| 593cd01 | Denis Yuen | 23 May 2018, 19:45:51 UTC | [maven-release-plugin] prepare release 1.5.0-alpha.1 | 23 May 2018, 19:45:51 UTC |
| 2186ac0 | Gary Luu | 22 May 2018, 16:59:55 UTC | Feature/1370/login with google (#1424) * Initial implementation * Use oauth2 api, don't error on updateMetadata when using google * Check auth user for Github * Update google user profile * Allow GitHub and Google to co-exist * Add prefix for all google accounts (keep github the same) * Update dockstore.yml * Make google optional * Renaming, update Google token * update secret archive * Add encrypt.sh * Add @NotEmpty | 22 May 2018, 16:59:55 UTC |
| d9ca0cc | Denis Yuen | 22 May 2018, 15:27:34 UTC | commit ids (#1429) * Add commit id column and reduce migration false positives * Minor performance improvement for tool refresh * Tests for commit id | 22 May 2018, 15:27:34 UTC |
| a2503cc | Denis Yuen | 18 May 2018, 18:09:44 UTC | Hookup and tests for WDL metadata (#1426) * Hookup and tests for WDL metadata. * will likely need tests to make this more robust for malformed WDL * Exclude SlowTests * Minor performance improvement for tool refresh | 18 May 2018, 18:09:44 UTC |
| f348850 | Denis Yuen | 17 May 2018, 18:18:21 UTC | Feature/nextflow temporary dag tool listing (#1425) * Save WIP Nextflow handler for DAG and tool listing * Add tests for nextflow dag and tool listing * Override detected swagger type to get rid of odd issue * Typing things and adding documentation in prep for refactor | 17 May 2018, 18:18:21 UTC |
| d4dd502 | Andrew Duncan | 15 May 2018, 19:56:03 UTC | Feature/entry type endpoint restrictions (#1423) * extension of hosted workflows * restricted use of some endpoints on hosted workflows * fix failing tests | 15 May 2018, 19:56:03 UTC |
| 705849f | Gary Luu | 11 May 2018, 14:55:43 UTC | Feature/864/file format search (#1383) * Extract file formats * Add tests * Add FileFormat DAO and FileFormat | 11 May 2018, 14:55:43 UTC |
| a3ff147 | Denis Yuen | 10 May 2018, 20:06:02 UTC | Minimize temp files for #1404 (#1409) | 10 May 2018, 20:06:02 UTC |
| 13835e3 | Denis Yuen | 10 May 2018, 20:05:45 UTC | Record who edited to create a revision of a workflow/tool (#1408) * also test and migration | 10 May 2018, 20:05:45 UTC |
| 205d6a4 | Denis Yuen | 10 May 2018, 18:11:55 UTC | Implement for gitlab and add test (#1406) * Implement tag and branch tracking for gitlab and add test * also use a new library for gitlab | 10 May 2018, 18:11:55 UTC |
| d5759aa | Andrew Duncan | 08 May 2018, 17:00:35 UTC | added patch to allowed verbs (#1392) | 08 May 2018, 17:00:35 UTC |
| e89ce2e | Andrew Duncan | 03 May 2018, 19:02:32 UTC | Feature/cromwell update (#1388) * added tests for issue 1211, update cromwell to 30.2 | 03 May 2018, 19:02:32 UTC |
| e262dca | Denis Yuen | 01 May 2018, 22:12:00 UTC | Feature/crud dates (#1382) * Add dates and hook up workflow ownership properly | 01 May 2018, 22:12:00 UTC |
| 31d6333 | Denis Yuen | 30 April 2018, 18:31:49 UTC | Fix merge problems | 01 May 2018, 18:52:16 UTC |
| 2e012ab | Denis Yuen | 30 April 2018, 16:43:20 UTC | More elastic manager update | 01 May 2018, 18:52:16 UTC |
| 53f26aa | Denis Yuen | 27 April 2018, 20:55:47 UTC | Moved some code to avoid cyclic dependency * Before this, swagger-java-client depends on the webservice which * depends on the dockstore-client which depends on the * swagger-java-client, so you'd need to build twice for updates, once to * generate swagger.yaml and again to actually get a generated client * from it | 01 May 2018, 18:52:16 UTC |
| 295ac33 | Denis Yuen | 27 April 2018, 20:04:23 UTC | Add tests | 01 May 2018, 18:52:16 UTC |
| 66d50e9 | Denis Yuen | 27 April 2018, 16:15:40 UTC | More generics cleanup of casting | 01 May 2018, 18:52:16 UTC |
| b5aeca9 | Denis Yuen | 27 April 2018, 14:43:42 UTC | Locally functional WIP * needs testing and cleanup | 01 May 2018, 18:52:16 UTC |
| 9fcd228 | Denis Yuen | 26 April 2018, 15:51:45 UTC | Remove content from overall calls for homepage | 01 May 2018, 18:52:16 UTC |
| 905d3fb | Denis Yuen | 26 April 2018, 15:06:28 UTC | Remove admin only endpoint | 01 May 2018, 18:52:16 UTC |
| beb2c59 | Andrew Duncan | 30 April 2018, 18:20:42 UTC | Feature/wdl4s update (#1377) * update wdl4s from 0.6 to 0.15 | 30 April 2018, 18:20:42 UTC |
| ad4b177 | Denis Yuen | 25 April 2018, 15:36:01 UTC | Feature/record ref type (#1362) * also refactor all methods in SourceCodeRepoInterface to use repositoryIDs for future simplification * Tighten enforcer rules * Fix typo in gitignore * Add tests and fix tests for branch detection for tools and workflows * Add bitbucket branch support * properly type token source * properly type workflow sourcecontrol | 25 April 2018, 15:36:01 UTC |
| 564e0a1 | Gary Luu | 24 April 2018, 14:42:13 UTC | Sort endpoints in swagger-ui (#1359) | 24 April 2018, 14:42:13 UTC |
| f134b91 | Gary Luu | 24 April 2018, 14:01:50 UTC | Feature/1220/requirements file (#1349) * 2 requirements files for python 2.x and 3.x * Add endpoint to check runner dependencies * Add client commands * Remove localstack temporarily due to pip issue with their dependencies | 24 April 2018, 14:01:50 UTC |
| 37e139e | Andrew Duncan | 23 April 2018, 18:57:25 UTC | fixed return issue (#1355) | 23 April 2018, 18:57:25 UTC |
| 6fbeeba | Denis Yuen | 23 April 2018, 18:00:13 UTC | Standardize model boilerplate (#1356) * Standardize comparing, tostring, equals, and hashcode for all model * Organize third party licenses in anticipation of more * remove un-unused admin method * The cli should not die on permissions check if webservice is down | 23 April 2018, 18:00:13 UTC |
| 2bf22d6 | Denis Yuen | 20 April 2018, 19:38:43 UTC | Update LICENSE | 20 April 2018, 19:38:43 UTC |
| e270e1c | Denis Yuen | 20 April 2018, 19:37:57 UTC | Update LICENSE | 20 April 2018, 19:37:57 UTC |
| c3232d3 | Andrew Duncan | 20 April 2018, 16:19:46 UTC | Feature/convert manual to auto (#1352) * manual tools that can be converted to auto are now converted | 20 April 2018, 16:19:46 UTC |
| 602c17a | Gary Luu | 19 April 2018, 18:10:00 UTC | Feature/1297/delete tag then refresh (#1348) * Add test * Remove localstack temporarily due to pip issue with their dependencies | 19 April 2018, 18:10:00 UTC |
| 8c96710 | Denis Yuen | 18 April 2018, 21:53:39 UTC | Update various dependencies (#1345) * remove extra yaml processing library since we had two * remove duplicate httpclient dependency * Fix up mocked test for new updates | 18 April 2018, 21:53:39 UTC |
| a6e5425 | Andrew Duncan | 18 April 2018, 18:57:49 UTC | Feature/stub confidential migrations (#1343) Adds stub confidential migrations files to appease running db migrations. | 18 April 2018, 18:57:49 UTC |
| a87db6a | Denis Yuen | 18 April 2018, 17:16:21 UTC | Update to more up-to-date maven plugin versions (#1340) * Update to more up-to-date maven plugin versions * Remove localstack temporarily due to pip issue with their dependencies | 18 April 2018, 17:16:21 UTC |
| 2ee9087 | Denis Yuen | 17 April 2018, 19:51:35 UTC | Fix toil with update to toil 3.15.0 (#1339) * Fix toil with update to toil 3.15.0 * also toil seems to handle hints differently * Toil doesn't seem to include cwl-runner * Remove localstack temporarily due to pip issue with their dependencies | 17 April 2018, 19:51:35 UTC |
| 9253b65 | Denis Yuen | 17 April 2018, 14:17:12 UTC | Feature/dropwizard update (#1341) * Update dropwizard to 1.3.1 | 17 April 2018, 14:17:12 UTC |
| 1c12485 | Denis Yuen | 17 April 2018, 14:11:41 UTC | Split out testing of dockstore-client, switch to jacoco (#1329) * Split out dockstore-client under its own skip variable * Remove deploy until we have this nailed down * Looks like cobertura is dead, give jacoco a try * Potential jacoco aggregation based on https://github.com/jacoco/jacoco/wiki/MavenMultiModule | 17 April 2018, 14:11:41 UTC |
| d2010d8 | Andrew Duncan | 16 April 2018, 19:35:55 UTC | include the io.github package from the client in the webservice (#1335) | 16 April 2018, 19:35:55 UTC |
| 7879c32 | Denis Yuen | 16 April 2018, 17:43:17 UTC | Check for provided config file (#1334) | 16 April 2018, 17:43:17 UTC |
| 35d7a5d | Denis Yuen | 16 April 2018, 14:24:37 UTC | Optimize conditional requests, re-use cache, clean build log (#1330) * endpoint for cache performance * remove egit in favour of kohsuke/github-api, use conditional requests where possible https://developer.github.com/v3/#conditional-requests * webservice will now wait when out of rate limit and disallow additional requests * webservice will re-use okhttp request cache between launches * some build log cleanup | 16 April 2018, 14:24:37 UTC |
| 6bf8ff2 | Andrew Duncan | 12 April 2018, 17:42:35 UTC | subworkflows will show inherited docker in dag (#1325) | 12 April 2018, 17:42:35 UTC |
| 93d8472 | Andrew Duncan | 12 April 2018, 15:04:23 UTC | Feature/cwl dag hints (#1315) Fix CWL hint parsing (for DAG and tools tabs) | 12 April 2018, 15:04:23 UTC |
| 9991d46 | Denis Yuen | 11 April 2018, 14:15:45 UTC | Travis-testing (#1293) Attempting to clean up the build somewhat * install dependencies only for jobs that need them * run integration tests only when unit tests pass * run coverage only when integration tests pass * Also experiment with auto-deploy script and shaded jar * make tests that depend on cwltool integration tests so unit tests can move toward having no dependencies | 11 April 2018, 14:15:45 UTC |
| 4363080 | Denis Yuen | 10 April 2018, 14:53:34 UTC | Redo due to release glitch | 10 April 2018, 14:53:34 UTC |
| 5900e76 | Denis Yuen | 10 April 2018, 14:52:11 UTC | Merge tag '1.4.1' into develop [maven-release-plugin] copy for tag 1.4.1 | 10 April 2018, 14:52:11 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 |
