The server is back up. Thanks for reporting this issue.

Dan

> On Dec 19, 2016, at 10:02 AM, Nicola Soranzo <nsora...@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-boun...@lists.galaxyproject.org>galaxy-dev-boun...@lists.galaxyproject.org
>>  <mailto:galaxy-dev-boun...@lists.galaxyproject.org>> on behalf of Nate 
>> Coraor <n...@bx.psu.edu <mailto:n...@bx.psu.edu>>
>> Date: Thursday, December 15, 2016 at 3:13 PM
>> To: " 
>> <mailto:galaxy-annou...@lists.galaxyproject.org>galaxy-annou...@lists.galaxyproject.org
>>  <mailto:galaxy-annou...@lists.galaxyproject.org>" 
>> <galaxy-annou...@lists.galaxyproject.org 
>> <mailto:galaxy-annou...@lists.galaxyproject.org>>
>> Cc: Galaxy Committers <galaxy-committ...@lists.galaxyproject.org 
>> <mailto:galaxy-committ...@lists.galaxyproject.org>>, Galaxy Dev List 
>> <galaxy-dev@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-committ...@lists.galaxyproject.org 
>> <mailto:galaxy-committ...@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"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
>> 
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/ 
>> <http://galaxyproject.org/search/mailinglists/>
> ___________________________________________________________
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