1 Introduction

##1.1 Purpose:

This user manual is a comprehensive guide to walk through the steps that it takes to install fedora, taverna, virtual machine and how to add different microservices. The easy steps that has been described in the manual will be very beneficial for the users who are new in this area. This will also help the user to understand how the overall process works in terms of system requirement.

Also, it will describe how to create a t2workflow and how the JMS listener works in the proposed architecture. Most importantly, this will guide the user to add existing micro services as well as the new microservices that is under development. Once the system, is completely built, it will help new user greatly to get all the system running in their local machine.

1.2 System Overview

1.2.1 system structure

JMS Listener

The JMS listener listen to the changes from fedora. JMS listener pulls t2flow document from the content model to taverna server when changes happen.

The JMS listener include:

1. TavernaSender.php which is to sent and run t2flow on taverna sender.

2. Connect.php which is to listen a single change.

3. listener.php which start connections.

4. TavernaConnectionException.php which is to deal with Exceptions.

5. tuque which is the API that TavernaSender uses.

The JMS listener uses HTTP REST to post and run t2flow to taverna.

To use JMS listener, a trigger datastream xml file should be added into the content model. It defines which methods are triggered and which t2flows are used.

To use JMS listener, t2flows that uses should be added into the content model.

PHP SOAP listener.

The PHP SOAP listener is to provide WSDL and SOAP services.

The PHP SOAP listener defines microservices via WSDL 1.1 which users can import to taverna workbanch and make t2flows.

The PHP SOAP listener includes:

1. The includes folder which executes the microservices.

2. soap_serv.php which is to provide the WSDL and SOAP services.

3. The soap_test folder which is to test soap_serv.

4. The tuque API which is the API soap_serv uses.

Taverna Workbanch

Taverna workbanch is to make t2flow.

Users can import microservices if PHP SOAP listener is correctly installed.

Users should add the t2flows they made to content model so that JMS listener can post them to taverna server.

It is located at : http://www.taverna.org.uk/download/workbench/

Taverna Server

The taverna server process REST call from JMS listener.

The t2flow runs at the Taverna server.

The taverna server calls the services defined in PHP SOAP listener to execute microservices.

The taverna server calls the external Web service to execute external services.

1.2.2 System Requirements

In addition to the Islandora Requirements, the following is needed to execute the Taverna Integrated workflows:

A working Taverna Server (TavernaServer 2.4.1 tested.)

Updated php_listeners code currently located here:

https://github.com/roblib/php_listeners/

PHP PEAR SOAP Server (version 0.13.0 tested)

1.2.3 Taverna Workbench System Requirements:

Operating System:

Taverna Workbench has been successfully tested on the system below:

Windows XP.

Windows Vista.

Windows 7.

Mac OSX (10.4) and various versions of Linux.

Memory:

At least 1GB of RAM for better performance.

JAVA:

Requires at least JRE version 6 or later from Oracle.

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