1.14.0-beta.0

For testing on staging

What's Changed

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

New Contributors

• @hyunnaye made their first contribution in #5241

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