| 67657e5 | Denis Yuen | 11 June 2018, 15:11:57 UTC | [maven-release-plugin] prepare release 1.4.4 | 11 June 2018, 15:11:57 UTC |
| 1124f0c | Denis Yuen | 11 June 2018, 15:04:40 UTC | Fix url and add tests (#1473) * Add a convenience script for expanding our confidential bundle * Disable build steps that are failing non-deterministically * Skip slow tests * These tests broken due to Gitlab dropping v3 | 11 June 2018, 15:04:40 UTC |
| 8435e47 | Denis Yuen | 05 June 2018, 20:37:44 UTC | Refresh fix (#1463) * Fix duplicate creation of test json for tools * Properly calculate relative paths for files endpoint * More tests | 05 June 2018, 20:37:44 UTC |
| 28e1481 | Andrew Duncan | 05 June 2018, 00:02:39 UTC | 1446/recursive imports wdl (#1453) * fix recursive imports * small cleanup * fix for infinite loop * Update WDLHandler.java * fixes for pr * changed list to set * changed set to hashmap * Update WDLHandler.java * moved pattern to a static final | 05 June 2018, 00:02:39 UTC |
| 4452e9b | Denis Yuen | 28 May 2018, 20:35:23 UTC | Merge branch 'hotfix/1.4.2' | 28 May 2018, 20:35:23 UTC |
| 2e2f266 | Denis Yuen | 28 May 2018, 20:30:46 UTC | [maven-release-plugin] prepare for next development iteration | 28 May 2018, 20:30:46 UTC |
| 704d680 | Denis Yuen | 28 May 2018, 20:30:41 UTC | [maven-release-plugin] prepare release 1.4.3 | 28 May 2018, 20:30:41 UTC |
| c280032 | Denis Yuen | 28 May 2018, 20:28:31 UTC | Fix odd state | 28 May 2018, 20:28:31 UTC |
| 07ba979 | Denis Yuen | 28 May 2018, 20:20:45 UTC | [maven-release-plugin] prepare for next development iteration | 28 May 2018, 20:20:45 UTC |
| 9c7c17d | Denis Yuen | 28 May 2018, 20:19:39 UTC | Revert "[maven-release-plugin] prepare release 1.4.2" This reverts commit 1db15ac62c03f39263a6bcabc0421d275dad0c4b. | 28 May 2018, 20:19:39 UTC |
| 37491af | Denis Yuen | 28 May 2018, 20:18:20 UTC | Merge branch 'hotfix/1.4.2' of github.com:ga4gh/dockstore into hotfix/1.4.2 | 28 May 2018, 20:18:20 UTC |
| 1db15ac | Denis Yuen | 28 May 2018, 20:16:34 UTC | [maven-release-plugin] prepare release 1.4.2 | 28 May 2018, 20:16:34 UTC |
| 4c3d5b5 | Denis Yuen | 28 May 2018, 20:11:55 UTC | Messed up generated urls (#1441) * Show TEST_CWL_FILE, TEST_WDL_FILE, PLAIN_... test parameter files for relative paths endpoint * More tests, flatten relative paths endpoint output * Change implementation, also allow containerfiles to be output * Refactor and get rid of table generation * Add tests and fix odd broken v1 call * Add more tests | 28 May 2018, 20:11:55 UTC |
| abea2ba | Andrew Duncan | 23 May 2018, 15:27:55 UTC | 1415/seven bridges support (#1433) * support for seven bridges docker reg * sbg images can have custom image registry paths * added test for sbg | 23 May 2018, 15:27:55 UTC |
| 4d1b201 | Andrew Duncan | 23 May 2018, 00:50:53 UTC | 1419/metadata issue (#1430) * handle metadata when default version is set * added test for issue 1419 | 23 May 2018, 00:50:53 UTC |
| d34d53a | Andrew Duncan | 16 April 2018, 15:07:57 UTC | include the io.github package from the client in the webservice | 26 April 2018, 19:06:34 UTC |
| 69f43cb | Denis Yuen | 20 April 2018, 19:37:32 UTC | Update LICENSE | 20 April 2018, 19:37:32 UTC |
| 0618036 | Andrew Duncan | 19 April 2018, 17:39:04 UTC | Dag test fix (#1350) * fix for cwl hints not working | 19 April 2018, 17:39:04 UTC |
| c604705 | Denis Yuen | 17 April 2018, 15:32:48 UTC | Remove localstack temporarily due to pip issue with their dependencies | 17 April 2018, 18:47:13 UTC |
| 978b28c | Denis Yuen | 10 April 2018, 14:52:08 UTC | Merge branch 'release/1.4.1' | 10 April 2018, 14:52:08 UTC |
| e281354 | Denis Yuen | 09 April 2018, 19:57:39 UTC | [maven-release-plugin] prepare for next development iteration | 09 April 2018, 19:57:39 UTC |
| 7d8116d | Denis Yuen | 09 April 2018, 19:57:34 UTC | [maven-release-plugin] prepare release 1.4.1 | 09 April 2018, 19:57:34 UTC |
| 771bd47 | Denis Yuen | 09 April 2018, 19:55:47 UTC | Iterate versions | 09 April 2018, 19:55:47 UTC |
| d198ea4 | Gary Luu | 09 April 2018, 19:52:37 UTC | Feature/1295/ga4 gh invalid id handling (#1296) * Handle invalid tool ID | 09 April 2018, 19:52:37 UTC |
| d6ca567 | Denis Yuen | 06 April 2018, 15:20:20 UTC | Test out fix for tool refresh issue | 06 April 2018, 15:20:20 UTC |
| beaa2d2 | Denis Yuen | 05 April 2018, 20:11:44 UTC | Merge branch 'master' into release/1.4.1 | 05 April 2018, 20:11:44 UTC |
| 457af72 | Denis Yuen | 05 April 2018, 20:11:31 UTC | Iterate version numbers | 05 April 2018, 20:11:31 UTC |
| 7fd7be5 | Denis Yuen | 05 April 2018, 20:00:53 UTC | Merge tag '1.4.0' [maven-release-plugin] copy for tag 1.4.0 | 05 April 2018, 20:00:53 UTC |
| 53cc8ae | Denis Yuen | 04 April 2018, 21:48:47 UTC | [maven-release-plugin] prepare for next development iteration | 04 April 2018, 21:48:47 UTC |
| 9dc87ae | Denis Yuen | 04 April 2018, 21:48:42 UTC | [maven-release-plugin] prepare release 1.4.0 | 04 April 2018, 21:48:42 UTC |
| b135a4b | Andrew Duncan | 04 April 2018, 21:45:54 UTC | fix for issue, also fix for another issue (#1277) * fix for #1268 | 04 April 2018, 21:45:54 UTC |
| a4a52c8 | Gary Luu | 04 April 2018, 19:40:55 UTC | Fix containerfile endpoint return type and also add dummy self_link h… (#1275) * Fix containerfile endpoint return type and also add dummy self_link header * Fix V2 ToolContainerfile to V1 ToolDockerfile conversion | 04 April 2018, 19:40:55 UTC |
| 81d8c68 | Gary Luu | 04 April 2018, 19:14:13 UTC | Feature/fix regression tests (#1251) * Fix client regression tests * Fix general regression IT * Enable regression tests * Use confidential data for regression tests too * Bypass issue #1264 * Remove test that was also removed in normal IT | 04 April 2018, 19:14:13 UTC |
| 46e878d | Denis Yuen | 03 April 2018, 18:18:21 UTC | [maven-release-plugin] prepare for next development iteration | 03 April 2018, 18:18:21 UTC |
| 29172f9 | Denis Yuen | 03 April 2018, 18:18:16 UTC | [maven-release-plugin] prepare release 1.4.0-rc.2 | 03 April 2018, 18:18:16 UTC |
| 459309d | Gary Luu | 03 April 2018, 17:03:54 UTC | Feature/test tool url ga4 gh (#1272) * Populate with test_tool_url with workflow path * Get has_checker and checker_url in GA4GH Tool * Update swagger, openapi.yaml, pom for new TRS | 03 April 2018, 17:03:54 UTC |
| 76299f7 | Gary Luu | 03 April 2018, 14:59:20 UTC | Help change (#1255) * Help change * Output proper error when --yaml used with WDL | 03 April 2018, 14:59:20 UTC |
| b562ddc | Denis Yuen | 03 April 2018, 14:52:18 UTC | Feature/trs validation fix (#1265) * Avoid nulls for validation check * Hook up test for validation fix | 03 April 2018, 14:52:18 UTC |
| 2468b92 | Denis Yuen | 03 April 2018, 14:49:19 UTC | Fix exit code for Cromwell (#1270) * Fix exit code for Cromwell * Add system rules for Cromwell tests | 03 April 2018, 14:49:19 UTC |
| 5ca56cb | Andrew Duncan | 03 April 2018, 13:17:42 UTC | block updating of descriptor type for a workflow if not a stub (#1262) * block updating of descriptor type for a workflow if not a stub | 03 April 2018, 13:17:42 UTC |
| 2eeecdd | Denis Yuen | 29 March 2018, 21:36:38 UTC | [maven-release-plugin] prepare for next development iteration | 29 March 2018, 21:36:38 UTC |
| 4ef1a93 | Denis Yuen | 29 March 2018, 21:36:33 UTC | [maven-release-plugin] prepare release 1.4.0-rc.1 | 29 March 2018, 21:36:33 UTC |
| 6ac5613 | Denis Yuen | 29 March 2018, 21:30:05 UTC | Fix on the webservice side for #1250 (#1252) * Fix on the webservice side for #1250 * Clear checker workflow when stubbing * Refresh issue and reassociation with checkers on unstub | 29 March 2018, 21:30:05 UTC |
| 88e7a7c | Andrew Duncan | 29 March 2018, 17:57:32 UTC | Feature/no toolname workflowname update (#1256) * cannot update toolname or workflowname from CLI or webservice * fix tests | 29 March 2018, 17:57:32 UTC |
| 1c4c526 | Andrew Duncan | 28 March 2018, 18:29:18 UTC | Feature/checker workflow tests (#1247) * fix for existing tests * added wdl test for checker workflows | 28 March 2018, 18:29:18 UTC |
| 12b32af | Denis Yuen | 23 March 2018, 20:31:40 UTC | [maven-release-plugin] prepare for next development iteration | 23 March 2018, 20:31:40 UTC |
| 7d99e60 | Denis Yuen | 23 March 2018, 20:31:36 UTC | [maven-release-plugin] prepare release 1.4.0-beta.3 | 23 March 2018, 20:31:36 UTC |
| a4c0674 | Gary Luu | 23 March 2018, 17:19:19 UTC | Feature/feature/1176/test old client (#1224) * Add ClientIT successful tests for old client * Add tests for GeneralIT * Tests for GeneralWorkflowIT * Fix for registry enum change * Move generalworkflowIT tests * Move to regression tests * Add test for workflow launch * Add tool launch * Remove regression tests from normal integration-test | 23 March 2018, 17:19:19 UTC |
| 3932057 | Andrew Duncan | 22 March 2018, 20:40:57 UTC | Feature/checker cli (#1238) Added Checker commands to the CLI. | 22 March 2018, 20:40:57 UTC |
| 0755ae6 | Denis Yuen | 20 March 2018, 16:52:06 UTC | Allow launch of unpublished tools and workflows with valid token (#1227) * Allow launch of unpublished tools and workflows with valid token * Add test launching unpublished tools * also fix issue with imports | 20 March 2018, 16:52:06 UTC |
| 91cfe5b | Andrew Duncan | 19 March 2018, 19:29:51 UTC | Feature/workflowname fix (#1234) Fixed issue with null workflow names creating checker workflows with the string null in the name. | 19 March 2018, 19:29:51 UTC |
| 2f284f8 | Denis Yuen | 19 March 2018, 14:55:45 UTC | Feature/trs hotfix (#1235) * odd fix to trs, test later * [maven-release-plugin] prepare release 1.4.0-beta.2 * [maven-release-plugin] prepare for next development iteration * Property copy issue with Booleans | 19 March 2018, 14:55:45 UTC |
| 86894e1 | Gary Luu | 16 March 2018, 15:31:45 UTC | Feature/1146/openapi generate (#1225) * Auto-generate openapi.yaml * Initial openapi.yaml * Install swagger2openapi * Specify version * Change phase to compile, should be ran after swagger generation * Update README.md | 16 March 2018, 15:31:45 UTC |
| 84c1c07 | Andrew Duncan | 15 March 2018, 19:37:09 UTC | Feature/migrate toolname nullable (#1229) Toolname can now be null and is no longer required, instead of using an empty string. | 15 March 2018, 19:37:09 UTC |
| 7013c6d | Denis Yuen | 14 March 2018, 17:19:44 UTC | [maven-release-plugin] prepare for next development iteration | 14 March 2018, 17:19:44 UTC |
| ae61cf1 | Denis Yuen | 14 March 2018, 17:19:40 UTC | [maven-release-plugin] prepare release 1.4.0-beta.0 | 14 March 2018, 17:19:40 UTC |
| 2b9bdb6 | Denis Yuen | 14 March 2018, 17:07:05 UTC | Migration fix for odd workflows with corrupt giturl (#1223) | 14 March 2018, 17:07:05 UTC |
| 2530d57 | Denis Yuen | 14 March 2018, 14:15:19 UTC | Feature/process improvements (#1221) * add script and template for re-generating run-tests when encrypting a new bundle * add method for ignoring yaml sort order when comparing new swagger.yaml generation | 14 March 2018, 14:15:19 UTC |
| 0b59791 | Andrew Duncan | 13 March 2018, 18:59:17 UTC | Feature/create checker workflow endpoint (#1209) Adds support for adding checker workflows. | 13 March 2018, 18:59:17 UTC |
| 0afe356 | Denis Yuen | 13 March 2018, 15:54:46 UTC | Feature/trs endpoint update (#1208) * Update server endpoints to current TRSV2 * Auto-generate much more of the server classes * Remove V2 from current classes (more trouble than it is worth) * Use mustache templates to insert paths, context, and @UnitOfWork * Silence migrations * Add source for generated classes for coverage | 13 March 2018, 15:54:46 UTC |
| e64a770 | Denis Yuen | 13 March 2018, 15:54:13 UTC | Lock down index update #1158 (#1217) * Lock down index update #1158 | 13 March 2018, 15:54:13 UTC |
| d13386c | Gary Luu | 12 March 2018, 15:02:37 UTC | Custom http user agent for CLI (#1196) | 12 March 2018, 15:02:37 UTC |
| 0648ded | Denis Yuen | 08 March 2018, 19:36:17 UTC | Feature/jar library versions (#1207) Checking in WIP, includes work on * specify version for Cromwell in config file #1137, bunny version * generic cwl-runner interface and toil as options for cwlrunner #1119 * prototype local launch for nextflow and show nextflow commands in ui #1041 * return nextflow resources from TRS and our own endpoints properly * squash liquibase migration otuput which is getting overwhelming | 08 March 2018, 19:36:17 UTC |
| f201199 | Gary Luu | 05 March 2018, 20:10:14 UTC | More tests, fix workflow id (#1205) | 05 March 2018, 20:10:14 UTC |
| 5558550 | Denis Yuen | 28 February 2018, 17:23:26 UTC | Merge tag '1.3.4' into develop [maven-release-plugin] copy for tag 1.3.4 | 28 February 2018, 17:23:26 UTC |
| af9352c | Denis Yuen | 27 February 2018, 22:25:31 UTC | Merge branch 'hotfix/1.3.4' | 27 February 2018, 22:25:31 UTC |
| a49554f | Andrew Duncan | 27 February 2018, 15:42:43 UTC | Release/1.4.0 alpha.8 (#1193) * [maven-release-plugin] prepare release 1.4.0-alpha.8 * [maven-release-plugin] prepare for next development iteration | 27 February 2018, 15:42:43 UTC |
| 492342e | Andrew Duncan | 27 February 2018, 02:39:19 UTC | Feature/convert enum to path (#1191) * Convert registry/source control to strings (path) * Removed custom docker registry path used for tools with custom paths | 27 February 2018, 02:39:19 UTC |
| f498161 | Denis Yuen | 26 February 2018, 20:18:33 UTC | Feature/non confidential unit tests (#1190) * Try out unit tests without confidential bundles * Simplify test handling for #1161 * Cobertura seems to be invoked improperly for unit tests * Tighten checks for tests | 26 February 2018, 20:18:33 UTC |
| c6d1dbf | Andrew Duncan | 26 February 2018, 19:54:46 UTC | Feature/checker workflow db changes (#1182) Added migrations for checker workflow, added properties to entry classes | 26 February 2018, 19:54:46 UTC |
| 60e318e | Denis Yuen | 23 February 2018, 21:02:13 UTC | Date everything with database-managed dates (#1185) * Date everything with database-managed dates Working on #331 * Add back disabled workflow version dates from source control | 23 February 2018, 21:02:13 UTC |
| 21b5194 | Andrew Duncan | 22 February 2018, 20:07:45 UTC | Feature/fix swagger positions (#1183) * fixed position of swagger properties | 22 February 2018, 20:07:45 UTC |
| e7183b0 | Andrew Duncan | 22 February 2018, 19:45:23 UTC | Release/1.4.0 alpha.7 (#1181) * [maven-release-plugin] prepare release 1.4.0-alpha.7 * [maven-release-plugin] prepare for next development iteration | 22 February 2018, 19:45:23 UTC |
| 3e91622 | Denis Yuen | 22 February 2018, 14:56:50 UTC | [maven-release-plugin] prepare for next development iteration | 22 February 2018, 14:56:50 UTC |
| 7441ae1 | Denis Yuen | 22 February 2018, 14:56:46 UTC | [maven-release-plugin] prepare release 1.3.6 | 22 February 2018, 14:56:46 UTC |
| 03b9515 | Denis Yuen | 22 February 2018, 14:55:19 UTC | Iterate laggard version numbers | 22 February 2018, 14:55:19 UTC |
| 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 |
