/lib/galaxy/webapps/community/controllers/repository.py
Python | 1144 lines | 1081 code | 7 blank | 56 comment | 56 complexity | aa433671131278cfec4260685f873f4f MD5 | raw file
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1import os, logging, urllib, ConfigParser, tempfile, shutil 2from time import strftime 3from datetime import date, datetime 4from galaxy import util 5from galaxy.datatypes.checkers import * 6from galaxy.web.base.controller import * 7from galaxy.web.form_builder import CheckboxField 8from galaxy.webapps.community import model 9from galaxy.webapps.community.model import directory_hash_id 10from galaxy.web.framework.helpers import time_ago, iff, grids 11from galaxy.util.json import from_json_string, to_json_string 12from galaxy.model.orm import * 13from common import * 14from mercurial import hg, ui, patch, commands 15 16log = logging.getLogger( __name__ ) 17 18# Characters that must be html escaped 19MAPPED_CHARS = { '>' :'>', 20 '<' :'<', 21 '"' : '"', 22 '&' : '&', 23 '\'' : ''' } 24MAX_CONTENT_SIZE = 32768 25VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) 26VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) 27 28class CategoryListGrid( grids.Grid ): 29 class NameColumn( grids.TextColumn ): 30 def get_value( self, trans, grid, category ): 31 return category.name 32 class DescriptionColumn( grids.TextColumn ): 33 def get_value( self, trans, grid, category ): 34 return category.description 35 class RepositoriesColumn( grids.TextColumn ): 36 def get_value( self, trans, grid, category ): 37 if category.repositories: 38 viewable_repositories = 0 39 for rca in category.repositories: 40 viewable_repositories += 1 41 return viewable_repositories 42 return 0 43 44 # Grid definition 45 webapp = "community" 46 title = "Categories" 47 model_class = model.Category 48 template='/webapps/community/category/grid.mako' 49 default_sort_key = "name" 50 columns = [ 51 NameColumn( "Name", 52 key="Category.name", 53 link=( lambda item: dict( operation="repositories_by_category", id=item.id, webapp="community" ) ), 54 attach_popup=False ), 55 DescriptionColumn( "Description", 56 key="Category.description", 57 attach_popup=False ), 58 # Columns that are valid for filtering but are not visible. 59 RepositoriesColumn( "Repositories", 60 model_class=model.Repository, 61 attach_popup=False ) 62 ] 63 # Override these 64 default_filter = {} 65 global_actions = [] 66 operations = [] 67 standard_filters = [] 68 num_rows_per_page = 50 69 preserve_state = False 70 use_paging = True 71 72class RepositoryListGrid( grids.Grid ): 73 class NameColumn( grids.TextColumn ): 74 def get_value( self, trans, grid, repository ): 75 return repository.name 76 class RevisionColumn( grids.GridColumn ): 77 def __init__( self, col_name ): 78 grids.GridColumn.__init__( self, col_name ) 79 def get_value( self, trans, grid, repository ): 80 """ 81 Display a SelectField whose options are the changeset_revision 82 strings of all downloadable_revisions of this repository. 83 """ 84 select_field = build_changeset_revision_select_field( trans, repository ) 85 if len( select_field.options ) > 1: 86 return select_field.get_html() 87 return repository.revision 88 class DescriptionColumn( grids.TextColumn ): 89 def get_value( self, trans, grid, repository ): 90 return repository.description 91 class CategoryColumn( grids.TextColumn ): 92 def get_value( self, trans, grid, repository ): 93 rval = '<ul>' 94 if repository.categories: 95 for rca in repository.categories: 96 rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s&webapp=community">%s</a></li>' \ 97 % ( trans.security.encode_id( rca.category.id ), rca.category.name ) 98 else: 99 rval += '<li>not set</li>' 100 rval += '</ul>' 101 return rval 102 class RepositoryCategoryColumn( grids.GridColumn ): 103 def filter( self, trans, user, query, column_filter ): 104 """Modify query to filter by category.""" 105 if column_filter == "All": 106 return query 107 return query.filter( model.Category.name == column_filter ) 108 class UserColumn( grids.TextColumn ): 109 def get_value( self, trans, grid, repository ): 110 if repository.user: 111 return repository.user.username 112 return 'no user' 113 class EmailColumn( grids.TextColumn ): 114 def filter( self, trans, user, query, column_filter ): 115 if column_filter == 'All': 116 return query 117 return query.filter( and_( model.Repository.table.c.user_id == model.User.table.c.id, 118 model.User.table.c.email == column_filter ) ) 119 class EmailAlertsColumn( grids.TextColumn ): 120 def get_value( self, trans, grid, repository ): 121 if trans.user and repository.email_alerts and trans.user.email in from_json_string( repository.email_alerts ): 122 return 'yes' 123 return '' 124 # Grid definition 125 title = "Repositories" 126 model_class = model.Repository 127 template='/webapps/community/repository/grid.mako' 128 default_sort_key = "name" 129 columns = [ 130 NameColumn( "Name", 131 key="name", 132 link=( lambda item: dict( operation="view_or_manage_repository", 133 id=item.id, 134 webapp="community" ) ), 135 attach_popup=True ), 136 DescriptionColumn( "Synopsis", 137 key="description", 138 attach_popup=False ), 139 RevisionColumn( "Revision" ), 140 CategoryColumn( "Category", 141 model_class=model.Category, 142 key="Category.name", 143 attach_popup=False ), 144 UserColumn( "Owner", 145 model_class=model.User, 146 link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), 147 attach_popup=False, 148 key="User.username" ), 149 grids.CommunityRatingColumn( "Average Rating", key="rating" ), 150 EmailAlertsColumn( "Alert", attach_popup=False ), 151 # Columns that are valid for filtering but are not visible. 152 EmailColumn( "Email", 153 model_class=model.User, 154 key="email", 155 visible=False ), 156 RepositoryCategoryColumn( "Category", 157 model_class=model.Category, 158 key="Category.name", 159 visible=False ), 160 grids.DeletedColumn( "Deleted", 161 key="deleted", 162 visible=False, 163 filterable="advanced" ) 164 ] 165 columns.append( grids.MulticolFilterColumn( "Search repository name, description", 166 cols_to_filter=[ columns[0], columns[1] ], 167 key="free-text-search", 168 visible=False, 169 filterable="standard" ) ) 170 operations = [ grids.GridOperation( "Receive email alerts", 171 allow_multiple=False, 172 condition=( lambda item: not item.deleted ), 173 async_compatible=False ) ] 174 standard_filters = [] 175 default_filter = dict( deleted="False" ) 176 num_rows_per_page = 50 177 preserve_state = False 178 use_paging = True 179 def build_initial_query( self, trans, **kwd ): 180 return trans.sa_session.query( self.model_class ) \ 181 .join( model.User.table ) \ 182 .outerjoin( model.RepositoryCategoryAssociation.table ) \ 183 .outerjoin( model.Category.table ) 184 185class DownloadableRepositoryListGrid( RepositoryListGrid ): 186 class RevisionColumn( grids.GridColumn ): 187 def __init__( self, col_name ): 188 grids.GridColumn.__init__( self, col_name ) 189 def get_value( self, trans, grid, repository ): 190 """ 191 Display a SelectField whose options are the changeset_revision 192 strings of all downloadable_revisions of this repository. 193 """ 194 select_field = build_changeset_revision_select_field( trans, repository ) 195 if len( select_field.options ) > 1: 196 return select_field.get_html() 197 return repository.revision 198 title = "Downloadable repositories" 199 columns = [ 200 RepositoryListGrid.NameColumn( "Name", 201 key="name", 202 attach_popup=True ), 203 RepositoryListGrid.DescriptionColumn( "Synopsis", 204 key="description", 205 attach_popup=False ), 206 RevisionColumn( "Revision" ), 207 RepositoryListGrid.UserColumn( "Owner", 208 model_class=model.User, 209 attach_popup=False, 210 key="User.username" ) 211 ] 212 columns.append( grids.MulticolFilterColumn( "Search repository name, description", 213 cols_to_filter=[ columns[0], columns[1] ], 214 key="free-text-search", 215 visible=False, 216 filterable="standard" ) ) 217 operations = [] 218 def build_initial_query( self, trans, **kwd ): 219 return trans.sa_session.query( self.model_class ) \ 220 .join( model.RepositoryMetadata.table ) \ 221 .join( model.User.table ) 222 223class RepositoryController( BaseUIController, ItemRatings ): 224 225 downloadable_repository_list_grid = DownloadableRepositoryListGrid() 226 repository_list_grid = RepositoryListGrid() 227 category_list_grid = CategoryListGrid() 228 229 @web.expose 230 def index( self, trans, **kwd ): 231 params = util.Params( kwd ) 232 message = util.restore_text( params.get( 'message', '' ) ) 233 status = params.get( 'status', 'done' ) 234 return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) 235 @web.expose 236 def browse_categories( self, trans, **kwd ): 237 if 'f-free-text-search' in kwd: 238 # Trick to enable searching repository name, description from the CategoryListGrid. 239 # What we've done is rendered the search box for the RepositoryListGrid on the grid.mako 240 # template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako. 241 # Since we are searching repositories and not categories, redirect to browse_repositories(). 242 if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: 243 # The value of 'id' has been set to the search string, which is a repository name. 244 # We'll try to get the desired encoded repository id to pass on. 245 try: 246 repository = get_repository_by_name( trans, kwd[ 'id' ] ) 247 kwd[ 'id' ] = trans.security.encode_id( repository.id ) 248 except: 249 pass 250 return self.browse_repositories( trans, **kwd ) 251 if 'operation' in kwd: 252 operation = kwd['operation'].lower() 253 if operation in [ "repositories_by_category", "repositories_by_user" ]: 254 # Eliminate the current filters if any exist. 255 for k, v in kwd.items(): 256 if k.startswith( 'f-' ): 257 del kwd[ k ] 258 return trans.response.send_redirect( web.url_for( controller='repository', 259 action='browse_repositories', 260 **kwd ) ) 261 # Render the list view 262 return self.category_list_grid( trans, **kwd ) 263 @web.expose 264 def browse_downloadable_repositories( self, trans, **kwd ): 265 # Set the toolshedgalaxyurl cookie so we can get back 266 # to the calling local Galaxy instance. 267 galaxy_url = kwd.get( 'galaxy_url', None ) 268 if galaxy_url: 269 trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) 270 repository_id = kwd.get( 'id', None ) 271 if 'operation' in kwd: 272 operation = kwd[ 'operation' ].lower() 273 if operation == "preview_tools_in_changeset": 274 repository = get_repository( trans, repository_id ) 275 return trans.response.send_redirect( web.url_for( controller='repository', 276 action='preview_tools_in_changeset', 277 repository_id=repository_id, 278 changeset_revision=repository.tip ) ) 279 280 # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change 281 # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One 282 # of the many select fields on the grid performed the refresh_on_change, so we loop through 283 # all of the received values to see which value is not the repository tip. If we find it, we 284 # know the refresh_on_change occurred, and we have the necessary repository id and change set 285 # revision to pass on. 286 for k, v in kwd.items(): 287 changset_revision_str = 'changeset_revision_' 288 if k.startswith( changset_revision_str ): 289 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) 290 repository = get_repository( trans, repository_id ) 291 if repository.tip != v: 292 return trans.response.send_redirect( web.url_for( controller='repository', 293 action='preview_tools_in_changeset', 294 repository_id=trans.security.encode_id( repository.id ), 295 changeset_revision=v ) ) 296 url_args = dict( action='browse_downloadable_repositories', 297 operation='preview_tools_in_changeset', 298 repository_id=repository_id ) 299 self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install tools", 300 url_args=url_args, 301 allow_multiple=False, 302 async_compatible=False ) ] 303 304 # Render the list view 305 return self.downloadable_repository_list_grid( trans, **kwd ) 306 @web.expose 307 def preview_tools_in_changeset( self, trans, repository_id, **kwd ): 308 params = util.Params( kwd ) 309 message = util.restore_text( params.get( 'message', '' ) ) 310 status = params.get( 'status', 'done' ) 311 repository = get_repository( trans, repository_id ) 312 changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) 313 repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) 314 if repository_metadata: 315 metadata = repository_metadata.metadata 316 else: 317 metadata = None 318 revision_label = get_revision_label( trans, repository, changeset_revision ) 319 changeset_revision_select_field = build_changeset_revision_select_field( trans, 320 repository, 321 selected_value=changeset_revision, 322 add_id_to_name=False ) 323 return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', 324 repository=repository, 325 changeset_revision=changeset_revision, 326 revision_label=revision_label, 327 changeset_revision_select_field=changeset_revision_select_field, 328 metadata=metadata, 329 display_for_install=True, 330 message=message, 331 status=status ) 332 @web.expose 333 def install_repository_revision( self, trans, repository_id, **kwd ): 334 params = util.Params( kwd ) 335 message = util.restore_text( params.get( 'message', '' ) ) 336 status = params.get( 'status', 'done' ) 337 galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) 338 repository = get_repository( trans, repository_id ) 339 changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) 340 # Redirect back to local Galaxy to perform install. 341 tool_shed_url = trans.request.host 342 repository_clone_url = generate_clone_url( trans, repository_id ) 343 # TODO: support https in the following url. 344 url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repository_name=%s&repository_clone_url=%s&changeset_revision=%s' % \ 345 ( galaxy_url, tool_shed_url, repository.name, repository_clone_url, changeset_revision ) 346 return trans.response.send_redirect( url ) 347 @web.expose 348 def browse_repositories( self, trans, **kwd ): 349 # We add params to the keyword dict in this method in order to rename the param 350 # with an "f-" prefix, simulating filtering by clicking a search link. We have 351 # to take this approach because the "-" character is illegal in HTTP requests. 352 if 'operation' in kwd: 353 operation = kwd['operation'].lower() 354 if operation == "view_or_manage_repository": 355 repository_id = kwd[ 'id' ] 356 repository = get_repository( trans, repository_id ) 357 is_admin = trans.user_is_admin() 358 if is_admin or repository.user == trans.user: 359 return trans.response.send_redirect( web.url_for( controller='repository', 360 action='manage_repository', 361 **kwd ) ) 362 else: 363 return trans.response.send_redirect( web.url_for( controller='repository', 364 action='view_repository', 365 **kwd ) ) 366 elif operation == "edit_repository": 367 return trans.response.send_redirect( web.url_for( controller='repository', 368 action='edit_repository', 369 **kwd ) ) 370 elif operation == "repositories_by_user": 371 # Eliminate the current filters if any exist. 372 for k, v in kwd.items(): 373 if k.startswith( 'f-' ): 374 del kwd[ k ] 375 if 'user_id' in kwd: 376 user = get_user( trans, kwd[ 'user_id' ] ) 377 kwd[ 'f-email' ] = user.email 378 del kwd[ 'user_id' ] 379 else: 380 # The received id is the repository id, so we need to get the id of the user 381 # that uploaded the repository. 382 repository_id = kwd.get( 'id', None ) 383 repository = get_repository( trans, repository_id ) 384 kwd[ 'f-email' ] = repository.user.email 385 elif operation == "my_repositories": 386 # Eliminate the current filters if any exist. 387 for k, v in kwd.items(): 388 if k.startswith( 'f-' ): 389 del kwd[ k ] 390 kwd[ 'f-email' ] = trans.user.email 391 elif operation == "repositories_by_category": 392 # Eliminate the current filters if any exist. 393 for k, v in kwd.items(): 394 if k.startswith( 'f-' ): 395 del kwd[ k ] 396 category_id = kwd.get( 'id', None ) 397 category = get_category( trans, category_id ) 398 kwd[ 'f-Category.name' ] = category.name 399 elif operation == "receive email alerts": 400 if trans.user: 401 if kwd[ 'id' ]: 402 return trans.response.send_redirect( web.url_for( controller='repository', 403 action='set_email_alerts', 404 **kwd ) ) 405 else: 406 kwd[ 'message' ] = 'You must be logged in to set email alerts.' 407 kwd[ 'status' ] = 'error' 408 del kwd[ 'operation' ] 409 # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change 410 # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One 411 # of the many select fields on the grid performed the refresh_on_change, so we loop through 412 # all of the received values to see which value is not the repository tip. If we find it, we 413 # know the refresh_on_change occurred, and we have the necessary repository id and change set 414 # revision to pass on. 415 for k, v in kwd.items(): 416 changset_revision_str = 'changeset_revision_' 417 if k.startswith( changset_revision_str ): 418 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) 419 repository = get_repository( trans, repository_id ) 420 if repository.tip != v: 421 return trans.response.send_redirect( web.url_for( controller='repository', 422 action='browse_repositories', 423 operation='view_or_manage_repository', 424 id=trans.security.encode_id( repository.id ), 425 changeset_revision=v ) ) 426 # Render the list view 427 return self.repository_list_grid( trans, **kwd ) 428 @web.expose 429 def create_repository( self, trans, **kwd ): 430 params = util.Params( kwd ) 431 message = util.restore_text( params.get( 'message', '' ) ) 432 status = params.get( 'status', 'done' ) 433 categories = get_categories( trans ) 434 if not categories: 435 message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ 436 'An administrator needs to create some via the Administrator control panel before creating repositories.', 437 status = 'error' 438 return trans.response.send_redirect( web.url_for( controller='repository', 439 action='browse_repositories', 440 message=message, 441 status=status ) ) 442 name = util.restore_text( params.get( 'name', '' ) ) 443 description = util.restore_text( params.get( 'description', '' ) ) 444 long_description = util.restore_text( params.get( 'long_description', '' ) ) 445 category_ids = util.listify( params.get( 'category_id', '' ) ) 446 selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] 447 if params.get( 'create_repository_button', False ): 448 error = False 449 message = self.__validate_repository_name( name, trans.user ) 450 if message: 451 error = True 452 if not description: 453 message = 'Enter a description.' 454 error = True 455 if not error: 456 # Add the repository record to the db 457 repository = trans.app.model.Repository( name=name, 458 description=description, 459 long_description=long_description, 460 user_id=trans.user.id ) 461 # Flush to get the id 462 trans.sa_session.add( repository ) 463 trans.sa_session.flush() 464 # Determine the repository's repo_path on disk 465 dir = os.path.join( trans.app.config.file_path, *directory_hash_id( repository.id ) ) 466 # Create directory if it does not exist 467 if not os.path.exists( dir ): 468 os.makedirs( dir ) 469 # Define repo name inside hashed directory 470 repository_path = os.path.join( dir, "repo_%d" % repository.id ) 471 # Create local repository directory 472 if not os.path.exists( repository_path ): 473 os.makedirs( repository_path ) 474 # Create the local repository 475 repo = hg.repository( get_configured_ui(), repository_path, create=True ) 476 # Add an entry in the hgweb.config file for the local repository 477 # This enables calls to repository.repo_path 478 self.__add_hgweb_config_entry( trans, repository, repository_path ) 479 # Create a .hg/hgrc file for the local repository 480 self.__create_hgrc_file( repository ) 481 flush_needed = False 482 if category_ids: 483 # Create category associations 484 for category_id in category_ids: 485 category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) 486 rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) 487 trans.sa_session.add( rca ) 488 flush_needed = True 489 if flush_needed: 490 trans.sa_session.flush() 491 message = "Repository '%s' has been created." % repository.name 492 trans.response.send_redirect( web.url_for( controller='repository', 493 action='view_repository', 494 message=message, 495 id=trans.security.encode_id( repository.id ) ) ) 496 return trans.fill_template( '/webapps/community/repository/create_repository.mako', 497 name=name, 498 description=description, 499 long_description=long_description, 500 selected_categories=selected_categories, 501 categories=categories, 502 message=message, 503 status=status ) 504 def __validate_repository_name( self, name, user ): 505 # Repository names must be unique for each user, must be at least four characters 506 # in length and must contain only lower-case letters, numbers, and the '_' character. 507 if name in [ 'None', None, '' ]: 508 return 'Enter the required repository name.' 509 for repository in user.active_repositories: 510 if repository.name == name: 511 return "You already have a repository named '%s', so choose a different name." % name 512 if len( name ) < 4: 513 return "Repository names must be at least 4 characters in length." 514 if len( name ) > 80: 515 return "Repository names cannot be more than 80 characters in length." 516 if not( VALID_REPOSITORYNAME_RE.match( name ) ): 517 return "Repository names must contain only lower-case letters, numbers and underscore '_'." 518 return '' 519 def __make_hgweb_config_copy( self, trans, hgweb_config ): 520 # Make a backup of the hgweb.config file 521 today = date.today() 522 backup_date = today.strftime( "%Y_%m_%d" ) 523 hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) 524 shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) 525 def __add_hgweb_config_entry( self, trans, repository, repository_path ): 526 # Add an entry in the hgweb.config file for a new repository. 527 # An entry looks something like: 528 # repos/test/mira_assembler = database/community_files/000/repo_123. 529 hgweb_config = "%s/hgweb.config" % trans.app.config.root 530 # Make a backup of the hgweb.config file since we're going to be changing it. 531 self.__make_hgweb_config_copy( trans, hgweb_config ) 532 entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) 533 if os.path.exists( hgweb_config ): 534 output = open( hgweb_config, 'a' ) 535 else: 536 output = open( hgweb_config, 'w' ) 537 output.write( '[paths]\n' ) 538 output.write( "%s\n" % entry ) 539 output.close() 540 def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): 541 # Change an entry in the hgweb.config file for a repository. This only happens when 542 # the owner changes the name of the repository. An entry looks something like: 543 # repos/test/mira_assembler = database/community_files/000/repo_123. 544 hgweb_config = "%s/hgweb.config" % trans.app.config.root 545 # Make a backup of the hgweb.config file since we're going to be changing it. 546 self.__make_hgweb_config_copy( trans, hgweb_config ) 547 repo_dir = repository.repo_path 548 old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) 549 old_entry = "%s = %s" % ( old_lhs, repo_dir ) 550 new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) 551 tmp_fd, tmp_fname = tempfile.mkstemp() 552 new_hgweb_config = open( tmp_fname, 'wb' ) 553 for i, line in enumerate( open( hgweb_config ) ): 554 if line.startswith( old_lhs ): 555 new_hgweb_config.write( new_entry ) 556 else: 557 new_hgweb_config.write( line ) 558 shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) 559 def __create_hgrc_file( self, repository ): 560 # At this point, an entry for the repository is required to be in the hgweb.config 561 # file so we can call repository.repo_path. 562 # Create a .hg/hgrc file that looks something like this: 563 # [web] 564 # allow_push = test 565 # name = convert_characters1 566 # push_ssl = False 567 # Since we support both http and https, we set push_ssl to False to override 568 # the default (which is True) in the mercurial api. 569 repo = hg.repository( get_configured_ui(), path=repository.repo_path ) 570 fp = repo.opener( 'hgrc', 'wb' ) 571 fp.write( '[paths]\n' ) 572 fp.write( 'default = .\n' ) 573 fp.write( 'default-push = .\n' ) 574 fp.write( '[web]\n' ) 575 fp.write( 'allow_push = %s\n' % repository.user.username ) 576 fp.write( 'name = %s\n' % repository.name ) 577 fp.write( 'push_ssl = false\n' ) 578 fp.close() 579 @web.expose 580 def browse_repository( self, trans, id, **kwd ): 581 params = util.Params( kwd ) 582 message = util.restore_text( params.get( 'message', '' ) ) 583 status = params.get( 'status', 'done' ) 584 commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) 585 repository = get_repository( trans, id ) 586 repo = hg.repository( get_configured_ui(), repository.repo_path ) 587 current_working_dir = os.getcwd() 588 # Update repository files for browsing. 589 update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) 590 is_malicious = change_set_is_malicious( trans, id, repository.tip ) 591 return trans.fill_template( '/webapps/community/repository/browse_repository.mako', 592 repo=repo, 593 repository=repository, 594 commit_message=commit_message, 595 is_malicious=is_malicious, 596 message=message, 597 status=status ) 598 @web.expose 599 def contact_owner( self, trans, id, **kwd ): 600 params = util.Params( kwd ) 601 message = util.restore_text( params.get( 'message', '' ) ) 602 status = params.get( 'status', 'done' ) 603 repository = get_repository( trans, id ) 604 if trans.user and trans.user.email: 605 return trans.fill_template( "/webapps/community/repository/contact_owner.mako", 606 repository=repository, 607 message=message, 608 status=status ) 609 else: 610 # Do all we can to eliminate spam. 611 return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) 612 @web.expose 613 def send_to_owner( self, trans, id, message='' ): 614 repository = get_repository( trans, id ) 615 if not message: 616 message = 'Enter a message' 617 status = 'error' 618 elif trans.user and trans.user.email: 619 smtp_server = trans.app.config.smtp_server 620 from_address = trans.app.config.email_from 621 if smtp_server is None or from_address is None: 622 return trans.show_error_message( "Mail is not configured for this Galaxy tool shed instance" ) 623 to_address = repository.user.email 624 # Get the name of the server hosting the tool shed instance. 625 host = trans.request.host 626 # Build the email message 627 body = string.Template( contact_owner_template ) \ 628 .safe_substitute( username=trans.user.username, 629 repository_name=repository.name, 630 email=trans.user.email, 631 message=message, 632 host=host ) 633 subject = "Regarding your tool shed repository named %s" % repository.name 634 # Send it 635 try: 636 util.send_mail( from_address, to_address, subject, body, trans.app.config ) 637 message = "Your message has been sent" 638 status = "done" 639 except Exception, e: 640 message = "An error occurred sending your message by email: %s" % str( e ) 641 status = "error" 642 else: 643 # Do all we can to eliminate spam. 644 return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) 645 return trans.response.send_redirect( web.url_for( controller='repository', 646 action='contact_owner', 647 id=id, 648 message=message, 649 status=status ) ) 650 @web.expose 651 def select_files_to_delete( self, trans, id, **kwd ): 652 params = util.Params( kwd ) 653 message = util.restore_text( params.get( 'message', '' ) ) 654 status = params.get( 'status', 'done' ) 655 commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) 656 repository = get_repository( trans, id ) 657 repo_dir = repository.repo_path 658 repo = hg.repository( get_configured_ui(), repo_dir ) 659 selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) 660 if params.get( 'select_files_to_delete_button', False ): 661 if selected_files_to_delete: 662 selected_files_to_delete = selected_files_to_delete.split( ',' ) 663 current_working_dir = os.getcwd() 664 # Get the current repository tip. 665 tip = repository.tip 666 for selected_file in selected_files_to_delete: 667 try: 668 commands.remove( repo.ui, repo, repo_file, force=True ) 669 except Exception, e: 670 # I never have a problem with commands.remove on a Mac, but in the test/production 671 # tool shed environment, it throws an exception whenever I delete all files from a 672 # repository. If this happens, we'll try the following. 673 relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) 674 repo.dirstate.remove( relative_selected_file ) 675 repo.dirstate.write() 676 absolute_selected_file = os.path.abspath( selected_file ) 677 if os.path.isdir( absolute_selected_file ): 678 try: 679 os.rmdir( absolute_selected_file ) 680 except OSError, e: 681 # The directory is not empty 682 pass 683 elif os.path.isfile( absolute_selected_file ): 684 os.remove( absolute_selected_file ) 685 dir = os.path.split( absolute_selected_file )[0] 686 try: 687 os.rmdir( dir ) 688 except OSError, e: 689 # The directory is not empty 690 pass 691 # Commit the change set. 692 if not commit_message: 693 commit_message = 'Deleted selected files' 694 try: 695 commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) 696 except Exception, e: 697 # I never have a problem with commands.commit on a Mac, but in the test/production 698 # tool shed environment, it occasionally throws a "TypeError: array item must be char" 699 # exception. If this happens, we'll try the following. 700 repo.dirstate.write() 701 repo.commit( user=trans.user.username, text=commit_message ) 702 handle_email_alerts( trans, repository ) 703 # Update the repository files for browsing. 704 update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) 705 # Get the new repository tip. 706 repo = hg.repository( get_configured_ui(), repo_dir ) 707 if tip != repository.tip: 708 message = "The selected files were deleted from the repository." 709 else: 710 message = 'No changes to repository.' 711 # Set metadata on the repository tip 712 error_message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) 713 if error_message: 714 message = '%s<br/>%s' % ( message, error_message ) 715 return trans.response.send_redirect( web.url_for( controller='repository', 716 action='manage_repository', 717 id=id, 718 message=message, 719 status=status ) ) 720 else: 721 message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." 722 status = "error" 723 is_malicious = change_set_is_malicious( trans, id, repository.tip ) 724 return trans.fill_template( '/webapps/community/repository/browse_repository.mako', 725 repo=repo, 726 repository=repository, 727 commit_message=commit_message, 728 is_malicious=is_malicious, 729 message=message, 730 status=status ) 731 @web.expose 732 def view_repository( self, trans, id, **kwd ): 733 params = util.Params( kwd ) 734 message = util.restore_text( params.get( 'message', '' ) ) 735 status = params.get( 'status', 'done' ) 736 repository = get_repository( trans, id ) 737 repo = hg.repository( get_configured_ui(), repository.repo_path ) 738 avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) 739 changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) 740 display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) 741 alerts = params.get( 'alerts', '' ) 742 alerts_checked = CheckboxField.is_checked( alerts ) 743 if repository.email_alerts: 744 email_alerts = from_json_string( repository.email_alerts ) 745 else: 746 email_alerts = [] 747 user = trans.user 748 if user and params.get( 'receive_email_alerts_button', False ): 749 flush_needed = False 750 if alerts_checked: 751 if user.email not in email_alerts: 752 email_alerts.append( user.email ) 753 repository.email_alerts = to_json_string( email_alerts ) 754 flush_needed = True 755 else: 756 if user.email in email_alerts: 757 email_alerts.remove( user.email ) 758 repository.email_alerts = to_json_string( email_alerts ) 759 flush_needed = True 760 if flush_needed: 761 trans.sa_session.add( repository ) 762 trans.sa_session.flush() 763 checked = alerts_checked or ( user and user.email in email_alerts ) 764 alerts_check_box = CheckboxField( 'alerts', checked=checked ) 765 changeset_revision_select_field = build_changeset_revision_select_field( trans, 766 repository, 767 selected_value=changeset_revision, 768 add_id_to_name=False ) 769 revision_label = get_revision_label( trans, repository, changeset_revision ) 770 repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) 771 if repository_metadata: 772 metadata = repository_metadata.metadata 773 else: 774 metadata = None 775 is_malicious = change_set_is_malicious( trans, id, repository.tip ) 776 if is_malicious: 777 if trans.app.security_agent.can_push( trans.user, repository ): 778 message += malicious_error_can_push 779 else: 780 message += malicious_error 781 status = 'error' 782 return trans.fill_template( '/webapps/community/repository/view_repository.mako', 783 repo=repo, 784 repository=repository, 785 metadata=metadata, 786 avg_rating=avg_rating, 787 display_reviews=display_reviews, 788 num_ratings=num_ratings, 789 alerts_check_box=alerts_check_box, 790 changeset_revision=changeset_revision, 791 changeset_revision_select_field=changeset_revision_select_field, 792 revision_label=revision_label, 793 is_malicious=is_malicious, 794 message=message, 795 status=status ) 796 @web.expose 797 @web.require_login( "manage repository" ) 798 def manage_repository( self, trans, id, **kwd ): 799 params = util.Params( kwd ) 800 message = util.restore_text( params.get( 'message', '' ) ) 801 status = params.get( 'status', 'done' ) 802 repository = get_repository( trans, id ) 803 repo_dir = repository.repo_path 804 repo = hg.repository( get_configured_ui(), repo_dir ) 805 repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) 806 changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) 807 description = util.restore_text( params.get( 'description', repository.description ) ) 808 long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) 809 avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) 810 display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) 811 alerts = params.get( 'alerts', '' ) 812 alerts_checked = CheckboxField.is_checked( alerts ) 813 category_ids = util.listify( params.get( 'category_id', '' ) ) 814 if repository.email_alerts: 815 email_alerts = from_json_string( repository.email_alerts ) 816 else: 817 email_alerts = [] 818 allow_push = params.get( 'allow_push', '' ) 819 error = False 820 user = trans.user 821 if params.get( 'edit_repository_button', False ): 822 flush_needed = False 823 # TODO: add a can_manage in the security agent. 824 if user != repository.user: 825 message = "You are not the owner of this repository, so you cannot manage it." 826 status = error 827 return trans.response.send_redirect( web.url_for( controller='repository', 828 action='view_repository', 829 id=id, 830 message=message, 831 status=status ) ) 832 if repo_name != repository.name: 833 message = self.__validate_repository_name( repo_name, user ) 834 if message: 835 error = True 836 else: 837 self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name ) 838 repository.name = repo_name 839 flush_needed = True 840 if description != repository.description: 841 repository.description = description 842 flush_needed = True 843 if long_description != repository.long_description: 844 repository.long_description = long_description 845 flush_needed = True 846 if flush_needed: 847 trans.sa_session.add( repository ) 848 trans.sa_session.flush() 849 message = "The repository information has been updated." 850 elif params.get( 'manage_categories_button', False ): 851 flush_needed = False 852 # Delete all currently existing categories. 853 for rca in repository.categories: 854 trans.sa_session.delete( rca ) 855 trans.sa_session.flush() 856 if category_ids: 857 # Create category associations 858 for category_id in category_ids: 859 category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) 860 rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) 861 trans.sa_session.add( rca ) 862 trans.sa_session.flush() 863 message = "The repository information has been updated." 864 elif params.get( 'user_access_button', False ): 865 if allow_push not in [ 'none' ]: 866 remove_auth = params.get( 'remove_auth', '' ) 867 if remove_auth: 868 usernames = '' 869 else: 870 user_ids = util.listify( allow_push ) 871 usernames = [] 872 for user_id in user_ids: 873 user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) 874 usernames.append( user.username ) 875 usernames = ','.join( usernames ) 876 repository.set_allow_push( usernames, remove_auth=…
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