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From: Gale Naylor <GaleN@noventussolutions.com>
Date: Tue, 16 Feb 2016 23:28:02 +0000
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Subject: Re: Functionality in next release?
To: dev@taverna.incubator.apache.org
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Thanks, Stian. I'm sure that's why I was confused about the release notes -
because they were addressing more than just Taverna Language.

Is there any reason to wait on the RC/vote?

Thanks for the other release note info/background. When we can all edit the
release notes, it will be easier.

Gale


On Mon, Feb 15, 2016 at 8:46 AM Stian Soiland-Reyes <stain@apache.org>
wrote:

> 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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