On Wed, Mar 6, 2013 at 12:22 PM, John Chilton <chil...@msi.umn.edu> wrote:

> This whole concept puts a lot of onus on the tool developer. A
> biologist who has taken a two week course on perl could probably write
> a Galaxy tool, they probably couldn't write a secure tool for a public
> LWR. I think some experience in thinking about how to secure web
> accessible applications and prevent injection style attacks is needed.
> I will update the documentation urging additional caution with respect
> to this.

What I'm trying to understand is whether this model for a public LWR
makes sense. It appears that your LWR will take a command line, and
then apply a series of validations to it. This set of validations
would need to be very comprehensive -- perhaps impossibly
comprehensive -- to be secure.

To me it would make more sense that the LWR takes an input values dict
and constructs the command line itself after validating everything (it
already has the toolbox, so this should be possible).

> That said, there have been in the recent past multiple tools on public
> Galaxy servers (main included) that were developed by serious
> programmers that allowed arbitrary code execution. This is something
> the whole community (or at least that subset hosting public servers)
> needs to address and take more seriously.

I could not agree more, though I see this as a somewhat different
issue. There are a number of things that would be really helpful here:

- Some automatic validation of command line construction to look for
common exploits (again, impossible to do comprehensively)
- Some kind of sandboxing, through support for chroot, zones, jails,
or (dare I dream) running under native client.

> there is some malicious command that could get through. I cannot
> guarantee that it is secure, but I would be eager for counter examples
> or specific issues I can address.

I think this is what concerned me as well. I'm always worried about
security through comprehensive screening, someone almost always finds
a way around it. This is why the original python sandbox failed.
Constructing the command line from validated inputs seems safer (as
long as you trust the template that builds the command line).

> If we are honest and accept that there are going to security problems
> with the tools we wrap, one idea that might be worth pursuing for both
> the LWR and Galaxy itself is running tools in chrooted environments or
> at least as a different user then the webapp.

On this we completely agree.
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