LIMS Server

Introduction This document describes how to get started with the Biocode LIMS Server . The server is a Java web application and is bundled in a war file. Theoretically it can run in any Java Web Application Server that provides Servlet API 3.0 or greater, but at this time it is being developed and tested with Jetty v9. This document tries to provide generic instructions alongside specific instructions for Jetty v9.

Let Biomatters know if you wish to use another application server.

Jetty Instructions Jetty can be obtained from many Linux repositories. However it is also available as a standalone distribution at http://www.eclipse.org/jetty/ and can be installed on a variety of operating systems including Microsoft Windows.

The full Jetty documentation can be found at http://www.eclipse.org/jetty/documentation/current/index.html.

Follow Part I: Quick Start Guide to get Jetty running on your server. Running Jetty as a service is covered under Part III: Jetty Administration and is not covered by this document.

User Access In the next phase of development we will be adding systems for authentication and authorization separating user data access based on project role. For this alpha version the LIMS server will take advantage of the user authentication provided by the application server. The LIMS server will allow anyone with the role of lims to connect.

Jetty Instructions Jetty does not start with any user authentication so this will need to be added before the BiocodeLIMS server will start up correctly.

Authentication in Jetty can be configured in a number of ways. Consult the documentation if you wish to explore the methods available. For the purposes of getting started quickly two configuration files have been supplied along with this document that can be used to quickly set up a user to connect with. BiocodeLIMS.xml - Defines file based authentication. Place this in your webapps directory. biocode-users.properties - Defines user accounts and passwords. Place this under the [jetty home]/etc directory. Typically jetty home is the jetty installation directory.

Configuration The server will need to connect to an external LIMS database. The server will get it’s connection configuration from a properties file in the home directory of the user the server runs under. For example if your server’s home directory is /home/server then the configuration file will be read from /home/server/.biocode-lims/connection.properties. The server will create this file the first time it starts if the file is missing.

Jetty Instructions A typical jetty installation will have the server running as a user named jetty. The home directory is usually the jetty installation directory or /usr/share/jetty on Linux systems.

If unsure about where to locate this file. Then deploy the war file first and let it create the default connection.properties file. The index page located at [Jetty Server URL]/BiocodeLIMS will tell you where the file is located.

Deployment Once your application server is installed and a user account set up with the lims role, you are ready to deploy the BiocodeLIMS.war file into your application server. Jetty Instructions The easiest way to deploy the application is to drop the war file into the [jetty home directory]/webapps

After Deployment Once the server is started and the application is deployed you should be able to visit [server url]/BiocodeLIMS. If there was any problems connecting to your FIMS or LIMS this page will show errors. Otherwise everything should be good to go.

You can test this by viewing [server url]/BiocodeLIMS/biocode/fims/fields/tissue in a web browser. This should return an XML document that describes your fims tissue field as below.

Connecting with Geneious It is not possible to connect to the server using the public release version of the Biocode plugin. The server can only be connected to using version 2.90.0 of the Biocode plugin contained in the folder with these instructions.

The new plugin will allow you to choose Through Biocode Server as the connection method. Specify your URL, username and password to connect.

The server provides all the functionality of the standalone plugin with the exception of the reporting module.