| 5e9391a | Thomas B. Mooney | 13 November 2014, 13:35:31 UTC | Merge pull request #198 from tmooney/fix_anp_refseq_assignment Fix ReferenceSequence AnP Assignment | 13 November 2014, 13:35:31 UTC |
| c6cbd26 | APipe Tester | 13 November 2014, 13:19:27 UTC | Updated `genome` tab completion. | 13 November 2014, 13:19:27 UTC |
| 3630ccc | APipe Tester | 13 November 2014, 13:16:32 UTC | Updated class browser cache. | 13 November 2014, 13:16:32 UTC |
| 2d50114 | David Morton | 13 November 2014, 00:38:28 UTC | Merge pull request #193 from davidlmorton/resultify_generate_reports Resultify generate reports | 13 November 2014, 00:38:28 UTC |
| 4947874 | dmorton | 12 November 2014, 20:52:11 UTC | Remove UR::Context::Transaction from Command::DelegatesToResult The use of the transaction exposed cases where we were incompletely constructing objects. These objects are not DB backed and their references fall out of scope, but the transaction still knows about them and when we commit it determines that they are in an un-savable state. All of those cases need to be addressed before we can use a transaction here. | 12 November 2014, 20:52:11 UTC |
| 7d174ad | APipe Tester | 12 November 2014, 16:44:28 UTC | updated jenkins submodule to 86c5301 | 12 November 2014, 16:44:28 UTC |
| d1ea1c5 | Thomas B. Mooney | 12 November 2014, 15:10:06 UTC | Merge pull request #196 from tmooney/display_names_in_anp_view Parse Configuration in AnP View | 12 November 2014, 15:10:06 UTC |
| 4f20896 | Thomas Mooney | 12 November 2014, 14:49:15 UTC | Remove disused "File::Spec" include. | 12 November 2014, 14:49:15 UTC |
| 10eec8a | Thomas Mooney | 11 November 2014, 23:17:05 UTC | Fix test: SomVal factory now makes extra model so now ours is second. | 11 November 2014, 23:17:05 UTC |
| 91eb589 | Thomas Mooney | 11 November 2014, 23:12:17 UTC | Basic real test of SomVal's CreateAssembledContigReference for indels. | 11 November 2014, 23:12:17 UTC |
| 450a082 | David Morton | 11 November 2014, 23:09:51 UTC | Merge pull request #194 from davidlmorton/vrdb Genome::Process | 11 November 2014, 23:09:51 UTC |
| caf10aa | Thomas Mooney | 11 November 2014, 22:58:42 UTC | Basic real test of SomVal's CreateAssembledContigReference for SVs. | 11 November 2014, 22:58:42 UTC |
| 9ef322a | Thomas Mooney | 11 November 2014, 22:58:11 UTC | Require a reference to be defined on SomVal test models. | 11 November 2014, 22:58:11 UTC |
| 2587b3f | dmorton | 11 November 2014, 22:51:10 UTC | Add tag to sqitch.plan | 11 November 2014, 22:51:10 UTC |
| cffbdda | Thomas Mooney | 11 November 2014, 21:39:08 UTC | Allow analysis_projects to be specified when called in code. | 11 November 2014, 21:39:08 UTC |
| f45c495 | Thomas Mooney | 11 November 2014, 21:12:13 UTC | Warn if we couldn't find an object. | 11 November 2014, 21:12:13 UTC |
| 07f18b2 | Thomas Mooney | 11 November 2014, 19:02:32 UTC | Tighten regexes now that we're doing global replace. | 11 November 2014, 19:02:32 UTC |
| ab47410 | Thomas Mooney | 11 November 2014, 18:59:44 UTC | Allow shorter IDs (to match legacy processing profiles) | 11 November 2014, 18:59:44 UTC |
| b53abee | Thomas Mooney | 11 November 2014, 18:58:01 UTC | Save on repeat search queries by replacing all matches at once. | 11 November 2014, 18:58:01 UTC |
| f6eae6c | dmorton | 11 November 2014, 18:55:59 UTC | Make shortcut/execute exception safe and use a transaction | 11 November 2014, 18:55:59 UTC |
| 85d3024 | Thomas B. Mooney | 11 November 2014, 18:32:09 UTC | Merge pull request #195 from tmooney/improve_add_menu_item_test Improve add-menu-item test | 11 November 2014, 18:32:09 UTC |
| 3ed911a | Eddie Belter | 11 November 2014, 17:59:36 UTC | RDP: test fixes for training set updates | 11 November 2014, 17:59:36 UTC |
| b5b9b14 | Thomas Mooney | 11 November 2014, 15:01:12 UTC | Attempt to translate IDs to display names when printing configuration. | 11 November 2014, 15:01:12 UTC |
| d5302e1 | Thomas Mooney | 11 November 2014, 15:00:42 UTC | Documentation improvements. | 11 November 2014, 15:00:42 UTC |
| 8212799 | dmorton | 11 November 2014, 01:59:41 UTC | Just die if we cannot symlink | 11 November 2014, 01:59:41 UTC |
| efd819d | dmorton | 11 November 2014, 01:53:26 UTC | Revert "Make output_directory no longer an output" This reverts commit ed2b45ac4389945954f591caf583fdae4d049077. | 11 November 2014, 01:53:26 UTC |
| 78a315c | dmorton | 11 November 2014, 00:46:43 UTC | Ensure we return 1 from post_get_or_create | 11 November 2014, 00:46:43 UTC |
| b5e64e5 | dmorton | 10 November 2014, 22:52:18 UTC | Use gsc.wustl.edu as email | 10 November 2014, 22:52:18 UTC |
| 8e17361 | dmorton | 10 November 2014, 22:50:10 UTC | Reuse $pkg instead of spelling it out | 10 November 2014, 22:50:10 UTC |
| ed2b45a | dmorton | 10 November 2014, 22:39:53 UTC | Make output_directory no longer an output | 10 November 2014, 22:39:53 UTC |
| 0169784 | dmorton | 10 November 2014, 22:24:08 UTC | Use $pkg instead of spelling it out again | 10 November 2014, 22:26:39 UTC |
| 2c4399a | dmorton | 10 November 2014, 22:23:00 UTC | Pull returns out of branches | 10 November 2014, 22:26:39 UTC |
| 515b72c | dmorton | 10 November 2014, 22:22:04 UTC | Expect post_get_or_create to return undef on failure | 10 November 2014, 22:26:39 UTC |
| a865ce5 | Thomas B. Mooney | 10 November 2014, 20:51:02 UTC | Merge pull request #190 from tmooney/set_anps_on_subordinate_models Propagate the AnalysisProject on SomaticValidation to its subordinate RefSeq models | 10 November 2014, 20:51:02 UTC |
| ac439aa | Susanna Siebert | 10 November 2014, 20:15:05 UTC | Another case where we need to modify the SCALAR_CACHE | 10 November 2014, 20:15:05 UTC |
| 06834c2 | Susanna Siebert | 10 November 2014, 19:46:52 UTC | Since this subroutine returns a list, we need to modify the SCALAR_CACHE | 10 November 2014, 19:46:52 UTC |
| 5af7265 | dmorton | 10 November 2014, 19:00:04 UTC | Make sure Memoized is used. | 10 November 2014, 19:00:04 UTC |
| a2a7fdb | dmorton | 10 November 2014, 18:59:47 UTC | Use LIST_CACHE => 'MERGE' for memoized functions | 10 November 2014, 18:59:47 UTC |
| 8d46aea | dmorton | 10 November 2014, 18:04:02 UTC | Removed redundant process_process in index names | 10 November 2014, 18:39:49 UTC |
| 6d35c95 | dmorton | 10 November 2014, 18:29:24 UTC | Use Try::Tiny instead of eval | 10 November 2014, 18:29:24 UTC |
| 22dbca6 | dmorton | 10 November 2014, 18:22:35 UTC | Don't import Memoize's stuff into our namespace | 10 November 2014, 18:22:35 UTC |
| 0553989 | dmorton | 10 November 2014, 18:19:01 UTC | Remove 1; from inline package declarations | 10 November 2014, 18:19:01 UTC |
| 0e82e68 | dmorton | 10 November 2014, 18:13:57 UTC | Deduplicate shortcut and execute | 10 November 2014, 18:13:57 UTC |
| e41b76a | dmorton | 10 November 2014, 17:45:03 UTC | Restore sqitch.conf to original (inadvertent change) | 10 November 2014, 17:45:03 UTC |
| d82e502 | Thomas Mooney | 10 November 2014, 17:01:40 UTC | Test that our objects are valid. | 10 November 2014, 17:01:49 UTC |
| 2564012 | Thomas Mooney | 10 November 2014, 17:00:05 UTC | Add required description field. | 10 November 2014, 17:01:49 UTC |
| 2a68ce1 | Thomas Mooney | 10 November 2014, 16:58:36 UTC | Use test factory so they're valid objects. | 10 November 2014, 17:01:49 UTC |
| b6043cd | Thomas B. Mooney | 10 November 2014, 16:54:04 UTC | Merge pull request #192 from tmooney/set_status_for_menu_item_based_configs Set status to active when creating a profile item from a menu item. | 10 November 2014, 16:54:04 UTC |
| da3d3ec | Thomas B. Mooney | 10 November 2014, 16:23:07 UTC | Merge pull request #183 from tmooney/remove_old_inline_config Remove old G:M:Alignment inline configurations. | 10 November 2014, 16:23:07 UTC |
| 636264c | Thomas Mooney | 10 November 2014, 16:19:05 UTC | Test that the created objects can be committed. | 10 November 2014, 16:19:05 UTC |
| e05af5f | APipe Tester | 10 November 2014, 15:22:44 UTC | updated ur submodule to da25be6 | 10 November 2014, 15:22:44 UTC |
| ef77a53 | Thomas B. Mooney | 10 November 2014, 13:53:27 UTC | Merge pull request #191 from tmooney/remove_old_constraints Remove old constraints from Meta DB | 10 November 2014, 13:53:27 UTC |
| 3db6969 | dmorton | 10 November 2014, 02:37:39 UTC | Add Genome::Process::StatusEvent Also have update_status set 'created_at', 'started_at', and 'ended_at'. | 10 November 2014, 02:53:18 UTC |
| f5cb61e | dmorton | 10 November 2014, 02:50:51 UTC | Sqitch: add index for status_event timestamp | 10 November 2014, 02:53:17 UTC |
| 47d04bc | dmorton | 10 November 2014, 01:59:29 UTC | Sqitch: add process status_event table | 10 November 2014, 02:53:17 UTC |
| 0ddb866 | dmorton | 10 November 2014, 02:31:19 UTC | Add Genome::Process This is designed to be a very light-weight base class for keeping meta-data about commands that run workflows. | 10 November 2014, 02:53:17 UTC |
| d643022 | dmorton | 09 November 2014, 22:48:32 UTC | Sqitch: add index for process subclass_name | 10 November 2014, 02:02:41 UTC |
| f91c647 | dmorton | 09 November 2014, 22:43:32 UTC | Sqitch: add indexes for process timestamps | 10 November 2014, 02:02:35 UTC |
| d6a0ce0 | dmorton | 09 November 2014, 21:13:30 UTC | Sqitch: add index for process created_by | 10 November 2014, 01:09:00 UTC |
| f1b29aa | dmorton | 09 November 2014, 21:04:12 UTC | Sqitch: add index for process status | 10 November 2014, 01:09:00 UTC |
| 2a53a14 | dmorton | 08 November 2014, 04:00:04 UTC | Sqitch: add process schema and table | 10 November 2014, 01:08:59 UTC |
| e2ed17f | dmorton | 09 November 2014, 03:11:02 UTC | Allow automatic creation of SR::Users and add tests | 09 November 2014, 03:11:55 UTC |
| 2210742 | dmorton | 09 November 2014, 03:10:41 UTC | Fix Debug statement formatting | 09 November 2014, 03:10:41 UTC |
| 987d26e | dmorton | 09 November 2014, 01:51:34 UTC | Store the got/created SoftwareResult on the Command | 09 November 2014, 03:10:17 UTC |
| 0601297 | dmorton | 08 November 2014, 19:34:25 UTC | Create and use Genome::Command::DelegatesToResult This just defines a shortcut and execute that delegates the real work to the 'result_class' and does some logging. | 08 November 2014, 20:42:18 UTC |
| caa9ff2 | David Morton | 08 November 2014, 19:16:18 UTC | Merge pull request #185 from davidlmorton/color Remove redefinition of inherited property | 08 November 2014, 19:16:18 UTC |
| f3e4abb | APipe Tester | 07 November 2014, 13:21:30 UTC | Updated `gmt` tab completion. | 07 November 2014, 13:21:30 UTC |
| e8110af | APipe Tester | 07 November 2014, 13:20:05 UTC | Updated `genome` tab completion. | 07 November 2014, 13:20:05 UTC |
| f2e39d5 | APipe Tester | 07 November 2014, 13:16:57 UTC | Updated class browser cache. | 07 November 2014, 13:16:57 UTC |
| e10b6b7 | David Morton | 07 November 2014, 03:20:16 UTC | Merge pull request #188 from davidlmorton/vr_cleanup Remove unused VariantReporting integration | 07 November 2014, 03:20:16 UTC |
| 9800e27 | dmorton | 07 November 2014, 03:13:30 UTC | SoftwareResultify GenerateReport | 07 November 2014, 03:13:30 UTC |
| 1cb5084 | dmorton | 07 November 2014, 01:49:56 UTC | GenerateReports takes provider_json instead of translations Since we plan to create a SoftwareResult for this command, and a HASH type input cannot be a SoftwareResult::Param, and provider_json is already an input to all of the Expert adaptors, it seemed like it makes sense to just use provider_json. | 07 November 2014, 01:49:56 UTC |
| 7c7c2f4 | Thomas Mooney | 06 November 2014, 23:55:35 UTC | Set status to active when creating a profile item from a menu item. | 06 November 2014, 23:55:35 UTC |
| fe1ed79 | dmorton | 06 November 2014, 23:49:05 UTC | Rename ReportGenerator to GenerateReport Commands should be named like verbs not nouns. | 06 November 2014, 23:49:05 UTC |
| dfee1fc | dmorton | 06 November 2014, 22:12:15 UTC | Fix data-type of plan_json parameter | 06 November 2014, 23:16:13 UTC |
| 4984560 | David Morton | 06 November 2014, 23:15:39 UTC | Merge pull request #173 from apregier/resource_provider_refactor Change resource provider to translations-only | 06 November 2014, 23:15:39 UTC |
| ad6bd58 | Thomas B. Mooney | 06 November 2014, 22:46:53 UTC | Merge pull request #187 from tmooney/make_status_required Make profile item status a required property. | 06 November 2014, 22:46:53 UTC |
| ced1501 | Travis Abbott | 06 November 2014, 22:17:29 UTC | add bam-window 0.5 | 06 November 2014, 22:17:29 UTC |
| 77ddd79 | apregier | 06 November 2014, 22:15:52 UTC | Eliminate temporary variable | 06 November 2014, 22:15:52 UTC |
| bdbd84e | Thomas Mooney | 06 November 2014, 20:38:26 UTC | Remove constraints for non-existent table config.set | 06 November 2014, 20:38:26 UTC |
| 7bf1e50 | Thomas Mooney | 06 November 2014, 20:27:54 UTC | Remove constraints for non-existent table config.analysis_menu_item | 06 November 2014, 20:27:54 UTC |
| 77d1996 | apregier | 06 November 2014, 18:58:48 UTC | Merge pull request #175 from apregier/tcga_additions Tcga additions | 06 November 2014, 18:58:48 UTC |
| 6d10322 | jhundal | 06 November 2014, 17:48:39 UTC | Merge pull request #184 from jhundal/master Epitope prediction : new module added. | 06 November 2014, 17:48:39 UTC |
| 08e5a03 | dmorton | 06 November 2014, 17:28:53 UTC | Add missing use File::Slurp statement. | 06 November 2014, 17:28:53 UTC |
| f7f0c14 | David Morton | 06 November 2014, 17:18:21 UTC | Merge pull request #186 from davidlmorton/cleanup Remove unused command | 06 November 2014, 17:18:21 UTC |
| 7cf04af | Thomas Mooney | 06 November 2014, 15:25:07 UTC | Set the AnP on our refseq models if we have one. | 06 November 2014, 16:15:24 UTC |
| 280bcd7 | APipe Tester | 06 November 2014, 13:22:07 UTC | Updated `gmt` tab completion. | 06 November 2014, 13:22:07 UTC |
| 7dac533 | APipe Tester | 06 November 2014, 13:20:40 UTC | Updated `genome` tab completion. | 06 November 2014, 13:20:40 UTC |
| 28f3c66 | APipe Tester | 06 November 2014, 13:17:20 UTC | Updated class browser cache. | 06 November 2014, 13:17:20 UTC |
| 6da8528 | dmorton | 06 November 2014, 02:37:24 UTC | Remove unused VariantReporting integration | 06 November 2014, 02:37:24 UTC |
| 513b513 | dmorton | 06 November 2014, 02:16:26 UTC | Update test data for Define-docs.t | 06 November 2014, 02:16:26 UTC |
| 1af9e52 | dmorton | 06 November 2014, 01:47:18 UTC | Add Genome::Command::WithColor This is a Command::V2 so its attributes can 'is_param'. This is needed in order to have an attribute show up in the help or be accepted as a command-line argument. | 06 November 2014, 01:51:39 UTC |
| 3e0ca15 | dmorton | 06 November 2014, 01:41:41 UTC | Make doc clearer | 06 November 2014, 01:41:41 UTC |
| 8d4007c | dmorton | 06 November 2014, 01:38:52 UTC | Move ColorMixin from Command to Utility Since it does not inherit from Command it belongs someplace else. | 06 November 2014, 01:38:52 UTC |
| a589c4b | Chris Miller | 05 November 2014, 23:52:16 UTC | Merge pull request #180 from chrisamiller/master adding tumor purity correction option to some plotting tools. | 05 November 2014, 23:52:16 UTC |
| 50f9921 | Thomas Mooney | 05 November 2014, 22:26:47 UTC | Make profile item status a required property. Values in the database have been backfilled. | 05 November 2014, 23:09:16 UTC |
| ff6dc8f | Thomas B. Mooney | 05 November 2014, 22:15:15 UTC | Merge pull request #177 from tmooney/move_phase_variants Move "PhaseVariants" tool under GMT. | 05 November 2014, 22:15:15 UTC |
| 0adbf6b | Jasreet Hundal | 05 November 2014, 21:32:48 UTC | Epitope Prediction - changes to AddCoords.pm v3 | 05 November 2014, 21:32:48 UTC |
| f88cdfc | apregier | 05 November 2014, 21:17:40 UTC | Rename example resource_files | 05 November 2014, 21:17:40 UTC |
| 23770d4 | dmorton | 05 November 2014, 21:10:51 UTC | Remove unused command This was created during prototyping and should have been removed earlier. | 05 November 2014, 21:10:51 UTC |
