/lib/galaxy/web/controllers/visualization.py
Python | 457 lines | 446 code | 7 blank | 4 comment | 12 complexity | 10d22404979008dff44e127c3831f4d4 MD5 | raw file
1from galaxy import model 2from galaxy.model.item_attrs import * 3from galaxy.web.base.controller import * 4from galaxy.web.framework.helpers import time_ago, grids, iff 5from galaxy.util.sanitize_html import sanitize_html 6 7 8class VisualizationListGrid( grids.Grid ): 9 # Grid definition 10 title = "Saved Visualizations" 11 model_class = model.Visualization 12 default_sort_key = "-update_time" 13 default_filter = dict( title="All", deleted="False", tags="All", sharing="All" ) 14 columns = [ 15 grids.TextColumn( "Title", key="title", attach_popup=True, 16 link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), 17 grids.TextColumn( "Dbkey", key="dbkey" ), 18 grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), 19 grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), 20 grids.GridColumn( "Created", key="create_time", format=time_ago ), 21 grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), 22 ] 23 columns.append( 24 grids.MulticolFilterColumn( 25 "Search", 26 cols_to_filter=[ columns[0], columns[2] ], 27 key="free-text-search", visible=False, filterable="standard" ) 28 ) 29 global_actions = [ 30 grids.GridAction( "Create new visualization", dict( action='create' ) ) 31 ] 32 operations = [ 33 grids.GridOperation( "View/Edit", allow_multiple=False, url_args=dict( controller='tracks', action='browser' ) ), 34 grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ), 35 grids.GridOperation( "Clone", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ), 36 grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), 37 grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ), 38 ] 39 def apply_query_filter( self, trans, query, **kwargs ): 40 return query.filter_by( user=trans.user, deleted=False ) 41 42class VisualizationAllPublishedGrid( grids.Grid ): 43 # Grid definition 44 use_panels = True 45 use_async = True 46 title = "Published Visualizations" 47 model_class = model.Visualization 48 default_sort_key = "update_time" 49 default_filter = dict( title="All", username="All" ) 50 columns = [ 51 grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), 52 grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), 53 grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), 54 grids.CommunityRatingColumn( "Community Rating", key="rating" ), 55 grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), 56 grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) 57 ] 58 columns.append( 59 grids.MulticolFilterColumn( 60 "Search title, annotation, owner, and tags", 61 cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], 62 key="free-text-search", visible=False, filterable="standard" ) 63 ) 64 def build_initial_query( self, trans, **kwargs ): 65 # Join so that searching history.user makes sense. 66 return trans.sa_session.query( self.model_class ).join( model.User.table ) 67 def apply_query_filter( self, trans, query, **kwargs ): 68 return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) 69 70 71class VisualizationController( BaseUIController, Sharable, UsesAnnotations, 72 UsesHistoryDatasetAssociation, UsesVisualization, 73 UsesItemRatings ): 74 _user_list_grid = VisualizationListGrid() 75 _published_list_grid = VisualizationAllPublishedGrid() 76 77 @web.expose 78 def list_published( self, trans, *args, **kwargs ): 79 grid = self._published_list_grid( trans, **kwargs ) 80 if 'async' in kwargs: 81 return grid 82 else: 83 # Render grid wrapped in panels 84 return trans.fill_template( "visualization/list_published.mako", grid=grid ) 85 86 @web.expose 87 @web.require_login( "use Galaxy visualizations", use_panels=True ) 88 def index( self, trans, *args, **kwargs ): 89 """ Lists user's saved visualizations. """ 90 return self.list( trans, *args, **kwargs ) 91 92 @web.expose 93 @web.require_login() 94 def clone(self, trans, id, *args, **kwargs): 95 visualization = self.get_visualization( trans, id, check_ownership=False ) 96 user = trans.get_user() 97 owner = ( visualization.user == user ) 98 new_title = "Copy of '%s'" % visualization.title 99 if not owner: 100 new_title += " shared by %s" % visualization.user.email 101 102 cloned_visualization = visualization.copy( user=trans.user, title=new_title ) 103 104 # Persist 105 session = trans.sa_session 106 session.add( cloned_visualization ) 107 session.flush() 108 109 # Display the management page 110 trans.set_message( 'Copy created with name "%s"' % cloned_visualization.title ) 111 return self.list( trans ) 112 113 @web.expose 114 @web.require_login( "use Galaxy visualizations", use_panels=True ) 115 def list( self, trans, *args, **kwargs ): 116 # Handle operation 117 if 'operation' in kwargs and 'id' in kwargs: 118 session = trans.sa_session 119 operation = kwargs['operation'].lower() 120 ids = util.listify( kwargs['id'] ) 121 for id in ids: 122 item = session.query( model.Visualization ).get( trans.security.decode_id( id ) ) 123 if operation == "delete": 124 item.deleted = True 125 if operation == "share or publish": 126 return self.sharing( trans, **kwargs ) 127 session.flush() 128 129 # Build list of visualizations shared with user. 130 shared_by_others = trans.sa_session \ 131 .query( model.VisualizationUserShareAssociation ) \ 132 .filter_by( user=trans.get_user() ) \ 133 .join( model.Visualization.table ) \ 134 .filter( model.Visualization.deleted == False ) \ 135 .order_by( desc( model.Visualization.update_time ) ) \ 136 .all() 137 138 return trans.fill_template( "visualization/list.mako", grid=self._user_list_grid( trans, *args, **kwargs ), shared_by_others=shared_by_others ) 139 140 @web.expose 141 @web.require_login( "modify Galaxy visualizations" ) 142 def set_slug_async( self, trans, id, new_slug ): 143 """ Set item slug asynchronously. """ 144 visualization = self.get_visualization( trans, id ) 145 if visualization: 146 visualization.slug = new_slug 147 trans.sa_session.flush() 148 return visualization.slug 149 150 @web.expose 151 @web.require_login( "use Galaxy visualizations" ) 152 def set_accessible_async( self, trans, id=None, accessible=False ): 153 """ Set visualization's importable attribute and slug. """ 154 visualization = self.get_visualization( trans, id ) 155 156 # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed. 157 importable = accessible in ['True', 'true', 't', 'T']; 158 if visualization and visualization.importable != importable: 159 if importable: 160 self._make_item_accessible( trans.sa_session, visualization ) 161 else: 162 visualization.importable = importable 163 trans.sa_session.flush() 164 165 return 166 167 @web.expose 168 @web.require_login( "rate items" ) 169 @web.json 170 def rate_async( self, trans, id, rating ): 171 """ Rate a visualization asynchronously and return updated community data. """ 172 173 visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) 174 if not visualization: 175 return trans.show_error_message( "The specified visualization does not exist." ) 176 177 # Rate visualization. 178 visualization_rating = self.rate_item( trans.sa_session, trans.get_user(), visualization, rating ) 179 180 return self.get_ave_item_rating_data( trans.sa_session, visualization ) 181 182 @web.expose 183 @web.require_login( "share Galaxy visualizations" ) 184 def imp( self, trans, id ): 185 """ Import a visualization into user's workspace. """ 186 # Set referer message. 187 referer = trans.request.referer 188 if referer is not "": 189 referer_message = "<a href='%s'>return to the previous page</a>" % referer 190 else: 191 referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) 192 193 # Do import. 194 session = trans.sa_session 195 visualization = self.get_visualization( trans, id, check_ownership=False ) 196 if visualization.importable == False: 197 return trans.show_error_message( "The owner of this visualization has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) 198 elif visualization.deleted: 199 return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) 200 else: 201 # Create imported visualization via copy. 202 # TODO: need to handle custom db keys. 203 204 imported_visualization = visualization.copy( user=trans.user, title="imported: " + visualization.title ) 205 206 # Persist 207 session = trans.sa_session 208 session.add( imported_visualization ) 209 session.flush() 210 211 # Redirect to load galaxy frames. 212 return trans.show_ok_message( 213 message="""Visualization "%s" has been imported. <br>You can <a href="%s">start using this visualization</a> or %s.""" 214 % ( visualization.title, web.url_for( controller='visualization' ), referer_message ), use_panels=True ) 215 216 217 @web.expose 218 @web.require_login( "share Galaxy visualizations" ) 219 def sharing( self, trans, id, **kwargs ): 220 """ Handle visualization sharing. """ 221 222 # Get session and visualization. 223 session = trans.sa_session 224 visualization = self.get_visualization( trans, id, check_ownership=True ) 225 226 # Do operation on visualization. 227 if 'make_accessible_via_link' in kwargs: 228 self._make_item_accessible( trans.sa_session, visualization ) 229 elif 'make_accessible_and_publish' in kwargs: 230 self._make_item_accessible( trans.sa_session, visualization ) 231 visualization.published = True 232 elif 'publish' in kwargs: 233 visualization.published = True 234 elif 'disable_link_access' in kwargs: 235 visualization.importable = False 236 elif 'unpublish' in kwargs: 237 visualization.published = False 238 elif 'disable_link_access_and_unpublish' in kwargs: 239 visualization.importable = visualization.published = False 240 elif 'unshare_user' in kwargs: 241 user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) 242 if not user: 243 error( "User not found for provided id" ) 244 association = session.query( model.VisualizationUserShareAssociation ) \ 245 .filter_by( user=user, visualization=visualization ).one() 246 session.delete( association ) 247 248 session.flush() 249 250 return trans.fill_template( "/sharing_base.mako", item=visualization, use_panels=True ) 251 252 @web.expose 253 @web.require_login( "share Galaxy visualizations" ) 254 def share( self, trans, id=None, email="", use_panels=False ): 255 """ Handle sharing a visualization with a particular user. """ 256 msg = mtype = None 257 visualization = self.get_visualization( trans, id, check_ownership=True ) 258 if email: 259 other = trans.sa_session.query( model.User ) \ 260 .filter( and_( model.User.table.c.email==email, 261 model.User.table.c.deleted==False ) ) \ 262 .first() 263 if not other: 264 mtype = "error" 265 msg = ( "User '%s' does not exist" % email ) 266 elif other == trans.get_user(): 267 mtype = "error" 268 msg = ( "You cannot share a visualization with yourself" ) 269 elif trans.sa_session.query( model.VisualizationUserShareAssociation ) \ 270 .filter_by( user=other, visualization=visualization ).count() > 0: 271 mtype = "error" 272 msg = ( "Visualization already shared with '%s'" % email ) 273 else: 274 share = model.VisualizationUserShareAssociation() 275 share.visualization = visualization 276 share.user = other 277 session = trans.sa_session 278 session.add( share ) 279 self.create_item_slug( session, visualization ) 280 session.flush() 281 trans.set_message( "Visualization '%s' shared with user '%s'" % ( visualization.title, other.email ) ) 282 return trans.response.send_redirect( url_for( action='sharing', id=id ) ) 283 return trans.fill_template( "/ind_share_base.mako", 284 message = msg, 285 messagetype = mtype, 286 item=visualization, 287 email=email, 288 use_panels=use_panels ) 289 290 291 @web.expose 292 def display_by_username_and_slug( self, trans, username, slug ): 293 """ Display visualization based on a username and slug. """ 294 295 # Get visualization. 296 session = trans.sa_session 297 user = session.query( model.User ).filter_by( username=username ).first() 298 visualization = trans.sa_session.query( model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first() 299 if visualization is None: 300 raise web.httpexceptions.HTTPNotFound() 301 302 # Security check raises error if user cannot access visualization. 303 self.security_check( trans, visualization, False, True) 304 305 # Get rating data. 306 user_item_rating = 0 307 if trans.get_user(): 308 user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), visualization ) 309 if user_item_rating: 310 user_item_rating = user_item_rating.rating 311 else: 312 user_item_rating = 0 313 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, visualization ) 314 315 # Display. 316 visualization_config = self.get_visualization_config( trans, visualization ) 317 return trans.stream_template_mako( "visualization/display.mako", item = visualization, item_data = visualization_config, 318 user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings, 319 content_only=True ) 320 321 @web.expose 322 @web.json 323 @web.require_login( "get item name and link" ) 324 def get_name_and_link_async( self, trans, id=None ): 325 """ Returns visualization's name and link. """ 326 visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) 327 328 if self.create_item_slug( trans.sa_session, visualization ): 329 trans.sa_session.flush() 330 return_dict = { "name" : visualization.title, "link" : url_for( action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) } 331 return return_dict 332 333 @web.expose 334 def get_item_content_async( self, trans, id ): 335 """ Returns item content in HTML format. """ 336 337 # Get visualization, making sure it's accessible. 338 visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) 339 if visualization is None: 340 raise web.httpexceptions.HTTPNotFound() 341 342 # Return content. 343 visualization_config = self.get_visualization_config( trans, visualization ) 344 return trans.fill_template_mako( "visualization/item_content.mako", encoded_id=trans.security.encode_id(visualization.id), 345 item=visualization, item_data=visualization_config, content_only=True ) 346 347 @web.expose 348 @web.require_login( "create visualizations" ) 349 def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="" ): 350 """ 351 Create a new visualization 352 """ 353 user = trans.get_user() 354 visualization_title_err = visualization_slug_err = visualization_annotation_err = "" 355 if trans.request.method == "POST": 356 if not visualization_title: 357 visualization_title_err = "visualization name is required" 358 elif not visualization_slug: 359 visualization_slug_err = "visualization id is required" 360 elif not VALID_SLUG_RE.match( visualization_slug ): 361 visualization_slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" 362 elif trans.sa_session.query( model.Visualization ).filter_by( user=user, slug=visualization_slug, deleted=False ).first(): 363 visualization_slug_err = "visualization id must be unique" 364 else: 365 # Create the new stored visualization 366 visualization = model.Visualization() 367 visualization.title = visualization_title 368 visualization.slug = visualization_slug 369 visualization.dbkey = visualization_dbkey 370 visualization.type = 'trackster' # HACK: set visualization type to trackster since it's the only viz 371 visualization_annotation = sanitize_html( visualization_annotation, 'utf-8', 'text/html' ) 372 self.add_item_annotation( trans.sa_session, trans.get_user(), visualization, visualization_annotation ) 373 visualization.user = user 374 375 # And the first (empty) visualization revision 376 visualization_revision = model.VisualizationRevision() 377 visualization_revision.title = visualization_title 378 visualization_revision.config = {} 379 visualization_revision.dbkey = visualization_dbkey 380 visualization_revision.visualization = visualization 381 visualization.latest_revision = visualization_revision 382 383 # Persist 384 session = trans.sa_session 385 session.add(visualization) 386 session.add(visualization_revision) 387 session.flush() 388 389 return trans.response.send_redirect( web.url_for( action='list' ) ) 390 391 return trans.show_form( 392 web.FormBuilder( web.url_for(), "Create new visualization", submit_text="Submit" ) 393 .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) 394 .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, 395 help="""A unique identifier that will be used for 396 public links to this visualization. A default is generated 397 from the visualization title, but can be edited. This field 398 must contain only lowercase letters, numbers, and 399 the '-' character.""" ) 400 .add_select( "visualization_dbkey", "Visualization DbKey/Build", value=visualization_dbkey, options=self._get_dbkeys( trans ), error=None) 401 .add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err, 402 help="A description of the visualization; annotation is shown alongside published visualizations."), 403 template="visualization/create.mako" ) 404 405 @web.expose 406 @web.require_login( "edit visualizations" ) 407 def edit( self, trans, id, visualization_title="", visualization_slug="", visualization_annotation="" ): 408 """ 409 Edit a visualization's attributes. 410 """ 411 visualization = self.get_visualization( trans, id, check_ownership=True ) 412 session = trans.sa_session 413 414 visualization_title_err = visualization_slug_err = visualization_annotation_err = "" 415 if trans.request.method == "POST": 416 if not visualization_title: 417 visualization_title_err = "Visualization name is required" 418 elif not visualization_slug: 419 visualization_slug_err = "Visualization id is required" 420 elif not VALID_SLUG_RE.match( visualization_slug ): 421 visualization_slug_err = "Visualization identifier must consist of only lowercase letters, numbers, and the '-' character" 422 elif visualization_slug != visualization.slug and trans.sa_session.query( model.Visualization ).filter_by( user=visualization.user, slug=visualization_slug, deleted=False ).first(): 423 visualization_slug_err = "Visualization id must be unique" 424 else: 425 visualization.title = visualization_title 426 visualization.slug = visualization_slug 427 if visualization_annotation != "": 428 visualization_annotation = sanitize_html( visualization_annotation, 'utf-8', 'text/html' ) 429 self.add_item_annotation( trans.sa_session, trans.get_user(), visualization, visualization_annotation ) 430 session.flush() 431 # Redirect to visualization list. 432 return trans.response.send_redirect( web.url_for( action='list' ) ) 433 else: 434 visualization_title = visualization.title 435 # Create slug if it's not already set. 436 if visualization.slug is None: 437 self.create_item_slug( trans.sa_session, visualization ) 438 visualization_slug = visualization.slug 439 visualization_annotation = self.get_item_annotation_str( trans.sa_session, trans.user, visualization ) 440 if not visualization_annotation: 441 visualization_annotation = "" 442 return trans.show_form( 443 web.FormBuilder( web.url_for( id=id ), "Edit visualization attributes", submit_text="Submit" ) 444 .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) 445 .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, 446 help="""A unique identifier that will be used for 447 public links to this visualization. A default is generated 448 from the visualization title, but can be edited. This field 449 must contain only lowercase letters, numbers, and 450 the '-' character.""" ) 451 .add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err, 452 help="A description of the visualization; annotation is shown alongside published visualizations."), 453 template="visualization/create.mako" ) 454 455 def get_item( self, trans, id ): 456 return self.get_visualization( trans, id ) 457