What's Changed

DOCK-2605: Fix TRS endpoint response code by @svonworl in https://github.com/dockstore/dockstore/pull/6114
SEAB-7184: Generate DOI for workflow with existent-but-empty author name by @svonworl in https://github.com/dockstore/dockstore/pull/6120
SEAB-7157: Fix TRS 500 by @svonworl in https://github.com/dockstore/dockstore/pull/6121
Return 404 if tooltester logs don't exist in S3 by @kathy-t in https://github.com/dockstore/dockstore/pull/6128
Add database constraints to prevent duplicate DOI initiator types by @kathy-t in https://github.com/dockstore/dockstore/pull/6126

Full Changelog: https://github.com/dockstore/dockstore/compare/1.17.0...1.17.1

- Java
Published by kathy-t about 1 year ago

What's Changed

DOCK-2589: Only add utf-8 charset to text and json mime types by @svonworl in https://github.com/dockstore/dockstore/pull/6014
Feature/cwlavro update by @denis-yuen in https://github.com/dockstore/dockstore/pull/6030
trs extensions to facilitate toil development by @denis-yuen in https://github.com/dockstore/dockstore/pull/6005
SEAB-5762: Implement pagination to getWorkflowVersions endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/6001
Harvest GitHub-Zenodo DOIs based on latestReleaseDate by @coverbeck in https://github.com/dockstore/dockstore/pull/6035
DOCK-2582: Better exception messages by @svonworl in https://github.com/dockstore/dockstore/pull/6037
DOCK-2571: Improve relative readMePath error message by @svonworl in https://github.com/dockstore/dockstore/pull/6040
Use reusable deploy artifacts workflow by @kathy-t in https://github.com/dockstore/dockstore/pull/6043
Add id-token write permisson for deploying db docs by @kathy-t in https://github.com/dockstore/dockstore/pull/6047
update dropwizard to 4.0.11 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5804
DOCK-2591: Sort "representative" version first by default by @svonworl in https://github.com/dockstore/dockstore/pull/6042
Adjust quay image sha by @svonworl in https://github.com/dockstore/dockstore/pull/6052
SEAB-6464: Infer .dockstore.yml by @svonworl in https://github.com/dockstore/dockstore/pull/5939
Revert reusable workflow revert by @kathy-t in https://github.com/dockstore/dockstore/pull/6054
DOCK-2600: Fix backlinks from Zenodo DOI records by @svonworl in https://github.com/dockstore/dockstore/pull/6053
SEAB-6341: add include query param to version endpoints by @hyunnaye in https://github.com/dockstore/dockstore/pull/6055
fix runner dependencies metadata resource call and add test by @denis-yuen in https://github.com/dockstore/dockstore/pull/6062
test with postgres 16.4 by @denis-yuen in https://github.com/dockstore/dockstore/pull/6063
Update Surefire to non-milestone version by @coverbeck in https://github.com/dockstore/dockstore/pull/5981
put image digest in both places for dockstore-deploy builds by @denis-yuen in https://github.com/dockstore/dockstore/pull/6068
Feature/fix swagger validation by @denis-yuen in https://github.com/dockstore/dockstore/pull/6069
update to newer dropwizard and logback by @denis-yuen in https://github.com/dockstore/dockstore/pull/6070
Add lastModified and selectedconceptdoi to elastic search object for search cards by @kathy-t in https://github.com/dockstore/dockstore/pull/6071
fix regression integration tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/6072
SEAB-6917: add Toil to Partner enum by @hyunnaye in https://github.com/dockstore/dockstore/pull/6073
Fix bad openapi.yaml merge by @kathy-t in https://github.com/dockstore/dockstore/pull/6079
Put back reusable deploy workflow by @kathy-t in https://github.com/dockstore/dockstore/pull/6080
test action ubuntu version by @denis-yuen in https://github.com/dockstore/dockstore/pull/6082
DOCK-2608: Incorporate other signals into version sorting by @svonworl in https://github.com/dockstore/dockstore/pull/6081
DOCK-2591: Change default version sort order to descending by @svonworl in https://github.com/dockstore/dockstore/pull/6083
SEAB-6995: Reenable "authorless" DOIs by @svonworl in https://github.com/dockstore/dockstore/pull/6084
SEAB-6803: Implement "versions needing a retroactive DOI" endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/6086
SEAB-6803: Create retroactive automatic DOI endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/6087
Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/6091
Snakemake tests and some clean-up by @denis-yuen in https://github.com/dockstore/dockstore/pull/6085
add markdown conversion to html and run current tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/6093
SEAB-6978: Lock down "platform partner" users by @svonworl in https://github.com/dockstore/dockstore/pull/6089
SEAB-7080: Use tag creation date as DOI publication date by @svonworl in https://github.com/dockstore/dockstore/pull/6096
Add snakemake plugin to webservice image by @denis-yuen in https://github.com/dockstore/dockstore/pull/6097
SEAB-7089: Fix slow-loading user profile "Activity" section by @svonworl in https://github.com/dockstore/dockstore/pull/6098
DOCK-2585: remove restub functionality by @hyunnaye in https://github.com/dockstore/dockstore/pull/6094
SMK app log tweak based on qa testing by @denis-yuen in https://github.com/dockstore/dockstore/pull/6099
Cherry-pick notebook commit to release by @svonworl in https://github.com/dockstore/dockstore/pull/6105
SEAB-6978: Correct "metrics robot" design by @svonworl in https://github.com/dockstore/dockstore/pull/6104
SEAB-7134: Fix auth-related 500 by @svonworl in https://github.com/dockstore/dockstore/pull/6106
further sanitize sourcefiles, strict by @denis-yuen in https://github.com/dockstore/dockstore/pull/6103
update snakemake plugin by @denis-yuen in https://github.com/dockstore/dockstore/pull/6107
Bump snakemake plugin version by @kathy-t in https://github.com/dockstore/dockstore/pull/6109

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.6...1.17.0

- Java
Published by denis-yuen about 1 year ago

What's Changed

Cherry-pick notebook commit to release by @svonworl in https://github.com/dockstore/dockstore/pull/6105
SEAB-6978: Correct "metrics robot" design by @svonworl in https://github.com/dockstore/dockstore/pull/6104
SEAB-7134: Fix auth-related 500 by @svonworl in https://github.com/dockstore/dockstore/pull/6106
further sanitize sourcefiles, strict by @denis-yuen in https://github.com/dockstore/dockstore/pull/6103
update snakemake plugin by @denis-yuen in https://github.com/dockstore/dockstore/pull/6107

Full Changelog: https://github.com/dockstore/dockstore/compare/1.17.0-beta.0...1.17.0-beta.1

- Java
Published by denis-yuen about 1 year ago

What's Changed

DOCK-2589: Only add utf-8 charset to text and json mime types by @svonworl in https://github.com/dockstore/dockstore/pull/6014
Feature/cwlavro update by @denis-yuen in https://github.com/dockstore/dockstore/pull/6030
trs extensions to facilitate toil development by @denis-yuen in https://github.com/dockstore/dockstore/pull/6005
SEAB-5762: Implement pagination to getWorkflowVersions endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/6001
Harvest GitHub-Zenodo DOIs based on latestReleaseDate by @coverbeck in https://github.com/dockstore/dockstore/pull/6035
DOCK-2582: Better exception messages by @svonworl in https://github.com/dockstore/dockstore/pull/6037
DOCK-2571: Improve relative readMePath error message by @svonworl in https://github.com/dockstore/dockstore/pull/6040
Use reusable deploy artifacts workflow by @kathy-t in https://github.com/dockstore/dockstore/pull/6043
Add id-token write permisson for deploying db docs by @kathy-t in https://github.com/dockstore/dockstore/pull/6047
update dropwizard to 4.0.11 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5804
DOCK-2591: Sort "representative" version first by default by @svonworl in https://github.com/dockstore/dockstore/pull/6042
Adjust quay image sha by @svonworl in https://github.com/dockstore/dockstore/pull/6052
SEAB-6464: Infer .dockstore.yml by @svonworl in https://github.com/dockstore/dockstore/pull/5939
Revert reusable workflow revert by @kathy-t in https://github.com/dockstore/dockstore/pull/6054
DOCK-2600: Fix backlinks from Zenodo DOI records by @svonworl in https://github.com/dockstore/dockstore/pull/6053
SEAB-6341: add include query param to version endpoints by @hyunnaye in https://github.com/dockstore/dockstore/pull/6055
fix runner dependencies metadata resource call and add test by @denis-yuen in https://github.com/dockstore/dockstore/pull/6062
test with postgres 16.4 by @denis-yuen in https://github.com/dockstore/dockstore/pull/6063
Update Surefire to non-milestone version by @coverbeck in https://github.com/dockstore/dockstore/pull/5981
put image digest in both places for dockstore-deploy builds by @denis-yuen in https://github.com/dockstore/dockstore/pull/6068
Feature/fix swagger validation by @denis-yuen in https://github.com/dockstore/dockstore/pull/6069
update to newer dropwizard and logback by @denis-yuen in https://github.com/dockstore/dockstore/pull/6070
Add lastModified and selectedconceptdoi to elastic search object for search cards by @kathy-t in https://github.com/dockstore/dockstore/pull/6071
fix regression integration tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/6072
SEAB-6917: add Toil to Partner enum by @hyunnaye in https://github.com/dockstore/dockstore/pull/6073
Fix bad openapi.yaml merge by @kathy-t in https://github.com/dockstore/dockstore/pull/6079
Put back reusable deploy workflow by @kathy-t in https://github.com/dockstore/dockstore/pull/6080
test action ubuntu version by @denis-yuen in https://github.com/dockstore/dockstore/pull/6082
DOCK-2608: Incorporate other signals into version sorting by @svonworl in https://github.com/dockstore/dockstore/pull/6081
DOCK-2591: Change default version sort order to descending by @svonworl in https://github.com/dockstore/dockstore/pull/6083
SEAB-6995: Reenable "authorless" DOIs by @svonworl in https://github.com/dockstore/dockstore/pull/6084
SEAB-6803: Implement "versions needing a retroactive DOI" endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/6086
SEAB-6803: Create retroactive automatic DOI endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/6087
Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/6091
Snakemake tests and some clean-up by @denis-yuen in https://github.com/dockstore/dockstore/pull/6085
add markdown conversion to html and run current tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/6093
SEAB-6978: Lock down "platform partner" users by @svonworl in https://github.com/dockstore/dockstore/pull/6089
SEAB-7080: Use tag creation date as DOI publication date by @svonworl in https://github.com/dockstore/dockstore/pull/6096
Add snakemake plugin to webservice image by @denis-yuen in https://github.com/dockstore/dockstore/pull/6097
SEAB-7089: Fix slow-loading user profile "Activity" section by @svonworl in https://github.com/dockstore/dockstore/pull/6098
DOCK-2585: remove restub functionality by @hyunnaye in https://github.com/dockstore/dockstore/pull/6094
SMK app log tweak based on qa testing by @denis-yuen in https://github.com/dockstore/dockstore/pull/6099

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.6...1.17.0-beta.0

- Java
Published by denis-yuen over 1 year ago

What's Changed

SEAB-6700: Generate automatic DOIs for all new tags by @svonworl in https://github.com/dockstore/dockstore/pull/6074
SEAB-6971: Commit to hotfix branch by @hyunnaye in https://github.com/dockstore/dockstore/pull/6077

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.5...1.16.6

- Java
Published by kathy-t over 1 year ago

What's Changed

Cherry pick "DOCK-2600: Fix backlinks from Zenodo DOI records" to hotfix by @svonworl in https://github.com/dockstore/dockstore/pull/6058
SEAB-6831: Fix aborted DOI alias creation during bot push by @svonworl in https://github.com/dockstore/dockstore/pull/6057
postgres 16.4 update by @denis-yuen in https://github.com/dockstore/dockstore/pull/6064
Fix http imports from a local secondary file by @denis-yuen in https://github.com/dockstore/dockstore/pull/6066

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.3...1.16.5

- Java
Published by denis-yuen over 1 year ago

dockstore - 1.16.3

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.1...1.16.3

What's Changed

DOCK-2571: Cherry pick "improve relative readMePath error message" to hotfix branch by @svonworl in https://github.com/dockstore/dockstore/pull/6041
Add enableAutoDois field to .dockstore.yml and allow disabling auto DOIs by @kathy-t in https://github.com/dockstore/dockstore/pull/6045
Handle expired GitHub token by @coverbeck in https://github.com/dockstore/dockstore/pull/6051

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.0...1.16.3

- Java
Published by denis-yuen over 1 year ago

What's Changed

DOCK-2571: Cherry pick "improve relative readMePath error message" to hotfix branch by @svonworl in https://github.com/dockstore/dockstore/pull/6041
Add enableAutoDois field to .dockstore.yml and allow disabling auto DOIs by @kathy-t in https://github.com/dockstore/dockstore/pull/6045
Handle expired GitHub token by @coverbeck in https://github.com/dockstore/dockstore/pull/6051

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.0...1.16.2

- Java
Published by denis-yuen over 1 year ago

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 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

- Java
Published by denis-yuen over 1 year ago

What's Changed

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

Full Changelog: https://github.com/dockstore/dockstore/compare/1.16.0-beta.7...1.16.0-beta.8

- Java
Published by kathy-t over 1 year ago

dockstore - 1.16.0-beta.7

- Java
Published by david4096 almost 2 years ago

dockstore - 1.16.0-beta.5

- Java
Published by david4096 almost 2 years ago

What's Changed

fix engine version metadata update and add test (#5953) by @denis-yuen in https://github.com/dockstore/dockstore/pull/5956
Add latest cwltool requirements by @david4096 in https://github.com/dockstore/dockstore/pull/5958
Update postgres JDBC version by @david4096 in https://github.com/dockstore/dockstore/pull/5971
SEAB-6535: Improve logging of mapped Exceptions (hotfix) by @svonworl in https://github.com/dockstore/dockstore/pull/5974

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.3...1.15.4

- Java
Published by kathy-t almost 2 years ago

What's Changed

Make athena life easier - duration in seconds by @denis-yuen in https://github.com/dockstore/dockstore/pull/5842
Update deprecated CircleCI images by @denis-yuen in https://github.com/dockstore/dockstore/pull/5896
fix regex for comments in .dockstore.yml and add test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5910

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.2...1.15.3

- Java
Published by denis-yuen about 2 years ago

What's Changed

Fix basic search authors by @denis-yuen in https://github.com/dockstore/dockstore/pull/5819

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.1...1.15.2

- Java
Published by coverbeck over 2 years ago

What's Changed

DOCK-2512: Fix pushes of annotated tags by @svonworl in https://github.com/dockstore/dockstore/pull/5809

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.0...1.15.1

- Java
Published by denis-yuen over 2 years ago

Highlighted Changes

General release of notebooks and metrics
improved display of github app logs before first successful registration to aid debugging
improved validation and debugging display for workflows with a partially correct .dockstore.yml
bugfixes for searching full-text, workflows without authors, search display for starred workflows
deployment improvements behind-the-scenes to allow for drift detection, between release deployment of supporting infrastructure
cli validation tool for .dockstore.yml files
cwltool and cromwell support update

What's Changed

Feature/dropwizard update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5477
add joda time to classpath by @denis-yuen in https://github.com/dockstore/dockstore/pull/5488
SEAB-5113: Implement notebook snapshotting by @svonworl in https://github.com/dockstore/dockstore/pull/5499
SEAB-5438: Support old notebooks by @svonworl in https://github.com/dockstore/dockstore/pull/5507
deal with expired docker image by @denis-yuen in https://github.com/dockstore/dockstore/pull/5512
Dropwizard update 4.0 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5483
SEAB-5121: Add config properties for Colab and Mybinder launch urls by @svonworl in https://github.com/dockstore/dockstore/pull/5515
remove event consumer by @denis-yuen in https://github.com/dockstore/dockstore/pull/5511
SEAB-5437: added notebook to getUserEntries endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/5522
SEAB-5530: Change test notebook IDs so they will never collide by @svonworl in https://github.com/dockstore/dockstore/pull/5526
Fix failing metrics test from 1.14 merge by @kathy-t in https://github.com/dockstore/dockstore/pull/5529
what if new dependency cache by @denis-yuen in https://github.com/dockstore/dockstore/pull/5530
DOCK-2374: Switch to new codecov uploader by @y-ng in https://github.com/dockstore/dockstore/pull/5532
SEAB-5548: Optimize database migrations by @svonworl in https://github.com/dockstore/dockstore/pull/5531
SEAB-5387: get notebook counts in collections and add Service support in collections by @hyunnaye in https://github.com/dockstore/dockstore/pull/5519
Add getPublishedContainer to OpenAPI by @coverbeck in https://github.com/dockstore/dockstore/pull/5539
test out potentially temporary fix for es indexing issue by @denis-yuen in https://github.com/dockstore/dockstore/pull/5536
Feature/refactor project by @denis-yuen in https://github.com/dockstore/dockstore/pull/5547
DOCK-2397: Redirect 500 error for invalid filters to a 400 by @hyunnaye in https://github.com/dockstore/dockstore/pull/5543
Fix slow endpoints with checker workflows by @coverbeck in https://github.com/dockstore/dockstore/pull/5546
Only apply CORS headers to TRS endpoints by @david4096 in https://github.com/dockstore/dockstore/pull/5544
Update zenodo client by @denis-yuen in https://github.com/dockstore/dockstore/pull/5555
Switch jackson annotations and add tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/5563
remove obsolete column by @denis-yuen in https://github.com/dockstore/dockstore/pull/5569
cwlavro update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5564
Move things that dockstore-support uses to dockstore-common by @kathy-t in https://github.com/dockstore/dockstore/pull/5562
Remove unused getSpecificUser endpoint by @coverbeck in https://github.com/dockstore/dockstore/pull/5572
SEAB-5602: Fix Events for Notebooks and Services by @svonworl in https://github.com/dockstore/dockstore/pull/5574
Feature/seab 5519/privaterepos by @coverbeck in https://github.com/dockstore/dockstore/pull/5570
Remove some dependencies from the Dockerfile by @david4096 in https://github.com/dockstore/dockstore/pull/5579
SEAB-5576: Allow some Entries to be deleted by @svonworl in https://github.com/dockstore/dockstore/pull/5545
Restore curl by @denis-yuen in https://github.com/dockstore/dockstore/pull/5583
actually restore curl by @denis-yuen in https://github.com/dockstore/dockstore/pull/5585
SEAB-5613: added new lambdaEvents endpoint for admins by @hyunnaye in https://github.com/dockstore/dockstore/pull/5580
Feature/openapi swagger attempt 3 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5589
Add cost metric by @kathy-t in https://github.com/dockstore/dockstore/pull/5577
Add description endpoint for version description by @coverbeck in https://github.com/dockstore/dockstore/pull/5590
Check license using action from workflow-actions by @coverbeck in https://github.com/dockstore/dockstore/pull/5599
Feature/new sam cli by @denis-yuen in https://github.com/dockstore/dockstore/pull/5604
Use versionName for deleteEntryFromCollection by @y-ng in https://github.com/dockstore/dockstore/pull/5597
openapi diff for backwards compatibitlity by @denis-yuen in https://github.com/dockstore/dockstore/pull/5607
SEAB-5703: Update event code for services and notebooks by @svonworl in https://github.com/dockstore/dockstore/pull/5608
Bump okio from 2.6.0 to 3.4.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5596
Bump actions/upload-pages-artifact from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/5593
cleanup compose setup version by @denis-yuen in https://github.com/dockstore/dockstore/pull/5601
Record entry names in lambda event by @kathy-t in https://github.com/dockstore/dockstore/pull/5611
Add OpenAPI Auth annotation by @coverbeck in https://github.com/dockstore/dockstore/pull/5620
Feature/dropwizard update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5622
DOCK-2429: Enable 'Rerun failed tests only' in CircleCI by @y-ng in https://github.com/dockstore/dockstore/pull/5616
SEAB-5655: removed id check for admins and curators for getUserTokens endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/5630
split out dev dependencies by @denis-yuen in https://github.com/dockstore/dockstore/pull/5629
Remove some items from AIDE logs by @david4096 in https://github.com/dockstore/dockstore/pull/5632
Hook up X-GitHub-Delivery to LambdaEvent deliveryId by @kathy-t in https://github.com/dockstore/dockstore/pull/5626
SEAB-5660: Remove getErrorMessage from CustomWebApplicationException by @svonworl in https://github.com/dockstore/dockstore/pull/5628
DOCK-2412: Reenable migration caching by @svonworl in https://github.com/dockstore/dockstore/pull/5633
Bump aws-actions/configure-aws-credentials from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/5639
SEAB-3957: Handle search text containing special characters by @y-ng in https://github.com/dockstore/dockstore/pull/5634
Services Issues by @coverbeck in https://github.com/dockstore/dockstore/pull/5650
SEAB-5770: Implement GitHub App event "ref inspection" scheme by @svonworl in https://github.com/dockstore/dockstore/pull/5653
add broad mirror by @denis-yuen in https://github.com/dockstore/dockstore/pull/5656
Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5655
Feature/openapi hierarchy simple by @denis-yuen in https://github.com/dockstore/dockstore/pull/5643
Feature/debug macos by @denis-yuen in https://github.com/dockstore/dockstore/pull/5661
SEAB-5849: Add verified platforms to version metadata by @svonworl in https://github.com/dockstore/dockstore/pull/5658
run with ea by @denis-yuen in https://github.com/dockstore/dockstore/pull/5663
DOCK-2415: invalidates relative file paths in dockstore.yml by @hyunnaye in https://github.com/dockstore/dockstore/pull/5641
Bump docker/login-action from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/5665
SEAB-5849: Make ElasticListener retrieve sourcefiles sparingly by @svonworl in https://github.com/dockstore/dockstore/pull/5659
DOCK-2415 follow-up: add notnull to test parameters by @hyunnaye in https://github.com/dockstore/dockstore/pull/5667
SEAB-5849: Restructure delete webhook to reduce Hibernate overhead by @svonworl in https://github.com/dockstore/dockstore/pull/5662
Bump docker/build-push-action from 4 to 5 by @dependabot in https://github.com/dockstore/dockstore/pull/5664
Bump aws-actions/configure-aws-credentials from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5660
Add blurb to PR template to cover privacy by @david4096 in https://github.com/dockstore/dockstore/pull/5672
Feature/hierarchy revert by @denis-yuen in https://github.com/dockstore/dockstore/pull/5678
update to 4.0.2 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5679
enable pgp across the board by @denis-yuen in https://github.com/dockstore/dockstore/pull/5681
Set default service paths to be absolute by @coverbeck in https://github.com/dockstore/dockstore/pull/5682
Feature/even simpler openapi cleanup by @denis-yuen in https://github.com/dockstore/dockstore/pull/5684
SEAB-5913: Avoid indexing .dockstore.yml, improve es tokenization by @svonworl in https://github.com/dockstore/dockstore/pull/5686
SEAB-811: Add archive endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/5687
DOCK-2464: Display ignored GitHub events by @svonworl in https://github.com/dockstore/dockstore/pull/5691
Add execution and validation metrics to ES. by @coverbeck in https://github.com/dockstore/dockstore/pull/5693
Followup to #5693 by @coverbeck in https://github.com/dockstore/dockstore/pull/5695
DOCK-1195: Populate versions in archive/unarchive endpoint response by @svonworl in https://github.com/dockstore/dockstore/pull/5698
Deprecate aggregated metrics field for metric submission endpoint by @kathy-t in https://github.com/dockstore/dockstore/pull/5699
add total count and tests - lambda events by @denis-yuen in https://github.com/dockstore/dockstore/pull/5688
DOCK-1195: Add "archived" property to "my workflows" retrieval by @svonworl in https://github.com/dockstore/dockstore/pull/5700
DOCK-2442: Fix sluggish events endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/5697
SEAB-5780: Ensure Workflow Run RO-Crate compatibility by @hyunnaye in https://github.com/dockstore/dockstore/pull/5702
Upgrade to latest pf4j by @coverbeck in https://github.com/dockstore/dockstore/pull/5709
Use offset indexing for sourcefile content and apply text_analyzer by @kathy-t in https://github.com/dockstore/dockstore/pull/5707
Add topic field in .dockstore.yml for GitHub app tools, workflows, and notebooks by @kathy-t in https://github.com/dockstore/dockstore/pull/5713
Add AI topic column and AI topic selection option by @kathy-t in https://github.com/dockstore/dockstore/pull/5716
SEAB-5951: Notebook "launch to GitHub Codespace" support by @svonworl in https://github.com/dockstore/dockstore/pull/5721
SEAB-5951: Add GitHub codespace import URL property to UI config by @svonworl in https://github.com/dockstore/dockstore/pull/5725
SEAB-6002: Enable search in notebook EntryTypeMetadata by @svonworl in https://github.com/dockstore/dockstore/pull/5732
DOCK-2441: remove global security property to remove unneeded auth padlocks by @hyunnaye in https://github.com/dockstore/dockstore/pull/5739
DOCK-2440: added sort and filter values on GitHub Apps Logs endpoints by @hyunnaye in https://github.com/dockstore/dockstore/pull/5730
Update cromwell version to latest on jfrog by @david4096 in https://github.com/dockstore/dockstore/pull/5741
Feature/seab 5786/secretuser by @coverbeck in https://github.com/dockstore/dockstore/pull/5734
Bump org.json:json from 20230227 to 20231013 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5710
DOCK-1946: Remove "dockstore.org" from allowable values for "delete stubbed workflow" endpoint by @svonworl in https://github.com/dockstore/dockstore/pull/5747
Allow the submission of task metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5738
SEAB-5422: Don't display certain Events when the referenced entry is unpublished by @svonworl in https://github.com/dockstore/dockstore/pull/5736
DOCK-2440: allow null values in sorting in the github apps logs table by @hyunnaye in https://github.com/dockstore/dockstore/pull/5749
SEAB-6022: Fix updateWorkflow endpoint for Services and Notebooks by @svonworl in https://github.com/dockstore/dockstore/pull/5750
Restore disabled BitBucket test by @coverbeck in https://github.com/dockstore/dockstore/pull/5762
Bump ch.qos.logback:logback-core from 1.4.11 to 1.4.12 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5757
Bump ch.qos.logback:logback-classic from 1.4.11 to 1.4.12 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5761
SEAB-6025: Add endpoint that retrieves an Entry by alias by @svonworl in https://github.com/dockstore/dockstore/pull/5763
Bump actions/setup-java from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5764
Fix silly zenodo api change by @denis-yuen in https://github.com/dockstore/dockstore/pull/5755
SEAB-2476: Fix nextflow 500 error in getContent() by @svonworl in https://github.com/dockstore/dockstore/pull/5754
Review tables for dbcreatedate and dbupdatedate by @coverbeck in https://github.com/dockstore/dockstore/pull/5767
DOCK-2376: remove deprecated author and email field in Entry by @hyunnaye in https://github.com/dockstore/dockstore/pull/5706
enforce entryname is null or nonempty for lambda events - sorting issue by @denis-yuen in https://github.com/dockstore/dockstore/pull/5769
Cwlavro update release by @denis-yuen in https://github.com/dockstore/dockstore/pull/5776
test postgres 13.13 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5780
SEAB-6100: Reduce memory consumption of TRS tools get by @svonworl in https://github.com/dockstore/dockstore/pull/5781
SEAB-6096: Add version event on tagged GitHub release by @svonworl in https://github.com/dockstore/dockstore/pull/5783
Add Aborted and Failed statuses, and new endpoint to support ingesting broad metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5768
Add update execution metrics endpoint by @kathy-t in https://github.com/dockstore/dockstore/pull/5778
Decode metrics S3 key components by @kathy-t in https://github.com/dockstore/dockstore/pull/5788
Fix duplicate validator versions in get aggregated metrics response for "ALL" platform by @kathy-t in https://github.com/dockstore/dockstore/pull/5789
add zenodo patch by @denis-yuen in https://github.com/dockstore/dockstore/pull/5795
search workflow version as well as default version for authors by @denis-yuen in https://github.com/dockstore/dockstore/pull/5797
Separate execution metrics by status by @kathy-t in https://github.com/dockstore/dockstore/pull/5800

New Contributors

@y-ng made their first contribution in https://github.com/dockstore/dockstore/pull/5532

Full Changelog: https://github.com/dockstore/dockstore/compare/1.14.3...1.15.0

- Java
Published by denis-yuen over 2 years ago

What's Changed

add zenodo patch by @denis-yuen in https://github.com/dockstore/dockstore/pull/5795
search workflow version as well as default version for authors by @denis-yuen in https://github.com/dockstore/dockstore/pull/5797
Separate execution metrics by status by @kathy-t in https://github.com/dockstore/dockstore/pull/5800

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.0-rc.1...1.15.0-rc.2

- Java
Published by denis-yuen over 2 years ago

What's Changed

Decode metrics S3 key components by @kathy-t in https://github.com/dockstore/dockstore/pull/5788
Fix duplicate validator versions in get aggregated metrics response for "ALL" platform by @kathy-t in https://github.com/dockstore/dockstore/pull/5789

Full Changelog: https://github.com/dockstore/dockstore/compare/1.15.0-rc.0...1.15.0-rc.1

- Java
Published by denis-yuen over 2 years ago

dockstore - 1.15.0-rc.0

- Java
Published by denis-yuen over 2 years ago

dockstore - 1.15.0-beta.0

- Java
Published by denis-yuen over 2 years ago

dockstore - 1.14.3

- Java
Published by coverbeck over 2 years ago

dockstore -

- Java
Published by denis-yuen almost 3 years ago

What's Changed

Enable non-curator to update org by @coverbeck in https://github.com/dockstore/dockstore/pull/5565
Return 415 if invalid JSON for search endpoint by @kathy-t in https://github.com/dockstore/dockstore/pull/5566
DOCK-2391: return 415 for google token endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/5573
Fix connection pool health check by @kathy-t in https://github.com/dockstore/dockstore/pull/5586

Full Changelog: https://github.com/dockstore/dockstore/compare/1.14.0...1.14.1

- Java
Published by denis-yuen about 3 years ago

Highlighted new features

Public preview for notebooks, get in touch if you wish to integrate with us for notebooks or have suggestions!
Public preview for metrics, as above get in touch if you're interested!
New dashboard provides a cleaner and (we think!) more elegant look at your workflows and tools
- Also monitor your favorite (starred) workflows for new versions and changes
- Keep an eye on your favorite or your own organizations and collections
- A better onboarding experience for new users to register workflows
Initial GA4GH TRS 2.0.1 support
Dockstore now parses and enables search for language versions (think searching for Nextflow DSL2, CWL v1.2, WDL 1.1, or Galaxy gxformat2 specifically)
Dockstore also parses and makes a best effort to allow search for workflows using open data
Improved .dockstore.yml validator in the CLI
Numerous security updates and upgrades for our own dependencies
Inside baseball: a pile of updates to our own software development practices, build processes, and deployment procedures

Breaking changes

CLI now requires Java 17 (Note, Java 11 active support ends in September)
On the language front cromwell support and bindings have been updated to version 84, cwltool has been updated to 3.1.20230201224320 so expect possible changes when running workflows locally via the CLI (or potentially when parsing WDL workflows)

Full Changelog

ensure token refresh before checking repo validity by @denis-yuen in https://github.com/dockstore/dockstore/pull/5114
Update PR template for docs by @denis-yuen in https://github.com/dockstore/dockstore/pull/5134
Feature/dock 2170/replace cwlavro by cwljava by @svonworl in https://github.com/dockstore/dockstore/pull/5063
Bump char0n/swagger-editor-validate from 1.3.1 to 1.3.2 by @dependabot in https://github.com/dockstore/dockstore/pull/5147
Update cromwell and WDL bindings by @kathy-t in https://github.com/dockstore/dockstore/pull/5153
SEAB-4499: Optimize integration test database migrations by @svonworl in https://github.com/dockstore/dockstore/pull/5161
SEAB-4042: Fix Staging Discuss Entry Backlinks by @svonworl in https://github.com/dockstore/dockstore/pull/5140
Add basic file integrity verification by @david4096 in https://github.com/dockstore/dockstore/pull/5148
SEAB-4903: Update circleci setupremotedocker docker version by @svonworl in https://github.com/dockstore/dockstore/pull/5170
Update Kohsuke GitHub library by @kathy-t in https://github.com/dockstore/dockstore/pull/5176
Iterate CircleCI cache by @kathy-t in https://github.com/dockstore/dockstore/pull/5209
Bump actions/cache from 3.0.8 to 3.0.11 by @dependabot in https://github.com/dockstore/dockstore/pull/5177
Feature/even more dropwizard by @denis-yuen in https://github.com/dockstore/dockstore/pull/5206
Add review instructions by @coverbeck in https://github.com/dockstore/dockstore/pull/5196
Correctly discover existing workflows by @coverbeck in https://github.com/dockstore/dockstore/pull/5199
Remove 5 "the the" instances by @denis-yuen in https://github.com/dockstore/dockstore/pull/5225
Remove code for refreshing GitHub tokens by @kathy-t in https://github.com/dockstore/dockstore/pull/5230
DOCK-2194: Improve .dockstore.yml validation by @svonworl in https://github.com/dockstore/dockstore/pull/5212
DOCK-2170: Fix tools and DAG generation problem by @svonworl in https://github.com/dockstore/dockstore/pull/5232
Tidy up SAM sharing code by @coverbeck in https://github.com/dockstore/dockstore/pull/5137
Feature/reduce ci pin by @denis-yuen in https://github.com/dockstore/dockstore/pull/5239
add reviewers [skip ci] by @denis-yuen in https://github.com/dockstore/dockstore/pull/5240
Feature/python deps by @denis-yuen in https://github.com/dockstore/dockstore/pull/5242
lgtm migration by @denis-yuen in https://github.com/dockstore/dockstore/pull/5244
TRS 2.0.1 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5246
DOCK-2228 Added apptools in RSS feed by @hyunnaye in https://github.com/dockstore/dockstore/pull/5241
Allow organization admins to view pending and rejected invitations by @kathy-t in https://github.com/dockstore/dockstore/pull/5243
parallel circleci unit tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/5259
DOCK-2237: Reimplemented ignored integration test by @hyunnaye in https://github.com/dockstore/dockstore/pull/5264
Add workflow language version for SourceFile and Version & implement it for WDL by @kathy-t in https://github.com/dockstore/dockstore/pull/5266
Feature/user permissions cleanup by @denis-yuen in https://github.com/dockstore/dockstore/pull/5271
DOCK-5245: Replace cwljava with cwlavro by @svonworl in https://github.com/dockstore/dockstore/pull/5281
fix trs 2.0.1 issues, hook up language version by @denis-yuen in https://github.com/dockstore/dockstore/pull/5275
SEAB-3978: check for null GitHub user input by @hyunnaye in https://github.com/dockstore/dockstore/pull/5277
Bump commons-net from 3.3 to 3.9.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5265
Remove unused bom entry by @david4096 in https://github.com/dockstore/dockstore/pull/5278
Bump postgresql from 42.4.1 to 42.4.3 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5251
set install and deploy at end to avoid partial deploy by @denis-yuen in https://github.com/dockstore/dockstore/pull/5282
Feature/language versions plugins and java 17 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5279
Update pull request template with security section by @coverbeck in https://github.com/dockstore/dockstore/pull/5289
code coverage improvement by @denis-yuen in https://github.com/dockstore/dockstore/pull/5286
catch runtime exceptions by @denis-yuen in https://github.com/dockstore/dockstore/pull/5288
DOCK-2299: Improve handling of WDL with recursive remote import by @svonworl in https://github.com/dockstore/dockstore/pull/5291
junit 5 with compatibility (legacy) layer by @denis-yuen in https://github.com/dockstore/dockstore/pull/5292
DOCK-2004: Flag missing nextflow main script by @svonworl in https://github.com/dockstore/dockstore/pull/5294
rotate bundle by @denis-yuen in https://github.com/dockstore/dockstore/pull/5298
Add language version to search by @kathy-t in https://github.com/dockstore/dockstore/pull/5295
convert dockstore-common, webservice, most integration tests to junit 5 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5297
Update Dockerfile galaxy plugin by @denis-yuen in https://github.com/dockstore/dockstore/pull/5303
DOCK-2293: Parse CWL language version by @svonworl in https://github.com/dockstore/dockstore/pull/5300
Update test for junit 5 by @svonworl in https://github.com/dockstore/dockstore/pull/5305
hoverfly upgrade and powermock removal by @denis-yuen in https://github.com/dockstore/dockstore/pull/5302
Dependabot/simulate update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5309
SEAB-5104: Add Notebook entity and related stuff by @svonworl in https://github.com/dockstore/dockstore/pull/5311
Language version parsing for Nextflow by @coverbeck in https://github.com/dockstore/dockstore/pull/5307
Feature/redesign cache by @denis-yuen in https://github.com/dockstore/dockstore/pull/5312
Remove unnecessary log messages by default by @fhembroff in https://github.com/dockstore/dockstore/pull/5314
Feature/citation change by @denis-yuen in https://github.com/dockstore/dockstore/pull/5316
fix link zip behaviour, and add tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/5310
Feature/bitbucket simple retry by @denis-yuen in https://github.com/dockstore/dockstore/pull/5313
Move language descriptor versions to different tables by @coverbeck in https://github.com/dockstore/dockstore/pull/5315
Create an S3 prototype for metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5306
SEAB-5107: Index notebooks in Elasticsearch by @svonworl in https://github.com/dockstore/dockstore/pull/5322
maintenance update for vfs2 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5326
Bump testng from 7.0.0-beta1 to 7.7.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5323
SEAB-5182: modified endpoints to get notebooks by @hyunnaye in https://github.com/dockstore/dockstore/pull/5327
Create DB schema prototype for metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5324
Bump docker/build-push-action from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5336
SEAB-5105: Add Jupyter ipynb notebook language handler by @svonworl in https://github.com/dockstore/dockstore/pull/5329
Add open data availability to ES index by @coverbeck in https://github.com/dockstore/dockstore/pull/5333
Update Language Versions by @coverbeck in https://github.com/dockstore/dockstore/pull/5332
Feature/release tinkering by @denis-yuen in https://github.com/dockstore/dockstore/pull/5335
Unpublish GH App workflow if it has no versions by @kathy-t in https://github.com/dockstore/dockstore/pull/5337
update cwltool version by @denis-yuen in https://github.com/dockstore/dockstore/pull/5345
github rate limit checker - sleep by @denis-yuen in https://github.com/dockstore/dockstore/pull/5346
SEAB-5106: Add notebooks support to .dockstore.yml and GitHub apps webhooks by @svonworl in https://github.com/dockstore/dockstore/pull/5352
simple fixes by @denis-yuen in https://github.com/dockstore/dockstore/pull/5359
SEAB-5132: Reimplement MuteForSuccessfulTests equivalent for Junit 5 by @svonworl in https://github.com/dockstore/dockstore/pull/5358
add null check, start test split by @denis-yuen in https://github.com/dockstore/dockstore/pull/5353
new constraints for workflow and tool names by @denis-yuen in https://github.com/dockstore/dockstore/pull/5351
SEAB-4704: delete entries that are not considered any of the EntryTypes by @hyunnaye in https://github.com/dockstore/dockstore/pull/5360
add test for regex for weird github references by @denis-yuen in https://github.com/dockstore/dockstore/pull/5354
fix bitbucket profile and transfer worst tests to it by @denis-yuen in https://github.com/dockstore/dockstore/pull/5361
SEAB-5242: Improve MuteForSuccessfulTests extension by @svonworl in https://github.com/dockstore/dockstore/pull/5366
commit stub files by @denis-yuen in https://github.com/dockstore/dockstore/pull/5369
Create endpoint to send metrics to S3 by @kathy-t in https://github.com/dockstore/dockstore/pull/5357
attempt db documentation generation by @denis-yuen in https://github.com/dockstore/dockstore/pull/5370
SEAB-5108: Adjust webservice endpoints for notebooks by @svonworl in https://github.com/dockstore/dockstore/pull/5371
hack for galaxy version parsing for existing workflows by @denis-yuen in https://github.com/dockstore/dockstore/pull/5374
SEAB-5111: added test for starring notebook by @hyunnaye in https://github.com/dockstore/dockstore/pull/5375
Feature/jwt refactor by @denis-yuen in https://github.com/dockstore/dockstore/pull/5373
SEAB-5428: Change "ipynb" naming to "jupyter" by @svonworl in https://github.com/dockstore/dockstore/pull/5378
SEAB-5205: Additional ES-related notebook test by @svonworl in https://github.com/dockstore/dockstore/pull/5379
SEAB-5108: TRS notebooks updates by @svonworl in https://github.com/dockstore/dockstore/pull/5380
Corrected Typos in dockstore/dockstore by @fhembroff in https://github.com/dockstore/dockstore/pull/5387
SEAB-5112: Test notebook collections by @hyunnaye in https://github.com/dockstore/dockstore/pull/5377
Feature/move webhook class by @denis-yuen in https://github.com/dockstore/dockstore/pull/5386
SEAB-5103: Notebook support in RSS Feed by @hyunnaye in https://github.com/dockstore/dockstore/pull/5383
Feature/events for user orgs by @denis-yuen in https://github.com/dockstore/dockstore/pull/5391
workflow-level README by @denis-yuen in https://github.com/dockstore/dockstore/pull/5384
Add endpoint to post aggregated metrics, fix S3 client region by @kathy-t in https://github.com/dockstore/dockstore/pull/5381
dropwizard 2.1.5 update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5392
Bump aws-actions/configure-aws-credentials from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/5405
SEAB-5270: Add additional type information to Entry by @svonworl in https://github.com/dockstore/dockstore/pull/5403
Feature/triple 2 record by @denis-yuen in https://github.com/dockstore/dockstore/pull/5404
Checking for open data by @coverbeck in https://github.com/dockstore/dockstore/pull/5347
add platform partner role by @denis-yuen in https://github.com/dockstore/dockstore/pull/5408
SEAB-5239: Add user-specified kernel reference to notebook by @svonworl in https://github.com/dockstore/dockstore/pull/5411
SEAB-5281: Overhaul branch discovery during github app install by @svonworl in https://github.com/dockstore/dockstore/pull/5419
update to docker compose v2 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5420
add create dates for join table entries via postgres by @denis-yuen in https://github.com/dockstore/dockstore/pull/5425
use same regex for webhook delete as for create events by @denis-yuen in https://github.com/dockstore/dockstore/pull/5424
SEAB-5116: Miscellaneous notebook tweaks by @svonworl in https://github.com/dockstore/dockstore/pull/5429
Fix file name in getToolTesterLogs by @kathy-t in https://github.com/dockstore/dockstore/pull/5431
SEAB-5122 starred notebook endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/5406
hook up flag and cache behaviour by @denis-yuen in https://github.com/dockstore/dockstore/pull/5426
Bump actions/deploy-pages from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/5434
Feature/5385/cwlparams by @coverbeck in https://github.com/dockstore/dockstore/pull/5430
Capture Nextflow Engine version by @coverbeck in https://github.com/dockstore/dockstore/pull/5433
Feature/apptool count fix by @denis-yuen in https://github.com/dockstore/dockstore/pull/5439
make migration survive next change by @denis-yuen in https://github.com/dockstore/dockstore/pull/5442
add a null check by @denis-yuen in https://github.com/dockstore/dockstore/pull/5448
Add validation metric to support miniwdl validation by @kathy-t in https://github.com/dockstore/dockstore/pull/5447
swap readme precedence and add test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5454
SEAB-5318: Created GET endpoints for TRS metrics by @hyunnaye in https://github.com/dockstore/dockstore/pull/5449
Feature/public orcid api fallback by @denis-yuen in https://github.com/dockstore/dockstore/pull/5453
Make Generate Key Public by @fhembroff in https://github.com/dockstore/dockstore/pull/5463
Open Data Check for Hosted Workflows by @coverbeck in https://github.com/dockstore/dockstore/pull/5460
Bump json from 20220924 to 20230227 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5465
null check and add test for cwl location by @denis-yuen in https://github.com/dockstore/dockstore/pull/5468
Add multiple authors to Entry and fix authors in search by @kathy-t in https://github.com/dockstore/dockstore/pull/5461
Fix description update for existing workflow version by @kathy-t in https://github.com/dockstore/dockstore/pull/5470
Feature/5397/s3gs by @coverbeck in https://github.com/dockstore/dockstore/pull/5487
Feature/seab 5364/opendata by @coverbeck in https://github.com/dockstore/dockstore/pull/5473
DOCK-2367: hide category events from regular users by @hyunnaye in https://github.com/dockstore/dockstore/pull/5478
Allow platforms to submit aggregated metrics; aggregate metrics across all platforms by @kathy-t in https://github.com/dockstore/dockstore/pull/5486
Remove trailing slash from the lambda url by @coverbeck in https://github.com/dockstore/dockstore/pull/5490
Handle StackOverflowError that Cromwell throws by @coverbeck in https://github.com/dockstore/dockstore/pull/5497
Tweak API message for hosted entries by @coverbeck in https://github.com/dockstore/dockstore/pull/5500
Set default descriptor type for tools by @kathy-t in https://github.com/dockstore/dockstore/pull/5498
DOCK-2004: Calculate Version validity later by @svonworl in https://github.com/dockstore/dockstore/pull/5502
Add ORCID when publishing to Zenodo by @coverbeck in https://github.com/dockstore/dockstore/pull/5506
Hardcode region for ToolTester S3Client to us-east-1 by @kathy-t in https://github.com/dockstore/dockstore/pull/5514
Test 1.13 CLI with 1.14 webservice by @kathy-t in https://github.com/dockstore/dockstore/pull/5518
update constraint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5521

Full Changelog: https://github.com/dockstore/dockstore/compare/1.13.1...1.14.0

- Java
Published by denis-yuen about 3 years ago

What's Changed

Handle StackOverflowError that Cromwell throws by @coverbeck in https://github.com/dockstore/dockstore/pull/5497
Tweak API message for hosted entries by @coverbeck in https://github.com/dockstore/dockstore/pull/5500
Set default descriptor type for tools by @kathy-t in https://github.com/dockstore/dockstore/pull/5498
DOCK-2004: Calculate Version validity later by @svonworl in https://github.com/dockstore/dockstore/pull/5502
Add ORCID when publishing to Zenodo by @coverbeck in https://github.com/dockstore/dockstore/pull/5506
Hardcode region for ToolTester S3Client to us-east-1 by @kathy-t in https://github.com/dockstore/dockstore/pull/5514
Test 1.13 CLI with 1.14 webservice by @kathy-t in https://github.com/dockstore/dockstore/pull/5518
update constraint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5521

Full Changelog: https://github.com/dockstore/dockstore/compare/1.14.0-beta.0...1.14.0-rc.0

- Java
Published by kathy-t about 3 years ago

What's Changed

ensure token refresh before checking repo validity by @denis-yuen in https://github.com/dockstore/dockstore/pull/5114
Update PR template for docs by @denis-yuen in https://github.com/dockstore/dockstore/pull/5134
Feature/dock 2170/replace cwlavro by cwljava by @svonworl in https://github.com/dockstore/dockstore/pull/5063
Bump char0n/swagger-editor-validate from 1.3.1 to 1.3.2 by @dependabot in https://github.com/dockstore/dockstore/pull/5147
Update cromwell and WDL bindings by @kathy-t in https://github.com/dockstore/dockstore/pull/5153
SEAB-4499: Optimize integration test database migrations by @svonworl in https://github.com/dockstore/dockstore/pull/5161
SEAB-4042: Fix Staging Discuss Entry Backlinks by @svonworl in https://github.com/dockstore/dockstore/pull/5140
Add basic file integrity verification by @david4096 in https://github.com/dockstore/dockstore/pull/5148
SEAB-4903: Update circleci setupremotedocker docker version by @svonworl in https://github.com/dockstore/dockstore/pull/5170
Update Kohsuke GitHub library by @kathy-t in https://github.com/dockstore/dockstore/pull/5176
Iterate CircleCI cache by @kathy-t in https://github.com/dockstore/dockstore/pull/5209
Bump actions/cache from 3.0.8 to 3.0.11 by @dependabot in https://github.com/dockstore/dockstore/pull/5177
Feature/even more dropwizard by @denis-yuen in https://github.com/dockstore/dockstore/pull/5206
Add review instructions by @coverbeck in https://github.com/dockstore/dockstore/pull/5196
Correctly discover existing workflows by @coverbeck in https://github.com/dockstore/dockstore/pull/5199
Remove 5 "the the" instances by @denis-yuen in https://github.com/dockstore/dockstore/pull/5225
Remove code for refreshing GitHub tokens by @kathy-t in https://github.com/dockstore/dockstore/pull/5230
DOCK-2194: Improve .dockstore.yml validation by @svonworl in https://github.com/dockstore/dockstore/pull/5212
DOCK-2170: Fix tools and DAG generation problem by @svonworl in https://github.com/dockstore/dockstore/pull/5232
Tidy up SAM sharing code by @coverbeck in https://github.com/dockstore/dockstore/pull/5137
Feature/reduce ci pin by @denis-yuen in https://github.com/dockstore/dockstore/pull/5239
add reviewers [skip ci] by @denis-yuen in https://github.com/dockstore/dockstore/pull/5240
Feature/python deps by @denis-yuen in https://github.com/dockstore/dockstore/pull/5242
lgtm migration by @denis-yuen in https://github.com/dockstore/dockstore/pull/5244
TRS 2.0.1 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5246
DOCK-2228 Added apptools in RSS feed by @hyunnaye in https://github.com/dockstore/dockstore/pull/5241
Allow organization admins to view pending and rejected invitations by @kathy-t in https://github.com/dockstore/dockstore/pull/5243
parallel circleci unit tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/5259
DOCK-2237: Reimplemented ignored integration test by @hyunnaye in https://github.com/dockstore/dockstore/pull/5264
Add workflow language version for SourceFile and Version & implement it for WDL by @kathy-t in https://github.com/dockstore/dockstore/pull/5266
Feature/user permissions cleanup by @denis-yuen in https://github.com/dockstore/dockstore/pull/5271
DOCK-5245: Replace cwljava with cwlavro by @svonworl in https://github.com/dockstore/dockstore/pull/5281
fix trs 2.0.1 issues, hook up language version by @denis-yuen in https://github.com/dockstore/dockstore/pull/5275
SEAB-3978: check for null GitHub user input by @hyunnaye in https://github.com/dockstore/dockstore/pull/5277
Bump commons-net from 3.3 to 3.9.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5265
Remove unused bom entry by @david4096 in https://github.com/dockstore/dockstore/pull/5278
Bump postgresql from 42.4.1 to 42.4.3 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5251
set install and deploy at end to avoid partial deploy by @denis-yuen in https://github.com/dockstore/dockstore/pull/5282
Feature/language versions plugins and java 17 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5279
Update pull request template with security section by @coverbeck in https://github.com/dockstore/dockstore/pull/5289
code coverage improvement by @denis-yuen in https://github.com/dockstore/dockstore/pull/5286
catch runtime exceptions by @denis-yuen in https://github.com/dockstore/dockstore/pull/5288
DOCK-2299: Improve handling of WDL with recursive remote import by @svonworl in https://github.com/dockstore/dockstore/pull/5291
junit 5 with compatibility (legacy) layer by @denis-yuen in https://github.com/dockstore/dockstore/pull/5292
DOCK-2004: Flag missing nextflow main script by @svonworl in https://github.com/dockstore/dockstore/pull/5294
rotate bundle by @denis-yuen in https://github.com/dockstore/dockstore/pull/5298
Add language version to search by @kathy-t in https://github.com/dockstore/dockstore/pull/5295
convert dockstore-common, webservice, most integration tests to junit 5 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5297
Update Dockerfile galaxy plugin by @denis-yuen in https://github.com/dockstore/dockstore/pull/5303
DOCK-2293: Parse CWL language version by @svonworl in https://github.com/dockstore/dockstore/pull/5300
Update test for junit 5 by @svonworl in https://github.com/dockstore/dockstore/pull/5305
hoverfly upgrade and powermock removal by @denis-yuen in https://github.com/dockstore/dockstore/pull/5302
Dependabot/simulate update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5309
SEAB-5104: Add Notebook entity and related stuff by @svonworl in https://github.com/dockstore/dockstore/pull/5311
Language version parsing for Nextflow by @coverbeck in https://github.com/dockstore/dockstore/pull/5307
Feature/redesign cache by @denis-yuen in https://github.com/dockstore/dockstore/pull/5312
Remove unnecessary log messages by default by @fhembroff in https://github.com/dockstore/dockstore/pull/5314
Feature/citation change by @denis-yuen in https://github.com/dockstore/dockstore/pull/5316
fix link zip behaviour, and add tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/5310
Feature/bitbucket simple retry by @denis-yuen in https://github.com/dockstore/dockstore/pull/5313
Move language descriptor versions to different tables by @coverbeck in https://github.com/dockstore/dockstore/pull/5315
Create an S3 prototype for metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5306
SEAB-5107: Index notebooks in Elasticsearch by @svonworl in https://github.com/dockstore/dockstore/pull/5322
maintenance update for vfs2 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5326
Bump testng from 7.0.0-beta1 to 7.7.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5323
SEAB-5182: modified endpoints to get notebooks by @hyunnaye in https://github.com/dockstore/dockstore/pull/5327
Create DB schema prototype for metrics by @kathy-t in https://github.com/dockstore/dockstore/pull/5324
Bump docker/build-push-action from 3 to 4 by @dependabot in https://github.com/dockstore/dockstore/pull/5336
SEAB-5105: Add Jupyter ipynb notebook language handler by @svonworl in https://github.com/dockstore/dockstore/pull/5329
Add open data availability to ES index by @coverbeck in https://github.com/dockstore/dockstore/pull/5333
Update Language Versions by @coverbeck in https://github.com/dockstore/dockstore/pull/5332
Feature/release tinkering by @denis-yuen in https://github.com/dockstore/dockstore/pull/5335
Unpublish GH App workflow if it has no versions by @kathy-t in https://github.com/dockstore/dockstore/pull/5337
update cwltool version by @denis-yuen in https://github.com/dockstore/dockstore/pull/5345
github rate limit checker - sleep by @denis-yuen in https://github.com/dockstore/dockstore/pull/5346
SEAB-5106: Add notebooks support to .dockstore.yml and GitHub apps webhooks by @svonworl in https://github.com/dockstore/dockstore/pull/5352
simple fixes by @denis-yuen in https://github.com/dockstore/dockstore/pull/5359
SEAB-5132: Reimplement MuteForSuccessfulTests equivalent for Junit 5 by @svonworl in https://github.com/dockstore/dockstore/pull/5358
add null check, start test split by @denis-yuen in https://github.com/dockstore/dockstore/pull/5353
new constraints for workflow and tool names by @denis-yuen in https://github.com/dockstore/dockstore/pull/5351
SEAB-4704: delete entries that are not considered any of the EntryTypes by @hyunnaye in https://github.com/dockstore/dockstore/pull/5360
add test for regex for weird github references by @denis-yuen in https://github.com/dockstore/dockstore/pull/5354
fix bitbucket profile and transfer worst tests to it by @denis-yuen in https://github.com/dockstore/dockstore/pull/5361
SEAB-5242: Improve MuteForSuccessfulTests extension by @svonworl in https://github.com/dockstore/dockstore/pull/5366
commit stub files by @denis-yuen in https://github.com/dockstore/dockstore/pull/5369
Create endpoint to send metrics to S3 by @kathy-t in https://github.com/dockstore/dockstore/pull/5357
attempt db documentation generation by @denis-yuen in https://github.com/dockstore/dockstore/pull/5370
SEAB-5108: Adjust webservice endpoints for notebooks by @svonworl in https://github.com/dockstore/dockstore/pull/5371
hack for galaxy version parsing for existing workflows by @denis-yuen in https://github.com/dockstore/dockstore/pull/5374
SEAB-5111: added test for starring notebook by @hyunnaye in https://github.com/dockstore/dockstore/pull/5375
Feature/jwt refactor by @denis-yuen in https://github.com/dockstore/dockstore/pull/5373
SEAB-5428: Change "ipynb" naming to "jupyter" by @svonworl in https://github.com/dockstore/dockstore/pull/5378
SEAB-5205: Additional ES-related notebook test by @svonworl in https://github.com/dockstore/dockstore/pull/5379
SEAB-5108: TRS notebooks updates by @svonworl in https://github.com/dockstore/dockstore/pull/5380
Corrected Typos in dockstore/dockstore by @fhembroff in https://github.com/dockstore/dockstore/pull/5387
SEAB-5112: Test notebook collections by @hyunnaye in https://github.com/dockstore/dockstore/pull/5377
Feature/move webhook class by @denis-yuen in https://github.com/dockstore/dockstore/pull/5386
SEAB-5103: Notebook support in RSS Feed by @hyunnaye in https://github.com/dockstore/dockstore/pull/5383
Feature/events for user orgs by @denis-yuen in https://github.com/dockstore/dockstore/pull/5391
workflow-level README by @denis-yuen in https://github.com/dockstore/dockstore/pull/5384
Add endpoint to post aggregated metrics, fix S3 client region by @kathy-t in https://github.com/dockstore/dockstore/pull/5381
dropwizard 2.1.5 update by @denis-yuen in https://github.com/dockstore/dockstore/pull/5392
Bump aws-actions/configure-aws-credentials from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/5405
SEAB-5270: Add additional type information to Entry by @svonworl in https://github.com/dockstore/dockstore/pull/5403
Feature/triple 2 record by @denis-yuen in https://github.com/dockstore/dockstore/pull/5404
Checking for open data by @coverbeck in https://github.com/dockstore/dockstore/pull/5347
add platform partner role by @denis-yuen in https://github.com/dockstore/dockstore/pull/5408
SEAB-5239: Add user-specified kernel reference to notebook by @svonworl in https://github.com/dockstore/dockstore/pull/5411
SEAB-5281: Overhaul branch discovery during github app install by @svonworl in https://github.com/dockstore/dockstore/pull/5419
update to docker compose v2 by @denis-yuen in https://github.com/dockstore/dockstore/pull/5420
add create dates for join table entries via postgres by @denis-yuen in https://github.com/dockstore/dockstore/pull/5425
use same regex for webhook delete as for create events by @denis-yuen in https://github.com/dockstore/dockstore/pull/5424
SEAB-5116: Miscellaneous notebook tweaks by @svonworl in https://github.com/dockstore/dockstore/pull/5429
Fix file name in getToolTesterLogs by @kathy-t in https://github.com/dockstore/dockstore/pull/5431
SEAB-5122 starred notebook endpoint by @hyunnaye in https://github.com/dockstore/dockstore/pull/5406
hook up flag and cache behaviour by @denis-yuen in https://github.com/dockstore/dockstore/pull/5426
Bump actions/deploy-pages from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/5434
Feature/5385/cwlparams by @coverbeck in https://github.com/dockstore/dockstore/pull/5430
Capture Nextflow Engine version by @coverbeck in https://github.com/dockstore/dockstore/pull/5433
Feature/apptool count fix by @denis-yuen in https://github.com/dockstore/dockstore/pull/5439
make migration survive next change by @denis-yuen in https://github.com/dockstore/dockstore/pull/5442
add a null check by @denis-yuen in https://github.com/dockstore/dockstore/pull/5448
Add validation metric to support miniwdl validation by @kathy-t in https://github.com/dockstore/dockstore/pull/5447
swap readme precedence and add test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5454
SEAB-5318: Created GET endpoints for TRS metrics by @hyunnaye in https://github.com/dockstore/dockstore/pull/5449
Feature/public orcid api fallback by @denis-yuen in https://github.com/dockstore/dockstore/pull/5453
Make Generate Key Public by @fhembroff in https://github.com/dockstore/dockstore/pull/5463
Open Data Check for Hosted Workflows by @coverbeck in https://github.com/dockstore/dockstore/pull/5460
Bump json from 20220924 to 20230227 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5465
null check and add test for cwl location by @denis-yuen in https://github.com/dockstore/dockstore/pull/5468
Add multiple authors to Entry and fix authors in search by @kathy-t in https://github.com/dockstore/dockstore/pull/5461
Fix description update for existing workflow version by @kathy-t in https://github.com/dockstore/dockstore/pull/5470
Feature/5397/s3gs by @coverbeck in https://github.com/dockstore/dockstore/pull/5487
Feature/seab 5364/opendata by @coverbeck in https://github.com/dockstore/dockstore/pull/5473
DOCK-2367: hide category events from regular users by @hyunnaye in https://github.com/dockstore/dockstore/pull/5478
Allow platforms to submit aggregated metrics; aggregate metrics across all platforms by @kathy-t in https://github.com/dockstore/dockstore/pull/5486
Remove trailing slash from the lambda url by @coverbeck in https://github.com/dockstore/dockstore/pull/5490

New Contributors

@hyunnaye made their first contribution in https://github.com/dockstore/dockstore/pull/5241

Full Changelog: https://github.com/dockstore/dockstore/compare/1.13.1...1.14.0-beta.0###

- Java
Published by denis-yuen about 3 years ago

What's Changed

SEAB-4903: Update circleci setupremotedocker docker version (on hotfix branch) by @svonworl in https://github.com/dockstore/dockstore/pull/5171
Update dropwizard to 2.1.3 by @kathy-t in https://github.com/dockstore/dockstore/pull/5167
DOCK-2256: ORCID identifiers can end with 'X' by @svonworl in https://github.com/dockstore/dockstore/pull/5172
SEAB-4880: Include galaxy plugin in webservice docker image by @svonworl in https://github.com/dockstore/dockstore/pull/5208
Always index only one version's source files by @coverbeck in https://github.com/dockstore/dockstore/pull/5168
Create metadata health check endpoint by @kathy-t in https://github.com/dockstore/dockstore/pull/5198

Full Changelog: https://github.com/dockstore/dockstore/compare/1.13.0...1.13.1

- Java
Published by denis-yuen over 3 years ago

Highlighted new features

performance improvements for GA4GH TRS and for UI display for workflows with many versions
cwltool and cromwell support update
improved display of github app logs before first successful registration to aid debugging
improved validation and debugging display for workflows with a partially correct .dockstore.yml
bugfixes for searching full-text, workflows without authors, search display for starred workflows
deployment improvements behind-the-scenes to allow for drift detection, between release deployment of supporting infrastructure
cli validation tool for .dockstore.yml files # Breaking changes
none intended

Full Changelog

changes to support Snakemake by @wshands in https://github.com/dockstore/dockstore/pull/4686
Update README.md by @denis-yuen in https://github.com/dockstore/dockstore/pull/4708
Disable this test till we get TRS working with both paging and apptools by @denis-yuen in https://github.com/dockstore/dockstore/pull/4726
Add LGTM suppression comment for false positive by @david4096 in https://github.com/dockstore/dockstore/pull/4725
Bump postgresql from 42.2.25 to 42.3.3 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/4733
bump cromwell artifacts versions and dependencies by @wshands in https://github.com/dockstore/dockstore/pull/4759
Remove language specific code to simplify adding a new language by @wshands in https://github.com/dockstore/dockstore/pull/4757
don't ignore get over 500 tags test by @wshands in https://github.com/dockstore/dockstore/pull/4780
Feature/java 17 finally by @denis-yuen in https://github.com/dockstore/dockstore/pull/4792
builds with CI friendly versions by @denis-yuen in https://github.com/dockstore/dockstore/pull/4789
switch to temurin image for Java 17 by @denis-yuen in https://github.com/dockstore/dockstore/pull/4806
Update swagger/openapi clients and plugins by @denis-yuen in https://github.com/dockstore/dockstore/pull/4799
Feature/checkstyle spotbugs update by @denis-yuen in https://github.com/dockstore/dockstore/pull/4807
dependabot.yml fine tune by @denis-yuen in https://github.com/dockstore/dockstore/pull/4809
Regression test with 1.10 by @coverbeck in https://github.com/dockstore/dockstore/pull/4824
typo by @denis-yuen in https://github.com/dockstore/dockstore/pull/4826
Bump char0n/swagger-editor-validate from 1.2.1 to 1.3.1 by @dependabot in https://github.com/dockstore/dockstore/pull/4828
Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/4827
Bump actions/cache from 1 to 3.0.1 by @dependabot in https://github.com/dockstore/dockstore/pull/4829
Allow query parameter to load user profiles by @Richard-Hansen in https://github.com/dockstore/dockstore/pull/4837
aws encryption now with v2 support by @denis-yuen in https://github.com/dockstore/dockstore/pull/4841
Bump actions/setup-java from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/4846
Bump actions/cache from 3.0.1 to 3.0.2 by @dependabot in https://github.com/dockstore/dockstore/pull/4849
try out latest dropwizard patch by @denis-yuen in https://github.com/dockstore/dockstore/pull/4847
used descriptor and new galaxy default desc name by @wshands in https://github.com/dockstore/dockstore/pull/4825
bump cwltool version support by @wshands in https://github.com/dockstore/dockstore/pull/4848
move out to github actions by @denis-yuen in https://github.com/dockstore/dockstore/pull/4850
Feature/dock 2105/log negative validations in GitHub apps logs by @svonworl in https://github.com/dockstore/dockstore/pull/4844
Update deploy_snapshot.yml by @denis-yuen in https://github.com/dockstore/dockstore/pull/4864
Rename user_profile bio to link and sync GitHub bio by @kathy-t in https://github.com/dockstore/dockstore/pull/4865
optimize github apps log retrieval for common cases by @svonworl in https://github.com/dockstore/dockstore/pull/4861
improve performance of fetching descriptor file via trs by @svonworl in https://github.com/dockstore/dockstore/pull/4866
Convert empty string names and links in user profiles to null by @kathy-t in https://github.com/dockstore/dockstore/pull/4868
Add security policy markdown by @david4096 in https://github.com/dockstore/dockstore/pull/4869
fix circleci by @svonworl in https://github.com/dockstore/dockstore/pull/4891
DOCK-2105: change GitHub apps log separator to newlines by @svonworl in https://github.com/dockstore/dockstore/pull/4895
Bump docker/login-action from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/4899
Bump docker/build-push-action from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/4900
remove context from unit tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/4903
Use integer offsets on /published endpoints (SEAB-3979) by @amarjandu in https://github.com/dockstore/dockstore/pull/4896
Update PULLREQUESTTEMPLATE.md by @denis-yuen in https://github.com/dockstore/dockstore/pull/4898
Query events by user id by @Richard-Hansen in https://github.com/dockstore/dockstore/pull/4901
Modified config.yml so that it sends coverage results for the unit test to codecov by @fhembroff in https://github.com/dockstore/dockstore/pull/4905
just reissue the tokens and see what happens by @denis-yuen in https://github.com/dockstore/dockstore/pull/4911
DOCK-2033: fix cwl hint precedence by @svonworl in https://github.com/dockstore/dockstore/pull/4912
Feature/flynn/4268/seperate bitbucket tests by @fhembroff in https://github.com/dockstore/dockstore/pull/4913
bring us into dropwizard 2.1 by @denis-yuen in https://github.com/dockstore/dockstore/pull/4919
Bump actions/cache from 3.0.2 to 3.0.3 by @dependabot in https://github.com/dockstore/dockstore/pull/4938
Add pattern validation for /metadata/runner_dependencies (#SEAB-3980) by @amarjandu in https://github.com/dockstore/dockstore/pull/4915
Feature/seab 4046/fix messagebodywriter exception by @svonworl in https://github.com/dockstore/dockstore/pull/4937
Updated the version numbers on several google clients by @fhembroff in https://github.com/dockstore/dockstore/pull/4942
Bump actions/cache from 3.0.3 to 3.0.4 by @dependabot in https://github.com/dockstore/dockstore/pull/4943
Standardize OpenAPI security field (#4671) by @amarjandu in https://github.com/dockstore/dockstore/pull/4944
Feature/seab 3896/remove trs caching code by @svonworl in https://github.com/dockstore/dockstore/pull/4949
Simplify language support by @wshands in https://github.com/dockstore/dockstore/pull/4940
re-create snyk suggestion by @denis-yuen in https://github.com/dockstore/dockstore/pull/4958
Add apple silicon setup to readme by @wshands in https://github.com/dockstore/dockstore/pull/4955
new api to get cli version by @wshands in https://github.com/dockstore/dockstore/pull/4948
fix api links by @denis-yuen in https://github.com/dockstore/dockstore/pull/4965
hook up initiator user to events endpoint and test by @denis-yuen in https://github.com/dockstore/dockstore/pull/4960
update to official maven wrapper by @denis-yuen in https://github.com/dockstore/dockstore/pull/4959
restrict to tags for now by @denis-yuen in https://github.com/dockstore/dockstore/pull/4966
Feature/dock 2110/continue processing dockstore yml after error by @svonworl in https://github.com/dockstore/dockstore/pull/4924
Feature/seab 4083/parrallel tests by @fhembroff in https://github.com/dockstore/dockstore/pull/4970
Merge to develop sanity check by @coverbeck in https://github.com/dockstore/dockstore/pull/4986
Remove unused constructors (SEAB-4055) by @amarjandu in https://github.com/dockstore/dockstore/pull/4952
Update SEMVERSTRING to support prereleases (#4981) by @amarjandu in https://github.com/dockstore/dockstore/pull/4982
order events by date by @denis-yuen in https://github.com/dockstore/dockstore/pull/4991
batch process index index creation by @denis-yuen in https://github.com/dockstore/dockstore/pull/4973
dropwizard 2.1.1 by @denis-yuen in https://github.com/dockstore/dockstore/pull/4988
Add non-empty constraints to user_profile table (#4871) by @amarjandu in https://github.com/dockstore/dockstore/pull/4994
Changed version number of hibernate-validator by @fhembroff in https://github.com/dockstore/dockstore/pull/5004
syntax github workflow by @denis-yuen in https://github.com/dockstore/dockstore/pull/5011
Bump commons-configuration2 from 2.7 to 2.8.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/4997
Bump actions/cache from 3.0.4 to 3.0.5 by @dependabot in https://github.com/dockstore/dockstore/pull/5020
SEAB-4269: Configurable SourceFile path restriction by @svonworl in https://github.com/dockstore/dockstore/pull/5005
Tweak new Sourcefile path-related integration test by @svonworl in https://github.com/dockstore/dockstore/pull/5022
pom simplification for how liquibase-core is included by @denis-yuen in https://github.com/dockstore/dockstore/pull/5021
support grab-bag of updates by @denis-yuen in https://github.com/dockstore/dockstore/pull/5032
Check if user exists in user endpoints by @kathy-t in https://github.com/dockstore/dockstore/pull/5031
Removed Liquibase Changeset Message from Output in CircleCI by @fhembroff in https://github.com/dockstore/dockstore/pull/5033
Update PR template by @coverbeck in https://github.com/dockstore/dockstore/pull/5034
Feature/restub snapshot by @denis-yuen in https://github.com/dockstore/dockstore/pull/5035
Fix failed openapi validation by @kathy-t in https://github.com/dockstore/dockstore/pull/5036
Don't terminate indexing after an indexing failure by @coverbeck in https://github.com/dockstore/dockstore/pull/5024
Fix collectionsLength for starred organizations by @coverbeck in https://github.com/dockstore/dockstore/pull/5038
SEAB-4403: Refactor user-level permissions checks by @svonworl in https://github.com/dockstore/dockstore/pull/4989
add test and hook up verified to collection endpoint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5037
ninjaed by @denis-yuen in https://github.com/dockstore/dockstore/pull/5048
index source files properly and test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5042
what if index by id by @denis-yuen in https://github.com/dockstore/dockstore/pull/5052
Link MacOS instructions to GitHub action by @fhembroff in https://github.com/dockstore/dockstore/pull/5043
Fix user-level permission check for workflow version ORCID authors endpoint by @kathy-t in https://github.com/dockstore/dockstore/pull/5055
Bump actions/cache from 3.0.5 to 3.0.6 by @dependabot in https://github.com/dockstore/dockstore/pull/5067
Feature/user permissions profile page by @denis-yuen in https://github.com/dockstore/dockstore/pull/5062
deal with n/a author searching by @denis-yuen in https://github.com/dockstore/dockstore/pull/5075
Bump actions/cache from 3.0.6 to 3.0.7 by @dependabot in https://github.com/dockstore/dockstore/pull/5077
DOCK-2159: Handle duplicate keys in .dockstore.yml parse by @svonworl in https://github.com/dockstore/dockstore/pull/5074
Removing BitBucket Tokens from non-bitbucket tests by @fhembroff in https://github.com/dockstore/dockstore/pull/5076
repair dockstore-cli failing nightly build by @denis-yuen in https://github.com/dockstore/dockstore/pull/5079
allow topic update on hosted by @denis-yuen in https://github.com/dockstore/dockstore/pull/5071
Revert "repair dockstore-cli failing nightly build" by @denis-yuen in https://github.com/dockstore/dockstore/pull/5080
Bump postgresql from 42.3.3 to 42.4.1 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5064
Add a type query parameter to fetch user entries. by @coverbeck in https://github.com/dockstore/dockstore/pull/5084
Feature/fix for paths maybe by @denis-yuen in https://github.com/dockstore/dockstore/pull/5083
turn on pgp signature checks by @denis-yuen in https://github.com/dockstore/dockstore/pull/5087
SEAB-4403: Revise permissions check changes by @svonworl in https://github.com/dockstore/dockstore/pull/5082
Improved Github app handling for logs by @coverbeck in https://github.com/dockstore/dockstore/pull/5070
Missed new param in merge by @coverbeck in https://github.com/dockstore/dockstore/pull/5090
Index Elasticsearch if mappings don't exist by @kathy-t in https://github.com/dockstore/dockstore/pull/5081
optimize files get endpoint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5092
Bump actions/cache from 3.0.7 to 3.0.8 by @dependabot in https://github.com/dockstore/dockstore/pull/5095
Feature/debug GitHub action by @denis-yuen in https://github.com/dockstore/dockstore/pull/5098
add git permissions check for workflows by @denis-yuen in https://github.com/dockstore/dockstore/pull/5094
SEAB-4625: Harmonize EntryVersionHelper "sourcefiles" methods by @svonworl in https://github.com/dockstore/dockstore/pull/5089
Fix multi-arch Quay images by @kathy-t in https://github.com/dockstore/dockstore/pull/5093
check whether a manual tool repo is valid by @denis-yuen in https://github.com/dockstore/dockstore/pull/5096
Sync GitHub app entry metadata with default version by @kathy-t in https://github.com/dockstore/dockstore/pull/5101
Automatically regenerate github tokens in old style on start-up by @denis-yuen in https://github.com/dockstore/dockstore/pull/5102
Add connection pool health check by @kathy-t in https://github.com/dockstore/dockstore/pull/5112
Feature/dock 2058/fix relative absolute file conversion bug by @svonworl in https://github.com/dockstore/dockstore/pull/5110
SEAB-4837: Fix sourcefile retrieval - SAM - google token bug by @svonworl in https://github.com/dockstore/dockstore/pull/5115
Fix failing workflow snapshot by @kathy-t in https://github.com/dockstore/dockstore/pull/5120
update regression test requirements by @denis-yuen in https://github.com/dockstore/dockstore/pull/5126
SEAB-4849: Fix SAM access to hosted workflows by @svonworl in https://github.com/dockstore/dockstore/pull/5127

New Contributors

@fhembroff made their first contribution in https://github.com/dockstore/dockstore/pull/4905

- Java
Published by denis-yuen almost 4 years ago

Highlighted new features

eLWazi launch with
https://www.youtube.com/watch?v=GWBg8gJDpiw
Usability and performance improvements, particularly to TRS and proprietary API for fetching workflows, github app validation/parsing messages for debugging
security updates

Breaking changes

none intended

- Java
Published by denis-yuen about 4 years ago

Highlighted new features include

GitHub app support expanded to CWL tools
- More details here
- improved error handling for github apps including unknown properties in .dockstore.yml
Enhanced support for GA4GH WES, more to come on this topic
Support for biologically-relevant (or other fields) categories that can be managed by Dockstore curators, more to come on this topic
Expanded checksum gathering for workflows and tools that use Amazon ECR and GitHub Container registry docker images to help support reproducible and immutable production-ready workflows
detection of open data in parameter json for workflows, to help evaluate workflow FAIRness
continued UI redesign to simplify and improve the end-user experience
- more consistent UI elements throughout
- harvesting of more descriptions and topics from github repos to improve search experience (can also be manually specified)
improved experience for exporting orcid workflows to multiple users
improved organization and collections experience
- for example, deletion of collections
performance enhancements to a number of endpoints including GA4GH TRS
a large number of fixes for everything from image linking, multi-file input types in CWL, multi-architecture quay.io images
a large number of behind the scenes improvements to our deployment and compliance processes

See a whole lot more in the full list of our changes on GitHub

Breaking changes

Major

none anticipated

Minor

none anticipated

- Java
Published by denis-yuen over 4 years ago

dockstore - 1.12.0-rc.1

- Java
Published by denis-yuen over 4 years ago

dockstore - 1.11.12

bugfixes and performance improvements

- Java
Published by denis-yuen over 4 years ago

dockstore - 1.11.11

launch-with removal DNAstack
security updates

- Java
Published by denis-yuen over 4 years ago

dockstore - 1.11.10

Maintenance release including

Wrong link from tool to GitHub #4540
Security update

- Java
Published by coverbeck over 4 years ago

dockstore - 1.11.8

Maintenance release including

fix for some GUI text formatting issues
fix for database transactions on github app error
fix for boolean WDL metadata parsing
security updates

- Java
Published by wshands almost 5 years ago

Highlighted new features include

GitHub app support for control over publishing status and setting the default tag that users see when looking at your workflow
- More details here.
Support for exporting selected workflows to your ORCID profile
- including improved wizard for snapshot, DOI minting
launch-with support for multiple Galaxy instances
simple support for launch-with for Nextflow Tower
redesigned logged-off homepage and about page with more information on Dockstore's mission and tutorials
updates to search for both usability and performance
a large number of fixes for anything from date modified for github app workflows, navigation in collections, search page filtering, truncating long names, and event tracking
performance improvements for github apps
update to test version of cromwell from 41 to 60
a large number of behind the scenes improvements to our deployment and compliance processes

See a full list of our changes on GitHub

Breaking changes

Major

Regretfully, CLI users will need to update to 1.11 due to some changes in how workflows are loaded for performance reasons
Some behind the scenes changes will tighten up the way GitHub login is performed, If you experience difficulty logging into your Dockstore account after our update, create a help desk ticket on Discuss. For verification purposes make sure your Discuss account is linked to your GitHub account before creating a ticket.

Minor

none

- Java
Published by denis-yuen about 5 years ago

dockstore - 1.10.2

Optimization for github releases with large repos Updated TOS Minor bugfixes

Details at https://github.com/dockstore/dockstore/compare/1.10.1...1.10.2

- Java
Published by wshands over 5 years ago

dockstore - 1.10.1

bugfixes

Details at https://github.com/dockstore/dockstore/compare/1.10.0...1.10.1

- Java
Published by denis-yuen over 5 years ago

Highlighted new features include

GitHub app support for filters to allow for more control over which tags and branches are automatically reported to Dockstore.
- More details here.
Ability to select a specific version of a workflow or tool when adding them to a collection ("I vouch for specifically version X of workflow Y").
Update support for cwltool from 1.0.20190621234233 to 3.0.20200807132242.
GitHub apps patches for more reliable processing of automatic updates.
Performance improvements for large repositories with lots of branches and tags.
Performance improvements for GA4GH TRS implementation.
Initial phase of a more consistent visual experience for the site.
Behind the scenes:
- A large number of deployment and architectural changes to facilitate better security and regulatory compliance.
- Updates to elastic search and angular.
A significant number of bugfixes for everything from WDL parsing, UI display issues, editing of hosted workflows, and command-line interface fixes.

See a full list of our changes on GitHub

Breaking changes

Major

None intended

Minor

none

- Java
Published by denis-yuen over 5 years ago

dockstore - 1.9.2

Minor bugfixes and performance improvements

- Java
Published by coverbeck almost 6 years ago

dockstore -

performance improvements
galaxy compatibility fixes
quay.io fix
github app message fix

See last half of https://github.com/dockstore/dockstore/compare/1.9.0...1.9.1 due to "Fix bad merge to master" for details

- Java
Published by denis-yuen almost 6 years ago

dockstore - 1.9.0

Changelog for overall changes from 1.8.0 to 1.9.0

Highlighted new features include:

language plugin support, allowing for additional of Galaxy workflows as a preview feature
performance improvements for a large variety of endpoints
GitHub app support in preview to allow for automated update of workflow content
implementation of the TRS v2 final standard ** TRS v2 beta standard support is deprecated but still present
capture of file and docker image checksums from GitHub, quay.io, Gitlab, and Docker Hub on workflow snapshot to support immutable workflows (see breakdown for details here)
support for linking ORCID profiles user profiles ** currently displayed in organization and stargazer views
a large number of usability improvements and fixes to the user interface website
partial API migration from swagger 2.0 to openapi 3.0 for the Dockstore API
a large variety of security updates and bug fixes

As always, see our full list of changes on GitHub

Breaking changes

Major

None intended

Minor

If upgrading the Dockstore CLI, our Dockstore script has changed and should be downloaded anew from the onboarding wizard
CLI website management features (refresh) will be broken until CLI version is upgraded, workflow launching should remain

- Java
Published by denis-yuen about 6 years ago

dockstore -

With the https://github.com/dockstore/dockstore-cli/releases/download/1.9.0-beta.0/dockstore dockstore script

- Java
Published by garyluu about 6 years ago

dockstore - 1.9.0-beta.0

- Java
Published by agduncan94 about 6 years ago

dockstore - 1.9.0-alpha.10

- Java
Published by agduncan94 about 6 years ago

dockstore - 1.9.0-alpha.9

- Java
Published by agduncan94 about 6 years ago

dockstore - 1.8.6

Bugfixes and performance improvements

improve performance of My Workflows and collection views
improve performance of events
fix tool deletion with events

Details at https://github.com/dockstore/dockstore/milestone/34

- Java
Published by denis-yuen about 6 years ago

dockstore - 1.8.5

Performance improvements and bug-fixes * stability issues * collection performance improvements * funding text

- Java
Published by denis-yuen about 6 years ago

dockstore - 1.8.4

Performance improvements and bug-fixes

stability issues
collection performance improvements
funding text

- Java
Published by denis-yuen about 6 years ago

dockstore - 1.8.3

Performance improvements and bug-fixes

stability issues
collection performance improvements
funding text

- Java
Published by denis-yuen about 6 years ago

dockstore - 1.9.0-alpha.8

- Java
Published by agduncan94 over 6 years ago

dockstore - 1.8.2

Performance improvements and bug-fixes

improvements have been made to the performance of the webservice and search
bugfixes have been made to prevent overlapping refreshes from creating invalid content

- Java
Published by coverbeck over 6 years ago

New Features

Launch with BioData Catalyst buttons

- Java
Published by coverbeck over 6 years ago

Highlighted new features include:

New launch-with partners
- AnVIL
Redesigned logged-in homepage displays more information for returning users including
- News and updates
- Featured content such as new organizations and workflows
- Recently modified tools, workflows and orgs
Notification system for news such as TOS updates, pending system updates
Security updates
Performance improvements
Usability improvements
Can source workflow descriptions from README.md if not present in workflow itself
DOI landing pages hosted at Zenodo will now link to exact versions of workflows
Preview feature
Services are now reachable from many parts of the UI
Behind the scenes work on CI/CD, infrastructure improvements, more frequent releases
Also some behind the scenes work leading up to the implementation of the final v2 GA4GH TRS standard

As always, see our full list of changes on GitHub

Breaking changes

Major

None intended

Minor

If upgrading the Dockstore CLI, our Dockstore script has changed and should be downloaded anew from the onboarding wizard

- Java
Published by denis-yuen over 6 years ago

dockstore - 1.8.0-rc.0

- Java
Published by denis-yuen over 6 years ago

dockstore - 1.8.0-beta.9

- Java
Published by agduncan94 over 6 years ago

dockstore - 1.8.0-beta.8

- Java
Published by agduncan94 over 6 years ago

dockstore - 1.8.0-beta.7

- Java
Published by agduncan94 over 6 years ago

dockstore - 1.8.0-beta.6

- Java
Published by denis-yuen over 6 years ago

dockstore - 1.8.0-beta.0

- Java
Published by denis-yuen over 6 years ago

dockstore - 1.7.4

performance fix

- Java
Published by denis-yuen over 6 years ago

dockstore - 1.8.0-alpha.2

built cli separately with synced version numbers

- Java
Published by denis-yuen over 6 years ago

dockstore - 1.7.3

includes fix for google login issue

- Java
Published by denis-yuen over 6 years ago

Fixes include

correctly parse complex WDL workflows

- Java
Published by agduncan94 over 6 years ago

dockstore - 1.8.0-alpha.1

- Java
Published by agduncan94 over 6 years ago