/lib/galaxy/web/controllers/request_type.py
Python | 460 lines | 453 code | 4 blank | 3 comment | 15 complexity | 29b4384fb167dc029904ce694f4848c6 MD5 | raw file
1from galaxy.web.base.controller import * 2from galaxy.web.framework.helpers import time_ago, iff, grids 3from galaxy.model.orm import * 4from galaxy import model, util 5from galaxy.web.form_builder import * 6from galaxy.web.controllers.requests_common import invalid_id_redirect 7import logging, os 8 9log = logging.getLogger( __name__ ) 10 11class RequestTypeGrid( grids.Grid ): 12 # Custom column types 13 class NameColumn( grids.TextColumn ): 14 def get_value(self, trans, grid, request_type): 15 return request_type.name 16 class DescriptionColumn( grids.TextColumn ): 17 def get_value(self, trans, grid, request_type): 18 return request_type.desc 19 class RequestFormColumn( grids.TextColumn ): 20 def get_value(self, trans, grid, request_type): 21 return request_type.request_form.name 22 class SampleFormColumn( grids.TextColumn ): 23 def get_value(self, trans, grid, request_type): 24 return request_type.sample_form.name 25 class ExternalServiceColumn( grids.IntegerColumn ): 26 def get_value(self, trans, grid, request_type): 27 if request_type.external_services: 28 return len( request_type.external_services ) 29 return 'No external service assigned' 30 # Grid definition 31 webapp = "galaxy" 32 title = "Request Types" 33 template = "admin/request_type/grid.mako" 34 model_class = model.RequestType 35 default_sort_key = "-create_time" 36 num_rows_per_page = 50 37 preserve_state = True 38 use_paging = True 39 default_filter = dict( deleted="False" ) 40 columns = [ 41 NameColumn( "Name", 42 key="name", 43 link=( lambda item: iff( item.deleted, None, dict( operation="view_request_type", id=item.id ) ) ), 44 attach_popup=True, 45 filterable="advanced" ), 46 DescriptionColumn( "Description", 47 key='desc', 48 filterable="advanced" ), 49 RequestFormColumn( "Request Form", 50 link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.request_form.id ) ) ) ), 51 SampleFormColumn( "Sample Form", 52 link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.sample_form.id ) ) ) ), 53 ExternalServiceColumn( "External Services" ), 54 grids.DeletedColumn( "Deleted", 55 key="deleted", 56 visible=False, 57 filterable="advanced" ) 58 ] 59 columns.append( grids.MulticolFilterColumn( "Search", 60 cols_to_filter=[ columns[0], columns[1] ], 61 key="free-text-search", 62 visible=False, 63 filterable="standard" ) ) 64 operations = [ 65 grids.GridOperation( "Edit request type", allow_multiple=False, condition=( lambda item: not item.deleted ) ), 66 grids.GridOperation( "Edit permissions", allow_multiple=False, condition=( lambda item: not item.deleted ) ), 67 grids.GridOperation( "Use run details template", allow_multiple=False, condition=( lambda item: not item.deleted and not item.run_details ) ), 68 grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted ) ), 69 grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), 70 ] 71 global_actions = [ 72 grids.GridAction( "Create new request type", dict( controller='request_type', action='create_request_type' ) ) 73 ] 74 75class RequestType( BaseUIController, UsesFormDefinitions ): 76 request_type_grid = RequestTypeGrid() 77 78 @web.expose 79 @web.require_admin 80 def browse_request_types( self, trans, **kwd ): 81 if 'operation' in kwd: 82 operation = kwd['operation'].lower() 83 obj_id = kwd.get( 'id', None ) 84 if operation == "view_form_definition": 85 return self.view_form_definition( trans, **kwd ) 86 elif operation == "view_request_type": 87 return self.view_request_type( trans, **kwd ) 88 elif operation == "use run details template": 89 return trans.response.send_redirect( web.url_for( controller='requests_admin', 90 action='add_template', 91 cntrller='requests_admin', 92 item_type='request_type', 93 form_type=trans.model.FormDefinition.types.RUN_DETAILS_TEMPLATE, 94 request_type_id=obj_id ) ) 95 elif operation == "edit request type": 96 return self.view_editable_request_type( trans, **kwd ) 97 elif operation == "delete": 98 return self.delete_request_type( trans, **kwd ) 99 elif operation == "undelete": 100 return self.undelete_request_type( trans, **kwd ) 101 elif operation == "edit permissions": 102 return self.request_type_permissions( trans, **kwd ) 103 elif operation == "view_external_service": 104 return trans.response.send_redirect( web.url_for( controller='external_service', 105 action='view_external_service', 106 **kwd ) ) 107 # Render the grid view 108 return self.request_type_grid( trans, **kwd ) 109 @web.expose 110 @web.require_admin 111 def create_request_type( self, trans, **kwd ): 112 params = util.Params( kwd ) 113 message = util.restore_text( params.get( 'message', '' ) ) 114 status = params.get( 'status', 'done' ) 115 rt_info_widgets, rt_states_widgets = self.__get_populated_request_type_widgets( trans, **kwd ) 116 external_service_select_fields_list = [] 117 # get all the external services selected till now 118 external_services_list = self.__get_external_services( trans, **kwd ) 119 for index, external_service in enumerate( external_services_list ): 120 external_service_select_field = self.__build_external_service_select_field( trans, 121 'external_service_id_%i' % index, 122 external_service ) 123 external_service_select_fields_list.append( external_service_select_field ) 124 if params.get( 'add_state_button', False ): 125 # Append a new tuple to the set of states which will result in 126 # empty state name and description TextFields being displayed on 127 # the form. 128 rt_states_widgets.append( ( "", "" ) ) 129 elif params.get( 'remove_state_button', False ): 130 index = int( params.get( 'remove_state_button', '' ).split( " " )[2] ) 131 del rt_states_widgets[ index-1 ] 132 elif params.get( 'add_external_service_button', False ): 133 # create a new one 134 external_service_select_field = self.__build_external_service_select_field( trans, 135 'external_service_id_%i' % len( external_services_list ) ) 136 external_service_select_fields_list.append( external_service_select_field ) 137 elif params.get( 'create_request_type_button', False ): 138 self.__save_request_type( trans, action='create_request_type', **kwd ) 139 message = 'The request type has been created.' 140 return trans.response.send_redirect( web.url_for( controller='request_type', 141 action='browse_request_types', 142 message=message, 143 status=status ) ) 144 # A request_type requires at least one possible sample state so that 145 # it can be used to create a sequencing request 146 if not len( rt_states_widgets ): 147 rt_states_widgets.append( ( "New", "First sample state" ) ) 148 return trans.fill_template( '/admin/request_type/create_request_type.mako', 149 rt_info_widgets=rt_info_widgets, 150 rt_states_widgets=rt_states_widgets, 151 external_service_select_fields_list=external_service_select_fields_list, 152 message=message, 153 status=status ) 154 def __get_external_services(self, trans, request_type=None, **kwd): 155 params = util.Params( kwd ) 156 external_services_list = [] 157 i = 0 158 while True: 159 if kwd.has_key( 'external_service_id_%i' % i ): 160 id = params.get( 'external_service_id_%i' % i, '' ) 161 try: 162 external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( id ) ) 163 except: 164 return invalid_id_redirect( trans, 'request_type', id, 'external service', action='browse_request_types' ) 165 external_services_list.append( external_service ) 166 i += 1 167 else: 168 break 169 return external_services_list 170 @web.expose 171 @web.require_admin 172 def view_editable_request_type( self, trans, **kwd ): 173 params = util.Params( kwd ) 174 message = util.restore_text( params.get( 'message', '' ) ) 175 status = params.get( 'status', 'done' ) 176 request_type_id = params.get( 'id', None ) 177 try: 178 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 179 except: 180 return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' ) 181 # See if we have any associated templates 182 widgets = request_type.get_template_widgets( trans ) 183 widget_fields_have_contents = self.widget_fields_have_contents( widgets ) 184 # get all the external services selected till now 185 external_service_select_fields_list = [] 186 for index, external_service in enumerate( request_type.external_services ): 187 external_service_select_field = self.__build_external_service_select_field( trans, 188 'external_service_id_%i' % index, 189 external_service ) 190 external_service_select_fields_list.append( external_service_select_field ) 191 return trans.fill_template( '/admin/request_type/edit_request_type.mako', 192 request_type=request_type, 193 widgets=widgets, 194 widget_fields_have_contents=widget_fields_have_contents, 195 external_service_select_fields_list=external_service_select_fields_list, 196 message=message, 197 status=status ) 198 @web.expose 199 @web.require_admin 200 def edit_request_type( self, trans, **kwd ): 201 params = util.Params( kwd ) 202 message = util.restore_text( params.get( 'message', '' ) ) 203 status = params.get( 'status', 'done' ) 204 request_type_id = params.get( 'id', None ) 205 try: 206 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 207 except: 208 return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' ) 209 # See if we have any associated templates 210 widgets = request_type.get_template_widgets( trans ) 211 widget_fields_have_contents = self.widget_fields_have_contents( widgets ) 212 # get all the external services selected till now 213 external_service_select_fields_list = [] 214 external_services_list = self.__get_external_services( trans, request_type, **kwd ) 215 if params.get( 'edit_request_type_button', False ): 216 request_type = self.__save_request_type( trans, action='edit_request_type', **kwd ) 217 message = 'Changes made to request type (%s) have been saved' % request_type.name 218 elif params.get( 'add_external_service_button', False ): 219 external_services_list.append( None ) 220 elif params.get( 'remove_external_service_button', False ): 221 index = int( kwd[ 'remove_external_service_button' ].split(' ')[3] ) - 1 222 del external_services_list[index] 223 #if external_services_list 224 for index, external_service in enumerate( external_services_list ): 225 external_service_select_field = self.__build_external_service_select_field( trans, 226 'external_service_id_%i' % index, 227 external_service ) 228 external_service_select_fields_list.append( external_service_select_field ) 229 return trans.fill_template( '/admin/request_type/edit_request_type.mako', 230 request_type=request_type, 231 widgets=widgets, 232 widget_fields_have_contents=widget_fields_have_contents, 233 external_service_select_fields_list=external_service_select_fields_list, 234 message=message, 235 status=status ) 236 def __save_request_type( self, trans, action, **kwd ): 237 # Here we save a newly created request_type or save changed 238 # attributes of an existing request_type. 239 params = util.Params( kwd ) 240 request_type_id = params.get( 'id', None ) 241 name = util.restore_text( params.get( 'name', '' ) ) 242 desc = util.restore_text( params.get( 'desc', '' ) ) 243 request_form_id = params.get( 'request_form_id', 'none' ) 244 sample_form_id = params.get( 'sample_form_id', 'none' ) 245 external_service_id = params.get( 'external_service_id', 'none' ) 246 # validate 247 if not name or request_form_id == 'none' or sample_form_id == 'none': 248 message = 'Enter the name, request form, sample form and at least one sample state associated with this request type.' 249 return trans.response.send_redirect( web.url_for( controller='request_type', 250 action=action, 251 message=message, 252 status='error' ) ) 253 try: 254 request_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( request_form_id ) ) 255 except: 256 return invalid_id_redirect( trans, 'request_type', request_type_id, 'form definition', action='browse_request_types' ) 257 258 try: 259 sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( sample_form_id ) ) 260 except: 261 return invalid_id_redirect( trans, 'request_type', request_type_id, 'form definition', action='browse_request_types' ) 262 if request_type_id: 263 # We're saving changed attributes of an existing request_type. 264 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 265 request_type.name = name 266 request_type.desc = desc 267 request_type.request_form = request_form 268 request_type.sample_form = sample_form 269 for sample_state in request_type.states: 270 sample_state_id = trans.security.encode_id( sample_state.id ) 271 name = util.restore_text( params.get( 'state_name_%s' % sample_state_id, '' ) ) 272 desc = util.restore_text( params.get( 'state_desc_%s' % sample_state_id, '' ) ) 273 sample_state.name = name 274 sample_state.desc = desc 275 trans.sa_session.add( sample_state ) 276 trans.sa_session.flush() 277 trans.sa_session.add( request_type ) 278 trans.sa_session.flush() 279 else: 280 # We're saving a newly created request_type 281 request_type = trans.model.RequestType( name=name, 282 desc=desc, 283 request_form=request_form, 284 sample_form=sample_form ) 285 trans.sa_session.add( request_type ) 286 trans.sa_session.flush() 287 i = 0 288 while True: 289 if kwd.has_key( 'state_name_%i' % i ): 290 name = util.restore_text( params.get( 'state_name_%i' % i, '' ) ) 291 desc = util.restore_text( params.get( 'state_desc_%i' % i, '' ) ) 292 sample_state = trans.model.SampleState( name, desc, request_type ) 293 trans.sa_session.add( sample_state ) 294 trans.sa_session.flush() 295 i += 1 296 else: 297 break 298 # delete existing associations 299 request_type.delete_external_service_associations( trans ) 300 # save the external services associated with this request_type 301 external_services_list = self.__get_external_services( trans, **kwd ) 302 for external_service in external_services_list: 303 request_type.add_external_service_association( trans, external_service ) 304 return request_type 305 def __get_populated_request_type_widgets( self, trans, **kwd ): 306 request_form_definitions = self.get_all_forms( trans, 307 filter=dict( deleted=False ), 308 form_type=trans.model.FormDefinition.types.REQUEST ) 309 sample_form_definitions = self.get_all_forms( trans, 310 filter=dict( deleted=False ), 311 form_type=trans.model.FormDefinition.types.SAMPLE ) 312 if not request_form_definitions or not sample_form_definitions: 313 return [],[] 314 params = util.Params( kwd ) 315 request_form_id = params.get( 'request_form_id', 'none' ) 316 sample_form_id = params.get( 'sample_form_id', 'none' ) 317 request_form_id_select_field = build_select_field( trans, 318 objs=request_form_definitions, 319 label_attr='name', 320 select_field_name='request_form_id', 321 selected_value=request_form_id, 322 refresh_on_change=False ) 323 sample_form_id_select_field = build_select_field( trans, 324 objs=sample_form_definitions, 325 label_attr='name', 326 select_field_name='sample_form_id', 327 selected_value=sample_form_id, 328 refresh_on_change=False ) 329 rt_info_widgets = [ dict( label='Name', 330 widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ), 331 dict( label='Description', 332 widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ), 333 dict( label='Request form', 334 widget=request_form_id_select_field ), 335 dict( label='Sample form', 336 widget=sample_form_id_select_field ) ] 337 # Unsaved sample states being defined for this request type 338 rt_states = [] 339 i=0 340 while True: 341 if kwd.has_key( 'state_name_%i' % i ): 342 rt_states.append( ( util.restore_text( params.get( 'state_name_%i' % i, '' ) ), 343 util.restore_text( params.get( 'state_desc_%i' % i, '' ) ) ) ) 344 i += 1 345 else: 346 break 347 return rt_info_widgets, rt_states 348 349 @web.expose 350 @web.require_admin 351 def view_request_type( self, trans, **kwd ): 352 params = util.Params( kwd ) 353 message = util.restore_text( params.get( 'message', '' ) ) 354 status = params.get( 'status', 'done' ) 355 request_type_id = kwd.get( 'id', None ) 356 try: 357 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 358 except: 359 return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' ) 360 # See if we have any associated templates 361 widgets = request_type.get_template_widgets( trans ) 362 widget_fields_have_contents = self.widget_fields_have_contents( widgets ) 363 return trans.fill_template( '/admin/request_type/view_request_type.mako', 364 request_type=request_type, 365 widgets=widgets, 366 widget_fields_have_contents=widget_fields_have_contents, 367 message=message, 368 status=status ) 369 @web.expose 370 @web.require_admin 371 def delete_request_type( self, trans, **kwd ): 372 request_type_id = kwd.get( 'id', '' ) 373 request_type_id_list = util.listify( request_type_id ) 374 for request_type_id in request_type_id_list: 375 try: 376 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 377 except: 378 return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' ) 379 request_type.deleted = True 380 trans.sa_session.add( request_type ) 381 trans.sa_session.flush() 382 status = 'done' 383 message = '%i request types has been deleted' % len( request_type_id_list ) 384 return trans.response.send_redirect( web.url_for( controller='request_type', 385 action='browse_request_types', 386 message=message, 387 status='done' ) ) 388 @web.expose 389 @web.require_admin 390 def undelete_request_type( self, trans, **kwd ): 391 request_type_id = kwd.get( 'id', '' ) 392 request_type_id_list = util.listify( request_type_id ) 393 for request_type_id in request_type_id_list: 394 try: 395 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 396 except: 397 return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' ) 398 request_type.deleted = False 399 trans.sa_session.add( request_type ) 400 trans.sa_session.flush() 401 status = 'done' 402 message = '%i request types have been undeleted' % len( request_type_id_list ) 403 return trans.response.send_redirect( web.url_for( controller='request_type', 404 action='browse_request_types', 405 message=message, 406 status=status ) ) 407 @web.expose 408 @web.require_admin 409 def request_type_permissions( self, trans, **kwd ): 410 params = util.Params( kwd ) 411 message = util.restore_text( params.get( 'message', '' ) ) 412 status = params.get( 'status', 'done' ) 413 request_type_id = kwd.get( 'id', '' ) 414 try: 415 request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) 416 except: 417 return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' ) 418 roles = trans.sa_session.query( trans.model.Role ) \ 419 .filter( trans.model.Role.table.c.deleted==False ) \ 420 .order_by( trans.model.Role.table.c.name ) 421 if params.get( 'update_roles_button', False ): 422 permissions = {} 423 for k, v in trans.model.RequestType.permitted_actions.items(): 424 in_roles = [ trans.sa_session.query( trans.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] 425 permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles 426 trans.app.security_agent.set_request_type_permissions( request_type, permissions ) 427 trans.sa_session.refresh( request_type ) 428 message = "Permissions updated for request type '%s'" % request_type.name 429 return trans.fill_template( '/admin/request_type/request_type_permissions.mako', 430 request_type=request_type, 431 roles=roles, 432 status=status, 433 message=message ) 434 @web.expose 435 @web.require_admin 436 def view_form_definition( self, trans, **kwd ): 437 form_definition_id = kwd.get( 'id', None ) 438 try: 439 form_definition = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( form_definition_id ) ) 440 except: 441 return invalid_id_redirect( trans, 'request_type', form_definition_id, 'form definition', action='browse_request_types' ) 442 return trans.fill_template( '/admin/forms/view_form_definition.mako', 443 form_definition=form_definition ) 444 445 # ===== Methods for building SelectFields used on various admin_requests forms 446 def __build_external_service_select_field( self, trans, select_field_name, external_service=None ): 447 if external_service: 448 selected_value = trans.security.encode_id( external_service.id ) 449 else: 450 selected_value = 'none' 451 all_external_services = trans.sa_session.query( trans.model.ExternalService ).filter( trans.model.ExternalService.table.c.deleted==False ).all() 452 for e in all_external_services: 453 external_service_type = e.get_external_service_type( trans ) 454 e.label = '%s - %s' % ( e.name, external_service_type.name ) 455 return build_select_field( trans, 456 objs=all_external_services, 457 label_attr='label', 458 select_field_name=select_field_name, 459 selected_value=selected_value, 460 refresh_on_change=False )