introduction to ontology development

At work, during preperation of a conference paper related to semantic web, i luckily had a chance to use protege for ontology development.. Protege (http://protege.stanford.edu/) is an ontology editor and knowledge acquisition system. In this series of posts, i write down my experience of using protege as an ontology editor..
The paper at http://protege.stanford.edu/publications/ontology_development/ontology101.html proposes a methodology for developing an ontology. According to that paper, the domain and scope of the ontology should be defined properly before the design phase. After that, ontologies that have been developed so far in that domain should be checked. Using previous ontologies provides compatibility with applications using that ontology. Then the next step is writing down all the terms you can think of related to the concerned domain. Those terms are than examined and determined if they are classes or not. The terms that are decided to be classes are organized in a hierarchy with one of top-down, bottom-up approaches or a combination of them. Then, the slots are determined by using the generated class hierarchy and previously written and marked as not-class terms. The slots have domains and ranges and facets(restriction) can be defined on them. Afterwards, instances are created and the knowledge base is so close to be complete. However, ontology development is an iterative work and some of these steps should be carried out over and over in order to catch the balance: the developed ontology should be neither too generic nor too specific.
I will continue with new posts focusing on more specific issues and usage of protege.

migration from open esb + glassfish to apache tomcat + ode

In our project, we develop web services using jax-ws and deploy them to glassfish v2 coming with netbeans 6.5 ide. btw, we installed netbeans 6.5 with open esb selected, since we use it for our bpel s. Bpels are also deployed to the same glassfish as web services. Development and deployment are quite easy and fast. However, when we ran all the bpels one after the other during unit tests, the server seems to be very slow and after a few runs out of memory error comes up.. we tried to configure glassfish, but it did not work as we expected.. (the database is postgresql, but currently this is irrelevant.)

So, now i want to deploy web services and bpels to apache-tomcat-6.0.24 + apache-ode-war-1.3.3 just to see what happens.. (in order to deploy ode to tomcat, just download the zip files, extract them and copy ode.war under webapps folder of tomcat and start tomcat..)
Now, lets follow the migration step by step..

The first step is deploying war of web services generated by netbeans (under dist folder of the project) to tomcat. So, i just copied the war file under tomcat-home/webapps and restarted the server. As i expected, the deployment seemed successful in terms of a regular web application, however it can not process the web services since no wsit runtime is installed on tomcat. (in other words, i can not see the wsdl..) In order to fix this, we have to install metro on tomcat.. a helpful link is http://blog.theunical.com/webservers/tomcat/installation-and-configuration-of-jax-ws-metro-on-tomcat-6/
following the link,

• i downloaded and unzipped metro 2.0,
• edited tomcat-home/conf/catalina.properties by replacing shared.loader= line with shared.loader=metro-home/lib/*.jar,
• set CATALINA_HOME environment variable with the command export CATALINA_HOME=path to tomcat-home and chech with echo $CATALINA_HOME
• run the command ant -f metro-on-tomcat.xml from metro-home
  

changes in web service project (generated in netbeans ide as netbeans project):
we have to modify web.xml and add sun-jaxws.xml under project-home/web/WEB-INF in netbeans project. actually, i got help from fromjava example of metro samples package for figuring out how to change the configuration files.

• in web.xml, add servlet definitions and in sun-jaxws.xml modify endpoint definitions accordingly..
• build the project in netbeans and copy the war under project-home/dist folder to tomcat-home/webapps folder for deployment.

now, you should see the wsdl at the endpoint you specified in sun-jaxws.xml.

At this point, we have deployed web services successfully, and now is the time to deploy the bpels..

Bpel files and the corresponding wsdl are collected under a bpel module of netbeans ide.
The major necessity is a deploy.xml. Get one from ode-home/examples folder and copy under bpel-module-home. i used the one from sample HelloWorld2.
here is some info about ode deployment descriptor: http://ode.apache.org/creating-a-process.html

After modifying deploy.xml, clean and build the netbeans bpel module.
Before deploying your actual bpel module under tomcat-home/webapps/ode/WEB-INF/processes folder, you may want to try one of the samples coming with ode package just to see if it is working on its own samples.. It is good to note that the bpels i am about to deploy are using the above deployed web services..

Now, lets try to note down what i have to change:

• some minor namespace errors come up, but they were easy to solve, just read the error log in tomcat-come/logs/catalina.out file.
• the major restriction is it forced all endpoint addreses to format http://hostname:port/ode/processes/myProcessEndpointName for example http://localhost:8080/Balistika2010Ws/ode/processes/SeriesServiceService?wsdl and http://localhost:8080/ode/processes/AddParameter?wsdl are both valid endpoints..

now, build the bpel module in netbeans and make sure thedeploy.xml is under build folder, if it is not, copy it manually and copy the build folder under tomcat-home/webapps/ode/processes . you may want to rename the folder build with a more meaningful name.
now, check http://localhost:8080/ode/processes.html. If successful, the process must be seen at that address..
An important point is the wsdls for bpels are generated with axis2 anymore because of ode, not jaxws..

Some errors due to the differtence between bpel engines might arise.. For instance i got the following error from my previosly working bpel:

javax.xml.ws.soap.SOAPFaultException: axis2ns62:selectionFailure
at com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:111)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:108)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
at $Proxy33.lightLoginWsdlOperation(Unknown Source)
at odebpelclient.Main.main(Main.java:28)

Here is a discussion about the problem: http://mail-archives.apache.org/mod_mbox/ode-user/200810.mbox/%3Cfbdc6a970810200738i75692ac6qb47d3263e9aefe1c@mail.gmail.com%3E
Ode does not automatically initialize the variables, since this is not part of the standard.. This might be an extension provided by Open Esb.. So, lets initialize all the variables and redeploy..

i end this post here, i think the point is clear..

Note: btw, x-home in italics means the location where x is installed.

Edit on 8/3/2010, 14:08:
i get the following error when i called one of the bpels from client:

from server log:
DEBUG - GeronimoLog.debug(66) | Fault response message: {http://docs.oasis-open.org/wsbpel/2.0/process/executable}uninitializedPartnerRole

from client log:
javax.xml.ws.soap.SOAPFaultException: axis2ns6:uninitializedPartnerRole
at com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:111)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:108)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
at $Proxy33.lightLoginWsdlOperation(Unknown Source)
at odebpelclient.Main.main(Main.java:28)

himm, that error was due to a mistake in deploy.xml of bpels.. i had to use keyword invoke instead of provide for invoked web services. So, for writing deploy.xml file, ode-home/examples/DynPartner maybe a better example than HelloWorld2.
and besides, check the existence of initializePartnerRole=yes attribute, when partnerRole exists in partner link.
That solution worked for me :)

Edit on 10/3/2010, 11:37:
in our case, we want to write bpel s that works both with ode and open esb. Here is an example variable initialization that works with both:

<copy>
<from>
<literal>
<ns1:authorizeUserResponse>
<ns1:return> </ns1:return>
</ns1:authorizeUserResponse>
</literal>
</from>
<to variable="AuthorizeUserOut" part="parameters"/>
</copy>

btw, the empty string between returns is necessary..

java.lang.NoSuchMethodError: org.objectweb.asm.ClassWriter.(Z)V when deploying to glassfish

i have recently downloaded glassfish v2.1.1 and got the following error while trying to deploy my app:

javax.persistence.PersistenceException: No Persistence provider for EntityManager named CleanerPU: Provider named org.hibernate.ejb.HibernatePersistence threw unexpected exception at create EntityManagerFactory:
java.lang.NoSuchMethodError
java.lang.NoSuchMethodError: org.objectweb.asm.ClassWriter.(Z)V
at net.sf.cglib.core.DebuggingClassWriter.(DebuggingClassWriter.java:47)
...

i googled for a while and found: http://tai-dev.blog.co.uk/2010/01/21/nosuchmethoderror-org-objectweb-asm-classwriter-when-deploying-your-app-to-a-new-instance-of-glassfish-v2-1-1-it-looks-like-the-upgraded-fins-are-7849068/
according to the link this is due to lib differences between glassfish v2.1.0 and v2.1.1
and the solution is manually deleting the asm-3.1.jar file in the glassfish-install-dir/lib/directory and copy an old version of asm-.jar in its place. i replaced with the asm.jar coming with netbeans 6.5.1 ide and it worked!

trouble in persisting type List <String> in jpa

Trying to persist an attribute with type List causes trouble in jpa.
here is a link: http://stackoverflow.com/questions/287201/how-to-persist-a-property-of-type-liststringin-jpa
the solution is changing from List to String with separated values with delimiter..
the explanation by Bill James at Nov 13 '08 at 15:34 (the above link) seems good..

OpenJms

in this post, i note down some links related to openjms and i try to give a summary.. here is my prev post on the issue: http://hilaltarakci.blogspot.com/2010/02/intro-to-jms.html

http://www.devx.com/Java/Article/20903
here is a presentation about openjms: http://www.oreillynet.com/pub/d/834
a summary from the presentation by Jim Alateras:

• two messaging models: Queues(point to point), Topics(publish and subscribe)
• two message delivery modes: persistent (provider attempts to deliver the message at most once to the consumer. If the consumer is unavailable, provider persist the message and deliver it when the consumer is reactivated. ), non-persistent ( provider attempts to deliver non-persistent messages at most once. If the consumer is unavailable or inactive, then consumer will never receive the message. Non persistent messages should only be used if the subscribers can tolerate lost messages.)
• five message types: text, byte, object map and stream. most applications use xml.
• syncronous (consumers pull messages from the provider by calling receive ) & asyncronous (if consumer registers a listener, provider push messages to consumer ) message consumption
• selectors, used by consumers to selectively process messages
• 10 priority levels 1 being the lowest and 10 being the highest. Publishers assign priority levels to messages, which effect the order that they are queued by provider.
• QueueBrowser, specific to queue destinations and is used to browse messages on a queue.
• two transaction modes Local( use the chained transaction model and applied to transacted sessions) & Distributed (use 2 phase commit protocol and are defined by a set of XA interfaces. XA interfaces are part of the advanced server facility)
  

Queues:

• Senders publish messages to queue and receivers consumer messages of queue.More than one sender or receiver can be attached to queue.
• Messages on a queue are delivered to only one consumer and JMS does not define delivery semantics when more than one subscriber is attached to the queue. a message is only sent to one of the registered subscribers.
• Priority effects the order that messages are queued for delivery. Higher priority messages are queued for delivery before lower priority messages
• Non-persistent messages delivered at most once.
• Persistent messages delivered exactly once.
  

Topics:

• Publishers publish messages and subscribers consume them. A topic with once subscriber and one publisher acts similar to a queue.
• When you have multiple publishers and subscribers ,the publishers send messages to the provider, who queues them for delivery and then each of the subscribers receive a copy of each published message.
• As for Queues priority effects the order that messages queued for delivery and selectors effect the order that messages are consumed.
• Similar to queues persistent and non-persistent delivery