Drop old repositories, group repo functions in one module

galaxyproject · Sep 20, 2023 · cde5fdd · cde5fdd
1 parent 1d8f696
commit cde5fdd
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Showing 9 changed files with 11 additions and 13 deletions.
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
@@ -37,7 +37,7 @@
 )
 from galaxy.model import UserQuotaUsage
 from galaxy.model.base import transaction
-from galaxy.model.repositories.user import (
+from galaxy.model.repositories import (
     get_user_by_email,
     get_user_by_username,
 )

diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
@@ -26,7 +26,6 @@
     web,
 )
 from galaxy.model.base import transaction
-from galaxy.model.repositories.tool_shed_repository import ToolShedRepositoryRepository as tsr_repo
 from galaxy.model.scoped_session import install_model_scoped_session
 from galaxy.model.tool_shed_install import ToolShedRepository
 from galaxy.tool_shed.util import basic_util
@@ -70,7 +69,7 @@ def check_for_updates(
             message += "Unable to retrieve status from the tool shed for the following repositories:\n"
             message += ", ".join(repository_names_not_updated)
     else:
-        repository = tsr_repo(install_model_context).get(repository_id)
+        repository = install_model_context.get(ToolShedRepository, repository_id)
         ok, updated = _check_or_update_tool_shed_status_for_installed_repository(
             tool_shed_registry, install_model_context, repository
         )
@@ -633,7 +632,7 @@ def get_tool_shed_from_clone_url(repository_clone_url):
 def get_tool_shed_repository_by_id(app, repository_id) -> ToolShedRepository:
     """Return a tool shed repository database record defined by the id."""
     # This method is used only in Galaxy, not the tool shed.
-    return tsr_repo(app.install_model.context).get(app.security.decode_id(repository_id))
+    return app.install_model.context.get(ToolShedRepository, app.security.decode_id(repository_id))
 
 
 def get_tool_shed_status_for(tool_shed_registry: Registry, repository: ToolShedRepository):

diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -16,12 +16,12 @@
 )
 from galaxy.managers import histories
 from galaxy.managers.sharable import SlugBuilder
+from galaxy.model import Role
 from galaxy.model.base import transaction
 from galaxy.model.item_attrs import (
     UsesAnnotations,
     UsesItemRatings,
 )
-from galaxy.model.repositories.role import RoleRepository
 from galaxy.structured_app import StructuredApp
 from galaxy.util import (
     listify,
@@ -576,10 +576,9 @@ def permissions(self, trans, payload=None, **kwd):
         else:
             self.history_manager.error_unless_mutable(history)
             permissions = {}
-            _role_repo = RoleRepository(trans.sa_session)
             for action_key, action in trans.app.model.Dataset.permitted_actions.items():
                 in_roles = payload.get(action_key) or []
-                in_roles = [_role_repo.get(trans.security.decode_id(x)) for x in in_roles]
+                in_roles = [trans.sa_session.get(Role, trans.security.decode_id(x)) for x in in_roles]
                 permissions[trans.app.security_agent.get_action(action.action)] = in_roles
             trans.app.security_agent.history_set_default_permissions(history, permissions)
             return {"message": "Default history '%s' dataset permissions have been changed." % history.name}

diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -18,7 +18,7 @@
 )
 from galaxy.exceptions import Conflict
 from galaxy.managers import users
-from galaxy.model.repositories.user import get_user_by_email
+from galaxy.model.repositories import get_user_by_email
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_publicname,

diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py
@@ -10,7 +10,7 @@
 import galaxy.model
 import galaxy.model.tool_shed_install
 import tool_shed.webapp.model as model
-from galaxy.model.repositories.user import get_user_by_username
+from galaxy.model.repositories import get_user_by_username
 
 log = logging.getLogger("test.tool_shed.test_db_util")
 

diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
@@ -25,7 +25,7 @@
     web,
 )
 from galaxy.model.base import transaction
-from galaxy.model.repositories.user import get_user_by_username
+from galaxy.model.repositories import get_user_by_username
 from galaxy.tool_shed.util import dependency_display
 from galaxy.tools.repositories import ValidationContext
 from galaxy.web.form_builder import (

diff --git a/test/integration/test_user_preferences.py b/test/integration/test_user_preferences.py
@@ -8,7 +8,7 @@
     put,
 )
 
-from galaxy.model.repositories.user import get_user_by_email
+from galaxy.model.repositories import get_user_by_email
 from galaxy_test.driver import integration_util
 
 TEST_USER_EMAIL = "[email protected]"

diff --git a/test/integration/test_vault_extra_prefs.py b/test/integration/test_vault_extra_prefs.py
@@ -10,7 +10,7 @@
     put,
 )
 
-from galaxy.model.repositories.user import get_user_by_email
+from galaxy.model.repositories import get_user_by_email
 from galaxy_test.driver import integration_util
 
 TEST_USER_EMAIL = "[email protected]"

diff --git a/test/integration/test_vault_file_source.py b/test/integration/test_vault_file_source.py
@@ -1,7 +1,7 @@
 import os
 import tempfile
 
-from galaxy.model.repositories.user import get_user_by_email
+from galaxy.model.repositories import get_user_by_email
 from galaxy.security.vault import UserVaultWrapper
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator