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111 Commits
Author SHA1 Message Date
Matthias Bernt 0c321cb86e removed config.ini parameter from cleanup scripts 
fixes https://github.com/galaxyproject/galaxy/issues/5941
 2018-04-23 14:58:48 +02:00
John Chilton fea7953410 Remove two scripts - dataset purging hasn't worked this way for a very long time. 2018-03-23 16:14:49 -04:00
John Chilton 16d821e12e Mark scripts/* that don't work with YAML configuraiton options as deprecated. 2018-03-23 16:14:49 -04:00
John Chilton 5f3f792f6f Unification of Galaxy configuration parsing for scripts/* 2018-03-23 16:14:49 -04:00
Nicola Soranzo 74d0bcb353 Merge branch 'release_17.09' into release_18.01 2018-03-19 17:50:57 +00:00
Nicola Soranzo 3b87dac780 Add Galaxy lib directory to Python path for 2 scripts 
Also fix check introduced in commit 0763cab37a .

Fix https://github.com/galaxyproject/galaxy/issues/5722 .
 2018-03-19 14:53:19 +00:00
mvdbeek 89d45416fb Import Registry directly 2018-01-19 15:27:55 +01:00
mvdbeek ca51898bc4 Fix cleanup datasets script 2018-01-19 14:50:08 +01:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nate Coraor b8dfceb72a Merge branch 'release_17.09' into dev 2017-10-23 10:38:14 -04:00
Nate Coraor 646a8d1092 Support a log directory argument for pgcleanup.py 2017-10-20 12:43:09 -04:00
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 e32ad2864f Remove container config log message from cleanup scripts logs 2017-08-18 12:35:04 +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 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 
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() . 
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 
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. 
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. 
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. 
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