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Posted to dev@taverna.apache.org by Abraham NIEVA DE LA HIDALGA <ab...@uppuebla.edu.mx> on 2015/07/09 23:30:14 UTC
Taverna Player Internationalization Issues
Hi,
We have installed a customised version of the BioVeL portal which uses
Taverna Player to facilitate workflow execution online. Our aim is to
introduce the tool to spanish speaking users (biotechnology scientists
specifically).
The portal is available at http://lvbupp.at.uppuebla.edu.mx/.
Overall, the portal works and lets users execute workflows. However,
workflows with interactions seem to have problems. We have tested and found
two kinds of problems: interactions not shown properly and responded
interactions not being registered. In both cases, the problem is that the
workflow will not continue execution unless the interactions is responded
by the user and as a result the workflow cannot finish.
For an example of the first case, we have tried running the "Bayesian
Phylogenetic Inference: Select Model For Me - Submission" workflow (
http://www.myexperiment.org/workflows/3410.html). The firs interaction
cannot be found so the popup shows a blank screen and the state of the run
reamins as "Waiting for user input".
For an example of the second case, we executed the "Matrix Population Model
analysis v12" workflow (http://www.myexperiment.org/workflows/3686.html).
The first interaction is presented correctly, After selecting values and
pressing on confirm, the popup shows the legend stages submited However,
nothing else happens, the popup stays on and the state of the run remains
"Waiting for user input".
In both cases, the runs stay on and is not possible to continue exevution,
consequently they must be cancelled.
I think the problem needs to be addressed by ensuring that Taverna Player
maps interaction URLs correctly so that the workers that poll the
interaction queue and Taverna server can detect which interactions have
been answered.
In the mean time ther should be a work around so that routes interpreted
correctly.
If any one has had a similar problem or is addressing a similar issue, or
knows of a workaround, please let us know.
Regards
Abraham
Re: Taverna Player Internationalization Issues
Posted by Stian Soiland-Reyes <st...@apache.org>.
Our problem was I think related to the internal communication between
the WebDav, Portal and Server. It all worked fine when the interaction
server was set as 'localhost', but then the client would only work on
actually localhost - thus not on a real portal. Setting it as the
external host name (e.g. http://server1.example.com:8080/something )
did not work, as within the docker container for the portal, the
server is on the hostname "server" within the other docker container.
Thus requests would be seen as coming from "10.54.12.3" or whatever
Docker's internal network would have, which was not permitted by the S
It's hard to predict in advance from the Taverna Server docker
container what IP the other Portal container would get - supporitng a
subnet could work, but would need to list basically 10.0.0.0/8 etc. I
am not sure why the webdav could not be openly accessible (relying on
regular firewalls which with Docker is "nothing exposed").. is there
not an authentication code as well?
I don't think Finn reported this in Jira - do you think this is an
issue with the Server, Portal or the Interaction activity?
On 10 July 2015 at 16:14, Ian Dunlop <ia...@manchester.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hello,
>
> Stian & Finn encountered the same (or at least very similar) issue on
> a recent taverna player install on one of our servers. I don't think
> they have found a fix yet.
>
> Cheers,
>
> Ian
>
> On 10/07/15 09:10, Christian Brenninkmeijer wrote:
>> I don't know if it is related but it is worth checking that the
>> interaction screen is not hiding behind another screen.
>>
>> If you are like me and start doing something else while waiting for
>> the interaction screen it may not get or instantly loose the
>> focus.
>>
>> Try minimizing everything so you see only the background and for me
>> in the past the interaction was hiding behind something else.
>>
>> Christian ________________________________________ From: Abraham
>> NIEVA DE LA HIDALGA [abraham.nieva@uppuebla.edu.mx] Sent: Thursday,
>> July 09, 2015 10:30 PM To: dev@taverna.incubator.apache.org Cc:
>> Alan Williams; Stian Soiland-Reyes; Finn Bacall Subject: Taverna
>> Player Internationalization Issues
>>
>> Hi,
>>
>> We have installed a customised version of the BioVeL portal which
>> uses Taverna Player to facilitate workflow execution online. Our
>> aim is to introduce the tool to spanish speaking users
>> (biotechnology scientists specifically).
>>
>> The portal is available at http://lvbupp.at.uppuebla.edu.mx/.
>>
>> Overall, the portal works and lets users execute workflows.
>> However, workflows with interactions seem to have problems. We have
>> tested and found two kinds of problems: interactions not shown
>> properly and responded interactions not being registered. In both
>> cases, the problem is that the workflow will not continue execution
>> unless the interactions is responded by the user and as a result
>> the workflow cannot finish.
>>
>> For an example of the first case, we have tried running the
>> "Bayesian Phylogenetic Inference: Select Model For Me - Submission"
>> workflow ( http://www.myexperiment.org/workflows/3410.html). The
>> firs interaction cannot be found so the popup shows a blank screen
>> and the state of the run reamins as "Waiting for user input".
>>
>> For an example of the second case, we executed the "Matrix
>> Population Model analysis v12" workflow
>> (http://www.myexperiment.org/workflows/3686.html). The first
>> interaction is presented correctly, After selecting values and
>> pressing on confirm, the popup shows the legend stages submited
>> However, nothing else happens, the popup stays on and the state of
>> the run remains "Waiting for user input".
>>
>> In both cases, the runs stay on and is not possible to continue
>> exevution, consequently they must be cancelled.
>>
>> I think the problem needs to be addressed by ensuring that Taverna
>> Player maps interaction URLs correctly so that the workers that
>> poll the interaction queue and Taverna server can detect which
>> interactions have been answered.
>>
>> In the mean time ther should be a work around so that routes
>> interpreted correctly.
>>
>> If any one has had a similar problem or is addressing a similar
>> issue, or knows of a workaround, please let us know.
>>
>> Regards
>>
>> Abraham
>>
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--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Taverna Player Internationalization Issues
Posted by Ian Dunlop <ia...@manchester.ac.uk>.
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hello,
Stian & Finn encountered the same (or at least very similar) issue on
a recent taverna player install on one of our servers. I don't think
they have found a fix yet.
Cheers,
Ian
On 10/07/15 09:10, Christian Brenninkmeijer wrote:
> I don't know if it is related but it is worth checking that the
> interaction screen is not hiding behind another screen.
>
> If you are like me and start doing something else while waiting for
> the interaction screen it may not get or instantly loose the
> focus.
>
> Try minimizing everything so you see only the background and for me
> in the past the interaction was hiding behind something else.
>
> Christian ________________________________________ From: Abraham
> NIEVA DE LA HIDALGA [abraham.nieva@uppuebla.edu.mx] Sent: Thursday,
> July 09, 2015 10:30 PM To: dev@taverna.incubator.apache.org Cc:
> Alan Williams; Stian Soiland-Reyes; Finn Bacall Subject: Taverna
> Player Internationalization Issues
>
> Hi,
>
> We have installed a customised version of the BioVeL portal which
> uses Taverna Player to facilitate workflow execution online. Our
> aim is to introduce the tool to spanish speaking users
> (biotechnology scientists specifically).
>
> The portal is available at http://lvbupp.at.uppuebla.edu.mx/.
>
> Overall, the portal works and lets users execute workflows.
> However, workflows with interactions seem to have problems. We have
> tested and found two kinds of problems: interactions not shown
> properly and responded interactions not being registered. In both
> cases, the problem is that the workflow will not continue execution
> unless the interactions is responded by the user and as a result
> the workflow cannot finish.
>
> For an example of the first case, we have tried running the
> "Bayesian Phylogenetic Inference: Select Model For Me - Submission"
> workflow ( http://www.myexperiment.org/workflows/3410.html). The
> firs interaction cannot be found so the popup shows a blank screen
> and the state of the run reamins as "Waiting for user input".
>
> For an example of the second case, we executed the "Matrix
> Population Model analysis v12" workflow
> (http://www.myexperiment.org/workflows/3686.html). The first
> interaction is presented correctly, After selecting values and
> pressing on confirm, the popup shows the legend stages submited
> However, nothing else happens, the popup stays on and the state of
> the run remains "Waiting for user input".
>
> In both cases, the runs stay on and is not possible to continue
> exevution, consequently they must be cancelled.
>
> I think the problem needs to be addressed by ensuring that Taverna
> Player maps interaction URLs correctly so that the workers that
> poll the interaction queue and Taverna server can detect which
> interactions have been answered.
>
> In the mean time ther should be a work around so that routes
> interpreted correctly.
>
> If any one has had a similar problem or is addressing a similar
> issue, or knows of a workaround, please let us know.
>
> Regards
>
> Abraham
>
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Re: Taverna Player Internationalization Issues
Posted by Alan R Williams <al...@manchester.ac.uk>.
On 10/07/2015 09:10, Christian Brenninkmeijer wrote:
> I don't know if it is related but it is worth checking that the
> interaction screen is not hiding behind another screen.
I don't think that matches Abraham's description. It is important to
look at the console log when this type of problem occurs. There have
been difficulties in the past if a website/player is running as https
and part of the interaction is http. That will not work (on most modern
browsers).
They had to do special tweaks to the Apache config for it to work on the
BioVeL portal because of these problems.
The problem should not happen with a built-in interaction. So...
@Abraham - does a simple interaction like ask work OK?
[snip]
> Christian
Alan
RE: Taverna Player Internationalization Issues
Posted by Christian Brenninkmeijer <ch...@manchester.ac.uk>.
I don't know if it is related but it is worth checking that the interaction screen is not hiding behind another screen.
If you are like me and start doing something else while waiting for the interaction screen it may not get or instantly loose the focus.
Try minimizing everything so you see only the background and for me in the past the interaction was hiding behind something else.
Christian
________________________________________
From: Abraham NIEVA DE LA HIDALGA [abraham.nieva@uppuebla.edu.mx]
Sent: Thursday, July 09, 2015 10:30 PM
To: dev@taverna.incubator.apache.org
Cc: Alan Williams; Stian Soiland-Reyes; Finn Bacall
Subject: Taverna Player Internationalization Issues
Hi,
We have installed a customised version of the BioVeL portal which uses
Taverna Player to facilitate workflow execution online. Our aim is to
introduce the tool to spanish speaking users (biotechnology scientists
specifically).
The portal is available at http://lvbupp.at.uppuebla.edu.mx/.
Overall, the portal works and lets users execute workflows. However,
workflows with interactions seem to have problems. We have tested and found
two kinds of problems: interactions not shown properly and responded
interactions not being registered. In both cases, the problem is that the
workflow will not continue execution unless the interactions is responded
by the user and as a result the workflow cannot finish.
For an example of the first case, we have tried running the "Bayesian
Phylogenetic Inference: Select Model For Me - Submission" workflow (
http://www.myexperiment.org/workflows/3410.html). The firs interaction
cannot be found so the popup shows a blank screen and the state of the run
reamins as "Waiting for user input".
For an example of the second case, we executed the "Matrix Population Model
analysis v12" workflow (http://www.myexperiment.org/workflows/3686.html).
The first interaction is presented correctly, After selecting values and
pressing on confirm, the popup shows the legend stages submited However,
nothing else happens, the popup stays on and the state of the run remains
"Waiting for user input".
In both cases, the runs stay on and is not possible to continue exevution,
consequently they must be cancelled.
I think the problem needs to be addressed by ensuring that Taverna Player
maps interaction URLs correctly so that the workers that poll the
interaction queue and Taverna server can detect which interactions have
been answered.
In the mean time ther should be a work around so that routes interpreted
correctly.
If any one has had a similar problem or is addressing a similar issue, or
knows of a workaround, please let us know.
Regards
Abraham