Hi, How can I use the taverna-language API to know what will the inputs and what will the outputs of workflow?
I don't get any proper guide or code. Thanks On Fri, Sep 2, 2016 at 6:37 PM, Stian Soiland-Reyes <[email protected]> wrote: > Yes, you should use taverna-language to load the .t2flow and inspect it. > > You should not really need to make any Java beans for it as the > workflow wouldn't be constructed on the phone (although you could do > that with the Taverna Language API), but loaded from $somewhere as > previously saved from the Taverna Workbench or downloaded from > myExperiment - however you can use the API to inspect the workflow, > e.g. list the input port names of the main workflow. > > > See: > > https://taverna.incubator.apache.org/download/language/ > > Javadoc: > https://taverna.incubator.apache.org/javadoc/taverna- > language/org/apache/taverna/scufl2/api/package-summary.html > > Example: > https://github.com/apache/incubator-taverna-language/ > blob/master/taverna-scufl2-examples/src/main/java/org/ > apache/taverna/examples/ProcessorNames.java > > On 29 August 2016 at 14:39, Ian Dunlop <[email protected]> wrote: > > Hello, > > > > There is an xsd for t2flow available in the taverna-language module > > https://github.com/apache/incubator-taverna-language/ > blob/master/taverna-scufl2-t2flow/src/main/resources/org/ > apache/taverna/scufl2/translator/t2flow/xsd/t2flow.xsd > > You should be able to re-use taverna-language to parse t2flow rather than > > build your own parser. Perhaps using > > https://github.com/apache/incubator-taverna-language/ > tree/master/taverna-scufl2-t2flow. > > No readme though. Maybe some other devs can advise how to use it. > > > > Cheers, > > > > Ian > > > > On 28 August 2016 at 18:23, Sagar <[email protected]> wrote: > > > >> Hi, > >> > >> Is there any predefined tree structure for t2flow xml file ? > >> > >> if yes, then provide me so that I am able to create java beans for it. > >> otherwise, I will create it according to any t2flow xml file. > >> > >> Please revert ASAP. > >> > >> Thanks > >> > >> On Fri, Aug 26, 2016 at 3:54 PM, Finn Bacall < > [email protected] > >> > > >> wrote: > >> > >> > This wouldn't be that hard to implement, you can get the unique ID for > >> the > >> > workflow from the parser gem, see: > >> > > >> > https://github.com/myExperiment/workflow_parser-t2flow/blob/ > >> > master/lib/t2flow/model.rb#L136 > >> > > >> > Then you'd just need to extract it in the parsing method: > >> > > >> > https://github.com/myGrid/taverna-player-portal/blob/master/ > >> > app/models/workflow.rb#L40 > >> > > >> > and store it in a new field in the database. > >> > > >> > Cheers, > >> > > >> > Finn > >> > > >> > > >> > On 26/08/2016 09:32, Ian Dunlop wrote: > >> > > >> >> Hello, > >> >> > >> >> I think you are pretty much spot on with your diagnosis. I agree it > is a > >> >> bit of a pain that the workflow ids are different. However, each > >> workflow > >> >> does have a unique uuid internally (with t2flow anyway) so that > could be > >> >> used to check if a workflow on myexperiment and the portal are the > same. > >> >> Look for the element <dataflow id="0f5e83c1-bbb5-42e7-9ba3- > >> 438f645d3d17" > >> >> role="top"> in a t2flow file. This probably means that the portal > would > >> >> need an extension to search by workflow uuid. For now I would just > treat > >> >> each run as having a unique workflow and we can always improve it > later. > >> >> > >> >> Cheers, > >> >> > >> >> Ian > >> >> > >> >> On 26 August 2016 at 08:02, Sagar <[email protected]> wrote: > >> >> > >> >> Hello, > >> >>> > >> >>> Thank you for providing code. Now, I am working on it. > >> >>> > >> >>> Currently, I have understood that I need following steps to run a > >> >>> workflow > >> >>> on taverna player portal > >> >>> > >> >>> 1) Download workflow content. > >> >>> 2) Upload it to taverna player portal. > >> >>> 3) Run it on taverna player portal. > >> >>> 4) Show output of the complete workflow's run. > >> >>> > >> >>> I have also understood that there is no link between myExperiment > >> >>> workflow > >> >>> and Taverna Player workflow that's why I can't retain myExperiment's > >> >>> workflow running history on Taverna player portal and also I can't > >> search > >> >>> the same workflow in taverna player portal. For each new run, I > have to > >> >>> upload it again. > >> >>> > >> >>> > >> >>> If I have understood correct then Please revert back . > >> >>> > >> >>> If not then, Please correct me. > >> >>> > >> >>> Thanks > >> >>> > >> >>> > >> >>> On Wed, Aug 24, 2016 at 8:48 PM, Ian Dunlop <[email protected]> > >> >>> wrote: > >> >>> > >> >>> Hello, > >> >>>> > >> >>>> This is where the upload code is in the current mobile code > >> >>>> https://github.com/apache/incubator-taverna-mobile/blob/ > >> >>>> 4daa91d3f42b5a4474303fd39c7a7ec1483cebff/app/src/main/java/ > >> >>>> org/apache/taverna/mobile/fragments/workflowdetails/ > >> >>>> WorkflowdetailFragment.java#L655 > >> >>>> > >> >>>> Cheers, > >> >>>> > >> >>>> Ian > >> >>>> > >> >>>> On 24 August 2016 at 14:40, Ian Dunlop <[email protected]> > wrote: > >> >>>> > >> >>>> Hello, > >> >>>>> > >> >>>>> That upload code should already be available in the mobile app. > >> Larry, > >> >>>>> myself and Finn spent a few hours figuring all that stuff out last > >> time > >> >>>>> round. > >> >>>>> I have added an API call in the taverna-player-portal to get the > runs > >> >>>>> > >> >>>> for > >> >>> > >> >>>> a user eg /users/1/runs. Pull request waiting in github (hint hint > >> >>>>> > >> >>>> Finn). I > >> >>>> > >> >>>>> even added some tests. > >> >>>>> > >> >>>>> Cheers, > >> >>>>> > >> >>>>> Ian > >> >>>>> > >> >>>>> On 24 August 2016 at 10:57, Finn Bacall < > >> [email protected]> > >> >>>>> wrote: > >> >>>>> > >> >>>>> On 23/08/2016 11:38, Sagar wrote: > >> >>>>>> > >> >>>>>> Hi, > >> >>>>>>> > >> >>>>>>> I think there is some problem as mention below > >> >>>>>>> > >> >>>>>>> 1) How can I upload a workflow using API ? > >> >>>>>>> > >> >>>>>>> here's a gist of some Java code someone wrote to upload a > workflow > >> to > >> >>>>>> > >> >>>>> the > >> >>>> > >> >>>>> portal: > >> >>>>>> https://gist.github.com/larrytech7/957cc61a3bdd82e3e030 > >> >>>>>> > >> >>>>>> Basically the format is: > >> >>>>>> > >> >>>>>> { "workflow" : { "document" : "data:application/octet- > >> >>>>>> > >> >>>>> stream;base64,<<<Insert > >> >>>> > >> >>>>> base64 encoded workflow here>>>" } } > >> >>>>>> > >> >>>>>> Finn > >> >>>>>> > >> >>>>>> > >> >>>>> > >> >>> > >> >>> -- > >> >>> > >> >>> *With warm regards * > >> >>> *Sincerely yours* > >> >>> Sagar > >> >>> > >> >>> > >> >>> *Student ,(7th Semester )B.Tech IT and mathematical innovation* > >> >>> *Cluster Innovation Centre* > >> >>> *University of Delhi * > >> >>> > >> >>> > >> > > >> > >> > >> -- > >> > >> *With warm regards * > >> *Sincerely yours* > >> Sagar > >> > >> > >> *Student ,(7th Semester )B.Tech IT and mathematical innovation* > >> *Cluster Innovation Centre* > >> *University of Delhi * > >> > > > > -- > Stian Soiland-Reyes > Apache Taverna (incubating), Apache Commons > http://orcid.org/0000-0001-9842-9718 > -- *With warm regards * *Sincerely yours* Sagar *Student ,(7th Semester )B.Tech IT and mathematical innovation* *Cluster Innovation Centre* *University of Delhi *
