088a1a2 | Anthony Brummett | 27 August 2013, 21:08:46 UTC | typo | 27 August 2013, 21:08:46 UTC |
5e26e7d | Nathan Nutter | 27 August 2013, 20:50:33 UTC | IDs are Text now so have to be quoted in JSON... in XSL... in XML... | 27 August 2013, 20:50:55 UTC |
d88a845 | APipe Tester | 27 August 2013, 20:46:48 UTC | Updated `genome` tab completion. | 27 August 2013, 20:46:48 UTC |
3a80cb7 | APipe Tester | 27 August 2013, 20:44:54 UTC | Updated class browser cache. | 27 August 2013, 20:44:54 UTC |
9cc0d97 | Anthony Brummett | 27 August 2013, 20:34:16 UTC | Instead of picking the "latest" library, exit when there are more than one with the given name As part of the postgres-id-sorting change, we can't rely on the "highest" ID being the newest thing anymore. There's no obvious time associated with a library so no good way to keep the old behavior, which seems bad anyway | 27 August 2013, 20:34:16 UTC |
8cd41b3 | Anthony Brummett | 27 August 2013, 20:33:54 UTC | Can't sort numerically be ID anymore | 27 August 2013, 20:33:54 UTC |
f3bd359 | Anthony Brummett | 27 August 2013, 20:33:13 UTC | Can't sort things by ID as a surrogate for sorting by creation order | 27 August 2013, 20:33:13 UTC |
841cbb1 | Adam Coffman | 27 August 2013, 19:58:47 UTC | remove unused sub | 27 August 2013, 19:58:47 UTC |
3a7faf9 | Adam Coffman | 27 August 2013, 19:58:28 UTC | compare ids as strings instead of numbers | 27 August 2013, 19:58:28 UTC |
52f1a4e | Adam Coffman | 27 August 2013, 19:57:48 UTC | sort ids as strings instead of numbers | 27 August 2013, 19:57:48 UTC |
51bade9 | Adam Coffman | 27 August 2013, 19:57:28 UTC | sort on date_scheduled instead of build id | 27 August 2013, 19:57:28 UTC |
9ceb84e | Adam Coffman | 27 August 2013, 19:56:34 UTC | use last_succeeded_build | 27 August 2013, 19:56:34 UTC |
c9de8fb | Adam Coffman | 27 August 2013, 19:55:43 UTC | sort bamqc result by new best_guess_date value on software results | 27 August 2013, 19:55:43 UTC |
48f6172 | Adam Coffman | 27 August 2013, 19:54:25 UTC | sort on creation_date and date_scheduled instead of id | 27 August 2013, 19:54:25 UTC |
cf30083 | Adam Coffman | 27 August 2013, 19:54:02 UTC | sort instrument data ids as strings | 27 August 2013, 19:54:02 UTC |
730ae22 | Adam Coffman | 27 August 2013, 19:53:15 UTC | sort models on creation date instead of id | 27 August 2013, 19:53:15 UTC |
2478e2e | Adam Coffman | 27 August 2013, 19:52:24 UTC | sort models on creation date instead of id | 27 August 2013, 19:52:24 UTC |
10a5c10 | Adam Coffman | 27 August 2013, 19:51:57 UTC | sort instrument data ids as strings | 27 August 2013, 19:51:57 UTC |
9e4b959 | Adam Coffman | 27 August 2013, 19:51:35 UTC | sort build ids as strings instead of numbers | 27 August 2013, 19:51:35 UTC |
3e5f6ef | Adam Coffman | 27 August 2013, 19:51:18 UTC | sort builds on date_scheduled instead of id | 27 August 2013, 19:51:18 UTC |
647e572 | Adam Coffman | 27 August 2013, 19:42:00 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 August 2013, 19:42:00 UTC |
0fd5d84 | Adam Coffman | 27 August 2013, 19:41:49 UTC | add new best_guess_date sub for sorting software result | 27 August 2013, 19:41:49 UTC |
57ea583 | APipe Tester | 27 August 2013, 19:31:54 UTC | updated ur submodule to e3864f9 | 27 August 2013, 19:31:54 UTC |
5d5987f | APipe Tester | 27 August 2013, 19:24:34 UTC | updated graphite submodule to da9443f | 27 August 2013, 19:24:34 UTC |
255d147 | Nathan Nutter | 27 August 2013, 18:41:30 UTC | remove old datasources | 27 August 2013, 18:41:30 UTC |
b99328f | Travis Abbott | 27 August 2013, 18:33:19 UTC | update model set coverage view to find correct builds it previously tried to sort builds by id, but build ids are no longer numeric. now, $model->builds returns builds newest first, which is what this thing wants anyway. | 27 August 2013, 18:34:33 UTC |
f77e912 | Travis Abbott | 27 August 2013, 17:43:38 UTC | Genome::Model->builds now returns builds in order (newest first) they are ordered by date_scheduled (descending) | 27 August 2013, 18:34:33 UTC |
078c0df | APipe Tester | 27 August 2013, 18:17:56 UTC | updated graphite submodule to f4151f8 | 27 August 2013, 18:17:56 UTC |
02423fb | Gabriel Sanderson | 27 August 2013, 17:57:21 UTC | Merge branch 'master' into gb_master | 27 August 2013, 17:57:21 UTC |
a88ea93 | Gabriel Sanderson | 27 August 2013, 17:56:26 UTC | Add a VERY rudimentary check to the beginning that will look for the common problem that we have "chr" chromosomes without a nimblegen reference sequence. | 27 August 2013, 17:56:26 UTC |
1eb3b61 | APipe Tester | 27 August 2013, 15:47:05 UTC | updated graphite submodule to 1629c7e | 27 August 2013, 15:47:05 UTC |
05b227e | Mark Burnett | 27 August 2013, 15:37:38 UTC | G:D:Allocation test -- seed RNG on fork This should fix the bug related to my previous commit. | 27 August 2013, 15:37:38 UTC |
d98687b | Mark Burnett | 27 August 2013, 15:30:16 UTC | change G:D:A test allocation_paths This is an attempt to fix this error: ERROR: Failed to create directory (/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing//tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/allocation_lock_testing_1_pKhDg6d) with return value = '', and error: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 ERROR: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 I could not reproduce the error, but this change should fix the odd, nested path. | 27 August 2013, 15:32:18 UTC |
4c1b012 | Thomas Mooney | 27 August 2013, 15:23:44 UTC | Take fail count into consideration when deciding which data to process. | 27 August 2013, 15:23:44 UTC |
1e078c6 | Mark Burnett | 27 August 2013, 13:33:39 UTC | G:M:T:Picard monitors both stdout and stderr for activity | 27 August 2013, 14:09:50 UTC |
cf50bfc | Mark Burnett | 27 August 2013, 13:32:55 UTC | make sure InstrumentData::delete removes BamQc results | 27 August 2013, 14:09:49 UTC |
c0325c1 | Mark Burnett | 23 August 2013, 14:56:16 UTC | add note indicating a build is run using flow | 27 August 2013, 14:09:49 UTC |
61bcd43 | Thomas Mooney | 27 August 2013, 14:05:30 UTC | Updates to account for transition to UUIDs. | 27 August 2013, 14:05:30 UTC |
29bd72e | Thomas Mooney | 27 August 2013, 13:49:27 UTC | Improve error message--print just class name instead of metaobject hash. | 27 August 2013, 13:49:27 UTC |
9cda567 | APipe Tester | 26 August 2013, 23:22:02 UTC | updated workflow submodule to f9affd1 | 26 August 2013, 23:22:02 UTC |
62ea041 | Feiyu Du | 26 August 2013, 22:22:39 UTC | add output default to STDOUT | 26 August 2013, 22:22:39 UTC |
8b473d9 | APipe Tester | 26 August 2013, 20:48:40 UTC | Updated `gmt` tab completion. | 26 August 2013, 20:48:40 UTC |
9dfa0d2 | APipe Tester | 26 August 2013, 20:47:39 UTC | Updated `genome` tab completion. | 26 August 2013, 20:47:39 UTC |
050a1f8 | APipe Tester | 26 August 2013, 20:45:49 UTC | Updated class browser cache. | 26 August 2013, 20:45:49 UTC |
18f5021 | Dan Koboldt | 26 August 2013, 20:21:36 UTC | Writing something here. Merge branch 'master' of git+ssh://git/srv/git/genome | 26 August 2013, 20:21:36 UTC |
f85d020 | APipe Tester | 26 August 2013, 20:19:12 UTC | Updated `gmt` tab completion. | 26 August 2013, 20:19:12 UTC |
0af579a | APipe Tester | 26 August 2013, 20:18:06 UTC | Updated `genome` tab completion. | 26 August 2013, 20:18:06 UTC |
d8af0fa | APipe Tester | 26 August 2013, 20:15:43 UTC | Updated class browser cache. | 26 August 2013, 20:15:43 UTC |
06a4444 | Dan Koboldt | 26 August 2013, 20:11:12 UTC | Updates to Mendelian analysis tools | 26 August 2013, 20:11:12 UTC |
3f18253 | Nathan Nutter | 26 August 2013, 19:26:48 UTC | Merge Postgres transition branch | 26 August 2013, 19:26:48 UTC |
810d6bf | Nathan Nutter | 23 August 2013, 20:26:50 UTC | remove Genome::DataSource::Main | 26 August 2013, 19:18:30 UTC |
3134ae7 | Nathan Nutter | 23 August 2013, 20:26:41 UTC | remove use of Genome::DataSource::Main | 26 August 2013, 19:18:30 UTC |
ef4bca8 | Nathan Nutter | 23 August 2013, 19:00:09 UTC | remove Genome::DataSource::PGTest | 26 August 2013, 19:18:29 UTC |
f36c89b | Nathan Nutter | 23 August 2013, 18:59:31 UTC | remove GENOME_QUERY_POSTGRES | 26 August 2013, 19:18:29 UTC |
32a3b9c | Nathan Nutter | 23 August 2013, 18:59:10 UTC | remove use of GENOME_QUERY_POSTGRES | 26 August 2013, 19:18:28 UTC |
8b03865 | Anthony Brummett | 22 August 2013, 20:38:23 UTC | Data source pointed to the old Oracle schema The graphite metrics collector will use this to look up session info. We'd like to see the session count drop to 0 | 26 August 2013, 19:18:27 UTC |
d1227d1 | Anthony Brummett | 20 August 2013, 23:47:17 UTC | fix expected output wrt oracle date vs pg date format | 26 August 2013, 19:18:27 UTC |
ef4425e | Anthony Brummett | 20 August 2013, 23:28:40 UTC | Make Model/Command/Import/Metadata.t test pass This replays part of commit 89ebc0cbd7398ca5e8c31445e46ea6a8afc336de which was undone by commit 65e970fb2b36deef08d1773fafec1b419dd892eb | 26 August 2013, 19:18:26 UTC |
38a760e | Nathan Nutter | 13 August 2013, 20:08:38 UTC | add OldGMSchema | 26 August 2013, 19:18:26 UTC |
6a92d5a | Nathan Nutter | 02 August 2013, 03:46:40 UTC | update Meta DB for Postgres | 26 August 2013, 19:18:25 UTC |
dbd6ab0 | Ben Oberkfell | 30 July 2013, 23:43:02 UTC | columns are case sensitive | 26 August 2013, 19:18:24 UTC |
f1d449d | Ben Oberkfell | 30 July 2013, 17:15:07 UTC | fix expected output wrt oracle date vs pg date format | 26 August 2013, 19:18:24 UTC |
94f1bd9 | Nathan Nutter | 26 July 2013, 21:44:18 UTC | update channel_for_model to work with UUIDs | 26 August 2013, 19:18:23 UTC |
54cac01 | Nathan Nutter | 14 August 2013, 01:39:35 UTC | IDs are now 32 character text (UUID) | 26 August 2013, 19:18:23 UTC |
947fbc6 | Nathan Nutter | 15 August 2013, 17:37:24 UTC | all classes now use UUID generators | 26 August 2013, 19:18:21 UTC |
69525a8 | Nathan Nutter | 15 August 2013, 17:36:19 UTC | update table_names to match Postgres schema | 26 August 2013, 19:18:21 UTC |
449cc3e | Nathan Nutter | 23 August 2013, 20:23:37 UTC | remove GMSchemaOracle | 26 August 2013, 19:18:20 UTC |
bf9bf19 | Ben Oberkfell | 11 July 2013, 21:39:16 UTC | switch GMSchema to Postgres | 26 August 2013, 19:18:19 UTC |
eaaad3c | APipe Tester | 26 August 2013, 14:46:47 UTC | updated ur submodule to f88cc7d | 26 August 2013, 14:46:47 UTC |
5cd7c6b | Nathan Nutter | 25 August 2013, 16:18:17 UTC | Revert "factor in GENOME_SOFTWARE_RESULT_TEST_NAME into the version" This reverts commit b76311302c51a1c82828e8f1f00a5ca498f9566d. GENOME_SOFTWARE_RESULT_TEST_NAME is not always set so this had no effect. Will look for an alternative solution. | 25 August 2013, 16:18:17 UTC |
b763113 | Nathan Nutter | 25 August 2013, 01:13:55 UTC | factor in GENOME_SOFTWARE_RESULT_TEST_NAME into the version | 25 August 2013, 01:14:21 UTC |
7894d8f | Nathan Nutter | 25 August 2013, 01:07:17 UTC | extract repeated expression into temp variable | 25 August 2013, 01:14:20 UTC |
2362379 | Nathan Nutter | 25 August 2013, 01:04:24 UTC | whitespace | 25 August 2013, 01:14:19 UTC |
79aa1fa | Nathan Nutter | 24 August 2013, 05:06:25 UTC | whitespace | 24 August 2013, 05:06:25 UTC |
8e30c22 | Nathan Nutter | 24 August 2013, 05:04:55 UTC | silence 'Build * For Model' emails in these tests | 24 August 2013, 05:04:55 UTC |
e3d6e39 | Nathan Nutter | 24 August 2013, 01:45:39 UTC | add ability to silence 'Build * For Model' emails | 24 August 2013, 01:45:39 UTC |
adf3b56 | Nathan Nutter | 23 August 2013, 20:24:23 UTC | Genome::DataSource::OldPostgres | 23 August 2013, 22:13:07 UTC |
07b71f2 | Nathan Nutter | 23 August 2013, 20:25:49 UTC | Genome::DataSource::Dgidb | 23 August 2013, 22:13:06 UTC |
2271eed | Adam Coffman | 23 August 2013, 21:17:05 UTC | update expected | 23 August 2013, 21:17:05 UTC |
4c19479 | Eddie Belter | 23 August 2013, 19:06:48 UTC | Sync: create then execute update command | 23 August 2013, 19:07:09 UTC |
fe267c8 | Eddie Belter | 23 August 2013, 18:49:10 UTC | Fix SQL db links in site sync setup proj seq product | 23 August 2013, 19:07:08 UTC |
34181f2 | Eddie Belter | 23 August 2013, 18:48:27 UTC | Inst data tests abandoning builds and deleting associated alignment results upon delete | 23 August 2013, 19:07:08 UTC |
936c00e | Eddie Belter | 23 August 2013, 18:45:06 UTC | Alignment results cascade delete their bam qc results | 23 August 2013, 19:07:07 UTC |
509fd5e | Adam Coffman | 23 August 2013, 19:00:14 UTC | update expected test output | 23 August 2013, 19:00:14 UTC |
d720c63 | Dan Koboldt | 23 August 2013, 17:59:59 UTC | Update to allow VCF output option | 23 August 2013, 17:59:59 UTC |
b36d97c | APipe Tester | 23 August 2013, 17:10:20 UTC | Updated `gmt` tab completion. | 23 August 2013, 17:10:20 UTC |
66f485e | APipe Tester | 23 August 2013, 17:09:18 UTC | Updated `genome` tab completion. | 23 August 2013, 17:09:18 UTC |
40a566e | APipe Tester | 23 August 2013, 17:07:15 UTC | Updated class browser cache. | 23 August 2013, 17:07:15 UTC |
6b771f2 | Travis Abbott | 23 August 2013, 16:49:14 UTC | update PC burden test code | 23 August 2013, 16:49:58 UTC |
fc0ed6b | Nathan Nutter | 23 August 2013, 14:21:20 UTC | enable nounset later | 23 August 2013, 14:21:38 UTC |
9b7653c | APipe Tester | 22 August 2013, 22:48:08 UTC | Updated `genome` tab completion. | 22 August 2013, 22:48:08 UTC |
8de3247 | APipe Tester | 22 August 2013, 22:46:24 UTC | Updated class browser cache. | 22 August 2013, 22:46:24 UTC |
fa2fd54 | Nathan Nutter | 22 August 2013, 22:35:08 UTC | add genome-env CHANGELOG: Moved most of `genome-test-env` to a new command, `genome-env`, so people can use `genome-env` to setup for running builds, etc. with the correct UR and Workflow. They can also continue to use `genome-test-env` to setup for running tests which basically just turns off database commits in addition to running `genome-env`. | 22 August 2013, 22:38:02 UTC |
22064a3 | Nathan Nutter | 22 August 2013, 22:13:07 UTC | remove unused/incomplete command | 22 August 2013, 22:38:01 UTC |
eafe8cf | Feiyu Du | 22 August 2013, 22:18:46 UTC | remove use_error_rate_pileup and add error_rate_version for RnaSeq | 22 August 2013, 22:19:42 UTC |
0e5bbfe | APipe Tester | 22 August 2013, 21:38:56 UTC | updated graphite submodule to a20ecce | 22 August 2013, 21:38:56 UTC |
c3338e7 | Travis Abbott | 22 August 2013, 16:51:51 UTC | Merge commit '47bfd70e20b45afad8fdd4c88bbb0badaa6a6785' as 'lib/perl/Genome/Model/Tools/Germline/BurdenTest' | 22 August 2013, 16:51:51 UTC |
47bfd70 | Travis Abbott | 22 August 2013, 16:51:51 UTC | Squashed 'lib/perl/Genome/Model/Tools/Germline/BurdenTest/' content from commit b6d5eb4 git-subtree-dir: lib/perl/Genome/Model/Tools/Germline/BurdenTest git-subtree-split: b6d5eb456b61cada90b07ce9419a4545225bd45b | 22 August 2013, 16:51:51 UTC |
7aed89b | APipe Tester | 22 August 2013, 15:47:31 UTC | updated ur submodule to 5f86690 | 22 August 2013, 15:47:31 UTC |
be99232 | Nathan Nutter | 22 August 2013, 15:45:32 UTC | fixup! remove Genome::Model::Varaint and Genome::Model::BuildVariant Missed a reference to Genome::Model::BuildVariant. | 22 August 2013, 15:46:29 UTC |