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Author SHA1 Message Date
Martin Cech 182fbd1bc6 fix the data source tools for modendcode with proper URLs 2015-05-19 16:53:25 -04:00
John Chilton 74cba741bc Merge pull request #255 from guerler/fix_none_selection 
[15.05] Accept 'None' as valid value for selections
 2015-05-13 13:24:21 -05:00
guerler e5d19d9999 Accept 'None' as valid value 2015-05-13 11:24:32 -04:00
Nate Coraor ada867bb00 Merge pull request #254 from carlfeberhard/fix.history-state 
[15.05] Histories, API: do not consider deleted datasets when calculating his…
 2015-05-13 09:22:41 -04:00
Carl Eberhard d1c14bd1a1 Histories, API: do not consider deleted datasets when calculating history state; test 2015-05-12 16:57:17 -04:00
Nate Coraor 32edb07930 Merge pull request #247 from blankenberg/baseurl-fix 
[15.05] Fixes for BaseURLToolParameter. Data source tools will now work again…
 2015-05-11 16:14:35 -04:00
John Chilton 781fb12a27 Merge pull request #252 from blankenberg/pysam-fix 
[15.05] Supress pysam binary incompatibility warning when using datatypes in binary.py.
 2015-05-11 14:27:54 -05:00
Daniel Blankenberg 830b9f4d35 Supress pysam binary incompatibility warning when using datatypes in binary.py. 2015-05-11 15:04:09 -04:00
Daniel Blankenberg 539df779d9 Merge pull request #251 from jmchilton/ts_test_fixes 
[15.05] Tool shed test fixes for 15.05.
 2015-05-11 12:23:25 -04:00
John Chilton 4d69f2e8c0 Fix a variety of tool shed tests broken with a24e206. 2015-05-11 11:57:05 -04:00
John Chilton 593d38fcf0 Fix a variety of tool shed tests broken with PR #75. 2015-05-11 11:56:26 -04:00
Dannon Baker 9d4099ac36 Merge pull request #245 from blankenberg/tool-data-table-enhancements 
[15.05] Allow a tool data table to declare that duplicate entries are not allowed.
 2015-05-08 11:34:41 -04:00
Daniel Blankenberg a3d694de70 Fixes for BaseURLToolParameter. Data source tools will now work again. Restores consistency to various ways that one might get the parameter value. 2015-05-08 09:30:04 -04:00
Daniel Blankenberg 7483b043f6 Allow a tool data table to declare that duplicate entries are not allowed. 2015-05-07 16:41:43 -04:00
Dannon Baker 95d7108b1b Merge pull request #244 from guerler/tool_form_001 
[15.05] Remove redundant version ids from version selector
 2015-05-07 16:27:37 -04:00
guerler 784d76d3db Remove redundant versions from version selector 2015-05-07 16:07:29 -04:00
Daniel Blankenberg 1709b7fae7 Merge pull request #242 from natefoo/release_15.05 
[15.05] Fix lib/galaxy/main.py for changes in starting control queue
 2015-05-07 15:07:09 -04:00
Nate Coraor e6b75a1000 Fix lib/galaxy/main.py for changes in starting control queue. 2015-05-07 15:04:01 -04:00
Dannon Baker f85ef347d8 Merge pull request #235 from jmchilton/qunit_travis 
[15.05] Backport QUnit Test Fixes + Add to CI
 2015-05-07 14:26:14 -04:00
John Chilton 30f4b335a5 Merge pull request #236 from natefoo/clean_job_workdir 
[15.05] Fix job resubmission
 2015-05-07 12:54:28 -05:00
Carl Eberhard a0bd971beb Testing, qunit: rename paired-collection-creator test to match actual mvc script, update README to include silent error warning 2015-05-07 13:26:39 -04:00
Carl Eberhard 19d00d6ac6 Testing, qunit: remove unfortunately silent error of missing global Galaxy when running via require and phantom by checking scope first, update list of pairs tests with recent option changes, remove debugging cruft 2015-05-07 13:26:38 -04:00
John Chilton 87d8f5762a Add qunit tests to Travis CI. 2015-05-07 13:26:38 -04:00
John Chilton 0964464f12 Merge pull request #238 from martenson/gitignore-tox 
[15.05] add .tox folder to gitignore
 2015-05-07 11:59:22 -05:00
Martin Cech 3d586739dd add .tox folder to gitignore 2015-05-07 12:57:21 -04:00
Nate Coraor c1a97465bb Fix perfectly PEP-8 valid hanging indents that flake8 says are invalid. =P 2015-05-07 12:35:17 -04:00
Nate Coraor 90c01d551d Add an is_valid column to job_external_output_metadata so that the 
temp files can be regenerated when the job is resubmitted.
 2015-05-07 12:21:11 -04:00
Nate Coraor 599fd97749 Allow a job working directory to be "cleared" (its contents will be 
moved to a directory underneath the top-level working dir)
 2015-05-07 12:15:19 -04:00
Nate Coraor 2268cbe8b9 Add a somewhat more appropriate obj_dir kwarg to the object store to 
cause the creation of a directory named by the object's ID inside the
directory hash, useful for things like job working directories.
Previously this was done with `extra_dir=str(obj.id)`.
 2015-05-07 12:10:59 -04:00
Nate Coraor 9fafded1b6 Deindent the walltime/memory limit resubmission state handler. 2015-05-07 12:06:43 -04:00
Nate Coraor 049e9e8024 Merge remote-tracking branch 'upstream/release_15.03' into release_15.05 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
 2015-05-07 11:57:59 -04:00
Dannon Baker 7a936f824a Merge pull request #222 from jmchilton/tox_switch_and_fixes 
[15.05] Switch Travis testing to tox and associated fixes.
 2015-05-07 11:41:46 -04:00
Dannon Baker ac9b46c92d Merge pull request #234 from carlfeberhard/fix.metadownload-btn 
[STABLE] History UI: in published/annotated panels, fix metafile download drop…
 2015-05-07 11:10:33 -04:00
Carl Eberhard c2d52fdddd History UI: in published/annotated panels, fix metafile download dropdowns (BAM files, etc.) to open properly, remove console statement in template 2015-05-07 10:53:30 -04:00
Dannon Baker da9142c9c0 Merge pull request #232 from jmchilton/test_fix 
[15.05] Fix problem with twill's custom subprocess module.
 2015-05-06 20:43:19 -04:00
John Chilton 5d31ce641a Fix problem with twill's custom subprocess module. 
There has been for some time a scary warning when testing (http://dev.list.galaxyproject.org/run-test-sh-ImportError-cannot-import-name-args-from-interpreter-flags-td4666277.html) that I now understand is the result of Twill being packaged with its own custom subprocess module that conflicts with modules using multiprocessing (e.g. kombu).

After the #198 this scary warning has become an exception that prevents exception of tests (see https://travis-ci.org/galaxyproject/planemo/jobs/61547827 for instance). Importing subprocess seems to force Python to use the system module instead of twills - which seems to prevent these problems.

There have been other reports of this problem with Twill in other projects and removing the subprocess module didn't seem to break anything for them either.
 2015-05-06 20:24:50 -04:00
John Chilton 32a1f8f178 Merge pull request #231 from cganote/pull_req 
Made a small fix to the collectl.py file
 2015-05-06 18:18:10 -05:00
cganote f180b99b00 Made a small fix to the collectl.py file 2015-05-06 19:01:12 -04:00
Daniel Blankenberg f18d3567ce Merge pull request #226 from martenson/fix-tool-search 
[15.05] avoid adding data managers to the tool search index
 2015-05-06 16:51:15 -04:00
John Chilton 23d1e39e2d Merge pull request #228 from martenson/fix-ts-logo-margin 
[15.05] TS is not using masthead.js so mako needs to be updated too
 2015-05-06 15:27:28 -05:00
Martin Cech dd133cb0d1 TS is not using masthead.js so mako needs to be updated too 2015-05-06 16:17:20 -04:00
John Chilton 9da20a30ed Merge pull request #216 from nsoranzo/release_15.05 
[15.05] Fix AuthManager.active_authenticators(). Partially re...
 2015-05-06 15:15:19 -05:00
Nate Coraor e462b40921 Merge branch 'release_15.03' into release_15.05 2015-05-06 15:22:21 -04:00
Martin Cech d0451b86c8 avoid adding data managers to the tool search index 
this would occur if you have some DM installed and you install another
tool trigerring the reindexing and then non-admin user uses the
searchbox in the tool panel to search for something that also returns
the data manager tool resulting in API giving you 404 and logging
that user without proper permissions tried to access DM
 2015-05-06 14:38:08 -04:00
Nate Coraor 281233f7e5 Fix Pulsar remote staging that I broke when adding nginx_upload_module 
support in #110.
 2015-05-06 14:15:16 -04:00
John Chilton bc48ac15d5 Update tool tests to reflect get_tool is non-deterministic... 
... if supplied a short id instead of a GUID and there are multiple versions of a shed tool with the same short id installed.
 2015-05-06 14:06:16 -04:00
John Chilton a15a2bd2b2 Fix Python 2.6 incompat in script_entry_point.mako. 2015-05-06 14:06:16 -04:00
John Chilton 499108432a Attempt to fix manager, viz, and web unit tests for Python 2.6... 
... using unittest2.
 2015-05-06 14:06:16 -04:00
John Chilton 32eb76e143 Exclude some more non-Galaxy code from unit tests. 
These functions were imported from an external module and contain non-deterministic doctests.
 2015-05-06 12:40:07 -04:00
John Chilton 5ddc4934d4 Fix some doctests that were assuming fixed Python hashing. 
Tests are more correct and perhaps less strong as result.
 2015-05-06 12:40:07 -04:00