diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 4035a8c5c5c..bd823b6cb09 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -5,6 +5,10 @@ from mercurial import (
     hg,
     ui,
 )
+from sqlalchemy import (
+    false,
+    select,
+)
 from whoosh.writing import AsyncWriter
 
 import tool_shed.webapp.model.mapping as ts_mapping
@@ -91,21 +95,11 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
     """
     hgwcm = hgweb_config_manager
     hgwcm.hgweb_config_dir = hgweb_config_dir
-    # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
-    q = (
-        sa_session.query(model.Repository)
-        .filter_by(deleted=False)
-        .filter_by(deprecated=False)
-        .order_by(model.Repository.update_time.desc())
-    )
-    q = q.filter(model.Repository.type != "tool_dependency_definition")
-    for repo in q:
+    for repo in get_repositories_for_indexing(sa_session):
         category_names = []
-        for rca in sa_session.query(model.RepositoryCategoryAssociation).filter(
-            model.RepositoryCategoryAssociation.repository_id == repo.id
-        ):
-            for category in sa_session.query(model.Category).filter(model.Category.id == rca.category.id):
-                category_names.append(category.name.lower())
+        for rca in get_repo_cat_associations(sa_session, repo.id):
+            category = sa_session.get(model.Category, rca.category.id)
+            category_names.append(category.name.lower())
         categories = (",").join(category_names)
         repo_id = repo.id
         name = repo.name
@@ -118,7 +112,7 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
 
         repo_owner_username = ""
         if repo.user_id is not None:
-            user = sa_session.query(model.User).filter(model.User.id == repo.user_id).one()
+            user = sa_session.get(model.User, repo.user_id)
             repo_owner_username = user.username.lower()
 
         last_updated = pretty_print_time_interval(repo.update_time)
@@ -196,3 +190,23 @@ def load_one_dir(path):
                 )
                 tools_in_dir.append(tool)
     return tools_in_dir
+
+
+def get_repositories_for_indexing(session):
+    # Do not index deleted, deprecated, or "tool_dependency_definition" type repositories.
+    Repository = model.Repository
+    stmt = (
+        select(Repository)
+        .where(Repository.deleted == false())
+        .where(Repository.deprecated == false())
+        .where(Repository.type != "tool_dependency_definition")
+        .order_by(Repository.update_time.desc())
+    )
+    return session.scalars(stmt)
+
+
+def get_repo_cat_associations(session, repository_id):
+    stmt = select(model.RepositoryCategoryAssociation).where(
+        model.RepositoryCategoryAssociation.repository_id == repository_id
+    )
+    return session.scalars(stmt)