Version:
+ 0.1.0.0, alpha version
Authors:
+ Sopasakis Pantelis
+ Charalampos Chomenidis
Description:
+ ToxOtis is the Greek word for Sagittarius, that actually means ‘archer’. ToxOtis is a Java interface to the predictive toxicology services of OpenTox. ToxOtis is being developed to help both those who need a painless way to consume OpenTox services and for ambitious service providers that don’t want to spend half of their time in RDF parsing and creation. ToxOtis-Persistence is a persistence module for ToxOtis. Loading the jar file in your classpath along with ToxOtis.jar will provide persistence functionalities.
This project depends on the following libraries (Should be downloaded and added in your classpath).
- The latest version of ToxOtis. We remind that ToxOtis has the following three dependencies:
- Jena, version 2.6.2 : Download Jena from this link. [Make sure to download version 2.6.2. otherwise there is no guarantee it will work as expected.]
- Weka, version 3.6.2 : Download weka and add weka.jar in your classpath.
- JFreeChart 1.0.13 : Download JFreeChart and enjoy free charts.
- Hibernate version 3.6.0.
- MySQL Connector or other connector with the database server you will choose (This is configurable).
In order to persist ToxOtis objects using Hibernate you have to have installed on your machine a relational datbase server supported by Hibernate. Among other MySQL, PostgreSQL, Apache Derby and lots of other (This module is tested with MySQL but is believed to work with other DBs as well). Copy the file example.cfg.xml into hibernate.cfg.xml in the same folder (src/org/opentox/toxotis/persistence/config) and set the jdbc URL and password accordingly. Here is an example:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE hibernate-configuration PUBLIC "-//Hibernate/Hibernate Configuration DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<!-- Database connection settings -->
<property name="connection.driver_class">com.mysql.jdbc.Driver</property>
<!-- Using MySQL -->
<property name="connection.url">jdbc:mysql://localhost/toxotis</property>
<!-- Database user -->
<property name="connection.username">root</property>
<!-- Your password goes here... -->
<property name="connection.password">opensess@me</property>
<!-- JDBC connection pool (use the built-in) -->
<property name="connection.pool_size">1</property>
<!-- SQL dialect -->
<property name="dialect">org.hibernate.dialect.MySQLDialect</property>
<!-- Enable Hibernate's automatic session context management -->
<property name="current_session_context_class">thread</property>
<!-- Disable the second-level cache -->
<property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>
<!-- Echo all executed SQL to stdout -->
<property name="show_sql">false</property>
<!-- Drop and re-create the database schema on startup -->
<property name="hbm2ddl.auto">update</property>
<mapping resource="./org/opentox/toxotis/persistence/config/LiteralValueMapping.hbm.xml"/>
<mapping resource="./org/opentox/toxotis/persistence/config/ResourceValue.hbm.xml"/>
<mapping resource="./org/opentox/toxotis/persistence/config/MetaInfoMapping.hbm.xml"/>
<mapping resource="./org/opentox/toxotis/persistence/config/OTComponentMapping.hbm.xml"/>
<mapping resource="./org/opentox/toxotis/persistence/config/OntologicalClassMapping.hbm.xml"/>
<mapping resource="./org/opentox/toxotis/persistence/config/UserMapping.hbm.xml"/>
</session-factory>
</hibernate-configuration>
This project, as well as all other projects developed by the NTUA developers team under OpeTox, is licensed under the GNU GPL license version 3. There is a considerable debate taking place in the open source community regarding the use of the GPL or LGPL, while a variety of other licenses can be found on the web as well. However it is GNU itself that prompts developers to use GPL (read this article).