On Nov 5, 2013, at 6:28 PM, Nate Coraor <n...@bx.psu.edu> wrote:

> Hi Ido,
> 
> Thanks for the feedback.  Replies below.
> 
> On Nov 5, 2013, at 9:54 AM, Ido Tamir wrote:
> 
>> This seems to happen often e.g. 
>> http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
> 
> I'm not sure I'd agree that it's often - we've had 4 or 5 vulnerabilities 
> over the life of the project.  2 allowed arbitrary code execution, the others 
> were less severe.
> 
But these were written by experts, not by people like me, that don't know what 
the galaxy framework really does/does not do with the input, so I guess I make 
many more mistakes.

>> a) are there general guidelines in the wiki on how to avoid these problems 
>> when creating tools?
> 
> The guidelines for writing a Galaxy tool are no different from best practices 
> for writing secure code.  In specific for this vulnerability, execution of 
> user input should be handled with extreme care, and this tool had some gaps 
> in its input validation and sanitization.  For what it's worth, the filter 
> tool (on which the other vulnerable tools were based) is one of the few tools 
> surviving from the very early days of Galaxy, and would not be implemented 
> the same way if written today.

I think it would be nice to have a small outline on the wiki of what galaxy 
does with the input data and how it could affect a tool.
What sanitisation is there by default so I don't have to worry about it, but 
what could happen I if I don't care to check/remove sanitise ' | or " ..., 
maybe with examples.

>> b) is there a way to check automatically if all input fields are correctly 
>> escaped in a tool?
> 
> I am not sure how Galaxy could do this.  Galaxy sanitizes the command line so 
> that input fields passed to a tool as command line arguments cannot be 
> crafted to exploit the shell's parsing rules.  
Thats good

best,
ido


> What the tool itself does with its inputs are out of Galaxy's control.
> 
> --nate
> 
>> 
>> A search for security in the wiki brings up:
>>      • Admin/Data Libraries/Library Security
>> 0.0k - rev: 1 (current) last modified: 2013-01-02 23:54:33
>>      • Admin/DataLibraries/LibrarySecurity
>> 19.2k - rev: 4 (current) last modified: 2013-01-03 00:12:36
>>      • HelpOnConfiguration/SecurityPolicy
>> 1.9k - rev: 1 (current) last modified: 0
>>      • Learn/Security Features
>> 7.0k - rev: 3 (current) last modified: 2011-09-13 16:52:08
>>      • News/2013_04_08_Galaxy_Security_Release
>> 1.3k - rev: 3 (current) last modified: 2013-04-08 16:56:41
>> 
>> "escape" does not bring up anything.
>> 
>> thank you very much,
>> ido
>> 
>> 
>> On Nov 5, 2013, at 12:45 AM, Nate Coraor <n...@bx.psu.edu> wrote:
>> 
>>> A security vulnerability was recently discovered by John Chilton with 
>>> Galaxy's "Filter data on any column using simple expressions" and "Filter 
>>> on ambiguities in polymorphism datasets" tools that can allow for arbitrary 
>>> execution of code on the command line.
>>> 
>>> The fix for these tools has been committed to the Galaxy source.  The 
>>> timing of this commit coincides with the next Galaxy stable release (which 
>>> has also been pushed out today).
>>> 
>>> To apply the fix and simultaneously update to the new Galaxy stable 
>>> release, ensure you are on the stable branch and upgrade to the latest 
>>> changeset:
>>> 
>>> % hg branch
>>> stable
>>> 
>>> % hg pull -u
>>> 
>>> For Galaxy installations that administrators are not yet ready to upgrade 
>>> to the latest release, there are three workarounds.
>>> 
>>> First, for Galaxy installations running on a relatively new version of the 
>>> stable release (e.g. release_2013.08.12), Galaxy can be updated to the 
>>> specific changeset that that contains the fix.  This will include all of 
>>> the stable (non-feature) commits that have been accumulated since the 8/12 
>>> release plus any new features included with (and prior to) the 8/12 
>>> release, but without all of the new features included in the 11/4 release.  
>>> Ensure you are on the stable branch and then upgrade to the specific 
>>> changeset:
>>> 
>>> % hg pull -u -r e094c73fed4d
>>> 
>>> Second, the patch can be downloaded and applied manually:
>>> 
>>> % wget -o security.patch 
>>> https://bitbucket.org/galaxy/galaxy-central/commits/e094c73fed4dc66b589932edb83412cb8b827cd3raw/
>>> 
>>> and then:
>>> 
>>> % hg patch security.patch
>>> 
>>> or:
>>> 
>>> % patch -p1 < security.patch
>>> 
>>> Third, the tools can be completely disabled by removing them from the tool 
>>> configuration file (by default, tool_conf.xml) and restarting all Galaxy 
>>> server processes.  The relevant lines in tool_conf.xml are:
>>> 
>>> <tool file="stats/dna_filtering.xml" />
>>> <tool file="stats/filtering.xml" />
>>> 
>>> The full 11/4 Galaxy Distribution News Brief will be available later today 
>>> and will contain details of changes since the last release.
>>> 
>>> --nate
>>> Galaxy Team
>>> ___________________________________________________________
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>> 
>> 
> 


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