Reinout van Schouwen wrote:
> 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?)
I think this may be an issue with the CredentialManager failing to gain
information, possibly because it is running headless (as part of the
server). I would guess that you would see the same bug if you run the
workflow in the command line tool.
> 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.
Yes please create the Jira issues. You can put them in the Taverna 2 or
Taverna 3 projects. I will get notification that they have gone in and
can assign them correctly.
> regards,
Alan
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