Nicola Soranzo
3d57c22b63
Fix I201 errors from flake8-import-order
...
Also fix Python3 compatibility.
Remove unused method
galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() .
2016-11-23 18:31:04 +00:00
Nicola Soranzo
1d17a29c79
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +00:00
Nicola Soranzo
cd13423953
Python3: small fixes to previous commits
2016-06-26 02:43:57 -04:00
Junzhou Wang
f68a8198da
Python3: scripts/cleanup_datasets scripts/data_libraries
2016-06-25 21:49:25 -04:00
Nicola Soranzo
cc336f61c0
Make some files compatible with Python3
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Also enlarge the set of files tested with flake8 under Python3
2016-06-03 19:24:46 +01:00
Nicola Soranzo
6ba6f798ec
Fix more E203 flake8 errors
2016-05-17 23:53:16 +01:00
Nicola Soranzo
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
Nicola Soranzo
d85db9daa6
Use __file__ when adding paths to sys.path instead of os.getcwd() .
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Also insert additional paths in position 1 unless strictly necessary.
2016-02-18 15:45:15 +00:00
Dannon Baker
89e7c3df95
Address W503 and E721 errors now enforced by pep8 1.7.
2016-01-12 18:26:20 -05:00
Nate Coraor
c893afda00
Merge branch 'dev' into smash_eggs
2015-10-19 11:46:58 -04:00
Dannon Baker
b77496ec63
Update other quota manipulations to use the new user.adjust_quota_usage function.
2015-10-13 13:53:15 -04:00
Nate Coraor
0469ed29e0
Remove egg cruft from scripts/
2015-09-21 15:55:07 -04:00
Nicola Soranzo
0f883ef776
Merge branch 'release_15.07' into dev
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Conflicts:
lib/galaxy/model/__init__.py
2015-08-20 14:12:27 +01:00
Nicola Soranzo
a34f13a9f6
Merge branch 'release_15.05' into release_15.07
2015-08-20 14:07:09 +01:00
Nicola Soranzo
238d908cce
Fix purging datasets whose total_size is None.
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Fix the error:
Removing disk, file /opt/galaxy/database/files/000/dataset_192.dat
Error attempting to purge data file: /opt/galaxy/database/files/000/dataset_192.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType'
when running:
python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r
2015-08-19 15:33:54 +01:00
Nicola Soranzo
cc9b0bed85
Fix all E712 errors. Standardize sqlalchemy imports.
2015-07-14 20:49:34 +01:00
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
John Chilton
732abcc0db
Merge remote-tracking branch 'jmchilton/release_15.05' into dev
2015-06-08 14:04:28 -04:00
Nicola Soranzo
292d16a593
Mark also HDAs as purged when purging datasets via cleanup script.
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This will make purged datasets be shown as purged in histories,
preventing them to be undeleted through the UI.
This will not fix datasets previously purged through this script,
scripts/cleanup_datasets/pgcleanup.py may be used for that.
2015-06-04 18:06:01 +01:00
dpryan79
00eb96923f
Add a missing period in populate_uuid.py
2015-05-20 13:01:40 +02:00
dpryan79
0ff5a050d5
Indentation fix
2015-05-19 21:55:36 +02:00
dpryan79
0763cab37a
Update the remainder of the python cleanup scripts
2015-05-19 21:53:45 +02:00
dpryan79
4c20494011
Make python scripts executable. Tweak remove_renamed_datasets_from_disk.py.
2015-05-12 18:25:32 +02:00
dpryan79
a092aa2f59
Start providing usage information for the various cleanup scripts
2015-05-12 17:53:18 +02:00
Nicola Soranzo
b4acf247df
Uniform configuration of "From" field of sent emails.
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Subsume activation_email in email_from (used also in tool_shed.ini).
Try also getfqdn in PJA.
Default to 'galaxy-no-reply@' instead of 'galaxy-noreply@' in PJA.
2015-03-13 01:07:57 +00:00
Lance Parsons
b4c9f2fb10
Added pkg_resources to load required Mako package
2014-12-03 14:50:56 -05:00
Nate Coraor
acd078a65c
merge.
2014-09-15 16:57:28 -04:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Nate Coraor
4306560237
Remove unused "Main" versions of cleanup convenienence wrappers.
2014-09-15 15:34:03 -04:00
Dannon Baker
038f6dc6d5
Switch to_json_string/from_json_string in galaxy/scripts.
2014-09-09 10:04:28 -04:00
Kyle Ellrott
47f0f822f0
Refactoring work to add in Workflow UUIDs
2014-08-20 14:10:43 -07:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Kyle Ellrott
e4f45e04e3
Adding script to generate UUIDs for datasets where the value is null. This is to backfill previously generated records (from now on UUID will be generated during creation)
2014-03-04 15:46:10 -08:00
Nate Coraor
5a8c6457b9
Fix username argument to PostgreSQL connection in pgcleanup.py
2014-01-09 10:46:01 -05:00
Dannon Baker
eed1f76001
Merged in lance_parsons/galaxy-central-pull-requests/dataset-cleanup (pull request #158 )
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Basic administrative dataset cleanup script
2013-09-10 13:14:10 -04:00
Lance Parsons
91ba836a00
Fix unicode issue when printing history names in cleanup_datasets.py script
2013-07-22 14:24:13 -04:00
Nate Coraor
c1fb32d7c6
Update pgcleanup.py for dialect name change.
2013-05-29 16:16:11 -04:00
Lance Parsons
d37fabc834
Fix admin_cleanup_datasets.py for copied datasets
2013-04-18 15:43:00 -04:00
Lance Parsons
bd8cd477bc
Basic administrative dataset cleanup script
2013-04-18 11:24:09 -04:00
Nate Coraor
1e2256fe0e
pgcleanup: Print a useful message if no options are given.
2012-10-01 13:45:37 -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
459d3a2c1d
More pgcleanup.py fixes and addition of cleanup event tables for library items.
2012-09-17 12:51:17 -04:00
Nate Coraor
71d7f7c132
Distributed object store fixes for pgcleanup.py.
2012-09-11 12:22:03 -04:00
Nate Coraor
0e1b041cde
Bug fixes for pgcleanup.py
2012-09-10 16:59:33 -04:00
Nate Coraor
c8e49cdd6d
Bugfix for pgcleanup.py
2012-09-10 14:07:05 -04:00
Nate Coraor
e19092e9c5
Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial.
2012-09-10 12:03:23 -04:00
Nate Coraor
35dd4e1ef9
Fix for cleanup_datasets.py when database_connection is the uncommented default in the config file.
2012-04-16 10:07:10 -04:00
Nate Coraor
9aed5a36d8
Fix for dataset cleanup scripts and object store.
2012-01-31 14:07:14 -05:00
Nate Coraor
3a1526ac8a
Decrease user disk usage when files are removed from disk by the cleanup_datasets.py.
2011-08-22 16:19:49 -04:00
Nicola Soranzo