1.16.0
Highlighted Changes
- AI topic sentences for workflows
- Pilot for automatic DOIs
- Harvested DOIs from Zenodo-GitHub integration
- Galaxy planemo information in launch-with
- Numerous usability improvements like
- Track whether a GitHub tracked workflow is successfully syncing
- Relax workflow names for odd names including pairs of hyphens and underscores
- Sorting in github app logs
- Dynamic landing page when registering workflows with more helpful and relevant information
- Improved search result presentation
- Display Nextflow engine versions instead of DSL1/2
- Switch to AWS Athena for metrics back-end processing
- Numerous security and dependency updates
Breaking Changes
- None known/intended
What's Changed
- Bump actions/deploy-pages from 2 to 3 by @dependabot in #5765
- Bump actions/configure-pages from 3 to 4 by @dependabot in #5766
- Bump actions/deploy-pages from 3 to 4 by @dependabot in #5773
- cwlavro upgrade by @denis-yuen in #5772
- Bump actions/upload-pages-artifact from 2 to 3 by @dependabot in #5774
- Bump github/codeql-action from 2 to 3 by @dependabot in #5770
- SEAB-6096: Add version Event on tagged GitHub release by @svonworl in #5782
- clean-up zenodo reference to wrong repo by @denis-yuen in #5784
- Bump org.apache.commons:commons-compress from 1.22 to 1.24.0 in /bom-internal by @dependabot in #5775
- Bump actions/cache from 3 to 4 by @dependabot in #5787
- Partial update to java 21 by @denis-yuen in #5805
- SEAB-6083: Remove deprecated properties from Entry by @svonworl in #5811
- Bump org.postgresql:postgresql from 42.4.3 to 42.7.2 in /bom-internal by @dependabot in #5814
- fix scala bytecode compilation and make property by @denis-yuen in #5820
- Bump org.apache.commons:commons-compress from 1.24.0 to 1.26.0 in /bom-internal by @dependabot in #5816
- SEAB-6266: Update deprecated CircleCI images by @ll5zh in #5823
- Remove deprecated aggregated executions field by @kathy-t in #5824
- SEAB-5910: add topic selection to elasticsearch by @hyunnaye in #5827
- DOCK-2468: Improve error message when .dockstore.yml contains a scalar where a list is expected by @svonworl in #5825
- Add security checklist checkbox by @denis-yuen in #5826
- Update reference for breaking API changes plugin by @denis-yuen in #5830
- upgrade postgres versions by @denis-yuen in #5812
- Record number of skipped executions for aggregated metrics by @kathy-t in #5822
- SEAB-5195: Automatically set default version if appropriate by @svonworl in #5829
- Feature/param version openapi by @denis-yuen in #5840
- what if MyWorkflows (and some related objects) was a record by @denis-yuen in #5836
- add tests and fix 500s - weird registries and languages by @denis-yuen in #5838
- add workaround for quay test by @denis-yuen in #5841
- For executions endpoints, fetch workflow version using JPA by @coverbeck in #5832
- SEAB-5965: Optimize non-BioWorkflow "my entry" endpoints by @svonworl in #5845
- Bump org.apache.commons:commons-configuration2 from 2.8.0 to 2.10.1 in /bom-internal by @dependabot in #5849
- SEAB-6225/4825: Add Liquibase lock and Elasticsearch consistency checks by @svonworl in #5843
- Add endpoint to upload AI topic & increase max topic length by @kathy-t in https://github.com //pull/5847
- SEAB-6000: Track GitHub App UNINSTALL events by @svonworl in #5852
- Verify Java imports are sorted by @coverbeck in #5853
- Update ES index after updating AI topic by @kathy-t in #5856
- Bump actions/configure-pages from 4 to 5 by @dependabot in #5857
- SEAB-5015: Use [skip] to run partial CI build by @ll5zh in #5833
- Add skipTests documentation by @ll5zh in #5861
- DOCK-2477: Accept pairs of internal hyphens/underscores in entry names by @svonworl in #5858
- SEAB-6170: "weird tags and ids" fuzzing bug fixes by @svonworl in #5859
- Fix bug in skipTests by @ll5zh in #5863
- SEAB-6173: Remove getPublishedContainerSchema endpoint by @svonworl in #5860
- SEAB-6173: Fix miscellaneous "fuzzing bugs" by @svonworl in #5862
- SEAB-6342: Ignore frozen cwltool dependencies by @ll5zh in #5870
- Don't check OpenAPI for tag builds by @coverbeck in #5867
- DOCK-2312: Add "is this Entry automatically syncing?" endpoint by @svonworl in #5865
- SEAB-6148: Log more diagnostic information by @svonworl in #5821
- SEAB-6174: fix fuzzing 500 errors by @hyunnaye in #5874
- Feature/metrics registry by @denis-yuen in #5873
- fix unit for metric unload for calculated db load by @denis-yuen in #5876
- unit fix for calculated load metric by @denis-yuen in #5877
- SEAB-6388: No longer periodically log diagnostic database pool information by @svonworl in #5882
- SEAB-6310: Log privileged endpoints at webservice startup by @svonworl in #5881
- Feature/remove deprecated endpoint by @denis-yuen in #5886
- save a few bucks on circle ci artifacts by @denis-yuen in #5885
- Make ConnectionPoolHealthCheck always healthy by @coverbeck in #5888
- lambda pagination limit by @denis-yuen in #5889
- SEAB-6420: Add new health check names to endpoint
allowableValuesby @svonworl in #5883 - modest update bouncycastle via transitive by @denis-yuen in #5895
- Autocreate Zenodo DOIs and create shared access links by @kathy-t in #5879
- DOCK-2523: Fix formatting of conceptDOI by @hyunnaye in #5894
- Fix DOI migration by @kathy-t in #5902
- SEAB-6465 Add DB fields to aid periodic tasks - topics by @denis-yuen in #5897
- Add conceptdoi to mocked Zenodo responses by @kathy-t in #5903
- SEAB-6423: Consistently impose SourceFile limits by @svonworl in #5893
- SEAB-6448: Make various WorkflowResource endpoints refuse to update .dockstore.yml-based workflows by @svonworl in #5905
- SEAB-6449: Improve TransactionHelper by @svonworl in #5909
- add skipped limit check by @denis-yuen in #5908
- Bump docker/build-push-action from 5 to 6 by @dependabot in #5914
- (Sonar) Fixed finding: "@OverRide should be used on overriding and implementing methods" by @pixeeai in #5907
- fix up bad merge by @denis-yuen in #5915
- Bump char0n/swagger-editor-validate from 1.3.2 to 1.4.0 by @dependabot in #5916
- Bump urllib3 from 1.26.14 to 1.26.19 in /dockstore-webservice/src/main/resources/requirements/1.14.0 by @dependabot in #5912
- Try ignoring all python dependabot dependencies by @david4096 in #5928
- GitHub pr experiment by @denis-yuen in #5923
- SEAB-6489: Version-level sourcefile size limits by @svonworl in #5932
- SEAB-6488: Modify SourceFile to flag errors by @svonworl in #5934
- Allow DOI selection by @kathy-t in #5940
- Fix sourcefile state field migration by using defaultValue insetad of value by @kathy-t in #5943
- Track AI topic approval by workflow owner by @kathy-t in #5949
- fix engine version metadata update and add test by @denis-yuen in #5953
- Track GitHub release date by @coverbeck in #5950
- DOCK-2534: Fully support CWLs that contain .nan or .inf values by @svonworl in #5968
- new linux machine executor with Java 21 by @denis-yuen in #5961
- Serialize webhook's release payload published_at property as a string by @coverbeck in #5966
- Set successful in lambda release event by @coverbeck in #5975
- More cli docs by @denis-yuen in #5979
- DOCK-2557: Add topic to CollectionEntry by @hyunnaye in #5980
- Support Userless workflows by @coverbeck in #5976
- Add endpoint that gets entry versions that need to be aggregated by @kathy-t in #5970
- Harvest DOIs from Zenodo by @coverbeck in #5880
- DOCK-2565: Notebook name/path clash improvements by @svonworl in #5984
- Fix publishing a userless workflow by @coverbeck in #5985
- SEAB-6484: Improve "representative" version selection by @svonworl in #5991
- Update AWS SDK for AWS Bedrock by @kathy-t in #6003
- SEAB-6508: Allow workflows with DOIs to be restubbed by @svonworl in #6002
- Enabling DOI generation for tags by @coverbeck in #6008
- DOCK-2573: Fix 500 related to AI topic + frozen version by @svonworl in #6011
- Add endpoint that gets all AI topic candidates by @kathy-t in #6006
- DOCK-2589: Fix content type of TRS zip response by @svonworl in #6013
- DOCK-2589: Cherry pick "Only add utf-8 charset parameter to text and json mime types" pr to release branch by @svonworl in #6021
- Upload metrics for other entry types to the correct S3 directory by @kathy-t in #6022
- Add other TRS entry types to getToolId so other entry types can be aggregated by @kathy-t in #6028
New Contributors
Full Changelog: 1.15.4...1.16.0
Contributors
coverbeck, denis-yuen, and 8 other contributors