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Posted to dev@taverna.apache.org by Stian Soiland-Reyes <st...@apache.org> on 2016/04/11 17:30:19 UTC
Re: Enquiry about the features of Taverna 2.5
Hi!
(Folks, Khalid help do lots of work on research object, wfprov and
wfdesc which we use in taverna-language and
taverna-engine/taverna-prov)
On 11 April 2016 at 15:17, Khalid Belhajjame <kb...@googlemail.com> wrote:
> I would like to enquiry about some of the current features of Taverna. I
> have an answer for most of the question, but I would like to know the status
> with respect to the current version (2.5) of Taverna. I will be grateful if
> you could take the time to answer them.
>
> 1- In the current version of Taverna (2.5), I can see that the provenance
> can be saved as PROV, but not as OPM. I am guessing that OPM export was
> deprecated. Let me know if I am wrong. Regarding the PROV export, you are
> using TavernaProv isn’t it? If so, do you have TavernaProv documented
> somewhere? I would like to see how it compares to wfprov.
Yes, you are correct in that the OPM export was deprecated in 2.5 - it
was also less in match with what was happening in the workflow so it
was rather removed.
TavernaProv became part of Taverna from 2.5. Documentation and example here:
https://github.com/apache/incubator-taverna-engine/tree/master/taverna-prov
(It's not yet fully integrated into Taverna 3)
TavernaProv is basically wfprov+prov+taverna - you will see that
everything is stated both with pure prov and in wfprov - which often
provides shortcuts. For details such as at which iteration something
happened you have to use the tavernaprov aspects - which also adds a
cnt:chars for embedding smaller values, and checksums like
tavernaprov:sha512.
> 2- Are there any utilities/means that help users to either deploy workflows
> on the cloud or call services/use resource on the cloud? I remember the work
> of Sonja with Unicore. Is there any other work that was conducted on this
> front?
A bit related - we have a GSOC student working on Docker:
https://issues.apache.org/jira/browse/TAVERNA-879
As for actually managing cloud instances or grid jobs I am not aware
of any current initiatives. Perhaps Dmitry or Vadim Surpin knows of
something?
I think the http://www.vph-dare.eu/ project is using VPH Share and
local Grid infrastructure via Taverna Server - but I'm not sure of the
details.
> 3- is the CWL used somehow to allow for the exchange of workflow
> specifications between workflow systems?
In CWL we are discussing how we can use wfprov and some aspects of
tavernaprov. See
https://github.com/common-workflow-language/common-workflow-language/issues/84
We are working on CWL support in Apache Taverna this summer - we might
get three Google Summer Of Code students this year:
https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+GSOC+2016
And I will pick up some work here as well for http://bioexcel.eu/ - my
use case is to use CWL and Docker with Open PHACTS and
Taverna/Galaxy/Knime - with deployment on the EGI grid/cloud:
http://slides.com/soilandreyes/2016-02-11-bioexcel-use-case-open-phacts
> 4-Is there anything that has been done in relation to initiatives such as
> iPython?
I think Alan might know about iPython and Jupyter.. Not sure if
anything was done since this:
http://www.taverna.org.uk/2014/05/20/calling-taverna-workflows-from-ipython-notebook/
Does the Taverna Player still support iPython in such a way?
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Enquiry about the features of Taverna 2.5
Posted by Khalid Belhajjame <kb...@googlemail.com>.
Thanks alot Stian,
These are very helpful.
best wishes,
khalid
On 11 April 2016 at 17:30, Stian Soiland-Reyes <st...@apache.org> wrote:
> Hi!
>
> (Folks, Khalid help do lots of work on research object, wfprov and
> wfdesc which we use in taverna-language and
> taverna-engine/taverna-prov)
>
> On 11 April 2016 at 15:17, Khalid Belhajjame <kb...@googlemail.com>
> wrote:
> > I would like to enquiry about some of the current features of Taverna. I
> > have an answer for most of the question, but I would like to know the
> status
> > with respect to the current version (2.5) of Taverna. I will be grateful
> if
> > you could take the time to answer them.
> >
> > 1- In the current version of Taverna (2.5), I can see that the provenance
> > can be saved as PROV, but not as OPM. I am guessing that OPM export was
> > deprecated. Let me know if I am wrong. Regarding the PROV export, you are
> > using TavernaProv isn’t it? If so, do you have TavernaProv documented
> > somewhere? I would like to see how it compares to wfprov.
>
>
> Yes, you are correct in that the OPM export was deprecated in 2.5 - it
> was also less in match with what was happening in the workflow so it
> was rather removed.
>
> TavernaProv became part of Taverna from 2.5. Documentation and example
> here:
>
> https://github.com/apache/incubator-taverna-engine/tree/master/taverna-prov
>
> (It's not yet fully integrated into Taverna 3)
>
>
> TavernaProv is basically wfprov+prov+taverna - you will see that
> everything is stated both with pure prov and in wfprov - which often
> provides shortcuts. For details such as at which iteration something
> happened you have to use the tavernaprov aspects - which also adds a
> cnt:chars for embedding smaller values, and checksums like
> tavernaprov:sha512.
>
>
> > 2- Are there any utilities/means that help users to either deploy
> workflows
> > on the cloud or call services/use resource on the cloud? I remember the
> work
> > of Sonja with Unicore. Is there any other work that was conducted on this
> > front?
>
> A bit related - we have a GSOC student working on Docker:
>
> https://issues.apache.org/jira/browse/TAVERNA-879
>
> As for actually managing cloud instances or grid jobs I am not aware
> of any current initiatives. Perhaps Dmitry or Vadim Surpin knows of
> something?
>
> I think the http://www.vph-dare.eu/ project is using VPH Share and
> local Grid infrastructure via Taverna Server - but I'm not sure of the
> details.
>
>
> > 3- is the CWL used somehow to allow for the exchange of workflow
> > specifications between workflow systems?
>
>
> In CWL we are discussing how we can use wfprov and some aspects of
> tavernaprov. See
>
> https://github.com/common-workflow-language/common-workflow-language/issues/84
>
>
> We are working on CWL support in Apache Taverna this summer - we might
> get three Google Summer Of Code students this year:
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+GSOC+2016
>
> And I will pick up some work here as well for http://bioexcel.eu/ - my
> use case is to use CWL and Docker with Open PHACTS and
> Taverna/Galaxy/Knime - with deployment on the EGI grid/cloud:
>
> http://slides.com/soilandreyes/2016-02-11-bioexcel-use-case-open-phacts
>
>
> > 4-Is there anything that has been done in relation to initiatives such as
> > iPython?
>
>
> I think Alan might know about iPython and Jupyter.. Not sure if
> anything was done since this:
>
>
> http://www.taverna.org.uk/2014/05/20/calling-taverna-workflows-from-ipython-notebook/
>
> Does the Taverna Player still support iPython in such a way?
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Enquiry about the features of Taverna 2.5
Posted by alaninmcr <al...@googlemail.com>.
On 11/04/2016 16:30, Stian Soiland-Reyes wrote:
> Hi!
[snip]
>> 4-Is there anything that has been done in relation to initiatives such as
>> iPython?
>
>
> I think Alan might know about iPython and Jupyter.. Not sure if
> anything was done since this:
>
> http://www.taverna.org.uk/2014/05/20/calling-taverna-workflows-from-ipython-notebook/
>
> Does the Taverna Player still support iPython in such a way?
That is really IPython calling Taverna workflows. It should still work.
Alan
Re: Enquiry about the features of Taverna 2.5
Posted by Khalid Belhajjame <kb...@googlemail.com>.
Thanks alot Stian,
These are very helpful.
best wishes,
khalid
On 11 April 2016 at 17:30, Stian Soiland-Reyes <st...@apache.org> wrote:
> Hi!
>
> (Folks, Khalid help do lots of work on research object, wfprov and
> wfdesc which we use in taverna-language and
> taverna-engine/taverna-prov)
>
> On 11 April 2016 at 15:17, Khalid Belhajjame <kb...@googlemail.com>
> wrote:
> > I would like to enquiry about some of the current features of Taverna. I
> > have an answer for most of the question, but I would like to know the
> status
> > with respect to the current version (2.5) of Taverna. I will be grateful
> if
> > you could take the time to answer them.
> >
> > 1- In the current version of Taverna (2.5), I can see that the provenance
> > can be saved as PROV, but not as OPM. I am guessing that OPM export was
> > deprecated. Let me know if I am wrong. Regarding the PROV export, you are
> > using TavernaProv isn’t it? If so, do you have TavernaProv documented
> > somewhere? I would like to see how it compares to wfprov.
>
>
> Yes, you are correct in that the OPM export was deprecated in 2.5 - it
> was also less in match with what was happening in the workflow so it
> was rather removed.
>
> TavernaProv became part of Taverna from 2.5. Documentation and example
> here:
>
> https://github.com/apache/incubator-taverna-engine/tree/master/taverna-prov
>
> (It's not yet fully integrated into Taverna 3)
>
>
> TavernaProv is basically wfprov+prov+taverna - you will see that
> everything is stated both with pure prov and in wfprov - which often
> provides shortcuts. For details such as at which iteration something
> happened you have to use the tavernaprov aspects - which also adds a
> cnt:chars for embedding smaller values, and checksums like
> tavernaprov:sha512.
>
>
> > 2- Are there any utilities/means that help users to either deploy
> workflows
> > on the cloud or call services/use resource on the cloud? I remember the
> work
> > of Sonja with Unicore. Is there any other work that was conducted on this
> > front?
>
> A bit related - we have a GSOC student working on Docker:
>
> https://issues.apache.org/jira/browse/TAVERNA-879
>
> As for actually managing cloud instances or grid jobs I am not aware
> of any current initiatives. Perhaps Dmitry or Vadim Surpin knows of
> something?
>
> I think the http://www.vph-dare.eu/ project is using VPH Share and
> local Grid infrastructure via Taverna Server - but I'm not sure of the
> details.
>
>
> > 3- is the CWL used somehow to allow for the exchange of workflow
> > specifications between workflow systems?
>
>
> In CWL we are discussing how we can use wfprov and some aspects of
> tavernaprov. See
>
> https://github.com/common-workflow-language/common-workflow-language/issues/84
>
>
> We are working on CWL support in Apache Taverna this summer - we might
> get three Google Summer Of Code students this year:
>
> https://cwiki.apache.org/confluence/display/TAVERNADEV/2016-03+GSOC+2016
>
> And I will pick up some work here as well for http://bioexcel.eu/ - my
> use case is to use CWL and Docker with Open PHACTS and
> Taverna/Galaxy/Knime - with deployment on the EGI grid/cloud:
>
> http://slides.com/soilandreyes/2016-02-11-bioexcel-use-case-open-phacts
>
>
> > 4-Is there anything that has been done in relation to initiatives such as
> > iPython?
>
>
> I think Alan might know about iPython and Jupyter.. Not sure if
> anything was done since this:
>
>
> http://www.taverna.org.uk/2014/05/20/calling-taverna-workflows-from-ipython-notebook/
>
> Does the Taverna Player still support iPython in such a way?
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>