| 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 |
| 11bc6bc | Denis Yuen | 20 April 2021, 19:56:00 UTC | Feature/missing timestamps (#4197) * Making sure propose migration scripts works | 20 April 2021, 19:56:00 UTC |
| 182cdc4 | Denis Yuen | 20 April 2021, 14:32:30 UTC | Db consistency take 2 (#4195) * Update to deal with https://github.com/dockstore/dockstore/security/dependabot/bom-internal/pom.xml/org.eclipse.jetty:jetty-io/open * Remove exceptions for liquibase diff * Bad merge and snyk warning | 20 April 2021, 14:32:30 UTC |
| 07aef63 | Gary Luu | 16 April 2021, 22:51:54 UTC | Feature/seab 2797/oom (#4190) * Disable most tests, remove Java memory limit * Remove manual cgroup setting | 16 April 2021, 22:51:54 UTC |
| 580c3e6 | Gary Luu | 16 April 2021, 18:03:54 UTC | Feature/seab 2783/orcid token details (#4189) * Save scope and expiration date * Add migration * Update previous rows * Make scope an enum | 16 April 2021, 18:03:54 UTC |
| 38d2dd5 | Denis Yuen | 16 April 2021, 15:22:19 UTC | Update to deal with jetty warning (#4181) * Update to deal with https://github.com/dockstore/dockstore/security/dependabot/bom-internal/pom.xml/org.eclipse.jetty:jetty-io/open * Will need to hold back liquibase | 16 April 2021, 15:22:19 UTC |
| 580a271 | Denis Yuen | 15 April 2021, 18:34:04 UTC | Feature/trs update (#4187) * Galaxy parameters * WIP in attempt to get access to 3.0.21 and repair custon template behaviour * Seems better, but still not totally fixed https://github.com/swagger-api/swagger-codegen/issues/10107 * Might as well * Add back fix for #3284 * Thank you for tests, seems like transient templates need to be included Even if not modified | 15 April 2021, 18:34:04 UTC |
| 706f271 | David Steinberg | 15 April 2021, 18:02:19 UTC | Add openAPI schema annotations to match swagger for Version.java (#4188) * Add openAPI schema annotations to match swagger * Update openapi.yaml | 15 April 2021, 18:02:19 UTC |
| 6265e21 | David Steinberg | 14 April 2021, 20:57:27 UTC | Add sonarcloud scanning to CircleCI (#4183) * Try using the pom method of scanning with sonar * Sonar collides on multimodule projects * Add sonar version to pluginmanagement | 14 April 2021, 20:57:27 UTC |
| e3ab4f5 | Charles Overbeck | 13 April 2021, 23:01:48 UTC | Upgrade Hibernate and run unit tests with PG 11 (#4167) https://ucsc-cgl.atlassian.net/browse/SEAB-2676, Change unit tests to use PG 11, which opened a whole can of worms. Lots of details in SEAB-2676. Short version here: Postgres 10 introduced support for SQL Identity. Pre PG-10, Liquibase/Hibernate would simulate SQL Identity with SQL Sequence. When we upgraded from PG 9 to PG11, Liquibase took advantage of SQL Identity, but Hibernate didn't, leading to the propose_migrations failures (Liquibase would generate identity, Hibernate would generate Sequence) We need to tell Hibernate to use the PG10 dialect in the dockstore.yml, so that it will also generate Identity, but our version of Hibernate doesn't have that dialect. So, upgrade Hibernate to a version that has the PostgreSQL10 dialect. The version bundled with DropWizard (we were behind), supports it. So upgrading it just means not pinning to an older version. And then chasing down the enforcer plugin errors. Also: Run CWL tests in CircleCI, remove Travis And, saw some OOM errors, which removing the unused scala plugin seemed to fix. | 13 April 2021, 23:01:48 UTC |
| 039e8f7 | Denis Yuen | 12 April 2021, 15:47:37 UTC | Add endpoint to retrieve user organizations on github (#4171) * PR feedback, added test | 12 April 2021, 15:47:37 UTC |
| f14750d | David Steinberg | 09 April 2021, 22:43:28 UTC | Change POM Flatten behavior (#4173) * Move flatten to validate phase and rename outputs * Add renamed poms * Remove old filenames. | 09 April 2021, 22:43:28 UTC |
| c7072e5 | NatalieEO | 09 April 2021, 20:30:34 UTC | search term length limit (#4177) *https://ucsc-cgl.atlassian.net/browse/SEAB-2515 Fail request when search term is over length limit to prevent ES from going down. | 09 April 2021, 20:30:34 UTC |
| 0cc0769 | NatalieEO | 09 April 2021, 19:18:20 UTC | 4080/lazy load versions more often (#4135) #4080 Pairs with dockstore/dockstore-ui2#1180 Created new columns and migration to fill to replace the calculated columns for input and output file formats of an entry. This ties into lazy loading versions because those calculated columns were made the versions always get fetched despite the lazy setting being enabled. | 09 April 2021, 19:18:20 UTC |
| 517d6e1 | Wendy Zhang | 09 April 2021, 18:48:49 UTC | Feature/4052/entry languages (#4150) * modified collectionentry constructor * getting descriptor type for workflows * Added testGetWorkflowDescriptor * returns "verified" boolean * list of descriptor types * Get it to compile * Fix DAO for tool descriptor * else if added * fixed getWorkflowsDescriptorTypes * clean up getWorkflowsDescriptorTypes * getSingleResult instead of getResultList Co-authored-by: Gary Luu <garylau.work@gmail.com> | 09 April 2021, 18:48:49 UTC |
| 711b0d7 | Denis Yuen | 08 April 2021, 14:04:29 UTC | Feature/round up (#4170) * Null check for #3635 * Comment for #3255 * Doc for #3255 and error message for #3855 | 08 April 2021, 14:04:29 UTC |
| 803e86d | Walter Shands | 07 April 2021, 23:59:53 UTC | upgrade cromwell artifacts (#4169) * upgrade cromwell artifacts * update licenses | 07 April 2021, 23:59:53 UTC |
| 6ca6dbf | Gary Luu | 07 April 2021, 18:05:27 UTC | Feature/seab 2402/orcid put code (#4162) * Add columns * Add migration * Add ORCID put * Modify endpoint to update when already exported | 07 April 2021, 18:05:27 UTC |
| 7d3668c | Richard-Hansen | 06 April 2021, 19:32:50 UTC | Feature/2669/flattenedPOMs (#4158) Generating flattened POMs. SEAB-2669. | 06 April 2021, 19:32:50 UTC |
| f1171b6 | Walter Shands | 05 April 2021, 18:38:08 UTC | return 422 on Galaxy plugin call lint exception (#4160) * return 422 on Galaxy plugin call lint exception * handle missing descriptor | 05 April 2021, 18:38:08 UTC |
| 0e34849 | Walter Shands | 05 April 2021, 15:25:43 UTC | catch nextflow parsing exception (#4159) | 05 April 2021, 15:25:43 UTC |
| 2f3e0b8 | Gary Luu | 05 April 2021, 14:50:26 UTC | Feature/4121/ignore unknown properties (#4156) * Ignore unknown properties * Modify test | 05 April 2021, 14:50:26 UTC |
| 36dd73d | Walter Shands | 02 April 2021, 03:34:25 UTC | fix scala warnings for one artifact (#4155) * fix scala warnings for one artifact | 02 April 2021, 03:34:25 UTC |
| 4fda4e8 | Gary Luu | 01 April 2021, 19:06:31 UTC | Truncate description length (#4157) * Truncate description length * Fix checkstyle | 01 April 2021, 19:06:31 UTC |
| 74699b9 | David Steinberg | 01 April 2021, 17:00:37 UTC | Upgrade packages in the docker build to check if quay vulns are fixed (#4151) Add upgrade to same line as rest of apt commands following dockerfile best practices | 01 April 2021, 17:00:37 UTC |
| 50fa284 | Walter Shands | 31 March 2021, 22:10:04 UTC | Send 422 instead of 400 on cwl or wdl parse errors (#4154) * return 422 for WDL parse errors * send 422 for CWL parse error Addresses #1322 | 31 March 2021, 22:10:04 UTC |
| 42945da | Wendy Zhang | 31 March 2021, 17:44:19 UTC | get labels (#4138) * get labels * getting labels(not the most optimal way) * discard unused imports * remove comments * resolve merge conflicts * update | 31 March 2021, 17:44:19 UTC |
| f90f59f | Gary Luu | 31 March 2021, 14:23:13 UTC | Update postgres of plugin version (#4153) | 31 March 2021, 14:23:13 UTC |
| 8eb270a | Denis Yuen | 30 March 2021, 23:22:52 UTC | Feature/http client risky cleanup (#4124) * Stuff that I noticed during https://github.com/dockstore/dockstore/pull/4120 But wasn't sure if it would break anything if I cleaned it up | 30 March 2021, 23:22:52 UTC |
| 18217ad | Wendy Zhang | 30 March 2021, 15:37:41 UTC | Feature/workflows tools lengths 2 (#4118) * cherry pick the added get workflow & tools lengths methods * modified test for getting workflows and tools lengths * Modified testWorkflowsToolsLength * Update .gitignore * test for getting number of tools * added 2 tests for getting number of workflows and tools length correctly * number of workflows/tools displayed in collection now is the same as the actual * Update OrganizationIT.java * yq version 3.3.2 build * different versions of workflows are counted(assertion is failing) * Revert "different versions of workflows are counted(assertion is failing)" This reverts commit 2a1e7730809be73f0558ad2b3c58b0ed5c1e68c4. * Update openapi.yaml * typo in comments * getting correct number of workflows even with versions * using enum and generated description for two variables in openapi | 30 March 2021, 15:37:41 UTC |
| 6541fe3 | Charles Overbeck | 30 March 2021, 00:10:22 UTC | Switch to ES 7.9.3 (#4142) AWS Elasticsearch does not yet support 7.10 | 30 March 2021, 00:10:22 UTC |
| a341c5b | Denis Yuen | 29 March 2021, 23:59:29 UTC | Feature/docker client swap (#4147) * Swap docker client * See if this is better now | 29 March 2021, 23:59:29 UTC |
| b9cf6cb | Denis Yuen | 29 March 2021, 16:12:10 UTC | Feature/release cli update (#4148) * [maven-release-plugin] prepare release 1.11.0-alpha.1 * [maven-release-plugin] prepare for next development iteration | 29 March 2021, 16:12:10 UTC |
| 8d31427 | Charles Overbeck | 26 March 2021, 20:35:16 UTC | Signal Retry to Lambda on GitHub Rate Limit failure (#4134) #3770 Use a variant of RateLimitHandler.FAIL to cause failure, then throw 500 error for Lambda. In looking at this, I now consider the RateLimitHandler.WAIT we used to use as a possible culprit for our most recent prod incident. The default WAIT handler will wait until the GitHub rate limit resets, which can be be lots of minutes, since the rate limit resets every hour. I couldn't find any proof of it, but it would block a thread and have an open DB transaction, so it does seem potentially dangerous. Regarding other points on the ticket, a ConstraintViolation already signals retry -- it happens when committing the transaction fails, and that gets translated to a 5xx error. | 26 March 2021, 20:35:16 UTC |
| 5d36822 | Denis Yuen | 26 March 2021, 17:20:03 UTC | Whitelist dependencies for PGP plugin (#4145) * Well * think keysmap is the one that counts | 26 March 2021, 17:20:03 UTC |
| f59cd56 | Denis Yuen | 26 March 2021, 15:12:40 UTC | formatting fix [skip CI] (#4144) | 26 March 2021, 15:12:40 UTC |
| f80e216 | Gary Luu | 25 March 2021, 22:31:55 UTC | Feature/add publish request setter (#4131) * Add PublishRequest setter * update swagger * Fix | 25 March 2021, 22:31:55 UTC |
| f7c347b | Gary Luu | 25 March 2021, 20:44:03 UTC | Handle decode issue everywhere in TRS (#4122) | 25 March 2021, 20:44:03 UTC |
| 1200a9f | Denis Yuen | 25 March 2021, 20:18:11 UTC | deterministic sorting of openapi yaml? (#4136) * deterministic sorting with updated swagger * Make sure build works without yq Is PGP failure deterministic? (turns out no, it is transient) | 25 March 2021, 20:18:11 UTC |
| 007ef12 | Walter Shands | 24 March 2021, 21:27:54 UTC | WDL 1.1 early support (#4115) * skip validation for WDL 1.1 * adjust error message if version 1.1 | 24 March 2021, 21:27:54 UTC |
| 65eded6 | Wendy Zhang | 24 March 2021, 21:00:36 UTC | Feature/collections length (#4129) * added the method to return collections length, without tests * test for getting number of collections * Update openapi.yaml * Update openapi.yaml * yq 3.3.2? * make sure no collection returns 0 Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> | 24 March 2021, 21:00:36 UTC |
| 1c34928 | Charles Overbeck | 24 March 2021, 18:17:19 UTC | External elasticsearch #3519 More options for ES in configuration. I was going initially going to connect with https using basic auth, but then decided against it. So the additional parameters aren't being used, but I figured I leave them in You're only supposed to have one RestHighLevelClient for your application, so changed. Noticed in trying to figure out performance differences. I still close the ES client on shutdown, although it's probably overkill, using DropWizard lifecycle, which is a new dependency. | 24 March 2021, 18:17:19 UTC |
| 30272d6 | Denis Yuen | 23 March 2021, 18:39:26 UTC | Feature/snyk round up (#4128) * Netty update SEAB-2606 2607 2608 2625 2631 etc * SEAB-2602 2614 2655 etc * Address CVE * dealing with https://github.com/eclipse/jetty.project/issues/6001 | 23 March 2021, 18:39:26 UTC |
| b29dedc | Gary Luu | 22 March 2021, 20:06:35 UTC | Remove warnings (#4125) | 22 March 2021, 20:06:35 UTC |
| 5f17ec1 | Gary Luu | 22 March 2021, 18:51:04 UTC | Feature/seab 2622/cromwell test failures (#4130) * Remove client tests * Remove dockstore-client dependency | 22 March 2021, 18:51:04 UTC |
| 66207e4 | Gregory F J Hogue | 22 March 2021, 14:12:51 UTC | liquibase-maven-plugin 3.6.3 -> 3.10.3 (#4126) * switch unit_test to use PG11 on Circle * take migrations from circle unit_test * no default values * reapply sourcefile policy * fix drop policy * split off policy changesets * more policies * correct table * try bumping liquibase-maven-plugin * revert unit tests Postgres to 9 (admit defeat for now) | 22 March 2021, 14:12:51 UTC |
| 10ef956 | Gary Luu | 19 March 2021, 21:36:07 UTC | Feature/3785/publish orcid endpoint (#4097) * initial endpoint * Update openapi * Handle version and check DOI * Fixes * Update openapi * Add test * PR changes * Missed one * Last PR changes * Oops | 19 March 2021, 21:36:07 UTC |
| cbd4248 | Denis Yuen | 19 March 2021, 18:34:06 UTC | namespace cache for testing on circle CI (#4120) * WIP, namespace cache for testing on circle CI https://github.com/square/okhttp/issues/6214 interceptors would be a choice to add a fragment as suggested https://square.github.io/okhttp/interceptors/ but non-logging interceptors seem broken in the kohsuke library * My skin is not my own * It's not who I am underneath, but what I do that defines me. * duh, need this to actually save a new cache * Badge will never work since we now push images Let's me test the performance of the new cache | 19 March 2021, 18:34:06 UTC |
| 16ee350 | Gary Luu | 18 March 2021, 19:03:31 UTC | Feature/2488/double registry property (#4108) * Add comments fix enum * Update openapi * Remove comments | 18 March 2021, 19:03:31 UTC |
