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Author SHA1 Message Date
Nicola Soranzo d807ed0f75 Merge branch 'release_17.05' into dev 
Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/bundled/login.bundled.js.map
 2017-06-02 15:05:14 +01:00
Aysam Guerler 0272e188a8 Merge pull request #4139 from dannon/tag_sorting 
[17.05] Tag fixes
 2017-06-02 02:05:44 -04:00
Dannon Baker 20d2303d34 Merge remote-tracking branch 'upstream/release_17.05' into dev 2017-06-01 13:39:36 -04:00
Dannon Baker b0c46cc4d0 Merge pull request #4140 from blankenberg/17.05_data_tables_URL_fix 
[17.05] Fix for Data Tables loaded from a URL.
 2017-06-01 13:36:28 -04:00
Dannon Baker c1d822d96d Merge pull request #4141 from erasche/wiki-links 
Swap over all URLs to new wiki location
 2017-06-01 13:26:42 -04:00
E Rasche 2f992d90ae Rebase 2017-06-01 16:43:21 +00:00
Daniel Blankenberg c2348340cf Fix for Data Tables loaded from a URL. 2017-06-01 12:36:37 -04:00
Dannon Baker e43ef79576 Merge pull request #4077 from martenson/improve-release-process 
Improve release checklist
 2017-06-01 11:46:15 -04:00
Dannon Baker 0954290e5d Combine list comprehensions, slightly tweak logic. 2017-06-01 10:38:18 -04:00
Dannon Baker 12905321ca Allow hashtag usage in workflow PJA tag addition mechanism 2017-06-01 10:38:18 -04:00
Dannon Baker 0c43954e8d Slight tweak of logic in tag filtering PJA 2017-06-01 10:38:18 -04:00
Dannon Baker 967c363786 Filter tags for empties (fixes #4127) 2017-06-01 10:38:18 -04:00
Dannon Baker c260e0b0c8 Sort tags for display (note, this is stupid to have in 3 places -- refactor) 2017-06-01 10:38:13 -04:00
Martin Cech 8b7b5b6c8e Merge pull request #4138 from dannon/workflow_display_styling 
Improved styling of workflow list.
 2017-06-01 10:31:47 -04:00
Dannon Baker f3aa53261d Improved styling of workflow list. Removed unused class, used hierarchy in base.less. 2017-06-01 09:48:44 -04:00
Dannon Baker 75028ac1ee Merge pull request #4133 from guerler/escape_regex 
[17.05] Properly escape potential regex expression in workflow parameters
 2017-05-31 19:20:44 -04:00
Martin Cech f6ced00ef0 Merge pull request #4135 from blankenberg/17.05_zipfile 
[17.05] Fix for returning a fileobject in compression_utils.py when handling a zipfile.
 2017-05-31 18:48:01 -04:00
Daniel Blankenberg a9d0d3671a Fix for returning a fileobject in compression_utils.py when handling a zipfile. 
Will return the first named object in the archive. zipfile.os_zipfile does not exist...
 2017-05-31 16:55:32 -04:00
guerler c409572ef8 Handle potential regex expression in workflow parameter names 2017-05-31 16:28:18 -04:00
Dannon Baker b6597d43f3 Merge remote-tracking branch 'upstream/release_17.05' into dev 2017-05-31 15:06:35 -04:00
Nicola Soranzo 5845af2562 Merge pull request #4126 from manabuishii/patch-5 
Fix typo
 2017-05-31 08:12:05 +01:00
Manabu ISHII 7037a57a42 Fix typo 2017-05-31 13:45:25 +09:00
Aysam Guerler d61ab1644b Merge pull request #4124 from dannon/fix_workflow_menu_escaping 
New workflow menu message fix
 2017-05-30 15:06:19 -04:00
Dannon Baker 5c954139fa Since we're using addClass to inject status type, it's not necessary to escape this one. 2017-05-30 14:27:06 -04:00
Dannon Baker 8080c08ae6 Fix escaping of status/message passed by querystring in the new workflow 
menu.
 2017-05-30 14:24:59 -04:00
Dannon Baker 9896fc0e9f Merge pull request #4092 from bgruening/workflowexport_mako 
New Configure Workflow Menu UI
 2017-05-30 13:36:12 -04:00
Martin Cech 42e274d334 Merge pull request #4122 from galaxyproject/release_17.01 
[17.05] merge Release 17.01
 2017-05-30 10:11:51 -04:00
Martin Cech aa7d701cbc Merge pull request #4121 from peterjc/locales_string_letters 
Avoid locale specific string.letters for job_name
 2017-05-29 22:56:18 -04:00
peterjc 54d6a54367 Avoid locale specific string.letters for job_name 
The job_name sanitation can fail if the locale specific
string.letters contains unexpected characters. e.g.
Saravanaraj Ayyampalayam reported getting the following
under locale en_US.iso885915

Traceback (most recent call last):
  File /.../galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 397, in <genexpr>
    job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name )
UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128)

See http://dev.list.galaxyproject.org/Issue-with-job-name-UnicodeDecodeError-in-drmaa-td4670784.html
or https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-May/025687.html

The downside of this proposed change would be to mask
reasonable non ASCII letters from the job name on a
well defined system with consistent locale settings
for both Galaxy and the Cluster. But ASCII only seems
safer.
 2017-05-29 17:40:37 +01:00
Marius van den Beek 96e1cf58f4 Merge pull request #4117 from jmchilton/genome_diversity_fixes 
[17.01] Fix legacy Python path for genome diversity tools from miller lab.
 2017-05-29 13:13:37 +02:00
John Chilton 55336d2c31 Fix legacy Python path for genome diversity tools from miller lab. 
Fixes #4108.
 2017-05-28 19:34:20 -04:00
Marius van den Beek 3d16319a15 Merge pull request #4114 from dannon/force_uniqueness_preserved_tags 
[17.05] Force uniqueness of preserved tags
 2017-05-27 08:38:04 +02:00
Dannon Baker 2ac04bbf09 Uniqueify hashtag display 2017-05-26 13:30:21 +01:00
Dannon Baker dd06a01746 Handle *both* paths for tag appending using the now-dict correctly. 2017-05-26 10:22:13 +01:00
Dannon Baker b6e8d3e8ac Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. 2017-05-26 10:14:48 +01:00
Dannon Baker 68433b1eff Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) 2017-05-25 15:33:09 +01:00
Martin Cech 64d6ffd59d Merge pull request #4112 from guerler/fix_populate 
Fix failed merge for populate model
 2017-05-24 14:10:34 -04:00
guerler 6f5e76eecc Fix bad merge for populate model 2017-05-24 12:59:30 -04:00
Martin Cech 18ef6a6ab0 Update version to 17.05 v17.05 2017-05-24 10:47:27 -04:00
Martin Cech d7a0fdfaa7 Merge branch 'release_17.05' into dev 2017-05-24 10:47:27 -04:00
Martin Cech e50c787aa7 Merge branch 'release_17.05' into dev 2017-05-24 10:47:20 -04:00
Martin Cech d8c21e1fd9 Merge pull request #4110 from nsoranzo/release_17.05 
[17.05] Improve 17.05 release notes
 2017-05-24 10:38:05 -04:00
Nicola Soranzo 4294663d53 Improve 17.05 release notes 
Also add 4 pull requests merged in the last few days.
 2017-05-24 12:10:05 +01:00
Nicola Soranzo 31015a83af Remove residual comment 
Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
 2017-05-24 11:18:47 +01:00
Nicola Soranzo e0c0111524 Merge branch 'release_17.05' into dev 2017-05-23 23:32:33 +01:00
Martin Cech 0268f5078c Merge pull request #4107 from guerler/fix_repeats_in_workflows 
[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
 2017-05-23 13:50:26 -04:00
Martin Cech 3d1da8e11d Merge pull request #4089 from mvdbeek/no_global_changes 
[17.05] Do not modify self.app.config.tool_data_path
 2017-05-23 13:19:41 -04:00
Martin Cech aa8aafb109 Merge pull request #4104 from dannon/tags_continued 
[17.05] Change to only inheriting 'name' tags
 2017-05-23 13:01:19 -04:00
guerler 4dcc145dbf Remove composite api function and duplicate resource connector 2017-05-23 12:19:03 -04:00
guerler 6f8472e525 Fixes repeat handling in workflow editor, store values as passed from ui 2017-05-23 08:08:28 -04:00