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15832 Commits
Author SHA1 Message Date
John Chilton 5e584bbe55 Update various Galaxy requirements. 
At least requests and Babel are required to get the latest "locked" version of the dev requirements compatible with our current locked versions in requirements.txt.

Removed repoze.lru from an earlier variant of this since the wheel didn't work - good catch @nsoranzo.
 2017-10-27 12:53:29 -04:00
Dannon Baker de9f8a6094 Merge branch 'selten/dev' into dev 2017-10-26 17:51:45 -04:00
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
Peter Selten 89e843730e Ensure galaxy can boot even with a malformed tour. 2017-10-25 19:43:12 +02:00
Peter Selten b3866bae16 Ensure Galaxy doesn't crash when a tour is malformed. 2017-10-25 19:40:09 +02:00
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
Peter Selten a3c00c122c Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 2017-10-19 21:26:17 +02:00
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
Peter Selten dea036f66a Use tags instead of groups 2017-10-19 19:31:55 +02:00
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