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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected] > > > >> 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 < > [email protected]> > >> >>> 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 >
