The server is back up. Thanks for reporting this issue.
Dan
On Dec 19, 2016, at 10:02 AM, Nicola Soranzo
<nsoranzo(a)tiscali.it> wrote:
Thanks David,
the issue has been already reported, see
https://github.com/galaxyproject/galaxy/issues/3332
<
https://github.com/galaxyproject/galaxy/issues/3332> , hopefully someone from the
Galaxy Team will look into this soon.
You can get the patch from GitHub in the mean time, it has been applied to all branches
starting from release_14.10 .
Cheers,
Nicola
On 19/12/16 14:39, Lapointe, David wrote:
> This site does not seem to be working for getting patches.
depot.galaxyproject.org
> --
> David Lapointe Ph.D.
> Sr. Bioinformatics Specialist
> Research Technology (RT)
> Tufts Technology Services (TTS)
> 16 Dearborn Road
> Somerville MA 02144
>
> Phone: 617-627-5319
> Fax: 617-627-3667
>
http://it.tufts.edu <
http://it.tufts.edu/>
>
> From: galaxy-dev <
<mailto:galaxy-dev-bounces@lists.galaxyproject.org>galaxy-dev-bounces@lists.galaxyproject.org
<mailto:galaxy-dev-bounces@lists.galaxyproject.org>> on behalf of Nate Coraor
<nate(a)bx.psu.edu <mailto:nate@bx.psu.edu>>
> Date: Thursday, December 15, 2016 at 3:13 PM
> To: "
<mailto:galaxy-announce@lists.galaxyproject.org>galaxy-announce@lists.galaxyproject.org
<mailto:galaxy-announce@lists.galaxyproject.org>"
<galaxy-announce(a)lists.galaxyproject.org
<mailto:galaxy-announce@lists.galaxyproject.org>>
> Cc: Galaxy Committers <galaxy-committers(a)lists.galaxyproject.org
<mailto:galaxy-committers@lists.galaxyproject.org>>, Galaxy Dev List
<galaxy-dev(a)lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>>
> Subject: [galaxy-dev] Galaxy Security Vulnerability - Arbitrary code execution
>
> *DESCRIPTION*
>
> A security vulnerability was recently discovered by David Wyde in two Galaxy tools
that are provided with and enabled by default in the Galaxy server. These vulnerabilities
allow malicious actors to execute arbitrary code as the user running the Galaxy server.
>
> The vulnerable tools are "Filter GFF data by attribute" and "Filter
GFF data by feature count", two tools which share code with each other and the more
general "Filter data on any column using simple expressions" tool. The latter
was fixed in a previous security disclosure but these GFF variants of the tool were missed
when updating the Filter tool.
>
> These tools use the Python `eval` and `exec` functions and do not properly sanitize
input to these functions.
>
> Additionally, an XSS vulnerability with the upload tool: An uploaded file's name
was not properly sanitized, and so a specially crafted filename uploaded to the Galaxy
server could be used as an XSS attack vector. This vulnerability has already been fixed in
the 16.07 and 16.10 Galaxy releases.
>
> The Galaxy Committers would like to thank David for disclosing these vulnerabilities.
If you discover security vulnerabilities in Galaxy, please report them to the Galaxy
Committers at galaxy-committers(a)lists.galaxyproject.org
<mailto:galaxy-committers@lists.galaxyproject.org>.
>
> *AFFECTED VERSIONS*
>
> These arbitrary code execution vulnerability is present in all known releases of
Galaxy using the default tool config or a tool config in which these tools are loaded. To
determine if your Galaxy server is affected, check your tool_conf.xml for the following
lines:
>
> <tool file="filters/gff/gff_filter_by_attribute.xml" />
> <tool file="filters/gff/gff_filter_by_feature_count.xml" />
>
> If you are unsure, you can also check to see if the tools have loaded by searching
for them in your Galaxy server logs, e.g.:
>
> % grep gff_filter paster.log
> galaxy.tools.toolbox.base DEBUG 2016-12-08 13:25:16,930 Loaded tool id:
gff_filter_by_attribute, version: 0.1 into tool panel..
> galaxy.tools.toolbox.base DEBUG 2016-12-08 13:25:16,930 Loaded tool id:
gff_filter_by_feature_count, version: 0.1 into tool panel..
>
> *IMPACT*
>
> This vulnerability can be exploited to execute arbitrary code as the user that runs
Galaxy jobs on any system where Galaxy runs those jobs (potentially a cluster). Such code
can be used to provide a remote shell to an attacker, or read/write/delete files that the
Galaxy user has appropriate permissions on.
>
> *SOLUTION*
>
> Multiple solutions exist for the arbitrary code execution vulnerability:
>
> 1. Update your Galaxy code. A fix for the issue has been applied to stable releases
of Galaxy back to version 14.10.
>
> 2. Disable the affected tools.
>
> 3. Patch the affected tools. Patches to fix the vulnerabilities (depending on the
version of Galaxy that you are running) can be found below.
>
> *INSTRUCTIONS*
>
> 1. To apply the fix, first identify your current Galaxy release version using the
`git branch` command. If you are on a 'release_YY.MM' branch, you can update
with:
>
> % git pull
>
> The process above can also be used to update to the 16.10 release if you are on the
'master' git branch. If you are on the 'master' branch and wish to remain
on your current Galaxy major release, check the 'lib/galaxy/version.py' file to
determine your major release version, then update to the appropriate branch:
>
> % git fetch origin
> % git checkout -b release_YY.MM origin/release_YY.MM
> % git pull
>
> 2. To disable the tools, locate and remove the following lines from your
tool_conf.xml, then restart Galaxy:
>
> <tool file="filters/gff/gff_filter_by_attribute.xml" />
> <tool file="filters/gff/gff_filter_by_feature_count.xml" />
>
> 3. To manually patch the tools, use the appropriate patch file below:
>
> For Galaxy releases 16.01 to dev:
>
>
https://depot.galaxyproject.org/patch/filter_security_16_01.patch
<
https://depot.galaxyproject.org/patch/filter_security_16_01.patch>
>
> For Galaxy releases 15.07 to 15.10:
>
>
https://depot.galaxyproject.org/patch/filter_security_15_07.patch
<
https://depot.galaxyproject.org/patch/filter_security_15_07.patch>
>
> For Galaxy releases 14.10 to 15.05:
>
>
https://depot.galaxyproject.org/patch/filter_security_14_10.patch
<
https://depot.galaxyproject.org/patch/filter_security_14_10.patch>
>
> To apply the patch, navigate to the root of your Galaxy directory, then execute
(replacing <patch_url> with the url above appropriate for your current Galaxy
release):
>
> % wget -O filter_security.patch <patch_url>
>
> or:
>
> % curl -o filter_security.patch <patch_url>
>
> and then test applying the patch:
>
> % patch -p1 --dry-run < filter_security.patch
> checking file tools/filters/gff/gff_filter_by_attribute.py
> checking file tools/filters/gff/gff_filter_by_attribute.xml
> checking file tools/filters/gff/gff_filter_by_feature_count.py
> checking file tools/filters/gff/gff_filter_by_feature_count.xml
>
> If this succeeds without error (applying successfully with fuzz/offset is
> fine), apply with:
>
> % patch -p1 < filter_security.patch
> patching file tools/filters/gff/gff_filter_by_attribute.py
> patching file tools/filters/gff/gff_filter_by_attribute.xml
> patching file tools/filters/gff/gff_filter_by_feature_count.py
> patching file tools/filters/gff/gff_filter_by_feature_count.xml
>
> In all cases, for the changes to take effect, *YOU MUST RESTART ALL GALAXY
> SERVER PROCESSES*.
>
> On behalf of the Galaxy Committers,
> --nate
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
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>
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>
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<
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