Add scripts to fix association null values

lib/galaxy/model/scripts/association_table_fixer.py

@@ -0,0 +1,87 @@
+import os
+import sys
+from abc import (
+    ABC,
+    abstractmethod,
+)
+
+from sqlalchemy import (
+    create_engine,
+    delete,
+    func,
+    null,
+    or_,
+    select,
+)
+
+from galaxy.model import (
+    Base,
+    GroupRoleAssociation,
+    UserGroupAssociation,
+    UserRoleAssociation,
+)
+from galaxy.model.orm.scripts import get_config
+
+
+class AssociationNullFix(ABC):
+
+    def __init__(self, association_model: Base):
+        self.assoc_model = association_model
+        self.assoc_name = association_model.__tablename__
+        self.where_clause = self.build_where_clause()
+
+    def run(self):
+        config = get_config(sys.argv, use_argparse=False, cwd=os.getcwd())
+        engine = create_engine(config["db_url"])
+
+        invalid_assocs = self.count_associations_with_nulls(engine)
+        if not invalid_assocs:
+            print(f"Your database does not contain invalid {self.assoc_name} records")
+            return
+
+        print(f"Your database contains {invalid_assocs} invalid {self.assoc_name} records")
+        answer = input(f'Delete {invalid_assocs} invalid records? (type "yes" to confirm)\n')
+        if answer.lower() == "yes":
+            self.delete_associations_with_nulls(engine)
+        else:
+            print("Operation aborted")
+
+    def count_associations_with_nulls(self, engine):
+        """
+        Retrieve association records where one or both associated item ids are null.
+        """
+        select_stmt = select(func.count()).where(self.where_clause)
+        with engine.connect() as conn:
+            return conn.scalar(select_stmt)
+
+    def delete_associations_with_nulls(self, engine):
+        """
+        Delete association records where one or both associated item ids are null.
+        """
+        delete_stmt = delete(self.assoc_model).where(self.where_clause)
+        with engine.begin() as conn:
+            result = conn.execute(delete_stmt)
+            conn.commit()
+        print(f"{result.rowcount} invalid records have been deleted")
+
+    @abstractmethod
+    def build_where_clause(self):
+        """Build where clause for filtering records containing nulls instead of associated item ids"""
+
+
+class UserGroupAssociationNullFix(AssociationNullFix):
+
+    def build_where_clause(self):
+        return or_(UserGroupAssociation.user_id == null(), UserGroupAssociation.group_id == null())
+
+
+class UserRoleAssociationNullFix(AssociationNullFix):
+
+    def build_where_clause(self):
+        return or_(UserRoleAssociation.user_id == null(), UserRoleAssociation.role_id == null())
+
+
+class GroupRoleAssociationNullFix(AssociationNullFix):
+
+    def build_where_clause(self):
+        return or_(GroupRoleAssociation.group_id == null(), GroupRoleAssociation.role_id == null())

scripts/db/fix_group_role_association_nulls.py

@@ -1 +1,11 @@
-# TODO
+import os
+import sys
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
+
+from galaxy.model import GroupRoleAssociation
+from galaxy.model.scripts.association_table_fixer import GroupRoleAssociationNullFix
+
+if __name__ == "__main__":
+    assoc_fix = GroupRoleAssociationNullFix(GroupRoleAssociation)
+    assoc_fix.run()

scripts/db/fix_user_group_association_nulls.py

@@ -1 +1,11 @@
-# TODO
+import os
+import sys
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
+
+from galaxy.model import UserGroupAssociation
+from galaxy.model.scripts.association_table_fixer import UserGroupAssociationNullFix
+
+if __name__ == "__main__":
+    assoc_fix = UserGroupAssociationNullFix(UserGroupAssociation)
+    assoc_fix.run()

scripts/db/fix_user_role_association_nulls.py

@@ -1 +1,11 @@
-# TODO
+import os
+import sys
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
+
+from galaxy.model import UserRoleAssociation
+from galaxy.model.scripts.association_table_fixer import UserRoleAssociationNullFix
+
+if __name__ == "__main__":
+    assoc_fix = UserRoleAssociationNullFix(UserRoleAssociation)
+    assoc_fix.run()