Sources for the BioAssay Research Database
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README.md

BARD REST API

This repository hosts the BARD REST API that provides query access to the backend BARD database. The API is designed using the Jersey framework and is meant to be hosted in an application container. Currently, we have tested it in Tomcat 6 and (GlassFish, but it should work in any other compliant application container such as Jetty.

Dependencies

The backend database currently runs on MySQL. The repository does not contain the MySQL ODBC connector. Instead it should be available within the gloabl classpath of the application container. In addition, some resources implemented by the current code have a dependency on the ChemAxon jchem.jar file. Due to license restrictions this is not included in the repository. You should obtain an appropriately licensed version and place it under lib/.

Building

The REST API is deployed as a WAR file which can be generated using

ant war-rest

You can then copy deploy/bard.war to the application containers' webapp directory and restart the server (if required)

Tomcat Configuration

The API code employs JDBC pooling and is currently using MySQL as the backend database. If you plan to host the API locally, you will need an instance of the backend database as well. After that has been set up, ensure that you have the MySQL ODBC connector located in the global Tomcat classpath and then add the following entry to config/context.xml in the Tomcat home directory.

  <Resource
      name="jdbc/bard"
      scope="Shareable"
      type="javax.sql.DataSource"
      url="jdbc:mysql://data.base.server:portnum/dbname?zeroDateTimeBehavior=convertToNull" 
      driverClassName="com.mysql.jdbc.Driver"
      username="bard"
      password="bard"
      maxIdle="3"
      maxActive="20"
      removeAbandoned="true"
      removeAbandonedTimeout="60"
      testOnBorrow="true"
      validationQuery="select 1"
      logAbandoned="true"
      debug="99"/>

Plugins

The REST API also supports the concept of plugins - user contributed Java classes that appear as resources in the REST hierarchy. See the plugin repository for some examples. A more detailed description of how plugins should be written can be found here. Plugins are built & deployed separately from the main BARD API. A proxy server in front of all BARD resources performs the appropriate redirection