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
Nicola Soranzo
7f04b5d698
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
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
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
...
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
Helena Rasche
887aae2ab3
Refactor into model
2019-08-14 16:15:49 +02:00
Helena Rasche
58f4f65a4a
new method
2019-08-14 16:08:04 +02:00
John Chilton
5f3f792f6f
Unification of Galaxy configuration parsing for scripts/*
2018-03-23 16:14:49 -04:00
Nicola Soranzo
14259b11d9
Python3: finish first pass on whole codebase
2017-12-14 12:01:01 +00:00
Nicola Soranzo
d1bc98dfcb
Python3: fix remaining print statements
...
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
2017-10-12 18:34:29 +01:00
Nicola Soranzo
a353b2e88f
Fix E127 errors introduced by previous commit
...
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
1d17a29c79
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +00:00
Nicola Soranzo
d85db9daa6
Use __file__ when adding paths to sys.path instead of os.getcwd() .
...
Also insert additional paths in position 1 unless strictly necessary.
2016-02-18 15:45:15 +00:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +01:00
Nicola Soranzo
6569c2dcc3
Partially lint scripts/ .
2015-07-13 20:13:28 +01:00
Dannon Baker
fe226e1a9b
Refactoring of set_user_disk_usage and admin controller disk usage to use the same pgcalc
2015-02-25 12:52:47 -05:00
Dannon Baker
c733ce370b
Fix path insertion vs appending of <galaxy>/lib for all scripts.
2015-02-12 10:34:51 -05:00
Nate Coraor
bc5ec4fec4
Bug fixes to scripts for config subdir.
2014-09-15 16:52:50 -04:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Nate Coraor
ed9fc69f33
Fix a few postgres dialect renaming misses.
2013-09-26 09:34:27 -04:00
Lance Parsons
f98cf656a2
Fix for Postgres versions < 9 (see https://trello.com/c/Z0EynAV2 )
2012-12-10 16:23:11 -05:00
Nate Coraor
9213c344db
Fix reporting in the set_user_disk_usage.py script.
2012-10-03 13:40:54 -04:00
Nate Coraor
8193489dda
pgcleanup/set_user_disk_usage: set usage to 0, not null, when the user has no active data.
2012-09-28 16:11:38 -04:00
Nate Coraor
caa06bbc20
Allow Postgres users to update user disk usage with a fast wCTE rather than a slower computation in Python.
2012-09-28 14:30:10 -04:00
Nate Coraor
c8f4c93799
Make set_user_disk_usage.py object store-aware.
2012-02-09 13:26:14 -05:00
John Duddy
a2c0328241
Merge
2011-10-07 13:25:19 -07:00
Nate Coraor
d9126aa807
Clarify output messages of set_user_disk_usage.py
2011-09-07 15:07:05 -04:00
Nate Coraor
eea0b7a81a
Be more forgiving about running the disk accounting scripts from outside the galaxy-dist directory.
2011-09-07 09:05:52 -04:00
Nate Coraor
0756941512
Move a number of dataset-related methods from the root controller to the dataset controller and encode their ids. Also add user disk usage accounting.
2011-07-26 13:30:07 -04:00
John Chilton