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
