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Loading prefetched small variants results is slow #371

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holtgrewe opened this issue Mar 7, 2022 · 2 comments · Fixed by #372
Closed

Loading prefetched small variants results is slow #371

holtgrewe opened this issue Mar 7, 2022 · 2 comments · Fixed by #372
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bug Something isn't working
Milestone
athenea-1.1.0 (RC)

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@holtgrewe
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Describe the bug
Loading prefetched small variant resuls is slow.

To Reproduce
Create small variant query. Make varfish fetch the result. Look at the query results.

Expected behavior
Should be quite speedy.

Additional context
N/A
@holtgrewe holtgrewe added the bug Something isn't working label Mar 7, 2022
@holtgrewe holtgrewe added this to the athenea-1.1.0 (RC) milestone Mar 7, 2022
@holtgrewe
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Root Cause Analysis
The query to fetch the small variant results does not incorporate case_id, thus all table partitions need to be queried.

@holtgrewe
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Resolution Proposal
Make the queries to fetch the results also consider case_id to make queries on the partition tables fast.

Affected Components
Varfish server.

Affected Modules/Files

  • variants.queries

Required Architectural Changes

  • None

Resolution Sketch

  • See above, make the queries also check the case_id column.

holtgrewe added a commit that referenced this issue Mar 7, 2022
@holtgrewe
Improving performance for fetching result queries (#371)
9a8b5ee 
Closes: #371
holtgrewe added a commit that referenced this issue Mar 7, 2022
@holtgrewe
Improving performance for fetching result queries (#371)
35321f7 
Closes: #371
@holtgrewe holtgrewe mentioned this issue Mar 7, 2022
Merged
holtgrewe added a commit that referenced this issue Mar 7, 2022
@holtgrewe
Improving performance for fetching result queries (#371) (#372)
be2ed28 
Closes: #371
holtgrewe added a commit that referenced this issue Mar 7, 2022
@holtgrewe
Optimize retrieving query IDs via API (#371)
f9a4dce
holtgrewe added a commit that referenced this issue Mar 7, 2022
@holtgrewe
Optimize retrieving query IDs via API (#371) (#373)
034c311
snesic added a commit to snesic/varfish-server that referenced this issue Mar 9, 2022
@snesic
Add extra annotations scores to the filtered variants (varfish-org#242).
838611d 
Squashed commit of the following:

commit 5a0ff15
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Wed Mar 9 11:14:51 2022 +0100

    Documenting release cycle and branch names

commit 7c50327
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Wed Mar 9 11:13:04 2022 +0100

    Capping max. number of cases to query at once (varfish-org#372) (varfish-org#377)

commit cc29127
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Wed Mar 9 08:41:46 2022 +0100

    Fixing problem with sodar-core upgrade (varfish-org#375) (varfish-org#376)

commit 034c311
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Mon Mar 7 15:52:05 2022 +0100

    Optimize retrieving query IDs via API (varfish-org#371) (varfish-org#373)

commit bdb49c8
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Mon Mar 7 15:40:35 2022 +0100

    Fix to support sodar-core v0.10.10.

commit be2ed28
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Mon Mar 7 14:41:25 2022 +0100

    Improving performance for fetching result queries (varfish-org#371) (varfish-org#372)

    Closes: varfish-org#371

commit c0fbd74
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Mon Mar 7 11:40:52 2022 +0100

    Fixing minor bug in _ClosingWrapper.

commit 00ab43f
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Mar 4 17:24:31 2022 +0100

    Documenting Clinical Beacon v1 protocol.

commit b954c1e
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Mar 4 16:48:19 2022 +0100

    Changing branch for badge to main

commit 005f7d4
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Mar 4 16:44:36 2022 +0100

    Splitting UNION queries in joint mode (varfish-org#241) (varfish-org#352)

commit 5e04b4d
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Mar 4 16:42:18 2022 +0100

    Fixing beaconsite queries with dots in the key id (varfish-org#369) (varfish-org#370)

    Closes: varfish-org#369

commit dc32e7e
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Mar 4 16:16:01 2022 +0100

    Adding REST API for small variants (varfish-org#332) (varfish-org#341)

commit bb8a9c1
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Mar 4 14:46:31 2022 +0100

    Fixing problem with ACMD classification (varfish-org#359) (varfish-org#368)

    Closes: varfish-org#359

commit fbfc86c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Mar 4 14:02:42 2022 +0100

    Bump url-parse from 1.5.4 to 1.5.10 in /varfish/vueapp (varfish-org#365)

    Bumps [url-parse](https://github.com/unshiftio/url-parse) from 1.5.4 to 1.5.10.
    - [Release notes](https://github.com/unshiftio/url-parse/releases)
    - [Commits](unshiftio/url-parse@1.5.4...1.5.10)

    ---
    updated-dependencies:
    - dependency-name: url-parse
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <support@github.com>

    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit b06b258
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Mar 4 14:02:36 2022 +0100

    Bump follow-redirects from 1.14.7 to 1.14.8 in /varfish/vueapp (varfish-org#356)

    Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.7 to 1.14.8.
    - [Release notes](https://github.com/follow-redirects/follow-redirects/releases)
    - [Commits](follow-redirects/follow-redirects@v1.14.7...v1.14.8)

    ---
    updated-dependencies:
    - dependency-name: follow-redirects
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <support@github.com>

    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit b017ad2
Author: Svetozar N <snesic@gmail.com>
Date:   Fri Mar 4 14:01:57 2022 +0100

    Updates to developer_installation.rst (varfish-org#340)

commit 00bfc89
Author: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date:   Fri Feb 25 10:23:55 2022 +0100

    Removing `display_hgmd_public_membership` (varfish-org#363)

commit 2898ef0
Author: Oliver Stolpe <oliver.stolpe@bih-charite.de>
Date:   Wed Feb 23 11:30:11 2022 +0100

    Extending developers documentation with topics git and running specific tests (varfish-org#362)

commit 21a6e75
Author: Oliver Stolpe <oliver.stolpe@bih-charite.de>
Date:   Tue Feb 22 17:32:47 2022 +0100

    Fixing broken case detail page that has comments on svs. (varfish-org#360)
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Improving performance for fetching result queries (#371) varfish-org/varfish-server
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@holtgrewe