mvdbeek 88f3bd0135 Migrate Query.get() calls to Session.get() ...

Query.get() is a legacy SQLAlchemy 1.x construct that emits
LegacyAPIWarning on every invocation. Session.get() is the 2.0
replacement.

Also guard against None primary keys in
tools/parameters/basic.py where the value can legitimately be
absent (previously triggered 'SAWarning: fully NULL primary key
identity cannot load any object').

2026-04-11 13:39:26 +02:00

..

__init__.py

Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util.

2013-02-26 15:52:51 -05:00

basic_util.py

Remove unused code from basic_util.

2022-09-22 11:29:19 -04:00

commit_util.py

Code cleanups from pyupgrade

2025-07-31 11:17:22 +01:00

common_util.py

Remove unused handle_tool_shed_url_protocol

2026-02-25 15:14:47 +01:00

container_util.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

encoding_util.py

Replace toolshed util symlink with package safe re-export.

2019-11-10 21:27:31 -05:00

hg_util.py

Merge branch 'release_24.2' into release_25.0

2025-06-07 18:00:47 +01:00

hgweb_config.py

Make repository creation slightly safer

2024-06-03 15:55:11 +02:00

metadata_util.py

Clean up invalid tool error message handling: produce plain text, not HTML

2026-03-10 18:41:02 +01:00

readme_util.py

Delete unused middleware, decorators, utility_containers, and dead code.

2026-03-17 08:21:24 -04:00

repository_content_util.py

Use CompressedFile.open_tar() to open tar files

2025-01-18 15:03:02 +00:00

repository_util.py

Migrate Query.get() calls to Session.get()

2026-04-11 13:39:26 +02:00

search_util.py

Use model classes from `galaxy.model instead of app.model` object

2025-02-26 12:41:40 +00:00

shed_index.py

Fix last updated time

2025-12-10 18:06:56 +01:00

shed_util_common.py

Delete dead code: is_path_within_*, empty framework dir, stale refs.

2026-03-17 08:21:24 -04:00

tool_dependency_util.py

Refactor tool_shed.util.tool_dependency_util into galaxy.

2019-11-10 23:03:53 -05:00

tool_util.py

Delete unused middleware, decorators, utility_containers, and dead code.

2026-03-17 08:21:24 -04:00

web_util.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

xml_util.py

Move create_element into the only place it is used.

2022-09-14 09:07:43 -04:00