Fix SA2.0 usage in tool_shed.util.shed_util_common

lib/tool_shed/util/shed_util_common.py

@@ -5,10 +5,10 @@ import socket
 import string
 from typing import TYPE_CHECKING
 
-import sqlalchemy.orm.exc
 from sqlalchemy import (
-    and_,
     false,
+    func,
+    select,
     true,
 )
 
@@ -89,46 +89,41 @@ changes were made to the repository named "${repository_name}".
 
 
 def count_repositories_in_category(app: "ToolShedApp", category_id: str) -> int:
-    sa_session = app.model.session
-    return (
-        sa_session.query(app.model.RepositoryCategoryAssociation)
-        .filter(app.model.RepositoryCategoryAssociation.table.c.category_id == app.security.decode_id(category_id))
-        .count()
+    stmt = (
+        select(func.count())
+        .select_from(app.model.RepositoryCategoryAssociation)
+        .where(app.model.RepositoryCategoryAssociation.category_id == app.security.decode_id(category_id))
     )
+    return app.model.session.scalar(stmt)
 
 
 def get_categories(app: "ToolShedApp"):
     """Get all categories from the database."""
     sa_session = app.model.session
-    return (
-        sa_session.query(app.model.Category)
-        .filter(app.model.Category.table.c.deleted == false())
-        .order_by(app.model.Category.table.c.name)
-        .all()
-    )
+    stmt = select(app.model.Category).where(app.model.Category.deleted == false()).order_by(app.model.Category.name)
+    return sa_session.scalars(stmt).all()
 
 
 def get_category(app: "ToolShedApp", id: str):
     """Get a category from the database."""
     sa_session = app.model.session
-    return sa_session.query(app.model.Category).get(app.security.decode_id(id))
+    return sa_session.get(app.model.Category, app.security.decode_id(id))
 
 
 def get_category_by_name(app: "ToolShedApp", name: str):
     """Get a category from the database via name."""
     sa_session = app.model.session
-    try:
-        return sa_session.query(app.model.Category).filter_by(name=name).one()
-    except sqlalchemy.orm.exc.NoResultFound:
-        return None
+    stmt = select(app.model.Category).filter_by(name=name).limit(1)
+    return sa_session.scalars(stmt).first()
 
 
 def get_repository_categories(app, id):
     """Get categories of a repository on the tool shed side from the database via id"""
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryCategoryAssociation).filter(
-        app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id)
+    stmt = select(app.model.RepositoryCategoryAssociation).where(
+        app.model.RepositoryCategoryAssociation.repository_id == app.security.decode_id(id)
     )
+    return sa_session.scalars(stmt).all()
 
 
 def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
@@ -336,9 +331,7 @@ def handle_email_alerts(app, host, repository, content_alert_str="", new_repo_al
             subject = f"Galaxy tool shed alert for new repository named {str(repository.name)}"
             subject = subject[:80]
             email_alerts = []
-            for user in sa_session.query(app.model.User).filter(
-                and_(app.model.User.table.c.deleted == false(), app.model.User.table.c.new_repo_alert == true())
-            ):
+            for user in get_users_with_repo_alert(sa_session.query, app.model.User):
                 if admin_only:
                     if user.email in admin_users:
                         email_alerts.append(user.email)
@@ -468,3 +461,8 @@ __all__ = (
     "set_image_paths",
     "tool_shed_is_this_tool_shed",
 )
+
+
+def get_users_with_repo_alert(session, user_model):
+    stmt = select(user_model).where(user_model.deleted == false()).where(user_model.new_repo_alert == true())
+    return session.scalars(stmt)