BioDWH2 / BioDWH2-OrientDB-Server

OrientDB server utility for the BioDWH2 tool. Create and explore a OrientDB database from any BioDWH2 workspace.

BioDWH2-OrientDB-Server

BioDWH2 is an easy-to-use, automated, graph-based data warehouse and mapping tool for bioinformatics and medical informatics. The main repository can be found here.

This repository contains the BioDWH2-OrientDB-Server utility which can be used to create and explore a OrientDB graph database from any BioDWH2 workspace. There is no need for any OrientDB installation. All necessary components are bundled with this tool.

Download

The latest release version of BioDWH2-OrientDB-Server can be downloaded here.

Usage

BioDWH2-OrientDB-Server requires the Java Runtime Environment version 8. The JRE 8 is available here.

Creating a database from any workspace is done using the following command. Every time the workspace is updated or changed, the create command has to be executed again.

> java -jar BioDWH2-OrientDB-Server.jar --create /path/to/workspace

Once the database has been created, the database and OrientDB Studio can be started as follows:

> java -jar BioDWH2-OrientDB-Server.jar --start /path/to/workspace

By default, two users are created for OrientDB Studio:

• username: biodwh2, password: biodwh2
• username: root, password: root

Help

Usage: BioDWH2-OrientDB-Server.jar [-h] [-c <workspacePath>] [-cs <workspacePath>]
                                   [-s <workspacePath>] [-p <port>] [-sp <studioPort>]
  -h, --help                            print this message
  -s, --start <workspacePath>           Start an OrientDB server for the workspace
  -c, --create <workspacePath>          Create a OrientDB database from the workspace graph
  -cs, --create-start <workspacePath>   Create and start a OrientDB database from the workspace graph
  -p, --port <port>                     Specifies the OrientDB server port(-range) (default 2424-2430)
  -sp, --studio-port <studioPort>       Specifies the OrientDB Studio port(-range) (default 2480-2490)