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30,744 Commits 62 Branches 243 Tags
08cb278cc9612a70dcb9dd77ff3bfbdfd333ce2b
Commit Graph
15825 Commits
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
Nicola Soranzo e780b0fe91 Require flake8-import-order >=0.14 2017-10-26 12:13:39 +01:00
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
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
Martin Cech 52b16ecd32 Merge pull request #4841 from bgruening/Analyze75 
add Analyze75 datatype
 2017-10-24 16:49:23 -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
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Dannon Baker 2f2acb98e0 Merge remote-tracking branch 'guerler/remove_toolshed_grids' into dev 2017-10-23 17:23:46 -04:00
Martin Cech d11ed538c6 tie sample tracking api controllers functionality to config 
introduce enable_legacy_sample_tracking_api config option that controls that
disable by default
 2017-10-23 15:11:10 -04:00
Martin Cech 7c3fdbe1a5 Merge branch 'dev' into remove_samples_000 2017-10-23 14:43:32 -04:00
Martin Cech 7e667170cd optimize the admin query 2017-10-23 14:20:45 -04:00
mvdbeek dd609265a2 Only subqueryload latest_workflow instead of all workflows 2017-10-23 18:15:44 +02:00
Nate Coraor 8bc242abc1 Security: Switch GIE Popen() calls to run without shell=True to fix an 
ACE vulnerability.
 2017-10-23 10:25:22 -04:00
Nate Coraor 92d63977a9 Security: Fix issues with path handling in libraries and in general. 2017-10-23 10:25:22 -04:00
Nate Coraor c3fd90a36d Security: Switch GIE Popen() calls to run without shell=True to fix an 
ACE vulnerability.
 2017-10-23 10:24:50 -04:00
Nate Coraor f02cd7ddb6 Security: Fix issues with path handling in libraries and in general. 2017-10-23 10:24:50 -04:00
Björn Grüning 319d1cb794 lint fixes 2017-10-21 16:53:48 +02:00
Bjoern Gruening 72dd4a3a79 add Analyze75 datatype 2017-10-21 16:33:13 +02:00
Martin Cech f6737618e3 expose state, stdout, stderr, uuid in the API 
fix few bugs and UI/UX glitches
 2017-10-20 16:27:00 -04:00
Nate Coraor 17b45ff6d1 Fix the case where 'Labels' in a docker node inspect exists but is null. 2017-10-20 15:37:06 -04:00
Nate Coraor 206f5ec034 Merge remote-tracking branch 'origin/release_17.09' into dev 2017-10-20 14:43:43 -04:00
guerler 799fda61db Filter library dataset by user 2017-10-20 11:57:37 -04:00
guerler 42dc7b3617 Filter histories for visualization grids by user 2017-10-20 11:35:32 -04:00
Daniel Blankenberg 3b03b5b6cc Fix for single select list initial value when multiple options are selected by default. 2017-10-19 13:35:40 -04:00
Nate Coraor 9f8d3ee444 Security: Switch GIE Popen() calls to run without shell=True to fix an 
ACE vulnerability.
 2017-10-19 10:27:56 -04:00
Nate Coraor e8a72252ef Security: Fix issues with path handling in libraries and in general. 2017-10-19 10:27:53 -04:00
Nate Coraor 1bccbefbff Security: Fix issues with path handling in libraries and in general. 2017-10-19 10:26:44 -04:00
Nate Coraor ed045cd570 Security: Fix issues with path handling in libraries and in general. 2017-10-19 10:26:23 -04:00
Nate Coraor 93a8bfc7cb Security: Fix issues with path handling in libraries and in general. 2017-10-19 10:26:08 -04:00
Nate Coraor 0447ec7ea0 Merge remote-tracking branch 'origin/release_17.09' into dev 2017-10-19 09:19:18 -04:00
Nate Coraor acc59e4d5d Merge remote-tracking branch 'origin/release_17.05' into release_17.09 2017-10-19 09:18:41 -04:00
Nate Coraor f0e9767912 Merge remote-tracking branch 'origin/release_17.01' into release_17.05 2017-10-19 09:14:02 -04:00