RE: Dockerization of Taverna Server - Vimig Socrates
Hello, I wonder if using --network="host" in your docker run command would help. That should make the docker container use the host network. Of course it might break other things in the TavServ container and it only works on linux. https://docs.docker.com/network/host/ Cheers, Ian Sent from Mail for Windows 10 From: Vimig Socrates Sent: 04 April 2019 00:42 To: users@taverna.incubator.apache.org Subject: Re: Dockerization of Taverna Server - Vimig Socrates Hi, Yes, I incorporated a portion of the Dockerfile from the released taverna-server Docker container. After some more digging, looks like it is an issue with my workflow file. I try to connect to the http://localhost:8080/tavernaserver/rest/runs endpoint using a REST service in my workflow and since Docker sees localhost as the host machine, that doesn't work. Has anyone else run into this issue? If so, any help would be appreciated! Thank you! -- Vimig Socrates Case Western Reserve University Class of 2018 On Wed, Apr 3, 2019 at 5:52 AM Ian Dunlop wrote: Hello, Hi Vimig. Have you had a look at https://hub.docker.com/r/taverna/taverna-server/ which is a taverna server in Tomcat 8. I haven’t used this recently but I think it used to work. Are you required to use Tomcat 7? What workflow were you trying to run. It looks like the code that is causing the issue are: at org.taverna.server.master.worker.RemoteRunDelegate.getStatus(RemoteRunDelegate.java:214) at org.taverna.server.master.worker.RunDatabase.checkForFinishNow(RunDatabase.java:83) though I don’t know why they are trying to connect to 127.0.0.1. I’m not sure if its the workflow causing the problem or the TavServ itself. Cheers, Ian Sent from Mail for Windows 10 From: Vimig Socrates Sent: 03 April 2019 03:56 To: users@taverna.incubator.apache.org Subject: Dockerization of Taverna Server - Vimig Socrates Hello everyone! I am currently trying to Dockerize a Taverna Server v2.5.4 deployed on a Tomcat 7 server. I am having some issues when I actually try to run a workflow. I get a Connection Refused error as below: java.rmi.ConnectException: Connection refused to host: 127.0.0.1; nested exception is: java.net.ConnectException: Connection refused (Connection refused) at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:619) at sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:216) ... at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.net.ConnectException: Connection refused (Connection refused) at java.net.PlainSocketImpl.socketConnect(Native Method) ... at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:613) ... 21 more I've attached the full tavserv.out file for reference. I believe the reason is that 127.0.0.1 refers to the host computer through the Docker bridge, but I am not sure how to fix that. Do I need to add something to the tavernaserver.properties file? Thanks for the help! -- Vimig Socrates Case Western Reserve University Class of 2018
RE: Dockerization of Taverna Server - Vimig Socrates
Hello, Hi Vimig. Have you had a look at https://hub.docker.com/r/taverna/taverna-server/ which is a taverna server in Tomcat 8. I haven’t used this recently but I think it used to work. Are you required to use Tomcat 7? What workflow were you trying to run. It looks like the code that is causing the issue are: at org.taverna.server.master.worker.RemoteRunDelegate.getStatus(RemoteRunDelegate.java:214) at org.taverna.server.master.worker.RunDatabase.checkForFinishNow(RunDatabase.java:83) though I don’t know why they are trying to connect to 127.0.0.1. I’m not sure if its the workflow causing the problem or the TavServ itself. Cheers, Ian Sent from Mail for Windows 10 From: Vimig Socrates Sent: 03 April 2019 03:56 To: users@taverna.incubator.apache.org Subject: Dockerization of Taverna Server - Vimig Socrates Hello everyone! I am currently trying to Dockerize a Taverna Server v2.5.4 deployed on a Tomcat 7 server. I am having some issues when I actually try to run a workflow. I get a Connection Refused error as below: java.rmi.ConnectException: Connection refused to host: 127.0.0.1; nested exception is: java.net.ConnectException: Connection refused (Connection refused) at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:619) at sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:216) ... at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.net.ConnectException: Connection refused (Connection refused) at java.net.PlainSocketImpl.socketConnect(Native Method) ... at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:613) ... 21 more I've attached the full tavserv.out file for reference. I believe the reason is that 127.0.0.1 refers to the host computer through the Docker bridge, but I am not sure how to fix that. Do I need to add something to the tavernaserver.properties file? Thanks for the help! -- Vimig Socrates Case Western Reserve University Class of 2018
RE: Taverna Server 2.5.4 Provenance File Location
Hello,
I probably got version number confusion. I think 2.5.4 is the latest available
from launchpad according to https://launchpad.net/taverna-server. It has that
API capability according to the docs.
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 24 February 2019 21:14
To: users@taverna.incubator.apache.org
Subject: Re: Taverna Server 2.5.4 Provenance File Location
Hi,
I thought that 2.5.5 was the most recent release of the Taverna
(pre-Apache). I don't see it on the Github repo either. Please let me know
where the war file is. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2019
On Sun, Feb 24, 2019 at 4:11 PM Vimig Socrates wrote:
Hi,
I thought that 2.5.5 was the most recent release of the Taverna (pre-Apache). I
don't see any on the Github repo either. Please let me know where the war file
is. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Fri, Feb 22, 2019 at 4:47 AM Ian Dunlop wrote:
Hi Vimig,
I see you are using 2.5.4 . However, in the 2.5.5 server the provenance is also
contained in the run bundle for the workflow run via /runs/{id}/run-bundle.
It’s detailed in
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle.
Maybe it’s worth switching the 2.5.5 to give it a try. I’ve never tried this
provenance/run-bundle API call though so fingers crossed.
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 19 February 2019 22:22
To: users@taverna.incubator.apache.org
Subject: Taverna Server 2.5.4 Provenance File Location
Hi,
I was wondering if there was a way to change the location that the files are
generated from calling with REST /generate-provenance from Taverna Server
2.5.4. They seem to be currently placed in /tmp on Ubuntu16.04 and those get
deleted every day.
I'd like access to the .wfbundle file so I can rerun the workflow easily.
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
RE: Taverna Server 2.5.4 Provenance File Location
Hi Vimig,
I see you are using 2.5.4 . However, in the 2.5.5 server the provenance is also
contained in the run bundle for the workflow run via /runs/{id}/run-bundle.
It’s detailed in
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle.
Maybe it’s worth switching the 2.5.5 to give it a try. I’ve never tried this
provenance/run-bundle API call though so fingers crossed.
Cheers,
Ian
Sent from Mail for Windows 10
From: Vimig Socrates
Sent: 19 February 2019 22:22
To: users@taverna.incubator.apache.org
Subject: Taverna Server 2.5.4 Provenance File Location
Hi,
I was wondering if there was a way to change the location that the files are
generated from calling with REST /generate-provenance from Taverna Server
2.5.4. They seem to be currently placed in /tmp on Ubuntu16.04 and those get
deleted every day.
I'd like access to the .wfbundle file so I can rerun the workflow easily.
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
RE: Resources to create UI using Workflow on Workbench
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 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 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
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 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
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: Opening .xml workflow files in Taverna
Hello, xml workflows are from Taverna 1. The latest version of Taverna 2 can only load Taverna 2 t2flow files. Previous versions could load all types of Taverna workflows, I think 2.4.0 can load it. You can then convert it to t2flow for use in the 2.5 version. Try installing the workbench from https://launchpad.net/taverna/+milestone/2.4.0 Cheers, Ian On 13/11/2015 16:03, Danielle Harris wrote: > I’ve downloaded a set of workflows in .xml format, and the SOP files tell me > simply to open the files via File>Open Workflow>Workflow.xml. I see in the > user manual that the files should be in .t2flow format, so I am wondering > whether there is a plugin I am missing? I’ve tried to find the information > online, but have been unsuccessful. > > Sincerely, > Danielle > -- Ian Dunlop, eScience Lab School of Computer Science The University of Manchester http://orcid.org/-0001-7066-3350
