I think you won't get the annotation content for the mimetype without also using
https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/annotation/AnnotationTools.html

but that would add dependency on Jena, which latest versions require
Java 7 and I'm not sure if it works well on Android.


Perhaps using just the XSD mapping from taverna-scufl2-t2flow would be
a bit easier? You still need to trundle through the annotations which
in .t2flow were serialized in a perhaps awkward way (an annotation
chain which then contains a set of revisioned annotations).



On 15 September 2016 at 11:29, Ian Dunlop <ianwdun...@gmail.com> wrote:
> Hello,
>
> @sagar did you use the maven profile idea? If so could you send a pull
> request so that we can keep this for the future.
>
> I've never used the scufl2-api. I did find
> https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/core/Workflow.html#getInputPorts--
> which has
> https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/common/Named.html#getName--
> I remember from way back that the mime types were hidden inside an
> annotation on the port. So maybe try
> https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/api/common/AbstractNamed.html#getAnnotations--
> and have a look at what is there.
>
> Cheers,
>
> Ian
>
> On 15 September 2016 at 10:36, Sagar <kumarsagar15...@gmail.com> wrote:
>
>> Hi,
>>
>> I have build taverna-scufl2-api as jar using java 7 .
>>
>> Can you tell me how to use it to get all input and output MIME type and
>> their name?
>>
>>
>> On Mon, Sep 12, 2016 at 6:05 PM, Stian Soiland-Reyes <st...@apache.org>
>> wrote:
>>
>> > Thanks - from this I would say Taverna Mobile can target KitKat (API
>> > level 19), get 80% share - which would rise by the time we release the
>> > app.
>> >
>> > But that still grounds us on Java 6 features - and even in latest
>> > Android SDK API the package java.nio.file is not there - so robundle
>> > would not work anyway.
>> >
>> > On 8 September 2016 at 19:24, Gale Naylor <ga...@noventussolutions.com>
>> > wrote:
>> > > Here is the distribution of Android API levels in use as of Aug 1:
>> > > https://developer.android.com/about/dashboards/index.html
>> > >
>> > > According to this, only 15% of all Android devices are running API 23.
>> > >
>> > >
>> > > On Thu, Sep 8, 2016 at 6:29 AM Ian Dunlop <ianwdun...@gmail.com>
>> wrote:
>> > >
>> > >> Hello,
>> > >>
>> > >> That page is typically clear as mud! I think it is implying that jdk 7
>> > is
>> > >> fine for all API levels but for jdk 8 you need API 23 and (if special
>> > >> language features required) a different compiler. So as long as we
>> don't
>> > >> use jdk 8 features we will be ok (maybe).  I guess that means
>> > >> taverna-language can be used (until we go all lambda crazy).
>> > >>
>> > >> Cheers,
>> > >>
>> > >> Ian
>> > >>
>> > >> On 8 September 2016 at 14:24, Stian Soiland-Reyes <st...@apache.org>
>> > >> wrote:
>> > >>
>> > >> > I don't think we use any Java 8 features in taverna-language (e.g.
>> > >> > Stream or lambdas) - but taverna-robundle use java.nio.Path from
>> Java
>> > >> > 7.  I think it should be possible to make a subset of
>> Taverna-language
>> > >> > you need compile for JAva 6 (e.g. taverna-scufl2-api,
>> > >> > taverna-scufl2-t2flow and taverna-scufl2-ucfpackage) - perhaps as a
>> > >> > Maven profile?
>> > >> >
>> > >> > https://developer.android.com/guide/platform/j8-jack.html says you
>> > can
>> > >> > use Java 7/8 features from API level 23-24.
>> > >> >
>> > >> > How do we decide which Android API level we want to support..?
>> > >> >
>> > >> > On 8 September 2016 at 10:56, Sagar <kumarsagar15...@gmail.com>
>> > wrote:
>> > >> > > Hi,
>> > >> > >
>> > >> > > I was reading the readme and I found Taverna-language-API will
>> only
>> > >> work
>> > >> > > with JAVA 8 and newer.
>> > >> > > We can't use in taverna-mobile because Android API 16 works with
>> > JAVA
>> > >> 6.
>> > >> > >
>> > >> > > So, Now provide me with the schema of the .t2flow file.
>> > >> > >
>> > >> > > Thanks
>> > >> > >
>> > >> > > On Thu, Sep 8, 2016 at 2:13 PM, Sagar <kumarsagar15...@gmail.com>
>> > >> wrote:
>> > >> > >
>> > >> > >> 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 <
>> > st...@apache.org
>> > >> >
>> > >> > >> 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-languag
>> > >> > >>> e/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 <ianwdun...@gmail.com>
>> > 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 <kumarsagar15...@gmail.com>
>> > >> 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 <
>> > >> > >>> finn.bac...@manchester.ac.uk
>> > >> > >>> >> >
>> > >> > >>> >> 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 <
>> > kumarsagar15...@gmail.com>
>> > >> > >>> 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 <
>> > >> > ianwdun...@gmail.com>
>> > >> > >>> >> >>> wrote:
>> > >> > >>> >> >>>
>> > >> > >>> >> >>> Hello,
>> > >> > >>> >> >>>>
>> > >> > >>> >> >>>> This is where the upload code is in the current mobile
>> > code
>> > >> > >>> >> >>>> https://github.com/apache/
>> incubator-taverna-mobile/blob/
>> > >> > >>> >> >>>> 4daa91d3f42b5a4474303fd39c7a7e
>> > c1483cebff/app/src/main/java/
>> > >> > >>> >> >>>> org/apache/taverna/mobile/fragments/workflowdetails/
>> > >> > >>> >> >>>> WorkflowdetailFragment.java#L655
>> > >> > >>> >> >>>>
>> > >> > >>> >> >>>> Cheers,
>> > >> > >>> >> >>>>
>> > >> > >>> >> >>>> Ian
>> > >> > >>> >> >>>>
>> > >> > >>> >> >>>> On 24 August 2016 at 14:40, Ian Dunlop <
>> > ianwdun...@gmail.com
>> > >> >
>> > >> > >>> 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 <
>> > >> > >>> >> finn.bac...@manchester.ac.uk>
>> > >> > >>> >> >>>>> 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 *
>> > >> > >>
>> > >> > >>
>> > >> > >
>> > >> > >
>> > >> > > --
>> > >> > >
>> > >> > > *With warm regards  *
>> > >> > > *Sincerely yours*
>> > >> > > Sagar
>> > >> > >
>> > >> > >
>> > >> > > *Student ,(7th Semester )B.Tech IT and mathematical innovation*
>> > >> > > *Cluster Innovation Centre*
>> > >> > > *University of Delhi *
>> > >> >
>> > >> >
>> > >> >
>> > >> > --
>> > >> > Stian Soiland-Reyes
>> > >> > http://orcid.org/0000-0001-9842-9718
>> > >> >
>> > >>
>> >
>> >
>> >
>> > --
>> > Stian Soiland-Reyes
>> > 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 *
>>



-- 
Stian Soiland-Reyes
http://orcid.org/0000-0001-9842-9718

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