opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
16,684 Commits 69 Branches 243 Tags
4d347dcfe1efebda631845d48deff697c3de64ad
Commit Graph
16684 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
guerler 4d347dcfe1 Fix select2 field arrow style 2015-03-09 13:55:18 -04:00
guerler f515e29504 Enable remap condition 2015-03-06 15:28:22 -05:00
guerler 949b785fac Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-03-06 15:26:24 -05:00
guerler d079ad8f8c Add resume option for job dependencies 2015-03-06 15:24:31 -05:00
Daniel Blankenberg 18d77b008f Make api/config /version usable as sessionless in addition to anonymous. 2015-03-06 14:18:48 -05:00
guerler f0bebc997f Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-03-05 22:16:54 -05:00
guerler 1a1f5a33c9 Fix dataset and collection mapping for re-run in imported histories 2015-03-05 22:15:21 -05:00
Daniel Blankenberg 9316cccbb5 Fix for displaying Tools in ToolShed that use Dynamically Generated multiple selects as checkboxes and for displaying select lists using old-style dynamic options. 2015-03-05 17:02:45 -05:00
Dannon Baker 6db6b7e93b Tweaks to the password reset email template to help email clients not mangle it, and when they do, to suggest copying and pasting. 2015-03-05 13:27:22 -05:00
Dannon Baker 826f69fb62 Python 2.6 has a bug in deepcopy that causes an error when attempting to copy datasets between users (which uses deepcopy). Py2.7 worked fine. Now they both should. 2015-03-04 18:04:00 -05:00
John Chilton 9364b9d3c5 API fixes for tools and datatypes. 
By replacing _future_expose_api_anonymous with _future_expose_api_anonymous_and_sessionless.
 2015-03-04 14:51:43 -05:00
Carl Eberhard aa9c7e604e Fix: in multi-history order properly instantiate Dates for comparison and handle variadic better 2015-03-04 13:13:29 -05:00
Dannon Baker 5cba38827b Update .gitignore to include run_api_tests.html 2015-03-04 09:27:23 -05:00
Carl Eberhard d0b9664160 UI, multi-history: swap 'done' and 'create' buttons for better rtl intuition 2015-03-04 09:23:19 -05:00
Carl Eberhard d390ef2955 Fix to safari that still uses prefixed flexbox attributes 2015-03-03 13:13:26 -05:00
Daniel Blankenberg 2e3bebbfe2 Fix for reports app not running mysql. 2015-03-03 11:55:47 -05:00
Daniel Blankenberg 853f5156c0 When loading Dynamic Display application links, allow the application to load even if one set of links does not. 2015-03-03 10:49:12 -05:00
Daniel Blankenberg 05ff2aa6ce Add a 10 second timeout to loading data URLs for Tool Data Tables. 2015-03-03 10:24:58 -05:00
John Chilton f823278efd Fix bug in workflows test for implicit connections between steps. 
It would fail when being run with the rest of the suite and not on its own - because it was using the same id for the workflow id and invocation id - which is obviously wrong unless it is a completely fresh database :).
 2015-03-03 09:37:30 -05:00
John Chilton fc0a6d8764 Fix intermittently failing test test_workflow_run_dynamic_output_collections. 
Love it when the bugs correspond to actual TODOs I left in the code.
 2015-03-03 09:30:55 -05:00
John Chilton 391abd5fd6 Remove assert False from test/api/test_workflows_from_yaml.py. 
These aren't ideal tests - but it is some indication that things are working that the API will import the workflow and produce a representation. Should follow up at some point and verify the representation is in fact the correct one.
 2015-03-02 22:39:58 -05:00
John Chilton f8bfe89c42 Clarify failing test test_tools.py. 2015-03-02 22:39:58 -05:00
John Chilton a20938fc48 Attempt to fix intermittently failing jobs API test. 
Retry check several times in case there is some sort of timing problem where a history turns okay - before a job. Improve assertion error message.
 2015-03-02 22:39:50 -05:00
John Chilton b1f3654208 Tool data API testing fixes. 
- Add files I didn't commit previously in test/functional/tool-data/.
 - Comment out test for tool data table deletion since Dan fixed the problem of regular users running data managers through the API (https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634e69378f1f020) that I previously exploited to write the test.
 2015-03-02 22:36:24 -05:00
guerler 0d62ee6960 Parameters: Fix collection selection for multiple dataset input field 2015-03-02 18:25:46 -05:00
guerler 434aa056a2 Parameters: Cover additional case for multiple hdas 2015-03-02 18:12:34 -05:00
Martin Cech 8e6fbe34ca tweak toolbox search to provide better (and more) results 
with the inclusion of toolhelp in index and with more versions
of the same tools being massively installed the search results were
inconsistent and inaccurate and incomplete.
addresses https://trello.com/c/6Bvbduci/2486-toolbox-search-is-behaving-wrongly-differently
 2015-03-02 16:33:43 -05:00
Dannon Baker 1b23706b8f Rearranging the layers of middleware to allow sentry and debug to coexist without exploding (but you probably don't want to use both at once anyway) 2015-03-02 14:54:29 -05:00
Carl Eberhard ebda6ac03d Fix to remove validation of genome builds since some data source tools will assign invalid genome builds and later validation makes these hdas un-updatable 2015-03-02 14:22:00 -05:00
John Chilton 589b3fb226 Update basic.py to allow collection reduction with new tool form. 2015-03-02 13:53:17 -05:00
guerler 5bee11df4c Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful) 2015-02-28 12:12:10 -05:00
guerler 76a337bd24 ToolForm: Use default closing behaviour for progress modal 2015-02-28 04:37:37 -05:00
guerler 1bf37afec0 ToolForm: Do not show submission error if user closes progress modal 2015-02-28 04:30:14 -05:00
guerler 54eba77d91 Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-02-28 01:36:21 -05:00
guerler 772f08d6d2 ToolForm: Update biostar url for tool search 2015-02-28 01:33:15 -05:00
Daniel Blankenberg 1260d07a28 Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37). 2015-02-27 15:50:28 -05:00
Daniel Blankenberg 9f68fe0792 Allow External display applications to use Tool Data Tables. 2015-02-27 15:50:13 -05:00
Dannon Baker 10f8b6e21f Merge branch 'release_15.03' of github.com:galaxyproject/galaxy into release_15.03 2015-02-27 15:19:32 -05:00
dannon f73467f19d Fix server_starttime being in app for reports, toolshed. I will be refactoring this shortly to have a base UniverseApplication from which things inherit. 2015-02-27 15:19:17 -05:00
Nate Coraor 002fef995a Fix a typo in datatypes_conf.xml.sample 2015-02-27 14:21:22 -05:00
guerler f6afc9b238 ToolForm: Make deep copy of current state in order to be on the safe side 2015-02-27 13:43:39 -05:00
guerler 6080ff92e6 Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-02-27 10:17:05 -05:00
guerler 3c11c856a2 ToolForm: Fix dataset order for multi select run 2015-02-27 10:12:13 -05:00
Carl Eberhard fe523237c6 Fix display_structure by using serializer; fix structure by removing extra decode_id 2015-02-27 10:03:47 -05:00
guerler d4b6df5330 ToolForm/Ui: Restrict available option requirement to single select fields 2015-02-27 04:36:20 -05:00
guerler e0ad2d78e1 Parameters: Set hidden attribute for hidden dataset parameter 2015-02-27 04:26:15 -05:00
guerler d58d2abf57 Parameters: Fix deleted datasets validation message 2015-02-27 01:59:43 -05:00
guerler 5a78162f6f ToolForm/Ui: Limit selection to available options 2015-02-27 01:57:39 -05:00
guerler 0207fc1035 Parameters: Prevent uncaught exception on unavailable datasets in column validation 2015-02-27 01:49:53 -05:00
guerler c7943f33b5 ToolForm/Collections: Re-introduce parameter expansion 2015-02-27 01:35:38 -05:00