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Source code for galaxy.managers.tags

import logging
import re

from galaxy.util import unicodify
from six import string_types
from sqlalchemy.sql import select
from sqlalchemy.sql.expression import func

log = logging.getLogger( __name__ )


# Item-specific information needed to perform tagging.
[docs]class ItemTagAssocInfo( object ):
[docs] def __init__( self, item_class, tag_assoc_class, item_id_col ): self.item_class = item_class self.tag_assoc_class = tag_assoc_class self.item_id_col = item_id_col
[docs]class TagManager( object ): """ Manages CRUD operations related to tagging objects. """
[docs] def __init__( self, app ): self.app = app # Minimum tag length. self.min_tag_len = 2 # Maximum tag length. self.max_tag_len = 255 # Tag separator. self.tag_separators = ',;' # Hierarchy separator. self.hierarchy_separator = '.' # Key-value separator. self.key_value_separators = "=:" # Initialize with known classes - add to this in subclasses. self.item_tag_assoc_info = {}
[docs] def add_tags_from_list( self, user, item, new_tags_list ): new_tags_set = set( new_tags_list ) if item.tags: new_tags_set.update( self.get_tags_str( item.tags ).split( ',' ) ) return self.set_tags_from_list( user, item, new_tags_set )
[docs] def set_tags_from_list( self, user, item, new_tags_list ): # precondition: item is already security checked against user # precondition: incoming tags is a list of sanitized/formatted strings self.delete_item_tags( user, item ) new_tags_str = ','.join( new_tags_list ) self.apply_item_tags( user, item, unicodify( new_tags_str, 'utf-8' ) ) self.app.model.context.flush() return item.tags
[docs] def get_tag_assoc_class( self, item_class ): """Returns tag association class for item class.""" return self.item_tag_assoc_info[item_class.__name__].tag_assoc_class
[docs] def get_id_col_in_item_tag_assoc_table( self, item_class ): """Returns item id column in class' item-tag association table.""" return self.item_tag_assoc_info[item_class.__name__].item_id_col
[docs] def get_community_tags( self, item=None, limit=None ): """Returns community tags for an item.""" # Get item-tag association class. item_class = item.__class__ item_tag_assoc_class = self.get_tag_assoc_class( item_class ) if not item_tag_assoc_class: return [] # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count( '*' ) ] from_obj = item_tag_assoc_class.table.join( item_class.table ).join( self.app.model.Tag.table ) where_clause = ( self.get_id_col_in_item_tag_assoc_table( item_class ) == item.id ) order_by = [ func.count( "*" ).desc() ] group_by = item_tag_assoc_class.table.c.tag_id # Do query and get result set. query = select( columns=cols_to_select, from_obj=from_obj, whereclause=where_clause, group_by=group_by, order_by=order_by, limit=limit ) result_set = self.app.model.context.execute( query ) # Return community tags. community_tags = [] for row in result_set: tag_id = row[0] community_tags.append( self.get_tag_by_id( tag_id ) ) return community_tags
[docs] def get_tool_tags( self ): result_set = self.app.model.context.execute( select( columns=[ self.app.model.ToolTagAssociation.table.c.tag_id ], from_obj=self.app.model.ToolTagAssociation.table ).distinct() ) tags = [] for row in result_set: tag_id = row[0] tags.append( self.get_tag_by_id( tag_id ) ) return tags
[docs] def remove_item_tag( self, user, item, tag_name ): """Remove a tag from an item.""" # Get item tag association. item_tag_assoc = self._get_item_tag_assoc( user, item, tag_name ) # Remove association. if item_tag_assoc: # Delete association. self.app.model.context.delete( item_tag_assoc ) item.tags.remove( item_tag_assoc ) return True return False
[docs] def delete_item_tags( self, user, item ): """Delete tags from an item.""" # Delete item-tag associations. for tag in item.tags: self.app.model.context.delete( tag ) # Delete tags from item. del item.tags[:]
[docs] def item_has_tag( self, user, item, tag ): """Returns true if item is has a given tag.""" # Get tag name. if isinstance( tag, string_types ): tag_name = tag elif isinstance( tag, self.app.model.Tag ): tag_name = tag.name # Check for an item-tag association to see if item has a given tag. item_tag_assoc = self._get_item_tag_assoc( user, item, tag_name ) if item_tag_assoc: return True return False
[docs] def apply_item_tag( self, user, item, name, value=None ): # Use lowercase name for searching/creating tag. lc_name = name.lower() # Get or create item-tag association. item_tag_assoc = self._get_item_tag_assoc( user, item, lc_name ) # If the association does not exist, or if it has a different value, add another. # We do allow multiple associations with different values. if not item_tag_assoc or (item_tag_assoc and item_tag_assoc.value != value): # Create item-tag association. # Create tag; if None, skip the tag (and log error). tag = self._get_or_create_tag( lc_name ) if not tag: log.warning( "Failed to create tag with name %s" % lc_name ) return # Create tag association based on item class. item_tag_assoc_class = self.get_tag_assoc_class( item.__class__ ) item_tag_assoc = item_tag_assoc_class() # Add tag to association. item.tags.append( item_tag_assoc ) item_tag_assoc.tag = tag item_tag_assoc.user = user # Apply attributes to item-tag association. Strip whitespace from user name and tag. lc_value = None if value: lc_value = value.lower() item_tag_assoc.user_tname = name item_tag_assoc.user_value = value item_tag_assoc.value = lc_value return item_tag_assoc
[docs] def apply_item_tags( self, user, item, tags_str ): """Apply tags to an item.""" # Parse tags. parsed_tags = self.parse_tags( tags_str ) # Apply each tag. for name, value in parsed_tags: self.apply_item_tag( user, item, name, value )
[docs] def get_tags_str( self, tags ): """Build a string from an item's tags.""" # Return empty string if there are no tags. if not tags: return "" # Create string of tags. tags_str_list = list() for tag in tags: tag_str = tag.user_tname if tag.value is not None: tag_str += ":" + tag.user_value tags_str_list.append( tag_str ) return ", ".join( tags_str_list )
[docs] def get_tag_by_id( self, tag_id ): """Get a Tag object from a tag id.""" return self.app.model.context.query( self.app.model.Tag ).filter_by( id=tag_id ).first()
[docs] def get_tag_by_name( self, tag_name ): """Get a Tag object from a tag name (string).""" if tag_name: return self.app.model.context.query( self.app.model.Tag ).filter_by( name=tag_name.lower() ).first() return None
def _create_tag( self, tag_str ): """Create a Tag object from a tag string.""" tag_hierarchy = tag_str.split( self.hierarchy_separator ) tag_prefix = "" parent_tag = None for sub_tag in tag_hierarchy: # Get or create subtag. tag_name = tag_prefix + self._scrub_tag_name( sub_tag ) tag = self.app.model.context.query( self.app.model.Tag ).filter_by( name=tag_name).first() if not tag: tag = self.app.model.Tag( type=0, name=tag_name ) # Set tag parent. tag.parent = parent_tag # Update parent and tag prefix. parent_tag = tag tag_prefix = tag.name + self.hierarchy_separator return tag def _get_or_create_tag( self, tag_str ): """Get or create a Tag object from a tag string.""" # Scrub tag; if tag is None after being scrubbed, return None. scrubbed_tag_str = self._scrub_tag_name( tag_str ) if not scrubbed_tag_str: return None # Get item tag. tag = self.get_tag_by_name( scrubbed_tag_str ) # Create tag if necessary. if tag is None: tag = self._create_tag( scrubbed_tag_str ) return tag def _get_item_tag_assoc( self, user, item, tag_name ): """ Return ItemTagAssociation object for a user, item, and tag string; returns None if there is no such association. """ scrubbed_tag_name = self._scrub_tag_name( tag_name ) for item_tag_assoc in item.tags: if ( item_tag_assoc.user == user ) and ( item_tag_assoc.user_tname == scrubbed_tag_name ): return item_tag_assoc return None
[docs] def parse_tags( self, tag_str ): """ Returns a list of raw (tag-name, value) pairs derived from a string; method scrubs tag names and values as well. Return value is a list of (tag_name, tag_value) tuples. """ # Gracefully handle None. if not tag_str: return dict() # Split tags based on separators. reg_exp = re.compile( '[' + self.tag_separators + ']' ) raw_tags = reg_exp.split( tag_str ) # Extract name-value pairs. name_value_pairs = [] for raw_tag in raw_tags: nv_pair = self._get_name_value_pair( raw_tag ) scrubbed_name = self._scrub_tag_name( nv_pair[0] ) scrubbed_value = self._scrub_tag_value( nv_pair[1] ) # Append tag_name, tag_value tuple -- TODO use NamedTuple name_value_pairs.append(( scrubbed_name, scrubbed_value )) return name_value_pairs
def _scrub_tag_value( self, value ): """Scrub a tag value.""" # Gracefully handle None: if not value: return None # Remove whitespace from value. reg_exp = re.compile( '\s' ) scrubbed_value = re.sub( reg_exp, "", value ) return scrubbed_value def _scrub_tag_name( self, name ): """Scrub a tag name.""" # Gracefully handle None: if not name: return None # Remove whitespace from name. reg_exp = re.compile( '\s' ) scrubbed_name = re.sub( reg_exp, "", name ) # Ignore starting ':' char. if scrubbed_name.startswith( self.hierarchy_separator ): scrubbed_name = scrubbed_name[1:] # If name is too short or too long, return None. if len( scrubbed_name ) < self.min_tag_len or len( scrubbed_name ) > self.max_tag_len: return None return scrubbed_name def _scrub_tag_name_list( self, tag_name_list ): """Scrub a tag name list.""" scrubbed_tag_list = list() for tag in tag_name_list: scrubbed_tag_list.append( self._scrub_tag_name( tag ) ) return scrubbed_tag_list def _get_name_value_pair( self, tag_str ): """Get name, value pair from a tag string.""" # Use regular expression to parse name, value. reg_exp = re.compile( "[" + self.key_value_separators + "]" ) name_value_pair = reg_exp.split( tag_str ) # Add empty slot if tag does not have value. if len( name_value_pair ) < 2: name_value_pair.append( None ) return name_value_pair
[docs]class GalaxyTagManager( TagManager ):
[docs] def __init__( self, app ): from galaxy import model TagManager.__init__( self, app ) self.item_tag_assoc_info["History"] = ItemTagAssocInfo( model.History, model.HistoryTagAssociation, model.HistoryTagAssociation.table.c.history_id ) self.item_tag_assoc_info["HistoryDatasetAssociation"] = \ ItemTagAssocInfo( model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, model.HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id ) self.item_tag_assoc_info["HistoryDatasetCollectionAssociation"] = \ ItemTagAssocInfo( model.HistoryDatasetCollectionAssociation, model.HistoryDatasetCollectionTagAssociation, model.HistoryDatasetCollectionTagAssociation.table.c.history_dataset_collection_id ) self.item_tag_assoc_info["Page"] = ItemTagAssocInfo( model.Page, model.PageTagAssociation, model.PageTagAssociation.table.c.page_id ) self.item_tag_assoc_info["StoredWorkflow"] = ItemTagAssocInfo( model.StoredWorkflow, model.StoredWorkflowTagAssociation, model.StoredWorkflowTagAssociation.table.c.stored_workflow_id ) self.item_tag_assoc_info["Visualization"] = ItemTagAssocInfo( model.Visualization, model.VisualizationTagAssociation, model.VisualizationTagAssociation.table.c.visualization_id )
[docs]class CommunityTagManager( TagManager):
[docs] def __init__( self, app ): TagManager.__init__( self, app )