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Set sorting field types to 64 bit long #279

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wants to merge 38 commits into from
Closed

Set sorting field types to 64 bit long #279

wants to merge 38 commits into from

Commits on Jun 19, 2024

  1. Set sorting field types to 64 bit long

    @bbimber
    Sebastian Benjamin authored and bbimber committed Jun 19, 2024
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Commits on Jun 20, 2024

  1. remove usages of HtmlView(String,String)

    @labkey-matthewb
    labkey-matthewb authored and Sebastian Benjamin committed Jun 20, 2024
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  2. HtmlView.unsafe()

    @labkey-matthewb
    labkey-matthewb authored and Sebastian Benjamin committed Jun 20, 2024
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  3. Update gradle plugin ids (#258)

    @labkey-susanh
    labkey-susanh authored and Sebastian Benjamin committed Jun 20, 2024
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  4. replace usages of q() with h() where appropriate

    @labkey-matthewb
    labkey-matthewb authored and Sebastian Benjamin committed Jun 20, 2024
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  5. Tomcat 10 - Update namespace of Jakarta EE packages (#268) 

    Co-authored-by: Adam Rauch <[email protected]>
Co-authored-by: Josh Eckels <[email protected]>
    @labkey-tchad @labkey-adam @labkey-jeckels
    3 people authored and Sebastian Benjamin committed Jun 20, 2024
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  6. Fix more tests that launch ClusterStartup (#270)

    @labkey-jeckels
    labkey-jeckels authored and Sebastian Benjamin committed Jun 20, 2024
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  7. Switch a few URLs to path-first (#271)

    @labkey-adam
    labkey-adam authored and Sebastian Benjamin committed Jun 20, 2024
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  8. Add null check

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  9. Set allowable values for HOMOZYGOUS_VAR

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  10. Update error message

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  11. Update error message

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  12. Update error message

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  13. Adjust sort field name

    Sebastian Benjamin committed Jun 20, 2024
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  14. Improve and debug SequenceAnalysisMaintenanceTask

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  15. Add LRUQueryCache (#273) 

    * Add LRUQueryCache

* Custom query caching policy

* Query strategy works on BooleanQuery with MatchAllDocs predicate

* Use proper Cache and add action to report cache info

* Improve handling of lucene cache

* Add code to cache the first page of each mGAP JBrowse session

* Add logging and clear cache prior to adding default query

---------

Co-authored-by: Sebastian Benjamin <[email protected]>
Co-authored-by: bbimber <[email protected]>
    @hextraza @bbimber
    3 people committed Jun 20, 2024
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  16. Reduce length of description field

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  17. Update parameter name

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  18. Ensure savedSeuratObjects.txt file has unique name per job

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  19. Fix typo

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  20. Add link to single cell management page

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  21. Add support for useLeiden

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  22. Update default for requireRiraImmune

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  23. Bump braces from 3.0.2 to 3.0.3 in /jbrowse 

    Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3.
- [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md)
- [Commits](micromatch/braces@3.0.2...3.0.3)

---
updated-dependencies:
- dependency-name: braces
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored and Sebastian Benjamin committed Jun 20, 2024
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  24. Update nimble arguments

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  25. Add Classify_Myeloid to RIRA step

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  26. Support GATK SVAnnotateStep

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  27. Drop unused bissnp code

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  28. Drop unused DockerHTCondorExecutionEngine code

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  29. Correct parameter label

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  30. Support bcftools as optional liftover tool

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  31. Inital support for paraGRAPH

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  32. Update library type terms

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  33. Add step to re-process Seurat prototypes

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  34. Support parameter for collapsing Gamma-only cells to Gamma/Delta

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  35. Set sorting field types to 64 bit long

    Sebastian Benjamin committed Jun 20, 2024
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  36. Update DimplotLogic to allow missing reductions

    @bbimber
    bbimber authored and Sebastian Benjamin committed Jun 20, 2024
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  37. Merge branch '23.4_fb_sortingLongFix' of github.com:BimberLab/DiscvrL… 

    …abKeyModules into 23.4_fb_sortingLongFix
    Sebastian Benjamin committed Jun 20, 2024
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