[2] | 1 | """ |
---|
| 2 | Contains functionality needed in every web interface |
---|
| 3 | """ |
---|
| 4 | import os, time, logging, re, string, sys, glob |
---|
| 5 | from datetime import datetime, timedelta |
---|
| 6 | from galaxy import config, tools, web, util |
---|
| 7 | from galaxy.web import error, form, url_for |
---|
| 8 | from galaxy.model.orm import * |
---|
| 9 | from galaxy.workflow.modules import * |
---|
| 10 | from galaxy.web.framework import simplejson |
---|
| 11 | from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField |
---|
| 12 | from galaxy.visualization.tracks.data_providers import get_data_provider |
---|
| 13 | |
---|
| 14 | from Cheetah.Template import Template |
---|
| 15 | |
---|
| 16 | log = logging.getLogger( __name__ ) |
---|
| 17 | |
---|
| 18 | # States for passing messages |
---|
| 19 | SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" |
---|
| 20 | |
---|
| 21 | # RE that tests for valid slug. |
---|
| 22 | VALID_SLUG_RE = re.compile( "^[a-z0-9\-]+$" ) |
---|
| 23 | |
---|
| 24 | class BaseController( object ): |
---|
| 25 | """ |
---|
| 26 | Base class for Galaxy web application controllers. |
---|
| 27 | """ |
---|
| 28 | def __init__( self, app ): |
---|
| 29 | """Initialize an interface for application 'app'""" |
---|
| 30 | self.app = app |
---|
| 31 | def get_toolbox(self): |
---|
| 32 | """Returns the application toolbox""" |
---|
| 33 | return self.app.toolbox |
---|
| 34 | def get_class( self, trans, class_name ): |
---|
| 35 | """ Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>). """ |
---|
| 36 | if class_name == 'History': |
---|
| 37 | item_class = trans.model.History |
---|
| 38 | elif class_name == 'HistoryDatasetAssociation': |
---|
| 39 | item_class = trans.model.HistoryDatasetAssociation |
---|
| 40 | elif class_name == 'Page': |
---|
| 41 | item_class = trans.model.Page |
---|
| 42 | elif class_name == 'StoredWorkflow': |
---|
| 43 | item_class = trans.model.StoredWorkflow |
---|
| 44 | elif class_name == 'Visualization': |
---|
| 45 | item_class = trans.model.Visualization |
---|
| 46 | elif class_name == 'Tool': |
---|
| 47 | item_class = trans.model.Tool |
---|
| 48 | elif class_name == 'Job': |
---|
| 49 | item_class == trans.model.Job |
---|
| 50 | else: |
---|
| 51 | item_class = None |
---|
| 52 | return item_class |
---|
| 53 | |
---|
| 54 | Root = BaseController |
---|
| 55 | |
---|
| 56 | class SharableItemSecurity: |
---|
| 57 | """ Mixin for handling security for sharable items. """ |
---|
| 58 | def security_check( self, user, item, check_ownership=False, check_accessible=False ): |
---|
| 59 | """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ |
---|
| 60 | if check_ownership: |
---|
| 61 | # Verify ownership. |
---|
| 62 | if not user: |
---|
| 63 | error( "Must be logged in to manage Galaxy items" ) |
---|
| 64 | if item.user != user: |
---|
| 65 | error( "%s is not owned by current user" % item.__class__.__name__ ) |
---|
| 66 | if check_accessible: |
---|
| 67 | # Verify accessible. |
---|
| 68 | if ( item.user != user ) and ( not item.importable ) and ( user not in item.users_shared_with_dot_users ): |
---|
| 69 | error( "%s is not accessible to current user" % item.__class__.__name__ ) |
---|
| 70 | return item |
---|
| 71 | |
---|
| 72 | # |
---|
| 73 | # TODO: need to move UsesHistory, etc. mixins to better location - perhaps lib/galaxy/model/XXX ? |
---|
| 74 | # |
---|
| 75 | |
---|
| 76 | class UsesHistoryDatasetAssociation: |
---|
| 77 | """ Mixin for controllers that use HistoryDatasetAssociation objects. """ |
---|
| 78 | def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False ): |
---|
| 79 | """ Get an HDA object by id. """ |
---|
| 80 | # DEPRECATION: We still support unencoded ids for backward compatibility |
---|
| 81 | try: |
---|
| 82 | data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) |
---|
| 83 | if data is None: |
---|
| 84 | raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) |
---|
| 85 | except: |
---|
| 86 | try: |
---|
| 87 | data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) |
---|
| 88 | except: |
---|
| 89 | data = None |
---|
| 90 | if not data: |
---|
| 91 | raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid dataset id: %s." % str( dataset_id ) ) |
---|
| 92 | if check_ownership: |
---|
| 93 | # Verify ownership. |
---|
| 94 | user = trans.get_user() |
---|
| 95 | if not user: |
---|
| 96 | error( "Must be logged in to manage Galaxy items" ) |
---|
| 97 | if data.history.user != user: |
---|
| 98 | error( "%s is not owned by current user" % data.__class__.__name__ ) |
---|
| 99 | if check_accessible: |
---|
| 100 | current_user_roles = trans.get_current_user_roles() |
---|
| 101 | if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): |
---|
| 102 | if data.state == trans.model.Dataset.states.UPLOAD: |
---|
| 103 | return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) |
---|
| 104 | else: |
---|
| 105 | error( "You are not allowed to access this dataset" ) |
---|
| 106 | return data |
---|
| 107 | def get_data( self, dataset, preview=True ): |
---|
| 108 | """ Gets a dataset's data. """ |
---|
| 109 | # Get data from file, truncating if necessary. |
---|
| 110 | truncated = False |
---|
| 111 | dataset_data = None |
---|
| 112 | if os.path.exists( dataset.file_name ): |
---|
| 113 | max_peek_size = 1000000 # 1 MB |
---|
| 114 | if preview and os.stat( dataset.file_name ).st_size > max_peek_size: |
---|
| 115 | dataset_data = open( dataset.file_name ).read(max_peek_size) |
---|
| 116 | truncated = True |
---|
| 117 | else: |
---|
| 118 | dataset_data = open( dataset.file_name ).read(max_peek_size) |
---|
| 119 | truncated = False |
---|
| 120 | return truncated, dataset_data |
---|
| 121 | |
---|
| 122 | class UsesVisualization( SharableItemSecurity ): |
---|
| 123 | """ Mixin for controllers that use Visualization objects. """ |
---|
| 124 | |
---|
| 125 | len_files = None |
---|
| 126 | |
---|
| 127 | def _get_dbkeys( self, trans ): |
---|
| 128 | """ Returns all valid dbkeys that a user can use in a visualization. """ |
---|
| 129 | |
---|
| 130 | # Read len files. |
---|
| 131 | if not self.len_files: |
---|
| 132 | len_files = glob.glob(os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "*.len" )) |
---|
| 133 | self.len_files = [ os.path.split(f)[1].split(".len")[0] for f in len_files ] # get xxx.len |
---|
| 134 | |
---|
| 135 | user_keys = {} |
---|
| 136 | user = trans.get_user() |
---|
| 137 | if 'dbkeys' in user.preferences: |
---|
| 138 | user_keys = from_json_string( user.preferences['dbkeys'] ) |
---|
| 139 | |
---|
| 140 | dbkeys = [ (v, k) for k, v in trans.db_builds if k in self.len_files or k in user_keys ] |
---|
| 141 | return dbkeys |
---|
| 142 | |
---|
| 143 | def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): |
---|
| 144 | """ Get a Visualization from the database by id, verifying ownership. """ |
---|
| 145 | # Load workflow from database |
---|
| 146 | id = trans.security.decode_id( id ) |
---|
| 147 | visualization = trans.sa_session.query( trans.model.Visualization ).get( id ) |
---|
| 148 | if not visualization: |
---|
| 149 | error( "Visualization not found" ) |
---|
| 150 | else: |
---|
| 151 | return self.security_check( trans.get_user(), visualization, check_ownership, check_accessible ) |
---|
| 152 | |
---|
| 153 | def get_visualization_config( self, trans, visualization ): |
---|
| 154 | """ Returns a visualization's configuration. Only works for trackster visualizations right now. """ |
---|
| 155 | |
---|
| 156 | config = None |
---|
| 157 | if visualization.type == 'trackster': |
---|
| 158 | # Trackster config; taken from tracks/browser |
---|
| 159 | latest_revision = visualization.latest_revision |
---|
| 160 | tracks = [] |
---|
| 161 | |
---|
| 162 | # Set tracks. |
---|
| 163 | if 'tracks' in latest_revision.config: |
---|
| 164 | hda_query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) |
---|
| 165 | for t in visualization.latest_revision.config['tracks']: |
---|
| 166 | dataset_id = t['dataset_id'] |
---|
| 167 | try: |
---|
| 168 | prefs = t['prefs'] |
---|
| 169 | except KeyError: |
---|
| 170 | prefs = {} |
---|
| 171 | dataset = hda_query.get( dataset_id ) |
---|
| 172 | track_type, _ = dataset.datatype.get_track_type() |
---|
| 173 | track_data_provider_class = get_data_provider( original_dataset=dataset ) |
---|
| 174 | track_data_provider = track_data_provider_class( original_dataset=dataset ) |
---|
| 175 | |
---|
| 176 | tracks.append( { |
---|
| 177 | "track_type": track_type, |
---|
| 178 | "name": dataset.name, |
---|
| 179 | "dataset_id": dataset.id, |
---|
| 180 | "prefs": simplejson.dumps(prefs), |
---|
| 181 | "filters": track_data_provider.get_filters() |
---|
| 182 | } ) |
---|
| 183 | |
---|
| 184 | config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), |
---|
| 185 | "tracks": tracks, "chrom": "", "dbkey": visualization.dbkey } |
---|
| 186 | |
---|
| 187 | return config |
---|
| 188 | |
---|
| 189 | class UsesStoredWorkflow( SharableItemSecurity ): |
---|
| 190 | """ Mixin for controllers that use StoredWorkflow objects. """ |
---|
| 191 | def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): |
---|
| 192 | """ Get a StoredWorkflow from the database by id, verifying ownership. """ |
---|
| 193 | # Load workflow from database |
---|
| 194 | id = trans.security.decode_id( id ) |
---|
| 195 | stored = trans.sa_session.query( trans.model.StoredWorkflow ).get( id ) |
---|
| 196 | if not stored: |
---|
| 197 | error( "Workflow not found" ) |
---|
| 198 | else: |
---|
| 199 | return self.security_check( trans.get_user(), stored, check_ownership, check_accessible ) |
---|
| 200 | def get_stored_workflow_steps( self, trans, stored_workflow ): |
---|
| 201 | """ Restores states for a stored workflow's steps. """ |
---|
| 202 | for step in stored_workflow.latest_workflow.steps: |
---|
| 203 | if step.type == 'tool' or step.type is None: |
---|
| 204 | # Restore the tool state for the step |
---|
| 205 | module = module_factory.from_workflow_step( trans, step ) |
---|
| 206 | # Any connected input needs to have value DummyDataset (these |
---|
| 207 | # are not persisted so we need to do it every time) |
---|
| 208 | module.add_dummy_datasets( connections=step.input_connections ) |
---|
| 209 | # Store state with the step |
---|
| 210 | step.module = module |
---|
| 211 | step.state = module.state |
---|
| 212 | # Error dict |
---|
| 213 | if step.tool_errors: |
---|
| 214 | errors[step.id] = step.tool_errors |
---|
| 215 | else: |
---|
| 216 | ## Non-tool specific stuff? |
---|
| 217 | step.module = module_factory.from_workflow_step( trans, step ) |
---|
| 218 | step.state = step.module.get_runtime_state() |
---|
| 219 | # Connections by input name |
---|
| 220 | step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) |
---|
| 221 | |
---|
| 222 | class UsesHistory( SharableItemSecurity ): |
---|
| 223 | """ Mixin for controllers that use History objects. """ |
---|
| 224 | def get_history( self, trans, id, check_ownership=True, check_accessible=False ): |
---|
| 225 | """Get a History from the database by id, verifying ownership.""" |
---|
| 226 | # Load history from database |
---|
| 227 | id = trans.security.decode_id( id ) |
---|
| 228 | history = trans.sa_session.query( trans.model.History ).get( id ) |
---|
| 229 | if not history: |
---|
| 230 | err+msg( "History not found" ) |
---|
| 231 | else: |
---|
| 232 | return self.security_check( trans.get_user(), history, check_ownership, check_accessible ) |
---|
| 233 | def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False): |
---|
| 234 | """ Returns history's datasets. """ |
---|
| 235 | query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ |
---|
| 236 | .filter( trans.model.HistoryDatasetAssociation.history == history ) \ |
---|
| 237 | .options( eagerload( "children" ) ) \ |
---|
| 238 | .join( "dataset" ).filter( trans.model.Dataset.purged == False ) \ |
---|
| 239 | .options( eagerload_all( "dataset.actions" ) ) \ |
---|
| 240 | .order_by( trans.model.HistoryDatasetAssociation.hid ) |
---|
| 241 | if not show_deleted: |
---|
| 242 | query = query.filter( trans.model.HistoryDatasetAssociation.deleted == False ) |
---|
| 243 | return query.all() |
---|
| 244 | |
---|
| 245 | class UsesFormDefinitionWidgets: |
---|
| 246 | """Mixin for controllers that use Galaxy form objects.""" |
---|
| 247 | def get_all_forms( self, trans, all_versions=False, filter=None, form_type='All' ): |
---|
| 248 | """ |
---|
| 249 | Return all the latest forms from the form_definition_current table |
---|
| 250 | if all_versions is set to True. Otherwise return all the versions |
---|
| 251 | of all the forms from the form_definition table. |
---|
| 252 | """ |
---|
| 253 | if all_versions: |
---|
| 254 | return trans.sa_session.query( trans.app.model.FormDefinition ) |
---|
| 255 | if filter: |
---|
| 256 | fdc_list = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).filter_by( **filter ) |
---|
| 257 | else: |
---|
| 258 | fdc_list = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ) |
---|
| 259 | if form_type == 'All': |
---|
| 260 | return [ fdc.latest_form for fdc in fdc_list ] |
---|
| 261 | else: |
---|
| 262 | return [ fdc.latest_form for fdc in fdc_list if fdc.latest_form.type == form_type ] |
---|
| 263 | def widget_fields_have_contents( self, widgets ): |
---|
| 264 | # Return True if any of the fields in widgets contain contents, widgets is a list of dictionaries that looks something like: |
---|
| 265 | # [{'widget': <galaxy.web.form_builder.TextField object at 0x10867aa10>, 'helptext': 'Field 0 help (Optional)', 'label': 'Field 0'}] |
---|
| 266 | for i, field in enumerate( widgets ): |
---|
| 267 | if ( isinstance( field[ 'widget' ], TextArea ) or isinstance( field[ 'widget' ], TextField ) ) and field[ 'widget' ].value: |
---|
| 268 | return True |
---|
| 269 | if isinstance( field[ 'widget' ], SelectField ) and field[ 'widget' ].options: |
---|
| 270 | for option_label, option_value, selected in field['widget'].options: |
---|
| 271 | if selected: |
---|
| 272 | return True |
---|
| 273 | if isinstance( field[ 'widget' ], CheckboxField ) and field[ 'widget' ].checked: |
---|
| 274 | return True |
---|
| 275 | if isinstance( field[ 'widget' ], WorkflowField ) and str( field[ 'widget' ].value ).lower() not in [ 'none' ]: |
---|
| 276 | return True |
---|
| 277 | if isinstance( field[ 'widget' ], AddressField ) and str( field[ 'widget' ].value ).lower() not in [ 'none' ]: |
---|
| 278 | return True |
---|
| 279 | return False |
---|
| 280 | def clean_field_contents( self, widgets, **kwd ): |
---|
| 281 | field_contents = [] |
---|
| 282 | for index, widget_dict in enumerate( widgets ): |
---|
| 283 | widget = widget_dict[ 'widget' ] |
---|
| 284 | value = kwd.get( widget.name, '' ) |
---|
| 285 | if isinstance( widget, CheckboxField ): |
---|
| 286 | # CheckboxField values are lists if the checkbox is checked |
---|
| 287 | value = str( widget.is_checked( value ) ).lower() |
---|
| 288 | elif isinstance( widget, AddressField ): |
---|
| 289 | # If the address was new, is has already been saved and widget.value is the new address.id |
---|
| 290 | value = widget.value |
---|
| 291 | field_contents.append( util.restore_text( value ) ) |
---|
| 292 | return field_contents |
---|
| 293 | def field_param_values_ok( self, index, widget_type, **kwd ): |
---|
| 294 | # Make sure required fields have contents, etc |
---|
| 295 | params = util.Params( kwd ) |
---|
| 296 | if widget_type == 'AddressField': |
---|
| 297 | if not util.restore_text( params.get( 'field_%i_short_desc' % index, '' ) ) \ |
---|
| 298 | or not util.restore_text( params.get( 'field_%i_name' % index, '' ) ) \ |
---|
| 299 | or not util.restore_text( params.get( 'field_%i_institution' % index, '' ) ) \ |
---|
| 300 | or not util.restore_text( params.get( 'field_%i_address' % index, '' ) ) \ |
---|
| 301 | or not util.restore_text( params.get( 'field_%i_city' % index, '' ) ) \ |
---|
| 302 | or not util.restore_text( params.get( 'field_%i_state' % index, '' ) ) \ |
---|
| 303 | or not util.restore_text( params.get( 'field_%i_postal_code' % index, '' ) ) \ |
---|
| 304 | or not util.restore_text( params.get( 'field_%i_country' % index, '' ) ): |
---|
| 305 | return False |
---|
| 306 | return True |
---|
| 307 | def save_widget_field( self, trans, field_obj, index, **kwd ): |
---|
| 308 | # Save a form_builder field object |
---|
| 309 | params = util.Params( kwd ) |
---|
| 310 | if isinstance( field_obj, trans.model.UserAddress ): |
---|
| 311 | field_obj.desc = util.restore_text( params.get( 'field_%i_short_desc' % index, '' ) ) |
---|
| 312 | field_obj.name = util.restore_text( params.get( 'field_%i_name' % index, '' ) ) |
---|
| 313 | field_obj.institution = util.restore_text( params.get( 'field_%i_institution' % index, '' ) ) |
---|
| 314 | field_obj.address = util.restore_text( params.get( 'field_%i_address' % index, '' ) ) |
---|
| 315 | field_obj.city = util.restore_text( params.get( 'field_%i_city' % index, '' ) ) |
---|
| 316 | field_obj.state = util.restore_text( params.get( 'field_%i_state' % index, '' ) ) |
---|
| 317 | field_obj.postal_code = util.restore_text( params.get( 'field_%i_postal_code' % index, '' ) ) |
---|
| 318 | field_obj.country = util.restore_text( params.get( 'field_%i_country' % index, '' ) ) |
---|
| 319 | field_obj.phone = util.restore_text( params.get( 'field_%i_phone' % index, '' ) ) |
---|
| 320 | trans.sa_session.add( field_obj ) |
---|
| 321 | trans.sa_session.flush() |
---|
| 322 | def populate_widgets_from_kwd( self, trans, widgets, **kwd ): |
---|
| 323 | # A form submitted via refresh_on_change requires us to populate the widgets with the contents of |
---|
| 324 | # the form fields the user may have entered so that when the form refreshes the contents are retained. |
---|
| 325 | params = util.Params( kwd ) |
---|
| 326 | populated_widgets = [] |
---|
| 327 | for widget_dict in widgets: |
---|
| 328 | widget = widget_dict[ 'widget' ] |
---|
| 329 | if params.get( widget.name, False ): |
---|
| 330 | # The form included a field whose contents should be used to set the |
---|
| 331 | # value of the current widget (widget.name is field_0, field_1, etc). |
---|
| 332 | if isinstance( widget, AddressField ): |
---|
| 333 | value = util.restore_text( params.get( widget.name, '' ) ) |
---|
| 334 | if value == 'new': |
---|
| 335 | # Adding a new address |
---|
| 336 | widget.value = value |
---|
| 337 | widget_dict[ 'widget' ] = widget |
---|
| 338 | elif value == 'none': |
---|
| 339 | widget.value = '' |
---|
| 340 | widget_dict[ 'widget' ] = widget |
---|
| 341 | else: |
---|
| 342 | # An existing address object was selected |
---|
| 343 | widget_dict[ 'widget' ] = widget |
---|
| 344 | # Populate the AddressField params with the form field contents |
---|
| 345 | widget_params_dict = {} |
---|
| 346 | for field_name, label, help_text in widget.fields(): |
---|
| 347 | form_param_name = '%s_%s' % ( widget.name, field_name ) |
---|
| 348 | widget_params_dict[ form_param_name ] = util.restore_text( params.get( form_param_name, '' ) ) |
---|
| 349 | widget.params = widget_params_dict |
---|
| 350 | elif isinstance( widget, CheckboxField ): |
---|
| 351 | # Check the value from kwd since util.Params would have |
---|
| 352 | # stringify'd the list if the checkbox is checked. |
---|
| 353 | value = kwd.get( widget.name, '' ) |
---|
| 354 | if CheckboxField.is_checked( value ): |
---|
| 355 | widget.value = 'true' |
---|
| 356 | widget_dict[ 'widget' ] = widget |
---|
| 357 | elif isinstance( widget, SelectField ): |
---|
| 358 | # Ensure the selected option remains selected. |
---|
| 359 | value = util.restore_text( params.get( widget.name, '' ) ) |
---|
| 360 | processed_options = [] |
---|
| 361 | for option_label, option_value, option_selected in widget.options: |
---|
| 362 | selected = value == option_value |
---|
| 363 | processed_options.append( ( option_label, option_value, selected ) ) |
---|
| 364 | widget.options = processed_options |
---|
| 365 | else: |
---|
| 366 | widget.value = util.restore_text( params.get( widget.name, '' ) ) |
---|
| 367 | widget_dict[ 'widget' ] = widget |
---|
| 368 | populated_widgets.append( widget_dict ) |
---|
| 369 | return populated_widgets |
---|
| 370 | |
---|
| 371 | class Sharable: |
---|
| 372 | """ Mixin for a controller that manages an item that can be shared. """ |
---|
| 373 | # Implemented methods. |
---|
| 374 | @web.expose |
---|
| 375 | @web.require_login( "share Galaxy items" ) |
---|
| 376 | def set_public_username( self, trans, id, username, **kwargs ): |
---|
| 377 | """ Set user's public username and delegate to sharing() """ |
---|
| 378 | trans.get_user().username = username |
---|
| 379 | trans.sa_session.flush |
---|
| 380 | return self.sharing( trans, id, **kwargs ) |
---|
| 381 | # Abstract methods. |
---|
| 382 | @web.expose |
---|
| 383 | @web.require_login( "modify Galaxy items" ) |
---|
| 384 | def set_slug_async( self, trans, id, new_slug ): |
---|
| 385 | """ Set item slug asynchronously. """ |
---|
| 386 | pass |
---|
| 387 | @web.expose |
---|
| 388 | @web.require_login( "share Galaxy items" ) |
---|
| 389 | def sharing( self, trans, id, **kwargs ): |
---|
| 390 | """ Handle item sharing. """ |
---|
| 391 | pass |
---|
| 392 | @web.expose |
---|
| 393 | @web.require_login( "share Galaxy items" ) |
---|
| 394 | def share( self, trans, id=None, email="", **kwd ): |
---|
| 395 | """ Handle sharing an item with a particular user. """ |
---|
| 396 | pass |
---|
| 397 | @web.expose |
---|
| 398 | def display_by_username_and_slug( self, trans, username, slug ): |
---|
| 399 | """ Display item by username and slug. """ |
---|
| 400 | pass |
---|
| 401 | @web.expose |
---|
| 402 | @web.json |
---|
| 403 | @web.require_login( "get item name and link" ) |
---|
| 404 | def get_name_and_link_async( self, trans, id=None ): |
---|
| 405 | """ Returns item's name and link. """ |
---|
| 406 | pass |
---|
| 407 | @web.expose |
---|
| 408 | @web.require_login("get item content asynchronously") |
---|
| 409 | def get_item_content_async( self, trans, id ): |
---|
| 410 | """ Returns item content in HTML format. """ |
---|
| 411 | pass |
---|
| 412 | # Helper methods. |
---|
| 413 | def _make_item_accessible( self, sa_session, item ): |
---|
| 414 | """ Makes item accessible--viewable and importable--and sets item's slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes. """ |
---|
| 415 | item.importable = True |
---|
| 416 | self.create_item_slug( sa_session, item ) |
---|
| 417 | def create_item_slug( self, sa_session, item ): |
---|
| 418 | """ Create item slug. Slug is unique among user's importable items for item's class. Returns true if item's slug was set; false otherwise. """ |
---|
| 419 | if item.slug is None or item.slug == "": |
---|
| 420 | # Item can have either a name or a title. |
---|
| 421 | if hasattr( item, 'name' ): |
---|
| 422 | item_name = item.name |
---|
| 423 | elif hasattr( item, 'title' ): |
---|
| 424 | item_name = item.title |
---|
| 425 | # Replace whitespace with '-' |
---|
| 426 | slug_base = re.sub( "\s+", "-", item_name.lower() ) |
---|
| 427 | # Remove all non-alphanumeric characters. |
---|
| 428 | slug_base = re.sub( "[^a-zA-Z0-9\-]", "", slug_base ) |
---|
| 429 | # Remove trailing '-'. |
---|
| 430 | if slug_base.endswith('-'): |
---|
| 431 | slug_base = slug_base[:-1] |
---|
| 432 | # Make sure that slug is not taken; if it is, add a number to it. |
---|
| 433 | slug = slug_base |
---|
| 434 | count = 1 |
---|
| 435 | while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=slug, importable=True ).count() != 0: |
---|
| 436 | # Slug taken; choose a new slug based on count. This approach can handle numerous histories with the same name gracefully. |
---|
| 437 | slug = '%s-%i' % ( slug_base, count ) |
---|
| 438 | count += 1 |
---|
| 439 | item.slug = slug |
---|
| 440 | return True |
---|
| 441 | return False |
---|
| 442 | |
---|
| 443 | """ |
---|
| 444 | Deprecated: `BaseController` used to be available under the name `Root` |
---|
| 445 | """ |
---|
| 446 | class ControllerUnavailable( Exception ): |
---|
| 447 | pass |
---|
| 448 | |
---|
| 449 | class Admin( object ): |
---|
| 450 | # Override these |
---|
| 451 | user_list_grid = None |
---|
| 452 | role_list_grid = None |
---|
| 453 | group_list_grid = None |
---|
| 454 | |
---|
| 455 | @web.expose |
---|
| 456 | @web.require_admin |
---|
| 457 | def index( self, trans, **kwd ): |
---|
| 458 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 459 | params = util.Params( kwd ) |
---|
| 460 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 461 | status = params.get( 'status', 'done' ) |
---|
| 462 | if webapp == 'galaxy': |
---|
| 463 | return trans.fill_template( '/webapps/galaxy/admin/index.mako', |
---|
| 464 | webapp=webapp, |
---|
| 465 | message=message, |
---|
| 466 | status=status ) |
---|
| 467 | else: |
---|
| 468 | return trans.fill_template( '/webapps/community/admin/index.mako', |
---|
| 469 | webapp=webapp, |
---|
| 470 | message=message, |
---|
| 471 | status=status ) |
---|
| 472 | @web.expose |
---|
| 473 | @web.require_admin |
---|
| 474 | def center( self, trans, **kwd ): |
---|
| 475 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 476 | if webapp == 'galaxy': |
---|
| 477 | return trans.fill_template( '/webapps/galaxy/admin/center.mako' ) |
---|
| 478 | else: |
---|
| 479 | return trans.fill_template( '/webapps/community/admin/center.mako' ) |
---|
| 480 | @web.expose |
---|
| 481 | @web.require_admin |
---|
| 482 | def reload_tool( self, trans, **kwd ): |
---|
| 483 | params = util.Params( kwd ) |
---|
| 484 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 485 | status = params.get( 'status', 'done' ) |
---|
| 486 | return trans.fill_template( '/admin/reload_tool.mako', |
---|
| 487 | toolbox=self.app.toolbox, |
---|
| 488 | message=message, |
---|
| 489 | status=status ) |
---|
| 490 | @web.expose |
---|
| 491 | @web.require_admin |
---|
| 492 | def tool_reload( self, trans, tool_version=None, **kwd ): |
---|
| 493 | params = util.Params( kwd ) |
---|
| 494 | tool_id = params.tool_id |
---|
| 495 | self.app.toolbox.reload( tool_id ) |
---|
| 496 | message = 'Reloaded tool: ' + tool_id |
---|
| 497 | return trans.fill_template( '/admin/reload_tool.mako', |
---|
| 498 | toolbox=self.app.toolbox, |
---|
| 499 | message=message, |
---|
| 500 | status='done' ) |
---|
| 501 | |
---|
| 502 | # Galaxy Role Stuff |
---|
| 503 | @web.expose |
---|
| 504 | @web.require_admin |
---|
| 505 | def roles( self, trans, **kwargs ): |
---|
| 506 | if 'operation' in kwargs: |
---|
| 507 | operation = kwargs['operation'].lower() |
---|
| 508 | if operation == "roles": |
---|
| 509 | return self.role( trans, **kwargs ) |
---|
| 510 | if operation == "create": |
---|
| 511 | return self.create_role( trans, **kwargs ) |
---|
| 512 | if operation == "delete": |
---|
| 513 | return self.mark_role_deleted( trans, **kwargs ) |
---|
| 514 | if operation == "undelete": |
---|
| 515 | return self.undelete_role( trans, **kwargs ) |
---|
| 516 | if operation == "purge": |
---|
| 517 | return self.purge_role( trans, **kwargs ) |
---|
| 518 | if operation == "manage users and groups": |
---|
| 519 | return self.manage_users_and_groups_for_role( trans, **kwargs ) |
---|
| 520 | if operation == "rename": |
---|
| 521 | return self.rename_role( trans, **kwargs ) |
---|
| 522 | # Render the list view |
---|
| 523 | return self.role_list_grid( trans, **kwargs ) |
---|
| 524 | @web.expose |
---|
| 525 | @web.require_admin |
---|
| 526 | def create_role( self, trans, **kwd ): |
---|
| 527 | params = util.Params( kwd ) |
---|
| 528 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 529 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 530 | status = params.get( 'status', 'done' ) |
---|
| 531 | if params.get( 'create_role_button', False ): |
---|
| 532 | name = util.restore_text( params.name ) |
---|
| 533 | description = util.restore_text( params.description ) |
---|
| 534 | in_users = util.listify( params.get( 'in_users', [] ) ) |
---|
| 535 | in_groups = util.listify( params.get( 'in_groups', [] ) ) |
---|
| 536 | create_group_for_role = params.get( 'create_group_for_role', 'no' ) |
---|
| 537 | if not name or not description: |
---|
| 538 | message = "Enter a valid name and a description" |
---|
| 539 | elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==name ).first(): |
---|
| 540 | message = "A role with that name already exists" |
---|
| 541 | else: |
---|
| 542 | # Create the role |
---|
| 543 | role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN ) |
---|
| 544 | trans.sa_session.add( role ) |
---|
| 545 | # Create the UserRoleAssociations |
---|
| 546 | for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]: |
---|
| 547 | ura = trans.app.model.UserRoleAssociation( user, role ) |
---|
| 548 | trans.sa_session.add( ura ) |
---|
| 549 | # Create the GroupRoleAssociations |
---|
| 550 | for group in [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in in_groups ]: |
---|
| 551 | gra = trans.app.model.GroupRoleAssociation( group, role ) |
---|
| 552 | trans.sa_session.add( gra ) |
---|
| 553 | if create_group_for_role == 'yes': |
---|
| 554 | # Create the group |
---|
| 555 | group = trans.app.model.Group( name=name ) |
---|
| 556 | trans.sa_session.add( group ) |
---|
| 557 | message = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ |
---|
| 558 | ( group.name, role.name, len( in_users ), len( in_groups ) ) |
---|
| 559 | else: |
---|
| 560 | message = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) |
---|
| 561 | trans.sa_session.flush() |
---|
| 562 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 563 | action='roles', |
---|
| 564 | webapp=webapp, |
---|
| 565 | message=util.sanitize_text( message ), |
---|
| 566 | status='done' ) ) |
---|
| 567 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 568 | action='create_role', |
---|
| 569 | webapp=webapp, |
---|
| 570 | message=util.sanitize_text( message ), |
---|
| 571 | status='error' ) ) |
---|
| 572 | out_users = [] |
---|
| 573 | for user in trans.sa_session.query( trans.app.model.User ) \ |
---|
| 574 | .filter( trans.app.model.User.table.c.deleted==False ) \ |
---|
| 575 | .order_by( trans.app.model.User.table.c.email ): |
---|
| 576 | out_users.append( ( user.id, user.email ) ) |
---|
| 577 | out_groups = [] |
---|
| 578 | for group in trans.sa_session.query( trans.app.model.Group ) \ |
---|
| 579 | .filter( trans.app.model.Group.table.c.deleted==False ) \ |
---|
| 580 | .order_by( trans.app.model.Group.table.c.name ): |
---|
| 581 | out_groups.append( ( group.id, group.name ) ) |
---|
| 582 | return trans.fill_template( '/admin/dataset_security/role/role_create.mako', |
---|
| 583 | in_users=[], |
---|
| 584 | out_users=out_users, |
---|
| 585 | in_groups=[], |
---|
| 586 | out_groups=out_groups, |
---|
| 587 | webapp=webapp, |
---|
| 588 | message=message, |
---|
| 589 | status=status ) |
---|
| 590 | @web.expose |
---|
| 591 | @web.require_admin |
---|
| 592 | def rename_role( self, trans, **kwd ): |
---|
| 593 | params = util.Params( kwd ) |
---|
| 594 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 595 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 596 | status = params.get( 'status', 'done' ) |
---|
| 597 | id = params.get( 'id', None ) |
---|
| 598 | if not id: |
---|
| 599 | message = "No role ids received for renaming" |
---|
| 600 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 601 | action='roles', |
---|
| 602 | webapp=webapp, |
---|
| 603 | message=message, |
---|
| 604 | status='error' ) ) |
---|
| 605 | role = get_role( trans, id ) |
---|
| 606 | if params.get( 'rename_role_button', False ): |
---|
| 607 | old_name = role.name |
---|
| 608 | new_name = util.restore_text( params.name ) |
---|
| 609 | new_description = util.restore_text( params.description ) |
---|
| 610 | if not new_name: |
---|
| 611 | message = 'Enter a valid name' |
---|
| 612 | status='error' |
---|
| 613 | elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first(): |
---|
| 614 | message = 'A role with that name already exists' |
---|
| 615 | status = 'error' |
---|
| 616 | else: |
---|
| 617 | role.name = new_name |
---|
| 618 | role.description = new_description |
---|
| 619 | trans.sa_session.add( role ) |
---|
| 620 | trans.sa_session.flush() |
---|
| 621 | message = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) |
---|
| 622 | return trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 623 | action='roles', |
---|
| 624 | webapp=webapp, |
---|
| 625 | message=util.sanitize_text( message ), |
---|
| 626 | status='done' ) ) |
---|
| 627 | return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', |
---|
| 628 | role=role, |
---|
| 629 | webapp=webapp, |
---|
| 630 | message=message, |
---|
| 631 | status=status ) |
---|
| 632 | @web.expose |
---|
| 633 | @web.require_admin |
---|
| 634 | def manage_users_and_groups_for_role( self, trans, **kwd ): |
---|
| 635 | params = util.Params( kwd ) |
---|
| 636 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 637 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 638 | status = params.get( 'status', 'done' ) |
---|
| 639 | id = params.get( 'id', None ) |
---|
| 640 | if not id: |
---|
| 641 | message = "No role ids received for managing users and groups" |
---|
| 642 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 643 | action='roles', |
---|
| 644 | webapp=webapp, |
---|
| 645 | message=message, |
---|
| 646 | status='error' ) ) |
---|
| 647 | role = get_role( trans, id ) |
---|
| 648 | if params.get( 'role_members_edit_button', False ): |
---|
| 649 | in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] |
---|
| 650 | for ura in role.users: |
---|
| 651 | user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id ) |
---|
| 652 | if user not in in_users: |
---|
| 653 | # Delete DefaultUserPermissions for previously associated users that have been removed from the role |
---|
| 654 | for dup in user.default_permissions: |
---|
| 655 | if role == dup.role: |
---|
| 656 | trans.sa_session.delete( dup ) |
---|
| 657 | # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role |
---|
| 658 | for history in user.histories: |
---|
| 659 | for dhp in history.default_permissions: |
---|
| 660 | if role == dhp.role: |
---|
| 661 | trans.sa_session.delete( dhp ) |
---|
| 662 | trans.sa_session.flush() |
---|
| 663 | in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] |
---|
| 664 | trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups ) |
---|
| 665 | trans.sa_session.refresh( role ) |
---|
| 666 | message = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) |
---|
| 667 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 668 | action='roles', |
---|
| 669 | webapp=webapp, |
---|
| 670 | message=util.sanitize_text( message ), |
---|
| 671 | status=status ) ) |
---|
| 672 | in_users = [] |
---|
| 673 | out_users = [] |
---|
| 674 | in_groups = [] |
---|
| 675 | out_groups = [] |
---|
| 676 | for user in trans.sa_session.query( trans.app.model.User ) \ |
---|
| 677 | .filter( trans.app.model.User.table.c.deleted==False ) \ |
---|
| 678 | .order_by( trans.app.model.User.table.c.email ): |
---|
| 679 | if user in [ x.user for x in role.users ]: |
---|
| 680 | in_users.append( ( user.id, user.email ) ) |
---|
| 681 | else: |
---|
| 682 | out_users.append( ( user.id, user.email ) ) |
---|
| 683 | for group in trans.sa_session.query( trans.app.model.Group ) \ |
---|
| 684 | .filter( trans.app.model.Group.table.c.deleted==False ) \ |
---|
| 685 | .order_by( trans.app.model.Group.table.c.name ): |
---|
| 686 | if group in [ x.group for x in role.groups ]: |
---|
| 687 | in_groups.append( ( group.id, group.name ) ) |
---|
| 688 | else: |
---|
| 689 | out_groups.append( ( group.id, group.name ) ) |
---|
| 690 | library_dataset_actions = {} |
---|
| 691 | if webapp == 'galaxy': |
---|
| 692 | # Build a list of tuples that are LibraryDatasetDatasetAssociationss followed by a list of actions |
---|
| 693 | # whose DatasetPermissions is associated with the Role |
---|
| 694 | # [ ( LibraryDatasetDatasetAssociation [ action, action ] ) ] |
---|
| 695 | for dp in role.dataset_actions: |
---|
| 696 | for ldda in trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ |
---|
| 697 | .filter( trans.app.model.LibraryDatasetDatasetAssociation.dataset_id==dp.dataset_id ): |
---|
| 698 | root_found = False |
---|
| 699 | folder_path = '' |
---|
| 700 | folder = ldda.library_dataset.folder |
---|
| 701 | while not root_found: |
---|
| 702 | folder_path = '%s / %s' % ( folder.name, folder_path ) |
---|
| 703 | if not folder.parent: |
---|
| 704 | root_found = True |
---|
| 705 | else: |
---|
| 706 | folder = folder.parent |
---|
| 707 | folder_path = '%s %s' % ( folder_path, ldda.name ) |
---|
| 708 | library = trans.sa_session.query( trans.app.model.Library ) \ |
---|
| 709 | .filter( trans.app.model.Library.table.c.root_folder_id == folder.id ) \ |
---|
| 710 | .first() |
---|
| 711 | if library not in library_dataset_actions: |
---|
| 712 | library_dataset_actions[ library ] = {} |
---|
| 713 | try: |
---|
| 714 | library_dataset_actions[ library ][ folder_path ].append( dp.action ) |
---|
| 715 | except: |
---|
| 716 | library_dataset_actions[ library ][ folder_path ] = [ dp.action ] |
---|
| 717 | return trans.fill_template( '/admin/dataset_security/role/role.mako', |
---|
| 718 | role=role, |
---|
| 719 | in_users=in_users, |
---|
| 720 | out_users=out_users, |
---|
| 721 | in_groups=in_groups, |
---|
| 722 | out_groups=out_groups, |
---|
| 723 | library_dataset_actions=library_dataset_actions, |
---|
| 724 | webapp=webapp, |
---|
| 725 | message=message, |
---|
| 726 | status=status ) |
---|
| 727 | @web.expose |
---|
| 728 | @web.require_admin |
---|
| 729 | def mark_role_deleted( self, trans, **kwd ): |
---|
| 730 | params = util.Params( kwd ) |
---|
| 731 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 732 | id = kwd.get( 'id', None ) |
---|
| 733 | if not id: |
---|
| 734 | message = "No role ids received for deleting" |
---|
| 735 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 736 | action='roles', |
---|
| 737 | webapp=webapp, |
---|
| 738 | message=message, |
---|
| 739 | status='error' ) ) |
---|
| 740 | ids = util.listify( id ) |
---|
| 741 | message = "Deleted %d roles: " % len( ids ) |
---|
| 742 | for role_id in ids: |
---|
| 743 | role = get_role( trans, role_id ) |
---|
| 744 | role.deleted = True |
---|
| 745 | trans.sa_session.add( role ) |
---|
| 746 | trans.sa_session.flush() |
---|
| 747 | message += " %s " % role.name |
---|
| 748 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 749 | action='roles', |
---|
| 750 | webapp=webapp, |
---|
| 751 | message=util.sanitize_text( message ), |
---|
| 752 | status='done' ) ) |
---|
| 753 | @web.expose |
---|
| 754 | @web.require_admin |
---|
| 755 | def undelete_role( self, trans, **kwd ): |
---|
| 756 | params = util.Params( kwd ) |
---|
| 757 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 758 | id = kwd.get( 'id', None ) |
---|
| 759 | if not id: |
---|
| 760 | message = "No role ids received for undeleting" |
---|
| 761 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 762 | action='roles', |
---|
| 763 | webapp=webapp, |
---|
| 764 | message=message, |
---|
| 765 | status='error' ) ) |
---|
| 766 | ids = util.listify( id ) |
---|
| 767 | count = 0 |
---|
| 768 | undeleted_roles = "" |
---|
| 769 | for role_id in ids: |
---|
| 770 | role = get_role( trans, role_id ) |
---|
| 771 | if not role.deleted: |
---|
| 772 | message = "Role '%s' has not been deleted, so it cannot be undeleted." % role.name |
---|
| 773 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 774 | action='roles', |
---|
| 775 | webapp=webapp, |
---|
| 776 | message=util.sanitize_text( message ), |
---|
| 777 | status='error' ) ) |
---|
| 778 | role.deleted = False |
---|
| 779 | trans.sa_session.add( role ) |
---|
| 780 | trans.sa_session.flush() |
---|
| 781 | count += 1 |
---|
| 782 | undeleted_roles += " %s" % role.name |
---|
| 783 | message = "Undeleted %d roles: %s" % ( count, undeleted_roles ) |
---|
| 784 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 785 | action='roles', |
---|
| 786 | webapp=webapp, |
---|
| 787 | message=util.sanitize_text( message ), |
---|
| 788 | status='done' ) ) |
---|
| 789 | @web.expose |
---|
| 790 | @web.require_admin |
---|
| 791 | def purge_role( self, trans, **kwd ): |
---|
| 792 | # This method should only be called for a Role that has previously been deleted. |
---|
| 793 | # Purging a deleted Role deletes all of the following from the database: |
---|
| 794 | # - UserRoleAssociations where role_id == Role.id |
---|
| 795 | # - DefaultUserPermissions where role_id == Role.id |
---|
| 796 | # - DefaultHistoryPermissions where role_id == Role.id |
---|
| 797 | # - GroupRoleAssociations where role_id == Role.id |
---|
| 798 | # - DatasetPermissionss where role_id == Role.id |
---|
| 799 | params = util.Params( kwd ) |
---|
| 800 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 801 | id = kwd.get( 'id', None ) |
---|
| 802 | if not id: |
---|
| 803 | message = "No role ids received for purging" |
---|
| 804 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 805 | action='roles', |
---|
| 806 | webapp=webapp, |
---|
| 807 | message=util.sanitize_text( message ), |
---|
| 808 | status='error' ) ) |
---|
| 809 | ids = util.listify( id ) |
---|
| 810 | message = "Purged %d roles: " % len( ids ) |
---|
| 811 | for role_id in ids: |
---|
| 812 | role = get_role( trans, role_id ) |
---|
| 813 | if not role.deleted: |
---|
| 814 | message = "Role '%s' has not been deleted, so it cannot be purged." % role.name |
---|
| 815 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 816 | action='roles', |
---|
| 817 | webapp=webapp, |
---|
| 818 | message=util.sanitize_text( message ), |
---|
| 819 | status='error' ) ) |
---|
| 820 | # Delete UserRoleAssociations |
---|
| 821 | for ura in role.users: |
---|
| 822 | user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id ) |
---|
| 823 | # Delete DefaultUserPermissions for associated users |
---|
| 824 | for dup in user.default_permissions: |
---|
| 825 | if role == dup.role: |
---|
| 826 | trans.sa_session.delete( dup ) |
---|
| 827 | # Delete DefaultHistoryPermissions for associated users |
---|
| 828 | for history in user.histories: |
---|
| 829 | for dhp in history.default_permissions: |
---|
| 830 | if role == dhp.role: |
---|
| 831 | trans.sa_session.delete( dhp ) |
---|
| 832 | trans.sa_session.delete( ura ) |
---|
| 833 | # Delete GroupRoleAssociations |
---|
| 834 | for gra in role.groups: |
---|
| 835 | trans.sa_session.delete( gra ) |
---|
| 836 | # Delete DatasetPermissionss |
---|
| 837 | for dp in role.dataset_actions: |
---|
| 838 | trans.sa_session.delete( dp ) |
---|
| 839 | trans.sa_session.flush() |
---|
| 840 | message += " %s " % role.name |
---|
| 841 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 842 | action='roles', |
---|
| 843 | webapp=webapp, |
---|
| 844 | message=util.sanitize_text( message ), |
---|
| 845 | status='done' ) ) |
---|
| 846 | |
---|
| 847 | # Galaxy Group Stuff |
---|
| 848 | @web.expose |
---|
| 849 | @web.require_admin |
---|
| 850 | def groups( self, trans, **kwargs ): |
---|
| 851 | if 'operation' in kwargs: |
---|
| 852 | operation = kwargs['operation'].lower() |
---|
| 853 | if operation == "groups": |
---|
| 854 | return self.group( trans, **kwargs ) |
---|
| 855 | if operation == "create": |
---|
| 856 | return self.create_group( trans, **kwargs ) |
---|
| 857 | if operation == "delete": |
---|
| 858 | return self.mark_group_deleted( trans, **kwargs ) |
---|
| 859 | if operation == "undelete": |
---|
| 860 | return self.undelete_group( trans, **kwargs ) |
---|
| 861 | if operation == "purge": |
---|
| 862 | return self.purge_group( trans, **kwargs ) |
---|
| 863 | if operation == "manage users and roles": |
---|
| 864 | return self.manage_users_and_roles_for_group( trans, **kwargs ) |
---|
| 865 | if operation == "rename": |
---|
| 866 | return self.rename_group( trans, **kwargs ) |
---|
| 867 | # Render the list view |
---|
| 868 | return self.group_list_grid( trans, **kwargs ) |
---|
| 869 | @web.expose |
---|
| 870 | @web.require_admin |
---|
| 871 | def rename_group( self, trans, **kwd ): |
---|
| 872 | params = util.Params( kwd ) |
---|
| 873 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 874 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 875 | status = params.get( 'status', 'done' ) |
---|
| 876 | id = params.get( 'id', None ) |
---|
| 877 | if not id: |
---|
| 878 | message = "No group ids received for renaming" |
---|
| 879 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 880 | action='groups', |
---|
| 881 | webapp=webapp, |
---|
| 882 | message=message, |
---|
| 883 | status='error' ) ) |
---|
| 884 | group = get_group( trans, id ) |
---|
| 885 | if params.get( 'rename_group_button', False ): |
---|
| 886 | old_name = group.name |
---|
| 887 | new_name = util.restore_text( params.name ) |
---|
| 888 | if not new_name: |
---|
| 889 | message = 'Enter a valid name' |
---|
| 890 | status = 'error' |
---|
| 891 | elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first(): |
---|
| 892 | message = 'A group with that name already exists' |
---|
| 893 | status = 'error' |
---|
| 894 | else: |
---|
| 895 | group.name = new_name |
---|
| 896 | trans.sa_session.add( group ) |
---|
| 897 | trans.sa_session.flush() |
---|
| 898 | message = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) |
---|
| 899 | return trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 900 | action='groups', |
---|
| 901 | webapp=webapp, |
---|
| 902 | message=util.sanitize_text( message ), |
---|
| 903 | status='done' ) ) |
---|
| 904 | return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', |
---|
| 905 | group=group, |
---|
| 906 | webapp=webapp, |
---|
| 907 | message=message, |
---|
| 908 | status=status ) |
---|
| 909 | @web.expose |
---|
| 910 | @web.require_admin |
---|
| 911 | def manage_users_and_roles_for_group( self, trans, **kwd ): |
---|
| 912 | params = util.Params( kwd ) |
---|
| 913 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 914 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 915 | status = params.get( 'status', 'done' ) |
---|
| 916 | group = get_group( trans, params.id ) |
---|
| 917 | if params.get( 'group_roles_users_edit_button', False ): |
---|
| 918 | in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.in_roles ) ] |
---|
| 919 | in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] |
---|
| 920 | trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=in_roles, users=in_users ) |
---|
| 921 | trans.sa_session.refresh( group ) |
---|
| 922 | message += "Group '%s' has been updated with %d associated roles and %d associated users" % ( group.name, len( in_roles ), len( in_users ) ) |
---|
| 923 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 924 | action='groups', |
---|
| 925 | webapp=webapp, |
---|
| 926 | message=util.sanitize_text( message ), |
---|
| 927 | status=status ) ) |
---|
| 928 | in_roles = [] |
---|
| 929 | out_roles = [] |
---|
| 930 | in_users = [] |
---|
| 931 | out_users = [] |
---|
| 932 | for role in trans.sa_session.query(trans.app.model.Role ) \ |
---|
| 933 | .filter( trans.app.model.Role.table.c.deleted==False ) \ |
---|
| 934 | .order_by( trans.app.model.Role.table.c.name ): |
---|
| 935 | if role in [ x.role for x in group.roles ]: |
---|
| 936 | in_roles.append( ( role.id, role.name ) ) |
---|
| 937 | else: |
---|
| 938 | out_roles.append( ( role.id, role.name ) ) |
---|
| 939 | for user in trans.sa_session.query( trans.app.model.User ) \ |
---|
| 940 | .filter( trans.app.model.User.table.c.deleted==False ) \ |
---|
| 941 | .order_by( trans.app.model.User.table.c.email ): |
---|
| 942 | if user in [ x.user for x in group.users ]: |
---|
| 943 | in_users.append( ( user.id, user.email ) ) |
---|
| 944 | else: |
---|
| 945 | out_users.append( ( user.id, user.email ) ) |
---|
| 946 | message += 'Group %s is currently associated with %d roles and %d users' % ( group.name, len( in_roles ), len( in_users ) ) |
---|
| 947 | return trans.fill_template( '/admin/dataset_security/group/group.mako', |
---|
| 948 | group=group, |
---|
| 949 | in_roles=in_roles, |
---|
| 950 | out_roles=out_roles, |
---|
| 951 | in_users=in_users, |
---|
| 952 | out_users=out_users, |
---|
| 953 | webapp=webapp, |
---|
| 954 | message=message, |
---|
| 955 | status=status ) |
---|
| 956 | @web.expose |
---|
| 957 | @web.require_admin |
---|
| 958 | def create_group( self, trans, **kwd ): |
---|
| 959 | params = util.Params( kwd ) |
---|
| 960 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 961 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 962 | status = params.get( 'status', 'done' ) |
---|
| 963 | if params.get( 'create_group_button', False ): |
---|
| 964 | name = util.restore_text( params.name ) |
---|
| 965 | in_users = util.listify( params.get( 'in_users', [] ) ) |
---|
| 966 | in_roles = util.listify( params.get( 'in_roles', [] ) ) |
---|
| 967 | if not name: |
---|
| 968 | message = "Enter a valid name" |
---|
| 969 | elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first(): |
---|
| 970 | message = "A group with that name already exists" |
---|
| 971 | else: |
---|
| 972 | # Create the group |
---|
| 973 | group = trans.app.model.Group( name=name ) |
---|
| 974 | trans.sa_session.add( group ) |
---|
| 975 | trans.sa_session.flush() |
---|
| 976 | # Create the UserRoleAssociations |
---|
| 977 | for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]: |
---|
| 978 | uga = trans.app.model.UserGroupAssociation( user, group ) |
---|
| 979 | trans.sa_session.add( uga ) |
---|
| 980 | trans.sa_session.flush() |
---|
| 981 | # Create the GroupRoleAssociations |
---|
| 982 | for role in [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in in_roles ]: |
---|
| 983 | gra = trans.app.model.GroupRoleAssociation( group, role ) |
---|
| 984 | trans.sa_session.add( gra ) |
---|
| 985 | trans.sa_session.flush() |
---|
| 986 | message = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_users ), len( in_roles ) ) |
---|
| 987 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 988 | action='groups', |
---|
| 989 | webapp=webapp, |
---|
| 990 | message=util.sanitize_text( message ), |
---|
| 991 | status='done' ) ) |
---|
| 992 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 993 | action='create_group', |
---|
| 994 | webapp=webapp, |
---|
| 995 | message=util.sanitize_text( message ), |
---|
| 996 | status='error' ) ) |
---|
| 997 | out_users = [] |
---|
| 998 | for user in trans.sa_session.query( trans.app.model.User ) \ |
---|
| 999 | .filter( trans.app.model.User.table.c.deleted==False ) \ |
---|
| 1000 | .order_by( trans.app.model.User.table.c.email ): |
---|
| 1001 | out_users.append( ( user.id, user.email ) ) |
---|
| 1002 | out_roles = [] |
---|
| 1003 | for role in trans.sa_session.query( trans.app.model.Role ) \ |
---|
| 1004 | .filter( trans.app.model.Role.table.c.deleted==False ) \ |
---|
| 1005 | .order_by( trans.app.model.Role.table.c.name ): |
---|
| 1006 | out_roles.append( ( role.id, role.name ) ) |
---|
| 1007 | return trans.fill_template( '/admin/dataset_security/group/group_create.mako', |
---|
| 1008 | in_users=[], |
---|
| 1009 | out_users=out_users, |
---|
| 1010 | in_roles=[], |
---|
| 1011 | out_roles=out_roles, |
---|
| 1012 | webapp=webapp, |
---|
| 1013 | message=message, |
---|
| 1014 | status=status ) |
---|
| 1015 | @web.expose |
---|
| 1016 | @web.require_admin |
---|
| 1017 | def mark_group_deleted( self, trans, **kwd ): |
---|
| 1018 | params = util.Params( kwd ) |
---|
| 1019 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 1020 | id = params.get( 'id', None ) |
---|
| 1021 | if not id: |
---|
| 1022 | message = "No group ids received for marking deleted" |
---|
| 1023 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1024 | action='groups', |
---|
| 1025 | webapp=webapp, |
---|
| 1026 | message=message, |
---|
| 1027 | status='error' ) ) |
---|
| 1028 | ids = util.listify( id ) |
---|
| 1029 | message = "Deleted %d groups: " % len( ids ) |
---|
| 1030 | for group_id in ids: |
---|
| 1031 | group = get_group( trans, group_id ) |
---|
| 1032 | group.deleted = True |
---|
| 1033 | trans.sa_session.add( group ) |
---|
| 1034 | trans.sa_session.flush() |
---|
| 1035 | message += " %s " % group.name |
---|
| 1036 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1037 | action='groups', |
---|
| 1038 | webapp=webapp, |
---|
| 1039 | message=util.sanitize_text( message ), |
---|
| 1040 | status='done' ) ) |
---|
| 1041 | @web.expose |
---|
| 1042 | @web.require_admin |
---|
| 1043 | def undelete_group( self, trans, **kwd ): |
---|
| 1044 | params = util.Params( kwd ) |
---|
| 1045 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 1046 | id = kwd.get( 'id', None ) |
---|
| 1047 | if not id: |
---|
| 1048 | message = "No group ids received for undeleting" |
---|
| 1049 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1050 | action='groups', |
---|
| 1051 | webapp=webapp, |
---|
| 1052 | message=message, |
---|
| 1053 | status='error' ) ) |
---|
| 1054 | ids = util.listify( id ) |
---|
| 1055 | count = 0 |
---|
| 1056 | undeleted_groups = "" |
---|
| 1057 | for group_id in ids: |
---|
| 1058 | group = get_group( trans, group_id ) |
---|
| 1059 | if not group.deleted: |
---|
| 1060 | message = "Group '%s' has not been deleted, so it cannot be undeleted." % group.name |
---|
| 1061 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1062 | action='groups', |
---|
| 1063 | webapp=webapp, |
---|
| 1064 | message=util.sanitize_text( message ), |
---|
| 1065 | status='error' ) ) |
---|
| 1066 | group.deleted = False |
---|
| 1067 | trans.sa_session.add( group ) |
---|
| 1068 | trans.sa_session.flush() |
---|
| 1069 | count += 1 |
---|
| 1070 | undeleted_groups += " %s" % group.name |
---|
| 1071 | message = "Undeleted %d groups: %s" % ( count, undeleted_groups ) |
---|
| 1072 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1073 | action='groups', |
---|
| 1074 | webapp=webapp, |
---|
| 1075 | message=util.sanitize_text( message ), |
---|
| 1076 | status='done' ) ) |
---|
| 1077 | @web.expose |
---|
| 1078 | @web.require_admin |
---|
| 1079 | def purge_group( self, trans, **kwd ): |
---|
| 1080 | # This method should only be called for a Group that has previously been deleted. |
---|
| 1081 | # Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations. |
---|
| 1082 | params = util.Params( kwd ) |
---|
| 1083 | webapp = params.get( 'webapp', 'galaxy' ) |
---|
| 1084 | id = kwd.get( 'id', None ) |
---|
| 1085 | if not id: |
---|
| 1086 | message = "No group ids received for purging" |
---|
| 1087 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1088 | action='groups', |
---|
| 1089 | webapp=webapp, |
---|
| 1090 | message=util.sanitize_text( message ), |
---|
| 1091 | status='error' ) ) |
---|
| 1092 | ids = util.listify( id ) |
---|
| 1093 | message = "Purged %d groups: " % len( ids ) |
---|
| 1094 | for group_id in ids: |
---|
| 1095 | group = get_group( trans, group_id ) |
---|
| 1096 | if not group.deleted: |
---|
| 1097 | # We should never reach here, but just in case there is a bug somewhere... |
---|
| 1098 | message = "Group '%s' has not been deleted, so it cannot be purged." % group.name |
---|
| 1099 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1100 | action='groups', |
---|
| 1101 | webapp=webapp, |
---|
| 1102 | message=util.sanitize_text( message ), |
---|
| 1103 | status='error' ) ) |
---|
| 1104 | # Delete UserGroupAssociations |
---|
| 1105 | for uga in group.users: |
---|
| 1106 | trans.sa_session.delete( uga ) |
---|
| 1107 | # Delete GroupRoleAssociations |
---|
| 1108 | for gra in group.roles: |
---|
| 1109 | trans.sa_session.delete( gra ) |
---|
| 1110 | trans.sa_session.flush() |
---|
| 1111 | message += " %s " % group.name |
---|
| 1112 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1113 | action='groups', |
---|
| 1114 | webapp=webapp, |
---|
| 1115 | message=util.sanitize_text( message ), |
---|
| 1116 | status='done' ) ) |
---|
| 1117 | |
---|
| 1118 | # Galaxy User Stuff |
---|
| 1119 | @web.expose |
---|
| 1120 | @web.require_admin |
---|
| 1121 | def create_new_user( self, trans, **kwargs ): |
---|
| 1122 | webapp = kwargs.get( 'webapp', 'galaxy' ) |
---|
| 1123 | return trans.response.send_redirect( web.url_for( controller='user', |
---|
| 1124 | action='create', |
---|
| 1125 | webapp=webapp, |
---|
| 1126 | admin_view=True ) ) |
---|
| 1127 | @web.expose |
---|
| 1128 | @web.require_admin |
---|
| 1129 | def reset_user_password( self, trans, **kwd ): |
---|
| 1130 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 1131 | id = kwd.get( 'id', None ) |
---|
| 1132 | if not id: |
---|
| 1133 | message = "No user ids received for resetting passwords" |
---|
| 1134 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1135 | action='users', |
---|
| 1136 | webapp=webapp, |
---|
| 1137 | message=message, |
---|
| 1138 | status='error' ) ) |
---|
| 1139 | ids = util.listify( id ) |
---|
| 1140 | if 'reset_user_password_button' in kwd: |
---|
| 1141 | message = '' |
---|
| 1142 | status = '' |
---|
| 1143 | for user_id in ids: |
---|
| 1144 | user = get_user( trans, user_id ) |
---|
| 1145 | password = kwd.get( 'password', None ) |
---|
| 1146 | confirm = kwd.get( 'confirm' , None ) |
---|
| 1147 | if len( password ) < 6: |
---|
| 1148 | message = "Please use a password of at least 6 characters" |
---|
| 1149 | status = 'error' |
---|
| 1150 | break |
---|
| 1151 | elif password != confirm: |
---|
| 1152 | message = "Passwords do not match" |
---|
| 1153 | status = 'error' |
---|
| 1154 | break |
---|
| 1155 | else: |
---|
| 1156 | user.set_password_cleartext( password ) |
---|
| 1157 | trans.sa_session.add( user ) |
---|
| 1158 | trans.sa_session.flush() |
---|
| 1159 | if not message and not status: |
---|
| 1160 | message = "Passwords reset for %d users" % len( ids ) |
---|
| 1161 | status = 'done' |
---|
| 1162 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1163 | action='users', |
---|
| 1164 | webapp=webapp, |
---|
| 1165 | message=util.sanitize_text( message ), |
---|
| 1166 | status=status ) ) |
---|
| 1167 | users = [ get_user( trans, user_id ) for user_id in ids ] |
---|
| 1168 | if len( ids ) > 1: |
---|
| 1169 | id=','.join( id ) |
---|
| 1170 | return trans.fill_template( '/admin/user/reset_password.mako', |
---|
| 1171 | id=id, |
---|
| 1172 | users=users, |
---|
| 1173 | password='', |
---|
| 1174 | confirm='', |
---|
| 1175 | webapp=webapp ) |
---|
| 1176 | @web.expose |
---|
| 1177 | @web.require_admin |
---|
| 1178 | def mark_user_deleted( self, trans, **kwd ): |
---|
| 1179 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 1180 | id = kwd.get( 'id', None ) |
---|
| 1181 | if not id: |
---|
| 1182 | message = "No user ids received for deleting" |
---|
| 1183 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1184 | action='users', |
---|
| 1185 | webapp=webapp, |
---|
| 1186 | message=message, |
---|
| 1187 | status='error' ) ) |
---|
| 1188 | ids = util.listify( id ) |
---|
| 1189 | message = "Deleted %d users: " % len( ids ) |
---|
| 1190 | for user_id in ids: |
---|
| 1191 | user = get_user( trans, user_id ) |
---|
| 1192 | user.deleted = True |
---|
| 1193 | trans.sa_session.add( user ) |
---|
| 1194 | trans.sa_session.flush() |
---|
| 1195 | message += " %s " % user.email |
---|
| 1196 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1197 | action='users', |
---|
| 1198 | webapp=webapp, |
---|
| 1199 | message=util.sanitize_text( message ), |
---|
| 1200 | status='done' ) ) |
---|
| 1201 | @web.expose |
---|
| 1202 | @web.require_admin |
---|
| 1203 | def undelete_user( self, trans, **kwd ): |
---|
| 1204 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 1205 | id = kwd.get( 'id', None ) |
---|
| 1206 | if not id: |
---|
| 1207 | message = "No user ids received for undeleting" |
---|
| 1208 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1209 | action='users', |
---|
| 1210 | webapp=webapp, |
---|
| 1211 | message=message, |
---|
| 1212 | status='error' ) ) |
---|
| 1213 | ids = util.listify( id ) |
---|
| 1214 | count = 0 |
---|
| 1215 | undeleted_users = "" |
---|
| 1216 | for user_id in ids: |
---|
| 1217 | user = get_user( trans, user_id ) |
---|
| 1218 | if not user.deleted: |
---|
| 1219 | message = "User '%s' has not been deleted, so it cannot be undeleted." % user.email |
---|
| 1220 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1221 | action='users', |
---|
| 1222 | webapp=webapp, |
---|
| 1223 | message=util.sanitize_text( message ), |
---|
| 1224 | status='error' ) ) |
---|
| 1225 | user.deleted = False |
---|
| 1226 | trans.sa_session.add( user ) |
---|
| 1227 | trans.sa_session.flush() |
---|
| 1228 | count += 1 |
---|
| 1229 | undeleted_users += " %s" % user.email |
---|
| 1230 | message = "Undeleted %d users: %s" % ( count, undeleted_users ) |
---|
| 1231 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1232 | action='users', |
---|
| 1233 | webapp=webapp, |
---|
| 1234 | message=util.sanitize_text( message ), |
---|
| 1235 | status='done' ) ) |
---|
| 1236 | @web.expose |
---|
| 1237 | @web.require_admin |
---|
| 1238 | def purge_user( self, trans, **kwd ): |
---|
| 1239 | # This method should only be called for a User that has previously been deleted. |
---|
| 1240 | # We keep the User in the database ( marked as purged ), and stuff associated |
---|
| 1241 | # with the user's private role in case we want the ability to unpurge the user |
---|
| 1242 | # some time in the future. |
---|
| 1243 | # Purging a deleted User deletes all of the following: |
---|
| 1244 | # - History where user_id = User.id |
---|
| 1245 | # - HistoryDatasetAssociation where history_id = History.id |
---|
| 1246 | # - Dataset where HistoryDatasetAssociation.dataset_id = Dataset.id |
---|
| 1247 | # - UserGroupAssociation where user_id == User.id |
---|
| 1248 | # - UserRoleAssociation where user_id == User.id EXCEPT FOR THE PRIVATE ROLE |
---|
| 1249 | # - UserAddress where user_id == User.id |
---|
| 1250 | # Purging Histories and Datasets must be handled via the cleanup_datasets.py script |
---|
| 1251 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 1252 | id = kwd.get( 'id', None ) |
---|
| 1253 | if not id: |
---|
| 1254 | message = "No user ids received for purging" |
---|
| 1255 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1256 | action='users', |
---|
| 1257 | webapp=webapp, |
---|
| 1258 | message=util.sanitize_text( message ), |
---|
| 1259 | status='error' ) ) |
---|
| 1260 | ids = util.listify( id ) |
---|
| 1261 | message = "Purged %d users: " % len( ids ) |
---|
| 1262 | for user_id in ids: |
---|
| 1263 | user = get_user( trans, user_id ) |
---|
| 1264 | if not user.deleted: |
---|
| 1265 | # We should never reach here, but just in case there is a bug somewhere... |
---|
| 1266 | message = "User '%s' has not been deleted, so it cannot be purged." % user.email |
---|
| 1267 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1268 | action='users', |
---|
| 1269 | webapp=webapp, |
---|
| 1270 | message=util.sanitize_text( message ), |
---|
| 1271 | status='error' ) ) |
---|
| 1272 | private_role = trans.app.security_agent.get_private_user_role( user ) |
---|
| 1273 | # Delete History |
---|
| 1274 | for h in user.active_histories: |
---|
| 1275 | trans.sa_session.refresh( h ) |
---|
| 1276 | for hda in h.active_datasets: |
---|
| 1277 | # Delete HistoryDatasetAssociation |
---|
| 1278 | d = trans.sa_session.query( trans.app.model.Dataset ).get( hda.dataset_id ) |
---|
| 1279 | # Delete Dataset |
---|
| 1280 | if not d.deleted: |
---|
| 1281 | d.deleted = True |
---|
| 1282 | trans.sa_session.add( d ) |
---|
| 1283 | hda.deleted = True |
---|
| 1284 | trans.sa_session.add( hda ) |
---|
| 1285 | h.deleted = True |
---|
| 1286 | trans.sa_session.add( h ) |
---|
| 1287 | # Delete UserGroupAssociations |
---|
| 1288 | for uga in user.groups: |
---|
| 1289 | trans.sa_session.delete( uga ) |
---|
| 1290 | # Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE |
---|
| 1291 | for ura in user.roles: |
---|
| 1292 | if ura.role_id != private_role.id: |
---|
| 1293 | trans.sa_session.delete( ura ) |
---|
| 1294 | # Delete UserAddresses |
---|
| 1295 | for address in user.addresses: |
---|
| 1296 | trans.sa_session.delete( address ) |
---|
| 1297 | # Purge the user |
---|
| 1298 | user.purged = True |
---|
| 1299 | trans.sa_session.add( user ) |
---|
| 1300 | trans.sa_session.flush() |
---|
| 1301 | message += "%s " % user.email |
---|
| 1302 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1303 | action='users', |
---|
| 1304 | webapp=webapp, |
---|
| 1305 | message=util.sanitize_text( message ), |
---|
| 1306 | status='done' ) ) |
---|
| 1307 | @web.expose |
---|
| 1308 | @web.require_admin |
---|
| 1309 | def users( self, trans, **kwargs ): |
---|
| 1310 | if 'operation' in kwargs: |
---|
| 1311 | operation = kwargs['operation'].lower() |
---|
| 1312 | if operation == "roles": |
---|
| 1313 | return self.user( trans, **kwargs ) |
---|
| 1314 | if operation == "reset password": |
---|
| 1315 | return self.reset_user_password( trans, **kwargs ) |
---|
| 1316 | if operation == "delete": |
---|
| 1317 | return self.mark_user_deleted( trans, **kwargs ) |
---|
| 1318 | if operation == "undelete": |
---|
| 1319 | return self.undelete_user( trans, **kwargs ) |
---|
| 1320 | if operation == "purge": |
---|
| 1321 | return self.purge_user( trans, **kwargs ) |
---|
| 1322 | if operation == "create": |
---|
| 1323 | return self.create_new_user( trans, **kwargs ) |
---|
| 1324 | if operation == "information": |
---|
| 1325 | return self.user_info( trans, **kwargs ) |
---|
| 1326 | if operation == "manage roles and groups": |
---|
| 1327 | return self.manage_roles_and_groups_for_user( trans, **kwargs ) |
---|
| 1328 | if operation == "tools_by_user": |
---|
| 1329 | # This option is called via the ToolsColumn link in a grid subclass, |
---|
| 1330 | # so we need to add user_id to kwargs since id in the subclass is tool.id, |
---|
| 1331 | # and update the current sort filter, using the grid subclass's default |
---|
| 1332 | # sort filter instead of this class's. |
---|
| 1333 | kwargs[ 'user_id' ] = kwargs[ 'id' ] |
---|
| 1334 | kwargs[ 'sort' ] = 'name' |
---|
| 1335 | return trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1336 | action='browse_tools', |
---|
| 1337 | **kwargs ) ) |
---|
| 1338 | # Render the list view |
---|
| 1339 | return self.user_list_grid( trans, **kwargs ) |
---|
| 1340 | @web.expose |
---|
| 1341 | @web.require_admin |
---|
| 1342 | def user_info( self, trans, **kwd ): |
---|
| 1343 | ''' |
---|
| 1344 | This method displays the user information page which consists of login |
---|
| 1345 | information, public username, reset password & other user information |
---|
| 1346 | obtained during registration |
---|
| 1347 | ''' |
---|
| 1348 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 1349 | user_id = kwd.get( 'id', None ) |
---|
| 1350 | if not user_id: |
---|
| 1351 | message += "Invalid user id (%s) received" % str( user_id ) |
---|
| 1352 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1353 | action='users', |
---|
| 1354 | webapp=webapp, |
---|
| 1355 | message=util.sanitize_text( message ), |
---|
| 1356 | status='error' ) ) |
---|
| 1357 | user = get_user( trans, user_id ) |
---|
| 1358 | return trans.response.send_redirect( web.url_for( controller='user', |
---|
| 1359 | action='show_info', |
---|
| 1360 | user_id=user.id, |
---|
| 1361 | admin_view=True, |
---|
| 1362 | **kwd ) ) |
---|
| 1363 | @web.expose |
---|
| 1364 | @web.require_admin |
---|
| 1365 | def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): |
---|
| 1366 | """Return autocomplete data for user emails""" |
---|
| 1367 | ac_data = "" |
---|
| 1368 | for user in trans.sa_session.query( User ).filter_by( deleted=False ).filter( func.lower( User.email ).like( q.lower() + "%" ) ): |
---|
| 1369 | ac_data = ac_data + user.email + "\n" |
---|
| 1370 | return ac_data |
---|
| 1371 | @web.expose |
---|
| 1372 | @web.require_admin |
---|
| 1373 | def manage_roles_and_groups_for_user( self, trans, **kwd ): |
---|
| 1374 | webapp = kwd.get( 'webapp', 'galaxy' ) |
---|
| 1375 | user_id = kwd.get( 'id', None ) |
---|
| 1376 | message = '' |
---|
| 1377 | status = '' |
---|
| 1378 | if not user_id: |
---|
| 1379 | message += "Invalid user id (%s) received" % str( user_id ) |
---|
| 1380 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1381 | action='users', |
---|
| 1382 | webapp=webapp, |
---|
| 1383 | message=util.sanitize_text( message ), |
---|
| 1384 | status='error' ) ) |
---|
| 1385 | user = get_user( trans, user_id ) |
---|
| 1386 | private_role = trans.app.security_agent.get_private_user_role( user ) |
---|
| 1387 | if kwd.get( 'user_roles_groups_edit_button', False ): |
---|
| 1388 | # Make sure the user is not dis-associating himself from his private role |
---|
| 1389 | out_roles = kwd.get( 'out_roles', [] ) |
---|
| 1390 | if out_roles: |
---|
| 1391 | out_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( out_roles ) ] |
---|
| 1392 | if private_role in out_roles: |
---|
| 1393 | message += "You cannot eliminate a user's private role association. " |
---|
| 1394 | status = 'error' |
---|
| 1395 | in_roles = kwd.get( 'in_roles', [] ) |
---|
| 1396 | if in_roles: |
---|
| 1397 | in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( in_roles ) ] |
---|
| 1398 | out_groups = kwd.get( 'out_groups', [] ) |
---|
| 1399 | if out_groups: |
---|
| 1400 | out_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( out_groups ) ] |
---|
| 1401 | in_groups = kwd.get( 'in_groups', [] ) |
---|
| 1402 | if in_groups: |
---|
| 1403 | in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( in_groups ) ] |
---|
| 1404 | if in_roles: |
---|
| 1405 | trans.app.security_agent.set_entity_user_associations( users=[ user ], roles=in_roles, groups=in_groups ) |
---|
| 1406 | trans.sa_session.refresh( user ) |
---|
| 1407 | message += "User '%s' has been updated with %d associated roles and %d associated groups (private roles are not displayed)" % \ |
---|
| 1408 | ( user.email, len( in_roles ), len( in_groups ) ) |
---|
| 1409 | trans.response.send_redirect( web.url_for( controller='admin', |
---|
| 1410 | action='users', |
---|
| 1411 | webapp=webapp, |
---|
| 1412 | message=util.sanitize_text( message ), |
---|
| 1413 | status='done' ) ) |
---|
| 1414 | in_roles = [] |
---|
| 1415 | out_roles = [] |
---|
| 1416 | in_groups = [] |
---|
| 1417 | out_groups = [] |
---|
| 1418 | for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted==False ) \ |
---|
| 1419 | .order_by( trans.app.model.Role.table.c.name ): |
---|
| 1420 | if role in [ x.role for x in user.roles ]: |
---|
| 1421 | in_roles.append( ( role.id, role.name ) ) |
---|
| 1422 | elif role.type != trans.app.model.Role.types.PRIVATE: |
---|
| 1423 | # There is a 1 to 1 mapping between a user and a PRIVATE role, so private roles should |
---|
| 1424 | # not be listed in the roles form fields, except for the currently selected user's private |
---|
| 1425 | # role, which should always be in in_roles. The check above is added as an additional |
---|
| 1426 | # precaution, since for a period of time we were including private roles in the form fields. |
---|
| 1427 | out_roles.append( ( role.id, role.name ) ) |
---|
| 1428 | for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted==False ) \ |
---|
| 1429 | .order_by( trans.app.model.Group.table.c.name ): |
---|
| 1430 | if group in [ x.group for x in user.groups ]: |
---|
| 1431 | in_groups.append( ( group.id, group.name ) ) |
---|
| 1432 | else: |
---|
| 1433 | out_groups.append( ( group.id, group.name ) ) |
---|
| 1434 | message += "User '%s' is currently associated with %d roles and is a member of %d groups" % \ |
---|
| 1435 | ( user.email, len( in_roles ), len( in_groups ) ) |
---|
| 1436 | if not status: |
---|
| 1437 | status = 'done' |
---|
| 1438 | return trans.fill_template( '/admin/user/user.mako', |
---|
| 1439 | user=user, |
---|
| 1440 | in_roles=in_roles, |
---|
| 1441 | out_roles=out_roles, |
---|
| 1442 | in_groups=in_groups, |
---|
| 1443 | out_groups=out_groups, |
---|
| 1444 | webapp=webapp, |
---|
| 1445 | message=message, |
---|
| 1446 | status=status ) |
---|
| 1447 | @web.expose |
---|
| 1448 | @web.require_admin |
---|
| 1449 | def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): |
---|
| 1450 | if self.app.memdump is None: |
---|
| 1451 | return trans.show_error_message( "Memdump is not enabled (set <code>use_memdump = True</code> in universe_wsgi.ini)" ) |
---|
| 1452 | heap = self.app.memdump.get() |
---|
| 1453 | p = util.Params( kwd ) |
---|
| 1454 | msg = None |
---|
| 1455 | if p.dump: |
---|
| 1456 | heap = self.app.memdump.get( update = True ) |
---|
| 1457 | msg = "Heap dump complete" |
---|
| 1458 | elif p.setref: |
---|
| 1459 | self.app.memdump.setref() |
---|
| 1460 | msg = "Reference point set (dump to see delta from this point)" |
---|
| 1461 | ids = ids.split( ',' ) |
---|
| 1462 | sorts = sorts.split( ',' ) |
---|
| 1463 | if new_id is not None: |
---|
| 1464 | ids.append( new_id ) |
---|
| 1465 | sorts.append( 'None' ) |
---|
| 1466 | elif new_sort is not None: |
---|
| 1467 | sorts[-1] = new_sort |
---|
| 1468 | breadcrumb = "<a href='%s' class='breadcrumb'>heap</a>" % web.url_for() |
---|
| 1469 | # new lists so we can assemble breadcrumb links |
---|
| 1470 | new_ids = [] |
---|
| 1471 | new_sorts = [] |
---|
| 1472 | for id, sort in zip( ids, sorts ): |
---|
| 1473 | new_ids.append( id ) |
---|
| 1474 | if id != 'None': |
---|
| 1475 | breadcrumb += "<a href='%s' class='breadcrumb'>[%s]</a>" % ( web.url_for( ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), id ) |
---|
| 1476 | heap = heap[int(id)] |
---|
| 1477 | new_sorts.append( sort ) |
---|
| 1478 | if sort != 'None': |
---|
| 1479 | breadcrumb += "<a href='%s' class='breadcrumb'>.by('%s')</a>" % ( web.url_for( ids=','.join( new_ids ), sorts=','.join( new_sorts ) ), sort ) |
---|
| 1480 | heap = heap.by( sort ) |
---|
| 1481 | ids = ','.join( new_ids ) |
---|
| 1482 | sorts = ','.join( new_sorts ) |
---|
| 1483 | if p.theone: |
---|
| 1484 | breadcrumb += ".theone" |
---|
| 1485 | heap = heap.theone |
---|
| 1486 | return trans.fill_template( '/admin/memdump.mako', heap = heap, ids = ids, sorts = sorts, breadcrumb = breadcrumb, msg = msg ) |
---|
| 1487 | |
---|
| 1488 | @web.expose |
---|
| 1489 | @web.require_admin |
---|
| 1490 | def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, job_lock = None, **kwd ): |
---|
| 1491 | deleted = [] |
---|
| 1492 | msg = None |
---|
| 1493 | status = None |
---|
| 1494 | if not trans.app.config.get_bool( "enable_job_running", True ): |
---|
| 1495 | return trans.show_error_message( 'This Galaxy instance is not configured to run jobs. If using multiple servers, please directly access the job running instance to manage jobs.' ) |
---|
| 1496 | job_ids = util.listify( stop ) |
---|
| 1497 | if job_ids and stop_msg in [ None, '' ]: |
---|
| 1498 | msg = 'Please enter an error message to display to the user describing why the job was terminated' |
---|
| 1499 | status = 'error' |
---|
| 1500 | elif job_ids: |
---|
| 1501 | if stop_msg[-1] not in string.punctuation: |
---|
| 1502 | stop_msg += '.' |
---|
| 1503 | for job_id in job_ids: |
---|
| 1504 | trans.app.job_manager.job_stop_queue.put( job_id, error_msg="This job was stopped by an administrator: %s For more information or help" % stop_msg ) |
---|
| 1505 | deleted.append( str( job_id ) ) |
---|
| 1506 | if deleted: |
---|
| 1507 | msg = 'Queued job' |
---|
| 1508 | if len( deleted ) > 1: |
---|
| 1509 | msg += 's' |
---|
| 1510 | msg += ' for deletion: ' |
---|
| 1511 | msg += ', '.join( deleted ) |
---|
| 1512 | status = 'done' |
---|
| 1513 | if job_lock == 'lock': |
---|
| 1514 | trans.app.job_manager.job_queue.job_lock = True |
---|
| 1515 | elif job_lock == 'unlock': |
---|
| 1516 | trans.app.job_manager.job_queue.job_lock = False |
---|
| 1517 | cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) |
---|
| 1518 | jobs = trans.sa_session.query( trans.app.model.Job ) \ |
---|
| 1519 | .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, |
---|
| 1520 | or_( trans.app.model.Job.state == trans.app.model.Job.states.NEW, |
---|
| 1521 | trans.app.model.Job.state == trans.app.model.Job.states.QUEUED, |
---|
| 1522 | trans.app.model.Job.state == trans.app.model.Job.states.RUNNING, |
---|
| 1523 | trans.app.model.Job.state == trans.app.model.Job.states.UPLOAD ) ) ) \ |
---|
| 1524 | .order_by( trans.app.model.Job.table.c.update_time.desc() ) |
---|
| 1525 | last_updated = {} |
---|
| 1526 | for job in jobs: |
---|
| 1527 | delta = datetime.utcnow() - job.update_time |
---|
| 1528 | if delta > timedelta( minutes=60 ): |
---|
| 1529 | last_updated[job.id] = '%s hours' % int( delta.seconds / 60 / 60 ) |
---|
| 1530 | else: |
---|
| 1531 | last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) |
---|
| 1532 | return trans.fill_template( '/admin/jobs.mako', |
---|
| 1533 | jobs = jobs, |
---|
| 1534 | last_updated = last_updated, |
---|
| 1535 | cutoff = cutoff, |
---|
| 1536 | msg = msg, |
---|
| 1537 | status = status, |
---|
| 1538 | job_lock = trans.app.job_manager.job_queue.job_lock ) |
---|
| 1539 | |
---|
| 1540 | ## ---- Utility methods ------------------------------------------------------- |
---|
| 1541 | |
---|
| 1542 | def get_user( trans, id ): |
---|
| 1543 | """Get a User from the database by id.""" |
---|
| 1544 | # Load user from database |
---|
| 1545 | id = trans.security.decode_id( id ) |
---|
| 1546 | user = trans.sa_session.query( trans.model.User ).get( id ) |
---|
| 1547 | if not user: |
---|
| 1548 | return trans.show_error_message( "User not found for id (%s)" % str( id ) ) |
---|
| 1549 | return user |
---|
| 1550 | def get_role( trans, id ): |
---|
| 1551 | """Get a Role from the database by id.""" |
---|
| 1552 | # Load user from database |
---|
| 1553 | id = trans.security.decode_id( id ) |
---|
| 1554 | role = trans.sa_session.query( trans.model.Role ).get( id ) |
---|
| 1555 | if not role: |
---|
| 1556 | return trans.show_error_message( "Role not found for id (%s)" % str( id ) ) |
---|
| 1557 | return role |
---|
| 1558 | def get_group( trans, id ): |
---|
| 1559 | """Get a Group from the database by id.""" |
---|
| 1560 | # Load user from database |
---|
| 1561 | id = trans.security.decode_id( id ) |
---|
| 1562 | group = trans.sa_session.query( trans.model.Group ).get( id ) |
---|
| 1563 | if not group: |
---|
| 1564 | return trans.show_error_message( "Group not found for id (%s)" % str( id ) ) |
---|
| 1565 | return group |
---|