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Paper: Patterns for Introducing a Superclass for Test Classes

kinow @ Sep 25, 2012 17:58:09 ()

Few days ago we had SugarLoafPlop 2012 in Natal - RN

It is a conference on pattern languages of programming. About six months ago I saw a tweet by Eduardo Guerra asking if anyone had some cases where certain patterns were applied. It was a big coincidence, since I was working on Apache Commons Functor and some Jenkins plugins, both projects with cases that could be used in his paper.

So I joined Guerra and gave my small contribution to the paper that has been accepted for this edition of SugarLoafPlop. Guerra also went there to give a talk and participate in an open discussion about several papers, including ours. I simply love when these things happen, it was great work with Guerra, and even better for being able to use Open Source examples in our paper.

Bioinformatics tools: Stacks

kinow @ Sep 25, 2012 16:08:03 ()

It is the first post about bioinformatics tools, but I will try to post more about other tools such as MrBayes, Structure, maybe some next generation sequencing tools too, and Bioperl, Biojava, and so on.

As I am more a computer geek, rather than a bioinformatics one, I will focus on requirements for running these tools on clusters and the requirements to install them on your machine. The instructions require that you have an intermediary knowledge on *nix OS and sometimes a bit of programming experience.

I will be using tutorials available on the Internet and hosting my code in GitHub/kinow. Hammer time!

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Running word-count example on a Hadoop commodity-hardware cluster and on a Hadoop local installation

kinow @ Sep 20, 2012 21:49:38 ()

Last weekend I spent some hours assembling old computer parts to create my commodity hardware cluster for running Hadoop. I already had a local installation in my notebook, so I thought it would be cool to run the word-count example in both scenarios to see what would be the results.

But first, let’s review the hardware configurations:

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Integrating Nutch 2.x, MySQL and Solr

kinow @ Sep 14, 2012 00:02:31 ()

Right now we are working on a new project using Apache Nutch 2.x, Apache Hadoop, Apache Solr 4 and a lot of other cool tools/modules/API’s/etc. After following the instructions found on http://nlp.solutions.asia/?p=180, I’ve successfully connected Apache Nutch, MySQL and Apache Solr.

mysql_hadoop_solr_nutch

In summary:

  • Create a database to hold your data
  • Use SQLDataStore and add configuration for your MySQL server
  • Update Apache Nutch configuration
  • Update Solr schema

Now our Apache Nutch uses MySQL as data store (the place where it keeps the result of the crawling process, such as URL, text content, metadata, and so on). That’s grand, but there is one part missing in the Solr Schema provided in the blog post.

Due to SOLR-3432, after following the tutorial and replacing the schema, we couldn’t delete the whole index anymore. After following the instructions in the bug comments, and adding the following entry in schema.xml it worked again.

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Invoking Testopia XML-RPC or JSON methods using Java

kinow @ Sep 09, 2012 16:08:09 ()

Most TestLink [1] users are aware that there is an external API, maybe for the external API token being displayed in the user profile section. Today after a meeting with Peter Florijn [2], I realized that the same may not be true for Testopia [3] users.

I am quite new to Testopia, and there are many features that I haven’t used yet. But if I understand it correctly, the database is interfaced by several Perl scripts that are, by its turns, exposed as Web Service (most of them). The web services are available via a JSON and a XML-RPC API (what is very useful, TestLink supports supports only XML-RPC).

The communication between different programming languages and the external API’s is accomplished by a client API. In TestLink you have testlink-java-api [4] and testlink-api-java-client [5].

Testopia has a Java client too, available in Testopia source repository [6] and can be used to integrate your existing Java code with Testopia.

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