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Author SHA1 Message Date
guerler 5d5dfb5f64 Revise ui-misc 2016-01-14 15:37:07 -05:00
Martin Cech f617f739dc Merge pull request #1510 from martenson/log-user-exceptions-properly 
[16.01] catch Exception and properly log errors
 2016-01-14 12:57:23 -05:00
Martin Cech 12445a0524 use log.exception instead of log.error to retain the stacktrace 2016-01-14 12:53:23 -05:00
Martin Cech 3ee94d58e0 catch Exception and properly log errors 2016-01-14 11:35:11 -05:00
Nicola Soranzo 669d65c327 Merge pull request #1505 from jmchilton/dev_merge_0 
Fix Python 3 problem causing Travis failure of dev.
 2016-01-14 15:35:59 +00:00
Dannon Baker be7c0dfcbf Merge pull request #1463 from guerler/tour_000 
Scratchbook tour
 2016-01-14 09:43:34 -05:00
guerler e52626b279 Apply fix from 16.01 2016-01-14 09:09:57 -05:00
guerler 30c472a388 Add flat id attribute to form parameters 2016-01-14 09:05:31 -05:00
guerler 0ccb72160a Refactor masthead render to improve readibility 2016-01-14 09:04:41 -05:00
guerler b38bc293d7 Add Scratchbook tour 2016-01-14 09:02:29 -05:00
guerler 94443625d8 Cleanup settings view 2016-01-14 09:02:27 -05:00
John Chilton aeafcb1d6d Merge pull request #1504 from jmchilton/dev_merge_0 
Merge release 16.01 into dev.
 2016-01-14 07:46:53 -05:00
Dannon Baker 33a3ae4562 Merge pull request #1489 from nsoranzo/flake8_fixes 
Fix all E731 "errors".
 2016-01-14 07:38:22 -05:00
Björn Grüning be4ddb26d4 Merge pull request #1473 from jmchilton/job_shell 
[16.01] Allow override of job shell (for conda resolver).
 2016-01-14 13:35:53 +01:00
Björn Grüning 1dac5f3bb6 Merge pull request #1502 from jmchilton/planemo_fix 
[16.01] Fix a few problems discovered through planemo.
 2016-01-14 11:31:00 +01:00
John Chilton 7de3bcdd7e Merge pull request #1495 from natefoo/pin-release-wheels 
[16.01] Pin release wheel versions
 2016-01-14 04:23:28 -05:00
John Chilton f41550f69f Merge pull request #1488 from martenson/fix-jobparam-hack 
fix old jobparam hack for importing files to library
 2016-01-14 04:21:59 -05:00
John Chilton eb3fc642fc Merge pull request #1498 from blankenberg/tab_mime 
[16.01] Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes.
 2016-01-14 04:12:27 -05:00
John Chilton 0902c23f34 Merge pull request #1501 from guerler/fix_disabled_000 
[16.01] Fix disabled css
 2016-01-14 04:08:18 -05:00
John Chilton ba592a79fe Fix Python 3.4 problem causing Travis failure of dev. 2016-01-14 07:51:45 +00:00
John Chilton 793fbdbedc Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0 
Conflicts:
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2016-01-14 07:44:48 +00:00
John Chilton f2c3eaaf64 Merge branch 'release_16.01' into dev_merge_0 
Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2016-01-14 07:41:29 +00:00
John Chilton 602dc7f664 Switch default job shell back to /bin/sh for 16.01. 2016-01-14 06:17:45 +00:00
John Chilton e69638277f Fix tab problem in test tool. 
dash will convert the literal characters \t to a tab, bash doesn't seem to do this. Use portable printf as suggested by nicola.
 2016-01-14 06:17:45 +00:00
John Chilton 3e47aa23b8 Switch to bash as default shell (for conda resolver). 
I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now.
 2016-01-14 06:17:43 +00:00
Martin Cech 2e62388b2f Merge pull request #1494 from jmchilton/tool_command_integrity 
[16.01] Fix to ensure integrity of tool_script.sh also.
 2016-01-14 00:41:57 -05:00
guerler 4b5b970d78 Fix disabled css 2016-01-13 20:50:40 -05:00
Nicola Soranzo 487ece0f40 Fix all E731 "errors". 2016-01-14 01:19:01 +00:00
Dannon Baker 9d52a4a31d Merge pull request #1493 from guerler/undo_user_000 
[16.01] Undo user icon in masthead
 2016-01-13 18:46:11 -05:00
John Chilton f78756cb79 Fix a few problems discovered through planemo. 
Including 'TypeError: _get_config_option() got multiple values for keyword argument 'prefix' and problem when planemo's cwltool is installed in Galaxy's virtualenv.
 2016-01-13 22:32:56 +00:00
Daniel Blankenberg 0bcfa74ea1 Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Fixes the issue of losing newlines and actual spacing (i.e. do not treat as html). 2016-01-13 16:28:59 -05:00
Martin Cech 84fd89d67a Merge pull request #1496 from guerler/labels_000 
Revise label handling in form
 2016-01-13 16:28:51 -05:00
guerler e14449e62d Revise label handling in form 2016-01-13 16:23:38 -05:00
John Chilton 91fe9d09aa Merge pull request #1497 from jmchilton/dev_merge_0 
Merge 16.01 into dev.
 2016-01-13 16:09:17 -05:00
Nate Coraor 9d91be8dd3 Pin release wheel verisons. pinned-requirements.txt renamed to 
pinned-hashed-requirements.txt as unfortunately even Galaxy pip does not
support --hash
 2016-01-13 14:47:57 -05:00
guerler 37f8038d63 Undo user icon in masthead 2016-01-13 14:31:40 -05:00
Nate Coraor becffe93a3 Merge pull request #1485 from jmchilton/common_startup_fixes 
[16.01] Fix common_startup options for planemo.
 2016-01-13 14:20:56 -05:00
Martin Cech 74afe4127a fix old jobparam hack for importing files to library 2016-01-13 12:16:53 -05:00
Martin Cech 86158cbc7f Merge pull request #1487 from dannon/release_16.01 
[16.01] Cherrypick of pep8 fixes.
 2016-01-13 11:18:50 -05:00
John Chilton e13fb12569 Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0 2016-01-13 16:08:13 +00:00
Dannon Baker 2f1dbeee68 Address W503 and E721 errors now enforced by pep8 1.7. 2016-01-13 10:41:27 -05:00
Dannon Baker b559cf303c Drop E731 from flake8 enforcement (though we should revisit this and see if we *do* want to follow this or not) 2016-01-13 10:41:19 -05:00
Aysam Guerler 790953e6e7 Merge pull request #1478 from dannon/lparsons_bad_urls 
URL generation tweaks for utils.js
 2016-01-13 09:59:36 -05:00
John Chilton 55677f2d3d Fix to ensure integrity of tool_script.sh also. 
Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected.

Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable.
 2016-01-13 14:58:28 +00:00
Dannon Baker 46e5e480cb Merge remote-tracking branch 'upstream/dev' into lparsons_bad_urls 2016-01-13 09:32:48 -05:00
John Chilton 8fd83df665 Allow override of location of virtual env Galaxy manages. 2016-01-13 13:55:36 +00:00
John Chilton 9dc9ddf8cd Add --replace-pip option to common_startup.sh. 
Needed to restore correct functionality to planemo.
 2016-01-13 13:55:35 +00:00
John Chilton 0a6f6c3da4 Merge pull request #1483 from dannon/fix_lint_new_flake8 
Fix project linting for new pep8
 2016-01-12 20:51:57 -05:00
John Chilton ea5c082e88 Merge pull request #1402 from bgruening/remove_ipython 
Remove IPython IE, which was replaced by Jupyter IE.
 2016-01-12 18:53:07 -05:00
Dannon Baker 89e7c3df95 Address W503 and E721 errors now enforced by pep8 1.7. 2016-01-12 18:26:20 -05:00