Merge pull request #16833 from jdavcs/dev_ts20_sa20_3

Another batch of SA2.0 edits in TS2.0 (part 3)

lib/galaxy/managers/users.py

@@ -844,8 +844,11 @@ def get_users_by_ids(session: Session, user_ids):
 # the tool_shed app, which has its own User model, which is different from
 # galaxy.model.User. In that case, the tool_shed user model should be passed as
 # the model_class argument.
-def get_user_by_email(session, email: str, model_class=User):
-    stmt = select(model_class).filter(model_class.email == email).limit(1)
+def get_user_by_email(session, email: str, model_class=User, case_sensitive=True):
+    filter_clause = model_class.email == email
+    if not case_sensitive:
+        filter_clause = func.lower(model_class.email) == func.lower(email)
+    stmt = select(model_class).where(filter_clause).limit(1)
     return session.scalars(stmt).first()
 
 

lib/tool_shed/managers/categories.py

@@ -5,6 +5,8 @@
     List,
 )
 
+from sqlalchemy import select
+
 import tool_shed.util.shed_util_common as suc
 from galaxy import (
     exceptions,
@@ -41,14 +43,9 @@ def create(self, trans: ProvidesUserContext, category_request: CreateCategoryReq
             raise exceptions.RequestParameterMissingException('Missing required parameter "name".')
 
     def index_db(self, trans: ProvidesUserContext, deleted: bool) -> List[Category]:
-        category_db_objects: List[Category] = []
         if deleted and not trans.user_is_admin:
             raise exceptions.AdminRequiredException("Only administrators can query deleted categories.")
-        for category in (
-            trans.sa_session.query(Category).filter(Category.table.c.deleted == deleted).order_by(Category.table.c.name)
-        ):
-            category_db_objects.append(category)
-        return category_db_objects
+        return list(get_categories_by_deleted(trans.sa_session, deleted))
 
     def index(self, trans: ProvidesUserContext, deleted: bool) -> List[Dict[str, Any]]:
         category_dicts: List[Dict[str, Any]] = []
@@ -80,3 +77,8 @@ def to_model(self, category: Category) -> CategoryResponse:
 def get_value_mapper(app: ToolShedApp) -> Dict[str, Callable]:
     value_mapper = {"id": app.security.encode_id}
     return value_mapper
+
+
+def get_categories_by_deleted(session, deleted):
+    stmt = select(Category).where(Category.deleted == deleted).order_by(Category.name)
+    return session.scalars(stmt)

lib/tool_shed/managers/groups.py

@@ -5,6 +5,7 @@
 
 from sqlalchemy import (
     false,
+    select,
     true,
 )
 from sqlalchemy.orm.exc import (
@@ -47,13 +48,11 @@ def get(self, trans, decoded_group_id=None, name=None):
         if decoded_group_id is None and name is None:
             raise RequestParameterInvalidException("You must supply either ID or a name of the group.")
 
-        name_query = trans.sa_session.query(trans.app.model.Group).filter(trans.app.model.Group.table.c.name == name)
-        id_query = trans.sa_session.query(trans.app.model.Group).filter(
-            trans.app.model.Group.table.c.id == decoded_group_id
-        )
-
         try:
-            group = id_query.one() if decoded_group_id else name_query.one()
+            if decoded_group_id:
+                group = trans.sa_session.get(trans.app.model.Group, decoded_group_id)
+            else:
+                group = get_group_by_name(trans.sa_session, name, trans.app.model.Group)
         except MultipleResultsFound:
             raise InconsistentDatabase("Multiple groups found with the same identifier.")
         except NoResultFound:
@@ -121,16 +120,21 @@ def list(self, trans, deleted=False):
         :returns: query that will emit all groups
         :rtype:   sqlalchemy query
         """
-        is_admin = trans.user_is_admin
-        query = trans.sa_session.query(trans.app.model.Group)
-        if is_admin:
+        Group = trans.app.model.Group
+        stmt = select(Group)
+        if trans.user_is_admin:
             if deleted is None:
                 #  Flag is not specified, do not filter on it.
                 pass
             elif deleted:
-                query = query.filter(trans.app.model.Group.table.c.deleted == true())
+                stmt = stmt.where(Group.deleted == true())
             else:
-                query = query.filter(trans.app.model.Group.table.c.deleted == false())
+                stmt = stmt.where(Group.deleted == false())
         else:
-            query = query.filter(trans.app.model.Group.table.c.deleted == false())
-        return query
+            stmt = stmt.where(Group.deleted == false())
+        return trans.sa_session.scalars(stmt)
+
+
+def get_group_by_name(session, name, group_model):
+    stmt = select(group_model).where(group_model.name == name)
+    return session.execute(stmt).scalar_one()

lib/tool_shed/managers/repositories.py

@@ -17,8 +17,8 @@
 
 from pydantic import BaseModel
 from sqlalchemy import (
-    and_,
     false,
+    select,
 )
 
 from galaxy import web
@@ -202,17 +202,7 @@ def check_updates(app: ToolShedApp, request: UpdatesRequest) -> Union[str, Dict[
 def guid_to_repository(app: ToolShedApp, tool_id: str) -> "Repository":
     # tool_id = remove_protocol_and_user_from_clone_url(tool_id)
     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,
-        )
-    ]
-    repository = app.model.context.query(app.model.Repository).filter(*clause_list).first()
-    return repository
+    return _get_repository_by_name_and_owner(app.model.context, name, owner, app.model.User)
 
 
 def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
@@ -222,16 +212,7 @@ def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
         repository = guid_to_repository(app, tool_id)
         owner = repository.user.username
         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,
-            )
-        ]
-        repository = app.model.context.current.sa_session.query(app.model.Repository).filter(*clause_list).first()
+        repository = _get_repository_by_name_and_owner(app.model.context.current, name, owner, app.model.User)
         if not repository:
             log.warning(f"Repository {owner}/{name} does not exist, skipping")
             continue
@@ -273,27 +254,7 @@ 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,
-        )
-    ]
-    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,
-            )
-        )
-    if name is not None:
-        clause_list.append(app.model.Repository.table.c.name == name)
-    repositories = []
-    for repository in (
-        app.model.context.query(app.model.Repository).filter(*clause_list).order_by(app.model.Repository.table.c.name)
-    ):
-        repositories.append(repository)
-    return repositories
+    return list(_get_repository_by_name_and_owner_and_deleted(app.model.context, name, owner, deleted, app.model.User))
 
 
 def can_manage_repo(trans: ProvidesUserContext, repository: Repository) -> bool:
@@ -616,3 +577,27 @@ def upload_tar_and_set_metadata(
     else:
         raise InternalServerError(message)
     return message
+
+
+def _get_repository_by_name_and_owner(session, name, owner, user_model):
+    stmt = (
+        select(Repository)
+        .where(Repository.deprecated == false())
+        .where(Repository.deleted == false())
+        .where(Repository.name == name)
+        .where(user_model.username == owner)
+        .where(Repository.user_id == user_model.id)
+        .limit(1)
+    )
+    return session.scalars(stmt).first()
+
+
+def _get_repository_by_name_and_owner_and_deleted(session, name, owner, deleted, user_model):
+    stmt = select(Repository).where(Repository.deprecated == false()).where(Repository.deleted == deleted)
+    if owner is not None:
+        stmt = stmt.where(user_model.username == owner)
+        stmt = stmt.where(Repository.user_id == user_model.id)
+    if name is not None:
+        stmt = stmt.where(Repository.name == name)
+    stmt = stmt.order_by(Repository.name).limit(1)
+    return session.scalars(stmt).first()

lib/tool_shed/managers/users.py

@@ -1,5 +1,7 @@
 from typing import List
 
+from sqlalchemy import select
+
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.model.base import transaction
 from galaxy.security.validate_user_input import (
@@ -18,11 +20,7 @@
 
 def index(app: ToolShedApp, deleted: bool) -> List[ApiUser]:
     users: List[ApiUser] = []
-    for user in (
-        app.model.context.query(app.model.User)
-        .filter(app.model.User.table.c.deleted == deleted)
-        .order_by(app.model.User.table.c.username)
-    ):
+    for user in get_users_by_deleted(app.model.context, app.model.User, deleted):
         users.append(get_api_user(app, user))
     return users
 
@@ -77,3 +75,8 @@ def _validate(trans: ProvidesUserContext, email: str, password: str, confirm: st
         )
     ).rstrip()
     return message
+
+
+def get_users_by_deleted(session, user_model, deleted):
+    stmt = select(user_model).where(user_model.deleted == deleted).order_by(user_model.username)
+    return session.scalars(stmt)