Dannon Baker
8215f03082
Merge.
2015-02-09 14:50:00 -05:00
Dannon Baker
b901d64866
Prevent last_action column from being populated with time.now() in the entire database and function correctly with null values here. Related bugfixes.
2015-02-09 14:49:35 -05:00
John Chilton
c26c8a86cb
When copying individual collections via the GUI - copy HDAs by default also.
...
We may want to be able to turn this off someday in certain scenarios - but usually this will result in less confusion for the user.
Doing this for whole histories also needs to be done - but it is a bit trickier (don't want the HDA copied twice). Might be better on the other side of eliminating the nessecity that these things have HIDs.
2015-02-09 13:29:45 -05:00
John Chilton
a6ed01ced8
Do not import argparse unconditionally in lib/galaxy/tools/deps/brew_exts.py.
2015-02-09 12:22:22 -05:00
Dannon Baker
fd2f5dce47
Merge.
2015-02-09 12:16:01 -05:00
Carl Eberhard
0e37a931ce
API, configuration: doc and clean up
2015-02-09 11:49:49 -05:00
Nate Coraor
19ce7033d3
Fix warning causing tool failure:
...
FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
2015-02-09 11:43:26 -05:00
Dannon Baker
022143ecfb
Merge.
2015-02-09 11:36:45 -05:00
Carl Eberhard
7abdea1eaa
Managers, users: add tags_used and requests to user serializer to match info bootstrapped in galaxy.masthead.mako and galaxy_client_app.mako
2015-02-09 11:34:47 -05:00
Carl Eberhard
cb0428e94a
UI: better defesive prog in metrics logger
2015-02-09 11:18:11 -05:00
Carl Eberhard
2b8fca4a03
Visualizations, scatterplot: update handlebars since server runtime was updated
2015-02-09 11:02:31 -05:00
Nate Coraor
2e9a80b5e2
Remove escaping of quotes in the slurm cli status checks, I don't think they should be there (the format args should in fact be quoted).
2015-02-09 09:59:36 -06:00
Carl Eberhard
b1ecf26c5a
Dataproviders, column: allow filtering data by parsed column values (numeric, list, and string)
2015-02-09 10:36:43 -05:00
Nate Coraor
440d623ffd
Add a _future_expose_api_raw_anonymous_and_sessionless to restore functionality
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that was previously available with _future_expose_api_raw_anonymous.
2015-02-09 09:17:53 -06:00
Aysam Guerler
637b43f67b
ToolForm: Set missing values to null
2015-02-09 09:15:25 -05:00
Aysam Guerler
3ece75b4fa
Parameters: Fix initial value for drill downs, Workflow/ToolForm: Move module building to api
2015-02-08 23:49:24 -05:00
John Chilton
a69db7a7fb
Link to "easiest ways to start" card in CONTRIBUTING.md.
2015-02-08 18:17:10 -05:00
Dannon Baker
c74448cd57
Allow specifying connection at launch of GalaxyQueueWorker.
2015-02-08 18:02:26 -05:00
John Chilton
8c05b4e3da
Merge.
2015-02-08 15:31:45 -05:00
John Chilton
0e3c165c12
Add link to actual presentation slides to CONTRIBUTING.md.
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For people who want to follow along with Dannon at home.
2015-02-08 15:29:02 -05:00
Dannon Baker
8b03d0f9d9
Merge.
2015-02-08 15:09:23 -05:00
John Chilton
82fe547a93
First crack at a CONTRIBUTING file for galaxy-central.
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Ideally this would come in through a pull request but I am trying to rush through documentation related to Galaxy development ahead of a GSOC application - by all means I would encourage comments related to this commit as well as well as direct modifications.
CONTRIBUTING files are meant to encourge developers to contribute to open source projects by spelling out how to contribute and what is expected from contributions. More resources related to CONTRIBUTION files include:
- http://contribute.md/
- https://github.com/blog/1184-contributing-guidelines
This isn't coming at the expense of wiki documentation - I have already made dozens of enhancements to the Develop section of the wiki today and I am planning a huge walkthrough of how to contribute and learn about various aspect of the broader Galaxy community from a new developer perspective. Having this file in place though I feel is an important part of that however.
2015-02-08 15:02:54 -05:00
Dannon Baker
a831c6e148
Minor formatting, spelling in workflow scheduling_manager.
2015-02-08 11:21:42 -05:00
Dannon Baker
4dc04e1472
Fix a few instances of incorrect (deprecated) use of value instead of identity testing in xml parsing.
2015-02-08 11:16:14 -05:00
John Chilton
0e582719fe
Fix running tool tests for recent control reworking.
2015-02-07 19:32:16 -05:00
John Chilton
9e0d530c0c
Rework control queue setup to work in non-web contexts.
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Namely in the new lib/galaxy/main.py. I think this break down of the code makes more sense also since control queues aren't inheriently something web-y so lib/galaxy/app.py makes more sense for configuring them. Dannon feel free to reorganize if you dislike this particular organization - I just wanted to make sure lib/galaxy/main.py could share in the new stuff.
2015-02-07 19:32:16 -05:00
Aysam Guerler
05787784c2
Ui: Use placeholder title
2015-02-06 23:32:58 -05:00
Aysam Guerler
0718fca13f
ToolForm: Update repeat blocks
2015-02-06 23:23:26 -05:00
Aysam Guerler
3dd4207f03
ToolForm: More style adjustments
2015-02-06 22:03:33 -05:00
John Chilton
7f5f15b4f3
Merged in JenCabral/galaxy-central/tool_shed_test_fix-DB_initialization (pull request #662 )
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Fix tool shed tests - create database directory
2015-02-06 21:33:49 -05:00
Aysam Guerler
57b9fefb07
Ui: Repack styles
2015-02-06 20:49:58 -05:00
Aysam Guerler
1750027b57
Ui: Add tooltip to options
2015-02-06 20:47:28 -05:00
Aysam Guerler
aca45c1b36
ToolForm: Try new data selector style
2015-02-06 19:09:53 -05:00
Aysam Guerler
50c0ce8228
Ui: Fix slider value element
2015-02-06 16:38:11 -05:00
Carl Eberhard
0547725d03
Fix to 8c71422: add the file
2015-02-06 13:56:31 -05:00
Carl Eberhard
242f2634cf
API, configuration: expand exposed settings to include those needed by the masthead in galaxy.masthead.mako, add serializers for config
2015-02-06 13:38:53 -05:00
JenCabral
d0dedc8404
adding a comment and moving out of else statement
2015-02-06 11:05:04 -06:00
JenCabral
ee3fe10503
checks to see if directory for database exists if not creates the directory
2015-02-06 10:59:53 -06:00
Daniel Blankenberg
1155ead7ff
Fix for SelectToolParameters that utilize dynamic options and that make use of __trans__ failing at get_legal_values().
2015-02-06 11:56:54 -05:00
Jennifer Cabral
940bfc48a2
Created new branch tool_shed_test_fix-DB_initialization
2015-02-06 16:51:03 +00:00
Dannon Baker
f4ec978d9e
Relocate uwsgi test to the beginning of config, since this might affect other config options down the road.
2015-02-06 11:40:47 -05:00
Dannon Baker
c6cda49498
Merge.
2015-02-06 11:33:45 -05:00
Dannon Baker
f457c09f07
Adjust generated queue names to match with new postfork manipulation of config.server_name
2015-02-06 11:33:33 -05:00
Aysam Guerler
68d9ea0fad
Ui: Fix class name
2015-02-06 11:23:19 -05:00
Aysam Guerler
928f558b08
Merge
2015-02-06 11:06:29 -05:00
Aysam Guerler
836b3bb913
Ui: Revise portlet margins
2015-02-06 11:05:23 -05:00
Dannon Baker
7adff59c5f
Force postfork unique servername on uwsgi workers in the format of 'servername.workername'. Use this for correctly routing messages.
2015-02-06 11:05:06 -05:00
Dannon Baker
5eff5db70d
Minor formatting of routes in buildapp.py
2015-02-06 10:55:15 -05:00
Dannon Baker
2fed958e86
The other half of d89864b9f5daaec89dfda0ad5772a13aed72536b.
2015-02-06 09:00:12 -05:00
Dannon Baker
9f826acff7
Merge.
2015-02-06 08:56:03 -05:00
Dannon Baker