Fix SA2.0 usage in tool_shed.util.metadata_util

lib/tool_shed/util/metadata_util.py

@@ -5,7 +5,7 @@
     TYPE_CHECKING,
 )
 
-from sqlalchemy import and_
+from sqlalchemy import select
 
 from galaxy.model.base import transaction
 from galaxy.tool_shed.util.hg_util import (
@@ -30,7 +30,6 @@ def get_all_dependencies(app, metadata_entry, processed_dependency_links=None):
     encoder = app.security.encode_id
     value_mapper = {"repository_id": encoder, "id": encoder, "user_id": encoder}
     metadata = metadata_entry.to_dict(value_mapper=value_mapper, view="element")
-    db = app.model.session
     returned_dependencies = []
     required_metadata = get_dependencies_for_metadata_revision(app, metadata)
     if required_metadata is None:
@@ -41,7 +40,9 @@ def get_all_dependencies(app, metadata_entry, processed_dependency_links=None):
         if dependency_link in processed_dependency_links:
             continue
         processed_dependency_links.append(dependency_link)
-        repository = db.query(app.model.Repository).get(app.security.decode_id(dependency_dict["repository_id"]))
+        repository = app.model.session.get(
+            app.model.Repository, app.security.decode_id(dependency_dict["repository_id"])
+        )
         dependency_dict["repository"] = repository.to_dict(value_mapper=value_mapper)
         if dependency_metadata.includes_tools:
             dependency_dict["tools"] = dependency_metadata.metadata["tools"]
@@ -123,7 +124,7 @@ def get_latest_downloadable_changeset_revision(app, repository):
 def get_latest_repository_metadata(app, decoded_repository_id, downloadable=False):
     """Get last metadata defined for a specified repository from the database."""
     sa_session = app.model.session
-    repository = sa_session.query(app.model.Repository).get(decoded_repository_id)
+    repository = sa_session.get(app.model.Repository, decoded_repository_id)
     if downloadable:
         changeset_revision = get_latest_downloadable_changeset_revision(app, repository)
     else:
@@ -258,16 +259,10 @@ def repository_metadata_by_changeset_revision(
     # Make sure there are no duplicate records, and return the single unique record for the changeset_revision.
     # Duplicate records were somehow created in the past.  The cause of this issue has been resolved, but we'll
     # leave this method as is for a while longer to ensure all duplicate records are removed.
+
     sa_session = model_mapping.context
-    all_metadata_records = (
-        sa_session.query(model_mapping.RepositoryMetadata)
-        .filter(
-            and_(
-                model_mapping.RepositoryMetadata.table.c.repository_id == id,
-                model_mapping.RepositoryMetadata.table.c.changeset_revision == changeset_revision,
-            )
-        )
-        .all()
+    all_metadata_records = get_metadata_by_changeset(
+        sa_session, id, changeset_revision, model_mapping.RepositoryMetadata
     )
     if len(all_metadata_records) > 1:
         # Delete all records older than the last one updated.
@@ -285,7 +280,7 @@ def repository_metadata_by_changeset_revision(
 def get_repository_metadata_by_id(app, id):
     """Get repository metadata from the database"""
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryMetadata).get(app.security.decode_id(id))
+    return sa_session.get(app.model.RepositoryMetadata, app.security.decode_id(id))
 
 
 def get_repository_metadata_by_repository_id_changeset_revision(app, id, changeset_revision, metadata_only=False):
@@ -348,3 +343,12 @@ def is_malicious(app, id, changeset_revision, **kwd):
     if repository_metadata:
         return repository_metadata.malicious
     return False
+
+
+def get_metadata_by_changeset(session, repository_id, changeset_revision, repository_metadata_model):
+    stmt = (
+        select(repository_metadata_model)
+        .where(repository_metadata_model.repository_id == repository_id)
+        .where(repository_metadata_model.changeset_revision == changeset_revision)
+    )
+    return session.scalars(stmt).all()