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Source code for tool_shed.repository_registry

import logging

from sqlalchemy import and_, false, or_

import tool_shed.repository_types.util as rt_util
from galaxy.webapps.tool_shed import model
from tool_shed.util import hg_util
from tool_shed.util import metadata_util

log = logging.getLogger( __name__ )


[docs]class Registry( object ):
[docs] def __init__( self, app ): log.debug( "Loading the repository registry..." ) self.app = app self.certified_level_one_clause_list = self.get_certified_level_one_clause_list() # The following lists contain tuples like ( repository.name, repository.user.username, changeset_revision ) # where the changeset_revision entry is always the latest installable changeset_revision.. self.certified_level_one_repository_and_suite_tuples = [] self.certified_level_one_suite_tuples = [] # These category dictionaries contain entries where the key is the category and the value is the integer count # of viewable repositories within that category. self.certified_level_one_viewable_repositories_and_suites_by_category = {} self.certified_level_one_viewable_suites_by_category = {} self.certified_level_two_repository_and_suite_tuples = [] self.certified_level_two_suite_tuples = [] self.certified_level_two_viewable_repositories_and_suites_by_category = {} self.certified_level_two_viewable_suites_by_category = {} self.repository_and_suite_tuples = [] self.suite_tuples = [] self.viewable_repositories_and_suites_by_category = {} self.viewable_suites_by_category = {} self.viewable_valid_repositories_and_suites_by_category = {} self.viewable_valid_suites_by_category = {} self.load_viewable_repositories_and_suites_by_category() self.load_repository_and_suite_tuples()
[docs] def add_category_entry( self, category ): category_name = str( category.name ) if category_name not in self.viewable_repositories_and_suites_by_category: self.viewable_repositories_and_suites_by_category[ category_name ] = 0 if category_name not in self.viewable_suites_by_category: self.viewable_suites_by_category[ category_name ] = 0 if category_name not in self.viewable_valid_repositories_and_suites_by_category: self.viewable_valid_repositories_and_suites_by_category[ category_name ] = 0 if category_name not in self.viewable_valid_suites_by_category: self.viewable_valid_suites_by_category[ category_name ] = 0 if category_name not in self.certified_level_one_viewable_repositories_and_suites_by_category: self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 0 if category_name not in self.certified_level_one_viewable_suites_by_category: self.certified_level_one_viewable_suites_by_category[ category_name ] = 0
[docs] def add_entry( self, repository ): try: if repository: is_valid = self.is_valid( repository ) certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple for rca in repository.categories: category = rca.category category_name = str( category.name ) if category_name in self.viewable_repositories_and_suites_by_category: self.viewable_repositories_and_suites_by_category[ category_name ] += 1 else: self.viewable_repositories_and_suites_by_category[ category_name ] = 1 if is_valid: if category_name in self.viewable_valid_repositories_and_suites_by_category: self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1 else: self.viewable_valid_repositories_and_suites_by_category[ category_name ] = 1 if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if category_name in self.viewable_suites_by_category: self.viewable_suites_by_category[ category_name ] += 1 else: self.viewable_suites_by_category[ category_name ] = 1 if is_valid: if category_name in self.viewable_valid_suites_by_category: self.viewable_valid_suites_by_category[ category_name ] += 1 else: self.viewable_valid_suites_by_category[ category_name ] = 1 if is_level_one_certified: if category_name in self.certified_level_one_viewable_repositories_and_suites_by_category: self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] += 1 else: self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 1 if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if category_name in self.certified_level_one_viewable_suites_by_category: self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 else: self.certified_level_one_viewable_suites_by_category[ category_name ] = 1 self.load_repository_and_suite_tuple( repository ) if is_level_one_certified: self.load_certified_level_one_repository_and_suite_tuple( repository ) except Exception: # The viewable repository numbers and the categorized (filtered) lists of repository tuples # may be slightly skewed, but that is no reason to result in a potential server error. All # will be corrected at next server start. log.exception( "Handled error adding entry to repository registry" )
[docs] def edit_category_entry( self, old_name, new_name ): if old_name in self.viewable_repositories_and_suites_by_category: val = self.viewable_repositories_and_suites_by_category[ old_name ] del self.viewable_repositories_and_suites_by_category[ old_name ] self.viewable_repositories_and_suites_by_category[ new_name ] = val else: self.viewable_repositories_and_suites_by_category[ new_name ] = 0 if old_name in self.viewable_valid_repositories_and_suites_by_category: val = self.viewable_valid_repositories_and_suites_by_category[ old_name ] del self.viewable_valid_repositories_and_suites_by_category[ old_name ] self.viewable_valid_repositories_and_suites_by_category[ new_name ] = val else: self.viewable_valid_repositories_and_suites_by_category[ new_name ] = 0 if old_name in self.viewable_suites_by_category: val = self.viewable_suites_by_category[ old_name ] del self.viewable_suites_by_category[ old_name ] self.viewable_suites_by_category[ new_name ] = val else: self.viewable_suites_by_category[ new_name ] = 0 if old_name in self.viewable_valid_suites_by_category: val = self.viewable_valid_suites_by_category[ old_name ] del self.viewable_valid_suites_by_category[ old_name ] self.viewable_valid_suites_by_category[ new_name ] = val else: self.viewable_valid_suites_by_category[ new_name ] = 0 if old_name in self.certified_level_one_viewable_repositories_and_suites_by_category: val = self.certified_level_one_viewable_repositories_and_suites_by_category[ old_name ] del self.certified_level_one_viewable_repositories_and_suites_by_category[ old_name ] self.certified_level_one_viewable_repositories_and_suites_by_category[ new_name ] = val else: self.certified_level_one_viewable_repositories_and_suites_by_category[ new_name ] = 0 if old_name in self.certified_level_one_viewable_suites_by_category: val = self.certified_level_one_viewable_suites_by_category[ old_name ] del self.certified_level_one_viewable_suites_by_category[ old_name ] self.certified_level_one_viewable_suites_by_category[ new_name ] = val else: self.certified_level_one_viewable_suites_by_category[ new_name ] = 0
[docs] def get_certified_level_one_clause_list( self ): certified_level_one_tuples = [] clause_list = [] for repository in self.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false() ) ): certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple if is_level_one_certified: certified_level_one_tuples.append( certified_level_one_tuple ) clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id, repository.id, model.RepositoryMetadata.table.c.changeset_revision, latest_installable_changeset_revision ) ) return clause_list
[docs] def get_certified_level_one_tuple( self, repository ): """ Return True if the latest installable changeset_revision of the received repository is level one certified. """ if repository is None: return ( None, False ) if repository.deleted or repository.deprecated: return ( None, False ) repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) # Get the latest installable changeset revision since that is all that is currently configured for testing. latest_installable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision( self.app, repository, repo ) if latest_installable_changeset_revision not in [ None, hg_util.INITIAL_CHANGELOG_HASH ]: encoded_repository_id = self.app.security.encode_id( repository.id ) repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app, encoded_repository_id, latest_installable_changeset_revision ) if repository_metadata: # No repository_metadata. return ( latest_installable_changeset_revision, True ) else: # No installable changeset_revision. return ( None, False )
[docs] def is_level_one_certified( self, repository_metadata ): if repository_metadata: repository = repository_metadata.repository if repository: if repository.deprecated or repository.deleted: return False tuple = ( str( repository.name ), str( repository.user.username ), str( repository_metadata.changeset_revision ) ) if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: return tuple in self.certified_level_one_suite_tuples else: return tuple in self.certified_level_one_repository_and_suite_tuples return False
[docs] def is_valid( self, repository ): if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions: return True return False
[docs] def load_certified_level_one_repository_and_suite_tuple( self, repository ): # The received repository has been determined to be level one certified. name = str( repository.name ) owner = str( repository.user.username ) tip_changeset_hash = repository.tip( self.app ) if tip_changeset_hash != hg_util.INITIAL_CHANGELOG_HASH: certified_level_one_tuple = ( name, owner, tip_changeset_hash ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if certified_level_one_tuple not in self.certified_level_one_suite_tuples: self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) else: if certified_level_one_tuple not in self.certified_level_one_repository_and_suite_tuples: self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple )
[docs] def load_repository_and_suite_tuple( self, repository ): name = str( repository.name ) owner = str( repository.user.username ) for repository_metadata in repository.metadata_revisions: changeset_revision = str( repository_metadata.changeset_revision ) tuple = ( name, owner, changeset_revision ) if tuple not in self.repository_and_suite_tuples: self.repository_and_suite_tuples.append( tuple ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if tuple not in self.suite_tuples: self.suite_tuples.append( tuple )
[docs] def load_repository_and_suite_tuples( self ): # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples. for repository in self.sa_session.query( model.Repository ) \ .join( model.RepositoryMetadata.table ) \ .filter( or_( *self.certified_level_one_clause_list ) ) \ .join( model.User.table ): self.load_certified_level_one_repository_and_suite_tuple( repository ) # Load self.repository_and_suite_tuples and self.suite_tuples for repository in self.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false() ) ) \ .join( model.User.table ): self.load_repository_and_suite_tuple( repository )
[docs] def load_viewable_repositories_and_suites_by_category( self ): # Clear all dictionaries just in case they were previously loaded. self.certified_level_one_viewable_repositories_and_suites_by_category = {} self.certified_level_one_viewable_suites_by_category = {} self.certified_level_two_viewable_repositories_and_suites_by_category = {} self.certified_level_two_viewable_suites_by_category = {} self.viewable_repositories_and_suites_by_category = {} self.viewable_suites_by_category = {} self.viewable_valid_repositories_and_suites_by_category = {} self.viewable_valid_suites_by_category = {} for category in self.sa_session.query( model.Category ): category_name = str( category.name ) if category not in self.certified_level_one_viewable_repositories_and_suites_by_category: self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.certified_level_one_viewable_suites_by_category: self.certified_level_one_viewable_suites_by_category[ category_name ] = 0 if category not in self.viewable_repositories_and_suites_by_category: self.viewable_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.viewable_suites_by_category: self.viewable_suites_by_category[ category_name ] = 0 if category not in self.viewable_valid_repositories_and_suites_by_category: self.viewable_valid_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.viewable_valid_suites_by_category: self.viewable_valid_suites_by_category[ category_name ] = 0 for rca in category.repositories: repository = rca.repository if not repository.deleted and not repository.deprecated: is_valid = self.is_valid( repository ) encoded_repository_id = self.app.security.encode_id( repository.id ) tip_changeset_hash = repository.tip( self.app ) repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app, encoded_repository_id, tip_changeset_hash ) self.viewable_repositories_and_suites_by_category[ category_name ] += 1 if is_valid: self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1 if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: self.viewable_suites_by_category[ category_name ] += 1 if is_valid: self.viewable_valid_suites_by_category[ category_name ] += 1 if self.is_level_one_certified( repository_metadata ): self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] += 1 if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: self.certified_level_one_viewable_suites_by_category[ category_name ] += 1
[docs] def remove_category_entry( self, category ): catgeory_name = str( category.name ) if catgeory_name in self.viewable_repositories_and_suites_by_category: del self.viewable_repositories_and_suites_by_category[ catgeory_name ] if catgeory_name in self.viewable_valid_repositories_and_suites_by_category: del self.viewable_valid_repositories_and_suites_by_category[ catgeory_name ] if catgeory_name in self.viewable_suites_by_category: del self.viewable_suites_by_category[ catgeory_name ] if catgeory_name in self.viewable_valid_suites_by_category: del self.viewable_valid_suites_by_category[ catgeory_name ] if catgeory_name in self.certified_level_one_viewable_repositories_and_suites_by_category: del self.certified_level_one_viewable_repositories_and_suites_by_category[ catgeory_name ] if catgeory_name in self.certified_level_one_viewable_suites_by_category: del self.certified_level_one_viewable_suites_by_category[ catgeory_name ]
[docs] def remove_entry( self, repository ): try: if repository: is_valid = self.is_valid( repository ) certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple for rca in repository.categories: category = rca.category category_name = str( category.name ) if category_name in self.viewable_repositories_and_suites_by_category: if self.viewable_repositories_and_suites_by_category[ category_name ] > 0: self.viewable_repositories_and_suites_by_category[ category_name ] -= 1 else: self.viewable_repositories_and_suites_by_category[ category_name ] = 0 if is_valid: if category_name in self.viewable_valid_repositories_and_suites_by_category: if self.viewable_valid_repositories_and_suites_by_category[ category_name ] > 0: self.viewable_valid_repositories_and_suites_by_category[ category_name ] -= 1 else: self.viewable_valid_repositories_and_suites_by_category[ category_name ] = 0 if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if category_name in self.viewable_suites_by_category: if self.viewable_suites_by_category[ category_name ] > 0: self.viewable_suites_by_category[ category_name ] -= 1 else: self.viewable_suites_by_category[ category_name ] = 0 if is_valid: if category_name in self.viewable_valid_suites_by_category: if self.viewable_valid_suites_by_category[ category_name ] > 0: self.viewable_valid_suites_by_category[ category_name ] -= 1 else: self.viewable_valid_suites_by_category[ category_name ] = 0 if is_level_one_certified: if category_name in self.certified_level_one_viewable_repositories_and_suites_by_category: if self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] > 0: self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] -= 1 else: self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 0 if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if category_name in self.certified_level_one_viewable_suites_by_category: if self.certified_level_one_viewable_suites_by_category[ category_name ] > 0: self.certified_level_one_viewable_suites_by_category[ category_name ] -= 1 else: self.certified_level_one_viewable_suites_by_category[ category_name ] = 0 self.unload_repository_and_suite_tuple( repository ) if is_level_one_certified: self.unload_certified_level_one_repository_and_suite_tuple( repository ) except Exception: # The viewable repository numbers and the categorized (filtered) lists of repository tuples # may be slightly skewed, but that is no reason to result in a potential server error. All # will be corrected at next server start. log.exception( "Handled error removing entry from repository registry" )
@property def sa_session( self ): return self.app.model.context.current
[docs] def unload_certified_level_one_repository_and_suite_tuple( self, repository ): # The received repository has been determined to be level one certified. name = str( repository.name ) owner = str( repository.user.username ) tip_changeset_hash = repository.tip( self.app ) if tip_changeset_hash != hg_util.INITIAL_CHANGELOG_HASH: certified_level_one_tuple = ( name, owner, tip_changeset_hash ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if certified_level_one_tuple in self.certified_level_one_suite_tuples: self.certified_level_one_suite_tuples.remove( certified_level_one_tuple ) else: if certified_level_one_tuple in self.certified_level_one_repository_and_suite_tuples: self.certified_level_one_repository_and_suite_tuples.remove( certified_level_one_tuple )
[docs] def unload_repository_and_suite_tuple( self, repository ): name = str( repository.name ) owner = str( repository.user.username ) for repository_metadata in repository.metadata_revisions: changeset_revision = str( repository_metadata.changeset_revision ) tuple = ( name, owner, changeset_revision ) if tuple in self.repository_and_suite_tuples: self.repository_and_suite_tuples.remove( tuple ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: if tuple in self.suite_tuples: self.suite_tuples.remove( tuple )