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Author SHA1 Message Date
Max Schaefer 43ddd47320 Add missing var declarations. 
In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global.
 2017-08-16 15:22:42 +01:00
Max Schaefer 7ef9b4cdaf Remove spurious null check. 2017-08-16 15:22:10 +01:00
Dannon Baker c5a91491c6 Merge pull request #4432 from guerler/fix_role_association_check 
Fix private role validation
 2017-08-16 09:27:50 -04:00
Björn Grüning b6f0600e98 Merge pull request #4387 from jmchilton/tool_unit_test_cleanup 
Cleanup of Unit Test Code for Loading Tools
 2017-08-16 14:55:14 +02:00
John Chilton 8eb487e7c1 Merge pull request #4431 from mvdbeek/break_connections 
Break connection in workflow editor if necessary
 2017-08-15 22:05:16 -04:00
guerler 522ca9e5c2 Fix private role validation 2017-08-15 17:22:41 -04:00
mvdbeek 09c4b1037b Break connection in workflow editor if necessary 
When switching tool versions in the workflow editor connections are
maintained by default. If a tool changes the datatype one may end up
with a connection between incompatible input/outputs. Therefore we
update the datatypes and explicitly destroy invalid connections.
 2017-08-15 21:50:08 +02:00
Martin Cech 4bddd617fe Merge pull request #4405 from guerler/admin_grid_groups 
Admin grid groups revision
 2017-08-15 14:41:59 -04:00
guerler e72948cb74 Merge branch 'dev' into admin_grid_groups 2017-08-15 12:12:53 -04:00
Dannon Baker 462b7def5d Merge pull request #4427 from nsoranzo/merge_release_17.05 
Merge release_17.05 into dev
 2017-08-15 11:36:16 -04:00
Martin Cech 27be249638 Merge pull request #4373 from mvdbeek/switch_versions_in_workflows 
Allow switching tool versions in workflow editor
 2017-08-15 11:34:37 -04:00
Martin Cech aa7be28960 Merge branch 'dev' into switch_versions_in_workflows 2017-08-15 11:25:03 -04:00
Nicola Soranzo 07a3049999 Merge branch 'release_17.05' into dev 
Conflicts:
	lib/galaxy/model/tool_shed_install/__init__.py
 2017-08-15 16:24:32 +01:00
John Chilton 44548f8f2f Merge pull request #4409 from nsoranzo/fix_conda_channel_order 
Update conda channel order to sync with Bioconda
 2017-08-15 09:32:54 -04:00
John Chilton 8721da8ca2 Merge pull request #4426 from erasche/local-runner-unicode 
some unicoding for local runner
 2017-08-15 09:27:38 -04:00
John Chilton 7f78ee7b18 Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast 
[17.05] Don't cast tool_version to string if tool_version is None-type
 2017-08-15 09:26:58 -04:00
E Rasche 68555f5571 some unicoding 2017-08-15 14:04:05 +02:00
guerler fd5f42dc17 Merge branch 'dev' into admin_grid_groups 2017-08-14 10:57:39 -04:00
guerler eccdc8c248 Removed unreached message line 2017-08-14 10:56:20 -04:00
Nicola Soranzo cdbac056cb Override channel list on the command line instead of modifying condarc 
The way we were modifying condarc in the ensure_channels_configured()
method was broken because we were appending the missing channels at the
end, so the final order may not be the one specified in
conda_ensure_channels .

Also:
- not modifying the user condarc is a much better approach
- overriding the channel list on the command line will make debugging
  easier
 2017-08-14 15:27:15 +01:00
Nicola Soranzo 420e7a4f34 Remove _ensure_conda_context() function 
and make conda_context argument mandatory in functions/methods.
This should help making sure the correct context (e.g. channels)
is used for all Conda operations.

Also remove unused is_target_available() function.
 2017-08-14 14:38:23 +01:00
Nicola Soranzo 4dd503046f Update conda channel order to sync with Bioconda 2017-08-14 12:18:39 +01:00
Nicola Soranzo 9cbabef17e Merge branch 'release_17.05' into dev 
Conflicts:
	static/maps/mvc/library/library-foldertoolbar-view.js.map
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/mvc/library/library-foldertoolbar-view.js
 2017-08-14 12:07:17 +01:00
Nicola Soranzo 4faf496c98 Merge branch 'release_17.01' into release_17.05 
Conflicts:
	tox.ini
 2017-08-14 11:54:55 +01:00
Marius van den Beek 0f5ad34eaf Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes 
[17.01] Add missing chemical formats to datatypes_conf.xml.sample
 2017-08-14 12:27:14 +02:00
Marius van den Beek e594152de2 Merge pull request #4394 from jmchilton/subworkflow_loading_fix 
Bugfix for loading subworkflows from workflow descriptions.
 2017-08-14 12:25:47 +02:00
Marius van den Beek 8e192dbf4c Merge pull request #4397 from jmchilton/api_test_enhancement 
Better Error Summaries for API Tests
 2017-08-14 12:22:34 +02:00
mvdbeek 6ad6fd9252 Rebuild tool_version_cache on DetachedInstanceError 2017-08-14 11:58:48 +02:00
Björn Grüning f849c7e6fe Merge pull request #4417 from jmchilton/upload_enhance 
Fixes and enhancements for the upload API
 2017-08-14 10:18:45 +02:00
mvdbeek 73f4141d96 Add static JS 2017-08-14 00:21:25 +02:00
mvdbeek d0b06a3b1d Don't cast tool_version to string if tool_version is None-type 
If a version is not specifically requested a wrong version (`None` cast to
`'None'`) of a tool will be loaded in the workflow editor instead of the
latest version.

That should address @martenson's remark in
https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674
(and maybe also
https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153).
 2017-08-14 00:09:33 +02:00
mvdbeek df91881c1f Remove unused workflow outputs 2017-08-13 23:50:15 +02:00
mvdbeek 31c423a45a Fix typo and remove leftover comment (thanks @nsoranzo) 2017-08-13 23:50:14 +02:00
mvdbeek 2e95026317 Remove unused old_version variable 2017-08-13 23:50:14 +02:00
mvdbeek 1c286b158a Remove extra newlines 2017-08-13 23:50:14 +02:00
mvdbeek 92fedc0ae8 Fix logic for adding and removing outputs 2017-08-13 23:50:14 +02:00
mvdbeek bc95f5e81b Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic 2017-08-13 23:50:14 +02:00
mvdbeek ea1f4f8666 Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date 2017-08-13 23:50:14 +02:00
mvdbeek db2ea853f6 Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow 2017-08-13 23:50:14 +02:00
mvdbeek 526e98e372 Reset outputs when changing tool versions in wf-editor 2017-08-13 23:50:14 +02:00
mvdbeek 36ce9113f7 Keep spacing consistent (thx @nsoranzo) 2017-08-13 23:50:14 +02:00
mvdbeek 5afe490822 Fix qunit test 2017-08-13 23:50:14 +02:00
mvdbeek 25e05b62c7 Do postchange action only when modifiying tool versions in the workflow editor 2017-08-13 23:50:14 +02:00
mvdbeek 5f1b7d5a50 Show verison button in workflow editor and trigger on_change 2017-08-13 23:50:14 +02:00
John Chilton 06ca789f92 Configuration tests for the last few upload enhancements. 2017-08-12 07:13:05 -04:00
John Chilton fc861cdf38 Merge pull request #3064 from manabuishii/install_workflow_and_tools 
Install tools and workflow
 2017-08-12 06:49:01 -04:00
John Chilton fec1eab82d Add ability to arbitrarily not decompress files on upload via API. 2017-08-12 06:36:50 -04:00
John Chilton bee6af1e41 Allow API tests to work with admin users (not just admin keys). 2017-08-12 06:36:50 -04:00
John Chilton 53b0b25456 Better error reporting in test/base/populators.py. 2017-08-12 06:36:50 -04:00
John Chilton 59aa11864a Add configuration option to disable upload content checking. 2017-08-12 06:36:50 -04:00