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4378 Commits
Author SHA1 Message Date
John Chilton ef29b72e00 Integration test for 'outputs_to_working_directory' with Pulsar. 2019-07-16 10:23:33 -04:00
Sergey Golitsynskiy f3f979fd5d Fix linting errors (import stms) 2019-07-13 19:28:31 -04:00
Sergey Golitsynskiy 3d59d94aa8 Restructure/modify environ context manager + tests 
Factor out __environ context manager into helper class (and rename).

Move context manager tests into separate test module. Improve tests.

Refactor context manager:
- Change default arg to None
- Simplify: I don't think we need to keep track of new keys;
  environ.clear() + environ.update(old_environ) should be sufficient.
  We significantly reduce complexity at the minor cost of a little more
  space.
- Instead of wrapping in a try/except block, just check if key exists
  before deleting.

Modify test_tool_deps to use the new context manager.
 2019-07-13 13:08:59 -04:00
Sergey Golitsynskiy 205d82e3f6 Merge remote-tracking branch 'upstream/dev' into dev_unittest_bugfix 2019-07-13 12:43:13 -04:00
Nicola Soranzo de798d4829 Merge pull request #8329 from mvdbeek/fix_py3_startup 
Cast uwsgi option to unicode, fixes startup under python 3
 2019-07-13 15:50:17 +01:00
mvdbeek 7f8c42421f Fix test_400_on_invalid_embedded_content on python 3 2019-07-13 10:47:30 +02:00
Sergey Golitsynskiy 9713184b03 Move tools/verify/ into tool_util/verify/ 
Ref: https://github.com/galaxyproject/galaxy/issues/8073
 2019-07-12 18:06:53 +01:00
Enis Afgan 33f442f0c8 Merge pull request #8311 from telukir/f-kt-r19.05-jwt1 
walltime_limit added for the k8s jobs
 2019-07-12 08:30:29 +02:00
Martin Cech b415dfddfa Merge pull request #8294 from bwlang/library_date_propagate 
Library date propagate
 2019-07-11 13:55:31 -04:00
mvdbeek ff0d1f142e Add test for k8s_walltime_limit 2019-07-10 17:16:08 +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
Nicola Soranzo ea32667142 Merge branch 'release_19.05' into dev 2019-07-09 18:43:43 +01:00
guerler deaa583890 Merge branch 'dev' into activate_toolshed 2019-07-09 13:58:01 +02:00
Marius van den Beek 2691a4470d Merge pull request #8310 from dglaetzer/dev 
Add and run tests for auth package
 2019-07-09 13:07:40 +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
Brad Langhorst 50011c1e98 linting fixes 2019-07-09 04:09:11 -04:00
Sergey Golitsynskiy 73cd69a13f Fix lint errors 2019-07-09 00:39:21 +02:00
Sergey Golitsynskiy 6e78cc6847 Fix bug in a unit test 
There was a bug in a context manager inside a unit test. This caused
nondeterministic behavior of some unit tests after a refactoring.

Bug fixed; added 3 unit tests to test the context manager.
 2019-07-08 17:59:25 +02:00
dglaetzer 2a1dd4b1a6 Update test_auth.py 2019-07-08 17:52:36 +02:00
dglaetzer ec454313ea dummy tests for auth package 2019-07-08 17:28:32 +02:00
John Chilton c9ef1b6fad Merge pull request #8302 from dglaetzer/dev 
dummy tests for containers package
 2019-07-08 15:41:48 +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
dglaetzer 4a6ecd0b61 linting 2019-07-08 13:07:56 +02:00
dglaetzer 2a42853bfa add tests 2019-07-08 12:55:43 +02:00
Brad Langhorst 4f99db9d3f starting point for a test… 
Failing on sqlite
 2019-07-08 06:29:57 -04:00
Nate Coraor 058fabc121 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-08 12:27:21 +02:00
John Chilton 1815a6547a Bring top-level galaxy Python files into galaxy-app. 2019-07-07 19:45:48 +02:00
Nate Coraor a0b1d0066f Unit test fixes 2019-07-07 16:29:58 +02:00
Nate Coraor 2034980b77 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-07 13:50:41 +02:00
Nate Coraor caef1d6711 Fix datatypes_conf.xml.sample path for upload integration test 2019-07-07 13:10:37 +02:00
John Chilton d194520fdf Merge pull request #8152 from jmchilton/tool_deps_serialize 
Re-try dependency manager serialization and embedded config.
 2019-07-07 12:44:35 +02:00
Nate Coraor 37522f5e8e Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-05 16:05:17 +02:00
Dannon 72cc063451 Merge pull request #7905 from ValentinMarcon/toolrefs 
Implement "xref" tag on the tool structure (with visualisation)
 2019-07-05 09:54:24 -04:00
Nate Coraor cdb9040e26 Merge remote-tracking branch 'origin/dev' into installable 2019-07-05 15:51:15 +02:00
guerler d8e089308a Merge branch 'dev' into activate_toolshed 2019-07-05 14:09:08 +02:00
Dannon e23f0c5f45 Merge pull request #8231 from mvdbeek/fix_job_check_for_cancelled_jobs 
[19.05] Fix cancelling jobs with a message from the admin panel
 2019-07-01 09:43:34 -04:00
Marius van den Beek 71d315cf36 Merge pull request #8246 from mvdbeek/merge_8221 
Merge 19.05 into dev
 2019-06-29 09:24:02 +02:00
Marius van den Beek 49d09e2c45 Merge pull request #8090 from guerler/new_toolshed 
Convert repository client to vue
 2019-06-29 09:17:36 +02:00
mvdbeek 928f9453e5 Merge branch 'release_19.05' into dev 2019-06-29 00:24:51 +01:00
Martin Cech 6d6aec80ee Merge pull request #7811 from dannon/dm-cleanup 
Data Manager interface - use standard card header styles without extra markup
 2019-06-28 09:46:00 -04:00
Marius van den Beek aa98a29686 Merge pull request #8233 from VJalili/test_base_api 
Refactor setup_user_get_key method to return the created test user and its API key
 2019-06-28 11:14:36 +02:00
ValentinMarcon 03ba7a3c01 standardization of 'reftype' & 'value' 2019-06-28 11:02:57 +02:00
ValentinMarcon 6a6ade54fa xrefs yaml parser 2019-06-27 15:39:07 +02:00
ValentinMarcon 7347e57509 add parsing xml and yaml test 2019-06-27 11:41:31 +02:00
John Chilton 584c117df3 Refactor to cleanup dependencies around galaxy.web.stack. 
Move galaxy.web.stack.database_heartbeat into galaxy.model - since it was the only thing in galaxy.web.stack that used galaxy.model at all and it didn't import anything else from galaxy.web.stack.

Once that was done, I refactored this whole package (galaxy.web.stack) into galaxy.web_stack. It doesn't use the framework setup or exported by the base galaxy.web package so it wouldn't seem to belong there. It also has very different dependencies than the rest of that. And finally and most importantly, this elimiantes almost all dependency from galaxy.jobs and galaxy.tools and galaxy.workflows to anything in galaxy.web.
 2019-06-26 18:54:52 -04:00
vahid d3cbb985a3 Refactor a test method to return a create test user with its api key. 2019-06-26 12:36:13 -07:00
mvdbeek 54a60a6aaa Looks like we never actually cancel the job? 2019-06-26 15:53:25 +02:00
mvdbeek 5016dedac7 Add test that ensures cancelling job in admin interface works 2019-06-26 12:08:49 +02:00
mvdbeek 05a5628df0 Add test for fetching section by label 2019-06-25 18:29:52 +02:00