Hi Nicola,
Just thought I'd write back since I added a Wiki page in Admin/Config area for implementing access control.
Thank you for sharing the snippets you posted in the email thread you linked me!
Eric Rasche
06.11.2013, 18:57, "Eric Rasche" <rasche.eric@yandex.ru>:

Hi Nicola,

Oh, excellent. I must've skipped over that, given the strange title of
the thread.

Your solution at the end of that thread is very promising, and certainly
handles failure MUCH better than mine does (i.e. raising exceptions and
not breaking a workflow if the user isn't permitted access.)

(Did you put it on the galaxy wiki anywhere? If it weren't for you
linking that, I never would've known about it and that's very useful info!)

In my organisation's case; if a user isn't allowed access to a given
tool, we believe that

- - galaxy has no reason to admit it exists
- - galaxy should not share default information about a tool

Which is a bit different from the case of having a license to use a
tool. For licensing issues, naturally it would be fine to say "yes this
exists and if you can't run it, obtain a license".

For my org's case, we might want to store administrative tools (for
other services) in galaxy. It's a very convenient platform for more than
just bioinformatics and we have some non-technical people on staff who
occasionally need to pull various data sets from various services/make
database backups/etc. Students and clients who use our galaxy instance
don't need to know that these tools are available.


On 11/06/2013 12:12 PM, Nicola Soranzo wrote:

Hi Eric,
please also take a look at this mailing list thread:


If you are interested in the is_user_in_group solution, I have a
slightly updated version which also uses roles instead of groups.


Il giorno mer, 06/11/2013 alle 11.38 -0600, Eric Rasche ha scritto:
Howdy devs,

I've implemented some rather basic tool access control and am looking
for feedback on my implementation.

# Why

Our organisation wanted the ability to restrict tools to different
users/roles. As such I've implemented as an "execute" tag which can be
applied to either <section> or <tools> in the tool configuration file.

# Example galaxy-admin changes

For example:

<section execute="a@b.co,b@b.co" id="EncodeTools" name="ENCODE Tools">
<tool file="encode/gencode_partition.xml" />
<tool execute="b@b.co" file="encode/random_intervals.xml" />

which would allow A and B to access gencode_parition, but only B would
be able to access random_intervals. To put it explicity

- by default, everyone can access all tools
- if section level permissions are set, then those are set as defaults
for all tools in that section
- if tool permissions are set, they will override the defaults.

# Pros and Cons

There are some good features

- non-accessible tools won't show up in the left hand panel, based on user
- non-accessible tools cannot be run or accessed.

There are some caveats however.

- existence of tools is not completely hidden.
- Labels are not hidden at all.
- workflows break completely if a tool is unavailable to a shared user
and the user copies+edits. They can be copied, and viewed (says tool not
found), but cannot be edited.

Tool names/id/version info can be found in the javascript object due to
the call to app.toolbox.tool_panel.items() in
templates/webapps/galaxy/workflow/editor.mako, as that returns the raw
tool list, rather than one that's filtered on whether or not the user
has access. I'm yet to figure out a clean fix for this. Additionally,
empty sections are still shown even if there aren't tools listed in them.

For a brief overview of my changes, please see the attached diff. (It's
missing one change because I wasn't being careful and started work on
multiple different features)

# Changeset overview

In brief, most of the changes consist of
- new method in model.User to check if an array of roles overlaps at all
with a user's roles
- modifications to appropriate files for reading in the new
tool_config.xml's options
- modification to get_tool to pass user information, as whether or not a
tool exists is now dependent on who is asking.

Please let me know if you have input on this before I create a pull
request on this feature.

# Fixes

I believe this will fix a number of previously brought up issues (at
least to my understanding of the issues listed)

+ https://trello.com/c/Zo7FAXlM/286-24-add-ability-to-password-secure-tools
+ (I saw some solution where they were adding "_beta" to tool names
which gave permissions to developers somewhere, but cannot find that now)

Eric Rasche

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Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843

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Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843