Dr. Taylor,

Thanks for the e-mail. I think that is a solid instinct, it makes me
nervous too, though most things do. I am responding to the list
because I think others are going to have the same concern

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.

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 guess the other big question is is there something inherently
insecure about the framework - to me the most obvious attack vector
there is the regular expression that is generated. I worry if that is
that too porous somehow, if there some XML that a developer would
write that would reasonably make the tool look secure but in fact
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.

The one thing I will say is over and over, things are whitelisted -
not blacklisted - which is generally securer.

After that level, I think the LWR does still have issues, but they are
all the same issues Galaxy itself has. Can you do a denial of service
type attack, yes pretty easily, though I think I could hit any public
Galaxy the same way. Also are the tools and wrappers themselves
secure, is there some fastq file you could give to bowtie to cause it
to run an arbitrary command? My guess is probably, but there is not
much the framework could do to prevent that.

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.

Thanks again,

On Wed, Mar 6, 2013 at 10:01 AM, James Taylor <ja...@jamestaylor.org> wrote:
> John, something about this makes me really nervous security wise. Need
> to think hard on it.
> (Not a complaint, or criticism, or copied to the list, just letting
> you know it caught my attention).
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
> On Tue, Mar 5, 2013 at 10:19 PM, John Chilton <chil...@msi.umn.edu> wrote:
>> I have been extending the LWR so that one can now stand up public LWR
>> servers 
>> (https://lwr.readthedocs.org/en/latest/#setting-up-a-public-lwr-server),
>> the idea is that you can publicly share data and computation with any
>> Galaxy instances in the world easily and seamlessly via vanilla Galaxy
>> tools. This could serve the foundation of a distributed service
>> architecture where tools are the contracts, Galaxy instances the
>> clients, and LWRs the server containers.
>> One thing that did need to change with the LWR is that inputs need to
>> be validated. It would obviously not be a good idea to allow arbitrary
>> command-line or script executions to unauthenticated clients.
>> This was accomplished in part by allowing you to configure a Galaxy
>> toolbox or tool_conf file for the LWR. The LWR reads validation logic
>> for command-line and configfiles from the XML and verifies them before
>> execution.
>> The test cases I used to build up this validation extension to the
>> tool XML can be found here:
>> https://bitbucket.org/jmchilton/lwr/src/tip/test/validator_test.py
>> Question 1: Would Galaxy benefit from implementing this validation
>> stuff in the core framework as well? I think of myself as fairly
>> security conscious and my sense is no, but it could I see the
>> argument. There are potentially complex interactions between user
>> inputs and cheetah templates that one might sleep better knowing
>> everything is being validated before execution (the user didn't cause
>> the cheetah template to somehow render "; rm -rf /").
>> Question 2: Looking back on the validation stuff, it seems I am just
>> rewriting in XML what cheetah is doing. The duplication makes me think
>> the validation stuff might serve the foundation for a better (or at
>> least more secure) way to build up commands.
>> <command interpreter="python">
>>   <tool_wrapper>tophat_wrapper.py</tool_wrapper>
>>   <if>
>>     <cond>
>>       <equals left="$refGenomeSource.genomeSource" right="history">
>>       <then>
>>          <parameter name="--own_file">$refGenomeSource.ownFile</parameter>
>>    ....
>> The client could easily compile that into a cheetah template to build
>> the command, the server could compile it into a regular expression to
>> validate the input.
>> These aren't things that pressingly need to be added to the core
>> Galaxy framework, but things to think about longer term. If there is
>> any interest from the core Galaxy team I would be happy to implement
>> any of this with any desired changes.
>> Thanks all,
>> -John
>> ------------------------------------------------
>> John Chilton
>> Senior Software Developer
>> University of Minnesota Supercomputing Institute
>> Office: 612-625-0917
>> Cell: 612-226-9223
>> https://twitter.com/jmchilton
>> https://bitbucket.org/jmchilton
>> https://github.com/jmchilton
>> ___________________________________________________________
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