like. 

    NOTE: All 3 properties are needed...don't skip any!

Listing 3: The pom <scm> tag 

    scm:svn:svn+ssh://my.subversion.com/data1/svns_repo/path/to/my/project/trunk
    scm:svn:svn+ssh://my.subversion.com/data1/svns_repo/path/to/my/project/trunk
    scm:svn:svn+ssh://my.subversion.com/data1/svns_repo/path/to/my/project/trunk

Next the maven-release-plugin version needs to be configured. The default version of the maven-release-plugin for Maven 3.0.4 has some bugs in it, most notibly when trying to use this configuration to perform mult-module reactor builds.  So your project pom.xml must be configured to use a more recent version of the maven-release-plugin.  Listing 4 shows this.

Listing 4: The maven-release-plugin version

  
    
      
        org.apache.maven.plugins
        maven-release-plugin
        2.5.1
        
          false
        
      
    
  

Hopefully this fully documents everything that's needed.  Enjoy!

References
Maven Encryption. (2015, June 21). maven.apache.org. Retrieved June 23, 2015 from https://maven.apache.org/guides/mini/guide-encryption.html