| 0e145bb | Thomas Mooney | 29 November 2012, 20:02:13 UTC | Just make it optional so we don't try to save NULL to the db. | 29 November 2012, 20:02:13 UTC |
| ad462f6 | Mark Burnett | 29 November 2012, 19:36:00 UTC | change Disk::Allocation to not rely on perl 5.10 | 29 November 2012, 19:36:00 UTC |
| 2016dcf | Mark Burnett | 29 November 2012, 19:24:31 UTC | Db:E:AnnotationStructuresm now updates lookup_hash when it changes test_name | 29 November 2012, 19:26:33 UTC |
| 1ef2954 | Mark Burnett | 29 November 2012, 19:24:00 UTC | add remove_test_name function to SoftwareResult | 29 November 2012, 19:26:33 UTC |
| 382ac2e | APipe Tester | 29 November 2012, 18:59:29 UTC | Merge remote-tracking branch 'origin/master' | 29 November 2012, 18:59:29 UTC |
| 4dc5046 | Eddie Belter | 29 November 2012, 18:19:07 UTC | Misc update: improve test for SKIPs; add site tgi class method | 29 November 2012, 18:19:13 UTC |
| 9facbfc | Mark Burnett | 29 November 2012, 17:54:14 UTC | disable Model/ClinSeq/Command/GetBamReadCounts.t This test was blocking us from deploying an important SoftwareResult change. It appears that the test data were not updated when code was changed. | 29 November 2012, 17:54:14 UTC |
| 94564f3 | Mark Burnett | 29 November 2012, 17:34:07 UTC | fix DbSnpConcordance.t | 29 November 2012, 17:34:07 UTC |
| 26ab9ab | Mark Burnett | 29 November 2012, 17:28:43 UTC | fix chimerascan result test | 29 November 2012, 17:29:26 UTC |
| d71ebac | Adam Coffman | 29 November 2012, 17:20:11 UTC | Revert "Override test_name accessor instead of introducing new set method" __ syntax doesn't seem to work for delegated property accessors This reverts commit 0d3b3c3d22c803071c83ae4c53f7988e1d9144f8. | 29 November 2012, 17:20:11 UTC |
| 0d3b3c3 | Adam Coffman | 29 November 2012, 17:01:17 UTC | Override test_name accessor instead of introducing new set method | 29 November 2012, 17:01:17 UTC |
| 01f3582 | Thomas Mooney | 29 November 2012, 16:35:06 UTC | Fixes for the combine test: actually set the inputs on the VCF results *This changes the diff of the generated VCF for one test, so the data has been updated as well. | 29 November 2012, 16:35:06 UTC |
| 2141de7 | Mark Burnett | 29 November 2012, 16:33:32 UTC | add command: 'genome software-result set-test-name' | 29 November 2012, 16:33:32 UTC |
| 84b91d5 | Mark Burnett | 29 November 2012, 16:25:20 UTC | decrease chunk size for FillLookupHashes | 29 November 2012, 16:25:20 UTC |
| 15f11bf | Mark Burnett | 29 November 2012, 15:56:16 UTC | add set_test_name to SoftwareResult | 29 November 2012, 15:56:16 UTC |
| ac65dc3 | Mark Burnett | 29 November 2012, 15:30:23 UTC | make sample optional in DV2:Result:Manual | 29 November 2012, 15:30:23 UTC |
| f09f95e | Mark Burnett | 29 November 2012, 15:23:34 UTC | Merge remote-tracking branch 'origin/master' into software_result_hashing | 29 November 2012, 15:23:34 UTC |
| 0a0ead9 | Mark Burnett | 29 November 2012, 15:19:43 UTC | change expected test count for ID:AR:Bwa | 29 November 2012, 15:21:23 UTC |
| f52a17f | Mark Burnett | 29 November 2012, 15:17:43 UTC | make roi_track_name optional in ID:AR:CoverageStats | 29 November 2012, 15:21:23 UTC |
| 7355fda | Thomas Mooney | 29 November 2012, 15:19:32 UTC | The aligned_reads_sample isn't needed for combine VCFs--it comes from inputs. Since it's required in the base class, just give it a default value to satisfy existence. | 29 November 2012, 15:19:32 UTC |
| 6e42a38 | Mark Burnett | 29 November 2012, 15:03:09 UTC | fix SR/Stagable.t | 29 November 2012, 15:03:09 UTC |
| 081d802 | Mark Burnett | 29 November 2012, 14:54:14 UTC | fix expected test count in ID:AR:Bsmap.t | 29 November 2012, 14:54:14 UTC |
| a644a4b | Thomas Mooney | 29 November 2012, 14:09:38 UTC | No combine results appear to have "version" set, so make it optional. | 29 November 2012, 14:09:38 UTC |
| 9b1618b | Malachi Griffith | 29 November 2012, 05:51:39 UTC | Fixed bug with check of instrument data type checking in clin-seq update-analysis | 29 November 2012, 05:51:39 UTC |
| 9eeb023 | Malachi Griffith | 29 November 2012, 05:29:16 UTC | Major clean-up of CnView tool in advance of further refactor | 29 November 2012, 05:29:16 UTC |
| 3bd0b96 | Scott Smith | 29 November 2012, 05:25:55 UTC | fixed bug in which genome model input update would not allow a value to be set to zero | 29 November 2012, 05:25:55 UTC |
| bd465c3 | Mark Burnett | 29 November 2012, 00:46:20 UTC | Merge branch 'software_result_hashing' of ssh://git/srv/git/genome into software_result_hashing | 29 November 2012, 00:46:20 UTC |
| e6e3a4a | Mark Burnett | 29 November 2012, 00:45:19 UTC | add lookup_hash to stagable SR test | 29 November 2012, 00:45:19 UTC |
| a47b8ec | Mark Burnett | 29 November 2012, 00:42:29 UTC | make SR get_with_lock confess when underspecified | 29 November 2012, 00:42:29 UTC |
| 7e5503f | Thomas Mooney | 28 November 2012, 23:56:56 UTC | Cleanup this result--make optional things that should be, properly make hash. | 28 November 2012, 23:56:56 UTC |
| 9b3c3de | Mark Burnett | 28 November 2012, 23:54:56 UTC | Merge branch 'software_result_hashing' of ssh://git/srv/git/genome into software_result_hashing | 28 November 2012, 23:54:56 UTC |
| 8ad34d1 | dmorton | 28 November 2012, 23:49:15 UTC | Changed many ->get to ->get_with_lock ->get_with_lock is appropriate for software_results if expecting a single result. This is because it will use the new faster hashing lookup instead of the old slow queries. | 28 November 2012, 23:49:15 UTC |
| 4545ee8 | Mark Burnett | 28 November 2012, 23:44:06 UTC | roi_track_name is not optional in AR:Merged:RefCov.t | 28 November 2012, 23:44:06 UTC |
| dee22f0 | Thomas Mooney | 28 November 2012, 23:23:55 UTC | We need to get the individual results one-at-a-time. | 28 November 2012, 23:23:55 UTC |
| abfdb05 | Thomas Mooney | 28 November 2012, 23:03:23 UTC | Add more lookup hashes to software results __defined__. | 28 November 2012, 23:03:23 UTC |
| c36ff9c | Thomas Mooney | 28 November 2012, 22:48:51 UTC | Calculate the hash after adding all the inputs. | 28 November 2012, 22:48:51 UTC |
| cc81b32 | Scott Smith | 28 November 2012, 22:44:46 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 November 2012, 22:44:46 UTC |
| 6e2f597 | Scott Smith | 28 November 2012, 22:44:05 UTC | ignore mutation diagram stderr files in clinseq test diff | 28 November 2012, 22:44:05 UTC |
| 436a3a3 | Mark Burnett | 28 November 2012, 22:37:45 UTC | bug fixes in some alignment tests | 28 November 2012, 22:37:45 UTC |
| 9ece52d | Mark Burnett | 28 November 2012, 22:37:07 UTC | bug fixes to new SR lookup | 28 November 2012, 22:37:07 UTC |
| aa957bc | Mark Burnett | 28 November 2012, 22:35:51 UTC | fix uninitialized value bug in DV2:Result:Merged | 28 November 2012, 22:35:51 UTC |
| 1ec57d0 | Adam Coffman | 28 November 2012, 21:50:15 UTC | Allow watching of Projects on creation if desired. We don't want all projects to be watched automatically, but when created manually from the web interface, they should be watched by default. | 28 November 2012, 21:50:15 UTC |
| 3dfff39 | Mark Burnett | 28 November 2012, 21:39:13 UTC | Merge branch 'software_result_hashing' of ssh://git/srv/git/genome into software_result_hashing | 28 November 2012, 21:39:13 UTC |
| 0931a6d | Mark Burnett | 28 November 2012, 21:38:42 UTC | add lookup hashes to other tests | 28 November 2012, 21:38:42 UTC |
| 5810dc4 | Thomas Mooney | 28 November 2012, 21:37:07 UTC | Add some lookup hashes to tests. | 28 November 2012, 21:37:07 UTC |
| fbdc43e | Eddie Belter | 28 November 2012, 21:34:50 UTC | Misc update: change reporting a bit | 28 November 2012, 21:34:50 UTC |
| cdcc50c | Eddie Belter | 28 November 2012, 21:31:16 UTC | Misc update: rename SKIPPED status to SKIP | 28 November 2012, 21:31:16 UTC |
| d9c169c | Eddie Belter | 28 November 2012, 21:30:19 UTC | Misc update: add SKIPPED status for ignored lims properties | 28 November 2012, 21:30:19 UTC |
| fec3cab | Eddie Belter | 28 November 2012, 21:14:49 UTC | Reconcile misc update: update date b/c of oracle datr formating | 28 November 2012, 21:14:49 UTC |
| b56ad92 | Mark Burnett | 28 November 2012, 21:06:52 UTC | bug fixes to new SR hashing | 28 November 2012, 21:07:36 UTC |
| a193646 | Mark Burnett | 28 November 2012, 20:07:09 UTC | make SR::_faster_get use the new hash column | 28 November 2012, 20:19:59 UTC |
| 5bb6873 | Mark Burnett | 28 November 2012, 18:22:42 UTC | SR:calculate_query pre-fetches inputs and params | 28 November 2012, 20:19:58 UTC |
| 74b5466 | Mark Burnett | 28 November 2012, 18:14:38 UTC | add SR:Command:FillLookupHashes | 28 November 2012, 20:19:57 UTC |
| 6fb1f3b | Eddie Belter | 28 November 2012, 20:09:18 UTC | Misc update: rm error msg setting from failure | 28 November 2012, 20:09:39 UTC |
| 8debd19 | Eddie Belter | 28 November 2012, 18:55:04 UTC | Sync: rm unused ReconcileUpdates | 28 November 2012, 20:09:38 UTC |
| 782c080 | Eddie Belter | 28 November 2012, 18:54:38 UTC | Reconcile Misc Update: complete reporting | 28 November 2012, 20:09:38 UTC |
| 7f17c4c | Eddie Belter | 28 November 2012, 18:28:27 UTC | Reconcile Misc Update: modify test to not create multi misc updates, but get them to verify | 28 November 2012, 20:09:38 UTC |
| 7a0e924 | Eddie Belter | 28 November 2012, 18:16:19 UTC | Sync: reconcile misc updates mostly functional | 28 November 2012, 20:09:37 UTC |
| 3e95817 | Eddie Belter | 28 November 2012, 17:48:08 UTC | Sync multi misc update - added checks when getting genoem entity params | 28 November 2012, 20:09:37 UTC |
| 264b4da | Eddie Belter | 28 November 2012, 17:47:33 UTC | Sync: misc update - added helper methods; added perform update | 28 November 2012, 20:09:36 UTC |
| 9e266c9 | Eddie Belter | 28 November 2012, 17:05:19 UTC | Sync: add class to represent misc updates that have multiple entities for one insert/delete. | 28 November 2012, 20:09:36 UTC |
| 53b8c48 | Eddie Belter | 28 November 2012, 16:40:16 UTC | Sync classes: change method lims_name_to_genome_name to lims_property_name_to_genome_property_name | 28 November 2012, 20:09:35 UTC |
| 3be65f7 | Eddie Belter | 21 November 2012, 21:54:54 UTC | Sync: sort p[op group memeber by pop group id then member id | 28 November 2012, 20:09:35 UTC |
| 08af356 | Eddie Belter | 21 November 2012, 21:53:42 UTC | Add mapping of lims attr name to apipe attr name | 28 November 2012, 20:09:34 UTC |
| 12cb8e7 | Eddie Belter | 21 November 2012, 19:13:32 UTC | Sync: add test for reconcile misc update | 28 November 2012, 20:09:34 UTC |
| cf6e5ae | Eddie Belter | 21 November 2012, 19:13:15 UTC | Sync: update class name for reconcile misc update | 28 November 2012, 20:09:33 UTC |
| 1199492 | Eddie Belter | 21 November 2012, 19:06:23 UTC | Sync: add reconcile misc update | 28 November 2012, 20:09:33 UTC |
| 1828d0f | Eddie Belter | 21 November 2012, 19:05:55 UTC | Sync: added class to represent misc update | 28 November 2012, 20:09:32 UTC |
| 9a00557 | Eddie Belter | 21 November 2012, 19:05:32 UTC | Sync: add clearly defined classes for syncing taxon, ind, pop group and sample | 28 November 2012, 20:09:32 UTC |
| f2e61c0 | Adam Coffman | 28 November 2012, 19:53:26 UTC | Add clear error message when given incorrect model type | 28 November 2012, 19:53:26 UTC |
| c1b3562 | Mark Burnett | 28 November 2012, 18:14:08 UTC | add lookup_hash field to software result | 28 November 2012, 18:16:52 UTC |
| f33bf45 | Mark Burnett | 28 November 2012, 16:10:38 UTC | add hook for SR subclasses to modify hash calculation | 28 November 2012, 18:16:51 UTC |
| 3ceea88 | Mark Burnett | 28 November 2012, 15:12:25 UTC | rename "hash" to lookup_hash | 28 November 2012, 18:16:51 UTC |
| 7a8156f | Mark Burnett | 28 November 2012, 14:51:49 UTC | check that meta->data_type is defined before use | 28 November 2012, 18:16:51 UTC |
| ba213e5 | Thomas Mooney | 28 November 2012, 00:36:49 UTC | Basics of hashing inputs/params for efficient software result lookup | 28 November 2012, 18:16:50 UTC |
| dcfcdc8 | Malachi Griffith | 28 November 2012, 18:16:18 UTC | Improve mapping of FPKM gene expression values to Tier1 SNVs in ClinSeq | 28 November 2012, 18:16:18 UTC |
| 6df88e9 | Malachi Griffith | 28 November 2012, 18:13:47 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 November 2012, 18:13:47 UTC |
| 9f408a3 | Malachi Griffith | 28 November 2012, 18:13:35 UTC | Cosmetic update to SummarizeBuilds | 28 November 2012, 18:13:35 UTC |
| 014aa6c | Dan Koboldt | 28 November 2012, 17:26:01 UTC | New tool for extracting sample variants with annotation from VCF | 28 November 2012, 17:26:01 UTC |
| 58fb0e0 | Scott Smith | 28 November 2012, 17:08:48 UTC | added one more file to the clinseq diff exception list | 28 November 2012, 17:08:48 UTC |
| 19ea294 | Scott Smith | 28 November 2012, 17:06:58 UTC | added files to the cliseq list of files to ignore during diff | 28 November 2012, 17:06:58 UTC |
| f0314f3 | Scott Smith | 28 November 2012, 17:03:33 UTC | made build files_ignored_by_diff() fall back to model files_ignored_by_build_diff() | 28 November 2012, 17:03:33 UTC |
| 77937c1 | Scott Smith | 28 November 2012, 16:54:23 UTC | renamed method from build to prevent autoload bug for clinseq | 28 November 2012, 16:54:23 UTC |
| 13db31c | Scott Smith | 28 November 2012, 16:27:05 UTC | fixed bug in latest update to ClinSeq.t | 28 November 2012, 16:27:05 UTC |
| 2977920 | Scott Smith | 28 November 2012, 16:19:31 UTC | updated the way the build diff exceptions list is implemented for clinseq | 28 November 2012, 16:19:31 UTC |
| 44ebbeb | Mark Burnett | 28 November 2012, 01:11:42 UTC | Remove lots of duplicate code Remove duplicate copies of _gather_params_for_get_or_create in various sub classes of SR. | 28 November 2012, 01:15:39 UTC |
| 6ba9c96 | Obi Griffith | 28 November 2012, 00:30:58 UTC | Added option to allow files for review to be specified and copied into folder along with newly created xml session files | 28 November 2012, 00:30:58 UTC |
| 8a422a5 | Obi Griffith | 28 November 2012, 00:30:14 UTC | Fixed bug where sample with parentheses killed summarizeBuilds | 28 November 2012, 00:30:14 UTC |
| f789090 | Ian Ferguson | 27 November 2012, 23:41:00 UTC | Fixed warnings when unarchiving an allocation In some cases, unarchiving an allocation would print warnings about attempting to touch an 'ALLOCATION_DELETED' file in the shadow allocation used by the unarchiving process. This was caused by NFS caching attributes used by the stat() syscall. Even after the shadow allocation path was moved to the final path, NFS would report that the original shadow allocation path still existed. The solution was to flush the cache by attempting to opendir() the path in question before testing its existence with -d. | 27 November 2012, 23:41:00 UTC |
| b8256c2 | Scott Smith | 27 November 2012, 23:25:27 UTC | add logic to ensure clinseq build diffs ignore the correct files | 27 November 2012, 23:25:27 UTC |
| e145180 | Scott Smith | 27 November 2012, 22:43:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 November 2012, 22:43:02 UTC |
| a7caecd | Scott Smith | 27 November 2012, 22:42:51 UTC | updated ClinSeq.t to use the new snapshot at 2012-11-27, and added masking for the clonality plot tsv | 27 November 2012, 22:42:51 UTC |
| c3a35d2 | Brian Derickson | 27 November 2012, 21:24:51 UTC | fixed a few bugs | 27 November 2012, 21:24:59 UTC |
| d82c790 | Mark Burnett | 27 November 2012, 20:32:36 UTC | add input blacklist and params whitelist to SR::_faster_get This will make us fall back on old behavior when a software result has only inputs of the specified name. This is desirable, because the new get is slow in cases where the inputs correspond to many software results. Additionally, add params whitelist so we can search on highly selective params by default. | 27 November 2012, 20:55:20 UTC |
| efae32e | Mark Burnett | 27 November 2012, 20:11:56 UTC | make new SR::_faster_get act more like UR's get This fixes 3 failing perl tests, by reducing restrictions on what is considered a matching object (mimicing the lax comparisons implemented by UR get, like undef == ''). | 27 November 2012, 20:13:26 UTC |
| 9aad289 | APipe Tester | 27 November 2012, 19:55:39 UTC | updated ur submodule to 71d1cdc | 27 November 2012, 19:55:39 UTC |
| 0b09864 | Nathan Nutter | 16 November 2012, 03:06:26 UTC | symlink after move Change-Id: Ia8e8c93ad032fe53db1d470457a63dd04f9bdd68 | 27 November 2012, 19:22:15 UTC |
| 1cf95f5 | Malachi Griffith | 27 November 2012, 18:58:11 UTC | Updated test case for clin-seq update-analysis | 27 November 2012, 18:58:11 UTC |
| 859baa0 | Malachi Griffith | 27 November 2012, 18:53:57 UTC | Added option to skip problem instrument data and consolidated check for solexa instrument data type in clinseq update-analysis | 27 November 2012, 18:53:57 UTC |
| e215f7f | Nathan Nutter | 27 November 2012, 18:40:03 UTC | fix: cannot re-execute a command | 27 November 2012, 18:46:58 UTC |
