Il giorno ven, 20/09/2013 alle 10.25 -0500, John Chilton ha scritto:
On Fri, Sep 20, 2013 at 9:08 AM, Nicola Soranzo <soranzo@crs4.it> wrote:
First step is to create a new dynamic job destination, this is demonstrated in job_conf.xml in the above changeset. This demonstrates the new style job_conf section - this will need to be adapted for the old style runners but is still doable.
Then you will want to add a dynamic job runner rule that implements this logic. This is the file lib/galaxy/jobs/rules/license_checker.py.
Is there a way to specify in job_conf.xml a per-tool final destination after the has_license filtering ? E.g.:
<tool id="cat1" destination="has_license" final_destination="local" /> <tool id="cat2" destination="has_license" final_destination="remote_cluster" />
The 'final_destination' attribute would then be used in has_license function instead of returning DEFAULT_JOB_DESTINATION_ID.
There is no way currently to pass information from the tool tag to the dynamic runner or to have the dynamic runner "pass" on making a decision in some way. It could potentially make sense to add these - but I would put forward a workaround that in my opinion is actually a little better: ...
I have actually found a way to implement my idea of specifying a final destination! I also generalized your approach giving the possibility to also specify a per-tool required group in jobs_conf.xml . job_conf.xml : <?xml version="1.0"?> <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" /> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" /> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="remote_cluster"> <destination id="local" runner="local" /> <destination id="is_user_in_group" runner="dynamic"> <param id="function">is_user_in_group</param> </destination> <destination id="remote_cluster" runner="drmaa" /> </destinations> <tools> <tool id="tool1" destination="is_user_in_group" required_group="other_group" /> <tool id="tool2" destination="is_user_in_group" final_destination="local" /> </tools> </job_conf> lib/galaxy/jobs/rules/is_user_in_group.py : from galaxy.jobs.mapper import JobMappingException DEFAULT_GROUP = 'have_license' def is_user_in_group(user, app, tool_id): # app is a galaxy.app.UniverseApplication object if user is None: raise JobMappingException('You must login to use this tool!') user_group_assocs = user.groups or [] default_destination_id = app.job_config.get_destination(None) for jtc in app.job_config.get_job_tool_configurations(tool_id): # app.job_config.get_job_tool_configurations(tool_id) returns a list of galaxy.jobs.JobToolConfiguration objects if not jtc.params: required_group = jtc.get('required_group', DEFAULT_GROUP) final_destination = jtc.get('final_destination', default_destination_id) break else: required_group = DEFAULT_GROUP final_destination = default_destination_id user_in_group = required_group in [user_group_assoc.group.name for user_group_assoc in user_group_assocs] if not user_in_group: raise JobMappingException('This tool is restricted to users in the %s group, please contact a site administrator to be authorized!' % required_group) else: return final_destination Hope that helps, Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/
There is no longer any need to display such tools to the user thanks to dynamic toolbox filters. This is that last file: lib/galaxy/tools/filters/license_filter.py. This will prevent any tool in the list 'LICENSED_TOOLS' from even being seen by unlicensed users. You do need to specify this filter is being used by adding the line:
tool_filters = license_filter:has_license
in the [app:main] section of universe_wsgi.ini.
I think that something like this:
# Tool filtering. Multiple such filters can be specified by giving # module (relative to galaxy.tools.filters) and function names for each # as a comma separated list. # See lib/galaxy/tools/filters/examples.py.sample for some examples. #tool_filters = #tool_label_filters = #tool_section_filters =
should be added to universe_wsgi.ini.sample , otherwise this wonderful feature is very difficult to discover.
Do you mean to suggest that merely documenting my contributions to Galaxy on my Twitter feed is insufficient? Hmm I don't know about that...
Seriously though, Björn has implemented some extensions to dynamic toolbox filters that include this:
https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-a...
I have added more options to Galaxy then I have documented in that file and I am always unsure whether to add them or not, the hesitation is that I think that file has too cluttered. I have missed really important modifications that should have been made because I didn't see them in that file.
These filters may rise to the level that they belong in there, I am not certain, but they should certainly be documented at least on the wiki somewhere
-John
Hope this helps!
-John
Thanks again!
Nicola
On Thu, Sep 19, 2013 at 2:45 AM, Vandeweyer Geert <geert.vandeweyer@uantwerpen.be> wrote:
Hi,
Could somebody point me to the place where I can create a ticket for the following feature:
- We want to have tools available only to users who provided a licence for this tool. - To prevent very long email lists (see example on dev-only tools), I'd like to have a group 'have_licence' - in dynamic job runner function : check if user is in usergroup : ok => run ; fail => give message.
Or can I hide tools from the menu based on usergroup?
Best,
Geert