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From Vimig Socrates <vsocra...@case.edu>
Subject Re: Dockerization of Taverna Server - Vimig Socrates
Date Mon, 08 Apr 2019 01:54:22 GMT
Hi,

Thank you all for your help. It turns out I just needed to increase the
memory limit on the Docker container. I am not sure how that manifested
itself in a 127.0.0.1 Connection Refused error. Thank you for your help
however.

--
Vimig Socrates
Case Western Reserve University Class of 2018


On Fri, Apr 5, 2019 at 4:09 PM Vimig Socrates <vsocrates@case.edu> wrote:

> 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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