davelopez a66ec96dfe Prevent deletion of user-defined object stores ...

Skips the physical file removal process for datasets stored in user-defined object stores. These storage locations cannot be resolved by the cleanup script, so the database records are updated while the external files remain intact to prevent potential errors or data loss.

2026-06-08 12:41:24 +02:00

..

api

Apply 2026 black style

2026-01-20 10:25:45 +00:00

auth

Apply black formatting.

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

cleanup_datasets

Prevent deletion of user-defined object stores

2026-06-08 12:41:24 +02:00

grt

Apply 2026 black style

2026-01-20 10:25:45 +00:00

loc_files

Apply 2026 black style

2026-01-20 10:25:45 +00:00

metagenomics

Fix UP031 errors

2024-11-24 21:35:23 +00:00

microbes

Fix new ruff 0.11.0 errors

2025-03-15 17:12:02 +00:00

objectstore

Apply black formatting.

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

slideshow

Apply black formatting.

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

taxonomy

…

tool_shed

Fix repo metadata persistence in fix_tool_config_paths.py

2026-03-09 15:09:45 +01:00

tools

Apply 2026 black style

2026-01-20 10:25:45 +00:00

__init__.py

…

apply_tags.py

Code cleanups from pyupgrade

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

bootstrap_test_shed.py

Code cleanups from pyupgrade

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

build_toolbox.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

celery_shell.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

check_and_update_purged_on_duplicated_uuid.py

Add migration that makes dataset uuid unique

2024-09-20 10:40:12 +02:00

check_eggs.py

…

check_model.py

Remove future, autocommit args from session and engine creation

2024-04-05 13:54:39 -04:00

check_python.py

Drop support for Python 3.9

2026-01-19 18:39:16 +00:00

common_startup_functions.sh

activate the conda env before the python venv

2023-07-21 00:58:35 +01:00

common_startup.sh

Drop --frozen-lockfile from prebuilt client install

2026-04-16 17:30:10 -04:00

config_parse.py

Use `load_app_properties()` to load Galaxy config file

2022-04-26 09:48:18 +01:00

config_sample_to_kwalify.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

cwl_conformance_to_test_cases.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

db_dev.py

Add --repair argument to upgrade/downgrade commands on db_dev script

2023-04-26 08:53:35 -04:00

db_dev.sh

Split script into admin and dev

2022-09-28 15:45:00 -04:00

db_shell.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

db.py

Edit db wrapper scripts for consistency, add TS script

2023-02-08 00:33:48 -05:00

drmaa_external_killer.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

drmaa_external_runner.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

dump_library_paths.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

dump_openapi_schema.py

Drop unused code from dump_openapi_schema.py

2024-01-10 17:43:30 +01:00

edam_mapping.py

Create wrapper for requests with default user agent

2024-04-16 17:54:29 +02:00

external_chown_script.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

extract_dataset_part.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

extract_toolbox_sections.py

Apply black formatting.

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

fetch_eggs.py

Apply black formatting.

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

fix_dm_versions.py

Enable flake8-comprehensions ruff rules

2024-03-09 19:11:20 +00:00

galaxy_main.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

galaxy_schemadisp.py

Apply black formatting.

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

galaxy-main

Adjust galaxy-main script so we can import from it for easy app setup

2020-12-22 11:18:00 +01:00

helper.py

Replace file_name property with get_file_name function

2023-11-08 17:17:14 -05:00

maintenance.sh

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00

manage_db.py

Remove legacy ref to sqlalchemy migrate

2024-05-22 14:57:53 -04:00

manage_tool_dependencies.py

Apply black formatting.

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

mypy_config_utils.py

Script for finding unused mypy.ini entries.

2022-09-15 13:20:04 -04:00

pages_identifier_conversion.py

Remove transaction helper from scripts

2025-01-23 11:39:25 -05:00

patch.sh

Add the script I used to create security patches

2016-02-24 16:54:30 -05:00

plugin_staging.py

Apply black formatting.

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

release-diff.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

release.sh

Shellcheck fixes

2025-10-29 18:45:26 +00:00

reorganize_tool_data.py

Run make format

2025-05-09 10:53:43 +02:00

resumable_upload.py

Revert some requests import changes

2024-05-23 15:55:56 +01:00

rst2html.py

Enable flake8-implicit-str-concat ruff rules

2024-04-29 13:37:54 +01:00

run_alembic.py

Add shell wrapper for alembic CLI, improve inline docs

2022-09-30 10:34:58 -04:00

run_alembic.sh

Add shell wrapper for alembic CLI, improve inline docs

2022-09-30 10:34:58 -04:00

runtime_stats.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

secret_decoder_ring.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

set_dataset_sizes.py

Type annotation improvements

2025-02-21 15:46:14 +00:00

set_user_disk_usage.py

Type annotation improvements

2025-02-21 15:46:14 +00:00

summarize_timings.py

Apply black formatting.

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

tests_markdown_compare.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

tests_markdown.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

tests_markdown.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

toolshed_db.py

Edit db wrapper scripts for consistency, add TS script

2023-02-08 00:33:48 -05:00

update_cwl_conformance_tests.sh

Adjust update_cwl_conformance_tests.sh for removed branch

2024-04-05 13:49:31 +02:00

update_shed_config_path.py

Remove transaction helper from scripts

2025-01-23 11:39:25 -05:00

validate_tools.sh

Switch to lxml for xml parsing

2020-05-12 15:00:27 +02:00

validate_tours.sh

Tour validation.

2022-06-02 14:53:55 -04:00