Taverna 1.7.1 released

Taverna 1.7.1 was released today, including an updated preview of t2, the enactor of Taverna 2.0 scheduled for June 2008.

You can download 1.7.1 from SourceForge.

This update to Taverna resolves a number of issues with Taverna and the preview of the new t2 enactor.

For instance, you should now be able to run a workflow in the Taverna 2 preview perspective and see the progress graphically with progress bars. If you run a sufficiently advanced workflow, such as one of Paul Fisher’s workflows– you should be able to see the streaming of t2 in effect, where a processor downstream will start iterating over the results even if the one above has not yet finished. This alone should be able to give a nice speed-up to workflows iterating over many items.

We’ve also reintroduced the interactive diagram editor to complement the normal, static diagram. Now, we know it’s still not 100% stable, so that’s why there is that little “experimental” there in the title, but many users find this much easier to work with. You can simply click on a processor in the diagram to select it, right click, select Connect output and draw a line to the processor you want to connect. You can even make connections the other way around, if you know you need an input, but don’t remember quite sure from where! You should also be able to drag services from Available services and onto this diagram to add them to the workflow.

Although this won’t be the editor you will see in Taverna 2.0 that we have scheduled for end of June 2008, but we’re aiming for a similar way to edit workflows, as one of many, as we’ll shine up the graphical user interface to go better with the new enactor. We’ll also now be working on security aspects, such as support for various grid systems, as you might have seen discussed on taverna-hackers.

If you’ve been using nested workflows and have had complains from your friends on myExperiment because their Taverna can’t find F:\workflows\nested\mynestedworkflow.xml – 1.7.1 has a solution for you. When you save a workflow, tick the Embed nested workflows checkbox, and all of your nested workflows will be embedded in the saved Scufl instead of referenced by filename.

Note that if you actually find the referenced nested workflows useful, say because you update the nested workflow on disk and want the new version to be used in all the workflows including that nested workflows, make sure you save the workflow without the checkbox ticked to keep the references. We’ll be looking at further improving the GUI so that it’s more obvious when a nested workflow is included by reference (ie. filename) or embedded – but expect this to look slightly different for Taverna 2.0 anyway.

The t2 plugin is now able to render results such as images and JMol data as in Taverna 1. Note that we’re still working on improving the user experience in the t2 result browser, as it’s still not optimal. For instance you currently need to expand the data document, select the first entry, right click and select Render as image.

Under the official plugin list we’ve included the GT4 processor and scavenger contributed by Wei Tan and Ravi Madduri of the caGrid project, note that this is still in it’s early stages as we’re sorting out issues to do with WSRF, security, etc. in tight cooperation with caGrid.

If you’re missing the alternative way to find services of Taverna 2 Activity Palette that was introduced in 1.7.0, you can also find this under available plugins, we chose to no longer include this by default as Taverna 2.0 will include a different activity palette and it would not be a realistic preview.

The source code download of 1.7.1 should also be more complete including the code for the plugins and the t2 preview – although we still recommend doing an anonymous CVS checkout.

We’ve resolved these issues according to Jira:

Spring release 2008 – presumable last release before 2.0
Bug TAV-553 FIXED Fetching results unpredictable Critical Resolved
Bug TAV-709 FIXED T2 Enactment Error with pauls workflow Critical Resolved
Bug TAV-700 FIXED Column ‘thing’ too short in LogBook database schema Major Resolved
Refinement TAV-735 FIXED Improved workflow editor adding improved drag and drop abilities Major Resolved
Bug TAV-716 FIXED Remote execution service using outdated Taverna profile Major Resolved
Bug TAV-721 FIXED T2 Valdation fails for processors containing merged ports. Major Resolved
Bug TAV-732 FIXED documentation is out of date Major Resolved
Bug TAV-740 NOT A BUG Workflow example directory does not replace previous installation Major Resolved
Bug TAV-694 BY DESIGN t2: Conditionals fire even on errors Major Resolved
Task TAV-737 FIXED Allow multiple implementations of the Monitor interface. Major Closed
Improvement TAV-682 FIXED Disconnected outputs fails workflow Major Closed
Improvement TAV-726 FIXED Mac OS X plist file improvements Major Closed
New Feature TAV-664 FIXED Serialise bean to stream instead of file Major Closed
Bug TAV-724 FIXED T2 FileDataManager and FileBlobStore uses File.mkdirs which isn’t thread-safe Major Closed
New Feature TAV-736 FIXED T2 Renderers Major Closed
Bug TAV-710 FIXED T2 input dialogue doesn’t open after an error Major Closed
Improvement TAV-244 FIXED The execution version of the workflow should be the same as the edit version. Major Closed
Bug TAV-731 FIXED goViz is not there Major Closed
Improvement TAV-722 WON’T FIX Increase default memory size Major Closed
Bug TAV-706 NOT A BUG T2 XMLInputSplitterActivity problem Major Closed
Bug TAV-741 NOT A BUG T2 plugin initially disabled Major Closed
Improvement TAV-675 BY DESIGN t2 should support implicit iteration in input port Major Closed
Bug TAV-715 FIXED Avoid Raven/maven dependency for remote execution service Minor Resolved
Bug TAV-680 FIXED Failing workflows goes to empty results Minor Resolved
Bug TAV-742 FIXED JTidyWorkerTest fails due to character set assumptions Minor Resolved
Bug TAV-649 FIXED SVG renderer does not work Minor Resolved
Bug TAV-713 FIXED Workflow scavenger dropping ports and script content for Rshell Minor Resolved
Bug TAV-679 FIXED Default “Metadata” tab for input/output ports confusing Minor Closed
Improvement TAV-574 IMPLEMENTED Nested workflow location Minor Closed
Bug TAV-719 FIXED TestJavaProcess failed during Maven build Trivial Resolved
Improvement TAV-728 FIXED Add Unknown Host Exception in PluginManager Trivial Closed

Well, that’s about what I remember for now, let’s hope you’ll enjoy the release, and as always, report any bugs, issues and questions to our mailing lists.

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