In order to successfully use the Taverna Plugin, the user needs to install the following software in the local computer:
The user needs to have an account in the MI or in Biomed Town to be able to access the web services required for the plugin (see Registration and Log in section for more details.
Installing Taverna Plugin
To install the plugin the user needs to register this repository on the current Taverna Workbench by pressing F12 or using Advance >> Updates and Plugins menu option.
To add the repository click on Find new plugin button following by the “Add update site”
After that check the plugin and click on the Install button; only the plugins available for the specific Taverna Workbench version will be showed.
Importing VPH-Share services
Once the plugin is installed, the user is requested to restart Taverna . After that operation is complete, a new entry is shown when pressing the Import new service button VPH-Share services.
After this, the user needs to import VPH-Share services into Taverna before opening or creating any workflows. There are two ways to do this:
If the user has several WSDL URLs, he/she needs to perform this task for each one of them.
- If the user is provided with an XML file with all necessary services. Import these services by right-clicking on the folder Available services, located right below the Import new service button, and then selecting the option Import services from file in the pop-up menu. See the following image for reference.
A message window will pop up asking whether the user would like to replace the current services or append the new ones to the existing service. We recommend to press the Add to current services button. See the following image for reference.
After either of these two steps, if this is the first time the user uses Taverna Workbench, the user will be asked to setup the master password of Taverna’s Credential Manager. See the image below. The user can introduce any password of convenience. Be careful to remember this password, as it will be asked every time Taverna starts.
Then, the user will be required to introduce a Biomed Town user and password. The user will be required to enter this information only once, as long as this is saved in the Taverna’s Credential Manager. See the image below.
Once this is done, new entries will appear on Available services, with the name of the VPH-Share Applications that corresponded to the added WSDLs. Under each application name, the list of operations available through the application will show up, which can now be used to build workflows. See the following image for reference.
Unable to access to the Taverna Keystore
In order to enable the use of long password the user will be required to upgrade to Java Cryptography Extension (JCE) Unlimited Strength, if not done already.
The user has to download the correct version depending on the JRE that is running
and copy files on the security folder under the JRE location, replacing the previous version.
NoMachine plugin not installed or blocked
The VPH-Share plugin relies on the NoMachine web client (https://www.nomachine.com/) as the remote desktop application for the user to interact with some web services. This application requires the browser to support Java applets. If it does not, the following image will appear the first time the user tries to use the web client.
This indicates that the user has to install the support for Java Plugins first. Please do so, and after installing it please refresh the web page where the NoMachine client was attempted to start.
Timeouts when executing workflows for long times
By default, the execution of VPH-Share services has a blocking behaviour. This means that when the VPH-Share plugin invokes a VPH-Share service, the plugin’s execution is interrupted until the service returns a response. This is perfectly valid for services that return a response promptly, but it can pose a problem for those services with long execution times, since the connection can be taken down by any intervening web proxies or firewalls, as the communication is flagged as timed out. This is the typical source of errors such as “Bad gateway” or “Timeout” when running VPH-Share services.
In order to avoid this, the VPH-Share Taverna plugin supports a non-blocking communication mechanism, in which the plugin starts the execution of the service in an asynchronous fashion, and then monitors the execution status of the service every few seconds. When the plugin detects that the service is finished, it collects the response and continues the execution of the workflow. This can be easily activated in a per-service base, by selecting a service and then displaying its details. In the “Details” tab, a “Configure” button will show up. By pressing this button, the configuration dialog will appear, in which the user can activate the non-blocking behaviour by clicking on the check-box next to “Execute service in non-blocking mode”. See the following image for reference.