Fix SA2.0 usage in tool_shed.util.repository_util

lib/tool_shed/util/repository_util.py

@@ -9,9 +9,12 @@
 )
 
 from markupsafe import escape
-from sqlalchemy import false
+from sqlalchemy import (
+    delete,
+    false,
+    select,
+)
 from sqlalchemy.orm import joinedload
-from sqlalchemy.sql import select
 
 import tool_shed.dependencies.repository
 from galaxy import (
@@ -232,7 +235,7 @@ def create_repository(
     if category_ids:
         # Create category associations
         for category_id in category_ids:
-            category = sa_session.query(app.model.Category).get(app.security.decode_id(category_id))
+            category = sa_session.get(app.model.Category, app.security.decode_id(category_id))
             rca = app.model.RepositoryCategoryAssociation(repository, category)
             sa_session.add(rca)
             flush_needed = True
@@ -335,39 +338,20 @@ def get_repo_info_dict(trans: "ProvidesRepositoriesContext", repository_id, chan
 def get_repositories_by_category(
     app: "ToolShedApp", category_id, installable=False, sort_order="asc", sort_key="name", page=None, per_page=25
 ):
-    sa_session = app.model.session
-    query = (
-        sa_session.query(app.model.Repository)
-        .join(
-            app.model.RepositoryCategoryAssociation,
-            app.model.Repository.id == app.model.RepositoryCategoryAssociation.repository_id,
-        )
-        .join(app.model.User, app.model.User.id == app.model.Repository.user_id)
-        .filter(app.model.RepositoryCategoryAssociation.category_id == category_id)
-    )
-    if installable:
-        subquery = select(app.model.RepositoryMetadata.table.c.repository_id)
-        query = query.filter(app.model.Repository.id.in_(subquery))
-    if sort_key == "owner":
-        query = (
-            query.order_by(app.model.User.username)
-            if sort_order == "asc"
-            else query.order_by(app.model.User.username.desc())
-        )
-    else:
-        query = (
-            query.order_by(app.model.Repository.name)
-            if sort_order == "asc"
-            else query.order_by(app.model.Repository.name.desc())
-        )
-    if page is not None:
-        page = int(page)
-        query = query.limit(per_page)
-        if page > 1:
-            query = query.offset((page - 1) * per_page)
-    resultset = query.all()
     repositories = []
-    for repository in resultset:
+    for repository in get_repositories(
+        app.model.session,
+        app.model.Repository,
+        app.model.RepositoryCategoryAssociation,
+        app.model.User,
+        app.model.RepositoryMetadata,
+        category_id,
+        installable,
+        sort_order,
+        sort_key,
+        page,
+        per_page,
+    ):
         default_value_mapper = {
             "id": app.security.encode_id,
             "user_id": app.security.encode_id,
@@ -396,7 +380,7 @@ def handle_role_associations(app: "ToolShedApp", role, repository, **kwd):
     repository_owner = repository.user
     if kwd.get("manage_role_associations_button", False):
         in_users_list = util.listify(kwd.get("in_users", []))
-        in_users = [sa_session.query(app.model.User).get(x) for x in in_users_list]
+        in_users = [sa_session.get(app.model.User, x) for x in in_users_list]
         # Make sure the repository owner is always associated with the repostory's admin role.
         owner_associated = False
         for user in in_users:
@@ -408,7 +392,7 @@ def handle_role_associations(app: "ToolShedApp", role, repository, **kwd):
             message += "The repository owner must always be associated with the repository's administrator role.  "
             status = "error"
         in_groups_list = util.listify(kwd.get("in_groups", []))
-        in_groups = [sa_session.query(app.model.Group).get(x) for x in in_groups_list]
+        in_groups = [sa_session.get(app.model.Group, x) for x in in_groups_list]
         in_repositories = [repository]
         app.security_agent.set_entity_role_associations(
             roles=[role], users=in_users, groups=in_groups, repositories=in_repositories
@@ -424,20 +408,12 @@ def handle_role_associations(app: "ToolShedApp", role, repository, **kwd):
     out_users = []
     in_groups = []
     out_groups = []
-    for user in (
-        sa_session.query(app.model.User)
-        .filter(app.model.User.table.c.deleted == false())
-        .order_by(app.model.User.table.c.email)
-    ):
+    for user in get_current_users(sa_session, app.model.User):
         if user in [x.user for x in role.users]:
             in_users.append((user.id, user.email))
         else:
             out_users.append((user.id, user.email))
-    for group in (
-        sa_session.query(app.model.Group)
-        .filter(app.model.Group.table.c.deleted == false())
-        .order_by(app.model.Group.table.c.name)
-    ):
+    for group in get_current_groups(sa_session, app.model.Group):
         if group in [x.group for x in role.groups]:
             in_groups.append((group.id, group.name))
         else:
@@ -467,7 +443,7 @@ def update_repository(trans: "ProvidesUserContext", id: str, **kwds) -> Tuple[Op
     message = None
     flush_needed = False
     sa_session = app.model.session
-    repository = sa_session.query(app.model.Repository).get(app.security.decode_id(id))
+    repository = sa_session.get(app.model.Repository, app.security.decode_id(id))
     if repository is None:
         return None, "Unknown repository ID"
 
@@ -483,17 +459,14 @@ def update_repository(trans: "ProvidesUserContext", id: str, **kwds) -> Tuple[Op
             flush_needed = True
 
     if "category_ids" in kwds and isinstance(kwds["category_ids"], list):
-        # Get existing category associations
-        category_associations = sa_session.query(app.model.RepositoryCategoryAssociation).filter(
-            app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id)
+        # Remove existing category associations
+        delete_repository_category_associations(
+            sa_session, app.model.RepositoryCategoryAssociation, app.security.decode_id(id)
         )
-        # Remove all of them
-        for rca in category_associations:
-            sa_session.delete(rca)
 
         # Then (re)create category associations
         for category_id in kwds["category_ids"]:
-            category = sa_session.query(app.model.Category).get(app.security.decode_id(category_id))
+            category = sa_session.get(app.model.Category, app.security.decode_id(category_id))
             if category:
                 rca = app.model.RepositoryCategoryAssociation(repository, category)
                 sa_session.add(rca)
@@ -562,6 +535,66 @@ def validate_repository_name(app: "ToolShedApp", name, user):
     return ""
 
 
+def get_repositories(
+    session,
+    repository_model,
+    repository_category_assoc_model,
+    user_model,
+    repository_metadata_model,
+    category_id,
+    installable,
+    sort_order,
+    sort_key,
+    page,
+    per_page,
+):
+    Repository = repository_model
+    RepositoryCategoryAssociation = repository_category_assoc_model
+    User = user_model
+    RepositoryMetadata = repository_metadata_model
+
+    stmt = (
+        select(Repository)
+        .join(
+            RepositoryCategoryAssociation,
+            Repository.id == RepositoryCategoryAssociation.repository_id,
+        )
+        .join(User, User.id == Repository.user_id)
+        .where(RepositoryCategoryAssociation.category_id == category_id)
+    )
+    if installable:
+        stmt1 = select(RepositoryMetadata.repository_id)
+        stmt = stmt.where(Repository.id.in_(stmt1))
+    if sort_key == "owner":
+        stmt = stmt.order_by(User.username)
+    else:
+        stmt = stmt.order_by(Repository.name)
+    if sort_order == "desc":
+        stmt = stmt.desc()
+    if page is not None:
+        page = int(page)
+        stmt = stmt.limit(per_page)
+        if page > 1:
+            stmt = stmt.offset((page - 1) * per_page)
+
+    return session.scalars(stmt)
+
+
+def get_current_users(session, user_model):
+    stmt = select(user_model).where(user_model.deleted == false()).order_by(user_model.email)
+    return session.scalars(stmt)
+
+
+def get_current_groups(session, group_model):
+    stmt = select(group_model).where(group_model.deleted == false()).order_by(group_model.name)
+    return session.scalars(stmt)
+
+
+def delete_repository_category_associations(session, repository_category_assoc_model, repository_id):
+    stmt = delete(repository_category_assoc_model).where(repository_category_assoc_model.repository_id == repository_id)
+    return session.execute(stmt)
+
+
 __all__ = (
     "change_repository_name_in_hgrc_file",
     "create_or_update_tool_shed_repository",