What's Changed

• SEAB-7285: Make "missing dockstore.yml" user notifications happen less by @svonworl in #6168
• Fix broken migration by @svonworl in #6170
• test zenodo client update by @denis-yuen in #6177
• SEAB-7226: Add endpoint to identify "missing" DOIs by @svonworl in #6175
• SEAB-7226: Address DOI creation failures by @svonworl in #6174
• Fix cwltool bug and bump version by @svonworl in #6187

Full Changelog: 1.18.0...1.18.2

Highlighted Changes

• Time series metrics (view workflow runs over previous weeks) and breakdowns of execution status
• Wizard that can infer (guess) at a .dockstore.yml based on repository contents to aid with registration
• Numerous security updates

Breaking Changes

• None known/intended

What's Changed

• SEAB-6958: Make notebook registration error message more explanatory by @svonworl in #6100
• Bump org.apache.httpcomponents.client5:httpclient5 from 5.4.1 to 5.4.3 in /dockstore-integration-testing/generated/src/main/resources by @dependabot[bot] in #6101
• update bundle by @denis-yuen in #6113
• routine dropwizard update by @denis-yuen in #6115
• Bump commons-beanutils:commons-beanutils from 1.9.4 to 1.11.0 in /bom-internal by @dependabot[bot] in #6116
• update swagger ui - 5.22.0 - cve by @denis-yuen in #6117
• cve update - java docker by @denis-yuen in #6119
• update aws in order to update netty by @denis-yuen in #6118
• Revert "how bad is it if we just don't restart elasticsearch" and add docker schema test by @denis-yuen in #6123
• patch and test with empty repository by @denis-yuen in #6124
• Bump org.apache.commons:commons-lang3 from 3.17.0 to 3.18.0 in /dockstore-common/generated/src/main/resources by @dependabot[bot] in #6129
• update postgres to avoid deprecation by @denis-yuen in #6133
• jpa loading of starred entries by @denis-yuen in #6130
• new location for broad artifacts by @denis-yuen in #6134
• try newer async http by @denis-yuen in #6136
• dropwizard 4.0.15 by @denis-yuen in #6137
• SEAB-7194: Add "time series" metric database entity by @svonworl in #6127
• fix docker hub pull of tag images by @denis-yuen in #6140
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #6138
• Bump actions/setup-java from 4 to 5 by @dependabot[bot] in #6143
• SEAB-7194: Add weekly execution count time series metric by @svonworl in #6144
• Bump actions/upload-pages-artifact from 3 to 4 by @dependabot[bot] in #6145
• Update dependabot.yml - exclude requirement files for cwltool by @denis-yuen in #6148
• Create user notification for .dockstore.yml inference by @kathy-t in #6147
• SEAB-7194: Add max weekly execution count endpoint by @svonworl in #6156
• SEAB-7194: Correct openapi description of new "max weekly execution counts" endpoint by @svonworl in #6157
• SEAB-6531: Notify trigger user after install on repo with no .dockstore.yml by @svonworl in #6160
• Bump aws-actions/configure-aws-credentials from 4 to 5 by @dependabot[bot] in #6154
• New exclude-paths for dependabot.yml by @denis-yuen in #6155
• SEAB-6531: Fix some .dockstore.yml inference bugs, reset version by @svonworl in #6162

Full Changelog: 1.17.2...1.18.0

What's Changed

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

Full Changelog: 1.17.0...1.17.1

Highlighted Changes

• R Jupyter notebook support
• Preview of Snakemake support
• Search cards (makes it easier to review search results)
• Toil and Terra anonymous metrics integration
• Automatic DOI enhancements
  • back-end changes for retroactive issuing
• many bugfixes and tweaks

Breaking Changes

• None known/intended

What's Changed

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

Full Changelog: 1.16.6...1.17.0

What's Changed

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

Full Changelog: 1.17.0-beta.0...1.17.0-beta.1

What's Changed

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

Full Changelog: 1.16.6...1.17.0-beta.0

What's Changed

• SEAB-6700: Generate automatic DOIs for all new tags by @svonworl in #6074
• SEAB-6971: Commit to hotfix branch by @hyunnaye in #6077

Full Changelog: 1.16.5...1.16.6

What's Changed

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

Full Changelog: 1.16.3...1.16.5

Full Changelog: 1.16.1...1.16.3

What's Changed

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

Full Changelog: 1.16.0...1.16.3