Start migrating sqlalchemy in tool shed 2.0 to newer SA.

jmchilton · Sep 27, 2023 · 45f2126 · 45f2126
1 parent 439daea
commit 45f2126
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Showing 3 changed files with 56 additions and 49 deletions.
diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
@@ -19,6 +19,7 @@
 from sqlalchemy import (
     and_,
     false,
+    select,
 )
 
 from galaxy import web
@@ -204,14 +205,14 @@ def guid_to_repository(app: ToolShedApp, tool_id: str) -> "Repository":
     shed, _, owner, name, rest = tool_id.split("/", 5)
     clause_list = [
         and_(
-            app.model.Repository.table.c.deprecated == false(),
-            app.model.Repository.table.c.deleted == false(),
-            app.model.Repository.table.c.name == name,
-            app.model.User.table.c.username == owner,
-            app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+            app.model.Repository.deprecated == false(),
+            app.model.Repository.deleted == false(),
+            app.model.Repository.name == name,
+            app.model.User.username == owner,
+            app.model.Repository.user_id == app.model.User.id,
         )
     ]
-    repository = app.model.context.query(app.model.Repository).filter(*clause_list).first()
+    repository = app.model.context.scalars(select(app.model.Repository).where(*clause_list).limit(1)).first()
     return repository
 
 
@@ -224,14 +225,16 @@ def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
         name = repository.name
         clause_list = [
             and_(
-                app.model.Repository.table.c.deprecated == false(),
-                app.model.Repository.table.c.deleted == false(),
-                app.model.Repository.table.c.name == name,
-                app.model.User.table.c.username == owner,
-                app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+                app.model.Repository.deprecated == false(),
+                app.model.Repository.deleted == false(),
+                app.model.Repository.name == name,
+                app.model.User.username == owner,
+                app.model.Repository.user_id == app.model.User.id,
             )
         ]
-        repository = app.model.context.current.sa_session.query(app.model.Repository).filter(*clause_list).first()
+        repository = app.model.context.current.sa_session.scalars(
+            select(app.model.Repository).where(*clause_list).limit(1)
+        ).first()
         if not repository:
             log.warning(f"Repository {owner}/{name} does not exist, skipping")
             continue
@@ -275,22 +278,22 @@ def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
 def index_repositories(app: ToolShedApp, name: Optional[str], owner: Optional[str], deleted: bool):
     clause_list = [
         and_(
-            app.model.Repository.table.c.deprecated == false(),
-            app.model.Repository.table.c.deleted == deleted,
+            app.model.Repository.deprecated == false(),
+            app.model.Repository.deleted == deleted,
         )
     ]
     if owner is not None:
         clause_list.append(
             and_(
-                app.model.User.table.c.username == owner,
-                app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+                app.model.User.username == owner,
+                app.model.Repository.user_id == app.model.User.id,
             )
         )
     if name is not None:
-        clause_list.append(app.model.Repository.table.c.name == name)
+        clause_list.append(app.model.Repository.name == name)
     repositories = []
     for repository in (
-        app.model.context.query(app.model.Repository).filter(*clause_list).order_by(app.model.Repository.table.c.name)
+        app.model.context.query(app.model.Repository).filter(*clause_list).order_by(app.model.Repository.name)
     ):
         repositories.append(repository)
     return repositories

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -11,6 +11,7 @@
     and_,
     false,
     or_,
+    select,
 )
 
 from galaxy import util
@@ -164,16 +165,14 @@ def handle_repository_elem(self, repository_elem, only_if_compiling_contained_td
                 is_valid = False
                 return repository_dependency_tup, is_valid, error_message
             try:
-                repository = (
-                    self.sa_session.query(self.app.model.Repository)
-                    .filter(
+                repository = self.sa_session.execute(
+                    select(self.app.model.Repository).where(
                         and_(
                             self.app.model.Repository.table.c.name == name,
                             self.app.model.Repository.table.c.user_id == user.id,
                         )
                     )
-                    .one()
-                )
+                ).scalar_one()
             except Exception:
                 error_message = f"Ignoring repository dependency definition for tool shed {toolshed},"
                 error_message += f"name {name}, owner {owner}, "

diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py
@@ -8,6 +8,7 @@
     and_,
     false,
     true,
+    select,
 )
 
 import galaxy.model
@@ -53,42 +54,46 @@ def get_all_repositories():
 def get_all_installed_repositories(session=None) -> List[galaxy.model.tool_shed_install.ToolShedRepository]:
     if session is None:
         session = install_session()
-    return list(
-        session.query(galaxy.model.tool_shed_install.ToolShedRepository)
-        .filter(
-            and_(
-                galaxy.model.tool_shed_install.ToolShedRepository.table.c.deleted == false(),
-                galaxy.model.tool_shed_install.ToolShedRepository.table.c.uninstalled == false(),
-                galaxy.model.tool_shed_install.ToolShedRepository.table.c.status
-                == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED,
+    return session.scalars(
+        session.execute(
+            select(galaxy.model.tool_shed_install.ToolShedRepository).where(
+                and_(
+                    galaxy.model.tool_shed_install.ToolShedRepository.deleted == false(),
+                    galaxy.model.tool_shed_install.ToolShedRepository.uninstalled == false(),
+                    galaxy.model.tool_shed_install.ToolShedRepository.status
+                    == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED,
+                )
             )
         )
-        .all()
-    )
+    ).all()
 
 
 def get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision):
-    return (
-        install_session()
-        .query(galaxy.model.tool_shed_install.ToolShedRepository)
-        .filter(
-            and_(
-                galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,
-                galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner,
-                galaxy.model.tool_shed_install.ToolShedRepository.table.c.changeset_revision == changeset_revision,
+    session = install_session()
+    return session.scalars(
+        session.execute(
+            select(galaxy.model.tool_shed_install.ToolShedRepository)
+            .where(
+                and_(
+                    galaxy.model.tool_shed_install.ToolShedRepository.name == repository_name,
+                    galaxy.model.tool_shed_install.ToolShedRepository.owner == owner,
+                    galaxy.model.tool_shed_install.ToolShedRepository.changeset_revision == changeset_revision,
+                )
             )
+            .limit(1)
         )
-        .first()
-    )
+    ).first()
 
 
 def get_installed_repository_by_id(repository_id):
-    return (
-        install_session()
-        .query(galaxy.model.tool_shed_install.ToolShedRepository)
-        .filter(galaxy.model.tool_shed_install.ToolShedRepository.table.c.id == repository_id)
-        .first()
-    )
+    session = install_session()
+    return session.scalars(
+        session.execute(
+            select(galaxy.model.tool_shed_install.ToolShedRepository)
+            .where(galaxy.model.tool_shed_install.ToolShedRepository.id == repository_id)
+            .limit(1)
+        )
+    ).first()
 
 
 def get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False, session=None):