This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.model.item_attrs

import logging

from sqlalchemy.sql.expression import func

# Cannot import galaxy.model b/c it creates a circular import graph.
import galaxy

log = logging.getLogger(__name__)

[docs]class UsesItemRatings(object): """ Mixin for getting and setting item ratings. Class makes two assumptions: (1) item-rating association table is named <item_class>RatingAssocation (2) item-rating association table has a column with a foreign key referencing item table that contains the item's id. """
[docs] def get_ave_item_rating_data(self, db_session, item, webapp_model=None): """ Returns the average rating for an item.""" if webapp_model is None: webapp_model = galaxy.model item_rating_assoc_class = self._get_item_rating_assoc_class(item, webapp_model=webapp_model) if not item_rating_assoc_class: raise Exception("Item does not have ratings: %s" % item.__class__.__name__) item_id_filter = self._get_item_id_filter_str(item, item_rating_assoc_class) ave_rating = db_session.query(func.avg(item_rating_assoc_class.rating)).filter(item_id_filter).scalar() # Convert ave_rating to float; note: if there are no item ratings, ave rating is None. if ave_rating: ave_rating = float(ave_rating) else: ave_rating = 0 num_ratings = int(db_session.query(func.count(item_rating_assoc_class.rating)).filter(item_id_filter).scalar()) return (ave_rating, num_ratings)
[docs] def rate_item(self, db_session, user, item, rating, webapp_model=None): """ Rate an item. Return type is <item_class>RatingAssociation. """ if webapp_model is None: webapp_model = galaxy.model item_rating = self.get_user_item_rating(db_session, user, item, webapp_model=webapp_model) if not item_rating: # User has not yet rated item; create rating. item_rating_assoc_class = self._get_item_rating_assoc_class(item, webapp_model=webapp_model) item_rating = item_rating_assoc_class() item_rating.user = user item_rating.set_item(item) item_rating.rating = rating db_session.add(item_rating) db_session.flush() elif item_rating.rating != rating: # User has rated item; update rating. item_rating.rating = rating db_session.flush() return item_rating
[docs] def get_user_item_rating(self, db_session, user, item, webapp_model=None): """ Returns user's rating for an item. Return type is <item_class>RatingAssociation. """ if webapp_model is None: webapp_model = galaxy.model item_rating_assoc_class = self._get_item_rating_assoc_class(item, webapp_model=webapp_model) if not item_rating_assoc_class: raise Exception("Item does not have ratings: %s" % item.__class__.__name__) # Query rating table by user and item id. item_id_filter = self._get_item_id_filter_str(item, item_rating_assoc_class) return db_session.query(item_rating_assoc_class).filter_by(user=user).filter(item_id_filter).first()
def _get_item_rating_assoc_class(self, item, webapp_model=None): """ Returns an item's item-rating association class. """ if webapp_model is None: webapp_model = galaxy.model item_rating_assoc_class = '%sRatingAssociation' % item.__class__.__name__ return getattr(webapp_model, item_rating_assoc_class, None) def _get_item_id_filter_str(self, item, item_rating_assoc_class, webapp_model=None): # Get foreign key in item-rating association table that references item table. if webapp_model is None: webapp_model = galaxy.model item_fk = get_foreign_key(item_rating_assoc_class, item) # TODO: can we provide a better filter than a raw string? return "%s=%i" % (item_fk.parent.name, item.id)
[docs]class UsesAnnotations(object): """ Mixin for getting and setting item annotations. """
[docs] def get_item_annotation_str(self, db_session, user, item): return get_item_annotation_str(db_session, user, item)
[docs] def get_item_annotation_obj(self, db_session, user, item): return get_item_annotation_obj(db_session, user, item)
[docs] def add_item_annotation(self, db_session, user, item, annotation): return add_item_annotation(db_session, user, item, annotation)
[docs] def delete_item_annotation(self, db_session, user, item): annotation_assoc = get_item_annotation_obj(db_session, user, item) if annotation_assoc: db_session.delete(annotation_assoc) db_session.flush()
[docs] def copy_item_annotation(self, db_session, source_user, source_item, target_user, target_item): """ Copy an annotation from a user/item source to a user/item target. """ if source_user and target_user: annotation_str = self.get_item_annotation_str(db_session, source_user, source_item) if annotation_str: annotation = self.add_item_annotation(db_session, target_user, target_item, annotation_str) return annotation return None
def get_item_annotation_obj(db_session, user, item): """Returns a user's annotation object for an item.""" # Get annotation association class. annotation_assoc_class = _get_annotation_assoc_class(item) if not annotation_assoc_class: return None # Get annotation association object. annotation_assoc = db_session.query(annotation_assoc_class).filter_by(user=user) # TODO: use filtering like that in _get_item_id_filter_str() if item.__class__ == galaxy.model.History: annotation_assoc = annotation_assoc.filter_by(history=item) elif item.__class__ == galaxy.model.HistoryDatasetAssociation: annotation_assoc = annotation_assoc.filter_by(hda=item) elif item.__class__ == galaxy.model.HistoryDatasetCollectionAssociation: annotation_assoc = annotation_assoc.filter_by(history_dataset_collection=item) elif item.__class__ == galaxy.model.StoredWorkflow: annotation_assoc = annotation_assoc.filter_by(stored_workflow=item) elif item.__class__ == galaxy.model.WorkflowStep: annotation_assoc = annotation_assoc.filter_by(workflow_step=item) elif item.__class__ == galaxy.model.Page: annotation_assoc = annotation_assoc.filter_by(page=item) elif item.__class__ == galaxy.model.Visualization: annotation_assoc = annotation_assoc.filter_by(visualization=item) return annotation_assoc.first() def get_item_annotation_str(db_session, user, item): """ Returns a user's annotation string for an item. """ if hasattr(item, 'annotations'): # If we already have an annotations object we use it. annotation_obj = None for annotation in item.annotations: if annotation.user == user: annotation_obj = annotation break else: annotation_obj = get_item_annotation_obj(db_session, user, item) if annotation_obj: return galaxy.util.unicodify(annotation_obj.annotation) return None def add_item_annotation(db_session, user, item, annotation): """ Add or update an item's annotation; a user can only have a single annotation for an item. """ # Get/create annotation association object. annotation_assoc = get_item_annotation_obj(db_session, user, item) if not annotation_assoc: annotation_assoc_class = _get_annotation_assoc_class(item) if not annotation_assoc_class: return None annotation_assoc = annotation_assoc_class() item.annotations.append(annotation_assoc) annotation_assoc.user = user # Set annotation. annotation_assoc.annotation = annotation return annotation_assoc def _get_annotation_assoc_class(item): """ Returns an item's item-annotation association class. """ class_name = '%sAnnotationAssociation' % item.__class__.__name__ return getattr(galaxy.model, class_name, None)
[docs]def get_foreign_key(source_class, target_class): """ Returns foreign key in source class that references target class. """ target_fk = None for fk in source_class.table.foreign_keys: if fk.references(target_class.table): target_fk = fk break if not target_fk: raise Exception("No foreign key found between objects: %s, %s" % source_class.table, target_class.table) return target_fk
__all__ = ( 'get_foreign_key', 'UsesAnnotations', 'UsesItemRatings', )