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user.py

リビジョン 2, 55.4 KB (コミッタ: hatakeyama, 14 年前)
import galaxy-central

行番号
1	"""
2	Contains the user interface in the Universe class
3	"""
4	from galaxy.web.base.controller import *
5	from galaxy.model.orm import *
6	from galaxy import util
7	import logging, os, string, re, smtplib, socket
8	from random import choice
9	from email.MIMEText import MIMEText
10	from galaxy.web.form_builder import *
11	from galaxy.util.json import from_json_string, to_json_string
12	from galaxy.web.framework.helpers import iff
13
14	log = logging.getLogger( __name__ )
15
16	require_login_template = """
17	<h1>Welcome to Galaxy</h1>
18
19	<p>
20	This installation of Galaxy has been configured such that only users who are logged in may use it.%s
21	</p>
22	<p/>
23	"""
24	require_login_nocreation_template = require_login_template % ""
25	require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>."
26
27	VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" )
28
29	class User( BaseController, UsesFormDefinitionWidgets ):
30	@web.expose
31	def index( self, trans, webapp='galaxy', **kwd ):
32	return trans.fill_template( '/user/index.mako', webapp=webapp )
33	@web.expose
34	def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ):
35	referer = kwd.get( 'referer', trans.request.referer )
36	use_panels = util.string_as_bool( kwd.get( 'use_panels', True ) )
37	message = kwd.get( 'message', '' )
38	status = kwd.get( 'status', 'done' )
39	header = ''
40	user = None
41	email = kwd.get( 'email', '' )
42	if kwd.get( 'login_button', False ):
43	password = kwd.get( 'password', '' )
44	referer = kwd.get( 'referer', '' )
45	if webapp == 'galaxy' and not refresh_frames:
46	if trans.app.config.require_login:
47	refresh_frames = [ 'masthead', 'history', 'tools' ]
48	else:
49	refresh_frames = [ 'masthead', 'history' ]
50	user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first()
51	if not user:
52	message = "No such user"
53	status = 'error'
54	elif user.deleted:
55	message = "This account has been marked deleted, contact your Galaxy administrator to restore the account."
56	status = 'error'
57	elif user.external:
58	message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
59	status = 'error'
60	elif not user.check_password( password ):
61	message = "Invalid password"
62	status = 'error'
63	else:
64	trans.handle_user_login( user, webapp )
65	trans.log_event( "User logged in" )
66	message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \
67	( user.email, referer, url_for( '/' ) )
68	if trans.app.config.require_login:
69	message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' )
70	redirect_url = referer
71	if not user and trans.app.config.require_login:
72	if trans.app.config.allow_user_creation:
73	header = require_login_creation_template % web.url_for( action='create' )
74	else:
75	header = require_login_nocreation_template
76	return trans.fill_template( '/user/login.mako',
77	webapp=webapp,
78	email=email,
79	header=header,
80	use_panels=use_panels,
81	redirect_url=redirect_url,
82	referer=referer,
83	refresh_frames=refresh_frames,
84	message=message,
85	status=status,
86	active_view="user" )
87	@web.expose
88	def logout( self, trans, webapp='galaxy' ):
89	if webapp == 'galaxy':
90	if trans.app.config.require_login:
91	refresh_frames = [ 'masthead', 'history', 'tools' ]
92	else:
93	refresh_frames = [ 'masthead', 'history' ]
94	else:
95	refresh_frames = [ 'masthead' ]
96	# Since logging an event requires a session, we'll log prior to ending the session
97	trans.log_event( "User logged out" )
98	trans.handle_user_logout()
99	message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \
100	( trans.request.referer, url_for( '/' ) )
101	return trans.fill_template( '/user/logout.mako',
102	webapp=webapp,
103	refresh_frames=refresh_frames,
104	message=message,
105	status='done',
106	active_view="user" )
107	@web.expose
108	def create( self, trans, redirect_url='', refresh_frames=[], **kwd ):
109	params = util.Params( kwd )
110	webapp = params.get( 'webapp', 'galaxy' )
111	use_panels = util.string_as_bool( kwd.get( 'use_panels', True ) )
112	email = util.restore_text( params.get( 'email', '' ) )
113	# Do not sanitize passwords, so take from kwd
114	# instead of params ( which were sanitized )
115	password = kwd.get( 'password', '' )
116	confirm = kwd.get( 'confirm', '' )
117	username = util.restore_text( params.get( 'username', '' ) )
118	subscribe = params.get( 'subscribe', '' )
119	subscribe_checked = CheckboxField.is_checked( subscribe )
120	admin_view = util.string_as_bool( params.get( 'admin_view', False ) )
121	message = util.restore_text( params.get( 'message', '' ) )
122	status = params.get( 'status', 'done' )
123	referer = kwd.get( 'referer', trans.request.referer )
124	if not refresh_frames:
125	if webapp == 'galaxy':
126	if trans.app.config.require_login:
127	refresh_frames = [ 'masthead', 'history', 'tools' ]
128	else:
129	refresh_frames = [ 'masthead', 'history' ]
130	else:
131	refresh_frames = [ 'masthead' ]
132	error = ''
133	if not trans.app.config.allow_user_creation and not trans.user_is_admin():
134	error = 'User registration is disabled. Please contact your Galaxy administrator for an account.'
135	# Create the user, save all the user info and login to Galaxy
136	elif params.get( 'create_user_button', False ):
137	# Check email and password validity
138	error = self.__validate( trans, params, email, password, confirm, username, webapp )
139	if not error:
140	# all the values are valid
141	user = trans.app.model.User( email=email )
142	user.set_password_cleartext( password )
143	user.username = username
144	trans.sa_session.add( user )
145	trans.sa_session.flush()
146	trans.app.security_agent.create_private_user_role( user )
147	message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) )
148	if webapp == 'galaxy':
149	# We set default user permissions, before we log in and set the default history permissions
150	trans.app.security_agent.user_set_default_permissions( user,
151	default_access_private=trans.app.config.new_user_dataset_access_role_default_private )
152	# save user info
153	self.__save_user_info( trans, user, action='create', new_user=True, **kwd )
154	if subscribe_checked:
155	# subscribe user to email list
156	if trans.app.config.smtp_server is None:
157	error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance."
158	else:
159	msg = MIMEText( 'Join Mailing list.\n' )
160	to = msg[ 'To' ] = trans.app.config.mailing_join_addr
161	frm = msg[ 'From' ] = email
162	msg[ 'Subject' ] = 'Join Mailing List'
163	try:
164	s = smtplib.SMTP()
165	s.connect( trans.app.config.smtp_server )
166	s.sendmail( frm, [ to ], msg.as_string() )
167	s.close()
168	except:
169	error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed."
170	if not error and not admin_view:
171	# The handle_user_login() method has a call to the history_set_default_permissions() method
172	# (needed when logging in with a history), user needs to have default permissions set before logging in
173	trans.handle_user_login( user, webapp )
174	trans.log_event( "User created a new account" )
175	trans.log_event( "User logged in" )
176	elif not error:
177	trans.response.send_redirect( web.url_for( controller='admin',
178	action='users',
179	message='Created new user account (%s)' % user.email,
180	status='done' ) )
181	elif not admin_view:
182	# Must be logging into the community space webapp
183	trans.handle_user_login( user, webapp )
184	if not error:
185	redirect_url = referer
186	if error:
187	message=error
188	status='error'
189	if webapp == 'galaxy':
190	user_info_select, user_info_form, widgets = self.__user_info_ui( trans, **kwd )
191	else:
192	user_info_select = []
193	user_info_form = []
194	widgets = []
195	return trans.fill_template( '/user/register.mako',
196	email=email,
197	password=password,
198	confirm=confirm,
199	username=username,
200	subscribe_checked=subscribe_checked,
201	admin_view=admin_view,
202	user_info_select=user_info_select,
203	user_info_form=user_info_form,
204	widgets=widgets,
205	webapp=webapp,
206	use_panels=use_panels,
207	referer=referer,
208	redirect_url=redirect_url,
209	refresh_frames=refresh_frames,
210	message=message,
211	status=status )
212	def __save_user_info(self, trans, user, action, new_user=True, **kwd):
213	'''
214	This method saves the user information for new users as well as editing user
215	info for existing users. For new users, the user info form is retrieved from
216	the one that user has selected. And for existing users, the user info form is
217	retrieved from the db.
218	'''
219	params = util.Params( kwd )
220	# get all the user information forms
221	user_info_forms = self.get_all_forms( trans, filter=dict(deleted=False),
222	form_type=trans.app.model.FormDefinition.types.USER_INFO )
223	if new_user:
224	# if there are no user forms available then there is nothing to save
225	if not len( user_info_forms ):
226	return
227	user_info_type = params.get( 'user_info_select', 'none' )
228	try:
229	user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(user_info_type))
230	except:
231	return trans.response.send_redirect( web.url_for( controller='user',
232	action=action,
233	message='Invalid user information form id',
234	status='error') )
235	else:
236	if user.values:
237	user_info_form = user.values.form_definition
238	else:
239	# user was created before any of the user_info forms were created
240	if len(user_info_forms) > 1:
241	# when there are multiple user_info forms and the user or admin
242	# can change the user_info form
243	user_info_type = params.get( 'user_info_select', 'none' )
244	try:
245	user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(user_info_type))
246	except:
247	return trans.response.send_redirect( web.url_for( controller='user',
248	action=action,
249	message='Invalid user information form id',
250	status='error') )
251	else:
252	# when there is only one user_info form then there is no way
253	# to change the user_info form
254	user_info_form = user_info_forms[0]
255	values = []
256	for index, field in enumerate(user_info_form.fields):
257	if field['type'] == 'AddressField':
258	value = util.restore_text(params.get('field_%i' % index, ''))
259	if value == 'new':
260	# save this new address in the list of this user's addresses
261	user_address = trans.app.model.UserAddress( user=user )
262	self.save_widget_field( trans, user_address, index, **kwd )
263	trans.sa_session.refresh( user )
264	values.append(int(user_address.id))
265	elif value == unicode('none'):
266	values.append('')
267	else:
268	values.append(int(value))
269	elif field['type'] == 'CheckboxField':
270	values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') ))
271	else:
272	values.append(util.restore_text(params.get('field_%i' % index, '')))
273	if new_user or not user.values:
274	# new user or existing
275	form_values = trans.app.model.FormValues(user_info_form, values)
276	trans.sa_session.add( form_values )
277	trans.sa_session.flush()
278	user.values = form_values
279	elif user.values:
280	# editing the user info of an existing user with existing user info
281	user.values.content = values
282	trans.sa_session.add( user.values )
283	trans.sa_session.add( user )
284	trans.sa_session.flush()
285	def __validate_email( self, trans, email, user=None ):
286	error = None
287	if user and user.email == email:
288	return None
289	if len( email ) == 0 or "@" not in email or "." not in email:
290	error = "Enter a real email address"
291	elif len( email ) > 255:
292	error = "Email address exceeds maximum allowable length"
293	elif trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first():
294	error = "User with that email already exists"
295	return error
296	def __validate_username( self, trans, username, user=None ):
297	# User names must be at least four characters in length and contain only lower-case
298	# letters, numbers, and the '-' character.
299	if username in [ 'None', None, '' ]:
300	return None
301	if user and user.username == username:
302	return None
303	if len( username ) < 4:
304	return "User name must be at least 4 characters in length"
305	if len( username ) > 255:
306	return "User name cannot be more than 255 characters in length"
307	if not( VALID_USERNAME_RE.match( username ) ):
308	return "User name must contain only lower-case letters, numbers and '-'"
309	if trans.sa_session.query( trans.app.model.User ).filter_by( username=username ).first():
310	return "This user name is not available"
311	return None
312	def __validate_password( self, trans, password, confirm ):
313	error = None
314	if len( password ) < 6:
315	error = "Use a password of at least 6 characters"
316	elif password != confirm:
317	error = "Passwords do not match"
318	return error
319	def __validate( self, trans, params, email, password, confirm, username, webapp ):
320	# If coming from the community webapp, we'll require a public user name
321	if webapp == 'community' and not username:
322	return "A public user name is required"
323	error = self.__validate_email( trans, email )
324	if not error:
325	error = self.__validate_password( trans, password, confirm )
326	if not error and username:
327	error = self.__validate_username( trans, username )
328	if not error:
329	if webapp == 'galaxy':
330	if len( self.get_all_forms( trans,
331	filter=dict( deleted=False ),
332	form_type=trans.app.model.FormDefinition.types.USER_INFO ) ):
333	if not params.get( 'user_info_select', False ):
334	return "Select the user's type and information"
335	return error
336	def __user_info_ui( self, trans, user=None, **kwd ):
337	'''
338	This method creates the user type select box & user information form widgets
339	and is called during user registration and editing user information.
340	If there exists only one user information form then show it after main
341	login info. However, if there are more than one user info forms then
342	show a selectbox containing all the forms, then the user can select
343	the one that fits the user's description the most
344	'''
345	params = util.Params( kwd )
346	# get all the user information forms
347	user_info_forms = self.get_all_forms( trans,
348	filter=dict( deleted=False ),
349	form_type=trans.app.model.FormDefinition.types.USER_INFO )
350	user_info_select = None
351	if user:
352	if user.values:
353	selected_user_form_id = user.values.form_definition.id
354	else:
355	selected_user_form_id = params.get( 'user_info_select', 'none' )
356	else:
357	selected_user_form_id = params.get( 'user_info_select', 'none' )
358	# when there are more than one user information forms then show a select box
359	# list all these forms
360	if len(user_info_forms) > 1:
361	# create the select box
362	user_info_select = SelectField('user_info_select', refresh_on_change=True,
363	refresh_on_change_values=[str(u.id) for u in user_info_forms])
364	if selected_user_form_id == 'none':
365	user_info_select.add_option('Select one', 'none', selected=True)
366	else:
367	user_info_select.add_option('Select one', 'none')
368	for u in user_info_forms:
369	if selected_user_form_id == str(u.id):
370	user_info_select.add_option(u.name, u.id, selected=True)
371	else:
372	user_info_select.add_option(u.name, u.id)
373	# when there is just one user information form the just render that form
374	elif len(user_info_forms) == 1:
375	selected_user_form_id = user_info_forms[0].id
376	# user information
377	try:
378	user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(selected_user_form_id))
379	except:
380	return user_info_select, None, None
381	if user:
382	if user.values:
383	widgets = user_info_form.get_widgets(user=user,
384	contents=user.values.content,
385	**kwd)
386	else:
387	widgets = user_info_form.get_widgets(None, contents=[], **kwd)
388	else:
389	widgets = user_info_form.get_widgets(None, contents=[], **kwd)
390	return user_info_select, user_info_form, widgets
391	@web.expose
392	def show_info( self, trans, **kwd ):
393	'''
394	This method displays the user information page which consists of login
395	information, public user name, reset password & other user information
396	obtained during registration
397	'''
398	params = util.Params( kwd )
399	user_id = params.get( 'user_id', None )
400	webapp = params.get( 'webapp', 'galaxy' )
401	if user_id:
402	user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
403	else:
404	user = trans.user
405	if not user:
406	raise AssertionError, "The user id (%s) is not valid" % str( user_id )
407	email = util.restore_text( params.get( 'email', user.email ) )
408	# Do not sanitize passwords, so take from kwd
409	# instead of params ( which were sanitized )
410	current = kwd.get( 'current', '' )
411	password = kwd.get( 'password', '' )
412	confirm = kwd.get( 'confirm', '' )
413	username = util.restore_text( params.get( 'username', '' ) )
414	if not username:
415	username = user.username
416	admin_view = util.string_as_bool( params.get( 'admin_view', False ) )
417	message = util.restore_text( params.get( 'message', '' ) )
418	status = params.get( 'status', 'done' )
419	if webapp == 'galaxy':
420	user_info_select, user_info_form, widgets = self.__user_info_ui( trans, user, **kwd )
421	# user's addresses
422	show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) )
423	if show_filter == 'All':
424	addresses = [address for address in user.addresses]
425	elif show_filter == 'Deleted':
426	addresses = [address for address in user.addresses if address.deleted]
427	else:
428	addresses = [address for address in user.addresses if not address.deleted]
429	user_info_forms = self.get_all_forms( trans,
430	filter=dict( deleted=False ),
431	form_type=trans.app.model.FormDefinition.types.USER_INFO )
432	return trans.fill_template( '/webapps/galaxy/user/info.mako',
433	user=user,
434	email=email,
435	current=current,
436	password=password,
437	confirm=confirm,
438	username=username,
439	user_info_select=user_info_select,
440	user_info_forms=user_info_forms,
441	user_info_form=user_info_form,
442	widgets=widgets,
443	addresses=addresses,
444	show_filter=show_filter,
445	admin_view=admin_view,
446	webapp=webapp,
447	message=message,
448	status=status )
449	else:
450	return trans.fill_template( '/webapps/community/user/info.mako',
451	user=user,
452	email=email,
453	current=current,
454	password=password,
455	confirm=confirm,
456	username=username,
457	admin_view=False,
458	webapp=webapp,
459	message=message,
460	status=status )
461	@web.expose
462	def edit_info( self, trans, **kwd ):
463	params = util.Params( kwd )
464	user_id = params.get( 'user_id', None )
465	admin_view = util.string_as_bool( params.get( 'admin_view', False ) )
466	webapp = params.get( 'webapp', 'galaxy' )
467	message = util.restore_text( params.get( 'message', '' ) )
468	status = params.get( 'status', 'done' )
469	if user_id:
470	user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
471	else:
472	user = trans.user
473	# Editing login info ( email & username )
474	if params.get( 'login_info_button', False ):
475	email = util.restore_text( params.get( 'email', '' ) )
476	username = util.restore_text( params.get( 'username', '' ) ).lower()
477	# validate the new values
478	error = self.__validate_email( trans, email, user )
479	if not error and username:
480	error = self.__validate_username( trans, username, user )
481	if error:
482	return trans.response.send_redirect( web.url_for( controller='user',
483	action='show_info',
484	webapp=webapp,
485	message=error,
486	status='error') )
487	# The user's private role name must match the user's login ( email )
488	private_role = trans.app.security_agent.get_private_user_role( user )
489	private_role.name = email
490	private_role.description = 'Private role for ' + email
491	# Now change the user info
492	user.email = email
493	user.username = username
494	trans.sa_session.add_all( ( user, private_role ) )
495	trans.sa_session.flush()
496	message = 'The login information has been updated with the changes'
497	if webapp == 'galaxy' and admin_view:
498	return trans.response.send_redirect( web.url_for( controller='user',
499	action='show_info',
500	user_id=user.id,
501	admin_view=admin_view,
502	webapp=webapp,
503	message=message,
504	status='done' ) )
505	return trans.response.send_redirect( web.url_for( controller='user',
506	action='show_info',
507	webapp=webapp,
508	message=message,
509	status='done') )
510	# Change password
511	elif params.get( 'change_password_button', False ):
512	# Do not sanitize passwords, so get from kwd and not params
513	# ( which were sanitized ).
514	password = kwd.get( 'password', '' )
515	confirm = kwd.get( 'confirm', '' )
516	# When from the user perspective, validate the current password
517	if not webapp == 'galaxy' and not admin_view:
518	# Do not sanitize passwords, so get from kwd and not params
519	# ( which were sanitized ).
520	current = kwd.get( 'current', '' )
521	if not trans.user.check_password( current ):
522	return trans.response.send_redirect( web.url_for( controller='user',
523	action='show_info',
524	webapp=webapp,
525	message='Invalid current password',
526	status='error') )
527	# validate the new values
528	error = self.__validate_password( trans, password, confirm )
529	if error:
530	if webapp == 'galaxy' and admin_view:
531	return trans.response.send_redirect( web.url_for( controller='user',
532	action='show_info',
533	webapp=webapp,
534	user_id=user.id,
535	admin_view=admin_view,
536	message=error,
537	status='error' ) )
538	return trans.response.send_redirect( web.url_for( controller='user',
539	action='show_info',
540	webapp=webapp,
541	message=error,
542	status='error') )
543	# save new password
544	user.set_password_cleartext( password )
545	trans.sa_session.add( user )
546	trans.sa_session.flush()
547	trans.log_event( "User change password" )
548	message = 'The password has been changed.'
549	if webapp == 'galaxy' and admin_view:
550	return trans.response.send_redirect( web.url_for( controller='user',
551	action='show_info',
552	webapp=webapp,
553	user_id=user.id,
554	admin_view=admin_view,
555	message=message,
556	status='done' ) )
557	return trans.response.send_redirect( web.url_for( controller='user',
558	action='show_info',
559	webapp=webapp,
560	message=message,
561	status='done') )
562	# Edit user information - webapp MUST BE 'galaxy'
563	elif params.get( 'edit_user_info_button', False ):
564	self.__save_user_info(trans, user, "show_info", new_user=False, **kwd)
565	message = "The user information has been updated with the changes."
566	if admin_view:
567	return trans.response.send_redirect( web.url_for( controller='user',
568	action='show_info',
569	webapp=webapp,
570	user_id=user.id,
571	admin_view=admin_view,
572	message=message,
573	status='done' ) )
574	return trans.response.send_redirect( web.url_for( controller='user',
575	action='show_info',
576	webapp=webapp,
577	message=message,
578	status='done') )
579	else:
580	if webapp == 'galaxy' and admin_view:
581	return trans.response.send_redirect( web.url_for( controller='user',
582	action='show_info',
583	webapp=webapp,
584	user_id=user.id,
585	admin_view=admin_view ) )
586	return trans.response.send_redirect( web.url_for( controller='user',
587	action='show_info',
588	webapp=webapp ) )
589	@web.expose
590	def reset_password( self, trans, email=None, webapp='galaxy', **kwd ):
591	if trans.app.config.smtp_server is None:
592	return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact an administrator." )
593	message = util.restore_text( kwd.get( 'message', '' ) )
594	status = 'done'
595	if kwd.get( 'reset_password_button', False ):
596	reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first()
597	user = trans.get_user()
598	if reset_user:
599	if user and user.id != reset_user.id:
600	message = "You may only reset your own password"
601	status = 'error'
602	else:
603	chars = string.letters + string.digits
604	new_pass = ""
605	for i in range(15):
606	new_pass = new_pass + choice(chars)
607	host = trans.request.host.split(':')[0]
608	if host == 'localhost':
609	host = socket.getfqdn()
610	msg = MIMEText( 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass ) )
611	to = msg[ 'To' ] = email
612	frm = msg[ 'From' ] = 'galaxy-no-reply@' + host
613	msg[ 'Subject' ] = 'Galaxy Password Reset'
614	try:
615	s = smtplib.SMTP()
616	s.connect( trans.app.config.smtp_server )
617	s.sendmail( frm, [ to ], msg.as_string() )
618	s.close()
619	reset_user.set_password_cleartext( new_pass )
620	trans.sa_session.add( reset_user )
621	trans.sa_session.flush()
622	trans.log_event( "User reset password: %s" % email )
623	message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( action='login' ) )
624	except Exception, e:
625	message = 'Failed to reset password: %s' % str( e )
626	status = 'error'
627	return trans.response.send_redirect( web.url_for( controller='user',
628	action='reset_password',
629	message=message,
630	status=status ) )
631	elif email != None:
632	message = "The specified user does not exist"
633	status = 'error'
634	elif email is None:
635	email = ""
636	return trans.fill_template( '/user/reset_password.mako',
637	webapp=webapp,
638	message=message,
639	status=status )
640	@web.expose
641	def set_default_permissions( self, trans, **kwd ):
642	"""Sets the user's default permissions for the new histories"""
643	if trans.user:
644	if 'update_roles_button' in kwd:
645	p = util.Params( kwd )
646	permissions = {}
647	for k, v in trans.app.model.Dataset.permitted_actions.items():
648	in_roles = p.get( k + '_in', [] )
649	if not isinstance( in_roles, list ):
650	in_roles = [ in_roles ]
651	in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in in_roles ]
652	action = trans.app.security_agent.get_action( v.action ).action
653	permissions[ action ] = in_roles
654	trans.app.security_agent.user_set_default_permissions( trans.user, permissions )
655	return trans.show_ok_message( 'Default new history permissions have been changed.' )
656	return trans.fill_template( 'user/permissions.mako' )
657	else:
658	# User not logged in, history group must be only public
659	return trans.show_error_message( "You must be logged in to change your default permitted actions." )
660	@web.expose
661	@web.require_login( "to get most recently used tool" )
662	@web.json_pretty
663	def get_most_recently_used_tool_async( self, trans ):
664	""" Returns information about the most recently used tool. """
665
666	# Get most recently used tool.
667	query = trans.sa_session.query( self.app.model.Job.tool_id ).join( self.app.model.History ). \
668	filter( self.app.model.History.user==trans.user ). \
669	order_by( self.app.model.Job.create_time.desc() ).limit(1)
670	tool_id = query[0][0] # Get first element in first row of query.
671	tool = self.get_toolbox().tools_by_id[ tool_id ]
672
673	# Return tool info.
674	tool_info = {
675	"id" : tool.id,
676	"link" : url_for( controller='tool_runner', tool_id=tool.id ),
677	"target" : tool.target,
678	"name" : tool.name, ## TODO: translate this using _()
679	"minsizehint" : tool.uihints.get( 'minwidth', -1 ),
680	"description" : tool.description
681	}
682	return tool_info
683	@web.expose
684	def manage_addresses(self, trans, **kwd):
685	if trans.user:
686	params = util.Params( kwd )
687	message = util.restore_text( params.get( 'message', '' ) )
688	status = params.get( 'status', 'done' )
689	show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) )
690	if show_filter == 'All':
691	addresses = [address for address in trans.user.addresses]
692	elif show_filter == 'Deleted':
693	addresses = [address for address in trans.user.addresses if address.deleted]
694	else:
695	addresses = [address for address in trans.user.addresses if not address.deleted]
696	return trans.fill_template( 'user/address.mako',
697	addresses=addresses,
698	show_filter=show_filter,
699	message=message,
700	status=status)
701	else:
702	# User not logged in, history group must be only public
703	return trans.show_error_message( "You must be logged in to change your default permitted actions." )
704	@web.expose
705	def new_address( self, trans, **kwd ):
706	params = util.Params( kwd )
707	message = util.restore_text( params.get( 'message', '' ) )
708	status = params.get( 'status', 'done' )
709	admin_view = util.string_as_bool( params.get( 'admin_view', False ) )
710	user_id = params.get( 'user_id', False )
711	if not user_id:
712	# User must be logged in to create a new address
713	return trans.show_error_message( "You must be logged in to create a new address." )
714	user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
715	short_desc = util.restore_text( params.get( 'short_desc', '' ) )
716	name = util.restore_text( params.get( 'name', '' ) )
717	institution = util.restore_text( params.get( 'institution', '' ) )
718	address = util.restore_text( params.get( 'address', '' ) )
719	city = util.restore_text( params.get( 'city', '' ) )
720	state = util.restore_text( params.get( 'state', '' ) )
721	postal_code = util.restore_text( params.get( 'postal_code', '' ) )
722	country = util.restore_text( params.get( 'country', '' ) )
723	phone = util.restore_text( params.get( 'phone', '' ) )
724	ok = True
725	if not trans.app.config.allow_user_creation and not trans.user_is_admin():
726	return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' )
727	if params.get( 'new_address_button', False ):
728	if not short_desc:
729	ok = False
730	message = 'Enter a short description for this address'
731	elif not name:
732	ok = False
733	message = 'Enter the name'
734	elif not institution:
735	ok = False
736	message = 'Enter the institution associated with the user'
737	elif not address:
738	ok = False
739	message = 'Enter the address'
740	elif not city:
741	ok = False
742	message = 'Enter the city'
743	elif not state:
744	ok = False
745	message = 'Enter the state/province/region'
746	elif not postal_code:
747	ok = False
748	message = 'Enter the postal code'
749	elif not country:
750	ok = False
751	message = 'Enter the country'
752	if ok:
753	user_address = trans.model.UserAddress( user=user,
754	desc=short_desc,
755	name=name,
756	institution=institution,
757	address=address,
758	city=city,
759	state=state,
760	postal_code=postal_code,
761	country=country,
762	phone=phone )
763	trans.sa_session.add( user_address )
764	trans.sa_session.flush()
765	message = 'Address (%s) has been added' % user_address.desc
766	if admin_view:
767	return trans.response.send_redirect( web.url_for( controller='user',
768	action='show_info',
769	admin_view=admin_view,
770	user_id=user.id,
771	message=message,
772	status='done' ) )
773	return trans.response.send_redirect( web.url_for( controller='user',
774	action='show_info',
775	message=message,
776	status='done' ) )
777	# Display the address form with the current values filled in
778	return trans.fill_template( 'user/new_address.mako',
779	user=user,
780	admin_view=admin_view,
781	short_desc=short_desc,
782	name=name,
783	institution=institution,
784	address=address,
785	city=city,
786	state=state,
787	postal_code=postal_code,
788	country=country,
789	phone=phone,
790	message=message,
791	status=status )
792	@web.expose
793	def edit_address( self, trans, **kwd ):
794	params = util.Params( kwd )
795	message = util.restore_text( params.get( 'message', '' ) )
796	status = params.get( 'status', 'done' )
797	admin_view = util.string_as_bool( params.get( 'admin_view', False ) )
798	user_id = params.get( 'user_id', False )
799	if not user_id:
800	# User must be logged in to create a new address
801	return trans.show_error_message( "You must be logged in to create a new address." )
802	user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
803	address_id = params.get( 'address_id', None )
804	if not address_id:
805	return trans.show_error_message( "No address_id received for editing." )
806	address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( int( address_id ) )
807	if params.get( 'edit_address_button', False ):
808	short_desc = util.restore_text( params.get( 'short_desc', '' ) )
809	name = util.restore_text( params.get( 'name', '' ) )
810	institution = util.restore_text( params.get( 'institution', '' ) )
811	address = util.restore_text( params.get( 'address', '' ) )
812	city = util.restore_text( params.get( 'city', '' ) )
813	state = util.restore_text( params.get( 'state', '' ) )
814	postal_code = util.restore_text( params.get( 'postal_code', '' ) )
815	country = util.restore_text( params.get( 'country', '' ) )
816	phone = util.restore_text( params.get( 'phone', '' ) )
817	ok = True
818	if not short_desc:
819	ok = False
820	message = 'Enter a short description for this address'
821	elif not name:
822	ok = False
823	message = 'Enter the name'
824	elif not institution:
825	ok = False
826	message = 'Enter the institution associated with the user'
827	elif not address:
828	ok = False
829	message = 'Enter the address'
830	elif not city:
831	ok = False
832	message = 'Enter the city'
833	elif not state:
834	ok = False
835	message = 'Enter the state/province/region'
836	elif not postal_code:
837	ok = False
838	message = 'Enter the postal code'
839	elif not country:
840	ok = False
841	message = 'Enter the country'
842	if ok:
843	address_obj.desc = short_desc
844	address_obj.name = name
845	address_obj.institution = institution
846	address_obj.address = address
847	address_obj.city = city
848	address_obj.state = state
849	address_obj.postal_code = postal_code
850	address_obj.country = country
851	address_obj.phone = phone
852	trans.sa_session.add( address_obj )
853	trans.sa_session.flush()
854	message = 'Address (%s) has been updated.' % address_obj.desc
855	if admin_view:
856	return trans.response.send_redirect( web.url_for( controller='user',
857	action='show_info',
858	user_id=user.id,
859	admin_view=admin_view,
860	message=message,
861	status='done' ) )
862	return trans.response.send_redirect( web.url_for( controller='user',
863	action='show_info',
864	message=message,
865	status='done' ) )
866	# Display the address form with the current values filled in
867	return trans.fill_template( 'user/edit_address.mako',
868	user=user,
869	address_obj=address_obj,
870	admin_view=admin_view,
871	message=message,
872	status=status )
873	@web.expose
874	def delete_address( self, trans, address_id=None, user_id=None, admin_view=False ):
875	try:
876	user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( int( address_id ) )
877	except:
878	return trans.response.send_redirect( web.url_for( controller='user',
879	action='show_info',
880	user_id=user_id,
881	admin_view=admin_view,
882	message='Invalid address ID',
883	status='error' ) )
884	user_address.deleted = True
885	trans.sa_session.add( user_address )
886	trans.sa_session.flush()
887	return trans.response.send_redirect( web.url_for( controller='user',
888	action='show_info',
889	admin_view=admin_view,
890	user_id=user_id,
891	message='Address (%s) deleted' % user_address.desc,
892	status='done') )
893	@web.expose
894	def undelete_address( self, trans, address_id=None, user_id=None, admin_view=False ):
895	try:
896	user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( int( address_id ) )
897	except:
898	return trans.response.send_redirect( web.url_for( controller='user',
899	action='show_info',
900	user_id=user_id,
901	admin_view=admin_view,
902	message='Invalid address ID',
903	status='error' ) )
904	user_address.deleted = False
905	trans.sa_session.flush()
906	return trans.response.send_redirect( web.url_for( controller='user',
907	action='show_info',
908	admin_view=admin_view,
909	user_id=user_id,
910	message='Address (%s) undeleted' % user_address.desc,
911	status='done') )
912	@web.expose
913	def set_user_pref_async( self, trans, pref_name, pref_value ):
914	""" Set a user preference asynchronously. If user is not logged in, do nothing. """
915	if trans.user:
916	trans.log_action( trans.get_user(), "set_user_pref", "", { pref_name : pref_value } )
917	trans.user.preferences[pref_name] = pref_value
918	trans.sa_session.flush()
919	@web.expose
920	def log_user_action_async( self, trans, action, context, params ):
921	""" Log a user action asynchronously. If user is not logged in, do nothing. """
922	if trans.user:
923	trans.log_action( trans.get_user(), action, context, params )
924	@web.expose
925	@web.require_login()
926	def dbkeys( self, trans, **kwds ):
927	user = trans.get_user()
928	message = None
929	lines_skipped = 0
930	if 'dbkeys' not in user.preferences:
931	dbkeys = {}
932	else:
933	dbkeys = from_json_string(user.preferences['dbkeys'])
934
935	if 'delete' in kwds:
936	key = kwds.get('key', '')
937	if key and key in dbkeys:
938	del dbkeys[key]
939
940	elif 'add' in kwds:
941	name = kwds.get('name', '')
942	key = kwds.get('key', '')
943	len_file = kwds.get('len_file', None)
944	if getattr(len_file, "file", None): # Check if it's a FieldStorage object
945	len_text = len_file.file.read()
946	else:
947	len_text = kwds.get('len_text', '')
948	if not name or not key or not len_text:
949	message = "You must specify values for all the fields."
950	else:
951	# Create new len file
952	new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session )
953	trans.sa_session.add( new_len )
954	new_len.name = name
955	new_len.visible = False
956	new_len.state = trans.app.model.Job.states.OK
957	new_len.info = "custom build .len file"
958	trans.sa_session.flush()
959
960	counter = 0
961	f = open(new_len.file_name, "w")
962	for line in len_text.split("\n"):
963	lst = line.strip().split()
964	if not lst or len(lst) < 2:
965	lines_skipped += 1
966	continue
967	chrom, length = lst[0], lst[1]
968	try:
969	length = int(length)
970	except ValueError:
971	lines_skipped += 1
972	continue
973	counter += 1
974	f.write("%s\t%s\n" % (chrom, length))
975	f.close()
976	dbkeys[key] = { "name": name, "len": new_len.id, "count": counter }
977
978	user.preferences['dbkeys'] = to_json_string(dbkeys)
979	trans.sa_session.flush()
980
981	return trans.fill_template( 'user/dbkeys.mako',
982	user=user,
983	dbkeys=dbkeys,
984	message=message,
985	lines_skipped=lines_skipped )
986	@web.expose
987	def api_keys( self, trans, **kwd ):
988	params = util.Params( kwd )
989	message = util.restore_text( params.get( 'message', '' ) )
990	status = params.get( 'status', 'done' )
991	error = ''
992	if params.get( 'new_api_key_button', None ) == 'Generate a new key now':
993	new_key = trans.app.model.APIKeys()
994	new_key.user_id = trans.user.id
995	new_key.key = trans.app.security.get_new_guid()
996	trans.sa_session.add( new_key )
997	trans.sa_session.flush()
998	message = "Generated a new web API key"
999	status = "done"
1000	return trans.fill_template( 'webapps/galaxy/user/api_keys.mako',
1001	user=trans.user,
1002	message=message,
1003	status=status )

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root/galaxy-central/lib/galaxy/web/controllers/user.py

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