Re: [VOTE] Retire Taverna from Apache Incubator?

[Gale Naylor]

Thank you, Stian!

On Wed, Feb 19, 2020, 4:57 AM Stian Soiland-Reyes  wrote:

> +1 Retire
>
> Thank you, Sagar and everyone!
>
> On Wed, 19 Feb 2020 13:28:06 +0530, Sagar 
> wrote:
> > [+1] Learned a lot with you. Thanks
> >
> > On Thu, 6 Feb, 2020, 12:52 am Serban Mardaloescu, <
> > serban.stefan...@gmail.com> wrote:
> >
> > >   [ -1] Do not retire Taverna
> > >
> > > În lun., 3 feb. 2020 la 16:08, Stian Soiland-Reyes 
> a
> > > scris:
> > >
> > > > Hi,
> > > >
> > > > I think we have to be honest with ourselves.
> > > >
> > > > While we had a good go at Taverna in the Apache Incubator, and lots
> of
> > > > great effort over the years, we seem to have ground to a standstill.
> > > >
> > > > It looks now almost impossible that we will graduate from the
> incubator
> > > > and continue to thrive as a top-level Apache project.
> > > >
> > > > I am as guilty as everyone - emails missed, builds not updated,
> releases
> > > > not completed. The tasks were not large, but they still demand
> continued
> > > > volunteer effort, which sadly we now seem to have not got anymore.
> > > >
> > > >
> > > > I think I speak for all of you when I am grateful for all the time
> > > > and effort everyone has committed since we moved to Apache Software
> > > > Foundation in 2014.
> > > >
> > > >
> > > > It is therefore with sadness that I call this vote on retiring
> > > > Taverna from the Apache Incubator.
> > > >
> > > >
> > > > I don't think there is any shame if we come to this conclusion,
> > > > this project started 2003-02-24 and the world of bioinformatics and
> web
> > > > services has changed significantly since then.
> > > >
> > > >
> > > > For more information about what retirement means, see
> > > > https://incubator.apache.org/guides/retirement.html
> > > >
> > > > In terms of codebase my suggestion is that we move the git
> repositories
> > > > to http://github.com/taverna/ with a clear README indication that
> > > > they are no longer maintained.
> > > >
> > > > I think we should invite anyone on this list to join that GitHub
> > > > organization for a passive curator role, or to delegate if someone
> > > > later wants to reboot the activity.
> > > >
> > > >
> > > > See also previous discussion from 2019-09:
> > > >
> > > >
> > >
> https://lists.apache.org/thread.html/f9db87bf752c1b3f2f0ac5be9afd34d29a7cff76d66728a0f713%40%3Cdev.taverna.apache.org%3E
> > > >
> > > >
> > > >
> > > > PLEASE INDICATE YOUR VOTE:
> > > >
> > > > [ ] +1 Retire Taverna
> > > > [ ]  0 Undecided
> > > > [ ] -1 Do not retire Taverna
> > > >
> > > > The vote is open for at least 72 hours for anyone on this list, with
> a
> > > > lazy consensus.
> > > >
> > > > --
> > > > Stian Soiland-Reyes
> > > > https://orcid.org/-0001-9842-9718
> > > >
> > > >
> > >
>

Re: [VOTE] Retire Taverna from Apache Incubator?

[Gale Naylor]

[+1] Grateful for being along for the ride

On Mon, Feb 3, 2020, 7:27 AM Sube Singh  wrote:

> [ -1]  Do not retire Taverna
>
> -Original Message-
> From: Stian Soiland-Reyes 
> Sent: 03 February 2020 07:38 PM
> To: dev@taverna.incubator.apache.org
> Subject: [VOTE] Retire Taverna from Apache Incubator?
>
> Hi,
>
> I think we have to be honest with ourselves.
>
> While we had a good go at Taverna in the Apache Incubator, and lots of
> great effort over the years, we seem to have ground to a standstill.
>
> It looks now almost impossible that we will graduate from the incubator
> and continue to thrive as a top-level Apache project.
>
> I am as guilty as everyone - emails missed, builds not updated, releases
> not completed. The tasks were not large, but they still demand continued
> volunteer effort, which sadly we now seem to have not got anymore.
>
>
> I think I speak for all of you when I am grateful for all the time and
> effort everyone has committed since we moved to Apache Software Foundation
> in 2014.
>
>
> It is therefore with sadness that I call this vote on retiring Taverna
> from the Apache Incubator.
>
>
> I don't think there is any shame if we come to this conclusion, this
> project started 2003-02-24 and the world of bioinformatics and web services
> has changed significantly since then.
>
>
> For more information about what retirement means, see
> https://incubator.apache.org/guides/retirement.html
>
> In terms of codebase my suggestion is that we move the git repositories
> to http://github.com/taverna/ with a clear README indication that
> they are no longer maintained.
>
> I think we should invite anyone on this list to join that GitHub
> organization for a passive curator role, or to delegate if someone
> later wants to reboot the activity.
>
>
> See also previous discussion from 2019-09:
>
> https://lists.apache.org/thread.html/f9db87bf752c1b3f2f0ac5be9afd34d29a7cff76d66728a0f713%40%3Cdev.taverna.apache.org%3E
>
>
>
> PLEASE INDICATE YOUR VOTE:
>
> [ ] +1 Retire Taverna
> [ ]  0 Undecided
> [ ] -1 Do not retire Taverna
>
> The vote is open for at least 72 hours for anyone on this list, with a
> lazy consensus.
>
> --
> Stian Soiland-Reyes
> https://orcid.org/-0001-9842-9718
>
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Re: [DISCUSS] Retiring Taverna from incubator?

[Gale Naylor]

GitHub sounds like a good option to me.

Thanks, Ian! Working at Facebook is going great. I'm very happy. Hope you
and Stian are doing well also.

Gale


On Sun, Sep 22, 2019, 8:45 AM Ian Dunlop  wrote:

> Hello
>
> I think a "GitHub organisation" seems like a good idea. Staying in Apache
> would obviously be great but the release process seems to keep hitting
> barriers. I would have liked the minimal amount of projects to stay in
> Apache but who could do that. I almost got a release of mobile out and knew
> what to do but in the end couldn't find time plus I wasn't sure if
> releasing code without having a clear purpose or community was a good idea.
> Maybe getting core repos to graduation. Maybe mobile. Move the others to
> github. That could be an idea.
>
> Cheers
>
> Ian
>
> Ps nice to hear from you gale. Hope things are going well for you.
>
> On Tue, 10 Sep 2019, 10:12 Stian Soiland-Reyes,  wrote:
>
>> On Thu, 5 Sep 2019 05:41:34 -0700, Gale Naylor <
>> ga...@noventussolutions.com> wrote:
>> > Stian, is an "incubator release ... to verify that the Intellectual
>> > Property is clean" the same thing as the "token release" that lets
>> Taverna
>> > graduate?
>>
>> That was not my intention, the release would be all proper, just that
>> its main purpose would be to clear IP rather than provide it to the
>> user.
>>
>> I think one challenge for us is the many git repositories for different
>> modules and we have released them separately, e.g. to correspond with
>> git tags.
>>
>> As some of the modules were not in a mature enough state code-wise or
>> build-wise they have not been released yet. We could do a incubator
>> release of these which would primarily be to ensure their code base has
>> been through the incubator and cleared their IP. Then their code can
>> join us in graduation.
>>
>> Some repos like Taverna Language we have already released, so they are
>> IP clear and have mature code/build systems. If we were to drop the
>> other repositories, with these it is almost trivial to do a release,
>> which we could do as a "token release" to show the IPMC is still working
>> and able to vote on releases.
>>
>>
>> The Taverna Mobile is dfferent - it is mature in a sense both in
>> code and build, and have clean IP as fresh project, but it has a
>> different build system without assisted release. Here I think just
>> manual work (or script) is needed - but it is a bit tedious.
>>
>> So in a sense we have many options, but I would say they all require
>> making and voting on releases.
>>
>>
>>
>>

Re: [DISCUSS] Retiring Taverna from incubator?

[Gale Naylor]

Stian, is an "incubator release ... to verify that the Intellectual
Property is clean" the same thing as the "token release" that lets Taverna
graduate?

Gale

On Thu, Sep 5, 2019, 2:27 AM Stian Soiland-Reyes <
soiland-re...@manchester.ac.uk> wrote:

> Hi,
>
> It saddens me, but we have to discuss the reality.
>
> Taverna have progressed well in the incubator, if slowly.
>
> But I think you will agree with me that the activity level has dropped
> to a minimum during the last year.
>
> Note that it is perfectly OK for an Apache project to not be in active
> development. If you go through the ASF list you will find several mature
> projects in that state.
>
>
> We said we would release the remaining code bases (e.g. taverna-mobile,
> taverna-workbench), which beyond "re-engate PPMC" is the only remaining
> hurdle before we can graduate.
>
>
> While we had some starts at this, we did not go through with it.
>
> What distinguishes a "dead" project from a "sleeping" project at ASF
> will be the ability to prepare, vote and publish releases. This requires
> a PPMC that is engaged, and volunteer release managers.
>
>
> Now I think we still have enough PPMC folks to do the vote (let's see
> how many engages in this thread).
>
> What we don't seem to have is enough energy/time to prepare and publish
> releases.  I am as guilty as anyone - I had promised to prepare several
> release candidates for a vote, but dropped the ball.
>
> I will admit that preparing release candidates at ASF does take a bit
> more effort than a quick "git tag" - although we mostly have our
> instructions and Maven tooling now set up to do it fairly easy.
>
>
> As I pointed out in the September report - given the lack of progress I
> think we need to seriously discuss the possibility of
> retiring Taverna from the incubator.
>
>
> There is no shame in this - we've had a good run and done lots of
> progress - which could live on in a more lightweight fashion, e.g. a
> GitHub organization. Recently even an active podling retired from the
> incubator to do this, (although that was over political differences).
>
> Retiring means giving up on the Apache name and *.apache.org resources.
> We could simply change the name back to just "Taverna" and keep it under
> the Apache License. Practically the package name and Maven coordinates
> would need to change, as we did for modules we moved to taverna-extra
> GitHub group earlier.
>
>
> One alternative we have discussed before: shrink the size of Taverna
> code-base so it's largely what we have already done releases for. We
> could drop taverna-workbench-* and some plugins.
>
> If we then just do a "token" release to show we are still alive then we
> would be able to crawl into a graduation proposal.
>
>
> After graduation to an ASF project we would need to do board reports and
> any PMC-level management (typically respond to email requests), but ASF
> board is not interferring in how often releases are done etc.
>
> Given that taverna-mobile is freshly started in the incubator with ASF
> copyright it would admitedly be a shame to "leave it behind" graduation,
> but it could be possible to bring it back later. The easiest would
> however be to do a incubator release of this now to verify that
> the Intellectual Property is clean.
>
>
> What are your views on the future directions of the Taverna project?
> Please feel free to contribute, however small comment.
>
> --
> Stian Soiland-Reyes
> https://orcid.org/-0001-9842-9718
>
>

Re: [VOTE] Retire legacy taverna repos to taverna-extras

[Gale Naylor]

+1

On Wed, Jun 6, 2018 at 4:04 PM Stian Soiland-Reyes  wrote:

>
> We don't seem to get much progress in these legacy git repositories:
>
> https://github.com/apache/incubator-taverna-plugin-component
> https://github.com/apache/incubator-taverna-plugin-bioinformatics
>
> Both have been failing in Jenkins for a long time.
>
>
> The Component plugin I think still needs some more work for Taverna 3. I
> just fixed now some typos like broken  not enough to get it to compile.
>
>
> The Bioinformatics plugin has activities for Biomart, Biomoby,
> NCBI and Soaplab web services. I don't believe any of these are
> particularly relevant anymore. The plugin also have some dependencies
> with unclear or incompatible open source license (martj.jar)
>
>
>
> I propose we retire these repos and ask to transfer their ownership to:
> https://github.com/taverna-extras/
>
> Their license and file headers would remain.
>
> As this would mean ASF giving up on holding their code base I think we
> should decide this formally.
>
> Please Vote:
>
> [ ] +1: Yes, retire them to taverna-extras
> [ ]  0: Either way
> [ ] -1: No, don't retire
>
> This vote will be open for at least 72 hours. Anyone can vote, not just
> Taverna PPMC members.
>
> --
> Stian Soiland-Reyes
> https://orcid.org/-0001-9842-9718
>
>

Re: [ANNOUNCE] Welcome Sagar to Apache Taverna PPMC

[Gale Naylor]

Congratulations!

On Feb 26, 2018 9:07 AM, "Sagar"  wrote:

> Thank you :)
>
>
>
> ‌
>
> On Mon, Feb 26, 2018 at 10:29 PM, Stian Soiland-Reyes 
> wrote:
>
> > The Taverna PPMC has voted to invite Sagar to become a new member of the
> > Taverna Project Management Committee, and we are proud to announce that
> > he has accepted.
> >
> > Sagar has shown great enthusiasm and contributed strongly to the
> > project, in particular to Taverna Mobile, but also mentoring
> > GSOC students and helping the project overall.
> >
> > We are sure Sagar will be a great addition to the PPMC.
> >
> > Please join me in welcoming Sagar and congratulate him on his new role!
> >
> >
> > --
> > Stian Soiland-Reyes
> > http://orcid.org/-0001-9842-9718
> >
> >
>
>
> --
>
> Warmest regards
> Sagar
> Software Developer
> Lattice Innovations Pvt. Ltd.
>

Re: Taverna Server documentation

[Gale Naylor]

Awesome! Thanks :)

On Fri, Jan 19, 2018, 6:48 AM Stian Soiland-Reyes  wrote:

> On 19 January 2018 at 03:14, Gale Naylor 
> wrote:
> > Happy New Year @Ian and @Stian and all! Things are going well. Keep
> > thinking I'll have time to do more than lurk, but not so far. :)
> > Looks like things are going well for you, too!
>
> Cheers! I guess we're trundling along! :)
>
> No worries if you don't have time, it's limited for all of us..
>
> Any effort welcome folks, small or large; opinions, code, docs and
> bitcoins welcome :)  And don't feel bad if you are busy, let's keep it
> fun.
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

RE: Taverna Server documentation

[Gale Naylor]

Happy New Year @Ian and @Stian and all! Things are going well. Keep
thinking I'll have time to do more than lurk, but not so far. :)

Looks like things are going well for you, too!

Cheers!

Gale

On Jan 18, 2018 6:22 AM, "Ian Dunlop"  wrote:

> Hello,
>
> Styling seems to have gone a bit crazy on the install guide “Configuration
> Property List” part, lot’s of bold headers. (http://taverna.staging.
> apache.org/documentation/server/3.1/install)
> In http://taverna.staging.apache.org/documentation/server/3.1/usage some
> of the code blocks haven’t rendered correctly, you can still see the ```xml
> markup in some places.
> Also why is the workflow state not rendered as a Taverna workflow (BTW
> that’s a joke 😉)
>
> Overall, good job.
> @Gale Happy New Year. Great to hear from you. Hope things are going well
> for you.
>
> Cheers,
>
> Ian
>
> Sent from Mail for Windows 10
>
> From: Stian Soiland-Reyes
> Sent: 18 January 2018 12:41
> To: dev@taverna.incubator.apache.org
> Subject: Re: Taverna Server documentation
>
> I think we can say the distinction is if the documentation is
> code-related (stays in git aka GitHub) or user-related (stays on our
> website).  With Taverna Server it's a bit tighter together.. all the
> API examples could change from one release to another and easily be
> outdated.
>
> Agree on that the headers and code sections looks better in GtHub
> rendering.
>
> It could be that we can make some tweaks to our website CSS to make it
> more similar?
> I think we are using Bootstrap and a couple of custom overrides in
> https://github.com/apache/incubator-taverna-site/tree/trunk/content/css
>
> On 5 January 2018 at 15:50, Gale Naylor 
> wrote:
> > Happy New Year, all!
> >
> > I was only able to take a quick look on my phone. But the docs look
> pretty
> > good!
> >
> > Stian, what would be the advantage of the docs being on the Apache site
> vs
> > GitHub? I do like the headers and code sections better in GitHub.
> > Personally, the Apache CMS headings seem large and h1/h2 are fairly
> > similar. Also, I like the gray code rendering. But not a big deal.
> >
> > Cheers!
> >
> > Gale
> >
> > On Thu, Jan 4, 2018, 7:18 AM Stian Soiland-Reyes 
> wrote:
> >
> >> I updated
> >> https://github.com/apache/incubator-taverna-server/blob/master/usage.md
> >> to include some table of content - it's still very long and could
> >> probably be split into multiple pages.
> >>
> >> As I fixed some things in its example XML I think it would be cumbersome
> >> to also maintain a OpenOffice version, so I removed those.
> >>
> >> Would this documentation live in GitHub as it is now, or as
> >> separate pages under
> >> https://taverna.incubator.apache.org/documentation/server/ ?
> >>
> >> I had a quick go:
> >>
> >> http://taverna.staging.apache.org/documentation/server/3.1/
> >> http://taverna.staging.apache.org/documentation/server/3.1/install
> >> http://taverna.staging.apache.org/documentation/server/3.1/usage
> >>
> >> Stylistically I think those look quite nice.. your views?
> >>
> >> (Compare with GitHub rendering
> >> https://github.com/apache/incubator-taverna-server/blob/
> master/README.md
> >> https://github.com/apache/incubator-taverna-server/blob/
> master/install.md
> >> https://github.com/apache/incubator-taverna-server/blob/master/usage.md
> >> )
> >>
> >> Note as I just copied from GitHub, that there are a couple of MarkDown
> >> differences that makes the /usage examples look broken or perhaps too
> red.
> >>
> >>
> >>
> >> On Wed, 6 Dec 2017 11:12:04 +, Stian Soiland-Reyes <
> st...@apache.org>
> >> wrote:
> >> > I had a look at the documentation included in the Taverna Server git
> >> > repository https://github.com/apache/incubator-taverna-server
> >> >
> >> > Both install and usage are quite extensive, and describes both how to
> >> > install it and how the services are invoked.
> >> >
> >> > For some reason these where in the repository as binary PDF and DOCX
> >> > files which personally I find a bit odd for a server product.
> >> >
> >> > They also had some outdated references to Univ of Manchester and
> >> > Taverna 2.5.
> >> >
> >> >
> >> > So I changed it to more open formats MarkDown and ODT and added the
> >> > Apache License heade

Re: Taverna Server documentation

[Gale Naylor]

Happy New Year, all!

I was only able to take a quick look on my phone. But the docs look pretty
good!

Stian, what would be the advantage of the docs being on the Apache site vs
GitHub? I do like the headers and code sections better in GitHub.
Personally, the Apache CMS headings seem large and h1/h2 are fairly
similar. Also, I like the gray code rendering. But not a big deal.

Cheers!

Gale

On Thu, Jan 4, 2018, 7:18 AM Stian Soiland-Reyes  wrote:

> I updated
> https://github.com/apache/incubator-taverna-server/blob/master/usage.md
> to include some table of content - it's still very long and could
> probably be split into multiple pages.
>
> As I fixed some things in its example XML I think it would be cumbersome
> to also maintain a OpenOffice version, so I removed those.
>
> Would this documentation live in GitHub as it is now, or as
> separate pages under
> https://taverna.incubator.apache.org/documentation/server/ ?
>
> I had a quick go:
>
> http://taverna.staging.apache.org/documentation/server/3.1/
> http://taverna.staging.apache.org/documentation/server/3.1/install
> http://taverna.staging.apache.org/documentation/server/3.1/usage
>
> Stylistically I think those look quite nice.. your views?
>
> (Compare with GitHub rendering
> https://github.com/apache/incubator-taverna-server/blob/master/README.md
> https://github.com/apache/incubator-taverna-server/blob/master/install.md
> https://github.com/apache/incubator-taverna-server/blob/master/usage.md
> )
>
> Note as I just copied from GitHub, that there are a couple of MarkDown
> differences that makes the /usage examples look broken or perhaps too red.
>
>
>
> On Wed, 6 Dec 2017 11:12:04 +, Stian Soiland-Reyes 
> wrote:
> > I had a look at the documentation included in the Taverna Server git
> > repository https://github.com/apache/incubator-taverna-server
> >
> > Both install and usage are quite extensive, and describes both how to
> > install it and how the services are invoked.
> >
> > For some reason these where in the repository as binary PDF and DOCX
> > files which personally I find a bit odd for a server product.
> >
> > They also had some outdated references to Univ of Manchester and
> > Taverna 2.5.
> >
> >
> > So I changed it to more open formats MarkDown and ODT and added the
> > Apache License headers:
> >
> >
> https://github.com/apache/incubator-taverna-server/blob/master/install.md
> >
> https://github.com/apache/incubator-taverna-server/blob/master/install.odt
> > https://github.com/apache/incubator-taverna-server/blob/master/usage.md
> > https://github.com/apache/incubator-taverna-server/blob/master/usage.odt
> >
> > Some more tidy-up could be done (e.g. use ```code``` blocks for the XML
> > examples).
> >
> >
> > The documentation seems very overlapping (or equal) to the 2.5
> > Taverna Server documentation that also lives online in the old wiki:
> >
> > https://taverna.incubator.apache.org/documentation/server/
> >
> > .. but I have not checked this page by page.
> >
> >
> >
> > What do you think:
> >
> > Is the Markdown version more or less maintainable?
> >   (e.g. the tables can get messy)
> >
> > Do we keep maintaining the OpenDocument versions (packaged as PDF in
> release)?
> >
> > Do we keep the Markdown documentation as part of the git repository (and
> > hence the Taverna Server distribution), or move it to the
> > taverna.apache.org website? (it would probably work out of the
> > box)
> >
> >
> > --
> > Stian Soiland-Reyes
> > http://orcid.org/-0001-9842-9718
> >
>

Re: Podling Report Reminder - March 2017

[Gale Naylor]

>but we can make this manageable by
> progressing step by step.

Agree. I honestly don't have time to keep up with gitter, but if the list
of tasks is clearly broken down into small steps and articulated on dev@,
it seems like it would be easier for more people to participate.

Keeping code that needs a lot of work in a separate location makes a lot of
sense to me.

Gale

On Sun, Mar 12, 2017, 1:46 AM Andy Seaborne  wrote:

>
>
> On 01/03/17 15:06, Stian Soiland-Reyes wrote:
> > On Wed, 1 Mar 2017 08:44:27 +, Andy Seaborne 
> wrote:
> >> Ian's put some notes in but it needs completing.
> >>
> >> Where is everyone?
> >>
> >> There has been a big dropoff of activity on dev@ in this reporting
> period.
> >
> > Thanks. I augmented the report a bit:
> >
> >> How has the community developed since the last report?
> >>
> >>  List has gone a bit more quiet, while activity on the
> >>  Gitter chat https://gitter.im/apache/taverna
> >>  has remained at same level. Need to re-focus use of
> >>  mailing list and community development.
> >
> >>
> >> Comments:
> >> Activity has stalled a bit in the drive towards graduation, as
> >> some (perhaps tedious) IP review remains. Ambition levels
> >> might need adjustment, e.g. don't include all repositories
> >> in graduation to TLP.
> >
> > Agree there has been a big dropoff in the dev@ activity - not sure how
> much we
> > can blame this on the Gitter chat (which has not been as quiet), but we
> should
> > refocus our activity here on this list.
>
> Gitter is great for within team discussions but it's pretty opaque to
> people outside, which is the value of dev@
>
> > I know I am partially to blame as I have not been able to contribute
> much these
> > months - it's been quite hectic with work; lots of documents, emails and
> calls,
> > and I have not been able to help where I should.
> >
> > I must admit I have lacked motiviation to help on the remaining IP
> review -
> > it's not something that is too easy to pick up late at night when the
> kids
> > are at bed.. I might not be alone here - but we can make this manageable
> by
> > progressing step by step.
> >
> >
> > Andy - do you think if we don't include a repository in graduation it
> would be
> > easy to add back on later from GitHub? As it's not SVN it is not as easy
> to
> > keep around; I know this helped in Jena, where you had some "extra
> stuff" at an
> > SVN tag that you could pick up again at a later time.  Perhaps we could
> do some
> > kind of "legacy" or "sandbox" apache-taverna git repository with specific
> > branches under there?
>
> At graduation, what is in Apache source code control will need to be
> IP-clean.  Incubation has more latitude.
>
> There is no distinction of some repos of a TLP being "good" and some
> "parking space" that I know of.  People are free to pick up Apache code
> direct from repos and some notes in a README don't really meet a
> reasonable level of notice.
>
> You can keep code elsewhere and contribute later.
>
>  Andy
>
> >
> >
>

Re: Podling graduation rally on incubator list

[Gale Naylor]

>Decide which code is in/out: "... keep
our future options open
>to bring in the rest of the code later without a second software grant."

That sounds like a good plan. What do we have to do to find out if we can
bring the rest of the code in later without a new grant?

A weekly status sounds like a good way to keep this moving.

Gale

On Wed, Mar 1, 2017, 8:49 AM Stian Soiland-Reyes  wrote:

> On Fri, 17 Feb 2017 17:31:59 +, Andy Seaborne  wrote:
> > > There is a recent thread regarding getting podlings to graduate on the
> > > incubator mailing list. Perhaps we can add Taverna to their list. We
> may
> > > have stalled again. Any thoughts? What really, really, really needs
> done
> > > to graduate? Let's move out any non essential components. We've already
> > > released several so they are ready to go. Of the rest what do we really
> > > need to keep? I can't see any that are essential.
> >
> > I think you've described the situation accurately.
> >
> > * Decide which code is in and which is not.
>
> This is the tricky bit.. I guess we have been undecided, as there is
> more we think "should" keep than we have been able to get ready.
>
> We have to be more realistic and cut our ambitions to align with the
> actual effort we have available. It would be good if we can still keep
> our future options open to bring in the rest of the code later without a
> second software grant.
>
>
> > * Release the "in" code.
>
> Agreed. This should be not be too much work for taverna-server, and even
> for taverna-workbench-* (although they might not be release-ready for
> the public).
>
>
> > * Don't stall :-)
>
> Let's start a weekly status roll to avoid stalling. We can do it
>
>
> > Good would be to have more PPMC diversity of organisation.
>
> Technically we've got higher diversity now that Ian no longer
> works at The University of Manchester, Christian and Donal are in a
> different group and Gale got a new job :-) - but I see your point -
> particularly in consideration of what is effectively the *active* PPMC.
>
> > Graduation needs the codebase to be ASF-clean and verified; that's
> > Tavernas main item in my view.  A release does that best.
>
> I suggest we do a source code release of what we have, and don't promote
> too much on the website anything that is not at user-ready.
>
> Taverna Mobile would be interesting to release as well - as there's
> never been an Android release through the incubator before, and those
> have their own (it turns out) proprietary build chains.
>
>
> > Maybe Taverna isn't quite at the point to be rallied.  The other
> > podlings are mostly all done, just need to do the grdauation step itself.
>
> Agree on this ; while we're pretty much ready to graduate, for the IPMC
> to evaluate that this is the case would take a bit longer than in the
> projects in the rally.
>
> I think Ian has done well on our license review under
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-09+License+review
> and sub pages, which fits into
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+Taverna+Graduation+Maturity+Assessment
>
> However the above still needs filling in for the remaining parts, from
> RE40 and below.
>
> --
> Stian Soiland-Reyes
> The University of Manchester
> http://www.esciencelab.org.uk/
> http://orcid.org/-0001-9842-9718
>
>

Re: Graduation?

[Gale Naylor]

+1

On Thu, Jan 26, 2017, 3:38 AM Alan Williams 
wrote:

> On 26-Jan-17 11:33, Ian Dunlop wrote:
> > Hello,
> >
> > This sounds like a horribly tangled web that we should just ignore for
> > the moment. Perhaps the biomoby-activity-ui can be moved to the
> > taverna-extras repo until we clear this up. To me it doesn't seem worth
> > expending  effort when most of the other apache taverna repos are almost
> > there regards licences.
>
> +1
>
> > Cheers,
> >
> > Ian
>
> Alan
>
>

Re: Presentations on the Taverna website

[Gale Naylor]

OK! I added a Presentations page under the Publications and References
pages in the Community menu. If you would like anything changed (or want me
to add the link), just let me know!

Gale

On Tue, Jan 10, 2017 at 2:09 AM Alan Williams 
wrote:

> On 09-Jan-17 21:03, Gale Naylor wrote:
> > Hi Alan,
> >
> > I don't think we have a place to put presentations. I could put a
> > Presentations page under Community, where we have Publications and
> > References.
> >
> > Anyone have a better idea?
>
> No - your idea sounds good to me.
>
> > Gale
>
> Alan
>
-- 

*Give me your tired, your poor,*
*Your huddled masses yearning to breathe free,*
*The wretched refuse of your teeming shore.*
*Send these, the homeless, tempest-tost to me,*
*I lift my lamp beside the golden door!"*
-- Emma Lazarus

Re: Presentations on the Taverna website

[Gale Naylor]

Or a different idea? ;-)

On Mon, Jan 9, 2017, 1:03 PM Gale Naylor 
wrote:

> Hi Alan,
>
> I don't think we have a place to put presentations. I could put a
> Presentations page under Community, where we have Publications and
> References.
>
> Anyone have a better idea?
>
> Gale
>
> On Mon, Jan 9, 2017, 5:10 AM alaninmcr  wrote:
>
> Hello everyone
>
> Is there anywhere on the Taverna website to put links to presentations?
> There is an interesting talk I'd like to link to.
>
> Alan
>
> --
>
> *Give me your tired, your poor,*
> *Your huddled masses yearning to breathe free,*
> *The wretched refuse of your teeming shore.*
> *Send these, the homeless, tempest-tost to me,*
> *I lift my lamp beside the golden door!"*
> -- Emma Lazarus
>
>
-- 

*Give me your tired, your poor,*
*Your huddled masses yearning to breathe free,*
*The wretched refuse of your teeming shore.*
*Send these, the homeless, tempest-tost to me,*
*I lift my lamp beside the golden door!"*
-- Emma Lazarus

Re: Presentations on the Taverna website

[Gale Naylor]

Hi Alan,

I don't think we have a place to put presentations. I could put a
Presentations page under Community, where we have Publications and
References.

Anyone have a better idea?

Gale

On Mon, Jan 9, 2017, 5:10 AM alaninmcr  wrote:

> Hello everyone
>
> Is there anywhere on the Taverna website to put links to presentations?
> There is an interesting talk I'd like to link to.
>
> Alan
>
-- 

*Give me your tired, your poor,*
*Your huddled masses yearning to breathe free,*
*The wretched refuse of your teeming shore.*
*Send these, the homeless, tempest-tost to me,*
*I lift my lamp beside the golden door!"*
-- Emma Lazarus

Re: Podling Report Reminder - December 2016

[Gale Naylor]

Looks great! I'm glad you're signing on as (official) mentor, Stian. It's a
good fit.  :)

On Dec 6, 2016 3:22 AM, "Stian Soiland-Reyes"  wrote:

> My fault - I accidentally moved Suresh and Marlon down to "Emeritus
> Mentor" - but as they never formally retired in podlings.xml I guess
> they should be moved back up. (Done)
>
> Good point to announce it on general@.
>
> On 6 December 2016 at 10:55, Andy Seaborne  wrote:
> >> Signed-off-by:
> >>
> >>   [ ](taverna) Andy Seaborne
> >>   [ ](taverna) Daniel J Debrunner
> >>   [x](taverna) Stian Soiland-Reyes
> >>   [ ](taverna) Suresh Srinivas
> >>   [ ](taverna) Suresh Marru
> >>   [ ](taverna) Marlon Pierce
> >
> >
> > Glad to see that Stian has signed up as mentor.  (Was this announced on
> > general@?)
> >
> > http://incubator.apache.org/projects/taverna.html
> >
> > only lists 3 mentors.
> >
> > Andy
>
>
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

Re: Towards graduation of Taverna

[Gale Naylor]

Congratulations, Stian! Even though we appear to be close to graduation, is
there any reason, *not* to add yourself as a mentor? You can add it to your
resume. ;)

On Wed, Nov 23, 2016, 6:42 AM Stian Soiland-Reyes  wrote:

On 23 November 2016 at 14:10, Andy Seaborne  wrote:
> PS Stian - I don't see why you can't add your self as a mentor.

No need for that if we graduate? :-)


Folks - Andy is referring to the fact I was just voted to be a member
of the Incubator PMC.  So technically I could now be a mentor for
Taverna (and i guess Andy relax slightly).

Should I add myself as mentor?


BTW, I see we also need to update
http://incubator.apache.org/projects/taverna.html to list the new
committers.

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

Re: Create 'develop' branch for tavmob

[Gale Naylor]

I was thinking the master was the latest release, too, but I have no strong
feelings either way.

On Nov 4, 2016 10:28 AM, "Ian Dunlop"  wrote:

Hello

Maybe having a separate develop branch fits in with the commit then review
model (see other recent thread). I guess I have got into the idea that
master is the latest release. As with all these things I'm happy to go with
the consensus. If we make it clear in the readme and website that pull
requests should be against develop then that will help. People will still
sometimes pull against wrong branch but I guess that is just life.

Cheers

Ian

Cheers

Ian

On 4 Nov 2016 14:59, "Stian Soiland-Reyes"  wrote:

Agree to wait with any split before we have done a first Mobile release.

I am not quite sure why we need a separate develop branch, would you attend
for "master" branch to always be equal to the latest Apache Taverna Mobile
source release or to regularly sync up with devel ?

Who are the intended users of the master branch? This could confuse work
for pull requests going against the "wrong" branch.

If a moving master is for others than developers on this list, then you
have introduced an in-between "release" which don't follow the ASF release
policy.

Some larger projects use this approach with pure feature branches. Then
selecting a release is to select feature branches into a release branch
forked off master. This allows more immature or unstable features to be
excluded from a release. But this requires a lot of git management, quite a
few git rebase or merges. Also there's the problem of when you need to
build one feature branches of another that you end up with a "develop"
branch that is no longer directly mergable with master.

So my recommendation is to be careful :-)

On 3 Nov 2016 4:02 pm, "Ian Dunlop"  wrote:

> Hello,
>
> Yes we can tag the master branch and then create develop from it.
>
> Cheers,
>
> Ian
>
> On 03/11/16 13:56, Rajan Maurya wrote:
> > It's one of the Cool thing to manage the code, It's awesome but I think,
> we
> > should make at least a github relase before shifting the master a main
> > default branch.
> >
> > Thanks.
> >
>
>
>

Re: To pull or not to pull

[Gale Naylor]

Thanks for the explanation. :)

On Fri, Nov 4, 2016, 7:59 AM Stian Soiland-Reyes  wrote:

> It's very low tech, subscribe to commits (or look at archive), just look at
> quickly at every email and reply (back to dev@) if something is unclear.
> Revert git commit if something breaks.
>
> (But no-one are necessarily "on watch" so commits might go unnoticed.)
>
> Apache Commons work like that, which is a bit important there as they have
> granted all ASF committers write access and the Commons libraries have
> hundreds of thousands of users.
>
> You could also look at the git log locally or at GitHub, but we have many
> repositories and a couple of branches. This might be good before a release.
>
> On 4 Nov 2016 1:39 pm, "Gale Naylor"  wrote:
>
> > RTC for large changes and CTR for maintenance sounds good. I'm curious -
> > What is the process for CTR with the @commits list?
> >
> > On Fri, Nov 4, 2016, 5:31 AM Stian Soiland-Reyes 
> wrote:
> >
> > > CTR can be done with the commits@ list, but with git it can be way too
> > > noisy to follow or understand. Pull Request have very good UI for code
> > > review. I think we also have an ASF Gerrit instance we can use.
> > >
> > > How about we do RTC for large things or where a committer is not quite
> > > sure, but CTR for maintenance things?
> > >
> > > Also I would put an informal 1w deadline on any pull requests after
> which
> > > the committer just merges themselves.
> > >
> > > On 4 Nov 2016 11:48 am, "Andy Seaborne"  wrote:
> > >
> > > > There are two styles
> > > >
> > > > CTR - "Commit then review" -- its still up for review
> > > > RTC - "Review then commit"
> > > >
> > > > and hybrid forms such as committers doing CTR for small, "obvious"
> > things
> > > > (e.g. "Doh!" bug fixes; emergency repair) and RTC via PR when larger
> or
> > > the
> > > > committer is seeking review.
> > > >
> > > > Andy
> > > >
> > > > On 04/11/16 04:11, Thilina Manamgoda wrote:
> > > >
> > > >> HI,
> > > >>
> > > >> I think this is a good idea. There may be mistakes in my code
> because
> > > >> still  i am not a expert thus code review is a good approach.
> > > >>
> > > >> Regards,
> > > >> Thilina
> > > >>
> > > >> On Thu, Nov 3, 2016 at 10:05 PM, Ian Dunlop 
> > > wrote:
> > > >>
> > > >> Hello,
> > > >>>
> > > >>> I think we need a policy decision on how to add new code to
> existing
> > > >>> projects. Apache Taverna commiters can just merge straight into
> > master
> > > >>> but perhaps we should have a policy of using pull requests so that
> we
> > > >>> can review the code first. It might mean there is a slight overhead
> > but
> > > >>> maybe long term it means we get better code out of it. Myself and
> > Sagar
> > > >>> were just having a chat about this with respect to the TavMob
> project
> > > so
> > > >>> it might not be appropriate for every repo.
> > > >>>
> > > >>> Discuss.
> > > >>>
> > > >>> Cheers,
> > > >>>
> > > >>> Ian
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>
> > >
> >
>

Re: To pull or not to pull

[Gale Naylor]

RTC for large changes and CTR for maintenance sounds good. I'm curious -
What is the process for CTR with the @commits list?

On Fri, Nov 4, 2016, 5:31 AM Stian Soiland-Reyes  wrote:

> CTR can be done with the commits@ list, but with git it can be way too
> noisy to follow or understand. Pull Request have very good UI for code
> review. I think we also have an ASF Gerrit instance we can use.
>
> How about we do RTC for large things or where a committer is not quite
> sure, but CTR for maintenance things?
>
> Also I would put an informal 1w deadline on any pull requests after which
> the committer just merges themselves.
>
> On 4 Nov 2016 11:48 am, "Andy Seaborne"  wrote:
>
> > There are two styles
> >
> > CTR - "Commit then review" -- its still up for review
> > RTC - "Review then commit"
> >
> > and hybrid forms such as committers doing CTR for small, "obvious" things
> > (e.g. "Doh!" bug fixes; emergency repair) and RTC via PR when larger or
> the
> > committer is seeking review.
> >
> > Andy
> >
> > On 04/11/16 04:11, Thilina Manamgoda wrote:
> >
> >> HI,
> >>
> >> I think this is a good idea. There may be mistakes in my code because
> >> still  i am not a expert thus code review is a good approach.
> >>
> >> Regards,
> >> Thilina
> >>
> >> On Thu, Nov 3, 2016 at 10:05 PM, Ian Dunlop 
> wrote:
> >>
> >> Hello,
> >>>
> >>> I think we need a policy decision on how to add new code to existing
> >>> projects. Apache Taverna commiters can just merge straight into master
> >>> but perhaps we should have a policy of using pull requests so that we
> >>> can review the code first. It might mean there is a slight overhead but
> >>> maybe long term it means we get better code out of it. Myself and Sagar
> >>> were just having a chat about this with respect to the TavMob project
> so
> >>> it might not be appropriate for every repo.
> >>>
> >>> Discuss.
> >>>
> >>> Cheers,
> >>>
> >>> Ian
> >>>
> >>>
> >>>
> >>>
> >>
>

Re: Create 'develop' branch for tavmob

[Gale Naylor]

That makes a lot of sense to me.

Gale

On Nov 3, 2016 5:15 AM, "Ian Dunlop"  wrote:

> Hello,
>
> Up until now we have been pushing  to the master branch on the taverna
> mobile project. I think it is good practice to create a 'develop' branch
> which is the one that code changes are made to until we are ready to
> release. Then we merge it with master and start the release process.
>
> Thoughts?
>
> Cheers,
>
> Ian
>
>
>

Re: Welcome to Sagar and Rajan

[Gale Naylor]

Welcome, Sagar and Rajan!

On Nov 1, 2016 2:05 AM, "Ian Dunlop"  wrote:

> Hello,
>
> The Apache Taverna PPMC would like to formally welcome Rajan Maurya
> (rajanmaurya...@apache.org) and Sagar (sa...@apache.org) to the Apache
> Taverna community. They have both been helping out a lot with many great
> code contributions over the last few months and are now Apache Taverna
> committers. Welcome to you both.
>
> Cheers,
>
> Ian
>
>
>

Re: Fwd: Re: ASF for Google Code-In

[Gale Naylor]

I like the ideas Stian suggested. Sounds like a good way to give back!

Gale

On Oct 31, 2016 7:35 AM, "Stian Soiland-Reyes"  wrote:

Google Code In was mentioned on the chat, now there is ASF interest to
register as well. (See below)

I think we can have a go, it is true that it will be many small efforts as
the participants are high-school age (13-17) with perhaps not much coding
experience, but we can ask them to do non-coding things as well.

Some ideas:

* Test Android app on phones in the wild, report bugs/glitches
* Style up our homepage, just some css and bootstrap skills
* Make a new Taverna cog logo, preferably in svg
* Twitter rep - find Taverna stuff and blog/tweet it

Views..?
-- Forwarded message --
From: "Stian Soiland-Reyes" 
Date: 31 Oct 2016 2:27 pm
Subject: Re: ASF for Google Code-In
To: 
Cc:

+1 to have a go, we discussed it in Taverna as well, we could give them
> something to do in the Android app.
>
> It would be a bit similar to HelpWanted.apache.org I guess, but with
> mentoring..? It would have to be quite bite-sized for high school
students,
> but you would probably also be surprised as to what some of them can do!
>
> On 30 Oct 2016 11:22 pm, "Roman Shaposhnik"  wrote:
>
>> Hi!
>>
>> a project I mentor got interested in:
>>  https://developers.google.com/open-source/gci/
>>
>> Has there been any attempts to have ASF
>> as a mentoring organization there?
>>
>> The current list of orgs is pretty eclectic:
>>https://codein.withgoogle.com/archive/2015/organization/
>> but given that folks like Ubuntu are on the list
>> I don't see why ASF shouldn't be.
>>
>> Thanks,
>> Roman.
>>
>> -
>> To unsubscribe, e-mail: dev-unsubscr...@community.apache.org
>> For additional commands, e-mail: dev-h...@community.apache.org
>>
>>

Re: Website community updates

[Gale Naylor]

I like the changes! (Especially the Who Are We page and separators for the
web menu.) I also like the extended Incubator status.

I wonder if we need to have the incubator status on the Who Are We page? It
seems to me it's enough to put it on the home page.

>>   Community -> Contribute now goes to
>>
https://taverna.incubator.apache.org/download/code/#contribute-to-apache-taverna
>>   instead of the confusing section
>>   https://taverna.incubator.apache.org/community/#contribute

I like changing the Contribute link to the download/code page. And I agree
that the contribute section on the community home page was confusing.

I reformatted the contribute section on the Community/home page to make it
less confusing (I hope). Let me know what you think about the change. (I
also put mailing lists/ chat/ report bugs in it's own section called How to
Communicate. Otherwise, it seemed like chat and bug reporting were a subset
of mailing list.)

If we create a separate page for How to Contribute would it include what's
on the home page and the download/code page? Would it be useful to add more
content about contributing workflows and hosting services, etc?

Do we have something written about "How to become a committer?" It seems
logical to me to put that information on a future How to Contribute page.

Thanks!
Gale

On Sun, Sep 25, 2016 at 8:07 PM Stian Soiland-Reyes 
wrote:

> Hi, I've updated the Taverna website
>
> https://taverna.incubator.apache.org/community/lists
> * Added ASF Code of conduct
>
> https://taverna.incubator.apache.org/community/irc
> * Redirects to /community/chat
>
>
> https://taverna.incubator.apache.org/community/chat
> * Describe Gitter room
> * ..but use mailing list for decisions!
>
> https://taverna.incubator.apache.org/about/
> * Added Thilina as committer
> * Listed contributors (including recent GSOC students)
> * Incubator status: Linked to Graduation assessment
>
> https://taverna.incubator.apache.org/community/
> * Moved Incubator status to the bottom
> * Added Incubator disclaimer and link to Graduation assessment
> * Added Web chat link
>
>
> Menu changes:
>
> Added:
> Community -> Who Are We?
> https://taverna.incubator.apache.org/about/
> (This was just linked to from the /community/ text before)
>
>
> Community -> Contribute
> now goes to
>
> https://taverna.incubator.apache.org/download/code/#contribute-to-apache-taverna
> instead of the confusing section
> https://taverna.incubator.apache.org/community/#contribute
>
> (should these merge to become a linkable /community/contribute page to
> include non-code contribs -- perhaps this could also show how to
> become a committer?)
>
>
> Community ->
> * Reordered items
> * Added separators
>
>
> You may have to do a Ctrl-Shift-R reload to see the changes.
>
>
> Spot any Norwenglish typos or other comments?
>
>
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

Re: Welcome Thilina!

[Gale Naylor]

Welcome!

On Sun, Sep 25, 2016, 4:59 PM Stian Soiland-Reyes  wrote:

> The Apache Taverna PPMC is pleased to announce that Thilina Manamgoda
> (maana...@apache.org) has become a committer and joined the Taverna
> team.
>
> Welcome, Thilina!
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

Re: Move taverna-perspective-biocatalogue to GitHub?

[Gale Naylor]

Thanks for clarifying. We can include the Taverna 3 process for using the
web services in our documentation (helping with backward-compatibility).

I also agree with moving it for now.

Gale

On Wed, Sep 21, 2016 at 8:09 AM Thilina Manamgoda 
wrote:

> Hi,
>
> I think  that's a good idea. We can fix those license issue seperatly and
> bring it back.
>
> Thanks,
> Thilina
>
>
> On Wed, Sep 21, 2016 at 8:21 PM, Ian Dunlop  wrote:
>
> > Hello,
> >
> > They can still use the web services - just takes a little bit more effort
> > since they have to find and configure them themselves. I guess this is
> what
> > the biocat perspective brings to the table. I think it is safer to move
> it
> > to extras for the time being rather than spending effort on chasing down
> > the provenance of some files.
> >
> > Cheers,
> >
> > Ian
> >
> > On 21 September 2016 at 15:49, Gale Naylor 
> > wrote:
> >
> > > If we don't release the BioCatalogue perspective as part of Taverna 3,
> is
> > > there a way for users to continue using those BioCatalogue web
> services,
> > or
> > > do we lose that capability?
> > >
> > > Gale
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Sep 21, 2016 at 6:56 AM alaninmcr 
> > > wrote:
> > >
> > > > On 21/09/2016 13:26, Stian Soiland-Reyes wrote:
> > > > [snip]
> > > >
> > > > > I don't know how much the Biocatalogue perspective is used in
> Taverna
> > > > > 2.5 - I know it can be very useful to find and use lots of web
> > > > > services - so arguably it would be a bit of a loss. It also has
> lots
> > > > > of code to replicate in Java Swing what is also on the
> > > > > biocatalogue.org website - that is perhaps not as needed.
> > > >
> > > > My long-standing opinion is that Taverna should not attempt to
> > replicate
> > > > a website, whether biocatalogue or myExperiment :)
> > > >
> > > > > What's your take?
> > > >
> > > > I agree with moving it out to extras.
> > > >
> > > > Alan
> > > >
> > > >
> > >
> >
>

Re: Taverna Mobile NOTICE

[Gale Naylor]

That sounds good!

On Wed, Sep 21, 2016 at 8:02 AM Rajan Maurya 
wrote:

> Yes, We can show opensource licences of all the library in the menu action
> button.
>
> For an example : open google gmail app -> click navigation home button ->
> scroll to botton -> click on Settings -> open settings action menu -> click
> on Help & feedback ->
> open Help & feedback action menu -> click on "Open-source liceneces".
>
> I think this is sufficient.
>
>
>
> On Wed, Sep 21, 2016 at 2:01 PM, Ian Dunlop  wrote:
>
> > Hello,
> >
> > I agree with Gale that we can add it to the play read more but we also
> need
> > to think about people who will just download the apk. So maybe we do need
> > to add some details to the "about" section within the app. It's not a big
> > deal to do. I guess we will discover what to do when we release. We could
> > ask these questions on general@incubator, I wonder what they do for iOS.
> >
> > Cheers,
> >
> > Ian
> >
> > On 20 September 2016 at 18:44, Stian Soiland-Reyes 
> > wrote:
> >
> > > Yes, I think that would somewhat count as "provided with" in these
> cloud
> > > days  :-)
> > >
> > > (I am not a lawyer, etc)
> > >
> > > On 20 Sep 2016 5:48 p.m., "Gale Naylor" 
> > > wrote:
> > >
> > > > Could we put the license and notice in the "read more" section of the
> > > play
> > > > store window that is used to describe the app? Or a summary of the
> > info?
> > > >
> > > > On Tue, Sep 20, 2016, 3:12 AM Stian Soiland-Reyes 
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > If we're going to release a Taverna Mobile binary .apk (or whatever
> > > > > the extension is today) - then that would also bundle the
> third-party
> > > > > dependencies, right?
> > > > >
> > > > > We would then need to include a variant of the LICENSE and NOTICE
> > file
> > > > > - but how can that be readable from within the app?  (As you
> wouldn't
> > > > > "unzip" the app before installing it).  Do we need to use a "About"
> > > > > menu button where the user can scroll through the license?
> > > > >
> > > > >
> > > > > Also it would be good to check on the dependencies if they have
> their
> > > > > own NOTICE files - it should be easy by just looking inside their
> JAR
> > > > > files and copy out whatever is there. If they don't have, and they
> > are
> > > > > also Apache licensed, then there should be nothing more to do. BSD
> > > > > licensed ones however would need to comply with
> > > > >
> > > > > > 2. Redistributions in binary form must reproduce the above
> > copyright
> > > > > notice, this list of conditions and the following disclaimer in the
> > > > > documentation and/or other materials provided with the
> distribution.
> > > > >
> > > > > I am not sure if we could get away with that by not providing
> > > > > documentation or materials :)
> > > > >
> > > > > --
> > > > > Stian Soiland-Reyes
> > > > > http://orcid.org/-0001-9842-9718
> > > > >
> > > >
> > >
> >
>
>
>
> --
> *Thanks*
> *Namaste*
>
> Rajan Maurya
> Contact Number : +91 8010665248
> Github : https://github.com/therajanmaurya
> College : Cluster Innovation Centre, University of Delhi
> Student : B.Tech. (Information Technology & Mathematical Innovations)
>

Re: Move taverna-perspective-biocatalogue to GitHub?

[Gale Naylor]

If we don't release the BioCatalogue perspective as part of Taverna 3, is
there a way for users to continue using those BioCatalogue web services, or
do we lose that capability?

Gale





On Wed, Sep 21, 2016 at 6:56 AM alaninmcr  wrote:

> On 21/09/2016 13:26, Stian Soiland-Reyes wrote:
> [snip]
>
> > I don't know how much the Biocatalogue perspective is used in Taverna
> > 2.5 - I know it can be very useful to find and use lots of web
> > services - so arguably it would be a bit of a loss. It also has lots
> > of code to replicate in Java Swing what is also on the
> > biocatalogue.org website - that is perhaps not as needed.
>
> My long-standing opinion is that Taverna should not attempt to replicate
> a website, whether biocatalogue or myExperiment :)
>
> > What's your take?
>
> I agree with moving it out to extras.
>
> Alan
>
>

Re: Taverna Mobile NOTICE

[Gale Naylor]

Could we put the license and notice in the "read more" section of the play
store window that is used to describe the app? Or a summary of the info?

On Tue, Sep 20, 2016, 3:12 AM Stian Soiland-Reyes  wrote:

> Hi,
>
> If we're going to release a Taverna Mobile binary .apk (or whatever
> the extension is today) - then that would also bundle the third-party
> dependencies, right?
>
> We would then need to include a variant of the LICENSE and NOTICE file
> - but how can that be readable from within the app?  (As you wouldn't
> "unzip" the app before installing it).  Do we need to use a "About"
> menu button where the user can scroll through the license?
>
>
> Also it would be good to check on the dependencies if they have their
> own NOTICE files - it should be easy by just looking inside their JAR
> files and copy out whatever is there. If they don't have, and they are
> also Apache licensed, then there should be nothing more to do. BSD
> licensed ones however would need to comply with
>
> > 2. Redistributions in binary form must reproduce the above copyright
> notice, this list of conditions and the following disclaimer in the
> documentation and/or other materials provided with the distribution.
>
> I am not sure if we could get away with that by not providing
> documentation or materials :)
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

Re: Replace the #taverna IRC channel with Gitter webchat?

[Gale Naylor]

I signed up and signed it. Looks interesting.

On Fri, Sep 16, 2016 at 3:54 AM Stian Soiland-Reyes 
wrote:

> Hi,
>
> On https://taverna.incubator.apache.org/community/irc
>
> we suggest the #taverna IRC channel as an informal chat. However by
> its synchronous nature and our various time zones it has not really
> seen any use.
>
> I think it's good that we primarily use the mailing list.
>
> Should we remove the above IRC page from our website?
>
>
> One web-chat that is very popular in open source communities these
> days is Gitter, which is free for open source communities. It's
> semi-asynchronous - as it keeps the backlog for you (channels are open
> by default), and you can turn on/off email notifications.
>
> Some of the nice features are how you can paste code examples etc. See
> for instance how it's used by the Common Workflow Language community:
>
> https://gitter.im/common-workflow-language/common-workflow-language
>
>
>
> However to log in and chat you need either a GitHub or Twitter
> account. So it's not as open as IRC. (but you can use
> https://irc.gitter.im/ with an IRC client if you have an account!)
>
>
> As a test I made an Apache Taverna Gitter room:
>
>   https://gitter.im/apache/taverna
>
> What do you think?
>
>
> As always - remember: "If it didn't happen on the mailing list, it
> didn't happen!"
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

Re: Taverna Player Portal JSON API queries ( Apache Taverna Mobile )

[Gale Naylor]

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  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 
> 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  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 
> 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  >
> > >> 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  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 
> 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:
> > >>> >> >
> > >>> >> 

Re: No apache License headers in taverna-workbench module

[Gale Naylor]

>>Any volunteers? We can add sections at the >>end of the wiki with the
>>rat output for each.

Volunteers to manually add headers to non-java files, or ?

On Wed, Sep 7, 2016, 8:09 AM Ian Dunlop  wrote:

> Hello,
>
> Added page
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/Taverna+Mobile+Licence+Review
> and linked to the licence review page.
>
> Cheers,
>
> Ian
>
> On 7 September 2016 at 16:02, Ian Dunlop  wrote:
>
> > Hello,
> >
> > Found a rat plugin for gradle. We need this for the mobile app, no maven
> > here! I am currently testing it out (and raising minor issues!)
> >
> > https://plugins.gradle.org/plugin/org.nosphere.apache.rat
> >
> > Cheers,
> >
> > Ian
> >
> > On 7 September 2016 at 14:50, Stian Soiland-Reyes 
> > wrote:
> >
> >> I've updated the table on
> >>
> >> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-
> >> 09+License+review
> >>
> >> so that now there's now just a (?)-mark  on the repositories where I
> >> added ASF headers to *.java, but which apache-rat might not have
> >> checked - e.g. there would be the odd XML file left - perhaps some
> >> PNGs etc.
> >>
> >>
> >> Any volunteers? We can add sections at the end of the wiki with the
> >> rat output for each.
> >>
> >>
> >>
> >>
> >>
> >> I've added comments to NOTICE where something was unclear and left
> >> their header in place.. e.g.
> >>
> >> https://github.com/apache/incubator-taverna-workbench/blob/
> >> master/NOTICE#L12
> >>
> >> .. which indicate a file I find didn't have any open source license at
> >> all (copied from a blog).
> >>
> >> Each of these should become JIRA issues - at least we would notice in
> >> the NOTICE file!
> >>
> >>
> >> On 7 September 2016 at 14:47, Stian Soiland-Reyes 
> >> wrote:
> >> > Thanks - I did something similar - although now it turns out the
> >> > "wrong order" with 'package' on top (that was easier with sed)
> >> >
> >> > cd incubator-taverna-plugin-bioinformatics/
> >> > git status
> >> > git checkout master
> >> > git pull
> >> >
> >> > # files that probably are OK
> >> > grep -r "Licensed to the Apache Software" . | cut -d : -f 1 > OK
> >> >
> >> > # Find Java files - naive
> >> > grep -r ^package . | grep src | cut -d ":" -f 1 | grep java$  > CHECK
> >> >
> >> > # Find the differences
> >> > grep -v -f OK CHECK  > MISSING
> >> >
> >> > # Check there are not any nonsense here
> >> > head MISSING  | less
> >> >
> >> > # Check the current file headers
> >> > xargs -a MISSING head | less
> >> >
> >> > # Remove /* sillyness
> >> > cat MISSING | xargs sed -i '\,^.\*\*\*\*\*\*.*, d'
> >> >
> >> >  git diff
> >> >  git commit -m "Removed /*** comments" tav*
> >> >  git status
> >> >
> >> > Now let's add the header.  I put the /* .. */  text in a file
> >> LICENSE-header.txt
> >> >
> >> > vi LICENSE-header.txt
> >> > /*
> >> >  * Licensed to the Apache Software Foundation (ASF) under one or more
> >> >  * contributor license agreements.  See the NOTICE file distributed
> with
> >> >  * this work for additional information regarding copyright ownership.
> >> >  * The ASF licenses this file to You under the Apache License, Version
> >> 2.0
> >> >  * (the "License"); you may not use this file except in compliance
> with
> >> >  * the License.  You may obtain a copy of the License at
> >> >  *
> >> >  *  http://www.apache.org/licenses/LICENSE-2.0
> >> >  *
> >> >  * Unless required by applicable law or agreed to in writing, software
> >> >  * distributed under the License is distributed on an "AS IS" BASIS,
> >> >  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
> >> implied.
> >> >  * See the License for the specific language governing permissions and
> >> >  * limitations under the License.
> >> >  */
> >> >
> >> > cat MISSING | xargs sed -i '/^package/ r LICENSE-header.txt'
> >> >
> >> > git diff
> >> > git commit -m "Added ASF license header" taverna-*
> >> > git push
> >> >
> >> > # Tidy
> >> > rm CHECK LICENSE-header.txt MISSING OK
> >> > git status
> >> >
> >> > But sadly this means the comment was added below the 'package' line..
> >> > Sorry about that.
> >> >
> >> > On 7 September 2016 at 14:15, Andy Seaborne  wrote:
> >> >> PS
> >> >>
> >> >> /**
> >> >>  License
> >> >> */
> >> >>
> >> >> then
> >> >>
> >> >> package org.apache.taverna ... ;
> >> >>
> >> >> is the usual way - not package then license comment.
> >> >>
> >> >> Andy
> >> >>
> >> >>
> >> >> On 07/09/16 14:08, Andy Seaborne wrote:
> >> >>>
> >> >>>
> >> >>>
> >> >>> On 07/09/16 12:04, Stian Soiland-Reyes wrote:
> >> 
> >>  It should - if the script or maven plugin is able to cleanly remove
> >>  the old header.
> >> >>>
> >> >>>
> >> >>> I use perl:
> >> >>>
> >> >>> undef $/ ;
> >> >>> s!/.*?\npackage!\npackage!s ;
> >> >>>
> >> >>> i.e. remove everything up until the "package" on the start of a
> line.
> >> >>>
> >> >>> This avoids having to match different layouts.
> >> >>>
> >> >>> Andy
> >> >>>
> >> >>> #!/usr/bin/perl
> >> >>> # find . -

Re: Taverna License review wiki page

[Gale Naylor]

Regarding using the Mojohaus Maven license plugin, I figured some things
out and got a simple
test case to work, but then I ran into a problem regarding a real
repository with multiple
modules. Specifically, using {project.baseUri}/src/license to describe the
location of the license file
only works for files at the root of the project. This Q&A on on
StackOverflow
(
http://stackoverflow.com/questions/23274539/maven-license-plugin-use-license-for-parentpom-for-all-children
)
says to use a classpath:// protocol, instead of the {project.baleUri} but
then it also says:
"you really do need to have a separate package with the license files.
There doesn't seem to be a way to keep this information in the parent pom
project."

I don't quite understand how to create a separate package and where to put
it in the directory structure.
Can anyone point me to information that would help me understand what to
do? Is this worth pursuing?


Meanwhile, here is what I learned about the Mojohaus Maven license plugin:

1) You DO need a license/ folder under src/.

2) Inside the license/ folder you need a file called licenses.properties
(Some of the documentation
erroneously says "license.properties" instead of "licenses" - with an "s"
at the end.)

3) The licenses.properties file lists the licenses and needs one line per
license: e.g., apache_v2=Apache 2.0

4) Inside the license/ folder you also need a sub-folder with the name of
your license: e.g., apache_v2

5) Inside the apache_v2/ folder are the header.txt and license.txt files.

6) You can run mvn license:license-list to see the license names to use.
(Plus you can check licenses,
download licenses, get 3rd party reports, etc.)

7) This plugin inserts control characters (#%L and %%)  into the license,
for example:
/*-
 * #%L
 * Apache Taverna Server
 * %%
 * Copyright (C) 2015 - 2016 The Apache Software Foundation
 * %%
 * Licensed under the Apache License

8) Add the following to the pom.xml (Mojohaus apparently still uses
org.codehaus.mojo):

org.codehaus.mojo
license-maven-plugin
1.9

apache_v2
${project.baseUri}/src/license



generate-license-headers

update-file-header

process-sources


src/main/java








On Mon, Sep 5, 2016 at 10:17 AM Gale Naylor 
wrote:

> Oh! That's what you meant. Sorry - I thought you meant you added an Apache
> header. Thanks!!!
>
> On Mon, Sep 5, 2016 at 10:16 AM Stian Soiland-Reyes 
> wrote:
>
>> But I updated and removed all the mygrid links:
>>
>> https://github.com/apache/incubator-taverna-server/blob/master/.opf.yml
>>
>>
>> On 5 September 2016 at 17:20, Gale Naylor 
>> wrote:
>> > I'll have another look at the maven license header tomorrow. (Today is a
>> > holiday here.) And thanks for the information about settings: I just
>> took
>> > the defaults because I couldn't find answers in the documentation.
>> >
>> > As for the OPF file, my real questions are:
>> >
>> > Is there a reason to keep the pre-Apache information in an Apache
>> release?
>> > (Maybe we should update the information?)
>> >
>> > In particular, I'm wondering about pointing people to the Taverna Server
>> > 2.4 home page and to mygrid.org.uk for issues. Won't that be
>> > confusing/out-of-date?
>> >
>> > Thanks,
>> >
>> > Gale
>> >
>> > On Mon, Sep 5, 2016, 9:05 AM Stian Soiland-Reyes 
>> wrote:
>> >
>> >> Thanks for having a go!
>> >>
>> >> I am not sure to be honest what is the correct configuration of
>> >> license-maven-plugin.. I just spotted it had a update-file-header
>> >>
>> >> (BTW - We should not add SVN keywords, we use git!)
>> >>
>> >> One problem is that the codehaus.org has since disappeared - which
>> >> hosted many useful Maven plugins.
>> >>
>> >> Most of them are rescued here: http://www.mojohaus.org/ - aka
>> >> http://www.mojohaus.org/license-maven-plugin/
>> >>
>> >>
>> >>
>> >>
>> >> There's also the competing
>> >> http://code.mycila.com/license-maven-plugin/ which has a slightly
>> >> different kind of configuration.
>> >>
>> >>
>> >> It might be you would have to add a license template to a folder under
>> >> src/ somewhere first.
>> >>
>> >> On 2 September 2016 at 22:38, Gale Naylor > >
>> >> wrote:
>> >> > Also, I tried using the maven license plugin to add a license header
>> (to
>> >> a
>> >> > loc

Question Jenkins build failures

[Gale Naylor]

When I look at the Jenkins builds in this link (
https://builds.apache.org/user/stain/my-views/view/taverna/) most of the
builds are failing. There was some discussion recently about the
commandline build failing and needing to upgrade Java and Maven -- or
possibly using different servers? I've read the Jenkins wiki and a few of
the introductory articles, but don't yet understand enough of the process
to know the consequences of failed builds.

Is this a concern, or is it something that typically happens and will
eventually be cleared up? It's just that, since we're referencing the
Jenkins builds in our Graduation Maturity Document, it seems odd that most
of the recent ones are failing.

Thanks,

Gale

Re: Taverna License review wiki page

[Gale Naylor]

Oh! That's what you meant. Sorry - I thought you meant you added an Apache
header. Thanks!!!

On Mon, Sep 5, 2016 at 10:16 AM Stian Soiland-Reyes 
wrote:

> But I updated and removed all the mygrid links:
>
> https://github.com/apache/incubator-taverna-server/blob/master/.opf.yml
>
>
> On 5 September 2016 at 17:20, Gale Naylor 
> wrote:
> > I'll have another look at the maven license header tomorrow. (Today is a
> > holiday here.) And thanks for the information about settings: I just took
> > the defaults because I couldn't find answers in the documentation.
> >
> > As for the OPF file, my real questions are:
> >
> > Is there a reason to keep the pre-Apache information in an Apache
> release?
> > (Maybe we should update the information?)
> >
> > In particular, I'm wondering about pointing people to the Taverna Server
> > 2.4 home page and to mygrid.org.uk for issues. Won't that be
> > confusing/out-of-date?
> >
> > Thanks,
> >
> > Gale
> >
> > On Mon, Sep 5, 2016, 9:05 AM Stian Soiland-Reyes 
> wrote:
> >
> >> Thanks for having a go!
> >>
> >> I am not sure to be honest what is the correct configuration of
> >> license-maven-plugin.. I just spotted it had a update-file-header
> >>
> >> (BTW - We should not add SVN keywords, we use git!)
> >>
> >> One problem is that the codehaus.org has since disappeared - which
> >> hosted many useful Maven plugins.
> >>
> >> Most of them are rescued here: http://www.mojohaus.org/ - aka
> >> http://www.mojohaus.org/license-maven-plugin/
> >>
> >>
> >>
> >>
> >> There's also the competing
> >> http://code.mycila.com/license-maven-plugin/ which has a slightly
> >> different kind of configuration.
> >>
> >>
> >> It might be you would have to add a license template to a folder under
> >> src/ somewhere first.
> >>
> >> On 2 September 2016 at 22:38, Gale Naylor 
> >> wrote:
> >> > Also, I tried using the maven license plugin to add a license header
> (to
> >> a
> >> > local file copies), but kept getting this error: "licenseName can not
> be
> >> > null nor empty." It's probably because I don't quite know how to use
> this
> >> > plugin. I followed the instructions here (
> >> >
> >>
> http://www.mojohaus.org/license-maven-plugin/examples/update-file-header-config.html
> >> )
> >> > and here (
> >> >
> >>
> http://stackoverflow.com/questions/22549517/how-to-use-the-the-license-maven-plugin
> >> )
> >> > and added the license plugin to the project pom.xml, but could not
> >> resolve
> >> > the error. One thing I couldn't find: where does the plugin get the
> text
> >> > for the license header?
> >> >
> >> > Here is what I added to the pom:
> >> >
> >> >
> >> >       
> >> > org.codehaus.mojo
> >> > license-maven-plugin
> >> > 1.9
> >> > 
> >> >   false
> >> >   true
> >> > 
> >> > 
> >> >   
> >> > generate-license-headers
> >> > 
> >> >   update-file-header
> >> > 
> >> > process-sources
> >> > 
> >> >   Apache 2.0
> >> >   
> >> > src/main/java
> >> >   
> >> > 
> >> >   
> >> > 
> >> >   
> >> >
> >> > Cheers! Have a nice weekend.
> >> >
> >> > Gale
> >> >
> >> >
> >> > On Fri, Sep 2, 2016 at 2:33 PM Gale Naylor <
> ga...@noventussolutions.com>
> >> > wrote:
> >> >
> >> >> I downloaded a zip of incubator-taverna-server from GitHub and ran
> the
> >> RAT
> >> >> check from the command line on each of the main and sub folders. It
> >> looks
> >> >> like almost all the files need a header.
> >> >>
> >> >> One if the files is the .opf.yml file, which contains references to
> >> >> mygrid.org.uk and taverna.org.uk.:
> >> >>
> >> >> name: Taverna Server
> >

Re: Taverna License review wiki page

[Gale Naylor]

I'll have another look at the maven license header tomorrow. (Today is a
holiday here.) And thanks for the information about settings: I just took
the defaults because I couldn't find answers in the documentation.

As for the OPF file, my real questions are:

Is there a reason to keep the pre-Apache information in an Apache release?
(Maybe we should update the information?)

In particular, I'm wondering about pointing people to the Taverna Server
2.4 home page and to mygrid.org.uk for issues. Won't that be
confusing/out-of-date?

Thanks,

Gale

On Mon, Sep 5, 2016, 9:05 AM Stian Soiland-Reyes  wrote:

> Thanks for having a go!
>
> I am not sure to be honest what is the correct configuration of
> license-maven-plugin.. I just spotted it had a update-file-header
>
> (BTW - We should not add SVN keywords, we use git!)
>
> One problem is that the codehaus.org has since disappeared - which
> hosted many useful Maven plugins.
>
> Most of them are rescued here: http://www.mojohaus.org/ - aka
> http://www.mojohaus.org/license-maven-plugin/
>
>
>
>
> There's also the competing
> http://code.mycila.com/license-maven-plugin/ which has a slightly
> different kind of configuration.
>
>
> It might be you would have to add a license template to a folder under
> src/ somewhere first.
>
> On 2 September 2016 at 22:38, Gale Naylor 
> wrote:
> > Also, I tried using the maven license plugin to add a license header (to
> a
> > local file copies), but kept getting this error: "licenseName can not be
> > null nor empty." It's probably because I don't quite know how to use this
> > plugin. I followed the instructions here (
> >
> http://www.mojohaus.org/license-maven-plugin/examples/update-file-header-config.html
> )
> > and here (
> >
> http://stackoverflow.com/questions/22549517/how-to-use-the-the-license-maven-plugin
> )
> > and added the license plugin to the project pom.xml, but could not
> resolve
> > the error. One thing I couldn't find: where does the plugin get the text
> > for the license header?
> >
> > Here is what I added to the pom:
> >
> >
> >   
> > org.codehaus.mojo
> > license-maven-plugin
> > 1.9
> > 
> >   false
> >   true
> > 
> > 
> >   
> > generate-license-headers
> > 
> >   update-file-header
> >         
> > process-sources
> > 
> >   Apache 2.0
> >   
> > src/main/java
> >   
> > 
> >   
> > 
> >   
> >
> > Cheers! Have a nice weekend.
> >
> > Gale
> >
> >
> > On Fri, Sep 2, 2016 at 2:33 PM Gale Naylor 
> > wrote:
> >
> >> I downloaded a zip of incubator-taverna-server from GitHub and ran the
> RAT
> >> check from the command line on each of the main and sub folders. It
> looks
> >> like almost all the files need a header.
> >>
> >> One if the files is the .opf.yml file, which contains references to
> >> mygrid.org.uk and taverna.org.uk.:
> >>
> >> name: Taverna Server
> >> vendor: The University of Manchester
> >> maintainer:
> >> name: Donal Fellows
> >> email: donal.k.fellows( AT )manchester.ac.uk
> >> platform: "Java 6+, Tomcat 6, POSIX"
> >> download: http://www.taverna.org.uk/download/server/
> >> # Really the documentation page as the overall home page is shared with
> >> the workbench but will do for now
> >> homepage:
> http://dev.mygrid.org.uk/wiki/display/taverna/Taverna+Server+2.4
> >> issues: http://dev.mygrid.org.uk/issues/browse/TAVSERV
> >> # Note, no anti-spam armouring required for this one
> >> support-contact: supp...@mygrid.org.uk
> >>
> >> I'm guessing this information needs to be updated, too?
> >>
> >> Gale
> >>
> >> On Fri, Sep 2, 2016 at 8:41 AM Stian Soiland-Reyes <
> >> soiland-re...@cs.manchester.ac.uk> wrote:
> >>
> >>> Hi,
> >>>
> >>> I've made
> >>>
> >>>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-09+License+review
> >>>
> >>> so we can track license review progress.
> >>>
> >>>
> >>> Anyone is welcome to keep checking/fixing those that are not complete
> >>> - as I've mentioned it's fine to remove the (C) Manchester/LGPL
> >>> headers as they are part oft he software grant.
> >>>
> >>> It should be possible to do the license header updates using the maven
> >>> license plugin rather than a large vim session..
> >>>
> >>> --
> >>> Stian Soiland-Reyes, eScience Lab
> >>> School of Computer Science
> >>> The University of Manchester
> >>> http://orcid.org/-0001-9842-9718
> >>>
> >>
>
>
>
> --
> Stian Soiland-Reyes
> http://orcid.org/-0001-9842-9718
>

Re: Taverna License review wiki page

[Gale Naylor]

Also, I tried using the maven license plugin to add a license header (to a
local file copies), but kept getting this error: "licenseName can not be
null nor empty." It's probably because I don't quite know how to use this
plugin. I followed the instructions here (
http://www.mojohaus.org/license-maven-plugin/examples/update-file-header-config.html)
and here (
http://stackoverflow.com/questions/22549517/how-to-use-the-the-license-maven-plugin)
and added the license plugin to the project pom.xml, but could not resolve
the error. One thing I couldn't find: where does the plugin get the text
for the license header?

Here is what I added to the pom:


  
org.codehaus.mojo
license-maven-plugin
1.9

  false
  true


  
generate-license-headers

  update-file-header

process-sources

  Apache 2.0
  
src/main/java
  

  

  

Cheers! Have a nice weekend.

Gale


On Fri, Sep 2, 2016 at 2:33 PM Gale Naylor 
wrote:

> I downloaded a zip of incubator-taverna-server from GitHub and ran the RAT
> check from the command line on each of the main and sub folders. It looks
> like almost all the files need a header.
>
> One if the files is the .opf.yml file, which contains references to
> mygrid.org.uk and taverna.org.uk.:
>
> name: Taverna Server
> vendor: The University of Manchester
> maintainer:
> name: Donal Fellows
> email: donal.k.fellows( AT )manchester.ac.uk
> platform: "Java 6+, Tomcat 6, POSIX"
> download: http://www.taverna.org.uk/download/server/
> # Really the documentation page as the overall home page is shared with
> the workbench but will do for now
> homepage: http://dev.mygrid.org.uk/wiki/display/taverna/Taverna+Server+2.4
> issues: http://dev.mygrid.org.uk/issues/browse/TAVSERV
> # Note, no anti-spam armouring required for this one
> support-contact: supp...@mygrid.org.uk
>
> I'm guessing this information needs to be updated, too?
>
> Gale
>
> On Fri, Sep 2, 2016 at 8:41 AM Stian Soiland-Reyes <
> soiland-re...@cs.manchester.ac.uk> wrote:
>
>> Hi,
>>
>> I've made
>>
>> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-09+License+review
>>
>> so we can track license review progress.
>>
>>
>> Anyone is welcome to keep checking/fixing those that are not complete
>> - as I've mentioned it's fine to remove the (C) Manchester/LGPL
>> headers as they are part oft he software grant.
>>
>> It should be possible to do the license header updates using the maven
>> license plugin rather than a large vim session..
>>
>> --
>> Stian Soiland-Reyes, eScience Lab
>> School of Computer Science
>> The University of Manchester
>> http://orcid.org/-0001-9842-9718
>>
>

Re: Taverna License review wiki page

[Gale Naylor]

I downloaded a zip of incubator-taverna-server from GitHub and ran the RAT
check from the command line on each of the main and sub folders. It looks
like almost all the files need a header.

One if the files is the .opf.yml file, which contains references to
mygrid.org.uk and taverna.org.uk.:

name: Taverna Server
vendor: The University of Manchester
maintainer:
name: Donal Fellows
email: donal.k.fellows( AT )manchester.ac.uk
platform: "Java 6+, Tomcat 6, POSIX"
download: http://www.taverna.org.uk/download/server/
# Really the documentation page as the overall home page is shared with the
workbench but will do for now
homepage: http://dev.mygrid.org.uk/wiki/display/taverna/Taverna+Server+2.4
issues: http://dev.mygrid.org.uk/issues/browse/TAVSERV
# Note, no anti-spam armouring required for this one
support-contact: supp...@mygrid.org.uk

I'm guessing this information needs to be updated, too?

Gale

On Fri, Sep 2, 2016 at 8:41 AM Stian Soiland-Reyes <
soiland-re...@cs.manchester.ac.uk> wrote:

> Hi,
>
> I've made
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-09+License+review
>
> so we can track license review progress.
>
>
> Anyone is welcome to keep checking/fixing those that are not complete
> - as I've mentioned it's fine to remove the (C) Manchester/LGPL
> headers as they are part oft he software grant.
>
> It should be possible to do the license header updates using the maven
> license plugin rather than a large vim session..
>
> --
> Stian Soiland-Reyes, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/-0001-9842-9718
>

Re: Taverna Player integration ( Apache Taverna Mobile )

[Gale Naylor]

>>In the previous version, the simple button had used to run workflow but I
will use floating action button for it.

FAB will be very cool. Looking forward to it!

On Wed, Aug 17, 2016 at 12:53 PM Gale Naylor 
wrote:

> Regarding target API levels:
>
> >>In
>
> https://github.com/apache/incubator-taverna-mobile/blob/master/app/build.gradle
>
> the min sdk is 16 and  the target 21. I think these translate as Jelly Bean
> and Lollypop respectively
>
> Forgot I could look up the targets in the build.gradle file, but what I
> was really wondering is -- shouldn't this information be in the readme?
>
> On Wed, Aug 17, 2016 at 2:57 AM Sagar  wrote:
>
>> Sorry, i mean taverna player portal, not taverna player .
>>
>

Re: Taverna Player integration ( Apache Taverna Mobile )

[Gale Naylor]

Regarding target API levels:

>>In
https://github.com/apache/incubator-taverna-mobile/blob/master/app/build.gradle
the min sdk is 16 and  the target 21. I think these translate as Jelly Bean
and Lollypop respectively

Forgot I could look up the targets in the build.gradle file, but what I was
really wondering is -- shouldn't this information be in the readme?

On Wed, Aug 17, 2016 at 2:57 AM Sagar  wrote:

> Sorry, i mean taverna player portal, not taverna player .
>

Re: Towards graduation?

[Gale Naylor]

Is there a typical or accepted method for making sure the code (including
dependencies) is licence-clean?

On Sat, Aug 13, 2016 at 10:44 AM Andy Seaborne  wrote:

> On 12/08/16 12:19, Stian Soiland-Reyes wrote:
> > It would be ideal to have the Server and Workbench released as well -
> > but I agree with Ian that should not be a blocker for graduation.
>
> It would be good to make sure the code is licence-clean, including
> dependencies.
>
> All the code does not have to have been through a release as far as i
> know but repo needs to be "clean" and this would be proof of that.
>
>  Andy
>
>

Re: Towards graduation?

[Gale Naylor]

Sounds good to me. What does everyone else think?

Once we decide to go for it, should we fill out the graduation assessment
form? Or?

On Thu, Aug 11, 2016 at 8:51 AM Ian Dunlop  wrote:

> Hello,
>
> I don't think we need to release the server or workbench to consider
> graduation. I think Taverna is ready now. We don't want to hover in that
> perpetual state of "just one more bit of functionality" (you know like you
> always wait to buy a new laptop or phone because the next version has the
> new widgetron that makes life amazing).
> I guess in a nutshell the workbench is the UI that can be used to design
> and run workflows interactively rather than via the command line. The
> server allows you to run workflows on a remote machine. I think the current
> code gives enough of the functionality that we should just go for it :)
>
> Cheers,
>
> Ian
>
> On 11 August 2016 at 16:46, Gale Naylor 
> wrote:
>
> > Thanks, Donal, for the description of Server issues that need to be
> > addressed.
> >
> > On Thu, Aug 11, 2016 at 8:45 AM Gale Naylor  >
> > wrote:
> >
> > > I was thinking it would make sense to fill out the Graduation Maturity
> > > Assessment (
> > > https://cwiki.apache.org/confluence/display/TAVERNADEV/
> > 2016-03+Taverna+Graduation+Maturity+Assessment)
> > > and then evaluate where we think we are relative to graduation.
> > > Interestingly, at least the way I read the maturity assessment, it's
> > geared
> > > more towards process and structure (also important) rather than
> released
> > > content - specifically, it doesn't mention how much of the code we want
> > to
> > > release and doesn't mention soft goals, such as engagement.
> > >
> > > Perhaps we should add something about released content to the
> assessment?
> > >
> > > Shall we plan to release the Server and evaluate engagement at that
> time
> > > (with an eye toward graduation) or do we think we need to release the
> > > Workbench as well? (Are we talking user engagement vs developer
> > > engagement?) I'd love to know what specific user functionality is added
> > > with the Server and what will not be available until we release the
> > > Workbench.
> > >
> > > Gale
> > >
> > >
> > >
> > > On Wed, Aug 10, 2016 at 7:56 AM Donal K. Fellows <
> > > donal.k.fell...@manchester.ac.uk> wrote:
> > >
> > >> On 08/08/2016 20:31, Andy Seaborne wrote:
> > >> > What do others on the PPMC think?
> > >> [...]
> > >> >>> I remember we said the 3 most important points were
> > >> >>>
> > >> >>>   1. Community growth
> > >> >>
> > >> >> Taverna is like many ASF projects - the size of the active (I)PMC
> is
> > >> not
> > >> >> that great.  This, in my experience, is normal.  We hear and see
> the
> > >> ASF
> > >> >> mega-projects but in terms of numbers of projects, they are a
> > minority.
> > >> >>
> > >> >> It would be good to see some of the IPMC active. The critical thing
> > >> here
> > >> >> is whether people are available to get releases out, not "3 days,
> > now"
> > >> >> but "in the next month could you...".
> > >>
> > >> At the moment, my workload is pretty high with other things going on,
> so
> > >> I can only occasionally pay proper attention here. I'm afraid I've
> been
> > >> relying on others to pick things up and let me know explicitly when my
> > >> input is desired, and that's a bit naughty of me.
> > >>
> > >> I'll parachute effort and attention in when I can.
> > >>
> > >> >>>   2. Release more of the imported code to create engagement
> > >> >>
> > >> >> What is the current state of imported/released?
> > >>
> > >> There are two main items out of the imported set that haven't yet made
> > >> it to release: the Server and the Workbench. With the Server, I think
> > >> the effort to release it isn't too massive, under the assumption that
> we
> > >> don't take on doing a huge functionality revision. While there's some
> > >> bits that need work, I'm guessing that it isn't too much unless we go
> > >> for some of the more elaborate i

Re: Apache Taverna Commandline

[Gale Naylor]

Here are a couple of links that might help you test the Java Doc fixes:

http://docs.oracle.com/javase/7/docs/technotes/tools/windows/javadoc.html

https://maven.apache.org/plugins/maven-javadoc-plugin/test-javadoc-mojo.html

On Thu, Aug 11, 2016 at 8:50 AM Gale Naylor 
wrote:

> Hi Chamini,
>
> Were you able to generate the Java Doc errors in Eclipse without errors?
>
> Gale
>
> On Wed, Aug 3, 2016 at 6:56 PM Gale Naylor 
> wrote:
>
>> Thank you for clarifying, Chamini!
>>
>> The Java Doc warnings listed in Taverna 982 occurred when the
>> Command-line Tool was being BUILT, not when it was running. The
>> Command-line Tool actually RUNS without errors (at least on the Hello World
>> example in the README file).
>>
>> If you are using an IDE, like Eclipse, can you generate the Java Docs
>> using Eclipse and see that there are no errors?
>>
>> I'm not sure how else to test that the issues have been resolved. Anyone
>> else have any suggestions?
>>
>> Gale
>>
>> On Wed, Aug 3, 2016 at 5:32 PM Chamini Prashakthi Jayasinghe <
>> webcha...@gmail.com> wrote:
>>
>>> Gale,
>>> I tried to test case because i worked on Taverna 982 bug.How could i know
>>> the correctness of my code without running testcases.
>>> Regards Chamini
>>>
>>>
>>> On Thu, Aug 4, 2016 at 5:57 AM, Chamini Prashakthi Jayasinghe <
>>> webcha...@gmail.com> wrote:
>>>
>>> > hI,
>>> > I got this kind of errors after run the testcase without comment mark.
>>> > Error:(32, 43) java:
>>> > org.apache.taverna.commandline.options.CommandLineOptions is abstract;
>>> > cannot be instantiated
>>> > Error:(35, 70) java: cannot find symbol
>>> >   symbol:   variable DataManagementConfiguration
>>> >   location: class
>>> > org.apache.taverna.commandline.TestDatabaseConfigurationHandler
>>> > Error:(36, 37) java: cannot find symbol
>>> >   symbol:   variable DataManagementConfiguration
>>> >   location: class
>>> > org.apache.taverna.commandline.TestDatabaseConfigurationHandler
>>> >
>>> > Regards chamini
>>> >
>>> > On Thu, Aug 4, 2016 at 5:53 AM, Gale Naylor <
>>> ga...@noventussolutions.com>
>>> > wrote:
>>> >
>>> >> I think Chamini is getting errors AFTER un-commenting all the code in
>>> >> the TestDatabaseConfigurationHandler
>>> >> class. https://github.com/apache/
>>> >>
>>> >>
>>> incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
>>> >>
>>> >> I presume the code was commented out for a good reason (thus the
>>> errors),
>>> >> and I wonder why the TestDatabaseConfigurationHandler.java file is
>>> >> included
>>> >> in the distribution if all the code is commented out.
>>> >>
>>> >> Chamini, the README file (
>>> >>
>>> >>
>>> https://github.com/apache/incubator-taverna-commandline/blob/master/README.md
>>> >> )
>>> >> contains an example of using the command-line tool. Does this help? If
>>> >> not,
>>> >> can you provide a little more information about what you are trying to
>>> >> test
>>> >> and why?
>>> >>
>>> >> Thanks,
>>> >>
>>> >> Gale
>>> >>
>>> >>
>>> >> On Wed, Aug 3, 2016 at 11:30 AM Gale Naylor <
>>> ga...@noventussolutions.com>
>>> >> wrote:
>>> >>
>>> >> > I'm wondering why the class TestDatabaseConfigurationHandler is
>>> >> commented
>>> >> > out...
>>> >> >
>>> >> >
>>> >> >
>>> >>
>>> https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
>>> >> >
>>> >> >
>>> >> > On Wed, Aug 3, 2016 at 10:19 AM Alan Williams <
>>> alanin...@googlemail.com
>>> >> >
>>> >> > wrote:
>>> >> >
>>> >> >> On 03-Aug-16 03:50, Chamini Prashakthi Jayasinghe wrote:
>>> >> >> > Hi all,
>>> >> >> > can someone explain me how to run the test case in Apache Taverna
>>> >> >> > Commandline common module.it is all commented and after remove
>>> >> comment
>>> >> >> mark
>>> >> >> > it shows errors.
>>> >> >>
>>> >> >> What errors are you getting?
>>> >> >>
>>> >> >> > regards chamini
>>> >> >>
>>> >> >> Alan
>>> >> >>
>>> >> >>
>>> >>
>>> >
>>> >
>>>
>>

Re: Apache Taverna Commandline

[Gale Naylor]

Hi Chamini,

Were you able to generate the Java Doc errors in Eclipse without errors?

Gale

On Wed, Aug 3, 2016 at 6:56 PM Gale Naylor 
wrote:

> Thank you for clarifying, Chamini!
>
> The Java Doc warnings listed in Taverna 982 occurred when the Command-line
> Tool was being BUILT, not when it was running. The Command-line Tool
> actually RUNS without errors (at least on the Hello World example in the
> README file).
>
> If you are using an IDE, like Eclipse, can you generate the Java Docs
> using Eclipse and see that there are no errors?
>
> I'm not sure how else to test that the issues have been resolved. Anyone
> else have any suggestions?
>
> Gale
>
> On Wed, Aug 3, 2016 at 5:32 PM Chamini Prashakthi Jayasinghe <
> webcha...@gmail.com> wrote:
>
>> Gale,
>> I tried to test case because i worked on Taverna 982 bug.How could i know
>> the correctness of my code without running testcases.
>> Regards Chamini
>>
>>
>> On Thu, Aug 4, 2016 at 5:57 AM, Chamini Prashakthi Jayasinghe <
>> webcha...@gmail.com> wrote:
>>
>> > hI,
>> > I got this kind of errors after run the testcase without comment mark.
>> > Error:(32, 43) java:
>> > org.apache.taverna.commandline.options.CommandLineOptions is abstract;
>> > cannot be instantiated
>> > Error:(35, 70) java: cannot find symbol
>> >   symbol:   variable DataManagementConfiguration
>> >   location: class
>> > org.apache.taverna.commandline.TestDatabaseConfigurationHandler
>> > Error:(36, 37) java: cannot find symbol
>> >   symbol:   variable DataManagementConfiguration
>> >   location: class
>> > org.apache.taverna.commandline.TestDatabaseConfigurationHandler
>> >
>> > Regards chamini
>> >
>> > On Thu, Aug 4, 2016 at 5:53 AM, Gale Naylor <
>> ga...@noventussolutions.com>
>> > wrote:
>> >
>> >> I think Chamini is getting errors AFTER un-commenting all the code in
>> >> the TestDatabaseConfigurationHandler
>> >> class. https://github.com/apache/
>> >>
>> >>
>> incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
>> >>
>> >> I presume the code was commented out for a good reason (thus the
>> errors),
>> >> and I wonder why the TestDatabaseConfigurationHandler.java file is
>> >> included
>> >> in the distribution if all the code is commented out.
>> >>
>> >> Chamini, the README file (
>> >>
>> >>
>> https://github.com/apache/incubator-taverna-commandline/blob/master/README.md
>> >> )
>> >> contains an example of using the command-line tool. Does this help? If
>> >> not,
>> >> can you provide a little more information about what you are trying to
>> >> test
>> >> and why?
>> >>
>> >> Thanks,
>> >>
>> >> Gale
>> >>
>> >>
>> >> On Wed, Aug 3, 2016 at 11:30 AM Gale Naylor <
>> ga...@noventussolutions.com>
>> >> wrote:
>> >>
>> >> > I'm wondering why the class TestDatabaseConfigurationHandler is
>> >> commented
>> >> > out...
>> >> >
>> >> >
>> >> >
>> >>
>> https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
>> >> >
>> >> >
>> >> > On Wed, Aug 3, 2016 at 10:19 AM Alan Williams <
>> alanin...@googlemail.com
>> >> >
>> >> > wrote:
>> >> >
>> >> >> On 03-Aug-16 03:50, Chamini Prashakthi Jayasinghe wrote:
>> >> >> > Hi all,
>> >> >> > can someone explain me how to run the test case in Apache Taverna
>> >> >> > Commandline common module.it is all commented and after remove
>> >> comment
>> >> >> mark
>> >> >> > it shows errors.
>> >> >>
>> >> >> What errors are you getting?
>> >> >>
>> >> >> > regards chamini
>> >> >>
>> >> >> Alan
>> >> >>
>> >> >>
>> >>
>> >
>> >
>>
>

Re: Towards graduation?

[Gale Naylor]

Thanks, Donal, for the description of Server issues that need to be
addressed.

On Thu, Aug 11, 2016 at 8:45 AM Gale Naylor 
wrote:

> I was thinking it would make sense to fill out the Graduation Maturity
> Assessment (
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+Taverna+Graduation+Maturity+Assessment)
> and then evaluate where we think we are relative to graduation.
> Interestingly, at least the way I read the maturity assessment, it's geared
> more towards process and structure (also important) rather than released
> content - specifically, it doesn't mention how much of the code we want to
> release and doesn't mention soft goals, such as engagement.
>
> Perhaps we should add something about released content to the assessment?
>
> Shall we plan to release the Server and evaluate engagement at that time
> (with an eye toward graduation) or do we think we need to release the
> Workbench as well? (Are we talking user engagement vs developer
> engagement?) I'd love to know what specific user functionality is added
> with the Server and what will not be available until we release the
> Workbench.
>
> Gale
>
>
>
> On Wed, Aug 10, 2016 at 7:56 AM Donal K. Fellows <
> donal.k.fell...@manchester.ac.uk> wrote:
>
>> On 08/08/2016 20:31, Andy Seaborne wrote:
>> > What do others on the PPMC think?
>> [...]
>> >>> I remember we said the 3 most important points were
>> >>>
>> >>>   1. Community growth
>> >>
>> >> Taverna is like many ASF projects - the size of the active (I)PMC is
>> not
>> >> that great.  This, in my experience, is normal.  We hear and see the
>> ASF
>> >> mega-projects but in terms of numbers of projects, they are a minority.
>> >>
>> >> It would be good to see some of the IPMC active. The critical thing
>> here
>> >> is whether people are available to get releases out, not "3 days, now"
>> >> but "in the next month could you...".
>>
>> At the moment, my workload is pretty high with other things going on, so
>> I can only occasionally pay proper attention here. I'm afraid I've been
>> relying on others to pick things up and let me know explicitly when my
>> input is desired, and that's a bit naughty of me.
>>
>> I'll parachute effort and attention in when I can.
>>
>> >>>   2. Release more of the imported code to create engagement
>> >>
>> >> What is the current state of imported/released?
>>
>> There are two main items out of the imported set that haven't yet made
>> it to release: the Server and the Workbench. With the Server, I think
>> the effort to release it isn't too massive, under the assumption that we
>> don't take on doing a huge functionality revision. While there's some
>> bits that need work, I'm guessing that it isn't too much unless we go
>> for some of the more elaborate ideas that we've mooted in the past (and
>> I'm not convinced any more that they're the right way).
>>
>> Concretely, the key things are:
>>
>>* Review the internal message bus mechanism for security. JRMP is
>>  convenient, but it requires very tight security and isn't really
>>  designed to work that way. Attention required and not just from me
>>  because I'm probably too close to the existing code to see any dumb
>>  problems in it.
>>
>>* Reworking the server so that it supports something less horrible
>>  than baclava files for packaged data import and export. For export,
>>  most people have been just downloading zip files, but the import
>>  side is more of an issue.
>>
>>* Throw out the mess that was the listeners and the notification
>>  mechanism. That never really worked right. The bits that did work
>>  are already mostly partially elsewhere, but we ought to clear this
>>  bit of swamp instead of keeping the alligators for ass-backward
>>  compatibility reasons.
>>
>> Aside from the usual release engineering stuff (license checks, etc) of
>> course.
>>
>> The Workbench is a whole different problem.
>>
>> Donal.
>>
>

Re: Towards graduation?

[Gale Naylor]

I was thinking it would make sense to fill out the Graduation Maturity
Assessment (
https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+Taverna+Graduation+Maturity+Assessment)
and then evaluate where we think we are relative to graduation.
Interestingly, at least the way I read the maturity assessment, it's geared
more towards process and structure (also important) rather than released
content - specifically, it doesn't mention how much of the code we want to
release and doesn't mention soft goals, such as engagement.

Perhaps we should add something about released content to the assessment?

Shall we plan to release the Server and evaluate engagement at that time
(with an eye toward graduation) or do we think we need to release the
Workbench as well? (Are we talking user engagement vs developer
engagement?) I'd love to know what specific user functionality is added
with the Server and what will not be available until we release the
Workbench.

Gale



On Wed, Aug 10, 2016 at 7:56 AM Donal K. Fellows <
donal.k.fell...@manchester.ac.uk> wrote:

> On 08/08/2016 20:31, Andy Seaborne wrote:
> > What do others on the PPMC think?
> [...]
> >>> I remember we said the 3 most important points were
> >>>
> >>>   1. Community growth
> >>
> >> Taverna is like many ASF projects - the size of the active (I)PMC is not
> >> that great.  This, in my experience, is normal.  We hear and see the ASF
> >> mega-projects but in terms of numbers of projects, they are a minority.
> >>
> >> It would be good to see some of the IPMC active. The critical thing here
> >> is whether people are available to get releases out, not "3 days, now"
> >> but "in the next month could you...".
>
> At the moment, my workload is pretty high with other things going on, so
> I can only occasionally pay proper attention here. I'm afraid I've been
> relying on others to pick things up and let me know explicitly when my
> input is desired, and that's a bit naughty of me.
>
> I'll parachute effort and attention in when I can.
>
> >>>   2. Release more of the imported code to create engagement
> >>
> >> What is the current state of imported/released?
>
> There are two main items out of the imported set that haven't yet made
> it to release: the Server and the Workbench. With the Server, I think
> the effort to release it isn't too massive, under the assumption that we
> don't take on doing a huge functionality revision. While there's some
> bits that need work, I'm guessing that it isn't too much unless we go
> for some of the more elaborate ideas that we've mooted in the past (and
> I'm not convinced any more that they're the right way).
>
> Concretely, the key things are:
>
>* Review the internal message bus mechanism for security. JRMP is
>  convenient, but it requires very tight security and isn't really
>  designed to work that way. Attention required and not just from me
>  because I'm probably too close to the existing code to see any dumb
>  problems in it.
>
>* Reworking the server so that it supports something less horrible
>  than baclava files for packaged data import and export. For export,
>  most people have been just downloading zip files, but the import
>  side is more of an issue.
>
>* Throw out the mess that was the listeners and the notification
>  mechanism. That never really worked right. The bits that did work
>  are already mostly partially elsewhere, but we ought to clear this
>  bit of swamp instead of keeping the alligators for ass-backward
>  compatibility reasons.
>
> Aside from the usual release engineering stuff (license checks, etc) of
> course.
>
> The Workbench is a whole different problem.
>
> Donal.
>

Re: CWL code questions

[Gale Naylor]

Hi Alan,

Thank you for the explanation and the link. It makes much more sense now.

Gale

On Fri, Aug 5, 2016 at 1:23 PM Alan Williams 
wrote:

> On 05-Aug-16 18:42, Gale Naylor wrote:
>
> Hello Gale
>
> > In CwlContextualView.java (I used the wrong filename in my previous
> email)
> > I'm also curious about the two private, final (but not static) constants
> > (?): configurationBean and activity.
> >
> > I'm not sure this StackOverflow answer is 100% relevant because
> > configurationBean and activity do not have initial values, but this is
> all
> > I've been able to find online:
> >
> http://stackoverflow.com/questions/1415955/private-final-static-attribute-vs-private-final-attribute
>
> If an attribute is not static then each instance of the class has its
> own attribute. So,
>
> private final CwlActivityConfigurationBean configurationBean;
>
> means that each CwlContextualView has its own configurationBean value.
>
> If an attribute is declared as static, then all instances of the class
> share the same attribute value.
>
> The private means that the value of the configurationBean cannot be
> accessed (directly) outside of the CwlContextualView. So
>
> fred = myCwlContextualView.configurationBean // will not work
>
> The final means that once the attribute has a value it cannot be
> changed. Even stronger, the value must be specified either in the
> declaration of the attribute, or when you construct an instance of
> CwlContextualView. (There are weird exceptions to the last sentence that
> are best ignored and never mentioned in polite company.)
>
> If you look at
>
> public CwlContextualView(CwlDumyActivity activity)
>
> which makes a CwlContextualView, it contains the line:
>
> this.configurationBean = activity.getConfiguration();
>
> So once you have made a CwlConfigurationView, it has a configurationBean
> attribute, that nothing else can see, and that has a fixed value.
>
> > Can anyone point me to information that would help me understand this
> > nomenclature?
>
> I think
>
> http://stackoverflow.com/questions/13772827/difference-between-static-and-final
> explains static and final well.
>
> > Thanks,
> >
> > Gale
>
> Alan
>
>

Re: CWL code questions

[Gale Naylor]

In CwlContextualView.java, should cwutil be cwlUtil?

Also, I notice in this CWL User Guide (
http://www.commonwl.org/draft-3/UserGuide.html ) it says the basecommand
field comes before the input and output parameters.

Gale

On Fri, Aug 5, 2016 at 10:42 AM Gale Naylor 
wrote:

> In CwlContextualView.java (I used the wrong filename in my previous email)
> I'm also curious about the two private, final (but not static) constants
> (?): configurationBean and activity.
>
> I'm not sure this StackOverflow answer is 100% relevant because
> configurationBean and activity do not have initial values, but this is all
> I've been able to find online:
> http://stackoverflow.com/questions/1415955/private-final-static-attribute-vs-private-final-attribute
> .
>
> Can anyone point me to information that would help me understand this
> nomenclature?
>
> Thanks,
>
> Gale
>
> On Fri, Aug 5, 2016 at 10:24 AM Gale Naylor 
> wrote:
>
>> I have a couple of additional questions/observations about the CWL code.
>>
>> In CwlContextView.java:
>>
>> - Starting in line 101, is a String called "summery" - I think this may
>> mean "summary". (It looks like the CWL configuration information is being
>> summarized here.)
>>
>> - I'm wondering if in lines 121 and 122 it's permissible to use the
>> DESCRIPTION constant instead of the hard-coded value "description"?
>>
>> Thanks,
>>
>> Gale
>>
>> On Thu, Aug 4, 2016 at 5:56 AM Gale Naylor 
>> wrote:
>>
>>> Great!
>>>
>>> Gale
>>>
>>> On Wed, Aug 3, 2016, 9:22 PM Thilina Manamgoda 
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Thanks for pointing that out. I have fixed them
>>>> https://github.com/apache/incubator-taverna-common-activities/pull/13
>>>>
>>>> Thanks !
>>>>
>>>> On Thu, Aug 4, 2016 at 12:18 AM, Gale Naylor <
>>>> ga...@noventussolutions.com>
>>>> wrote:
>>>>
>>>> > I have a couple of questions about the CWL code.
>>>> >
>>>> > (1) In CwlServiceDesc.java, line 50:
>>>> > Should CwlDumyActivity.class be called CwlDummyActivity.class?
>>>> > (Because it looks like the code creates a "dummy" class.)
>>>> >
>>>> > (2) In CwlServiceProvider.java, lines 47 and 48:
>>>> > Should the constant names be upper case? e.g., PROVIDER_NAME and
>>>> > PROVIDER_ID?
>>>> >
>>>> > Thanks!
>>>> > Gale
>>>> >
>>>>
>>>

Re: CWL code questions

[Gale Naylor]

In CwlContextualView.java (I used the wrong filename in my previous email)
I'm also curious about the two private, final (but not static) constants
(?): configurationBean and activity.

I'm not sure this StackOverflow answer is 100% relevant because
configurationBean and activity do not have initial values, but this is all
I've been able to find online:
http://stackoverflow.com/questions/1415955/private-final-static-attribute-vs-private-final-attribute
.

Can anyone point me to information that would help me understand this
nomenclature?

Thanks,

Gale

On Fri, Aug 5, 2016 at 10:24 AM Gale Naylor 
wrote:

> I have a couple of additional questions/observations about the CWL code.
>
> In CwlContextView.java:
>
> - Starting in line 101, is a String called "summery" - I think this may
> mean "summary". (It looks like the CWL configuration information is being
> summarized here.)
>
> - I'm wondering if in lines 121 and 122 it's permissible to use the
> DESCRIPTION constant instead of the hard-coded value "description"?
>
> Thanks,
>
> Gale
>
> On Thu, Aug 4, 2016 at 5:56 AM Gale Naylor 
> wrote:
>
>> Great!
>>
>> Gale
>>
>> On Wed, Aug 3, 2016, 9:22 PM Thilina Manamgoda 
>> wrote:
>>
>>> Hi,
>>>
>>> Thanks for pointing that out. I have fixed them
>>> https://github.com/apache/incubator-taverna-common-activities/pull/13
>>>
>>> Thanks !
>>>
>>> On Thu, Aug 4, 2016 at 12:18 AM, Gale Naylor <
>>> ga...@noventussolutions.com>
>>> wrote:
>>>
>>> > I have a couple of questions about the CWL code.
>>> >
>>> > (1) In CwlServiceDesc.java, line 50:
>>> > Should CwlDumyActivity.class be called CwlDummyActivity.class?
>>> > (Because it looks like the code creates a "dummy" class.)
>>> >
>>> > (2) In CwlServiceProvider.java, lines 47 and 48:
>>> > Should the constant names be upper case? e.g., PROVIDER_NAME and
>>> > PROVIDER_ID?
>>> >
>>> > Thanks!
>>> > Gale
>>> >
>>>
>>

Re: CWL code questions

[Gale Naylor]

I have a couple of additional questions/observations about the CWL code.

In CwlContextView.java:

- Starting in line 101, is a String called "summery" - I think this may
mean "summary". (It looks like the CWL configuration information is being
summarized here.)

- I'm wondering if in lines 121 and 122 it's permissible to use the
DESCRIPTION constant instead of the hard-coded value "description"?

Thanks,

Gale

On Thu, Aug 4, 2016 at 5:56 AM Gale Naylor 
wrote:

> Great!
>
> Gale
>
> On Wed, Aug 3, 2016, 9:22 PM Thilina Manamgoda 
> wrote:
>
>> Hi,
>>
>> Thanks for pointing that out. I have fixed them
>> https://github.com/apache/incubator-taverna-common-activities/pull/13
>>
>> Thanks !
>>
>> On Thu, Aug 4, 2016 at 12:18 AM, Gale Naylor > >
>> wrote:
>>
>> > I have a couple of questions about the CWL code.
>> >
>> > (1) In CwlServiceDesc.java, line 50:
>> > Should CwlDumyActivity.class be called CwlDummyActivity.class?
>> > (Because it looks like the code creates a "dummy" class.)
>> >
>> > (2) In CwlServiceProvider.java, lines 47 and 48:
>> > Should the constant names be upper case? e.g., PROVIDER_NAME and
>> > PROVIDER_ID?
>> >
>> > Thanks!
>> > Gale
>> >
>>
>

Re: CWL code questions

[Gale Naylor]

Great!

Gale

On Wed, Aug 3, 2016, 9:22 PM Thilina Manamgoda 
wrote:

> Hi,
>
> Thanks for pointing that out. I have fixed them
> https://github.com/apache/incubator-taverna-common-activities/pull/13
>
> Thanks !
>
> On Thu, Aug 4, 2016 at 12:18 AM, Gale Naylor 
> wrote:
>
> > I have a couple of questions about the CWL code.
> >
> > (1) In CwlServiceDesc.java, line 50:
> > Should CwlDumyActivity.class be called CwlDummyActivity.class?
> > (Because it looks like the code creates a "dummy" class.)
> >
> > (2) In CwlServiceProvider.java, lines 47 and 48:
> > Should the constant names be upper case? e.g., PROVIDER_NAME and
> > PROVIDER_ID?
> >
> > Thanks!
> > Gale
> >
>

Re: Apache Taverna Commandline

[Gale Naylor]

Thank you for clarifying, Chamini!

The Java Doc warnings listed in Taverna 982 occurred when the Command-line
Tool was being BUILT, not when it was running. The Command-line Tool
actually RUNS without errors (at least on the Hello World example in the
README file).

If you are using an IDE, like Eclipse, can you generate the Java Docs using
Eclipse and see that there are no errors?

I'm not sure how else to test that the issues have been resolved. Anyone
else have any suggestions?

Gale

On Wed, Aug 3, 2016 at 5:32 PM Chamini Prashakthi Jayasinghe <
webcha...@gmail.com> wrote:

> Gale,
> I tried to test case because i worked on Taverna 982 bug.How could i know
> the correctness of my code without running testcases.
> Regards Chamini
>
>
> On Thu, Aug 4, 2016 at 5:57 AM, Chamini Prashakthi Jayasinghe <
> webcha...@gmail.com> wrote:
>
> > hI,
> > I got this kind of errors after run the testcase without comment mark.
> > Error:(32, 43) java:
> > org.apache.taverna.commandline.options.CommandLineOptions is abstract;
> > cannot be instantiated
> > Error:(35, 70) java: cannot find symbol
> >   symbol:   variable DataManagementConfiguration
> >   location: class
> > org.apache.taverna.commandline.TestDatabaseConfigurationHandler
> > Error:(36, 37) java: cannot find symbol
> >   symbol:   variable DataManagementConfiguration
> >   location: class
> > org.apache.taverna.commandline.TestDatabaseConfigurationHandler
> >
> > Regards chamini
> >
> > On Thu, Aug 4, 2016 at 5:53 AM, Gale Naylor  >
> > wrote:
> >
> >> I think Chamini is getting errors AFTER un-commenting all the code in
> >> the TestDatabaseConfigurationHandler
> >> class. https://github.com/apache/
> >>
> >>
> incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
> >>
> >> I presume the code was commented out for a good reason (thus the
> errors),
> >> and I wonder why the TestDatabaseConfigurationHandler.java file is
> >> included
> >> in the distribution if all the code is commented out.
> >>
> >> Chamini, the README file (
> >>
> >>
> https://github.com/apache/incubator-taverna-commandline/blob/master/README.md
> >> )
> >> contains an example of using the command-line tool. Does this help? If
> >> not,
> >> can you provide a little more information about what you are trying to
> >> test
> >> and why?
> >>
> >> Thanks,
> >>
> >> Gale
> >>
> >>
> >> On Wed, Aug 3, 2016 at 11:30 AM Gale Naylor <
> ga...@noventussolutions.com>
> >> wrote:
> >>
> >> > I'm wondering why the class TestDatabaseConfigurationHandler is
> >> commented
> >> > out...
> >> >
> >> >
> >> >
> >>
> https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
> >> >
> >> >
> >> > On Wed, Aug 3, 2016 at 10:19 AM Alan Williams <
> alanin...@googlemail.com
> >> >
> >> > wrote:
> >> >
> >> >> On 03-Aug-16 03:50, Chamini Prashakthi Jayasinghe wrote:
> >> >> > Hi all,
> >> >> > can someone explain me how to run the test case in Apache Taverna
> >> >> > Commandline common module.it is all commented and after remove
> >> comment
> >> >> mark
> >> >> > it shows errors.
> >> >>
> >> >> What errors are you getting?
> >> >>
> >> >> > regards chamini
> >> >>
> >> >> Alan
> >> >>
> >> >>
> >>
> >
> >
>

Re: Apache Taverna Commandline

[Gale Naylor]

I think Chamini is getting errors AFTER un-commenting all the code in
the TestDatabaseConfigurationHandler
class. https://github.com/apache/
incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java

I presume the code was commented out for a good reason (thus the errors),
and I wonder why the TestDatabaseConfigurationHandler.java file is included
in the distribution if all the code is commented out.

Chamini, the README file (
https://github.com/apache/incubator-taverna-commandline/blob/master/README.md)
contains an example of using the command-line tool. Does this help? If not,
can you provide a little more information about what you are trying to test
and why?

Thanks,

Gale


On Wed, Aug 3, 2016 at 11:30 AM Gale Naylor 
wrote:

> I'm wondering why the class TestDatabaseConfigurationHandler is commented
> out...
>
>
> https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java
>
>
> On Wed, Aug 3, 2016 at 10:19 AM Alan Williams 
> wrote:
>
>> On 03-Aug-16 03:50, Chamini Prashakthi Jayasinghe wrote:
>> > Hi all,
>> > can someone explain me how to run the test case in Apache Taverna
>> > Commandline common module.it is all commented and after remove comment
>> mark
>> > it shows errors.
>>
>> What errors are you getting?
>>
>> > regards chamini
>>
>> Alan
>>
>>

CWL code questions

[Gale Naylor]

I have a couple of questions about the CWL code.

(1) In CwlServiceDesc.java, line 50:
Should CwlDumyActivity.class be called CwlDummyActivity.class?
(Because it looks like the code creates a "dummy" class.)

(2) In CwlServiceProvider.java, lines 47 and 48:
Should the constant names be upper case? e.g., PROVIDER_NAME and
PROVIDER_ID?

Thanks!
Gale

Re: [jira] [Updated] (TAVERNA-1007) warnings in javadoc in taverna command line tool

[Gale Naylor]

The links all seem to work. I wonder what is causing the Java Doc errors.
Anyone seen something like this before?

On Wed, Aug 3, 2016 at 11:36 AM Gale Naylor (JIRA)  wrote:

>
>  [
> https://issues.apache.org/jira/browse/TAVERNA-1007?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
> ]
>
> Gale Naylor updated TAVERNA-1007:
> -
> Description:
> In addition to javadoc warnings in Taverna 982, there are some other
> javadoc warnings in the command line tool.
> fix them
> [WARNING] Javadoc Warnings
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-language/
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-osgi/
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-engine/
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-common-activities/
>
>   was:
> except taverna 982 bug of warnings there are some anothere javadoc
> warnings in the command line tool.
> fix them
> [WARNING] Javadoc Warnings
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-language/
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-osgi/
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-engine/
> [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-common-activities/
>
>
> > warnings in javadoc in taverna command line tool
> > 
> >
> > Key: TAVERNA-1007
> > URL: https://issues.apache.org/jira/browse/TAVERNA-1007
> > Project: Apache Taverna
> >  Issue Type: Bug
> >  Components: Taverna Command-line Tool
> >Affects Versions: command-line 3.1.0
> > Environment: java doc
> >Reporter: Chamini Prashakthi
> >  Labels: build
> > Fix For: command-line 3.1.0
> >
> >
> > In addition to javadoc warnings in Taverna 982, there are some other
> javadoc warnings in the command line tool.
> > fix them
> > [WARNING] Javadoc Warnings
> > [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-language/
> > [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-osgi/
> > [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-engine/
> > [WARNING] javadoc: warning - Error fetching URL:
> https://taverna.incubator.apache.org/javadoc/taverna-common-activities/
>
>
>
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>

[jira] [Updated] (TAVERNA-1007) warnings in javadoc in taverna command line tool

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-1007?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-1007:
-
Description: 
In addition to javadoc warnings in Taverna 982, there are some other javadoc 
warnings in the command line tool.
fix them
[WARNING] Javadoc Warnings
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-language/
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-osgi/
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-engine/
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-common-activities/

  was:
except taverna 982 bug of warnings there are some anothere javadoc warnings in 
the command line tool.
fix them
[WARNING] Javadoc Warnings
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-language/
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-osgi/
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-engine/
[WARNING] javadoc: warning - Error fetching URL: 
https://taverna.incubator.apache.org/javadoc/taverna-common-activities/


> warnings in javadoc in taverna command line tool
> 
>
> Key: TAVERNA-1007
> URL: https://issues.apache.org/jira/browse/TAVERNA-1007
> Project: Apache Taverna
>  Issue Type: Bug
>  Components: Taverna Command-line Tool
>Affects Versions: command-line 3.1.0
> Environment: java doc
>Reporter: Chamini Prashakthi
>  Labels: build
> Fix For: command-line 3.1.0
>
>
> In addition to javadoc warnings in Taverna 982, there are some other javadoc 
> warnings in the command line tool.
> fix them
> [WARNING] Javadoc Warnings
> [WARNING] javadoc: warning - Error fetching URL: 
> https://taverna.incubator.apache.org/javadoc/taverna-language/
> [WARNING] javadoc: warning - Error fetching URL: 
> https://taverna.incubator.apache.org/javadoc/taverna-osgi/
> [WARNING] javadoc: warning - Error fetching URL: 
> https://taverna.incubator.apache.org/javadoc/taverna-engine/
> [WARNING] javadoc: warning - Error fetching URL: 
> https://taverna.incubator.apache.org/javadoc/taverna-common-activities/



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Re: Apache Taverna Commandline

[Gale Naylor]

I'm wondering why the class TestDatabaseConfigurationHandler is commented
out...

https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/test/java/org/apache/taverna/commandline/TestDatabaseConfigurationHandler.java


On Wed, Aug 3, 2016 at 10:19 AM Alan Williams 
wrote:

> On 03-Aug-16 03:50, Chamini Prashakthi Jayasinghe wrote:
> > Hi all,
> > can someone explain me how to run the test case in Apache Taverna
> > Commandline common module.it is all commented and after remove comment
> mark
> > it shows errors.
>
> What errors are you getting?
>
> > regards chamini
>
> Alan
>
>

Re: Wiki access?

[Gale Naylor]

It's kind of up to you. The How-to-article gives you some structure you can
use (if you like the way it's designed). With the blank page you can decide
on your own sections. Either one will work. Just try one and see how you
like it!

Gale

On Thu, Jul 21, 2016 at 10:47 AM Thilina Manamgoda 
wrote:

> HI,
>
>
>  Thank you very much  ! . Which one should i select for tutorial(Upgrading
> Taverna Ui plugin to Taverna version 3) ?. "Blank page" or "How-to article"
> ?
>
> regards,
> Thilina
>
> On Thu, Jul 21, 2016 at 10:42 PM, Gale Naylor  >
> wrote:
>
> > I just added user maanafunedu.
> >
> > Thilina, let me know if you have any problems, but you should now have
> > write access to the wiki.
> >
> > Gale
> >
> > On Thu, Jul 21, 2016, 7:08 AM Stian Soiland-Reyes 
> > wrote:
> >
> > > Gale, could you see if the wiki user maanafunedu have write access to
> > > edit https://cwiki.apache.org/confluence/display/TAVERNADEV ?
> > >
> > > --
> > > Stian Soiland-Reyes
> > > Apache Taverna (incubating), Apache Commons
> > > http://orcid.org/-0001-9842-9718
> > >
> >
>

Re: Wiki access?

[Gale Naylor]

I just added user maanafunedu.

Thilina, let me know if you have any problems, but you should now have
write access to the wiki.

Gale

On Thu, Jul 21, 2016, 7:08 AM Stian Soiland-Reyes  wrote:

> Gale, could you see if the wiki user maanafunedu have write access to
> edit https://cwiki.apache.org/confluence/display/TAVERNADEV ?
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Add new publication?

[Gale Naylor]

Well. Where was my brain yesterday?  :) Thank you, Arzu, I'll just add the
page numbers.

Gale

On Wed, Jul 20, 2016 at 12:28 AM  wrote:

> Dear Gale,
>
> It our paper, it is already in the Taverna publication list :)
>
>
> Regards,
>
> Arzu Tugce Guler
> Leiden University Medical Center
> Center for Proteomics and Metabolomics
> P.O. Box 9600, Zone S3
> 2300 RC Leiden
> The Netherlands
> Tel: +31 (0)71 526 8745
>
>
>
> -Original Message-
> From: Gale Naylor [mailto:ga...@noventussolutions.com]
> Sent: dinsdag 19 juli 2016 21:43
> To: Apache Dev
> Subject: Add new publication?
>
> I saw this publication on the Twitter feed. It looks like a good one to
> add to our publication list:
>
> Arzu Tugce Guler, Cathelijn J.F. Waaijer, Yassene Mohammed, Magnus
> Palmblad. (2016 August).
> **Automating bibliometric analyses using Taverna scientific workflows: A
> tutorial on integrating Web Services.**
> In: *Journal of Informetrics*. **10**(3): 830–841.
> doi:[
>
> doi.org/10.1016/j.joi.2016.05.002](http://dx.doi.org/10.1016/j.joi.2016.05.002)
> <http://doi.org/10.1016/j.joi.2016.05.002%5D(http://dx.doi.org/10.1016/j.joi.2016.05.002)>
> <
> http://doi.org/10.1016/j.joi.2016.05.002%5D(http://dx.doi.org/10.1016/j.joi.2016.05.002)
> >
>
> Direct link:
> http://www.sciencedirect.com/science/article/pii/S1751157716300141
>
> Silent consensus in 48 hours... :)
>
> Thanks,
>
> Gale
>

Add new publication?

[Gale Naylor]

I saw this publication on the Twitter feed. It looks like a good one to add
to our publication list:

Arzu Tugce Guler, Cathelijn J.F. Waaijer, Yassene Mohammed, Magnus
Palmblad. (2016 August).
**Automating bibliometric analyses using Taverna scientific workflows: A
tutorial on integrating Web Services.**
In: *Journal of Informetrics*. **10**(3): 830–841.
doi:[
doi.org/10.1016/j.joi.2016.05.002](http://dx.doi.org/10.1016/j.joi.2016.05.002)


Direct link:
http://www.sciencedirect.com/science/article/pii/S1751157716300141

Silent consensus in 48 hours... :)

Thanks,

Gale

Re: Update notice on Maven repo page?

[Gale Naylor]

Okay. I'll take care of that today.

On Fri, Jul 15, 2016, 12:05 AM Stian Soiland-Reyes  wrote:

> Yes, I think that disclaimer would be misleading and should be removed.
> There might be others around the pages, Christian added them whenever a
> page was "ahead of its code" in a way.
>
> We should keep the section about 2.5 pre-Apache mygrid repo, as that is
> needed for Workbench 2.5 plugins (e.g. as some of the student projects are
> doing).
>
> On 14 Jul 2016 12:31 a.m., "Gale Naylor" 
> wrote:
>
> > Currently the Maven repository page (
> > https://taverna.incubator.apache.org/download/maven/) has a disclaimer
> > that
> > reads, in part:
> >
> > Currently there is no Apache release of any Taverna products.
> >
> > Would it be appropriate to update this now to reflect the release of the
> > Command-line Tool, or should we just leave it until after the next
> > release(s)?
> >
> > Gale
> >
>

Re: [jira] [Commented] (TAVERNA-998) Fix compile errors in taverna-workbench-impl

[Gale Naylor]

Since users tended not to register, do you think they may be more inclined
to follow Taverna on Twitter? If so, we could use Twitter for announcements.

On Thu, Jul 14, 2016 at 8:55 AM Alan Williams 
wrote:

> On 14-Jul-16 16:03, Gale Naylor wrote:
> > Just wondering: Are users required to register somewhere else?
>
> Elsewhere in Taverna - no. Registration was always optional in the
> workbench, so most users did not register :-)
>
> There is a "notice" capability in the Taverna 2.* workbench that pops up
> a message if we had anything important to announce. I am not sure if
> that is still in Taverna 3 workbench. We would have to decide where it
> read the notice from.
>
> Alan
>
>
>

Re: [jira] [Commented] (TAVERNA-998) Fix compile errors in taverna-workbench-impl

[Gale Naylor]

Just wondering: Are users required to register somewhere else?

On Thu, Jul 14, 2016, 7:14 AM Stian Soiland-Reyes (JIRA) 
wrote:

>
> [
> https://issues.apache.org/jira/browse/TAVERNA-998?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15376987#comment-15376987
> ]
>
> Stian Soiland-Reyes commented on TAVERNA-998:
> -
>
> Solved by removing all the User Registration code - I don't think we want
> to do user registration pop-ups as Apache software?
>
> > Fix compile errors in taverna-workbench-impl
> > 
> >
> > Key: TAVERNA-998
> > URL: https://issues.apache.org/jira/browse/TAVERNA-998
> > Project: Apache Taverna
> >  Issue Type: Sub-task
> >  Components: Taverna Workbench
> >Affects Versions: workbench 3.1.0
> >Reporter: Stian Soiland-Reyes
> >Priority: Blocker
> > Fix For: workbench 3.1.0
> >
> >
> > Compiling taverna-workbench-impl fails with:
> > {code}
> > [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile
> (default-compile) on project workbench-impl: Compilation failure:
> Compilation failure:
> > [ERROR]
> /home/stain/src/taverna/incubator-taverna-workbench/taverna-workbench-impl/src/main/java/org/apache/taverna/workbench/ui/impl/UserRegistrationHook.java:[95,78]
> error: incompatible types: Path cannot be converted to File
> > [ERROR]
> /home/stain/src/taverna/incubator-taverna-workbench/taverna-workbench-impl/src/main/java/org/apache/taverna/workbench/ui/impl/UserRegistrationHook.java:[150,60]
> error: incompatible types: Path cannot be converted to File
> > {code}
>
>
>
> --
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> (v6.3.4#6332)
>

Update notice on Maven repo page?

[Gale Naylor]

Currently the Maven repository page (
https://taverna.incubator.apache.org/download/maven/) has a disclaimer that
reads, in part:

Currently there is no Apache release of any Taverna products.

Would it be appropriate to update this now to reflect the release of the
Command-line Tool, or should we just leave it until after the next
release(s)?

Gale

Re: Website Updates

[Gale Naylor]

Sounds good, thanks! I'll try to remember the magic words, "silent
consensus in 48h." :)

On Tue, Jul 12, 2016 at 1:35 PM Stian Soiland-Reyes 
wrote:

> "Silent consensus in 48h" is often a good option :-)
>
> I think you can update at will right away if you want - the 'embargo'
> was because of the download pages before the release was public.
>
> On 12 July 2016 at 19:24, Gale Naylor  wrote:
> > If there is a need NOT to publish changes to web pages, please let me
> know.
> > Otherwise, I will start publishing changes in 48 hours.
> >
> > Thanks!
> >
> > Gale
> >
> > On Mon, Jul 11, 2016 at 5:31 PM Gale Naylor  >
> > wrote:
> >
> >> I know for a while we were not publishing website updates because we had
> >> pages that needed to stay "staged."
> >>
> >> Is it okay to publish pages now? I've made a few minor corrections.
> >>
> >> Thanks,
> >>
> >> Gale
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Website Updates

[Gale Naylor]

If there is a need NOT to publish changes to web pages, please let me know.
Otherwise, I will start publishing changes in 48 hours.

Thanks!

Gale

On Mon, Jul 11, 2016 at 5:31 PM Gale Naylor 
wrote:

> I know for a while we were not publishing website updates because we had
> pages that needed to stay "staged."
>
> Is it okay to publish pages now? I've made a few minor corrections.
>
> Thanks,
>
> Gale
>

Website Updates

[Gale Naylor]

I know for a while we were not publishing website updates because we had
pages that needed to stay "staged."

Is it okay to publish pages now? I've made a few minor corrections.

Thanks,

Gale

Re: taverna command line

[Gale Naylor]

That seems to be the problem. I disconnected from the network and it ran
just fine - no errors.

Can anyone tell me the syntax for running the helloanyone.wfbundle example?
Thanks.

On Sat, Jul 9, 2016 at 2:02 AM Stian Soiland-Reyes  wrote:

> Thanks for checking.
>
> I think the "content is not allowed" is coming from Jena when opening or
> closing the (implicit) workflow bundle when it is reading the manifest 's
> @context. It should in theory read it from the class path cache instead of
> the internet, but this being within OSGi the class path might not include
> the cache file.
>
> Could you try with your network disconnected and see if the warning is the
> same or if you get a network error? (The helloworld workflow itself does
> not require internet, so this should in theory work)
>
> On 8 Jul 2016 6:11 p.m., "Gale Naylor" 
> wrote:
>
> > Yes, the workflow created the Hello_World_output folder with the greeting
> > file inside it, which I was then able to write to the console using the
> > "type" command. So, it looks like it worked, in spite of the error.
> >
> > This is the content of the Hello_World.rdf file. (I opened in in Atom.)
> I'm
> > not that familiar with XML; does anyone see any extraneous characters?:
> >
> > 
> > http://ns.taverna.org.uk/2010/scufl2#"; xmlns:rdf="
> > http://www.w3.org/1999/02/22-rdf-syntax-ns#"; xmlns:rdfs="
> > http://www.w3.org/2000/01/rdf-schema#"; xmlns:xsi="
> > http://www.w3.org/2001/XMLSchema-instance"; xsi:type="WorkflowDocument"
> > xml:base="Hello_World/" xsi:schemaLocation="
> > http://ns.taverna.org.uk/2010/scufl2#
> > http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd
> > http://www.w3.org/1999/02/22-rdf-syntax-ns#
> > http://ns.taverna.org.uk/2010/scufl2/rdf.xsd";>
> > 
> > Hello_World
> > http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/
> > "/>
> > 
> > 
> > greeting
> > 
> > 
> > 
> > 
> > hello
> > 
> >  > rdf:about="processor/hello/out/value">
> > value
> > http://www.w3.org/2001/XMLSchema#integer";>0
> > http://www.w3.org/2001/XMLSchema#integer";>0
> > 
> > 
> > 
> >  > rdf:about="processor/hello/iterationstrategy/"/>
> > 
> > 
> > 
> > 
> >  > rdf:about="datalink?from=processor/hello/out/value&to=out/greeting">
> > 
> > 
> > 
> > 
> > 
> > 
> >
> >
> > On Fri, Jul 8, 2016 at 8:23 AM Ian Dunlop  wrote:
> >
> > > Hello,
> > >
> > > The content not allowed in prolog error usually means there is as xml
> > > parsing issue with the workflow and that the start of the file has some
> > > extraneous characters. I wonder what it means here. Did you get an
> output
> > > from the workflow? The log says it can be found here:
> > >  Outputs will be saved to the directory:
> > > C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\
> > > taverna-commandline-product\target\apache-taverna-
> > > commandline-3.1.0-incubating\Hello_World_output
> > >
> > > Cheers,
> > >
> > > Ian
> > >
> > > On 7 July 2016 at 19:54, Gale Naylor 
> > wrote:
> > >
> > > > Update: I ran the example hello world workflow several times without
> an
> > > > issue (other than the "Content is not allowed..." error), but now I
> am
> > > > getting the log4j warnings:
> > > >
> > > >
> > > >
> > >
> >
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
> > > > examples\helloworld.wfbundle
> > > > log4j:WARN No appenders could be found for logger
> > > >
> (org.springframework.beans.factory.support.DefaultListableBeanFactory).
> > > > log4j:WARN Please initialize the log4j system properly.
> > > > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
> > for
> > &g

Re: taverna command line

[Gale Naylor]

Yes, the workflow created the Hello_World_output folder with the greeting
file inside it, which I was then able to write to the console using the
"type" command. So, it looks like it worked, in spite of the error.

This is the content of the Hello_World.rdf file. (I opened in in Atom.) I'm
not that familiar with XML; does anyone see any extraneous characters?:


http://ns.taverna.org.uk/2010/scufl2#"; xmlns:rdf="
http://www.w3.org/1999/02/22-rdf-syntax-ns#"; xmlns:rdfs="
http://www.w3.org/2000/01/rdf-schema#"; xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance"; xsi:type="WorkflowDocument"
xml:base="Hello_World/" xsi:schemaLocation="
http://ns.taverna.org.uk/2010/scufl2#
http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd
http://www.w3.org/1999/02/22-rdf-syntax-ns#
http://ns.taverna.org.uk/2010/scufl2/rdf.xsd";>

Hello_World
http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/
"/>


greeting




hello


value
http://www.w3.org/2001/XMLSchema#integer";>0
http://www.w3.org/2001/XMLSchema#integer";>0

















On Fri, Jul 8, 2016 at 8:23 AM Ian Dunlop  wrote:

> Hello,
>
> The content not allowed in prolog error usually means there is as xml
> parsing issue with the workflow and that the start of the file has some
> extraneous characters. I wonder what it means here. Did you get an output
> from the workflow? The log says it can be found here:
>  Outputs will be saved to the directory:
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\
> taverna-commandline-product\target\apache-taverna-
> commandline-3.1.0-incubating\Hello_World_output
>
> Cheers,
>
> Ian
>
> On 7 July 2016 at 19:54, Gale Naylor  wrote:
>
> > Update: I ran the example hello world workflow several times without an
> > issue (other than the "Content is not allowed..." error), but now I am
> > getting the log4j warnings:
> >
> >
> >
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
> > examples\helloworld.wfbundle
> > log4j:WARN No appenders could be found for logger
> > (org.springframework.beans.factory.support.DefaultListableBeanFactory).
> > log4j:WARN Please initialize the log4j system properly.
> > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> > more info.
> > log4j:WARN No appenders could be found for logger
> >
> >
> (org.springframework.osgi.service.importer.support.OsgiServiceProxyFactoryBean).
> > log4j:WARN No appenders could be found for logger
> >
> >
> (org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager).
> > log4j:WARN Please initialize the log4j system properly.
> > log4j:WARN No appenders could be found for logger
> >
> >
> (org.springframework.osgi.service.importer.support.OsgiServiceCollectionProxyFactoryBean).
> > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> > more info.
> > log4j:WARN Please initialize the log4j system properly.
> > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> > more info.
> > log4j:WARN Please initialize the log4j system properly.
> > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> > more info.
> > Outputs will be saved to the directory:
> >
> >
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating\Hello_World_output
> > ERROR 2016-07-07 11:46:45,132 (org.apache.jena.riot:84) - [line: 1, col:
> 1
> > ] Content is not allowed in prolog.
> > Workflow completed.
> >
> >
> >
> > On Thu, Jul 7, 2016 at 11:39 AM Gale Naylor  >
> > wrote:
> >
> > > Although the helloworld.wfbundle example gave me an error, it did work.
> > > For Windows the command is  "type Hello_World_output\greeting". I'll
> > update
> > > the README.
> > >
> > > Gale
> > >
> > > On Thu, Jul 7, 2016 at 10:42 AM Gale Naylor <
> ga...@noventussolutions.com
> > >
> > > wrote:
> > >
> > >> Hello all,
&g

Re: taverna command line

[Gale Naylor]

Update: I ran the example hello world workflow several times without an
issue (other than the "Content is not allowed..." error), but now I am
getting the log4j warnings:

C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
examples\helloworld.wfbundle
log4j:WARN No appenders could be found for logger
(org.springframework.beans.factory.support.DefaultListableBeanFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
log4j:WARN No appenders could be found for logger
(org.springframework.osgi.service.importer.support.OsgiServiceProxyFactoryBean).
log4j:WARN No appenders could be found for logger
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN No appenders could be found for logger
(org.springframework.osgi.service.importer.support.OsgiServiceCollectionProxyFactoryBean).
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
Outputs will be saved to the directory:
C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating\Hello_World_output
ERROR 2016-07-07 11:46:45,132 (org.apache.jena.riot:84) - [line: 1, col: 1
] Content is not allowed in prolog.
Workflow completed.



On Thu, Jul 7, 2016 at 11:39 AM Gale Naylor 
wrote:

> Although the helloworld.wfbundle example gave me an error, it did work.
> For Windows the command is  "type Hello_World_output\greeting". I'll update
> the README.
>
> Gale
>
> On Thu, Jul 7, 2016 at 10:42 AM Gale Naylor 
> wrote:
>
>> Hello all,
>>
>> I tried running the helloworld.wfbundle example in Windows 10 (Version
>> 10.0.10586) using cmd.exe and got an error:
>>
>> ERROR 2016-07-07 09:27:41,603 (org.apache.jena.riot:84) - [line: 1, col:
>> 1 ] Content is not allowed in prolog.
>>
>> I then tried running the helloanyone.wfbundle example. When I ran it
>> without an input, I got an error that it expected 'Name", but when I tried
>> entering a name in singe quotes, I still got an error (see below). I also
>> tried the command with no quotation marks at all (log4j errors) and with
>> double quotation marks (similar/same error as with singe quotes).
>>
>> Is there a step I'm missing?
>>
>> Thanks,
>> Gale
>>
>>
>> HELLOANYONE ERRORS: input = 'Gale'
>>
>> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\
>> taverna-commandline-product\target\apache-taverna-
>> commandline-3.1.0-incubating>executeworkflow.bat
>> examples/helloanyone.wfbundle 'Gale'
>>
>> ERROR 2016-07-07 09:58:28,042
>> (org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52)
>> - Application context refresh failed
>> (OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common,
>> config=osgibundle:/META-INF/spring/*.xml))
>> org.springframework.beans.factory.BeanCreationException: Error creating
>> bean with name 'commandLineTool' defined in URL
>> [bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]:
>> Invocation of init method failed; nested exception is
>> java.lang.reflect.UndeclaredThrowableException
>> at
>> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
>> (more error text available)
>>
>> 
>>
>> HELLOANYONE ERRORS when input does not match expected input
>>
>> *
>> *** input without single quotes
>>
>> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
>> examples/helloanyone.wfbundle Gale
>>
>> log4j:WARN No appenders could be found for logger
>> (org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager).
>> log4j:WARN No appenders could be found for logger
>> (org.springframework.osgi.service.dependency.internal.DefaultMandatoryDependencyManager).
>> log4j:WARN No appenders could be found for 

Re: taverna command line

[Gale Naylor]

Although the helloworld.wfbundle example gave me an error, it did work. For
Windows the command is  "type Hello_World_output\greeting". I'll update the
README.

Gale

On Thu, Jul 7, 2016 at 10:42 AM Gale Naylor 
wrote:

> Hello all,
>
> I tried running the helloworld.wfbundle example in Windows 10 (Version
> 10.0.10586) using cmd.exe and got an error:
>
> ERROR 2016-07-07 09:27:41,603 (org.apache.jena.riot:84) - [line: 1, col: 1
> ] Content is not allowed in prolog.
>
> I then tried running the helloanyone.wfbundle example. When I ran it
> without an input, I got an error that it expected 'Name", but when I tried
> entering a name in singe quotes, I still got an error (see below). I also
> tried the command with no quotation marks at all (log4j errors) and with
> double quotation marks (similar/same error as with singe quotes).
>
> Is there a step I'm missing?
>
> Thanks,
> Gale
>
>
> HELLOANYONE ERRORS: input = 'Gale'
>
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\
> taverna-commandline-product\target\apache-taverna-
> commandline-3.1.0-incubating>executeworkflow.bat
> examples/helloanyone.wfbundle 'Gale'
>
> ERROR 2016-07-07 09:58:28,042
> (org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52)
> - Application context refresh failed
> (OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common,
> config=osgibundle:/META-INF/spring/*.xml))
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'commandLineTool' defined in URL
> [bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]:
> Invocation of init method failed; nested exception is
> java.lang.reflect.UndeclaredThrowableException
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
> (more error text available)
>
> 
>
> HELLOANYONE ERRORS when input does not match expected input
>
> *
> *** input without single quotes
>
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
> examples/helloanyone.wfbundle Gale
>
> log4j:WARN No appenders could be found for logger
> (org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager).
> log4j:WARN No appenders could be found for logger
> (org.springframework.osgi.service.dependency.internal.DefaultMandatoryDependencyManager).
> log4j:WARN No appenders could be found for logger
> (org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor).
> log4j:WARN Please initialize the log4j system properly.
> log4j:WARN No appenders could be found for logger
> (org.springframework.osgi.service.importer.support.OsgiServiceProxyFactoryBean).
> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> more info.
> log4j:WARN Please initialize the log4j system properly.
> log4j:WARN Please initialize the log4j system properly.
> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> more info.
> log4j:WARN Please initialize the log4j system properly.
>   log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
> for more info.
> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> more info.
> ERROR 2016-07-07 10:01:59,775
> (org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52)
> - Application context refresh failed
> (OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common,
> config=osgibundle:/META-INF/spring/*.xml))
>  org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'commandLineTool' defined in URL
> [bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]:
> Invocation of init method failed; nested exception is
> java.lang.reflect.UndeclaredThrowableException
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
>
> 
>  input using double quotes
>
> C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
> examples/helloanyone.wfbundle "Gale"
>
> ERROR 2016-07-07 10:15:48,443
> (org.springframework.osgi.extender.internal

Re: taverna command line

[Gale Naylor]

Hello all,

I tried running the helloworld.wfbundle example in Windows 10 (Version
10.0.10586) using cmd.exe and got an error:

ERROR 2016-07-07 09:27:41,603 (org.apache.jena.riot:84) - [line: 1, col: 1
] Content is not allowed in prolog.

I then tried running the helloanyone.wfbundle example. When I ran it
without an input, I got an error that it expected 'Name", but when I tried
entering a name in singe quotes, I still got an error (see below). I also
tried the command with no quotation marks at all (log4j errors) and with
double quotation marks (similar/same error as with singe quotes).

Is there a step I'm missing?

Thanks,
Gale


HELLOANYONE ERRORS: input = 'Gale'

C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\
taverna-commandline-product\target\apache-taverna-
commandline-3.1.0-incubating>executeworkflow.bat
examples/helloanyone.wfbundle 'Gale'

ERROR 2016-07-07 09:58:28,042
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52)
- Application context refresh failed
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common,
config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'commandLineTool' defined in URL
[bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]:
Invocation of init method failed; nested exception is
java.lang.reflect.UndeclaredThrowableException
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
(more error text available)



HELLOANYONE ERRORS when input does not match expected input

*
*** input without single quotes

C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
examples/helloanyone.wfbundle Gale

log4j:WARN No appenders could be found for logger
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyServiceManager).
log4j:WARN No appenders could be found for logger
(org.springframework.osgi.service.dependency.internal.DefaultMandatoryDependencyManager).
log4j:WARN No appenders could be found for logger
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN No appenders could be found for logger
(org.springframework.osgi.service.importer.support.OsgiServiceProxyFactoryBean).
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
log4j:WARN Please initialize the log4j system properly.
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
for more info.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
ERROR 2016-07-07 10:01:59,775
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52)
- Application context refresh failed
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common,
config=osgibundle:/META-INF/spring/*.xml))
 org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'commandLineTool' defined in URL
[bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]:
Invocation of init method failed; nested exception is
java.lang.reflect.UndeclaredThrowableException
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)


 input using double quotes

C:\src\_RC3_CL\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating>executeworkflow.bat
examples/helloanyone.wfbundle "Gale"

ERROR 2016-07-07 10:15:48,443
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52)
- Application context refresh failed
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.commandline.taverna-commandline-common,
config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'commandLineTool' defined in URL
[bundle://127.0:0/META-INF/spring/taverna-commandline-common-context.xml]:
Invocation of init method failed; nested exception is
java.lang.reflect.UndeclaredThrowableException
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)



HELLOANYONE ERRORS: (no input) - included for completene

Re: draft release notes for Taverna cmd line 3.1.0

[Gale Naylor]

I think the banner is great!

Gale

On Mon, Jul 4, 2016 at 4:35 AM Ian Dunlop  wrote:

> Hello,
>
> I added a little alert banner on the home page for the 3.1.0 release
> because I think it's a big deal and we should be shouting about it. Feel
> free to disagree and change etc.
>
> Cheers,
>
> Ian
>
> On 4 July 2016 at 10:44, Alan Williams  wrote:
>
> > On 04-Jul-16 10:23, Ian Dunlop wrote:
> >
> >> Hello,
> >>
> >> Who can add the release to the google plus feed? If it's not being used
> >> then there is not much point having it.
> >>
> >
> > Good point Ian. I have added a Google+ post which should appear in the
> > feed.
> >
> > Cheers,
> >>
> >> Ian
> >>
> >
> > Alan
> >
>

Re: [GitHub] incubator-taverna-commandline pull request #2: Update Command-line README ty...

[Gale Naylor]

Thanks, Ian. Will do.

Gale

On Mon, Jul 4, 2016 at 2:01 AM Ian Dunlop  wrote:

> Hello,
>
> Merged it in Gale.  Fee free to commit these changes directly to the Apache
> repository rather than ask for a pull request via Github. You should have
> full committer rights to do that I think.
>
> Cheers,
>
> Ian
>
> On 1 July 2016 at 15:33, galejwnaylor  wrote:
>
> > GitHub user galejwnaylor opened a pull request:
> >
> > https://github.com/apache/incubator-taverna-commandline/pull/2
> >
> > Update Command-line README typos and grammar
> >
> > Just a few minor changes to word order, adding "-",
> > and fixing a typo.
> >
> > I will do this directly next time, but today this
> > was quicker. Thanks.
> >
> > You can merge this pull request into a Git repository by running:
> >
> > $ git pull
> > https://github.com/galejwnaylor/incubator-taverna-commandline patch-2
> >
> > Alternatively you can review and apply these changes as the patch at:
> >
> > https://github.com/apache/incubator-taverna-commandline/pull/2.patch
> >
> > To close this pull request, make a commit to your master/trunk branch
> > with (at least) the following in the commit message:
> >
> > This closes #2
> >
> > 
> > commit 5d371a797b2f512f967879df13b65aba4317b6fb
> > Author: galejwnaylor 
> > Date:   2016-07-01T14:33:04Z
> >
> > Update Command-line README typos and grammar
> >
> > Just a few minor changes to word order, adding "-",
> > and fixing a typo.
> >
> > 
> >
> >
> > ---
> > If your project is set up for it, you can reply to this email and have
> your
> > reply appear on GitHub as well. If your project does not have this
> feature
> > enabled and wishes so, or if the feature is enabled but not working,
> please
> > contact infrastructure at infrastruct...@apache.org or file a JIRA
> ticket
> > with INFRA.
> > ---
> >
>

Re: draft release notes for Taverna cmd line 3.1.0

[Gale Naylor]

Good point. :)

On Fri, Jul 1, 2016 at 6:40 AM Stian Soiland-Reyes  wrote:

> OK, I updated the download pages to say 2016-07-01
>
> (not "7/1" !! :)
>
> On 1 July 2016 at 14:36, Gale Naylor  wrote:
> > 7/1 is fine with me.
> >
> > On Fri, Jul 1, 2016 at 6:33 AM Stian Soiland-Reyes 
> wrote:
> >
> >> I don't know how people calculate the release date.. I pushed the
> >> button yesterday so it could be in all the mirrors today - but we we
> >> didn't reveal/announce it until today.
> >>
> >> On https://taverna.incubator.apache.org/download/commandline/ I said:
> >>
> >>
> >> > Apache Taverna Command-line 3.1.0-incubating was published on
> 2016-06-30
> >>
> >> But then of course if you look at
> >>
> >>
> https://www.apache.org/dist/incubator/taverna/source/taverna-commandline-3.1.0-incubating/
> >>
> >> it will actually say 2016-06-06 as that is when the RC3 was uploaded.
> >>
> >>
> >> and Maven will say 2016-06-30:
> >>
> >> https://repo1.maven.org/maven2/org/apache/taverna/engine/
> >>
> >>
> >>
> >> Shall we just say 2016-07-01 as today is when we "Publish" publically?
> >>
> >>
> >> On 1 July 2016 at 14:25, Gale Naylor 
> wrote:
> >> > Hi Stian,
> >> >
> >> > In the release notes, do you want the release date to be 6/30 or 7/1?
> >> >
> >> > Gale
> >> >
> >> > On Fri, Jul 1, 2016 at 6:21 AM Gale Naylor <
> ga...@noventussolutions.com>
> >> > wrote:
> >> >
> >> >> Hi Alan,
> >> >>
> >> >> You should have access to editing (and everything else) now.
> >> >>
> >> >> Gale
> >> >>
> >> >> On Fri, Jul 1, 2016 at 5:07 AM Alan Williams <
> alanin...@googlemail.com>
> >> >> wrote:
> >> >>
> >> >>> On 01-Jul-16 12:51, Stian Soiland-Reyes wrote:
> >> >>> > I have made live the download pages for 3.1.0 and friends:
> >> >>> > https://taverna.incubator.apache.org/download/commandline/
> >> >>> >
> >> >>> > (You may spot that I've re-arranged the items in the Download menu
> >> and
> >> >>> > /download/ front page)
> >> >>> >
> >> >>> >
> >> >>> > And drafted release email:
> >> >>> >
> >> >>> >
> >> >>>
> >>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/Taverna+Command+Line+3.1.0
> >> >>>
> >> >>> What is the easiest way to comment / edit the draft? I can log into
> the
> >> >>> cwiki but do not seem to have access to the page.
> >> >>>
> >> >>> > I'll clean up/remove the TBD bits.
> >> >>> >
> >> >>> >
> >> >>> > Any edits/comments for the release notes? I'll post it in a
> couple of
> >> >>> hours. :)
> >> >>> >
> >> >>> > Thanks everyone!
> >> >>>
> >> >>> Alan
> >> >>>
> >> >>>
> >> >>>
> >>
> >>
> >>
> >> --
> >> Stian Soiland-Reyes
> >> Apache Taverna (incubating), Apache Commons
> >> http://orcid.org/-0001-9842-9718
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: draft release notes for Taverna cmd line 3.1.0

[Gale Naylor]

7/1 is fine with me.

On Fri, Jul 1, 2016 at 6:33 AM Stian Soiland-Reyes  wrote:

> I don't know how people calculate the release date.. I pushed the
> button yesterday so it could be in all the mirrors today - but we we
> didn't reveal/announce it until today.
>
> On https://taverna.incubator.apache.org/download/commandline/ I said:
>
>
> > Apache Taverna Command-line 3.1.0-incubating was published on 2016-06-30
>
> But then of course if you look at
>
> https://www.apache.org/dist/incubator/taverna/source/taverna-commandline-3.1.0-incubating/
>
> it will actually say 2016-06-06 as that is when the RC3 was uploaded.
>
>
> and Maven will say 2016-06-30:
>
> https://repo1.maven.org/maven2/org/apache/taverna/engine/
>
>
>
> Shall we just say 2016-07-01 as today is when we "Publish" publically?
>
>
> On 1 July 2016 at 14:25, Gale Naylor  wrote:
> > Hi Stian,
> >
> > In the release notes, do you want the release date to be 6/30 or 7/1?
> >
> > Gale
> >
> > On Fri, Jul 1, 2016 at 6:21 AM Gale Naylor 
> > wrote:
> >
> >> Hi Alan,
> >>
> >> You should have access to editing (and everything else) now.
> >>
> >> Gale
> >>
> >> On Fri, Jul 1, 2016 at 5:07 AM Alan Williams 
> >> wrote:
> >>
> >>> On 01-Jul-16 12:51, Stian Soiland-Reyes wrote:
> >>> > I have made live the download pages for 3.1.0 and friends:
> >>> > https://taverna.incubator.apache.org/download/commandline/
> >>> >
> >>> > (You may spot that I've re-arranged the items in the Download menu
> and
> >>> > /download/ front page)
> >>> >
> >>> >
> >>> > And drafted release email:
> >>> >
> >>> >
> >>>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/Taverna+Command+Line+3.1.0
> >>>
> >>> What is the easiest way to comment / edit the draft? I can log into the
> >>> cwiki but do not seem to have access to the page.
> >>>
> >>> > I'll clean up/remove the TBD bits.
> >>> >
> >>> >
> >>> > Any edits/comments for the release notes? I'll post it in a couple of
> >>> hours. :)
> >>> >
> >>> > Thanks everyone!
> >>>
> >>> Alan
> >>>
> >>>
> >>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: draft release notes for Taverna cmd line 3.1.0

[Gale Naylor]

Hi Stian,

In the release notes, do you want the release date to be 6/30 or 7/1?

Gale

On Fri, Jul 1, 2016 at 6:21 AM Gale Naylor 
wrote:

> Hi Alan,
>
> You should have access to editing (and everything else) now.
>
> Gale
>
> On Fri, Jul 1, 2016 at 5:07 AM Alan Williams 
> wrote:
>
>> On 01-Jul-16 12:51, Stian Soiland-Reyes wrote:
>> > I have made live the download pages for 3.1.0 and friends:
>> > https://taverna.incubator.apache.org/download/commandline/
>> >
>> > (You may spot that I've re-arranged the items in the Download menu and
>> > /download/ front page)
>> >
>> >
>> > And drafted release email:
>> >
>> >
>> https://cwiki.apache.org/confluence/display/TAVERNADEV/Taverna+Command+Line+3.1.0
>>
>> What is the easiest way to comment / edit the draft? I can log into the
>> cwiki but do not seem to have access to the page.
>>
>> > I'll clean up/remove the TBD bits.
>> >
>> >
>> > Any edits/comments for the release notes? I'll post it in a couple of
>> hours. :)
>> >
>> > Thanks everyone!
>>
>> Alan
>>
>>
>>

Re: draft release notes for Taverna cmd line 3.1.0

[Gale Naylor]

Hi Alan,

You should have access to editing (and everything else) now.

Gale

On Fri, Jul 1, 2016 at 5:07 AM Alan Williams 
wrote:

> On 01-Jul-16 12:51, Stian Soiland-Reyes wrote:
> > I have made live the download pages for 3.1.0 and friends:
> > https://taverna.incubator.apache.org/download/commandline/
> >
> > (You may spot that I've re-arranged the items in the Download menu and
> > /download/ front page)
> >
> >
> > And drafted release email:
> >
> >
> https://cwiki.apache.org/confluence/display/TAVERNADEV/Taverna+Command+Line+3.1.0
>
> What is the easiest way to comment / edit the draft? I can log into the
> cwiki but do not seem to have access to the page.
>
> > I'll clean up/remove the TBD bits.
> >
> >
> > Any edits/comments for the release notes? I'll post it in a couple of
> hours. :)
> >
> > Thanks everyone!
>
> Alan
>
>
>

Re: [RESULT] [VOTE] Release Apache Taverna Command-line Tool 3.1.0-incubating RC3

[Gale Naylor]

Great!

On Thu, Jun 30, 2016, 4:25 AM Stian Soiland-Reyes  wrote:

> On 17 June 2016 at 14:26, Stian Soiland-Reyes  wrote:
> > The Taverna PPMC has successfully voted for the source release of
> >
> >   Apache Taverna Engine 3.1.0-incubating
> >   Apache Taverna Common Activities 2.1.0-incubating
> >   Apache Taverna Command-line Tool 3.1.0-incubating
>
>
> I'm happy to announce the result of the IPMC vote:
>
> +3 IPMC binding:
>
> +1 Justin Mclean (jmclean)
> +1 Sergio Fernández (wikier)
> +1 Josh Elser (elserj)
>
>
> No 0 or -1 votes.
>
>
> Thanks to all who helped!
>
> I will proceed with the publishing the release.
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Checkstyle/Findbugs LGPL - does it matter

[Gale Naylor]

If they are not part of the distribution, where are they? Are they in the
repositories?

On Wed, Jun 15, 2016 at 11:04 AM Donal Fellows <
donal.k.fell...@manchester.ac.uk> wrote:

> The plugins should be fine. They are not required to build anything (if
> anyone is super-worried, they can be put in a maven profile; it can be
> enabled by default for our convenience) and there is a lot of precedent for
> allowing LGPL tools to work with Apache products.
>
> Donal.
>
> Ian Dunlop  wrote:
>
> >Hello,
> >
> >I noticed that the checkstyle and findbugs code analysis tools are LGPL
> >licensed. I don't think that matters as long as they are not part of the
> >distribution. Any thoughts?
> >
> >Cheers,
> >
> >Ian
>

[jira] [Created] (TAVERNA-982) Fix Command-line Tool Javadoc Warnings

[Gale Naylor (JIRA)]

Gale Naylor created TAVERNA-982:
---

 Summary: Fix Command-line Tool Javadoc Warnings
 Key: TAVERNA-982
 URL: https://issues.apache.org/jira/browse/TAVERNA-982
 Project: Apache Taverna
  Issue Type: Bug
  Components: Taverna Command-line Tool
Affects Versions: command-line 3.1.0
Reporter: Gale Naylor


Fix the following Javadoc Warnings in Command-line tool Common:

[WARNING] 
C:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-common\src\main\java\org\apache\taverna\commandline\data\SaveResultsHandler.java:39:
 warning - Tag @link: reference not found: CommandLineResultListener

[WARNING] 
C:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-common\src\main\java\org\apache\taverna\commandline\data\SaveResultsHandler.java:39:
 warning - Tag @see: reference not found: BaclavaHandler

[WARNING] 
C:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-common\src\main\java\org\apache\taverna\commandline\data\SaveResultsHandler.java:39:
 warning - Tag @see: reference not found: CommandLineResultListener

[WARNING] 
C:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-common\src\main\java\org\apache\taverna\commandline\data\SaveResultsHandler.java:39:
 warning - Tag @link: reference not found: CommandLineResultListener

[WARNING] 
C:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-common\src\main\java\org\apache\taverna\commandline\data\SaveResultsHandler.java:39:
 warning - Tag @link: reference not found: CommandLineResultListener





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[jira] [Updated] (TAVERNA-981) Fix Common Activities Javadoc Warnings

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-981?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-981:

Attachment: Taverna-CommonActivities-Javadoc-Warnings.xlsx

Javadoc warnings for:

   - Beanshell Activity
   - External Tool Activity
   - REST Activity
   - Spreadsheet Import Activity
   - WSDL-generic Library
   - WSDL Activity


> Fix Common Activities Javadoc Warnings
> --
>
> Key: TAVERNA-981
> URL: https://issues.apache.org/jira/browse/TAVERNA-981
> Project: Apache Taverna
>  Issue Type: Bug
>  Components: Taverna Common Activities
>Affects Versions: common activities 2.1.0
>    Reporter: Gale Naylor
> Attachments: Taverna-CommonActivities-Javadoc-Warnings.xlsx
>
>
> See attached Excel File - Javadoc warnings in:
>    - Beanshell Activity
>    - External Tool Activity
>    - REST Activity
>    - Spreadsheet Import Activity
>    - WSDL-generic Library
>    - WSDL Activity



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[jira] [Created] (TAVERNA-981) Fix Common Activities Javadoc Warnings

[Gale Naylor (JIRA)]

Gale Naylor created TAVERNA-981:
---

 Summary: Fix Common Activities Javadoc Warnings
 Key: TAVERNA-981
 URL: https://issues.apache.org/jira/browse/TAVERNA-981
 Project: Apache Taverna
  Issue Type: Bug
  Components: Taverna Common Activities
Affects Versions: common activities 2.1.0
Reporter: Gale Naylor


See attached Excel File - Javadoc warnings in:

   - Beanshell Activity
   - External Tool Activity
   - REST Activity
   - Spreadsheet Import Activity
   - WSDL-generic Library
   - WSDL Activity




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[jira] [Updated] (TAVERNA-980) Fix Engine Javadoc Warnings

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-980?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-980:

Attachment: Taverna-Engine-Javadoc-Warnings.xlsx

Javadoc warnings for the following are listed in the Excel file (on different 
tabs):

  - Reference Manager API
  - Observer pattern
  - Workflow Model API
  - Workflow Model Extension Points
  - Workflow Model impl
  - Reference Manager impl; 
  - Platform Capability API
  - Credential Manager API
  - Credential Manager impl
  - Platform Report Service
  - Platform Execution Service API
  - Platform Run Service API

> Fix Engine Javadoc Warnings
> ---
>
> Key: TAVERNA-980
> URL: https://issues.apache.org/jira/browse/TAVERNA-980
> Project: Apache Taverna
>  Issue Type: Bug
>  Components: Taverna Engine
>Affects Versions: engine 3.1.0
>    Reporter: Gale Naylor
> Attachments: Taverna-Engine-Javadoc-Warnings.xlsx
>
>
> See attached Excel file.



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[jira] [Created] (TAVERNA-980) Fix Engine Javadoc Warnings

[Gale Naylor (JIRA)]

Gale Naylor created TAVERNA-980:
---

 Summary: Fix Engine Javadoc Warnings
 Key: TAVERNA-980
 URL: https://issues.apache.org/jira/browse/TAVERNA-980
 Project: Apache Taverna
  Issue Type: Bug
  Components: Taverna Engine
Affects Versions: engine 3.1.0
Reporter: Gale Naylor


See attached Excel file.



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[jira] [Updated] (TAVERNA-960) Add Content to Taverna Podling Maturity Assessment

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-960?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-960:

Summary: Add Content to Taverna Podling Maturity Assessment  (was: Taverna 
Podling Maturity Assessment)

> Add Content to Taverna Podling Maturity Assessment
> --
>
> Key: TAVERNA-960
> URL: https://issues.apache.org/jira/browse/TAVERNA-960
> Project: Apache Taverna
>  Issue Type: Task
>        Reporter: Gale Naylor
>Priority: Minor
>  Labels: documentation
>
> The outline of the Taverna Podling Maturity Assessment (AKA Graduation Plan) 
> is now on the TavernaDev wiki.
> It is ready for content to be added.



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[jira] [Updated] (TAVERNA-978) Fix Common Activities build warnings

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-978?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-978:

Summary: Fix Common Activities build warnings   (was: Fix build warnings 
from RC3)

> Fix Common Activities build warnings 
> -
>
> Key: TAVERNA-978
> URL: https://issues.apache.org/jira/browse/TAVERNA-978
> Project: Apache Taverna
>  Issue Type: Bug
>  Components: Taverna Common Activities
>Affects Versions: common activities 2.1.0
>    Reporter: Gale Naylor
>  Labels: build
>
>- Common Activities: empty jar warning
> [WARNING] JAR will be empty - no content was marked for inclusion!
> [INFO] Building jar: 
> c:\src\CARC3\apache-taverna-common-activities-2.1.0-incubating\target\apache-taverna-common-activities-2.1.0-incubating-tests.jar



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[jira] [Updated] (TAVERNA-979) Fix build warnings Command-line Tool

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-979?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-979:

Summary: Fix build warnings Command-line Tool  (was: Fix build warnings in 
RC3)

> Fix build warnings Command-line Tool
> 
>
> Key: TAVERNA-979
> URL: https://issues.apache.org/jira/browse/TAVERNA-979
> Project: Apache Taverna
>  Issue Type: Bug
>  Components: Taverna Command-line Tool
>Affects Versions: command-line 3.1.0
>    Reporter: Gale Naylor
>
> Summary: empty jar, missing POMs, "not an OSGi bundle"
> [WARNING] JAR will be empty - no content was marked for inclusion!
> [INFO] Building jar: 
> c:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\target\apache-taverna-commandline-3.1.0-incubating-tests.jar
> ---
> [WARNING] The POM for 
> org.springframework:org.springframework.aop:jar:3.0.0.RC1 is missing, no 
> dependency information available
> [WARNING] The POM for 
> org.springframework:org.springframework.core:jar:3.0.0.RC1 is missing, no 
> dependency information available
> [WARNING] The POM for 
> org.springframework:org.springframework.asm:jar:3.0.0.RC1 is missing, no 
> dependency information available
> [WARNING] The POM for 
> org.springframework:org.springframework.context:jar:3.0.0.RC1 is missing, no 
> dependency information available
> ---
> [WARNING] Not an OSGi bundle : org.osgi:org.osgi.core:jar:4.3.1
> [WARNING] Not an OSGi bundle : org.osgi:org.osgi.compendium:jar:4.3.1
> [WARNING] Not an OSGi bundle : commons-logging:commons-logging:jar:1.1.1
> [WARNING] Not an OSGi bundle : org.apache.poi:poi:jar:3.6
> [WARNING] Not an OSGi bundle : org.apache.poi:poi-ooxml:jar:3.6
> [WARNING] Not an OSGi bundle : org.opensaml:opensaml:jar:2.5.1-1
> [WARNING] Not an OSGi bundle : 
> org.apache.taverna.commandline:taverna-commandline-launcher:jar:3.1.0-incubating
> [WARNING] Not an OSGi bundle : xml-apis:xml-apis:jar:1.4.01
> [WARNING] Not an OSGi bundle : junit:junit:jar:4.11



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[jira] [Updated] (TAVERNA-977) Fix Engine build warnings

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-977?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-977:

Summary: Fix Engine build warnings  (was: Fix build warnings from RC3)

> Fix Engine build warnings
> -
>
> Key: TAVERNA-977
> URL: https://issues.apache.org/jira/browse/TAVERNA-977
> Project: Apache Taverna
>  Issue Type: Bug
>  Components: Taverna Engine
>Affects Versions: engine 3.1.0
>    Reporter: Gale Naylor
>  Labels: build
>
> Summary:
> - Workflow Model impl - private reference
> - Reference Manager impl - unused package warning
> - Activity archetype: missing plug-in warnings, empty jar warning, 
>   and unresolved package dependency warnings  
> Details:
> - Workflow Model impl -
> [WARNING] Bundle 
> org.apache.taverna.engine:taverna-workflowmodel-impl:bundle:3.1.0-incubating 
> : Export org.apache.taverna.workflowmodel.impl,  has 1,  private references 
> [org.apache.taverna.workflowmodel.processor.dispatch.impl], 
> - Reference Manager impl -
> [WARNING] Bundle 
> org.apache.taverna.engine:taverna-reference-impl:bundle:3.1.0-incubating : 
> Unused Import-Package instructions: [org.springframework.orm.*] 
> - Activity Archetype -
> [INFO] [WARNING] Some problems were encountered while building the effective 
> model for 
> com.example:dummy-taverna-plugin-plugin:taverna-plugin:0.1.0-SNAPSHOT
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 22, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 50, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-jar-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 40, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-source-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 29, column 12
> INFO] [WARNING] Some problems were encountered while building the effective 
> model for com.example:dummy-taverna-plugin-activity:bundle:0.1.0-SNAPSHOT
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 22, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 50, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-jar-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 40, column 12
> [INFO] [WARNING] 'build.plugins.plugin.version' for 
> org.apache.maven.plugins:maven-source-plugin is missing. @ 
> com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
> C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
>  line 29, column 12
> [INFO] [WARNING] Some problems were encountered while building the effective 
> model for com.example:dummy-taverna-plugin:pom:0.1.0-S

[jira] [Created] (TAVERNA-979) Fix build warnings in RC3

[Gale Naylor (JIRA)]

Gale Naylor created TAVERNA-979:
---

 Summary: Fix build warnings in RC3
 Key: TAVERNA-979
 URL: https://issues.apache.org/jira/browse/TAVERNA-979
 Project: Apache Taverna
  Issue Type: Bug
  Components: Taverna Command-line Tool
Affects Versions: command-line 3.1.0
Reporter: Gale Naylor


Summary: empty jar, missing POMs, "not an OSGi bundle"


[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: 
c:\src\CLRC3\apache-taverna-commandline-3.1.0-incubating\target\apache-taverna-commandline-3.1.0-incubating-tests.jar

---

[WARNING] The POM for org.springframework:org.springframework.aop:jar:3.0.0.RC1 
is missing, no dependency information available

[WARNING] The POM for 
org.springframework:org.springframework.core:jar:3.0.0.RC1 is missing, no 
dependency information available

[WARNING] The POM for org.springframework:org.springframework.asm:jar:3.0.0.RC1 
is missing, no dependency information available

[WARNING] The POM for 
org.springframework:org.springframework.context:jar:3.0.0.RC1 is missing, no 
dependency information available

---

[WARNING] Not an OSGi bundle : org.osgi:org.osgi.core:jar:4.3.1
[WARNING] Not an OSGi bundle : org.osgi:org.osgi.compendium:jar:4.3.1
[WARNING] Not an OSGi bundle : commons-logging:commons-logging:jar:1.1.1
[WARNING] Not an OSGi bundle : org.apache.poi:poi:jar:3.6
[WARNING] Not an OSGi bundle : org.apache.poi:poi-ooxml:jar:3.6
[WARNING] Not an OSGi bundle : org.opensaml:opensaml:jar:2.5.1-1
[WARNING] Not an OSGi bundle : 
org.apache.taverna.commandline:taverna-commandline-launcher:jar:3.1.0-incubating
[WARNING] Not an OSGi bundle : xml-apis:xml-apis:jar:1.4.01
[WARNING] Not an OSGi bundle : junit:junit:jar:4.11




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[jira] [Updated] (TAVERNA-978) Fix build warnings from RC3

[Gale Naylor (JIRA)]

 [ 
https://issues.apache.org/jira/browse/TAVERNA-978?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gale Naylor updated TAVERNA-978:

Affects Version/s: (was: engine 3.1.0)
   common activities 2.1.0
  Description: 
   - Common Activities: empty jar warning

[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: 
c:\src\CARC3\apache-taverna-common-activities-2.1.0-incubating\target\apache-taverna-common-activities-2.1.0-incubating-tests.jar


  was:
Summary:
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning, 
  and unresolved package dependency warnings  

Details:

- Workflow Model impl -

[WARNING] Bundle 
org.apache.taverna.engine:taverna-workflowmodel-impl:bundle:3.1.0-incubating : 
Export org.apache.taverna.workflowmodel.impl,  has 1,  private references 
[org.apache.taverna.workflowmodel.processor.dispatch.impl], 

- Reference Manager impl -

[WARNING] Bundle 
org.apache.taverna.engine:taverna-reference-impl:bundle:3.1.0-incubating : 
Unused Import-Package instructions: [org.springframework.orm.*] 

- Activity Archetype -

[INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin-plugin:taverna-plugin:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 29, column 12

INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin-activity:bundle:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 29, column 12

[INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin:pom:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ line 40, 

[jira] [Created] (TAVERNA-978) Fix build warnings from RC3

[Gale Naylor (JIRA)]

Gale Naylor created TAVERNA-978:
---

 Summary: Fix build warnings from RC3
 Key: TAVERNA-978
 URL: https://issues.apache.org/jira/browse/TAVERNA-978
 Project: Apache Taverna
  Issue Type: Bug
  Components: Taverna Engine
Affects Versions: engine 3.1.0
Reporter: Gale Naylor


Summary:
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning, 
  and unresolved package dependency warnings  

Details:

- Workflow Model impl -

[WARNING] Bundle 
org.apache.taverna.engine:taverna-workflowmodel-impl:bundle:3.1.0-incubating : 
Export org.apache.taverna.workflowmodel.impl,  has 1,  private references 
[org.apache.taverna.workflowmodel.processor.dispatch.impl], 

- Reference Manager impl -

[WARNING] Bundle 
org.apache.taverna.engine:taverna-reference-impl:bundle:3.1.0-incubating : 
Unused Import-Package instructions: [org.springframework.orm.*] 

- Activity Archetype -

[INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin-plugin:taverna-plugin:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 29, column 12

INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin-activity:bundle:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 29, column 12

[INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin:pom:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ line 29, column 12

---

[INFO] [WARNING] JAR w

[jira] [Created] (TAVERNA-977) Fix build warnings from RC3

[Gale Naylor (JIRA)]

Gale Naylor created TAVERNA-977:
---

 Summary: Fix build warnings from RC3
 Key: TAVERNA-977
 URL: https://issues.apache.org/jira/browse/TAVERNA-977
 Project: Apache Taverna
  Issue Type: Bug
  Components: Taverna Engine
Affects Versions: engine 3.1.0
Reporter: Gale Naylor


Summary:
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning, 
  and unresolved package dependency warnings  

Details:

- Workflow Model impl -

[WARNING] Bundle 
org.apache.taverna.engine:taverna-workflowmodel-impl:bundle:3.1.0-incubating : 
Export org.apache.taverna.workflowmodel.impl,  has 1,  private references 
[org.apache.taverna.workflowmodel.processor.dispatch.impl], 

- Reference Manager impl -

[WARNING] Bundle 
org.apache.taverna.engine:taverna-reference-impl:bundle:3.1.0-incubating : 
Unused Import-Package instructions: [org.springframework.orm.*] 

- Activity Archetype -

[INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin-plugin:taverna-plugin:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 29, column 12

INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin-activity:bundle:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ 
com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT, 
C:\src\ERC3\apache-taverna-engine-3.1.0-incubating\taverna-activity-archetype\target\test-classes\projects\dummyActivity\project\dummy-taverna-plugin\pom.xml,
 line 29, column 12

[INFO] [WARNING] Some problems were encountered while building the effective 
model for com.example:dummy-taverna-plugin:pom:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 22, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 50, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-jar-plugin is missing. @ line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for 
org.apache.maven.plugins:maven-source-plugin is missing. @ line 29, column 12

---

[INFO] [WARNING] JAR w

Re: [] Release Apache Taverna Command-line Tool 3.1.0-incubating RC3

[Gale Naylor]

+1

taverna-engine, taverna-common-activities, and taverna-commandline all build
successfully on my Windows 10 machine running Maven 3.3.9 and Java 1.8.0_91.

Add the following warnings to JIRA:

---
Warnings (other than Javadoc warnings) - Individual JIRA issues
---
  taverna-engine
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning,
  and unresolved package dependency warnings

  taverna-common-activities
- Common Activities: empty jar warning

  taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Product: missing POMs

---
Detailed summary (including Javadoc warnings)
---

taverna-engine
  - Engine and Platform: empty jar warning
  - Reference Manager API: Javadoc warnings
  - Observer pattern: Javadoc warnings
  - Workflow Model API: Javadoc warnings
  - Workflow Model Extension Points: Javadoc warnings
  - Workflow Model impl: Javadoc warnings; private reference warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-workflowmodel-
  impl:bundle:3.1.0-incubating :
  Export org.apache.taverna.workflowmodel.impl,  has 1,  private
references
  [org.apache.taverna.workflowmodel.processor.dispatch.impl],

  - Reference Manager impl: Javadoc warnings; unused package warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-reference-
  impl:bundle:3.1.0-incubating : Unused Import-Package instructions:
  [org.springframework.orm.*]

  - Activity archetype: missing plug-in warnings, empty jar warning,
and unresolved package dependency warnings
  EXAMPLE 1: [INFO] [WARNING] 'build.plugins.plugin.version' for
  org.apache.maven.plugins:maven-compiler-plugin is missing.
  @ com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
  ...\taverna-activity-archetype\target\test-classes\projects\
  dummyActivity\project\dummy-taverna-plugin\pom.xml, line 22, column 12

  EXAMPLE 2: [INFO] [WARNING] Bundle : org.springframework:
  org.springframework.context:jar:3.0.5.RELEASE has unresolved package
  dependencies: org.apache.commons.logging;version="[1.1.1,2.0.0)"

  - Platform Capability API: Javadoc warnings
  - Credential Manager API: Javadoc warnings
  - Credential Manager impl: Javadoc warnings
  - Platform Report Service: Javadoc warnings
  - Platform Execution Service API: Javadoc warnings
  - Platform Run Service API: Javadoc warnings

taverna-common-activities
   - Common Activities: empty jar warning
   - Beanshell Activity: Javadoc warnings
   - External Tool Activity: Javadoc warnings
   - REST Activity: Javadoc warnings
   - Spreadsheet Import Activity: Javadoc warnings
   - WSDL-generic Library: Javadoc warnings
   - WSDL Activity: Javadoc warnings

taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Common: a few Javadoc warnings
- Command-line tool Product: missing POMs
EXAMPLE: [WARNING] Missing POM for org.springframework:org.
springframework.aop:jar:3.0.0.RC1




On Mon, Jun 13, 2016 at 9:49 AM Stian Soiland-Reyes 
wrote:

> On 13 June 2016 at 10:04, Andy Seaborne  wrote:
> > One of the few issues that Taverna has before graduation is getting VOTEs
> > done.  When a TLP, the future-PMC is going to have to be able to muster
> the
> > necessary 3 votes for a releases.  The active PPMC of Taverna is looking
> > minimal.
> >
> > 1/ What about this vote?
>
> Thanks for raising this, Andy.
>
>
> I agree we need to be speedier on a VOTE - but I think it's fair that
> we have due review of the very first release of this particular code -
> e.g. we dropped a RC because of misleading copyright headers; which I
> think shows a functioning PMC.
>
>
> One thing I think is important is that we should not strive for code
> perfection, as a small project I am afraid we don't have that luxury.
> We should rather try to Release Early, Release Often.
>
>
> > 2/ How can the pool of active (P)PMC members be grown?
>
> We still need new members, but I think we also need to keep the
> existing PPMC members engaged.
>
> ASF processes come with.. well, some overhead. I guess that can be
> tiring sometimes.
>
>
> I know everyone is busy - perhaps the remaining part of the PPMC [1]
> could chip in on what we could do to get you to review/vote? :)
>
>
> Have we made the release process [2][3] too big?   Or is it too much
> to review 3 artifacts at once?
>
> Note that everyone don't have to test everything on the list!
>
>
> [1] https://taverna.incubator.apache.org/about/
> [2]
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+How+to+Review+a+Release+and+Vote
> [3]
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+Details%3A+How+to+Review+a+Release
>
>
> --
> Stian Soiland-Reyes
> 

Re: [DISCUSS] The third RC of Taverna Command Line 3.1.0

[Gale Naylor]

I do not think any of the issues I raised should stop the release. I agree
to adding the non-Javadoc warnings individually to JIRA. There are a lot of
Javadoc warnings, can we have one JIRA issue for each component that
collects all of the Javadoc warnings?

I'm ready to [VOTE].

On Mon, Jun 13, 2016 at 9:17 AM Stian Soiland-Reyes 
wrote:

> Thanks, Alan.. would you feel ready to [VOTE]..?
>
> On 6 June 2016 at 17:31, Alan Williams  wrote:
> > It all builds OK on my Maven 3.3.3
> >
> > Alan
> >
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: [DISCUSS] The third RC of Taverna Command Line 3.1.0

[Gale Naylor]

taverna-engine, taverna-common-activities, and taverna-commandline all build
successfully on my Windows 10 machine running Maven 3.3.9 and Java 1.8.0_91.

I do not have time to perform a detailed check of the source headers
for the common-activities or commandline files at this time, or check the
dependencies. (But Alan has done a GitHub search for copyrights and the
files are clean.)

These warnings in Activity archetype seem to be the most serious:

[INFO] [WARNING] Some problems were encountered while building the
effective model for com.example:dummy-taverna-plugin:pom:0.1.0-SNAPSHOT
[INFO] [WARNING] 'build.plugins.plugin.version' for
org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 22,
column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for
org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 50,
column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for
org.apache.maven.plugins:maven-jar-plugin is missing. @ line 40, column 12
[INFO] [WARNING] 'build.plugins.plugin.version' for
 org.apache.maven.plugins:maven-source-plugin is missing. @ line 29, column
12


Can we release with these warnings?


See a summary of the non-Javadoc warnings below, followed by
a summary of all warnings (including Javadoc warnings).

---
Warnings (other than Javadoc warnings):
---
  taverna-engine
- Workflow Model impl - private reference
- Reference Manager impl - unused package warning
- Activity archetype: missing plug-in warnings, empty jar warning,
  and unresolved package dependency warnings

  taverna-common-activities
- Common Activities: empty jar warning

  taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Product: missing POMs

---
Detailed summary (including Javadoc warnings)
---

taverna-engine
  - Engine and Platform: empty jar warning
  - Reference Manager API: Javadoc warnings
  - Observer pattern: Javadoc warnings
  - Workflow Model API: Javadoc warnings
  - Workflow Model Extension Points: Javadoc warnings
  - Workflow Model impl: Javadoc warnings; private reference warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-workflowmodel-
  impl:bundle:3.1.0-incubating :
  Export org.apache.taverna.workflowmodel.impl,  has 1,  private
references
  [org.apache.taverna.workflowmodel.processor.dispatch.impl],

  - Reference Manager impl: Javadoc warnings; unused package warning
  [WARNING] Bundle org.apache.taverna.engine:taverna-reference-
  impl:bundle:3.1.0-incubating : Unused Import-Package instructions:
  [org.springframework.orm.*]

  - Activity archetype: missing plug-in warnings, empty jar warning,
and unresolved package dependency warnings
  EXAMPLE 1: [INFO] [WARNING] 'build.plugins.plugin.version' for
  org.apache.maven.plugins:maven-compiler-plugin is missing.
  @ com.example:dummy-taverna-plugin:0.1.0-SNAPSHOT,
  ...\taverna-activity-archetype\target\test-classes\projects\
  dummyActivity\project\dummy-taverna-plugin\pom.xml, line 22, column 12

  EXAMPLE 2: [INFO] [WARNING] Bundle : org.springframework:
  org.springframework.context:jar:3.0.5.RELEASE has unresolved package
  dependencies: org.apache.commons.logging;version="[1.1.1,2.0.0)"

  - Platform Capability API: Javadoc warnings
  - Credential Manager API: Javadoc warnings
  - Credential Manager impl: Javadoc warnings
  - Platform Report Service: Javadoc warnings
  - Platform Execution Service API: Javadoc warnings
  - Platform Run Service API: Javadoc warnings

taverna-common-activities
   - Common Activities: empty jar warning
   - Beanshell Activity: Javadoc warnings
   - External Tool Activity: Javadoc warnings
   - REST Activity: Javadoc warnings
   - Spreadsheet Import Activity: Javadoc warnings
   - WSDL-generic Library: Javadoc warnings
   - WSDL Activity: Javadoc warnings

taverna-commandline
- Command-line tool: empty jar warning
- Command-line tool Common: a few Javadoc warnings
- Command-line tool Product: missing POMs
EXAMPLE: [WARNING] Missing POM for org.springframework:org.
springframework.aop:jar:3.0.0.RC1

Packages/modules (what is the correct term?) that are not listed
have no warnings.


Gale

On Wed, Jun 8, 2016 at 3:49 AM Stian Soiland-Reyes  wrote:

> Thilina Manamgoda wrote:
> > i  have updated the maven to 3.3.9 and i got this failure
> >
> > Failed to execute goal
> > org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test (default-test)
> > on project taverna-credential-manager-impl: There are test failures.
>
> Do you have any more details of this test error? It should look like a
> stack trace mentioning which tests fail.
>
> You can also look in the *.txt files in
> taverna-credential-manager-impl/target/surefire-reports/
>
> In case you built with -T1.5C, (which would build mult

Re: [DISCUSS] Release candidate 2 of Command-line Tool 3.1.0-incubating

[Gale Naylor]

Yes, I think we can do the package.html file headers after the release.


On Mon, Jun 6, 2016 at 7:27 AM Stian Soiland-Reyes  wrote:

> On 4 June 2016 at 17:30, Gale Naylor  wrote:
> > Thanks for the explanations, Stian. A vote-email script might not be a
> bad
> > idea! It certainly
> > seems to be a complicated thing to pull together.
> >
> > In response to Stian's email, I found some additional, related ASF
> > resources that support not
> > requiring license headers in files whose content cannot be copyrighted
> > (e.g., files that contain
> > "Hello"). Here is the link:
> > http://www.apache.org/legal/src-headers.html#faq-exceptions
> >
> > The exception also applies to "Test data for which the addition of a
> source
> > header would cause
> > the tests to fail."
> >
> > It seems that most of the files that currently do not have license
> headers,
> > including
> > files in the services sub-directories, meet the criteria of being exempt
> > from the license header
> > requirement.
>
> Ah, great. So we're generally good to go with those test files then,
> and can just list them in the apache-rat excludes - which I think is a
> good way to say "Yeah, we know about this file, 's fine".
>
>
> > However, it sounds like we SHOULD add license headers to the
> > package.html files.
> > Do we want to do that way now, and then later convert to
> > package-info.java files?
>
> Just convert them right away, I think.. it's generally just rename and
> add the ASF header and the Java "package " line.
>
> The only tricky thing about them is that you need to use the two
> different Java comment blocks carefully so that the ASF header does
> not become the JAvadoc, that is
>
> src/main/java/org/apache/taverna/foo/package-info.java
>
> /* ASF */
> /** javadoc for this package **/
> package org.apache.taverna.foo;
>
> And we should have such package info for all API-like packages at
> least.. like in all the *-api bits in taverna-engine.   (It might just
> have a one-liner with the description from README)
>
>
> Shall we do this after this release?
>
>
>
> > I also found an ASF link that confirms what Stian said about only BUNDLED
> > dependencies
> > needing to be included in NOTICE files. Good to know.
> > (http://www.apache.org/dev/licensing-howto.html#bundled-vs-non-bundled)
>
> Yes - so bundled would be when we make a binaries/ upload.
>
> Not sure if this also covers any bundling in Maven Central - e.g.
>
>
> http://central.maven.org/maven2/org/apache/taverna/language/taverna-tavlang-tool/0.15.1-incubating/taverna-tavlang-tool-0.15.1-incubating.jar
> includes bundled JARs, but the Maven plugins seem to have managed to
> combine the contained META-INF/NOTICE. (Thanks, Menaka)
>
>
>
> > Also, regarding 3rd party copyrighted works:  I found an ASF link that
> > explicitly states:
> > -- not to modify/remove copyright headers from 3rd party works;
> > -- not to add the standard ASF license header to 3rd party works.
> > http://www.apache.org/legal/src-headers.html#3party
>
> OK, so we'll leave those BSD copyrights in place in say the
> taverna-engine hadoop crossproduct.java
>
>
> > One remaining question about 3rd party license in
> > src/license/THIRD-PARTY.properties:
> >
> > javax.transaction--com.springsource.javax.transaction--1.1.0  (CDDL
> 1.0)
> >
> > Is this an exception to the category-b license "binary only" rule
> because
> > we use only
> > a small amount of source code?
>
> But it's not included - we don't distribute javax.transaction in the
> source archive; it's downloaded from Maven repositories.  You won't
> see it until you have built the commandline product:
>
>  Directory of
> D:\src\apache-taverna-commandline-3.1.0-incubating\taverna-commandline-product\target\apache-taverna-commandline-3.1.0-incubating\lib\javax.transaction
>
> 2016-06-06  14:10  .
> 2016-06-06  14:10  ..
> 2016-05-31  16:2315,518
> com.springsource.javax.transaction-1.1.0.jar
>
> (or look in ~/.m2/repository/javax/transaction)
>
> > One observation about headers in JSON files
> > Most of the JSON files have the header you described (
> http://purl.org.
> > ..).
>
> Yeah.. some kind of JSON-LD-like workaround -- the key is unlikely to
> be used for anything but for licenses - and generally JSON consumers
> ignore extra keys.
>
>
> > Is it okay if the JSON file header uses ##? (Se

Added Structure to Confluence Wiki Pages

[Gale Naylor]

I organized the wiki pages so that all the GSOC-related pages are under a
parent page called GSOC 2016, which serves as a table of contents.

I also added a parent page called Releases, which has all the
release-related pages, and acts as a table of contents.

Does this seem reasonable?

Gale

Re: Code Analysis Tools Implementation

[Gale Naylor]

If you only need one page, go ahead and use this one:

https://cwiki.apache.org/confluence/display/TAVERNADEV/GSOC+2016+Apache+Taverna+Mobile

If you need multiple pages, go ahead and create them - we can always sort
out the organization later.

On Thu, Jun 9, 2016 at 10:54 AM Gale Naylor 
wrote:

> I created a GSOC 2016 Apache Taverna Mobile parent page. You can add wiki
> page(s) as child pages. Let me know if you have any problems.
>
> Gale
>
> On Thu, Jun 9, 2016 at 10:27 AM Gale Naylor 
> wrote:
>
>> You should be all set, Sagar!
>>
>> On Thu, Jun 9, 2016 at 10:01 AM Sagar  wrote:
>>
>>> Hi Gale,
>>>
>>> I sign-up here : https://cwiki.apache.org/confluence/signup.action
>>>
>>> my username : sagar15795
>>>
>>> Thanks.
>>> Sagar
>>>
>>> On Thu, Jun 9, 2016 at 8:00 PM, Gale Naylor >> >
>>> wrote:
>>>
>>> > Hi Rajan,
>>> >
>>> > You should be able to add a wiki now. Please let me know if you have
>>> any
>>> > difficulties.
>>> >
>>> > Thanks,
>>> > Gale
>>> >
>>> > On Thu, Jun 9, 2016 at 4:08 AM Rajan Maurya 
>>> > wrote:
>>> >
>>> > > Hi,
>>> > >
>>> > > I sign-up here : https://cwiki.apache.org/confluence/signup.action
>>> > >
>>> > > my username : therajanmaurya
>>> > >
>>> > > Thanks.
>>> > >
>>> > >
>>> > > On Wed, Jun 8, 2016 at 9:40 PM, Stian Soiland-Reyes <
>>> st...@apache.org>
>>> > > wrote:
>>> > >
>>> > > > On 6 June 2016 at 06:02, Rajan Maurya 
>>> > wrote:
>>> > > > > Hi Sagar,
>>> > > > >
>>> > > > > I have looked you #PR
>>> > > > > <https://github.com/apache/incubator-taverna-mobile/pull/14>.
>>> It's
>>> > now
>>> > > > > completed. You did a good job.
>>> > > >
>>> > > > Thanks for your good mentoring, Rajan! Pull request merged.
>>> > > >
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > *Thanks*
>>> > > *Namaste*
>>> > >
>>> > > Rajan Maurya
>>> > > Contact Number : +91 8010665248
>>> > > Github : https://github.com/therajanmaurya
>>> > > College : Cluster Innovation Centre, University of Delhi
>>> > > Student : B.Tech. (Information Technology & Mathematical Innovations)
>>> > >
>>> >
>>>
>>>
>>>
>>> --
>>>
>>> *With warm regards  *
>>> *Sincerely yours*
>>> Sagar
>>>
>>>
>>> *Student ,(6th Semester )B.Tech IT and mathematical innovation*
>>> *Cluster Innovation Centre*
>>> *University of Delhi *
>>>
>>