impact/mygrid hackathon - introduction to taverna

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Katy Wolstencroft gives an introduction to Taverna at the IMPACT/myGrid Taverna Hackathon, 14th November 2011

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  • 1. An Introduction to Designing, Executing and Sharing Workflows with TavernaKaty Wolstencroft myGrid University of Manchester IMPACT/Taverna Hackathon 2011

2. Exercise 1: Exploring the Workbench

  • Taverna can be downloaded from
  • http://www.taverna.org.uk/
  • Go to the page and find the latest (2.3)
  • Download the correct version for your operating system
  • Follow the instructions in the Taverna installer
  • The following page shows a screenshot of Taverna and the different panels that make up the workbench

3. Taverna Workbench Workflow Diagram Services Panel Workflow Explorer 4. 1. Workflow Diagram

  • The visual representation of workflow
  • Shows inputs/outputs, services and control flows
  • Allows editing of the workflow by dragging and dropping and connecting services together
  • Enables saving of workflow diagrams for publishing and sharing

5. 1. Workflow Explorer

  • The Workflow Explorer shows the detailed view of your workflow. It shows default values and descriptions for service inputs and outputs and it shows where remote services are located. It also shows configuration details, such as iteration and looping (we will come back to these things later).
  • Workflow validation details can also be found here. Before a workflow is run, Taverna checks to see if it is connected correctly and if its services are available.

6. 1. Available Services Panel

  • Lists services available by default in Taverna
    • Local java services
    • WSDL Web Service secure and public
    • RESTful Services
    • R Processor services (for statistical analyses)
    • Beanshell scripts
    • Xpath scripts
  • Allows the user to add new services or workflows from the web or from file systems there are loads more available!

7.

  • In the Services panel, type imageinto the search box.
  • Select Get Image from URL
  • This is a local service, but web services work the same way
  • Many historical documents are stored as images on the web. This is a simple, but useful service to help gather data

Exercise 2: Building a Simple Workflow

  • Drag this service across to the workflow diagram panel

8. Exercise 2: Building a Simple Workflow

  • In a blank space in the workflow diagram, right-click and select Add Workflow Input Port
  • Type a name (e.g. URL) for this input in the pop-up window and click ok
  • Do the same to create a new workflow output. Call this output image

9. Exercise 2: Building a Simple Workflow

  • You now have 3 boxes in the diagram and we need to connect them up into a workflow
  • First, we need to find out how many inputs and outputs the get image from URL service has
  • At the top of the workflow diagram, select the show ports icon

Show Ports 10. Exercise 2: Building a Simple Workflow

  • Click on the workflow input box and drag the linking arrow across to the URL input of the get_image_from_URL service.

Link the image output of get_image_from_url to the workflow output port 11. Exercise 2: Building a Simple Workflow

  • You have now built your first workflow! It should look something like this.
  • In many cases, you have to supply input data for EVERY service input port. In this case, however, the base input is optional, so we will leave it.
  • Save the workflow by going to file -> save workflow

12. Exercise 2: Building a Simple Workflow

  • Run the workflow by selecting file -> run workflow, or by clicking on the play button at the top of the workbench

13. Exercise 2: Building a Simple Workflow

  • An input window will appear. As you can see, we have not yet added a description of the workflow or of the input

Click on New Value in the input window and add the url http://www.archives.gov/exhibits/featured_documents/magna_carta/images/magna_carta.jpg where it says some input data goes here 14. Exercise 2: Building a Simple Workflow

  • Click run workflow
  • In the bottom left of the results window, click on the results. You will now see an image from the specified web page
  • Workflow results can be saved here if required by clicking on save all values

15. 2: Adding a Workflow Description

  • Right-click on a blank part of the workflow diagram and select show details
  • In the workflow explorer panel, the details page will open up. Add some details about the workflow (e.g. who is the author, what does the workflow do).
  • You can also add examples and descriptions for the workflow inputs by selecting them in the explorer panel and selecting details
  • Adding this metadata makes the workflow much more reusable
  • Save the workflow by going to File -> save workflow

16.

  • New services can be gathered from anywhere on the web
  • We will find a new service and add it to the workbench
  • IMPACT and SACPE have a whole suite of services. We will add one (you will be using it later on today)
  • Go tohttps://fue.onb.ac.at/synapse . Here you will find a list of IMPACT services
  • Click onIMPACTTesseractV3Proxyand copy the link you are directed to.
  • This is the WSDL address and is what Taverna needs to run the service

Exercise 3: Adding New Services 17. 3. Adding New Services

  • Go to theservicespanel in Taverna and click import new services. For each type of service, you are given the option to add a new service
  • Select WSDL serviceA window will pop-up asking for a web address

18. 3. Adding New Services

  • Enter the service address you just copied
  • Scroll down theServiceslist, you will see your new service there

19. Exercise 4: Sharing and Reusing Workflows

  • Go tohttp://www.myexperiment.org
  • myExperiment is a social networking site for sharing workflows and workflow expertise and experiences
  • Browse around the site and see what it contains
  • Find everything that has been tagged with text mining, for example
  • Look at the text mining workflows. You will see some that are specific to biology, some that are generally applicable, and some that are specific to other scientific disciplines

20. 4. Sharing and Reusing workflows

  • IMPACT have many workflows on myExperiment, but they are not public. You must join an IMPACT group before you can see them and use them.
  • Create yourself an account and join the group called IMPACT-myGrid-Hackathon ( NOTE : you need to join this group to access content for future exercises)
  • Explore the shared items in this group. These are examples of the types of tasks IMPACT workflows can perform

21. 5. Using Workflows from myExperiment

  • You can download and run the workflows from the myExperiment website, or you can use myExperiment directly from Taverna
  • To use workflows from the website, you can either download them, or copy the workflow file location into the open workflows from the web option in Tavernas file menu.

22. 5. Using Workflows from myExperiment

  • Go back to Taverna and click on the myExperiment icon at the top of the workbench
  • Go to my stuff and log in (using the same credentials as the web page)
  • Find the IMPACT-myGrid-Hackathon group by using the search option.
  • Look at the shared items and find the workflow called Text to List
  • Click on open and this workflow will be automatically imported into your Taverna design window

23. 5. Validate your Workflow

  • Taverna checks to see that everything is connected properly and that all the required services are available
  • Go to the workflow explorer and click on validation report
  • See if Taverna has found any problems with the workflow. Errors will be displayed in red, warnings in yellow. Workflows with warnings often still run.
  • If there are problems, follow the instructions to resolve them by clicking on the Solution tab
  • If not, run the workflow

24. 5. Using Workflows from myExperiment

  • Use the default input suggested to run the workflow. The workflow will collect and list some example data stored at the given URL
  • It returns a list of image files
  • We can now combine this workflow with the one we made earlier to return the actual images.
  • In Taverna, you can add workflows as if they were any other kind of service these are called Nested Workflows

25. 6. Reusing and connecting Workflows

  • From the current workflow design window, go to
  • Insert -> Nested workflow
  • Import the workflow you made earlier, by selecting import from file
  • You can see a small