dockstore/dockstore: 1.16.0

What's Changed

• Bump actions/deploy-pages from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/5765
• Bump actions/configure-pages from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5766
• Bump actions/deploy-pages from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5773
• cwlavro upgrade by @denis-yuen in https://github.com/dockstore/dockstore/pull/5772
• Bump actions/upload-pages-artifact from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/5774
• Bump github/codeql-action from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/5770
• SEAB-6096: Add version Event on tagged GitHub release by @svonworl in https://github.com/dockstore/dockstore/pull/5782
• clean-up zenodo reference to wrong repo by @denis-yuen in https://github.com/dockstore/dockstore/pull/5784
• Bump org.apache.commons:commons-compress from 1.22 to 1.24.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5775
• Bump actions/cache from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5787
• Partial update to java 21 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5805
• SEAB-6083: Remove deprecated properties from Entry by @svonworl in https://github.com/dockstore/dockstore/pull/5811
• Bump org.postgresql:postgresql from 42.4.3 to 42.7.2 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5814
• fix scala bytecode compilation and make property by @denis-yuen in https://github.com/dockstore/dockstore/pull/5820
• Bump org.apache.commons:commons-compress from 1.24.0 to 1.26.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5816
• SEAB-6266: Update deprecated CircleCI images by @ll5zh in https://github.com/dockstore/dockstore/pull/5823
• Remove deprecated aggregated executions field by @kathy-t in https://github.com/dockstore/dockstore/pull/5824
• SEAB-5910: add topic selection to elasticsearch by @hyunnaye in https://github.com/dockstore/dockstore/pull/5827
• DOCK-2468: Improve error message when .dockstore.yml contains a scalar where a list is expected by @svonworl in https://github.com/dockstore/dockstore/pull/5825
• Add security checklist checkbox by @denis-yuen in https://github.com/dockstore/dockstore/pull/5826
• Update reference for breaking API changes plugin by @denis-yuen in https://github.com/dockstore/dockstore/pull/5830
• upgrade postgres versions by @denis-yuen in https://github.com/dockstore/dockstore/pull/5812
• Record number of skipped executions for aggregated metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5822
• SEAB-5195: Automatically set default version if appropriate by @svonworl in https://github.com/dockstore/dockstore/pull/5829
• Feature/param version openapi by @denis-yuen in https://github.com/dockstore/dockstore/pull/5840
• what if MyWorkflows (and some related objects) was a record by @denis-yuen in https://github.com/dockstore/dockstore/pull/5836
• add tests and fix 500s - weird registries and languages by @denis-yuen in https://github.com/dockstore/dockstore/pull/5838
• add workaround for quay test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5841
• For executions endpoints, fetch workflow version using JPA by @coverbeck in https://github.com/dockstore/dockstore/pull/5832
• SEAB-5965: Optimize non-BioWorkflow "my entry" endpoints by @svonworl in https://github.com/dockstore/dockstore/pull/5845
• Bump org.apache.commons:commons-configuration2 from 2.8.0 to 2.10.1 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5849
• SEAB-6225/4825: Add Liquibase lock and Elasticsearch consistency checks by @svonworl in https://github.com/dockstore/dockstore/pull/5843
• Add endpoint to upload AI topic & increase max topic length by @kathy-t in https://github.com/dockstore/dockstore/pull/5847
• SEAB-6000: Track GitHub App UNINSTALL events by @svonworl in https://github.com/dockstore/dockstore/pull/5852
• Verify Java imports are sorted by @coverbeck in https://github.com/dockstore/dockstore/pull/5853
• Update ES index after updating AI topic by @kathy-t in https://github.com/dockstore/dockstore/pull/5856
• Bump actions/configure-pages from 4 to 5 by @dependabot in https://github.com/dockstore/dockstore/pull/5857
• SEAB-5015: Use [skip] to run partial CI build by @ll5zh in https://github.com/dockstore/dockstore/pull/5833
• Add skipTests documentation by @ll5zh in https://github.com/dockstore/dockstore/pull/5861
• DOCK-2477: Accept pairs of internal hyphens/underscores in entry names by @svonworl in https://github.com/dockstore/dockstore/pull/5858
• SEAB-6170: "weird tags and ids" fuzzing bug fixes by @svonworl in https://github.com/dockstore/dockstore/pull/5859
• Fix bug in skipTests by @ll5zh in https://github.com/dockstore/dockstore/pull/5863
• SEAB-6173: Remove getPublishedContainerSchema endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/5860
• SEAB-6173: Fix miscellaneous "fuzzing bugs" by @svonworl in https://github.com/dockstore/dockstore/pull/5862
• SEAB-6342: Ignore frozen cwltool dependencies by @ll5zh in https://github.com/dockstore/dockstore/pull/5870
• Don't check OpenAPI for tag builds by @coverbeck in https://github.com/dockstore/dockstore/pull/5867
• DOCK-2312: Add "is this Entry automatically syncing?" endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/5865
• SEAB-6148: Log more diagnostic information by @svonworl in https://github.com/dockstore/dockstore/pull/5821
• SEAB-6174: fix fuzzing 500 errors by @hyunnaye in https://github.com/dockstore/dockstore/pull/5874
• Feature/metrics registry by @denis-yuen in https://github.com/dockstore/dockstore/pull/5873
• fix unit for metric unload for calculated db load by @denis-yuen in https://github.com/dockstore/dockstore/pull/5876
• unit fix for calculated load metric by @denis-yuen in https://github.com/dockstore/dockstore/pull/5877
• SEAB-6388: No longer periodically log diagnostic database pool information by @svonworl in https://github.com/dockstore/dockstore/pull/5882
• SEAB-6310: Log privileged endpoints at webservice startup by @svonworl in https://github.com/dockstore/dockstore/pull/5881
• Feature/remove deprecated endpoint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5886
• save a few bucks on circle ci artifacts by @denis-yuen in https://github.com/dockstore/dockstore/pull/5885
• Make ConnectionPoolHealthCheck always healthy by @coverbeck in https://github.com/dockstore/dockstore/pull/5888
• lambda pagination limit by @denis-yuen in https://github.com/dockstore/dockstore/pull/5889
• SEAB-6420: Add new health check names to endpoint allowableValues by @svonworl in https://github.com/dockstore/dockstore/pull/5883
• modest update bouncycastle via transitive by @denis-yuen in https://github.com/dockstore/dockstore/pull/5895
• Autocreate Zenodo DOIs and create shared access links by @kathy-t in https://github.com/dockstore/dockstore/pull/5879
• DOCK-2523: Fix formatting of conceptDOI by @hyunnaye in https://github.com/dockstore/dockstore/pull/5894
• Fix DOI migration by @kathy-t in https://github.com/dockstore/dockstore/pull/5902
• SEAB-6465 Add DB fields to aid periodic tasks - topics by @denis-yuen in https://github.com/dockstore/dockstore/pull/5897
• Add conceptdoi to mocked Zenodo responses by @kathy-t in https://github.com/dockstore/dockstore/pull/5903
• SEAB-6423: Consistently impose SourceFile limits by @svonworl in https://github.com/dockstore/dockstore/pull/5893
• SEAB-6448: Make various WorkflowResource endpoints refuse to update .dockstore.yml-based workflows by @svonworl in https://github.com/dockstore/dockstore/pull/5905
• SEAB-6449: Improve TransactionHelper by @svonworl in https://github.com/dockstore/dockstore/pull/5909
• add skipped limit check by @denis-yuen in https://github.com/dockstore/dockstore/pull/5908
• Bump docker/build-push-action from 5 to 6 by @dependabot in https://github.com/dockstore/dockstore/pull/5914
• (Sonar) Fixed finding: "@Override should be used on overriding and implementing methods" by @pixeeai in https://github.com/dockstore/dockstore/pull/5907
• fix up bad merge by @denis-yuen in https://github.com/dockstore/dockstore/pull/5915
• Bump char0n/swagger-editor-validate from 1.3.2 to 1.4.0 by @dependabot in https://github.com/dockstore/dockstore/pull/5916
• Bump urllib3 from 1.26.14 to 1.26.19 in /dockstore-webservice/src/main/resources/requirements/1.14.0 by @dependabot in https://github.com/dockstore/dockstore/pull/5912
• Try ignoring all python dependabot dependencies by @david4096 in https://github.com/dockstore/dockstore/pull/5928
• GitHub pr experiment by @denis-yuen in https://github.com/dockstore/dockstore/pull/5923
• SEAB-6489: Version-level sourcefile size limits by @svonworl in https://github.com/dockstore/dockstore/pull/5932
• SEAB-6488: Modify SourceFile to flag errors by @svonworl in https://github.com/dockstore/dockstore/pull/5934
• Allow DOI selection by @kathy-t in https://github.com/dockstore/dockstore/pull/5940
• Fix sourcefile state field migration by using defaultValue insetad of value by @kathy-t in https://github.com/dockstore/dockstore/pull/5943
• Track AI topic approval by workflow owner by @kathy-t in https://github.com/dockstore/dockstore/pull/5949
• fix engine version metadata update and add test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5953
• Track GitHub release date by @coverbeck in https://github.com/dockstore/dockstore/pull/5950
• DOCK-2534: Fully support CWLs that contain .nan or .inf values by @svonworl in https://github.com/dockstore/dockstore/pull/5968
• new linux machine executor with Java 21 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5961
• Serialize webhook's release payload published_at property as a string by @coverbeck in https://github.com/dockstore/dockstore/pull/5966
• Set successful in lambda release event by @coverbeck in https://github.com/dockstore/dockstore/pull/5975
• More cli docs by @denis-yuen in https://github.com/dockstore/dockstore/pull/5979
• DOCK-2557: Add topic to CollectionEntry by @hyunnaye in https://github.com/dockstore/dockstore/pull/5980
• Support Userless workflows by @coverbeck in https://github.com/dockstore/dockstore/pull/5976
• Add endpoint that gets entry versions that need to be aggregated by @kathy-t in https://github.com/dockstore/dockstore/pull/5970
• Harvest DOIs from Zenodo by @coverbeck in https://github.com/dockstore/dockstore/pull/5880
• DOCK-2565: Notebook name/path clash improvements by @svonworl in https://github.com/dockstore/dockstore/pull/5984
• Fix publishing a userless workflow by @coverbeck in https://github.com/dockstore/dockstore/pull/5985
• SEAB-6484: Improve "representative" version selection by @svonworl in https://github.com/dockstore/dockstore/pull/5991
• Update AWS SDK for AWS Bedrock by @kathy-t in https://github.com/dockstore/dockstore/pull/6003
• SEAB-6508: Allow workflows with DOIs to be restubbed by @svonworl in https://github.com/dockstore/dockstore/pull/6002
• Enabling DOI generation for tags by @coverbeck in https://github.com/dockstore/dockstore/pull/6008
• DOCK-2573: Fix 500 related to AI topic + frozen version by @svonworl in https://github.com/dockstore/dockstore/pull/6011
• Add endpoint that gets all AI topic candidates by @kathy-t in https://github.com/dockstore/dockstore/pull/6006
• DOCK-2589: Fix content type of TRS zip response by @svonworl in https://github.com/dockstore/dockstore/pull/6013
• DOCK-2589: Cherry pick "Only add utf-8 charset parameter to text and json mime types" pr to release branch by @svonworl in https://github.com/dockstore/dockstore/pull/6021
• Upload metrics for other entry types to the correct S3 directory by @kathy-t in https://github.com/dockstore/dockstore/pull/6022
• Add other TRS entry types to getToolId so other entry types can be aggregated by @kathy-t in https://github.com/dockstore/dockstore/pull/6028

New Contributors

• @ll5zh made their first contribution in https://github.com/dockstore/dockstore/pull/5823
• @pixeeai made their first contribution in https://github.com/dockstore/dockstore/pull/5907

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.4...1.16.0