John Chilton
886e7adfd6
Job metrics - ensure all text values are unicode before persisting.
...
Gets rid of the following warning: "SAWarning: Unicode type received non-unicode bind param value.".
2014-04-22 21:25:04 -05:00
John Chilton
2ec1f3e9af
Merge pull request #352 .
2014-04-22 21:06:03 -05:00
Greg Von Kuster
0e80b456af
More quickly stop the process of checking for migrated tools when starting Galaxy if there is no internet connection to the tool shed.
2014-04-22 11:45:10 -04:00
Greg Von Kuster
646bba4b8c
Handle case where no network is available when attempting to determine repository dependencies for an installed repository.
2014-04-22 10:33:42 -04:00
Dannon Baker
a329745571
Merge.
2014-04-21 17:10:48 -04:00
Dannon Baker
e5052df2a4
Convert cloudlaunch over to bioblend egg/launching, unifying the two approaches. The bioblend codebase will be where improvements (vpc, etc) happen moving forward.
2014-04-21 17:10:23 -04:00
Martin Cech
e520630b7e
data libraries: don't allow adding dataset within deleted library; better error message handling
2014-04-21 16:28:14 -04:00
Martin Cech
2c0c472f09
data libraries: don't allow creating folders within deleted library
2014-04-21 15:48:19 -04:00
John Chilton
7e56d2dc20
Fix comment in lib/galaxy/workflow/run.py
2014-04-21 14:26:56 -05:00
Dave Bouvier
45ff30f6e1
Fix for registering an account with custom user information when only one custom user info form is defined. Fix editing user info when custom user info forms are defined. Fix functional tests for user info.
2014-04-21 12:41:05 -04:00
Daniel Blankenberg
9835de1a26
Prevent redirect misuse on user log in.
2014-04-21 12:11:49 -04:00
John Chilton
989950c037
Workflow running - modify var names/comment to reflect 773951eb2bbf.
2014-04-21 08:36:43 -05:00
John Chilton
263efe1321
Bugfix for 439510f (reported by @saketkc).
...
Previous logic for determining if state had been calculated for workflow steps in workflow run module would only work for data input steps - this new logic should work for data input or tools.
2014-04-21 08:01:22 -05:00
John Chilton
02425e7c4f
Refactor workflow API logic related to module population into run module.
...
Also moves runtime parameter override logic into that module as well. This is a good refactoring because it thins out a fat controllers (slightly) - but it is of particular interest because it makes it easier to recursively invoke potentially nested workflows from the workflow running module itself. It is still an open question whether that is desirable - see discussion on Pull Request #370 - but if it proves to be this can help enable it.
2014-04-19 11:40:19 -05:00
John Chilton
073ee18f1d
Refactor galaxy.workflow.run interface to use config object.
...
Number of ways to paramemterize workflow is a little bit sprawling already and it is about to get worse.
2014-04-19 11:40:19 -05:00
Carl Eberhard
3fcfd3ecad
Improve visualization registry warning info when datatype class not found by lookup
2014-04-18 18:04:13 -04:00
Martin Cech
8891243e69
data libraries: small API changes; bugfix; deferred queue for adding datasets from history to library; permission handling work
2014-04-18 17:16:58 -04:00
Dave Bouvier
b48712928b
Merge fix from stable.
2014-04-18 14:58:04 -04:00
Dave Bouvier
0c1c0add3f
If a tool shed repository was updated after a tool migration without a new installable changeset revision being generated, for example by adding or removing a readme file, the migration install framework would be unable to find repository dependencies. This changeset resolves that.
2014-04-18 13:58:51 -04:00
John Chilton
960cf077f5
Merged in dan/galaxy-central-stable-prs/stable (pull request #369 )
...
BioStar fixes
2014-04-17 15:02:44 -05:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Daniel Blankenberg
9aa9f7d018
Add an option to biostar integration to never authenticate.
2014-04-17 15:38:42 -04:00
Daniel Blankenberg
3ed326601a
Add an option to biostar integration to never authenticate.
2014-04-17 15:38:42 -04:00
Dave Bouvier
30bc77e7ea
Fix most of the failing functional tests in test_sample_tracking.py.
2014-04-17 15:16:57 -04:00
Daniel Blankenberg
2d2c2e8344
Some better error handling for external display applications when e.g. files have been deleted but are still active in applications.
2014-04-17 15:05:18 -04:00
John Chilton
53a154df2f
Fix library permissions API controller.
2014-04-17 13:46:57 -05:00
John Chilton
54aac81f4a
Fix library permissions API controller.
2014-04-17 13:46:57 -05:00
Daniel Blankenberg
69924df39b
Remove 'galaxy' tag as default now that we are using a custom biostar site.
2014-04-17 13:03:02 -04:00
Daniel Blankenberg
1899f37cd1
Remove 'galaxy' tag as default now that we are using a custom biostar site.
2014-04-17 13:03:02 -04:00
Daniel Blankenberg
322a9b9a6e
Allow disabling biostar bug reports through config settings.
2014-04-17 12:34:33 -04:00
Daniel Blankenberg
98664286e7
Allow disabling biostar bug reports through config settings.
2014-04-17 12:34:33 -04:00
Martin Cech
db752de9d3
data libraries: API improvements; add datasets from history to folder; folder contents sorting; progressive rendering; new error code; new API endpoint; js model comparators; Galaxy.currUser defensive programming;
2014-04-16 16:27:13 -04:00
John Chilton
54f33ef537
If 'populating' state from tool API request - stop processing tree on conditional test param error.
...
Attempting to populate the state below the conditional parameter can result in uncaught exceptions in some cases. See Peter's post here - http://dev.list.galaxyproject.org/Unclear-API-and-Twill-test-failure-for-undefined-datatype-tt4664216.html for example.
2014-04-16 09:11:31 -05:00
Dave Bouvier
ebaba221f5
Remove stray debug output.
2014-04-16 09:23:09 -04:00
Daniel Blankenberg
fde5ca9093
Allow copying Histories directly from the list of Saved Histories.
2014-04-15 14:24:14 -04:00
Daniel Blankenberg
6f846d50fc
Provide run and edit links for workflows after extraction from history.
2014-04-15 14:01:21 -04:00
Nate Coraor
7458911e43
Remove old platforms and versions from platform string manipulation. Egg compatibility enhancements for OS X. Galaxy's prepackaged OS X eggs should now work on any Python interpreter on Intel versions of OS X 10.6 and newer.
2014-04-15 13:27:36 -04:00
Daniel Blankenberg
2e72df832e
merge next stable
2014-04-14 16:30:29 -04:00
Daniel Blankenberg
f5d289c2ba
Fix for rerun of unvalidated parameters for multiple selects.
2014-04-14 16:29:46 -04:00
Daniel Blankenberg
7e8859923f
merge next-stable
2014-04-14 15:47:01 -04:00
Daniel Blankenberg
2cf20ccfc9
Fix for workflow editor in call to check_param on input parameters that need late validation but were attempting to run validators.
2014-04-14 15:44:36 -04:00
Carl Eberhard
6672b8db2c
Metrics: remove double parsing of JSON from server-side, add GalaxyApp object with config and user, tie metrics-logger to GalaxyApp
2014-04-14 13:00:06 -04:00
Carl Eberhard
a65f3bc0e1
Configuration API: use new api decorator for error serialization
2014-04-14 11:07:58 -04:00
Carl Eberhard
be686fbc4f
Configuration API: clean up controller interface
2014-04-14 11:01:15 -04:00
Martin Cech
01cd002652
data libraries: API improvements, access permissions work, started with UI for adding files from history work
2014-04-11 17:29:36 -04:00
Dannon Baker
1bbe1b28c9
Merged in jlhg/galaxy-central (pull request #365 )
...
Update the job exit codes
2014-04-11 11:33:20 -04:00
Jian-Long Huang
fbdf57aa63
Update the job exit codes
2014-04-11 21:41:39 +08:00
Nicola Soranzo
46641daaa7
Merge galaxy/galaxy-central default branch.
2014-04-11 12:00:39 +02:00
Jeremy Goecks
80b603902a
Merge next-stable branch to default.
2014-04-10 17:21:38 -04:00
Jeremy Goecks
28ddf4bcc2
Updates to Sweepster to get it working again.
2014-04-10 17:21:00 -04:00
John Chilton