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Author SHA1 Message Date
Nicola Soranzo 08cb278cc9 Add various elements to the Tool XML doc page 
In particular:
- macros
- edam_topics
- edam_operations
- environment_variables and subelement
- request_param_translation and subelements

Also:
- reorder elements to follow IUC coding style
- in examples:
  - use lowercase ``true`` and ``false`` for boolean attributes
  - add/use single quotes
- minor doc fixes
 2017-10-26 15:43:12 +01:00
Nate Coraor 7cfbb56a55 Merge remote-tracking branch 'origin/release_17.09' into dev 2017-10-26 10:29:56 -04:00
Nate Coraor 800a7faf27 Merge pull request #4863 from jmchilton/data_source_security_tests 
Simple tests for data source responses.
 2017-10-26 09:47:10 -04:00
Nate Coraor b9adcc81e8 Merge pull request #4844 from mvdbeek/workflow_performance_issues 
[17.09] Only subqueryload latest_workflow instead of all workflows
 2017-10-26 09:45:33 -04:00
John Chilton acf39e8e02 Fix tool XSD for data source tools. 
I guess it has never been applied to a data source?
 2017-10-26 08:39:48 -04:00
John Chilton 1ceb778b63 Merge pull request #4869 from nsoranzo/flake8_0.14 
Require flake8-import-order >=0.14
 2017-10-26 08:34:28 -04:00
Nicola Soranzo e780b0fe91 Require flake8-import-order >=0.14 2017-10-26 12:13:39 +01:00
Martin Cech 561ccfe815 Merge pull request #4867 from dannon/plumber 
Add a gulp plumber.
 2017-10-25 17:09:59 -04:00
Dannon Baker 6fd17e3669 Add a gulp plumber. 2017-10-25 16:46:21 -04:00
John Chilton 162bddd96c Simple tests for data source responses. 
- Verify a simple data source works when responding via the API.
- Verify a data source sending back a file:// parameter is blocked (GX-2017-0004/GX-2017-0003 - it is tracked different ways in the commit message and in the security issue tracker).
 2017-10-25 14:46:16 -04:00
Nicola Soranzo 9b3d217a2e Merge branch 'release_17.09' into dev 2017-10-25 19:34:21 +01:00
Nicola Soranzo 1baed58e1e Backport fix for E201 and E202 errors 
From commit 9b4de72ca6
 2017-10-25 19:30:19 +01:00
Nicola Soranzo 986031bf19 Merge branch 'release_17.05' into release_17.09 
Conflicts:
	lib/galaxy/webapps/galaxy/controllers/library_common.py
 2017-10-25 19:13:00 +01:00
Nicola Soranzo 20621b7d09 Merge branch 'release_17.01' into release_17.05 2017-10-25 19:07:46 +01:00
Nicola Soranzo a7bf1601a1 Merge branch 'release_16.10' into release_17.01 2017-10-25 19:05:24 +01:00
Nicola Soranzo 90289b6116 Merge branch 'release_16.07' into release_16.10 2017-10-25 19:03:52 +01:00
Nicola Soranzo e3e28ddc2d Merge pull request #4856 from jmchilton/release_16.07_fix_in_directory 
[16.07] Fix galaxy.util.in_directory()...
 2017-10-25 19:02:00 +01:00
John Chilton 0f5927b628 Merge pull request #4839 from martenson/library-expose-state 
expose state, stdout, stderr, uuid in the library API
 2017-10-25 13:25:10 -04:00
Martin Cech a1f0895c92 Merge pull request #4526 from guerler/remove_samples_000 
Removes Sample request and External services makos/controllers
 2017-10-25 12:38:08 -04:00
John Chilton 7e08ba6f19 Rework in_directory fix to move realpath expansion into galaxy.util. 2017-10-25 12:08:03 -04:00
John Chilton 95f8f48416 Doc fix thanks to @nsoranzo. 2017-10-25 10:43:54 -04:00
John Chilton fcb23eb8f8 Some documentation to clarify discussion on #4856. 2017-10-25 10:34:35 -04:00
John Chilton 4b5dc399b9 Add basic test for in_directory. 2017-10-25 10:32:20 -04:00
John Chilton 899b0d8068 Fix galaxy.util.in_directory() - broken because it takes realpath of just one argument. 
Easy to see on Mac OS X since /tmp isn't really /tmp for instance:

```
% touch /tmp/moo
% python
>>> import galaxy.util
>>> galaxy.util.in_directory("/tmp/moo", "/tmp/moo")
False
```

... and this is why the Travis tests are failing under Mac OS X. Broken with 93a8bfc7cb.
 2017-10-24 22:49:24 -04:00
John Chilton a4a8f15537 Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions 
[16.07] Fix regressions in library API
 2017-10-24 21:55:23 -04:00
Martin Cech 52b16ecd32 Merge pull request #4841 from bgruening/Analyze75 
add Analyze75 datatype
 2017-10-24 16:49:23 -04:00
guerler 3dd45099ba Remove "Lab" from masthead 2017-10-24 16:42:44 -04:00
guerler 1e23a6397b Fix order in center panel information view 2017-10-24 16:16:33 -04:00
guerler d3a6af5f71 Add legacy data libraries link 2017-10-24 16:03:15 -04:00
guerler 8e9a7e8625 Remove unused import 2017-10-24 15:52:18 -04:00
guerler 52a566eb05 Remove api dependency on web controller 2017-10-24 15:19:06 -04:00
guerler 8f6e5eb6f5 Merge branch 'dev' into remove_samples_000 2017-10-24 14:57:02 -04:00
Nicola Soranzo 9791dd22d4 Fix regressions in library API 
Introduced in commit 93a8bfc7cb
 2017-10-24 19:36:19 +01:00
John Chilton 01b244a810 Merge pull request #4853 from martenson/improve-RN 
[17.09] release notes - add tldr for security
 2017-10-24 13:04:47 -04:00
John Chilton 62826a1160 Merge pull request #4847 from nsoranzo/flake8_3.5.0 
Fix all E722 errors and ignore E741
 2017-10-24 13:04:22 -04:00
Martin Cech fa295c0f63 Merge pull request #4852 from dannon/fix_jsutils_time 
Fix jsutils time - fixes charts visualize
 2017-10-24 12:56:37 -04:00
John Chilton cfb61e0696 Rework security wording a bit. 
I waffle on adding security notes for the 17.09-only issues...
 2017-10-24 12:54:31 -04:00
Martin Cech add3a97bb0 this is not markdown 2017-10-24 12:31:03 -04:00
Martin Cech f5981e6ef3 add tldr for security 2017-10-24 12:28:11 -04:00
Dannon Baker 546a8c6df9 Remove unnecessary (not sure what the intent was here) assignment in return. 2017-10-24 11:55:10 -04:00
Dannon Baker d97fcf3a8d Prettier pre-bugfix. 2017-10-24 11:53:42 -04:00
John Chilton 2db575b241 Merge pull request #4850 from martenson/bootstrap 
minor changes to release  checklist
 2017-10-24 11:25:07 -04:00
John Chilton 73b31ce319 Merge pull request #4772 from martenson/17.09_release_notes 
[17.09] release notes
 2017-10-24 10:56:17 -04:00
Martin Cech f08700b208 rename wiki to hub 2017-10-24 10:48:16 -04:00
Martin Cech 6bbf345c28 remove wrongly added files 2017-10-24 10:44:12 -04:00
Martin Cech fe440d2736 Merge branch '17.09_release_notes' of github.com:martenson/galaxy into 17.09_release_notes 2017-10-24 10:36:56 -04:00
Martin Cech d1190bb067 deprecate undocumented refresh_on_change functionality 2017-10-24 10:36:10 -04:00
John Chilton 00bc7a51f9 More 17.09 release note fixes. 
Merge more items, fix more sentences, etc...
 2017-10-24 10:34:18 -04:00
Martin Cech 1b5421c1df Merge pull request #24 from tnabtaf/17.09_release_notes 
17.09 release notes edits
 2017-10-24 09:51:05 -04:00
John Chilton 3e8bf27fca More release notes improvements. 
Move a couple things higher, merge a couple more things, improved language (toward sentences).
 2017-10-24 09:48:51 -04:00