Published September 12, 2022
| Version 1.13.0
Software
Open
dockstore/dockstore: 1.13.0
Authors/Creators
- Denis Yuen1
- Andrew Duncan2
- Gary Luu3
- Victor Liu
- Charles Overbeck
- Brian O'Connor4
- NatalieEO
- Walter Shands
- Kathy Tran
- Steve Von Worley
- Gregory F J Hogue5
- David Steinberg
- Richard-Hansen
- Emily Soth
- Louise Cabansay
- Flynn Hembroff
- amar jandu
- Nina Zhao
- oicr-vchung
- Andy Chen
- Peter Amstutz6
- Wendy Zhang
- kcao-guidewire
- Ryan Bautista
- Noah Warren
- Chaz Reid7
- dependabot-support
- Abraham
- C. Titus Brown8
- 1. @OICR_news
- 2. University of Toronto
- 3. OICR
- 4. Broad Institute & Nimbus Informatics, LLC
- 5. Ontario Institute for Cancer Research
- 6. @CuriiHQ @arvados
- 7. UCSC Genomics Institute
- 8. University of California, Davis
Description
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 # Breaking changes
- none intended
- 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 PULL_REQUEST_TEMPLATE.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 SEM_VER_STRING 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
- @fhembroff made their first contribution in https://github.com/dockstore/dockstore/pull/4905
Files
dockstore/dockstore-1.13.0.zip
Files
(2.0 MB)
| Name | Size | Download all |
|---|---|---|
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md5:7cb5a59e6b6f9872f23dff460289adc9
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2.0 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/dockstore/dockstore/tree/1.13.0 (URL)