 Carl Eberhard
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b44ca3c578
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History API: allow filtering, limit, and offset in index params; Implement managers/base.FilterParser to configure how models can be filtered; Change ModelManager.list to allow limit, offset, and post-query (functional) filters; Add user filter, limit, and offset parsers to BaseController; Add tests for previous; Remove some UserManager functions; Continue filling out Annotatable mixin
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2015-01-29 10:42:54 -05:00 |
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Nicola Soranzo
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2b7b5df7ba
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Fix INTEGRATED_TOOL_PANEL_DESCRIPTION .
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2015-01-29 13:52:19 +00:00 |
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Aysam Guerler
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28b83ba22a
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ToolForm: Update validation
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2015-01-29 04:30:33 -05:00 |
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Aysam Guerler
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08bc32ce42
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Parameters: Multiselect back to optional by default
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2015-01-29 00:57:59 -05:00 |
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Aysam Guerler
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d38ca6c5eb
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Workflow: Add tool form switch to config, fix late validation check
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2015-01-29 00:38:02 -05:00 |
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Aysam Guerler
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c4c6ba7534
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Workflow: Insert conditional tool model creation
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2015-01-28 23:53:19 -05:00 |
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Aysam Guerler
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9bad2c6648
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Parameters: Multiselect by default not optional
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2015-01-28 16:21:23 -05:00 |
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Nate Coraor
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23f3e479be
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Remove memdump, which probably has not worked for many years.
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2015-01-28 16:20:30 -05:00 |
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Martin Cech
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8a048be50b
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fix error in TS search schema
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2015-01-28 15:25:42 -05:00 |
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Martin Cech
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f10ed7d184
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way better search; dont query DB; repair final scoring functions
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2015-01-28 15:24:10 -05:00 |
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Aysam Guerler
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5db80b31bf
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Workflow: Disable new tool form
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2015-01-28 13:51:51 -05:00 |
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Nate Coraor
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e7bfac8046
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Merged in natefoo/galaxy-central/samtools1_bam_index (pull request #651)
Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1.
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2015-01-28 13:36:35 -05:00 |
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Nate Coraor
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43159db9fe
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Use subprocess.call() rather than Popen(), thanks Nicola.
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2015-01-28 13:25:11 -05:00 |
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Daniel Blankenberg
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bff841fa42
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Fix for XmlToolSource.parse_command() to return None when a command element does not exist or text is empty.
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2015-01-28 12:09:56 -05:00 |
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Nate Coraor
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11ae48a70f
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Use a symlink to the dataset in the same directory as the MetadataTempFile as the input to samtools index so there's no clobber risk. Thanks Dan.
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2015-01-28 11:58:23 -05:00 |
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Nate Coraor
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13e8b3e7de
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Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1.
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2015-01-28 10:38:22 -05:00 |
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Martin Cech
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3ac2b24451
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use the new pretty_print_time_interval method from utils
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2015-01-27 18:14:27 -05:00 |
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Martin Cech
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2c6f5cb5e9
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add pretty_print_time_interval to make time intervals more readable
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2015-01-27 18:13:50 -05:00 |
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Martin Cech
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2a405ef0e3
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Merge
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2015-01-27 17:19:07 -05:00 |
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Martin Cech
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fd8a7da910
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adjust schema, start dynamic scoring
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2015-01-27 17:15:18 -05:00 |
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Dannon Baker
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3f623e31b1
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Merge from stable.
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2015-01-27 15:34:24 -05:00 |
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Carl Eberhard
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43b2f4ffa1
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Remove paragraph tags from history/rename feedback messages
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2015-01-27 14:32:16 -05:00 |
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Martin Cech
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ad9ea20787
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query parser experiments, better formatted time delta
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2015-01-26 19:45:33 -05:00 |
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Daniel Blankenberg
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30f1815658
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Load genomes list from data tables for visualizations. Based off of Pull Request: https://bitbucket.org/galaxy/galaxy-central/pull-request/601/load-genomes-list-from-data-tables-for/diff
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2015-01-26 15:11:06 -05:00 |
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Martin Cech
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05e9ea637e
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initial version of TS search API and Index builder script
beware: always returns jsonp for now
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2015-01-26 13:08:16 -05:00 |
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Dannon Baker
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863d5d1720
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One more path permission increase for admins under remote_user.
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2015-01-26 10:43:02 -05:00 |
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Dannon Baker
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61a798a1db
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Allow admin users to change user information (like email addresses) when using remote_auth; otherwise should a user email address change you had to manually edit the database.
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2015-01-26 08:58:29 -05:00 |
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John Chilton
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663341e4cc
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Toolbox: Watch even empty directories if they are explicitly tool_dir specified.
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2015-01-25 19:18:53 -05:00 |
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John Chilton
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b5533cfe0e
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Merged in BjoernGruening/galaxy-central-1/compressed_upload (pull request #630)
Add CompressedArchive as datatype and do not uncomress it during upload.
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2015-01-23 14:13:25 -05:00 |
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Carl Eberhard
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a27e2a96d2
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Fix Ratable to add emtpy stubs
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2015-01-23 13:15:59 -05:00 |
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Carl Eberhard
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c1a0e03d55
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Managers: cleanup and removal of my awesome ascii art
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2015-01-23 13:09:42 -05:00 |
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Carl Eberhard
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b224959469
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Fix to replace get_dataset in visualization registry ResourceParser with hda_manager.get_accessible
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2015-01-23 12:44:46 -05:00 |
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John Chilton
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2d227d2daf
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Merged in BjoernGruening/galaxy-central-1/snpeff_datatype (pull request #640)
Add SnpEff datatypes
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2015-01-23 12:12:43 -05:00 |
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John Chilton
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c64c1bac0c
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Merged in BjoernGruening/galaxy-central-1/toolshed_blacklist_additions (pull request #627)
Add planemo test file to tool shed upoad blacklist.
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2015-01-23 12:11:03 -05:00 |
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Aysam Guerler
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178666baeb
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ToolForm: Fix optional dataset parameters, fix inconsistencies in parameter handling
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2015-01-23 12:04:50 -05:00 |
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Dannon Baker
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cdabbe2af8
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Add missing parameter in provenance controller.
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2015-01-23 08:13:45 -05:00 |
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Dannon Baker
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51043f8130
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Resolve scope issues in visualization controller, add missing imports and organize.
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2015-01-22 18:24:25 -05:00 |
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Dannon Baker
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e6d877196a
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Remove a trailing semicolon in the page controller.
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2015-01-22 18:19:08 -05:00 |
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Dannon Baker
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2bf6763dc6
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misc cleanup, pep8 in page controller
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2015-01-22 18:18:14 -05:00 |
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Dannon Baker
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91bc856cf5
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Remove cruft in history controller.
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2015-01-22 18:07:19 -05:00 |
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Dannon Baker
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cd585d91c9
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Import cleanup in history controller.
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2015-01-22 18:05:11 -05:00 |
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Dannon Baker
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f869d82fb4
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Merge.
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2015-01-22 17:57:15 -05:00 |
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Dannon Baker
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b0774dafc3
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Cleanup/pep8 in imp_exp.
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2015-01-22 17:57:04 -05:00 |
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Carl Eberhard
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1a48c1953e
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Fix: remove debugging statement
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2015-01-22 17:55:14 -05:00 |
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Dannon Baker
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dafc96e135
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Import cleanup in visualizations manager.
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2015-01-22 17:46:00 -05:00 |
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Dannon Baker
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a2e6b4504a
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Fix set_slug method in sharable manager / scope issues.
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2015-01-22 17:34:40 -05:00 |
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Carl Eberhard
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fe8bb01b78
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Sharable managers: Generate slug on user share only if needed
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2015-01-22 17:33:02 -05:00 |
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Dannon Baker
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421462bc76
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pep8 lddamanager
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2015-01-22 17:31:20 -05:00 |
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Dannon Baker
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950a67d7ed
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Remove unused imports from pages manager, minor formatting.
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2015-01-22 17:28:43 -05:00 |
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Dannon Baker
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e11ceb615e
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Fix missing required import in ldda manager.
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2015-01-22 17:22:39 -05:00 |
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