| 5f98301 | Scott Smith | 15 August 2013, 15:53:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 August 2013, 15:53:27 UTC |
| 3c90c0c | APipe Tester | 15 August 2013, 05:19:51 UTC | Updated `genome` tab completion. | 15 August 2013, 05:19:51 UTC |
| 6e10ed7 | APipe Tester | 15 August 2013, 05:17:31 UTC | Updated class browser cache. | 15 August 2013, 05:17:31 UTC |
| b3efd61 | Nathan Nutter | 15 August 2013, 05:11:25 UTC | default reason appends caller info so need a more flexible check | 15 August 2013, 05:11:25 UTC |
| 9ad12f4 | Nathan Nutter | 15 August 2013, 05:01:41 UTC | add diag and initialize count | 15 August 2013, 05:01:41 UTC |
| 98bf37d | Nathan Nutter | 15 August 2013, 04:29:05 UTC | add Informatics as valid lab | 15 August 2013, 04:29:05 UTC |
| f5fcb9b | Nathan Nutter | 15 August 2013, 04:27:30 UTC | fixup! remove unnecessary check that depends on ID being numeric | 15 August 2013, 04:27:30 UTC |
| 6b60733 | Nathan Nutter | 14 August 2013, 01:39:05 UTC | remove unnecessary check that depends on ID being numeric | 15 August 2013, 04:20:35 UTC |
| 56ecf89 | Nathan Nutter | 23 July 2013, 14:52:57 UTC | sort instrument data instead of assuming order | 15 August 2013, 04:20:13 UTC |
| 75936ea | Nathan Nutter | 15 July 2013, 21:22:17 UTC | refactor test to use subtests (there is still some interdependence) | 15 August 2013, 04:19:49 UTC |
| 028907d | Nathan Nutter | 15 July 2013, 18:33:23 UTC | also check notes on second object after create | 15 August 2013, 03:57:11 UTC |
| 0a39ca0 | Nathan Nutter | 15 July 2013, 18:31:31 UTC | remove need for temp variable (sort of) for counting | 15 August 2013, 03:56:47 UTC |
| 4e31410 | Nathan Nutter | 15 July 2013, 16:56:10 UTC | check that expected note exists instead of assuming order Since we do not have subsecond resolution on the entry_date of notes we cannot assume the order in this test is meaningful. | 15 August 2013, 03:56:16 UTC |
| 4e8edd7 | Ben Oberkfell | 30 July 2013, 19:26:50 UTC | remove dependence on sorting by ID | 15 August 2013, 03:55:49 UTC |
| 412776d | Nathan Nutter | 15 July 2013, 16:55:24 UTC | order by entry_date With IDs changing to UUIDs we cannot (and should never have) depended on the IDs representing temporal progression. | 14 August 2013, 22:27:41 UTC |
| 314bd64 | Nathan Nutter | 15 July 2013, 16:54:48 UTC | sort as UR would instead of assuming a hard-coded order | 14 August 2013, 22:27:37 UTC |
| 7ff2695 | Nathan Nutter | 14 August 2013, 17:15:35 UTC | Merge branch containing Postgres transition prep work | 14 August 2013, 22:27:34 UTC |
| 5d99b0e | Anthony Brummett | 10 July 2013, 23:07:29 UTC | More simple cases of moving to the Oltp or Dwrac data source | 14 August 2013, 22:27:30 UTC |
| c7296e3 | Anthony Brummett | 10 July 2013, 22:16:58 UTC | whitespace | 14 August 2013, 22:27:29 UTC |
| 555d192 | Anthony Brummett | 10 July 2013, 22:12:19 UTC | Switch to use the Dwrac data source This also nukes the union that pulls in Sanger rows. It was technically a problem because of the join on misc_attribute in the main Genome database with joins to Oltp and Dwrac on either side. The conclusion was that this class is only used by the data importer that migrates data from the LIMS database to Genome's, and Sanger data is handled via a completely different process - getting rows from the sequence_read table, making allocations for them and inserting them as imported instrument data. | 14 August 2013, 22:27:27 UTC |
| 9218e2a | Anthony Brummett | 10 July 2013, 21:51:27 UTC | Refactor to get work_order_id info from separate database We won't be able to join to OLTP anymore, so when filtering by work_order_id, first do a query to find out which models go with that work_order, then do a query to get the relevent info for those models | 14 August 2013, 22:27:23 UTC |
| 33ed3fd | Anthony Brummett | 10 July 2013, 19:44:17 UTC | Refactor to pass an iterator that does the query rather than just the query | 14 August 2013, 22:27:21 UTC |
| a2ef00c | Anthony Brummett | 10 July 2013, 19:56:23 UTC | make the test quiet | 14 August 2013, 22:27:19 UTC |
| 0343aca | Anthony Brummett | 10 July 2013, 20:33:48 UTC | Remove support for --subject-names option This required the subject_name column in the genome_model table, which hasn't existed in a while. If it's still needed, then support for joining to genome_subject will have to get added. | 14 August 2013, 22:27:16 UTC |
| 6c6d4f8 | Anthony Brummett | 10 July 2013, 17:53:31 UTC | Another simple case of switching data sources | 14 August 2013, 22:27:15 UTC |
| 66a44c7 | Anthony Brummett | 09 July 2013, 22:14:17 UTC | Step 1 of removing dblinks from raw SQL queries These are the simple cases | 14 August 2013, 22:27:14 UTC |
| db0ab42 | Anthony Brummett | 09 July 2013, 20:32:08 UTC | Limit disconnections to only Genome RDBMS datasources, not all UR RDBMS data sources | 14 August 2013, 22:27:12 UTC |
| a507bb2 | Anthony Brummett | 09 July 2013, 20:28:14 UTC | Refactor to inherit from Genome::DataSource::CommonRDBMS | 14 August 2013, 22:27:10 UTC |
| 69f8c85 | Anthony Brummett | 08 July 2013, 19:17:25 UTC | Add new class CommonRDBMS for logging and DB pausing Logging functions moved to CommonRDBMS and also used from GMSchema via Exporter Pausing functionality is only used in Dwrac and Oltp, but left a note for the switchover in GMSchema | 14 August 2013, 22:27:08 UTC |
| 9dd9f5a | Anthony Brummett | 03 July 2013, 21:24:18 UTC | Add data sources for the LIMS oracle databases | 14 August 2013, 22:27:07 UTC |
| 4146750 | APipe Tester | 14 August 2013, 22:23:50 UTC | updated workflow submodule to 071908d | 14 August 2013, 22:23:50 UTC |
| e9c5b35 | APipe Tester | 14 August 2013, 22:16:53 UTC | updated ur submodule to 0324309 | 14 August 2013, 22:16:53 UTC |
| 740c007 | Dave Larson | 14 August 2013, 22:09:37 UTC | Remove the die statement since Eddie has indicated these should exist in the future and the tool worked alright for data-transfer. | 14 August 2013, 22:09:37 UTC |
| a13186a | APipe Tester | 14 August 2013, 21:27:03 UTC | Updated `gmt` tab completion. | 14 August 2013, 21:27:03 UTC |
| ae77832 | APipe Tester | 14 August 2013, 21:25:36 UTC | Updated `genome` tab completion. | 14 August 2013, 21:25:36 UTC |
| 85ad399 | APipe Tester | 14 August 2013, 21:22:20 UTC | Updated class browser cache. | 14 August 2013, 21:22:20 UTC |
| 857c049 | Dan Koboldt | 14 August 2013, 21:14:19 UTC | Updates to make this tool compliant with new indel workflow | 14 August 2013, 21:14:19 UTC |
| 360323f | Dan Koboldt | 14 August 2013, 20:52:34 UTC | NOt sure why I have to write this Merge branch 'master' of git+ssh://git/srv/git/genome | 14 August 2013, 20:52:34 UTC |
| c6974c7 | Scott Smith | 14 August 2013, 20:06:37 UTC | better error messages on missing microarray files | 14 August 2013, 20:06:37 UTC |
| 7fab3b0 | Scott Smith | 14 August 2013, 20:06:11 UTC | handle an LSF without host groups | 14 August 2013, 20:06:11 UTC |
| 5227080 | Scott Smith | 14 August 2013, 18:30:43 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 August 2013, 18:30:43 UTC |
| 89ebc0c | Scott Smith | 14 August 2013, 18:29:05 UTC | refactor of genome model import/export metadata and tests | 14 August 2013, 18:29:05 UTC |
| 9fe0b12 | Scott Smith | 14 August 2013, 18:08:05 UTC | Rename Pcap/assemble.t to Pcap/Assemble.t, deleting the autogenerated test case. A pair of files with names like this messes up Mac checkouts. | 14 August 2013, 18:08:05 UTC |
| 35ede2a | apregier | 13 August 2013, 21:51:06 UTC | New version of strelka | 14 August 2013, 17:48:30 UTC |
| ca6ebca | Nathan Nutter | 14 August 2013, 16:56:55 UTC | can't use this lib since it is not installed for Perl 5.8 | 14 August 2013, 17:01:47 UTC |
| c8ad53c | APipe Tester | 14 August 2013, 15:37:32 UTC | Updated `gmt` tab completion. | 14 August 2013, 15:37:32 UTC |
| 9d32896 | APipe Tester | 14 August 2013, 15:36:26 UTC | Updated `genome` tab completion. | 14 August 2013, 15:36:26 UTC |
| 9b2f2e2 | APipe Tester | 14 August 2013, 15:34:13 UTC | Updated class browser cache. | 14 August 2013, 15:34:13 UTC |
| 3f41074 | Dan Koboldt | 14 August 2013, 15:31:53 UTC | Updates to some common analysis tools | 14 August 2013, 15:31:53 UTC |
| 482c6e5 | Dan Koboldt | 14 August 2013, 15:23:46 UTC | Pushing updates to Merge branch 'master' of git+ssh://git/srv/git/genome | 14 August 2013, 15:23:46 UTC |
| fc559cc | Dan Koboldt | 14 August 2013, 15:23:31 UTC | Updates to Mendelian analysis tools | 14 August 2013, 15:23:31 UTC |
| 8d74bd3 | Dan Koboldt | 14 August 2013, 15:23:10 UTC | New tools for Mendelian analysis | 14 August 2013, 15:23:10 UTC |
| 8506270 | Nathan Nutter | 14 August 2013, 15:15:15 UTC | all arguments must be array elements to pass an array to system | 14 August 2013, 15:15:15 UTC |
| 3551b91 | APipe Tester | 14 August 2013, 14:05:30 UTC | Updated `genome` tab completion. | 14 August 2013, 14:05:30 UTC |
| 2f35f4d | APipe Tester | 14 August 2013, 14:03:11 UTC | Updated class browser cache. | 14 August 2013, 14:03:11 UTC |
| 5b7e28e | dmorton | 14 August 2013, 13:19:23 UTC | Added UR_DBI_NO_COMMIT to Notable.t It seems someone added the entities it creates to the database by mistake somehow. | 14 August 2013, 13:19:23 UTC |
| ae6707b | dmorton | 10 August 2013, 00:03:34 UTC | Make _execute_system_command avoid invoking the shell That way arguments don't have to be escaped carefully. Escaping strings for the shell is difficult and almost everyone gets it wrong in some subtle way. IPC::System::Simple never invokes the shell and so avoids the issue entirely. | 14 August 2013, 12:53:17 UTC |
| 30f95ba | dmorton | 09 August 2013, 22:59:14 UTC | Ensure strings are properly formatted | 14 August 2013, 12:53:17 UTC |
| be7a6f4 | APipe Tester | 14 August 2013, 07:07:53 UTC | updated workflow submodule to c0449f9 | 14 August 2013, 07:07:53 UTC |
| d2af94f | Nathan Nutter | 14 August 2013, 06:38:43 UTC | bypass until expected data is updated | 14 August 2013, 06:38:43 UTC |
| 5a3080f | Nathan Nutter | 14 August 2013, 06:31:09 UTC | add ORA-03135 to retriable operations | 14 August 2013, 06:31:09 UTC |
| beea803 | Nathan Nutter | 14 August 2013, 02:46:44 UTC | should inherit from parent | 14 August 2013, 02:46:44 UTC |
| dadd613 | Thomas Mooney | 13 August 2013, 20:48:02 UTC | Update refalign build diffs to account for UUIDs. | 14 August 2013, 02:34:52 UTC |
| 43eafb7 | Thomas Mooney | 13 August 2013, 20:21:22 UTC | Update somval build diffs to account for UUIDs. | 14 August 2013, 02:34:40 UTC |
| ce29425 | Ben Oberkfell | 29 July 2013, 20:23:28 UTC | numeric comparison fails w/ uuids | 14 August 2013, 02:31:52 UTC |
| cdcd41e | Nathan Nutter | 26 July 2013, 22:04:56 UTC | deal with sort differences caused by UUIDs | 14 August 2013, 02:31:51 UTC |
| 7b01c61 | Nathan Nutter | 14 August 2013, 02:26:27 UTC | fix test counts after cherry-pick | 14 August 2013, 02:26:27 UTC |
| 86b8382 | Nathan Nutter | 26 July 2013, 21:42:41 UTC | put old test into a subtest | 14 August 2013, 02:22:22 UTC |
| d81ef62 | Nathan Nutter | 18 July 2013, 20:27:51 UTC | temporarily remove `genome disk allocation archive-expired` Due to PostgreSQL migration and poor date handling in UR::BoolExpr we are temporarily removing this command. We created AR-89 and AR-90 to address these issues at a later time. | 14 August 2013, 02:22:08 UTC |
| 21989b9 | Nathan Nutter | 23 July 2013, 19:18:42 UTC | sort order cannot be predetermined with UUIDs | 14 August 2013, 02:20:48 UTC |
| f072b80 | Nathan Nutter | 23 July 2013, 20:05:04 UTC | use appropriate sorter | 14 August 2013, 02:17:42 UTC |
| 586078c | Nathan Nutter | 25 July 2013, 15:48:26 UTC | extract method | 14 August 2013, 02:17:20 UTC |
| 1455741 | Nathan Nutter | 25 July 2013, 15:45:50 UTC | whitespace | 14 August 2013, 02:17:07 UTC |
| 76d73fc | Ben Oberkfell | 30 July 2013, 18:55:37 UTC | remove sorting assumption | 14 August 2013, 02:13:29 UTC |
| dbb772d | Nathan Nutter | 07 August 2013, 22:26:05 UTC | remove numeric comparison to ID | 14 August 2013, 02:03:26 UTC |
| 625b5ce | Nathan Nutter | 26 July 2013, 21:39:28 UTC | use is_equal_set instead of is_deeply and deal with sort difference | 14 August 2013, 01:45:24 UTC |
| a961c0d | Nathan Nutter | 26 July 2013, 21:39:11 UTC | add is_equal_set | 14 August 2013, 01:45:01 UTC |
| 2dbeefb | Nathan Nutter | 10 August 2013, 21:55:12 UTC | remove deprecated lock code This is follow up to 659c1fb. The deprecated lock code used subdirectories which leaves behind empty directories when the lock is removed. Since it is safe to assume all the old-lock-only code is no longer running we can now remove that. | 14 August 2013, 01:44:25 UTC |
| a98addf | Nathan Nutter | 09 August 2013, 21:09:48 UTC | add a SIGPIPE handler to BQM | 14 August 2013, 01:44:24 UTC |
| 9997bac | APipe Tester | 13 August 2013, 21:55:31 UTC | Updated `gmt` tab completion. | 13 August 2013, 21:55:31 UTC |
| d6968b6 | APipe Tester | 13 August 2013, 21:54:16 UTC | Updated `genome` tab completion. | 13 August 2013, 21:54:16 UTC |
| 6e4d0b9 | APipe Tester | 13 August 2013, 21:51:49 UTC | Updated class browser cache. | 13 August 2013, 21:51:49 UTC |
| 2f7e813 | Chris Miller | 13 August 2013, 21:37:43 UTC | adding test | 13 August 2013, 21:42:13 UTC |
| 71f6bb8 | Chris Miller | 13 August 2013, 21:17:47 UTC | first working version | 13 August 2013, 21:42:11 UTC |
| f996ad9 | Chris Miller | 13 August 2013, 17:33:58 UTC | removing testing code, reverting to older better version | 13 August 2013, 21:42:10 UTC |
| dfcc458 | Chris Miller | 13 August 2013, 17:33:01 UTC | updates - still nonfunctional | 13 August 2013, 21:42:10 UTC |
| ad7284a | Chris Miller | 12 August 2013, 20:46:47 UTC | initial commit of filter vcf info | 13 August 2013, 21:42:05 UTC |
| e1c70d4 | Chris Miller | 07 August 2013, 19:47:18 UTC | parsing info field by default | 13 August 2013, 21:42:05 UTC |
| 5e46f02 | Adam Coffman | 13 August 2013, 20:52:55 UTC | update approved docs for somatic validation define command | 13 August 2013, 20:52:55 UTC |
| f5cd3da | APipe Tester | 13 August 2013, 17:44:54 UTC | Updated `genome` tab completion. | 13 August 2013, 17:46:26 UTC |
| 64b1a2c | APipe Tester | 13 August 2013, 17:41:45 UTC | Updated class browser cache. | 13 August 2013, 17:46:26 UTC |
| 4edb203 | Eddie Belter | 13 August 2013, 17:42:35 UTC | InstData GATK: use sr user to get base recal in base recal bam result | 13 August 2013, 17:45:40 UTC |
| ee8f7d1 | Chris Miller | 09 August 2013, 17:15:52 UTC | adding --force option to somval to handle samples that don't match | 13 August 2013, 17:34:35 UTC |
| 4ef7050 | Eddie Belter | 13 August 2013, 17:29:27 UTC | Refine Reads GATK: rm setting user of indel realign; add tests for setting users of all gatk result generated | 13 August 2013, 17:29:27 UTC |
| 8e69a81 | Eddie Belter | 13 August 2013, 16:59:05 UTC | InstData GATK: add user to bam source; update tests; move status msgs to base class | 13 August 2013, 16:59:05 UTC |
| a78fccf | Eddie Belter | 13 August 2013, 16:58:24 UTC | InstData GATK: move known sites display to base class | 13 August 2013, 16:58:24 UTC |
| 38e0d19 | Eddie Belter | 13 August 2013, 16:45:39 UTC | InstData GATK: update var name in base recal bam result test | 13 August 2013, 16:45:39 UTC |
| 5804552 | Mark Burnett | 13 August 2013, 14:32:16 UTC | SomVal: add build_id to outputproperties for inner model | 13 August 2013, 14:33:29 UTC |
| 373ada8 | APipe Tester | 13 August 2013, 03:02:14 UTC | Updated `gmt` tab completion. | 13 August 2013, 03:02:14 UTC |
| aa1f308 | APipe Tester | 13 August 2013, 03:01:22 UTC | Updated `genome` tab completion. | 13 August 2013, 03:01:22 UTC |
