As you might know, we are developing Scufl2 as the next language and
model for specifying Taverna workflow. We have already successfully
used this model in an internal release of an OSGi-based command line
tool for executing Taverna workflows, and for Taverna 3 are working
towards using this as the workflow model being edited by the
workbench.
One of the motivations for moving from .t2flow to Scufl2 is to allow
third-party tools (like myExperiment) easier access to the workflow
structure, for reading, inspection, annotation and creation of
workflows. Ideally this should also allow the development of
alternative workflow building environments independent of the workflow
engine, like a simplified web-based editor.
Scufl2 as developed so far includes a Workflow Bundle format [1],
using structured folders (normally archived in a ZIP-file for
distribution purposes) of RDF/XML files - which can also be
created/parsed with an XML Schema if the appropriate xsi:type
attribute is included. [2]. (Note that the Scufl2 wiki pages are still
at a draft stage)
Although this format allows for all the Taverna language features to
be specified and used in an extensible manner, for instance allowing
bundling of data, provenance and runtime libraries, plugins to specify
which options they expect, etc., this format is more of an exchange
and bundling format than a format for manual editing.
The Scufl2 toolkit [3] allows reading and writing the common Scufl2
workflow model in many different formats, this is for instance how it
reads .t2flow and SCUFL 1 workflows at the moment. There is also an
internal textual "debug output" format. [4]
It has been raised a requirement to develop a more user-fronted
textual format for editing workflows by hand in an editor. The current
Scufl2 development is very much enabled to do so.
My suggestion is to do this as an additional SCUFL2 format, as a
simple text file in YAML or JSON, for writing regular straight-forward
workflows, with enough automagic (such as port depths and iteration
strategies) filled in by a combination of SCUFL2 tools and the engine.
For instance in made-up-JSON using the external tool activity:
{
"workflow" : {
"inputs": ("name"),
"outputs": ("greeting"),
"processors": {
"hello": {
"type": "tool",
"command": "echo Hello, %%name%%"
}
}
"links": {
"name": "hello:name",
"hello:STDOUT": "greeting"
}
}
}
Such a format would not be able to express every .t2flow or Scufl2 WB
workflow, but by limiting the scope we can avoid many details which
would make the format too verbose or magic, for instance port mapping,
alternative activities, and complex activity configurations.
I hereby propose a meeting/Skype call to discuss the need and
implementation plan of such an alternative serialisation format for
SCUFL2 workflows - with the aim of workflows to be easy to edit and
read by hand. If you are interested in attending the meeting (no
matter if you are part of the myGrid team or not), please mark your
availability in the Doodle poll [3].
[1] http://www.mygrid.org.uk/dev/wiki/display/developer/Taverna+Workflow+Bundle
[2] http://www.mygrid.org.uk/dev/wiki/display/developer/Scufl2-WorkflowBundle
[3] https://github.com/mygrid/scufl2/
[4]
https://github.com/myGrid/scufl2/blob/master/scufl2-api/src/test/resources/uk/org/taverna/scufl2/api/io/HelloWorld.txt
[5] http://www.doodle.com/ybruwger8mi5bnn7
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
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