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library_common.py

リビジョン 2, 156.1 KB (コミッタ: hatakeyama, 14 年前)
import galaxy-central

行番号
1	import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy, glob, string
2	from galaxy.web.base.controller import *
3	from galaxy import util, jobs
4	from galaxy.datatypes import sniff
5	from galaxy.security import RBACAgent
6	from galaxy.util.json import to_json_string
7	from galaxy.tools.actions import upload_common
8	from galaxy.model.orm import *
9	from galaxy.util.streamball import StreamBall
10	from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField
11	import logging, tempfile, zipfile, tarfile, os, sys
12
13	if sys.version_info[:2] < ( 2, 6 ):
14	zipfile.BadZipFile = zipfile.error
15	if sys.version_info[:2] < ( 2, 5 ):
16	zipfile.LargeZipFile = zipfile.error
17
18	log = logging.getLogger( __name__ )
19
20	# Test for available compression types
21	tmpd = tempfile.mkdtemp()
22	comptypes = []
23	for comptype in ( 'gz', 'bz2' ):
24	tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype )
25	try:
26	archive = tarfile.open( tmpf, 'w:' + comptype )
27	archive.close()
28	comptypes.append( comptype )
29	except tarfile.CompressionError:
30	log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype )
31	try:
32	os.unlink( tmpf )
33	except OSError:
34	pass
35	ziptype = '32'
36	tmpf = os.path.join( tmpd, 'compression_test.zip' )
37	try:
38	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
39	archive.close()
40	comptypes.append( 'zip' )
41	ziptype = '64'
42	except RuntimeError:
43	log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." )
44	except (TypeError, zipfile.LargeZipFile):
45	# ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped
46	log.warning( 'Max zip file size is 2GB, ZIP64 not supported' )
47	comptypes.append( 'zip' )
48	try:
49	os.unlink( tmpf )
50	except OSError:
51	pass
52	os.rmdir( tmpd )
53
54	class LibraryCommon( BaseController, UsesFormDefinitionWidgets ):
55	@web.json
56	def library_item_updates( self, trans, ids=None, states=None ):
57	# Avoid caching
58	trans.response.headers['Pragma'] = 'no-cache'
59	trans.response.headers['Expires'] = '0'
60	# Create new HTML for any that have changed
61	rval = {}
62	if ids is not None and states is not None:
63	ids = map( int, ids.split( "," ) )
64	states = states.split( "," )
65	for id, state in zip( ids, states ):
66	data = trans.sa_session.query( self.app.model.LibraryDatasetDatasetAssociation ).get( id )
67	if data.state != state:
68	job_ldda = data
69	while job_ldda.copied_from_library_dataset_dataset_association:
70	job_ldda = job_ldda.copied_from_library_dataset_dataset_association
71	force_history_refresh = False
72	rval[id] = {
73	"state": data.state,
74	"html": unicode( trans.fill_template( "library/common/library_item_info.mako", ldda=data ), 'utf-8' )
75	#"force_history_refresh": force_history_refresh
76	}
77	return rval
78	@web.expose
79	def browse_library( self, trans, cntrller, **kwd ):
80	params = util.Params( kwd )
81	message = util.restore_text( params.get( 'message', '' ) )
82	status = params.get( 'status', 'done' )
83	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
84	library_id = params.get( 'id', None )
85	if not library_id:
86	# To handle bots
87	message = "You must specify a library id."
88	status = 'error'
89	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
90	current_user_roles = trans.get_current_user_roles()
91	try:
92	library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
93	except:
94	# Protect against attempts to phish for valid keys that return libraries
95	library = None
96	# Most security for browsing libraries is handled in the template, but do a basic check here.
97	if not library or not ( is_admin or trans.app.security_agent.can_access_library( current_user_roles, library ) ):
98	message = "Invalid library id ( %s ) specified." % str( library_id )
99	status = 'error'
100	else:
101	# If use_panels is True, the library is being accessed via an external link
102	# which did not originate from within the Galaxy instance, and the library will
103	# be displayed correctly with the mast head.
104	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
105	created_ldda_ids = params.get( 'created_ldda_ids', '' )
106	hidden_folder_ids = util.listify( params.get( 'hidden_folder_ids', '' ) )
107	if created_ldda_ids and not message:
108	message = "%d datasets are uploading in the background to the library '%s' (each is selected). " % \
109	( len( created_ldda_ids.split( ',' ) ), library.name )
110	message += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the "
111	message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset."
112	status = "info"
113	comptypes_t = comptypes
114	if trans.app.config.nginx_x_archive_files_base:
115	comptypes_t = ['ngxzip']
116	for comptype in trans.app.config.disable_library_comptypes:
117	# TODO: do this once, not every time (we're gonna raise an
118	# exception every time after the first time)
119	try:
120	comptypes_t.remove( comptype )
121	except:
122	pass
123	return trans.fill_template( '/library/common/browse_library.mako',
124	cntrller=cntrller,
125	use_panels=use_panels,
126	library=library,
127	created_ldda_ids=created_ldda_ids,
128	hidden_folder_ids=hidden_folder_ids,
129	show_deleted=show_deleted,
130	comptypes=comptypes_t,
131	current_user_roles=current_user_roles,
132	message=message,
133	status=status )
134	return trans.response.send_redirect( web.url_for( use_panels=use_panels,
135	controller=cntrller,
136	action='browse_libraries',
137	default_action=params.get( 'default_action', None ),
138	message=util.sanitize_text( message ),
139	status=status ) )
140	@web.expose
141	def library_info( self, trans, cntrller, **kwd ):
142	params = util.Params( kwd )
143	message = util.restore_text( params.get( 'message', '' ) )
144	status = params.get( 'status', 'done' )
145	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
146	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
147	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
148	current_user_roles = trans.get_current_user_roles()
149	library_id = params.get( 'id', None )
150	try:
151	library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
152	except:
153	library = None
154	self._check_access( trans, cntrller, is_admin, library, current_user_roles, use_panels, library_id, show_deleted )
155	if params.get( 'library_info_button', False ):
156	self._check_modify( trans, cntrller, is_admin, library, current_user_roles, use_panels, library_id, show_deleted )
157	old_name = library.name
158	new_name = util.restore_text( params.get( 'name', 'No name' ) )
159	if not new_name:
160	message = 'Enter a valid name'
161	status='error'
162	else:
163	new_description = util.restore_text( params.get( 'description', '' ) )
164	new_synopsis = util.restore_text( params.get( 'synopsis', '' ) )
165	if new_synopsis in [ None, 'None' ]:
166	new_synopsis = ''
167	library.name = new_name
168	library.description = new_description
169	library.synopsis = new_synopsis
170	# Rename the root_folder
171	library.root_folder.name = new_name
172	library.root_folder.description = new_description
173	trans.sa_session.add_all( ( library, library.root_folder ) )
174	trans.sa_session.flush()
175	message = "Information updated for library '%s'." % library.name
176	return trans.response.send_redirect( web.url_for( controller='library_common',
177	action='library_info',
178	cntrller=cntrller,
179	use_panels=use_panels,
180	id=trans.security.encode_id( library.id ),
181	show_deleted=show_deleted,
182	message=util.sanitize_text( message ),
183	status='done' ) )
184	# See if we have any associated templates
185	info_association, inherited = library.get_info_association()
186	widgets = library.get_template_widgets( trans )
187	widget_fields_have_contents = self.widget_fields_have_contents( widgets )
188	return trans.fill_template( '/library/common/library_info.mako',
189	cntrller=cntrller,
190	use_panels=use_panels,
191	library=library,
192	widgets=widgets,
193	widget_fields_have_contents=widget_fields_have_contents,
194	current_user_roles=current_user_roles,
195	show_deleted=show_deleted,
196	info_association=info_association,
197	inherited=inherited,
198	message=message,
199	status=status )
200	@web.expose
201	def library_permissions( self, trans, cntrller, **kwd ):
202	params = util.Params( kwd )
203	message = util.restore_text( params.get( 'message', '' ) )
204	status = params.get( 'status', 'done' )
205	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
206	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
207	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
208	current_user_roles = trans.get_current_user_roles()
209	library_id = params.get( 'id', None )
210	try:
211	library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
212	except:
213	library = None
214	self._check_access( trans, cntrller, is_admin, library, current_user_roles, use_panels, library_id, show_deleted )
215	self._check_manage( trans, cntrller, is_admin, library, current_user_roles, use_panels, library_id, show_deleted )
216	if params.get( 'update_roles_button', False ):
217	# The user clicked the Save button on the 'Associate With Roles' form
218	permissions = {}
219	for k, v in trans.app.model.Library.permitted_actions.items():
220	in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
221	permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
222	trans.app.security_agent.set_all_library_permissions( library, permissions )
223	trans.sa_session.refresh( library )
224	# Copy the permissions to the root folder
225	trans.app.security_agent.copy_library_permissions( library, library.root_folder )
226	message = "Permissions updated for library '%s'." % library.name
227	return trans.response.send_redirect( web.url_for( controller='library_common',
228	action='library_permissions',
229	cntrller=cntrller,
230	use_panels=use_panels,
231	id=trans.security.encode_id( library.id ),
232	show_deleted=show_deleted,
233	message=util.sanitize_text( message ),
234	status='done' ) )
235	roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller )
236	return trans.fill_template( '/library/common/library_permissions.mako',
237	cntrller=cntrller,
238	use_panels=use_panels,
239	library=library,
240	current_user_roles=current_user_roles,
241	roles=roles,
242	show_deleted=show_deleted,
243	message=message,
244	status=status )
245	@web.expose
246	def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ):
247	params = util.Params( kwd )
248	message = util.restore_text( params.get( 'message', '' ) )
249	status = params.get( 'status', 'done' )
250	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
251	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
252	is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' )
253	current_user_roles = trans.get_current_user_roles()
254	try:
255	parent_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( parent_id ) )
256	except:
257	parent_folder = None
258	# Check the library which actually contains the user-supplied parent folder, not the user-supplied
259	# library, which could be anything.
260	if parent_folder:
261	parent_library = parent_folder.parent_library
262	self._check_access( trans, cntrller, is_admin, parent_folder, current_user_roles, use_panels, library_id, show_deleted )
263	self._check_add( trans, cntrller, is_admin, parent_folder, current_user_roles, use_panels, library_id, show_deleted )
264	if params.get( 'new_folder_button', False ) or cntrller == 'api':
265	new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ),
266	description=util.restore_text( params.description ) )
267	# We are associating the last used genome build with folders, so we will always
268	# initialize a new folder with the first dbkey in util.dbnames which is currently
269	# ? unspecified (?)
270	new_folder.genome_build = util.dbnames.default_value
271	parent_folder.add_folder( new_folder )
272	trans.sa_session.add( new_folder )
273	trans.sa_session.flush()
274	# New folders default to having the same permissions as their parent folder
275	trans.app.security_agent.copy_library_permissions( parent_folder, new_folder )
276	# If we're creating in the API, we're done
277	if cntrller == 'api':
278	return 200, dict( created=new_folder )
279	# If we have an inheritable template, redirect to the folder_info page so information
280	# can be filled in immediately.
281	widgets = []
282	info_association, inherited = new_folder.get_info_association()
283	if info_association and ( not( inherited ) or info_association.inheritable ):
284	widgets = new_folder.get_template_widgets( trans )
285	if info_association:
286	message = "The new folder named '%s' has been added to the data library. " % new_folder.name
287	message += "Additional information about this folder may be added using the inherited template."
288	return trans.fill_template( '/library/common/folder_info.mako',
289	cntrller=cntrller,
290	use_panels=use_panels,
291	folder=new_folder,
292	library_id=library_id,
293	widgets=widgets,
294	current_user_roles=current_user_roles,
295	show_deleted=show_deleted,
296	info_association=info_association,
297	inherited=inherited,
298	message=message,
299	status='done' )
300	# If not inheritable info_association, redirect to the library.
301	message = "The new folder named '%s' has been added to the data library." % new_folder.name
302	return trans.response.send_redirect( web.url_for( controller='library_common',
303	action='browse_library',
304	cntrller=cntrller,
305	use_panels=use_panels,
306	id=library_id,
307	show_deleted=show_deleted,
308	message=util.sanitize_text( message ),
309	status='done' ) )
310	# We do not render any template widgets on creation pages since saving the info_association
311	# cannot occur before the associated item is saved.
312	return trans.fill_template( '/library/common/new_folder.mako',
313	cntrller=cntrller,
314	use_panels=use_panels,
315	library_id=library_id,
316	folder=parent_folder,
317	show_deleted=show_deleted,
318	message=message,
319	status=status )
320	@web.expose
321	def folder_info( self, trans, cntrller, id, library_id, **kwd ):
322	params = util.Params( kwd )
323	message = util.restore_text( params.get( 'message', '' ) )
324	status = params.get( 'status', 'done' )
325	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
326	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
327	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
328	current_user_roles = trans.get_current_user_roles()
329	try:
330	folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) )
331	except:
332	folder = None
333	self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
334	if params.get( 'rename_folder_button', False ):
335	self._check_modify( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
336	old_name = folder.name
337	new_name = util.restore_text( params.name )
338	new_description = util.restore_text( params.description )
339	if not new_name:
340	message = 'Enter a valid name'
341	status='error'
342	else:
343	folder.name = new_name
344	folder.description = new_description
345	trans.sa_session.add( folder )
346	trans.sa_session.flush()
347	message = "Information updated for folder '%s'." % folder.name
348	return trans.response.send_redirect( web.url_for( controller='library_common',
349	action='folder_info',
350	cntrller=cntrller,
351	use_panels=use_panels,
352	id=id,
353	library_id=library_id,
354	show_deleted=show_deleted,
355	message=util.sanitize_text( message ),
356	status='done' ) )
357	# See if we have any associated templates
358	widgets = []
359	widget_fields_have_contents = False
360	info_association, inherited = folder.get_info_association()
361	if info_association and ( not( inherited ) or info_association.inheritable ):
362	widgets = folder.get_template_widgets( trans )
363	widget_fields_have_contents = self.widget_fields_have_contents( widgets )
364	return trans.fill_template( '/library/common/folder_info.mako',
365	cntrller=cntrller,
366	use_panels=use_panels,
367	folder=folder,
368	library_id=library_id,
369	widgets=widgets,
370	widget_fields_have_contents=widget_fields_have_contents,
371	current_user_roles=current_user_roles,
372	show_deleted=show_deleted,
373	info_association=info_association,
374	inherited=inherited,
375	message=message,
376	status=status )
377	@web.expose
378	def folder_permissions( self, trans, cntrller, id, library_id, **kwd ):
379	params = util.Params( kwd )
380	message = util.restore_text( params.get( 'message', '' ) )
381	status = params.get( 'status', 'done' )
382	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
383	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
384	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
385	current_user_roles = trans.get_current_user_roles()
386	try:
387	folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) )
388	except:
389	folder = None
390	self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
391	self._check_manage( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
392	if params.get( 'update_roles_button', False ):
393	# The user clicked the Save button on the 'Associate With Roles' form
394	permissions = {}
395	for k, v in trans.app.model.Library.permitted_actions.items():
396	if k != 'LIBRARY_ACCESS':
397	# LIBRARY_ACCESS is a special permission set only at the library level
398	# and it is not inherited.
399	in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
400	permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
401	trans.app.security_agent.set_all_library_permissions( folder, permissions )
402	trans.sa_session.refresh( folder )
403	message = "Permissions updated for folder '%s'." % folder.name
404	return trans.response.send_redirect( web.url_for( controller='library_common',
405	action='folder_permissions',
406	cntrller=cntrller,
407	use_panels=use_panels,
408	id=trans.security.encode_id( folder.id ),
409	library_id=library_id,
410	show_deleted=show_deleted,
411	message=util.sanitize_text( message ),
412	status='done' ) )
413	# If the library is public all roles are legitimate, but if the library
414	# is restricted, only those roles associated with the LIBRARY_ACCESS
415	# permission are legitimate.
416	roles = trans.app.security_agent.get_legitimate_roles( trans, folder.parent_library, cntrller )
417	return trans.fill_template( '/library/common/folder_permissions.mako',
418	cntrller=cntrller,
419	use_panels=use_panels,
420	folder=folder,
421	library_id=library_id,
422	current_user_roles=current_user_roles,
423	roles=roles,
424	show_deleted=show_deleted,
425	message=message,
426	status=status )
427	@web.expose
428	def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
429	params = util.Params( kwd )
430	message = util.restore_text( params.get( 'message', '' ) )
431	status = params.get( 'status', 'done' )
432	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
433	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
434	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
435	current_user_roles = trans.get_current_user_roles()
436	try:
437	ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
438	except:
439	ldda = None
440	self._check_access( trans, cntrller, is_admin, ldda, current_user_roles, use_panels, library_id, show_deleted )
441	self._check_modify( trans, cntrller, is_admin, ldda, current_user_roles, use_panels, library_id, show_deleted )
442	dbkey = params.get( 'dbkey', '?' )
443	if isinstance( dbkey, list ):
444	dbkey = dbkey[0]
445	file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
446	file_formats.sort()
447	# See if we have any associated templates
448	widgets = []
449	info_association, inherited = ldda.get_info_association()
450	if info_association and ( not( inherited ) or info_association.inheritable ):
451	widgets = ldda.get_template_widgets( trans )
452	if params.get( 'change', False ):
453	# The user clicked the Save button on the 'Change data type' form
454	if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
455	trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
456	trans.sa_session.flush()
457	message = "Data type changed for library dataset '%s'." % ldda.name
458	status = 'done'
459	else:
460	message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype )
461	status = 'error'
462	elif params.get( 'save', False ):
463	# The user clicked the Save button on the 'Edit Attributes' form
464	old_name = ldda.name
465	new_name = util.restore_text( params.get( 'name', '' ) )
466	new_info = util.restore_text( params.get( 'info', '' ) )
467	new_message = util.restore_text( params.get( 'message', '' ) )
468	if not new_name:
469	message = 'Enter a valid name'
470	status = 'error'
471	else:
472	ldda.name = new_name
473	ldda.info = new_info
474	ldda.message = new_message
475	# The following for loop will save all metadata_spec items
476	for name, spec in ldda.datatype.metadata_spec.items():
477	if spec.get("readonly"):
478	continue
479	optional = params.get( "is_" + name, None )
480	if optional and optional == 'true':
481	# optional element... == 'true' actually means it is NOT checked (and therefore ommitted)
482	setattr( ldda.metadata, name, None )
483	else:
484	setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) )
485	ldda.metadata.dbkey = dbkey
486	ldda.datatype.after_setting_metadata( ldda )
487	trans.sa_session.flush()
488	message = "Attributes updated for library dataset '%s'." % ldda.name
489	status = 'done'
490	elif params.get( 'detect', False ):
491	# The user clicked the Auto-detect button on the 'Edit Attributes' form
492	for name, spec in ldda.datatype.metadata_spec.items():
493	# We need to be careful about the attributes we are resetting
494	if name not in [ 'name', 'info', 'dbkey' ]:
495	if spec.get( 'default' ):
496	setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
497	ldda.datatype.set_meta( ldda )
498	ldda.datatype.after_setting_metadata( ldda )
499	trans.sa_session.flush()
500	message = "Information updated for library dataset '%s'." % ldda.name
501	status = 'done'
502	if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey:
503	# Copy dbkey into metadata, for backwards compatability
504	# This looks like it does nothing, but getting the dbkey
505	# returns the metadata dbkey unless it is None, in which
506	# case it resorts to the old dbkey. Setting the dbkey
507	# sets it properly in the metadata
508	ldda.metadata.dbkey = ldda.dbkey
509	return trans.fill_template( "/library/common/ldda_edit_info.mako",
510	cntrller=cntrller,
511	use_panels=use_panels,
512	ldda=ldda,
513	library_id=library_id,
514	file_formats=file_formats,
515	widgets=widgets,
516	current_user_roles=current_user_roles,
517	show_deleted=show_deleted,
518	info_association=info_association,
519	inherited=inherited,
520	message=message,
521	status=status )
522	@web.expose
523	def ldda_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
524	params = util.Params( kwd )
525	message = util.restore_text( params.get( 'message', '' ) )
526	status = params.get( 'status', 'done' )
527	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
528	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
529	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
530	current_user_roles = trans.get_current_user_roles()
531	try:
532	ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
533	except:
534	ldda = None
535	self._check_access( trans, cntrller, is_admin, ldda, current_user_roles, use_panels, library_id, show_deleted )
536	if is_admin:
537	# Get all associated hdas and lddas that use the same disk file.
538	associated_hdas = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \
539	.filter( and_( trans.model.HistoryDatasetAssociation.deleted == False,
540	trans.model.HistoryDatasetAssociation.dataset_id == ldda.dataset_id ) ) \
541	.all()
542	associated_lddas = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ) \
543	.filter( and_( trans.model.LibraryDatasetDatasetAssociation.deleted == False,
544	trans.model.LibraryDatasetDatasetAssociation.dataset_id == ldda.dataset_id,
545	trans.model.LibraryDatasetDatasetAssociation.id != ldda.id ) ) \
546	.all()
547	else:
548	associated_hdas = []
549	associated_lddas = []
550	# See if we have any associated templates
551	widgets = []
552	widget_fields_have_contents = False
553	info_association, inherited = ldda.get_info_association()
554	if info_association and ( not( inherited ) or info_association.inheritable ):
555	widgets = ldda.get_template_widgets( trans )
556	widget_fields_have_contents = self.widget_fields_have_contents( widgets )
557	return trans.fill_template( '/library/common/ldda_info.mako',
558	cntrller=cntrller,
559	use_panels=use_panels,
560	ldda=ldda,
561	library=ldda.library_dataset.folder.parent_library,
562	associated_hdas=associated_hdas,
563	associated_lddas=associated_lddas,
564	show_deleted=show_deleted,
565	widgets=widgets,
566	widget_fields_have_contents=widget_fields_have_contents,
567	current_user_roles=current_user_roles,
568	info_association=info_association,
569	inherited=inherited,
570	message=message,
571	status=status )
572	@web.expose
573	def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ):
574	params = util.Params( kwd )
575	message = util.restore_text( params.get( 'message', '' ) )
576	status = params.get( 'status', 'done' )
577	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
578	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
579	ids = util.listify( id )
580	lddas = []
581	libraries = []
582	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
583	current_user_roles = trans.get_current_user_roles()
584	for id in ids:
585	try:
586	ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
587	except:
588	ldda = None
589	if ldda:
590	library = ldda.library_dataset.folder.parent_library
591	self._check_access( trans, cntrller, is_admin, ldda, current_user_roles, use_panels, library_id, show_deleted )
592	lddas.append( ldda )
593	libraries.append( library )
594	library = libraries[0]
595	if filter( lambda x: x != library, libraries ):
596	message = "Library datasets specified span multiple libraries."
597	return trans.response.send_redirect( web.url_for( controller='library_common',
598	action='browse_library',
599	id=library_id,
600	cntrller=cntrller,
601	use_panels=use_panels,
602	message=util.sanitize_text( message ),
603	status='error' ) )
604	# If access to the dataset is restricted, then use the roles associated with the DATASET_ACCESS permission to
605	# determine the legitimate roles. If the dataset is public, see if access to the library is restricted. If
606	# it is, use the roles associated with the LIBRARY_ACCESS permission to determine the legitimate roles. If both
607	# the dataset and the library are public, all roles are legitimate. All of the datasets will have the same
608	# permissions at this point.
609	ldda = lddas[0]
610	if trans.app.security_agent.dataset_is_public( ldda.dataset ):
611	# The dataset is public, so check access to the library
612	roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller )
613	else:
614	roles = trans.app.security_agent.get_legitimate_roles( trans, ldda.dataset, cntrller )
615	if params.get( 'update_roles_button', False ):
616	a = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action )
617	permissions, in_roles, error, message = \
618	trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **kwd )
619	for ldda in lddas:
620	# Set the DATASET permissions on the Dataset.
621	if error:
622	# Keep the original role associations for the DATASET_ACCESS permission on the ldda.
623	permissions[ a ] = ldda.get_access_roles( trans )
624	trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
625	trans.sa_session.refresh( ldda.dataset )
626	# Set the LIBRARY permissions on the LibraryDataset. The LibraryDataset and
627	# LibraryDatasetDatasetAssociation will be set with the same permissions.
628	permissions = {}
629	for k, v in trans.app.model.Library.permitted_actions.items():
630	if k != 'LIBRARY_ACCESS':
631	# LIBRARY_ACCESS is a special permission set only at the library level and it is not inherited.
632	in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
633	permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
634	for ldda in lddas:
635	trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
636	trans.sa_session.refresh( ldda.library_dataset )
637	# Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
638	trans.app.security_agent.set_all_library_permissions( ldda, permissions )
639	trans.sa_session.refresh( ldda )
640	if error:
641	status = 'error'
642	else:
643	if len( lddas ) == 1:
644	message = "Permissions updated for dataset '%s'." % ldda.name
645	else:
646	message = 'Permissions updated for %d datasets.' % len( lddas )
647	status= 'done'
648	return trans.fill_template( "/library/common/ldda_permissions.mako",
649	cntrller=cntrller,
650	use_panels=use_panels,
651	lddas=lddas,
652	library_id=library_id,
653	roles=roles,
654	show_deleted=show_deleted,
655	message=message,
656	status=status )
657	if len( ids ) > 1:
658	# Ensure that the permissions across all library items are identical, otherwise we can't update them together.
659	check_list = []
660	for ldda in lddas:
661	permissions = []
662	# Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation
663	# will always be the same as the permissions on the associated LibraryDataset.
664	for library_permission in trans.app.security_agent.get_permissions( ldda.library_dataset ):
665	if library_permission.action not in permissions:
666	permissions.append( library_permission.action )
667	for dataset_permission in trans.app.security_agent.get_permissions( ldda.dataset ):
668	if dataset_permission.action not in permissions:
669	permissions.append( dataset_permission.action )
670	permissions.sort()
671	if not check_list:
672	check_list = permissions
673	if permissions != check_list:
674	message = 'The datasets you selected do not have identical permissions, so they can not be updated together'
675	trans.response.send_redirect( web.url_for( controller='library_common',
676	action='browse_library',
677	cntrller=cntrller,
678	use_panels=use_panels,
679	id=library_id,
680	show_deleted=show_deleted,
681	message=util.sanitize_text( message ),
682	status='error' ) )
683	# Display permission form, permissions will be updated for all lddas simultaneously.
684	return trans.fill_template( "/library/common/ldda_permissions.mako",
685	cntrller=cntrller,
686	use_panels=use_panels,
687	lddas=lddas,
688	library_id=library_id,
689	roles=roles,
690	show_deleted=show_deleted,
691	message=message,
692	status=status )
693	@web.expose
694	def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ):
695	params = util.Params( kwd )
696	message = util.restore_text( params.get( 'message', '' ) )
697	status = params.get( 'status', 'done' )
698	ldda_message = util.restore_text( params.get( 'ldda_message', '' ) )
699	deleted = util.string_as_bool( params.get( 'deleted', False ) )
700	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
701	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
702	replace_id = params.get( 'replace_id', None )
703	replace_dataset = None
704	upload_option = params.get( 'upload_option', 'upload_file' )
705	if params.get( 'files_0\|space_to_tab', False ):
706	space_to_tab = params.get( 'files_0\|space_to_tab', '' )
707	else:
708	space_to_tab = params.get( 'space_to_tab', '' )
709	link_data_only = params.get( 'link_data_only', '' )
710	dbkey = params.get( 'dbkey', '?' )
711	if isinstance( dbkey, list ):
712	last_used_build = dbkey[0]
713	else:
714	last_used_build = dbkey
715	roles = params.get( 'roles', '' )
716	is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' )
717	current_user_roles = trans.get_current_user_roles()
718	if replace_id not in [ None, 'None' ]:
719	try:
720	replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
721	except:
722	replace_dataset = None
723	self._check_access( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted )
724	self._check_modify( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted )
725	library = replace_dataset.folder.parent_library
726	folder = replace_dataset.folder
727	# The name is stored - by the time the new ldda is created, replace_dataset.name
728	# will point to the new ldda, not the one it's replacing.
729	replace_dataset_name = replace_dataset.name
730	if not last_used_build:
731	last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
732	# Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
733	upload_option = 'upload_file'
734	else:
735	folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
736	self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
737	self._check_add( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
738	library = folder.parent_library
739	if folder and last_used_build in [ 'None', None, '?' ]:
740	last_used_build = folder.genome_build
741	if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ) or cntrller == 'api':
742	error = False
743	if upload_option == 'upload_paths' and not trans.app.config.allow_library_path_paste:
744	error = True
745	message = '"allow_library_path_paste" is not defined in the Galaxy configuration file'
746	elif roles:
747	# Check to see if the user selected roles to associate with the DATASET_ACCESS permission
748	# on the dataset that would cause accessibility issues.
749	vars = dict( DATASET_ACCESS_in=roles )
750	permissions, in_roles, error, message = \
751	trans.app.security_agent.derive_roles_from_access( trans, library.id, cntrller, library=True, **vars )
752	if error:
753	if cntrller == 'api':
754	return 400, message
755	trans.response.send_redirect( web.url_for( controller='library_common',
756	action='upload_library_dataset',
757	cntrller=cntrller,
758	library_id=library_id,
759	folder_id=folder_id,
760	replace_id=replace_id,
761	upload_option=upload_option,
762	show_deleted=show_deleted,
763	message=util.sanitize_text( message ),
764	status='error' ) )
765
766	else:
767	# See if we have any inherited templates.
768	info_association, inherited = folder.get_info_association( inherited=True )
769	if info_association and info_association.inheritable:
770	template_id = str( info_association.template.id )
771	widgets = folder.get_template_widgets( trans, get_contents=True )
772	processed_widgets = []
773	# The list of widgets may include an AddressField which we need to save if it is new
774	for index, widget_dict in enumerate( widgets ):
775	widget = widget_dict[ 'widget' ]
776	if isinstance( widget, AddressField ):
777	value = util.restore_text( params.get( 'field_%i' % index, '' ) )
778	if value == 'new':
779	if self.field_param_values_ok( index, 'AddressField', **kwd ):
780	# Save the new address
781	address = trans.app.model.UserAddress( user=trans.user )
782	self.save_widget_field( trans, address, index, **kwd )
783	widget.value = str( address.id )
784	widget_dict[ 'widget' ] = widget
785	processed_widgets.append( widget_dict )
786	# It is now critical to update the value of 'field_%i', replacing the string
787	# 'new' with the new address id. This is necessary because the upload_dataset()
788	# method below calls the handle_library_params() method, which does not parse the
789	# widget fields, it instead pulls form values from kwd. See the FIXME comments in the
790	# handle_library_params() method, and the CheckboxField code in the next conditional.
791	kwd[ 'field_%i' % index ] = str( address.id )
792	else:
793	# The invalid address won't be saved, but we cannot display error
794	# messages on the upload form due to the ajax upload already occurring.
795	# When we re-engineer the upload process ( currently under way ), we
796	# will be able to check the form values before the ajax upload occurs
797	# in the background. For now, we'll do nothing...
798	pass
799	elif isinstance( widget, CheckboxField ):
800	# We need to check the value from kwd since util.Params would have munged the list if
801	# the checkbox is checked.
802	value = kwd.get( 'field_%i' % index, '' )
803	if CheckboxField.is_checked( value ):
804	widget.value = 'true'
805	widget_dict[ 'widget' ] = widget
806	processed_widgets.append( widget_dict )
807	kwd[ 'field_%i' % index ] = 'true'
808	else:
809	processed_widgets.append( widget_dict )
810	widgets = processed_widgets
811	else:
812	template_id = 'None'
813	widgets = []
814	created_outputs_dict = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
815	cntrller=cntrller,
816	library_id=trans.security.encode_id( library.id ),
817	folder_id=trans.security.encode_id( folder.id ),
818	template_id=template_id,
819	widgets=widgets,
820	replace_dataset=replace_dataset,
821	**kwd )
822	if created_outputs_dict:
823	if cntrller == 'api':
824	# created_outputs_dict can only ever be a string if cntrller == 'api'
825	if type( created_outputs_dict ) == str:
826	return 400, created_outputs_dict
827	return 200, created_outputs_dict
828	total_added = len( created_outputs_dict.keys() )
829	ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ]
830	created_ldda_ids=",".join( ldda_id_list )
831	if replace_dataset:
832	message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name )
833	else:
834	if not folder.parent:
835	# Libraries have the same name as their root_folder
836	message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name )
837	else:
838	message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name )
839	if cntrller == 'library_admin':
840	message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
841	status='done'
842	else:
843	# Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
844	# to check one of them to see if the current user can manage permissions on them.
845	check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
846	if trans.app.security_agent.can_manage_library_item( current_user_roles, check_ldda ):
847	if replace_dataset:
848	default_action = ''
849	else:
850	message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
851	default_action = 'manage_permissions'
852	else:
853	default_action = 'add'
854	trans.response.send_redirect( web.url_for( controller='library_common',
855	action='browse_library',
856	cntrller=cntrller,
857	id=library_id,
858	default_action=default_action,
859	created_ldda_ids=created_ldda_ids,
860	show_deleted=show_deleted,
861	message=util.sanitize_text( message ),
862	status='done' ) )
863	else:
864	created_ldda_ids = ''
865	message = "Upload failed"
866	status='error'
867	if cntrller == 'api':
868	return 400, message
869	response_code = 400
870	trans.response.send_redirect( web.url_for( controller='library_common',
871	action='browse_library',
872	cntrller=cntrller,
873	id=library_id,
874	created_ldda_ids=created_ldda_ids,
875	show_deleted=show_deleted,
876	message=util.sanitize_text( message ),
877	status=status ) )
878	# Note: if the upload form was submitted due to refresh_on_change for a form field, we cannot re-populate
879	# the field for the selected file ( files_0\|file_data ) if the user selected one. This is because the value
880	# attribute of the html input file type field is typically ignored by browsers as a security precaution.
881
882	# See if we have any inherited templates.
883	info_association, inherited = folder.get_info_association( inherited=True )
884	if info_association and info_association.inheritable:
885	widgets = folder.get_template_widgets( trans, get_contents=True )
886	# Retain contents of widget fields when form was submitted via refresh_on_change.
887	widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd )
888	else:
889	widgets = []
890	# Send list of data formats to the upload form so the "extension" select list can be populated dynamically
891	file_formats = trans.app.datatypes_registry.upload_file_formats
892	# Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
893	def get_dbkey_options( last_used_build ):
894	for dbkey, build_name in util.dbnames:
895	yield build_name, dbkey, ( dbkey==last_used_build )
896	dbkeys = get_dbkey_options( last_used_build )
897	# Send the current history to the form to enable importing datasets from history to library
898	history = trans.get_history()
899	trans.sa_session.refresh( history )
900	if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
901	# If we're using nginx upload, override the form action -
902	# url_for is intentionally not used on the base URL here -
903	# nginx_upload_path is expected to include the proxy prefix if the
904	# administrator intends for it to be part of the URL.
905	action = trans.app.config.nginx_upload_path + '?nginx_redir=' + web.url_for( controller='library_common', action='upload_library_dataset' )
906	else:
907	action = web.url_for( controller='library_common', action='upload_library_dataset' )
908	upload_option_select_list = self._build_upload_option_select_list( trans, upload_option )
909	roles_select_list = self._build_roles_select_list( trans, cntrller, library, util.listify( roles ) )
910	return trans.fill_template( '/library/common/upload.mako',
911	cntrller=cntrller,
912	upload_option_select_list=upload_option_select_list,
913	upload_option=upload_option,
914	action=action,
915	library_id=library_id,
916	folder_id=folder_id,
917	replace_dataset=replace_dataset,
918	file_formats=file_formats,
919	dbkeys=dbkeys,
920	last_used_build=last_used_build,
921	roles_select_list=roles_select_list,
922	history=history,
923	widgets=widgets,
924	space_to_tab=space_to_tab,
925	link_data_only=link_data_only,
926	show_deleted=show_deleted,
927	ldda_message=ldda_message,
928	message=message,
929	status=status )
930	def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ):
931	# Set up the traditional tool state/params
932	tool_id = 'upload1'
933	tool = trans.app.toolbox.tools_by_id[ tool_id ]
934	state = tool.new_state( trans )
935	errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd )
936	tool_params = state.inputs
937	dataset_upload_inputs = []
938	for input_name, input in tool.inputs.iteritems():
939	if input.type == "upload_dataset":
940	dataset_upload_inputs.append( input )
941	# Library-specific params
942	params = util.Params( kwd ) # is this filetoolparam safe?
943	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
944	message = util.restore_text( params.get( 'message', '' ) )
945	status = params.get( 'status', 'done' )
946	server_dir = util.restore_text( params.get( 'server_dir', '' ) )
947	if replace_dataset not in [ None, 'None' ]:
948	replace_id = trans.security.encode_id( replace_dataset.id )
949	else:
950	replace_id = None
951	upload_option = params.get( 'upload_option', 'upload_file' )
952	response_code = 200
953	if upload_option == 'upload_directory':
954	if server_dir in [ None, 'None', '' ]:
955	response_code = 400
956	if cntrller == 'library_admin' or ( cntrller == 'api' and trans.user_is_admin ):
957	import_dir = trans.app.config.library_import_dir
958	import_dir_desc = 'library_import_dir'
959	full_dir = os.path.join( import_dir, server_dir )
960	else:
961	import_dir = trans.app.config.user_library_import_dir
962	import_dir_desc = 'user_library_import_dir'
963	if server_dir == trans.user.email:
964	full_dir = os.path.join( import_dir, server_dir )
965	else:
966	full_dir = os.path.join( import_dir, trans.user.email, server_dir )
967	if import_dir:
968	message = 'Select a directory'
969	else:
970	response_code = 403
971	message = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
972	elif upload_option == 'upload_paths':
973	if not trans.app.config.allow_library_path_paste:
974	response_code = 403
975	message = '"allow_library_path_paste" is not defined in the Galaxy configuration file'
976	# Some error handling should be added to this method.
977	try:
978	# FIXME: instead of passing params here ( chiech have been process by util.Params(), the original kwd
979	# should be passed so that complex objects that may have been included in the initial request remain.
980	library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset )
981	except:
982	response_code = 500
983	message = "Unable to parse upload parameters, please report this error."
984	# Proceed with (mostly) regular upload processing if we're still errorless
985	if response_code == 200:
986	precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=cntrller )
987	if upload_option == 'upload_file':
988	tool_params = upload_common.persist_uploads( tool_params )
989	uploaded_datasets = upload_common.get_uploaded_datasets( trans, cntrller, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch )
990	elif upload_option == 'upload_directory':
991	uploaded_datasets, response_code, message = self.get_server_dir_uploaded_datasets( trans, cntrller, params, full_dir, import_dir_desc, library_bunch, response_code, message )
992	elif upload_option == 'upload_paths':
993	uploaded_datasets, response_code, message = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, response_code, message )
994	upload_common.cleanup_unused_precreated_datasets( precreated_datasets )
995	if upload_option == 'upload_file' and not uploaded_datasets:
996	response_code = 400
997	message = 'Select a file, enter a URL or enter text'
998	if response_code != 200:
999	if cntrller == 'api':
1000	return ( response_code, message )
1001	trans.response.send_redirect( web.url_for( controller='library_common',
1002	action='upload_library_dataset',
1003	cntrller=cntrller,
1004	library_id=library_id,
1005	folder_id=folder_id,
1006	replace_id=replace_id,
1007	upload_option=upload_option,
1008	show_deleted=show_deleted,
1009	message=util.sanitize_text( message ),
1010	status='error' ) )
1011	json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
1012	data_list = [ ud.data for ud in uploaded_datasets ]
1013	return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
1014	def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ):
1015	library_bunch.replace_dataset = None # not valid for these types of upload
1016	uploaded_dataset = util.bunch.Bunch()
1017	# Remove compressed file extensions, if any
1018	new_name = name
1019	if new_name.endswith( '.gz' ):
1020	new_name = new_name.rstrip( '.gz' )
1021	elif new_name.endswith( '.zip' ):
1022	new_name = new_name.rstrip( '.zip' )
1023	uploaded_dataset.name = new_name
1024	uploaded_dataset.path = path
1025	uploaded_dataset.type = type
1026	uploaded_dataset.ext = None
1027	uploaded_dataset.file_type = params.file_type
1028	uploaded_dataset.dbkey = params.dbkey
1029	uploaded_dataset.space_to_tab = params.space_to_tab
1030	if in_folder:
1031	uploaded_dataset.in_folder = in_folder
1032	uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch )
1033	if params.get( 'link_data_only', False ):
1034	uploaded_dataset.link_data_only = True
1035	uploaded_dataset.data.file_name = os.path.abspath( path )
1036	# Since we are not copying the file into Galaxy's managed
1037	# default file location, the dataset should never be purgable.
1038	uploaded_dataset.data.dataset.purgable = False
1039	trans.sa_session.add_all( ( uploaded_dataset.data, uploaded_dataset.data.dataset ) )
1040	trans.sa_session.flush()
1041	return uploaded_dataset
1042	def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, response_code, message ):
1043	files = []
1044	try:
1045	for entry in os.listdir( full_dir ):
1046	# Only import regular files
1047	path = os.path.join( full_dir, entry )
1048	if os.path.islink( full_dir ) and params.get( 'link_data_only', False ):
1049	# If we're linking instead of copying and the
1050	# sub-"directory" in the import dir is actually a symlink,
1051	# dereference the symlink, but not any of its contents.
1052	link_path = os.readlink( full_dir )
1053	if os.path.isabs( link_path ):
1054	path = os.path.join( link_path, entry )
1055	else:
1056	path = os.path.abspath( os.path.join( link_path, entry ) )
1057	elif os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ):
1058	# If we're linking instead of copying and the "file" in the
1059	# sub-directory of the import dir is actually a symlink,
1060	# dereference the symlink (one dereference only, Vasili).
1061	link_path = os.readlink( path )
1062	if os.path.isabs( link_path ):
1063	path = link_path
1064	else:
1065	path = os.path.abspath( os.path.join( os.path.dirname( path ), link_path ) )
1066	if os.path.isfile( path ):
1067	files.append( path )
1068	except Exception, e:
1069	message = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) )
1070	response_code = 500
1071	return None, response_code, message
1072	if not files:
1073	message = "The directory '%s' contains no valid files" % full_dir
1074	response_code = 400
1075	return None, response_code, message
1076	uploaded_datasets = []
1077	for file in files:
1078	name = os.path.basename( file )
1079	uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, file, 'server_dir', library_bunch ) )
1080	return uploaded_datasets, 200, None
1081	def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, response_code, message ):
1082	if params.get( 'filesystem_paths', '' ) == '':
1083	message = "No paths entered in the upload form"
1084	response_code = 400
1085	return None, response_code, message
1086	preserve_dirs = True
1087	if params.get( 'dont_preserve_dirs', False ):
1088	preserve_dirs = False
1089	# locate files
1090	bad_paths = []
1091	uploaded_datasets = []
1092	for line in [ l.strip() for l in params.filesystem_paths.splitlines() if l.strip() ]:
1093	path = os.path.abspath( line )
1094	if not os.path.exists( path ):
1095	bad_paths.append( path )
1096	continue
1097	# don't bother processing if we're just going to return an error
1098	if not bad_paths:
1099	if os.path.isfile( path ):
1100	name = os.path.basename( path )
1101	uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, path, 'path_paste', library_bunch ) )
1102	for basedir, dirs, files in os.walk( line ):
1103	for file in files:
1104	file_path = os.path.abspath( os.path.join( basedir, file ) )
1105	if preserve_dirs:
1106	in_folder = os.path.dirname( file_path.replace( path, '', 1 ).lstrip( '/' ) )
1107	else:
1108	in_folder = None
1109	uploaded_datasets.append( self.make_library_uploaded_dataset( trans,
1110	cntrller,
1111	params,
1112	file,
1113	file_path,
1114	'path_paste',
1115	library_bunch,
1116	in_folder ) )
1117	if bad_paths:
1118	message = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths )
1119	response_code = 400
1120	return None, response_code, message
1121	return uploaded_datasets, 200, None
1122	@web.expose
1123	def add_history_datasets_to_library( self, trans, cntrller, library_id, folder_id, hda_ids='', **kwd ):
1124	params = util.Params( kwd )
1125	message = util.restore_text( params.get( 'message', '' ) )
1126	status = params.get( 'status', 'done' )
1127	ldda_message = util.restore_text( params.get( 'ldda_message', '' ) )
1128	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1129	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1130	replace_id = params.get( 'replace_id', None )
1131	replace_dataset = None
1132	upload_option = params.get( 'upload_option', 'import_from_history' )
1133	if params.get( 'files_0\|space_to_tab', False ):
1134	space_to_tab = params.get( 'files_0\|space_to_tab', '' )
1135	else:
1136	space_to_tab = params.get( 'space_to_tab', '' )
1137	link_data_only = params.get( 'link_data_only', '' )
1138	dbkey = params.get( 'dbkey', '?' )
1139	if isinstance( dbkey, list ):
1140	last_used_build = dbkey[0]
1141	else:
1142	last_used_build = dbkey
1143	roles = params.get( 'roles', '' )
1144	is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' )
1145	current_user_roles = trans.get_current_user_roles()
1146	if replace_id not in [ None, 'None' ]:
1147	try:
1148	replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
1149	except:
1150	replace_dataset = None
1151	self._check_access( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted )
1152	self._check_modify( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted )
1153	library = replace_dataset.folder.parent_library
1154	folder = replace_dataset.folder
1155	last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
1156	else:
1157	folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
1158	self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
1159	self._check_add( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
1160	library = folder.parent_library
1161	last_used_build = folder.genome_build
1162	# See if the current history is empty
1163	history = trans.get_history()
1164	trans.sa_session.refresh( history )
1165	if not history.active_datasets:
1166	message = 'Your current history is empty'
1167	return trans.response.send_redirect( web.url_for( controller='library_common',
1168	action='browse_library',
1169	cntrller=cntrller,
1170	id=library_id,
1171	show_deleted=show_deleted,
1172	message=util.sanitize_text( message ),
1173	status='error' ) )
1174	if params.get( 'add_history_datasets_to_library_button', False ):
1175	hda_ids = util.listify( hda_ids )
1176	if hda_ids:
1177	dataset_names = []
1178	created_ldda_ids = ''
1179	for hda_id in hda_ids:
1180	try:
1181	hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) )
1182	except:
1183	hda = None
1184	self._check_access( trans, cntrller, is_admin, hda, current_user_roles, use_panels, library_id, show_deleted )
1185	if roles:
1186	role_ids = roles.split( ',' )
1187	role_obj_list = [ trans.sa_session.query( trans.model.Role ).get( role_id ) for role_id in role_ids ]
1188	else:
1189	role_obj_list = []
1190	ldda = hda.to_library_dataset_dataset_association( trans,
1191	target_folder=folder,
1192	replace_dataset=replace_dataset,
1193	roles=role_obj_list,
1194	ldda_message=ldda_message )
1195	created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
1196	dataset_names.append( ldda.name )
1197	if not replace_dataset:
1198	# If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new
1199	# LDDA and LibraryDataset.
1200	trans.app.security_agent.copy_library_permissions( folder, ldda )
1201	trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset )
1202	# Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
1203	trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda )
1204	if created_ldda_ids:
1205	created_ldda_ids = created_ldda_ids.lstrip( ',' )
1206	ldda_id_list = created_ldda_ids.split( ',' )
1207	total_added = len( ldda_id_list )
1208	if replace_dataset:
1209	message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name )
1210	else:
1211	if not folder.parent:
1212	# Libraries have the same name as their root_folder
1213	message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name )
1214	else:
1215	message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name )
1216	if cntrller == 'library_admin':
1217	message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
1218	else:
1219	# Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
1220	# to check one of them to see if the current user can manage permissions on them.
1221	check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
1222	if trans.app.security_agent.can_manage_library_item( current_user_roles, check_ldda ):
1223	if replace_dataset:
1224	default_action = ''
1225	else:
1226	message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
1227	default_action = 'manage_permissions'
1228	else:
1229	default_action = 'add'
1230	return trans.response.send_redirect( web.url_for( controller='library_common',
1231	action='browse_library',
1232	cntrller=cntrller,
1233	id=library_id,
1234	created_ldda_ids=created_ldda_ids,
1235	show_deleted=show_deleted,
1236	message=util.sanitize_text( message ),
1237	status='done' ) )
1238	else:
1239	message = 'Select at least one dataset from the list of active datasets in your current history'
1240	status = 'error'
1241	upload_option = params.get( 'upload_option', 'import_from_history' )
1242	widgets = self._get_populated_widgets( folder )
1243	# Send list of data formats to the upload form so the "extension" select list can be populated dynamically
1244	file_formats = trans.app.datatypes_registry.upload_file_formats
1245	# Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
1246	def get_dbkey_options( last_used_build ):
1247	for dbkey, build_name in util.dbnames:
1248	yield build_name, dbkey, ( dbkey==last_used_build )
1249	dbkeys = get_dbkey_options( last_used_build )
1250	# Send the current history to the form to enable importing datasets from history to library
1251	history = trans.get_history()
1252	trans.sa_session.refresh( history )
1253	action = 'add_history_datasets_to_library'
1254	upload_option_select_list = self._build_upload_option_select_list( trans, upload_option )
1255	roles_select_list = self._build_roles_select_list( trans, cntrller, library, util.listify( roles ) )
1256	return trans.fill_template( "/library/common/upload.mako",
1257	cntrller=cntrller,
1258	upload_option_select_list=upload_option_select_list,
1259	upload_option=upload_option,
1260	action=action,
1261	library_id=library_id,
1262	folder_id=folder_id,
1263	replace_dataset=replace_dataset,
1264	file_formats=file_formats,
1265	dbkeys=dbkeys,
1266	last_used_build=last_used_build,
1267	roles_select_list=roles_select_list,
1268	history=history,
1269	widgets=widgets,
1270	space_to_tab=space_to_tab,
1271	link_data_only=link_data_only,
1272	show_deleted=show_deleted,
1273	ldda_message=ldda_message,
1274	message=message,
1275	status=status )
1276	def _build_roles_select_list( self, trans, cntrller, library, selected_role_ids=[] ):
1277	# Get the list of legitimate roles to display on the upload form. If the library is public,
1278	# all active roles are legitimate. If the library is restricted by the LIBRARY_ACCESS permission, only
1279	# the set of all roles associated with users that have that permission are legitimate.
1280	legitimate_roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller )
1281	if legitimate_roles:
1282	# Build the roles multi-select list using the list of legitimate roles, making sure to select any that
1283	# were selected before refresh_on_change, if one occurred.
1284	roles_select_list = SelectField( "roles", multiple="true", size="5" )
1285	for role in legitimate_roles:
1286	selected = str( role.id ) in selected_role_ids
1287	roles_select_list.add_option( text=role.name, value=str( role.id ), selected=selected )
1288	return roles_select_list
1289	else:
1290	return None
1291	def _build_upload_option_select_list( self, trans, upload_option ):
1292	# Build the upload_option select list
1293	upload_refresh_on_change_values = [ option_value for option_value, option_label in trans.model.LibraryDataset.upload_options ]
1294	upload_option_select_list = SelectField( 'upload_option',
1295	refresh_on_change=True,
1296	refresh_on_change_values=upload_refresh_on_change_values )
1297	for option_value, option_label in trans.model.LibraryDataset.upload_options:
1298	upload_option_select_list.add_option( option_label, option_value, selected=option_value==upload_option )
1299	return upload_option_select_list
1300	def _get_populated_widgets( self, folder ):
1301	# See if we have any inherited templates.
1302	info_association, inherited = folder.get_info_association( inherited=True )
1303	if info_association and info_association.inheritable:
1304	widgets = folder.get_template_widgets( trans, get_contents=True )
1305	# Retain contents of widget fields when form was submitted via refresh_on_change.
1306	return self.populate_widgets_from_kwd( trans, widgets, **kwd )
1307	else:
1308	return []
1309	@web.expose
1310	def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ):
1311	"""Catches the dataset id and displays file contents as directed"""
1312	show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
1313	params = util.Params( kwd )
1314	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1315	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
1316	current_user_roles = trans.get_current_user_roles()
1317	try:
1318	ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
1319	except:
1320	ldda = None
1321	self._check_access( trans, cntrller, is_admin, ldda, current_user_roles, use_panels, library_id, show_deleted )
1322	composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
1323	ext = ldda.extension
1324	if ext in composite_extensions:
1325	# is composite - must return a zip of contents and the html file itself - ugh - should be reversible at upload!
1326	# use act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ) since it does what we need
1327	kwd['do_action'] = 'zip'
1328	return self.act_on_multiple_datasets( trans, cntrller, library_id, ldda_ids=[id,], **kwd )
1329	else:
1330	mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() )
1331	trans.response.set_content_type( mime )
1332	fStat = os.stat( ldda.file_name )
1333	trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
1334	valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
1335	fname = ldda.name
1336	fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
1337	trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s" % fname
1338	try:
1339	return open( ldda.file_name )
1340	except:
1341	message = 'This dataset contains no content'
1342	return trans.response.send_redirect( web.url_for( controller='library_common',
1343	action='browse_library',
1344	cntrller=cntrller,
1345	use_panels=use_panels,
1346	id=library_id,
1347	show_deleted=show_deleted,
1348	message=util.sanitize_text( message ),
1349	status='error' ) )
1350	@web.expose
1351	def library_dataset_info( self, trans, cntrller, id, library_id, **kwd ):
1352	params = util.Params( kwd )
1353	message = util.restore_text( params.get( 'message', '' ) )
1354	status = params.get( 'status', 'done' )
1355	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1356	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1357	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
1358	current_user_roles = trans.get_current_user_roles()
1359	try:
1360	library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( id ) )
1361	except:
1362	library_dataset = None
1363	self._check_access( trans, cntrller, is_admin, library_dataset, current_user_roles, use_panels, library_id, show_deleted )
1364	if params.get( 'edit_attributes_button', False ):
1365	self._check_modify( trans, cntrller, is_admin, library_dataset, current_user_roles, use_panels, library_id, show_deleted )
1366	old_name = library_dataset.name
1367	new_name = util.restore_text( params.get( 'name', '' ) )
1368	new_info = util.restore_text( params.get( 'info', '' ) )
1369	if not new_name:
1370	message = 'Enter a valid name'
1371	status = 'error'
1372	else:
1373	library_dataset.name = new_name
1374	library_dataset.info = new_info
1375	trans.sa_session.add( library_dataset )
1376	trans.sa_session.flush()
1377	message = "Information updated for library dataset '%s'." % library_dataset.name
1378	status = 'done'
1379	# See if we have any associated templates
1380	widgets = []
1381	widget_fields_have_contents = False
1382	info_association, inherited = library_dataset.library_dataset_dataset_association.get_info_association()
1383	if info_association and ( not( inherited ) or info_association.inheritable ):
1384	widgets = library_dataset.library_dataset_dataset_association.get_template_widgets( trans )
1385	widget_fields_have_contents = self.widget_fields_have_contents( widgets )
1386	return trans.fill_template( '/library/common/library_dataset_info.mako',
1387	cntrller=cntrller,
1388	use_panels=use_panels,
1389	library_dataset=library_dataset,
1390	library_id=library_id,
1391	current_user_roles=current_user_roles,
1392	info_association=info_association,
1393	inherited=inherited,
1394	widgets=widgets,
1395	widget_fields_have_contents=widget_fields_have_contents,
1396	show_deleted=show_deleted,
1397	message=message,
1398	status=status )
1399	@web.expose
1400	def library_dataset_permissions( self, trans, cntrller, id, library_id, **kwd ):
1401	params = util.Params( kwd )
1402	message = util.restore_text( params.get( 'message', '' ) )
1403	status = params.get( 'status', 'done' )
1404	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1405	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1406	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
1407	current_user_roles = trans.get_current_user_roles()
1408	try:
1409	library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( id ) )
1410	except:
1411	library_dataset = None
1412	self._check_access( trans, cntrller, is_admin, library_dataset, current_user_roles, use_panels, library_id, show_deleted )
1413	self._check_manage( trans, cntrller, is_admin, library_dataset, current_user_roles, use_panels, library_id, show_deleted )
1414	if params.get( 'update_roles_button', False ):
1415	# The user clicked the Save button on the 'Associate With Roles' form
1416	permissions = {}
1417	for k, v in trans.app.model.Library.permitted_actions.items():
1418	if k != 'LIBRARY_ACCESS':
1419	# LIBRARY_ACCESS is a special permission set only at the library level
1420	# and it is not inherited.
1421	in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
1422	permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
1423	# Set the LIBRARY permissions on the LibraryDataset
1424	# NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
1425	trans.app.security_agent.set_all_library_permissions( library_dataset, permissions )
1426	trans.sa_session.refresh( library_dataset )
1427	# Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
1428	trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions )
1429	trans.sa_session.refresh( library_dataset.library_dataset_dataset_association )
1430	message = "Permisisons updated for library dataset '%s'." % library_dataset.name
1431	status = 'done'
1432	roles = trans.app.security_agent.get_legitimate_roles( trans, library_dataset, cntrller )
1433	return trans.fill_template( '/library/common/library_dataset_permissions.mako',
1434	cntrller=cntrller,
1435	use_panels=use_panels,
1436	library_dataset=library_dataset,
1437	library_id=library_id,
1438	roles=roles,
1439	current_user_roles=current_user_roles,
1440	show_deleted=show_deleted,
1441	message=message,
1442	status=status )
1443	@web.expose
1444	def make_library_item_public( self, trans, cntrller, library_id, item_type, id, **kwd ):
1445	params = util.Params( kwd )
1446	message = util.restore_text( params.get( 'message', '' ) )
1447	status = params.get( 'status', 'done' )
1448	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1449	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1450	current_user_roles = trans.get_current_user_roles()
1451	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
1452	if item_type == 'library':
1453	library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( id ) )
1454	self._check_access( trans, cntrller, is_admin, library, current_user_roles, use_panels, library_id, show_deleted )
1455	self._check_manage( trans, cntrller, is_admin, library, current_user_roles, use_panels, library_id, show_deleted )
1456	contents = util.string_as_bool( params.get( 'contents', 'False' ) )
1457	trans.app.security_agent.make_library_public( library, contents=contents )
1458	if contents:
1459	message = "The data library (%s) and all it's contents have been made publicly accessible." % library.name
1460	else:
1461	message = "The data library (%s) has been made publicly accessible, but access to it's contents has been left unchanged." % library.name
1462	elif item_type == 'folder':
1463	folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( id ) )
1464	self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
1465	self._check_manage( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
1466	trans.app.security_agent.make_folder_public( folder )
1467	message = "All of the contents of folder (%s) have been made publicly accessible." % folder.name
1468	elif item_type == 'ldda':
1469	ldda = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
1470	self._check_access( trans, cntrller, is_admin, ldda.library_dataset, current_user_roles, use_panels, library_id, show_deleted )
1471	self._check_manage( trans, cntrller, is_admin, ldda.library_dataset, current_user_roles, use_panels, library_id, show_deleted )
1472	trans.app.security_agent.make_dataset_public( ldda.dataset )
1473	message = "The libary dataset (%s) has been made publicly accessible." % ldda.name
1474	else:
1475	message = "Invalid item_type (%s) received." % str( item_type )
1476	status = 'error'
1477	return trans.response.send_redirect( web.url_for( controller='library_common',
1478	action='browse_library',
1479	cntrller=cntrller,
1480	use_panels=use_panels,
1481	id=library_id,
1482	show_deleted=show_deleted,
1483	message=util.sanitize_text( message ),
1484	status=status ) )
1485	@web.expose
1486	def act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ):
1487	class NgxZip( object ):
1488	def __init__( self, url_base ):
1489	self.files = {}
1490	self.url_base = url_base
1491	def add( self, file, relpath ):
1492	self.files[file] = relpath
1493	def __str__( self ):
1494	rval = ''
1495	for fname, relpath in self.files.items():
1496	crc = '-'
1497	size = os.stat( fname ).st_size
1498	quoted_fname = urllib.quote_plus( fname, '/' )
1499	rval += '%s %i %s%s %s\r\n' % ( crc, size, self.url_base, quoted_fname, relpath )
1500	return rval
1501	# Perform an action on a list of library datasets.
1502	params = util.Params( kwd )
1503	message = util.restore_text( params.get( 'message', '' ) )
1504	status = params.get( 'status', 'done' )
1505	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1506	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1507	action = params.get( 'do_action', None )
1508	lddas = []
1509	error = False
1510	is_admin = trans.user_is_admin() and cntrller == 'library_admin'
1511	current_user_roles = trans.get_current_user_roles()
1512	if not ldda_ids:
1513	error = True
1514	message = 'You must select at least one dataset.'
1515	elif not action:
1516	error = True
1517	message = 'You must select an action to perform on the selected datasets.'
1518	else:
1519	# Set up the list of lddas for later, and get permission checks out of the way so we don't have to do it in multiple places later.
1520	ldda_ids = util.listify( ldda_ids )
1521	for ldda_id in ldda_ids:
1522	try:
1523	ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
1524	except:
1525	ldda = None
1526	if not ldda or ( not is_admin and not trans.app.security_agent.can_access_library_item( current_user_roles, ldda, trans.user ) ):
1527	error = True
1528	message = "Invalid library dataset id ( %s ) specified." % str( ldda_id )
1529	break
1530	lddas.append( ldda )
1531	if action == 'import_to_history' or action == 'add':
1532	if trans.get_history() is None:
1533	# Must be a bot sending a request without having a history.
1534	error = True
1535	message = "You do not have a current history"
1536	elif action == 'manage_permissions':
1537	if not is_admin:
1538	for ldda in lddas:
1539	if not ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \
1540	trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) ):
1541	error = True
1542	message = "You are not authorized to manage permissions on library dataset '%s'." % ldda.name
1543	break
1544	elif action == 'delete':
1545	if not is_admin:
1546	for ldda in lddas:
1547	if not trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ):
1548	error = True
1549	message = "You are not authorized to modify library dataset '%s'." % ldda.name
1550	break
1551	if error:
1552	return trans.response.send_redirect( web.url_for( controller='library_common',
1553	action='browse_library',
1554	cntrller=cntrller,
1555	use_panels=use_panels,
1556	id=library_id,
1557	show_deleted=show_deleted,
1558	message=util.sanitize_text( message ),
1559	status='error' ) )
1560	if action == 'import_to_history' or action == 'add':
1561	history = trans.get_history()
1562	total_imported_lddas = 0
1563	message = ''
1564	status = 'done'
1565	for ldda in lddas:
1566	if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]:
1567	message += "Cannot import dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state )
1568	status = 'error'
1569	elif ldda.dataset.state in [ 'ok', 'error' ]:
1570	hda = ldda.to_history_dataset_association( target_history=history, add_to_history=True )
1571	total_imported_lddas += 1
1572	if total_imported_lddas:
1573	trans.sa_session.add( history )
1574	trans.sa_session.flush()
1575	message += "%i dataset(s) have been imported into your history. " % total_imported_lddas
1576	elif action == 'manage_permissions':
1577	trans.response.send_redirect( web.url_for( controller='library_common',
1578	action='ldda_permissions',
1579	cntrller=cntrller,
1580	use_panels=use_panels,
1581	library_id=library_id,
1582	folder_id=trans.security.encode_id( lddas[0].library_dataset.folder.id ),
1583	id=",".join( ldda_ids ),
1584	show_deleted=show_deleted,
1585	message=util.sanitize_text( message ),
1586	status=status ) )
1587	elif action == 'delete':
1588	for ldda in lddas:
1589	# Do not delete the association, just delete the library_dataset. The
1590	# cleanup_datasets.py script handles everything else.
1591	ld = ldda.library_dataset
1592	ld.deleted = True
1593	trans.sa_session.add( ld )
1594	trans.sa_session.flush()
1595	message = "The selected datasets have been removed from this data library"
1596	elif action in ['zip','tgz','tbz','ngxzip']:
1597	error = False
1598	killme = string.punctuation + string.whitespace
1599	trantab = string.maketrans(killme,'_'*len(killme))
1600	try:
1601	outext = 'zip'
1602	if action == 'zip':
1603	# Can't use mkstemp - the file must not exist first
1604	tmpd = tempfile.mkdtemp()
1605	tmpf = os.path.join( tmpd, 'library_download.' + action )
1606	if ziptype == '64' and trans.app.config.upstream_gzip:
1607	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True )
1608	elif ziptype == '64':
1609	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
1610	elif trans.app.config.upstream_gzip:
1611	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED )
1612	else:
1613	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED )
1614	archive.add = lambda x, y: archive.write( x, y.encode('CP437') )
1615	elif action == 'tgz':
1616	if trans.app.config.upstream_gzip:
1617	archive = util.streamball.StreamBall( 'w\|' )
1618	outext = 'tar'
1619	else:
1620	archive = util.streamball.StreamBall( 'w\|gz' )
1621	outext = 'tgz'
1622	elif action == 'tbz':
1623	archive = util.streamball.StreamBall( 'w\|bz2' )
1624	outext = 'tbz2'
1625	elif action == 'ngxzip':
1626	archive = NgxZip( trans.app.config.nginx_x_archive_files_base )
1627	except (OSError, zipfile.BadZipfile):
1628	error = True
1629	log.exception( "Unable to create archive for download" )
1630	message = "Unable to create archive for download, please report this error"
1631	status = 'error'
1632	except:
1633	error = True
1634	log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0])
1635	message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0]
1636	status = 'error'
1637	if not error:
1638	composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
1639	seen = []
1640	for ldda in lddas:
1641	if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]:
1642	continue
1643	ext = ldda.extension
1644	is_composite = ext in composite_extensions
1645	path = ""
1646	parent_folder = ldda.library_dataset.folder
1647	while parent_folder is not None:
1648	# Exclude the now-hidden "root folder"
1649	if parent_folder.parent is None:
1650	path = os.path.join( parent_folder.library_root[0].name, path )
1651	break
1652	path = os.path.join( parent_folder.name, path )
1653	parent_folder = parent_folder.parent
1654	path += ldda.name
1655	while path in seen:
1656	path += '_'
1657	seen.append( path )
1658	zpath = os.path.split(path)[-1] # comes as base_name/fname
1659	outfname,zpathext = os.path.splitext(zpath)
1660	if is_composite:
1661	# need to add all the components from the extra_files_path to the zip
1662	if zpathext == '':
1663	zpath = '%s.html' % zpath # fake the real nature of the html file
1664	try:
1665	archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set
1666	except IOError:
1667	error = True
1668	log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
1669	message = "Unable to create archive for download, please report this error"
1670	status = 'error'
1671	continue
1672	flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'.')) # glob returns full paths
1673	for fpath in flist:
1674	efp,fname = os.path.split(fpath)
1675	if fname > '':
1676	fname = fname.translate(trantab)
1677	try:
1678	archive.add( fpath,fname )
1679	except IOError:
1680	error = True
1681	log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname))
1682	message = "Unable to create archive for download, please report this error"
1683	status = 'error'
1684	continue
1685	else: # simple case
1686	try:
1687	archive.add( ldda.dataset.file_name, path )
1688	except IOError:
1689	error = True
1690	log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name)
1691	message = "Unable to create archive for download, please report this error"
1692	status = 'error'
1693	if not error:
1694	lname = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ).name
1695	fname = lname.replace( ' ', '_' ) + '_files'
1696	if action == 'zip':
1697	archive.close()
1698	tmpfh = open( tmpf )
1699	# clean up now
1700	try:
1701	os.unlink( tmpf )
1702	os.rmdir( tmpd )
1703	except OSError:
1704	error = True
1705	log.exception( "Unable to remove temporary library download archive and directory" )
1706	message = "Unable to create archive for download, please report this error"
1707	status = 'error'
1708	if not error:
1709	trans.response.set_content_type( "application/x-zip-compressed" )
1710	trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext)
1711	return tmpfh
1712	elif action == 'ngxzip':
1713	trans.response.set_content_type( "application/zip" )
1714	trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext)
1715	trans.response.headers[ "X-Archive-Files" ] = "zip"
1716	return archive
1717	else:
1718	trans.response.set_content_type( "application/x-tar" )
1719	trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext)
1720	archive.wsgi_status = trans.response.wsgi_status()
1721	archive.wsgi_headeritems = trans.response.wsgi_headeritems()
1722	return archive.stream
1723	else:
1724	status = 'error'
1725	message = 'Invalid action ( %s ) specified.' % action
1726	return trans.response.send_redirect( web.url_for( controller='library_common',
1727	action='browse_library',
1728	cntrller=cntrller,
1729	use_panels=use_panels,
1730	id=library_id,
1731	show_deleted=show_deleted,
1732	message=util.sanitize_text( message ),
1733	status=status ) )
1734	def get_item_and_stuff( self, trans, item_type, library_id, folder_id, ldda_id, is_admin ):
1735	# Return an item, description, action and an id based on the item_type.
1736	message = None
1737	current_user_roles = trans.get_current_user_roles()
1738	if item_type == 'library':
1739	try:
1740	item = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
1741	except:
1742	item = None
1743	item_desc = 'data library'
1744	action = 'library_info'
1745	id = library_id
1746	elif item_type == 'folder':
1747	try:
1748	item = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
1749	except:
1750	item = None
1751	item_desc = 'folder'
1752	action = 'folder_info'
1753	id = folder_id
1754	elif item_type == 'ldda':
1755	try:
1756	item = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
1757	except:
1758	item = None
1759	item_desc = 'dataset'
1760	action = 'ldda_edit_info'
1761	id = ldda_id
1762	else:
1763	item = None
1764	message = "Invalid library item type ( %s )" % str( item_type )
1765	if not item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ):
1766	if message is None:
1767	message = "Invalid %s id ( %s ) specified." % ( item_desc, str( id ) )
1768	return trans.response.send_redirect( web.url_for( controller='library_common',
1769	action='browse_library',
1770	cntrller='library', # cheating a bit here
1771	id=library_id,
1772	message=util.sanitize_text( message ),
1773	status='error' ) )
1774	return item, item_desc, action, id
1775	@web.expose
1776	def add_template( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ):
1777	# Template can only be added to a Library, Folder or LibraryDatasetDatasetAssociation.
1778	forms = self.get_all_forms( trans,
1779	filter=dict( deleted=False ),
1780	form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE )
1781	if not forms:
1782	message = "There are no forms on which to base the template, so create a form and then add the template."
1783	return trans.response.send_redirect( web.url_for( controller='forms',
1784	action='create_request',
1785	message=message,
1786	status='done',
1787	form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) )
1788	params = util.Params( kwd )
1789	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1790	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1791	message = util.restore_text( params.get( 'message', '' ) )
1792	action = ''
1793	status = params.get( 'status', 'done' )
1794	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
1795	current_user_roles = trans.get_current_user_roles()
1796	try:
1797	item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id, is_admin )
1798	except ValueError:
1799	# At this point, the client has already redirected, so this is just here to prevent the unnecessary traceback
1800	return None
1801	if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
1802	message = "You are not authorized to modify %s '%s'." % ( item_desc, item.name )
1803	return trans.response.send_redirect( web.url_for( controller='library_common',
1804	action='browse_library',
1805	cntrller=cntrller,
1806	id=library_id,
1807	show_deleted=show_deleted,
1808	message=util.sanitize_text( message ),
1809	status='error' ) )
1810	# If the inheritable checkbox is checked, the param will be in the request
1811	inheritable = CheckboxField.is_checked( params.get( 'inheritable', '' ) )
1812	if params.get( 'add_template_button', False ):
1813	form_id = params.get( 'form_id', 'none' )
1814	if form_id not in [ None, 'None', 'none' ]:
1815	form = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id( form_id ) )
1816	form_values = trans.app.model.FormValues( form, [] )
1817	trans.sa_session.add( form_values )
1818	trans.sa_session.flush()
1819	if item_type == 'library':
1820	assoc = trans.app.model.LibraryInfoAssociation( item, form, form_values, inheritable=inheritable )
1821	elif item_type == 'folder':
1822	assoc = trans.app.model.LibraryFolderInfoAssociation( item, form, form_values, inheritable=inheritable )
1823	elif item_type == 'ldda':
1824	assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, form, form_values )
1825	trans.sa_session.add( assoc )
1826	trans.sa_session.flush()
1827	message = 'A template based on the form "%s" has been added to this %s.' % ( form.name, item_desc )
1828	trans.response.send_redirect( web.url_for( controller='library_common',
1829	action=action,
1830	cntrller=cntrller,
1831	use_panels=use_panels,
1832	library_id=library_id,
1833	folder_id=folder_id,
1834	id=id,
1835	show_deleted=show_deleted,
1836	message=message,
1837	status='done' ) )
1838	else:
1839	message = "Select a form on which to base the template."
1840	status = "error"
1841	def generate_template_stuff( trans, forms, form_id ):
1842	# Returns the following:
1843	# - a list of template ids
1844	# - a list of dictionaries whose keys are template ids and whose values are templates widgets.
1845	# The dictionary built using the received forms param
1846	# - a select list whose options are templates
1847	template_ids = [ 'none' ]
1848	widgets = []
1849	for form in forms:
1850	template_ids.append( trans.security.encode_id( form.id ) )
1851	template_select_list = SelectField( 'form_id',
1852	refresh_on_change=True,
1853	refresh_on_change_values=template_ids[1:] )
1854	if form_id == 'none':
1855	template_select_list.add_option( 'Select one', 'none', selected=True )
1856	decoded_form_id = None
1857	else:
1858	template_select_list.add_option( 'Select one', 'none' )
1859	decoded_form_id = trans.security.decode_id( form_id )
1860	for form in forms:
1861	if decoded_form_id and decoded_form_id == form.id:
1862	template_select_list.add_option( form.name, trans.security.encode_id( form.id ), selected=True )
1863	widgets = form.get_widgets( trans.user )
1864	else:
1865	template_select_list.add_option( form.name, trans.security.encode_id( form.id ) )
1866	return template_ids, widgets, template_select_list
1867	if params.get( 'refresh', False ):
1868	template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, kwd.get( 'form_id' ) )
1869	else:
1870	template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, 'none' )
1871	return trans.fill_template( '/library/common/select_template.mako',
1872	cntrller=cntrller,
1873	use_panels=use_panels,
1874	item_name=item.name,
1875	item_desc=item_desc,
1876	item_type=item_type,
1877	library_id=library_id,
1878	folder_id=folder_id,
1879	ldda_id=ldda_id,
1880	template_ids=template_ids,
1881	widgets=widgets,
1882	template_select_list=template_select_list,
1883	inheritable_checked=inheritable,
1884	show_deleted=show_deleted,
1885	message=message,
1886	status=status )
1887	@web.expose
1888	def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ):
1889	params = util.Params( kwd )
1890	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1891	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1892	message = util.restore_text( params.get( 'message', '' ) )
1893	status = params.get( 'status', 'done' )
1894	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
1895	current_user_roles = trans.get_current_user_roles()
1896	try:
1897	item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id, is_admin )
1898	except ValueError:
1899	return None
1900	if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
1901	message = "You are not authorized to modify %s '%s'." % ( item_desc, item.name )
1902	return trans.response.send_redirect( web.url_for( controller='library_common',
1903	action='browse_library',
1904	cntrller=cntrller,
1905	id=library_id,
1906	show_deleted=show_deleted,
1907	message=util.sanitize_text( message ),
1908	status='error' ) )
1909	info_association, inherited = item.get_info_association( restrict=True )
1910	if info_association:
1911	if info_association.inheritable:
1912	message = "The template for this %s will no longer be inherited to contained folders and datasets." % item_desc
1913	else:
1914	message = "The template for this %s will now be inherited to contained folders and datasets." % item_desc
1915	info_association.inheritable = not( info_association.inheritable )
1916	trans.sa_session.add( info_association )
1917	trans.sa_session.flush()
1918	return trans.response.send_redirect( web.url_for( controller='library_common',
1919	action=action,
1920	cntrller=cntrller,
1921	use_panels=use_panels,
1922	library_id=library_id,
1923	folder_id=folder_id,
1924	id=id,
1925	show_deleted=show_deleted,
1926	message=util.sanitize_text( message ),
1927	status='done' ) )
1928	@web.expose
1929	def edit_template( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, edited=False, **kwd ):
1930	# Edit the template itself, keeping existing field contents, if any.
1931	params = util.Params( kwd )
1932	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1933	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1934	message = util.restore_text( params.get( 'message', '' ) )
1935	status = params.get( 'status', 'done' )
1936	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
1937	current_user_roles = trans.get_current_user_roles()
1938	try:
1939	item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id, is_admin )
1940	except ValueError:
1941	return None
1942	if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
1943	message = "You are not authorized to modify %s '%s'." % ( item_desc, item.name )
1944	return trans.response.send_redirect( web.url_for( controller='library_common',
1945	action='browse_library',
1946	cntrller=cntrller,
1947	id=library_id,
1948	show_deleted=show_deleted,
1949	message=util.sanitize_text( message ),
1950	status='error' ) )
1951	# An info_association must exist at this point
1952	info_association, inherited = item.get_info_association( restrict=True )
1953	template = info_association.template
1954	info = info_association.info
1955	form_values = trans.sa_session.query( trans.app.model.FormValues ).get( info.id )
1956	if edited:
1957	# The form on which the template is based has been edited, so we need to update the
1958	# info_association with the current form
1959	fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).get( template.form_definition_current_id )
1960	info_association.template = fdc.latest_form
1961	trans.sa_session.add( info_association )
1962	trans.sa_session.flush()
1963	message = "The template for this %s has been updated with your changes." % item_desc
1964	return trans.response.send_redirect( web.url_for( controller='library_common',
1965	action=action,
1966	cntrller=cntrller,
1967	use_panels=use_panels,
1968	library_id=library_id,
1969	folder_id=folder_id,
1970	id=id,
1971	show_deleted=show_deleted,
1972	message=util.sanitize_text( message ),
1973	status='done' ) )
1974	# "template" is a FormDefinition, so since we're changing it, we need to use the latest version of it.
1975	vars = dict( id=trans.security.encode_id( template.form_definition_current_id ),
1976	response_redirect=web.url_for( controller='library_common',
1977	action='edit_template',
1978	cntrller=cntrller,
1979	item_type=item_type,
1980	library_id=library_id,
1981	folder_id=folder_id,
1982	ldda_id=ldda_id,
1983	edited=True,
1984	**kwd ) )
1985	return trans.response.send_redirect( web.url_for( controller='forms', action='edit', **vars ) )
1986	@web.expose
1987	def edit_template_info( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ):
1988	# Edit the contents of the template fields without altering the template itself.
1989	params = util.Params( kwd )
1990	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
1991	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
1992	message = util.restore_text( params.get( 'message', '' ) )
1993	status = params.get( 'status', 'done' )
1994	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
1995	current_user_roles = trans.get_current_user_roles()
1996	try:
1997	item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id, is_admin )
1998	except ValueError:
1999	return None
2000	if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
2001	message = "You are not authorized to modify %s '%s'." % ( item_desc, item.name )
2002	return trans.response.send_redirect( web.url_for( controller='library_common',
2003	action='browse_library',
2004	cntrller=cntrller,
2005	id=library_id,
2006	show_deleted=show_deleted,
2007	message=util.sanitize_text( message ),
2008	status='error' ) )
2009	# We need the type of each template field widget
2010	widgets = item.get_template_widgets( trans )
2011	# The list of widgets may include an AddressField which we need to save if it is new
2012	for index, widget_dict in enumerate( widgets ):
2013	widget = widget_dict[ 'widget' ]
2014	if isinstance( widget, AddressField ):
2015	value = util.restore_text( params.get( 'field_%i' % index, '' ) )
2016	if value == 'new':
2017	if params.get( 'edit_info_button', False ):
2018	if self.field_param_values_ok( index, 'AddressField', **kwd ):
2019	# Save the new address
2020	address = trans.app.model.UserAddress( user=trans.user )
2021	self.save_widget_field( trans, address, index, **kwd )
2022	widget.value = str( address.id )
2023	else:
2024	message = 'Required fields are missing contents.'
2025	return trans.response.send_redirect( web.url_for( controller='library_common',
2026	action=action,
2027	cntrller=cntrller,
2028	use_panels=use_panels,
2029	library_id=library_id,
2030	folder_id=folder_id,
2031	id=id,
2032	show_deleted=show_deleted,
2033	message=util.sanitize_text( message ),
2034	status='error' ) )
2035	else:
2036	# Form was submitted via refresh_on_change
2037	widget.value = 'new'
2038	elif value == unicode( 'none' ):
2039	widget.value = ''
2040	else:
2041	widget.value = value
2042	elif isinstance( widget, CheckboxField ):
2043	# We need to check the value from kwd since util.Params would have munged the list if
2044	# the checkbox is checked.
2045	value = kwd.get( 'field_%i' % index, '' )
2046	if CheckboxField.is_checked( value ):
2047	widget.value = 'true'
2048	else:
2049	widget.value = util.restore_text( params.get( 'field_%i' % index, '' ) )
2050	# Save updated template field contents
2051	field_contents = self.clean_field_contents( widgets, **kwd )
2052	if field_contents:
2053	# Since information templates are inherited, the template fields can be displayed on the information
2054	# page for a folder or ldda when it has no info_association object. If the user has added
2055	# field contents on an inherited template via a parent's info_association, we'll need to create a new
2056	# form_values and info_association for the current object. The value for the returned inherited variable
2057	# is not applicable at this level.
2058	info_association, inherited = item.get_info_association( restrict=True )
2059	if info_association:
2060	template = info_association.template
2061	info = info_association.info
2062	form_values = trans.sa_session.query( trans.app.model.FormValues ).get( info.id )
2063	# Update existing content only if it has changed
2064	if form_values.content != field_contents:
2065	form_values.content = field_contents
2066	trans.sa_session.add( form_values )
2067	trans.sa_session.flush()
2068	else:
2069	# Inherit the next available info_association so we can get the template
2070	info_association, inherited = item.get_info_association()
2071	template = info_association.template
2072	# Create a new FormValues object
2073	form_values = trans.app.model.FormValues( template, field_contents )
2074	trans.sa_session.add( form_values )
2075	trans.sa_session.flush()
2076	# Create a new info_association between the current library item and form_values
2077	if item_type == 'folder':
2078	# A LibraryFolder is a special case because if it inherited the template from it's parent,
2079	# we want to set inheritable to True for it's info_association. This allows for the default
2080	# inheritance to be False for each level in the Library hierarchy unless we're creating a new
2081	# level in the hierarchy, in which case we'll inherit the "inheritable" setting from the parent
2082	# level.
2083	info_association = trans.app.model.LibraryFolderInfoAssociation( item, template, form_values, inheritable=inherited )
2084	trans.sa_session.add( info_association )
2085	trans.sa_session.flush()
2086	elif item_type == 'ldda':
2087	# TODO: Currently info_associations at teh ldda level are not inheritable to the associated LibraryDataset.
2088	# We need to figure out if this is optimal.
2089	info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, template, form_values )
2090	trans.sa_session.add( info_association )
2091	trans.sa_session.flush()
2092	message = 'The information has been updated.'
2093	return trans.response.send_redirect( web.url_for( controller='library_common',
2094	action=action,
2095	cntrller=cntrller,
2096	use_panels=use_panels,
2097	library_id=library_id,
2098	folder_id=folder_id,
2099	id=id,
2100	show_deleted=show_deleted,
2101	message=util.sanitize_text( message ),
2102	status='done' ) )
2103	@web.expose
2104	def delete_template( self, trans, cntrller, item_type, library_id, id=None, folder_id=None, ldda_id=None, **kwd ):
2105	# Only adding a new template to a library or folder is currently allowed. Editing an existing template is
2106	# a future enhancement.
2107	params = util.Params( kwd )
2108	show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
2109	use_panels = util.string_as_bool( params.get( 'use_panels', False ) )
2110	message = util.restore_text( params.get( 'message', '' ) )
2111	status = params.get( 'status', 'done' )
2112	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
2113	current_user_roles = trans.get_current_user_roles()
2114	try:
2115	item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id, is_admin )
2116	except ValueError:
2117	return None
2118	if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
2119	message = "You are not authorized to modify %s '%s'." % ( item_desc, item.name )
2120	return trans.response.send_redirect( web.url_for( controller='library_common',
2121	action='browse_library',
2122	cntrller=cntrller,
2123	id=library_id,
2124	show_deleted=show_deleted,
2125	message=util.sanitize_text( message ),
2126	status='error' ) )
2127	info_association, inherited = item.get_info_association()
2128	if not info_association:
2129	message = "There is no template for this %s" % item_type
2130	status = 'error'
2131	else:
2132	info_association.deleted = True
2133	trans.sa_session.add( info_association )
2134	trans.sa_session.flush()
2135	message = 'The template for this %s has been deleted.' % item_type
2136	status = 'done'
2137	return trans.response.send_redirect( web.url_for( controller='library_common',
2138	action=action,
2139	cntrller=cntrller,
2140	use_panels=use_panels,
2141	library_id=library_id,
2142	folder_id=folder_id,
2143	id=id,
2144	show_deleted=show_deleted,
2145	message=util.sanitize_text( message ),
2146	status=status ) )
2147	@web.expose
2148	def delete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ):
2149	# This action will handle deleting all types of library items. State is saved for libraries and
2150	# folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously
2151	# deleted / purged contents will have the same state ). When a library or folder has been deleted for
2152	# the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its
2153	# contents will be purged. The association between this method and the cleanup_datasets.py script
2154	# enables clean maintenance of libraries and library dataset disk files. This is also why the item_types
2155	# are not any of the associations ( the cleanup_datasets.py script handles everything ).
2156	show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
2157	item_types = { 'library': trans.app.model.Library,
2158	'folder': trans.app.model.LibraryFolder,
2159	'library_dataset': trans.app.model.LibraryDataset }
2160	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
2161	current_user_roles = trans.get_current_user_roles()
2162	if item_type not in item_types:
2163	message = 'Bad item_type specified: %s' % str( item_type )
2164	status = 'error'
2165	else:
2166	if item_type == 'library_dataset':
2167	item_desc = 'Dataset'
2168	else:
2169	item_desc = item_type.capitalize()
2170	try:
2171	library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) )
2172	except:
2173	library_item = None
2174	if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ):
2175	message = 'Invalid %s id ( %s ) specifield.' % ( item_desc, item_id )
2176	status = 'error'
2177	elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ):
2178	message = "You are not authorized to delete %s '%s'." % ( item_desc, library_item.name )
2179	status = 'error'
2180	else:
2181	library_item.deleted = True
2182	trans.sa_session.add( library_item )
2183	trans.sa_session.flush()
2184	message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) )
2185	status = 'done'
2186	if item_type == 'library':
2187	return trans.response.send_redirect( web.url_for( controller=cntrller,
2188	action='browse_libraries',
2189	message=message,
2190	status=status ) )
2191	else:
2192	return trans.response.send_redirect( web.url_for( controller='library_common',
2193	action='browse_library',
2194	cntrller=cntrller,
2195	id=library_id,
2196	show_deleted=show_deleted,
2197	message=message,
2198	status=status ) )
2199	@web.expose
2200	def undelete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ):
2201	# This action will handle undeleting all types of library items
2202	show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
2203	item_types = { 'library': trans.app.model.Library,
2204	'folder': trans.app.model.LibraryFolder,
2205	'library_dataset': trans.app.model.LibraryDataset }
2206	is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
2207	current_user_roles = trans.get_current_user_roles()
2208	if item_type not in item_types:
2209	message = 'Bad item_type specified: %s' % str( item_type )
2210	status = ERROR
2211	else:
2212	if item_type == 'library_dataset':
2213	item_desc = 'Dataset'
2214	else:
2215	item_desc = item_type.capitalize()
2216	try:
2217	library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) )
2218	except:
2219	library_item = None
2220	if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ):
2221	message = 'Invalid %s id ( %s ) specifield.' % ( item_desc, item_id )
2222	status = 'error'
2223	elif library_item.purged:
2224	message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name )
2225	status = ERROR
2226	elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ):
2227	message = "You are not authorized to delete %s '%s'." % ( item_desc, library_item.name )
2228	status = 'error'
2229	else:
2230	library_item.deleted = False
2231	trans.sa_session.add( library_item )
2232	trans.sa_session.flush()
2233	message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) )
2234	status = SUCCESS
2235	if item_type == 'library':
2236	return trans.response.send_redirect( web.url_for( controller=cntrller,
2237	action='browse_libraries',
2238	message=message,
2239	status=status ) )
2240	else:
2241	return trans.response.send_redirect( web.url_for( controller='library_common',
2242	action='browse_library',
2243	cntrller=cntrller,
2244	id=library_id,
2245	show_deleted=show_deleted,
2246	message=message,
2247	status=status ) )
2248	def _check_access( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
2249	can_access = True
2250	if isinstance( item, trans.model.HistoryDatasetAssociation ):
2251	# Make sure the user has the DATASET_ACCESS permission on the history_dataset_association.
2252	if not item:
2253	message = "Invalid history dataset (%s) specified." % str( item )
2254	can_access = False
2255	elif not trans.app.security_agent.can_access_dataset( current_user_roles, item.dataset ) and item.history.user==trans.user:
2256	message = "You do not have permission to access the history dataset with id (%s)." % str( item.id )
2257	can_access = False
2258	else:
2259	# Make sure the user has the LIBRARY_ACCESS permission on the library item.
2260	if not item:
2261	message = "Invalid library item (%s) specified." % str( item )
2262	can_access = False
2263	elif not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ):
2264	if isinstance( item, trans.model.Library ):
2265	item_type = 'data library'
2266	elif isinstance( item, trans.model.LibraryFolder ):
2267	item_type = 'folder'
2268	else:
2269	item_type = '(unknown item type)'
2270	message = "You do not have permission to access the %s with id (%s)." % ( item_type, str( item.id ) )
2271	can_access = False
2272	if not can_access:
2273	if cntrller == 'api':
2274	return 400, message
2275	if isinstance( item, trans.model.Library ):
2276	return trans.response.send_redirect( web.url_for( controller=cntrller,
2277	action='browse_libraries',
2278	cntrller=cntrller,
2279	use_panels=use_panels,
2280	message=util.sanitize_text( message ),
2281	status='error' ) )
2282	return trans.response.send_redirect( web.url_for( controller='library_common',
2283	action='browse_library',
2284	cntrller=cntrller,
2285	use_panels=use_panels,
2286	id=library_id,
2287	show_deleted=show_deleted,
2288	message=util.sanitize_text( message ),
2289	status='error' ) )
2290	def _check_add( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
2291	# Deny access if the user is not an admin and does not have the LIBRARY_ADD permission.
2292	if not ( is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, item ) ):
2293	message = "You are not authorized to add an item to (%s)." % item.name
2294	# Redirect to the real parent library since we know we have access to it.
2295	if cntrller == 'api':
2296	return 403, message
2297	return trans.response.send_redirect( web.url_for( controller='library_common',
2298	action='browse_library',
2299	cntrller=cntrller,
2300	use_panels=use_panels,
2301	id=library_id,
2302	show_deleted=show_deleted,
2303	message=util.sanitize_text( message ),
2304	status='error' ) )
2305	def _check_manage( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
2306	if isinstance( item, trans.model.LibraryDataset ):
2307	# Deny access if the user is not an admin and does not have the LIBRARY_MANAGE and DATASET_MANAGE_PERMISSIONS permissions.
2308	if not ( is_admin or \
2309	( trans.app.security_agent.can_manage_library_item( current_user_roles, item ) and
2310	trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset ) ) ):
2311	message = "You are not authorized to manage permissions on library dataset (%s)." % library_dataset.name
2312	if cntrller == 'api':
2313	return 403, message
2314	return trans.response.send_redirect( web.url_for( controller='library_common',
2315	action='browse_library',
2316	id=library_id,
2317	cntrller=cntrller,
2318	use_panels=use_panels,
2319	message=util.sanitize_text( message ),
2320	status='error' ) )
2321	# Deny access if the user is not an admin and does not have the LIBRARY_MANAGE permission.
2322	if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, item ) ):
2323	message = "You are not authorized to manage permissions on (%s)." % item.name
2324	if cntrller == 'api':
2325	return 403, message
2326	return trans.response.send_redirect( web.url_for( controller='library_common',
2327	action='browse_library',
2328	id=library_id,
2329	cntrller=cntrller,
2330	use_panels=use_panels,
2331	message=util.sanitize_text( message ),
2332	status='error' ) )
2333	def _check_modify( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ):
2334	# Deny modification if the user is not an admin and does not have the LIBRARY_MODIFY permission.
2335	if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
2336	message = "You are not authorized to modify (%s)." % item.name
2337	if cntrller == 'api':
2338	return 403, message
2339	return trans.response.send_redirect( web.url_for( controller='library_common',
2340	action='browse_library',
2341	cntrller=cntrller,
2342	id=library_id,
2343	use_panels=use_panels,
2344	show_deleted=show_deleted,
2345	message=util.sanitize_text( message ),
2346	status='error' ) )
2347
2348	# ---- Utility methods -------------------------------------------------------
2349
2350	def active_folders( trans, folder ):
2351	# Much faster way of retrieving all active sub-folders within a given folder than the
2352	# performance of the mapper. This query also eagerloads the permissions on each folder.
2353	return trans.sa_session.query( trans.app.model.LibraryFolder ) \
2354	.filter_by( parent=folder, deleted=False ) \
2355	.options( eagerload_all( "actions" ) ) \
2356	.order_by( trans.app.model.LibraryFolder.table.c.name ) \
2357	.all()
2358	def activatable_folders( trans, folder ):
2359	return trans.sa_session.query( trans.app.model.LibraryFolder ) \
2360	.filter_by( parent=folder, purged=False ) \
2361	.options( eagerload_all( "actions" ) ) \
2362	.order_by( trans.app.model.LibraryFolder.table.c.name ) \
2363	.all()
2364	def active_folders_and_lddas( trans, folder ):
2365	folders = active_folders( trans, folder )
2366	# This query is much faster than the folder.active_library_datasets property
2367	lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
2368	.filter_by( deleted=False ) \
2369	.join( "library_dataset" ) \
2370	.filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
2371	.order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
2372	.all()
2373	return folders, lddas
2374	def activatable_folders_and_lddas( trans, folder ):
2375	folders = activatable_folders( trans, folder )
2376	# This query is much faster than the folder.activatable_library_datasets property
2377	lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
2378	.join( "library_dataset" ) \
2379	.filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
2380	.join( "dataset" ) \
2381	.filter( trans.app.model.Dataset.table.c.deleted==False ) \
2382	.order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
2383	.all()
2384	return folders, lddas
2385	def branch_deleted( folder ):
2386	# Return True if a folder belongs to a branch that has been deleted
2387	if folder.deleted:
2388	return True
2389	if folder.parent:
2390	return branch_deleted( folder.parent )
2391	return False
2392	def get_containing_library_from_library_dataset( trans, library_dataset ):
2393	"""Given a library_dataset, get the containing library"""
2394	folder = library_dataset.folder
2395	while folder.parent:
2396	folder = folder.parent
2397	# We have folder set to the library's root folder, which has the same name as the library
2398	for library in trans.sa_session.query( trans.model.Library ) \
2399	.filter( and_( trans.model.Library.table.c.deleted == False,
2400	trans.model.Library.table.c.name == folder.name ) ):
2401	# Just to double-check
2402	if library.root_folder == folder:
2403	return library
2404	return None

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

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