| e6662c0 | Denis Yuen | 09 February 2022, 22:00:23 UTC | [maven-release-plugin] prepare release 1.11.11 | 09 February 2022, 22:00:23 UTC |
| dc21d67 | Denis Yuen | 07 February 2022, 15:24:49 UTC | hotfix version of s3 update (#4683) | 07 February 2022, 15:24:49 UTC |
| 605511f | Richard-Hansen | 04 February 2022, 18:28:02 UTC | Bump postgres (#4707) * Bump postgres * Licenses * Ignore test for now Co-authored-by: Gary Luu <garylau.work@gmail.com> | 04 February 2022, 18:28:02 UTC |
| 27057eb | Gary Luu | 10 December 2021, 20:41:47 UTC | Update generated | 13 December 2021, 20:27:49 UTC |
| aa61857 | Gary Luu | 10 December 2021, 20:28:22 UTC | [maven-release-plugin] prepare for next development iteration | 13 December 2021, 20:27:49 UTC |
| b139a17 | Gary Luu | 10 December 2021, 20:28:19 UTC | [maven-release-plugin] prepare release 1.11.10 | 13 December 2021, 20:27:49 UTC |
| 0db3efd | Gary Luu | 10 December 2021, 20:04:32 UTC | Feature/4540/commit id fix (#4623) (#4625) * fix my mistake :( #4540 Co-authored-by: NatalieEO <nperez9@ucsc.edu> | 10 December 2021, 20:04:32 UTC |
| e72a639 | Gary Luu | 03 December 2021, 22:47:26 UTC | Hotfix/1.11.9 (#4603) * Fix/4460/readme update (#4463) * Update README description * Ignore cwltool tests for now * Add comment * Add test * fixed organization update to fail gracefully when no name specified (#4470) https://ucsc-cgl.atlassian.net/browse/DOCK-1900 #4442 * Use SnakeYAML SafeConstructor (#4564) * Add guards on .dockstore.yml reading * Add guards for CWL parsing * Ensure parsing doesn't happen after CWL is found unsafe * Use same assert pattern * Log parsing error and improve validation message * Log more places, and don't catch * Protect parameter yaml * Log the yaml exception * Assertion order matters * Feature/4540/get commit (#4584) * Check if object is of type tag or commit #4540 * [maven-release-plugin] prepare release dockstore-1.11.9 * [maven-release-plugin] prepare for next development iteration * mvn clean install -DskipTests * Change default tag name Co-authored-by: Stephen Von Worley <svonworl@ucsc.edu> Co-authored-by: David Steinberg <david@resium.com> Co-authored-by: NatalieEO <nperez9@ucsc.edu> | 03 December 2021, 22:47:26 UTC |
| 82e8fa5 | Walt Shands | 09 September 2021, 22:14:07 UTC | Merge branch 'hotfix/1.11.7' | 09 September 2021, 22:14:07 UTC |
| 7edaddb | Denis Yuen | 09 September 2021, 22:10:10 UTC | Snyk stuff | 09 September 2021, 22:10:10 UTC |
| b473f40 | Denis Yuen | 09 September 2021, 21:41:20 UTC | [maven-release-plugin] prepare for next development iteration | 09 September 2021, 21:41:20 UTC |
| eb35fb1 | Denis Yuen | 09 September 2021, 21:41:18 UTC | [maven-release-plugin] prepare release 1.11.8 | 09 September 2021, 21:41:18 UTC |
| 6ef0f9d | Walt Shands | 07 September 2021, 20:25:08 UTC | [maven-release-plugin] prepare for next development iteration | 07 September 2021, 20:25:08 UTC |
| 3dcfc61 | Walt Shands | 07 September 2021, 20:25:00 UTC | [maven-release-plugin] prepare release 1.11.7 | 07 September 2021, 20:25:00 UTC |
| 3937b49 | Charles Overbeck | 03 September 2021, 17:17:24 UTC | Rollback transaction on error (#4438) #4434 has the details. | 03 September 2021, 17:17:24 UTC |
| e263802 | Charles Overbeck | 01 September 2021, 00:13:45 UTC | Fix WDL parameter_meta with boolean values (#4433) #4431 Made the code a little more Scala-esque and avoid some duplication. Also improve logging | 01 September 2021, 00:13:45 UTC |
| 1a986f4 | Denis Yuen | 23 August 2021, 20:32:48 UTC | Merge branch 'hotfix/1.11.6' | 23 August 2021, 20:32:48 UTC |
| c36a6ad | Denis Yuen | 23 August 2021, 20:21:51 UTC | [maven-release-plugin] prepare for next development iteration | 23 August 2021, 20:21:51 UTC |
| 1c783f0 | Denis Yuen | 23 August 2021, 20:21:49 UTC | [maven-release-plugin] prepare release 1.11.6 | 23 August 2021, 20:21:49 UTC |
| b181e7a | Charles Overbeck | 21 July 2021, 16:56:20 UTC | Enable Hibernate statistics / use log4j for logging (#4362) https://ucsc-cgl.atlassian.net/browse/SEAB-3122 We added org.apache.logging.log4j.log4j-api as a dependency. Without the library, Hibernate was defaulting to using slf4j. With the library, Hibernate defaults to Log4j2. Set the system property to tell Hibernate to use slf4j. | 21 July 2021, 16:56:20 UTC |
| 8ddf947 | Denis Yuen | 19 July 2021, 13:17:16 UTC | low impact fix (#4361) | 19 July 2021, 13:17:16 UTC |
| c1bc057 | Gary Luu | 15 July 2021, 15:27:46 UTC | Grab user from DAO again (#4358) | 15 July 2021, 15:27:46 UTC |
| 93127a2 | Denis Yuen | 09 July 2021, 17:24:46 UTC | Merge branch 'hotfix/1.11.0' | 09 July 2021, 17:24:46 UTC |
| 4c3ccac | Denis Yuen | 07 July 2021, 20:26:34 UTC | Snyk iteration | 07 July 2021, 20:26:34 UTC |
| 6ff5e24 | Denis Yuen | 07 July 2021, 20:16:29 UTC | [maven-release-plugin] prepare for next development iteration | 07 July 2021, 20:16:29 UTC |
| 0dfca2f | Denis Yuen | 07 July 2021, 20:16:23 UTC | [maven-release-plugin] prepare release 1.11.5 | 07 July 2021, 20:16:23 UTC |
| 218a07b | Denis Yuen | 07 July 2021, 19:50:30 UTC | Merge branch 'hotfix/1.11.0' of github.com:dockstore/dockstore into hotfix/1.11.0 | 07 July 2021, 19:50:30 UTC |
| 7ddaa87 | Charles Overbeck | 06 July 2021, 20:50:22 UTC | Update generated POMs (#4343) | 06 July 2021, 20:50:22 UTC |
| 633f661 | Denis Yuen | 06 July 2021, 19:38:58 UTC | Merge branch 'hotfix/1.11.0' of github.com:dockstore/dockstore into hotfix/1.11.0 | 06 July 2021, 19:38:58 UTC |
| 3fb2396 | Denis Yuen | 06 July 2021, 19:38:45 UTC | Generated files | 06 July 2021, 19:38:45 UTC |
| e2c5298 | Charles Overbeck | 06 July 2021, 16:00:25 UTC | Add BatchSize to improve performance (#4340) #4338 | 06 July 2021, 16:00:25 UTC |
| 868d21c | Denis Yuen | 06 July 2021, 15:21:53 UTC | [maven-release-plugin] prepare for next development iteration | 06 July 2021, 15:21:53 UTC |
| f1a5e99 | Denis Yuen | 06 July 2021, 15:21:47 UTC | [maven-release-plugin] prepare release 1.11.4 | 06 July 2021, 15:21:47 UTC |
| 43471b6 | Gary Luu | 30 June 2021, 19:28:00 UTC | Error on wrong scope (#4329) * Error on wrong scope * Fix previous migration * Use TokenScope | 30 June 2021, 19:28:00 UTC |
| f13b351 | Denis Yuen | 23 June 2021, 14:13:49 UTC | Skip pgp but can revert to add cached keylist (#4318) * Might help in the future when one server starts working * [maven-release-plugin] prepare release 1.11.3-rc.0 * [maven-release-plugin] prepare for next development iteration * [maven-release-plugin] prepare release 1.11.3-rc.1 * [maven-release-plugin] prepare for next development iteration * Remove pgp * [maven-release-plugin] prepare release 1.11.3 * [maven-release-plugin] prepare for next development iteration | 23 June 2021, 14:13:49 UTC |
| 4244f28 | Denis Yuen | 21 June 2021, 21:29:46 UTC | [maven-release-plugin] prepare for next development iteration | 21 June 2021, 21:29:46 UTC |
| 6d26764 | Denis Yuen | 21 June 2021, 21:29:41 UTC | [maven-release-plugin] prepare release 1.11.2 | 21 June 2021, 21:29:41 UTC |
| 0958696 | Denis Yuen | 21 June 2021, 21:26:35 UTC | Try adding a keyserver | 21 June 2021, 21:26:35 UTC |
| 1d2159c | Denis Yuen | 21 June 2021, 20:00:53 UTC | Iterate snyk stuff | 21 June 2021, 20:00:53 UTC |
| 7305fbf | Denis Yuen | 21 June 2021, 19:46:37 UTC | [maven-release-plugin] prepare for next development iteration | 21 June 2021, 19:46:37 UTC |
| 4523a6d | Denis Yuen | 21 June 2021, 19:46:31 UTC | [maven-release-plugin] prepare release 1.11.1 | 21 June 2021, 19:46:31 UTC |
| f1d1c22 | NatalieEO | 21 June 2021, 16:38:14 UTC | get github ids again :( (#4317) Turns out I shouldn't have deleted that section of code. I need to try to get the GitHub id with all 3 methods | 21 June 2021, 16:38:14 UTC |
| 4bd8264 | Denis Yuen | 18 June 2021, 21:50:53 UTC | [maven-release-plugin] prepare for next development iteration | 18 June 2021, 21:50:53 UTC |
| 85f6d91 | Denis Yuen | 18 June 2021, 21:50:48 UTC | [maven-release-plugin] prepare release 1.11.0 | 18 June 2021, 21:50:48 UTC |
| c1ca36e | Denis Yuen | 18 June 2021, 14:33:39 UTC | Merge branch 'release/1.11' | 18 June 2021, 14:33:39 UTC |
| e4974dc | NatalieEO | 11 June 2021, 21:59:59 UTC | Get more github ids (#4294) * Get more github ids * forgot to add users that don't have a github token, add test | 11 June 2021, 21:59:59 UTC |
| fe59cee | Denis Yuen | 10 June 2021, 17:28:28 UTC | Iterate snyk and swagger stuff | 10 June 2021, 17:28:28 UTC |
| 4f40d77 | Denis Yuen | 10 June 2021, 17:19:55 UTC | [maven-release-plugin] prepare for next development iteration | 10 June 2021, 17:19:55 UTC |
| 57d064d | Denis Yuen | 10 June 2021, 17:19:49 UTC | [maven-release-plugin] prepare release 1.11.0-rc.0 | 10 June 2021, 17:19:49 UTC |
| 6bbc0c2 | Gary Luu | 10 June 2021, 17:16:01 UTC | Check not frozen before saving DAG (#4289) * Check not frozen before saving DAG Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> | 10 June 2021, 17:16:01 UTC |
| 382876a | Richard-Hansen | 10 June 2021, 16:16:45 UTC | Generated poms (#4290) Flattened pom update. | 10 June 2021, 16:16:45 UTC |
| 2b4803c | Gregory F J Hogue | 07 June 2021, 20:32:24 UTC | multiple authors & ORCID authors in .dockstore.yml (#4277) * dockstore yml authors - WIP * add orcid authors (WIP) * orcidauthor migration * remove validate key * authors in .dockstore.yml integration test * cascade orcidauthors * include versions in test workflow * test will pass, but EAGER :( * test passing with lazy orcidauthors :) | 07 June 2021, 20:32:24 UTC |
| cc466fb | Denis Yuen | 04 June 2021, 19:14:44 UTC | More snyk pom | 04 June 2021, 19:14:44 UTC |
| b120e84 | Denis Yuen | 04 June 2021, 19:10:01 UTC | [maven-release-plugin] prepare for next development iteration | 04 June 2021, 19:10:01 UTC |
| b7635d7 | Denis Yuen | 04 June 2021, 19:09:55 UTC | [maven-release-plugin] prepare release 1.11.0-beta.3 | 04 June 2021, 19:09:55 UTC |
| bb279b1 | Denis Yuen | 04 June 2021, 19:06:03 UTC | Need to skip flattened pom check on tags | 04 June 2021, 19:06:03 UTC |
| 5faa187 | Denis Yuen | 04 June 2021, 18:53:33 UTC | [maven-release-plugin] prepare for next development iteration | 04 June 2021, 18:53:33 UTC |
| effc98b | Denis Yuen | 04 June 2021, 18:53:27 UTC | [maven-release-plugin] prepare release 1.11.0-beta.2 | 04 June 2021, 18:53:27 UTC |
| 5028089 | Denis Yuen | 04 June 2021, 14:55:24 UTC | Iteratoe snyk stuff | 04 June 2021, 14:55:24 UTC |
| a33b017 | Denis Yuen | 04 June 2021, 14:41:43 UTC | [maven-release-plugin] prepare for next development iteration | 04 June 2021, 14:41:43 UTC |
| a372b29 | Denis Yuen | 04 June 2021, 14:41:37 UTC | [maven-release-plugin] prepare release 1.11.0-beta.1 | 04 June 2021, 14:41:37 UTC |
| 59ba43f | Denis Yuen | 02 June 2021, 19:47:31 UTC | Feature/featurednewsurl (#4269) * Missed this * Thought this was there already * For the UI | 02 June 2021, 19:47:31 UTC |
| 0394eb2 | Denis Yuen | 28 May 2021, 20:21:09 UTC | [maven-release-plugin] prepare for next development iteration | 28 May 2021, 20:21:09 UTC |
| c20afc8 | Denis Yuen | 28 May 2021, 20:21:04 UTC | [maven-release-plugin] prepare release 1.11.0-beta.0 | 28 May 2021, 20:21:04 UTC |
| 52333dd | Gregory F J Hogue | 27 May 2021, 20:44:10 UTC | Multiple Authors table, name/email migration (#4200) * start fresh authors branch * revert migration * version authors OneToMany * author version join-column; old authors DB migration * handle null case in old author/email getters * fix single-author behaviour for unit test * add default constructor for Author * Try eager-loading version authors * skip setting null author name * call isPresent() for Optional<Author> * use LAZY authors; fix string; add apimodelproperties * set back to eager for now | 27 May 2021, 20:44:10 UTC |
| aa5d280 | NatalieEO | 27 May 2021, 16:09:16 UTC | feature/addMoreLogging (#4264) * Add more logging so that we can see the endpoint is still running AND so that it's not necessary to debug if the endpoint somehow fails and we need to look up more users | 27 May 2021, 16:09:16 UTC |
| e7cdb3b | Gary Luu | 21 May 2021, 19:43:34 UTC | Feature/2988/auto default version set (#4244) * Add default version enum * Add assertions * Use boolean instead | 21 May 2021, 19:43:34 UTC |
| 3958779 | Richard-Hansen | 19 May 2021, 22:12:05 UTC | Updated ORCID scope in dockstore.yml (#4252) Updated ORCID scope in dockstore.yml and null check for code variable during ORCID OAuth | 19 May 2021, 22:12:05 UTC |
| cf9caf2 | Denis Yuen | 19 May 2021, 19:16:04 UTC | Feature/hook up sonar (#4251) * Cannot just upload coverage with sonar, instead we need to reanalyze in each nested job * luckily it only takes about a minute and a half in the parallel jobs https://community.sonarsource.com/t/jacoco-coverage-switch-from-deprecated-binary-to-xml-format-in-a-tycho-build-shows-0/10917/16 | 19 May 2021, 19:16:04 UTC |
| 5089ef4 | Denis Yuen | 18 May 2021, 20:27:51 UTC | add a couple indexes (#4249) | 18 May 2021, 20:27:51 UTC |
| e0ba762 | NatalieEO | 18 May 2021, 16:07:05 UTC | Add display name to CloudInstance (#4241) * #3764 Add display name to CloudInstance | 18 May 2021, 16:07:05 UTC |
| 2f5a8e1 | Denis Yuen | 14 May 2021, 21:32:47 UTC | Feature/small api suggestions (#4245) * suggestion 1 * Working on #4163 and #4165 * sonar cloud code smells | 14 May 2021, 21:32:47 UTC |
| 45e63c0 | Walter Shands | 12 May 2021, 02:41:25 UTC | don't append to dockstoreTest.yml multiple times (#4240) * don't append to dockstoreTest.yml multiple times | 12 May 2021, 02:41:25 UTC |
| f494cbc | Walter Shands | 10 May 2021, 15:13:42 UTC | update cli version and location (#4238) | 10 May 2021, 15:13:42 UTC |
| a756a1e | Richard-Hansen | 06 May 2021, 21:03:20 UTC | HTTP to HTTPS for apache license url (#4235) | 06 May 2021, 21:03:20 UTC |
| 9b8a89a | Gary Luu | 05 May 2021, 19:59:01 UTC | Change is_checker to isChecker (#4234) * Change is_checker to isChecker * Fix more | 05 May 2021, 19:59:01 UTC |
| 90e9a7a | Walter Shands | 03 May 2021, 18:35:55 UTC | use payload body for auth (#4228) * use payload body for auth | 03 May 2021, 18:35:55 UTC |
| aae19d6 | NatalieEO | 03 May 2021, 16:42:25 UTC | set last modified for github app workflows (#4224) * #4201 set last modified for github app workflows | 03 May 2021, 16:42:25 UTC |
| 0f610b1 | NatalieEO | 03 May 2021, 16:41:19 UTC | seab-2571/ Google ids through endpoint. (#4220) * https://ucsc-cgl.atlassian.net/browse/SEAB-2571 Try to gather Google ids through endpoint. Change the id type from long to string to accommodate Google. Do Google login by id and by username if id is not successful. Update/get Google id on login. | 03 May 2021, 16:41:19 UTC |
| c619cf4 | Richard-Hansen | 03 May 2021, 14:47:14 UTC | Check generated pom files during build (#4227) Check generated pom files during build | 03 May 2021, 14:47:14 UTC |
| c880113 | dependabot[bot] | 30 April 2021, 19:24:47 UTC | Bump openapi-generator-maven-plugin in /dockstore-webservice (#4225) Bumps openapi-generator-maven-plugin from 4.2.3 to 5.1.0. Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 30 April 2021, 19:24:47 UTC |
| 34a3bf8 | Kathy Tran | 30 April 2021, 14:36:37 UTC | Fix members count by only returning accepted members (#4222) | 30 April 2021, 14:36:37 UTC |
| 0b1fb9e | Charles Overbeck | 29 April 2021, 19:06:42 UTC | Upgrade to ES 7.10 (#4219) Now that AWS Elasticsearch supports it | 29 April 2021, 19:06:42 UTC |
| 5fbd8e9 | Gary Luu | 29 April 2021, 18:52:24 UTC | Feature/seab 2860/bitbucket rate limit (#4218) * Reduce bitbucket calls to 256 * Fix test repo url | 29 April 2021, 18:52:24 UTC |
| 760f2bb | Denis Yuen | 28 April 2021, 18:45:34 UTC | Upgrade random (#4217) * Looks like drop-in replacement locally * Codacy inspired cleanup | 28 April 2021, 18:45:34 UTC |
| fb6986a | Gary Luu | 28 April 2021, 17:24:06 UTC | Feature/4191/better orcid work sync (#4216) * Sync issues * Add test | 28 April 2021, 17:24:06 UTC |
| 3b396ae | Kathy Tran | 28 April 2021, 16:46:00 UTC | Don't expose tokens to users (#4214) * Use JsonViews to hide the actual token from users in getUserTokens * Don't show token for listToken endpoint * Hide token content in response for token endpoints not used for login * Restore ApiModelProperty positions * Hide onlineProfileId | 28 April 2021, 16:46:00 UTC |
| 8fc836e | Denis Yuen | 27 April 2021, 18:11:40 UTC | Discussion at OICR, think we can get rid of this too (#4215) | 27 April 2021, 18:11:40 UTC |
| 83e4193 | Denis Yuen | 26 April 2021, 16:55:10 UTC | Works locally (#4213) | 26 April 2021, 16:55:10 UTC |
| 6a29332 | Gary Luu | 23 April 2021, 16:46:49 UTC | Move test, limit memory (#4212) | 23 April 2021, 16:46:49 UTC |
| 6c53180 | NatalieEO | 23 April 2021, 16:33:01 UTC | github account linking by id, let admins delete another user (#4204) * https://ucsc-cgl.atlassian.net/browse/SEAB-2570 Gather IDs from GitHub with a one time use endpoint and use only the IDs to login to Dockstore. Let admins delete another user. Added unique indexes to token and user_profile tables to handle there not always being an id available for us to check against. | 23 April 2021, 16:33:01 UTC |
| 9863bd8 | Gary Luu | 22 April 2021, 20:23:37 UTC | The owner can now view their own unpublished hosted files (#4182) * See what breaks * Add assertion to confirm owner can get * Fix test | 22 April 2021, 20:23:37 UTC |
| 37828ed | David Steinberg | 22 April 2021, 19:41:41 UTC | Bump OpenJDK 11 Docker image version (#4210) * Update to latest JDK 11 image * CircleCI doesnt have the latest JDK cached yet | 22 April 2021, 19:41:41 UTC |
| 055b7d4 | Gary Luu | 22 April 2021, 01:19:41 UTC | Fix previous migration (#4208) | 22 April 2021, 01:19:41 UTC |
| 67b7713 | Gary Luu | 22 April 2021, 00:20:55 UTC | Feature/hoverfly orcid (#4196) * Update hoverfly * Redo with Java http client * Add some hoverfly test * Enhance test * Update plugin, increase memory | 22 April 2021, 00:20:55 UTC |
| 8c8bca1 | Denis Yuen | 21 April 2021, 20:59:44 UTC | [maven-release-plugin] prepare for next development iteration | 21 April 2021, 20:59:44 UTC |
| eac5528 | Denis Yuen | 21 April 2021, 20:59:37 UTC | [maven-release-plugin] prepare release 1.11.0-alpha.2 | 21 April 2021, 20:59:37 UTC |
| 9986f49 | Denis Yuen | 21 April 2021, 18:42:17 UTC | Standardize sequence increment value (#4205) | 21 April 2021, 18:42:17 UTC |
| 2c9ee26 | Charles Overbeck | 21 April 2021, 18:31:18 UTC | Only log privileged admin actions (#4199) Groundwork for https://ucsc-cgl.atlassian.net/browse/SEAB-2152 which requests an alert for privileged actions; currently it is logging all requests, and is very noisy. | 21 April 2021, 18:31:18 UTC |
| ed57274 | Charles Overbeck | 20 April 2021, 21:44:52 UTC | Rotate keys and reencrypt bundle (#4203) New variables because I don't want to break existing branches | 20 April 2021, 21:44:52 UTC |
