| 2bd9527 | apregier | 21 November 2014, 00:17:37 UTC | Merge pull request #238 from apregier/add_required_experts_docs Add required interpreters and experts section to reporter docs I am merging quickly to try to get this in a snapshot before our presentation tomorrow. | 21 November 2014, 00:17:37 UTC |
| 4b9e01a | David Morton | 21 November 2014, 00:09:20 UTC | Merge pull request #236 from davidlmorton/process_vr Make VariantReporting::Command::CreateReport use Genome::Process | 21 November 2014, 00:09:20 UTC |
| 612ab35 | apregier | 21 November 2014, 00:08:28 UTC | Rename methods requires_interpreters and requires_experts | 21 November 2014, 00:08:28 UTC |
| d98b23b | apregier | 20 November 2014, 23:26:09 UTC | Add required interpreters and experts section to reporter docs | 20 November 2014, 23:26:09 UTC |
| f2f2128 | Adam Coffman | 20 November 2014, 23:23:47 UTC | Merge pull request #237 from acoffman/bless_new_build Bless new test build | 20 November 2014, 23:23:47 UTC |
| f25f3c6 | apregier | 20 November 2014, 23:20:52 UTC | Merge pull request #233 from apregier/no_docs_for_transient Don't display transient properties | 20 November 2014, 23:20:52 UTC |
| 5511601 | Adam Coffman | 20 November 2014, 23:11:20 UTC | bless new test build | 20 November 2014, 23:11:20 UTC |
| 8000eb7 | apregier | 20 November 2014, 17:47:37 UTC | Don't display transient properties | 20 November 2014, 23:09:20 UTC |
| e35c0dc | dmorton | 20 November 2014, 22:43:02 UTC | Update docs | 20 November 2014, 22:43:02 UTC |
| cead689 | dmorton | 20 November 2014, 22:32:41 UTC | Make transients optional | 20 November 2014, 22:32:41 UTC |
| b8e1cf8 | dmorton | 20 November 2014, 21:40:12 UTC | Merge v3 and v4 into v5 test-data | 20 November 2014, 21:40:12 UTC |
| 083b0cf | dmorton | 20 November 2014, 21:23:46 UTC | Merge branch 'master' of github.com:genome/genome into process_vr Conflicts: lib/perl/Genome/VariantReporting/Suite/Joinx/Homopolymer/Expert.t | 20 November 2014, 21:23:46 UTC |
| becd9d4 | Susanna Siebert | 20 November 2014, 20:27:54 UTC | Merge pull request #222 from susannasiebert/component_descriptions Add documentation (doc lines) to variant reporting components | 20 November 2014, 20:27:54 UTC |
| cf6b506 | dmorton | 20 November 2014, 20:15:17 UTC | Add 'genome process list' command | 20 November 2014, 20:21:47 UTC |
| 18c8862 | dmorton | 20 November 2014, 19:36:30 UTC | CHANGELOG Remove output_directory property from CreateReport The 'genome variant-reporting create-report' command no longer takes an 'ouptut-directory'. The reports will be saved to a disk-allocation instead. To obtain symlinks to the reports run 'genome process symlink-result'. | 20 November 2014, 20:21:47 UTC |
| 6271c54 | dmorton | 20 November 2014, 20:06:28 UTC | Create command to symlink results of a Genome::Process | 20 November 2014, 20:21:47 UTC |
| dab4c0c | dmorton | 19 November 2014, 03:57:28 UTC | Update expected xml to expect process_id | 20 November 2014, 20:17:51 UTC |
| 9486112 | dmorton | 19 November 2014, 01:43:07 UTC | Pass process_id to Commands It will be used to set up appropriate SoftwareResult::User relationships. | 20 November 2014, 20:17:51 UTC |
| fee4328 | dmorton | 18 November 2014, 23:41:34 UTC | Allow Genome::Process to handle log-file location. | 20 November 2014, 20:17:51 UTC |
| b95ba2c | dmorton | 18 November 2014, 22:09:37 UTC | Make VariantReporting::Process::CreateReport | 20 November 2014, 20:17:51 UTC |
| 7322207 | Jim Weible | 20 November 2014, 19:49:57 UTC | Merge pull request #224 from jweible/AUE-305 Analysis Project Status Changes | 20 November 2014, 19:49:57 UTC |
| 330b011 | Susanna Siebert | 20 November 2014, 17:43:58 UTC | update expected lister test data | 20 November 2014, 19:16:57 UTC |
| af32e31 | Susanna Siebert | 20 November 2014, 17:27:50 UTC | documentation for reporters | 20 November 2014, 19:16:39 UTC |
| 87c9c62 | Susanna Siebert | 20 November 2014, 19:16:05 UTC | Merge branch 'master' into component_descriptions Conflicts: lib/perl/Genome/VariantReporting/Suite/BamReadcount/Adaptor.pm | 20 November 2014, 19:16:05 UTC |
| 92b122c | David Morton | 20 November 2014, 18:59:29 UTC | Merge pull request #225 from davidlmorton/misc_fixes Some miscellaneous fixes | 20 November 2014, 18:59:29 UTC |
| 2ccc73a | dmorton | 20 November 2014, 18:41:52 UTC | Fix merge mistake (missing },) | 20 November 2014, 18:41:52 UTC |
| d0b49ca | dmorton | 20 November 2014, 18:04:25 UTC | Merge branch 'master' of github.com:genome/genome into misc_fixes Conflicts: lib/perl/Genome/VariantReporting/Framework/ReportResult.pm | 20 November 2014, 18:04:25 UTC |
| 423238b | apregier | 20 November 2014, 17:46:03 UTC | Merge pull request #223 from apregier/improve-showdocs-cli Allow singular versions of component types | 20 November 2014, 17:46:03 UTC |
| 0fdcde8 | Jim Weible | 20 November 2014, 17:00:45 UTC | fix property name | 20 November 2014, 17:00:45 UTC |
| 0c4c81d | Jim Weible | 20 November 2014, 16:04:19 UTC | remove extra space | 20 November 2014, 16:04:19 UTC |
| ad3d60c | Thomas B. Mooney | 20 November 2014, 15:54:20 UTC | Merge pull request #230 from tmooney/use_test_data Use fake data for this test. (Except the reference...) | 20 November 2014, 15:54:20 UTC |
| 2cd448e | Thomas B. Mooney | 20 November 2014, 15:41:24 UTC | Merge pull request #220 from tmooney/add_menuitem_relations Add accessors to configs and projects using the menu item. | 20 November 2014, 15:41:24 UTC |
| 17d80ec | Jim Weible | 20 November 2014, 15:30:32 UTC | remove the other unnecessary "in" | 20 November 2014, 15:30:32 UTC |
| 8e6a749 | Jim Weible | 20 November 2014, 15:26:02 UTC | remove unnecessary "in" | 20 November 2014, 15:26:02 UTC |
| 6a3ef6d | Jim Weible | 20 November 2014, 15:23:40 UTC | remove references to removed flag and make the test assumptions make sense | 20 November 2014, 15:23:40 UTC |
| 86607d4 | Thomas Mooney | 20 November 2014, 14:44:46 UTC | Use fake data for this test. (Except the reference...) | 20 November 2014, 14:44:46 UTC |
| f844d04 | Susanna Siebert | 20 November 2014, 14:36:38 UTC | bugfixes and other minor improvements | 20 November 2014, 14:36:38 UTC |
| 74942f4 | Susanna Siebert | 20 November 2014, 14:31:06 UTC | bump homopolymer test data version | 20 November 2014, 14:31:06 UTC |
| ddfa76f | Susanna Siebert | 20 November 2014, 14:30:47 UTC | rename homo-polymer to homopolymer | 20 November 2014, 14:30:47 UTC |
| da585ea | Susanna Siebert | 20 November 2014, 14:13:38 UTC | rename HomoPolymer to Homopolymer | 20 November 2014, 14:13:38 UTC |
| b41fa0c | Susanna Siebert | 20 November 2014, 13:59:41 UTC | use q{} instead of escaping ' | 20 November 2014, 13:59:41 UTC |
| c05b79a | APipe Tester | 20 November 2014, 13:20:37 UTC | Updated `genome` tab completion. | 20 November 2014, 13:20:37 UTC |
| 94908d7 | APipe Tester | 20 November 2014, 13:17:09 UTC | Updated class browser cache. | 20 November 2014, 13:17:09 UTC |
| db5404c | dmorton | 19 November 2014, 21:52:55 UTC | Fix method signature | 19 November 2014, 21:52:55 UTC |
| 44e0f67 | David Morton | 19 November 2014, 21:29:38 UTC | Merge pull request #214 from davidlmorton/process_run Genome::Processes can run and be viewed | 19 November 2014, 21:29:38 UTC |
| 3980446 | Jim Weible | 19 November 2014, 20:42:43 UTC | correctly call the property analysis_projects and deal with the is_many | 19 November 2014, 20:42:43 UTC |
| 7f3dcdb | Nathaniel Nutter | 19 November 2014, 20:12:38 UTC | Merge pull request #221 from nnutter/misc updated genome-snapshot-deps URL | 19 November 2014, 20:12:38 UTC |
| 9a800ea | Jim Weible | 19 November 2014, 20:08:20 UTC | add template status for AnP | 19 November 2014, 20:08:20 UTC |
| 7211dd3 | Jim Weible | 19 November 2014, 20:07:48 UTC | remove deprecated approved status | 19 November 2014, 20:07:48 UTC |
| 37aac61 | Jim Weible | 19 November 2014, 20:00:13 UTC | Reqire reasonable analysis project statuses when adding models and remove means to subvert this check | 19 November 2014, 20:00:13 UTC |
| 1e26b7a | Jim Weible | 19 November 2014, 19:59:23 UTC | require a reasonable status for an analysis project before we screw with it | 19 November 2014, 19:59:23 UTC |
| ac28416 | dmorton | 19 November 2014, 19:17:15 UTC | Correct syntax with validate validate_pos(@_, OBJECT) is not the same as validate_Pos(@_, {type => OBJECT}). The former only validates that it is not undef, while the later ensures that it is an OBJECT. | 19 November 2014, 19:44:29 UTC |
| 4f2e33f | dmorton | 19 November 2014, 19:09:21 UTC | Eliminate need to create and execute coderefs | 19 November 2014, 19:44:22 UTC |
| 11532f2 | dmorton | 19 November 2014, 18:05:58 UTC | Only store md5_hex of plan_json and provider_json These values can easily exceed the 1000 character limit for these columns. | 19 November 2014, 19:44:13 UTC |
| 4900b11 | dmorton | 19 November 2014, 03:19:08 UTC | Fix return from catch block With Try::Tiny if you return from the catch block it only returns from the catch, not from the subroutine the catch is in. | 19 November 2014, 19:44:02 UTC |
| 3782ce7 | dmorton | 18 November 2014, 22:10:44 UTC | Delete temporarily constructed objects. | 19 November 2014, 19:43:49 UTC |
| 020e2ba | apregier | 19 November 2014, 19:43:03 UTC | Allow singular versions of component types This makes the command line make more sense when you are looking at the detailed view for a single component | 19 November 2014, 19:43:03 UTC |
| 804be33 | Susanna Siebert | 19 November 2014, 19:01:45 UTC | remove unneeded parameter | 19 November 2014, 19:01:45 UTC |
| 3458cf5 | Susanna Siebert | 19 November 2014, 19:01:31 UTC | bugfix: assignment of reference_fasta and alt_fasta was swapped | 19 November 2014, 19:01:31 UTC |
| 06b5cc5 | Susanna Siebert | 19 November 2014, 19:00:50 UTC | add vcf_id and vcf_description to filters | 19 November 2014, 19:00:50 UTC |
| 9ff2875 | Susanna Siebert | 19 November 2014, 19:00:13 UTC | Add documentation for parameters in Generic filters | 19 November 2014, 19:00:13 UTC |
| 5e1e1c6 | Susanna Siebert | 19 November 2014, 18:59:31 UTC | Add documentation for parameters in Vep related modules | 19 November 2014, 18:59:31 UTC |
| 1407468 | Susanna Siebert | 19 November 2014, 18:58:17 UTC | Add documention for parameters in Joinx related experts/adaptors | 19 November 2014, 18:58:17 UTC |
| 5d1bd24 | Susanna Siebert | 19 November 2014, 18:57:42 UTC | Add documentation for parameters in FPKM expert/adaptor | 19 November 2014, 18:57:42 UTC |
| 53c8c93 | Susanna Siebert | 19 November 2014, 18:57:11 UTC | Add documentation for parameters in FlankingRegion expert/adaptor | 19 November 2014, 18:57:11 UTC |
| 9dff9bd | Susanna Siebert | 19 November 2014, 18:56:35 UTC | Add documentation for parameters in BamReadcount related modules | 19 November 2014, 18:56:35 UTC |
| a08878b | Susanna Siebert | 19 November 2014, 18:55:00 UTC | General doc line for interpreters | 19 November 2014, 18:55:00 UTC |
| 1e96bd9 | Susanna Siebert | 19 November 2014, 18:52:17 UTC | General doc line for filters | 19 November 2014, 18:52:17 UTC |
| c36570a | Susanna Siebert | 19 November 2014, 18:49:57 UTC | General doc line for Adaptors/Experts | 19 November 2014, 18:49:57 UTC |
| 6448512 | apregier | 19 November 2014, 18:34:48 UTC | Merge pull request #211 from apregier/vr-show-docs VR show docs | 19 November 2014, 18:34:48 UTC |
| f51ca5b | Nathaniel Nutter | 19 November 2014, 17:58:14 UTC | Merge pull request #218 from nnutter/misc owner on GMSchema is optional | 19 November 2014, 17:58:14 UTC |
| d23d4f3 | Nathaniel Nutter | 19 November 2014, 17:56:59 UTC | updated genome-snapshot-deps URL genome-snapshot-deps has been migrated to GitHub so this updated the URL to point at the new location. | 19 November 2014, 17:56:59 UTC |
| e3f5398 | Jim Weible | 19 November 2014, 16:59:11 UTC | Fail when adding instrument-data to stuff that is done or archived or otherwise should not be added to | 19 November 2014, 16:59:11 UTC |
| 00508a9 | apregier | 19 November 2014, 16:49:01 UTC | Extract methods to clean up doc formating for properties Also, only say a property is undocumented if none of the doc fields are filled in | 19 November 2014, 16:49:01 UTC |
| c46a392 | Jim Weible | 19 November 2014, 16:41:16 UTC | remove deprecated "Approved" status | 19 November 2014, 16:41:16 UTC |
| e0f1d01 | Jim Weible | 19 November 2014, 16:40:40 UTC | Only CQID analysis projects that are "In Progress" | 19 November 2014, 16:40:40 UTC |
| cd1c62c | Jim Weible | 19 November 2014, 16:39:44 UTC | Add a Template status for Analysis Projects | 19 November 2014, 16:39:44 UTC |
| 8f57d09 | Adam Coffman | 19 November 2014, 16:29:49 UTC | Merge pull request #219 from acoffman/remove_cell_type_from_sync Remove cell_type from GMS | 19 November 2014, 16:29:49 UTC |
| 705243f | apregier | 19 November 2014, 16:28:24 UTC | This code was just copied over and is not really needed | 19 November 2014, 16:28:24 UTC |
| f5a381f | apregier | 19 November 2014, 16:25:43 UTC | is_structural should already exclude id properties | 19 November 2014, 16:25:43 UTC |
| f96aa5f | apregier | 19 November 2014, 16:24:19 UTC | Clarify hash construction | 19 November 2014, 16:24:19 UTC |
| dbe5df2 | apregier | 19 November 2014, 16:17:44 UTC | Simplify property lookup | 19 November 2014, 16:17:44 UTC |
| c81850a | apregier | 19 November 2014, 16:12:45 UTC | WithTranslatedInputs inherits from Component::Base These generic classes also need the is_structural attribute on their properties | 19 November 2014, 16:12:45 UTC |
| d9291df | Thomas B. Mooney | 19 November 2014, 15:38:10 UTC | Merge pull request #216 from tmooney/minor_import_fix Use ceiling when estimating needed disk space for imports | 19 November 2014, 15:38:10 UTC |
| 56317fe | Thomas Mooney | 19 November 2014, 15:36:17 UTC | Add accessors to configs and projects using the menu item. This allows usage such as: genome analysis-project create --analysis-menu-items \ analysis_projects.id=12345 to copy all menu items to a new project. | 19 November 2014, 15:36:17 UTC |
| e3c8ef6 | Adam Coffman | 18 November 2014, 23:50:04 UTC | update number of expected misc update entries | 18 November 2014, 23:50:04 UTC |
| af6ac68 | Adam Coffman | 18 November 2014, 23:49:19 UTC | update number of properties to copy | 18 November 2014, 23:49:19 UTC |
| a5a1914 | Adam Coffman | 18 November 2014, 23:47:13 UTC | update test data dir for UpdateAnalysis | 18 November 2014, 23:47:13 UTC |
| 1ede725 | Adam Coffman | 18 November 2014, 23:40:42 UTC | remove cell_type value from expected output | 18 November 2014, 23:40:42 UTC |
| 4e20142 | Adam Coffman | 18 November 2014, 23:04:06 UTC | remove trailing tabs | 18 November 2014, 23:04:06 UTC |
| f21b3be | Adam Coffman | 18 November 2014, 22:53:52 UTC | remove cell_type from ClinSeq commands | 18 November 2014, 22:53:52 UTC |
| de54a2b | Adam Coffman | 18 November 2014, 22:53:30 UTC | update metadata expected outputs | 18 November 2014, 22:53:30 UTC |
| 0272de8 | Adam Coffman | 18 November 2014, 22:53:15 UTC | remove cell_type from export commands | 18 November 2014, 22:53:15 UTC |
| 89f7a5d | Adam Coffman | 18 November 2014, 22:52:09 UTC | remove cell_type from views | 18 November 2014, 22:52:45 UTC |
| 2bdea0c | Adam Coffman | 18 November 2014, 22:51:41 UTC | remove cell_type attribute from sample classes | 18 November 2014, 22:51:41 UTC |
| e7f79b5 | Adam Coffman | 18 November 2014, 22:51:05 UTC | remove cell_type from sync classes | 18 November 2014, 22:51:05 UTC |
| 1935787 | Nathaniel Nutter | 18 November 2014, 20:52:39 UTC | owner on GMSchema is optional When using the GENOME_TEST_FILLDB feature this object fails error checking due to `owner` being `undef`. To correct this the `owner` should be labeled as optional. | 18 November 2014, 20:52:39 UTC |
| f2ddd2a | apregier | 18 November 2014, 16:34:25 UTC | Don't compare warning messages | 18 November 2014, 16:35:05 UTC |
| 6b48bd7 | Thomas Mooney | 18 November 2014, 15:29:58 UTC | Spelling: excute to execute. | 18 November 2014, 16:05:52 UTC |
| 6a7dc44 | Thomas Mooney | 18 November 2014, 15:26:05 UTC | Use ceiling when estimating needed disk space. (In my case, I was testing with a file <1KB in size and it estimated needing 0 disk, which is clearly too small.) | 18 November 2014, 16:05:51 UTC |
