BinBase Data Interface - Tools

The BDI tools are simple programs which use the hibernate access layer to work on the database and do simple tasks.

Reqiuerements

Installation

Please download the latest BDI-Tool distribution and unzip it in a directory of your choice. Please make sure that apache ant is in your current path.

Configuration

Please provide your database connection properties in the /config/database.properties file.

Usage

just execute one of the files in the /bin directory from a bash shell. We did not test these tools under windows but it is pretty easy. All what you have todo is to write a small *.bat file to call the provided ant script and executes the given target.

overview of tools

The current implementation of the tools provides the possibility to extract to bin table, bin references and calculates similarity matrices. The related issue is BINBASE-88

f.a.q

can I use the tools from Java applications?

yes they are all based on some simple java classes please check the ant task's for more details

how do I use the tools in my own ant tasks?

Please look at the run.ml file or the JUnit tests how to call and use the ant tasks, it's really quite simple.

I keep getting out of memory exceptions, what can I do?

Please set the variable ANT_OPTS to a sensible value, like ANT_OTPS=-Xmx1024M 

how I can reduce or increase the logging?

Please adjust the log4j.xml file in the log directory