Hi Eric, please also take a look at this mailing list thread: http://dev.list.galaxyproject.org/pass-user-groups-to-dynamic-job-runner-... If you are interested in the is_user_in_group solution, I have a slightly updated version which also uses roles instead of groups. Nicola 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=&quot;b(a)b.co&quot; file="encode/random_intervals.xml" /> > </section> > > 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) > > > > Cheers, > Eric Rasche > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/

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Thanks Eric, I'm sure this will be useful to many Galaxy admins! I've edited a bit the wiki page, in particular I've updated the code to use roles instead of groups, which is more appropriate in the context of access control. Best, Nicola Il 2013-12-07 03:07 Rasche Eric ha scritto: > Hi Nicola, >   > Just thought I'd write back since I added a Wiki page in > Admin/Config > [11] area for implementing access control. >   > Thank you for sharing the snippets you posted in the email thread > you > linked me! >   > http://wiki.galaxyproject.org/Admin/Config/Access%20Control [12] >   > Cheers, > Eric Rasche >   >   > 06.11.2013, 18:57, "Eric Rasche" <rasche.eric(a)yandex.ru&gt;: > >> 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. >> >> Thoughts? >> >> On 11/06/2013 12:12 PM, Nicola Soranzo wrote: >> >>>  Hi Eric, >>>  please also take a look at this mailing list thread: >>> >>> >> > >  http://dev.list.galaxyproject.org/pass-user-groups-to-dynamic-job-runner-... >>> [7] >>> >>>  If you are interested in the is_user_in_group solution, I have a >>>  slightly updated version which also uses roles instead of >>> groups. >>> >>>  Nicola >>> >>>  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=&quot;a(a)b.co [1],b(a)b.co [2]" id="EncodeTools" >>>> name="ENCODE Tools"> >>>>      <tool file="encode/gencode_partition.xml" /> >>>>      <tool execute=&quot;b(a)b.co [3]" >>>> file="encode/random_intervals.xml" /> >>>>    </section> >>>> >>>>  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 >>>> [4] >>>>  + (I saw some solution where they were adding "_beta" to tool >>>> names >>>>  which gave permissions to developers somewhere, but cannot >>>> find that now) >>>> >>>>  Cheers, >>>>  Eric Rasche >>>> >>>>  ___________________________________________________________ >>>>  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: >>>>    http://lists.bx.psu.edu/ [5] >>>> >>>>  To search Galaxy mailing lists use the unified search at: >>>>    http://galaxyproject.org/search/mailinglists/ [6] >> >> - -- >> Eric Rasche >> Programmer II >> Center for Phage Technology >> Texas A&M University >> College Station, TX 77843 >> 404-692-2048 >> esr(a)tamu.edu [9] >> rasche.eric(a)yandex.ru [10] >> > >   >   > -- > Eric Rasche > Programmer II > Center for Phage Technology > Texas A&M University > College Station, TX 77843 > 404-692-2048 > esr(a)tamu.edu [13] > rasche.eric(a)yandex.ru [14] > > Links: > ------ > [1] mailto:a@b.co > [2] mailto:b@b.co > [3] mailto:b@b.co > [4] > https://trello.com/c/Zo7FAXlM/286-24-add-ability-to-password-secure-tools > [5] http://lists.bx.psu.edu/ > [6] http://galaxyproject.org/search/mailinglists/ > [7] > > http://dev.list.galaxyproject.org/pass-user-groups-to-dynamic-job-runner-... > [8] http://www.enigmail.net/ > [9] mailto:esr@tamu.edu > [10] mailto:rasche.eric@yandex.ru > [11] http://wiki.galaxyproject.org/Admin/Config/ > [12] http://wiki.galaxyproject.org/Admin/Config/Access%20Control > [13] mailto:esr@tamu.edu > [14] mailto:rasche.eric@yandex.ru ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/