greg
3fdd4edc5c
Subclass IdeasPre from Html
2018-02-02 13:07:52 -05:00
greg
b5945ad3e3
Add IdeasPre datatype subclassed from Rgenetics
2018-02-02 09:22:10 -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
mvdbeek
414c031247
Follow IUC and Drop r channel from default cond channels
2018-01-29 17:35:49 +01:00
John Chilton
b1c5186e1c
Merge pull request #5397 from nsoranzo/release_18.01_conda_fixes
...
[18.01] Install latest conda and don't use shell=True
2018-01-26 10:19:00 -05:00
Nate Coraor
6333e83a65
Doc corrections from @nsoranzo
2018-01-26 10:18:53 -05:00
Dannon Baker
17fe5d635a
Merge branch 'release_17.09' into release_18.01
2018-01-26 10:06:29 -05:00
Dannon Baker
d6fb37071d
Merge pull request #5398 from mvdbeek/subworkflow_creation_fix
...
[17.09] Subworkflow creation fix
2018-01-26 10:03:40 -05:00
mvdbeek
f589a0cb5b
Build client
2018-01-26 14:22:15 +01:00
mvdbeek
74d57cfc1c
Fix subworkflow creation
...
This fixes #5396 . The problem was that we would override the content_id with an
undefined value. Broken in https://github.com/galaxyproject/galaxy/pull/5249 .
2018-01-26 14:22:15 +01:00
Nicola Soranzo
b8873c65ad
Install the latest version of conda and conda-build
...
Conda 4.3.33 contains a fix that should solve some conda env
creation programs:
https://github.com/conda/conda/pull/6766
Also support conda installation on x86 Linux architecture.
2018-01-26 11:34:52 +00:00
Nicola Soranzo
889aa29d02
Conda: pass subprocess arguments as list
2018-01-26 11:31:29 +00:00
Martin Cech
b6d0b14921
Merge pull request #5391 from dannon/release_17.09
...
[17.09] Constrain workflow tool panel entries to those not deleted.
2018-01-25 18:38:34 -05:00
Dannon Baker
9c187f0e5a
Constrain workflow tool panel entries to those not deleted.
2018-01-25 13:44:40 -05:00
Nate Coraor
fd96864bd6
Finish updates to framework dependencies doc
2018-01-25 12:36:11 -05:00
Nate Coraor
6bdd755aaf
WIP framework dependencies doc update
2018-01-25 12:36:11 -05:00
Nicola Soranzo
3b69c645da
Merge pull request #5387 from martenson/version-18.01
...
[18.01] Update version to 18.01.rc1
2018-01-25 17:10:46 +00:00
Martin Cech
392565489b
Update version to 18.01.rc1
2018-01-25 10:56:33 -05:00
Martin Cech
4e17ce81f4
Merge remote-tracking branch 'upstream/release_17.09' into dev
2018-01-25 10:55:41 -05:00
Martin Cech
5defdc7919
Merge pull request #5364 from dannon/history_multipanel_fixes
...
History multipanel fixes
2018-01-25 10:51:27 -05:00
greg