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Author SHA1 Message Date
mvdbeek bb38795e75 Give test data managers distinct ids and names 2019-11-06 14:33:45 +01:00
mvdbeek d6b69cf6d5 Use final_job_state in data manager exec_after_process 
This was all working correctly in my test, but removes some custom logic.
It was theoretically possible for the old logic to fail if there was
no output dataset for the job.
 2019-11-06 14:25:18 +01:00
Marius van den Beek 1b776b5b0b Merge pull request #8916 from jmchilton/data_req_fix 
[19.09] Fix galaxy-data package requirements.
 2019-11-04 11:45:58 +01:00
Nicola Soranzo 4b9c41503c [19.09] Fix TypeError in logging commands (#8925) 
[19.09] Fix `TypeError` in logging commands
 2019-11-04 09:49:41 +00:00
Sergey Golitsynskiy a855e2ca64 Fix TypeError in logging commands 
Fix the following exception:

```
TypeError: not all arguments converted during string formatting
```

Also, make other log format strings more consistent: %d for numeric object IDs.
 2019-11-03 21:35:07 +00:00
John Chilton fde0cd72cf Fix galaxy-data requirements. 
No longer pinning sqlalchemy to 1.2.
 2019-10-31 09:29:08 -04:00
John Chilton c554118a05 Merge pull request #8896 from ic4f/sg_config40_1909 
[19.09] If config_file is None, use cwd, not its parent
 2019-10-29 10:35:53 -04:00
Sergey Golitsynskiy bc611c1d3c If config_file is None, use cwd, not its parent 
Backport #8894

Context:
https://github.com/galaxyproject/galaxy/pull/921#discussion_r304351292
 2019-10-28 10:59:06 -04:00
Nicola Soranzo 7fb7862f55 Merge branch 'release_19.05' into release_19.09 2019-10-28 14:39:29 +00:00
Marius van den Beek fb1c0f8de2 Merge pull request #8895 from nsoranzo/release_19.05_followup_on_8891 
[19.05] Safer fix for ``unicodify`` on exceptions with bytestring message
 2019-10-28 15:18:27 +01:00
Nicola Soranzo 9c3be80a7c Safer fix for `unicodify` on exceptions with bytestring message 
Follow-up on https://github.com/galaxyproject/galaxy/pull/8891 .
Should be safer for `Exception` subclasses that override `__str__()`
/ ` __unicode__()` methods.
 2019-10-28 12:20:13 +00:00
Björn Grüning a7d664bb31 Merge pull request #8886 from mvdbeek/no_delete_queues 
[19.09] Discard messages created before QueueWorker was started
 2019-10-27 19:23:30 +01:00
John Chilton 70b2ba96b2 Merge pull request #8891 from mvdbeek/fix_unicodify_on_exceptions 
[19.05] Fix unicodify on exceptions with non-utf bytestring args
 2019-10-27 13:25:39 -04:00
John Chilton 47fa5760d3 Merge pull request #8887 from mvdbeek/dont_eagerload_unused_metadata 
[19.09] Fix excessive memory consumption by not loading repository.metadata column
 2019-10-27 13:23:26 -04:00
John Chilton 92d55ca43c Merge pull request #8879 from mvdbeek/ts_install_manager_test_and_hg_util_fixes 
[19.09] Install manager unit test and python 3 hg util exception handling fixes
 2019-10-27 13:13:44 -04:00
Marius van den BeekandNicola Soranzo 89d1f97f05 Only use value.args[0] if exception has a single argument. 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-10-27 16:15:10 +01:00
mvdbeek c5f70b9cd6 Cast ctx_rev coming from changset2rev to string 2019-10-27 14:47:00 +01:00
Nicola Soranzo 58118d1a59 Simplify code 2019-10-27 12:23:24 +00:00
Nicola Soranzo edb0cee8a4 Remove unused code 2019-10-27 12:20:10 +00:00
mvdbeek 57293086f7 Cast ctx_rev to str before passing it to subprocess command 
In some places `ctx_rev` is an `int`.
Fixes the toolshed tests. Uncovered by removing the string casting in
commit 732874badba3a60599fbf19a93af3c8aa85394d5 .
 2019-10-27 12:15:23 +00:00
mvdbeek 939754e6c3 Fix unicodify on exceptions with non-utf bytestring args 2019-10-27 11:08:48 +01:00
mvdbeek e4bc813a4f Use joined-loading only in ToolShedRepositoryCache query 2019-10-26 22:51:46 +02:00
mvdbeek 3a32948818 Fix metadata reset 2019-10-26 20:55:47 +02:00
mvdbeek 2e7f174e81 Limit lazy="joined" to tool_dependencies relation, defer repository.metadata loading 2019-10-26 19:30:01 +02:00
mvdbeek 3cc5a28006 Fallback for python2 not having math.inf 2019-10-26 18:42:45 +02:00
mvdbeek 9b18f5904d Add unit test that asserts past tasks won't be executed 2019-10-26 18:42:45 +02:00
mvdbeek a8b3e9dccf Discard messages created before QueueWorker was started 
And don't delete the local control queue. Deleting the local
control queue may throw off other consumers bound to that control
queue. This shouldn't happen, but apparently it can if Galaxy
runs in zerg mode ?
 2019-10-26 18:42:45 +02:00
John Chilton d659575c3c Merge pull request #8878 from natefoo/gxit-eu-fixes 
[19.09] Galaxy InteractiveTools cluster support fixes from EU
 2019-10-25 09:08:44 -04:00
mvdbeek 6924a0b01b Fix kwargs 2019-10-25 14:15:49 +02:00
Marius van den BeekandNicola Soranzo 56b8205e83 Improve phrasing of exception messages 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-10-25 14:15:49 +02:00
mvdbeek a8f6b2393f Add basic unit test for install repository manager 2019-10-25 14:15:49 +02:00
mvdbeek 5227655f16 Add basic test for create_or_update_tool_shed_repository 2019-10-25 14:15:49 +02:00
mvdbeek 82286827a3 Drop unnecessary casting and improve exception logging 2019-10-25 14:15:49 +02:00
mvdbeek 87525ee2f2 Simplify create_or_update_tool_shed_repository 2019-10-25 14:15:49 +02:00
mvdbeek 7ea3d240d3 Fix exception handling in hg_util on python 3 2019-10-25 14:15:49 +02:00
mvdbeek b46e422640 Use kwargs for long TS methods 
Was checking this during the review anyway, might as well add it in the
code.
 2019-10-25 14:15:49 +02:00
Nicola Soranzo 7f839ee36a Merge branch 'release_19.05' into release_19.09 2019-10-25 00:55:58 +01:00
Nicola Soranzo 4cb9941089 Backport oidc config file fix: yml to xml (#8869) 
Backport oidc config file fix: yml to xml
 2019-10-24 22:52:06 +01:00
Nate Coraor ddd950e209 Lint fixes 2019-10-24 17:46:28 -04:00
Nate Coraor 6445c9049d Check for container ports in DRMAA runner 2019-10-24 17:13:13 -04:00
Nate Coraor 1ea1990959 Galaxy InteractiveTools cluster fixes from EU 2019-10-24 17:12:21 -04:00
Sergey Golitsynskiy 9bdc0dd203 Backport #8859 2019-10-24 11:18:20 -04:00
John Chilton 7f559f290d Merge pull request #8853 from mvdbeek/fix_while_loop 
[19.09] Use pathlib for finding the parent repository dir
 2019-10-24 10:45:41 -04:00
Nate Coraor c79e15667e Merge pull request #8815 from natefoo/tsr-revision-update 
[19.09] Fix non-version (minor) tool shed repository updates when installing revisions through the API
 2019-10-24 09:46:05 -04:00
Martin Cech a1e9a174a9 Merge pull request #8854 from dannon/fix-ff-dropdown-glitch 
[19.09] Fix toolshed selection display glitch
 2019-10-23 10:53:26 -04:00
Martin Cech fc6491ea59 Merge pull request #8849 from mvdbeek/data_library_upload_explicit_error 
[19.09] Explicitly fail dataset upload with invalid extension
 2019-10-23 10:21:38 -04:00
Martin Cech e51daf2613 Merge pull request #8817 from mvdbeek/dmfix1909 
[19.09] Fix data_manager_manual with new data tables + cleanup and fixes
 2019-10-23 10:04:47 -04:00
mvdbeek b0624a5887 Make pathlib work on python2 using pathlib2 backport 2019-10-23 15:12:00 +02:00
Dannon Baker 2c0c0063c7 Fix dropdown popping out of line in the toolshed server selection 
interface
 2019-10-23 08:56:28 -04:00
John Chilton 75a7d685dc Merge pull request #8847 from mvdbeek/fix_trimmed_string_implementation 
[19.09] Cast to string in TrimmedString
 2019-10-23 08:41:46 -04:00