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Clickhouse implementation of study view #10304

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Closed

Clickhouse implementation of study view #10304

wants to merge 29 commits into from

Commits on Mar 15, 2023

  1. WIP

    @pvannierop
    pvannierop committed Mar 15, 2023
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Commits on Mar 16, 2023

  1. Move StudyViewFilter to webparams modules

    @pvannierop
    pvannierop committed Mar 16, 2023
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Commits on Mar 17, 2023

  1. Wip

    @pvannierop
    pvannierop committed Mar 17, 2023
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Commits on Mar 20, 2023

  1. Finalize second datasource

    @pvannierop
    pvannierop committed Mar 20, 2023
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Commits on Mar 26, 2023

  1. Fix clickhouse datasource

    @pvannierop
    pvannierop committed Mar 26, 2023
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  2. Wip

    @pvannierop
    pvannierop committed Mar 26, 2023
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Commits on Mar 30, 2023

  1. Wip

    @pvannierop
    pvannierop committed Mar 30, 2023
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Commits on Apr 1, 2023

  1. Working version of study view filter

    @pvannierop
    pvannierop committed Apr 1, 2023
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Commits on Apr 3, 2023

  1. Add mutated-genes via clickhouse

    @pvannierop
    pvannierop committed Apr 3, 2023
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Commits on Apr 6, 2023

  1. Fix ClinicalEventMapper.xml

    @pvannierop
    pvannierop committed Apr 6, 2023
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Commits on May 9, 2023

  1. Add comments

    @pvannierop
    pvannierop committed May 9, 2023
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Commits on May 10, 2023

  1. Deprecate need for connection to MySQL for clickhouse

    @pvannierop
    pvannierop committed May 10, 2023
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  2. Fix typo

    @pvannierop
    pvannierop committed May 10, 2023
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  3. Fix mapper

    @pvannierop
    pvannierop committed May 10, 2023
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  4. Externalize clickhouse connection string config

    @pvannierop
    pvannierop committed May 10, 2023
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Commits on May 15, 2023

  1. make clickhouse db params configurable

    @inodb
    inodb committed May 15, 2023
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Commits on May 17, 2023

  1. Sample Retrieval 

    - Add versionRange to pom.xml to conform to specifications
- Add ClickHouseDB query for retrieving sample_ids from sample table based on attribute
    @JREastonMarks
    JREastonMarks committed May 17, 2023
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Commits on May 25, 2023

  1. Use precomputed base64 encoded unique identifiers

    @pvannierop @inodb
    pvannierop authored and inodb committed May 25, 2023
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  2. Revert "Use precomputed base64 encoded unique identifiers" 

    This reverts commit c1e40be.
    @inodb
    inodb committed May 25, 2023
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Commits on May 31, 2023

  1. improved clickhouse specific example configuration

    @onursumer
    onursumer committed May 31, 2023
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Commits on Jun 5, 2023

  1. use base64 encoded columns for unique sample and patient keys

    @onursumer
    onursumer committed Jun 5, 2023
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Commits on Jun 26, 2023

  1. add mock data and config for clickhouse testing on filtered samples a… 

    …nd mutated genes (#10213)

Co-authored-by: Bryan Lai <[email protected]>
    @onursumer
    onursumer and Bryan Lai authored Jun 26, 2023
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Commits on Jun 27, 2023

  1. Revert original Study View endpoints (#10216) 

    * revert study view controller original endpoints and rename clickhouse endpoints

* add mybatiscolumnstore to test application context
    @onursumer
    onursumer authored Jun 27, 2023
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Commits on Jun 28, 2023

  1. Extract column store endpoints into StudyViewColumnStoreController (#… 

    …10245)

* Extract column store endpoints into StudyViewControllerColumnStore

* rename
    @haynescd
    haynescd authored Jun 28, 2023
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Commits on Jun 29, 2023

  1. add tests for clinical data filters (#10249)

    @onursumer
    onursumer authored Jun 29, 2023
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Commits on Jul 10, 2023

  1. Feature/add clinical data counts endpoint (#10262) 

    Migrate mutated-genes and clinical-data-counts to clickhouse-ish implementations
---------

Co-authored-by: haynescd <[email protected]>
    @alisman @haynescd
    alisman and haynescd authored Jul 10, 2023
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Commits on Jul 12, 2023

  1. add new clickhouse clinical data bin count end point (#10265)

    @onursumer
    onursumer authored Jul 12, 2023
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Commits on Jul 17, 2023

  1. Fix test to add Clinical Data

    @haynescd
    haynescd committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. Fix GeneFilters

    @haynescd
    haynescd committed Jul 18, 2023
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