Re: News pages was Re: Draft download pages

[alaninmcr]

On 10/05/2016 14:09, Ian Dunlop wrote:

Hello,

I guess its the G+ feed that needs updated. Who controls it? Looks like
some GSoC 2016 news/tweets are needed. No point having the social media
feeds if they are not used :(


It's strange as some posts have been made e.g. BioVeL = SEEK and Taverna 
addressing climate change.



Cheers,

Ian


Alan

Re: News pages was Re: Draft download pages

[Ian Dunlop]

Hello,

I guess its the G+ feed that needs updated. Who controls it? Looks like
some GSoC 2016 news/tweets are needed. No point having the social media
feeds if they are not used :(

Cheers,

Ian

On 10 May 2016 at 13:10, alaninmcr  wrote:

> Hello everyone,
>
> I noticed the News https://taverna.incubator.apache.org/community/news is
> very out of date compared with the Tweets.
>
> I think it would be better to hide out of date "News". Any ideas /
> comments?
>
> Alan
>

Re: Release of Taverna Command Line?

[Ian Dunlop]

Hello,

Engine and activites built ok on OSX Java 8 but there seem to be some
dependency issues with the commandline [1]. I guess my linux machine had
the artifacts already downloaded in the repo. This is the first time I have
tried building any of the taverna artifacts on this mac.

Cheers,

Ian

[1]:
 [ERROR] Failed to execute goal on project taverna-commandline-product:
Could not resolve dependencies for project
org.apache.taverna.commandline:taverna-commandline-product:jar:3.1.0-incubating-SNAPSHOT:
The following artifacts could not be resolved:
javax.mail:com.springsource.javax.mail:jar:1.4.1,
org.apache.xerces:com.springsource.org.apache.xerces:jar:2.9.1,
org.apache.xalan:com.springsource.org.apache.xalan:jar:2.7.1: Failure to
find javax.mail:com.springsource.javax.mail:jar:1.4.1 in
https://repo.maven.apache.org/maven2 was cached in the local repository,
resolution will not be reattempted until the update interval of central has
elapsed or updates are forced -> [Help 1]

On 8 May 2016 at 21:09, Stian Soiland-Reyes  wrote:

> Yes, great if you could have a go with the latest and greatest!
>
> I think from Oracle's JDK download page should work. Not sure if it works
> with the Java.com distribution, I think that would not include the Java
> compiler.
> On 8 May 2016 10:02 a.m., "Ian Dunlop"  wrote:
>
> > Hello,
> >
> > I might have a 64 bit mac running whatever the latest OS is called
> > (Yosemite? So long since I have used it). Is there Java 8 available?
> >
> > Cheers,
> >
> > Ian
> >
> > On 7 May 2016 at 12:27, Stian Soiland-Reyes  wrote:
> >
> > > Great! Then I say the only risk factor now is the notorious OS X
> > > Java.. anyone having the hardware?
> > >
> > > (I think my old Mac only runs 32-bit OSX 10.5, so it won't do Java 8
> > well)
> > >
> > >
> > >
> > > On 7 May 2016 at 11:20, Alan Williams 
> wrote:
> > > > On 06-May-16 12:14, Stian Soiland-Reyes wrote:
> > > >>
> > > >> Thanks for checking Ian!
> > > >>
> > > >> I think I updated all the READMEs to say we need Java 8 now.  We
> > > >> agreed to that update in
> > > >> https://issues.apache.org/jira/browse/TAVERNA-869
> > > >>
> > > >>
> > > >> I'm going to do a pre-flight test in Windows 10 as well so we don't
> > > >> need to do the dance on the RCs again..
> > > >>
> > > >> I'll be brave and even have a go inside the new Ubuntu in Windows
> > > >> subsystem... if it works there, then we have nothing to worry about
> :)
> > > >>
> > > >>
> > > >> Perhaps Alan can have a go in his temperamental Windows 8?
> > > >
> > > >
> > > > Alan had a go :)
> > > >
> > > > Windows 8.1
> > > > Java 1.8.0_51
> > > > Maven 3.3.3
> > > >
> > > > Engine, Common Activities and CommandLine all installed with no
> > problems.
> > > >
> > > > Alan
> > >
> > >
> > >
> > > --
> > > Stian Soiland-Reyes
> > > Apache Taverna (incubating), Apache Commons RDF (incubating)
> > > http://orcid.org/-0001-9842-9718
> > >
> >
>

News pages was Re: Draft download pages

[alaninmcr]

Hello everyone,

I noticed the News https://taverna.incubator.apache.org/community/news 
is very out of date compared with the Tweets.


I think it would be better to hide out of date "News". Any ideas / comments?

Alan

Re: Draft download pages

[alaninmcr]

On 09/05/2016 18:58, Stian Soiland-Reyes wrote:

OK, great if you could put it live!

I think now with the Command Line relesse is a good time to force old users
through the Apache Taverna pages, even if it might mean they go back to the
archive page to download the 2.5 Workbench.


It should be live now.

Alan

Re: Access/modify annotations in a WorkflowBundle

[Enrico Daga (enridaga)]

Dear Stian,

(sorry for this late reply, I’ve been away for few days)

I understand the problem from your explanation. I really appreciate you 
integrated the workaround in the current master.
I am OK on using the SNAPSHOT release for the time being, and happy to report 
any issues I might find.

Again, thank you for the help.

Best

Enrico


—
Enrico Daga (enridaga)
http://www.enridaga.net 
Il budda e’ nel parco.





> On 4 May 2016, at 12:04, Stian Soiland-Reyes  wrote:
> 
> I've added the wfbundle parser TAVERNA-71 workaround in master - see
> 
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java#L136
> 
> Do you think you could try out the latest SNAPSHOT?
> 
> 
>  org.apache.taverna.language
>  taverna-scufl2-wfbundle
>  0.15.2-incubating-SNAPSHOT
> 
> 
> 
>  
>
>  apache.snapshots
>  Apache Snapshot Repository
>  http://repository.apache.org/snapshots
>  
>false
>  
>
> 
> 
> 
> 
> (If this works, then you don't need your own version of parseAnnotations() )
> 
> On 4 May 2016 at 11:21, Stian Soiland-Reyes  wrote:
>> My apologies - you are right - I realize now that if you open a
>> wfbundle (as opposed to a .t2flow) - then getAnnotations() is always
>> empty.
>> 
>> It should work if you open a .t2flow as the T2flow parser populates
>> wfbundle.getAnnotations().
>> 
>> 
>> The reason is that the annotation links in wfbundle.getAnnotations()
>> are not stored in the wfbundle manifest (and not parsed).
>> 
>> some preliminary code for this was at:
>> 
>> https://github.com/apache/incubator-taverna-language/blob/0.15.1-incubating/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLSerializer.java#L549
>> 
>> To put it blunt - the t2flow parsed adds
>>  that describes
>>  - however the link between
>>  and
>>  is not
>> serialized - and so the only way to find annotation/ now is to go
>> through the annotation/ folder.
>> 
>> 
>> I think this relates to
>> https://issues.apache.org/jira/browse/TAVERNA-965 as the UCFPackage or
>> WorkflowBundle didn't have a mechanism to serialize which annotations
>> exist (it would basically need to replicate
>> https://w3id.org/bundle/#manifest-annotations ) - and so there would
>> not be any point in not moving to taverna-robundle for managing the
>> bundle and the annotations.
>> 
>> This bug was already tracked at
>> https://issues.apache.org/jira/browse/TAVERNA-71 - I've promoted this
>> to be Fix For Language 0.16.0.
>> 
>> I've shown you a workaround in
>> https://github.com/enridaga/taverna-sandbox/pull/1
>> to parse the wfbundle annotations
>> and I'm testing to add this to taverna-scufl2-wfbundle as a workaround.
>> 
>> 
>> 
>> 
>> On 3 May 2016 at 11:19, Enrico Daga (enridaga)  wrote:
>>> Hi Stian,
>>> 
>>> I tried with the latest release but I am still struggling on getting this 
>>> work.
>>> 
>>> I prepared a minimal project to test the issue [1], which contains a single 
>>> test using a workflow downloaded from my experiment (and converted to 
>>> wfbundle) [2].
>>> 
>>> This wf contains a set of annotations, particularly from input ports. I can 
>>> see them unpacking the bundle [3].
>>> 
>>> However, I cannot access them in the way you suggested (replicated here 
>>> [4]).
>>> 
>>> Best,
>>> 
>>> Enrico
>>> 
>>> 
>>> 
>>> [1] https://github.com/enridaga/taverna-sandbox 
>>> 
>>> [2] http://www.myexperiment.org/workflows/4303.html 
>>> 
>>> [3] 
>>> https://github.com/enridaga/taverna-sandbox/tree/master/src/test/resources/bundles/3Drec-v1/annotation
>>>  
>>> 
>>> [4] 
>>> https://github.com/enridaga/taverna-sandbox/blob/master/src/test/java/enridaga/AppTest.java
>>>  
>>> 
>>> 
>>> —
>>> Enrico Daga (enridaga)
>>> http://www.enridaga.net 
>>> Il budda e’ nel parco.
>>> 
>>> 
>>> 
>>> 
>>> 
 On 3 May 2016, at 09:01, Enrico Daga (enridaga)  
 wrote:
 
 Thank you Stian, this is gold.
 
 Will try the new release as well.
 
 It's good to have Taverna at Apache!
 
 Best,
 Enrico
 
 
 —
 Enrico Daga (enridaga)
 http://www.enridaga.net 
 Il budda e’ nel parco.
 
 
 
 
 
> On 2 May 2016, at 17:19, Stian Soiland-Reyes  > wrote:
> 
> BTW - another alternative - if you convert to wfdesc with tavlang convert 
> - see
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-tavlang-tool
>  
>