John Chilton
d7b4b36756
Change paired collections terminology from left/right to forward/reverse.
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If you have paired datasets in your database they will no longer work - send me an e-mail and I can give you an SQL update statement.
2014-05-15 13:01:36 -05:00
John Chilton
f1a322bc91
Order history.{active,visible}_dataset_collections by hid instead of id.
2014-05-15 12:04:58 -05:00
John Chilton
ededf2451d
PEP-8 fixes for DatasetInterface.copy_datasets.
2014-05-15 12:04:58 -05:00
John Chilton
a376cc7230
Allow 'Copy Datasets' page to copy collections as well.
2014-05-15 12:04:58 -05:00
John Chilton
ae1ea31eec
Bugfix: Copying datasets to existing and new history at same time.
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Previously would give error about set not having an append method.
2014-05-15 12:04:58 -05:00
Aysam Guerler
17d5ffad32
Charts: Fix multipanels in heatmap
2014-05-15 11:57:43 -04:00
Nate Coraor
dba55de9cf
Merged in erasche2/galaxy-central (pull request #393 )
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Added rolling restart script to kill servers sequentially
2014-05-15 11:33:20 -04:00
Eric Rasche
209bfcb2fb
Fixed typo on regex
2014-05-15 09:48:17 -05:00
Eric Rasche
d3bbb93fe7
Added line anchors for performance
2014-05-15 09:43:04 -05:00
Greg Von Kuster
2957700246
Refactoring cleanup in the Tool Shed's package installation framework.
2014-05-15 09:59:55 -04:00
Aysam Guerler
259ec14c2a
Charts: Fix style
2014-05-14 22:49:44 -04:00
Aysam Guerler
aecbac128c
Charts: Update panel
2014-05-14 22:21:36 -04:00
Aysam Guerler
eafa59209e
Charts: Update boxplots and stacked bar
2014-05-14 22:18:17 -04:00
Aysam Guerler
2caca37748
Charts: Add new selection panel, improve modularity, activate basic heat map
2014-05-14 22:11:59 -04:00
John Chilton
bdab215a8d
Bugfix: Yet another bug fix for workflow extraction with collection operations.
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Fail, fail, fail.
2014-05-14 18:25:50 -05:00
John Chilton
d6cea61cc5
Bugfix: Small fix for running workflows with subcollection mapping steps.
2014-05-14 18:25:50 -05:00
Greg Von Kuster
2d5c37a73f
Enhance the galaxy API for the Tool Shed to retrieve the latest installable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner.
2014-05-14 18:13:33 -04:00
Nate Coraor
d18dee991e
Add a config option for controlling the AMQP consumer timeout, catch socket.error and attempt to recover from it.
2014-05-14 16:34:15 -05:00
Daniel Blankenberg
e9391803bb
Fix for setting metadata when uploading directly to a library.
2014-05-14 17:26:41 -04:00
John Chilton
255e77c862
Remove stray log statements in previous commit.
2014-05-14 16:13:32 -05:00
John Chilton
11e0676490
Bugfixes: More bug fixes for extracting collection-y workflows from a history.
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The embarrassment continues...
2014-05-14 16:06:33 -05:00
Eric Rasche
f5e39af8e8
Added --daemon flag so user doesn't have to
2014-05-14 15:33:44 -05:00
Nate Coraor
5e32a8ae5b
Correctly handle the case where the AMQP SSL connection param parser gets params=None.
2014-05-14 15:27:28 -05:00
Eric Rasche
9c3b514693
Removed detach as --daemon flag will detach process
2014-05-14 15:23:26 -05:00
Eric Rasche
52f12b0729
Added rolling restart script to kill servers sequentially
2014-05-14 14:48:26 -05:00
Dave Bouvier
d682e58ad4
Fix missing imports, add self.app in a few more places.
2014-05-14 15:19:48 -04:00
John Chilton
75d47452f9
Merge.
2014-05-14 14:08:56 -05:00
John Chilton
61a28e9b28
Bugfix: Annotation, tags on collections update looking in old location.
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Moved to collection instances instead of collections a little before PR opened.
2014-05-14 14:08:03 -05:00
Greg Von Kuster
e31f73041d
Fix for tool migration manager to use self.app instead of trans.app.
2014-05-14 15:07:30 -04:00
Greg Von Kuster
5b3e02d5c3
Phase 2 of the tool dependency package installation framework rewrite: 1) rename the RecipeManager class to be the StepManager class and add a new TagManager class, both of which are contained in the recipe_manager.py module. 2) Add appropriate new classes for handling recipe tag sets to a new tag_handler.py module. Add a new InstallManager class with functions for installing tool dependencies. Eliminate the use of fabric_util.py and install_util.py.
2014-05-14 14:55:31 -04:00
Martin Cech
37d8aac8cd
data libraries: first take on api for requesting roles(assigned and assignable) for permissions; do not use - needs to be tested on test
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changes to UI, removed modal for dataset details, dissasembled into separate backbone view
2014-05-14 13:53:01 -04:00
Martin Cech
4605eeb541
extended ui-select module to support multiple inputs and on-demand ajax loading of paginated data
2014-05-14 13:50:15 -04:00
Daniel Blankenberg
9b170521ed
Fix for when hours_between_check is defined in ini.
2014-05-14 12:04:47 -04:00
Daniel Blankenberg
3f87380dea
Allow for an arbitrary number of tool_data_table_config_path files to be defined in ini file. Values are comma separated.
2014-05-14 11:52:20 -04:00
John Chilton
486dc41639
Bugfix for updating history dataset collection name.
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Thanks to Bjoern for the bug report.
This attribute had been DatasetCollection in earlier versions of this code and the update code was only partially cut-over to use the new location for name (on HistoryDatasetCollectionAssociation).
2014-05-14 05:26:21 -05:00
John Chilton
c79e4dcc40
Fix duplicated names in on_text when using multiple data inputs.
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Unit tests verifing the fixed, correct behavior included. Bug introduced in e8c84dd715782e7c1d709d8068e6033b835f7f39 as an unintended consequence of duplicating the first dataset in the dictionary of input datasets generated by the tool action code.
Fixes https://trello.com/c/LCEKxImR .
2014-05-13 17:47:57 -05:00
Dannon Baker
48ff27d6e3
Merge from stable.
2014-05-13 17:39:55 -04:00
John Chilton
e536ba727b
Merged in natefoo/galaxy-central (pull request #392 )
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SSL client certificate support for LWR AMQP connections
2014-05-13 15:38:04 -05:00
Nate Coraor
c9cc289a85
Allow specification of SSL client authentication parameters to the kombu
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connection. This is done via the `amqp_connect_ssl_*` options in `server.ini`.
2014-05-13 15:22:03 -05:00
Daniel Blankenberg
421e88cd05
Display line errors in data table registry display encountered when loading a location file.
2014-05-13 16:10:27 -04:00
Daniel Blankenberg
157812954d
More Data Manager UI fixes. Fix for viewing data manager job info when dataset has been deleted.
2014-05-13 15:47:54 -04:00
Daniel Blankenberg
a975b8f811
Allow tool_runner rerun to accept a job_id instead of a dataset_id.
2014-05-13 15:12:25 -04:00
Daniel Blankenberg
311034304a
More Data Manager UI tweaks.
2014-05-13 14:34:57 -04:00
Daniel Blankenberg
b02534af73
Alphabetize lists of Data Manager elements on index page.
2014-05-13 14:21:08 -04:00
Daniel Blankenberg
8090829a8b
Data Manager UI enhancements.
2014-05-13 14:07:07 -04:00
Daniel Blankenberg
c86e36f652
Add the ability for Admins to reload tool data table entries from disk without restarting the Galaxy server. This does not look for new <table> entries or contained new <file>s within XML files, but will e.g. make any changes to a .loc file become live immediately without restart.
2014-05-13 13:01:47 -04:00
Daniel Blankenberg
f5d2c1eb7d
When viewing tool data table registry in admin interface, provide link to manage data table interface for each tool data table.
2014-05-13 12:35:35 -04:00
John Chilton
98a560ccd1
Optimize/correct LWR remote metadata generation for working directory outputs.
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Previously I was attempting to mimic Galaxy's behavior of copying these files to a fixed output location after execution on the remote server before setting metadata. This was an un-needed copy since it appears to easier to just send the metadata generation code the expected path on the working directory.
2014-05-13 10:20:06 -05:00
John Chilton
f8e904a81d
Remove no longer valid log message.
2014-05-13 10:20:06 -05:00
John Chilton
3287af315d
Ensure new_file_path exists before set_metadata.py generates metadata.
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This directory is required to exist but usually unneeded because Galaxy creates this directory on startup. However, when setting metadata remotely with the LWR that remote Galaxy instance may have never been started and this directory may not exist.
2014-05-13 09:29:41 -05:00
John Chilton