Hi,
We have a Taverna server 2.2 installation running on a machine where we
also run Rserve, so that workflows with R scripts can access
localhost:6311. Outside connections on that port are blocked by a
firewall.
We found that a workflow created in Taverna 2.4 which uses an Rshell
activity with unauthenticated access to Rserve fails to execute from
Taverna server. The reason being that the workbench does not save
<username> and <password> elements to the .t2flow file when these values
aren't supplied. Consequently, the values for username and password are
null in the RshellConnectionSettings object that is passed to the
constructor of RshellConnection. And, because that constructor uses
username.equals("") instead of the safer expression "".equals(username),
a NullPointerException results. (But even if the safe comparison were
used, this check for empty username seems intended to prevent
unauthenticated access. Why?)
My workaround is to manually add empty <username> and <password>
elements to the .t2flow file. With that, the workflow executes
successfully. You can compare
http://www.myexperiment.org/workflows/3360.html and
http://www.myexperiment.org/workflows/3418.html if you like.
If you would like me to create a couple of JIRA issues about this,
please give me permission to do so. I already have an account.
regards,
--
Reinout van Schouwen <[email protected]>
LUMC
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