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
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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)
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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
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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 Cuccuru and Nicola Soranzo
9ebde5f1e9
Update scripts/cleanup_datasets/pgcleanup.py
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2020-12-01 15:32:06 +01:00
Gianmauro Cuccuru
7ceeb70f75
Add an option to the pgcleanup script to redirect logging to a different log file
2020-12-01 14:11:32 +01:00
Gianmauro Cuccuru
90e228cf91
Add an option to the pgcleanup script to redirect logging to stdout
2020-10-31 05:27:31 +01:00
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
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Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
Nicola Soranzo
56450de8a9
Print help if no action is selected
2020-03-05 13:26:28 +01:00
Nicola Soranzo
3525cf7a8e
Remove broken script
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None of the 3 other scripts called by this one exists anymore.
2020-02-03 18:48:57 +00:00
Nicola Soranzo
f5cd88465e
Make str.join()s more efficient
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by using generator expressions and tuples instead of lists.
2020-01-23 11:06:32 +00:00
Nicola Soranzo
303f9ec871
Merge pull request #8908 from bernt-matthias/topic/pgcleanup-also-delete
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make pgcleanup also delete HDAs
2019-11-04 10:21:04 +00:00
Sergey Golitsynskiy
a855e2ca64
Fix TypeError in logging commands
...
Fix the following exception:
```
TypeError: not all arguments converted during string formatting
```
Also, make other log format strings more consistent: %d for numeric object IDs.
2019-11-03 21:35:07 +00:00
M Bernt
6f010bd49c
make pgcleanup also delete HDAs
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follow up to https://github.com/galaxyproject/galaxy/pull/3572
2019-10-30 13:42:31 +01:00
John Chilton
e611797a77
Merge pull request #8470 from erasche/fix-975
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Fix #975
2019-08-16 14:42:24 -04:00
Helena Rasche
5f615168bc
Fix #975
2019-08-16 15:11:15 +02:00
Helena Rasche
b316bab722
Remove scripts deprecated since 1 year
2019-08-15 14:30:53 +02:00
M Bernt
f6ff679d63
cleanup: use logging instead of print
2019-08-01 09:25:13 +02:00
Nicola Soranzo
90a6c6d46b
Fix issues reported by ShellCheck
2019-06-13 12:53:26 +01:00
Nate Coraor
bd06628a3d
Fix use of pgcleanup's purge_deleted_users when there are no users to
...
purge
2019-05-17 16:37:19 -04:00
Nate Coraor
fc027182f7
Fix variable name for work mem in pgcleanup.py
2019-05-17 11:30:40 -04:00
Nate Coraor
e72d52c6df
Lint
2018-10-15 16:07:14 -04:00
Nate Coraor
e1a197676e
Refactor repetitive HDA purging stuff and add a function to purge HDAs
...
with null history_ids
2018-10-15 14:59:15 -04:00
John Davis