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Posted to users@taverna.apache.org by Matthieu Melcot <ma...@spaceapplications.com> on 2015/02/27 11:30:50 UTC
A few questions before choosing Taverna for our project
Dear Taverna Team,
I am currently looking for an orchestrator that could suit our project
needs.
I discovered Taverna and it seems very interesting.
I have a few questions that I would like to clarify before making the
choice of using Taverna in our project
The core of the project is the orchestration of WPS processes
(http://www.opengeospatial.org/standards/wps) which are Web Services for
Geospatial processing.
Basically, a client can request one of the 3 following
"GetCapabilities", "DescribeProcess", "Execute" and get a
response in XML
The WPS server implementation that we will use
(http://52north.org/communities/geoprocessing/wps/) doesn't embed the
WPS xml inside SOAP (even if the OGC WPS norm describes it), and their
are not WSDL capabilities.
1) Is it relatively easy to develop a component for Taverna that will
allow to add these WPS services into the "Services Available" for
building a workflow ? Which kind of effort would it represent ?
I read
(http://geoprocessing.forum.52north.org/Problem-with-Taverna-td4024997.html)
that some people try to use WPS with Taverna (Through WSDL however), but
they didnt succeed.
2) In the case that it is possible, is there some possibilities to
describe semantically the input and output of these WPS services (indeed
the input and outputs will always be URL (texts), but the URLs reference
different types of materials), so that it would be possible to check if
the connections are valid. It seems that Taverna has that kind of
mechanism...
3) My third question is about the monitoring and control of the workflow
execution.
Is there a way through the REST API to ask which part of a workflow is
actually executing.
4) Is there a simple Web Viewer/Controller (It seems that the "Taverna
Player" needs to be embedded in web pages in ruby). Is there a more
straightforward way to use this player in order to test it ?
5) Is there a mean to control and monitor the execution of a remote
workflow directly from the Taverna Workbench. It seems that "File / Open
Workflow Location" makes reference to a .t2flow remote file, and not a
workflow that would have been load into the Taverna Server.
Thanks in advance for your help
Matthieu Melcot
--
Matthieu Melcot
Software Engineer
Space Applications Services NV/SA
Leuvensesteenweg 325, 1932 Zaventem, Belgium
Direct: +32-(0)2-416.05.35
Main: +32-(0)2-721.54.84 Fax: +32-(0)2-721.54.44
www.spaceapplications.com
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Hello Vitor,
So your advice to run my workflow on the other project, this one:
https://github.com/myGrid/t2-server-jar/tree/next/src/main/java/uk/org/taverna/server/client
can I run it? , looks so complicated.
Regards
From: vitorfs@gmail.com [mailto:vitorfs@gmail.com] On Behalf Of Vitor Freitas
Sent: Wednesday, April 08, 2015 11:31 AM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Hello everyone,
Actually I started the development of this taverna java client [1] because I couldn't find at the time a client to work with the Taverna Server. Actually, later on I found it hidden in the server code base, as Alan said hehe.
I used a kind of naive implementation just to do some proof of concept, in order to integrate our experiment platform (which is written in java) with taverna.
About the provenance thing I will check it out, maybe it is something I haven't implemented on my client. Anyway, probably this client [2] is more complete... Would be good if it was detached from the server code base
[1] https://github.com/pgcc/taverna-java-client
[2] https://github.com/myGrid/t2-server-jar/tree/next/src/main/java/uk/org/taverna/server/client
On Tue, Mar 31, 2015 at 3:18 PM, Alan Williams <al...@googlemail.com> wrote:
On 31-Mar-15 12:21, Ian Dunlop wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hello,
Would this client code be usable from the taverna android app (see
previous GSoC discussions).
It probably needs to be separated out. I think I understand the history, but it is not helpful having it "hidden" in the server code base.
wrt Android I do not know, but it would be good if it could.
Cheers,
Ian
Alan
--
Vitor Freitas
vitorfs.com <http://vitorfs.com/>
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Hello,
Okay I will try this project to get the provenance data:
https://github.com/myGrid/t2-server-jar/
if anyone has sample client to run the workflow, please send it, so I can modify that and run my workflow.
Regards
From: vitorfs@gmail.com [mailto:vitorfs@gmail.com] On Behalf Of Vitor Freitas
Sent: Thursday, April 09, 2015 12:34 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Hello,
I am not planning to work on this java client at the moment, as I am working on another project... But you can fork the java client repository on GitHub and modify it yourself... Shouldn't be that hard
I suggest you take a look at the REST API docs and verify the TavernaServices file [1] if the service endpoint is there... probably this interface will do what you are looking for: public File getWorkingDirectoryCompressed(String uuid) throws TavernaException;
Afterwards just implement the service call, just like I did on the other cases, just modifying the TavernaClient file [2].
[1] https://github.com/pgcc/taverna-java-client/blob/master/TavernaClient/src/br/ufjf/taverna/core/TavernaServices.java
[2] https://github.com/pgcc/taverna-java-client/blob/master/TavernaClient/src/br/ufjf/taverna/core/TavernaClient.java
On Thu, Apr 9, 2015 at 1:12 PM, Ahmad Aburomman <ah...@rai.usc.es> wrote:
Hello everyone,
I tried client [2] but it is complicated, it is differ from the client [1] which I can add my workflow and can run it.
I need your help to add provenance data to the client [1], please can you add it?
regards
From: vitorfs@gmail.com [mailto:vitorfs@gmail.com] On Behalf Of Vitor Freitas
Sent: Wednesday, April 08, 2015 11:31 AM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Hello everyone,
Actually I started the development of this taverna java client [1] because I couldn't find at the time a client to work with the Taverna Server. Actually, later on I found it hidden in the server code base, as Alan said hehe.
I used a kind of naive implementation just to do some proof of concept, in order to integrate our experiment platform (which is written in java) with taverna.
About the provenance thing I will check it out, maybe it is something I haven't implemented on my client. Anyway, probably this client [2] is more complete... Would be good if it was detached from the server code base
[1] https://github.com/pgcc/taverna-java-client
[2] https://github.com/myGrid/t2-server-jar/tree/next/src/main/java/uk/org/taverna/server/client
On Tue, Mar 31, 2015 at 3:18 PM, Alan Williams <al...@googlemail.com> wrote:
On 31-Mar-15 12:21, Ian Dunlop wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hello,
Would this client code be usable from the taverna android app (see
previous GSoC discussions).
It probably needs to be separated out. I think I understand the history, but it is not helpful having it "hidden" in the server code base.
wrt Android I do not know, but it would be good if it could.
Cheers,
Ian
Alan
--
Vitor Freitas
vitorfs.com <http://vitorfs.com/>
--
Vitor Freitas
vitorfs.com <http://vitorfs.com/>
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Yes sure, just give me your account name, and let me know the time to talk
thanks
-----Original Message-----
From: Alan Williams [mailto:alaninmcr@googlemail.com]
Sent: Friday, April 10, 2015 2:23 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
On 09-Apr-15 18:27, Ahmad Aburomman wrote:
> My hangout is ahmad.aburoman@gmail.com
Can we try for a hangout on Monday?
Alan
Re: A few questions before choosing Taverna for our project
Posted by Alan Williams <al...@googlemail.com>.
On 09-Apr-15 18:27, Ahmad Aburomman wrote:
> My hangout is ahmad.aburoman@gmail.com
Can we try for a hangout on Monday?
Alan
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
My hangout is ahmad.aburoman@gmail.com
-----Original Message-----
From: Ahmad Aburomman [mailto:ahmad.aburomman@rai.usc.es]
Sent: Thursday, April 09, 2015 1:35 PM
To: users@taverna.incubator.apache.org
Subject: RE: A few questions before choosing Taverna for our project
Yes that will more easy.
-----Original Message-----
From: Alan Williams [mailto:alaninmcr@googlemail.com]
Sent: Thursday, April 09, 2015 1:04 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Hello everybody,
Would it make sense to have a Google hangout (or similar) to discuss what to do about Taverna Server client code?
Alan
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Yes that will more easy.
-----Original Message-----
From: Alan Williams [mailto:alaninmcr@googlemail.com]
Sent: Thursday, April 09, 2015 1:04 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Hello everybody,
Would it make sense to have a Google hangout (or similar) to discuss what to do about Taverna Server client code?
Alan
Re: A few questions before choosing Taverna for our project
Posted by Alan Williams <al...@googlemail.com>.
Hello everybody,
Would it make sense to have a Google hangout (or similar) to discuss
what to do about Taverna Server client code?
Alan
Re: A few questions before choosing Taverna for our project
Posted by Vitor Freitas <vi...@freitas.com>.
Hello,
I am not planning to work on this java client at the moment, as I am
working on another project... But you can fork the java client repository
on GitHub and modify it yourself... Shouldn't be that hard
I suggest you take a look at the REST API docs and verify the
TavernaServices file [1] if the service endpoint is there... probably this
interface will do what you are looking for: public File
getWorkingDirectoryCompressed(String uuid) throws TavernaException;
Afterwards just implement the service call, just like I did on the other
cases, just modifying the TavernaClient file [2].
[1]
https://github.com/pgcc/taverna-java-client/blob/master/TavernaClient/src/br/ufjf/taverna/core/TavernaServices.java
[2]
https://github.com/pgcc/taverna-java-client/blob/master/TavernaClient/src/br/ufjf/taverna/core/TavernaClient.java
On Thu, Apr 9, 2015 at 1:12 PM, Ahmad Aburomman <ah...@rai.usc.es>
wrote:
> Hello everyone,
>
>
>
> I tried client [2] but it is complicated, it is differ from the client [1]
> which I can add my workflow and can run it.
>
> I need your help to add provenance data to the client [1], please can you
> add it?
>
>
>
> regards
>
>
>
> *From:* vitorfs@gmail.com [mailto:vitorfs@gmail.com] *On Behalf Of *Vitor
> Freitas
> *Sent:* Wednesday, April 08, 2015 11:31 AM
> *To:* users@taverna.incubator.apache.org
> *Subject:* Re: A few questions before choosing Taverna for our project
>
>
>
> Hello everyone,
>
>
>
> Actually I started the development of this taverna java client [1] because
> I couldn't find at the time a client to work with the Taverna Server.
> Actually, later on I found it hidden in the server code base, as Alan said
> hehe.
>
>
>
> I used a kind of naive implementation just to do some proof of concept, in
> order to integrate our experiment platform (which is written in java) with
> taverna.
>
>
>
> About the provenance thing I will check it out, maybe it is something I
> haven't implemented on my client. Anyway, probably this client [2] is more
> complete... Would be good if it was detached from the server code base
>
>
>
> [1] https://github.com/pgcc/taverna-java-client
>
> [2]
> https://github.com/myGrid/t2-server-jar/tree/next/src/main/java/uk/org/taverna/server/client
>
>
>
> On Tue, Mar 31, 2015 at 3:18 PM, Alan Williams <al...@googlemail.com>
> wrote:
>
> On 31-Mar-15 12:21, Ian Dunlop wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA512
>
> Hello,
>
> Would this client code be usable from the taverna android app (see
> previous GSoC discussions).
>
>
> It probably needs to be separated out. I think I understand the history,
> but it is not helpful having it "hidden" in the server code base.
>
> wrt Android I do not know, but it would be good if it could.
>
> Cheers,
>
> Ian
>
>
> Alan
>
>
>
>
>
> --
>
> Vitor Freitas
>
> vitorfs.com
>
--
Vitor Freitas
vitorfs.com
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Hello everyone,
I tried client [2] but it is complicated, it is differ from the client [1] which I can add my workflow and can run it.
I need your help to add provenance data to the client [1], please can you add it?
regards
From: vitorfs@gmail.com [mailto:vitorfs@gmail.com] On Behalf Of Vitor Freitas
Sent: Wednesday, April 08, 2015 11:31 AM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Hello everyone,
Actually I started the development of this taverna java client [1] because I couldn't find at the time a client to work with the Taverna Server. Actually, later on I found it hidden in the server code base, as Alan said hehe.
I used a kind of naive implementation just to do some proof of concept, in order to integrate our experiment platform (which is written in java) with taverna.
About the provenance thing I will check it out, maybe it is something I haven't implemented on my client. Anyway, probably this client [2] is more complete... Would be good if it was detached from the server code base
[1] https://github.com/pgcc/taverna-java-client
[2] https://github.com/myGrid/t2-server-jar/tree/next/src/main/java/uk/org/taverna/server/client
On Tue, Mar 31, 2015 at 3:18 PM, Alan Williams <al...@googlemail.com> wrote:
On 31-Mar-15 12:21, Ian Dunlop wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hello,
Would this client code be usable from the taverna android app (see
previous GSoC discussions).
It probably needs to be separated out. I think I understand the history, but it is not helpful having it "hidden" in the server code base.
wrt Android I do not know, but it would be good if it could.
Cheers,
Ian
Alan
--
Vitor Freitas
vitorfs.com <http://vitorfs.com/>
Re: A few questions before choosing Taverna for our project
Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 08/04/2015 10:30, Vitor Freitas wrote:
> Actually I started the development of this taverna java client [1]
> because I couldn't find at the time a client to work with the Taverna
> Server. Actually, later on I found it hidden in the server code base, as
> Alan said hehe.
>
> I used a kind of naive implementation just to do some proof of concept,
> in order to integrate our experiment platform (which is written in java)
> with taverna.
>
> About the provenance thing I will check it out, maybe it is something I
> haven't implemented on my client. Anyway, probably this client [2] is
> more complete... Would be good if it was detached from the server code base
My original plan was to evolve that into a separate product library that
we could publish somewhere (like Maven Central?) but I got side-tracked
into a different project for the past couple of months. :-) The
t2-server-jar library hasn't had any commits for some time; I don't know
if it supports the current server API (if it doesn't, it'll only be
missing a few methods). It probably ought to be merged with the code in
the server codebase, which uses a somewhat different code-generation
technique (it derives the binding layer from WADL instead of building it
up from XSD directly).
Donal.
Re: A few questions before choosing Taverna for our project
Posted by Vitor Freitas <vi...@freitas.com>.
Hello everyone,
Actually I started the development of this taverna java client [1] because
I couldn't find at the time a client to work with the Taverna Server.
Actually, later on I found it hidden in the server code base, as Alan said
hehe.
I used a kind of naive implementation just to do some proof of concept, in
order to integrate our experiment platform (which is written in java) with
taverna.
About the provenance thing I will check it out, maybe it is something I
haven't implemented on my client. Anyway, probably this client [2] is more
complete... Would be good if it was detached from the server code base
[1] https://github.com/pgcc/taverna-java-client
[2]
https://github.com/myGrid/t2-server-jar/tree/next/src/main/java/uk/org/taverna/server/client
On Tue, Mar 31, 2015 at 3:18 PM, Alan Williams <al...@googlemail.com>
wrote:
> On 31-Mar-15 12:21, Ian Dunlop wrote:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA512
>>
>> Hello,
>>
>> Would this client code be usable from the taverna android app (see
>> previous GSoC discussions).
>>
>
> It probably needs to be separated out. I think I understand the history,
> but it is not helpful having it "hidden" in the server code base.
>
> wrt Android I do not know, but it would be good if it could.
>
> Cheers,
>>
>> Ian
>>
>
> Alan
>
>
--
Vitor Freitas
vitorfs.com
Re: A few questions before choosing Taverna for our project
Posted by Alan Williams <al...@googlemail.com>.
On 31-Mar-15 12:21, Ian Dunlop wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA512
>
> Hello,
>
> Would this client code be usable from the taverna android app (see
> previous GSoC discussions).
It probably needs to be separated out. I think I understand the history,
but it is not helpful having it "hidden" in the server code base.
wrt Android I do not know, but it would be good if it could.
> Cheers,
>
> Ian
Alan
Re: A few questions before choosing Taverna for our project
Posted by Ian Dunlop <ia...@manchester.ac.uk>.
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hello,
Would this client code be usable from the taverna android app (see
previous GSoC discussions).
Cheers,
Ian
On 31/03/2015 12:18, Alan Williams wrote:
> On 31-Mar-15 12:03, Stian Soiland-Reyes wrote:
>
> [snip]
>
>> I was confused as I thought he was talking about
>> https://github.com/myGrid/t2-server-jar/ .. which has not been
>> updated for Taverna 2.5 -- your code is made from scratch against
>> the 2.5 APIs, right?
>
> There is also the client code generated from the WADL (generated
> from the server code IIRC). It is at
>
> https://github.com/taverna/taverna-server/tree/2.5/server-client
>
> I think we need a discussion about how to do the Server clients. I
> think it is best to have the auto-generated one and then (if
> wanted) layer any "cleverer" code on top of that.
>
> Alan
>
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Re: A few questions before choosing Taverna for our project
Posted by Stian Soiland-Reyes <st...@apache.org>.
+1 to try a simple "clever stuff" layered over the auto generated one
The generated code would be deployed as separate module in Maven anyway,
so I think it is OK that it stays within the server code base, even though
it smells a lot of classic Axis1 style of client server development..
On 31 Mar 2015 12:18, "Alan Williams" <al...@googlemail.com> wrote:
> On 31-Mar-15 12:03, Stian Soiland-Reyes wrote:
>
> [snip]
>
> I was confused as I thought he was talking about
>> https://github.com/myGrid/t2-server-jar/
>> .. which has not been updated for Taverna 2.5 -- your code is made
>> from scratch against the 2.5 APIs, right?
>>
>
> There is also the client code generated from the WADL (generated from the
> server code IIRC). It is at
>
> https://github.com/taverna/taverna-server/tree/2.5/server-client
>
> I think we need a discussion about how to do the Server clients. I think
> it is best to have the auto-generated one and then (if wanted) layer any
> "cleverer" code on top of that.
>
> Alan
>
>
Re: A few questions before choosing Taverna for our project
Posted by Alan Williams <al...@googlemail.com>.
On 31-Mar-15 12:03, Stian Soiland-Reyes wrote:
[snip]
> I was confused as I thought he was talking about
> https://github.com/myGrid/t2-server-jar/
> .. which has not been updated for Taverna 2.5 -- your code is made
> from scratch against the 2.5 APIs, right?
There is also the client code generated from the WADL (generated from
the server code IIRC). It is at
https://github.com/taverna/taverna-server/tree/2.5/server-client
I think we need a discussion about how to do the Server clients. I think
it is best to have the auto-generated one and then (if wanted) layer any
"cleverer" code on top of that.
Alan
Re: A few questions before choosing Taverna for our project
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 31 March 2015 at 11:34, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Thanks a lot for your indeed reply, actually I'm using this project
> https://github.com/pgcc/taverna-java-client
Ah, that code is brand new to me and seems to be written for Taverna
Server 2.5 - we should invite Vitor to join the mailing list.
Vitor - Ahmad here have some questions about your taverna-java-client
and getting the provenance back
http://markmail.org/message/gplybw7ruvgef6o7
I was confused as I thought he was talking about
https://github.com/myGrid/t2-server-jar/
.. which has not been updated for Taverna 2.5 -- your code is made
from scratch against the 2.5 APIs, right?
Vitor, have you signed up to the Apache Taverna mailing lists? We
would love to have you on board and possibly join effort on the
Taverna Server client effort! Also it would be cool to hear what you
use Taverna for.
http://taverna.incubator.apache.org/contact/
> I have implemented the Provenance function in TavernaClient.java, it is okay now and enabled but still can't get the provenance data with the output
> You mentioned that I have to do some function to Baclava, can you guide me please or give me the exact script to update my project.
>
> Regards
> Ahmad
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 2:24 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> Not sure where you found that code, as I found they were implemented here:
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L344
>
>
> but in either case, the baclava input/output should NOT be used if you want the workflow run bundle back.
>
>
> Unfortunately the Taverna Server client code for Java has not been updated for the run bundle, which was new in 2.5 I think.
>
> It would be great if you could have a quick go - I think it should be quite doable, we've just not got around to it yet...
>
> Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
>
>
> By
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
> you need to send a PUT with "true" to /runs/{id}/generate-provenance
>
> so perhaps something like this could work?
>
>
> package uk.org.taverna.server.client.Run add two new methods, e.g.:
>
> similar to isBaclavaOutput and requestBaclavaOutput
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L404
>
> but with "generate-provenance" added to the run URL.
>
>
> Similarly add getRunBundle() similar to getOutputZip()
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L1140
>
> .. but requesting "run-bundle" added to the URL.
>
>
> To do it "proper REST-like" this can be generalized to find those two URI fragments from the runDescription as you see with getLink() in other bits of the code.
>
> On 27 March 2015 at 12:07, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>> Yes I see these code about baklava, but I don't know what to add exactly!
>>
>> @Override
>> public String getBaclavaInput(String uuid) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>> }
>>
>> @Override
>> public String setBaclavaInput(String uuid, String file) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>> }
>>
>>
>> @Override
>> public void setBaclavaOutput(String uuid, String file) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet.");
>>
>>
>>
>> -----Original Message-----
>> From: Stian Soiland-Reyes [mailto:stain@apache.org]
>> Sent: Friday, March 27, 2015 12:28 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
>>
>> On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>>> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
>>> Please explain more
>>>
>>> Thanks
>>>
>>> -----Original Message-----
>>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>>> Sent: Thursday, March 26, 2015 9:03 PM
>>> To: users@taverna.incubator.apache.org
>>> Subject: Re: A few questions before choosing Taverna for our project
>>>
>>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>>> Dear Stian,
>>>>
>>>> I'm working on workflow and I ran it perfectly (tomcat6 and
>>>> RESTful), I got the output without provenance bundle
>>>
>>> Before you started the run, did you set generate-provenance to true?
>>>
>>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>>
>>> See
>>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resourc
>>> e
>>> :/runs/{id}/generate-provenance
>>>
>>>> I don't know how to configure Taverna server to enable provenance
>>>> data, can you guide me please?
>>>
>>> It is not part of the server configuration. It is set for each run.
>>>
>>>> Kind regards
>>>>
>>>> Ahmad
>>>
>>> Alan
>>>
>>
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
So I have to build that, but it is very hard to build, I have no idea about it .
I'm also trying with Taverna Command Line Tool, also it is seem that there is no provenance data can be generate!!
I need a solution to run my workflow and get the output with the provenance data.
Regards
> Hello,
Hello
> I appreciate your time and cooperation, really thank you very much.
>
> But I got confused :(
Sorry about that.
> What I got that you want me to merge the client side from this project:
> https://github.com/taverna/taverna-server/tree/2.5/server-client
>
> with the server side from the this project:
> https://github.com/taverna/taverna-server.git
>
> the problem it the last project (https://github.com/taverna/taverna-server.git) is the same of the first one, it load the same one.
Yes. The client code is in
https://github.com/taverna/taverna-server/tree/2.5/server-client . To build it, you will (currently) have to build the whole of the Taverna Server code - but you can then just use the server-client.
Alan
Re: A few questions before choosing Taverna for our project
Posted by alaninmcr <al...@googlemail.com>.
On 23/04/2015 22:25, Ahmad Aburomman wrote:
> Hello,
Hello
> I appreciate your time and cooperation, really thank you very much.
>
> But I got confused :(
Sorry about that.
> What I got that you want me to merge the client side from this project:
> https://github.com/taverna/taverna-server/tree/2.5/server-client
>
> with the server side from the this project:
> https://github.com/taverna/taverna-server.git
>
> the problem it the last project (https://github.com/taverna/taverna-server.git) is the same of the first one, it load the same one.
Yes. The client code is in
https://github.com/taverna/taverna-server/tree/2.5/server-client . To
build it, you will (currently) have to build the whole of the Taverna
Server code - but you can then just use the server-client.
Alan
Re: A few questions before choosing Taverna for our project
Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 23/04/2015 22:25, Ahmad Aburomman wrote:
> But I got confused:(
You're not experienced with building fairly large Maven projects with
lots of dependencies? Get the build from our Artifactory. :-)
http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/uk/org/taverna/server/server-client/2.5.5-SNAPSHOT/server-client-2.5.5-20150425.104736-20.jar
That should be a largely self-contained JAR (85kB) with a few external
dependencies (org.jvnet.ws.wadl:wadl-core:1.1.6,
com.sun.jersey:jersey-client:1.8, commons-io:commons-io:2.4,
org.apache.tika:tika-core:1.5, com.google.code.findbugs:jsr305:1.3.7)
which we don't include since we don't normally repackage external
libraries in the Open Source world. ;-)
The above URL is not persistent; it is to a version that may go away
without warning (because we only keep a limited number of snapshot
versions). I'm not sure how to generate a link to the directory in the
Artifactory tree.
MAVEN INSTRUCTIONS
------------------
DO NOT USE THESE IF YOU AREN'T USING MAVEN FOR THE REST OF YOUR CLIENT.
THESE ASSUME THAT YOU KNOW HOW MAVEN WORKS ALREADY; WE WON'T TEACH YOU THAT!
It has the following Maven coordinates:
<dependency>
<groupId>uk.org.taverna.server</groupId>
<artifactId>server-client</artifactId>
<version>2.5.5-SNAPSHOT</version>
</dependency>
And that will depend on you having the myGrid repository set up:
<repositories>
<repository>
<releases />
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>mygrid-repository</id>
<name>myGrid Respository</name>
<url>http://www.mygrid.org.uk/maven/repository</url>
</repository>
<repository>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
<id>mygrid-snapshots</id>
<name>myGrid Snapshot Respository</name>
<url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
</repository>
</repositories>
Donal.
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Hello,
I appreciate your time and cooperation, really thank you very much.
But I got confused :(
What I got that you want me to merge the client side from this project:
https://github.com/taverna/taverna-server/tree/2.5/server-client
with the server side from the this project:
https://github.com/taverna/taverna-server.git
the problem it the last project (https://github.com/taverna/taverna-server.git) is the same of the first one, it load the same one.
_____________________________________________________
On 13/04/2015 13:27, alaninmcr wrote:
> I've started a hangout. If anyone else wants to join, the URL is
> https://plus.google.com/hangouts/_/gwg7xzlz4c6cyabi5popr6mohma
As was discussed, the code at:
https://github.com/myGrid/t2-server-jar
is really quite old, and is missing critical features. The client in the
server codebase:
https://github.com/taverna/taverna-server/tree/2.5/server-client
is up to date (and is part of what we've contributed to Apache, so it
will continue to be supported) though it is currently a bit awkward to
build and isn't a finished release yet. To build the 2.5 version (NB:
NOT Apache code, but equivalent to) check out the server code from github:
https://github.com/taverna/taverna-server.git
and then use maven to build it. I recommend 'mvn install' for that. That
will download the world a bit, but will eventually create the following
artefact in your system-local maven repository.
<dependency>
<groupId>uk.org.taverna.server</groupId>
<artifactId>server-client</artifactId>
<version>2.5.5-SNAPSHOT</version>
</dependency>
That should be quite fully featured enough to support generating
provenance (as part of the run bundle) provided you ask for it; you're
still expected to understand the general server usage patterns, which
are documented online currently at:
http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+Server+2.5
What we (well, probably I) will do next is to update the build so that a
proper client artefact is produced that doesn't have explicit
dependencies on other parts of the server build (currently it uses a
supporting library for handling Resource Usage Records) and get 2.5.5
released so that we can have an actual artefact that we can point to,
rather than some sort of SNAPSHOT.
Oh, and you *might* be able to use the build in our Artifactory:
http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/uk/org/taverna/server/server-client/2.5.5-SNAPSHOT/server-client-2.5.5-20150304.170355-11.jar
That's not a long-term guaranteed URL and I don't know if it has all the
dependencies you need. But maybe it will work? :-)
Donal.
Re: A few questions before choosing Taverna for our project
Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 13/04/2015 13:27, alaninmcr wrote:
> I've started a hangout. If anyone else wants to join, the URL is
> https://plus.google.com/hangouts/_/gwg7xzlz4c6cyabi5popr6mohma
As was discussed, the code at:
https://github.com/myGrid/t2-server-jar
is really quite old, and is missing critical features. The client in the
server codebase:
https://github.com/taverna/taverna-server/tree/2.5/server-client
is up to date (and is part of what we've contributed to Apache, so it
will continue to be supported) though it is currently a bit awkward to
build and isn't a finished release yet. To build the 2.5 version (NB:
NOT Apache code, but equivalent to) check out the server code from github:
https://github.com/taverna/taverna-server.git
and then use maven to build it. I recommend 'mvn install' for that. That
will download the world a bit, but will eventually create the following
artefact in your system-local maven repository.
<dependency>
<groupId>uk.org.taverna.server</groupId>
<artifactId>server-client</artifactId>
<version>2.5.5-SNAPSHOT</version>
</dependency>
That should be quite fully featured enough to support generating
provenance (as part of the run bundle) provided you ask for it; you're
still expected to understand the general server usage patterns, which
are documented online currently at:
http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+Server+2.5
What we (well, probably I) will do next is to update the build so that a
proper client artefact is produced that doesn't have explicit
dependencies on other parts of the server build (currently it uses a
supporting library for handling Resource Usage Records) and get 2.5.5
released so that we can have an actual artefact that we can point to,
rather than some sort of SNAPSHOT.
Oh, and you *might* be able to use the build in our Artifactory:
http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/uk/org/taverna/server/server-client/2.5.5-SNAPSHOT/server-client-2.5.5-20150304.170355-11.jar
That's not a long-term guaranteed URL and I don't know if it has all the
dependencies you need. But maybe it will work? :-)
Donal.
Re: A few questions before choosing Taverna for our project
Posted by alaninmcr <al...@googlemail.com>.
I've started a hangout. If anyone else wants to join, the URL is
https://plus.google.com/hangouts/_/gwg7xzlz4c6cyabi5popr6mohma
Alan
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Can we start hangout ?
-----Original Message-----
From: Donal K. Fellows [mailto:donal.k.fellows@manchester.ac.uk]
Sent: Friday, April 10, 2015 3:21 PM
To: Ahmad Aburomman
Cc: users@taverna.incubator.apache.org; Alan Williams
Subject: Re: A few questions before choosing Taverna for our project
On 06/04/2015 11:37, Ahmad Aburomman wrote:
> I modify the project of Vitor, here is the function:
> https://github.com/AhmadUsc/Java/blob/197819f798184721260789644f883221
> d166bb78/javaClient#L66
>
> Okay I didn't touch Baclava, I added Enable Provenance function I got
> the zip bundle but it was empty.
>
> Can you Vitor regenerate the code with provenance data enabling ?
> Here is Vitor project:
> https://github.com/pgcc/taverna-java-client
We were wondering whether you want a Google hangout so that you can discuss this with us. Perhaps sometime on Monday? That is, on 13/04/2015, some time between 0900 GMT and 1500 GMT, at least for preference. We can do other times by arrangement too (in which case we'll set up a doodle poll to arrange things) but they're the ones we can do with minimum fuss. :-)
Donal.
Re: A few questions before choosing Taverna for our project
Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 06/04/2015 11:37, Ahmad Aburomman wrote:
> I modify the project of Vitor, here is the function:
> https://github.com/AhmadUsc/Java/blob/197819f798184721260789644f883221d166bb78/javaClient#L66
>
> Okay I didn't touch Baclava, I added Enable Provenance function
> I got the zip bundle but it was empty.
>
> Can you Vitor regenerate the code with provenance data enabling ?
> Here is Vitor project:
> https://github.com/pgcc/taverna-java-client
We were wondering whether you want a Google hangout so that you can
discuss this with us. Perhaps sometime on Monday? That is, on
13/04/2015, some time between 0900 GMT and 1500 GMT, at least for
preference. We can do other times by arrangement too (in which case
we'll set up a doodle poll to arrange things) but they're the ones we
can do with minimum fuss. :-)
Donal.
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Hello,
I modify the project of Vitor, here is the function:
https://github.com/AhmadUsc/Java/blob/197819f798184721260789644f883221d166bb78/javaClient#L66
Okay I didn't touch Baclava, I added Enable Provenance function
I got the zip bundle but it was empty.
Can you Vitor regenerate the code with provenance data enabling ?
Here is Vitor project:
https://github.com/pgcc/taverna-java-client
Thanks in advance.
-----Original Message-----
From: Stian Soiland-Reyes [mailto:stain@apache.org]
Sent: Tuesday, March 31, 2015 1:05 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
No, you should not need to touch Baclava at all :)
You will need to retrieve the provenance bundle separately once the run has finished. It should be available at .../run-bundle in the REST
API:
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle
On 31 March 2015 at 11:34, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Thanks a lot for your indeed reply, actually I'm using this project
> https://github.com/pgcc/taverna-java-client
>
> I have implemented the Provenance function in TavernaClient.java, it
> is okay now and enabled but still can't get the provenance data with the output You mentioned that I have to do some function to Baclava, can you guide me please or give me the exact script to update my project.
>
> Regards
> Ahmad
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 2:24 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> Not sure where you found that code, as I found they were implemented here:
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org
> /taverna/server/client/Run.java#L344
>
>
> but in either case, the baclava input/output should NOT be used if you want the workflow run bundle back.
>
>
> Unfortunately the Taverna Server client code for Java has not been updated for the run bundle, which was new in 2.5 I think.
>
> It would be great if you could have a quick go - I think it should be quite doable, we've just not got around to it yet...
>
> Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
>
>
> By
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource
> :/runs/{id}/generate-provenance you need to send a PUT with "true" to
> /runs/{id}/generate-provenance
>
> so perhaps something like this could work?
>
>
> package uk.org.taverna.server.client.Run add two new methods, e.g.:
>
> similar to isBaclavaOutput and requestBaclavaOutput
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org
> /taverna/server/client/Run.java#L404
>
> but with "generate-provenance" added to the run URL.
>
>
> Similarly add getRunBundle() similar to getOutputZip()
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org
> /taverna/server/client/Run.java#L1140
>
> .. but requesting "run-bundle" added to the URL.
>
>
> To do it "proper REST-like" this can be generalized to find those two URI fragments from the runDescription as you see with getLink() in other bits of the code.
>
> On 27 March 2015 at 12:07, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>> Yes I see these code about baklava, but I don't know what to add exactly!
>>
>> @Override
>> public String getBaclavaInput(String uuid) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>> }
>>
>> @Override
>> public String setBaclavaInput(String uuid, String file) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>> }
>>
>>
>> @Override
>> public void setBaclavaOutput(String uuid, String file) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported
>> yet.");
>>
>>
>>
>> -----Original Message-----
>> From: Stian Soiland-Reyes [mailto:stain@apache.org]
>> Sent: Friday, March 27, 2015 12:28 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
>>
>> On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>>> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
>>> Please explain more
>>>
>>> Thanks
>>>
>>> -----Original Message-----
>>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>>> Sent: Thursday, March 26, 2015 9:03 PM
>>> To: users@taverna.incubator.apache.org
>>> Subject: Re: A few questions before choosing Taverna for our project
>>>
>>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>>> Dear Stian,
>>>>
>>>> I'm working on workflow and I ran it perfectly (tomcat6 and
>>>> RESTful), I got the output without provenance bundle
>>>
>>> Before you started the run, did you set generate-provenance to true?
>>>
>>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>>
>>> See
>>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resour
>>> c
>>> e
>>> :/runs/{id}/generate-provenance
>>>
>>>> I don't know how to configure Taverna server to enable provenance
>>>> data, can you guide me please?
>>>
>>> It is not part of the server configuration. It is set for each run.
>>>
>>>> Kind regards
>>>>
>>>> Ahmad
>>>
>>> Alan
>>>
>>
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: A few questions before choosing Taverna for our project
Posted by Stian Soiland-Reyes <st...@apache.org>.
No, you should not need to touch Baclava at all :)
You will need to retrieve the provenance bundle separately once the
run has finished. It should be available at .../run-bundle in the REST
API:
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle
On 31 March 2015 at 11:34, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Thanks a lot for your indeed reply, actually I'm using this project
> https://github.com/pgcc/taverna-java-client
>
> I have implemented the Provenance function in TavernaClient.java, it is okay now and enabled but still can't get the provenance data with the output
> You mentioned that I have to do some function to Baclava, can you guide me please or give me the exact script to update my project.
>
> Regards
> Ahmad
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 2:24 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> Not sure where you found that code, as I found they were implemented here:
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L344
>
>
> but in either case, the baclava input/output should NOT be used if you want the workflow run bundle back.
>
>
> Unfortunately the Taverna Server client code for Java has not been updated for the run bundle, which was new in 2.5 I think.
>
> It would be great if you could have a quick go - I think it should be quite doable, we've just not got around to it yet...
>
> Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
>
>
> By
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
> you need to send a PUT with "true" to /runs/{id}/generate-provenance
>
> so perhaps something like this could work?
>
>
> package uk.org.taverna.server.client.Run add two new methods, e.g.:
>
> similar to isBaclavaOutput and requestBaclavaOutput
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L404
>
> but with "generate-provenance" added to the run URL.
>
>
> Similarly add getRunBundle() similar to getOutputZip()
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L1140
>
> .. but requesting "run-bundle" added to the URL.
>
>
> To do it "proper REST-like" this can be generalized to find those two URI fragments from the runDescription as you see with getLink() in other bits of the code.
>
> On 27 March 2015 at 12:07, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>> Yes I see these code about baklava, but I don't know what to add exactly!
>>
>> @Override
>> public String getBaclavaInput(String uuid) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>> }
>>
>> @Override
>> public String setBaclavaInput(String uuid, String file) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
>> }
>>
>>
>> @Override
>> public void setBaclavaOutput(String uuid, String file) throws TavernaException {
>> throw new UnsupportedOperationException("Not supported yet.");
>>
>>
>>
>> -----Original Message-----
>> From: Stian Soiland-Reyes [mailto:stain@apache.org]
>> Sent: Friday, March 27, 2015 12:28 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
>>
>> On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>>> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
>>> Please explain more
>>>
>>> Thanks
>>>
>>> -----Original Message-----
>>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>>> Sent: Thursday, March 26, 2015 9:03 PM
>>> To: users@taverna.incubator.apache.org
>>> Subject: Re: A few questions before choosing Taverna for our project
>>>
>>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>>> Dear Stian,
>>>>
>>>> I'm working on workflow and I ran it perfectly (tomcat6 and
>>>> RESTful), I got the output without provenance bundle
>>>
>>> Before you started the run, did you set generate-provenance to true?
>>>
>>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>>
>>> See
>>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resourc
>>> e
>>> :/runs/{id}/generate-provenance
>>>
>>>> I don't know how to configure Taverna server to enable provenance
>>>> data, can you guide me please?
>>>
>>> It is not part of the server configuration. It is set for each run.
>>>
>>>> Kind regards
>>>>
>>>> Ahmad
>>>
>>> Alan
>>>
>>
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Thanks a lot for your indeed reply, actually I'm using this project
https://github.com/pgcc/taverna-java-client
I have implemented the Provenance function in TavernaClient.java, it is okay now and enabled but still can't get the provenance data with the output
You mentioned that I have to do some function to Baclava, can you guide me please or give me the exact script to update my project.
Regards
Ahmad
-----Original Message-----
From: Stian Soiland-Reyes [mailto:stain@apache.org]
Sent: Friday, March 27, 2015 2:24 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Not sure where you found that code, as I found they were implemented here:
https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L344
but in either case, the baclava input/output should NOT be used if you want the workflow run bundle back.
Unfortunately the Taverna Server client code for Java has not been updated for the run bundle, which was new in 2.5 I think.
It would be great if you could have a quick go - I think it should be quite doable, we've just not got around to it yet...
Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
By
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
you need to send a PUT with "true" to /runs/{id}/generate-provenance
so perhaps something like this could work?
package uk.org.taverna.server.client.Run add two new methods, e.g.:
similar to isBaclavaOutput and requestBaclavaOutput
https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L404
but with "generate-provenance" added to the run URL.
Similarly add getRunBundle() similar to getOutputZip()
https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L1140
.. but requesting "run-bundle" added to the URL.
To do it "proper REST-like" this can be generalized to find those two URI fragments from the runDescription as you see with getLink() in other bits of the code.
On 27 March 2015 at 12:07, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Yes I see these code about baklava, but I don't know what to add exactly!
>
> @Override
> public String getBaclavaInput(String uuid) throws TavernaException {
> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
> }
>
> @Override
> public String setBaclavaInput(String uuid, String file) throws TavernaException {
> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
> }
>
>
> @Override
> public void setBaclavaOutput(String uuid, String file) throws TavernaException {
> throw new UnsupportedOperationException("Not supported yet.");
>
>
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 12:28 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
>
> On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
>> Please explain more
>>
>> Thanks
>>
>> -----Original Message-----
>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>> Sent: Thursday, March 26, 2015 9:03 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>> Dear Stian,
>>>
>>> I'm working on workflow and I ran it perfectly (tomcat6 and
>>> RESTful), I got the output without provenance bundle
>>
>> Before you started the run, did you set generate-provenance to true?
>>
>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>
>> See
>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resourc
>> e
>> :/runs/{id}/generate-provenance
>>
>>> I don't know how to configure Taverna server to enable provenance
>>> data, can you guide me please?
>>
>> It is not part of the server configuration. It is set for each run.
>>
>>> Kind regards
>>>
>>> Ahmad
>>
>> Alan
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: A few questions before choosing Taverna for our project
Posted by Stian Soiland-Reyes <st...@apache.org>.
Not sure where you found that code, as I found they were implemented here:
https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L344
but in either case, the baclava input/output should NOT be used if you
want the workflow run bundle back.
Unfortunately the Taverna Server client code for Java has not been
updated for the run bundle, which was new in 2.5 I think.
It would be great if you could have a quick go - I think it should be
quite doable, we've just not got around to it yet...
Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
By
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
you need to send a PUT with "true" to /runs/{id}/generate-provenance
so perhaps something like this could work?
package uk.org.taverna.server.client.Run add two new methods, e.g.:
similar to isBaclavaOutput and requestBaclavaOutput
https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L404
but with "generate-provenance" added to the run URL.
Similarly add getRunBundle() similar to getOutputZip()
https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L1140
.. but requesting "run-bundle" added to the URL.
To do it "proper REST-like" this can be generalized to find those two
URI fragments from the runDescription as you see with getLink() in
other bits of the code.
On 27 March 2015 at 12:07, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Yes I see these code about baklava, but I don't know what to add exactly!
>
> @Override
> public String getBaclavaInput(String uuid) throws TavernaException {
> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
> }
>
> @Override
> public String setBaclavaInput(String uuid, String file) throws TavernaException {
> throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
> }
>
>
> @Override
> public void setBaclavaOutput(String uuid, String file) throws TavernaException {
> throw new UnsupportedOperationException("Not supported yet.");
>
>
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 12:28 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
>
> On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
>> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
>> Please explain more
>>
>> Thanks
>>
>> -----Original Message-----
>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>> Sent: Thursday, March 26, 2015 9:03 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>> Dear Stian,
>>>
>>> I'm working on workflow and I ran it perfectly (tomcat6 and RESTful),
>>> I got the output without provenance bundle
>>
>> Before you started the run, did you set generate-provenance to true?
>>
>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>
>> See
>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource
>> :/runs/{id}/generate-provenance
>>
>>> I don't know how to configure Taverna server to enable provenance
>>> data, can you guide me please?
>>
>> It is not part of the server configuration. It is set for each run.
>>
>>> Kind regards
>>>
>>> Ahmad
>>
>> Alan
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Yes I see these code about baklava, but I don't know what to add exactly!
@Override
public String getBaclavaInput(String uuid) throws TavernaException {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
@Override
public String setBaclavaInput(String uuid, String file) throws TavernaException {
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
@Override
public void setBaclavaOutput(String uuid, String file) throws TavernaException {
throw new UnsupportedOperationException("Not supported yet.");
-----Original Message-----
From: Stian Soiland-Reyes [mailto:stain@apache.org]
Sent: Friday, March 27, 2015 12:28 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
I think it should suffice in the client - although you might have to add support for it in the java client as the generate-provenance option was added recently.. Would you be willing to have a go at that?
On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
> Please explain more
>
> Thanks
>
> -----Original Message-----
> From: alaninmcr [mailto:alaninmcr@googlemail.com]
> Sent: Thursday, March 26, 2015 9:03 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>> Dear Stian,
>>
>> I'm working on workflow and I ran it perfectly (tomcat6 and RESTful),
>> I got the output without provenance bundle
>
> Before you started the run, did you set generate-provenance to true?
>
> Also, you need to make sure you are not sending the outputs to a Baclava file.
>
> See
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource
> :/runs/{id}/generate-provenance
>
>> I don't know how to configure Taverna server to enable provenance
>> data, can you guide me please?
>
> It is not part of the server configuration. It is set for each run.
>
>> Kind regards
>>
>> Ahmad
>
> Alan
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: A few questions before choosing Taverna for our project
Posted by Stian Soiland-Reyes <st...@apache.org>.
I think it should suffice in the client - although you might have to
add support for it in the java client as the generate-provenance
option was added recently.. Would you be willing to have a go at that?
On 27 March 2015 at 11:08, Ahmad Aburomman <ah...@rai.usc.es> wrote:
> Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
> Please explain more
>
> Thanks
>
> -----Original Message-----
> From: alaninmcr [mailto:alaninmcr@googlemail.com]
> Sent: Thursday, March 26, 2015 9:03 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>> Dear Stian,
>>
>> I'm working on workflow and I ran it perfectly (tomcat6 and RESTful),
>> I got the output without provenance bundle
>
> Before you started the run, did you set generate-provenance to true?
>
> Also, you need to make sure you are not sending the outputs to a Baclava file.
>
> See
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
>
>> I don't know how to configure Taverna server to enable provenance
>> data, can you guide me please?
>
> It is not part of the server configuration. It is set for each run.
>
>> Kind regards
>>
>> Ahmad
>
> Alan
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Okay, that seems to edit or modify some scripts, but which file should I do this? Inside Taverna server directory or in the java client?
Please explain more
Thanks
-----Original Message-----
From: alaninmcr [mailto:alaninmcr@googlemail.com]
Sent: Thursday, March 26, 2015 9:03 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
On 26/03/2015 19:45, Ahmad Aburomman wrote:
> Dear Stian,
>
> I'm working on workflow and I ran it perfectly (tomcat6 and RESTful),
> I got the output without provenance bundle
Before you started the run, did you set generate-provenance to true?
Also, you need to make sure you are not sending the outputs to a Baclava file.
See
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
> I don't know how to configure Taverna server to enable provenance
> data, can you guide me please?
It is not part of the server configuration. It is set for each run.
> Kind regards
>
> Ahmad
Alan
Re: A few questions before choosing Taverna for our project
Posted by alaninmcr <al...@googlemail.com>.
On 26/03/2015 19:45, Ahmad Aburomman wrote:
> Dear Stian,
>
> I'm working on workflow and I ran it perfectly (tomcat6 and RESTful),
> I got the output without provenance bundle
Before you started the run, did you set generate-provenance to true?
Also, you need to make sure you are not sending the outputs to a Baclava
file.
See
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
> I don't know how to configure Taverna server to enable provenance
> data, can you guide me please?
It is not part of the server configuration. It is set for each run.
> Kind regards
>
> Ahmad
Alan
RE: A few questions before choosing Taverna for our project
Posted by Ahmad Aburomman <ah...@rai.usc.es>.
Dear Stian,
I'm working on workflow and I ran it perfectly (tomcat6 and RESTful), I got the output without provenance bundle
I don't know how to configure Taverna server to enable provenance data, can you guide me please?
Kind regards
Ahmad
-----Original Message-----
From: Matthieu Melcot [mailto:matthieu.melcot@spaceapplications.com]
Sent: Tuesday, March 24, 2015 12:50 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project
Dear Stian,
Thank you for the answer, and the time you spent to give us details about Taverna specific points. It helped a lot!
We keep on testing Taverna, and I will come to you if I have other specific questions.
Best regards,
Matthieu
On 2015-03-02 14:06, Stian Soiland-Reyes wrote:
> Hi! Great that you are considering Taverna!
>
> On 27 February 2015 at 10:30, Matthieu Melcot
> <ma...@spaceapplications.com> wrote:
>
>> The core of the project is the orchestration of WPS processes
>> (http://www.opengeospatial.org/standards/wps) which are Web Services
>> for Geospatial processing.
>> Basically, a client can request one of the 3 following
>> "GetCapabilities", "DescribeProcess", "Execute" and get a response in
>> XML
> Great! Others here have already been using Taverna with WPS services -
> I know Alan Williams has some experience as well:
>
> http://markmail.org/message/y4elmrinjlyseoc4
>
>
>> The WPS server implementation that we will use
>> (http://52north.org/communities/geoprocessing/wps/) doesn't embed the
>> WPS xml inside SOAP (even if the OGC WPS norm describes it), and
>> their are not WSDL capabilities.
> But it does expose a SOAP/WSDL endpoint? Then it should in theory work
> out of the box - even though you would have to deal with the "service
> through a service" pattern of the generic DescribeProcess/ Execute
> calls.
>
>
>> 1) Is it relatively easy to develop a component for Taverna that will
>> allow to add these WPS services into the "Services Available" for
>> building a workflow ? Which kind of effort would it represent ?
> It's fairly easy to add a new Services Available plugin - see the Tutorial here:
>
> http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+dis
> covery+plugin
>
> Note that this tutorial is relevant for Taverna 2.5 , the upcoming
> Apache Taverna 3 would have slightly different ways of creating
> activities in the workbench.
>
>
> A service discovery module is allowed to return existing services
> (e.g. WSDL Activity) and don't have to create their own activity types
> (although the tutorial returns the HelloWorld type of activities)
>
> Note that creating WSDL activities programmatically could be slightly
> complicated if you need to add XML splitters for inputs and outputs -
> which I believe is needed for. You can have a look at the wsdl
> activity UI code for "Add XML splitter" for inspiration - See the
> Taverna 2 code here:
>
> https://github.com/taverna/taverna-wsdl-activity-ui/blob/maintenance/s
> rc/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLS
> plitterAction.java
>
> (Dmitry might have inputs on alternative ways to do this in Taverna 3
> - but for now I think you should target the Taverna 2 workbench as
> Apache Taverna 3 workbench probably won't be released before Q3 2015)
>
>
> A tighter integration with a "WPS Activity" plugin could give a much
> smoother expirence for the workflow design user, as you could expose a
> single step that interrogates the WPS server for input and output
> parameters and present these directly in Taverna as ports - this would
> take some more time - but has been done for many similar kind of
> service-in-a-service cases for Taverna, e.g. the Soaplab Activity.
>
>
> We did something similar when we created the AstroTaverna plugin for
> Taverna - but ended up making a new Perspective to have a richer
> search interface against the VO service registry -
> http://amiga.iaa.es/p/290-astrotaverna.htm
>
> Here the perspective allow a rich way to search and display
> information about VO compliant REST services, and then adding them to
> the workflow and/or Service Panel with a button.
>
>
>> I read
>> (http://geoprocessing.forum.52north.org/Problem-with-Taverna-td402499
>> 7.html) that some people try to use WPS with Taverna (Through WSDL
>> however), but they didnt succeed.
> Alan might be able to fill me in - but I believe this is mainly caused
> by an incomplete WSDL created by the WPS server.
>
>
>> 2) In the case that it is possible, is there some possibilities to
>> describe semantically the input and output of these WPS services
>> (indeed the input and outputs will always be URL (texts), but the
>> URLs reference different types of materials), so that it would be
>> possible to check if the connections are valid. It seems that Taverna has that kind of mechanism...
> Taverna does not have that kind of mechanism directly, but it is not
> far off from being able to do so. The main problem is the source of
> the semantic type annotations - a source like WPS service descriptions
> would be a good candidate.
>
> Mark Fortner has also shown interest in adding such a mechanism:
>
> http://markmail.org/message/zhmas3ifgmzccdsj
>
>
>
>> 3) My third question is about the monitoring and control of the
>> workflow execution.
>> Is there a way through the REST API to ask which part of a workflow
>> is actually executing.
> Not yet - but that is the plan as we are moving Taverna Server 3 to
> use the Taverna Platform directly instead running the engine through
> the command line.
>
> We will then be able to expose the workflow run report, which is a
> JSON document that details all processors and what they are doing,
> have done and still remains to do. Basically a detailed data structure
> similar to the Progress table at
> http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective#Result
> Perspective-ProgressReport
>
> You could access this today, but only through the Java API of the Engine.
>
>
>> 4) Is there a simple Web Viewer/Controller (It seems that the
>> "Taverna Player" needs to be embedded in web pages in ruby). Is there
>> a more straightforward way to use this player in order to test it ?
> Yes, Rob Haines and Finn Bacall made this basic portal so you won't
> have to make your Ruby portal to try it out:
>
> https://github.com/myGrid/taverna-player-portal
>
>
>
>
>> 5) Is there a mean to control and monitor the execution of a remote
>> workflow directly from the Taverna Workbench. It seems that "File /
>> Open Workflow Location" makes reference to a .t2flow remote file, and
>> not a workflow that would have been load into the Taverna Server.
> Not yet - but that is the goal of making the Taverna Platform binding
> to the Taverna Server API - the Taverna 3 workbench has the separation
> so that this is in theory easy. The main thing it is missing is that
> very same JSON report, which needs to be added also to the client
> code.
>
> Some simple UI code would also be needed to "Add your server".
>
> As an Apache project with open development, anyone can contribute to
> the development of Taverna.
>
> Do you think you (or your team) would be able to help out with
> updating and testing the Taverna Server for such an integration?
>
> For instance I think we need to clarify what should be the granularity
> of the report, how to deal with refreshing, loading intermediate data,
> etc.
>
--
Matthieu Melcot
Software Engineer
Space Applications Services NV/SA
Leuvensesteenweg 325, 1932 Zaventem, Belgium
Direct: +32-(0)2-416.05.35
Main: +32-(0)2-721.54.84 Fax: +32-(0)2-721.54.44 www.spaceapplications.com
Re: A few questions before choosing Taverna for our project
Posted by Matthieu Melcot <ma...@spaceapplications.com>.
Dear Stian,
Thank you for the answer, and the time you spent to give us details
about Taverna specific points. It helped a lot!
We keep on testing Taverna, and I will come to you if I have other
specific questions.
Best regards,
Matthieu
On 2015-03-02 14:06, Stian Soiland-Reyes wrote:
> Hi! Great that you are considering Taverna!
>
> On 27 February 2015 at 10:30, Matthieu Melcot
> <ma...@spaceapplications.com> wrote:
>
>> The core of the project is the orchestration of WPS processes
>> (http://www.opengeospatial.org/standards/wps) which are Web Services for
>> Geospatial processing.
>> Basically, a client can request one of the 3 following "GetCapabilities",
>> "DescribeProcess", "Execute" and get a
>> response in XML
> Great! Others here have already been using Taverna with WPS services -
> I know Alan Williams has some experience as well:
>
> http://markmail.org/message/y4elmrinjlyseoc4
>
>
>> The WPS server implementation that we will use
>> (http://52north.org/communities/geoprocessing/wps/) doesn't embed the WPS
>> xml inside SOAP (even if the OGC WPS norm describes it), and their are not
>> WSDL capabilities.
> But it does expose a SOAP/WSDL endpoint? Then it should in theory work
> out of the box - even though you would have to deal with the "service
> through a service" pattern of the generic DescribeProcess/ Execute
> calls.
>
>
>> 1) Is it relatively easy to develop a component for Taverna that will allow
>> to add these WPS services into the "Services Available" for building a
>> workflow ? Which kind of effort would it represent ?
> It's fairly easy to add a new Services Available plugin - see the Tutorial here:
>
> http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin
>
> Note that this tutorial is relevant for Taverna 2.5 , the upcoming
> Apache Taverna 3 would have slightly different ways of creating
> activities in the workbench.
>
>
> A service discovery module is allowed to return existing services
> (e.g. WSDL Activity) and don't have to create their own activity types
> (although the tutorial returns the HelloWorld type of activities)
>
> Note that creating WSDL activities programmatically could be slightly
> complicated if you need to add XML splitters for inputs and outputs -
> which I believe is needed for. You can have a look at the wsdl
> activity UI code for "Add XML splitter" for inspiration - See the
> Taverna 2 code here:
>
> https://github.com/taverna/taverna-wsdl-activity-ui/blob/maintenance/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
>
> (Dmitry might have inputs on alternative ways to do this in Taverna 3
> - but for now I think you should target the Taverna 2 workbench as
> Apache Taverna 3 workbench probably won't be released before Q3 2015)
>
>
> A tighter integration with a "WPS Activity" plugin could give a much
> smoother expirence for the workflow design user, as you could expose a
> single step that interrogates the WPS server for input and output
> parameters and present these directly in Taverna as ports - this would
> take some more time - but has been done for many similar kind of
> service-in-a-service cases for Taverna, e.g. the Soaplab Activity.
>
>
> We did something similar when we created the AstroTaverna plugin for
> Taverna - but ended up making a new Perspective to have a richer
> search interface against the VO service registry -
> http://amiga.iaa.es/p/290-astrotaverna.htm
>
> Here the perspective allow a rich way to search and display
> information about VO compliant REST services, and then adding them to
> the workflow and/or Service Panel with a button.
>
>
>> I read
>> (http://geoprocessing.forum.52north.org/Problem-with-Taverna-td4024997.html)
>> that some people try to use WPS with Taverna (Through WSDL however), but
>> they didnt succeed.
> Alan might be able to fill me in - but I believe this is mainly caused
> by an incomplete
> WSDL created by the WPS server.
>
>
>> 2) In the case that it is possible, is there some possibilities to describe
>> semantically the input and output of these WPS services (indeed the input
>> and outputs will always be URL (texts), but the URLs reference different
>> types of materials), so that it would be possible to check if the
>> connections are valid. It seems that Taverna has that kind of mechanism...
> Taverna does not have that kind of mechanism directly, but it is not
> far off from being able to do so. The main problem is the source of
> the semantic type annotations - a source like WPS service descriptions
> would be a good candidate.
>
> Mark Fortner has also shown interest in adding such a mechanism:
>
> http://markmail.org/message/zhmas3ifgmzccdsj
>
>
>
>> 3) My third question is about the monitoring and control of the workflow
>> execution.
>> Is there a way through the REST API to ask which part of a workflow is
>> actually executing.
> Not yet - but that is the plan as we are moving Taverna Server 3 to
> use the Taverna Platform directly instead running the engine through
> the command line.
>
> We will then be able to expose the workflow run report, which is a
> JSON document that details all processors and what they are doing,
> have done and still remains to do. Basically a detailed data structure
> similar to the Progress table at
> http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective#ResultPerspective-ProgressReport
>
> You could access this today, but only through the Java API of the Engine.
>
>
>> 4) Is there a simple Web Viewer/Controller (It seems that the "Taverna
>> Player" needs to be embedded in web pages in ruby). Is there a more
>> straightforward way to use this player in order to test it ?
> Yes, Rob Haines and Finn Bacall made this basic portal so you won't
> have to make your Ruby portal to try it out:
>
> https://github.com/myGrid/taverna-player-portal
>
>
>
>
>> 5) Is there a mean to control and monitor the execution of a remote workflow
>> directly from the Taverna Workbench. It seems that "File / Open Workflow
>> Location" makes reference to a .t2flow remote file, and not a workflow that
>> would have been load into the Taverna Server.
> Not yet - but that is the goal of making the Taverna Platform binding
> to the Taverna Server API - the Taverna 3 workbench has the separation
> so that this is in theory easy. The main thing it is missing is that
> very same JSON report, which needs to be added also to the client
> code.
>
> Some simple UI code would also be needed to "Add your server".
>
> As an Apache project with open development, anyone can contribute to
> the development of Taverna.
>
> Do you think you (or your team) would be able to help out with
> updating and testing the Taverna Server for such an integration?
>
> For instance I think we need to clarify what should be the granularity
> of the report, how to deal with refreshing, loading intermediate data,
> etc.
>
--
Matthieu Melcot
Software Engineer
Space Applications Services NV/SA
Leuvensesteenweg 325, 1932 Zaventem, Belgium
Direct: +32-(0)2-416.05.35
Main: +32-(0)2-721.54.84 Fax: +32-(0)2-721.54.44
www.spaceapplications.com
Re: A few questions before choosing Taverna for our project
Posted by Stian Soiland-Reyes <st...@apache.org>.
Hi! Great that you are considering Taverna!
On 27 February 2015 at 10:30, Matthieu Melcot
<ma...@spaceapplications.com> wrote:
> The core of the project is the orchestration of WPS processes
> (http://www.opengeospatial.org/standards/wps) which are Web Services for
> Geospatial processing.
> Basically, a client can request one of the 3 following "GetCapabilities",
> "DescribeProcess", "Execute" and get a
> response in XML
Great! Others here have already been using Taverna with WPS services -
I know Alan Williams has some experience as well:
http://markmail.org/message/y4elmrinjlyseoc4
> The WPS server implementation that we will use
> (http://52north.org/communities/geoprocessing/wps/) doesn't embed the WPS
> xml inside SOAP (even if the OGC WPS norm describes it), and their are not
> WSDL capabilities.
But it does expose a SOAP/WSDL endpoint? Then it should in theory work
out of the box - even though you would have to deal with the "service
through a service" pattern of the generic DescribeProcess/ Execute
calls.
> 1) Is it relatively easy to develop a component for Taverna that will allow
> to add these WPS services into the "Services Available" for building a
> workflow ? Which kind of effort would it represent ?
It's fairly easy to add a new Services Available plugin - see the Tutorial here:
http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin
Note that this tutorial is relevant for Taverna 2.5 , the upcoming
Apache Taverna 3 would have slightly different ways of creating
activities in the workbench.
A service discovery module is allowed to return existing services
(e.g. WSDL Activity) and don't have to create their own activity types
(although the tutorial returns the HelloWorld type of activities)
Note that creating WSDL activities programmatically could be slightly
complicated if you need to add XML splitters for inputs and outputs -
which I believe is needed for. You can have a look at the wsdl
activity UI code for "Add XML splitter" for inspiration - See the
Taverna 2 code here:
https://github.com/taverna/taverna-wsdl-activity-ui/blob/maintenance/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
(Dmitry might have inputs on alternative ways to do this in Taverna 3
- but for now I think you should target the Taverna 2 workbench as
Apache Taverna 3 workbench probably won't be released before Q3 2015)
A tighter integration with a "WPS Activity" plugin could give a much
smoother expirence for the workflow design user, as you could expose a
single step that interrogates the WPS server for input and output
parameters and present these directly in Taverna as ports - this would
take some more time - but has been done for many similar kind of
service-in-a-service cases for Taverna, e.g. the Soaplab Activity.
We did something similar when we created the AstroTaverna plugin for
Taverna - but ended up making a new Perspective to have a richer
search interface against the VO service registry -
http://amiga.iaa.es/p/290-astrotaverna.htm
Here the perspective allow a rich way to search and display
information about VO compliant REST services, and then adding them to
the workflow and/or Service Panel with a button.
> I read
> (http://geoprocessing.forum.52north.org/Problem-with-Taverna-td4024997.html)
> that some people try to use WPS with Taverna (Through WSDL however), but
> they didnt succeed.
Alan might be able to fill me in - but I believe this is mainly caused
by an incomplete
WSDL created by the WPS server.
> 2) In the case that it is possible, is there some possibilities to describe
> semantically the input and output of these WPS services (indeed the input
> and outputs will always be URL (texts), but the URLs reference different
> types of materials), so that it would be possible to check if the
> connections are valid. It seems that Taverna has that kind of mechanism...
Taverna does not have that kind of mechanism directly, but it is not
far off from being able to do so. The main problem is the source of
the semantic type annotations - a source like WPS service descriptions
would be a good candidate.
Mark Fortner has also shown interest in adding such a mechanism:
http://markmail.org/message/zhmas3ifgmzccdsj
> 3) My third question is about the monitoring and control of the workflow
> execution.
> Is there a way through the REST API to ask which part of a workflow is
> actually executing.
Not yet - but that is the plan as we are moving Taverna Server 3 to
use the Taverna Platform directly instead running the engine through
the command line.
We will then be able to expose the workflow run report, which is a
JSON document that details all processors and what they are doing,
have done and still remains to do. Basically a detailed data structure
similar to the Progress table at
http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective#ResultPerspective-ProgressReport
You could access this today, but only through the Java API of the Engine.
> 4) Is there a simple Web Viewer/Controller (It seems that the "Taverna
> Player" needs to be embedded in web pages in ruby). Is there a more
> straightforward way to use this player in order to test it ?
Yes, Rob Haines and Finn Bacall made this basic portal so you won't
have to make your Ruby portal to try it out:
https://github.com/myGrid/taverna-player-portal
> 5) Is there a mean to control and monitor the execution of a remote workflow
> directly from the Taverna Workbench. It seems that "File / Open Workflow
> Location" makes reference to a .t2flow remote file, and not a workflow that
> would have been load into the Taverna Server.
Not yet - but that is the goal of making the Taverna Platform binding
to the Taverna Server API - the Taverna 3 workbench has the separation
so that this is in theory easy. The main thing it is missing is that
very same JSON report, which needs to be added also to the client
code.
Some simple UI code would also be needed to "Add your server".
As an Apache project with open development, anyone can contribute to
the development of Taverna.
Do you think you (or your team) would be able to help out with
updating and testing the Taverna Server for such an integration?
For instance I think we need to clarify what should be the granularity
of the report, how to deal with refreshing, loading intermediate data,
etc.
--
Stian Soiland-Reyes
Apache Taverna (incubating)
http://orcid.org/0000-0001-9842-9718
Re: A few questions before choosing Taverna for our project
Posted by Alan Williams <al...@googlemail.com>.
On 27-Feb-15 10:30, Matthieu Melcot wrote:
> Dear Taverna Team,
Hello
I'll just fill in some additional information to Stian's answer.
> I am currently looking for an orchestrator that could suit our project
> needs.
>
> I discovered Taverna and it seems very interesting.
>
> I have a few questions that I would like to clarify before making the
> choice of using Taverna in our project
>
> The core of the project is the orchestration of WPS processes
> (http://www.opengeospatial.org/standards/wps) which are Web Services for
> Geospatial processing.
> Basically, a client can request one of the 3 following
> "GetCapabilities", "DescribeProcess", "Execute" and get a
> response in XML
Yes, I know WPS quite well. As part of the BioVeL project, I developed a
prototype WPS service for Taverna that talks to the WPS at iMarine
http://www.i-marine.eu/
> The WPS server implementation that we will use
> (http://52north.org/communities/geoprocessing/wps/) doesn't embed the
> WPS xml inside SOAP (even if the OGC WPS norm describes it), and their
> are not WSDL capabilities.
I do not understand what you are saying. Is it using the WPS REST
interface?
> 1) Is it relatively easy to develop a component for Taverna that will
> allow to add these WPS services into the "Services Available" for
> building a workflow ?
Relatively easy, yes. There are at least two prototype plugins for this
at https://github.com/zzpwelkin/taverna-wps-plugin.git and
https://github.com/alaninmcr/wps-taverna.git
> Which kind of effort would it represent ?
We have a Google Summer of Code project on it at
https://issues.apache.org/jira/browse/COMDEV-122 . I think it will
depend if you want to make sure that the extension works for most WPS or
just for yours. Also, the GSOC project includes getting the WPS support
into Taverna 3. It will be easier if you just do Taverna 2.5.
> I read
> (http://geoprocessing.forum.52north.org/Problem-with-Taverna-td4024997.html)
> that some people try to use WPS with Taverna (Through WSDL however), but
> they didnt succeed.
It is difficult to say anything reasonable about that problem as there
is no valid link to the problematic WSDL. It has localhost as the WSDL
server.
> 2) In the case that it is possible, is there some possibilities to
> describe semantically the input and output of these WPS services (indeed
> the input and outputs will always be URL (texts), but the URLs reference
> different types of materials), so that it would be possible to check if
> the connections are valid. It seems that Taverna has that kind of
> mechanism...
You could certainly write a validity check to see if the connections
matched up.
[snip]
> 4) Is there a simple Web Viewer/Controller (It seems that the "Taverna
> Player" needs to be embedded in web pages in ruby). Is there a more
> straightforward way to use this player in order to test it ?
The player does not need to be embedded in web pages in ruby. For
example, I developed a mechanism for including it in IPython Notebook -
see http://youtu.be/QVQwSOX5S08
[snip]
> Thanks in advance for your help
>
> Matthieu Melcot
Alan