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[hg] galaxy 2375: Remove direct references of the model from the...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7fd4f748b0ca changeset: 2375:7fd4f748b0ca user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 27 16:30:08 2009 -0400 description: Remove direct references of the model from the the cleanup_datasets_fix migration script. 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py diffs (709 lines): diff -r d0c905db68db -r 7fd4f748b0ca lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Mon Apr 27 16:30:08 2009 -0400 @@ -0,0 +1,705 @@ +import sys, logging, os, time, datetime, errno + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +from migrate import migrate_engine +from sqlalchemy import and_ + +from sqlalchemy import * +now = datetime.datetime.utcnow +from sqlalchemy.orm import * + +from galaxy.model.orm.ext.assignmapper import assign_mapper + +from galaxy.model.custom_types import * + +from galaxy.util.bunch import Bunch + + +metadata = MetaData( migrate_engine ) +context = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) + + +## classes +def get_permitted_actions( **kwds ): + return Bunch() + +def directory_hash_id( id ): + s = str( id ) + l = len( s ) + # Shortcut -- ids 0-999 go under ../000/ + if l < 4: + return [ "000" ] + # Pad with zeros until a multiple of three + padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s + # Drop the last three digits -- 1000 files per directory + padded = padded[:-3] + # Break into chunks of three + return [ padded[i*3:(i+1)*3] for i in range( len( padded ) // 3 ) ] + + +class Dataset( object ): + states = Bunch( NEW = 'new', + UPLOAD = 'upload', + QUEUED = 'queued', + RUNNING = 'running', + OK = 'ok', + EMPTY = 'empty', + ERROR = 'error', + DISCARDED = 'discarded' ) + permitted_actions = get_permitted_actions( filter='DATASET' ) + file_path = "/tmp/" + engine = None + def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True ): + self.id = id + self.state = state + self.deleted = False + self.purged = False + self.purgable = purgable + self.external_filename = external_filename + self._extra_files_path = extra_files_path + self.file_size = file_size + def get_file_name( self ): + if not self.external_filename: + assert self.id is not None, "ID must be set before filename used (commit the object)" + # First try filename directly under file_path + filename = os.path.join( self.file_path, "dataset_%d.dat" % self.id ) + # Only use that filename if it already exists (backward compatibility), + # otherwise construct hashed path + if not os.path.exists( filename ): + dir = os.path.join( self.file_path, *directory_hash_id( self.id ) ) + # Create directory if it does not exist + try: + os.makedirs( dir ) + except OSError, e: + # File Exists is okay, otherwise reraise + if e.errno != errno.EEXIST: + raise + # Return filename inside hashed directory + return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) + else: + filename = self.external_filename + # Make filename absolute + return os.path.abspath( filename ) + def set_file_name ( self, filename ): + if not filename: + self.external_filename = None + else: + self.external_filename = filename + file_name = property( get_file_name, set_file_name ) + @property + def extra_files_path( self ): + if self._extra_files_path: + path = self._extra_files_path + else: + path = os.path.join( self.file_path, "dataset_%d_files" % self.id ) + #only use path directly under self.file_path if it exists + if not os.path.exists( path ): + path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id ) + # Make path absolute + return os.path.abspath( path ) + def get_size( self ): + """Returns the size of the data on disk""" + if self.file_size: + return self.file_size + else: + try: + return os.path.getsize( self.file_name ) + except OSError: + return 0 + def set_size( self ): + """Returns the size of the data on disk""" + try: + if not self.file_size: + self.file_size = os.path.getsize( self.file_name ) + except OSError: + self.file_size = 0 + def has_data( self ): + """Detects whether there is any data""" + return self.get_size() > 0 + def mark_deleted( self, include_children=True ): + self.deleted = True + # FIXME: sqlalchemy will replace this + def _delete(self): + """Remove the file that corresponds to this data""" + try: + os.remove(self.data.file_name) + except OSError, e: + log.critical('%s delete error %s' % (self.__class__.__name__, e)) + +class DatasetInstance( object ): + """A base class for all 'dataset instances', HDAs, LDAs, etc""" + states = Dataset.states + permitted_actions = Dataset.permitted_actions + def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, + dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, + parent_id=None, validation_errors=None, visible=True, create_dataset = False ): + self.name = name or "Unnamed dataset" + self.id = id + self.info = info + self.blurb = blurb + self.peek = peek + self.extension = extension + self.designation = designation + self.metadata = metadata or dict() + if dbkey: #dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' + self.dbkey = dbkey + self.deleted = deleted + self.visible = visible + # Relationships + if not dataset and create_dataset: + dataset = Dataset( state=Dataset.states.NEW ) + dataset.flush() + self.dataset = dataset + self.parent_id = parent_id + self.validation_errors = validation_errors + @property + def ext( self ): + return self.extension + def get_dataset_state( self ): + return self.dataset.state + def set_dataset_state ( self, state ): + self.dataset.state = state + self.dataset.flush() #flush here, because hda.flush() won't flush the Dataset object + state = property( get_dataset_state, set_dataset_state ) + def get_file_name( self ): + return self.dataset.get_file_name() + def set_file_name (self, filename): + return self.dataset.set_file_name( filename ) + file_name = property( get_file_name, set_file_name ) + @property + def extra_files_path( self ): + return self.dataset.extra_files_path + @property + def datatype( self ): + return datatypes_registry.get_datatype_by_extension( self.extension ) + def get_metadata( self ): + if not hasattr( self, '_metadata_collection' ) or self._metadata_collection.parent != self: #using weakref to store parent (to prevent circ ref), does a context.clear() cause parent to be invalidated, while still copying over this non-database attribute? + self._metadata_collection = MetadataCollection( self ) + return self._metadata_collection + def set_metadata( self, bunch ): + # Needs to accept a MetadataCollection, a bunch, or a dict + self._metadata = self.metadata.make_dict_copy( bunch ) + metadata = property( get_metadata, set_metadata ) + # This provide backwards compatibility with using the old dbkey + # field in the database. That field now maps to "old_dbkey" (see mapping.py). + def get_dbkey( self ): + dbkey = self.metadata.dbkey + if not isinstance(dbkey, list): dbkey = [dbkey] + if dbkey in [[None], []]: return "?" + return dbkey[0] + def set_dbkey( self, value ): + if "dbkey" in self.datatype.metadata_spec: + if not isinstance(value, list): + self.metadata.dbkey = [value] + else: + self.metadata.dbkey = value + dbkey = property( get_dbkey, set_dbkey ) + def change_datatype( self, new_ext ): + self.clear_associated_files() + datatypes_registry.change_datatype( self, new_ext ) + def get_size( self ): + """Returns the size of the data on disk""" + return self.dataset.get_size() + def set_size( self ): + """Returns the size of the data on disk""" + return self.dataset.set_size() + def has_data( self ): + """Detects whether there is any data""" + return self.dataset.has_data() + def get_raw_data( self ): + """Returns the full data. To stream it open the file_name and read/write as needed""" + return self.datatype.get_raw_data( self ) + def write_from_stream( self, stream ): + """Writes data from a stream""" + self.datatype.write_from_stream(self, stream) + def set_raw_data( self, data ): + """Saves the data on the disc""" + self.datatype.set_raw_data(self, data) + def get_mime( self ): + """Returns the mime type of the data""" + return datatypes_registry.get_mimetype_by_extension( self.extension.lower() ) + def set_peek( self ): + return self.datatype.set_peek( self ) + def set_multi_byte_peek( self ): + return self.datatype.set_multi_byte_peek( self ) + def init_meta( self, copy_from=None ): + return self.datatype.init_meta( self, copy_from=copy_from ) + def set_meta( self, **kwd ): + self.clear_associated_files( metadata_safe = True ) + return self.datatype.set_meta( self, **kwd ) + def set_readonly_meta( self, **kwd ): + return self.datatype.set_readonly_meta( self, **kwd ) + def missing_meta( self, **kwd ): + return self.datatype.missing_meta( self, **kwd ) + def as_display_type( self, type, **kwd ): + return self.datatype.as_display_type( self, type, **kwd ) + def display_peek( self ): + return self.datatype.display_peek( self ) + def display_name( self ): + return self.datatype.display_name( self ) + def display_info( self ): + return self.datatype.display_info( self ) + def get_converted_files_by_type( self, file_type ): + valid = [] + for assoc in self.implicitly_converted_datasets: + if not assoc.deleted and assoc.type == file_type: + valid.append( assoc.dataset ) + return valid + def clear_associated_files( self, metadata_safe = False, purge = False ): + raise 'Unimplemented' + def get_child_by_designation(self, designation): + for child in self.children: + if child.designation == designation: + return child + return None + def get_converter_types(self): + return self.datatype.get_converter_types( self, datatypes_registry) + def find_conversion_destination( self, accepted_formats, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd ) + def add_validation_error( self, validation_error ): + self.validation_errors.append( validation_error ) + def extend_validation_errors( self, validation_errors ): + self.validation_errors.extend(validation_errors) + def mark_deleted( self, include_children=True ): + self.deleted = True + if include_children: + for child in self.children: + child.mark_deleted() + def mark_undeleted( self, include_children=True ): + self.deleted = False + if include_children: + for child in self.children: + child.mark_undeleted() + def undeletable( self ): + if self.purged: + return False + return True + @property + def source_library_dataset( self ): + def get_source( dataset ): + if isinstance( dataset, LibraryDatasetDatasetAssociation ): + if dataset.library_dataset: + return ( dataset, dataset.library_dataset ) + if dataset.copied_from_library_dataset_dataset_association: + source = get_source( dataset.copied_from_library_dataset_dataset_association ) + if source: + return source + if dataset.copied_from_history_dataset_association: + source = get_source( dataset.copied_from_history_dataset_association ) + if source: + return source + return ( None, None ) + return get_source( self ) + + +class HistoryDatasetAssociation( DatasetInstance ): + def __init__( self, + hid = None, + history = None, + copied_from_history_dataset_association = None, + copied_from_library_dataset_dataset_association = None, + **kwd ): + DatasetInstance.__init__( self, **kwd ) + self.hid = hid + # Relationships + self.history = history + self.copied_from_history_dataset_association = copied_from_history_dataset_association + self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + def copy( self, copy_children = False, parent_id = None, target_history = None ): + hda = HistoryDatasetAssociation( hid=self.hid, + name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset = self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_history_dataset_association=self, + history = target_history ) + hda.flush() + hda.set_size() + # Need to set after flushed, as MetadataFiles require dataset.id + hda.metadata = self.metadata + if copy_children: + for child in self.children: + child_copy = child.copy( copy_children = copy_children, parent_id = hda.id ) + if not self.datatype.copy_safe_peek: + # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + hda.set_peek() + hda.flush() + return hda + def to_library_dataset_dataset_association( self, target_folder, replace_dataset=None, parent_id=None ): + if replace_dataset: + # The replace_dataset param ( when not None ) refers to a LibraryDataset that is being replaced with a new version. + library_dataset = replace_dataset + else: + # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new + # LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset. + library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info ) + library_dataset.flush() + ldda = LibraryDatasetDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + library_dataset=library_dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_history_dataset_association=self, + user=self.history.user ) + ldda.flush() + # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset + # Must set metadata after ldda flushed, as MetadataFiles require ldda.id + ldda.metadata = self.metadata + if not replace_dataset: + target_folder.add_library_dataset( library_dataset, genome_build=ldda.dbkey ) + target_folder.flush() + library_dataset.library_dataset_dataset_association_id = ldda.id + library_dataset.flush() + for child in self.children: + child_copy = child.to_library_dataset_dataset_association( target_folder=target_folder, replace_dataset=replace_dataset, parent_id=ldda.id ) + if not self.datatype.copy_safe_peek: + # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + ldda.set_peek() + ldda.flush() + return ldda + def clear_associated_files( self, metadata_safe = False, purge = False ): + # metadata_safe = True means to only clear when assoc.metadata_safe == False + for assoc in self.implicitly_converted_datasets: + if not metadata_safe or not assoc.metadata_safe: + assoc.clear( purge = purge ) + + + +class LibraryDatasetDatasetAssociation( DatasetInstance ): + def __init__( self, + copied_from_history_dataset_association=None, + copied_from_library_dataset_dataset_association=None, + library_dataset=None, + user=None, + **kwd ): + DatasetInstance.__init__( self, **kwd ) + self.copied_from_history_dataset_association = copied_from_history_dataset_association + self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + self.library_dataset = library_dataset + self.user = user + def to_history_dataset_association( self, target_history, parent_id=None ): + hid = target_history._next_hid() + hda = HistoryDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_library_dataset_dataset_association=self, + history=target_history, + hid=hid ) + hda.flush() + hda.metadata = self.metadata #need to set after flushed, as MetadataFiles require dataset.id + for child in self.children: + child_copy = child.to_history_dataset_association( target_history=target_history, parent_id=hda.id ) + if not self.datatype.copy_safe_peek: + hda.set_peek() #in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + hda.flush() + return hda + def copy( self, copy_children = False, parent_id = None, target_folder = None ): + ldda = LibraryDatasetDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_library_dataset_dataset_association=self, + folder=target_folder ) + ldda.flush() + # Need to set after flushed, as MetadataFiles require dataset.id + ldda.metadata = self.metadata + if copy_children: + for child in self.children: + child_copy = child.copy( copy_children = copy_children, parent_id = ldda.id ) + if not self.datatype.copy_safe_peek: + # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + ldda.set_peek() + ldda.flush() + return ldda + def clear_associated_files( self, metadata_safe = False, purge = False ): + return + def get_library_item_info_templates( self, template_list=[], restrict=False ): + # If restrict is True, we'll return only those templates directly associated with this LibraryDatasetDatasetAssociation + if self.library_dataset_dataset_info_template_associations: + template_list.extend( [ lddita.library_item_info_template for lddita in self.library_dataset_dataset_info_template_associations if lddita.library_item_info_template not in template_list ] ) + self.library_dataset.get_library_item_info_templates( template_list, restrict ) + return template_list + + + +class LibraryDataset( object ): + # This class acts as a proxy to the currently selected LDDA + def __init__( self, folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd ): + self.folder = folder + self.order_id = order_id + self.name = name + self.info = info + self.library_dataset_dataset_association = library_dataset_dataset_association + def set_library_dataset_dataset_association( self, ldda ): + self.library_dataset_dataset_association = ldda + ldda.library_dataset = self + ldda.flush() + self.flush() + def get_info( self ): + if self.library_dataset_dataset_association: + return self.library_dataset_dataset_association.info + elif self._info: + return self._info + else: + return 'no info' + def set_info( self, info ): + self._info = info + info = property( get_info, set_info ) + def get_name( self ): + if self.library_dataset_dataset_association: + return self.library_dataset_dataset_association.name + elif self._name: + return self._name + else: + return 'Unnamed dataset' + def set_name( self, name ): + self._name = name + name = property( get_name, set_name ) + def display_name( self ): + self.library_dataset_dataset_association.display_name() + def get_purged( self ): + return self.library_dataset_dataset_association.dataset.purged + def set_purged( self, purged ): + if purged: + raise Exception( "Not implemented" ) + if not purged and self.purged: + raise Exception( "Cannot unpurge once purged" ) + purged = property( get_purged, set_purged ) + def get_library_item_info_templates( self, template_list=[], restrict=False ): + # If restrict is True, we'll return only those templates directly associated with this LibraryDataset + if self.library_dataset_info_template_associations: + template_list.extend( [ ldita.library_item_info_template for ldita in self.library_dataset_info_template_associations if ldita.library_item_info_template not in template_list ] ) + if restrict not in [ 'True', True ]: + self.folder.get_library_item_info_templates( template_list, restrict ) + return template_list + +##tables + + +Dataset.table = Table( "dataset", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "state", TrimmedString( 64 ) ), + Column( "deleted", Boolean, index=True, default=False ), + Column( "purged", Boolean, index=True, default=False ), + Column( "purgable", Boolean, default=True ), + Column( "external_filename" , TEXT ), + Column( "_extra_files_path", TEXT ), + Column( 'file_size', Numeric( 15, 0 ) ) ) + + + +HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), + Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), + Column( "hid", Integer ), + Column( "name", TrimmedString( 255 ) ), + Column( "info", TrimmedString( 255 ) ), + Column( "blurb", TrimmedString( 255 ) ), + Column( "peek" , TEXT ), + Column( "extension", TrimmedString( 64 ) ), + Column( "metadata", MetadataType(), key="_metadata" ), + Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), + Column( "designation", TrimmedString( 255 ) ), + Column( "deleted", Boolean, index=True, default=False ), + Column( "visible", Boolean ) ) + + +LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), index=True ), + Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ), + Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ), + Column( "name", TrimmedString( 255 ) ), + Column( "info", TrimmedString( 255 ) ), + Column( "blurb", TrimmedString( 255 ) ), + Column( "peek" , TEXT ), + Column( "extension", TrimmedString( 64 ) ), + Column( "metadata", MetadataType(), key="_metadata" ), + Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), + Column( "designation", TrimmedString( 255 ) ), + Column( "deleted", Boolean, index=True, default=False ), + Column( "visible", Boolean ), + Column( "message", TrimmedString( 255 ) ) ) + +LibraryDataset.table = Table( "library_dataset", metadata, + Column( "id", Integer, primary_key=True ), + Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected + Column( "order_id", Integer ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), key="_name" ), #when not None/null this will supercede display in library (but not when imported into user's history?) + Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) + Column( "deleted", Boolean, index=True, default=False ) ) + + + +##mappers + + +assign_mapper( context, Dataset, Dataset.table, + properties=dict( + history_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ) ), + active_history_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( ( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ) & ( HistoryDatasetAssociation.table.c.deleted == False ) ) ), + library_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) ), + active_library_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( ( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ) + ) ) + + +assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.table, + properties=dict( + dataset=relation( + Dataset, + primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), + # .history defined in History mapper + copied_to_history_dataset_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), + copied_to_library_dataset_dataset_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + children=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), + backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), + visible_children=relation( + HistoryDatasetAssociation, + primaryjoin=( ( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ) & ( HistoryDatasetAssociation.table.c.visible == True ) ) ) + ) ) + +assign_mapper( context, LibraryDatasetDatasetAssociation, LibraryDatasetDatasetAssociation.table, + properties=dict( + dataset=relation( Dataset ), + library_dataset = relation( LibraryDataset, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.library_dataset_id == LibraryDataset.table.c.id ) ), + copied_to_library_dataset_dataset_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), + copied_to_history_dataset_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + children=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "parent", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), + visible_children=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ) + ) ) + +assign_mapper( context, LibraryDataset, LibraryDataset.table, + properties=dict( + library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, primaryjoin=( LibraryDataset.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), + expired_datasets = relation( LibraryDatasetDatasetAssociation, foreign_keys=[LibraryDataset.table.c.id,LibraryDataset.table.c.library_dataset_dataset_association_id ], primaryjoin=( ( LibraryDataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.library_dataset_id ) & ( not_( LibraryDataset.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ) ), viewonly=True, uselist=True ) + ) ) + + +def __guess_dataset_by_filename( filename ): + """Return a guessed dataset by filename""" + try: + fields = os.path.split( filename ) + if fields: + if fields[-1].startswith( 'dataset_' ) and fields[-1].endswith( '.dat' ): #dataset_%d.dat + return Dataset.get( int( fields[-1][ len( 'dataset_' ): -len( '.dat' ) ] ) ) + except: + pass #some parsing error, we can't guess Dataset + return None + +def upgrade(): + log.debug( "Fixing a discrepancy concerning deleted shared history items." ) + affected_items = 0 + start_time = time.time() + for dataset in Dataset.filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ).all(): + for dataset_instance in dataset.history_associations + dataset.library_associations: + if not dataset_instance.deleted: + dataset.deleted = False + if dataset.file_size in [ None, 0 ]: + dataset.set_size() #Restore filesize + affected_items += 1 + break + context.flush() + log.debug( "%i items affected, and restored." % ( affected_items ) ) + log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) + + #fix share before hda + log.debug( "Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs." ) + dataset_by_filename = {} + changed_associations = 0 + start_time = time.time() + for dataset in Dataset.filter( Dataset.external_filename.like( '%dataset_%.dat' ) ).all(): + if dataset.file_name in dataset_by_filename: + guessed_dataset = dataset_by_filename[ dataset.file_name ] + else: + guessed_dataset = __guess_dataset_by_filename( dataset.file_name ) + if guessed_dataset and dataset.file_name != guessed_dataset.file_name:#not os.path.samefile( dataset.file_name, guessed_dataset.file_name ): + guessed_dataset = None + dataset_by_filename[ dataset.file_name ] = guessed_dataset + + if guessed_dataset is not None and guessed_dataset.id != dataset.id: #could we have a self referential dataset? + for dataset_instance in dataset.history_associations + dataset.library_associations: + dataset_instance.dataset = guessed_dataset + changed_associations += 1 + #mark original Dataset as deleted and purged, it is no longer in use, but do not delete file_name contents + dataset.deleted = True + dataset.external_filename = "Dataset was result of share before HDA, and has been replaced: %s mapped to Dataset %s" % ( dataset.external_filename, guessed_dataset.id ) + dataset.purged = True #we don't really purge the file here, but we mark it as purged, since this dataset is now defunct + context.flush() + log.debug( "%i items affected, and restored." % ( changed_associations ) ) + log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) + +def downgrade(): + log.debug( "Downgrade is not possible." ) +

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[hg] galaxy 2372: Added an option to mask non-CpG sites to the \...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ea9235523069 changeset: 2372:ea9235523069 user: guru date: Mon Apr 27 11:59:42 2009 -0400 description: Added an option to mask non-CpG sites to the \"Mask CpG sites\" tool. 2 file(s) affected in this change: tools/regVariation/maf_cpg_filter.py tools/regVariation/maf_cpg_filter.xml diffs (115 lines): diff -r 76bd876ed230 -r ea9235523069 tools/regVariation/maf_cpg_filter.py --- a/tools/regVariation/maf_cpg_filter.py Mon Apr 27 11:39:58 2009 -0400 +++ b/tools/regVariation/maf_cpg_filter.py Mon Apr 27 11:59:42 2009 -0400 @@ -1,5 +1,5 @@ #!/usr/bin/python - +#Guruprasad Ananda #Adapted from bx/scripts/maf_mask_cpg.py """ Mask out potential CpG sites from a maf. Restricted or inclusive definition @@ -27,12 +27,11 @@ def main(): options, args = doc_optparse.parse( __doc__ ) try: - inp_file, out_file, definition = args + inp_file, out_file, sitetype, definition = args if options.mask: mask = int(options.mask) else: mask = 0 - definition = int(definition) except: print >> sys.stderr, "Tool initialization error." sys.exit() @@ -43,14 +42,19 @@ mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'} mask = mask_chr_dict[mask] - if definition == 1: - cpgfilter = bx.align.sitemask.cpg.Restricted( mask=mask ) - defn = "Restricted" + if sitetype == "CpG": + if int(definition) == 1: + cpgfilter = bx.align.sitemask.cpg.Restricted( mask=mask ) + defn = "CpG-Restricted" + else: + cpgfilter = bx.align.sitemask.cpg.Inclusive( mask=mask ) + defn = "CpG-Inclusive" else: - cpgfilter = bx.align.sitemask.cpg.Inclusive( mask=mask ) - defn = "Inclusive" + cpgfilter = bx.align.sitemask.cpg.nonCpG( mask=mask ) + defn = "non-CpG" cpgfilter.run( reader, writer.write ) print "%2.2f percent bases masked; Mask character = %s, Definition = %s" %(float(cpgfilter.masked)/float(cpgfilter.total) * 100, mask, defn) + if __name__ == "__main__": main() diff -r 76bd876ed230 -r ea9235523069 tools/regVariation/maf_cpg_filter.xml --- a/tools/regVariation/maf_cpg_filter.xml Mon Apr 27 11:39:58 2009 -0400 +++ b/tools/regVariation/maf_cpg_filter.xml Mon Apr 27 11:59:42 2009 -0400 @@ -1,11 +1,16 @@ -<tool id="cpgFilter" name="Mask CpG sites"> +<tool id="cpgFilter" name="Mask CpG/non-CpG sites" version="1.0.0"> <description> from MAF file</description> <command interpreter="python"> maf_cpg_filter.py - $input - $out_file1 - $definition - -m $mask_char + $input + $out_file1 + $masksite.type + #if $masksite.type == "CpG": + $masksite.definition + #else: + "NA" + #end if + -m $mask_char </command> <inputs> <page> @@ -17,10 +22,19 @@ <option value="3">*</option> <option value="4">?</option> </param> - <param name="definition" size="5" type="select" label="Definition"> - <option value="0" selected="true">Inclusive</option> - <option value="1">Restricted</option> - </param> + <conditional name="masksite"> + <param name="type" size="5" type="select" label="Sites to be masked"> + <option value="CpG" selected="true">CpG sites</option> + <option value="nonCpG">non-CpG sites</option> + </param> + <when value="CpG"> + <param name="definition" size="5" type="select" label="Definition"> + <option value="0" selected="true">Inclusive</option> + <option value="1">Restricted</option> + </param> + </when> + <when value="nonCpG" /> + </conditional> </page> </inputs> <outputs> @@ -33,8 +47,16 @@ <test> <param name="input" value="6.maf"/> <param name="mask_char" value="0"/> + <param name="type" value="CpG" /> <param name="definition" value="0" /> <output name="out_file1" file="6_mask_cpg.maf"/> + </test> + <test> + <param name="input" value="6.maf"/> + <param name="mask_char" value="0"/> + <param name="type" value="nonCpG" /> + <param name="definition" value="NA" /> + <output name="out_file1" file="6_mask_noncpg.maf"/> </test> </tests> <help>

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[hg] galaxy 2371: Update bx-python for Guru
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/76bd876ed230 changeset: 2371:76bd876ed230 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Apr 27 11:39:58 2009 -0400 description: Update bx-python for Guru 1 file(s) affected in this change: eggs.ini diffs (19 lines): diff -r bb85df3f0baa -r 76bd876ed230 eggs.ini --- a/eggs.ini Mon Apr 27 10:50:17 2009 -0400 +++ b/eggs.ini Mon Apr 27 11:39:58 2009 -0400 @@ -59,13 +59,13 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r460 +bx_python = _dev_r130f083b56b9 nose = .dev_r101 ; source location, necessary for scrambling [source] numpy = http://downloads.sourceforge.net/numpy/numpy-1.2.1.tar.gz -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r460.tar.bz2 +bx_python = http://bitbucket.org/james_taylor/bx-python/get/130f083b56b9.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 2366: Deleting the cleanup_dataset migration script ...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e7492f6c18ca changeset: 2366:e7492f6c18ca user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 24 13:03:57 2009 -0400 description: Deleting the cleanup_dataset migration script until it is fixed, keeps it from being pushed to public. 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py diffs (78 lines): diff -r fb401a784261 -r e7492f6c18ca lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Thu Apr 23 12:42:05 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -import sys, logging, os, time - -log = logging.getLogger( __name__ ) -log.setLevel(logging.DEBUG) -handler = logging.StreamHandler( sys.stdout ) -format = "%(name)s %(levelname)s %(asctime)s %(message)s" -formatter = logging.Formatter( format ) -handler.setFormatter( formatter ) -log.addHandler( handler ) - -from migrate import migrate_engine -from sqlalchemy import and_ - -# load existing galaxy model, we are only changing data -import galaxy.model -from galaxy.model import mapping -model = mapping.init( galaxy.model.Dataset.file_path, str( migrate_engine.url ) ) - -def __guess_dataset_by_filename( filename ): - """Return a guessed dataset by filename""" - try: - fields = os.path.split( filename ) - if fields: - if fields[-1].startswith( 'dataset_' ) and fields[-1].endswith( '.dat' ): #dataset_%d.dat - return model.Dataset.get( int( fields[-1][ len( 'dataset_' ): -len( '.dat' ) ] ) ) - except: - pass #some parsing error, we can't guess Dataset - return None - -def upgrade(): - log.debug( "Fixing a discrepancy concerning deleted shared history items." ) - affected_items = 0 - start_time = time.time() - for dataset in model.Dataset.filter( and_( model.Dataset.c.deleted == True, model.Dataset.c.purged == False ) ).all(): - for dataset_instance in dataset.history_associations + dataset.library_associations: - if not dataset_instance.deleted: - dataset.deleted = False - if dataset.file_size in [ None, 0 ]: - dataset.set_size() #Restore filesize - affected_items += 1 - break - galaxy.model.mapping.Session.flush() - log.debug( "%i items affected, and restored." % ( affected_items ) ) - log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) - - #fix share before hda - log.debug( "Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs." ) - dataset_by_filename = {} - changed_associations = 0 - start_time = time.time() - for dataset in model.Dataset.filter( model.Dataset.external_filename.like( '%dataset_%.dat' ) ).all(): - if dataset.file_name in dataset_by_filename: - guessed_dataset = dataset_by_filename[ dataset.file_name ] - else: - guessed_dataset = __guess_dataset_by_filename( dataset.file_name ) - if guessed_dataset and dataset.file_name != guessed_dataset.file_name:#not os.path.samefile( dataset.file_name, guessed_dataset.file_name ): - guessed_dataset = None - dataset_by_filename[ dataset.file_name ] = guessed_dataset - - if guessed_dataset is not None and guessed_dataset.id != dataset.id: #could we have a self referential dataset? - for dataset_instance in dataset.history_associations + dataset.library_associations: - dataset_instance.dataset = guessed_dataset - changed_associations += 1 - #mark original Dataset as deleted and purged, it is no longer in use, but do not delete file_name contents - dataset.deleted = True - dataset.external_filename = "Dataset was result of share before HDA, and has been replaced: %s mapped to Dataset %s" % ( dataset.external_filename, guessed_dataset.id ) - dataset.purged = True #we don't really purge the file here, but we mark it as purged, since this dataset is now defunct - galaxy.model.mapping.Session.flush() - log.debug( "%i items affected, and restored." % ( changed_associations ) ) - log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) - -def downgrade(): - log.debug( "Downgrade is not possible." ) -

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[hg] galaxy 2367: Two fixes: add type checking for id when delet...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a1e84abd301a changeset: 2367:a1e84abd301a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 24 13:42:38 2009 -0400 description: Two fixes: add type checking for id when deleting datasets, ad checks to make sure at least 1 user can access a set of datasets when setting permissions on multiple datasets. 3 file(s) affected in this change: lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/dataset.py test/functional/test_security_and_libraries.py diffs (114 lines): diff -r e7492f6c18ca -r a1e84abd301a lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Apr 24 13:03:57 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Apr 24 13:42:38 2009 -0400 @@ -1495,9 +1495,36 @@ if action == 'permissions': if params.get( 'update_roles_button', False ): permissions = {} + accessible = False for k, v in trans.app.model.Dataset.permitted_actions.items(): in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible + if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + if len( in_roles ) > 1: + # Get the set of all users that are being associated with the dataset + in_roles_set = sets.Set() + for role in in_roles: + in_roles_set.add( role ) + users_set = sets.Set() + for role in in_roles: + for ura in role.users: + users_set.add( ura.user ) + # Make sure that at least 1 user has every role being associated with the dataset + for user in users_set: + user_roles_set = sets.Set() + for ura in user.roles: + user_roles_set.add( ura.role ) + if in_roles_set.issubset( user_roles_set ): + accessible = True + break + else: + accessible = True + if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions + # TODO: keep access permissions as they originally were, rather than automatically making public + permissions[ trans.app.security_agent.get_action( v.action ) ] = [] + else: + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles for ldda in lddas: # Set the DATASET permissions on the Dataset trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) @@ -1514,7 +1541,13 @@ # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation trans.app.security_agent.set_all_library_permissions( ldda, permissions ) ldda.refresh() - msg = 'Permissions and roles have been updated on %d datasets' % len( lddas ) + if not accessible: + msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas ) + msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, " + msg += "so access permissions were not set. All other permissions were updated for the datasets." + messagetype = 'error' + else: + msg = "Permissions have been updated on %d datasets" % len( lddas ) return trans.fill_template( "/admin/library/ldda_permissions.mako", ldda=lddas, library_id=library_id, diff -r e7492f6c18ca -r a1e84abd301a lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Apr 24 13:03:57 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Apr 24 13:42:38 2009 -0400 @@ -125,19 +125,20 @@ return trans.show_error_message( "You are not allowed to access this dataset" ) def _undelete( self, trans, id ): - history = trans.get_history() - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data and data.undeletable: - # Walk up parent datasets to find the containing history - topmost_parent = data - while topmost_parent.parent: - topmost_parent = topmost_parent.parent - assert topmost_parent in history.datasets, "Data does not belong to current history" - # Mark undeleted - data.mark_undeleted() - self.app.model.flush() - trans.log_event( "Dataset id %s has been undeleted" % str(id) ) - return True + if isinstance( id, type( 1 ) ): + history = trans.get_history() + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data and data.undeletable: + # Walk up parent datasets to find the containing history + topmost_parent = data + while topmost_parent.parent: + topmost_parent = topmost_parent.parent + assert topmost_parent in history.datasets, "Data does not belong to current history" + # Mark undeleted + data.mark_undeleted() + self.app.model.flush() + trans.log_event( "Dataset id %s has been undeleted" % str(id) ) + return True return False @web.expose diff -r e7492f6c18ca -r a1e84abd301a test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Apr 24 13:03:57 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Apr 24 13:42:38 2009 -0400 @@ -737,7 +737,7 @@ url = build_url( permissions, role_one ) self.home() self.visit_url( url ) - self.check_page_for_string( 'Permissions and roles have been updated on 3 datasets' ) + self.check_page_for_string( 'Permissions have been updated on 3 datasets' ) def check_edit_page1( lddas ): # Make sure the permissions have been correctly updated for the 3 datasets. Permissions should # be all of the above on any of the 3 datasets that are imported into a history @@ -785,7 +785,7 @@ url = build_url( permissions, role_one ) self.home() self.visit_url( url ) - self.check_page_for_string( 'Permissions and roles have been updated on 3 datasets' ) + self.check_page_for_string( 'Permissions have been updated on 3 datasets' ) def check_edit_page2( lddas ): # Make sure the permissions have been correctly updated for the 3 datasets. Permissions should # be all of the above on any of the 3 datasets that are imported into a history

1 0

[hg] galaxy 2368: Added column info to MB wrapper
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bc540363324d changeset: 2368:bc540363324d user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Apr 24 15:06:51 2009 -0400 description: Added column info to MB wrapper 2 file(s) affected in this change: static/welcome.html tools/metag_tools/megablast_wrapper.xml diffs (76 lines): diff -r a1e84abd301a -r bc540363324d static/welcome.html --- a/static/welcome.html Fri Apr 24 13:42:38 2009 -0400 +++ b/static/welcome.html Fri Apr 24 15:06:51 2009 -0400 @@ -14,6 +14,7 @@ .current-quickie { width: 100%; background: black; + borderRadius:10; } .quickie .head { font-size: 200%; diff -r a1e84abd301a -r bc540363324d tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml Fri Apr 24 13:42:38 2009 -0400 +++ b/tools/metag_tools/megablast_wrapper.xml Fri Apr 24 15:06:51 2009 -0400 @@ -2,20 +2,20 @@ <description> compare short reads against nt and wgs databases</description> <command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $evalue_cutoff $filter_query ${GALAXY_DATA_INDEX_DIR}</command> <inputs> - <param name="source_select" type="select" display="radio" label="Choose target database"> + <param name="input_query" type="data" format="fasta" label="Compare these sequences"/> + <param name="source_select" type="select" display="radio" label="against target database"> <options from_file="blastdb.loc"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> - <param name="input_query" type="data" format="fasta" label="Sequence file"/> - <param name="word_size" type="select" label="Word size (-W)" help="Size of best perfect match"> + <param name="word_size" type="select" label="using word size" help="Size of best perfect match"> <option value="28">28</option> <option value="16">16</option> </param> - <param name="iden_cutoff" type="float" size="15" value="90.0" label="Identity percentage cut-off (-p)" help="no cutoff if 0" /> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Expectation value (-e)" /> - <param name="filter_query" type="select" label="Filter query sequence (-F)"> + <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="filter_query" type="select" label="Filter out low complexity regions?"> <option value="T">Yes</option> <option value="F">No</option> </param> @@ -49,18 +49,27 @@ This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues. - ----- -**Parameters** +**Output format** -- *Word size* (**-W**) : the minimal length of an exact match -- *Identity percentage cut-off* (**-p**) : the minimal identity for an alignment -- *Expectation value* (**-e**) : the maximal expectation value for an alignment -- *Filter query sequence* (**-F**) : mask low-complexity regions in the query sequence +Output of this tool contains 13 columns delimited by Tabs: +1. Id of your sequence +2. GI of the database hit +3. Length of the database hit +4. % identity +5. Alignment length +6. # mismatches +7. # gaps +8. Start position in your sequence +9. End position in your sequence +10. Start position in database hit +11. End position in database hit +12. E-value +13. Bit score ------ +------- **Reference**

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[hg] galaxy 2369: Fixing accidental change
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0035ef5580bb changeset: 2369:0035ef5580bb user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Apr 24 15:08:22 2009 -0400 description: Fixing accidental change 1 file(s) affected in this change: static/welcome.html diffs (11 lines): diff -r bc540363324d -r 0035ef5580bb static/welcome.html --- a/static/welcome.html Fri Apr 24 15:06:51 2009 -0400 +++ b/static/welcome.html Fri Apr 24 15:08:22 2009 -0400 @@ -14,7 +14,6 @@ .current-quickie { width: 100%; background: black; - borderRadius:10; } .quickie .head { font-size: 200%;

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[hg] galaxy 2370: Fix for column_maker tool when input dataset h...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bb85df3f0baa changeset: 2370:bb85df3f0baa user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Apr 27 10:50:17 2009 -0400 description: Fix for column_maker tool when input dataset has missing or invalid metadata values. 1 file(s) affected in this change: tools/stats/column_maker.py diffs (33 lines): diff -r 0035ef5580bb -r bb85df3f0baa tools/stats/column_maker.py --- a/tools/stats/column_maker.py Fri Apr 24 15:08:22 2009 -0400 +++ b/tools/stats/column_maker.py Mon Apr 27 10:50:17 2009 -0400 @@ -13,15 +13,27 @@ sys.stderr.write( msg ) sys.exit() +data_err = "This tool can only be used with tab-delimited data." +columns_err = "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. " +column_types_err = "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. " +invalid_metadata_err = "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. " inp_file = sys.argv[1] out_file = sys.argv[2] expr = sys.argv[3] -round = sys.argv[4] +round = sys.argv[4] try: in_columns = int( sys.argv[5] ) +except: + stop_err( columns_err + data_err ) +if in_columns < 2: + # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method. + stop_err( columns_err + data_err ) +try: in_column_types = sys.argv[6].split( ',' ) except: - stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." ) + stop_err( column_types_err + data_err ) +if len( in_column_types ) != in_columns: + stop_err( invalid_metadata_err + data_err ) # Unescape if input has been escaped mapped_str = {

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[hg] galaxy 2365: Add ability for admins to delete and undelete ...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fb401a784261 changeset: 2365:fb401a784261 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Apr 23 12:42:05 2009 -0400 description: Add ability for admins to delete and undelete library items. Modify cleanup_datasets.py script and include a database migration script. 21 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/admin.py scripts/cleanup_datasets/cleanup_datasets.py scripts/cleanup_datasets/delete_userless_histories.sh scripts/cleanup_datasets/delete_userless_histories_main.sh scripts/cleanup_datasets/purge_datasets.sh scripts/cleanup_datasets/purge_datasets_main.sh scripts/cleanup_datasets/purge_folders.sh scripts/cleanup_datasets/purge_folders_main.sh scripts/cleanup_datasets/purge_histories.sh scripts/cleanup_datasets/purge_histories_main.sh scripts/cleanup_datasets/purge_libraries.sh scripts/cleanup_datasets/purge_libraries_main.sh static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/june_2007_style/blue/library.css static/june_2007_style/library.css.tmpl templates/admin/library/browse_library.mako templates/admin/library/common.mako diffs (1069 lines): diff -r f7336991d0ee -r fb401a784261 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Apr 23 12:42:05 2009 -0400 @@ -229,7 +229,7 @@ return des @property def activatable_datasets( self ): - return [ hda for hda in self.datasets if not hda.dataset.purged ] #this needs to be a list + return [ hda for hda in self.datasets if not hda.dataset.deleted ] #this needs to be a list class UserRoleAssociation( object ): def __init__( self, user, role ): @@ -707,6 +707,12 @@ @property def active_components( self ): return list( self.active_folders ) + list( self.active_datasets ) + @property + def activatable_datasets( self ): + return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.dataset.deleted ] #this needs to be a list + @property #make this a relation + def activatable_folders( self ): + return [ folder for folder in self.folders if not folder.purged ] #this needs to be a list class LibraryDataset( object ): # This class acts as a proxy to the currently selected LDDA @@ -743,6 +749,14 @@ name = property( get_name, set_name ) def display_name( self ): self.library_dataset_dataset_association.display_name() + def get_purged( self ): + return self.library_dataset_dataset_association.dataset.purged + def set_purged( self, purged ): + if purged: + raise Exception( "Not implemented" ) + if not purged and self.purged: + raise Exception( "Cannot unpurge once purged" ) + purged = property( get_purged, set_purged ) def get_library_item_info_templates( self, template_list=[], restrict=False ): # If restrict is True, we'll return only those templates directly associated with this LibraryDataset if self.library_dataset_info_template_associations: @@ -750,7 +764,7 @@ if restrict not in [ 'True', True ]: self.folder.get_library_item_info_templates( template_list, restrict ) return template_list - + class LibraryDatasetDatasetAssociation( DatasetInstance ): def __init__( self, copied_from_history_dataset_association=None, diff -r f7336991d0ee -r fb401a784261 lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Thu Apr 23 12:42:05 2009 -0400 @@ -0,0 +1,74 @@ +import sys, logging, os, time + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +from migrate import migrate_engine +from sqlalchemy import and_ + +# load existing galaxy model, we are only changing data +import galaxy.model +from galaxy.model import mapping +model = mapping.init( galaxy.model.Dataset.file_path, str( migrate_engine.url ) ) + +def __guess_dataset_by_filename( filename ): + """Return a guessed dataset by filename""" + try: + fields = os.path.split( filename ) + if fields: + if fields[-1].startswith( 'dataset_' ) and fields[-1].endswith( '.dat' ): #dataset_%d.dat + return model.Dataset.get( int( fields[-1][ len( 'dataset_' ): -len( '.dat' ) ] ) ) + except: + pass #some parsing error, we can't guess Dataset + return None + +def upgrade(): + log.debug( "Fixing a discrepancy concerning deleted shared history items." ) + affected_items = 0 + start_time = time.time() + for dataset in model.Dataset.filter( and_( model.Dataset.c.deleted == True, model.Dataset.c.purged == False ) ).all(): + for dataset_instance in dataset.history_associations + dataset.library_associations: + if not dataset_instance.deleted: + dataset.deleted = False + if dataset.file_size in [ None, 0 ]: + dataset.set_size() #Restore filesize + affected_items += 1 + break + galaxy.model.mapping.Session.flush() + log.debug( "%i items affected, and restored." % ( affected_items ) ) + log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) + + #fix share before hda + log.debug( "Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs." ) + dataset_by_filename = {} + changed_associations = 0 + start_time = time.time() + for dataset in model.Dataset.filter( model.Dataset.external_filename.like( '%dataset_%.dat' ) ).all(): + if dataset.file_name in dataset_by_filename: + guessed_dataset = dataset_by_filename[ dataset.file_name ] + else: + guessed_dataset = __guess_dataset_by_filename( dataset.file_name ) + if guessed_dataset and dataset.file_name != guessed_dataset.file_name:#not os.path.samefile( dataset.file_name, guessed_dataset.file_name ): + guessed_dataset = None + dataset_by_filename[ dataset.file_name ] = guessed_dataset + + if guessed_dataset is not None and guessed_dataset.id != dataset.id: #could we have a self referential dataset? + for dataset_instance in dataset.history_associations + dataset.library_associations: + dataset_instance.dataset = guessed_dataset + changed_associations += 1 + #mark original Dataset as deleted and purged, it is no longer in use, but do not delete file_name contents + dataset.deleted = True + dataset.external_filename = "Dataset was result of share before HDA, and has been replaced: %s mapped to Dataset %s" % ( dataset.external_filename, guessed_dataset.id ) + dataset.purged = True #we don't really purge the file here, but we mark it as purged, since this dataset is now defunct + galaxy.model.mapping.Session.flush() + log.debug( "%i items affected, and restored." % ( changed_associations ) ) + log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) + +def downgrade(): + log.debug( "Downgrade is not possible." ) + diff -r f7336991d0ee -r fb401a784261 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/util/__init__.py Thu Apr 23 12:42:05 2009 -0400 @@ -146,7 +146,7 @@ elif isinstance( value, list ): return map(sanitize_text, value) else: - raise Exception, 'Unknown parameter type' + raise Exception, 'Unknown parameter type (%s)' % ( type( value ) ) class Params: """ diff -r f7336991d0ee -r fb401a784261 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Thu Apr 23 12:42:05 2009 -0400 @@ -822,11 +822,13 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) created_ldda_ids = params.get( 'created_ldda_ids', '' ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) return trans.fill_template( '/admin/library/browse_library.mako', library=trans.app.model.Library.get( id ), created_ldda_ids=created_ldda_ids, msg=msg, - messagetype=messagetype ) + messagetype=messagetype, + show_deleted=show_deleted ) @web.expose @web.require_admin def library( self, trans, id=None, **kwd ): @@ -960,7 +962,8 @@ libraries=libraries, deleted=True, msg=msg, - messagetype=messagetype ) + messagetype=messagetype, + show_deleted = True ) @web.expose @web.require_admin def undelete_library( self, trans, **kwd ): @@ -2040,6 +2043,50 @@ id=library_id, msg=util.sanitize_text( msg ), messagetype=messagetype ) ) + + @web.expose + @web.require_admin + def delete_library_item( self, trans, library_id = None, library_item_id = None, library_item_type = None ): + #this action will handle deleting all types of library items in library browsing mode + library_item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, 'dataset': trans.app.model.LibraryDataset, } + if library_item_type not in library_item_types: + raise ValueError( 'Bad library_item_type specified: %s' % library_item_types ) + if library_item_id is None: + raise ValueError( 'library_item_id not specified' ) + library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) + library_item.deleted = True + library_item.flush() + #need to str because unicode isn't accepted... + msg = str( "%s '%s' has been marked deleted" % ( library_item_type, library_item.name ) ) + messagetype = str( "done" ) + if library_item_type == 'library' or library_id is None: + return self.browse_libraries( trans, msg = msg, messagetype = messagetype ) + else: + return self.browse_library( trans, id = library_id , msg = msg, messagetype = messagetype ) + + @web.expose + @web.require_admin + def undelete_library_item( self, trans, library_id = None, library_item_id = None, library_item_type = None ): + #this action will handle deleting all types of library items in library browsing mode + library_item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, 'dataset': trans.app.model.LibraryDataset, } + if library_item_type not in library_item_types: + raise ValueError( 'Bad library_item_type specified: %s' % library_item_types ) + if library_item_id is None: + raise ValueError( 'library_item_id not specified' ) + library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) + if library_item.purged: + raise ValueError( '%s %s cannot be undeleted' % ( library_item_type, library_item.name ) ) + library_item.deleted = False + library_item.flush() + msg = str( "%s '%s' has been undeleted" % ( library_item_type, library_item.name ) ) + messagetype = str( "done" ) + if library_item_type == 'library' or library_id is None: + return self.browse_libraries( trans, msg = msg, messagetype = messagetype ) + else: + return self.browse_library( trans, id = library_id , msg = msg, messagetype = messagetype ) + + + #(a)web.expose #(a)web.require_admin #def delete_dataset( self, trans, id=None, **kwd): diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Thu Apr 23 12:42:05 2009 -0400 @@ -1,6 +1,6 @@ #!/usr/bin/env python -import sys, os, time, ConfigParser +import sys, os, time, ConfigParser, shutil from datetime import datetime, timedelta from time import strftime from optparse import OptionParser @@ -15,7 +15,7 @@ pkg_resources.require( "SQLAlchemy >= 0.4" ) -from galaxy.model.orm import * +from galaxy.model.orm import and_, eagerload assert sys.version_info[:2] >= ( 2, 4 ) @@ -23,271 +23,172 @@ parser = OptionParser() parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (60)", default=60 ) parser.add_option( "-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False ) - parser.add_option( "-1", "--info_delete_userless_histories", action="store_true", dest="info_delete_userless_histories", default=False, help="info about the histories and datasets that will be affected by delete_userless_histories()" ) - parser.add_option( "-2", "--delete_userless_histories", action="store_true", dest="delete_userless_histories", default=False, help="delete userless histories and datasets" ) - parser.add_option( "-3", "--info_purge_histories", action="store_true", dest="info_purge_histories", default=False, help="info about histories and datasets that will be affected by purge_histories()" ) - parser.add_option( "-4", "--purge_histories", action="store_true", dest="purge_histories", default=False, help="purge deleted histories" ) - parser.add_option( "-5", "--info_purge_datasets", action="store_true", dest="info_purge_datasets", default=False, help="info about the datasets that will be affected by purge_datasets()" ) - parser.add_option( "-6", "--purge_datasets", action="store_true", dest="purge_datasets", default=False, help="purge deleted datasets" ) + parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False ) + + parser.add_option( "-1", "--delete_userless_histories", action="store_true", dest="delete_userless_histories", default=False, help="delete userless histories and datasets" ) + + parser.add_option( "-2", "--purge_histories", action="store_true", dest="purge_histories", default=False, help="purge deleted histories" ) + + parser.add_option( "-3", "--purge_datasets", action="store_true", dest="purge_datasets", default=False, help="purge deleted datasets" ) + + parser.add_option( "-4", "--purge_libraries", action="store_true", dest="purge_libraries", default=False, help="purge deleted libraries" ) + + parser.add_option( "-5", "--purge_folders", action="store_true", dest="purge_folders", default=False, help="purge deleted library folders" ) + + ( options, args ) = parser.parse_args() ini_file = args[0] - if not ( options.info_delete_userless_histories ^ options.delete_userless_histories ^ \ - options.info_purge_histories ^ options.purge_histories ^ \ - options.info_purge_datasets ^ options.purge_datasets ): + if not ( options.purge_folders ^ options.delete_userless_histories ^ \ + options.purge_libraries ^ options.purge_histories ^ \ + options.purge_datasets ): parser.print_help() sys.exit(0) + + if options.remove_from_disk and options.info_only: + parser.error( "remove_from_disk and info_only are mutually exclusive" ) conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) conf_parser.read( ini_file ) configuration = {} for key, value in conf_parser.items( "app:main" ): configuration[key] = value - database_connection = configuration['database_connection'] + + if 'database_connection' in configuration: + database_connection = configuration['database_connection'] + else: + database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % configuration["database_file"] file_path = configuration['file_path'] app = CleanupDatasetsApplication( database_connection=database_connection, file_path=file_path ) - h = app.model.History - d = app.model.Dataset - m = app.model.MetadataFile cutoff_time = datetime.utcnow() - timedelta( days=options.days ) now = strftime( "%Y-%m-%d %H:%M:%S" ) - + print "\n# %s - Handling stuff older than %i days\n" % ( now, options.days ) - - if options.info_delete_userless_histories: - info_delete_userless_histories( h, cutoff_time ) - elif options.delete_userless_histories: - delete_userless_histories( h, d, cutoff_time ) - if options.info_purge_histories: - info_purge_histories( h, d, cutoff_time ) + + if options.info_only: + print "# Displaying info only ( --info_only )\n" + elif options.remove_from_disk: + print "# Datasets will be removed from disk.\n" + else: + print "# Datasets will NOT be removed from disk.\n" + + if options.delete_userless_histories: + delete_userless_histories( app, cutoff_time, info_only = options.info_only ) elif options.purge_histories: - if options.remove_from_disk: - print "# Datasets will be removed from disk...\n" - else: - print "# Datasets will NOT be removed from disk...\n" - purge_histories( h, d, m, cutoff_time, options.remove_from_disk ) - elif options.info_purge_datasets: - info_purge_datasets( d, cutoff_time ) + purge_histories( app, cutoff_time, options.remove_from_disk, info_only = options.info_only ) elif options.purge_datasets: - if options.remove_from_disk: - print "# Datasets will be removed from disk...\n" - else: - print "# Datasets will NOT be removed from disk...\n" - purge_datasets( d, m, cutoff_time, options.remove_from_disk ) + purge_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only ) + elif options.purge_libraries: + purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only ) + elif options.purge_folders: + purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only ) + sys.exit(0) -def info_delete_userless_histories( h, cutoff_time ): - # Provide info about the histories and datasets that will be affected if the delete_userless_histories function is executed. +def delete_userless_histories( app, cutoff_time, info_only = False ): + # Deletes userless histories whose update_time value is older than the cutoff_time. + # The purge history script will handle marking DatasetInstances as deleted. + # Nothing is removed from disk yet. history_count = 0 - dataset_count = 0 - histories = h.filter( and_( h.table.c.user_id==None, - h.table.c.deleted==False, - h.table.c.update_time < cutoff_time ) ) \ - .options( eagerload( 'active_datasets' ) ).all() - - print '# The following datasets and associated userless histories will be deleted' + print '# The following datasets and associated userless histories have been deleted' start = time.clock() + histories = app.model.History.filter( and_( app.model.History.table.c.user_id==None, + app.model.History.table.c.deleted==False, + app.model.History.table.c.update_time < cutoff_time ) ).all()# \ for history in histories: - for dataset_assoc in history.active_datasets: - if not dataset_assoc.deleted: - # This check is not necessary since 'active_datasets' are not - # deleted, but just being cautious - print "dataset_%d" %dataset_assoc.dataset_id - dataset_count += 1 + if not info_only: + history.deleted = True print "%d" % history.id history_count += 1 + app.model.flush() stop = time.clock() - print "# %d histories ( including a total of %d datasets ) will be deleted\n" %( history_count, dataset_count ) - print "Elapsed time: ", stop - start, "\n" - -def delete_userless_histories( h, d, cutoff_time ): - # Deletes userless histories whose update_time value is older than the cutoff_time. - # The datasets associated with each history are also deleted. Nothing is removed from disk. - history_count = 0 - dataset_count = 0 - - print '# The following datasets and associated userless histories have been deleted' - start = time.clock() - histories = h.filter( and_( h.table.c.user_id==None, - h.table.c.deleted==False, - h.table.c.update_time < cutoff_time ) ) \ - .options( eagerload( 'active_datasets' ) ).all() - for history in histories: - for dataset_assoc in history.active_datasets: - if not dataset_assoc.deleted: - # Mark all datasets as deleted - datasets = d.filter( d.table.c.id==dataset_assoc.dataset_id ).all() - for dataset in datasets: - if not dataset.deleted: - dataset.deleted = True - dataset.flush() - # Mark the history_dataset_association as deleted - dataset_assoc.deleted = True - dataset_assoc.clear_associated_files() - dataset_assoc.flush() - print "dataset_%d" % dataset_assoc.dataset_id - dataset_count += 1 - history.deleted = True - history.flush() - print "%d" % history.id - history_count += 1 - stop = time.clock() - print "# Deleted %d histories ( including a total of %d datasets )\n" %( history_count, dataset_count ) + print "# Deleted %d histories.\n" % ( history_count ) print "Elapsed time: ", stop - start, "\n" -def info_purge_histories( h, d, cutoff_time ): - # Provide info about the histories and datasets that will be affected if the purge_histories function is executed. + +def purge_histories( app, cutoff_time, remove_from_disk, info_only = False ): + # Purges deleted histories whose update_time is older than the cutoff_time. + # The dataset associations of each history are also marked as deleted. + # The Purge Dataset method will purge each Dataset as necessary + # history.purged == True simply means that it can no longer be undeleted + # i.e. all associated datasets are marked as deleted history_count = 0 - dataset_count = 0 - disk_space = 0 - print '# The following datasets and associated deleted histories will be purged' + print '# The following datasets and associated deleted histories have been purged' start = time.clock() - histories = h.filter( and_( h.table.c.deleted==True, - h.table.c.purged==False, - h.table.c.update_time < cutoff_time ) ) \ + histories = app.model.History.filter( and_( app.model.History.table.c.deleted==True, + app.model.History.table.c.purged==False, + app.model.History.table.c.update_time < cutoff_time ) ) \ .options( eagerload( 'datasets' ) ).all() for history in histories: for dataset_assoc in history.datasets: - # Datasets can only be purged if their HistoryDatasetAssociation has been deleted. - if dataset_assoc.deleted: - datasets = d.filter( d.table.c.id==dataset_assoc.dataset_id ).all() - for dataset in datasets: - if dataset.purgable and not dataset.purged: - print "%s" % dataset.file_name - dataset_count += 1 - try: - disk_space += dataset.file_size - except: - pass + _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable + if not info_only: + history.purged = True print "%d" % history.id history_count += 1 + app.model.flush() stop = time.clock() - print '# %d histories ( including a total of %d datasets ) will be purged. Freed disk space: ' %( history_count, dataset_count ), disk_space, '\n' + print '# Purged %d histories.' % ( history_count ), '\n' print "Elapsed time: ", stop - start, "\n" -def purge_histories( h, d, m, cutoff_time, remove_from_disk ): - # Purges deleted histories whose update_time is older than the cutoff_time. - # The datasets associated with each history are also purged. - history_count = 0 - dataset_count = 0 - disk_space = 0 - file_size = 0 - errors = False - print '# The following datasets and associated deleted histories have been purged' +def purge_libraries( app, cutoff_time, remove_from_disk, info_only = False ): + # Purges deleted libraries whose update_time is older than the cutoff_time. + # The dataset associations of each library are also marked as deleted. + # The Purge Dataset method will purge each Dataset as necessary + # library.purged == True simply means that it can no longer be undeleted + # i.e. all associated LibraryDatasets/folders are marked as deleted + library_count = 0 + print '# The following libraries and associated folders have been purged' start = time.clock() - histories = h.filter( and_( h.table.c.deleted==True, - h.table.c.purged==False, - h.table.c.update_time < cutoff_time ) ) \ - .options( eagerload( 'datasets' ) ).all() - for history in histories: - errors = False - for dataset_assoc in history.datasets: - if dataset_assoc.deleted: - datasets = d.filter( d.table.c.id==dataset_assoc.dataset_id ).all() - for dataset in datasets: - if dataset.purgable and not dataset.purged: - file_size = dataset.file_size - dataset.deleted = True - dataset.file_size = 0 - if remove_from_disk: - dataset.flush() - errmsg = purge_dataset( dataset, d, m ) - if errmsg: - errors = True - print errmsg - else: - dataset.purged = True - dataset.flush() - print "%s" % dataset.file_name - # Mark all associated MetadataFiles as deleted and purged - print "The following metadata files associated with dataset '%s' have been marked purged" % dataset.file_name - for hda in dataset.history_associations: - for metadata_file in m.filter( m.table.c.hda_id==hda.id ).all(): - metadata_file.deleted = True - metadata_file.purged = True - metadata_file.flush() - print "%s" % metadata_file.file_name() - for lda in dataset.library_associations: - for metadata_file in m.filter( m.table.c.lda_id==lda.id ).all(): - metadata_file.deleted = True - metadata_file.purged = True - metadata_file.flush() - print "%s" % metadata_file.file_name() - dataset_count += 1 - try: - disk_space += file_size - except: - pass - if not errors: - history.purged = True - history.flush() - print "%d" % history.id - history_count += 1 + libraries = app.model.Library.filter( and_( app.model.Library.table.c.deleted==True, + app.model.Library.table.c.purged==False, + app.model.Library.table.c.update_time < cutoff_time ) ).all() + for library in libraries: + _purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only ) + if not info_only: + library.purged = True + print "%d" % library.id + library_count += 1 + app.model.flush() stop = time.clock() - print '# Purged %d histories ( including a total of %d datasets ). Freed disk space: ' %( history_count, dataset_count ), disk_space, '\n' + print '# Purged %d libraries .' % ( library_count ), '\n' print "Elapsed time: ", stop - start, "\n" -def info_purge_datasets( d, cutoff_time ): - # Provide info about the datasets that will be affected if the purge_datasets function is executed. - dataset_count = 0 - disk_space = 0 - print '# The following deleted datasets will be purged' +def purge_folders( app, cutoff_time, remove_from_disk, info_only = False ): + # Purges deleted folders whose update_time is older than the cutoff_time. + # The dataset associations of each folder are also marked as deleted. + # The Purge Dataset method will purge each Dataset as necessary + # libraryFolder.purged == True simply means that it can no longer be undeleted + # i.e. all associated LibraryDatasets/folders are marked as deleted + folder_count = 0 + print '# The following folders have been purged' start = time.clock() - datasets = d.filter( and_( d.table.c.deleted==True, - d.table.c.purgable==True, - d.table.c.purged==False, - d.table.c.update_time < cutoff_time ) ).all() - for dataset in datasets: - print "%s" % dataset.file_name - dataset_count += 1 - try: - disk_space += dataset.file_size - except: - pass + folders = app.model.LibraryFolder.filter( and_( app.model.LibraryFolder.table.c.deleted==True, + app.model.LibraryFolder.table.c.purged==False, + app.model.LibraryFolder.table.c.update_time < cutoff_time ) ).all() + for folder in folders: + _purge_folder( folder, app, remove_from_disk, info_only = info_only ) + print "%d" % folder.id + folder_count += 1 stop = time.clock() - print '# %d datasets will be purged. Freed disk space: ' %dataset_count, disk_space, '\n' + print '# Purged %d folders.' % ( folder_count ), '\n' print "Elapsed time: ", stop - start, "\n" -def purge_datasets( d, m, cutoff_time, remove_from_disk ): +def purge_datasets( app, cutoff_time, remove_from_disk, info_only = False ): # Purges deleted datasets whose update_time is older than cutoff_time. Files may or may # not be removed from disk. dataset_count = 0 disk_space = 0 - file_size = 0 print '# The following deleted datasets have been purged' start = time.clock() - datasets = d.filter( and_( d.table.c.deleted==True, - d.table.c.purgable==True, - d.table.c.purged==False, - d.table.c.update_time < cutoff_time ) ).all() + datasets = app.model.Dataset.filter( and_( app.model.Dataset.table.c.deleted==True, + app.model.Dataset.table.c.purgable==True, + app.model.Dataset.table.c.purged==False, + app.model.Dataset.table.c.update_time < cutoff_time ) ).all() for dataset in datasets: file_size = dataset.file_size - if remove_from_disk: - errmsg = purge_dataset( dataset, d, m ) - if errmsg: - print errmsg - else: - dataset_count += 1 - else: - dataset.purged = True - dataset.file_size = 0 - dataset.flush() - print "%s" % dataset.file_name - # Mark all associated MetadataFiles as deleted and purged - print "The following metadata files associated with dataset '%s' have been marked purged" % dataset.file_name - for hda in dataset.history_associations: - for metadata_file in m.filter( m.table.c.hda_id==hda.id ).all(): - metadata_file.deleted = True - metadata_file.purged = True - metadata_file.flush() - print "%s" % metadata_file.file_name() - for lda in dataset.library_associations: - for metadata_file in m.filter( m.table.c.lda_id==lda.id ).all(): - metadata_file.deleted = True - metadata_file.purged = True - metadata_file.flush() - print "%s" % metadata_file.file_name() - dataset_count += 1 + _purge_dataset( dataset, remove_from_disk, info_only = info_only ) + dataset_count += 1 try: disk_space += file_size except: @@ -298,68 +199,90 @@ print '# Freed disk space: ', disk_space, '\n' print "Elapsed time: ", stop - start, "\n" -def purge_dataset( dataset, d, m ): - # Removes the file from disk and updates the database accordingly. + +def _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children = True, info_only = False ): + #purging a dataset instance marks the instance as deleted, + #and marks the dataset as deleted if it is not associated with another DatsetInstance that is not deleted + if not info_only: + dataset_instance.mark_deleted( include_children = include_children ) + dataset_instance.clear_associated_files() + dataset_instance.flush() + dataset_instance.dataset.refresh() + if _dataset_is_deletable( dataset_instance.dataset ): + _delete_dataset( dataset_instance.dataset, app, remove_from_disk, info_only = info_only ) + #need to purge children here + if include_children: + for child in dataset_instance.children: + _purge_dataset_instance( child, app, remove_from_disk, include_children = include_children, info_only = info_only ) + +def _dataset_is_deletable( dataset ): + #a dataset is deletable when it no longer has any non-deleted associations + return not bool( dataset.active_history_associations or dataset.active_library_associations ) + +def _delete_dataset( dataset, app, remove_from_disk, info_only = False ): + #marks a base dataset as deleted, hdas/ldas associated with dataset can no longer be undeleted + #metadata files attached to associated dataset Instances is removed now + if not _dataset_is_deletable( dataset ): + print "# This Dataset (%i) is not deletable, associated Metadata Files will not be removed.\n" % ( dataset.id ) + else: + # Mark all associated MetadataFiles as deleted and purged and remove them from disk + print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id + metadata_files = [] + #lets create a list of metadata files, then perform actions on them + for hda in dataset.history_associations: + for metadata_file in app.model.MetadataFile.filter( app.model.MetadataFile.table.c.hda_id==hda.id ).all(): + metadata_files.append( metadata_file ) + for lda in dataset.library_associations: + for metadata_file in app.model.MetadataFile.filter( app.model.MetadataFile.table.c.lda_id==lda.id ).all(): + metadata_files.append( metadata_file ) + for metadata_file in metadata_files: + if not info_only: + if remove_from_disk: + try: + os.unlink( metadata_file.file_name ) + except Exception, e: + print "# Error, exception: %s caught attempting to purge metadata file %s\n" %( str( e ), metadata_file.file_name ) + metadata_file.purged = True + metadata_file.deleted = True + #metadata_file.flush() + print "%s" % metadata_file.file_name + print + dataset.deleted = True + #dataset.flush() + app.model.flush() + +def _purge_dataset( dataset, remove_from_disk, info_only = False ): if dataset.deleted: - purgable = True - # Remove files from disk and update the database try: - # See if the dataset has been shared - if dataset.external_filename: - # This check handles the pre-history_dataset_association approach to sharing. - shared_data = d.filter( and_( d.table.c.external_filename==dataset.external_filename, - d.table.c.deleted==False ) ).all() - if shared_data: - purgable = False - if purgable: - # This check handles the history_dataset_association approach to sharing. - for shared_data in dataset.history_associations: - # Check to see if another dataset is using this file. This happens when a user shares - # their history with another user. In this case, a new record is created in the dataset - # table for each dataset, but the dataset records point to the same data file on disk. So - # if 1 of the 2 users deletes the dataset from their history but the other doesn't, we need - # to keep the dataset on disk for the 2nd user. - if not shared_data.deleted: - purgable = False - break - if purgable: - # This check handles the library_dataset_dataset_association approach to sharing. - for shared_data in dataset.library_associations: - if not shared_data.deleted: - purgable = False - break - if purgable: - dataset.purged = True - dataset.file_size = 0 - dataset.flush() - # Remove dataset file from disk - os.unlink( dataset.file_name ) + if dataset.purgable and _dataset_is_deletable( dataset ): print "%s" % dataset.file_name - # Mark all associated MetadataFiles as deleted and purged and remove them from disk - print "The following metadata files associated with dataset '%s' have been purged" % dataset.file_name - for hda in dataset.history_associations: - for metadata_file in m.filter( m.table.c.hda_id==hda.id ).all(): - os.unlink( metadata_file.file_name() ) - metadata_file.deleted = True - metadata_file.purged = True - metadata_file.flush() - print "%s" % metadata_file.file_name() - for lda in dataset.library_associations: - for metadata_file in m.filter( m.table.c.lda_id==lda.id ).all(): - metadata_file.deleted = True - metadata_file.purged = True - metadata_file.flush() - print "%s" % metadata_file.file_name() - try: - # Remove associated extra files from disk if they exist - os.unlink( dataset.extra_files_path ) - except: - pass + if not info_only: + # Remove files from disk and update the database + if remove_from_disk: + os.unlink( dataset.file_name ) + # Remove associated extra files from disk if they exist + if dataset.extra_files_path and os.path.exists( dataset.extra_files_path ): + shutil.rmtree( dataset.extra_files_path ) #we need to delete the directory and its contents; os.unlink would always fail on a directory + dataset.purged = True + else: + print "# This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name ) except Exception, exc: - return "# Error, exception: %s caught attempting to purge %s\n" %( str( exc ), dataset.file_name ) + print "# Error, exception: %s caught attempting to purge %s\n" %( str( exc ), dataset.file_name ) else: - return "# Error: '%s' has not previously been deleted, so it cannot be purged\n" %dataset.file_name - return "" + print "# Error: '%s' has not previously been deleted, so it cannot be purged\n" % dataset.file_name + print "" + +def _purge_folder( folder, app, remove_from_disk, info_only = False ): + """Purges a folder and its contents, recursively""" + for ld in folder.datasets: + ld.deleted = True + for ldda in [ld.library_dataset_dataset_association] + ld.expired_datasets: + _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable + for sub_folder in folder.folders: + _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) + if not info_only: + folder.purged = True + folder.flush() class CleanupDatasetsApplication( object ): """Encapsulates the state of a Universe application""" diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/delete_userless_histories.sh --- a/scripts/cleanup_datasets/delete_userless_histories.sh Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/delete_userless_histories.sh Thu Apr 23 12:42:05 2009 -0400 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -2 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/delete_userless_histories_main.sh --- a/scripts/cleanup_datasets/delete_userless_histories_main.sh Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/delete_userless_histories_main.sh Thu Apr 23 12:42:05 2009 -0400 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -2 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_datasets.sh --- a/scripts/cleanup_datasets/purge_datasets.sh Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/purge_datasets.sh Thu Apr 23 12:42:05 2009 -0400 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_datasets_main.sh --- a/scripts/cleanup_datasets/purge_datasets_main.sh Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/purge_datasets_main.sh Thu Apr 23 12:42:05 2009 -0400 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -6 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_folders.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/cleanup_datasets/purge_folders.sh Thu Apr 23 12:42:05 2009 -0400 @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_folders_main.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/cleanup_datasets/purge_folders_main.sh Thu Apr 23 12:42:05 2009 -0400 @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_histories.sh --- a/scripts/cleanup_datasets/purge_histories.sh Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/purge_histories.sh Thu Apr 23 12:42:05 2009 -0400 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_histories_main.sh --- a/scripts/cleanup_datasets/purge_histories_main.sh Thu Apr 23 09:20:11 2009 -0400 +++ b/scripts/cleanup_datasets/purge_histories_main.sh Thu Apr 23 12:42:05 2009 -0400 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -4 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_libraries.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/cleanup_datasets/purge_libraries.sh Thu Apr 23 12:42:05 2009 -0400 @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log diff -r f7336991d0ee -r fb401a784261 scripts/cleanup_datasets/purge_libraries_main.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/cleanup_datasets/purge_libraries_main.sh Thu Apr 23 12:42:05 2009 -0400 @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log diff -r f7336991d0ee -r fb401a784261 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Thu Apr 23 09:20:11 2009 -0400 +++ b/static/june_2007_style/base.css.tmpl Thu Apr 23 12:42:05 2009 -0400 @@ -563,6 +563,7 @@ color: #333; font-size: 110%; font-weight: bold; + font-style: normal; white-space: nowrap; position: absolute; z-index: 20000; diff -r f7336991d0ee -r fb401a784261 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Thu Apr 23 09:20:11 2009 -0400 +++ b/static/june_2007_style/blue/base.css Thu Apr 23 12:42:05 2009 -0400 @@ -559,6 +559,7 @@ color: #333; font-size: 110%; font-weight: bold; + font-style: normal; white-space: nowrap; position: absolute; z-index: 20000; diff -r f7336991d0ee -r fb401a784261 static/june_2007_style/blue/library.css --- a/static/june_2007_style/blue/library.css Thu Apr 23 09:20:11 2009 -0400 +++ b/static/june_2007_style/blue/library.css Thu Apr 23 12:42:05 2009 -0400 @@ -4,6 +4,10 @@ .datasetHighlighted { background-color: #C1C9E5; +} + +.libraryItemDeleted-True { + font-style: italic; } div.historyItemBody { diff -r f7336991d0ee -r fb401a784261 static/june_2007_style/library.css.tmpl --- a/static/june_2007_style/library.css.tmpl Thu Apr 23 09:20:11 2009 -0400 +++ b/static/june_2007_style/library.css.tmpl Thu Apr 23 12:42:05 2009 -0400 @@ -4,6 +4,10 @@ .datasetHighlighted { background-color: $menu_bg_over; +} + +.libraryItemDeleted-True { + font-style: italic; } div.historyItemBody { diff -r f7336991d0ee -r fb401a784261 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Thu Apr 23 09:20:11 2009 -0400 +++ b/templates/admin/library/browse_library.mako Thu Apr 23 12:42:05 2009 -0400 @@ -93,7 +93,7 @@ %> %if not root_folder: <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"> - <div class="rowTitle"> + <div class="rowTitle libraryItemDeleted-${parent.deleted}"> <img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder )}" class="rowIcon"/> ${parent.name} %if parent.description: @@ -101,7 +101,7 @@ %endif <a id="folder-${parent.id}-popup" class="popup-arrow" style="display: none;">▼</a> </div> - %if not deleted: + %if not parent.deleted: <% library_item_ids = {} library_item_ids[ 'folder' ] = parent.id @@ -117,10 +117,11 @@ <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, folder_id=parent.id, new_template=True )}">Add an information template to this folder</a> %endif <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=parent.id, library_id=library_id )}">Edit this folder's permissions</a> - ## TODO: need to revamp the way folders and contained LibraryDatasets are deleted - ##%if subfolder: - ## <a class="action-button" confirm="Click OK to delete the folder '${parent.name}'" href="${h.url_for( action='folder', delete=True, id=parent.id, library_id=library_id )}">Remove this folder and its contents from the library</a> - ##%endif + <a class="action-button" confirm="Click OK to delete the folder '${parent.name}'" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library_id, library_item_id=parent.id, library_item_type='folder' )}">Remove this folder and its contents from the library</a> + </div> + %else: + <div popupmenu="folder-${parent.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library_id, library_item_id=parent.id, library_item_type='folder' )}">Undelete this folder</a> </div> %endif </li> @@ -130,10 +131,10 @@ %else: <ul> %endif - %if library.deleted: + %if deleted: <% - parent_folders = parent.folders - parent_datasets = parent.datasets + parent_folders = parent.activatable_folders + parent_datasets = parent.activatable_datasets %> %else: <% @@ -142,7 +143,7 @@ %> %endif %for folder in name_sorted( parent_folders ): - ${render_folder( folder, pad, library.deleted, created_ldda_ids, library.id )} + ${render_folder( folder, pad, deleted, created_ldda_ids, library.id )} %endfor %for library_dataset in name_sorted( parent_datasets ): <% @@ -182,17 +183,20 @@ <table cellspacing="0" cellpadding="0" border="0" width="100%" class="libraryTitle"> <th width="*"> <img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> - ${library.name} - %if library.description: - <i>- ${library.description}</i> - %endif + <span class="libraryItemDeleted-${library.deleted}"> + ${library.name} + %if library.description: + <i>- ${library.description}</i> + %endif + </span> <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="library-${library.id}-popup"> %if not library.deleted: <% library_item_ids = {} library_item_ids[ 'library' ] = library.id %> - <div popupmenu="library-${library.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this library's information</a> %if library.library_info_template_associations: <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> @@ -201,15 +205,16 @@ <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> %endif <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> - ## TODO: need to revamp the way libraries, folders, and contained LibraryDatasets are deleted - ##<a class="action-button" confirm="Current state will not be saved, so undeleting the library will restore all of its contents. Click OK to delete the library named '${library.name}'?" href="${h.url_for( controller='admin', action='library', delete=True, id=library.id )}">Delete this library and its contents</a> - </div> - ##%else: - ## <div popupmenu="library-${library.id}-popup"> - ## <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library', id=library.id )}">Undelete this library and its contents</a> - ## <a class="action-button" href="${h.url_for( controller='admin', action='purge_library', id=library.id )}">Purge this library and its contents</a> - ## </div> + <a class="action-button" confirm="Current state will not be saved, so undeleting the library will restore all of its contents. Click OK to delete the library named '${library.name}'?" href="${h.url_for( controller='admin', action='delete_library_item', library_item_type='library', library_item_id=library.id )}">Delete this library and its contents</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> + %else: + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> + %endif + %elif not library.purged: + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_item_type='library', library_item_id=library.id )}">Undelete this library</a> %endif + </div> </th> <th width="300">Information</th> <th width="150">Uploaded By</th> @@ -218,7 +223,7 @@ </div> </li> <ul> - ${render_folder( library.root_folder, 0, library.deleted, created_ldda_ids, library.id )} + ${render_folder( library.root_folder, 0, library.deleted or show_deleted, created_ldda_ids, library.id )} </ul> <br/> </ul> diff -r f7336991d0ee -r fb401a784261 templates/admin/library/common.mako --- a/templates/admin/library/common.mako Thu Apr 23 09:20:11 2009 -0400 +++ b/templates/admin/library/common.mako Thu Apr 23 12:42:05 2009 -0400 @@ -1,6 +1,6 @@ <% from time import strftime %> -<%def name="render_dataset( library_dataset, selected, library )"> +<%def name="render_dataset( library_dataset, selected, library, show_deleted = False )"> <% ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always @@ -27,13 +27,15 @@ %else: <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> %endif - <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:50]}</b></a> - %if not library.deleted: + <span class="libraryItemDeleted-${library_dataset.deleted}"> + <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:50]}</b></a> + </span> + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + %if not library_dataset.deleted: <% library_item_ids = {} library_item_ids[ 'ldda' ] = ldda.id %> - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use @@ -46,7 +48,11 @@ <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> %endif ##TODO: need to revamp the way we remove datasets from disk. - ##<a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, delete=True )}">Remove this dataset from the library</a> + <a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='dataset' )}">Remove this dataset from the library</a> + </div> + %else: + <div popupmenu="dataset-${ldda.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='dataset' )}">Undelete this dataset</a> </div> %endif </td>

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Not-So-Running Jobs
by Assaf Gordon 24 Apr '09

24 Apr '09

Hello, I've encountered a strange situation (at at least strange for me): Users are submitting jobs, and the jobs start almost immediately. However, the jobs look like they are running for very long time. Checking the report web page, a job looks like the attached image. The status is "running", but the command line is empty, and no program was executed for this job (I checked with "ps ax -H" and looked for python's child-processes). Some technical information: Running on Fedora with Python 2.4.3, PostgreSQL 8.0. The server is loaded but not too loaded ( 14.4 load average for 16 cores ). Relevant settings from universe_wsgi.ini: use_threadpool = true threadpool_workers = 10 local_job_queue_workers = 5 job_scheduler_policy = galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin job_queue_cleanup_interval = 30 Is this normal ? Thanks, Gordon.

2 3