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dataset.py

リビジョン 2, 41.5 KB (コミッタ: hatakeyama, 14 年前)
import galaxy-central

行番号
1	import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob, sys
2
3	from galaxy.web.base.controller import *
4	from galaxy.web.framework.helpers import time_ago, iff, grids
5	from galaxy import util, datatypes, jobs, web, model
6	from cgi import escape, FieldStorage
7	from galaxy.datatypes.display_applications.util import encode_dataset_user, decode_dataset_user
8	from galaxy.util.sanitize_html import sanitize_html
9	from galaxy.model.item_attrs import *
10
11	from email.MIMEText import MIMEText
12	import pkg_resources;
13	pkg_resources.require( "Paste" )
14	import paste.httpexceptions
15
16	if sys.version_info[:2] < ( 2, 6 ):
17	zipfile.BadZipFile = zipfile.error
18	if sys.version_info[:2] < ( 2, 5 ):
19	zipfile.LargeZipFile = zipfile.error
20
21	tmpd = tempfile.mkdtemp()
22	comptypes=[]
23	ziptype = '32'
24	tmpf = os.path.join( tmpd, 'compression_test.zip' )
25	try:
26	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
27	archive.close()
28	comptypes.append( 'zip' )
29	ziptype = '64'
30	except RuntimeError:
31	log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." )
32	except (TypeError, zipfile.LargeZipFile): # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped
33	log.warning( 'Max zip file size is 2GB, ZIP64 not supported' )
34	comptypes.append( 'zip' )
35	try:
36	os.unlink( tmpf )
37	except OSError:
38	pass
39	os.rmdir( tmpd )
40
41	log = logging.getLogger( __name__ )
42
43	error_report_template = """
44	GALAXY TOOL ERROR REPORT
45	------------------------
46
47	This error report was sent from the Galaxy instance hosted on the server
48	"${host}"
49	-----------------------------------------------------------------------------
50	This is in reference to dataset id ${dataset_id} from history id ${history_id}
51	-----------------------------------------------------------------------------
52	You should be able to view the history containing the related history item
53
54	${hid}: ${history_item_name}
55
56	by logging in as a Galaxy admin user to the Galaxy instance referenced above
57	and pointing your browser to the following link.
58
59	${history_view_link}
60	-----------------------------------------------------------------------------
61	The user '${email}' provided the following information:
62
63	${message}
64	-----------------------------------------------------------------------------
65	job id: ${job_id}
66	tool id: ${job_tool_id}
67	-----------------------------------------------------------------------------
68	job command line:
69	${job_command_line}
70	-----------------------------------------------------------------------------
71	job stderr:
72	${job_stderr}
73	-----------------------------------------------------------------------------
74	job stdout:
75	${job_stdout}
76	-----------------------------------------------------------------------------
77	job info:
78	${job_info}
79	-----------------------------------------------------------------------------
80	job traceback:
81	${job_traceback}
82	-----------------------------------------------------------------------------
83	(This is an automated message).
84	"""
85
86	class HistoryDatasetAssociationListGrid( grids.Grid ):
87	# Custom columns for grid.
88	class HistoryColumn( grids.GridColumn ):
89	def get_value( self, trans, grid, hda):
90	return hda.history.name
91
92	class StatusColumn( grids.GridColumn ):
93	def get_value( self, trans, grid, hda ):
94	if hda.deleted:
95	return "deleted"
96	return ""
97	def get_accepted_filters( self ):
98	""" Returns a list of accepted filters for this column. """
99	accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" }
100	accepted_filters = []
101	for label, val in accepted_filter_labels_and_vals.items():
102	args = { self.key: val }
103	accepted_filters.append( grids.GridColumnFilter( label, args) )
104	return accepted_filters
105
106	# Grid definition
107	title = "Saved Datasets"
108	model_class = model.HistoryDatasetAssociation
109	template='/dataset/grid.mako'
110	default_sort_key = "-update_time"
111	columns = [
112	grids.TextColumn( "Name", key="name",
113	# Link name to dataset's history.
114	link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ),
115	HistoryColumn( "History", key="history",
116	link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ),
117	grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ),
118	StatusColumn( "Status", key="deleted", attach_popup=False ),
119	grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
120	]
121	columns.append(
122	grids.MulticolFilterColumn(
123	"Search",
124	cols_to_filter=[ columns[0], columns[2] ],
125	key="free-text-search", visible=False, filterable="standard" )
126	)
127	operations = [
128	grids.GridOperation( "Copy to current history", condition=( lambda item: not item.deleted ), async_compatible=False ),
129	]
130	standard_filters = []
131	default_filter = dict( name="All", deleted="False", tags="All" )
132	preserve_state = False
133	use_paging = True
134	num_rows_per_page = 50
135	def build_initial_query( self, trans, **kwargs ):
136	# Show user's datasets that are not deleted, not in deleted histories, and not hidden.
137	# To filter HDAs by user, need to join model class/HDA and History table so that it is
138	# possible to filter by user. However, for dictionary-based filtering to work, need a
139	# primary table for the query.
140	return trans.sa_session.query( self.model_class ).select_from( self.model_class.table.join( model.History.table ) ) \
141	.filter( model.History.user == trans.user ) \
142	.filter( self.model_class.deleted==False ) \
143	.filter( model.History.deleted==False ) \
144	.filter( self.model_class.visible==True )
145
146	class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssociation, UsesItemRatings ):
147
148	stored_list_grid = HistoryDatasetAssociationListGrid()
149
150	@web.expose
151	def errors( self, trans, id ):
152	hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
153	return trans.fill_template( "dataset/errors.mako", hda=hda )
154	@web.expose
155	def stderr( self, trans, id ):
156	dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
157	job = dataset.creating_job_associations[0].job
158	trans.response.set_content_type( 'text/plain' )
159	return job.stderr
160	@web.expose
161	def report_error( self, trans, id, email='', message="" ):
162	smtp_server = trans.app.config.smtp_server
163	if smtp_server is None:
164	return trans.show_error_message( "Mail is not configured for this galaxy instance" )
165	to_address = trans.app.config.error_email_to
166	if to_address is None:
167	return trans.show_error_message( "Error reporting has been disabled for this galaxy instance" )
168	# Get the dataset and associated job
169	hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
170	job = hda.creating_job_associations[0].job
171	# Get the name of the server hosting the Galaxy instance from which this report originated
172	host = trans.request.host
173	history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) )
174	# Build the email message
175	msg = MIMEText( string.Template( error_report_template )
176	.safe_substitute( host=host,
177	dataset_id=hda.dataset_id,
178	history_id=hda.history_id,
179	hid=hda.hid,
180	history_item_name=hda.get_display_name(),
181	history_view_link=history_view_link,
182	job_id=job.id,
183	job_tool_id=job.tool_id,
184	job_command_line=job.command_line,
185	job_stderr=job.stderr,
186	job_stdout=job.stdout,
187	job_info=job.info,
188	job_traceback=job.traceback,
189	email=email,
190	message=message ) )
191	frm = to_address
192	# Check email a bit
193	email = email.strip()
194	parts = email.split()
195	if len( parts ) == 1 and len( email ) > 0:
196	to = to_address + ", " + email
197	else:
198	to = to_address
199	msg[ 'To' ] = to
200	msg[ 'From' ] = frm
201	msg[ 'Subject' ] = "Galaxy tool error report from " + email
202	# Send it
203	try:
204	s = smtplib.SMTP()
205	s.connect( smtp_server )
206	s.sendmail( frm, [ to ], msg.as_string() )
207	s.close()
208	return trans.show_ok_message( "Your error report has been sent" )
209	except Exception, e:
210	return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) )
211
212	@web.expose
213	def default(self, trans, dataset_id=None, **kwd):
214	return 'This link may not be followed from within Galaxy.'
215
216	@web.expose
217	def archive_composite_dataset( self, trans, data=None, **kwd ):
218	# save a composite object into a compressed archive for downloading
219	params = util.Params( kwd )
220	valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
221	outfname = data.name[0:150]
222	outfname = ''.join(c in valid_chars and c or '_' for c in outfname)
223	if (params.do_action == None):
224	params.do_action = 'zip' # default
225	msg = util.restore_text( params.get( 'msg', '' ) )
226	messagetype = params.get( 'messagetype', 'done' )
227	if not data:
228	msg = "You must select at least one dataset"
229	messagetype = 'error'
230	else:
231	error = False
232	try:
233	if (params.do_action == 'zip'):
234	# Can't use mkstemp - the file must not exist first
235	tmpd = tempfile.mkdtemp()
236	tmpf = os.path.join( tmpd, 'library_download.' + params.do_action )
237	if ziptype == '64':
238	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
239	else:
240	archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED )
241	archive.add = lambda x, y: archive.write( x, y.encode('CP437') )
242	elif params.do_action == 'tgz':
243	archive = util.streamball.StreamBall( 'w\|gz' )
244	elif params.do_action == 'tbz':
245	archive = util.streamball.StreamBall( 'w\|bz2' )
246	except (OSError, zipfile.BadZipFile):
247	error = True
248	log.exception( "Unable to create archive for download" )
249	msg = "Unable to create archive for %s for download, please report this error" % outfname
250	messagetype = 'error'
251	if not error:
252	current_user_roles = trans.get_current_user_roles()
253	ext = data.extension
254	path = data.file_name
255	fname = os.path.split(path)[-1]
256	efp = data.extra_files_path
257	htmlname = os.path.splitext(outfname)[0]
258	if not htmlname.endswith(ext):
259	htmlname = '%s_%s' % (htmlname,ext)
260	archname = '%s.html' % htmlname # fake the real nature of the html file
261	try:
262	archive.add(data.file_name,archname)
263	except IOError:
264	error = True
265	log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name)
266	msg = "Unable to create archive for download, please report this error"
267	messagetype = 'error'
268	flist = glob.glob(os.path.join(efp,'.')) # glob returns full paths
269	for fpath in flist:
270	efp,fname = os.path.split(fpath)
271	try:
272	archive.add( fpath,fname )
273	except IOError:
274	error = True
275	log.exception( "Unable to add %s to temporary library download archive" % fname)
276	msg = "Unable to create archive for download, please report this error"
277	messagetype = 'error'
278	continue
279	if not error:
280	if params.do_action == 'zip':
281	archive.close()
282	tmpfh = open( tmpf )
283	# clean up now
284	try:
285	os.unlink( tmpf )
286	os.rmdir( tmpd )
287	except OSError:
288	error = True
289	msg = "Unable to remove temporary library download archive and directory"
290	log.exception( msg )
291	messagetype = 'error'
292	if not error:
293	trans.response.set_content_type( "application/x-zip-compressed" )
294	trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.zip" % outfname
295	return tmpfh
296	else:
297	trans.response.set_content_type( "application/x-tar" )
298	outext = 'tgz'
299	if params.do_action == 'tbz':
300	outext = 'tbz'
301	trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext)
302	archive.wsgi_status = trans.response.wsgi_status()
303	archive.wsgi_headeritems = trans.response.wsgi_headeritems()
304	return archive.stream
305	return trans.show_error_message( msg )
306
307
308
309	@web.expose
310	def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd):
311	"""Catches the dataset id and displays file contents as directed"""
312	composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
313	composite_extensions.append('html') # for archiving composite datatypes
314	# DEPRECATION: We still support unencoded ids for backward compatibility
315	try:
316	data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
317	if data is None:
318	raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id )
319	except:
320	try:
321	data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) )
322	except:
323	data = None
324	if not data:
325	raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
326	current_user_roles = trans.get_current_user_roles()
327	if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
328	return trans.show_error_message( "You are not allowed to access this dataset" )
329
330	if data.state == trans.model.Dataset.states.UPLOAD:
331	return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." )
332
333	if filename and filename != "index":
334	# For files in extra_files_path
335	file_path = os.path.join( data.extra_files_path, filename )
336	if os.path.exists( file_path ):
337	mime, encoding = mimetypes.guess_type( file_path )
338	if not mime:
339	try:
340	mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] )
341	except:
342	mime = "text/plain"
343
344	trans.response.set_content_type( mime )
345	return open( file_path )
346	else:
347	return "Could not find '%s' on the extra files path %s." % (filename,file_path)
348
349	mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() )
350	trans.response.set_content_type(mime)
351	trans.log_event( "Display dataset id: %s" % str( dataset_id ) )
352
353	if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file
354	if data.extension in composite_extensions:
355	return self.archive_composite_dataset( trans, data, **kwd )
356	else:
357	trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size )
358	if not to_ext:
359	to_ext = data.extension
360	valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
361	fname = data.name
362	fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150]
363	trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext)
364	return open( data.file_name )
365	if not os.path.exists( data.file_name ):
366	raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name )
367
368	max_peek_size = 1000000 # 1 MB
369	if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size:
370	return open( data.file_name )
371	else:
372	trans.response.set_content_type( "text/html" )
373	return trans.stream_template_mako( "/dataset/large_file.mako",
374	truncated_data = open( data.file_name ).read(max_peek_size),
375	data = data )
376
377	@web.expose
378	@web.require_login( "see all available datasets" )
379	def list( self, trans, **kwargs ):
380	"""List all available datasets"""
381	status = message = None
382
383	if 'operation' in kwargs:
384	operation = kwargs['operation'].lower()
385	hda_ids = util.listify( kwargs.get( 'id', [] ) )
386
387	# Display no message by default
388	status, message = None, None
389
390	# Load the hdas and ensure they all belong to the current user
391	hdas = []
392	for encoded_hda_id in hda_ids:
393	hda_id = trans.security.decode_id( encoded_hda_id )
394	hda = trans.sa_session.query( model.HistoryDatasetAssociation ).filter_by( id=hda_id ).first()
395	if hda:
396	# Ensure history is owned by current user
397	if hda.history.user_id != None and trans.user:
398	assert trans.user.id == hda.history.user_id, "HistoryDatasetAssocation does not belong to current user"
399	hdas.append( hda )
400	else:
401	log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id )
402
403	if hdas:
404	if operation == "switch" or operation == "switch_history":
405	# Switch to a history that the HDA resides in.
406
407	# Convert hda to histories.
408	histories = []
409	for hda in hdas:
410	histories.append( hda.history )
411
412	# Use history controller to switch the history. TODO: is this reasonable?
413	status, message = trans.webapp.controllers['history']._list_switch( trans, histories )
414
415	# Current history changed, refresh history frame; if switching to a dataset, set hda seek.
416	trans.template_context['refresh_frames'] = ['history']
417	if operation == "switch":
418	hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ]
419	trans.template_context[ 'seek_hda_ids' ] = hda_ids
420	elif operation == "copy to current history":
421	# Copy a dataset to the current history.
422	target_histories = [ trans.get_history() ]
423	status, message = self._copy_datasets( trans, hda_ids, target_histories )
424
425	# Current history changed, refresh history frame.
426	trans.template_context['refresh_frames'] = ['history']
427
428	# Render the list view
429	return self.stored_list_grid( trans, status=status, message=message, **kwargs )
430
431	@web.expose
432	def imp( self, trans, dataset_id=None, **kwd ):
433	""" Import another user's dataset via a shared URL; dataset is added to user's current history. """
434	msg = ""
435
436	# Set referer message.
437	referer = trans.request.referer
438	if referer is not "":
439	referer_message = "<a href='%s'>return to the previous page</a>" % referer
440	else:
441	referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' )
442
443	# Error checking.
444	if not dataset_id:
445	return trans.show_error_message( "You must specify a dataset to import. You can %s." % referer_message, use_panels=True )
446
447	# Do import.
448	cur_history = trans.get_history( create=True )
449	status, message = self._copy_datasets( trans, [ dataset_id ], [ cur_history ], imported=True )
450	message = "Dataset imported. <br>You can <a href='%s'>start using the dataset</a> or %s." % ( url_for('/'), referer_message )
451	return trans.show_message( message, type=status, use_panels=True )
452
453	@web.expose
454	@web.json
455	@web.require_login( "use Galaxy datasets" )
456	def get_name_and_link_async( self, trans, id=None ):
457	""" Returns dataset's name and link. """
458	dataset = self.get_dataset( trans, id, False, True )
459	return_dict = { "name" : dataset.name, "link" : url_for( action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) ) }
460	return return_dict
461
462	@web.expose
463	def get_embed_html_async( self, trans, id ):
464	""" Returns HTML for embedding a dataset in a page. """
465	dataset = self.get_dataset( trans, id, False, True )
466	if dataset:
467	return "Embedded Dataset '%s'" % dataset.name
468
469	@web.expose
470	@web.require_login( "use Galaxy datasets" )
471	def set_accessible_async( self, trans, id=None, accessible=False ):
472	""" Does nothing because datasets do not have an importable/accessible attribute. This method could potentially set another attribute. """
473	return
474
475	@web.expose
476	@web.require_login( "rate items" )
477	@web.json
478	def rate_async( self, trans, id, rating ):
479	""" Rate a dataset asynchronously and return updated community data. """
480
481	dataset = self.get_dataset( trans, id, check_ownership=False, check_accessible=True )
482	if not dataset:
483	return trans.show_error_message( "The specified dataset does not exist." )
484
485	# Rate dataset.
486	dataset_rating = self.rate_item( rate_item, trans.get_user(), dataset, rating )
487
488	return self.get_ave_item_rating_data( trans.sa_session, dataset )
489
490	@web.expose
491	def display_by_username_and_slug( self, trans, username, slug, preview=True ):
492	""" Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id. """
493	dataset = self.get_dataset( trans, slug, False, True )
494	if dataset:
495	truncated, dataset_data = self.get_data( dataset, preview )
496	dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset )
497
498	# If data is binary or an image, stream without template; otherwise, use display template.
499	# TODO: figure out a way to display images in display template.
500	if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image):
501	mime = trans.app.datatypes_registry.get_mimetype_by_extension( dataset.extension.lower() )
502	trans.response.set_content_type( mime )
503	return open( dataset.file_name )
504	else:
505	# Get rating data.
506	user_item_rating = 0
507	if trans.get_user():
508	user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), dataset )
509	if user_item_rating:
510	user_item_rating = user_item_rating.rating
511	else:
512	user_item_rating = 0
513	ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, dataset )
514
515	return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, truncated=truncated,
516	user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings )
517	else:
518	raise web.httpexceptions.HTTPNotFound()
519
520	@web.expose
521	def get_item_content_async( self, trans, id ):
522	""" Returns item content in HTML format. """
523
524	dataset = self.get_dataset( trans, id, False, True )
525	if dataset is None:
526	raise web.httpexceptions.HTTPNotFound()
527	truncated, dataset_data = self.get_data( dataset, preview=True )
528	# Get annotation.
529	dataset.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, dataset )
530	return trans.stream_template_mako( "/dataset/item_content.mako", item=dataset, item_data=dataset_data, truncated=truncated )
531
532	@web.expose
533	def annotate_async( self, trans, id, new_annotation=None, **kwargs ):
534	dataset = self.get_dataset( trans, id, False, True )
535	if not dataset:
536	web.httpexceptions.HTTPNotFound()
537	if dataset and new_annotation:
538	# Sanitize annotation before adding it.
539	new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' )
540	self.add_item_annotation( trans.sa_session, trans.get_user(), dataset, new_annotation )
541	trans.sa_session.flush()
542	return new_annotation
543
544	@web.expose
545	def get_annotation_async( self, trans, id ):
546	dataset = self.get_dataset( trans, id, False, True )
547	if not dataset:
548	web.httpexceptions.HTTPNotFound()
549	return self.get_item_annotation_str( trans.sa_session, trans.user, dataset )
550
551	@web.expose
552	def display_at( self, trans, dataset_id, filename=None, **kwd ):
553	"""Sets up a dataset permissions so it is viewable at an external site"""
554	site = filename
555	data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
556	if not data:
557	raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
558	if 'display_url' not in kwd or 'redirect_url' not in kwd:
559	return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' )
560	try:
561	redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] )
562	except:
563	redirect_url = kwd['redirect_url'] # not all will need custom text
564	current_user_roles = trans.get_current_user_roles()
565	if trans.app.security_agent.dataset_is_public( data.dataset ):
566	return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac
567	if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
568	trans.app.host_security_agent.set_dataset_permissions( data, trans.user, site )
569	return trans.response.send_redirect( redirect_url )
570	else:
571	return trans.show_error_message( "You are not allowed to view this dataset at external sites. Please contact your Galaxy administrator to acquire management permissions for this dataset." )
572
573	@web.expose
574	def display_application( self, trans, dataset_id=None, user_id=None, app_name = None, link_name = None, app_action = None, action_param = None, **kwds ):
575	"""Access to external display applications"""
576	if kwds:
577	log.debug( "Unexpected Keywords passed to display_application: %s" % kwds ) #route memory?
578	#decode ids
579	data, user = decode_dataset_user( trans, dataset_id, user_id )
580	if not data:
581	raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
582	if user is None:
583	user = trans.user
584	if user:
585	user_roles = user.all_roles()
586	else:
587	user_roles = []
588	if None in [ app_name, link_name ]:
589	return trans.show_error_message( "A display application name and link name must be provided." )
590
591	if trans.app.security_agent.can_access_dataset( user_roles, data.dataset ):
592	msg = []
593	refresh = False
594	display_app = trans.app.datatypes_registry.display_applications.get( app_name )
595	assert display_app, "Unknown display application has been requested: %s" % app_name
596	dataset_hash, user_hash = encode_dataset_user( trans, data, user )
597	display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans )
598	assert display_link, "Unknown display link has been requested: %s" % link_name
599	if data.state == data.states.ERROR:
600	msg.append( ( 'This dataset is in an error state, you cannot view it at an external display application.', 'error' ) )
601	elif data.deleted:
602	msg.append( ( 'This dataset has been deleted, you cannot view it at an external display application.', 'error' ) )
603	elif data.state != data.states.OK:
604	msg.append( ( 'You must wait for this dataset to be created before you can view it at an external display application.', 'info' ) )
605	refresh = True
606	else:
607	#We have permissions, dataset is not deleted and is in OK state, allow access
608	if display_link.display_ready():
609	if app_action in [ 'data', 'param' ]:
610	assert action_param, "An action param must be provided for a data or param action"
611	#data is used for things with filenames that could be passed off to a proxy
612	#in case some display app wants all files to be in the same 'directory',
613	#data can be forced to param, but not the other way (no filename for other direction)
614	#get param name from url param name
615	action_param = display_link.get_param_name_by_url( action_param )
616	value = display_link.get_param_value( action_param )
617	assert value, "An invalid parameter name was provided: %s" % action_param
618	assert value.parameter.viewable, "This parameter is not viewable."
619	if value.parameter.type == 'data':
620	content_length = os.path.getsize( value.file_name )
621	rval = open( value.file_name )
622	else:
623	rval = str( value )
624	content_length = len( rval )
625	trans.response.set_content_type( value.mime_type() )
626	trans.response.headers[ 'Content-Length' ] = content_length
627	return rval
628	elif app_action == None:
629	#redirect user to url generated by display link
630	return trans.response.send_redirect( display_link.display_url() )
631	else:
632	msg.append( ( 'Invalid action provided: %s' % app_action, 'error' ) )
633	else:
634	if app_action == None:
635	if trans.history != data.history:
636	msg.append( ( 'You must import this dataset into your current history before you can view it at the desired display application.', 'error' ) )
637	else:
638	refresh = True
639	msg.append( ( 'This display application is being prepared.', 'info' ) )
640	if not display_link.preparing_display():
641	display_link.prepare_display()
642	else:
643	raise Exception( 'Attempted a view action (%s) on a non-ready display application' % app_action )
644	return trans.fill_template_mako( "dataset/display_application/display.mako", msg = msg, display_app = display_app, display_link = display_link, refresh = refresh )
645	return trans.show_error_message( 'You do not have permission to view this dataset at an external display application.' )
646
647	def _undelete( self, trans, id ):
648	try:
649	id = int( id )
650	except ValueError, e:
651	return False
652	history = trans.get_history()
653	data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
654	if data and data.undeletable:
655	# Walk up parent datasets to find the containing history
656	topmost_parent = data
657	while topmost_parent.parent:
658	topmost_parent = topmost_parent.parent
659	assert topmost_parent in history.datasets, "Data does not belong to current history"
660	# Mark undeleted
661	data.mark_undeleted()
662	trans.sa_session.flush()
663	trans.log_event( "Dataset id %s has been undeleted" % str(id) )
664	return True
665	return False
666
667	def _unhide( self, trans, id ):
668	try:
669	id = int( id )
670	except ValueError, e:
671	return False
672	history = trans.get_history()
673	data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
674	if data:
675	# Walk up parent datasets to find the containing history
676	topmost_parent = data
677	while topmost_parent.parent:
678	topmost_parent = topmost_parent.parent
679	assert topmost_parent in history.datasets, "Data does not belong to current history"
680	# Mark undeleted
681	data.mark_unhidden()
682	trans.sa_session.flush()
683	trans.log_event( "Dataset id %s has been unhidden" % str(id) )
684	return True
685	return False
686
687	@web.expose
688	def undelete( self, trans, id ):
689	if self._undelete( trans, id ):
690	return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) )
691	raise "Error undeleting"
692
693	@web.expose
694	def unhide( self, trans, id ):
695	if self._unhide( trans, id ):
696	return trans.response.send_redirect( web.url_for( controller='root', action='history', show_hidden = True ) )
697	raise "Error unhiding"
698
699
700	@web.expose
701	def undelete_async( self, trans, id ):
702	if self._undelete( trans, id ):
703	return "OK"
704	raise "Error undeleting"
705
706	@web.expose
707	def copy_datasets( self, trans, source_dataset_ids="", target_history_ids="", new_history_name="", do_copy=False, **kwd ):
708	params = util.Params( kwd )
709	user = trans.get_user()
710	history = trans.get_history()
711	create_new_history = False
712	refresh_frames = []
713	if source_dataset_ids:
714	if not isinstance( source_dataset_ids, list ):
715	source_dataset_ids = source_dataset_ids.split( "," )
716	source_dataset_ids = map( int, source_dataset_ids )
717	else:
718	source_dataset_ids = []
719	if target_history_ids:
720	if not isinstance( target_history_ids, list ):
721	target_history_ids = target_history_ids.split( "," )
722	if "create_new_history" in target_history_ids:
723	create_new_history = True
724	target_history_ids.remove( "create_new_history" )
725	target_history_ids = map( int, target_history_ids )
726	else:
727	target_history_ids = []
728	done_msg = error_msg = ""
729	if do_copy:
730	invalid_datasets = 0
731	if not source_dataset_ids or not ( target_history_ids or create_new_history ):
732	error_msg = "You must provide both source datasets and target histories."
733	if create_new_history:
734	target_history_ids.append( "create_new_history" )
735	else:
736	if create_new_history:
737	new_history = trans.app.model.History()
738	if new_history_name:
739	new_history.name = new_history_name
740	new_history.user = user
741	trans.sa_session.add( new_history )
742	trans.sa_session.flush()
743	target_history_ids.append( new_history.id )
744	if user:
745	target_histories = [ hist for hist in map( trans.sa_session.query( trans.app.model.History ).get, target_history_ids ) if ( hist is not None and hist.user == user )]
746	else:
747	target_histories = [ history ]
748	if len( target_histories ) != len( target_history_ids ):
749	error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) )
750	for data in map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, source_dataset_ids ):
751	if data is None:
752	error_msg = error_msg + "You tried to copy a dataset that does not exist. "
753	invalid_datasets += 1
754	elif data.history != history:
755	error_msg = error_msg + "You tried to copy a dataset which is not in your current history. "
756	invalid_datasets += 1
757	else:
758	for hist in target_histories:
759	hist.add_dataset( data.copy( copy_children = True ) )
760	if history in target_histories:
761	refresh_frames = ['history']
762	trans.sa_session.flush()
763	done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) )
764	trans.sa_session.refresh( history )
765	elif create_new_history:
766	target_history_ids.append( "create_new_history" )
767	source_datasets = history.active_datasets
768	target_histories = [history]
769	if user:
770	target_histories = user.active_histories
771	return trans.fill_template( "/dataset/copy_view.mako",
772	source_dataset_ids = source_dataset_ids,
773	target_history_ids = target_history_ids,
774	source_datasets = source_datasets,
775	target_histories = target_histories,
776	new_history_name = new_history_name,
777	done_msg = done_msg,
778	error_msg = error_msg,
779	refresh_frames = refresh_frames )
780
781	def _copy_datasets( self, trans, dataset_ids, target_histories, imported=False ):
782	""" Helper method for copying datasets. """
783	user = trans.get_user()
784	done_msg = error_msg = ""
785
786	invalid_datasets = 0
787	if not dataset_ids or not target_histories:
788	error_msg = "You must provide both source datasets and target histories."
789	else:
790	# User must own target histories to copy datasets to them.
791	for history in target_histories:
792	if user != history.user:
793	error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_histories ) )
794	for dataset_id in dataset_ids:
795	data = self.get_dataset( trans, dataset_id, False, True )
796	if data is None:
797	error_msg = error_msg + "You tried to copy a dataset that does not exist or that you do not have access to. "
798	invalid_datasets += 1
799	else:
800	for hist in target_histories:
801	dataset_copy = data.copy( copy_children = True )
802	if imported:
803	dataset_copy.name = "imported: " + dataset_copy.name
804	hist.add_dataset( dataset_copy )
805	trans.sa_session.flush()
806	num_datasets_copied = len( dataset_ids ) - invalid_datasets
807	done_msg = "%i dataset%s copied to %i histor%s." % \
808	( num_datasets_copied, iff( num_datasets_copied == 1, "", "s"), len( target_histories ), iff( len ( target_histories ) == 1, "y", "ies") )
809	trans.sa_session.refresh( history )
810
811	if error_msg != "":
812	status = ERROR
813	message = error_msg
814	else:
815	status = SUCCESS
816	message = done_msg
817	return status, message

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