Hi Alan, Alan R Williams wrote: > Hello Jits, > > I have two immediate questions: > > (1) How does your definition of a workflow component as including "Anything > that does > some processing" relate to the idea of data sources as first-class objects in > the > next gen workbench? >
At the moment, we're not quite sure and don't have a concrete proposal for handling data sources and data items. Though we definitely want to make them first class objects that can be easily added to workflows. In earlier work, we thought that data could be "wrapped" using the same components mechanism, but this quickly conflated the design discussions and led to some analysis paralysis. So in the interest of moving forward we focused on the process side of things first. There are a few considerations: - Based on discussions, users tend to want a clear separation between the "things that do some processing" and data sources. Hence the workbench has a "Components Palette" and a "Data" view (maybe we should call it "Data Palette"?) - There are very likely to be cases where components can be pre-packaged with data. For simple cases, like example data and default values, this is handled directly in the component definition. Or string constants within nested workflows can be used. But for more elaborate data packaging we need to think about this some more. Any thoughts / ideas on how we might do this? Internally, we will possibly use the Eclipse Resources framework [1] as there is a whole load of support for that in Eclipse RCP. We're also looking at VBrowser. > (2) How does the workbench component definition relate to, say, Galaxy tool > descriptions > Network Workbench algorithms or externalTool (was UseCase) definitions? > I've had a close look at Galaxy tool descriptions [2] and UseCase definitions (please could you remind me of the URL), but don't think I've come across NWB algorithms. Could you point me to the spec/template/examples please? In terms of Galaxy and externalTool, they cater for a bit simpler situation - wrapping command line tools only (I believe) so they have simple mappings to the underlying tech. There is still significant overlap with our components work, especially things like the UI configuration/fields in Galaxy tool configs. I can imagine we would be able to easily write a script to generate component definitions from externalTool definitions, or even just build a lightweight facade API over them. One thing, they don't seem to focus as much on metadata. I think things like help docs, tags, annotations, linking to related resources and helpers will (hopefully) add value once these workflow components live in repositories like a components library (building on our experiences with myExperiment and BioCatalogue). Cheers, Jits [1] http://help.eclipse.org/helios/index.jsp?topic=/org.eclipse.platform.doc.isv/guide/resInt.htm [2] http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax > Alan > > > ------------------------------------------------------------------------------ > Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! > Tap into the largest installed PC base & get more eyes on your game by > optimizing for Intel(R) Graphics Technology. Get started today with the > Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. > http://p.sf.net/sfu/intelisp-dev2dev > _______________________________________________ > taverna-hackers mailing list > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ > Developers Guide: http://www.taverna.org.uk/developers/ > ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ Developers Guide: http://www.taverna.org.uk/developers/
