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This commit is contained in:
Bjoern Gruening
2019-08-31 13:34:07 +02:00
parent 5232aefddd
commit 79da41de15
4 changed files with 19 additions and 19 deletions
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lib/galaxy/webapps/galaxy/api/tool_entry_points.py
+8 -8
View File
@@ -4,7 +4,7 @@ related to running and queued jobs.
import logging
from galaxy import exceptions, util
from galaxy.managers.realtime import RealTimeManager
from galaxy.managers.interactivetool import InteractiveToolManager
from galaxy.web import expose_api_anonymous_and_sessionless
from galaxy.webapps.base.controller import BaseAPIController
@@ -15,7 +15,7 @@ class ToolEntryPointsAPIController(BaseAPIController):
def __init__(self, app):
self.app = app
self.realtime_manager = RealTimeManager(app)
self.interactivetool_manager = InteractiveToolManager(app)
@expose_api_anonymous_and_sessionless
def index(self, trans, running=False, job_id=None, **kwd):
@@ -43,16 +43,16 @@ class ToolEntryPointsAPIController(BaseAPIController):
if job_id is not None:
job = trans.sa_session.query(trans.app.model.Job).get(self.decode_id(job_id))
if not self.realtime_manager.can_access_job(trans, job):
if not self.interactivetool_manager.can_access_job(trans, job):
raise exceptions.ItemAccessibilityException()
entry_points = job.realtimetool_entry_points
entry_points = job.interactivetool_entry_points
if running:
entry_points = self.realtime_manager.get_nonterminal_for_user_by_trans(trans)
entry_points = self.interactivetool_manager.get_nonterminal_for_user_by_trans(trans)
rval = []
for entry_point in entry_points:
as_dict = self.encode_all_ids(trans, entry_point.to_dict(), True)
target = self.realtime_manager.target_if_active(trans, entry_point)
target = self.interactivetool_manager.target_if_active(trans, entry_point)
if target:
as_dict["target"] = target
rval.append(as_dict)
@@ -68,10 +68,10 @@ class ToolEntryPointsAPIController(BaseAPIController):
:param id: Encoded entry point id
:rtype: dictionary
:returns: dictionary containing target for realtime entry point
:returns: dictionary containing target for interactivetool entry point
"""
# Because of auto id encoding needed for link from grid, the item.id keyword must be 'id'
if not id:
raise exceptions.RequestParameterMissingException("Must supply entry point ID.")
entry_point_id = self.decode_id(id)
return {"target": self.realtime_manager.access_entry_point_target(trans, entry_point_id)}
return {"target": self.interactivetool_manager.access_entry_point_target(trans, entry_point_id)}
lib/galaxy/webapps/galaxy/buildapp.py
+1 -1
View File
@@ -152,7 +152,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
webapp.add_client_route('/workflows/import')
webapp.add_client_route('/workflows/invocations/report')
webapp.add_client_route('/custom_builds')
webapp.add_client_route('/realtime_entry_points/list')
webapp.add_client_route('/interactivetool_entry_points/list')
# ==== Done
# Indicate that all configuration settings have been provided
lib/galaxy/webapps/galaxy/controllers/realtime.py → lib/galaxy/webapps/galaxy/controllers/interactivetool.py
+9 -9
View File
@@ -1,5 +1,5 @@
"""
Provides web interaction with RealTimeTools
Provides web interaction with InteractiveTools
"""
import logging
@@ -28,7 +28,7 @@ class EntryPointLinkColumn(grids.GridColumn):
return '<a class="entry-point-link" entry_point_id="%s">%s</a>' % (trans.security.encode_id(item.id), item.name)
class RealTimeToolEntryPointListGrid(grids.Grid):
class InteractiveToolEntryPointListGrid(grids.Grid):
use_panels = True
title = "Available InteractiveTools"
@@ -53,16 +53,16 @@ class RealTimeToolEntryPointListGrid(grids.Grid):
]
def build_initial_query(self, trans, **kwargs):
# Get list of user's active RealTimeTools
return trans.app.realtime_manager.get_nonterminal_for_user_by_trans(trans)
# Get list of user's active InteractiveTools
return trans.app.interactivetool_manager.get_nonterminal_for_user_by_trans(trans)
class RealTime(BaseUIController):
entry_point_grid = RealTimeToolEntryPointListGrid()
class InteractiveTool(BaseUIController):
entry_point_grid = InteractiveToolEntryPointListGrid()
@web.expose_api_anonymous
def list(self, trans, **kwargs):
"""List all available realtimetools"""
"""List all available interactivetools"""
if not trans.app.config.interactivetools_enable:
raise web.httpexceptions.HTTPNotFound()
operation = kwargs.get('operation', None)
@@ -77,7 +77,7 @@ class RealTime(BaseUIController):
for entry_point_id in ids:
entry_point_id = self.decode_id(entry_point_id)
entry_point = trans.sa_session.query(trans.app.model.InteractiveToolEntryPoint).get(entry_point_id)
if trans.app.realtime_manager.can_access_entry_point(trans, entry_point):
if trans.app.interactivetool_manager.can_access_entry_point(trans, entry_point):
eps.append(entry_point)
if eps:
failed = []
@@ -86,7 +86,7 @@ class RealTime(BaseUIController):
if operation == 'stop':
for ep in eps:
if ep.job not in jobs:
stopped = trans.app.realtime_manager.stop(trans, ep)
stopped = trans.app.interactivetool_manager.stop(trans, ep)
if stopped:
succeeded.append(ep)
jobs.append(ep.job)
lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+1 -1
View File
@@ -62,7 +62,7 @@ class ToolRunner(BaseUIController):
if not tool.allow_user_access(trans.user):
return __tool_404__()
# FIXME: Tool class should define behavior
if tool.tool_type in ['default', 'realtime']:
if tool.tool_type in ['default', 'interactivetool']:
return trans.response.send_redirect(url_for(controller='root', tool_id=tool_id))
# execute tool without displaying form (used for datasource tools)