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Author SHA1 Message Date
John Chilton 2f020ef944 Fix tool stdio level parsing for OOM level. 
Backend was enhanced to allow this in #5196 and a new entry point to setting exit code for such exit conditions but the custom parsing wasn't updated to allow it. Thanks to @nsoranzo for the catch.
 2018-02-05 12:18:22 -05:00
Dannon Baker 2cb3af5d60 Merge pull request #5447 from natefoo/server-name-fix 
[18.01] Fix server_name when config is a dict
 2018-02-05 10:43:03 -05:00
Dannon Baker 207f5faba0 Merge pull request #5449 from jmchilton/collection_mapping_fixes 
[18.01] Collection mapping fixes for regression in 18.01.
 2018-02-04 11:52:33 -05:00
John Chilton b2e8d891b7 Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable 
Fix setting job failure exception
 2018-02-03 15:01:17 -05:00
John Chilton 51e030f4f3 Bring in @mvdbeek's test cases from #5431. 2018-02-03 14:59:30 -05:00
John Chilton f99299f833 Pre-compute more collection state during mapping. 
Still dealing with fallout from 78babab645. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping.
 2018-02-03 14:59:30 -05:00
mvdbeek 7bbc46658a Fix setting job failure exception 
This can happen when the job's tool is unavailble and
outputs_to_working_directory is activated.
Fixes https://github.com/galaxyproject/galaxy/issues/5424.
 2018-02-03 18:09:57 +01:00
Martin Cech 1bd8c4fd26 Merge pull request #5455 from jmchilton/backport_flakey 
[18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests
 2018-02-03 11:45:16 -05:00
Nicola Soranzo 935b8c948c Add --skip_flakey_fails flag to CI script for API tests 
xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551
and following comments.
 2018-02-03 08:11:46 -05:00
Marius van den Beek 5aed347c30 Merge pull request #5418 from jmchilton/collection_pja 
[18.01] Implement more intuitive collection PJA
 2018-02-03 09:55:24 +01:00
Nate Coraor dac1ba5812 Fix failing integration tests for workflow handlers. 2018-02-02 15:40:22 -05:00
John Chilton 8e32e93d6d Implement more collection workflow post job actions. 
Implement hide, delete, add tag, and remove tag for output collections and mapped over collections.

Fixes https://github.com/galaxyproject/galaxy/issues/1680.
 2018-02-02 13:29:57 -05:00
Nate Coraor b0162ba543 Fix server_name when config is a dict. 2018-02-02 12:53:39 -05:00
Marius van den Beek fbfbdd51bb Merge pull request #5416 from jmchilton/rename_collections_pja 
[18.01] Fix rename post job actions to be more intuitive when mapping over collections.
 2018-02-02 17:53:37 +01:00
Marius van den Beek 6c013d0cb3 Merge pull request #5444 from dannon/multidelete_fix 
[18.01] Ensure jobStateSummariesCollection exists;
 2018-02-02 17:51:27 +01:00
John Chilton 0529153ac0 Fix bug in PJAs for collection mapping. 
Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157).
 2018-02-02 09:54:30 -05:00
John Chilton f6f9f9a891 Extend mapped collection output rename PJAs to include # replacements. 
Also make sure output collections in non-mapping scenarios are also properly renamed as well.
 2018-02-02 09:52:44 -05:00
John Chilton 2b8df110d0 Apply rename PJA to collection outputs including $ replacements. 
Update PJA collection test to test HDCA is renamed also.
 2018-02-02 09:52:44 -05:00
Dannon Baker a392b5750a Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail 2018-02-02 09:01:35 -05:00
Marius van den Beek 60561c2030 Merge pull request #5403 from jmchilton/collection_operation_tags 
[18.01] More robust nametag discovery and propagation.
 2018-02-02 09:05:08 +01:00
John Chilton 6022fe7d7e Handle optional inputs when collecting preserved tags. 
https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450
 2018-02-01 21:03:02 -05:00
John Chilton 6f40f7098d Cleanup collection operation tagging implementation thanks to @mvdbeek comments. 2018-02-01 21:02:01 -05:00
John Chilton 7490fd4520 More robust nametag discovery and propagation. 
- Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool.
- Nametags weren't being propagated to the outputs of collection operations.
 2018-02-01 21:02:01 -05:00
Martin Cech f24043e8a7 Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 
[18.01] Admin doc corrections
 2018-02-01 16:38:50 -05:00
Nate Coraor 6d8edce331 Admin doc corrections 2018-02-01 16:25:12 -05:00
Martin Cech ffaabe0a63 Merge pull request #5342 from dannon/integration.webhooks_improvements 
[18.01] Webhooks improvements
 2018-02-01 15:14:47 -05:00
Martin Cech a37b638491 Merge pull request #5390 from natefoo/framework-dependencies-doc-update 
[18.01] Update framework dependencies documentation
 2018-02-01 15:00:15 -05:00
Evgeny Anatskiy 29c766167a update webhooks docs 2018-02-01 12:22:21 -05:00
Evgeny Anatskiy 9b4465efd3 fix webhook's property name 2018-02-01 12:22:14 -05:00
Dannon Baker fa0ba22f97 Fix webhook filtering, make it a bit more defensive. Minor other tweaks. 2018-02-01 12:18:02 -05:00
Dannon Baker 22b0b2f2e9 Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes. 2018-02-01 12:18:02 -05:00
Dannon Baker 3b7daece04 Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported. 2018-02-01 12:18:02 -05:00
Dannon Baker 0ac7b7830d Fix import order in webhooks/__init__.py 2018-02-01 12:18:02 -05:00
Dannon Baker 57c1fc7804 Client formatting of webhooks changes. 2018-02-01 12:18:02 -05:00
Evgeny Anatskiy 90d59ac923 fix webhooks tests 2018-02-01 12:18:02 -05:00
Evgeny Anatskiy ada76931d8 add weighted random webhook pick 2018-02-01 12:18:01 -05:00
Evgeny Anatskiy 6070bf07e1 simplify Webhooks' structure 2018-02-01 12:18:01 -05:00
Martin Cech 6b0542f7c2 Merge pull request #5433 from davebx/release_18.01 
[18.01] Workaround for extra metadata revision creation
 2018-02-01 11:28:24 -05:00
Dave B 30ac9e940a Workaround for extra metadata revision creation 
Without this change, uploading non-metadata changes to a toolshed repository will display an error message and create a new metadata revision regardless of whether the code should determine that a new metadata revision is warranted.
 2018-02-01 09:21:16 -05:00
Nicola Soranzo baae416472 Merge pull request #5426 from jmchilton/fix_framework 
[18.01] Fix framework tests.
 2018-01-31 18:32:08 +00:00
John Chilton 73fe9bf827 Fix framework tests. 
Broken while framework tests were misconfigured. Thanks for @nsoranzo for tracking down the problem.
 2018-01-31 12:00:38 -05:00
Nicola Soranzo 5b23c0e87d Merge branch 'release_17.09' into release_18.01 
Conflicts:
	client/galaxy/scripts/mvc/workflow/workflow-node.js
	config/galaxy.ini.sample
	static/maps/mvc/workflow/workflow-node.js.map
	static/scripts/mvc/workflow/workflow-node.js
 2018-01-31 10:38:53 +00:00
Nicola Soranzo c0c95548a3 Merge branch 'release_17.05' into release_17.09 2018-01-31 10:16:33 +00:00
Björn Grüning 34421966d4 Merge pull request #5406 from mvdbeek/conda_and_channel_order_update 
[17.05] Follow IUC and drop r channel from default conda channels
 2018-01-31 10:15:01 +01:00
Marius van den Beek 8e5d2d3214 Merge pull request #5414 from jmchilton/skip_invalid_pja 
[17.09] Fix the PJA type issue when mapping renames over nested lists.
 2018-01-31 09:20:00 +01:00
John Chilton 54e07568be Merge pull request #5413 from mvdbeek/fix_dynamic_collection_output_18_01 
Allow map-over when discovering dataset collections
 2018-01-30 14:51:12 -05:00
mvdbeek cad17b07c3 Revert "Revert extra assertions that are causing unrelated issues to surface." 
This reverts commit 4925660ab4.
 2018-01-30 19:04:10 +01:00
John Chilton 9fcac13145 Fix the PJA type issue when mapping renames over nested lists. 2018-01-30 11:16:20 -05:00
mvdbeek eb506b25b9 Allow map-over when discovering dataset collections 
This would affect for example the mapping over of fastq-dump (and all other
tools in the sra-toolkit).

If one had attempted this previously the discovery phase would fail with:
```
galaxy.tools.parameters.output_collect ERROR 2018-01-30 08:56:46,369 Problem gathering output collection.
Traceback (most recent call last):
  File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 169, in collect_dynamic_collections
    collection
  File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/managers/collections.py", line 216, in collection_builder_for
    return builder.BoundCollectionBuilder(dataset_collection, collection_type_description)
  File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/dataset_collections/builder.py", line 84, in __init__
    raise Exception("Cannot reset elements of an already populated dataset collection.")
Exception: Cannot reset elements of an already populated dataset collection.
```

Instead we force the collection state to be new when we are discovering output collection datasets,
which seems reasonable to me. This includes an API testcase that would have failed previously.
 2018-01-30 14:48:42 +01:00
mvdbeek a70f2875b3 Remove r channel from more locations 2018-01-29 18:07:29 +01:00