External Tool Service and SSH

[Nina Wolfram <ni...@gmail.com>]

Hi everyone,

I recently started working with the Taverna Workbench 2.5. and want to
create a workflow running an External Tool on a remote machine.
Establishing the SSH connection works, but there seems to be an error when
creating the temporary directory for the invocation. The taverna logfiles
give me the following output:


*INFO  2016-10-19 13:12:53,440
(de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation:136)
- Changing remote directory to tmp/*
*INFO  2016-10-19 13:12:53,456
(net.sf.taverna.t2.activities.externaltool.ExternalToolActivity:237) - Run
id is 7b68322d-40f0-4b82-bb66-780a81f32c42*
*INFO  2016-10-19 13:12:53,456
(de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation:229)
- Full command is cd tmp/usecase-5420555556213764519 && java -version*
*INFO  2016-10-19 13:12:53,456
(de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshPool:46) - Reusing
session*
*WARN  2016-10-19 13:12:54,532
(net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) -
Failed (INVOCATION) invoking
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity@6d1e64d1 for
job DispatchJobEvent facade1:Workflow2:Tool[]: Invalid exit code 1:The
system cannot find the path specified.*
*de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException:
Invalid exit code 1:The system cannot find the path specified.*
* at
de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation.submit_wait_fetch_results(SshUseCaseInvocation.java:259)*
* at
net.sf.taverna.t2.activities.externaltool.ExternalToolActivity$1.run(ExternalToolActivity.java:258)*
* at java.lang.Thread.run(Thread.java:724)*

It seems there is one change of directory too much: in the filesystem I end
up with a directory structure of /tmp/tmp/usecase-5420555556213764519.
Is there any workaround for this? (Or am I maybe doing something wrong?)


I also have a follow-up question:
Eventually I'd like to run this workflow using the Taverna Player / Taverna
Player Portal on an installation of Taverna Server. How do I transmit the
credentials for the SSH connection in that scenario?

Thanks in advance for your help!

Nina

Re: External Tool Service and SSH

[alaninmcr <al...@googlemail.com>]

On 20/10/2016 12:25, Nina Wolfram wrote:
> Hi everyone,

Hello

For some reason, it seems to be using "tmp/" rather than "/tmp/" as the 
directory. Can you check the definition of the location you are running 
the tool on?

You can find that under File -> Preferences -> Tool invocation

> I recently started working with the Taverna Workbench 2.5. and want to
> create a workflow running an External Tool on a remote machine.
> Establishing the SSH connection works, but there seems to be an error
> when creating the temporary directory for the invocation. The taverna
> logfiles give me the following output:
> /
> /
> /INFO  2016-10-19 13:12:53,440
> (de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation:136)
> - Changing remote directory to tmp/

[snip]

> It seems there is one change of directory too much: in the filesystem I
> end up with a directory structure of /tmp/tmp/usecase-5420555556213764519.
> Is there any workaround for this? (Or am I maybe doing something wrong?)

I think the location is set incorrectly.

> I also have a follow-up question:
> Eventually I'd like to run this workflow using the Taverna Player /
> Taverna Player Portal on an installation of Taverna Server. How do I
> transmit the credentials for the SSH connection in that scenario?

I know how to do it on a Taverna Server instance using
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/security/credentials

I am not sure about the player.

> Thanks in advance for your help!
>
> Nina

Alan