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Author SHA1 Message Date
guerler 38037e487d Always open tool help links in a new window tab 2015-06-05 15:15:29 -04:00
John Chilton 2671df6244 Merge pull request #315 from carlfeberhard/fix.dataset-file 
[15.05] API, HDAs/Datasets: re-add file_name to detailed serializatio…
 2015-06-05 13:02:10 -04:00
Carl Eberhard 5097a9300a [15.05] API, HDAs/Datasets: re-add file_name to detailed serialization for admin users (resolve #313) 2015-06-05 11:45:58 -04:00
Dannon Baker f428443eff Merge pull request #310 from nsoranzo/release_15.05 
[15.05] Mark also HDAs as purged when purging datasets via cleanup script.
 2015-06-04 16:53:29 -04:00
Nicola Soranzo 292d16a593 Mark also HDAs as purged when purging datasets via cleanup script. 
This will make purged datasets be shown as purged in histories,
preventing them to be undeleted through the UI.
This will not fix datasets previously purged through this script,
scripts/cleanup_datasets/pgcleanup.py may be used for that.
 2015-06-04 18:06:01 +01:00
John Chilton cf44639ebf Merge pull request #305 from bgruening/IE-spinner-fix 
fix displaying the interactive environment spinner
 2015-06-02 14:33:33 -04:00
Bjoern Gruening 1cb06bd4ec fix path to spinner icon, grunting 2015-06-02 15:58:24 +02:00
Bjoern Gruening 654c216a77 fix path to spinner icon 2015-06-02 15:54:45 +02:00
Dannon Baker ae25e3054e Merge pull request #304 from jmchilton/1505_histories_share_fix 
[15.05] Backport Bjoern's bug in history sharing.
 2015-06-02 08:54:06 -04:00
Björn Grüning 7294bd0af3 Fix bug in history sharing. 2015-06-02 08:38:55 -04:00
Dannon Baker ef99cca5d1 Merge branch 'release_15.03' into release_15.05 2015-06-01 14:03:09 -04:00
Aysam Guerler 4445092410 Merge pull request #293 from jmchilton/history_tag_fix_15.03 
[15.03] Fix tag creation via /tags API endpoints.
 2015-05-28 11:44:53 -04:00
John Chilton 2ca8f7665b Fix tag creation via /tags API endpoints. 
Add test case to at least check for exceptions such as those reported.

Closes galaxyproject/bioblend#145.
 2015-05-27 12:51:53 -04:00
Dannon Baker 9f754357d9 Merge pull request #288 from jmchilton/history_tag_fix_15.05 
[15.05] Fix tag creation via /tags API endpoints.
 2015-05-26 11:42:19 -04:00
John Chilton 44c8e74c29 Fix tag creation via /tags API endpoints. 
Add test case to at least check for exceptions such as those reported.

Closes galaxyproject/bioblend#145.
 2015-05-25 22:31:09 -04:00
Daniel Blankenberg 4b35e18388 Merge pull request #283 from jmchilton/bool_shed_test_fix 
[15.05] Fix test parsing to adapt to tool shed expectations.
 2015-05-21 17:05:49 -04:00
John Chilton 00342bdd9e Fix test parsing to adapt to tool shed expectations. 
Should fix error reported by @nsoranzo (https://gist.github.com/nsoranzo/6cb3c34f051aaea8ec22).

This was broken with f469db3d7e (Pull Request #273).
 2015-05-21 13:16:11 -04:00
John Chilton 7c88e3624e Merge pull request #276 from guerler/tool_form_000 
[15.05] Revise checksum to detect tool form changes
 2015-05-20 14:42:39 -05:00
Nate Coraor 0dc7669646 Merge pull request #275 from martenson/data-source-fix 
[15.05] fix the data source tools for modendcode with proper URLs
 2015-05-20 15:15:33 -04:00
Daniel Blankenberg 9e67ba6de2 Merge pull request #278 from natefoo/load_speedup_cherrypick 
[15.05] Significant speedup of tool panel/homepage loading
 2015-05-20 12:49:18 -04:00
Daniel Blankenberg 8d2f9f77eb Update modencode dbkeys in gbrowse_build_sites.txt 2015-05-20 12:47:01 -04:00
Daniel Blankenberg af6172d14d Update default dbkey for worm_modencode.xml and bump version. 
ce10 is UCSC for WS220
 2015-05-20 12:42:05 -04:00
Daniel Blankenberg 93c51fa259 Update default dbkey for fly_modencode.xml and bump version. 
dm3 is UCSC for release 5
 2015-05-20 12:39:59 -04:00
Nate Coraor 27476764e9 Merge pull request #273 from jmchilton/test_bool_fixes 
[15.05] Fixes for boolean & select handling in test data elements.
 2015-05-20 12:29:44 -04:00
abretaud c567530723 handle adding/removing tools from toolshed 
(cherry picked from commit 911acd7a6e)
 2015-05-20 12:21:21 -04:00
abretaud 0d3c849d4f perf optimization: store tools' section in a dict instead of looping through the whole list of sections/tools for each tool 
(cherry picked from commit b8261db255)
 2015-05-20 12:21:15 -04:00
guerler 2fa3dabf0e Remove debug output 2015-05-19 17:39:27 -04:00
guerler 2db905c5c1 Add field id to checksum 2015-05-19 17:39:04 -04:00
guerler bf436582a8 Fix checksum to detect tool form changes 2015-05-19 17:32:04 -04:00
Martin Cech 182fbd1bc6 fix the data source tools for modendcode with proper URLs 2015-05-19 16:53:25 -04:00
John Chilton f469db3d7e Fixes for boolean & select handling in test data elements. 
- Allow boolean "truevalue"/"falsevalue" to be used in plain (non-conditional test element) parameters (see https://trello.com/c/iGk3f1pE).
 - Fix conditionals to use processed values - so this fix and 5b6c092aa0 are applid to these elements as well. (http://osdir.com/ml/general/2015-05/msg24402.html).

This also adds tests to verify these behaviors.

Run most relevant tests with commands:

    ./run_tests.sh -framework -id simple_constructs
    ./run_tests.sh -framework -id multi_select
    ./run_tests.sh -framework -id boolean_conditional
 2015-05-19 12:43:32 -04:00
Dannon Baker f1072db8b2 Merge pull request #271 from guerler/fix_empty_history_000 
[15.05] Disable automated history creation in data tool parameters
 2015-05-19 10:19:55 -04:00
guerler 15480dc4f1 Disable automated history creation in data tool parameters 2015-05-18 18:39:47 -04:00
Dannon Baker 55bc3ebb8a Merge pull request #265 from jmchilton/collection_fixes_15.05_2 
[15.05] Fix implicit output collection names when mapping over collections.
 2015-05-15 13:02:08 -04:00
John Chilton 2cac7e817b Fix implicit output collection names when mapping over collections. 2015-05-15 11:06:19 -04:00
Dannon Baker 41e7118a2a Merge pull request #262 from jmchilton/collection_fixes_15.05 
[15.05] Collection-y fixes for 15.05
 2015-05-15 09:56:13 -04:00
John Chilton 4ad4688fde Fix label's on output collections. 
Thanks to @kellrott for reporting the issue.

https://trello.com/c/Qc2A4rsw
 2015-05-14 16:33:39 -04:00
John Chilton fbaba4b463 Fix auto-hiding collections when mapping over tools. 
Broken by that moron @jmchilton in 44f7317fa5.
 2015-05-14 16:33:39 -04:00
Martin Cech 47aad5087f Merge pull request #260 from bgruening/release_15.05 
Pin the IPython Docker Image to the 15.05.
 2015-05-14 15:36:07 -04:00
Björn Grüning 8965dd2cbf Pin the IPython Docker Image to the 15.05. 
From now on we pin every Galaxy release to a special ipython-notebook image.
 2015-05-14 21:23:27 +02:00
Nate Coraor 0090d9a8cd Bump verison to 15.05 2015-05-13 17:09:38 -04:00
Nate Coraor 78ac97f9e9 Merge pull request #253 from jmchilton/release_notes_15.05 
[15.05] First crack at dev release notes for 15.05 release.
 2015-05-13 16:54:59 -04:00
Nate Coraor 981f175718 Merge pull request #256 from dannon/release_15.05 
[15.05] Fix workflow parameter/action display
 2015-05-13 16:54:34 -04:00
Dannon Baker cfea0386f4 Missed one. 2015-05-13 15:47:56 -04:00
Dannon Baker 0a7f50dbaa Change sanitization of workflow pja's for display in workflow/run to happen in get_short_str, trusting that output. This is probably still overzealous, and we should check if there's a way to exploit tool.output_names (and if not, pull back on that sanitization). 2015-05-13 15:45:01 -04:00
Martin Cech e44a0150ef Merge pull request #7 from natefoo/release_notes_15.05 
Add a stub for older release announcements
 2015-05-13 15:33:59 -04:00
Nate Coraor 959660f5c2 Add a stub for older release announcements. 2015-05-13 15:17:47 -04:00
John Chilton 5111e43b9a Add missing release to doc index. 2015-05-13 14:49:54 -04:00
Martin Cech 7f2922f9e2 update to transparent logo 2015-05-13 14:43:21 -04:00
John Chilton b1e6700087 Fill out doc stubs for releases through 13.01. 
These pages have the header and footer and links to the relevant pages on the wiki.

These are the ones on github and the ones that got at least a couple of the most serious bug fixes announced over the last year.
 2015-05-13 14:39:24 -04:00