| 56bc180 | Denis Yuen | 27 October 2022, 20:10:39 UTC | Iterate versions | 27 October 2022, 20:10:39 UTC |
| 7fcab72 | Kathy Tran | 27 October 2022, 14:53:05 UTC | Create metadata health check endpoint (#5198) https://ucsc-cgl.atlassian.net/browse/SEAB-4900 | 27 October 2022, 14:53:05 UTC |
| 1c3ecfc | Charles Overbeck | 26 October 2022, 00:00:34 UTC | Always index only one version's source files (#5168) #5154 | 26 October 2022, 00:00:34 UTC |
| 67b2d17 | Steve Von Worley | 25 October 2022, 19:51:50 UTC | include galaxy plugin in webservice docker image https://ucsc-cgl.atlassian.net/browse/SEAB-4880 | 25 October 2022, 19:51:50 UTC |
| d6838f9 | Steve Von Worley | 18 October 2022, 02:39:41 UTC | ORCID identifiers can end with 'X' https://ucsc-cgl.atlassian.net/browse/DOCK-2256 #5152 | 18 October 2022, 02:39:41 UTC |
| 69655e0 | Kathy Tran | 17 October 2022, 17:57:38 UTC | Update dropwizard to 2.1.3 (#5167) https://ucsc-cgl.atlassian.net/browse/SEAB-4867 | 17 October 2022, 17:57:38 UTC |
| 0e5e071 | Steve Von Worley | 10 October 2022, 23:30:17 UTC | update circleci setup_remote_docker docker version https://ucsc-cgl.atlassian.net/browse/SEAB-4903 | 10 October 2022, 23:30:17 UTC |
| e3618a5 | Denis Yuen | 14 September 2022, 21:53:42 UTC | Merge branch 'release/1.13.0' | 14 September 2022, 21:53:42 UTC |
| c4f86a7 | Steve Von Worley | 09 September 2022, 15:33:58 UTC | fix SAM access to hosted workflows https://ucsc-cgl.atlassian.net/browse/SEAB-4849 | 09 September 2022, 15:33:58 UTC |
| 3c3f5c1 | Denis Yuen | 08 September 2022, 14:07:17 UTC | update regression test requirements (#5126) | 08 September 2022, 14:07:17 UTC |
| c2f90a9 | Denis Yuen | 07 September 2022, 18:20:53 UTC | reset versions | 07 September 2022, 18:20:53 UTC |
| eb8d632 | Denis Yuen | 07 September 2022, 18:18:39 UTC | tagging release | 07 September 2022, 18:18:39 UTC |
| 301d57c | Kathy Tran | 07 September 2022, 15:10:38 UTC | Fix failing workflow snapshot (#5120) https://ucsc-cgl.atlassian.net/browse/SEAB-4832 * Handle images in galaxy workflows * Null check CWL workflow outputs | 07 September 2022, 15:10:38 UTC |
| 43c3a05 | Steve Von Worley | 06 September 2022, 23:23:04 UTC | fix sourcefile + sam permissions + google token bug https://ucsc-cgl.atlassian.net/browse/SEAB-4837 | 06 September 2022, 23:23:04 UTC |
| 3186c66 | Denis Yuen | 02 September 2022, 16:40:20 UTC | ensure token refresh before checking repo validity (#5114) | 02 September 2022, 16:45:05 UTC |
| ec6a84e | Denis Yuen | 31 August 2022, 20:31:17 UTC | reset versions | 31 August 2022, 20:31:17 UTC |
| b0c2ea0 | Denis Yuen | 31 August 2022, 20:28:47 UTC | release for ui testing | 31 August 2022, 20:28:47 UTC |
| d70b474 | Denis Yuen | 31 August 2022, 20:20:34 UTC | Merge tag '1.12.3' into develop 1.12.3 | 31 August 2022, 20:20:34 UTC |
| 5c7c4c6 | Denis Yuen | 31 August 2022, 20:06:47 UTC | Merge branch 'hotfix/1.12.3' | 31 August 2022, 20:06:47 UTC |
| a178667 | Steve Von Worley | 31 August 2022, 20:04:59 UTC | throw a nicer exception when parent path in conversion method is relative https://ucsc-cgl.atlassian.net/browse/DOCK-2058 #4715 | 31 August 2022, 20:04:59 UTC |
| a115571 | Kathy Tran | 31 August 2022, 20:00:49 UTC | Add connection pool health check (#5112) https://ucsc-cgl.atlassian.net/browse/SEAB-4508 | 31 August 2022, 20:00:49 UTC |
| b878a35 | Denis Yuen | 30 August 2022, 14:38:01 UTC | Automatically regenerate github tokens in old style on start-up (#5102) * new encrypted bundle with updated github token format * add automatic token reset for new github token format * PR feedback | 30 August 2022, 14:38:01 UTC |
| 995c2c8 | Kathy Tran | 29 August 2022, 12:39:03 UTC | Sync GitHub app entry metadata with default version (#5101) https://github.com/dockstore/dockstore/issues/4729 https://ucsc-cgl.atlassian.net/browse/DOCK-2065 | 29 August 2022, 12:39:03 UTC |
| 2bc1866 | Denis Yuen | 26 August 2022, 15:47:31 UTC | check whether a manual tool repo is valid (#5096) * check whether a manual tool repo is valid | 26 August 2022, 15:47:31 UTC |
| 19e0ec8 | Kathy Tran | 26 August 2022, 12:48:29 UTC | Fix multi-arch Quay images (#5093) https://ucsc-cgl.atlassian.net/browse/SEAB-3928 * Create an image for each multi arch manifest for a quay tag * Reuse methods from QuayImageRegistry for workflow images | 26 August 2022, 12:48:29 UTC |
| 4aae4e2 | Steve Von Worley | 25 August 2022, 22:17:28 UTC | harmonize EntryVersionHelper "sourcefiles" methods https://ucsc-cgl.atlassian.net/browse/SEAB-4625 | 25 August 2022, 22:17:28 UTC |
| ffc9d00 | Steve Von Worley | 25 August 2022, 22:15:10 UTC | better .dockstore.yml error message on missing author name+orcid https://ucsc-cgl.atlassian.net/browse/DOCK-2166 #4893 | 25 August 2022, 22:15:10 UTC |
| 3dfcb13 | Steve Von Worley | 25 August 2022, 16:19:02 UTC | handle push of conflicting descriptor languages gracefully https://ucsc-cgl.atlassian.net/browse/DOCK-2167 #4894 | 25 August 2022, 16:19:02 UTC |
| 1b9b860 | Denis Yuen | 25 August 2022, 14:36:00 UTC | add git permissions check for workflows (#5094) * add check for workflows * Update WorkflowResource.java * may as well add test | 25 August 2022, 14:36:00 UTC |
| de73f0a | Denis Yuen | 24 August 2022, 21:35:15 UTC | Feature/debug GitHub action (#5098) * are both java versions having issues? * looks like issue with unpinned java version | 24 August 2022, 21:35:15 UTC |
| 4bde527 | dependabot[bot] | 23 August 2022, 15:08:30 UTC | Bump actions/cache from 3.0.7 to 3.0.8 (#5095) Bumps [actions/cache](https://github.com/actions/cache) from 3.0.7 to 3.0.8. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3.0.7...v3.0.8) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 23 August 2022, 15:08:30 UTC |
| a271ce7 | Denis Yuen | 23 August 2022, 14:09:27 UTC | once more unto (#5092) | 23 August 2022, 14:09:27 UTC |
| 852f21b | Kathy Tran | 19 August 2022, 20:49:45 UTC | Index Elasticsearch if mappings don't exist (#5081) https://ucsc-cgl.atlassian.net/browse/SEAB-4598 | 19 August 2022, 20:49:45 UTC |
| 7a7b6bf | Charles Overbeck | 19 August 2022, 19:56:06 UTC | Missed new param in merge (#5090) | 19 August 2022, 19:56:06 UTC |
| 7ad9e6d | Charles Overbeck | 19 August 2022, 17:38:46 UTC | Improved Github app handling for logs (#5070) https://ucsc-cgl.atlassian.net/browse/SEAB-4304 #4845 | 19 August 2022, 17:38:46 UTC |
| ff101f7 | Steve Von Worley | 19 August 2022, 17:00:19 UTC | tighten some authorization checks https://ucsc-cgl.atlassian.net/browse/SEAB-4403 | 19 August 2022, 17:00:19 UTC |
| aabfe70 | Denis Yuen | 18 August 2022, 20:58:53 UTC | turn on pgp signature checks (#5087) * how is it now? * expand list | 18 August 2022, 20:58:53 UTC |
| 6647331 | Denis Yuen | 18 August 2022, 18:20:46 UTC | Feature/fix for paths maybe (#5083) * been here for a while, curious what tests break * this should not reverse | 18 August 2022, 18:20:46 UTC |
| c8ab72a | Charles Overbeck | 18 August 2022, 16:09:04 UTC | Add a type query parameter to fetch user entries. (#5084) Noticed that the endpoint wasn't returning app tools, fixed that also. https://ucsc-cgl.atlassian.net/browse/SEAB-4699 | 18 August 2022, 16:09:04 UTC |
| dbbe1ff | dependabot[bot] | 16 August 2022, 21:15:55 UTC | Bump postgresql from 42.3.3 to 42.4.1 in /bom-internal (#5064) * Bump postgresql from 42.3.3 to 42.4.1 in /bom-internal Bumps [postgresql](https://github.com/pgjdbc/pgjdbc) from 42.3.3 to 42.4.1. - [Release notes](https://github.com/pgjdbc/pgjdbc/releases) - [Changelog](https://github.com/pgjdbc/pgjdbc/blob/master/CHANGELOG.md) - [Commits](https://github.com/pgjdbc/pgjdbc/compare/REL42.3.3...REL42.4.1) --- updated-dependencies: - dependency-name: org.postgresql:postgresql dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * update generated Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> | 16 August 2022, 21:15:55 UTC |
| 55c5598 | Denis Yuen | 15 August 2022, 14:47:11 UTC | Revert "thrilling (#5079)" (#5080) This reverts commit 8106ab39b9c63eafa7e9db6feca8f6e78dd2b710. | 15 August 2022, 14:47:11 UTC |
| 672bf09 | Denis Yuen | 15 August 2022, 14:38:10 UTC | allow topic update on hosted (#5071) * allow topic update on hosted * fix bedmas type bug * why we link strings to tests * sonarcloud happiness | 15 August 2022, 14:38:10 UTC |
| 8106ab3 | Denis Yuen | 15 August 2022, 14:28:51 UTC | thrilling (#5079) | 15 August 2022, 14:28:51 UTC |
| dc2fb61 | Flynn Hembroff | 15 August 2022, 14:01:40 UTC | Removing BitBucket Tokens from non-bitbucket tests (#5076) * Removed BitBucket tokens * Added postgres to many function calls * Removed BitBucket tokens * Ensured testingPostgres wasn't null * Fixed errors * Added BitBucket tokens back in * Corrected spacing error * Corrected spacing error * Corrected spelling error * Corrected license * Corrected Codacy errors * Made deleteBitBucketToken private * Fixed sonarcloud issues * Crated class GeneralWorkflowBaseIT * Added Jacadoc * Removed accidental changes from BaseIT | 15 August 2022, 14:01:40 UTC |
| 7e8f480 | Steve Von Worley | 12 August 2022, 16:14:30 UTC | make readDockstoreYaml throw on duplicate keys https://ucsc-cgl.atlassian.net/browse/DOCK-2159 #4883 | 12 August 2022, 16:14:30 UTC |
| 2b5d329 | dependabot[bot] | 12 August 2022, 15:39:48 UTC | Bump actions/cache from 3.0.6 to 3.0.7 (#5077) Bumps [actions/cache](https://github.com/actions/cache) from 3.0.6 to 3.0.7. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3.0.6...v3.0.7) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 12 August 2022, 15:39:48 UTC |
| dfa2cd6 | Denis Yuen | 12 August 2022, 14:52:58 UTC | deal with n/a author searching (#5075) * Add starring sorting es (#5023) * put back generic versions in generated files * add number of stars into search index * explicitly index null authors as empty | 12 August 2022, 14:52:58 UTC |
| ef9785e | Denis Yuen | 10 August 2022, 14:10:06 UTC | Feature/user permissions profile page (#5062) * add test and loosen permissions to support user page * what if no email serialization * PR feedback | 10 August 2022, 14:10:06 UTC |
| 9f85da0 | dependabot[bot] | 08 August 2022, 14:28:07 UTC | Bump actions/cache from 3.0.5 to 3.0.6 (#5067) Bumps [actions/cache](https://github.com/actions/cache) from 3.0.5 to 3.0.6. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3.0.5...v3.0.6) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 08 August 2022, 14:28:07 UTC |
| 3eeed95 | Kathy Tran | 05 August 2022, 17:04:50 UTC | Fix user-level permission check for workflow version ORCID authors endpoint (#5051) (#5055) https://github.com/dockstore/dockstore/issues/4916 https://ucsc-cgl.atlassian.net/browse/DOCK-2173 * Make auth user optional * Add test | 05 August 2022, 17:04:50 UTC |
| 132fc05 | Flynn Hembroff | 05 August 2022, 14:26:22 UTC | Link MacOS instructions to GitHub action (#5043) * Created action to verify MacOS installation instructions, currently I just copy pasted the instructions into a yaml file, will change, just looking for proof of concept * Corrected error in macos_installation_instructions.yml (hopefully) [skip ci] * Corrected error in macos_installation_instructions.yml (hopefully) [skip circleci] * Disabled circleci * Disabled circleci * Added this branch to the action * Added continue on error to git. * Made it so circleci passes * Added "Print Working Directory and ls" * Added OpenJDK to path * Made it so compilers can find openjdk@17 * Implemented this step from the output of Install JDK 17 https://formulae.brew.sh/formula/openjdk@17 sudo ln -sfn /usr/local/opt/openjdk@17/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk-17.jdk * Checking java version number * Checking java version number * Correct syntax * Finding all installed JDK * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Updated the version of java that runs. * Updated the version of java that runs. * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Restored config.yml * Created action to verify MacOS installation instructions, currently I just copy pasted the instructions into a yaml file, will change, just looking for proof of concept * Corrected error in macos_installation_instructions.yml (hopefully) [skip ci] * Corrected error in macos_installation_instructions.yml (hopefully) [skip circleci] * Disabled circleci * Disabled circleci * Added this branch to the action * Added continue on error to git. * Made it so circleci passes * Added "Print Working Directory and ls" * Added OpenJDK to path * Made it so compilers can find openjdk@17 * Implemented this step from the output of Install JDK 17 https://formulae.brew.sh/formula/openjdk@17 sudo ln -sfn /usr/local/opt/openjdk@17/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk-17.jdk * Checking java version number * Checking java version number * Correct syntax * Finding all installed JDK * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Changed Java HOME * Updated the version of java that runs. * Updated the version of java that runs. * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Update macos_installation_instructions.yml * Restored config.yml * Added comment to README requesting users to update the workflow if changes are made * Added comment explaining where the instructions came from and defined environment variables for the directories. * Corrected syntax error * Double checking environment variables work as expected * Double checking environment variables work as expected * Double checking environment variables work as expected * Double checking environment variables work as expected * Double checking environment variables work as expected * Double checking environment variables work as expected * Double checking environment variables work as expected * Double checking environment variables work as expected * Verifiying that it works correctly. * Changed the format of my comment in README.md * Made it so the workflow runs every Monday at at 5:30am PST/8:30am EST * Made it so it only runs on develop * Removed branches * Removed unnecessary comments. * Added new line to seperate my "added" instructions from the README.md instructions * Added new line to seperate my "added" instructions from the README.md instructions * Made it so macos_instructions.json modifies README.md using information ins macos_instructions.json * Removed macos_instructions.json as it has been replaced by macos_instructions.yaml * Made it so instructions.md is generated by macos-instructions.sh and macos_instructions.yaml * Added a start and end tag to README.md so scripts/macos-instructions.sh knows where to put the instructions * README.md is generated by scripts/macos-instructions.sh * Made some syntax corrections and added comment explaining the keys * Made some minor corrections * Added new line to README * Added new line to macos-instructions.sh * Made it so github actions uses semi-colons. * Corrected macos_installation_instructions.yml * Update macos_installation_instructions.yml Testing action * Created check in CircleCI for MacOS instructions * Changed formatting slightly * Checking that script is working * Checking that script is working * Corrected mistakes introduced in macos_installation_instructions.yml and README.md * Removed extra line in config.yml * Added comment explaining which directory it should be run in. * Double checking action is working correctly. * Added comment explaining ; * Corrected name of macos_installation_instructions.yml * Changed some minor typos * Corrected directory for npm run build * Corrected directory for npm run build * Checking to see if issue still exists * Seeing if the original action file works * Seeing if it works with git clone * Seeing if it works with git clone * Checkout master * Changed it so the github actions uses actions/checkout@v3 * Removed "on push" check * Implemented some best practices from here https://kvz.io/bash-best-practices.html. I commented out set -o xtrace as it is unnecessary for general use, but a developer can uncomment it if necessary. Added (yes "" || true) as yes "" doesn't return 0 as an error code. This forces it to always return 0. * Changed continue-on-error: true to || true and configured macos-instructions.sh to ignore '|| true' when displaying code to user. * Made it so the action runs on this PR * Undid previous commit * Corrected syntax error * Corrected explanation of where to run macos-instructions.sh. * Added comment for how to install on yq on Mac. * Removed unnecessary working-directory keys in macos_instructions.yml. * Removed prebuild step. * Changed wording of where to run check_macos.sh * Corrected typo in the explanation of where to run the script * Testing the action * Undoing previous commit * Added comment stating which yq version this script was tested with. * Added bash recommendations to check_macos.sh https://kvz.io/bash-best-practices.html * Corrected typo in dockstore/dockstore and dockstore/dockstore-ui2 * Added comment as to why check_macos.sh copies. * Made scripts/macos-instructions.sh Mac Friendly * Changed format of if statements in check_macos.sh | 05 August 2022, 14:26:22 UTC |
| eb022e4 | Kathy Tran | 04 August 2022, 13:43:23 UTC | Fix user-level permission check for workflow version ORCID authors endpoint (#5051) https://github.com/dockstore/dockstore/issues/4916 https://ucsc-cgl.atlassian.net/browse/DOCK-2173 * Make auth user optional * Add test | 04 August 2022, 13:43:23 UTC |
| 1bf8045 | Denis Yuen | 03 August 2022, 18:22:41 UTC | what if index by id (#5052) * what if index by id * add documentation | 03 August 2022, 18:22:41 UTC |
| ea78846 | Denis Yuen | 02 August 2022, 14:07:30 UTC | index source files properly and test (#5042) | 02 August 2022, 14:07:30 UTC |
| 747671a | Denis Yuen | 01 August 2022, 16:25:40 UTC | ninjaed (#5048) | 01 August 2022, 16:25:40 UTC |
| 1cd477b | Denis Yuen | 29 July 2022, 22:08:55 UTC | add test and hook up verified to collection endpoint (#5037) * add test and hook up verified to collection endpoint * document the problematic code | 29 July 2022, 22:08:55 UTC |
| 0268774 | Steve Von Worley | 29 July 2022, 20:41:29 UTC | refactor user-level permissions checks https://ucsc-cgl.atlassian.net/browse/SEAB-4403 | 29 July 2022, 20:41:29 UTC |
| 39f5a75 | Charles Overbeck | 29 July 2022, 18:27:21 UTC | Fix collectionsLength for starred organizations (#5038) https://ucsc-cgl.atlassian.net/browse/SEAB-3136 This relies on the fact that we don't lazily fetch collections. But the existing code already does, so this is no worse, doesn't generate any additional queries, and on the plus side doesn't force developers to manually initialize the field. | 29 July 2022, 18:27:21 UTC |
| 26364e3 | Charles Overbeck | 29 July 2022, 00:09:47 UTC | Don't terminate indexing after an indexing failure (#5024) https://ucsc-cgl.atlassian.net/browse/SEAB-4596 | 29 July 2022, 00:09:47 UTC |
| 1b00406 | Kathy Tran | 27 July 2022, 20:10:39 UTC | Fix failed openapi validation (#5036) https://ucsc-cgl.atlassian.net/browse/SEAB-4593 | 27 July 2022, 20:10:39 UTC |
| ee317f3 | Denis Yuen | 27 July 2022, 18:51:46 UTC | Feature/restub snapshot (#5035) * add test to reveal issue * hook up check * fix query and distinguish error message * fix specific test * add check | 27 July 2022, 18:51:46 UTC |
| 760aaa1 | Charles Overbeck | 22 July 2022, 17:55:01 UTC | Update PR template (#5034) https://ucsc-cgl.atlassian.net/browse/SEAB-4603 | 22 July 2022, 17:55:01 UTC |
| 926543d | Flynn Hembroff | 22 July 2022, 14:33:01 UTC | Added "grep -v "^Running Changeset:"" to all commands that produce lines like, (#5033) Running Changeset: | 22 July 2022, 14:33:01 UTC |
| 0e4216d | Kathy Tran | 21 July 2022, 20:30:57 UTC | Check if user exists in user endpoints (#5031) https://ucsc-cgl.atlassian.net/browse/SEAB-3895 | 21 July 2022, 20:30:57 UTC |
| 10c86dd | Denis Yuen | 21 July 2022, 17:08:20 UTC | support grab-bag of updates (#5032) * support grab-bag of updates | 21 July 2022, 17:08:20 UTC |
| 9558614 | Denis Yuen | 19 July 2022, 14:29:05 UTC | Add starring sorting es (#5023) * put back generic versions in generated files * add number of stars into search index | 19 July 2022, 14:29:05 UTC |
| 65c8ee6 | Denis Yuen | 18 July 2022, 13:59:34 UTC | pom simplification for how liquibase-core is included (#5021) * curious * intellij pretty confused | 18 July 2022, 13:59:34 UTC |
| d2b2e8e | Charles Overbeck | 15 July 2022, 23:21:10 UTC | Revert "Don't terminate indexing after error on one item" This reverts commit 15740a211dcdd75ee6b8d9039f566f77a526bbde. | 15 July 2022, 23:21:10 UTC |
| 15740a2 | Charles Overbeck | 15 July 2022, 23:17:35 UTC | Don't terminate indexing after error on one item https://ucsc-cgl.atlassian.net/browse/SEAB-4596 | 15 July 2022, 23:17:35 UTC |
| 81223fa | Steve Von Worley | 15 July 2022, 16:32:47 UTC | tweak new SourceFile-path-related integration test https://ucsc-cgl.atlassian.net/browse/SEAB-4269 | 15 July 2022, 16:32:47 UTC |
| b89b6ad | Steve Von Worley | 14 July 2022, 23:22:55 UTC | restrict SourceFile paths to letters, numbers, dot, dash, slash, underscore, and space https://ucsc-cgl.atlassian.net/browse/SEAB-4269 | 14 July 2022, 23:22:55 UTC |
| b6f7702 | Denis Yuen | 14 July 2022, 16:53:43 UTC | remove old stuff [skip ci] | 14 July 2022, 16:53:43 UTC |
| c766c28 | dependabot[bot] | 14 July 2022, 13:54:08 UTC | Bump actions/cache from 3.0.4 to 3.0.5 (#5020) Bumps [actions/cache](https://github.com/actions/cache) from 3.0.4 to 3.0.5. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3.0.4...v3.0.5) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 14 July 2022, 13:54:08 UTC |
| 26b89d8 | dependabot[bot] | 13 July 2022, 14:12:16 UTC | Bump commons-configuration2 from 2.7 to 2.8.0 in /bom-internal (#4997) * Bump commons-configuration2 from 2.7 to 2.8.0 in /bom-internal Bumps commons-configuration2 from 2.7 to 2.8.0. --- updated-dependencies: - dependency-name: org.apache.commons:commons-configuration2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * update licenses * validation error Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> | 13 July 2022, 14:12:16 UTC |
| aba75e0 | Denis Yuen | 11 July 2022, 21:41:55 UTC | syntax (#5011) | 11 July 2022, 21:41:55 UTC |
| 2036f85 | Flynn Hembroff | 11 July 2022, 16:27:07 UTC | Changed version number of hibernate-validator (#5004) | 11 July 2022, 16:27:07 UTC |
| 683f7ca | amar jandu | 07 July 2022, 19:03:54 UTC | Add non-empty constraints to user_profile table (#4871, PR #4994) | 07 July 2022, 19:03:54 UTC |
| 26d9485 | Denis Yuen | 07 July 2022, 14:10:31 UTC | dropwizard 2.1.1 (#4988) | 07 July 2022, 14:10:31 UTC |
| c9106e4 | Denis Yuen | 07 July 2022, 14:10:20 UTC | batch process index index creation (#4973) * batch process index index creation | 07 July 2022, 14:10:20 UTC |
| 94e99b2 | Denis Yuen | 07 July 2022, 14:09:40 UTC | order events by date (#4991) | 07 July 2022, 14:09:40 UTC |
| d50cfd6 | amar jandu | 06 July 2022, 23:45:38 UTC | Update SEM_VER_STRING to support prereleases (#4981, PR #4982) | 06 July 2022, 23:45:38 UTC |
| e663b19 | Denis Yuen | 06 July 2022, 17:19:40 UTC | Merge tag '1.12.2' into develop testing out release process | 06 July 2022, 17:19:40 UTC |
| 1b1e531 | Denis Yuen | 06 July 2022, 17:15:00 UTC | Merge branch 'hotfix/1.12.2' | 06 July 2022, 17:15:00 UTC |
| ba8b26b | Denis Yuen | 06 July 2022, 15:30:04 UTC | following "changes!" in https://wiki.oicr.on.ca/display/DOC/Dockstore+Releases | 06 July 2022, 15:30:04 UTC |
| 258c293 | Denis Yuen | 06 July 2022, 15:27:08 UTC | builds with CI friendly versions (#4789) (#4987) * buildable with CI friendly versions * hook up trigger for release * needed this for liquibase * Update README.md | 06 July 2022, 15:27:08 UTC |
| cbbeda1 | amar jandu | 05 July 2022, 19:17:09 UTC | Remove unused constructors (SEAB-4055, PR #4952) * Normalize SuppressWarnings | 05 July 2022, 19:17:09 UTC |
| ccba9b1 | Charles Overbeck | 05 July 2022, 18:51:14 UTC | Merge remote-tracking branch 'origin/develop' into develop | 05 July 2022, 18:51:14 UTC |
| ef58572 | Charles Overbeck | 05 July 2022, 16:55:11 UTC | Merge tag '1.12.1' into develop 1.12.1 | 05 July 2022, 16:55:11 UTC |
| 701033f | Flynn Hembroff | 05 July 2022, 16:41:05 UTC | Feature/seab 4083/parrallel tests (#4970) * Made it so BitBucket tests are only treated as Integration tests in pom.xml. This is what was actually happening, I'm just making it official in pom.xml. * Created generate-test-lists.sh which does the following 1) Gets a list of all integration tests, using the same patterns failsafe would 2) Determines which tests belong to a profile and adds them to a new list and removes those files from the list of all integration tests. NOTE: This means all integration tests will be run, as the all integration test list is a catch. 3) converts file paths into Fully Qualified Class Names * config.yml now does the following, 1. Determine the test lists for ITs 2. Splits tests up using circleci test split * Corrected syntax errors in config.yml * Made it so "Generate test lists" runs before "build" * Added -DfailIfNoTests=false to config.yml. This is because some goals may not have any tests executed. * Undid changes to pom.xml to see if that speeds things up * Undid changes to pom.xml to see if that speeds things up * Moved all TRS tests from WorkflowIT.java to GaGhTRSAPIWorkflowIT.java and added common methods to BaseIT.java * Corrected indentation error in Ga4GhTRSAPIWorkflowIT * Moved all hosted workflow ITs from WorkflowIT to HostedWorkflowIT * Made it so generate-test-lists.sh generates files for unit tests * Made it so unit tests run in parallel * Attached the test lists * Moved Github Workflows from WorkflowIT to GitHubWorkflowIT and added common methods to BaseIT * Corrected config.yml so variables in unit-tests are kept * Added parallelism: 4 to unit-tests * Added pwd to unit-tests * Corrected unit-tests directory * Changed how the directory was persisted in circleci * Split out non-confidential tests from unit-tests * Split out non-confidential tests from generate-test-lists.sh * Made non-confidential tests a job * Removed the attach workspace from non-confidential-tests, as it is unneeded. * Corrected a line in running the non-confidential tests * Removed a few commands from unit-tests as they are done in non-confidential tests * Removed all parallelism from config.yml * Persisted workspace for non-confidential from build * Made it so non-confidential quickly builds first * Removed build * Removed parts of unit-tests that are done in non-confidential tests * Removed parts of unit-tests that are done in non-confidential tests * Made it so non-confidential tests only execute on the first node * Changed Parallelism as follows: integration-tests: 5 tool-integration-tests: 3 workflow-integration-tests: 5 bitbucket-tests: 2 Corrected errors in config.yml and deleted the job non-confidential tests * Attached workspace to unit-tests * Attached workspace (properly) * Added 4 parallelism to unit-test * Corrected typo * Restored unit-tests to the norm * Change parallelism integration-tests: 3 tool-integration-tests: 2 workflow-integration-tests: 3 bitbucket-tests: 3 * Running workflow-integration-tests with a parallelism of 2 * Added test to Ga4GhTRSAPIWorkflowIT that was accidentally skipped * Made it so generate-test-lists.sh does it checks if the category is commented out with // style comments * Removed unused file reference from config.yml * Removed unit tests and clarified comments in generate-test-lists.sh * Added a comment to config.yml and deleted unneeded commented out code * Corrected mistake in generate-test-lists.sh * Removed extra test from Ga4GhTRSAPIWorkflowIT * Cleaned up one of the commands in config.yml * Corrected comments in generate-test-lists.sh * Changed parallelism to integration-tests: 4 tool-integration-tests: 2 workflow-integration-tests: 3 bitbucket-tests: 1 language-parsing-tests: 1 * Corrected codacy problems * Corrected more codacy problems * Stored the test names in the build step * Stored the test names in the build step * Changed the naming pattern of the test lists. The following name changes occured - integration-tests.txt -> IT/integration-tests.txt - bitbucketIT.txt -> IT/bitbucket.txt - regressionIT.txt -> IT/regression.txt - workflowIT.txt -> IT/workflow.txt - toolIT.txt -> IT/tool.txt - non-confidentialIT.txt -> IT/non-confidential.txt - language-parsingIT.txt -> IT/language-parsing.txt * Commented out running sonar cloud for each IT, now should only run on unit_tests * Made generate_test_list a little easier to modify * Re-enabled sonar cloud on all jobs * Made it so there is no parallelism temporarily * Added parallelism back in * Adding a find statement to determine where jacoco files are being stored for each job. * Sonar cloud now only runs once (Hopefully) * Removed unneeded sonar cloud contexts * Corrected syntax error * Corrected syntax error * Corrected syntax error * Corrected syntax error * Corrected syntax error * Corrected syntax error * Removed the copying of .m2 and changed how files were persisted to the workspace * Running sonar-cloud with Docker * Syntax correction * Syntax correction * Modified config.yml so, it does a build and modified BitBucketSourceCodeRepo so that it has an extra function which should affect coverage, triggering an alert from sonarcloud * Added an extra line to check for coverage * Removed jacoco lines * Added extra line to test for coverage * Made sonar-cloud dependant on - regression-integration-tests * Checking coverage * Checking coverage * Restord files * Modified sonarcloud command * Testing coverage * READY FOR REVIEW reverted file used for testing back to normal * Made it so only one test file is generated | 05 July 2022, 16:41:05 UTC |
| d381cae | Charles Overbeck | 05 July 2022, 16:02:30 UTC | Merge branch 'hotfix/1.12.1' | 05 July 2022, 16:02:30 UTC |
| 589d0fd | Charles Overbeck | 30 June 2022, 18:12:49 UTC | Use versionNameFilter for proprietary API (#4977) #4975 | 30 June 2022, 18:12:49 UTC |
| 624fc05 | Steve Von Worley | 29 June 2022, 20:28:56 UTC | improve performance of fetching descriptor file via trs (#4974) https://ucsc-cgl.atlassian.net/browse/DOCK-1921 #4480 | 29 June 2022, 20:28:56 UTC |
| 59ea7fb | David Steinberg | 27 June 2022, 21:08:19 UTC | Upgrade swagger-ui to avoid XSS (#4971) * Upgrade swagger-ui to avoid XSS * Remove redundant version | 27 June 2022, 21:08:19 UTC |
| bb299a3 | Steve Von Worley | 25 June 2022, 01:00:51 UTC | include specified "filters" in TRS toolsGet next_page and last_page links https://ucsc-cgl.atlassian.net/browse/DOCK-2186 #4957 | 25 June 2022, 01:00:51 UTC |
| bb0c369 | Steve Von Worley | 24 June 2022, 22:55:20 UTC | continue processing .dockstore.yml after error https://ucsc-cgl.atlassian.net/browse/DOCK-2110 #4803 | 24 June 2022, 22:55:20 UTC |
| c4865ed | Denis Yuen | 24 June 2022, 15:38:17 UTC | restrict to tags for now [skip ci] (#4966) | 24 June 2022, 15:38:17 UTC |
| a99ec36 | Denis Yuen | 23 June 2022, 17:11:59 UTC | update to official maven wrapper (#4959) * update to official maven wrapper | 23 June 2022, 17:11:59 UTC |
| 451bd0f | Denis Yuen | 23 June 2022, 14:10:51 UTC | hook up initiator user to events endpoint and test (#4960) | 23 June 2022, 14:10:51 UTC |
| 2935885 | Denis Yuen | 22 June 2022, 19:25:13 UTC | fix api links (#4965) | 22 June 2022, 19:25:13 UTC |
| b1d8ff6 | Walter Shands | 22 June 2022, 15:24:09 UTC | new api to get cli version (#4948) New api to get cli information Addresses SEAB-3952 | 22 June 2022, 15:24:09 UTC |
