John Chilton
895c1d6971
Disable select2 for all multi-select inputs.
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These have been nothing but trouble (they have been disabled some places) and are awkward in those places that have not been changed.
Is there any place in Galaxy where multi-select inputs + select2 are being used to create a desirable UX? If yes, can we just create a class for these particular widgets and target it with a boolean expression on the same line?
2014-04-25 13:00:09 -05:00
Dave Bouvier
dbca5013cc
Fix for persisting data table entries generated by installed data managers.
2014-04-25 13:21:32 -04:00
Greg Von Kuster
42e9adb8b2
Add support for 3 new tool dependency installation recipe action tag types: assert_directory_exists, assert_file_exists and assert_file_executable.
2014-04-25 10:58:15 -04:00
Jeremy Goecks
c2d192810c
BAM data provider: hash to create read guids. This is line with other data providers and decreases payload size slightly.
2014-04-25 10:50:47 -04:00
Dave Bouvier
06c2434f6e
Fix functional tests for library templates.
2014-04-25 10:41:53 -04:00
Dave Bouvier
aecbc6da2a
Fix tool shed functional tests for roles and email notifications.
2014-04-25 10:41:34 -04:00
Jeremy Goecks
bae94cedc0
Simplification for dowsampler in bam data provider
2014-04-24 21:24:33 -04:00
Greg Von Kuster
c69b3f8065
Move some hg utility functions out of shed_util_common and into hg_util.
2014-04-24 15:45:55 -04:00
Greg Von Kuster
898a88fc42
Fix for the execute_step() method in the SetEnvironment class.
2014-04-24 15:11:43 -04:00
Greg Von Kuster
8d15b1e498
Fix tool shed unit tests I broke with my last commit.
2014-04-24 13:45:04 -04:00
Dave Bouvier
717395cf35
Get tool dependency status from the install model.
2014-04-24 11:24:24 -04:00
Dave Bouvier
5cb41fa42a
Update tool shed twilltestcase methods to reflect changes in the base twilltestcase's visit_url method. Fix functional tests for the tool shed. Update test tool dependencies to not actually compile EMBOSS and freebayes.
2014-04-24 11:23:03 -04:00
Dave Bouvier
1bd89b5357
Fix typo in step handler.
2014-04-24 11:06:59 -04:00
Dannon Baker
87131537f9
Add simplejson back again until 'anyjson' changes are pushed through bioblend.
2014-04-24 11:03:23 -04:00
Greg Von Kuster
8b4e15423c
Add a new recipe manager to support tool dependency package installation. Create new classes for each recipe step where classes contain both a prepare_step() and an execute_step() function. This implementation breaks up the very large loops in install_util.py (where recipe steps are prepared) and fabric_util.py (where recipe steps are executed). The recipe manager currently loads all of the recipe step classes when it is instantiated - this approach could be tweaked if desired.
2014-04-24 10:46:56 -04:00
Carl Eberhard
4a6c93e4fa
Client app: extract method on client app init to javascript_app so it isn't called twice when using parent.javascripts()
2014-04-24 10:34:24 -04:00
John Chilton
e8debf394c
Update LWR client through LWR changeset bd8d1cc.
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Needed for LWR runner to be able to use env tags from job conf file.
2014-04-24 00:31:57 -05:00
John Chilton
24e3e410de
Fix Python 3 incompat in galaxy.jobs.runners.util.
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Module shared with LWR so hoping for Python 3 compat.
2014-04-23 20:33:41 -05:00
Martin Cech
479337bd56
data libraries: default sorting; cleanup; refactor; jslint; start on getting rid of modals for library/folder creation
2014-04-23 17:31:01 -04:00
Dannon Baker
fb10c696a8
Add mock, poster eggs. Both may go away depending on which way bioblend goes w/ deps, but it keeps things working for now.
2014-04-23 17:07:39 -04:00
Dave Bouvier
83394adf1b
Twill test framework cleanup. Fix functional tests for history functions.
2014-04-23 16:46:14 -04:00
Jeremy Goecks
f37dd1a769
Fix divide-by-0 resulting from mean depth of 0 in bai data provider.
2014-04-23 16:31:23 -04:00
Carl Eberhard
45ec3b8e26
UI, History: first pass at making display_structured a bit more useful and clean up the styling; CSS: move hda styling out of history scope
2014-04-23 15:25:25 -04:00
Jeremy Goecks
a36ce7abba
Trackster: add color for read track histograms so that histograms are colorful. Read blocks are still gray to allow for seeing variants easily.
2014-04-23 13:56:26 -04:00
Carl Eberhard
2224045e8d
Visualization framework: remove deprecated 'template_root' element left from when visualizations were loaded from galaxy's template directory
2014-04-23 11:59:21 -04:00
Dannon Baker
733a63f234
Merge stable.
2014-04-23 09:48:48 -04:00
Dannon Baker
70ecfdf452
Merged in jmchilton/galaxy-central-fork-1/stable (pull request #373 )
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[stable] Bugfix for multiple input data parameters.
2014-04-23 09:44:28 -04:00
John Chilton
dfd9839185
Fix test_job_configuration.py for job metrics PR.
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Still need to go in and actually write some tests for the nested parsing that can happen.
2014-04-22 21:40:08 -05:00
John Chilton
886e7adfd6
Job metrics - ensure all text values are unicode before persisting.
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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
John Chilton
7ed40c36b5
Unit tests for job conf parsing.
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Update advanced job sample to fix "bugs" discovered during testing limit parsing.
2014-04-22 20:50:18 -05:00
Carl Eberhard
865805627e
History/HDA UI: pass allow_user_dataset_purge from Galaxy.config to history-panel and hda-edit and respect by not rendering purge controls if false
2014-04-22 13:16:50 -04:00
Dave Bouvier
88377749b4
Merge stable changes into default.
2014-04-22 12:59:21 -04:00
Dave Bouvier
b8981f4659
Fix library template functional tests. Revert change to user info tests that was breaking library template tests.
2014-04-22 12:58:42 -04:00
John Chilton
b5e97ea32b
Workflow Editor: Merge addDataInput and replaceDataInput into common method.
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Reduces some code duplication here and reduces even more code duplication downstream in dataset collections work.
2014-04-22 11:13:27 -05:00
John Chilton
cdeaba1f29
Workflow Editor: Replace instead of recreate terminal on update.
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This fixes at least one subtle bug related to multiple input data parameters (actually probably two bugs) because the old logic assumed there was only one connector per input terminal.
This should be more efficient, lead to some code duplication deletion in subsequent changesets, and really help dataset collections where terminals are much more complex (there are data inputs and collection inputs, and each can be mapped over by collections) - this helps manage complexity downstream.
2014-04-22 11:13:27 -05:00
John Chilton
553bbee7db
Workflow Editor: Rework InputTerminal to implement/use an update method (w/tests).
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This will enable replacing terminals instead of recreating them and reconnecting in subsequent changesets.
2014-04-22 11:13:27 -05:00
Carl Eberhard
10d5c0f920
UI: rework zh and ja locale data
2014-04-22 11:58:22 -04:00
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
Martin Cech
2a1ff52bd8
rename biostar menu link
2014-04-22 10:53:35 -04:00
Martin Cech
d70e804d65
rename biostar menu link
2014-04-22 10:53:35 -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
Dave Bouvier
16101f2038
Merge stable changes into default.
2014-04-22 10:09:40 -04:00
Dannon Baker
8c5f1d1c2d
Merged in dan/galaxy-central-stable-prs/stable (pull request #374 )
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Prevent redirect misuse on user log in.
2014-04-22 10:01:58 -04:00
Martin Cech
da5ba4c711
data libraries: improved chaincall for importing datasets into history, some cleanup
2014-04-21 17:31:36 -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
Dave Bouvier
fa15a53890
Fix functional tests for library features.
2014-04-21 16:51:05 -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