README

Hukilau Standalone Deployment :: http://hukilau.googlecode.com

This software is offered under the GNU Lesser GPL open source license.

Please contact codefor@systemsbiology.org for more information.

================================================================
Creating a Database
================================================================
1. Create Graph Database import configuration from template in config/graphDB.config

2. Configure Graph Database import configuration file (example.config)

3. Execute import utility:
    java -jar lib/DBImport.jar example.config

================================================================
Starting the Web Service
================================================================
1. Modify the service configuration to point at the path to your database
    $TOMCAT_HOME/lib/services/hukilau-svc.config

2. Add a service mapping for your new database
>>    {
>>        family: "/graphs",
>>        label: "Hukilau Graph Database Service",
>>        mappings: [
>>            {
>>                id: "test_db",
>>                label: "Test Database",
>>                location: "/local/hukilau/graphdbs/test.db"
>>            }
            ,
            {
                id: "example_db",
                label: "New Example Database",
                location: "/local/path/to/your/new/database/example.db"
            }
>>        ]
>>    }

3. Start tomcat web application server
    $TOMCAT_HOME/bin/startup.sh

4. Monitor tomcat log at
    $TOMCAT_HOME/logs/catalina.out

NOTE:
   To deploy a new database, or edit a database mapping, while TOMCAT is already running:
      touch $TOMCAT_HOME/webapps/hukilau-svc.war
   OR
      $TOMCAT_HOME/bin/shutdown.sh
      $TOMCAT_HOME/bin/startup.sh

================================================================
Accessing Web Application
================================================================
   Point your browser at http://localhost:8080/standalone.html

   To change the HTTP port, modify $TOMCAT_HOME/conf/server.xml
   Follow instructions here:  http://tomcat.apache.org/tomcat-7.0-doc/setup.html

Sample Query:
1. Select "Test Database" from Graph drop-down menu
2. Select "Node Query" tab
3. Select "sco" from "Node Type" drop-down menu
4. Select "gene_symbol" from "Node Property" drop-down menu
5. Enter "CLB5" in "Query Term" text box
6. Select "2 nodes" from "Traversal" drop-down menu
7. Press "Query" button

Results should show up on the right panel

View Results in Graph:
1. Select nodes from grid panel
2. Press "Add Nodes" button
3. Select "Graph" tab


================================================================
Modifying Web Application
================================================================
   All content for the web application is served from $TOMCAT_HOME/webapps/ROOT
   Any changes will be immediately available in the browser (if tomcat is running)