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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Functionality in next release?
Date Mon, 15 Feb 2016 16:46:21 GMT
No, the only provenance in tavlang (from taverna-language) is that
exported from the workflow definition itself within wfdesc export,
it's not related to workflow run provenance, which comes out of the
separate executeworkflow (taverna-commandline) - I think it's better
not to mention that.

The "RO Bundle" support in tavlang only saves the input as a Research
Object Bundle - that is it adds the RO manifest to a ZIP-file. I think
the supported inputs are other bundle formats listed here:

https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle#supported-bundle-formats


Note that Data Bundle is a specialization of an RO Bundle with certain
folders fixed (input, output, intermediates)- but I don't think
tavlang does anything particular with those as they are already RO
Bundles..


is that right, Menaka?


On 10 February 2016 at 20:55, Gale Naylor <GaleN@noventussolutions.com> wrote:
> Thank you Ian and Dmitry! I have a few more questions. (And, thank you, in
> advance, for answering my beginner's questions.)
>
> Just to clarify, we are going to be releasing _Taverna Language_ soon, not
> code from any other repository, right? (And the release notes will reflect
> only Taverna Language functionality?)
>
> ----------
> (1) Regarding saving workflow run provenance as workflow run bundle:
> ----------
>     (a) Is there a tavlang convert command option that saves workflow run
> provenance as a workflow run bundle, or are we saying, "the new
> functionality provided by the tavlang tool saves ... provenance as a
> workflow run bundle" ? (@Menaka)
>
>     (b) The tavlang readme does not mention provenance at all. As a new
> feature/ functionality, shouldn't it be mentioned? (@Menaka)
>
> ----------
> (2) WSDL Support
> ----------
>     (1) Based on Dmitry's additional information, I changed the WSDL
> Support paragraph to read:
>
> This release adds improved WSDL support using Apache Woden. The code has
> two parsers (wsdl 1.1 based on WSDL4j and 2.0 based on Woden) that
> implement a common interface (inherited from "wsdl-generic" based on AXIS
> 1.4). The service execution part is based on embedded JAX-WS API, but given
> that this part is calling the abstract interface there shouldn't be a
> significant change.
>
>     (b) Open action? -- "Probably we should check a SOAP version, because I
> think it's fixed to SOAP 1.1."
>
> Thanks!
>
> Gale
>
> On Wed, Feb 10, 2016 at 7:56 AM Dmitry <redmitry@list.ru> wrote:
>
>> Hello everybody,
>>
>> > https://ws.apache.org/woden/ implies that it has wsdl2 support - is this
>> > true in Taverna??? - Dmitry/Stian any ideas.
>> Yes.
>> Basically the code has two parsers (wsdl 1.1 based on WSDL4j and 2.0
>> based on Woden) that implement a common interface
>> (inherited from "wsdl-generic" based on AXIS 1.4).
>> The service execution part is based on embedded JAX-WS API, but given
>> that this part is calling the abstract interface there shouldn't be big
>> difference... Probably we should check a SOAP version, because I think
>> it's fixed to SOAP 1.1.
>>
>> Cheers,
>>
>> Dmitry
>>
>>
>> On 2/10/2016 4:38 PM, Ian Dunlop wrote:
>> > Hello,
>> >
>> > Great set of notes, here are some of my observations.
>> >
>> > * "One new functionality of the Taverna Command Line is the ability to
>> > save the workflow run provenance as a workflow run bundle. **(From this
>> > link it looks like saving provenance is in Taverna Engine (?). Is this
>> > really part of the Taverna *Language release?)***"
>> >
>> > I think the conversion tool is part of tavlang. So although the
>> > provenance is created by the engine, the conversion is by tavlang.
>> >
>> > * "This release adds improved WSDL support using Apache Woden. (Dmitri,
>> > is this change also giving WSDL2 support? What are the improvements
>> here?)"
>> >
>> > https://ws.apache.org/woden/ implies that it has wsdl2 support - is this
>> > true in Taverna??? - Dmitry/Stian any ideas.
>> >
>> > * "The OSGi support has been stabilized."
>> >
>> > Do we need a version?
>> >
>> > * "Activities - They are now maintained (??) separately as part of the
>> > Taverna Plugin Bioinformatics and Taverna Extras. (What does this mean?
>> > Will they be part of a future release?)"
>> >
>> > Are these part of "Apache" Taverna?? Or is it a "caveat emptor do what
>> > you want but you get no support from us approach". If we are not going
>> > to 'release' them then perhaps we should shift them out of the repo
>> > (unless they already have been).
>> >
>> > * "Taverna Language is no longer compatible with Java 1.7."
>> >
>> > I guess we should say that you need Java 1.8.
>> >
>> > * NPE does equal Null Pointer Exception :)
>> >
>> > Cheers,
>> >
>> > Ian
>> >
>> > On 01/02/2016 21:33, Gale Naylor wrote:
>> >> Here is a draft of the release notes based mostly on @stain's list:
>> >>
>> https://galenaylor.wordpress.com/2016/02/01/draft-taverna-language-release-notes-2/
>> >>
>> >> @Stian, I'm a little confused because some of the information seems to
>> >> apply to more than Taverna Language. (See comments and questions in
>> >> document.)
>> >>
>> >> I also noticed in that Menaka's readme refers to the tavlang tool (or
>> >> whatever we end up calling it) as a "planned" part of Taverna Language
>> and
>> >> as a GSOC "work in progress." These probably need to be changed to
>> reflect
>> >> that is is finished and being released?
>> >>
>> >> "This is planned as a command line for the Apache Taverna Language, an
>> API
>> >> for the Apache Taverna workflows.
>> >> This module is a work in progress as part of Google Summer of Code
>> 2015."
>> >>
>> >> Thanks,
>> >> Gale
>> >> On Mon, Feb 1, 2016 at 3:23 AM Stian Soiland-Reyes <stain@apache.org>
>> wrote:
>> >>
>> >>> Right - we will need proper release notes, won't we. Let's see..
>> >>> (sorry, this is not formatted as release notes)
>> >>>
>> >>>
>> >>> The taverna-language release would be an update that fixes some bugs
>> >>> (TAVERNA-874) and adds the tavlang command line, which we should say
>> >>> was contributed by Menaka Madushanka, sponsored by Google Summer of
>> >>> Code 2015. Mentors - would that be appropriate attribution?
>> >>>
>> >>>
>> >>> The release of taverna-osgi, taverna-engine, taverna-common-activities
>> >>> and taverna-commandline would give you a Taverna 3.1.0 command line
-
>> >>> which functionally is a follow-up from an earlier alpha-release before
>> >>> we went to Apache - see
>> >>> http://www.taverna.org.uk/developers/work-in-progress/taverna-3/ --
so
>> >>> in principle it is the same functionality, but now released by Apache,
>> >>> with a new license.
>> >>>
>> >>>
>> >>> Package names have changed to org.apache.taverna.* and the OSGi
>> >>> support has been stabilized. Source code has been reorganized - see
>> >>> http://taverna.incubator.apache.org/code/
>> >>>
>> >>>
>> >>> One new functionality of the taverna-commandline is the ability to
>> >>> save the workflow run provenance as a workflow run bundle - see
>> >>>
>> >>>
>> https://github.com/apache/incubator-taverna-engine/tree/master/taverna-prov#structure-of-exported-provenance
>> >>> (TODO: Move this doc to the website)
>> >>>
>> >>>
>> >>>
>> >>> The new release would add Dmitris improved WSDL support using Apache
>> >>> Woden - Dmitri, is this change also giving WSDL2 support? What are the
>> >>> improvements here?
>> >>>
>> >>>
>> >>>
>> >>> I think it is fair to mention the functionality that is
>> >>> disabled/missing compared to earlier, I think these activities are NO
>> >>> LONGER supported (they were part of 3.0.a2)
>> >>>
>> >>> RShell
>> >>> Soaplab
>> >>> Biomart
>> >>>
>> >>>
>> >>> They are now maintained (??) separately as part of the
>> >>> https://github.com/apache/incubator-taverna-plugin-bioinformatics/
>> >>> and https://github.com/taverna-extras/
>> >>>
>> >>>
>> >>> (I just moved RShell activity to taverna-extras and updated it, it
>> >>> seems we had forgotten it on https://github.com/taverna/ !)
>> >>>
>> >>>
>> >>>
>> >>> These plugins *ARE* included in the 3.1.0 release:
>> >>>
>> >>> Beanshell scripts
>> >>> External Tool
>> >>> Interaction service
>> >>> REST service
>> >>> Spreadsheet
>> >>> XML splitters
>> >>> WSDL services
>> >>> XPath
>> >>>
>> >>> (Which Alan is looking at workflows to test them all)
>> >>>
>> >>>
>> >>> On 23 January 2016 at 00:57, Gale Naylor <GaleN@noventussolutions.com>
>> >>> wrote:
>> >>>> Is there a description of what functionality will be available for
>> >>> Taverna
>> >>>> 3 users as a result of the upcoming release?
>> >>>>
>> >>>> Gale
>> >>>
>> >>>
>> >>> --
>> >>> Stian Soiland-Reyes
>> >>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> >>> http://orcid.org/0000-0001-9842-9718
>> >>>
>>
>>



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

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