This seems to happen often e.g.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
a) are there general guidelines in the wiki on how to avoid these problems when
creating tools?
b) is there a way to check automatically if all input fields are correctly
escaped in a tool?
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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