MURPA-Lin Wei-Week 5

In week 5, I spent the majority of my time fixing the opal.xml workflow, working on the OpalResource class design and studying the OpalClient.java. In terms of the workflow, it still doesn’t work. I have tried all the suggestions that were made by my supervisors and my own idea, but the error remains.

Opal.xml workflow

The actions I performed include:

Action	Detailed Step	Results
Colin’s suggestion	1. Install Nimrod/K and copy all the jar files that Colin gave me to Kepler 2. using this URL for the workflow: http://kryptonite.nbcr.net/app1267557427870/. Jane has double checked for me that this URL is a working URL. 3. On the workflow, update the Constant actor and update the all the "u" fields with this URL and update the "dpf" fields with the local copy (where kepler is) of 2HU4_B.dpf. 4. Run the workflow	ptolemy.kernel.util.IllegalActionException: We could not find the attribute filter_file in .opal.OpalClient_C0_TCA.OpalClient_C0 with tag colour {sequenceID=0, metadata={}, parameters={dpf="/home/linwei/kepler/2HU4_B.dpf", u="http://kryptonite.nbcr.net/app1267557427870/"}, hashcode=65311548} in .opal.OpalClient_C0_TCA.OpalClient_C0 at edu.sdsc.nbcr.opal.OpalClient._makeCmd(OpalClient.java:898) at edu.sdsc.nbcr.opal.OpalClient.fire(OpalClient.java:235) at org.monash.nimrod.NimrodDirector.NimrodProcessThread.run(NimrodProcessThread.java:394)
Wilfred’s suggestion	1. Export the OpalClient.java in Kepler 2.0 as an OpalClient.jar file 2. Replace the OpalClient.jar in Kepler 1.0 with the new OpalClient.jar 3. Run the workflow with the URL and the dpf file. I’m not sure if these are the correct steps. But the error message indicates that the OpalClient.java may be different because the OpalClient._makeCmd are on different lines	ptolemy.kernel.util.IllegalActionException: We could not find the attribute filter_file in .opal.OpalClient_C0_TCA.OpalClient_C0 with tag colour {sequenceID=0, metadata={}, parameters={dpf="/home/linwei/kepler/2HU4_B.dpf", u="http://kryptonite.nbcr.net/app1267557427870/"}, hashcode=65311548} in .opal.OpalClient_C0_TCA.OpalClient_C0 at edu.sdsc.nbcr.opal.OpalClient._makeCmd(OpalClient.java:893) at edu.sdsc.nbcr.opal.OpalClient.fire(OpalClient.java:235) at org.monash.nimrod.NimrodDirector.NimrodProcessThread.run(NimrodProcessThread.java:394)
My idea	1. Open the PDB2PQR.xml workflow that was created in Kepler 2.0 in Kepler 1.0 2. Open the opal.xml workflow in Kepler 1.0. 3. Copy the OpalClient actor in PDB2PQR workflow and paste it in opal.xml workflow to replace the original OpalClient actor. 4. Using the same serviceURL, u, dpf file and all other parameter values for the copied OpalClient actor. 5. Run the workflow and skip the error.	It is interesting that the workflow runs successfully with error messages flood the entire error message dialogue window. I showed Jane the generated web pages and she confirmed that the job was actually executed.

It remains unknown that if the OpalClient actor has been modified and used in the opal.xml workflow. All people involved in the opal.xml workflow development have been consulted and no one could tell what exactly he/she did when created the workflow. However, I suspect that the OpalClient actors are different because the interfaces of the actors in Kepler 2.0 and Kepler 1.0 are different. Here are the screenshots of the interfaces:

OpalClient interface in Kepler1.0

OpalClient Interface in Kepler 2

OpalResource class Design

The OpalResource class design needs to be modified. Wilfred points out that if we build the OpalResource class inside the OpalClient actor, the Opal actor will be dependent on the Nimrod/K API. Due to copyright issues, the Nimrod/K does not come with the standard Kepler distribution. The users have to agree to the licence, download and install the Nimrod/K manually. Wilfred suggests create an OpalNimrod actor which does the same job as the OpalResource class, but it adds burdens to maintenance since we will end up with two actors. We will discuss the design issues further with Colin in week 6.

Spirit Night

We went out to watch basketball competition at UCSD on spirit night. I was amazed by the passionate students and atmosphere of the competition. It’s a pity that Monash doesn’t have such sports event.