From 852cb9f00bfd4f8a10233d43e35e82fb8f1cda29 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 6 Oct 2023 11:12:25 -0400
Subject: [PATCH 01/22] Fix SA2.0 usage, refactor
 tool_shed.webapp.api.repository_revisions

---
 .../webapp/api/repository_revisions.py        | 44 +++++++++----------
 1 file changed, 21 insertions(+), 23 deletions(-)

diff --git a/lib/tool_shed/webapp/api/repository_revisions.py b/lib/tool_shed/webapp/api/repository_revisions.py
index 1b413827aced..be3b358adedf 100644
--- a/lib/tool_shed/webapp/api/repository_revisions.py
+++ b/lib/tool_shed/webapp/api/repository_revisions.py
@@ -4,7 +4,7 @@
     Dict,
 )
 
-from sqlalchemy import and_
+from sqlalchemy import select
 
 from galaxy import (
     util,
@@ -16,6 +16,7 @@
     metadata_util,
     repository_util,
 )
+from tool_shed.webapp.model import RepositoryMetadata
 from . import BaseShedAPIController
 
 log = logging.getLogger(__name__)
@@ -39,32 +40,15 @@ def index(self, trans, **kwd):
         Displays a collection (list) of repository revisions.
         """
         # Example URL: http://localhost:9009/api/repository_revisions
-        repository_metadata_dicts = []
-        # Build up an anded clause list of filters.
-        clause_list = []
-        # Filter by downloadable if received.
         downloadable = kwd.get("downloadable", None)
-        if downloadable is not None:
-            clause_list.append(trans.model.RepositoryMetadata.table.c.downloadable == util.asbool(downloadable))
-        # Filter by malicious if received.
         malicious = kwd.get("malicious", None)
-        if malicious is not None:
-            clause_list.append(trans.model.RepositoryMetadata.table.c.malicious == util.asbool(malicious))
-        # Filter by missing_test_components if received.
         missing_test_components = kwd.get("missing_test_components", None)
-        if missing_test_components is not None:
-            clause_list.append(
-                trans.model.RepositoryMetadata.table.c.missing_test_components == util.asbool(missing_test_components)
-            )
-        # Filter by includes_tools if received.
         includes_tools = kwd.get("includes_tools", None)
-        if includes_tools is not None:
-            clause_list.append(trans.model.RepositoryMetadata.table.c.includes_tools == util.asbool(includes_tools))
-        for repository_metadata in (
-            trans.sa_session.query(trans.app.model.RepositoryMetadata)
-            .filter(and_(*clause_list))
-            .order_by(trans.app.model.RepositoryMetadata.table.c.repository_id.desc())
-        ):
+        repository_metadata_dicts = []
+        all_repository_metadata = get_repository_metadata(
+            trans.sa_session, downloadable, malicious, missing_test_components, includes_tools
+        )
+        for repository_metadata in all_repository_metadata:
             repository_metadata_dict = repository_metadata.to_dict(
                 view="collection", value_mapper=self.__get_value_mapper(trans)
             )
@@ -222,3 +206,17 @@ def update(self, trans, payload, **kwd):
             controller="repository_revisions", action="show", id=repository_metadata_id
         )
         return repository_metadata_dict
+
+
+def get_repository_metadata(session, downloadable, malicious, missing_test_components, includes_tools):
+    stmt = select(RepositoryMetadata)
+    if downloadable is not None:
+        stmt = stmt.where(RepositoryMetadata.downloadable == util.asbool(downloadable))
+    if malicious is not None:
+        stmt = stmt.where(RepositoryMetadata.malicious == util.asbool(malicious))
+    if missing_test_components is not None:
+        stmt = stmt.where(RepositoryMetadata.missing_test_components == util.asbool(missing_test_components))
+    if includes_tools is not None:
+        stmt = stmt.where(RepositoryMetadata.includes_tools == util.asbool(includes_tools))
+    stmt = stmt.order_by(RepositoryMetadata.repository_id.desc())
+    return session.scalars(stmt)

From 49cafd053e67249c89833f99abeecf68979331bc Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 6 Oct 2023 12:26:08 -0400
Subject: [PATCH 02/22] Fix SA2.0 usage in tool_shed.webapp.api.groups

---
 lib/tool_shed/webapp/api/groups.py | 33 +++++++++++++++++++++---------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/lib/tool_shed/webapp/api/groups.py b/lib/tool_shed/webapp/api/groups.py
index 72329e20b787..14228462e675 100644
--- a/lib/tool_shed/webapp/api/groups.py
+++ b/lib/tool_shed/webapp/api/groups.py
@@ -4,6 +4,8 @@
     Dict,
 )
 
+from sqlalchemy import select
+
 from galaxy import (
     util,
     web,
@@ -24,6 +26,13 @@
 )
 from tool_shed.managers import groups
 from tool_shed.structured_app import ToolShedApp
+from tool_shed.webapp.model import (
+    Category,
+    Repository,
+    RepositoryCategoryAssociation,
+    RepositoryMetadata,
+    User,
+)
 from . import BaseShedAPIController
 
 log = logging.getLogger(__name__)
@@ -109,22 +118,14 @@ def _populate(self, trans, group):
         Turn the given group information from DB into a dict
         and add other characteristics like members and repositories.
         """
-        model = trans.app.model
         group_dict = group.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
         group_members = []
         group_repos = []
         total_downloads = 0
         for uga in group.users:
-            user = trans.sa_session.query(model.User).filter(model.User.table.c.id == uga.user_id).one()
+            user = trans.sa_session.get(User, uga.user_id)
             user_repos_count = 0
-            for repo in (
-                trans.sa_session.query(model.Repository)
-                .filter(model.Repository.table.c.user_id == uga.user_id)
-                .join(model.RepositoryMetadata.table)
-                .join(model.User.table)
-                .outerjoin(model.RepositoryCategoryAssociation.table)
-                .outerjoin(model.Category.table)
-            ):
+            for repo in get_user_repositories(trans.sa_session, uga.user_id):
                 categories = []
                 for rca in repo.categories:
                     cat_dict = dict(name=rca.category.name, id=trans.app.security.encode_id(rca.category.id))
@@ -169,3 +170,15 @@ def _populate(self, trans, group):
         group_dict["total_repos"] = len(group_repos)
         group_dict["total_downloads"] = total_downloads
         return group_dict
+
+
+def get_user_repositories(session, user_id):
+    stmt = (
+        select(Repository)
+        .where(Repository.user_id == user_id)
+        .join(RepositoryMetadata)
+        .join(User)
+        .outerjoin(RepositoryCategoryAssociation)
+        .outerjoin(Category)
+    )
+    return session.scalars(stmt)

From c4e1c9bc89330d3c81f6cb254f11d55b3e4185ee Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 6 Oct 2023 15:49:57 -0400
Subject: [PATCH 03/22] Fix SA2.0 usage in tool_shed.webapp.controllers.user

Also, add case_sensitive parameter to shared function in galaxy user manager
---
 lib/galaxy/managers/users.py             |  7 +++++--
 lib/tool_shed/webapp/controllers/user.py | 24 ++++++++----------------
 2 files changed, 13 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index c1ed9f992f3a..75dfcc7d6bd4 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -849,8 +849,11 @@ 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()
 
 
diff --git a/lib/tool_shed/webapp/controllers/user.py b/lib/tool_shed/webapp/controllers/user.py
index 1091647bc8e1..2740ee9f6c7d 100644
--- a/lib/tool_shed/webapp/controllers/user.py
+++ b/lib/tool_shed/webapp/controllers/user.py
@@ -2,13 +2,13 @@
 import socket
 
 from markupsafe import escape
-from sqlalchemy import func
 
 from galaxy import (
     util,
     web,
 )
 from galaxy.managers.api_keys import ApiKeyManager
+from galaxy.managers.users import get_user_by_email
 from galaxy.model.base import transaction
 from galaxy.security.validate_user_input import (
     validate_email,
@@ -247,18 +247,10 @@ def reset_password(self, trans, email=None, **kwd):
                     "Please check your email account for more instructions.  "
                     "If you do not receive an email shortly, please contact an administrator." % (escape(email))
                 )
-                reset_user = (
-                    trans.sa_session.query(trans.app.model.User)
-                    .filter(trans.app.model.User.table.c.email == email)
-                    .first()
-                )
+                reset_user = get_user_by_email(trans.sa_session, email, trans.app.model.User)
                 if not reset_user:
                     # Perform a case-insensitive check only if the user wasn't found
-                    reset_user = (
-                        trans.sa_session.query(trans.app.model.User)
-                        .filter(func.lower(trans.app.model.User.table.c.email) == func.lower(email))
-                        .first()
-                    )
+                    reset_user = get_user_by_email(trans.sa_session, email, trans.app.model.User, False)
                 if reset_user:
                     prt = trans.app.model.PasswordResetToken(reset_user)
                     trans.sa_session.add(prt)
@@ -291,7 +283,7 @@ def manage_user_info(self, trans, cntrller, **kwd):
         params = util.Params(kwd)
         user_id = params.get("id", None)
         if user_id:
-            user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
+            user = trans.sa_session.get(trans.app.model.User, trans.security.decode_id(user_id))
         else:
             user = trans.user
         if not user:
@@ -336,7 +328,7 @@ def edit_username(self, trans, cntrller, **kwd):
         status = params.get("status", "done")
         user_id = params.get("user_id", None)
         if user_id and is_admin:
-            user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
+            user = trans.sa_session.get(trans.app.model.User, trans.security.decode_id(user_id))
         else:
             user = trans.user
         if user and params.get("change_username_button", False):
@@ -371,7 +363,7 @@ def edit_info(self, trans, cntrller, **kwd):
         status = params.get("status", "done")
         user_id = params.get("user_id", None)
         if user_id and is_admin:
-            user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
+            user = trans.sa_session.get(trans.app.model.User, trans.security.decode_id(user_id))
         elif user_id and (not trans.user or trans.user.id != trans.security.decode_id(user_id)):
             message = "Invalid user id"
             status = "error"
@@ -422,8 +414,8 @@ def edit_info(self, trans, cntrller, **kwd):
             # Edit user information - webapp MUST BE 'galaxy'
             user_type_fd_id = params.get("user_type_fd_id", "none")
             if user_type_fd_id not in ["none"]:
-                user_type_form_definition = trans.sa_session.query(trans.app.model.FormDefinition).get(
-                    trans.security.decode_id(user_type_fd_id)
+                user_type_form_definition = trans.sa_session.get(
+                    trans.app.model.FormDefinition, trans.security.decode_id(user_type_fd_id)
                 )
             elif user.values:
                 user_type_form_definition = user.values.form_definition

From 3238b212805f35aa17906ee51296a08b491e0e4c Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Fri, 6 Oct 2023 16:06:57 -0400
Subject: [PATCH 04/22] Fix SA2.0 usage in
 tool_shed.webapp.controllers.repository

---
 .../webapp/controllers/repository.py          | 43 ++++++++++++-------
 1 file changed, 28 insertions(+), 15 deletions(-)

diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index b3c1725e8507..b9da8337fe55 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -12,9 +12,13 @@
     patch,
 )
 from sqlalchemy import (
-    and_,
     false,
     null,
+    select,
+)
+from toolshed.webapp.model import (
+    Repository,
+    RepositoryMetadata,
 )
 
 import tool_shed.grids.repository_grids as repository_grids
@@ -1498,7 +1502,7 @@ def index(self, trans, **kwd):
         message = escape(kwd.get("message", ""))
         status = kwd.get("status", "done")
         # See if there are any RepositoryMetadata records since menu items require them.
-        repository_metadata = trans.sa_session.query(trans.model.RepositoryMetadata).first()
+        repository_metadata = get_first_repository_metadata(trans.sa_session)
         current_user = trans.user
         # TODO: move the following to some in-memory register so these queries can be done once
         # at startup.  The in-memory register can then be managed during the current session.
@@ -1515,9 +1519,7 @@ def index(self, trans, **kwd):
                 if current_user.active_repositories:
                     can_administer_repositories = True
                 else:
-                    for repository in trans.sa_session.query(trans.model.Repository).filter(
-                        trans.model.Repository.table.c.deleted == false()
-                    ):
+                    for repository in get_current_repositories(trans.sa_session):
                         if trans.app.security_agent.user_can_administer_repository(current_user, repository):
                             can_administer_repositories = True
                             break
@@ -1615,16 +1617,7 @@ def manage_email_alerts(self, trans, **kwd):
         checked = new_repo_alert_checked or (user and user.new_repo_alert)
         new_repo_alert_check_box = CheckboxField("new_repo_alert", value=checked)
         email_alert_repositories = []
-        for repository in (
-            trans.sa_session.query(trans.model.Repository)
-            .filter(
-                and_(
-                    trans.model.Repository.table.c.deleted == false(),
-                    trans.model.Repository.table.c.email_alerts != null(),
-                )
-            )
-            .order_by(trans.model.Repository.table.c.name)
-        ):
+        for repository in get_current_email_alert_repositories(trans.sa_session):
             if user.email in repository.email_alerts:
                 email_alert_repositories.append(repository)
         return trans.fill_template(
@@ -2660,3 +2653,23 @@ def validate_changeset_revision(self, trans, changeset_revision, repository_id):
                         status="error",
                     )
                 )
+
+
+def get_first_repository_metadata(session):
+    stmt = select(RepositoryMetadata).limit(1)
+    return session.select(stmt).first()
+
+
+def get_current_repositories(session):
+    stmt = select(Repository).where(Repository.deleted == false())
+    return session.scalars(stmt)
+
+
+def get_current_email_alert_repositories(session):
+    stmt = (
+        select(Repository)
+        .where(Repository.deleted == false())
+        .where(Repository.email_alerts != null())
+        .order_by(Repository.name)
+    )
+    return session.scalars(stmt)

From f553b757c041862a92d9bb9d275f263687fd6d66 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 10 Oct 2023 15:45:26 -0400
Subject: [PATCH 05/22] Fix SA2.0 usage in
 tool_shed.webapp.controllers.repository

---
 lib/tool_shed/webapp/controllers/repository.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index b9da8337fe55..ce313c9d0821 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -60,6 +60,10 @@
 from tool_shed.util.web_util import escape
 from tool_shed.utility_containers import ToolShedUtilityContainerManager
 from tool_shed.webapp.framework.decorators import require_login
+from tool_shed.webapp.model import (
+    Category,
+    RepositoryCategoryAssociation,
+)
 from tool_shed.webapp.util import ratings_util
 
 log = logging.getLogger(__name__)
@@ -1685,8 +1689,8 @@ def manage_repository(self, trans, id, **kwd):
             if category_ids:
                 # Create category associations
                 for category_id in category_ids:
-                    category = trans.sa_session.query(trans.model.Category).get(trans.security.decode_id(category_id))
-                    rca = trans.app.model.RepositoryCategoryAssociation(repository, category)
+                    category = trans.sa_session.get(Category, trans.security.decode_id(category_id))
+                    rca = RepositoryCategoryAssociation(repository, category)
                     trans.sa_session.add(rca)
                     with transaction(trans.sa_session):
                         trans.sa_session.commit()
@@ -1700,7 +1704,7 @@ def manage_repository(self, trans, id, **kwd):
                     user_ids = util.listify(allow_push)
                     usernames = []
                     for user_id in user_ids:
-                        user = trans.sa_session.query(trans.model.User).get(trans.security.decode_id(user_id))
+                        user = trans.sa_session.get(trans.model.User, trans.security.decode_id(user_id))
                         usernames.append(user.username)
                     usernames = ",".join(usernames)
                 repository.set_allow_push(usernames, remove_auth=remove_auth)
@@ -1731,7 +1735,7 @@ def manage_repository(self, trans, id, **kwd):
         else:
             current_allow_push_list = []
         options = []
-        for user in trans.sa_session.query(trans.model.User):
+        for user in trans.sa_session.scalars(select(trans.model.User)):
             if user.username not in current_allow_push_list:
                 options.append(user)
         for obj in options:

From 6a6e5bf3e6dc2cc2ac28f19f8ad5a757055f9a2c Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 10 Oct 2023 15:56:02 -0400
Subject: [PATCH 06/22] Fix SA2.0 formatting in tool_shed.repository_registry +
 refactor

---
 lib/tool_shed/repository_registry.py | 50 +++++++++++++++++-----------
 1 file changed, 30 insertions(+), 20 deletions(-)

diff --git a/lib/tool_shed/repository_registry.py b/lib/tool_shed/repository_registry.py
index 941bd83285f2..6927b4e68e74 100644
--- a/lib/tool_shed/repository_registry.py
+++ b/lib/tool_shed/repository_registry.py
@@ -4,6 +4,7 @@
     and_,
     false,
     or_,
+    select,
 )
 
 import tool_shed.repository_types.util as rt_util
@@ -12,6 +13,11 @@
     metadata_util,
 )
 from tool_shed.webapp import model
+from tool_shed.webapp.model import (
+    Category,
+    Repository,
+    RepositoryMetadata,
+)
 
 log = logging.getLogger(__name__)
 
@@ -20,7 +26,6 @@ class Registry:
     def __init__(self, app):
         log.debug("Loading the repository registry...")
         self.app = app
-        self.certified_level_one_clause_list = self.get_certified_level_one_clause_list()
         # The following lists contain tuples like ( repository.name, repository.user.username, changeset_revision )
         # where the changeset_revision entry is always the latest installable changeset_revision..
         self.certified_level_one_repository_and_suite_tuples = []
@@ -143,19 +148,15 @@ def edit_category_entry(self, old_name, new_name):
             self.certified_level_one_viewable_suites_by_category[new_name] = 0
 
     def get_certified_level_one_clause_list(self):
-        certified_level_one_tuples = []
         clause_list = []
-        for repository in self.sa_session.query(model.Repository).filter(
-            and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())
-        ):
+        for repository in get_repositories(self.sa_session):
             certified_level_one_tuple = self.get_certified_level_one_tuple(repository)
             latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple
             if is_level_one_certified:
-                certified_level_one_tuples.append(certified_level_one_tuple)
                 clause_list.append(
                     and_(
-                        model.RepositoryMetadata.table.c.repository_id == repository.id,
-                        model.RepositoryMetadata.table.c.changeset_revision == latest_installable_changeset_revision,
+                        RepositoryMetadata.repository_id == repository.id,
+                        RepositoryMetadata.changeset_revision == latest_installable_changeset_revision,
                     )
                 )
         return clause_list
@@ -234,19 +235,11 @@ def load_repository_and_suite_tuple(self, repository):
 
     def load_repository_and_suite_tuples(self):
         # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples.
-        for repository in (
-            self.sa_session.query(model.Repository)
-            .join(model.RepositoryMetadata.table)
-            .filter(or_(*self.certified_level_one_clause_list))
-            .join(model.User.table)
-        ):
+        clauses = self.get_certified_level_one_clause_list()
+        for repository in get_certified_repositories_with_user(self.sa_session, clauses, model.User):
             self.load_certified_level_one_repository_and_suite_tuple(repository)
         # Load self.repository_and_suite_tuples and self.suite_tuples
-        for repository in (
-            self.sa_session.query(model.Repository)
-            .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false()))
-            .join(model.User.table)
-        ):
+        for repository in get_repositories_with_user(self.sa_session, model.User):
             self.load_repository_and_suite_tuple(repository)
 
     def load_viewable_repositories_and_suites_by_category(self):
@@ -259,7 +252,7 @@ def load_viewable_repositories_and_suites_by_category(self):
         self.viewable_suites_by_category = {}
         self.viewable_valid_repositories_and_suites_by_category = {}
         self.viewable_valid_suites_by_category = {}
-        for category in self.sa_session.query(model.Category):
+        for category in self.sa_session.scalars(select(Category)):
             category_name = str(category.name)
             if category not in self.certified_level_one_viewable_repositories_and_suites_by_category:
                 self.certified_level_one_viewable_repositories_and_suites_by_category[category_name] = 0
@@ -393,3 +386,20 @@ def unload_repository_and_suite_tuple(self, repository):
             if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION:
                 if tuple in self.suite_tuples:
                     self.suite_tuples.remove(tuple)
+
+
+def get_repositories(session):
+    stmt = select(Repository).where(Repository.deleted == false()).where(Repository.deprecated == false())
+    return session.scalars(stmt)
+
+
+def get_repositories_with_user(session, user_model):
+    stmt = (
+        select(Repository).where(Repository.deleted == false()).where(Repository.deprecated == false()).join(user_model)
+    )
+    return session.scalars(stmt)
+
+
+def get_certified_repositories_with_user(session, where_clauses, user_model):
+    stmt = select(Repository).join(RepositoryMetadata).where(or_(*where_clauses)).join(user_model)
+    return session.scalars(stmt)

From 70c7f03be9ef02bcdd405820ad68f1772f43a25d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 10:31:35 -0400
Subject: [PATCH 07/22] Fix SA2.0 usage in tool_shed.test.base.twilltestcase

---
 lib/tool_shed/test/base/twilltestcase.py | 31 ++++++++++++------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 8c15af3dc210..a4fbac8b6533 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -31,8 +31,8 @@
 )
 from playwright.sync_api import Page
 from sqlalchemy import (
-    and_,
     false,
+    select,
 )
 
 import galaxy.model.tool_shed_install as galaxy_model
@@ -572,20 +572,7 @@ def get_installed_repositories_by_name_owner(
     def get_installed_repository_for(
         self, owner: Optional[str] = None, name: Optional[str] = None, changeset: Optional[str] = None
     ) -> Optional[Dict[str, Any]]:
-        clause_list = []
-        if name is not None:
-            clause_list.append(galaxy_model.ToolShedRepository.table.c.name == name)
-        if owner is not None:
-            clause_list.append(galaxy_model.ToolShedRepository.table.c.owner == owner)
-        if changeset is not None:
-            clause_list.append(galaxy_model.ToolShedRepository.table.c.changeset_revision == changeset)
-        clause_list.append(galaxy_model.ToolShedRepository.table.c.deleted == false())
-        clause_list.append(galaxy_model.ToolShedRepository.table.c.uninstalled == false())
-
-        query = self._installation_target.install_model.context.query(galaxy_model.ToolShedRepository)
-        if len(clause_list) > 0:
-            query = query.filter(and_(*clause_list))
-        repository = query.one_or_none()
+        repository = get_installed_repository(self._installation_target.install_model.context, name, owner, changeset)
         if repository:
             return repository.to_dict()
         else:
@@ -2096,3 +2083,17 @@ def _get_tool_panel_section_from_repository_metadata(metadata):
     tool_panel_section_metadata = metadata["tool_panel_section"]
     tool_panel_section = tool_panel_section_metadata[tool_guid][0]["name"]
     return tool_panel_section
+
+
+def get_installed_repository(session, name, owner, changeset):
+    ToolShedRepository = galaxy_model.ToolShedRepository
+    stmt = select(ToolShedRepository)
+    if name is not None:
+        stmt = stmt.where(ToolShedRepository.name == name)
+    if owner is not None:
+        stmt = stmt.where(ToolShedRepository.owner == owner)
+    if changeset is not None:
+        stmt = stmt.wehre(ToolShedRepository.changeset_revision == changeset)
+    stmt = stmt.where(ToolShedRepository.deleted == false())
+    stmt = stmt.where(ToolShedRepository.uninstalled == false())
+    return session.scalars(stmt).one_or_none()

From a5110bcf1d5d64b077fa87d49d67b1f6da5fdc00 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 10:53:15 -0400
Subject: [PATCH 08/22] Drop unused functions from
 tool_shed.test.base.test_db_util

---
 lib/tool_shed/test/base/test_db_util.py | 51 -------------------------
 1 file changed, 51 deletions(-)

diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py
index 9081a007a097..840d7759b3d8 100644
--- a/lib/tool_shed/test/base/test_db_util.py
+++ b/lib/tool_shed/test/base/test_db_util.py
@@ -30,17 +30,6 @@ def install_session():
     return install_session
 
 
-def delete_obj(obj):
-    sa_session().delete(obj)
-    sa_session().flush()
-
-
-def delete_user_roles(user):
-    for ura in user.roles:
-        sa_session().delete(ura)
-    sa_session().flush()
-
-
 def flush(obj):
     sa_session().add(obj)
     sa_session().flush()
@@ -67,21 +56,6 @@ def get_all_installed_repositories(session=None) -> List[galaxy.model.tool_shed_
     )
 
 
-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,
-            )
-        )
-        .first()
-    )
-
-
 def get_installed_repository_by_id(repository_id):
     return (
         install_session()
@@ -131,21 +105,6 @@ def get_repository_by_id(repository_id):
     return sa_session().query(model.Repository).filter(model.Repository.table.c.id == repository_id).first()
 
 
-def get_repository_downloadable_revisions(repository_id):
-    revisions = (
-        sa_session()
-        .query(model.RepositoryMetadata)
-        .filter(
-            and_(
-                model.RepositoryMetadata.table.c.repository_id == repository_id,
-                model.RepositoryMetadata.table.c.downloadable == true(),
-            )
-        )
-        .all()
-    )
-    return revisions
-
-
 def get_repository_metadata_for_changeset_revision(
     repository_id: int, changeset_revision: Optional[str]
 ) -> model.RepositoryMetadata:
@@ -163,20 +122,10 @@ def get_repository_metadata_for_changeset_revision(
     return repository_metadata
 
 
-def get_role_by_name(role_name):
-    return sa_session().query(model.Role).filter(model.Role.table.c.name == role_name).first()
-
-
 def get_user(email):
     return sa_session().query(model.User).filter(model.User.table.c.email == email).first()
 
 
-def mark_obj_deleted(obj):
-    obj.deleted = True
-    sa_session().add(obj)
-    sa_session().flush()
-
-
 def refresh(obj):
     sa_session().refresh(obj)
 

From 5a70f2f69005b7ef4e190152c469a187b9d64a1c Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 12:40:23 -0400
Subject: [PATCH 09/22] Fix SA2.0 usage in tool_shed.test.base.test_db_util;
 refactor

---
 lib/tool_shed/test/base/test_db_util.py  | 121 ++++++++---------------
 lib/tool_shed/test/base/twilltestcase.py |   4 +-
 2 files changed, 44 insertions(+), 81 deletions(-)

diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py
index 840d7759b3d8..03b1bbcc7550 100644
--- a/lib/tool_shed/test/base/test_db_util.py
+++ b/lib/tool_shed/test/base/test_db_util.py
@@ -1,19 +1,18 @@
 import logging
-from typing import (
-    List,
-    Optional,
-)
+from typing import List
 
 from sqlalchemy import (
-    and_,
     false,
-    true,
+    select,
 )
 
 import galaxy.model
 import galaxy.model.tool_shed_install
 import tool_shed.webapp.model as model
-from galaxy.managers.users import get_user_by_username
+from galaxy.managers.users import (
+    get_user_by_email,
+    get_user_by_username,
+)
 
 log = logging.getLogger("test.tool_shed.test_db_util")
 
@@ -36,47 +35,38 @@ def flush(obj):
 
 
 def get_all_repositories():
-    return sa_session().query(model.Repository).all()
+    return sa_session().scalars(select(model.Repository)).all()
 
 
 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,
-            )
-        )
-        .all()
+    ToolShedRepository = galaxy.model.tool_shed_install.ToolShedRepository
+    stmt = (
+        select(ToolShedRepository)
+        .where(ToolShedRepository.deleted == false())
+        .where(ToolShedRepository.uninstalled == false())
+        .where(ToolShedRepository.status == ToolShedRepository.installation_status.INSTALLED)
     )
+    return session.scalars(stmt).all()
 
 
 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()
-    )
+    return install_session().get(galaxy.model.tool_shed_install.ToolShedRepository, repository_id)
 
 
 def get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False, session=None):
     if session is None:
         session = install_session()
-    query = 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,
-        )
+    ToolShedRepository = galaxy.model.tool_shed_install.ToolShedRepository
+    stmt = (
+        select(ToolShedRepository)
+        .where(ToolShedRepository.name == repository_name)
+        .where(ToolShedRepository.owner == owner)
     )
     if return_multiple:
-        return query.all()
-    return query.first()
+        return session.scalars(stmt).all()
+    return session.scalars(stmt.limit(1)).first()
 
 
 def get_role(user, role_name):
@@ -87,43 +77,21 @@ def get_role(user, role_name):
 
 
 def get_repository_role_association(repository_id, role_id):
-    rra = (
-        sa_session()
-        .query(model.RepositoryRoleAssociation)
-        .filter(
-            and_(
-                model.RepositoryRoleAssociation.table.c.role_id == role_id,
-                model.RepositoryRoleAssociation.table.c.repository_id == repository_id,
-            )
-        )
-        .first()
+    stmt = (
+        select(model.RepositoryRoleAssociation)
+        .where(model.RepositoryRoleAssociation.role_id == role_id)
+        .where(model.RepositoryRoleAssociation.repository_id == repository_id)
+        .limit(1)
     )
-    return rra
+    return sa_session().scalars(stmt).first()
 
 
 def get_repository_by_id(repository_id):
-    return sa_session().query(model.Repository).filter(model.Repository.table.c.id == repository_id).first()
-
-
-def get_repository_metadata_for_changeset_revision(
-    repository_id: int, changeset_revision: Optional[str]
-) -> model.RepositoryMetadata:
-    repository_metadata = (
-        sa_session()
-        .query(model.RepositoryMetadata)
-        .filter(
-            and_(
-                model.RepositoryMetadata.table.c.repository_id == repository_id,
-                model.RepositoryMetadata.table.c.changeset_revision == changeset_revision,
-            )
-        )
-        .first()
-    )
-    return repository_metadata
+    return sa_session().get(model.Repository, repository_id)
 
 
 def get_user(email):
-    return sa_session().query(model.User).filter(model.User.table.c.email == email).first()
+    return get_user_by_email(sa_session(), email, model.User)
 
 
 def refresh(obj):
@@ -136,25 +104,20 @@ def ga_refresh(obj):
 
 def get_repository_by_name_and_owner(name, owner_username, return_multiple=False):
     owner = get_user_by_username(sa_session(), owner_username, model.User)
-    repository = (
-        sa_session()
-        .query(model.Repository)
-        .filter(and_(model.Repository.table.c.name == name, model.Repository.table.c.user_id == owner.id))
-        .first()
+    stmt = (
+        select(model.Repository)
+        .where(model.Repository.name == name)
+        .where(model.Repository.user_id == owner.id)
+        .limit(1)
     )
-    return repository
+    return sa_session().scalars(stmt).first()
 
 
 def get_repository_metadata_by_repository_id_changeset_revision(repository_id, changeset_revision):
-    repository_metadata = (
-        sa_session()
-        .query(model.RepositoryMetadata)
-        .filter(
-            and_(
-                model.RepositoryMetadata.table.c.repository_id == repository_id,
-                model.RepositoryMetadata.table.c.changeset_revision == changeset_revision,
-            )
-        )
-        .first()
+    stmt = (
+        select(model.RepositoryMetadata)
+        .where(model.RepositoryMetadata.repository_id == repository_id)
+        .where(model.RepositoryMetadata.changeset_revision == changeset_revision)
+        .limit(1)
     )
-    return repository_metadata
+    return sa_session().scalars(stmt).first()
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index a4fbac8b6533..2d9b5e25c86f 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -1487,9 +1487,9 @@ def get_repository_metadata_for_db_object(self, repository: DbRepository):
         return [metadata_revision for metadata_revision in repository.metadata_revisions]
 
     def get_repository_metadata_by_changeset_revision(self, repository_id: int, changeset_revision):
-        return test_db_util.get_repository_metadata_for_changeset_revision(
+        return test_db_util.get_repository_metadata_by_repository_id_changeset_revision(
             repository_id, changeset_revision
-        ) or test_db_util.get_repository_metadata_for_changeset_revision(repository_id, None)
+        ) or test_db_util.get_repository_metadata_by_repository_id_changeset_revision(repository_id, None)
 
     def get_repository_metadata_revisions(self, repository: Repository) -> List[str]:
         return [

From 08b5a433e684caef67dd5d1ad64335c888eb3dff Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 12:55:33 -0400
Subject: [PATCH 10/22] Fix SA2.0 usage in tool_shed.managers.categories

---
 lib/tool_shed/managers/categories.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/lib/tool_shed/managers/categories.py b/lib/tool_shed/managers/categories.py
index 9176fef9e978..5341c4dea450 100644
--- a/lib/tool_shed/managers/categories.py
+++ b/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)

From ff8f6292bde1ec9f7b7d1a96cc18e36af31cdb28 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 13:00:45 -0400
Subject: [PATCH 11/22] Fix SA2.0 usage in tool_shed.managers.users

---
 lib/tool_shed/managers/users.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/lib/tool_shed/managers/users.py b/lib/tool_shed/managers/users.py
index 3514c6e76cf8..ef1ca01ff6f5 100644
--- a/lib/tool_shed/managers/users.py
+++ b/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)

From 77df9c9a73e6efd5233ec881a555855e913b3aaf Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 13:24:44 -0400
Subject: [PATCH 12/22] Fix SA2.0 usage in tool_shed.managers.repositories

---
 lib/tool_shed/managers/repositories.py | 71 ++++++++++----------------
 1 file changed, 28 insertions(+), 43 deletions(-)

diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index 805f716164c5..596aca642b0e 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/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()

From 4db5e3156300d6158987fd699d01fcf57746ad52 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 13:42:02 -0400
Subject: [PATCH 13/22] Fix SA2.0 usage in tool_shed.managers.groups

---
 lib/tool_shed/managers/groups.py | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/lib/tool_shed/managers/groups.py b/lib/tool_shed/managers/groups.py
index 50f5e06222f5..8ade7cb76c92 100644
--- a/lib/tool_shed/managers/groups.py
+++ b/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()

From a5a7d0675dd669470ec6ebf115da807ebe61f9cb Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 14:46:04 -0400
Subject: [PATCH 14/22] Fix SA2.0 usage in tool_shed.util.metadata_util

---
 lib/tool_shed/util/metadata_util.py | 32 ++++++++++++++++-------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
index c41b62b7a7c0..0ca15a8aa919 100644
--- a/lib/tool_shed/util/metadata_util.py
+++ b/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()

From 1711e96dacf02724ae7d7f73d8cbc02201e88477 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 17:14:44 -0400
Subject: [PATCH 15/22] Fix SA2.0 usage in tool_shed.util.shed_util_common

---
 lib/tool_shed/util/shed_util_common.py | 44 ++++++++++++--------------
 1 file changed, 21 insertions(+), 23 deletions(-)

diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 548f8ede40e4..3f107c652ab3 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -5,10 +5,10 @@
 import string
 from typing import TYPE_CHECKING
 
-import sqlalchemy.orm.exc
 from sqlalchemy import (
-    and_,
     false,
+    func,
+    select,
     true,
 )
 
@@ -89,46 +89,41 @@
 
 
 def count_repositories_in_category(app: "ToolShedApp", category_id: str) -> int:
-    sa_session = app.model.session
-    return (
-        sa_session.query(app.model.RepositoryCategoryAssociation)
-        .filter(app.model.RepositoryCategoryAssociation.table.c.category_id == app.security.decode_id(category_id))
-        .count()
+    stmt = (
+        select(func.count())
+        .select_from(app.model.RepositoryCategoryAssociation)
+        .where(app.model.RepositoryCategoryAssociation.category_id == app.security.decode_id(category_id))
     )
+    return app.model.session.scalar(stmt)
 
 
 def get_categories(app: "ToolShedApp"):
     """Get all categories from the database."""
     sa_session = app.model.session
-    return (
-        sa_session.query(app.model.Category)
-        .filter(app.model.Category.table.c.deleted == false())
-        .order_by(app.model.Category.table.c.name)
-        .all()
-    )
+    stmt = select(app.model.Category).where(app.model.Category.deleted == false()).order_by(app.model.Category.name)
+    return sa_session.scalars(stmt).all()
 
 
 def get_category(app: "ToolShedApp", id: str):
     """Get a category from the database."""
     sa_session = app.model.session
-    return sa_session.query(app.model.Category).get(app.security.decode_id(id))
+    return sa_session.get(app.model.Category, app.security.decode_id(id))
 
 
 def get_category_by_name(app: "ToolShedApp", name: str):
     """Get a category from the database via name."""
     sa_session = app.model.session
-    try:
-        return sa_session.query(app.model.Category).filter_by(name=name).one()
-    except sqlalchemy.orm.exc.NoResultFound:
-        return None
+    stmt = select(app.model.Category).filter_by(name=name).limit(1)
+    return sa_session.scalars(stmt).first()
 
 
 def get_repository_categories(app, id):
     """Get categories of a repository on the tool shed side from the database via id"""
     sa_session = app.model.session
-    return sa_session.query(app.model.RepositoryCategoryAssociation).filter(
-        app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id(id)
+    stmt = select(app.model.RepositoryCategoryAssociation).where(
+        app.model.RepositoryCategoryAssociation.repository_id == app.security.decode_id(id)
     )
+    return sa_session.scalars(stmt).all()
 
 
 def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
@@ -336,9 +331,7 @@ def handle_email_alerts(app, host, repository, content_alert_str="", new_repo_al
             subject = f"Galaxy tool shed alert for new repository named {str(repository.name)}"
             subject = subject[:80]
             email_alerts = []
-            for user in sa_session.query(app.model.User).filter(
-                and_(app.model.User.table.c.deleted == false(), app.model.User.table.c.new_repo_alert == true())
-            ):
+            for user in get_users_with_repo_alert(sa_session.query, app.model.User):
                 if admin_only:
                     if user.email in admin_users:
                         email_alerts.append(user.email)
@@ -468,3 +461,8 @@ def tool_shed_is_this_tool_shed(toolshed_base_url, trans=None):
     "set_image_paths",
     "tool_shed_is_this_tool_shed",
 )
+
+
+def get_users_with_repo_alert(session, user_model):
+    stmt = select(user_model).where(user_model.deleted == false()).where(user_model.new_repo_alert == true())
+    return session.scalars(stmt)

From d4a0cce03499d6486de1d48f0ae41ee2f2a6e4de Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 17:25:47 -0400
Subject: [PATCH 16/22] Fix SA2.0 usage in tool_shed.util.shed_index

---
 lib/tool_shed/util/shed_index.py | 44 +++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 15 deletions(-)

diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index 4035a8c5c5c3..bd823b6cb094 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -5,6 +5,10 @@
     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)

From b064064387918d2d5ac1426ece3ae6f07e40e8e2 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 17:30:46 -0400
Subject: [PATCH 17/22] Fix SA2.0 usage in tool_shed.util.search_util

---
 lib/tool_shed/util/search_util.py | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/lib/tool_shed/util/search_util.py b/lib/tool_shed/util/search_util.py
index 243d16a809c8..02e65c3f8288 100644
--- a/lib/tool_shed/util/search_util.py
+++ b/lib/tool_shed/util/search_util.py
@@ -1,8 +1,8 @@
 import logging
 
 from sqlalchemy import (
-    and_,
     false,
+    select,
     true,
 )
 
@@ -105,16 +105,7 @@ def search_repository_metadata(app, exact_matches_checked, tool_ids="", tool_nam
     match_tuples = []
     ok = True
     if tool_ids or tool_names or tool_versions:
-        for repository_metadata in (
-            sa_session.query(app.model.RepositoryMetadata)
-            .filter(app.model.RepositoryMetadata.table.c.includes_tools == true())
-            .join(app.model.Repository)
-            .filter(
-                and_(
-                    app.model.Repository.table.c.deleted == false(), app.model.Repository.table.c.deprecated == false()
-                )
-            )
-        ):
+        for repository_metadata in get_metadata(sa_session, app.model.RepositoryMetadata, app.model.Repository):
             metadata = repository_metadata.metadata
             if metadata:
                 tools = metadata.get("tools", [])
@@ -221,3 +212,14 @@ def search_repository_metadata(app, exact_matches_checked, tool_ids="", tool_nam
                         else:
                             ok = False
     return ok, match_tuples
+
+
+def get_metadata(session, repository_metadata_model, repository_model):
+    stmt = (
+        select(repository_metadata_model)
+        .where(repository_metadata_model.includes_tools == true())
+        .join(repository_model)
+        .where(repository_model.deleted == false())
+        .where(repository_model.deprecated == false())
+    )
+    return session.scalars(stmt)

From 43500cf6564cc75e5167f7528f0db7c6254f79a5 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 11 Oct 2023 17:33:24 -0400
Subject: [PATCH 18/22] Fix SA2.0 usage in tool_shed.util.commit_util

---
 lib/tool_shed/util/commit_util.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py
index e3e3148343c1..ab3864f8e98d 100644
--- a/lib/tool_shed/util/commit_util.py
+++ b/lib/tool_shed/util/commit_util.py
@@ -14,6 +14,7 @@
     Union,
 )
 
+from sqlalchemy import select
 from sqlalchemy.sql.expression import null
 
 import tool_shed.repository_types.util as rt_util
@@ -25,10 +26,10 @@
     hg_util,
     shed_util_common as suc,
 )
+from tool_shed.webapp.model import Repository
 
 if TYPE_CHECKING:
     from tool_shed.structured_app import ToolShedApp
-    from tool_shed.webapp.model import Repository
 
 log = logging.getLogger(__name__)
 
@@ -99,9 +100,7 @@ def check_file_contents_for_email_alerts(app: "ToolShedApp"):
     """
     sa_session = app.model.session
     admin_users = app.config.get("admin_users", "").split(",")
-    for repository in sa_session.query(app.model.Repository).filter(
-        app.model.Repository.table.c.email_alerts != null()
-    ):
+    for repository in get_repositories_with_alerts(sa_session, app.model.Repository):
         email_alerts = json.loads(repository.email_alerts)
         for user_email in email_alerts:
             if user_email in admin_users:
@@ -266,3 +265,8 @@ def uncompress(repository, uploaded_file_name, uploaded_file_filename, isgzip=Fa
     if isbz2:
         handle_bz2(repository, uploaded_file_name)
         return uploaded_file_filename.rstrip(".bz2")
+
+
+def get_repositories_with_alerts(session, repository_model):
+    stmt = select(repository_model).where(repository_model.email_alerts != null())
+    return session.scalars(stmt)

From bf919c049caeb8c78d0de0c94ea3b066b7849c2d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 12 Oct 2023 13:12:23 -0400
Subject: [PATCH 19/22] Fix SA2.0 usage in tool_shed.util.repository_util

---
 lib/tool_shed/util/repository_util.py | 143 ++++++++++++++++----------
 1 file changed, 88 insertions(+), 55 deletions(-)

diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 2f242a5d66f0..1cc1449bc40b 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/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",

From 68831ddcfc661ca13ce7b26cc7383589f185c65a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 12 Oct 2023 14:51:36 -0400
Subject: [PATCH 20/22] Fix SA2.0 usage in tool_shed.metadata, refactor

---
 .../metadata/repository_metadata_manager.py   | 109 +++++++++---------
 lib/tool_shed/webapp/api/repositories.py      |   5 +-
 2 files changed, 54 insertions(+), 60 deletions(-)

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 9ec1b29271b2..24b6e4bf46c3 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -8,9 +8,8 @@
 )
 
 from sqlalchemy import (
-    and_,
     false,
-    or_,
+    select,
 )
 
 from galaxy import util
@@ -150,11 +149,7 @@ def handle_repository_elem(self, repository_elem, only_if_compiling_contained_td
 
         if suc.tool_shed_is_this_tool_shed(toolshed, trans=self.trans):
             try:
-                user = (
-                    self.sa_session.query(self.app.model.User)
-                    .filter(self.app.model.User.table.c.username == owner)
-                    .one()
-                )
+                user = get_user_by_username(self.sa_session, owner, self.app.model.User)
             except Exception:
                 error_message = (
                     f"Ignoring repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, "
@@ -164,16 +159,7 @@ 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(
-                        and_(
-                            self.app.model.Repository.table.c.name == name,
-                            self.app.model.Repository.table.c.user_id == user.id,
-                        )
-                    )
-                    .one()
-                )
+                repository = get_repository(self.sa_session, self.app.model.Repository, name, user.id)
             except Exception:
                 error_message = f"Ignoring repository dependency definition for tool shed {toolshed},"
                 error_message += f"name {name}, owner {owner}, "
@@ -288,8 +274,7 @@ def build_repository_ids_select_field(
     ):
         """Generate the current list of repositories for resetting metadata."""
         repositories_select_field = SelectField(name=name, multiple=multiple, display=display)
-        query = self.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=True)
-        for repository in query:
+        for repository in self.get_repositories_for_setting_metadata(my_writable=my_writable, order=True):
             owner = str(repository.user.username)
             option_label = f"{str(repository.name)} ({owner})"
             option_value = f"{self.app.security.encode_id(repository.id)}"
@@ -303,13 +288,8 @@ def _clean_repository_metadata(self, changeset_revisions):
         # records with the same changeset revision value - no idea how this happens. We'll
         # assume we can delete the older records, so we'll order by update_time descending and
         # delete records that have the same changeset_revision we come across later.
-        for repository_metadata in (
-            self.sa_session.query(self.app.model.RepositoryMetadata)
-            .filter(self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id)
-            .order_by(
-                self.app.model.RepositoryMetadata.table.c.changeset_revision,
-                self.app.model.RepositoryMetadata.table.c.update_time.desc(),
-            )
+        for repository_metadata in get_repository_metadata(
+            self.sa_session, self.app.model.RepositoryMetadata, self.repository.id
         ):
             changeset_revision = repository_metadata.changeset_revision
             if changeset_revision not in changeset_revisions:
@@ -600,9 +580,9 @@ def _get_parent_id(self, id: int, old_id, version, guid, changeset_revisions):
             # The tool did not change through all of the changeset revisions.
             return old_id
 
-    def get_query_for_setting_metadata_on_repositories(self, my_writable=False, order=True):
+    def get_repositories_for_setting_metadata(self, my_writable=False, order=True):
         """
-        Return a query containing repositories for resetting metadata.  The order parameter
+        Return a list of repositories for resetting metadata.  The order parameter
         is used for displaying the list of repositories ordered alphabetically for display on
         a page.  When called from the Tool Shed API, order is False.
         """
@@ -611,46 +591,25 @@ def get_query_for_setting_metadata_on_repositories(self, my_writable=False, orde
         # repositories.
         if my_writable:
             username = self.user.username
-            clause_list = []
-            for repository in self.sa_session.query(self.app.model.Repository).filter(
-                self.app.model.Repository.table.c.deleted == false()
-            ):
+            repo_ids = []
+            for repository in get_current_repositories(self.sa_session, self.app.model.Repository):
                 # Always reset metadata on all repositories of types repository_suite_definition and
                 # tool_dependency_definition.
                 if repository.type in [rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION]:
-                    clause_list.append(self.app.model.Repository.table.c.id == repository.id)
+                    repo_ids.append(repository.id)
                 else:
                     allow_push = repository.allow_push()
                     if allow_push:
                         # Include all repositories that are writable by the current user.
                         allow_push_usernames = allow_push.split(",")
                         if username in allow_push_usernames:
-                            clause_list.append(self.app.model.Repository.table.c.id == repository.id)
-            if clause_list:
-                if order:
-                    return (
-                        self.sa_session.query(self.app.model.Repository)
-                        .filter(or_(*clause_list))
-                        .order_by(self.app.model.Repository.table.c.name, self.app.model.Repository.table.c.user_id)
-                    )
-                else:
-                    return self.sa_session.query(self.app.model.Repository).filter(or_(*clause_list))
+                            repo_ids.append(repository.id)
+            if repo_ids:
+                return get_filtered_repositories(self.sa_session, self.app.model.Repository, repo_ids, order)
             else:
-                # Return an empty query.
-                return self.sa_session.query(self.app.model.Repository).filter(
-                    self.app.model.Repository.table.c.id == -1
-                )
+                return []
         else:
-            if order:
-                return (
-                    self.sa_session.query(self.app.model.Repository)
-                    .filter(self.app.model.Repository.table.c.deleted == false())
-                    .order_by(self.app.model.Repository.table.c.name, self.app.model.Repository.table.c.user_id)
-                )
-            else:
-                return self.sa_session.query(self.app.model.Repository).filter(
-                    self.app.model.Repository.table.c.deleted == false()
-                )
+            return get_current_repositories(self.sa_session, self.app.model.Repository, order)
 
     def new_metadata_required_for_utilities(self):
         """
@@ -1107,3 +1066,39 @@ def _get_changeset_revisions_that_contain_tools(app: "ToolShedApp", repo, reposi
                 if metadata.get("tools", None):
                     changeset_revisions_that_contain_tools.append(changeset_revision)
     return changeset_revisions_that_contain_tools
+
+
+def get_user_by_username(session, username, user_model):
+    stmt = select(user_model).where(user_model.username == username)
+    return session.execute(stmt).scalar_one()
+
+
+def get_repository(session, repository_model, name, user_id):
+    stmt = select(repository_model).where(repository_model.name == name).where(repository_model.user_id == user_id)
+    return session.execute(stmt).scalar_one()
+
+
+def get_repository_metadata(session, repository_metadata_model, repository_id):
+    RepositoryMetadata = repository_metadata_model
+    stmt = (
+        select(RepositoryMetadata)
+        .where(RepositoryMetadata.repository_id == repository_id)
+        .order_by(RepositoryMetadata.changeset_revision, RepositoryMetadata.update_time.desc())
+    )
+    return session.scalars(stmt)
+
+
+def get_current_repositories(session, repository_model, order=False):
+    Repository = repository_model
+    stmt = select(Repository).where(Repository.deleted == false())
+    if order:
+        stmt = stmt.order_by(Repository.name, Repository.user_id)
+    return session.scalars(stmt)
+
+
+def get_filtered_repositories(session, repository_model, repo_ids, order):
+    Repository = repository_model
+    stmt = select(Repository).where(Repository.in_(repo_ids))
+    if order:
+        stmt = stmt.order_by(Repository.name, Repository.user_id)
+    return session.scalars(stmt)
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 4499534c0cdf..740f3a995421 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -427,9 +427,8 @@ def handle_repository(trans, repository, results):
             updating_installed_repository=False,
             persist=False,
         )
-        query = rmm.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=False)
         # First reset metadata on all repositories of type repository_dependency_definition.
-        for repository in query:
+        for repository in rmm.get_repositories_for_setting_metadata(my_writable=my_writable, order=False):
             encoded_id = trans.security.encode_id(repository.id)
             if encoded_id in encoded_ids_to_skip:
                 log.debug(
@@ -440,7 +439,7 @@ def handle_repository(trans, repository, results):
             elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
                 results = handle_repository(trans, repository, results)
         # Now reset metadata on all remaining repositories.
-        for repository in query:
+        for repository in rmm.get_repositories_for_setting_metadata(my_writable=my_writable, order=False):
             encoded_id = trans.security.encode_id(repository.id)
             if encoded_id in encoded_ids_to_skip:
                 log.debug(

From b0684fa9ff438caebf3872af66207fa28f1f7eda Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 12 Oct 2023 15:14:59 -0400
Subject: [PATCH 21/22] Import models

---
 .../metadata/repository_metadata_manager.py   | 37 +++++++++----------
 1 file changed, 18 insertions(+), 19 deletions(-)

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 24b6e4bf46c3..4cffd8d8cb19 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -35,7 +35,11 @@
     tool_util,
 )
 from tool_shed.util.metadata_util import repository_metadata_by_changeset_revision
-from tool_shed.webapp.model import Repository
+from tool_shed.webapp.model import (
+    Repository,
+    RepositoryMetadata,
+    User,
+)
 
 log = logging.getLogger(__name__)
 
@@ -149,7 +153,7 @@ def handle_repository_elem(self, repository_elem, only_if_compiling_contained_td
 
         if suc.tool_shed_is_this_tool_shed(toolshed, trans=self.trans):
             try:
-                user = get_user_by_username(self.sa_session, owner, self.app.model.User)
+                user = get_user_by_username(self.sa_session, owner)
             except Exception:
                 error_message = (
                     f"Ignoring repository dependency definition for tool shed {toolshed}, name {name}, owner {owner}, "
@@ -159,7 +163,7 @@ 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 = get_repository(self.sa_session, self.app.model.Repository, name, user.id)
+                repository = get_repository(self.sa_session, name, user.id)
             except Exception:
                 error_message = f"Ignoring repository dependency definition for tool shed {toolshed},"
                 error_message += f"name {name}, owner {owner}, "
@@ -288,9 +292,7 @@ def _clean_repository_metadata(self, changeset_revisions):
         # records with the same changeset revision value - no idea how this happens. We'll
         # assume we can delete the older records, so we'll order by update_time descending and
         # delete records that have the same changeset_revision we come across later.
-        for repository_metadata in get_repository_metadata(
-            self.sa_session, self.app.model.RepositoryMetadata, self.repository.id
-        ):
+        for repository_metadata in get_repository_metadata(self.sa_session, self.repository.id):
             changeset_revision = repository_metadata.changeset_revision
             if changeset_revision not in changeset_revisions:
                 self.sa_session.delete(repository_metadata)
@@ -592,7 +594,7 @@ def get_repositories_for_setting_metadata(self, my_writable=False, order=True):
         if my_writable:
             username = self.user.username
             repo_ids = []
-            for repository in get_current_repositories(self.sa_session, self.app.model.Repository):
+            for repository in get_current_repositories(self.sa_session):
                 # Always reset metadata on all repositories of types repository_suite_definition and
                 # tool_dependency_definition.
                 if repository.type in [rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION]:
@@ -605,11 +607,11 @@ def get_repositories_for_setting_metadata(self, my_writable=False, order=True):
                         if username in allow_push_usernames:
                             repo_ids.append(repository.id)
             if repo_ids:
-                return get_filtered_repositories(self.sa_session, self.app.model.Repository, repo_ids, order)
+                return get_filtered_repositories(self.sa_session, repo_ids, order)
             else:
                 return []
         else:
-            return get_current_repositories(self.sa_session, self.app.model.Repository, order)
+            return get_current_repositories(self.sa_session, order)
 
     def new_metadata_required_for_utilities(self):
         """
@@ -1068,18 +1070,17 @@ def _get_changeset_revisions_that_contain_tools(app: "ToolShedApp", repo, reposi
     return changeset_revisions_that_contain_tools
 
 
-def get_user_by_username(session, username, user_model):
-    stmt = select(user_model).where(user_model.username == username)
+def get_user_by_username(session, username):
+    stmt = select(User).where(User.username == username)
     return session.execute(stmt).scalar_one()
 
 
-def get_repository(session, repository_model, name, user_id):
-    stmt = select(repository_model).where(repository_model.name == name).where(repository_model.user_id == user_id)
+def get_repository(session, name, user_id):
+    stmt = select(Repository).where(Repository.name == name).where(Repository.user_id == user_id)
     return session.execute(stmt).scalar_one()
 
 
-def get_repository_metadata(session, repository_metadata_model, repository_id):
-    RepositoryMetadata = repository_metadata_model
+def get_repository_metadata(session, repository_id):
     stmt = (
         select(RepositoryMetadata)
         .where(RepositoryMetadata.repository_id == repository_id)
@@ -1088,16 +1089,14 @@ def get_repository_metadata(session, repository_metadata_model, repository_id):
     return session.scalars(stmt)
 
 
-def get_current_repositories(session, repository_model, order=False):
-    Repository = repository_model
+def get_current_repositories(session, order=False):
     stmt = select(Repository).where(Repository.deleted == false())
     if order:
         stmt = stmt.order_by(Repository.name, Repository.user_id)
     return session.scalars(stmt)
 
 
-def get_filtered_repositories(session, repository_model, repo_ids, order):
-    Repository = repository_model
+def get_filtered_repositories(session, repo_ids, order):
     stmt = select(Repository).where(Repository.in_(repo_ids))
     if order:
         stmt = stmt.order_by(Repository.name, Repository.user_id)

From 3c52785dabee077f23cc27eec860ed54a6009778 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 12 Oct 2023 15:30:23 -0400
Subject: [PATCH 22/22] Ignore typing error (see note)

RepositoryMetadata is mapped imperatively, so until the mapper creates
attributes based on Column definitions, the attribute does not exist on
the class. This class is mapped imperatively due to the complications
triggered by mapping the "metadata" attribute.
---
 lib/tool_shed/metadata/repository_metadata_manager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 4cffd8d8cb19..03c5562d5c02 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -1084,7 +1084,7 @@ def get_repository_metadata(session, repository_id):
     stmt = (
         select(RepositoryMetadata)
         .where(RepositoryMetadata.repository_id == repository_id)
-        .order_by(RepositoryMetadata.changeset_revision, RepositoryMetadata.update_time.desc())
+        .order_by(RepositoryMetadata.changeset_revision, RepositoryMetadata.update_time.desc())  # type: ignore[attr-defined]  # mapped attribute
     )
     return session.scalars(stmt)