| 3ffcaa8 | dmorton | 28 April 2014, 18:20:13 UTC | Add Joinx Adaptor/Expert and test | 28 April 2014, 18:20:13 UTC |
| 07bfc41 | dmorton | 28 April 2014, 17:21:02 UTC | make get_test_dir helper function | 28 April 2014, 18:19:42 UTC |
| 1652da0 | dmorton | 28 April 2014, 16:20:23 UTC | Pull a little more logic up to ExpertBase | 28 April 2014, 16:20:23 UTC |
| bc74073 | dmorton | 25 April 2014, 21:55:54 UTC | Add GRand as possible misidentification of gzipped/bgzipped files This file, created with 'bgzip' misidentifies: /gscmnt/ams1127/info/model_data/1C9/6A1D0CCBF11E3A4D7FFA12F9A8DCC/output_file.vcf.gz This bug is suppoed to be fixed in 'File 5.17' but even 14.04 doesn't have that package yet. | 28 April 2014, 15:11:29 UTC |
| fed2434 | Nathaniel Nutter | 25 April 2014, 22:14:02 UTC | refactor Genome/Sys/Lock.t to be independent of backends | 25 April 2014, 22:14:47 UTC |
| 363153a | Nathaniel Nutter | 25 April 2014, 22:10:02 UTC | refactor test to use MockBackend | 25 April 2014, 22:14:46 UTC |
| f571e82 | Nathaniel Nutter | 25 April 2014, 22:09:53 UTC | add MockBackend | 25 April 2014, 22:14:45 UTC |
| 0043072 | Nathaniel Nutter | 25 April 2014, 20:55:01 UTC | fix unwinding locks when one fails The previous code only happened to work because FileLock was always mandatory and was always first. | 25 April 2014, 22:14:44 UTC |
| b1ba842 | Gabriel Sanderson | 25 April 2014, 21:24:17 UTC | Move _link up to ExpertBase | 25 April 2014, 21:25:01 UTC |
| 1d07e7e | Gabriel Sanderson | 25 April 2014, 19:35:41 UTC | move build_adaptor_op up to the base class, rename it | 25 April 2014, 21:25:01 UTC |
| 6bc76c1 | Nathaniel Nutter | 25 April 2014, 20:28:38 UTC | refactor Nessy backend to be a non-singleton class | 25 April 2014, 20:28:38 UTC |
| b616046 | Nathaniel Nutter | 25 April 2014, 17:01:02 UTC | add genome_build_id and lsf_project to user_data | 25 April 2014, 20:16:35 UTC |
| 6d0a147 | Nathaniel Nutter | 25 April 2014, 16:49:42 UTC | clear_state is FileLock-specific so remove from API | 25 April 2014, 20:16:35 UTC |
| 13d14da | Nathaniel Nutter | 25 April 2014, 16:47:55 UTC | do not need to clear client after release_all | 25 April 2014, 20:16:34 UTC |
| aef8f8b | Nathaniel Nutter | 25 April 2014, 16:47:43 UTC | do not need to clear claims after unlocking | 25 April 2014, 20:16:34 UTC |
| e25a629 | Nathaniel Nutter | 25 April 2014, 16:46:21 UTC | missed a singleton call | 25 April 2014, 20:16:33 UTC |
| 178f873 | Nathaniel Nutter | 25 April 2014, 16:34:34 UTC | only check lock inconsistency when NessyBackend is installed | 25 April 2014, 20:16:32 UTC |
| ebb1323 | Nathaniel Nutter | 25 April 2014, 16:26:58 UTC | only install NessyBackend if GENOME_NESSY_SERVER is set | 25 April 2014, 20:16:31 UTC |
| 4c04151 | Nathaniel Nutter | 25 April 2014, 16:15:25 UTC | add instance validation subtest | 25 April 2014, 20:16:31 UTC |
| 46a6940 | Nathaniel Nutter | 25 April 2014, 16:15:14 UTC | move to subtest | 25 April 2014, 20:16:30 UTC |
| b810318 | Nathaniel Nutter | 25 April 2014, 16:14:14 UTC | should not return resource if claim failed | 25 April 2014, 20:16:30 UTC |
| 1b1277a | Nathaniel Nutter | 25 April 2014, 15:59:47 UTC | rename Genome::Sys::{NessyLock,Lock::NessyBackend} | 25 April 2014, 20:16:29 UTC |
| 49e7413 | Nathaniel Nutter | 25 April 2014, 15:51:40 UTC | remove UR::ModuleBase dependency | 25 April 2014, 20:16:28 UTC |
| 9e676c9 | Nathaniel Nutter | 25 April 2014, 01:48:10 UTC | replace class 'NESSY_LOCKS_TO_REMOVE' with instance 'claims' | 25 April 2014, 20:16:28 UTC |
| 76ea60b | Nathaniel Nutter | 25 April 2014, 01:13:00 UTC | allow mix of class/instance backends | 25 April 2014, 20:16:27 UTC |
| ee2ab9c | Nathaniel Nutter | 25 April 2014, 00:21:58 UTC | replace class variable 'LOCKING_CLIENT' with instance variable 'client' | 25 April 2014, 20:16:26 UTC |
| f67d637 | Nathaniel Nutter | 25 April 2014, 00:16:16 UTC | move GENOME_NESSY_SERVER to instance variable 'url' | 25 April 2014, 20:16:25 UTC |
| 5110b04 | Nathaniel Nutter | 25 April 2014, 01:14:01 UTC | *_messages need to be called on class not instance | 25 April 2014, 20:16:25 UTC |
| 8b2e437 | Nathaniel Nutter | 25 April 2014, 00:13:53 UTC | s/class/self/ | 25 April 2014, 20:16:24 UTC |
| 0517bcb | Nathaniel Nutter | 25 April 2014, 00:08:33 UTC | NessyLock implementes Genome::Sys::Lock::Backend | 25 April 2014, 20:16:24 UTC |
| 8cd1be0 | Nathaniel Nutter | 25 April 2014, 00:07:51 UTC | define a Genome::Sys::Lock::Backend role | 25 April 2014, 20:16:23 UTC |
| f6c0c43 | Nathaniel Nutter | 25 April 2014, 00:11:04 UTC | whitespace | 25 April 2014, 20:16:22 UTC |
| beee90c | Travis Abbott | 25 April 2014, 19:24:32 UTC | G:F:Fasta: divide_sequence_into_chunks_of_size for times when you want to do that | 25 April 2014, 19:25:48 UTC |
| 7e7b849 | Susanna Siebert | 25 April 2014, 16:54:15 UTC | make file_name a parameter on ReporterBase and use it instead of the reporter name | 25 April 2014, 18:57:34 UTC |
| 32b02d6 | Susanna Siebert | 25 April 2014, 16:28:59 UTC | move header printing functionality to ReporterWithHeaderBase | 25 April 2014, 18:47:25 UTC |
| a629107 | Nathaniel Nutter | 25 April 2014, 18:40:52 UTC | bump test data version v2 had a file_name in the params that is not defined on the class so was breaking tests. I fixed that in v3 and bumped the version here. | 25 April 2014, 18:41:36 UTC |
| f9f68a6 | Travis Abbott | 25 April 2014, 18:01:01 UTC | stop deleting objects then immediately trying to use them | 25 April 2014, 18:01:01 UTC |
| 40c7426 | Nathaniel Nutter | 25 April 2014, 15:47:19 UTC | add fatal message types to logger | 25 April 2014, 15:47:19 UTC |
| 24a3a7d | Nathaniel Nutter | 25 April 2014, 15:47:05 UTC | add fatal/fatalf | 25 April 2014, 15:47:05 UTC |
| 2171116 | Nathaniel Nutter | 25 April 2014, 15:40:57 UTC | instead of adding logger on import just extend the logger method | 25 April 2014, 15:40:57 UTC |
| b19d499 | Nathaniel Nutter | 25 April 2014, 15:39:56 UTC | default logger is tested by Genome/Logger.t | 25 April 2014, 15:39:56 UTC |
| 19f2f47 | Nathaniel Nutter | 25 April 2014, 14:55:13 UTC | add croak | 25 April 2014, 15:36:10 UTC |
| af135b2 | Nathaniel Nutter | 25 April 2014, 14:55:04 UTC | return message from logging | 25 April 2014, 15:35:51 UTC |
| 96a2f53 | Nathaniel Nutter | 25 April 2014, 15:16:39 UTC | reorder screen sub | 25 April 2014, 15:35:46 UTC |
| 7b0880c | Nathaniel Nutter | 25 April 2014, 15:30:38 UTC | flush_cache to ensure subtest has fresh logger | 25 April 2014, 15:34:58 UTC |
| 1493aaa | APipe Tester | 25 April 2014, 12:18:51 UTC | Updated `gmt` tab completion. | 25 April 2014, 12:18:51 UTC |
| 797ed90 | APipe Tester | 25 April 2014, 12:18:08 UTC | Updated `genome` tab completion. | 25 April 2014, 12:18:08 UTC |
| 541c3bd | APipe Tester | 25 April 2014, 12:16:36 UTC | Updated class browser cache. | 25 April 2014, 12:16:36 UTC |
| 6e1ef60 | Nathaniel Nutter | 25 April 2014, 00:04:23 UTC | hard-code Nessy backend until circular dependencies can be fixed | 25 April 2014, 00:05:01 UTC |
| 698be32 | Nathaniel Nutter | 24 April 2014, 23:38:44 UTC | remove use Genome::Sys | 25 April 2014, 00:05:01 UTC |
| a40f6a3 | Gabriel Sanderson | 24 April 2014, 23:27:46 UTC | Use awk instead of VcfToBed to create a region file. VcfToBed is not the tool we want for this. We don't actually want a bed file, we want a one-based region file. Moreover we do not actually care about sample information and their genotypes. We just want the positions where ANY variant was called. Awk is the easiest way to do this. | 24 April 2014, 23:31:05 UTC |
| 31a84d6 | Gabriel Sanderson | 24 April 2014, 21:36:24 UTC | If region list provided does not exist, touch the output file and warn (some legitimate cases exist in pipelines for this) | 24 April 2014, 23:31:04 UTC |
| 758720c | Gabriel Sanderson | 24 April 2014, 21:33:44 UTC | Refactored methods out of Expert.t into TestHelpers. | 24 April 2014, 23:31:04 UTC |
| d75d6b4 | Nathaniel Nutter | 24 April 2014, 22:27:54 UTC | first step towards allowing configurable lock backends There is still more work to be done but I believe this is in a working and semi-reasonable (but intermediate) state so I'm merging it back into master. | 24 April 2014, 22:27:54 UTC |
| a390ad4 | Nathaniel Nutter | 24 April 2014, 21:25:22 UTC | add test for Genome::Sys::Lock | 24 April 2014, 22:23:52 UTC |
| ab0e3bc | Nathaniel Nutter | 24 April 2014, 21:25:04 UTC | return failure if mandatory backend fails to unlock | 24 April 2014, 22:23:51 UTC |
| ca32f5f | Nathaniel Nutter | 24 April 2014, 20:56:05 UTC | allow timeout equal to min_timeout | 24 April 2014, 22:23:14 UTC |
| 5ca619f | Nathaniel Nutter | 24 April 2014, 20:55:12 UTC | fix typo | 24 April 2014, 22:23:13 UTC |
| 7812da4 | Nathaniel Nutter | 24 April 2014, 20:54:35 UTC | fix assumption that is_my_lock_target was equivalent to has_lock | 24 April 2014, 22:23:13 UTC |
| 075e8f8 | Nathaniel Nutter | 24 April 2014, 20:26:55 UTC | move Nessy backend to site config | 24 April 2014, 22:23:12 UTC |
| f0311ab | Nathaniel Nutter | 24 April 2014, 20:25:29 UTC | support add/remove backend | 24 April 2014, 22:22:32 UTC |
| e416f26 | Nathaniel Nutter | 24 April 2014, 01:08:05 UTC | rename self to class | 24 April 2014, 22:22:31 UTC |
| fa963d5 | Nathaniel Nutter | 23 April 2014, 23:12:35 UTC | change NessyLock's unlock to just take resource as argument | 24 April 2014, 22:22:31 UTC |
| cefa8cf | Nathaniel Nutter | 23 April 2014, 23:07:36 UTC | allow backends to reshape args | 24 April 2014, 22:22:30 UTC |
| ee7d89d | Nathaniel Nutter | 23 April 2014, 23:05:40 UTC | do not carry forward the use of resource_lock | 24 April 2014, 22:22:29 UTC |
| dc55d58 | Nathaniel Nutter | 23 April 2014, 23:04:44 UTC | fix broken lock unwinding | 24 April 2014, 22:22:29 UTC |
| 2e85f9b | Nathaniel Nutter | 23 April 2014, 23:03:21 UTC | make translate* part of the backend interface | 24 April 2014, 22:22:28 UTC |
| 4a42a43 | Nathaniel Nutter | 23 April 2014, 22:47:50 UTC | change order of methods | 24 April 2014, 22:22:28 UTC |
| d75471a | Nathaniel Nutter | 23 April 2014, 22:46:00 UTC | add basic NessyLock.t | 24 April 2014, 22:22:27 UTC |
| d9e56f4 | Nathaniel Nutter | 23 April 2014, 22:36:25 UTC | return empty if there is no Nessy locking client | 24 April 2014, 22:22:26 UTC |
| 3e84985 | Nathaniel Nutter | 23 April 2014, 22:35:16 UTC | return resource_lock instead of claim Return the resource_lock instead of the claim because the resource_lock is used to unlock. | 24 April 2014, 22:22:26 UTC |
| 8481e22 | Nathaniel Nutter | 23 April 2014, 22:34:52 UTC | translate wait_announce_interval for async use | 24 April 2014, 22:22:25 UTC |
| 063114c | Nathaniel Nutter | 23 April 2014, 22:19:43 UTC | validate inputs early | 24 April 2014, 22:22:24 UTC |
| 4b1ecbb | Nathaniel Nutter | 23 April 2014, 22:18:54 UTC | translate lock args | 24 April 2014, 22:22:24 UTC |
| 824715b | Nathaniel Nutter | 23 April 2014, 22:18:38 UTC | require timeout to be set as an arg | 24 April 2014, 22:22:23 UTC |
| 9db1fe0 | Nathaniel Nutter | 23 April 2014, 22:18:13 UTC | check that resource_lock was set | 24 April 2014, 22:22:22 UTC |
| c418dc8 | Nathaniel Nutter | 23 April 2014, 21:08:53 UTC | separate private methods out | 24 April 2014, 22:22:22 UTC |
| 9df8130 | Nathaniel Nutter | 23 April 2014, 21:04:33 UTC | add warning when releasing locks with release_all | 24 April 2014, 22:22:21 UTC |
| 3c7741c | Nathaniel Nutter | 23 April 2014, 21:01:34 UTC | fix calling wrong _resolve_resource_lock* method | 24 April 2014, 22:22:21 UTC |
| 9e866df | Nathaniel Nutter | 23 April 2014, 20:57:55 UTC | move methods to FileLock | 24 April 2014, 22:22:20 UTC |
| 06af081 | Nathaniel Nutter | 23 April 2014, 20:55:49 UTC | memoize cleanup_handler_check | 24 April 2014, 22:22:19 UTC |
| d7aa53e | Nathaniel Nutter | 23 April 2014, 20:55:34 UTC | replace exit_cleanup with release_all | 24 April 2014, 22:22:19 UTC |
| 3c599d3 | Nathaniel Nutter | 23 April 2014, 20:51:21 UTC | remove with_default_unlock_resource_args | 24 April 2014, 22:22:18 UTC |
| 125d12a | Nathaniel Nutter | 23 April 2014, 20:49:34 UTC | remove use of with_default_lock_resource_args in FileLock backend | 24 April 2014, 22:22:17 UTC |
| cb77323 | Nathaniel Nutter | 23 April 2014, 20:48:05 UTC | move FileLock specific defaults into FileLock backend | 24 April 2014, 22:22:17 UTC |
| 3e177be | Nathaniel Nutter | 23 April 2014, 20:39:20 UTC | add release_all to Genome::Sys::Lock API | 24 April 2014, 22:22:16 UTC |
| d94dc43 | Nathaniel Nutter | 18 April 2014, 21:23:53 UTC | document the used Genome::Sys::Lock API | 24 April 2014, 22:22:15 UTC |
| b5e8a31 | Nathaniel Nutter | 17 April 2014, 22:53:54 UTC | initial pass FileLock.t | 24 April 2014, 22:22:14 UTC |
| a097896 | Nathaniel Nutter | 16 April 2014, 19:54:56 UTC | separate the two backends | 24 April 2014, 22:22:13 UTC |
| 9c2881d | Nathaniel Nutter | 24 April 2014, 22:07:57 UTC | blacklist Db/Ensembl/Command/Run/Vep.d/ in compile.t | 24 April 2014, 22:08:45 UTC |
| 292a1d3 | Nathaniel Nutter | 24 April 2014, 22:08:32 UTC | fix issued exposed by UR update | 24 April 2014, 22:08:32 UTC |
| 92b57ff | Nathaniel Nutter | 24 April 2014, 22:02:41 UTC | remove code that was previously stomped over by UR Remove code that was never run until a recent UR change exposed that. | 24 April 2014, 22:08:16 UTC |
| 1cf99e9 | Nathaniel Nutter | 24 April 2014, 22:00:03 UTC | (don't) fix call to UR::Object::add_misc_update A UR update exposed that this method, add_misc_update, was not being executed before (becuase previously UR would stomp over it). The UR update changed the behavior to install to __add_misc_update instead of stomping over add_misc_update. Since the old code never ran I have reason to believe it doesn't actually work. However, I am making the fix that I think is equivalent to what was originally intended. | 24 April 2014, 22:08:15 UTC |
| c5c07cc | Nathaniel Nutter | 24 April 2014, 20:16:04 UTC | only load syslog logger if GENOME_DEV_MODE is off | 24 April 2014, 22:08:14 UTC |
| 792067b | Gabriel Sanderson | 24 April 2014, 21:25:51 UTC | Added a test for the one-based indel integration case | 24 April 2014, 21:25:51 UTC |
| e5b1c22 | Gabriel Sanderson | 24 April 2014, 21:24:30 UTC | No longer incorrectly increment start pos for indels | 24 April 2014, 21:24:52 UTC |
| c6b2d4a | apregier | 24 April 2014, 20:54:23 UTC | Need to be able to find vep scripts | 24 April 2014, 20:54:38 UTC |
| d170efd | Susanna Siebert | 24 April 2014, 20:34:31 UTC | module and test for simple report | 24 April 2014, 20:38:41 UTC |
| 1fc06e9 | Susanna Siebert | 24 April 2014, 20:33:00 UTC | added available_fields and fixed name | 24 April 2014, 20:38:40 UTC |
| 302a583 | Susanna Siebert | 24 April 2014, 18:39:58 UTC | move processing of vcf entry to ReporterPlan | 24 April 2014, 20:38:40 UTC |
