mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_17.01' into dev
Conflicts: lib/galaxy/managers/workflows.py Discarded all changes made to lib/galaxy/managers/workflows.py in https://github.com/galaxyproject/galaxy/pull/3681
This commit is contained in:
Nicola Soranzo
@@ -29,15 +29,17 @@ Highlights
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Thanks to `@abretaud <https://github.com/abretaud>`__, `@ashvark <https://github.com/ashvark>`__, `@jvolkening <https://github.com/jvolkening>`__, and `@mvdbeek <https://github.com/mvdbeek>`__.
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Implemented in `Pull Request 3145`_, `PullRequest 3510`_ and `PullRequest 3514`_.
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`Github <https://github.com/galaxyproject/galaxy>`__
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===========================================================
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Get Galaxy
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==========
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New Galaxy repository
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The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
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To get a new Galaxy repository run:
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.. code-block:: shell
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$ git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git
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Update of existing Galaxy repository
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To update an existing Galaxy repository run:
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.. code-block:: shell
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$ git checkout release_17.01 && git pull --ff-only origin release_17.01
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@@ -9,6 +9,7 @@ import time
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import galaxy.queues
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from galaxy import util
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from galaxy.model.util import pgcalc
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from kombu import Connection
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from kombu.mixins import ConsumerMixin
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@@ -18,7 +19,31 @@ logging.getLogger('kombu').setLevel(logging.WARNING)
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log = logging.getLogger(__name__)
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def send_local_control_task(app, task, kwargs={}):
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"""
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This sends a message to the process-local control worker, which is useful
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for one-time asynchronous tasks like recalculating user disk usage.
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"""
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log.info("Queuing async task %s." % task)
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payload = {'task': task,
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'kwargs': kwargs}
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try:
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c = Connection(app.config.amqp_internal_connection)
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with producers[c].acquire(block=True) as producer:
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producer.publish(payload,
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exchange=galaxy.queues.galaxy_exchange,
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declare=[galaxy.queues.galaxy_exchange] + [galaxy.queues.control_queue_from_config(app.config)],
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routing_key='control')
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except Exception:
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log.exception("Error queueing async task: %s." % payload)
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def send_control_task(app, task, noop_self=False, kwargs={}):
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"""
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This sends a control task out to all processes, useful for things like
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reloading a data table, which needs to happen individually in all
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processes.
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"""
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log.info("Sending %s control task." % task)
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payload = {'task': task,
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'kwargs': kwargs}
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@@ -112,6 +137,21 @@ def reload_sanitize_whitelist(app):
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app.config.reload_sanitize_whitelist()
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def recalculate_user_disk_usage(app, **kwargs):
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user_id = kwargs.get('user_id', None)
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sa_session = app.model.context
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if user_id:
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user = sa_session.query( app.model.User ).get( app.security.decode_id( user_id ) )
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if user:
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if sa_session.get_bind().dialect.name not in ( 'postgres', 'postgresql' ):
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new = user.calculate_disk_usage()
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else:
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new = pgcalc(sa_session, user.id)
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user.set_disk_usage(new)
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sa_session.add(user)
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sa_session.flush()
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def reload_tool_data_tables(app, **kwargs):
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params = util.Params(kwargs)
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log.debug("Executing tool data table reload for %s" % params.get('table_names', 'all tables'))
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@@ -135,7 +175,8 @@ control_message_to_task = { 'create_panel_section': create_panel_section,
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'reload_display_application': reload_display_application,
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'reload_tool_data_tables': reload_tool_data_tables,
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'admin_job_lock': admin_job_lock,
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'reload_sanitize_whitelist': reload_sanitize_whitelist}
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'reload_sanitize_whitelist': reload_sanitize_whitelist,
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'recalculate_user_disk_usage': recalculate_user_disk_usage}
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class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
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@@ -49,8 +49,9 @@ class ToolBoxSearch( object ):
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self.build_index( index_help )
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def build_index( self, index_help=True ):
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# Works around https://bitbucket.org/mchaput/whoosh/issues/391/race-conditions-with-temp-storage
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"""Prepare search index for tools loaded in toolbox."""
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RamStorage.temp_storage = _temp_storage
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# Works around https://bitbucket.org/mchaput/whoosh/issues/391/race-conditions-with-temp-storage
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self.storage = RamStorage()
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self.index = self.storage.create_index( self.schema )
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writer = self.index.writer()
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@@ -66,16 +67,15 @@ class ToolBoxSearch( object ):
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"section": to_unicode( tool.get_panel_section()[1] if len( tool.get_panel_section() ) == 2 else '' ),
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"help": to_unicode( "" )
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}
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# Hyphens are wildcards in Whoosh causing bad things
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if tool.name.find( '-' ) != -1:
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# Hyphens are wildcards in Whoosh causing bad things
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add_doc_kwds['name'] = (' ').join( [ token.text for token in self.rex( to_unicode( tool.name ) ) ] )
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else:
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add_doc_kwds['name'] = to_unicode( tool.name )
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# We do not want to search Tool Shed or version parts
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# of the long ids
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if id.find( '/' ) != -1:
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slash_indexes = [ m.start() for m in re.finditer( '/', id ) ]
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id_stub = id[ ( slash_indexes[1] + 1 ): slash_indexes[4] ]
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if tool.guid:
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# Create a stub consisting of owner, repo, and tool from guid
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slash_indexes = [ m.start() for m in re.finditer( '/', tool.guid ) ]
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id_stub = tool.guid[ ( slash_indexes[1] + 1 ): slash_indexes[4] ]
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add_doc_kwds['stub'] = (' ').join( [ token.text for token in self.rex( to_unicode( id_stub ) ) ] )
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else:
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add_doc_kwds['stub'] = to_unicode( id )
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@@ -17,6 +17,7 @@ from galaxy import model
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from galaxy import util
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from galaxy import web
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from galaxy.exceptions import ObjectInvalid
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from galaxy.queue_worker import send_local_control_task
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from galaxy.security.validate_user_input import (transform_publicname,
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validate_email,
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validate_password,
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@@ -624,9 +625,12 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
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refresh_frames = [ 'masthead', 'history', 'tools' ]
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else:
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refresh_frames = [ 'masthead', 'history' ]
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# Recalculate user disk usage.
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if trans.user:
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trans.user.calculate_disk_usage()
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# Queue a quota recalculation (async) task -- this takes a
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# while sometimes, so we don't want to block on logout.
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send_local_control_task( trans.app,
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'recalculate_user_disk_usage',
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{'user_id': trans.security.encode_id(trans.user.id)} )
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# Since logging an event requires a session, we'll log prior to ending the session
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trans.log_event( "User logged out" )
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else:
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@@ -1190,3 +1194,209 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
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message=message,
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display_top=kwd.get('redirect_home', False)
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)
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||||
|
||||
@web.expose
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@web.require_admin
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def edit_info( self, trans, cntrller, **kwd ):
|
||||
"""
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TEMPORARY ENDPOINT - added back to support admin-level user info
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editing prior to adminjs. This is code that was prematurely removed
|
||||
from the user controller when the user-side editing functionality was
|
||||
replaced.
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||||
|
||||
The method manage_user_info, which follows this, should also be removed
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at that time.
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Edit user information = username, email or password.
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"""
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params = util.Params( kwd )
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is_admin = cntrller == 'admin' and trans.user_is_admin()
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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user_id = params.get( 'user_id', None )
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if user_id and is_admin:
|
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user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) )
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elif user_id and ( not trans.user or trans.user.id != trans.security.decode_id( user_id ) ):
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message = 'Invalid user id'
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status = 'error'
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user = None
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else:
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user = trans.user
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if user and params.get( 'login_info_button', False ):
|
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# Editing email and username
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email = util.restore_text( params.get( 'email', '' ) )
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username = util.restore_text( params.get( 'username', '' ) ).lower()
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|
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# Validate the new values for email and username
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message = validate_email( trans, email, user )
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if not message and username:
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message = validate_publicname( trans, username, user )
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if message:
|
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status = 'error'
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else:
|
||||
if ( user.email != email ):
|
||||
# The user's private role name must match the user's login ( email )
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private_role = trans.app.security_agent.get_private_user_role( user )
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private_role.name = email
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||||
private_role.description = 'Private role for ' + email
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# Change the email itself
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user.email = email
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||||
trans.sa_session.add_all( ( user, private_role ) )
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||||
trans.sa_session.flush()
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||||
if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on:
|
||||
user.active = False
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trans.sa_session.add( user )
|
||||
trans.sa_session.flush()
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is_activation_sent = self.send_verification_email( trans, user.email, user.username )
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if is_activation_sent:
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message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.'
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else:
|
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message = 'Unable to send activation email, please contact your local Galaxy administrator.'
|
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if trans.app.config.error_email_to is not None:
|
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message += ' Contact: %s' % trans.app.config.error_email_to
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if ( user.username != username ):
|
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user.username = username
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trans.sa_session.add( user )
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||||
trans.sa_session.flush()
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message = 'The login information has been updated with the changes.'
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elif user and params.get( 'edit_user_info_button', False ):
|
||||
# Edit user information - webapp MUST BE 'galaxy'
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user_type_fd_id = params.get( 'user_type_fd_id', 'none' )
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||||
if user_type_fd_id not in [ 'none' ]:
|
||||
user_type_form_definition = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id( user_type_fd_id ) )
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||||
elif user.values:
|
||||
user_type_form_definition = user.values.form_definition
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||||
else:
|
||||
# User was created before any of the user_info forms were created
|
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user_type_form_definition = None
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||||
if user_type_form_definition:
|
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values = self.get_form_values( trans, user, user_type_form_definition, **kwd )
|
||||
else:
|
||||
values = {}
|
||||
flush_needed = False
|
||||
if user.values:
|
||||
# Editing the user info of an existing user with existing user info
|
||||
user.values.content = values
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||||
trans.sa_session.add( user.values )
|
||||
flush_needed = True
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elif values:
|
||||
form_values = trans.model.FormValues( user_type_form_definition, values )
|
||||
trans.sa_session.add( form_values )
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||||
user.values = form_values
|
||||
flush_needed = True
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if flush_needed:
|
||||
trans.sa_session.add( user )
|
||||
trans.sa_session.flush()
|
||||
message = "The user information has been updated with the changes."
|
||||
if user and trans.webapp.name == 'galaxy' and is_admin:
|
||||
kwd[ 'user_id' ] = trans.security.encode_id( user.id )
|
||||
kwd[ 'id' ] = user_id
|
||||
if message:
|
||||
kwd[ 'message' ] = util.sanitize_text( message )
|
||||
if status:
|
||||
kwd[ 'status' ] = status
|
||||
return trans.response.send_redirect( web.url_for( controller='user',
|
||||
action='manage_user_info',
|
||||
cntrller=cntrller,
|
||||
**kwd ) )
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def manage_user_info( self, trans, cntrller, **kwd ):
|
||||
'''TEMPORARY ENDPOINT - added back to support admin-level user info
|
||||
editing prior to adminjs. This is code that was prematurely removed
|
||||
from the user controller when the user-side editing functionality was
|
||||
replaced.
|
||||
|
||||
When this is removed, templates/webapps/galaxy/user/manage_info.mako
|
||||
should go as well.
|
||||
|
||||
Manage a user's login, password, public username, type,
|
||||
addresses, etc.'''
|
||||
|
||||
def __get_user_type_form_definition( trans, user=None, **kwd ):
|
||||
params = util.Params( kwd )
|
||||
if user and user.values:
|
||||
user_type_fd_id = trans.security.encode_id( user.values.form_definition.id )
|
||||
else:
|
||||
user_type_fd_id = params.get( 'user_type_fd_id', 'none' )
|
||||
if user_type_fd_id not in [ 'none' ]:
|
||||
user_type_form_definition = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id( user_type_fd_id ) )
|
||||
else:
|
||||
user_type_form_definition = None
|
||||
return user_type_form_definition
|
||||
|
||||
def __get_widgets( trans, user_type_form_definition, user=None, **kwd ):
|
||||
widgets = []
|
||||
if user_type_form_definition:
|
||||
if user:
|
||||
if user.values:
|
||||
widgets = user_type_form_definition.get_widgets( user=user,
|
||||
contents=user.values.content,
|
||||
**kwd )
|
||||
else:
|
||||
widgets = user_type_form_definition.get_widgets( None, contents={}, **kwd )
|
||||
else:
|
||||
widgets = user_type_form_definition.get_widgets( None, contents={}, **kwd )
|
||||
return widgets
|
||||
|
||||
def __build_user_type_fd_id_select_field( trans, selected_value ):
|
||||
from galaxy.web.form_builder import build_select_field
|
||||
# Get all the user information forms
|
||||
user_info_forms = self.get_all_forms( trans,
|
||||
filter=dict( deleted=False ),
|
||||
form_type=trans.model.FormDefinition.types.USER_INFO )
|
||||
return build_select_field( trans,
|
||||
objs=user_info_forms,
|
||||
label_attr='name',
|
||||
select_field_name='user_type_fd_id',
|
||||
initial_value='none',
|
||||
selected_value=selected_value,
|
||||
refresh_on_change=True )
|
||||
|
||||
params = util.Params( kwd )
|
||||
user_id = params.get( 'id', None )
|
||||
if user_id:
|
||||
user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) )
|
||||
else:
|
||||
user = trans.user
|
||||
if not user:
|
||||
raise AssertionError("The user id (%s) is not valid" % str( user_id ))
|
||||
email = util.restore_text( params.get( 'email', user.email ) )
|
||||
username = util.restore_text( params.get( 'username', '' ) )
|
||||
if not username:
|
||||
username = user.username
|
||||
message = escape( util.restore_text( params.get( 'message', '' ) ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
user_type_form_definition = __get_user_type_form_definition( trans, user=user, **kwd )
|
||||
user_type_fd_id = params.get( 'user_type_fd_id', 'none' )
|
||||
if user_type_fd_id == 'none' and user_type_form_definition is not None:
|
||||
user_type_fd_id = trans.security.encode_id( user_type_form_definition.id )
|
||||
user_type_fd_id_select_field = __build_user_type_fd_id_select_field( trans, selected_value=user_type_fd_id )
|
||||
widgets = __get_widgets( trans, user_type_form_definition, user=user, **kwd )
|
||||
# user's addresses
|
||||
show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) )
|
||||
if show_filter == 'All':
|
||||
addresses = [address for address in user.addresses]
|
||||
elif show_filter == 'Deleted':
|
||||
addresses = [address for address in user.addresses if address.deleted]
|
||||
else:
|
||||
addresses = [address for address in user.addresses if not address.deleted]
|
||||
user_info_forms = self.get_all_forms( trans,
|
||||
filter=dict( deleted=False ),
|
||||
form_type=trans.app.model.FormDefinition.types.USER_INFO )
|
||||
return trans.fill_template( '/webapps/galaxy/user/manage_info.mako',
|
||||
cntrller=cntrller,
|
||||
user=user,
|
||||
email=email,
|
||||
is_admin=True,
|
||||
username=username,
|
||||
user_type_fd_id_select_field=user_type_fd_id_select_field,
|
||||
user_info_forms=user_info_forms,
|
||||
user_type_form_definition=user_type_form_definition,
|
||||
user_type_fd_id=user_type_fd_id,
|
||||
widgets=widgets,
|
||||
addresses=addresses,
|
||||
show_filter=show_filter,
|
||||
message=message,
|
||||
status=status )
|
||||
|
||||
@@ -0,0 +1,40 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/user/info.mako" import="render_user_info" />
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
${render_user_info()}
|
||||
|
||||
%if user.values or user_info_forms:
|
||||
<p></p>
|
||||
<div class="toolForm">
|
||||
<form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" >
|
||||
<div class="toolFormTitle">User information</div>
|
||||
%if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) >= 1:
|
||||
<div class="form-row">
|
||||
<label>User type:</label>
|
||||
${user_type_fd_id_select_field.get_html()}
|
||||
</div>
|
||||
%else:
|
||||
<input type="hidden" name="user_type_fd_id" value="${trans.security.encode_id( user_type_fd_id )}"/>
|
||||
%endif
|
||||
%for field in widgets:
|
||||
<div class="form-row">
|
||||
<label>${field['label']}:</label>
|
||||
${field['widget'].get_html()}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${field['helptext']}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="edit_user_info_button" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
<p></p>
|
||||
%endif
|
||||
Reference in New Issue
Block a user