Carl Eberhard
3ec57d0833
UI, utils: modularize (AMD) naturalSort and move to utils
2015-02-10 13:42:59 -05:00
Carl Eberhard
b3f39b8d5a
UI, paired collection creator: move to underscore fn binding, allow name param in createList, add qunit test and data
2015-02-10 13:38:30 -05:00
Dannon Baker
663ada2d0b
Merged in nsoranzo/galaxy-central (pull request #658 )
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Don't abort restart if stop_daemon() failed.
2015-02-10 13:14:21 -05:00
Dannon Baker
59d73090fe
Add more accurate sample for specifying a swift object store in object_store_conf.sample
2015-02-10 09:55:03 -05:00
Dannon Baker
61b64b6f26
Merge.
2015-02-10 09:51:33 -05:00
Dannon Baker
ec0c3be798
Merged in charles_hsu/galaxy-central/fix-multipart-upload-in-swift-backend (pull request #648 )
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Fixed multipart-upload issue while use swift as object storage backend
2015-02-10 09:49:01 -05:00
Dannon Baker
51f32c8fc9
Actually use reduced redundancy only when specified.
2015-02-10 09:48:46 -05:00
Carl Eberhard
456a14d9df
UI, Paired collection creator: use scoped version of $.index instead of clumsy calculation
2015-02-09 18:09:27 -05:00
Carl Eberhard
ed32b63e50
UI, Paired collection creator: fix template function for 'Choose Filters'
2015-02-09 17:54:17 -05:00
Carl Eberhard
89d76ae929
UI: remove unused LazyDataLoader module
2015-02-09 17:47:30 -05:00
Carl Eberhard
f3aadb7e03
Fix to 389f0dcc1589: remove debugging code in index.mako
2015-02-09 17:42:13 -05:00
Carl Eberhard
eed33430d7
UI, Paired collection creator: when dragging within the paired section autoscroll the list when the mouse is within 'autoscrollDist' pixels of the top or bottom
2015-02-09 17:40:53 -05:00
Dannon Baker
61360355dd
Update objectstore sample to supply better defaults (and not host/port, which are unnecessary for s3).
2015-02-09 17:37:16 -05:00
Dannon Baker
27022833db
Merge.
2015-02-09 16:51:55 -05:00
Dannon Baker
18981016c6
Enable session timeout for tool_shed application (off by default, as with Galaxy).
2015-02-09 16:51:43 -05:00
Carl Eberhard
a49384046a
Merge
2015-02-09 16:41:04 -05:00
Carl Eberhard
13134f6269
UI, Paired collection creator: add rendered,rendered:inital events, add initial autopairing event
2015-02-09 16:40:18 -05:00
Martin Cech
b78858e0f9
load param as bool
2015-02-09 16:39:11 -05:00
Martin Cech
e7f754c2d5
minor adjustments to toolshed search
2015-02-09 16:29:31 -05:00
Dannon Baker
0f12fbdba5
Fix toolshed config/session timeout bug.
2015-02-09 16:17:47 -05:00
Dannon Baker
a101ee90ad
Merge.
2015-02-09 16:15:24 -05:00
Dannon Baker
1319fe5f58
More adjustments to queue kickoff to force webapps to initialize the connection prior to models; this (at least seems to, so far) fixes the concurrent mapper initialization race condition sqlalchemy issue.
2015-02-09 16:14:55 -05:00
Carl Eberhard
c6984b57d9
UI, History panel: show better feedback when 'Build List of Dataset Pairs' is clicked and no datasets are selected.
2015-02-09 15:53:26 -05:00
Carl Eberhard
5045c9c736
UI, Paired collection creator: create collection when enter is pressed in name field, remove debugging
2015-02-09 15:44:23 -05:00
Carl Eberhard
0f03877740
UI, Paired collection creator: fix pair template rendering bug
2015-02-09 15:30:16 -05:00
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.
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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:
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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
Carl Eberhard