Encyclopedia of Life is an ambitious project to create “.. electronic page for each species of organism on Earth..” and Freebase is a open structured data repository recently purchased by Google.

Go to app: http://eolfetch.freebaseapps.com/ (you need to have Freebase account)

The problem was with ActiveMQ flow control and transacted routes in Camel.

When you have slow consumers, to prevent queues from growing infinitely, ActiveMQ has a limit of how many messages you can put in a queue. When limit is reached, producer is, by default, forced to wait until the resources free. You can set these limits on system level or per queue level. Problem arises when you have transacted Camel route and system limit is reached.

Route that moves messages from queue A to queue B is inside a JMS transaction – you can’t remove message from queue A until the message is successfully placed on queue B.

If system limit is reached, no new messages can be sent to any queue. So, producers are forced to wait, transaction doesn’t complete, messages can’t be taken off queue A and no resource gets freed. The  whole processing freezes.

There are numerous ways you can work around this problem. You can turn off flow control and potentially let queues grow indefinitely.

In our case, solution was to set per-queue limits so that system limits can never be reached. Sum of limits for all queues needs to be less than the system limit. That way, as consumer takes messages from queue B, new messages can come in, transactions can complete and messages can be taken off queue A. Messages are consumed from queues A and B at the same pace and the whole system works fine.

In our case, I’ve set memoryLimit to 10m for our 13 queues and system memoryUsage to 180m.

For details see :

• ActiveMQ Producer Flow Control
• ActiveMQ Slow Consumer Handling

If you mix fields that filter out stop words (plain text) and fields that do not filter out stop words (like author names), your simple queries might end up with no results.

By default, DisMax will display only results that contain all the words from your query string. If your query has stop words like “ants of madagascar”, stop word “of” might not be found in any of the fields – it’s not in author names and it’s filtered out in article body – and you will get zero results.

Possible workarounds:

• Relax Minimum Match (mm) requirement.
  Downside: Lowering mm will increase number of results. mm of 50% on “ants madagascar” will return all documents that have “ants” and all docs that have “madagascar” in them.
• Do not filter out stop words.
  Downside: Your index can get large and you might get large number of less relevant results.
• Use other indexing schemes like N-Grams.

This article explains the details.

Also see this and this discussion.

I tested following transformers:

• Xalan 2.7.1:
  • org.apache.xalan.processor.TransformerFactoryImpl
  • org.apache.xalan.xsltc.trax.TransformerFactoryImpl
  • org.apache.xalan.xsltc.trax.SmartTransformerFactoryImpl
• Sun-Xalan (an internal transformer factory present in Sun JDK 5 and 6):
  • com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl
• Saxon 8.7:
  • net.sf.saxon.TransformerFactoryImpl

Here are the results for Mathematical Script Capital D character: 𝒟

Or, summarized in a table:

The results were the same regardless of the parser implementation. Xerces or Saxon.

Xalan’s handling of UTF-8 multi-byte characters seems to be seriously flawed. �� are not valid UTF-8 characters and both Xerces and Saxon parsers will throw SAXParseException when trying to parse documents that have them.

1. public class Test {
2.  
3.   public static interface Foo<T> {
4.     public T getX();
5.   }
6.  
7.   public static class Bar implements Foo<String> {
8.     public String getX() {
9.       return "Hello World";
10.     }
11.   }
12.  
13.   public static void main(String[] args) {
14.     Method[] methods = Bar.class.getDeclaredMethods();
15.  
16.     for (Method method : methods) {
17.       System.out.println(method.getReturnType().toString()+" "+method.getName());
18.     }
19.   }
20. }

Will return :

A) It’s illegal in Java to have two methods with the same signature returning different types.

B) The order in which these methods are returned would be completely random. For example, this can cause BeanUtils.copyProperties(..) to intermittently fail to copy some bean properties. BeanUtils would take the first get method returned, find that the return type is not matching corresponding set method and skip it.

The bug is present in both Java 5 and 6. There are several bugs filed around this problem. For example: 6422403 and 6528714. The bad news is that this is not going to be fixed until Java 7.

For example, go to this article. To view triples from the page use Firefox Operator plugin or GetN3. You should see following Dublin Core triples.

Currently supported DC terms are identifier, title, description, type, language, creator, subject, publisher

Read the article>

Laurie performed last weekend in play Birth by Karen Brody and directed by Aimée Miles. It was a performance for the Birth Fest 2008 in San Francisco. Birth Fest is an event created to support midwifery and natural birth.

Laurie got an additional applause after showing her belly !

Next week I will be starting as a software developer at Public Library of Science.

I spent more than 7 years at Xpiron. This is the longest time I spent at any company. I went through Xpiron’s ups and downs. Xpiron is now a stable company with solid number of customers and a promising future. It was a great experience.

I am really excited about PLoS. They have an unique architecture. Mulgara RDF database at back end, Fedora BLOB store, Topaz object-triplet mapping and Ambra publishing platform.

This year is a year of change of me. A new job, a new flat and I am becoming a father in October !

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