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From Vimig Socrates <vsocra...@case.edu>
Subject Re: Dockerization of Taverna Server - Vimig Socrates
Date Fri, 05 Apr 2019 20:09:31 GMT
I'm unsure which port those subprocesses are run on. I have tried curling
for port 80 and I receive a Connection Refused. I saw in the admin console
that the RMI server runs on port 1099, but that doesn't seem to work
either. Is that the correct approach?

Thanks for the help!

--
Vimig Socrates
Case Western Reserve University Class of 2018


On Fri, Apr 5, 2019 at 9:27 AM Stian Soiland-Reyes <stain@apache.org> wrote:

> While running, the Taverna Server spawns up sub-processes that talk back
> to the Taverna Server to set the status of the workflow run etc.
>
> I think what we're facing here is that the server gets confused as to
> its apparance outside vs inside the docker container.  Taverna Server
> will normally pick up its own hostname from the very first REST HTTP
> call from the outside.
>
> That said, 127.0.0.1 should still work inside the same container?
>
> Are you able to use "docker exec" to jump inside and try to test with
> curl?
>
> On Thu, 4 Apr 2019 19:58:19 -0400, Vimig Socrates <vsocrates@case.edu>
> wrote:
> > 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
> > >
> > >
> > >
> > >
> > >
> Non-text part: text/html
>

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