| 641d2e3 | Eddie Belter | 20 May 2015, 16:30:21 UTC | Merge pull request #761 from ebelter/site-tgi Sync: LIMS organism classes names are optional | 20 May 2015, 16:30:21 UTC |
| 1db0ab2 | Gue Su Chang | 20 May 2015, 14:51:07 UTC | Merge pull request #756 from gschang/master Minor bug fixation in R | 20 May 2015, 14:51:07 UTC |
| 1486ed8 | Anthony Brummett | 20 May 2015, 14:32:46 UTC | Merge pull request #747 from brummett/create_symlink Make Genome::Sys->create_symlink() idempotent | 20 May 2015, 14:32:46 UTC |
| b245abb | APipe Tester | 20 May 2015, 12:23:42 UTC | Updated `genome` tab completion. | 20 May 2015, 12:23:42 UTC |
| 2005883 | APipe Tester | 20 May 2015, 12:21:21 UTC | Updated class browser cache. | 20 May 2015, 12:21:21 UTC |
| b40a7ad | Eddie Belter | 19 May 2015, 23:38:42 UTC | Merge pull request #759 from ebelter/sync-usage Update the disk volume sync usage command | 19 May 2015, 23:38:42 UTC |
| 5a186e5 | Eddie Belter | 19 May 2015, 23:16:53 UTC | Merge pull request #754 from ebelter/instdata-import-process InstData Import: make the batch importer [formerly known as Manager, now called launch] a genome process. | 19 May 2015, 23:16:53 UTC |
| 682f285 | Eddie Belter | 19 May 2015, 21:24:55 UTC | Sync: LIMS organism classes names are optional | 19 May 2015, 21:24:55 UTC |
| 32af909 | Eddie Belter | 19 May 2015, 20:47:23 UTC | PR suggestions | 19 May 2015, 20:47:23 UTC |
| f201ea0 | Nathaniel Nutter | 19 May 2015, 20:47:07 UTC | Merge pull request #752 from nnutter/user validate values to hash | 19 May 2015, 20:47:07 UTC |
| 0bf9acb | Nathaniel Nutter | 19 May 2015, 20:46:52 UTC | Merge pull request #751 from nnutter/archivable avoid side effects if an allocation is rolled back | 19 May 2015, 20:46:52 UTC |
| 3ee2c46 | Nathaniel Nutter | 19 May 2015, 20:46:41 UTC | Merge pull request #750 from nnutter/start acquire build_requested lock before creating builds to start | 19 May 2015, 20:46:41 UTC |
| bcca514 | Eddie Belter | 19 May 2015, 20:15:50 UTC | Update the disk volume sync usage command | 19 May 2015, 20:15:50 UTC |
| 4836a35 | APipe Tester | 19 May 2015, 18:02:52 UTC | updated workflow submodule to 701271d | 19 May 2015, 18:02:52 UTC |
| 94bbafc | Gue Su Chang | 18 May 2015, 19:41:50 UTC | Minor bug fixation in R | 18 May 2015, 19:41:50 UTC |
| 1e73222 | Nathaniel Nutter | 18 May 2015, 14:18:52 UTC | add build ID to error message | 18 May 2015, 14:18:52 UTC |
| c6c2fbb | Nathaniel Nutter | 18 May 2015, 14:17:10 UTC | fix typo | 18 May 2015, 14:17:10 UTC |
| 0fd9af0 | APipe Tester | 18 May 2015, 12:17:02 UTC | Updated `genome` tab completion. | 18 May 2015, 12:17:02 UTC |
| f2f507c | APipe Tester | 18 May 2015, 12:15:05 UTC | Updated class browser cache. | 18 May 2015, 12:15:05 UTC |
| 0f086d9 | Nathaniel Nutter | 18 May 2015, 00:30:34 UTC | Merge pull request #635 from nnutter/config File-Backed Genome::Config Implementation | 18 May 2015, 00:30:34 UTC |
| cb0754c | Eddie Belter | 17 May 2015, 19:59:43 UTC | InstData Import: update create entity help | 17 May 2015, 19:59:43 UTC |
| 3fafe5b | Eddie Belter | 17 May 2015, 19:51:46 UTC | InstData Import: add process to instdata when ran through launch command | 17 May 2015, 19:51:46 UTC |
| 4114142 | Nathaniel Nutter | 17 May 2015, 15:57:29 UTC | Merge pull request #753 from nnutter/master fix `register_callback` call because subject is not valid for that API | 17 May 2015, 15:57:29 UTC |
| b9b6911 | Nathaniel Nutter | 16 May 2015, 20:36:04 UTC | fix `register_callback` call because subject is not valid for that API This was not caught by testing on the PR because `GENOME_NESSY_SERVER` isn't set on PR tests (yet). | 16 May 2015, 20:36:04 UTC |
| 9d224aa | Nathaniel Nutter | 16 May 2015, 17:24:48 UTC | Merge pull request #749 from nnutter/observers update Genome to use appropriate observer APIs | 16 May 2015, 17:24:48 UTC |
| f29504f | Nathaniel Nutter | 16 May 2015, 17:13:03 UTC | validate values to hash We had a case where no sponsor was found for a build which caused a warning about odd number of elements in the hash and then failed downstream. | 16 May 2015, 17:13:23 UTC |
| 8906afe | Nathaniel Nutter | 13 May 2015, 19:13:39 UTC | override __rollback_property__ to fix regression test for RT#105743 | 16 May 2015, 00:08:26 UTC |
| b1f2239 | Nathaniel Nutter | 13 May 2015, 19:13:09 UTC | add a regression test for RT#105743 | 16 May 2015, 00:08:25 UTC |
| d124949 | Nathaniel Nutter | 15 May 2015, 17:19:37 UTC | acquire build_requested lock before creating builds to start @tmooney pointed out that if something else were updating the model between when we created the build and turned off `build_requested` then we would turn off `build_requested` prematurely. This changes it so we disable `build_requested` (within a transaction) prior to even creating the build so that the `build_requested` locking prevents this race. | 15 May 2015, 22:06:11 UTC |
| a624aea | Nathaniel Nutter | 13 May 2015, 22:09:19 UTC | add test to ensure observers are not created during import If an observer is created during import of Genome packages it should use the `UR::Observer->register_callback` API so that they are rollback-safe. | 15 May 2015, 22:03:26 UTC |
| 5772c7d | Nathaniel Nutter | 13 May 2015, 20:42:33 UTC | convert old `create_subscription` calls to `add_observer` The `create_subscription` API is deprecated by the `add_observer` API. | 15 May 2015, 22:03:25 UTC |
| a2c8b10 | Nathaniel Nutter | 13 May 2015, 20:42:16 UTC | remove debug code | 15 May 2015, 22:03:24 UTC |
| a0bbfd8 | Nathaniel Nutter | 13 May 2015, 20:39:14 UTC | convert package-scoped observers to use register_callback Observers that are added as part of loading a package should be created with `UR::Observer->register_callback` so that they are rollback-safe. | 15 May 2015, 22:03:23 UTC |
| cca6030 | APipe Tester | 15 May 2015, 20:42:59 UTC | updated workflow submodule to e7a06a3 | 15 May 2015, 20:42:59 UTC |
| f40635b | APipe Tester | 15 May 2015, 20:42:48 UTC | updated ur submodule to fd4e58d | 15 May 2015, 20:42:48 UTC |
| 1516079 | Nathaniel Nutter | 15 May 2015, 20:31:59 UTC | Merge pull request #746 from nnutter/start cleaning up `genome model build start` a bit | 15 May 2015, 20:31:59 UTC |
| a3a8baa | Allison Penner Regier | 15 May 2015, 18:32:49 UTC | Merge pull request #743 from apregier/evaluate_bedpe Evaluate bedpe | 15 May 2015, 18:32:49 UTC |
| 54cc316 | Anthony Brummett | 15 May 2015, 16:54:11 UTC | Bug fix creating symlink over an already existing file Properly handle the case where it's asked to create a link, but that link name already exists as something that's not a link. | 15 May 2015, 16:54:11 UTC |
| 664b548 | Anthony Brummett | 15 May 2015, 15:26:17 UTC | Remove now-broken tests create_symlink() will now succeed for this case | 15 May 2015, 15:26:17 UTC |
| 9a73ca3 | Anthony Brummett | 15 May 2015, 15:23:14 UTC | Save the errno value before it can change | 15 May 2015, 15:23:14 UTC |
| 09e46c5 | Anthony Brummett | 15 May 2015, 15:22:35 UTC | avoid uninitialized value warning when readlink() is used on a non-symlink | 15 May 2015, 15:22:35 UTC |
| 876cd97 | APipe Tester | 15 May 2015, 12:17:10 UTC | Updated `genome` tab completion. | 15 May 2015, 12:17:10 UTC |
| 88312a5 | APipe Tester | 15 May 2015, 12:15:15 UTC | Updated class browser cache. | 15 May 2015, 12:15:15 UTC |
| 29d16fa | APipe Tester | 15 May 2015, 03:34:55 UTC | updated ur submodule to d8a4514 | 15 May 2015, 03:34:55 UTC |
| 9d686e3 | Anthony Brummett | 14 May 2015, 22:03:43 UTC | create_symlink() is now idempotent If the symlink exists, but already points to the requested target, succeed It still fails if the link exists but points somewhere else. | 14 May 2015, 22:03:43 UTC |
| d4616ba | Anthony Brummett | 14 May 2015, 22:00:30 UTC | Simplify create_symlink() Just go ahead and try to make the link and deal with the error afterward. Trying to verify entities on the filesystem exist beforehand is a race condition. | 14 May 2015, 22:00:30 UTC |
| 5da2c10 | Anthony Brummett | 14 May 2015, 21:54:30 UTC | Allow link names and targets to be '0' but not empty string | 14 May 2015, 21:54:30 UTC |
| 5ae839a | Anthony Brummett | 14 May 2015, 21:38:05 UTC | more tests for Genome::Sys->create_symlink() | 14 May 2015, 21:38:05 UTC |
| 004930e | Nathaniel Nutter | 14 May 2015, 20:37:56 UTC | consolidate code during start phase Some changes were made to fit the consolidated code but this was intended to be as close to a refactor as possible. | 14 May 2015, 20:40:20 UTC |
| a210179 | Nathaniel Nutter | 14 May 2015, 20:15:14 UTC | refactor: consolidate build create phase | 14 May 2015, 20:27:55 UTC |
| 38c158d | Nathaniel Nutter | 14 May 2015, 20:07:28 UTC | refactor: consolidate append_error | 14 May 2015, 20:15:44 UTC |
| 718e07d | Nathaniel Nutter | 14 May 2015, 20:01:24 UTC | catch eval errors immediately after their eval | 14 May 2015, 20:01:24 UTC |
| 8836a8a | Thomas B. Mooney | 14 May 2015, 19:41:29 UTC | Merge pull request #742 from tmooney/quote_for_shell_uses_string_shellquote Use String::QuoteShell to do quoting for shell. | 14 May 2015, 19:41:29 UTC |
| 8edf141 | Nathaniel Nutter | 14 May 2015, 19:21:48 UTC | Merge pull request #744 from nnutter/ur-prep fix (possible) bugs revealed by upcoming UR change | 14 May 2015, 19:21:48 UTC |
| 716ffda | apregier | 14 May 2015, 17:53:01 UTC | Print out stats | 14 May 2015, 17:53:01 UTC |
| 3fab00f | apregier | 14 May 2015, 17:37:50 UTC | Clarify doc | 14 May 2015, 17:37:50 UTC |
| 743d084 | apregier | 14 May 2015, 17:36:42 UTC | Fix spelling | 14 May 2015, 17:36:42 UTC |
| 03a2872 | Nathaniel Nutter | 14 May 2015, 15:56:51 UTC | add id_by to sx_result An upcoming change in UR started causing failures when trying to record a change of this property during a transaction. UR::Change would not accept the old object reference as `undo_data`. I believe giving this an `id_by` allows the value to be serialized. | 14 May 2015, 15:56:51 UTC |
| 43833d4 | Nathaniel Nutter | 14 May 2015, 15:49:40 UTC | add id_class_by and id_by to _leftover_object An upcoming change in UR started causing failures when trying to record a change of this property during a transaction. UR::Change would not accept the old object reference as `undo_data`. I believe giving this an `id_class_by` and `id_by` allows the value to be serialized. | 14 May 2015, 15:49:40 UTC |
| 3d6dea3 | Nathaniel Nutter | 14 May 2015, 15:31:46 UTC | remove `get` override from Genome::Report This change may be contriversal but if `get` really must not be allowed then I think this shouldn't even be a `UR::Object`. | 14 May 2015, 15:31:46 UTC |
| c54aebc | David Morton | 14 May 2015, 14:46:14 UTC | Merge pull request #724 from davidlmorton/abandonment_issues Ensure that errors are able to be displayed in G::M::B::Abandon | 14 May 2015, 14:46:14 UTC |
| dfab1aa | Thomas B. Mooney | 14 May 2015, 12:38:32 UTC | Merge pull request #739 from tmooney/falsepositivevcf_reports_progress Periodically report progress through the input VCF. | 14 May 2015, 12:38:32 UTC |
| 2575950 | Thomas B. Mooney | 14 May 2015, 12:38:23 UTC | Merge pull request #738 from tmooney/heartbeat_skips_parents_of_running_children Don't report idle parents of running children in heartbeat check. | 14 May 2015, 12:38:23 UTC |
| bb156be | Eddie Belter | 13 May 2015, 22:36:13 UTC | InstData Import: convert to be a process! | 13 May 2015, 22:36:13 UTC |
| d48ba52 | Eddie Belter | 13 May 2015, 22:14:19 UTC | InstData Import: remove generate output from csv parser | 13 May 2015, 22:14:23 UTC |
| 8fa1978 | apregier | 13 May 2015, 21:38:00 UTC | Add calculations for stats derived from the base stats | 13 May 2015, 21:38:00 UTC |
| 3bb24e0 | APipe Tester | 13 May 2015, 21:34:34 UTC | updated ur submodule to 2ef9718 | 13 May 2015, 21:34:34 UTC |
| 422a619 | Eddie Belter | 13 May 2015, 21:16:35 UTC | InstData Import: move command line instdata attr parsing to basic command from inputs | 13 May 2015, 21:16:35 UTC |
| 24b9a0e | apregier | 13 May 2015, 20:09:40 UTC | Refactor: extract method | 13 May 2015, 20:09:40 UTC |
| a121a20 | APipe Tester | 13 May 2015, 20:04:42 UTC | updated workflow submodule to 5ad0955 | 13 May 2015, 20:04:42 UTC |
| 3980d3d | Eddie Belter | 13 May 2015, 20:04:09 UTC | InstData Import: process! | 13 May 2015, 20:04:09 UTC |
| 794a711 | Thomas B. Mooney | 13 May 2015, 20:01:13 UTC | Merge pull request #737 from tmooney/heartbeat_check_only_if_operation_type Heartbeat check only if operation_type exists. | 13 May 2015, 20:01:13 UTC |
| 5e1b48f | apregier | 13 May 2015, 19:57:42 UTC | Add tool for comparing svs to a gold standard | 13 May 2015, 19:57:42 UTC |
| a3292d1 | Nathaniel Nutter | 13 May 2015, 19:49:13 UTC | Merge pull request #741 from nnutter/valid_signals add valid_signals | 13 May 2015, 19:49:13 UTC |
| a7dbf8b | Allison Penner Regier | 13 May 2015, 19:48:25 UTC | Merge pull request #736 from apregier/pairToPair Add wrapper for bedtools pairToPair | 13 May 2015, 19:48:25 UTC |
| 4e25031 | Thomas Mooney | 13 May 2015, 19:28:54 UTC | Use String::QuoteShell to do quoting for shell. | 13 May 2015, 19:28:54 UTC |
| 5c858fc | apregier | 13 May 2015, 19:02:59 UTC | quote files for shell | 13 May 2015, 19:04:52 UTC |
| 1a214f1 | Thomas B. Mooney | 13 May 2015, 18:57:31 UTC | Merge pull request #735 from tmooney/allow_derived_from_in_copycatsomaticwithbamwindow Search base references for CopyCat annotation data | 13 May 2015, 18:57:31 UTC |
| 34226e7 | Thomas B. Mooney | 13 May 2015, 18:25:14 UTC | Merge pull request #733 from tmooney/remove_tmooney_from_source Remove some old and obsolete comments. | 13 May 2015, 18:25:14 UTC |
| 292bd34 | Nathaniel Nutter | 13 May 2015, 17:22:47 UTC | Merge pull request #740 from nnutter/master fix circular dependency | 13 May 2015, 17:22:47 UTC |
| 68f6572 | Nathaniel Nutter | 13 May 2015, 16:15:57 UTC | pre-commit was not a valid signal | 13 May 2015, 16:15:57 UTC |
| 168edbb | APipe Tester | 13 May 2015, 12:16:05 UTC | Updated `genome` tab completion. | 13 May 2015, 12:16:05 UTC |
| 8a1dc32 | APipe Tester | 13 May 2015, 12:14:20 UTC | Updated class browser cache. | 13 May 2015, 12:14:20 UTC |
| d5e3467 | Chris Miller | 13 May 2015, 03:46:08 UTC | Merge pull request #734 from chrisamiller/master adding mutect support, cleaning trailing whitespace | 13 May 2015, 03:46:08 UTC |
| 24d4c1d | Eddie Belter | 13 May 2015, 01:04:31 UTC | InstData Import: rename manager to launch | 13 May 2015, 01:04:31 UTC |
| 8c5b4ab | Eddie Belter | 13 May 2015, 01:02:25 UTC | InstData Import: move basic logic to work flow run | 13 May 2015, 01:02:25 UTC |
| 62cbb42 | Eddie Belter | 13 May 2015, 00:58:47 UTC | InstData Import: add as_hashref to inputs | 13 May 2015, 00:58:47 UTC |
| 6f94e68 | Nathaniel Nutter | 13 May 2015, 00:32:41 UTC | add valid_signals An upcoming change to UR fixes a bug in the signal validation code that exposes cases where a class did not define `valid_signals` nor a `validate_subscription` method. This is one such example. | 13 May 2015, 00:32:41 UTC |
| 60c4bf2 | Eddie Belter | 13 May 2015, 00:32:29 UTC | InstData Import: add analysis project to inputs; consolidate error checking | 13 May 2015, 00:32:32 UTC |
| a32d0dc | Nathaniel Nutter | 13 May 2015, 00:26:56 UTC | fix circular dependency Can't require Genome::Model::Build at top of because it creates a circular dependency Genome::Model::Build uses Genome which uses Genome::Sys::Log which uses Genome::Model::Build. | 13 May 2015, 00:26:56 UTC |
| 92b6005 | Eddie Belter | 13 May 2015, 00:17:10 UTC | InstData Import: add getting instdata via original_data_path to inputs | 13 May 2015, 00:18:54 UTC |
| 885d640 | Eddie Belter | 13 May 2015, 00:03:42 UTC | InstData Import: add library property to inputs | 13 May 2015, 00:07:00 UTC |
| d8b779f | Eddie Belter | 12 May 2015, 23:59:05 UTC | InstData Import: update instance properties instead of using incoming params | 12 May 2015, 23:59:05 UTC |
| fa85b91 | Eddie Belter | 12 May 2015, 23:09:36 UTC | Merge pull request #730 from ebelter/instdata-import-cli-update InstData Import: update and consolidate the CLI. | 12 May 2015, 23:09:36 UTC |
| ad1085a | Eddie Belter | 12 May 2015, 23:07:57 UTC | Merge remote-tracking branch 'origin/master' into instdata-import-cli-update Conflicts: lib/perl/Genome/InstrumentData/Command/Import/Manager.pm lib/perl/Genome/InstrumentData/Command/Import/Manager.t | 12 May 2015, 23:07:57 UTC |
| 1be2209 | Eddie Belter | 12 May 2015, 22:48:45 UTC | Merge pull request #731 from ebelter/instdata-import-sf-objects InstData Import: use source file classes to get file size, md5 names and kb required. | 12 May 2015, 22:48:45 UTC |
| 53e0a1e | Thomas B. Mooney | 12 May 2015, 22:30:02 UTC | Merge pull request #729 from tmooney/heartbeat_stauts Spelling/grammar changes to Heartbeat Check | 12 May 2015, 22:30:02 UTC |
| 0ab2e69 | Thomas Mooney | 12 May 2015, 22:08:28 UTC | Periodically report progress through the input VCF. This should help reassure that progress is being made, both for manual inspection and the heartbeat check. | 12 May 2015, 22:08:28 UTC |
| 6637011 | Thomas Mooney | 12 May 2015, 21:49:13 UTC | Move setting of OK status outside of the loop. A parent with scheduled children otherwise fails to report OK. | 12 May 2015, 21:49:13 UTC |
| 8197333 | Thomas Mooney | 12 May 2015, 21:09:23 UTC | Don't report idle parents of running children in heartbeat check. | 12 May 2015, 21:09:23 UTC |
