Aysam Guerler
b67781ebda
Upload: Introduce progress button
2014-01-18 14:48:10 -05:00
Greg Von Kuster
4154e5e946
Improved logging in the tool shed's install and test framework.
2014-01-17 20:31:47 -05:00
Aysam Guerler
2f711d1a9f
DataViewer: Remove console output
2014-01-17 18:17:35 -05:00
Aysam Guerler
720bbdf41f
Upload: Add automated genome selection
2014-01-17 18:13:55 -05:00
Aysam Guerler
30186d6b87
Separate upload javascript into files and place into mvc directory
2014-01-17 17:55:15 -05:00
John Chilton
e45e22caa9
Merged in jmchilton/galaxy-central-fork-1 (pull request #300 )
...
Potential DRMAA fixes.
2014-01-17 16:04:39 -06:00
Greg Von Kuster
2bcaebf46b
Improved logging in the tool shed's install and test framework.
2014-01-17 16:57:18 -05:00
Greg Von Kuster
ac120fb0d1
Dict url entry changes and improved logging for the Tool Shed api.
2014-01-17 16:35:05 -05:00
Daniel Blankenberg
ca07eb79e9
Change log.error to log.debug.
2014-01-17 15:45:04 -05:00
Greg Von Kuster
a48cc46574
Enhance setting tool shed repository metadata to support tool dependency recipes that define installation of a binary but do not also include a recipe for installing and compiling from source.
2014-01-17 13:49:10 -05:00
Martin Cech
5137176626
library history ‘back’ button bug removal
2014-01-17 12:19:04 -05:00
John Chilton
766fbee77b
Handle subclassed DRMAA exceptions properly.
...
No clue if this was a problem, but realized it might be.
2014-01-17 09:48:17 -06:00
John Chilton
ae96c90894
Provide item style access to runner params.
2014-01-17 09:48:17 -06:00
Martin Cech
2404aca0bf
Merge
2014-01-17 09:55:27 -05:00
John Chilton
915948a305
Hide to_posix_lines in UI by default.
...
Galaxy still completely supports this option on backend - API tests still completely work and will hopefully ensure this functionality continues running. Any Galaxy deployements that wish to enable this option simply have to switch this one param from hidden to select. This is a ugly workaround - but it is a very small workaround - and will hopefully alleviate any potential fears Gert Hulselmans has of Galaxy diverging from his changes. This is only a stop gap until the Galaxy upload UI supports more advanced options.
I have previously outlined my concerns with the visual clutter on the upload.xml page - this is why I am hiding it by default. If anyone with commit access disagrees - please by all means backout of this individual changeset and restore the full functionality of pull request 171 (I have a terrible eye for this sort of GUI design stuff).
2014-01-17 00:03:26 -06:00
John Chilton
7be6b9758a
Functionally test various upload options via API.
2014-01-17 00:03:26 -06:00
John Chilton
658ea5966c
Merge pull request 171.
2014-01-16 23:57:43 -06:00
Daniel Blankenberg
2752bc74de
Fix for api/tools/show/ when no id is provided.
2014-01-16 16:52:39 -05:00
Daniel Blankenberg
fddb4b0ba6
Use toolbox.get_tool instead of toolbox.tools_by_id.get in tools api show().
2014-01-16 16:21:41 -05:00
Greg Von Kuster
9d49a65e60
Forgot None in my last commit
2014-01-16 16:13:47 -05:00
Greg Von Kuster
78b6229584
Re-include deprecated repositories when resetting metadata since they can be dependencies of installable repositories.
2014-01-16 16:02:39 -05:00
Martin Cech
0508ce36ff
Merge
2014-01-16 14:13:15 -05:00
Aysam Guerler
58899937a8
Merge
2014-01-16 14:10:56 -05:00
Aysam Guerler
92657b38db
Charts: Add configuration model, link all view functions to model events
2014-01-16 14:10:32 -05:00
Martin Cech
0d08258c11
PEP8 tweaks
2014-01-16 14:08:58 -05:00
Greg Von Kuster
212aa39901
Fixes in the tool shed api for mapping the repository user_id and for handling repository_dependency changeset_revision values that have been updated.
2014-01-16 14:07:28 -05:00
John Chilton
fc17db50cc
Fix database engine options when verifying tools using separate install database.
...
Bug report and fix thanks to Jim Johnson.
2014-01-16 13:00:30 -06:00
Martin Cech
9d6c849a94
new packed js
2014-01-16 13:37:04 -05:00
Martin Cech
a9b39936d6
remove doubled import
2014-01-16 13:35:51 -05:00
Martin Cech
34976050e5
removed obvious bugs in api_key retrieval through API using basic authentication
2014-01-16 13:30:53 -05:00
Martin Cech
e1ed16b74b
api_key retrieval through API using basic authentication
2014-01-16 13:20:10 -05:00
Aysam Guerler
17506f82e1
Charts: Update view organization
2014-01-16 12:24:47 -05:00
Dave Bouvier
d1114a1b0f
Fix deletion of test methods after tests have been run.
2014-01-16 11:30:25 -05:00
John Chilton
994ac18d73
Rearrange __handle_execute and handle_input in Tool...
...
Slightly cleaner this way (fewer exit points) and will enable extensions I am making downstream.
2014-01-16 09:30:01 -06:00
John Chilton
7e44ec4bb5
Add tool execution tests for various exceptional conditions.
...
Tool action raising exception, redirecting, and returning an error message.
2014-01-16 09:30:01 -06:00
Dannon Baker
33f83e1b77
Explicitly require UsesAnnotations mixin for the annotations api controller *after* UsesStoredWorkflowMixin.
2014-01-16 09:56:31 -05:00
Nicola Soranzo
966a7911e1
Add /api/workflows/import method to import a workflow shared by other users.
2014-01-15 18:28:21 +01:00
Nicola Soranzo
9953a948d6
Move core code for importing a shared workflow to UsesStoredWorkflowMixin.
2014-01-15 18:17:24 +01:00
Nicola Soranzo
94cf50b2eb
Add show_published param to /api/workflows index() method to display also published workflows.
2014-01-15 18:22:51 +01:00
Nicola Soranzo
89e443d9e1
Let /api/workflows show() method display also importable workflows.
2014-01-15 18:04:33 +01:00
Nicola Soranzo
9c61f80d13
PEP-8 and unused variables fixes.
2014-01-15 17:51:36 +01:00
Aysam Guerler
7a86e01751
Charts: Improve button selection
2014-01-16 01:38:06 -05:00
Aysam Guerler
6b3864591d
Merge
2014-01-16 00:43:19 -05:00
Aysam Guerler
8727ec9455
Charts: Show chart creation form on startup, add pie chart
2014-01-16 00:42:41 -05:00
John Chilton
3773f85a23
Merged in kellrott/galaxy-central/search (pull request #296 )
...
Adding update_time to dataset to_dict methods
2014-01-15 21:59:36 -06:00
Martin Cech
c14d433871
javascript library and modal refactoring, automatic even binding if flag provided
2014-01-15 18:11:09 -05:00
Greg Von Kuster
21e6f4448c
Display messages for repositories in the tool shed that have dependencies on deprecated repositories.
2014-01-15 15:35:41 -05:00
Dannon Baker
e26d6e56c7
Tweaks to scripts/api/common.py to fix JSONDecodeError removal and clean up code.
2014-01-15 09:05:38 -05:00
Dave Bouvier
37eb8a5b39
Fix tool configuration reload for changes in 5f6c670.
2014-01-15 08:54:33 -05:00
Dannon Baker
0a9f96e41a
Fix object not found wording.
2014-01-15 08:46:53 -05:00
Aysam Guerler