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1663c9e331ee2445ce86a2bca1a6cbd19dae64e1
Commit Graph
21565 Commits
Author SHA1 Message Date
Nicola Soranzo 1663c9e331 Check host_ip only once 2019-10-30 15:30:03 +00:00
John Chilton 391381d3c4 small doctest for docker port parsing 2019-10-30 11:08:27 -04:00
John Chilton ff08885c2e Only re-map container monitor host if can find IP and have 0.0.0.0. 2019-10-30 11:03:20 -04:00
John Chilton 352e751927 Revert hacking IPs in container monitor script. 
It breaks the Mac setup and seems just wrong, docker might not be on localhost. This needs to be made more specific in some way and should handle those socker commands not working on OS X.
 2019-10-29 10:12:38 -04:00
Nicola Soranzo 7fb7862f55 Merge branch 'release_19.05' into release_19.09 2019-10-28 14:39:29 +00:00
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 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 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
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 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
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
mvdbeek 5f4df5eb93 Use pathlib for finding the parent repository dir 
The previous code can be trapped in the while loop,
and I think this was the intention.
 2019-10-23 14:01:04 +02:00
Nate Coraor 71dac004af Refactor the controller method for updating minor 
(non-version-change) revisions of TS repos and attempt to automatically
perform updates when repo installs/updates are called via
/api/tool_shed_repositories/install_repository_revision.

Note: tool_shed.galaxy_install:InstallRepositoryManager.install checks
the TS for the version, so you won't actually get the requested
changeset_revision if it's not the newest for that tool version. This
reflects the current controller behavior, with the exception that in the
UI you don't specify a changeset ID.
 2019-10-23 07:24:43 -04:00
mvdbeek 1273db504c Load tool.tool_shed_repository from cache 2019-10-23 12:38:17 +02:00
Nicola Soranzo 233dd05a82 Merge branch 'release_19.05' into release_19.09 2019-10-23 11:19:53 +01:00
Aysam Guerler 3e713029ac Merge pull request #8848 from mvdbeek/clarify_disabled_visualizations 
[19.09] Only raise ObjectNotFound if visualization xml can't be found
 2019-10-22 19:43:06 -04:00
Nicola Soranzo f161be7ba7 Better use of dict get() 2019-10-22 23:11:08 +01:00
mvdbeek 508db6bba6 Drop more unnecessary default values 2019-10-22 23:28:18 +02:00
mvdbeek e4996a4fed Make sure ToolShedRepositoryMetadata is always a dict 2019-10-22 23:19:46 +02:00
Marius van den BeekandNicola Soranzo 28eba779c9 Drop unnecessary explicit default 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-10-22 23:19:46 +02:00
mvdbeek 210a79cf03 Implement get_tool_relative_path for ToolConfRepository 
This is needed in case data_manager_manual should create a new data
table.
 2019-10-22 23:19:46 +02:00
mvdbeek 7e11c99eba Don't use tool_shed_repository_id where not necessary 2019-10-22 23:19:46 +02:00