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From Vimig Socrates <vsocra...@case.edu>
Subject Re: Dockerization of Taverna Server - Vimig Socrates
Date Thu, 04 Apr 2019 23:58:19 GMT
Hi,

Yes, I gave that a shot too. I quickly realized that I can't run that on
Docker on Mac. I have to figure out if my program needs to be supported on
Mac and Windows as well.

If that is the case, I have thought about communicating between containers
but I run into a usability issue for non-developers there. Thanks for the
help!


--
Vimig Socrates
Case Western Reserve University Class of 2018


On Thu, Apr 4, 2019 at 8:13 AM Ian Dunlop <ianwdunlop@gmail.com> wrote:

> 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 <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates <vsocrates@case.edu>
> *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
> <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 <ianwdunlop@gmail.com> 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 <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates <vsocrates@case.edu>
> *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
>
>
>
>
>

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