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Posted to users@taverna.apache.org by Vimig Socrates <vs...@case.edu> on 2018/09/04 17:11:27 UTC
Resources to create UI using Workflow on Workbench
Hi everyone,
I am looking to run Taverna Server *version 2.5* and create a user
interface accessible from the internet that will update as the workflow
progresses. To that end, I would need an API that I could access to get an
update of a running workflow.
Can I do that with /runs/{id}/listeners and only using the given
*/runs/{id}/listeners/io/properties/stdout
*output? What if I want the entire workflow diagram to be shown in a web
interface? Is there any support for that?
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
RE: Resources to create UI using Workflow on Workbench
Posted by Alex Hardisty <Ha...@cardiff.ac.uk>.
Hi Vimig,
Take a look at the BioVeL portal – https://portal.biovel.eu/ . You may find this already does everything you need. It’s customised for biodiversity / ecology workflows executing on Taverna Server but is not limited to that specifically.
Kind regards
--
Alex
Alex Hardisty Alex Hardisty
Director of Informatics Projects Cyfarwyddwr y Prosiect Gwybodeg
School of Computer Science and Informatics Yr Ysgol Cyfrifiadureg a Gwybodeg
Cardiff University, Queens Buildings Prifysgol Caerdydd, Adeiladau’r Frenhines
5, The Parade, Cardiff CF24 3AA 5, The Parade, Caerdydd CF24 3AA
United Kingdom Y Deyrnas Unedig
tel: +44 (0)29 2087 4761 ffôn : +44 (0)29 2087 4761
email: hardistyar@cardiff.ac.uk<ma...@cardiff.ac.uk> ebost: hardistyar@caerdydd.ac.uk<ma...@caerdydd.ac.uk>
skype: alex.hardisty skype: alex.hardisty
orcid id: orcid.org/0000-0002-0767-4310<http://orcid.org/0000-0002-0767-4310>
From: Ian Dunlop <ia...@gmail.com>
Sent: 04 September 2018 18:16
To: users@taverna.incubator.apache.org
Subject: RE: Resources to create UI using Workflow on Workbench
Hello,
Have a look at https://github.com/taverna-extras/taverna-player-portal. This is a UI that uses the taverna server to run workflows and update progress.
I think there is some ruby code to get a png of the workflow diagram in it. There should also be some java code somewhere – anyone know where?
Cheers,
Ian
Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Vimig Socrates<ma...@case.edu>
Sent: 04 September 2018 18:11
To: users@taverna.incubator.apache.org<ma...@taverna.incubator.apache.org>
Subject: Resources to create UI using Workflow on Workbench
Hi everyone,
I am looking to run Taverna Server version 2.5 and create a user interface accessible from the internet that will update as the workflow progresses. To that end, I would need an API that I could access to get an update of a running workflow.
Can I do that with /runs/{id}/listeners and only using the given /runs/{id}/listeners/io/properties/stdout output? What if I want the entire workflow diagram to be shown in a web interface? Is there any support for that?
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
Re: Resources to create UI using Workflow on Workbench
Posted by Vimig Socrates <vs...@case.edu>.
Hi,
Just following up on this email. As a recap, I would like to embed the
image of the workflow (that I see on the Workbench) from the Taverna Server
2.5 into my Django app.
What is my best bet in doing this? Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Sat, Sep 22, 2018 at 2:28 AM Vimig Socrates <vs...@case.edu> wrote:
> Thank you for your fast reply Donal.
>
> In a related note, what if I want just the workflow image but don't need
> to update? I cannot use the Taverna Player plugin since the website I'm
> developing is made with Django, not Rails. The Taverna Player REST API also
> seems to not give an image of the workflow.
>
> Thank you all for your help so far!
>
> --
> Vimig Socrates
> Case Western Reserve University Class of 2018
>
>
> On Thu, Sep 20, 2018 at 3:49 PM Donal K. Fellows <
> donal.k.fellows@manchester.ac.uk> wrote:
>
>> On 20/09/2018 16:45, Ian Dunlop wrote:
>> > I’m not sure how to get deep inside an actual workflow run. Donal
>> > Fellows, the person who wrote most of the server code, might be able to
>> > help (if he is still reading these emails!). I can’t think of any
>> better
>> > suggestions beyond loading the code into a debugger. Although I think
>> > the actual workflow status, rather than workflow run status, is
>> probably
>> > handled by other code.
>> >
>>
>> I *sometimes* read these things. :-)
>>
>> When I last worked with the Server (some time ago) there wasn't a
>> mechanism for directly querying what the status of the parts of a
>> workflow were when it was running (because the workflow execution engine
>> process didn't publish that info; it only wrote things out at the end).
>> I believe we worked around this by modifying the workflows to
>> occasionally write something relating to their status to a “known
>> location” (either files or services would work for this) that the
>> exterior service could poll periodically. That's not a general solution,
>> not without a mechanism for automatically creating the operations for
>> recording the status (possible, but not something that existed the last
>> time I looked), but it will work fine if one is only supporting a
>> defined set of workflows.
>>
>> Or at least that's my first set of thoughts on how to do this.
>>
>> Donal.
>>
>
Re: Resources to create UI using Workflow on Workbench
Posted by Vimig Socrates <vs...@case.edu>.
Thank you for your fast reply Donal.
In a related note, what if I want just the workflow image but don't need to
update? I cannot use the Taverna Player plugin since the website I'm
developing is made with Django, not Rails. The Taverna Player REST API also
seems to not give an image of the workflow.
Thank you all for your help so far!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Thu, Sep 20, 2018 at 3:49 PM Donal K. Fellows <
donal.k.fellows@manchester.ac.uk> wrote:
> On 20/09/2018 16:45, Ian Dunlop wrote:
> > I’m not sure how to get deep inside an actual workflow run. Donal
> > Fellows, the person who wrote most of the server code, might be able to
> > help (if he is still reading these emails!). I can’t think of any better
> > suggestions beyond loading the code into a debugger. Although I think
> > the actual workflow status, rather than workflow run status, is probably
> > handled by other code.
> >
>
> I *sometimes* read these things. :-)
>
> When I last worked with the Server (some time ago) there wasn't a
> mechanism for directly querying what the status of the parts of a
> workflow were when it was running (because the workflow execution engine
> process didn't publish that info; it only wrote things out at the end).
> I believe we worked around this by modifying the workflows to
> occasionally write something relating to their status to a “known
> location” (either files or services would work for this) that the
> exterior service could poll periodically. That's not a general solution,
> not without a mechanism for automatically creating the operations for
> recording the status (possible, but not something that existed the last
> time I looked), but it will work fine if one is only supporting a
> defined set of workflows.
>
> Or at least that's my first set of thoughts on how to do this.
>
> Donal.
>
Re: Resources to create UI using Workflow on Workbench
Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 20/09/2018 16:45, Ian Dunlop wrote:
> I’m not sure how to get deep inside an actual workflow run. Donal
> Fellows, the person who wrote most of the server code, might be able to
> help (if he is still reading these emails!). I can’t think of any better
> suggestions beyond loading the code into a debugger. Although I think
> the actual workflow status, rather than workflow run status, is probably
> handled by other code.
>
I *sometimes* read these things. :-)
When I last worked with the Server (some time ago) there wasn't a
mechanism for directly querying what the status of the parts of a
workflow were when it was running (because the workflow execution engine
process didn't publish that info; it only wrote things out at the end).
I believe we worked around this by modifying the workflows to
occasionally write something relating to their status to a “known
location” (either files or services would work for this) that the
exterior service could poll periodically. That's not a general solution,
not without a mechanism for automatically creating the operations for
recording the status (possible, but not something that existed the last
time I looked), but it will work fine if one is only supporting a
defined set of workflows.
Or at least that's my first set of thoughts on how to do this.
Donal.
RE: Resources to create UI using Workflow on Workbench
Posted by Ian Dunlop <ia...@gmail.com>.
Hello,
I’m not sure how to get deep inside an actual workflow run. Donal Fellows, the person who wrote most of the server code, might be able to help (if he is still reading these emails!). I can’t think of any better suggestions beyond loading the code into a debugger. Although I think the actual workflow status, rather than workflow run status, is probably handled by other code.
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 19 September 2018 19:00
To: users@taverna.incubator.apache.org
Subject: Re: Resources to create UI using Workflow on Workbench
Hi,
I did look at the Taverna 2.5 equivalent (http://dev.mygrid.org.uk/wiki/display/tav250/REST+API). However, I didn't see any calls there that would give me the statuses beyond what you mentioned in your gitter message (Initial, initialized, operating, finished, destroyed & stopped).
I believe this is functionality I will need and it seems feasible since the workbench provides this capability. Could you point me in the right direction, if I wanted to make changes to the server code to get finer grain updates? Thank you!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Wed, Sep 19, 2018 at 9:11 AM Ian Dunlop <ia...@gmail.com> wrote:
Hello,
If you have a look at https://taverna.incubator.apache.org/documentation/server/3.1/usage you can see all the REST calls detailed. I’m assuming its much the same for 2.5.
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 17 September 2018 05:15
To: users@taverna.incubator.apache.org
Subject: Re: Resources to create UI using Workflow on Workbench
Hi,
Sorry for the late response. I tried running the player portal in docker and am having an issue. None of my workflows are running and whenever I try, the portal says "Server full - please wait; run will start soon".
With some debugging I've found that it is the Taverna Server that won't allow me to run anything on it. Using a REST client, I get a "503 Service Unavailable" error with the body as "failed to build workflow run worker".
As an additional question, I looked through the Rails code for the polling REST call, but don't see it. What REST endpoint should I hit to get an update of where along the workflow the system currently is?
Please let me know. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Tue, Sep 4, 2018 at 1:16 PM, Ian Dunlop <ia...@gmail.com> wrote:
Hello,
Have a look at https://github.com/taverna-extras/taverna-player-portal. This is a UI that uses the taverna server to run workflows and update progress.
I think there is some ruby code to get a png of the workflow diagram in it. There should also be some java code somewhere – anyone know where?
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 04 September 2018 18:11
To: users@taverna.incubator.apache.org
Subject: Resources to create UI using Workflow on Workbench
Hi everyone,
I am looking to run Taverna Server version 2.5 and create a user interface accessible from the internet that will update as the workflow progresses. To that end, I would need an API that I could access to get an update of a running workflow.
Can I do that with /runs/{id}/listeners and only using the given /runs/{id}/listeners/io/properties/stdout output? What if I want the entire workflow diagram to be shown in a web interface? Is there any support for that?
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
Re: Resources to create UI using Workflow on Workbench
Posted by Vimig Socrates <vs...@case.edu>.
Hi,
I did look at the Taverna 2.5 equivalent (
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API). However, I didn't
see any calls there that would give me the statuses beyond what you
mentioned in your gitter message (Initial, initialized, operating,
finished, destroyed & stopped).
I believe this is functionality I will need and it seems feasible since the
workbench provides this capability. Could you point me in the right
direction, if I wanted to make changes to the server code to get finer
grain updates? Thank you!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Wed, Sep 19, 2018 at 9:11 AM Ian Dunlop <ia...@gmail.com> wrote:
> Hello,
>
>
>
> If you have a look at
> https://taverna.incubator.apache.org/documentation/server/3.1/usage you
> can see all the REST calls detailed. I’m assuming its much the same for 2.5.
>
>
>
> Cheers,
>
>
>
> Ian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates <vs...@case.edu>
> *Sent: *17 September 2018 05:15
> *To: *users@taverna.incubator.apache.org
> *Subject: *Re: Resources to create UI using Workflow on Workbench
>
>
>
> Hi,
>
>
>
> Sorry for the late response. I tried running the player portal in docker
> and am having an issue. None of my workflows are running and whenever I
> try, the portal says "Server full - please wait; run will start soon".
>
>
>
> With some debugging I've found that it is the Taverna Server that won't
> allow me to run anything on it. Using a REST client, I get a "503 Service
> Unavailable" error with the body as "failed to build workflow run worker".
>
>
>
> As an *additional question*, I looked through the Rails code for the
> polling REST call, but don't see it. What REST endpoint should I hit to get
> an update of where along the workflow the system currently is?
>
>
>
> Please let me know. Thanks!
>
>
>
>
>
>
>
> --
>
> Vimig Socrates
>
> Case Western Reserve University Class of 2018
>
>
>
> On Tue, Sep 4, 2018 at 1:16 PM, Ian Dunlop <ia...@gmail.com> wrote:
>
> Hello,
>
>
>
> Have a look at https://github.com/taverna-extras/taverna-player-portal.
> This is a UI that uses the taverna server to run workflows and update
> progress.
>
> I think there is some ruby code to get a png of the workflow diagram in
> it. There should also be some java code somewhere – anyone know where?
>
>
>
> Cheers,
>
>
>
> Ian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates <vs...@case.edu>
> *Sent: *04 September 2018 18:11
> *To: *users@taverna.incubator.apache.org
> *Subject: *Resources to create UI using Workflow on Workbench
>
>
>
> Hi everyone,
>
>
>
> I am looking to run Taverna Server *version 2.5* and create a user
> interface accessible from the internet that will update as the workflow
> progresses. To that end, I would need an API that I could access to get an
> update of a running workflow.
>
>
>
> Can I do that with /runs/{id}/listeners and only using the given */runs/{id}/listeners/io/properties/stdout
> *output? What if I want the entire workflow diagram to be shown in a web
> interface? Is there any support for that?
>
>
>
> Thanks!
>
>
>
>
> --
>
> Vimig Socrates
>
> Case Western Reserve University Class of 2018
>
>
>
>
>
>
>
RE: Resources to create UI using Workflow on Workbench
Posted by Ian Dunlop <ia...@gmail.com>.
Hello,
If you have a look at https://taverna.incubator.apache.org/documentation/server/3.1/usage you can see all the REST calls detailed. I’m assuming its much the same for 2.5.
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 17 September 2018 05:15
To: users@taverna.incubator.apache.org
Subject: Re: Resources to create UI using Workflow on Workbench
Hi,
Sorry for the late response. I tried running the player portal in docker and am having an issue. None of my workflows are running and whenever I try, the portal says "Server full - please wait; run will start soon".
With some debugging I've found that it is the Taverna Server that won't allow me to run anything on it. Using a REST client, I get a "503 Service Unavailable" error with the body as "failed to build workflow run worker".
As an additional question, I looked through the Rails code for the polling REST call, but don't see it. What REST endpoint should I hit to get an update of where along the workflow the system currently is?
Please let me know. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Tue, Sep 4, 2018 at 1:16 PM, Ian Dunlop <ia...@gmail.com> wrote:
Hello,
Have a look at https://github.com/taverna-extras/taverna-player-portal. This is a UI that uses the taverna server to run workflows and update progress.
I think there is some ruby code to get a png of the workflow diagram in it. There should also be some java code somewhere – anyone know where?
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 04 September 2018 18:11
To: users@taverna.incubator.apache.org
Subject: Resources to create UI using Workflow on Workbench
Hi everyone,
I am looking to run Taverna Server version 2.5 and create a user interface accessible from the internet that will update as the workflow progresses. To that end, I would need an API that I could access to get an update of a running workflow.
Can I do that with /runs/{id}/listeners and only using the given /runs/{id}/listeners/io/properties/stdout output? What if I want the entire workflow diagram to be shown in a web interface? Is there any support for that?
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
Re: Resources to create UI using Workflow on Workbench
Posted by Vimig Socrates <vs...@case.edu>.
Hi,
Sorry for the late response. I tried running the player portal in docker
and am having an issue. None of my workflows are running and whenever I
try, the portal says "Server full - please wait; run will start soon".
With some debugging I've found that it is the Taverna Server that won't
allow me to run anything on it. Using a REST client, I get a "503 Service
Unavailable" error with the body as "failed to build workflow run worker".
As an *additional question*, I looked through the Rails code for the
polling REST call, but don't see it. What REST endpoint should I hit to get
an update of where along the workflow the system currently is?
Please let me know. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Tue, Sep 4, 2018 at 1:16 PM, Ian Dunlop <ia...@gmail.com> wrote:
> Hello,
>
>
>
> Have a look at https://github.com/taverna-extras/taverna-player-portal.
> This is a UI that uses the taverna server to run workflows and update
> progress.
>
> I think there is some ruby code to get a png of the workflow diagram in
> it. There should also be some java code somewhere – anyone know where?
>
>
>
> Cheers,
>
>
>
> Ian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates <vs...@case.edu>
> *Sent: *04 September 2018 18:11
> *To: *users@taverna.incubator.apache.org
> *Subject: *Resources to create UI using Workflow on Workbench
>
>
>
> Hi everyone,
>
>
>
> I am looking to run Taverna Server *version 2.5* and create a user
> interface accessible from the internet that will update as the workflow
> progresses. To that end, I would need an API that I could access to get an
> update of a running workflow.
>
>
>
> Can I do that with /runs/{id}/listeners and only using the given */runs/{id}/listeners/io/properties/stdout
> *output? What if I want the entire workflow diagram to be shown in a web
> interface? Is there any support for that?
>
>
>
> Thanks!
>
>
>
>
> --
>
> Vimig Socrates
>
> Case Western Reserve University Class of 2018
>
>
>
RE: Resources to create UI using Workflow on Workbench
Posted by Ian Dunlop <ia...@gmail.com>.
Hello,
Have a look at https://github.com/taverna-extras/taverna-player-portal. This is a UI that uses the taverna server to run workflows and update progress.
I think there is some ruby code to get a png of the workflow diagram in it. There should also be some java code somewhere – anyone know where?
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 04 September 2018 18:11
To: users@taverna.incubator.apache.org
Subject: Resources to create UI using Workflow on Workbench
Hi everyone,
I am looking to run Taverna Server version 2.5 and create a user interface accessible from the internet that will update as the workflow progresses. To that end, I would need an API that I could access to get an update of a running workflow.
Can I do that with /runs/{id}/listeners and only using the given /runs/{id}/listeners/io/properties/stdout output? What if I want the entire workflow diagram to be shown in a web interface? Is there any support for that?
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018