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Commit Graph
20953 Commits
Author SHA1 Message Date
Martin Cech b415dfddfa Merge pull request #8294 from bwlang/library_date_propagate 
Library date propagate
 2019-07-11 13:55:31 -04:00
John Chilton c2ac586669 Merge pull request #8296 from blankenberg/environment_variable-strip 
Add ability to strip whitespace from tool environment_variables.
 2019-07-11 16:28:29 +02:00
John Chilton 6a1c05fac2 Merge pull request #8300 from mvdbeek/skip_migration_for_new_databases 
Skip migrations on entirely clean new databases
 2019-07-11 16:24:07 +02:00
Vahid 731b3eb8d2 add r to regexp to escape \d & satisfy lint. 2019-07-10 13:49:33 -07:00
Vahid 40fe0a3e86 Enable user1 & user2 resolve to different usernames 2019-07-10 12:51:52 -07:00
Nicola Soranzo bdee798bc0 Fix kubernetes runner on py3 (#8321) 
Fix kubernetes runner on py3
 2019-07-10 15:59:37 +01:00
mvdbeek 888c03877d Fix kubernetes runner on py3 
instance_id is a string, so this can't be compared to an integer
on python 3. Broken in ac1b25ed4c,
prior to that the comparison was `len(self._galaxy_instance_id) > 0:`
 2019-07-10 13:49:53 +02:00
Brad Langhorst 485e0043a7 implements nicola's suggestion -> snakecase 2019-07-10 05:22:27 -04:00
Marius van den Beek ef9698895a Merge pull request #8319 from nsoranzo/lowercase_boolean_yaml 
Use lowercase true/false in config_schema.yml
 2019-07-10 11:18:19 +02:00
Marius van den Beek db3a1bac1d Merge pull request #8320 from nsoranzo/merge_19.05_20190709 
Merge 19.05 20190709
 2019-07-10 11:15:46 +02:00
Marius van den Beek bc7b48756b Merge pull request #7402 from guerler/activate_toolshed 
Activate api-based Toolshed interface in Admin panel
 2019-07-10 11:06:18 +02:00
guerler 95d69146be Restore tool metadata endpoint for old tool management grid 2019-07-10 08:21:38 +02:00
Nicola Soranzo d0c28f669b Use lowercase true/false in config_schema.yml 
since these are the only allowed values for booleans in YAML 1.2:
https://yaml.org/spec/1.2/spec.html#id2803629

make config-rebuild
 2019-07-09 18:58:51 +01:00
Nicola Soranzo ea32667142 Merge branch 'release_19.05' into dev 2019-07-09 18:43:43 +01:00
John Chilton 7fa24b191b Remove mimeparse package in lib/ root. 
Was added for trackster in 985f7c63fa for a tracks controller that no longer exists. Cannot find any references to this module.
 2019-07-09 14:13:12 +01:00
Marius van den Beek d22d7beaf4 Merge pull request #8305 from jmchilton/axe_log_tempfile 
Remove log_tempfile.
 2019-07-09 14:42:43 +02:00
guerler 4359029ef9 Remove legacy toolshed activation flag in config 2019-07-09 13:59:46 +02:00
guerler deaa583890 Merge branch 'dev' into activate_toolshed 2019-07-09 13:58:01 +02:00
Marius van den Beek ef86713754 Merge pull request #8304 from nsoranzo/remove_temp2.txt 
Use temporary file for sniff tests
 2019-07-09 12:55:25 +02:00
Nate Coraor 97bcd9c46a Merge pull request #8306 from jmchilton/axe_psyco_full 
Remove psyco_full.py - unused as far as I can tell.
 2019-07-09 11:01:09 +02:00
Brad Langhorst 50011c1e98 linting fixes 2019-07-09 04:09:11 -04:00
Brad Langhorst d35df5eca7 Sqlite3 compatible syntax 2019-07-08 13:10:35 -04:00
mvdbeek a01adf6da2 Do actually initialize tool shed mapping 2019-07-08 16:37:28 +02:00
mvdbeek ea0688146d Use correct install db url 2019-07-08 16:37:28 +02:00
mvdbeek d34142e420 Skip migrations on entirely clean new databases 
This should be a very nice speedup for ansible tutorials,
tests, planemo etc.
 2019-07-08 16:37:28 +02:00
John Chilton 1bed6c4931 Remove psyco_full.py - unused as far as I can tell. 
@natefoo didn't object.
 2019-07-08 14:59:52 +02:00
John Chilton 8a327db74d Remove log_tempfile. 
Simplify packaging - @natefoo said I could.
 2019-07-08 14:52:13 +02:00
Nicola Soranzo 8876f165d1 Use temporary file for tests 
Remove `lib/galaxy/datatypes/test/temp2.txt` which was added by
mistake in commit 54d2ca01f8 .
 2019-07-08 12:45:10 +01:00
Daniel BlankenbergandNicola Soranzo a5b3308a89 Update lib/galaxy/tool_util/xsd/galaxy.xsd 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-07-08 13:34:54 +02:00
Nate Coraor 058fabc121 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-08 12:27:21 +02:00
Daniel Blankenberg 3255284fb0 Fix for fetching strip if not defined 2019-07-08 12:17:38 +02:00
Daniel Blankenberg 7db36407cb Merge branch 'dev' of https://github.com/galaxyproject/galaxy into environment_variable-strip 2019-07-08 11:51:01 +02:00
Nate Coraor d187b28951 Stop trying to guess a web port from the config since most configs are not INI anymore anyway. 2019-07-08 11:43:11 +02:00
John Chilton 23241a29d7 Merge pull request #8280 from dglaetzer/dev 
get tests on data package running
 2019-07-08 11:41:36 +02:00
Nate Coraor 906413d07b Rework config locating logic (it was reading the sample again). 2019-07-08 11:28:31 +02:00
Nate Coraor 751503958f Fixes from PR review 2019-07-08 11:28:04 +02:00
Brad Langhorst dc26a388bb removes noisy debug output 2019-07-08 04:48:13 -04:00
Brad Langhorst 705ad4b21c Linting fixes 2019-07-08 04:42:26 -04:00
Martin Cech a8deae2404 format sql statement for readibility 2019-07-08 10:23:54 +02:00
Nate Coraor b6358f5333 Move remaining sample configs to lib/galaxy/config/sample 2019-07-08 10:19:11 +02:00
Brad Langhorst 3535efe20c minor cleanup 2019-07-08 04:01:20 -04:00
Brad Langhorst 2f1b120e31 Passing the trans was a bad idea… commit on that 
Caused user edits not to be saved
 2019-07-08 04:00:56 -04:00
Martin Cech 6cde398e62 add autocommit 2019-07-07 20:06:37 +02:00
Daniel Blankenberg 7e3ef30719 Add ability to strip whitespace from tool environment_variables. 2019-07-07 19:57:10 +02:00
Brad Langhorst 084cceffe3 tried passing in trans to avoid an additional session 
(Still not sticking)
 2019-07-07 13:39:47 -04:00
Brad Langhorst ac1a7c5593 calls time update during import to library too 2019-07-07 13:18:42 -04:00
Brad Langhorst e682d100e2 More logging to figure out why updates are not sticking 2019-07-07 13:17:55 -04:00
John Chilton a9f6c0cd1a Refactor config_watchers out of webapps so can be in galaxy-app package. 2019-07-07 19:10:12 +02:00
dglaetzer 20ba54eecd linked maf_utilities.py back to it's original place (now, finally) 2019-07-07 18:55:51 +02:00
Brad Langhorst c2f71cf4d8 propagates updates to library items up the folder tree 2019-07-07 11:15:48 -04:00