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Implement a faster query for sorted samples with search enabled and editing disabled #164

Merged
merged 23 commits into from
Sep 30, 2024
Merged

Implement a faster query for sorted samples with search enabled and editing disabled #164

merged 23 commits into from
Sep 30, 2024

Commits on Sep 26, 2024

  1. Optimized sample dashboard query (#162) 

    Refactor the samples query to call Neo4j directly
    @mandawilson
    mandawilson authored Sep 26, 2024
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Commits on Sep 27, 2024

  1. Update configs to work with new Neo4j version

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  2. Move nested fields returned in the new Samples query to the root level

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  3. Create a placeholder custom query and type for the new Samples query

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  4. Populate cancerType and cancerTypeDetailed fields with the new Sample… 

    …s query
    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  5. Enable searching in the all-samples view of Samples page

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  6. Populate recipe with the new Samples query

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  7. Add better error handling when getting oncotree data from cache

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  8. Search ct and ctDetailed fields more efficiently

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  9. Create a separate custom schema for dashboard samples

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  10. Add a context arg to the new samples query & enable WES view

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  11. Use the new samples query in the Request Samples view

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  12. Use the new samples query in the Patient Samples view

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  13. Use the new samples query in the Cohort Samples view

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  14. Resolve sample count using the new samples query

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  15. Clean up the old sample query's WHERE variables

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  16. Remove unnecessary React state 'parsedSearchVals' in Samples view

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  17. Remove dataloader package 

    We previously used dataloader to make a single query for samples via
the OGM. Otherwise, the `samples` and `samplesConnection` sub-queries
would be call it twice.

With the new approach, we use two slightly different queries to get
samples data and the count of samples. We could use dataloader to access
the oncotree cache, but this operation is very fast (< 0.05ms).
    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  18. Trigger search when search form is cleared

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  19. Trigger search when search form is cleared

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  20. Temporarily handle table element diffs between SamplesList and Record… 

    …sList components
    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  21. Add Investigator Sample ID column to WES Samples view

    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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  22. Increase sample polling interval from 2s to 5s and move investigatorS… 

    …ampleId column to the front
    @qu8n @ao508
    qu8n authored and ao508 committed Sep 27, 2024
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