Atlas v2.14 release candidate available for testing

[anthonysena]

Happy to announce that v2.14 of ATLAS/WebAPI is now available to the OHDSI Community for testing via this URL: http://atlas-preview.ohdsi.org:9090/atlas/#/home. This release is mainly focused on bug fixes which are listed in detail below but there are a few new features that we’d like to highlight:

• Ability to provide a date offset for cohort definitions – thanks @chrisknoll!
• Filter assets by read-only permissions: this allows for optionally hiding design assets (i.e. cohort definitions) from view when security is enabled - thanks @rkboyce. Unfortunately you won’t be able to see this in action on this instance of Atlas since security is not enabled but you can view: for details on this feature.
• A number of bug fixes for the ATLAS front-end and WebAPI back end including java library upgrades, SQL updates and fixes for Databricks (see below for more details). Many thanks to all of the developers that made contributions and to the 7 new contributors in this release!

If you encounter any issues while using this version of ATLAS please file them on GitHub here: Issues · OHDSI/Atlas · GitHub.

Atlas Release Notes

• Check for empty data condition. by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2834
• Concept added to a concept set has no Exclude/Descendants/Mapped flag #2838 by @anton-abushkevich in https://github.com/OHDSI/Atlas/pull/2839
• Pinned and updated dependency versions by @chgl in https://github.com/OHDSI/Atlas/pull/2683
• “Place of service distance” criteria for a Visit Occurrence criteria is misfunctional #2814 by @anton-abushkevich in https://github.com/OHDSI/Atlas/pull/2841
• Move databindings loading to application bootstrap. by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2852
• Adds ability to disable browser check via config by @alondhe in https://github.com/OHDSI/Atlas/pull/2863
• Correct vocabulary for person counts is used by @ssuvorov-fls in https://github.com/OHDSI/Atlas/pull/2860
• Add option to force authentication by @RowanErasmus in https://github.com/OHDSI/Atlas/pull/2861
• Fixed name of downloaded file by @ssuvorov-fls in https://github.com/OHDSI/Atlas/pull/2864
• Fix terms and conditions content by @jack5mil in https://github.com/OHDSI/Atlas/pull/2765
• Fixed PLE editor text for i18n. by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2871
• Make indexMessage respond to observable changes. by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2853
• Add read permissions (#2849) by @chrisknoll, @rkboyce in https://github.com/OHDSI/Atlas/pull/2879
• Reduce polling to /user/refresh by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2835
• Circe date offsets by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2880
• Ensure prism loads in correct order. by @chrisknoll in https://github.com/OHDSI/Atlas/pull/2877
• Prevent multiple calls to concept set list when loading cohort editor by @anthonysena in https://github.com/OHDSI/Atlas/pull/2888
• Reset feature analyses parameters after submission by @jack5mil in https://github.com/OHDSI/Atlas/pull/2768

New Contributors

• @alondhe made their first contribution in https://github.com/OHDSI/Atlas/pull/2863
• @RowanErasmus made their first contribution in https://github.com/OHDSI/Atlas/pull/2861
• @jack5mil made their first contribution in https://github.com/OHDSI/Atlas/pull/2765

Full Changelog: https://github.com/OHDSI/Atlas/compare/v2.13.0...v2.14.0](Apache Solr Setup Guide · OHDSI/WebAPI Wiki · GitHub)

WebAPI Release Notes

• TagRepository findXXXTagInfo() produces invalid SQL, should return minimal columns #2241 by @anton-abushkevich in https://github.com/OHDSI/WebAPI/pull/2242
• Refactored imports to depend on com.google.guava:guava by @ecruz165 in https://github.com/OHDSI/WebAPI/pull/2219
• Bump up several libraries by @ecruz165 in https://github.com/OHDSI/WebAPI/pull/2202
• Bump up maven tooling versions by @ecruz165 in https://github.com/OHDSI/WebAPI/pull/2200
• Hypersistence Optimizer Issues: Blocker: PooledSequenceOptimizerEvent by @ecruz165 in https://github.com/OHDSI/WebAPI/pull/2218
• Translated postgresql migration scripts to SQL Server up to v2.10 by @dsfrederic in https://github.com/OHDSI/WebAPI/pull/2238
• Webapi docker profile and TLS by @alondhe in https://github.com/OHDSI/WebAPI/pull/2235
• Added MAVEN_PARMS arg to Dockerfile by @alondhe in https://github.com/OHDSI/WebAPI/pull/2229
• Fix SQL in procedure drilldown report by @gebilaoman in https://github.com/OHDSI/WebAPI/pull/2224
• Set job status to failed when exception is thrown in listener. by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2217
• set default value for source.is_cache_enabled column to false by @chgl in https://github.com/OHDSI/WebAPI/pull/2133
• Fix cdmresults drill-down reports by @TomWhite-MedStar in https://github.com/OHDSI/WebAPI/pull/2257
• Enable PC and DPC for source and non-standard concepts by @TomWhite-MedStar in https://github.com/OHDSI/WebAPI/pull/2258
• Fix heracles 200 for spark by @TomWhite-MedStar in https://github.com/OHDSI/WebAPI/pull/2267
• Fix issue #2256 by @TomWhite-MedStar in https://github.com/OHDSI/WebAPI/pull/2269
• OpenID Connect custom parameters by @RowanErasmus in https://github.com/OHDSI/WebAPI/pull/2254
• limits for big query were changed to 10000 by @ssuvorov-fls in https://github.com/OHDSI/WebAPI/pull/2273
• Wildcard is not used now by default. User has to set it explicitly if needed by @ssuvorov-fls in https://github.com/OHDSI/WebAPI/pull/2277
• added permissions for downloading concepts by @ssuvorov-fls in https://github.com/OHDSI/WebAPI/pull/2279
• Added params to savePaths for spark dialect. by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2276
• raised versions of big query driver and libraries by @ssuvorov-fls in https://github.com/OHDSI/WebAPI/pull/2272
• Fixed PLE editor text for i18n. by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2290
• Enable OIDC authentication with a direct client by @RowanErasmus in https://github.com/OHDSI/WebAPI/pull/2289
• Bump circe to v1.11.0. by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2302
• Filter cohorts and concepts by permission (#2245) by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2301
• Update Dependencies and address defaultGlobalReadOnly param by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2305
• Dependabot Updates by @chrisknoll in https://github.com/OHDSI/WebAPI/pull/2309
• Fix: Sql syntax error on Update getConceptRecordCount.sql by @ww166 in https://github.com/OHDSI/WebAPI/pull/2311
• Finalizing externalizing Vocabulary Search Apache Solr implementation by @alex-odysseus in https://github.com/OHDSI/WebAPI/pull/2308
• Updated SqlRender v1.16.1 by @konstjar in https://github.com/OHDSI/WebAPI/pull/2313

New Contributors

• @ecruz165 made their first contribution in https://github.com/OHDSI/WebAPI/pull/2219
• @dsfrederic made their first contribution in https://github.com/OHDSI/WebAPI/pull/2238
• @gebilaoman made their first contribution in https://github.com/OHDSI/WebAPI/pull/2224
• @RowanErasmus made their first contribution in https://github.com/OHDSI/WebAPI/pull/2254
• @ww166 made their first contribution in https://github.com/OHDSI/WebAPI/pull/2311

Full Changelog: https://github.com/OHDSI/WebAPI/compare/v2.13.0...v2.14.0

[Ajit_Londhe]

Want to try this great new Atlas 2.14 release candidate on your own hardware and help test it? If you can run Docker, then you can in the time it takes to drink a cup of coffee! (depends on coffee cup size, ymmv, etc)

1. Clone Broadsea (repo located at https://github.com/OHDSI/Broadsea)
   I recommend using the Develop branch, as it has a bunch of bugfixes; we should release it officially soon

2. Modify these .env file settings:

    ATLAS_GITHUB_URL="https://github.com/OHDSI/Atlas.git#rc-2.14.0"
    WEBAPI_GITHUB_URL="https://github.com/OHDSI/WebAPI.git#rc-2.14.0"

    DOCKER_ARCH="linux/amd64" # change this to linux/arm64 if using Mac Silicon, 
                              # otherwise keep as-is

3. Run these command line steps while in the cloned directory:

    docker-compose up -d
    docker-compose --profile atlasdb up -d
    docker-compose --profile webapi-from-git up -d
    docker-compose --profile atlas-from-git up -d

4. Inspect everything is up and running
   View all docker logs, ensure everything is running and without any fatal errors

   

   Go to 127.0.0.1/WebAPI/info, ensure you see WebAPI’s version and status

   

   Go to 127.0.0.1/atlas, ensure Atlas loads

   

5. Switch to a celebratory beverage now that you have Atlas 2.14 Release Candidate up and running on your hardware (or a debugging beverage should these steps fail)

   Look at that fancy new date offset feature

   

   If the latter, please raise issues in the Broadsea GitHub repo.

[Sanjay_Udoshi]

A very impressive release! I just started testing today. Will report back with details. Huzzah!!! to everyone who contributed to this version!

[anthonysena]

An update for the community here: we’re nearly done testing and aiming to finalize the release of Atlas/WebAPI v2.14 at the end of this week. Thanks to everyone who has tested and provided feedback to date!