| 560234a | Denis Yuen | 21 February 2018, 22:21:33 UTC | [maven-release-plugin] prepare for next development iteration | 21 February 2018, 22:21:33 UTC |
| 7b03577 | Denis Yuen | 21 February 2018, 22:21:07 UTC | Revert "[maven-release-plugin] prepare release 1.3.5" This reverts commit 2c6ee4ee57c81e1f591b53cb818497518014f88b. | 21 February 2018, 22:21:07 UTC |
| 9846579 | Denis Yuen | 21 February 2018, 22:19:14 UTC | Merge branch 'hotfix/1.3.4' of github.com:ga4gh/dockstore into hotfix/1.3.4 | 21 February 2018, 22:19:14 UTC |
| 2c6ee4e | Denis Yuen | 21 February 2018, 22:18:57 UTC | [maven-release-plugin] prepare release 1.3.5 | 21 February 2018, 22:18:57 UTC |
| 550bd14 | Denis Yuen | 21 February 2018, 22:15:28 UTC | Secondary files continued (#1180) * Add test that says what we want for #1149 , will fail * Handle new cases with extra long extensions and without carets | 21 February 2018, 22:15:28 UTC |
| 79e8e10 | Andrew Duncan | 21 February 2018, 01:07:20 UTC | fix for get path (#1178) | 21 February 2018, 01:07:20 UTC |
| 96ea497 | Gary Luu | 20 February 2018, 14:26:18 UTC | Add custom log appender to webservice (#1173) * Add custom log appender to webservice * Remove logstash config file since it's in compose_setup | 20 February 2018, 14:26:18 UTC |
| c6dbf12 | Denis Yuen | 14 February 2018, 21:33:56 UTC | [maven-release-plugin] prepare for next development iteration | 14 February 2018, 21:33:56 UTC |
| 10bab2b | Denis Yuen | 14 February 2018, 21:33:51 UTC | [maven-release-plugin] prepare release 1.3.4 | 14 February 2018, 21:33:51 UTC |
| 164cdf5 | Gary Luu | 14 February 2018, 21:19:50 UTC | Feature/relative path with slashes (#1172) * Match all relative paths * Extend test to cover slash in relative path | 14 February 2018, 21:19:50 UTC |
| bb30836 | Andrew Duncan | 13 February 2018, 12:20:38 UTC | Release/1.4.0 alpha.6 (#1164) * [maven-release-plugin] prepare release 1.4.0-alpha.6 * [maven-release-plugin] prepare for next development iteration | 13 February 2018, 12:20:38 UTC |
| 99f3d01 | Andrew Duncan | 12 February 2018, 17:26:48 UTC | Feature/remove path (#1138) * Removes path field from entries * Rework of some path endpoints and DAO queries * Fix tests that include path * Change travis to run unit tests and integration tests separately | 12 February 2018, 17:26:48 UTC |
| a9d27b7 | Denis Yuen | 12 February 2018, 16:23:31 UTC | Investigate cwl features (#1154) * Import mixins * create directory structure properly when pulling down secondary files * Add test for mixins for #1151 * Add testing for #1151 symbolic links * Implement harvesting of description from include * needs follow-up with more robust implementation | 12 February 2018, 16:23:31 UTC |
| 57b95f0 | Denis Yuen | 07 February 2018, 21:01:07 UTC | Feature/message doi prototype (#1121) * Update AWS before experimenting with SQS * webservice -> SQS -> event-consumer done * awaiting zenodo and Docker prototype integration * rudimentary localstack testing prototype | 07 February 2018, 21:01:07 UTC |
| d37a899 | Denis Yuen | 07 February 2018, 18:33:41 UTC | More test fixing | 07 February 2018, 18:33:41 UTC |
| 518b1ba | Denis Yuen | 07 February 2018, 18:24:07 UTC | Fixing tests | 07 February 2018, 18:24:07 UTC |
| 4e35ec5 | Denis Yuen | 07 February 2018, 17:19:28 UTC | Fix formatting | 07 February 2018, 17:19:28 UTC |
| bfafa8e | Denis Yuen | 07 February 2018, 17:14:10 UTC | Feature/version dates (#1147) * Add the ability to retrieve workflow modification date * requires new github library and dropwizard update | 07 February 2018, 17:14:10 UTC |
| 06e4903 | Denis Yuen | 07 February 2018, 17:04:17 UTC | Handle #1149 and add test for it | 07 February 2018, 17:04:17 UTC |
| 6d5a707 | Gary Luu | 25 January 2018, 15:09:52 UTC | Feature/ga4 gh entry to ga4 gh tool fix (#1113) * Fix descriptor type in GA4GH * Refactor * Test for converting Entry to Tool * Fix tests for Travis * Sort verified sources * Expand test to include verified sources and verified checks * More tests * PR changes * PR fixes | 25 January 2018, 15:09:52 UTC |
| 47e0313 | Gary Luu | 25 January 2018, 15:07:53 UTC | CLI notifications (#1112) * Initial slack integration * Specify uuid in CLI, simplified message notifications * Handle failure notifications * Handle when no notifications webhook URL is specified * WDL launch notifications, move tests to seperate file * Generalize notifications client, same client but Slack-specific message * Check status upon NotificationsClient creation only * Change message structure * Always send notifications when url is present * Fast fail | 25 January 2018, 15:07:53 UTC |
| 90334f9 | Denis Yuen | 22 January 2018, 19:38:49 UTC | Is this still a thing? (#1122) | 22 January 2018, 19:38:49 UTC |
| cd13441 | Gary Luu | 19 January 2018, 14:45:34 UTC | Basic fix for incorrect descriptor type (#1115) | 19 January 2018, 14:45:34 UTC |
| dcf4acb | Gary Luu | 19 January 2018, 14:43:55 UTC | Feature/auto refresh all (#1110) * Return error when no GitHub token found * Return error when no token is found | 19 January 2018, 14:43:55 UTC |
| e2a1ada | Gary Luu | 16 January 2018, 19:41:36 UTC | Tests for different combination of workflow names and source code repo (#1106) * Tests for different combination of workflow names and source code repo * Adjust for new workflows added | 16 January 2018, 19:41:36 UTC |
| 96274b1 | Denis Yuen | 12 January 2018, 15:39:02 UTC | Feature/more nextflow mods (#1101) Working on #1041 Also updated to swagger 2.3.0 while we're at it (which introduces some style changes) and some refactoring to get prepared for DAG rendering on NextFlow when we're ready Still needed: DAG support CLI workflow execution | 12 January 2018, 15:39:02 UTC |
| 57ed0d2 | Gary Luu | 12 January 2018, 15:21:53 UTC | Listing files for GA4GH entries (#1098) * Include all newly generated methods/classes * Implement new endpoint * Swagger for the updated endpoint * Test endpoint * Remove the base metadata from swagger.yaml | 12 January 2018, 15:21:53 UTC |
| 98fece8 | Gary Luu | 11 January 2018, 20:12:23 UTC | Feature/issue 844 (#1095) * Search all similar paths * More relative paths testing * Don't clean database before each GA4GH read test | 11 January 2018, 20:12:23 UTC |
| a49c68a | Gary Luu | 10 January 2018, 15:56:30 UTC | Feature/trsv changes (#1093) * Append charset only when it isn't present * Add V2 endpoints, fixed endpoints to return correct object * Add newly generated swagger.yaml | 10 January 2018, 15:56:30 UTC |
| f9b72b5 | Denis Yuen | 08 January 2018, 20:59:01 UTC | Working on merge from hotfix | 08 January 2018, 20:59:01 UTC |
| 5df9987 | Denis Yuen | 08 January 2018, 20:58:34 UTC | Merge tag '1.3.3' into develop [maven-release-plugin] copy for tag 1.3.3 | 08 January 2018, 20:58:34 UTC |
| 1a5e904 | Denis Yuen | 08 January 2018, 20:36:52 UTC | Merge branch 'hotfix/1.3.3' | 08 January 2018, 20:36:52 UTC |
| 8fbb67c | Denis Yuen | 08 January 2018, 20:34:52 UTC | [maven-release-plugin] prepare for next development iteration | 08 January 2018, 20:34:52 UTC |
| 67e4d9d | Denis Yuen | 08 January 2018, 20:34:48 UTC | [maven-release-plugin] prepare release 1.3.3 | 08 January 2018, 20:34:48 UTC |
| 52fa2a0 | Denis Yuen | 05 January 2018, 21:25:20 UTC | [maven-release-plugin] prepare for next development iteration | 05 January 2018, 21:25:20 UTC |
| 1e1252b | Denis Yuen | 05 January 2018, 21:25:15 UTC | [maven-release-plugin] prepare release 1.4.0-alpha.4 | 05 January 2018, 21:25:15 UTC |
| f1d3696 | Denis Yuen | 05 January 2018, 21:23:32 UTC | Revert "[maven-release-plugin] prepare release 1.4.0-alpha.3" This reverts commit 7d768a2f96bf815b3b2614e9e548c7770a79779f. | 05 January 2018, 21:23:32 UTC |
| 7d768a2 | Denis Yuen | 05 January 2018, 21:05:26 UTC | [maven-release-plugin] prepare release 1.4.0-alpha.3 | 05 January 2018, 21:05:26 UTC |
| f68c864 | Denis Yuen | 05 January 2018, 21:02:15 UTC | This addresses an issue discovered with starting from an empty database (#1091) | 05 January 2018, 21:02:15 UTC |
| b012919 | Denis Yuen | 05 January 2018, 15:41:46 UTC | Catch and pass along more errors (#1090) * Catch and pass along more errors | 05 January 2018, 15:41:46 UTC |
| 7859737 | Charles Overbeck | 04 January 2018, 20:15:04 UTC | Improve error message for missing tag #1050 (#1088) * Error from dockstore-webservice now returns the tag name as part of its error message, so it's now `Invalid or missing tag <tag>.` instead of `Invalid version.`. * In ToolClient, only rely on the above message returned by dockstore-webservice and no longer prepend `Invalid tag`. This is the similar behavior when an entry, without the tag, is not present. | 04 January 2018, 20:15:04 UTC |
| 3d4c50a | Denis Yuen | 04 January 2018, 18:19:41 UTC | Add check for new metadata format and add test (#1087) * Add check for new metadata format and add test * Run hotfix and master tests on older VM | 04 January 2018, 18:19:41 UTC |
| b1579c9 | Denis Yuen | 03 January 2018, 19:25:13 UTC | Merge tag '1.3.2' into develop [maven-release-plugin] copy for tag 1.3.2 | 03 January 2018, 19:25:13 UTC |
| 90e785b | Denis Yuen | 03 January 2018, 19:23:54 UTC | Merge branch 'hotfix/1.3.2' | 03 January 2018, 19:23:54 UTC |
| 97a7053 | Denis Yuen | 03 January 2018, 19:06:45 UTC | Feature/parameters over http (#1081) * Implement json loading over http and add test | 03 January 2018, 19:06:45 UTC |
| 7fb1e36 | Gary Luu | 03 January 2018, 16:27:45 UTC | Feature/workflow to ga4gh fix (#1076) * Include registry in workflow path * Fix descriptor endpoint to return a property descriptor | 03 January 2018, 16:27:45 UTC |
| 0172157 | Denis Yuen | 02 January 2018, 20:18:54 UTC | this should detect a change to swagger.yaml (#1082) * this should detect a change to swagger.yaml * Fixed toolclient due to generated function parameter reordering, added new swagger | 02 January 2018, 20:18:54 UTC |
| 046daea | Denis Yuen | 21 December 2017, 18:55:09 UTC | Add odd missing testing resources | 21 December 2017, 18:55:09 UTC |
| bf5b733 | Denis Yuen | 21 December 2017, 18:23:25 UTC | [maven-release-plugin] prepare for next development iteration | 21 December 2017, 18:23:25 UTC |
| 635c405 | Denis Yuen | 21 December 2017, 18:23:20 UTC | [maven-release-plugin] prepare release 1.3.2 | 21 December 2017, 18:23:20 UTC |
| 7bbe32d | Denis Yuen | 21 December 2017, 18:17:02 UTC | Feature/nextflow experiment (#1067) * Refactoring refresh code * This fixes the odd travis-ci build issue by excluding jsr311 and silencing org.reflections * Cut down on unused code and add tests This gets NextFlow to the point that we index NextFlow config and the mainScript | 21 December 2017, 18:17:02 UTC |
| cfa8047 | Gary Luu | 21 December 2017, 17:09:15 UTC | Fix for workflow search SQL (#1063) * Change to null workflowname when empty * Convert empty string to null, not empty string constraint * Test refresh, manual publish, refreshAll | 21 December 2017, 17:09:15 UTC |
| 438cf33 | Denis Yuen | 21 December 2017, 17:07:20 UTC | Calculate language types for tools as well (#1078) | 21 December 2017, 17:07:20 UTC |
| 5b947f1 | Charles Overbeck | 20 December 2017, 19:32:08 UTC | Integration Tests on Mac Fix ga4gh/dockstore#1064 (#1069) Use -b instead of --bytes, as -b works on both BSD and GNU | 20 December 2017, 19:32:08 UTC |
| fad1716 | Charles Overbeck | 20 December 2017, 17:20:43 UTC | Exclude confidential tests ga4gh/dockstore#1068 (#1070) Add ConfidentialTest annotation to all tests that have a dependency on confidential data. CommonTestUtilities needs dockstoreTest.yml to be present, and that is only present with confidential data. I did try alternatively serving up a different .yml file, but the tests would then fail because of requirements for other confidential data, so just added the annotation to all tests that require dockstoreTest.yml. | 20 December 2017, 17:20:43 UTC |
| 79772b8 | Gary Luu | 20 December 2017, 16:48:19 UTC | Add allowable values to enum-like string (#1073) | 20 December 2017, 16:48:19 UTC |
| 36808f6 | Andrew Duncan | 19 December 2017, 20:57:34 UTC | [maven-release-plugin] prepare for next development iteration | 19 December 2017, 20:57:34 UTC |
| 0894b45 | Andrew Duncan | 19 December 2017, 20:57:29 UTC | [maven-release-plugin] prepare release 1.4.0-alpha.3 | 19 December 2017, 20:57:29 UTC |
| b2664da | Andrew Duncan | 19 December 2017, 20:14:56 UTC | fix registry bean to have enum name (#1074) * fix registry bean to have enum name | 19 December 2017, 20:14:56 UTC |
| 8e581c1 | Denis Yuen | 18 December 2017, 19:21:54 UTC | Fix tests | 18 December 2017, 19:21:54 UTC |
| f140ca2 | Denis Yuen | 14 December 2017, 22:18:03 UTC | WIP for #1072 | 14 December 2017, 22:18:03 UTC |
| 62eee9f | Denis Yuen | 14 December 2017, 21:36:08 UTC | Iterate | 14 December 2017, 21:36:08 UTC |
| 52285b9 | Denis Yuen | 14 December 2017, 21:09:13 UTC | [maven-release-plugin] prepare for next development iteration | 14 December 2017, 21:09:13 UTC |
| 4603dc0 | Denis Yuen | 14 December 2017, 21:09:09 UTC | [maven-release-plugin] prepare release 1.4.0-alpha.1 | 14 December 2017, 21:09:09 UTC |
| cb29be0 | Denis Yuen | 14 December 2017, 21:05:21 UTC | Iterate version number before standard release process | 14 December 2017, 21:05:21 UTC |
| ec75e43 | Denis Yuen | 14 December 2017, 19:45:44 UTC | Merge branch 'develop' of github.com:ga4gh/dockstore into develop | 14 December 2017, 19:45:44 UTC |
| a2bc682 | Denis Yuen | 13 December 2017, 18:15:49 UTC | This fixes the odd travis-ci build issue by excluding jsr311 and silencing org.reflections | 14 December 2017, 19:45:36 UTC |
| cffb1d8 | Andrew Duncan | 14 December 2017, 18:47:23 UTC | Feature/workflow add source control to path (#1062) * Update workflows to have source control in the path * Updated migrations for workflow source control * use deprecated dist | 14 December 2017, 18:47:23 UTC |
| 9281d52 | Denis Yuen | 11 December 2017, 22:23:54 UTC | Merge tag '1.3.1' into develop [maven-release-plugin] copy for tag 1.3.1 | 11 December 2017, 22:23:54 UTC |
| f2c15e9 | Denis Yuen | 11 December 2017, 22:20:42 UTC | Merge tag '1.3.1' [maven-release-plugin] copy for tag 1.3.1 | 11 December 2017, 22:20:42 UTC |
| e49d942 | Denis Yuen | 11 December 2017, 21:08:44 UTC | [maven-release-plugin] prepare release 1.3.1 | 11 December 2017, 21:08:44 UTC |
| 80b49dd | Denis Yuen | 08 December 2017, 21:32:11 UTC | [maven-release-plugin] prepare for next development iteration | 08 December 2017, 21:32:11 UTC |
| efc63df | Denis Yuen | 08 December 2017, 21:32:06 UTC | [maven-release-plugin] prepare release 1.3.1-rc.2 | 08 December 2017, 21:32:06 UTC |
| 6992b81 | Andrew Duncan | 08 December 2017, 17:40:53 UTC | Refresh hotfix (#1056) * fix for weird refresh bug * Add a warning message if the token is too old for github * Looks like some dependencies were missed, aborted update? | 08 December 2017, 17:40:53 UTC |
| cfde763 | Andrew Duncan | 05 December 2017, 21:02:43 UTC | fixed remaining poms | 05 December 2017, 21:02:43 UTC |
| 327a418 | Andrew Duncan | 05 December 2017, 20:59:40 UTC | fixed snapshot naming convention | 05 December 2017, 20:59:40 UTC |
| 8af0e22 | Andrew Duncan | 05 December 2017, 20:55:52 UTC | [maven-release-plugin] prepare for next development iteration | 05 December 2017, 20:55:52 UTC |
| 11b6e0e | Andrew Duncan | 05 December 2017, 18:07:27 UTC | Merge branch 'hotfix/1.3.1-SNAPSHOT' of github.com:ga4gh/dockstore into hotfix/1.3.1-SNAPSHOT | 05 December 2017, 18:07:27 UTC |
| b88b753 | Andrew Duncan | 05 December 2017, 18:04:07 UTC | Added some debug comments for refreshing workflows | 05 December 2017, 18:04:07 UTC |
| 63e502c | Denis Yuen | 05 December 2017, 16:44:56 UTC | [maven-release-plugin] prepare for next development iteration | 05 December 2017, 16:44:56 UTC |
| dd61ef1 | Denis Yuen | 05 December 2017, 16:44:52 UTC | [maven-release-plugin] prepare release 1.3.1-rc.0 | 05 December 2017, 16:44:52 UTC |
| 7d97a77 | Denis Yuen | 05 December 2017, 16:42:58 UTC | Revert "Iterate versions" This reverts commit 3a51e143474f972369fd12bd092116815eada625. | 05 December 2017, 16:42:58 UTC |
| 289953d | Denis Yuen | 05 December 2017, 16:40:33 UTC | Merge branch 'hotfix/1.3.1-SNAPSHOT' of github.com:ga4gh/dockstore into hotfix/1.3.1-SNAPSHOT | 05 December 2017, 16:40:33 UTC |
| 3a51e14 | Denis Yuen | 05 December 2017, 16:40:18 UTC | Iterate versions | 05 December 2017, 16:40:18 UTC |
| 6d32c7e | Denis Yuen | 29 November 2017, 16:56:08 UTC | Merge pull request #1039 from ga4gh/feature/testing_databases Feature/testing databases | 29 November 2017, 16:56:08 UTC |
| 13f65eb | Denis Yuen | 27 November 2017, 21:13:10 UTC | Delay this change for now | 27 November 2017, 21:13:10 UTC |
| 8e3611f | Denis Yuen | 27 November 2017, 19:48:55 UTC | Update swagger and flesh out registry response | 27 November 2017, 20:17:25 UTC |
| cccf576 | Denis Yuen | 27 November 2017, 16:27:12 UTC | Merge branch 'develop' into feature/testing_databases | 27 November 2017, 16:27:12 UTC |
| d757a2c | Denis Yuen | 24 November 2017, 21:25:56 UTC | Fix tests including mocked | 27 November 2017, 15:55:09 UTC |
| d1835a3 | Denis Yuen | 27 November 2017, 15:09:45 UTC | can now delete auto tools (#1035) | 27 November 2017, 15:09:45 UTC |
| 4c32926 | Denis Yuen | 24 November 2017, 20:47:30 UTC | Add script for creating proposed changes | 27 November 2017, 14:59:50 UTC |
| 9927dc2 | Denis Yuen | 24 November 2017, 19:51:46 UTC | Move to offline generation of swagger.yaml and WIP fixing tests * Fix migration test to be actually useful | 27 November 2017, 14:59:41 UTC |
| 9e401cf | Denis Yuen | 20 November 2017, 22:35:04 UTC | Add script and base for migrations * update secret archive * More test fixing | 27 November 2017, 14:59:24 UTC |
| 0c02918 | Denis Yuen | 20 November 2017, 15:48:49 UTC | Alter schema * update secret archive * Use new encrypted bundle * Add test enforcing that migration looks sane | 27 November 2017, 14:59:05 UTC |
| dc190b6 | Andrew Duncan | 21 November 2017, 18:48:08 UTC | can now delete auto tools (#1035) | 21 November 2017, 18:48:08 UTC |
| 0eba4fd | Denis Yuen | 17 November 2017, 21:11:46 UTC | Fix out of date readme (#1032) | 17 November 2017, 21:11:46 UTC |
| e4a3afd | Denis Yuen | 17 November 2017, 21:02:12 UTC | Update legacy.md | 17 November 2017, 21:02:12 UTC |
| 3083a87 | Denis Yuen | 09 November 2017, 18:34:02 UTC | Feature/multi experiment (#1021) * Concurrency for file provisioning with very basic progress display * Some tests to check for deadlock which can occur with vfs file size call | 09 November 2017, 18:34:02 UTC |
| 46f80b8 | Denis Yuen | 03 November 2017, 23:35:45 UTC | Add more useful message for ui2 (#1008) | 03 November 2017, 23:35:45 UTC |
| e897c64 | Gary Luu | 03 November 2017, 16:26:39 UTC | Feature/no content (#1005) * Appease swagger codegen * Check tokens before refresh all tools * Check tokens * Fix 1 test * Exit code expected on system exit * Longer error message | 03 November 2017, 16:26:39 UTC |
