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