Table update tracker anya #2764

anna-parker · 2024-09-11T06:54:37Z

related to: #2092

preview URL: https://table-update-tracker-anya.loculus.org/

Summary

Adds UpdateTrackerTable to database with last time a table in the database was modified.
Adds optional last-modified-if header to get-released-data, this accepts a Long = unix timestamp. If the database was modified since the value in last-modified-if get-released-data will respond with all released data and last-modified header, where last-modified is the time of the last database update. If the value in last-modified-if is equal or greater to the last time the database was modified get-released-data will respond with 304: NOT_MODIFIED and no last-modified header.
Updates silo_import_job.sh and silo_import_wrapper.sh to use the last-modified-if header. This significantly reduces the load on the database and backend, times are from after preprocessing has finished (CPU is in mCPU):

kubectl top pod --sum --containers --all-namespaces | egrep "backend|s-database" | egrep "main|tracker-anya" | sort -hk4                                           bs-mbpas-0092: Wed Sep 11 19:51:30 2024

prev-table-update-tracker-anya   loculus-backend-c859b6f4b-gj5k5                                   backend                              19m          421Mi
prev-table-update-tracker-anya   loculus-database-67f7d88557-9mf6v                                 database                             101m         326Mi
prev-main                        loculus-database-645647c886-kh5vf                                 database                             113m         234Mi
prev-main                        loculus-backend-55f5cdb6cb-p7p4f                                  backend                              300m         483Mi

Screenshot

PR Checklist

All necessary documentation has been adapted.
The implemented feature is covered by an appropriate test.
Now or in a later PR ensure that we are compliant https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/If-Modified-Since#syntax,

…D header

… was successfully sent to LAPIS - then echo $last_modified

corneliusroemer

Cool stuff, amazing this works, just some refactoring comments 😀

corneliusroemer · 2024-09-11T08:45:29Z

backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt

@@ -252,16 +256,30 @@ class SubmissionController(
    fun getReleasedData(
        @PathVariable @Valid organism: Organism,
        @RequestParam compression: CompressionFormat?,
+        @RequestHeader(value = HttpHeaders.IF_MODIFIED_SINCE, required = false) ifModifiedSince: Long?,


If we pass a long we are kind of violating HTTP specs which have a specific (annoying) format for this particular header. We might want to choose our own header field if we are not spec compliant to not confuse people.

We probably want extra millisecond precision here just to make sure we don't miss an update.

To make a potential cache race condition less impactful, we could always request all data after time X, say 1hr, then we are at most that much out of date, but this is best handled in client I think

Ah true - I see that the expected input is: https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/If-Modified-Since#syntax, so we could check if there is a way to convert a string to a sql.Timestamp object and then compare.

Or yeah we just make our own header field with unix timestamp - that is easiest

backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt

kubernetes/loculus/silo_import_job.sh

kubernetes/loculus/silo_import_wrapper.sh

corneliusroemer · 2024-09-11T08:57:13Z

kubernetes/loculus/silo_import_job.sh

    exit $exit_code
  fi
+
+  last_modified=$(grep '^last-modified:' "$new_input_header" | awk '{print $2}')
+  echo "$last_modified"


Should just use a variable here I think rather than using echo and subshell

corneliusroemer · 2024-09-11T09:01:03Z

Maybe we should turn the bash script into a Python script given the complexity. There are now multiple places where we return things or not. It's hard to wrap head round in bash I think.

We can add a rewrite to the todos though in case this here works ok for now.

kubernetes/loculus/silo_import_job.sh

fengelniederhammer · 2024-09-11T09:17:48Z

backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt

+        transaction {
+            lastTime = UpdateTrackerTable
+                .selectAll() // Select all rows
+                .mapNotNull { it[UpdateTrackerTable.lastTimeUpdatedDbColumn] } // Extract non-null datetime values
+                .maxOrNull()?.toTimestamp() // Find the maximum value
+        }


Actually we had the agreement that we don't put much logic in controller methods (especially database access). I would prefer if this was in a separate model/service class.

…t/loculus into table-update-tracker-anya

…s-project/loculus into table-update-tracker-anya

* Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation --------- Co-authored-by: Cornelius Roemer <[email protected]>

@anna-parker

co-authored with @anna-parker and Claude Sonnet try now it might work? Remove views fixup Change to a conditional update for useNewerProcessingPipelineIfPossible, add last_updated_db as a view. (#2741) Co-authored-by: Anna (Anya) Parker <[email protected]> Still return current newest version Return version from correct place Don't issue delete statement unless there's something to delete fix ktlint Adjust useNewerProcessingPipelineIfPossible to only update table when there are changes Table update tracker anya (#2764) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation --------- Co-authored-by: Cornelius Roemer <[email protected]> CR edits to table-update-tracker (#2767) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation * Use etag instead of modified-since for spec compliance * ktlin fix * Move logic into model * Fix etag formatting * Fix etag yet again --------- Co-authored-by: Anna (Anya) Parker <[email protected]> refactor(backend): streamline control flow refactor(backend): extract function Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Enable etag for /extract-unprocessed-data Use etag in prepro to skip preprocessing match case refactor Try fix fix logic fix! i'm stupid Force refresh every hour Add response code annotations Update preprocessing/nextclade/src/loculus_preprocessing/prepro.py Co-authored-by: Anna (Anya) Parker <[email protected]> Add etag to dummy preprocessing # Conflicts: # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionControllerDescriptions.kt # backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/UpdateTrackerTable.kt # backend/src/main/resources/db/migration/V1.2__add_table_update_tracker.sql # backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt # kubernetes/loculus/silo_import_job.sh

@anna-parker

co-authored with @anna-parker and Claude Sonnet try now it might work? Remove views fixup Change to a conditional update for useNewerProcessingPipelineIfPossible, add last_updated_db as a view. (#2741) Co-authored-by: Anna (Anya) Parker <[email protected]> Still return current newest version Return version from correct place Don't issue delete statement unless there's something to delete fix ktlint Adjust useNewerProcessingPipelineIfPossible to only update table when there are changes Table update tracker anya (#2764) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation --------- Co-authored-by: Cornelius Roemer <[email protected]> CR edits to table-update-tracker (#2767) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation * Use etag instead of modified-since for spec compliance * ktlin fix * Move logic into model * Fix etag formatting * Fix etag yet again --------- Co-authored-by: Anna (Anya) Parker <[email protected]> refactor(backend): streamline control flow refactor(backend): extract function Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Enable etag for /extract-unprocessed-data Use etag in prepro to skip preprocessing match case refactor Try fix fix logic fix! i'm stupid Force refresh every hour Add response code annotations Update preprocessing/nextclade/src/loculus_preprocessing/prepro.py Co-authored-by: Anna (Anya) Parker <[email protected]> Add etag to dummy preprocessing # Conflicts: # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionControllerDescriptions.kt # backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/UpdateTrackerTable.kt # backend/src/main/resources/db/migration/V1.2__add_table_update_tracker.sql # backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt # kubernetes/loculus/silo_import_job.sh

@anna-parker

co-authored with @anna-parker and Claude Sonnet try now it might work? Remove views fixup Change to a conditional update for useNewerProcessingPipelineIfPossible, add last_updated_db as a view. (#2741) Co-authored-by: Anna (Anya) Parker <[email protected]> Still return current newest version Return version from correct place Don't issue delete statement unless there's something to delete fix ktlint Adjust useNewerProcessingPipelineIfPossible to only update table when there are changes Table update tracker anya (#2764) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation --------- Co-authored-by: Cornelius Roemer <[email protected]> CR edits to table-update-tracker (#2767) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation * Use etag instead of modified-since for spec compliance * ktlin fix * Move logic into model * Fix etag formatting * Fix etag yet again --------- Co-authored-by: Anna (Anya) Parker <[email protected]> refactor(backend): streamline control flow refactor(backend): extract function Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Enable etag for /extract-unprocessed-data Use etag in prepro to skip preprocessing match case refactor Try fix fix logic fix! i'm stupid Force refresh every hour Add response code annotations Update preprocessing/nextclade/src/loculus_preprocessing/prepro.py Co-authored-by: Anna (Anya) Parker <[email protected]> Add etag to dummy preprocessing # Conflicts: # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionControllerDescriptions.kt # backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/UpdateTrackerTable.kt # backend/src/main/resources/db/migration/V1.2__add_table_update_tracker.sql # backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt # kubernetes/loculus/silo_import_job.sh

@anna-parker

co-authored with @anna-parker and Claude Sonnet try now it might work? Remove views fixup Change to a conditional update for useNewerProcessingPipelineIfPossible, add last_updated_db as a view. (#2741) Co-authored-by: Anna (Anya) Parker <[email protected]> Still return current newest version Return version from correct place Don't issue delete statement unless there's something to delete fix ktlint Adjust useNewerProcessingPipelineIfPossible to only update table when there are changes Table update tracker anya (#2764) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation --------- Co-authored-by: Cornelius Roemer <[email protected]> CR edits to table-update-tracker (#2767) * Add option to get-released-data to check last update time. * make name better * Make or short-circuiting * Only work with table_update_tracker - return lastTime in LAST_MODIFIED header * Remove unused functions * add back missing imports - somehow format removed this??? * Update bash scripts * Attempt to fix bash * 2nd little fix * echo value of last_modified not name * Do not update SILO if loculus responds with 304. * Always echo $lastSnapshot unless new data existed in loculus AND this was successfully sent to LAPIS - then echo $last_modified * save last snapshot to file * Update with loculus data anyways if longer than 1hour since last update * fix * Improve silo import scripts etc * add back BACKEND_BASE_URL * Log headers * Regularize * Better logs * Try to fix error * return 0 and never null in header * Fix read non-existent file bug * Better wrapper logging * fix delete after update snapshot * Make grep case insensitive * add back removed exit 0 * Improvement to logging * Add test * Add full process to test * Update documentation * Use etag instead of modified-since for spec compliance * ktlin fix * Move logic into model * Fix etag formatting * Fix etag yet again --------- Co-authored-by: Anna (Anya) Parker <[email protected]> refactor(backend): streamline control flow refactor(backend): extract function Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Update backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt Co-authored-by: Fabian Engelniederhammer <[email protected]> Enable etag for /extract-unprocessed-data Use etag in prepro to skip preprocessing match case refactor Try fix fix logic fix! i'm stupid Force refresh every hour Add response code annotations Update preprocessing/nextclade/src/loculus_preprocessing/prepro.py Co-authored-by: Anna (Anya) Parker <[email protected]> Add etag to dummy preprocessing # Conflicts: # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionController.kt # backend/src/main/kotlin/org/loculus/backend/controller/SubmissionControllerDescriptions.kt # backend/src/main/kotlin/org/loculus/backend/model/ReleasedDataModel.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt # backend/src/main/kotlin/org/loculus/backend/service/submission/UpdateTrackerTable.kt # backend/src/main/resources/db/migration/V1.2__add_table_update_tracker.sql # backend/src/test/kotlin/org/loculus/backend/controller/submission/GetReleasedDataEndpointTest.kt # kubernetes/loculus/silo_import_job.sh

anna-parker added 5 commits September 10, 2024 22:04

Add option to get-released-data to check last update time.

13efebd

make name better

ad2a106

Make or short-circuiting

758933c

Only work with table_update_tracker - return lastTime in LAST_MODIFIE…

42d23dd

…D header

Remove unused functions

a72afeb

anna-parker added the preview Triggers a deployment to argocd label Sep 11, 2024

anna-parker added 7 commits September 11, 2024 09:01

add back missing imports - somehow format removed this???

8135ce1

Update bash scripts

e2a8f2f

Attempt to fix bash

1ca0215

2nd little fix

7d3ddf8

echo value of last_modified not name

f046ff2

Do not update SILO if loculus responds with 304.

8036bb7

Always echo $lastSnapshot unless new data existed in loculus AND this…

01fe75f

… was successfully sent to LAPIS - then echo $last_modified

corneliusroemer requested changes Sep 11, 2024

View reviewed changes

corneliusroemer changed the base branch from main to table-update-tracker September 11, 2024 08:58

fengelniederhammer reviewed Sep 11, 2024

View reviewed changes

kubernetes/loculus/silo_import_job.sh Show resolved Hide resolved

fengelniederhammer reviewed Sep 11, 2024

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anna-parker mentioned this pull request Sep 11, 2024

Rewrite silo import job #2765

Open

anna-parker and others added 11 commits September 11, 2024 15:20

save last snapshot to file

f74dff0

Update with loculus data anyways if longer than 1hour since last update

18ba74d

fix

ae7425e

Improve silo import scripts etc

fab0ccc

Merge branch 'table-update-tracker-anya' of github.com:loculus-projec…

9e63e11

…t/loculus into table-update-tracker-anya

add back BACKEND_BASE_URL

8afdf44

Log headers

79e4b7e

Regularize

3eee83b

Better logs

aab360b

Try to fix error

8d51e5c

return 0 and never null in header

679ec99

corneliusroemer and others added 9 commits September 11, 2024 17:10

Fix read non-existent file bug

2c7d993

Better wrapper logging

c7c5bb4

fix delete after update snapshot

a9b4f79

Make grep case insensitive

8598145

Merge branch 'table-update-tracker-anya' of https://github.com/loculu…

6f02d56

…s-project/loculus into table-update-tracker-anya

add back removed exit 0

de31dfe

Improvement to logging

2c84609

Add test

a68b717

Add full process to test

247a6a7

anna-parker marked this pull request as ready for review September 11, 2024 17:55

Update documentation

7047c1f

corneliusroemer merged commit 573f7c9 into table-update-tracker Sep 11, 2024
13 checks passed

corneliusroemer deleted the table-update-tracker-anya branch September 11, 2024 20:27

corneliusroemer mentioned this pull request Sep 11, 2024

feat(backend,prepro): use etag to reduce database load #2768

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corneliusroemer mentioned this pull request Sep 13, 2024

don't merge: try out more postgres logging #2779

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Table update tracker anya #2764

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anna-parker commented Sep 11, 2024 •

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Table update tracker anya #2764

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