Taverna I Assignment

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Julianna Mosley
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Taverna I Assignment Taverna is an open source workflow system. It provides a language and software tools to facilitate easy composition of workflows.

1 Taverna I Assignment Taverna is an open source workflow system. It provides a language and software tools to facilitate easy composition of workflows. The aim of this tutorial is to become familiar with using Taverna for construction and enactment of scientific workflows. Requirements The tools used in the tutorial are: 1) Java Development Kit 1.5 ( 2) Taverna 1.7 ( Note: more resources about Taverna 1.7 can be downloaded from here: Taverna Installation 1. Unzip the downloaded file. 2. Start Taverna by double-clicking on the runme.bat batch file. The Taverna splash screen will appear followed shortly by the Scufl Workbench. The Scufl Workbench The Scufl Workbench provides the graphical user interface by which workflows can be created and enacted in Taverna. From here, you can compose a workflow, enact (run) it and browse the results and provenance information. The workbench acts as a container of windows, which provide various views and a controller to manipulate a workflow. On startup, the Scufl Model Explorer, Scufl Diagram view and processors palette are opened by default. Processors palette Scufl Diagram View Scufl Model Explorer

2 Importing a workflow into the Scufl Workbench To begin using Taverna, let's import a Scufl workflow into the Workbench. First download the sample workflow available on the assignment page Unpack the zip file Click on the File menu and then click on Open Workflow. Then select the unpacked file EuroToDollar.xml. This will load the EuroToDollar Scufl workflow into the Workbench. Your Workbench should now look similar to that shown below. You can see that the Scufl Diagram window provides a graphical view of the current Scufl workflow model. This is a read only view which is created from Taverna's internal model of the workflow. The graphical view consists of a network of nodes and edges, and consists of the following components as defined by the Scufl workflow language specification:

Scufl Component Description Symbol Workflow Input A source processor which executes instantaneously and makes the input value available on its virtual output port Web Service Processor Allows a

3 Scufl Component Description Symbol Workflow Input A source processor which executes instantaneously and makes the input value available on its virtual output port Web Service Processor Allows a single call on a Web service operation. The port names are derived from the message names in the Web Service Description Language (WSDL) file of the Web service for the identified operation. Web Service Processor Local Processor Can be used to add new local functions which are coded as classes to comply with a simple Java interface. Local Processor String Processor Has a single output port on which it returns a constant string value. This processor is of particular use where another processor in the same workflow requires a default value which acts as a parameter String Processor Data Link Define the flow of data between workflow inputs, processors and workflow outputs. In addition, these edges provide additional metadata about the data being linked between processors such as MIME type information and whether data is a singleton or a collection. Workflow Output A sink processor which receives a value from its virtual input port but never actually executes. The workflow that has just been loaded consists of two basic steps. Given the symbol of the currency that you want to convert into Dollars, the workflow will retrieve the exchange rate (through the ConversionRate web service). Then the workflow sends the retrieved rate to the NumberToDollar web service in order to get a textual representation of the retrieved exchange rate. The Scufl Model Explorer window provides a view of the state of the current model as a tree structure and is also used to edit workflows in the Scufl workbench. Expand the ConversionRateInput node to see its ports. There are fromcurrency and tocurrency input

4 ports and there is a 'output' output port. Later on in this tutorial, you will learn how to use the Scufl Model Explorer for manipulating workflows. Enacting (Executing) a workflow We will now enact the current workflow using the Scufl Workbench. Workflows are executed in the Scufl Workbench using the Results panel. To bring this panel up, click on the File menu and then click on 'Run Workflow '. This will switch to the Results window which consists of 3 panes: Status, Results and Process report. The Status pane provides information about the status of each processor in the workflow which is being enacted. Notice the change in status of each processor during the enactment of the workflow. When the workflow has completed running, click on the Results pane to view the results. The output of the workflow should be a textual representation of the current exchange rate.

step. This can be done through the status pane by selecting the

5 This represents the final result after running the two main steps but what about if you would like to see the output of the first step. This can be done through the status pane by selecting the ConversionRateOutput processor, then select the intermediate inputs pane.

Click on the Process report pane. This will show the provenance information which has been recorded about the workflow which has just been enacted.

6 Click on the Process report pane. This will show the provenance information which has been recorded about the workflow which has just been enacted. Currently, this provenance is technical in nature consisting of temporal information and the type of service invoked by each processor. Editing Workflows The simplest way to become familiar with the Taverna factilities for editing a workflow is to take an existing workflow model and make some changes to it. When changing a model, the main focus is on the Scufl Model Explorer window to identify the elements to be changed. The Scufl Model Explorer provides a constrained set of options so that you should only be able to create valid Scufl models. Any changes made in the Scufl model using the Explorer window are reflected in the Scufl Diagram and also the XScufl view. Edit string constant For the EuroToDollar workflow model that you have just loaded and ran above, one very simple change is to change the string constant processor so that it provides a different string. In the Scufl Model Explorer window: Select the FromCurrency processor. Right click to obtain the menu for this processor. Select edit string value as shown below. Supply the new value in the input dialog box, for example, GBP, and click ok.

They also provide a way of entering alternative inputs when running Scufl workflows in the Taverna workbench as we have done above.

7 Now that the string constant has a new value, run the revised model and get the corresponding results. Replace string constant with workflow input Scufl models with a string constant as its workflow input are very useful as test examples since new users do not have to guess an acceptable input. They also provide a way of entering alternative inputs when running Scufl workflows in the Taverna workbench as we have done above. However, using a workflow input element is more appropriate in other situations. Follow the steps below to replace a string constant with a workflow input. 1. Create a new workflow input - In the current workflow, add the new workflow input element by rightclicking on Workflow inputs in the Scufl Model Explorer window. - Provide a name, say "FromCurrencyInput" for the workflow input when requested. This name must be unique in the scope of the current model. - Check the presence of the new workflow input in the Scufl diagram.

2. Link workflow input with processor - Right-click on the newly created FromCurrencyInput workflow input in the Scufl Model Explorer window to see the nested list of destinations to which this input

The link will be added to the current model and the views updated. - Note that in Taverna data links are always made in the direction that the data will flow.

8 2. Link workflow input with processor - Right-click on the newly created FromCurrencyInput workflow input in the Scufl Model Explorer window to see the nested list of destinations to which this input can be linked. - Select the FromCurrency input port of the ConversionRateInput processor since this is the required destination of the workflow input. The link will be added to the current model and the views updated. - Note that in Taverna data links are always made in the direction that the data will flow. That is you start by selecting the source of the data (input or processor output) and then select the destination (output or processor input). 3. Delete String Processor - The string processor is now redundant and needs to be removed from the Scufl workflow. Right click on the processor EmblAccNumber in the Scufl Model Explorer window and select Remove from model. The processor will be removed from the current model and the views updated

Your modified workflow should now look like the one on the right. When you now run the workflow, you will need to enter a valid currency symbol. Type in EUR or GBP as an example.

xscufl" to make them easy to identify. You can choose to save the current XScufl model in a file with extension ".

9 Your modified workflow should now look like the one on the right. When you now run the workflow, you will need to enter a valid currency symbol. Type in EUR or GBP as an example. Saving workflows When required the File menu -> Save Workflow option can be used to save a copy of the current model to local file store. You can save files with the extension ".xscufl" to make them easy to identify. You can choose to save the current XScufl model in a file with extension ".xml", so that it is recognized as an XML file by other applications (including your browser). Editing workflows revisited: Adding a new processor Now, what we would like to do is to see how to add a new web service into our existing workflow. Suppose we would like to add a simple web service that inverts our output string case (Uppercase letters that are lowercase and lowercase letters that are uppercase). In order to do this, you have to following steps. 1. Populating the Service Palette with a new web service. Web services are added to the list of available services by providing the location of a Web Service Description Language (WSDL) to the WSDL Scavenger. It inspects the file and

Now, we would like to add our text handling we service: Right click on Available Processors in the Available services window. A menu describing ways of populating services will appear.

10 extracts all the information about the data types required to invoke the services described by the WSDL. For WSDL's that describe very complex data structures this can sometimes take a few seconds depending on network speed. Now, we would like to add our text handling we service: Right click on Available Processors in the Available services window. A menu describing ways of populating services will appear. Select Add new WSDL scavenger and enter the URL address of the text handling WSDL file. This will add the text handling web service as an available processor into the Service Palette within a folder. This folder contains all available methods which can be added as a single step into our existing model. In order to add the InvertStringCase method into your model, just right click on the method and select Add to Model. 2. Adding an XML splitter When expanding the list of inputs, or outputs, to the services, those that require a complex data structure will be described as having a mime type of 'text/xml' (or l'(text/xml') if it expects an array of complex data types). For many web services it is possible to provide the data directly by providing the XML, but this requires the user to have previous knowledge of the structure of the data that the service expects. For this reason, 'XML splitters' are provided which interrogate the data structure and present to the user the internal data elements. XML splitters resolve the XML data structure by a single level, revealing child elements that can be either base types or further complex types themselves. Child elements that are complex can be split further, and so on until all the required elements are revealed.

For inputs, values are then assigned in the standard manner, and when the workflow is run the splitters reconstruct the XML to then be used when invoking the service.

In both cases, arrays are handled by the standard iteration's mechanism.

11 For inputs, values are then assigned in the standard manner, and when the workflow is run the splitters reconstruct the XML to then be used when invoking the service. For outputs, the values can be passed on to downstream processors in the standard manner, and are extracted from the XML resulting from invoking the service. In both cases, arrays are handled by the standard iteration's mechanism. For example, the Text Handling service InvertStringCase input 'parameters' expects data according to the following structure: <InvertStringCase> <sastring> </sastring> </InvertStringCase> An XML splitter is added upstream by right-clicking on the parameters node and selecting 'Add XML splitter', or 'Add XML splitter with name' to explicitly provide a name. Add an XML splitter to the input parameters with the name InvertStringCaseInput Add an XML splitter to the output parameters with the name InvertStringCaseOutput Your modified workflow should now look like the one below.

NumbersToDollarOutput and the workflow s

12 3. Adjust the workflow s connections a. Connect the NumbersToDollarOutput to the InvertStringCaseInput b. Remove the redundant connection between NumbersToDollarOutput and the workflow s output c. Connect the InvertStringCaseOutput to the workflow s output

13 Your final workflow should now look like the one below. Enact the workflow to see the results generated by the InvertStringCase processor.

An Introduction to Taverna 1.3

An Introduction to Taverna 1.3 The Taverna workbench software allows the construction of complex in silico experiments in the form of workflows, with a particular focus on the bioinformatics domain. We