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Remove endpoints not needed in toolshed
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@guerler
guerler committed Jul 20, 2017
1 parent 97a4cb9 commit 917d2d9
Showing 1 changed file with 0 additions and 200 deletions.
200 changes: 0 additions & 200 deletions lib/tool_shed/util/admin_util.py
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Expand Up @@ -21,9 +21,6 @@ class Admin( object ):
user_list_grid = None
role_list_grid = None
group_list_grid = None
quota_list_grid = None
repository_list_grid = None
tool_version_list_grid = None
delete_operation = None
undelete_operation = None
purge_operation = None
Expand All @@ -46,55 +43,6 @@ def center( self, trans, **kwd ):
message=message,
status=status )

@web.expose
@web.require_admin
def package_tool( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
toolbox = self.app.toolbox
tool_id = None
if params.get( 'package_tool_button', False ):
tool_id = params.get('tool_id', None)
try:
tool_tarball = trans.app.toolbox.package_tool( trans, tool_id )
trans.response.set_content_type( 'application/x-gzip' )
download_file = open( tool_tarball )
os.unlink( tool_tarball )
tarball_path, filename = os.path.split( tool_tarball )
trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.tgz"' % ( tool_id )
return download_file
except Exception:
return trans.fill_template( '/admin/package_tool.mako',
tool_id=tool_id,
toolbox=toolbox,
message=message,
status='error' )

@web.expose
@web.require_admin
def reload_tool( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
toolbox = self.app.toolbox
tool_id = None
if params.get( 'reload_tool_button', False ):
tool_id = kwd.get( 'tool_id', None )
galaxy.queue_worker.send_control_task(trans.app, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} )
message, status = trans.app.toolbox.reload_tool_by_id( tool_id )
return trans.fill_template( '/admin/reload_tool.mako',
tool_id=tool_id,
toolbox=toolbox,
message=message,
status=status )

@web.expose
@web.require_admin
def tool_versions( self, trans, **kwd ):
if 'message' not in kwd or not kwd[ 'message' ]:
kwd[ 'message' ] = 'Tool ids for tools that are currently loaded into the tool panel are highlighted in green (click to display).'
return self.tool_version_list_grid( trans, **kwd )

@web.expose
@web.require_admin
def roles( self, trans, **kwargs ):
Expand Down Expand Up @@ -1008,154 +956,6 @@ def manage_roles_and_groups_for_user( self, trans, **kwd ):
message=message,
status=status )

@web.expose
@web.require_admin
def jobs( self, trans, stop=[], stop_msg=None, cutoff=180, job_lock=None, ajl_submit=None, **kwd ):
deleted = []
msg = None
status = None
job_ids = util.listify( stop )
if job_ids and stop_msg in [ None, '' ]:
msg = 'Please enter an error message to display to the user describing why the job was terminated'
status = 'error'
elif job_ids:
if stop_msg[-1] not in PUNCTUATION:
stop_msg += '.'
for job_id in job_ids:
error_msg = "This job was stopped by an administrator: %s <a href='%s' target='_blank'>Contact support</a> for additional help." \
% ( stop_msg, self.app.config.get("support_url", "https://galaxyproject.org/support/" ) )
if trans.app.config.track_jobs_in_database:
job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
job.stderr = error_msg
job.set_state( trans.app.model.Job.states.DELETED_NEW )
trans.sa_session.add( job )
else:
trans.app.job_manager.job_stop_queue.put( job_id, error_msg=error_msg )
deleted.append( str( job_id ) )
if deleted:
msg = 'Queued job'
if len( deleted ) > 1:
msg += 's'
msg += ' for deletion: '
msg += ', '.join( deleted )
status = 'done'
trans.sa_session.flush()
if ajl_submit:
if job_lock == 'on':
galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock',
kwargs={'job_lock': True } )
job_lock = True
else:
galaxy.queue_worker.send_control_task(trans.app, 'admin_job_lock',
kwargs={'job_lock': False } )
job_lock = False
else:
job_lock = trans.app.job_manager.job_lock
cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) )
jobs = trans.sa_session.query( trans.app.model.Job ) \
.filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time,
or_( trans.app.model.Job.state == trans.app.model.Job.states.NEW,
trans.app.model.Job.state == trans.app.model.Job.states.QUEUED,
trans.app.model.Job.state == trans.app.model.Job.states.RUNNING,
trans.app.model.Job.state == trans.app.model.Job.states.UPLOAD ) ) ) \
.order_by( trans.app.model.Job.table.c.update_time.desc() ).all()
recent_jobs = trans.sa_session.query( trans.app.model.Job ) \
.filter( and_( trans.app.model.Job.table.c.update_time > cutoff_time,
or_( trans.app.model.Job.state == trans.app.model.Job.states.ERROR,
trans.app.model.Job.state == trans.app.model.Job.states.OK) ) ) \
.order_by( trans.app.model.Job.table.c.update_time.desc() ).all()
last_updated = {}
for job in jobs:
delta = datetime.utcnow() - job.update_time
if delta.days > 0:
last_updated[job.id] = '%s hours' % ( delta.days * 24 + int( delta.seconds / 60 / 60 ) )
elif delta > timedelta( minutes=59 ):
last_updated[job.id] = '%s hours' % int( delta.seconds / 60 / 60 )
else:
last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 )
finished = {}
for job in recent_jobs:
delta = datetime.utcnow() - job.update_time
if delta.days > 0:
finished[job.id] = '%s hours' % ( delta.days * 24 + int( delta.seconds / 60 / 60 ) )
elif delta > timedelta( minutes=59 ):
finished[job.id] = '%s hours' % int( delta.seconds / 60 / 60 )
else:
finished[job.id] = '%s minutes' % int( delta.seconds / 60 )
return trans.fill_template( '/admin/jobs.mako',
jobs=jobs,
recent_jobs=recent_jobs,
last_updated=last_updated,
finished=finished,
cutoff=cutoff,
msg=msg,
status=status,
job_lock=job_lock)

@web.expose
@web.require_admin
def job_info( self, trans, jobid=None ):
job = None
if jobid is not None:
job = trans.sa_session.query( trans.app.model.Job ).get(jobid)
return trans.fill_template( '/webapps/reports/job_info.mako',
job=job,
message="<a href='jobs'>Back</a>" )

@web.expose
@web.require_admin
def manage_tool_dependencies( self,
trans,
install_dependencies=False,
uninstall_dependencies=False,
remove_unused_dependencies=False,
selected_tool_ids=None,
selected_environments_to_uninstall=None,
viewkey='View tool-centric dependencies'):
if not selected_tool_ids:
selected_tool_ids = []
if not selected_environments_to_uninstall:
selected_environments_to_uninstall = []
tools_by_id = trans.app.toolbox.tools_by_id
view = six.next(six.itervalues(trans.app.toolbox.tools_by_id))._view
if selected_tool_ids:
# install the dependencies for the tools in the selected_tool_ids list
if not isinstance(selected_tool_ids, list):
selected_tool_ids = [selected_tool_ids]
requirements = set([tools_by_id[tid].tool_requirements for tid in selected_tool_ids])
if install_dependencies:
[view.install_dependencies(r) for r in requirements]
elif uninstall_dependencies:
[view.uninstall_dependencies(index=None, requirements=r) for r in requirements]
if selected_environments_to_uninstall and remove_unused_dependencies:
if not isinstance(selected_environments_to_uninstall, list):
selected_environments_to_uninstall = [selected_environments_to_uninstall]
view.remove_unused_dependency_paths(selected_environments_to_uninstall)
return trans.fill_template( '/webapps/galaxy/admin/manage_dependencies.mako',
tools=tools_by_id,
requirements_status=view.toolbox_requirements_status,
tool_ids_by_requirements=view.tool_ids_by_requirements,
unused_environments=view.unused_dependency_paths,
viewkey=viewkey )

@web.expose
@web.require_admin
def sanitize_whitelist( self, trans, submit_whitelist=False, tools_to_whitelist=[]):
if submit_whitelist:
# write the configured sanitize_whitelist_file with new whitelist
# and update in-memory list.
with open(trans.app.config.sanitize_whitelist_file, 'wt') as f:
if isinstance(tools_to_whitelist, six.string_types):
tools_to_whitelist = [tools_to_whitelist]
new_whitelist = sorted([tid for tid in tools_to_whitelist if tid in trans.app.toolbox.tools_by_id])
f.write("\n".join(new_whitelist))
trans.app.config.sanitize_whitelist = new_whitelist
galaxy.queue_worker.send_control_task(trans.app, 'reload_sanitize_whitelist', noop_self=True)
# dispatch a message to reload list for other processes
return trans.fill_template( '/webapps/galaxy/admin/sanitize_whitelist.mako',
sanitize_all=trans.app.config.sanitize_all_html,
tools=trans.app.toolbox.tools_by_id )


# ---- Utility methods -------------------------------------------------------

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