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185 Commits
Author SHA1 Message Date
Ahmed Awan b80f41816c Merge remote-tracking branch 'upstream/release_24.2' into dev 2025-03-31 10:35:43 -05:00
John Davis 1bf72997a0 Handle "%" character in raw SQL 
This statement is prepared for SQLAlchemy but executed via psycopg2 in
the `pgcleanup.py` script. For psycopg2, the "%" character should be replaced
with %% (see docs
https://www.psycopg.org/docs/usage.html#passing-parameters-to-sql-queries).
SQLAlchemy already takes care of it automatically.
 2025-03-28 15:08:21 +00:00
Nicola Soranzo 5fe5b53bf3 Fix new ruff 0.11.0 errors 
Also:
- Add and fix type annotations
- Fix call of `object_store_allows_id_selection()` method
 2025-03-15 17:12:02 +00:00
Nicola Soranzo 9477c7773e Use model classes from `galaxy.model instead of app.model` object 
for proper type annotation of query results.

Also:
- Drop unused code from `lib/tool_shed/webapp/controllers/user.py`
- Drop Galaxy model code from
  `lib/tool_shed/util/admin_util.py:Admin.purge_user()`
 2025-02-26 12:41:40 +00:00
Nicola Soranzo dd80698e4b Removed deprecated `current` attribute of scoped_session 2025-02-21 09:29:41 +00:00
John DavisandNicola Soranzo 7886de0dd8 Fix typo 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-01-23 11:39:25 -05:00
John Davis 896d0848c2 Remove transaction helper from scripts 2025-01-23 11:39:25 -05:00
Nicola Soranzo 26a4e146e0 Fix UP031 errors 
reported by ruff 0.8.0 .
 2024-11-24 21:35:23 +00:00
Nicola Soranzo 534010a8cb Enable flake8-implicit-str-concat ruff rules 
See https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
 2024-04-29 13:37:54 +01:00
Nicola Soranzo 0629908541 Fix new UP031 errors from ruff 0.4.2 2024-04-29 00:09:38 +01:00
John Davis 0e61d61f47 Fix SA2.0 error: joinedload does not take str args 2024-04-02 10:08:53 -04:00
Nicola Soranzo a2018a5e60 Enable flake8-comprehensions ruff rules 
but allow `dict()` calls that make use of keyword arguments (e.g.,
`dict(a=1, b=2)`).
 2024-03-09 19:11:20 +00:00
Nate Coraor 90a0df5d48 Fix the purge historyless HDAs pgcleanup action 2024-01-29 11:25:30 -05:00
John Davis f91693dc6e Merge pull request #16783 from SergeyYakubov/get-rid-of-filename-property 
Replace file_name property with get_file_name function
 2023-11-08 17:19:40 -05:00
Yakubov, Sergey c30a4c06c2 Replace file_name property with get_file_name function 2023-11-08 17:17:14 -05:00
John Chilton 360b327de6 Augment pgcleanup to allow periodically deleting old datasets. 
... and restricting operations to specific object store ids.
 2023-09-25 15:10:13 -04:00
John Chilton da8ce00d88 Cleanup docs in admin_cleanup_datasets.py. 2023-09-25 14:49:45 -04:00
John Davis 09fe7b9a54 Fix select stmts in scripts 2023-07-19 11:05:55 -04:00
John Davis 0c895d1409 Wrap session.flush in admin_cleanup_datasets script 2023-06-09 13:05:26 -04:00
John Davis e7408dcd98 Wrap session.flush in populate_uuid script 2023-06-09 13:05:26 -04:00
John Davis 96e534122d Wrap session.flush in cleanup_datasets script 2023-06-09 13:05:26 -04:00
Nicola Soranzo c655360e4e Merge branch 'release_23.0' into dev 2023-04-05 12:39:43 +01:00
Nicola Soranzo bee3d2e7ac Merge branch 'release_22.05' into release_23.0 2023-04-03 16:31:48 +01:00
Nicola Soranzo c3139f246d Fix UP031 errors reported by ruff 2023-03-29 08:55:54 +01:00
Dannon Baker 9b1301e6ae Apply black to forward merge 2023-03-27 10:51:25 -04:00
Dannon Baker caaa3e4f62 Joinedload replaces eagerload 22.05 forward 2023-03-27 10:17:11 -04:00
Dannon Baker f959f05b97 Merge remote-tracking branch 'upstream/release_22.01' into release_22.05 2023-03-27 10:01:59 -04:00
mvdbeek 756d047e1c Merge branch 'release_23.0' into dev 2023-03-06 18:08:05 +01:00
mvdbeek d97adf6359 Fix slugified dataset display 
Fixes https://github.com/galaxyproject/galaxy/issues/15676.
 2023-03-03 18:39:34 +01:00
John Chilton 6d91292beb Lint fixes... 2023-02-21 14:18:57 -05:00
John Chilton f7a4992b4b Implement quota tracking options per ObjectStore. 2023-02-19 10:33:21 -05:00
Nicola Soranzo 30f60493c3 Format Python code with black 23.1.0 
with manual fixes to 3 files to make them compatible with black 22.12.0 .

We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
 2023-02-01 23:51:03 +00:00
John Davis dd553e805f Fix maintenance script bug 2022-12-16 10:15:21 -05:00
Sergey Golitsynskiy 158b9f0a70 s/eagerload/joinedload (SQLAlchemy 2.0) 
Ref: https://docs.sqlalchemy.org/en/14/orm/loading_relationships.html?highlight=eagerload#sqlalchemy.orm.eagerload
 2022-03-16 16:48:33 -04:00
Nicola Soranzo a62e86fc2e Merge branch 'release_22.01' into dev 2022-03-04 17:02:22 +00:00
Nicola Soranzo e886d38171 Merge branch 'release_21.09' into release_22.01 2022-03-04 16:16:15 +00:00
Nicola Soranzo 7f04b5d698 Merge branch 'release_22.01' into dev 2022-03-02 20:08:55 +00:00
Nate Coraor 6a20106694 Fix typo with metadata_file 2022-03-02 14:23:46 -05:00
Nate Coraor a9b4b632a9 Fix pgcleanup.py for datasets stored by UUID 2022-03-02 14:18:31 -05:00
mvdbeek 034f518e43 Move init_models_from_config to galaxy.model.mapping 2022-03-01 16:50:06 +01:00
mvdbeek c08a12f553 Drop get_database_url helper 
I don't see an advantage over accessing the config attribute instead.
 2022-03-01 16:50:06 +01:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
mvdbeek bab12662a9 Drop old sqlalchemy patterns 2021-12-16 12:30:49 +01:00
Nicola Soranzo 90a729e431 New pyupgrade fixes 
Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
 2021-10-24 12:10:34 +01:00
mvdbeek ecc54ba00c Merge branch 'release_21.05' into dev 2021-08-09 18:45:05 +02:00
Nate Coraor 038045a600 Add a GDPR-friendly user purge to pgcleanup. 2021-07-23 14:55:54 -04:00
Sergey Golitsynskiy 680db562f7 Do not use legacy string interpolation on URL obj 
This fixes the pgcleanup script and an integration test.

The test fails because of an error in the script.
The error is caused by incorrect string formatting.
The new SQLAlchemy URL object extends collections.namedtuple, and a
tuple is incompatible with printf-style formating.

Ref:
https://github.com/sqlalchemy/sqlalchemy/blob/18dbd6aa12a7eca0acb1e2c4f752088e24d6adae/lib/sqlalchemy/engine/url.py#L36
https://docs.python.org/3/library/stdtypes.html#printf-style-string-formatting
 2021-05-18 19:00:55 -04:00
mvdbeek 9e9343ccd2 Fix cleanup_datasets.py script 2021-05-11 18:34:30 +02:00
Nicola Soranzo d26b3d9848 Fix all E203, E741 and W504 flake8 errors 2021-01-18 10:35:41 +00:00
Gianmauro CuccuruandNicola Soranzo 9ebde5f1e9 Update scripts/cleanup_datasets/pgcleanup.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-12-01 15:32:06 +01:00