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 <sora...@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-ability-to-change-the-tool/diff#chg-universe_wsgi.ini.sample
>
> 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.vandewe...@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
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