Releases: dockstore/dockstore
Releases · dockstore/dockstore
1.17.1
What's Changed
- DOCK-2605: Fix TRS endpoint response code by @svonworl in #6114
- SEAB-7184: Generate DOI for workflow with existent-but-empty author name by @svonworl in #6120
- SEAB-7157: Fix TRS 500 by @svonworl in #6121
- Return 404 if tooltester logs don't exist in S3 by @kathy-t in #6128
- Add database constraints to prevent duplicate DOI initiator types by @kathy-t in #6126
Full Changelog: 1.17.0...1.17.1
Contributors
kathy-t and svonworl
Assets 2
1.17.0
Highlighted Changes
- R Jupyter notebook support
- Preview of Snakemake support
- Search cards (makes it easier to review search results)
- Toil and Terra anonymous metrics integration
- Automatic DOI enhancements
- back-end changes for retroactive issuing
- many bugfixes and tweaks
Breaking Changes
- None known/intended
What's Changed
- DOCK-2589: Only add utf-8 charset to text and json mime types by @svonworl in #6014
- Feature/cwlavro update by @denis-yuen in #6030
- trs extensions to facilitate toil development by @denis-yuen in #6005
- SEAB-5762: Implement pagination to getWorkflowVersions endpoint by @hyunnaye in #6001
- Harvest GitHub-Zenodo DOIs based on latestReleaseDate by @coverbeck in #6035
- DOCK-2582: Better exception messages by @svonworl in #6037
- DOCK-2571: Improve relative readMePath error message by @svonworl in #6040
- Use reusable deploy artifacts workflow by @kathy-t in #6043
- Add id-token write permisson for deploying db docs by @kathy-t in #6047
- update dropwizard to 4.0.11 by @denis-yuen in #5804
- DOCK-2591: Sort "representative" version first by default by @svonworl in #6042
- Adjust quay image sha by @svonworl in #6052
- SEAB-6464: Infer .dockstore.yml by @svonworl in #5939
- Revert reusable workflow revert by @kathy-t in #6054
- DOCK-2600: Fix backlinks from Zenodo DOI records by @svonworl in #6053
- SEAB-6341: add include query param to version endpoints by @hyunnaye in #6055
- fix runner dependencies metadata resource call and add test by @denis-yuen in #6062
- test with postgres 16.4 by @denis-yuen in #6063
- Update Surefire to non-milestone version by @coverbeck in #5981
- put image digest in both places for dockstore-deploy builds by @denis-yuen in #6068
- Feature/fix swagger validation by @denis-yuen in #6069
- update to newer dropwizard and logback by @denis-yuen in #6070
- Add lastModified and selected_concept_doi to elastic search object for search cards by @kathy-t in #6071
- fix regression integration tests by @denis-yuen in #6072
- SEAB-6917: add Toil to Partner enum by @hyunnaye in #6073
- Fix bad openapi.yaml merge by @kathy-t in #6079
- Put back reusable deploy workflow by @kathy-t in #6080
- test action ubuntu version by @denis-yuen in #6082
- DOCK-2608: Incorporate other signals into version sorting by @svonworl in #6081
- DOCK-2591: Change default version sort order to descending by @svonworl in #6083
- SEAB-6995: Reenable "authorless" DOIs by @svonworl in #6084
- SEAB-6803: Implement "versions needing a retroactive DOI" endpoint by @svonworl in #6086
- SEAB-6803: Create retroactive automatic DOI endpoint by @svonworl in #6087
- Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 in /bom-internal by @dependabot in #6091
- Snakemake tests and some clean-up by @denis-yuen in #6085
- add markdown conversion to html and run current tests by @denis-yuen in #6093
- SEAB-6978: Lock down "platform partner" users by @svonworl in #6089
- SEAB-7080: Use tag creation date as DOI publication date by @svonworl in #6096
- Add snakemake plugin to webservice image by @denis-yuen in #6097
- SEAB-7089: Fix slow-loading user profile "Activity" section by @svonworl in #6098
- DOCK-2585: remove restub functionality by @hyunnaye in #6094
- SMK app log tweak based on qa testing by @denis-yuen in #6099
- Cherry-pick notebook commit to release by @svonworl in #6105
- SEAB-6978: Correct "metrics robot" design by @svonworl in #6104
- SEAB-7134: Fix auth-related 500 by @svonworl in #6106
- further sanitize sourcefiles, strict by @denis-yuen in #6103
- update snakemake plugin by @denis-yuen in #6107
- Bump snakemake plugin version by @kathy-t in #6109
Full Changelog: 1.16.6...1.17.0
Contributors
coverbeck, denis-yuen, and 4 other contributors
Assets 2
1.17.0-beta.1
What's Changed
- Cherry-pick notebook commit to release by @svonworl in #6105
- SEAB-6978: Correct "metrics robot" design by @svonworl in #6104
- SEAB-7134: Fix auth-related 500 by @svonworl in #6106
- further sanitize sourcefiles, strict by @denis-yuen in #6103
- update snakemake plugin by @denis-yuen in #6107
Full Changelog: 1.17.0-beta.0...1.17.0-beta.1
Contributors
denis-yuen and svonworl
Assets 2
1.17.0-beta.0
What's Changed
- DOCK-2589: Only add utf-8 charset to text and json mime types by @svonworl in #6014
- Feature/cwlavro update by @denis-yuen in #6030
- trs extensions to facilitate toil development by @denis-yuen in #6005
- SEAB-5762: Implement pagination to getWorkflowVersions endpoint by @hyunnaye in #6001
- Harvest GitHub-Zenodo DOIs based on latestReleaseDate by @coverbeck in #6035
- DOCK-2582: Better exception messages by @svonworl in #6037
- DOCK-2571: Improve relative readMePath error message by @svonworl in #6040
- Use reusable deploy artifacts workflow by @kathy-t in #6043
- Add id-token write permisson for deploying db docs by @kathy-t in #6047
- update dropwizard to 4.0.11 by @denis-yuen in #5804
- DOCK-2591: Sort "representative" version first by default by @svonworl in #6042
- Adjust quay image sha by @svonworl in #6052
- SEAB-6464: Infer .dockstore.yml by @svonworl in #5939
- Revert reusable workflow revert by @kathy-t in #6054
- DOCK-2600: Fix backlinks from Zenodo DOI records by @svonworl in #6053
- SEAB-6341: add include query param to version endpoints by @hyunnaye in #6055
- fix runner dependencies metadata resource call and add test by @denis-yuen in #6062
- test with postgres 16.4 by @denis-yuen in #6063
- Update Surefire to non-milestone version by @coverbeck in #5981
- put image digest in both places for dockstore-deploy builds by @denis-yuen in #6068
- Feature/fix swagger validation by @denis-yuen in #6069
- update to newer dropwizard and logback by @denis-yuen in #6070
- Add lastModified and selected_concept_doi to elastic search object for search cards by @kathy-t in #6071
- fix regression integration tests by @denis-yuen in #6072
- SEAB-6917: add Toil to Partner enum by @hyunnaye in #6073
- Fix bad openapi.yaml merge by @kathy-t in #6079
- Put back reusable deploy workflow by @kathy-t in #6080
- test action ubuntu version by @denis-yuen in #6082
- DOCK-2608: Incorporate other signals into version sorting by @svonworl in #6081
- DOCK-2591: Change default version sort order to descending by @svonworl in #6083
- SEAB-6995: Reenable "authorless" DOIs by @svonworl in #6084
- SEAB-6803: Implement "versions needing a retroactive DOI" endpoint by @svonworl in #6086
- SEAB-6803: Create retroactive automatic DOI endpoint by @svonworl in #6087
- Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 in /bom-internal by @dependabot in #6091
- Snakemake tests and some clean-up by @denis-yuen in #6085
- add markdown conversion to html and run current tests by @denis-yuen in #6093
- SEAB-6978: Lock down "platform partner" users by @svonworl in #6089
- SEAB-7080: Use tag creation date as DOI publication date by @svonworl in #6096
- Add snakemake plugin to webservice image by @denis-yuen in #6097
- SEAB-7089: Fix slow-loading user profile "Activity" section by @svonworl in #6098
- DOCK-2585: remove restub functionality by @hyunnaye in #6094
- SMK app log tweak based on qa testing by @denis-yuen in #6099
Full Changelog: 1.16.6...1.17.0-beta.0
Contributors
coverbeck, denis-yuen, and 4 other contributors
Assets 2
1.16.6
Contributors
hyunnaye and svonworl
Assets 2
1.16.5
What's Changed
- Cherry pick "DOCK-2600: Fix backlinks from Zenodo DOI records" to hotfix by @svonworl in #6058
- SEAB-6831: Fix aborted DOI alias creation during bot push by @svonworl in #6057
- postgres 16.4 update by @denis-yuen in #6064
- Fix http imports from a local secondary file by @denis-yuen in #6066
Full Changelog: 1.16.3...1.16.5
Contributors
denis-yuen and svonworl
Assets 2
1.16.3
Full Changelog: 1.16.1...1.16.3
What's Changed
- DOCK-2571: Cherry pick "improve relative readMePath error message" to hotfix branch by @svonworl in #6041
- Add enableAutoDois field to .dockstore.yml and allow disabling auto DOIs by @kathy-t in #6045
- Handle expired GitHub token by @coverbeck in #6051
Full Changelog: 1.16.0...1.16.3
Contributors
coverbeck, kathy-t, and svonworl
Assets 2
1.16.2
What's Changed
- DOCK-2571: Cherry pick "improve relative readMePath error message" to hotfix branch by @svonworl in #6041
- Add enableAutoDois field to .dockstore.yml and allow disabling auto DOIs by @kathy-t in #6045
- Handle expired GitHub token by @coverbeck in #6051
Full Changelog: 1.16.0...1.16.2
Contributors
coverbeck, kathy-t, and svonworl
Assets 2
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 migrat...
Contributors
coverbeck, denis-yuen, and 8 other contributors
Assets 2
1.16.0-beta.8
What's Changed
Full Changelog: 1.16.0-beta.7...1.16.0-beta.8
Contributors
kathy-t