| 6523fb1 | Anthony Brummett | 21 August 2013, 22:07:44 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 21 August 2013, 22:07:44 UTC |
| 26b2def | Anthony Brummett | 21 August 2013, 22:06:15 UTC | Fix the test in advance of the switch to Postgres The Postgres datasource will have AutoCommit=1, and something in the test triggers a call to commit() the data source which generates this warning. | 21 August 2013, 22:06:15 UTC |
| 862c0e1 | APipe Tester | 21 August 2013, 21:55:46 UTC | updated ur submodule to c0fd575 | 21 August 2013, 21:55:46 UTC |
| 6e69c59 | Nathan Nutter | 21 August 2013, 18:44:56 UTC | fix for incorrect data_type in results The ALTERNATE_FROM_CLASS lookup stuff leads to objects with the incorrect data_type in the results. Really this whole thing needs to go in favor of people just explicitly "saying" what they need with UR::BoolExpr. | 21 August 2013, 18:46:46 UTC |
| e709235 | Nathan Nutter | 21 August 2013, 18:02:30 UTC | remove duplicate class Genome::Site::TGI::MiscAttribute Genome::Site::TGI::MiscAttribute was a duplicate of Genome::MiscAttribute so I updated the only user of it, Genome::Site::TGI::InstrumentData, to just use Genome::MiscAttribute. | 21 August 2013, 18:02:30 UTC |
| 77ffbf1 | Feiyu Du | 21 August 2013, 15:44:41 UTC | add error_rate_version as bamqc software result param | 21 August 2013, 15:44:41 UTC |
| 861b14c | Adam Coffman | 21 August 2013, 15:02:05 UTC | Mark use_error_rate_pileup as deprecated in RnaSeq error_rate_pileup was removed as a param for the underlying software result. This commit removes references to it in the BamQc command and marks it as deprecated in the RnaSeq model so that current processing profiles should continue to function. | 21 August 2013, 15:02:05 UTC |
| 7982841 | APipe Tester | 21 August 2013, 13:54:24 UTC | updated jenkins submodule to fd135da | 21 August 2013, 13:54:24 UTC |
| 1a063f6 | Dave Larson | 21 August 2013, 13:23:57 UTC | increase memory usage to large levels | 21 August 2013, 13:23:57 UTC |
| 9b4df09 | APipe Tester | 21 August 2013, 02:17:51 UTC | Updated `gmt` tab completion. | 21 August 2013, 02:17:51 UTC |
| 0e5c804 | APipe Tester | 21 August 2013, 02:16:49 UTC | Updated `genome` tab completion. | 21 August 2013, 02:16:49 UTC |
| 87cdf46 | APipe Tester | 21 August 2013, 02:14:56 UTC | Updated class browser cache. | 21 August 2013, 02:14:56 UTC |
| 4147882 | Dave Larson | 21 August 2013, 01:54:07 UTC | This tool is not actually for BED files and is used for DV2. Add an option to skip header lines to handle non-BED files. | 21 August 2013, 01:54:07 UTC |
| 768d060 | Dave Larson | 16 August 2013, 21:44:33 UTC | basic VCF converter for the native mutect output format | 21 August 2013, 01:51:09 UTC |
| 32854bb | Anthony Brummett | 20 August 2013, 22:10:16 UTC | Switch to string comparisons for this test The change works both in the Postgres branch and master | 20 August 2013, 22:10:16 UTC |
| 6c1784d | Anthony Brummett | 20 August 2013, 21:41:37 UTC | Switch to string comparisons for these tests The change works both in the Postgres branch and master | 20 August 2013, 21:41:37 UTC |
| b410c34 | Scott Smith | 20 August 2013, 19:33:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 August 2013, 19:33:11 UTC |
| d2de7ec | Scott Smith | 20 August 2013, 19:30:18 UTC | remove hard-coded expectation that log files are in /gscmnt, and that otherwise we should not log | 20 August 2013, 19:32:42 UTC |
| 41f7a07 | Nathan Nutter | 20 August 2013, 18:34:32 UTC | Update test output for 8e4f17f. | 20 August 2013, 19:32:41 UTC |
| 162d129 | Jim Weible | 20 August 2013, 15:57:47 UTC | Get a real test for GMT/Varscan/ConsensusVcfMatch | 20 August 2013, 19:32:41 UTC |
| c2019fe | Jim Weible | 20 August 2013, 15:57:41 UTC | cleanup | 20 August 2013, 19:32:40 UTC |
| 10813df | Jim Weible | 20 August 2013, 13:10:53 UTC | achieve feature parity with the original script | 20 August 2013, 19:32:40 UTC |
| 4961529 | Nathan Nutter | 20 August 2013, 18:34:32 UTC | Update test output for 8e4f17f. | 20 August 2013, 18:35:29 UTC |
| 6b9aeb3 | Jim Weible | 20 August 2013, 15:57:47 UTC | Get a real test for GMT/Varscan/ConsensusVcfMatch | 20 August 2013, 18:11:19 UTC |
| 8ff4482 | Jim Weible | 20 August 2013, 15:57:41 UTC | cleanup | 20 August 2013, 18:11:19 UTC |
| 9909b3a | Jim Weible | 20 August 2013, 13:10:53 UTC | achieve feature parity with the original script | 20 August 2013, 18:11:18 UTC |
| 0f14163 | Scott Smith | 20 August 2013, 16:24:55 UTC | updated exporter to include feature lists associated with instrument data target_region_set_name | 20 August 2013, 16:24:55 UTC |
| 4bf88ea | Anthony Brummett | 20 August 2013, 15:57:34 UTC | Switch to string comparisons for these tests The change works both in the Postgres branch and master | 20 August 2013, 15:57:34 UTC |
| b11a416 | Chris Miller | 20 August 2013, 13:33:34 UTC | documentation update | 20 August 2013, 13:33:34 UTC |
| 8e4f17f | Nathan Nutter | 20 August 2013, 02:18:34 UTC | make output (sort order) more deterministic when using UUIDs | 20 August 2013, 02:18:34 UTC |
| 507c55e | Nathan Nutter | 20 August 2013, 02:00:33 UTC | fix uninit warning | 20 August 2013, 02:00:33 UTC |
| 9128add | Nathan Nutter | 20 August 2013, 00:05:26 UTC | re-enable now that expected data has been updated | 20 August 2013, 00:05:26 UTC |
| 9439bac | APipe Tester | 19 August 2013, 23:33:06 UTC | Updated `genome` tab completion. | 19 August 2013, 23:33:06 UTC |
| 27597e9 | APipe Tester | 19 August 2013, 23:31:12 UTC | Updated class browser cache. | 19 August 2013, 23:31:12 UTC |
| 4b6ddf7 | Scott Smith | 19 August 2013, 23:20:10 UTC | better warning messages when creating seqdict for refseq | 19 August 2013, 23:21:29 UTC |
| 6033ba8 | Scott Smith | 19 August 2013, 23:19:06 UTC | better error messages in staged profiles | 19 August 2013, 23:21:28 UTC |
| f6f918b | APipe Tester | 19 August 2013, 23:12:24 UTC | updated workflow submodule to 6aaa1ec | 19 August 2013, 23:12:24 UTC |
| c0a25bb | APipe Tester | 19 August 2013, 22:39:22 UTC | updated ur submodule to 6c2d5ce | 19 August 2013, 22:39:22 UTC |
| f693de1 | Scott Smith | 19 August 2013, 22:26:36 UTC | add installer for file based COSMIC database | 19 August 2013, 22:26:36 UTC |
| 6757f4f | Scott Smith | 19 August 2013, 22:21:59 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 August 2013, 22:21:59 UTC |
| 5c30a7f | Nathan Nutter | 19 August 2013, 20:05:48 UTC | compare with eq so it will work with UUIDs | 19 August 2013, 20:07:37 UTC |
| 06bf8b3 | Nathan Nutter | 16 August 2013, 22:08:51 UTC | add subset_name to avoid the "invalid data for save" warnings | 19 August 2013, 20:07:37 UTC |
| a1fa4ea | Nathan Nutter | 15 August 2013, 20:07:32 UTC | IDs will not always be numeric so compare with eq | 19 August 2013, 20:07:36 UTC |
| 08b2205 | Nathan Nutter | 15 August 2013, 20:00:02 UTC | handle case where lane is not set | 19 August 2013, 20:07:35 UTC |
| cc3490d | Nathan Nutter | 15 August 2013, 19:59:05 UTC | whitespace | 19 August 2013, 20:07:35 UTC |
| c6012d0 | apregier | 16 August 2013, 17:49:36 UTC | Update docs | 19 August 2013, 17:00:57 UTC |
| d421456 | Chris Miller | 19 August 2013, 16:33:55 UTC | correct column uniq-ing | 19 August 2013, 16:34:35 UTC |
| c4839ef | Mark Burnett | 19 August 2013, 14:19:37 UTC | G:M:B:View -> play nice with Flow's running* status | 19 August 2013, 14:23:27 UTC |
| c6a454c | Mark Burnett | 19 August 2013, 14:18:53 UTC | PhenoCorr: wait for NFS cache | 19 August 2013, 14:23:26 UTC |
| 5846712 | apregier | 16 August 2013, 16:50:33 UTC | Vep plugin arguments work with our command line | 16 August 2013, 16:59:24 UTC |
| b31afe5 | APipe Tester | 16 August 2013, 13:53:46 UTC | updated workflow submodule to 92b7450 | 16 August 2013, 13:53:46 UTC |
| 56d23f6 | APipe Tester | 15 August 2013, 21:54:05 UTC | Updated `genome` tab completion. | 15 August 2013, 21:54:05 UTC |
| 1da3863 | APipe Tester | 15 August 2013, 21:51:56 UTC | Updated class browser cache. | 15 August 2013, 21:51:56 UTC |
| e99db69 | apregier | 15 August 2013, 21:38:19 UTC | Merge branch 'generator' into gb_master | 15 August 2013, 21:38:19 UTC |
| 7c61f0a | apregier | 15 August 2013, 21:30:17 UTC | Simplify submission-summary command | 15 August 2013, 21:35:18 UTC |
| 7ea7361 | apregier | 15 August 2013, 21:29:02 UTC | Add somatic validation test objects | 15 August 2013, 21:33:15 UTC |
| b97e1bb | Feiyu Du | 15 August 2013, 18:40:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 August 2013, 18:40:17 UTC |
| 47ffe44 | Feiyu Du | 15 August 2013, 18:37:55 UTC | test more parameters | 15 August 2013, 18:37:55 UTC |
| ac6dadf | APipe Tester | 15 August 2013, 17:54:21 UTC | Updated `genome` tab completion. | 15 August 2013, 17:54:21 UTC |
| 9bd219a | APipe Tester | 15 August 2013, 17:52:15 UTC | Updated class browser cache. | 15 August 2013, 17:52:15 UTC |
| e6d0a3d | Ben Oberkfell | 29 July 2013, 22:50:03 UTC | fix uuid sorting | 15 August 2013, 17:31:15 UTC |
| c027b28 | Ben Oberkfell | 29 July 2013, 20:57:54 UTC | match uuids as well as integers | 15 August 2013, 17:31:14 UTC |
| af72de6 | Nathan Nutter | 15 August 2013, 15:19:16 UTC | remove --newest-first option since it depends on implied information by instrument data IDs | 15 August 2013, 17:31:14 UTC |
| bcc63c1 | Nathan Nutter | 15 August 2013, 15:18:01 UTC | refactor test for more flexible handling of field comparisons | 15 August 2013, 17:31:13 UTC |
| 2ae9034 | Ben Oberkfell | 24 July 2013, 21:36:24 UTC | compare sets instead of arrays since order doesn't matter | 15 August 2013, 17:31:13 UTC |
| fd6555e | Nathan Nutter | 23 July 2013, 14:53:25 UTC | support numeric or hex (UUID) IDs | 15 August 2013, 17:31:12 UTC |
| e9125cd | Ben Oberkfell | 23 July 2013, 20:05:20 UTC | fix equality check for uuids | 15 August 2013, 17:31:11 UTC |
| 0a8c61b | Nathan Nutter | 15 August 2013, 14:29:12 UTC | explicitly import read_file | 15 August 2013, 17:31:11 UTC |
| 9235f46 | APipe Tester | 15 August 2013, 16:21:51 UTC | Updated `gmt` tab completion. | 15 August 2013, 16:21:51 UTC |
| 2a827b3 | APipe Tester | 15 August 2013, 16:20:46 UTC | Updated `genome` tab completion. | 15 August 2013, 16:20:46 UTC |
| 4cda859 | APipe Tester | 15 August 2013, 16:18:34 UTC | Updated class browser cache. | 15 August 2013, 16:18:34 UTC |
| 4c2d0a3 | Feiyu Du | 15 August 2013, 16:02:01 UTC | add unit test for gmt dgidb query-gene | 15 August 2013, 16:04:03 UTC |
| 922e855 | Feiyu Du | 14 August 2013, 22:09:09 UTC | Add a new tool to query gene from DGIDB database | 15 August 2013, 16:04:02 UTC |
| 29f3448 | Scott Smith | 15 August 2013, 15:58:22 UTC | updated model and build to have downstream_{model,build}_associations, respectively. | 15 August 2013, 15:58:22 UTC |
| 1d3396a | Scott Smith | 15 August 2013, 15:56:15 UTC | The unused "auto_build" flag (not to be confused with "auto_build_alignments", which automatically adds instrument data) will, when set, rebuild when input models rebuild. This can be turned on manually, and when not on has no effect. | 15 August 2013, 15:56:15 UTC |
| 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 |
