 Jeremy Goecks
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2e310f6cc6
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Small additions based on bdd35af2a18a
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2012-09-21 14:05:37 -04:00 |
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Jeremy Goecks
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6fefb40d4b
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Viz framework: (a) push data provider creation to registry to simplify provider creation; (b) fix bugs in filters module naming; (c) enable deeper sampling in BBI data provider.
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2012-09-21 14:00:09 -04:00 |
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Jeremy Goecks
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36e589d845
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Push data sources/converter methods from controller mixin to dataset object.
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2012-09-21 11:52:47 -04:00 |
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Greg Von Kuster
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f3070824b1
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Add the ability to review tools migration stages that are available for the current Galaxy instance.
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2012-09-21 11:21:38 -04:00 |
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Jeremy Goecks
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95b945b184
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Place track filters in their own file.
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2012-09-21 11:14:56 -04:00 |
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Jeremy Goecks
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75f936db5f
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Add requireJS support for data, visualization, tools and update dependencies.
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2012-09-21 10:12:01 -04:00 |
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Dannon Baker
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924cd349d3
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Workflows: Viewing and Downloading of workflows with missing tools now handled gracefully.
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2012-09-20 17:10:52 -04:00 |
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Jeremy Goecks
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53f26307c2
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Add utility function to circster that determines whether an element is visible.
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2012-09-20 15:39:57 -04:00 |
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Greg Von Kuster
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1b9513293c
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Display warning or error message if attempting to install tool dependencies defined in a tool shed repository when the tool_dependency_dir config setting is not set in the Galaxy config.
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2012-09-20 14:41:33 -04:00 |
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Dannon Baker
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8fec516f19
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Workflows: Fix for 0ba260ea43c4 to correctly display error message when attempting to run a workflow missing tools.
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2012-09-20 14:11:19 -04:00 |
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Greg Von Kuster
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9b063e395d
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Fixes for viewing tool metadata in a tool shed repository for tools the require data index (.loc) files.
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2012-09-20 13:43:42 -04:00 |
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Greg Von Kuster
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452249f806
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Fix for viewing tool metadata defined for tools in a repository that use the Galaxy ToolDataTableManager.
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2012-09-20 10:58:05 -04:00 |
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Jeremy Goecks
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1dd49b9ed4
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Circster: render wiggle data as a single path rather than many small paths.
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2012-09-19 18:31:30 -04:00 |
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Greg Von Kuster
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946fe73a82
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Fix and enhance the features for resetting a repository that encounted errors during the cloning process so the Galaxy admin can make another attempt to install it.
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2012-09-19 16:35:49 -04:00 |
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Dannon Baker
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1d67ba66b0
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Revert previous change to message.mako for now -- we do use html in the message box elsewhere (links, etc) and this breaks them.
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2012-09-19 13:20:45 -04:00 |
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Dannon Baker
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f1670541bf
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Prevent reflective XSS through message display.
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2012-09-19 10:32:19 -04:00 |
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Dannon Baker
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03694c29b2
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Cloud Launch - Fix for rare instance udpate() that happens when (rarely) Amazon doesn't have the instance fully registered before update() is called.
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2012-09-19 00:10:47 -04:00 |
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Jeremy Goecks
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ff226c3a4b
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Fix bug in setting dbkey for new track browser.
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2012-09-18 22:33:49 -04:00 |
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Dannon Baker
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ba6114ca3e
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Fix create_all_fasta_loc to work when inspect_dir is not set.
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2012-09-18 20:49:29 -04:00 |
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Jeremy Goecks
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b1d9046175
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Tophat2 wrapper fixes. Thanks to Jim Johnson and Lance Parsons.
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2012-09-18 17:11:18 -04:00 |
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Jeremy Goecks
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7bd55e2928
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Wrap Sweepster in a requireJS module and add needed module qualifications. Pack scripts.
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2012-09-18 16:50:45 -04:00 |
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Scott McManus
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0b221fee66
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Fixed call to check_tool_output for TaskWrapper.
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2012-09-18 14:10:56 -04:00 |
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Greg Von Kuster
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565fbaff4b
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Fix for getting updates for tool shed repositories installed into a local Galaxy instance.
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2012-09-18 13:54:19 -04:00 |
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Jeremy Goecks
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49632eab74
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Fix bugs in Trackster refactoring.
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2012-09-18 13:48:06 -04:00 |
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Jeremy Goecks
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79d9d25daa
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Remove dubugging statement from last commit.
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2012-09-18 13:14:49 -04:00 |
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Jeremy Goecks
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6d6b972951
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Enhancements for finding available visualizations: (a) use dataset rather than datatype and (b) only show scatterplot for tabular datasets with >=2 numerical columns.
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2012-09-18 13:10:04 -04:00 |
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Carl Eberhard
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8810a1c680
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fix to apply tooltips to running/queued datasets in history panel
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2012-09-18 12:39:13 -04:00 |
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Nate Coraor
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949ffbfe20
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Add $__user_name__ to job template.
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2012-09-18 12:13:02 -04:00 |
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Jeremy Goecks
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93f6810ed5
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Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.
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2012-09-18 11:40:57 -04:00 |
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Dannon Baker
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91ddfaff28
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Grammar. it's -> its in admin panel (and tests)
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2012-09-18 09:34:51 -04:00 |
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Greg Von Kuster
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ca4034cd32
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Apply fix from Jim Johnson for rendering tool dependencies defined in a tool shed repository.
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2012-09-18 09:03:39 -04:00 |
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Jeremy Goecks
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c66679cb26
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Fix bugs when converting BED to FLI and JS module references.
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2012-09-17 17:36:40 -04:00 |
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Carl Eberhard
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5d9348f1f2
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scatterplot.mako: some cleanup
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2012-09-17 17:19:53 -04:00 |
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Carl Eberhard
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68be41d2a9
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initial, un-wired prototype for scatterplot visualization
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2012-09-17 17:12:42 -04:00 |
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James Taylor
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a4216b5a74
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pack
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2012-09-17 16:24:27 -04:00 |
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James Taylor
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d8dac5bfcc
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trackster: moving more stuff out of mako into javascript
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2012-09-17 16:24:13 -04:00 |
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James Taylor
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bb08862dc6
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pack scripts
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2012-09-17 16:15:09 -04:00 |
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James Taylor
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8fbf7a3b0a
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trackster: misc fixes and reorganization
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2012-09-17 16:14:52 -04:00 |
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James Taylor
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893a610e8d
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trackster: fix adding bookmarks
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2012-09-17 15:41:35 -04:00 |
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James Taylor
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ae1a8a894c
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trackster: fix groups
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2012-09-17 15:38:46 -04:00 |
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James Taylor
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3fa6a8ab4e
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trackster fixes
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2012-09-17 15:36:11 -04:00 |
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James Taylor
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2297b49262
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trackster: adding packed scripts
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2012-09-17 15:23:45 -04:00 |
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Nate Coraor
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3bb0588147
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I missed some missing indexes...
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2012-09-17 14:23:00 -04:00 |
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Nate Coraor
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c51a9fb9fb
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Index galaxy_user.email and add a bunch of indexes for columns added to existing tables that were supposed to be indexed.
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2012-09-17 13:54:28 -04:00 |
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Dannon Baker
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987f9ad5fd
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Set header 'X-Content-Type-Options: nosniff' for dataset display. This will prevent IE8 from trying to render as html datasets served as text/plain.
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2012-09-17 13:19:32 -04:00 |
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Nate Coraor
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459d3a2c1d
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More pgcleanup.py fixes and addition of cleanup event tables for library items.
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2012-09-17 12:51:17 -04:00 |
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Nate Coraor
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2371873ccb
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Fix a typo in library permissions check.
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2012-09-17 12:47:13 -04:00 |
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Jeremy Goecks
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dd40fd7c05
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Data providers framework enhancements: (a) add registry object; (b) move all provider lookup code into registry; and (c) integrate ColumnDataProvider into raw_data requests.
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2012-09-17 12:29:48 -04:00 |
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Dannon Baker
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ba6980469c
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Prevent galaxy session cookie from being accessed via script. We don't use it via js anywhere, only other cookies specifically set for dynatree/genetrack.
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2012-09-17 12:27:03 -04:00 |
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James Taylor
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e6ce7b2895
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trackster: merge
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2012-09-17 12:06:02 -04:00 |
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