Hi,
On Tue, Mar 15, 2016 at 8:00 PM, Stian Soiland-Reyes <[email protected]> wrote: > On 15 March 2016 at 08:07, Thilina Manamgoda <[email protected]> > wrote: > > > I have gone through the tutorials Service invocation plugin > > < > http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+invocation+plugin > > > > and Service discovery plugin > > < > http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin > >. > > Great! Did you find any issues while doing so? > > > > So in order to bring CWL workflows to the Taverna i have to implement > Service > > discovery plugin > > < > http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin > > > > for CWL right ?. > > Yes, the TAVERNA-880 task is basically to implement a service > discovery plugin for CWL. > > The Service Invocation tutorial would be more relevant for > TAVERNA-878. It could be that to test your UI, to be able to drag a > CWL Tool into a workflow, you need to have a "dummy" Activity similar > to the one in the tutorial, even if it doesn't actually do any actual > invocation when it is run. That is, it would be a placeholder. > > > > 1. SCULF2 workflows are saved as workflow bundle document . > > Correct.. except it's a ZIP file of XML files, not a single document :-) > > > > 2. Service discovery plugin > > < > http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin > > > > Service > > Description is java bean and it's build using corresponding workflow > > bundle document . > > It's a java beans (in the Configuration), but as the tutorial is > according to Taverna 2.5 you will later need to update your Service > Discovery code for Taverna 3, where you will use the Taverna Language > SCUFL2 API - which is a java bean approach to the Workflow Bundle. > (those beans are then saved to the Workflow Bundle ZIP file, but that > is already handled). > > The beans are different though, the Taverna 2.5 beans have a > Configuration subclass per activity type, e.g. a ToolConfiguration - > while in Taverna 3 the Configuration class is not subclassed (instead > it declares a type URI), and all the actual configuration is in the > linked JSON object - which content would vary per configuration type. > > > > > 3. Activity has the logic of workflow .For example let's say service is > > addtiion of two numbers . Then two numbers are input and the addition is > > inside the Activity class . > > Exactly, the Activity is the thing that actually 'happens' in a box in > the workflow. The rest of the workflow is basically connections, > iterations and controls. > > > > 4.Activity class is also configured (build) using corresponding workflow > > bundle document . > > Yes. When a WorkflowBundle is set to run, the Taverna Engine will > select the corresponding Activity subclass based on its type URI, > instantiate it, and then configured it with a JsonObject (which exists > as a JSON file if the Workflow Bundle is saved as a ZIP file.) > > > There are different types of activities depending on what kind of > invocation they are doing, e.g. a RESTActivity that can do HTTP calls > (the configuration says which URI and headers), the ToolActivity can > execute a local or SSH command line (the configuration says which > command/host), or the BeanshellActivity can run a Beanshell script > (the configuration contains the script). There are thus different > configuration types, and a corresponding JSON Schema that says which > keys and value types to expect for a given type. > > > The imagined CWLActivity (TAVERNA-878) will be either a new kind of > activity, or just an alternative configuration of the ToolActivity - > as basically a CWL Tool is a command line that in theory may be > executed using the correct "docker run" syntax. In Taverna 3 it is > possible to have different kinds of configuration for the same > activity, the ToolActivity could be changed to recognize both its > existing "classic" Tool configuration and a new "CWL tool" > configuration. > > If you are interested in this execution logic, then it is probably > worth having an early stage investigation in the beginning of your > GSOC project to see to what extent the existing execution logic of the > ToolActivity can run a docker command line - e.g. experimenting in the > 2.5 Workbench and adding a Tool that executes a tool as in the CWL > Tool description, and then you would be able to see the configuration > mapping in a way. (But it could be that this reveals that say the > data handling of CWL Tools is different to how the Tool activity > handles input and output files - in which case a new CWLActivity would > be a better approach). > > As you write up your project proposal now, you should have some rough > estimates and time plans. Doing both TAVERNA-878 (activity) and > TAVERNA-880 (discovery) could be too much for the short duration of > GSOC, so if you are interested in both I would suggest to do one of > them only minimally. > > > > *5. when designing a CWL * Service discovery plugin > > < > http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin > > > > i > > Have to implement dummy Activity class for CWL . > > > Yes, with a "dummy activity" I mean one that can't actually execute > anything, it might just always say "Hello" on the output so that you > can see in the workbench that you have added something from your CWL > Service Discovery plugin. > > Also when you do this in Taverna 2.5 you need to have an actual > Activity subclass to add to the workflow - this is a problem in 2.5 in > that you couldn't build workflows with activities your local Taverna > didn't know how to execute. In Taverna 3 the workflow building is done > with plain java beans from the Taverna Language API, and those don't > know anything about execution, and so there it would be possible to > build workflows with activities that only run elsewhere (e.g. build a > workflow in Windows even though its activity can only run in Linux). > > > Alan - do you think in Taverna 2.5 phase we could let the CWL > Discovery plugin add a DisabledActivity instance and then chuck the > configuration JSON inside the XML? Would not then that XML be saved > directly to the .t2flow? It would be a bit cheating.. but then this > would be cheating anyway, and also it would mean it would both save > from Taverna Workbench 2 and load in Taverna 3. (We would need to add > a translator on the Taverna Language side though). > > > It should have logic to > > execute cwl-runner with corresponding tool and inputs and get the output > . > > > Executing cwlrunner from Taverna (configured with a CWL workflow > rather than a CWL tool) could be an interesting thing - that would be > a way to include a CWL workflow as a nested workflow in Taverna. > However I think that would be a different approach, so I've tracked > that as a new Jira task > https://issues.apache.org/jira/browse/TAVERNA-938 > > This could be some kind of intermediate approach you could explore if > you want, as you can execute any cwl tool by generating a one-step cwl > workflow and run cwlrunner. However then the user would need to have > cwlrunner AND Taverna installed, so it would be more of an > intermediate solution, which would however be great for demonstration > purposes - and mean that your GSOC work would be usable without > waiting for the other tasks. > > > Personally I am also going to try to work on the CWL support during > this spring/summer - so whatever tasks are not picked by an accepted > GSOC student would be something I would try to do - however I wouldn't > want the students to have to rely on this arriving in time, as your > GSOC evaluation (which determines if you get paid!) should be > independent of other concurrent work, including different GSOC > students. That doesn't mean you can't collaborate and discuss > solutions on this list - I would hope you do! Just don't build other > people's work into your project proposal like a blocker. > > > You are asking the right questions! Feel free to ask if you need help > with your project proposal! > > > -- > Stian Soiland-Reyes > Apache Taverna (incubating), Apache Commons RDF (incubating) > http://orcid.org/0000-0001-9842-9718 >
