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Source code for galaxy.model.item_attrs

import logging

from sqlalchemy import select
from sqlalchemy.sql.expression import func

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

log = logging.getLogger(__name__)

[docs]class UsesItemRatings: """ 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(f"Item does not have ratings: {item.__class__.__name__}") item_id_filter = self._get_item_id_filter_str(item, item_rating_assoc_class) ave_rating = db_session.scalar(select(func.avg(item_rating_assoc_class.rating)).where(item_id_filter)) # 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 = db_session.scalar(select(func.count(item_rating_assoc_class.rating)).where(item_id_filter)) 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(user, item, rating) db_session.add(item_rating) with transaction(db_session): db_session.commit() elif item_rating.rating != rating: # User has rated item; update rating. item_rating.rating = rating with transaction(db_session): db_session.commit() 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(f"Item does not have ratings: {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.scalars( select(item_rating_assoc_class).filter_by(user=user).where(item_id_filter).limit(1) ).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 = f"{item.__class__.__name__}RatingAssociation" return getattr(webapp_model, item_rating_assoc_class, None) def _get_item_id_filter_str(self, item, item_rating_assoc_class): # Get foreign key in item-rating association table that references item table. item_fk = get_foreign_key(item_rating_assoc_class, item) return item_fk.parent == item.id
[docs]class UsesAnnotations: """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): if annotation_assoc := get_item_annotation_obj(db_session, user, item): db_session.delete(annotation_assoc) with transaction(db_session): db_session.commit()
[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 or item.id is None: return None # Get annotation association object. annotation_assoc = select(annotation_assoc_class).filter_by(user=user) 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 db_session.scalars(annotation_assoc.limit(1)).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 = f"{item.__class__.__name__}AnnotationAssociation" 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(f"No foreign key found between objects: {source_class.__table__}, {target_class.__table__}") return target_fk
__all__ = ( "get_foreign_key", "UsesAnnotations", "UsesItemRatings", )