Backfill identifier_names to vulnerability_reads
What does this MR do and why?
New backfill migration for vulnerability_reads.identifier_names
as the old BBM is abandoned.
It is intended to be used for the filtering by identifier feature in #432419 (closed).
Changelog: other
Database
The estimate from db testing pipeline job for this migration to complete is available in !163088 (comment 2054374348).
Estimated Time to complete: 2 weeks, 3 days, 9 hours, 25 minutes, and 20 seconds
On production this is expected to finish sooner since we have migration optimization strategy.
We have set the Batch size to be 12000
and sub-batch size as 40
and with that we are getting:
Mean query time: 150.2 ms
Max query time: 12748.0 ms.
The max query time seems to be happen rarely when the DB is busy/congested and is not worth the effort for this one time migration task to further optimize.
Output of the post-deployment migration
bundle exec rake db:migrate:up:main VERSION=20241007115637
main: == [advisory_lock_connection] object_id: 128940, pg_backend_pid: 46825
main: == 20241007115637 QueueBackfillIdentifierNamesOfVulnerabilityReads: migrating =
main: == 20241007115637 QueueBackfillIdentifierNamesOfVulnerabilityReads: migrated (0.0772s)
main: == [advisory_lock_connection] object_id: 128940, pg_backend_pid: 46825
bundle exec rake db:migrate:down:main VERSION=20241007115637
main: == [advisory_lock_connection] object_id: 128920, pg_backend_pid: 47302
main: == 20241007115637 QueueBackfillIdentifierNamesOfVulnerabilityReads: reverting =
main: == 20241007115637 QueueBackfillIdentifierNamesOfVulnerabilityReads: reverted (0.0314s)
main: == [advisory_lock_connection] object_id: 128920, pg_backend_pid: 47302
Update query used in each sub-batch
UPDATE
vulnerability_reads vr
SET
identifier_names = selected_ids.names
FROM
(
WITH
batched_relation AS MATERIALIZED (
SELECT
vulnerability_reads.*
FROM
vulnerability_reads
WHERE
vulnerability_reads.id BETWEEN 104513160
AND 104513180
AND vulnerability_reads.id >= 104513160
AND vulnerability_reads.id < 104513201
LIMIT
40
)
SELECT
vulnerability_reads.id AS id,
array_agg(
vi.name
ORDER BY
vi.name
) AS names
FROM
batched_relation vulnerability_reads
JOIN vulnerability_occurrences vo ON vulnerability_reads.vulnerability_id = vo.vulnerability_id
JOIN vulnerability_occurrence_identifiers voi ON vo.id = voi.occurrence_id
JOIN vulnerability_identifiers vi ON voi.identifier_id = vi.id
GROUP BY
vulnerability_reads.id
) selected_ids
WHERE
vr.id = selected_ids.id
ModifyTable on public.vulnerability_reads vr (cost=105.69..159.44 rows=0 width=0) (actual time=699.540..699.565 rows=0 loops=1)
Buffers: shared hit=881 read=445 dirtied=82
I/O Timings: read=688.751 write=0.000
-> Nested Loop (cost=105.69..159.44 rows=15 width=102) (actual time=95.848..96.198 rows=7 loops=1)
Buffers: shared hit=142 read=37 dirtied=3
I/O Timings: read=94.390 write=0.000
-> Subquery Scan on selected_ids (cost=105.12..105.67 rows=15 width=104) (actual time=95.826..96.061 rows=7 loops=1)
Buffers: shared hit=107 read=37 dirtied=3
I/O Timings: read=94.390 write=0.000
-> Aggregate (cost=105.12..105.52 rows=15 width=40) (actual time=95.812..96.004 rows=7 loops=1)
Group Key: vulnerability_reads.id
Buffers: shared hit=107 read=37 dirtied=3
I/O Timings: read=94.390 write=0.000
CTE batched_relation
-> Limit (cost=0.57..24.42 rows=15 width=289) (actual time=14.061..16.777 rows=7 loops=1)
Buffers: shared hit=15 read=6
I/O Timings: read=16.610 write=0.000
-> Index Scan using vulnerability_reads_pkey on public.vulnerability_reads vulnerability_reads_1 (cost=0.57..24.42 rows=15 width=289) (actual time=14.057..16.764 rows=7 loops=1)
Index Cond: ((vulnerability_reads_1.id >= 104513160) AND (vulnerability_reads_1.id <= 104513180) AND (vulnerability_reads_1.id >= 104513160) AND (vulnerability_reads_1.id < 104513201))
Buffers: shared hit=15 read=6
I/O Timings: read=16.610 write=0.000
-> Sort (cost=80.70..80.77 rows=28 width=29) (actual time=95.684..95.697 rows=9 loops=1)
Sort Key: vulnerability_reads.id
Sort Method: quicksort Memory: 25kB
Buffers: shared hit=97 read=37 dirtied=3
I/O Timings: read=94.390 write=0.000
-> Nested Loop (cost=1.58..80.03 rows=28 width=29) (actual time=52.567..95.623 rows=9 loops=1)
Buffers: shared hit=94 read=37 dirtied=3
I/O Timings: read=94.390 write=0.000
-> Nested Loop (cost=1.14..67.17 rows=28 width=16) (actual time=47.017..75.644 rows=9 loops=1)
Buffers: shared hit=66 read=29 dirtied=3
I/O Timings: read=74.653 write=0.000
-> Nested Loop (cost=0.57..54.23 rows=15 width=16) (actual time=38.708..54.797 rows=7 loops=1)
Buffers: shared hit=39 read=17
I/O Timings: read=54.111 write=0.000
-> CTE Scan on batched_relation vulnerability_reads (cost=0.00..0.30 rows=15 width=16) (actual time=14.068..16.822 rows=7 loops=1)
Buffers: shared hit=15 read=6
I/O Timings: read=16.610 write=0.000
-> Index Scan using index_vulnerability_occurrences_on_vulnerability_id on public.vulnerability_occurrences vo (cost=0.57..3.58 rows=1 width=16) (actual time=5.417..5.419 rows=1 loops=7)
Index Cond: (vo.vulnerability_id = vulnerability_reads.vulnerability_id)
Buffers: shared hit=24 read=11
I/O Timings: read=37.501 write=0.000
-> Index Only Scan using index_vulnerability_occurrence_identifiers_on_unique_keys on public.vulnerability_occurrence_identifiers voi (cost=0.57..0.76 rows=10 width=16) (actual time=2.399..2.970 rows=1 loops=7)
Index Cond: (voi.occurrence_id = vo.id)
Heap Fetches: 3
Buffers: shared hit=27 read=12 dirtied=3
I/O Timings: read=20.543 write=0.000
-> Index Scan using vulnerability_identifiers_pkey on public.vulnerability_identifiers vi (cost=0.44..0.46 rows=1 width=29) (actual time=2.212..2.212 rows=1 loops=9)
Index Cond: (vi.id = voi.identifier_id)
Buffers: shared hit=28 read=8
I/O Timings: read=19.737 write=0.000
-> Index Scan using vulnerability_reads_pkey on public.vulnerability_reads vr (cost=0.57..3.58 rows=1 width=14) (actual time=0.013..0.013 rows=1 loops=7)
Index Cond: (vr.id = selected_ids.id)
Buffers: shared hit=35
I/O Timings: read=0.000 write=0.000
Time: 711.209 ms
- planning: 11.311 ms
- execution: 699.898 ms
- I/O read: 688.751 ms
- I/O write: 0.000 ms
Shared buffers:
- hits: 881 (~6.90 MiB) from the buffer pool
- reads: 445 (~3.50 MiB) from the OS file cache, including disk I/O
- dirtied: 82 (~656.00 KiB)
- writes: 0
https://console.postgres.ai/gitlab/gitlab-production-main/sessions/32350/commands/99928
Estimated Time to complete: 2 weeks, 3 days, 9 hours, 25 minutes, and 20 seconds
- Interval: 160s
- Total tuple count: 112712050
- Max batch size: 0
- Estimated seconds to complete: 1502720s
- Estimated number of batches: 9392
- Average batch time: 148.12s
- Batch size: 12000
- N. of batches sampled: 12
- N. of failed batches: 0
Time estimation is conservative and based on sampling production data in a test environment. It represents the max time that migration could take. The actual time may differ from this estimation.
Estimated Time to complete: 2 weeks, 3 days, 9 hours, 25 minutes, and 20 seconds
- Interval: 160s
- Total tuple count: 112712050
- Max batch size: 0
- Estimated seconds to complete: 1502720s
- Estimated number of batches: 9392
- Average batch time: 148.12s
- Batch size: 12000
- N. of batches sampled: 12
- N. of failed batches: 0
Time estimation is conservative and based on sampling production data in a test environment. It represents the max time that migration could take. The actual time may differ from this estimation.
Related to #460080 (closed)
Merge request reports
Activity
changed milestone to %17.4
assigned to @bala.kumar
added pipelinetier-1 label
- A deleted user
added database databasereview pending featureaddition typefeature labels
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updated too (unless the migration isn't changing the DB schema
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For more information, see:
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- The definition of done documentation.
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Dangeradded 1 commit
- 0e14e569 - Backfill migration for vulnerability_reads identifier_names
removed missed:17.2 label
Database migrations (on the main database)
Migrations included in this change have been executed on gitlab.com data for testing purposes. For details, please see the migration testing pipeline (limited access).
Migration Type Total runtime Result DB size change 20241007115637 - QueueBackfillIdentifierNamesOfVulnerabilityReads Post deploy 6.5 s +0.00 B Runtime Histogram for all migrations
Query Runtime Count 0 seconds - 0.01 seconds 0 0.01 seconds - 0.1 seconds 1 0.1 seconds - 1 second 6 1 second - 5 seconds 0 5 seconds - 15 seconds 0 15 seconds - 5 minutes 0 5 minutes + 0 Migration: 20241007115637 - QueueBackfillIdentifierNamesOfVulnerabilityReads
- Type: Post deploy
- Duration: 6.5 s
- Database size change: +0.00 B
Calls Total Time Max Time Mean Time Rows Query 1 11.0 ms 11.0 ms 11.0 ms 1 SELECT MAX("id")
FROM "vulnerability_reads"1 1.7 ms 1.7 ms 1.7 ms 1 INSERT INTO "batched_background_migrations" ("created_at", "updated_at", "max_value", "batch_size", "sub_batch_size", "interval", "status", "job_class_name", "table_name", "column_name", "total_tuple_count", "started_at", "gitlab_schema", "queued_migration_version") VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14) RETURNING "id"
1 0.8 ms 0.8 ms 0.8 ms 0 SELECT $1 AS one
FROM "batched_background_migrations" WHERE "batched_background_migrations"."job_class_name" = $2 AND "batched_background_migrations"."table_name" = $3 AND "batched_background_migrations"."column_name" = $4 AND (job_arguments = $5) AND "batched_background_migrations"."gitlab_schema" = $6
LIMIT $71 0.0 ms 0.0 ms 0.0 ms 1 SELECT "feature_gates"."key", "feature_gates"."value" FROM "feature_gates" WHERE "feature_gates"."feature_key" = $1
1 0.0 ms 0.0 ms 0.0 ms 0 SELECT $1 AS one
FROM "batched_background_migrations" WHERE "batched_background_migrations"."job_arguments" = $2 AND "batched_background_migrations"."job_class_name" = $3 AND "batched_background_migrations"."table_name" = $4 AND "batched_background_migrations"."column_name" = $5
LIMIT $62 0.0 ms 0.0 ms 0.0 ms 2 SELECT pg_backend_pid()
Histogram for QueueBackfillIdentifierNamesOfVulnerabilityReads
Query Runtime Count 0 seconds - 0.01 seconds 0 0.01 seconds - 0.1 seconds 1 0.1 seconds - 1 second 6 1 second - 5 seconds 0 5 seconds - 15 seconds 0 15 seconds - 5 minutes 0 5 minutes + 0 Background Migration: BackfillIdentifierNamesOfVulnerabilityReads
Sampled 12 batches. Estimated Time to complete: 2 weeks, 3 days, 9 hours, 25 minutes, and 20 seconds
- Interval: 160s
- Total tuple count: 112712050
- Max batch size: 0
- Estimated seconds to complete: 1502720s
- Estimated number of batches: 9392
- Average batch time: 148.12s
- Batch size: 12000
- N. of batches sampled: 12
- N. of failed batches: 0
Time estimation is conservative and based on sampling production data in a test environment. It represents the max time that migration could take. The actual time may differ from this estimation.
Consider changing max_batch_size and interval if this estimate is unacceptable.
Calls Total Time Max Time Mean Time Rows Query 3586 538489.7 ms 12748.0 ms 150.2 ms 135105 UPDATE vulnerability_reads vr
SET identifier_names = selected_ids.names
FROM (WITH batched_relation AS MATERIALIZED (
SELECT vulnerability_reads.*
FROM vulnerability_reads
WHERE vulnerability_reads.id BETWEEN $1 AND $2 AND vulnerability_reads.id >= $3 AND vulnerability_reads.id < $4
LIMIT $5
)
SELECT vulnerability_reads.id AS id, array_agg(vi.name ORDER BY vi.name) AS names
FROM batched_relation vulnerability_reads
JOIN vulnerability_occurrences vo ON vulnerability_reads.vulnerability_id = vo.vulnerability_id
JOIN vulnerability_occurrence_identifiers voi ON vo.id = voi.occurrence_id
JOIN vulnerability_identifiers vi ON voi.identifier_id = vi.id
GROUP BY vulnerability_reads.id
) selected_ids
WHERE vr.id = selected_ids.id12 1522.5 ms 415.3 ms 126.9 ms 409 UPDATE vulnerability_reads vr
SET identifier_names = selected_ids.names
FROM (WITH batched_relation AS MATERIALIZED (
SELECT vulnerability_reads.*
FROM vulnerability_reads
WHERE vulnerability_reads.id BETWEEN $1 AND $2 AND vulnerability_reads.id >= $3
LIMIT $4
)
SELECT vulnerability_reads.id AS id, array_agg(vi.name ORDER BY vi.name) AS names
FROM batched_relation vulnerability_reads
JOIN vulnerability_occurrences vo ON vulnerability_reads.vulnerability_id = vo.vulnerability_id
JOIN vulnerability_occurrence_identifiers voi ON vo.id = voi.occurrence_id
JOIN vulnerability_identifiers vi ON voi.identifier_id = vi.id
GROUP BY vulnerability_reads.id
) selected_ids
WHERE vr.id = selected_ids.id12 35.5 ms 15.8 ms 3.0 ms 12 UPDATE batched_background_migration_jobs
SET updated_at = $1, finished_at = $2, status = $3, metrics = $4
WHERE batched_background_migration_jobs.id = $53598 306.9 ms 10.4 ms 0.1 ms 3586 SELECT vulnerability_reads.id
FROM vulnerability_reads
WHERE vulnerability_reads.id BETWEEN $1 AND $2 AND vulnerability_reads.id >= $3
ORDER BY vulnerability_reads.id ASC
LIMIT $4
OFFSET $524 7.7 ms 3.6 ms 0.3 ms 24 INSERT INTO batched_background_migration_job_transition_logs (batched_background_migration_job_id, created_at, updated_at, previous_status, next_status) VALUES ($1, $2, $3, $4, $5) RETURNING id
12 2.0 ms 0.8 ms 0.2 ms 12 UPDATE batched_background_migration_jobs
SET updated_at = $1, started_at = $2, status = $3, attempts = $4
WHERE batched_background_migration_jobs.id = $524 2.4 ms 0.2 ms 0.1 ms 24 SELECT batched_background_migration_jobs.*
FROM batched_background_migration_jobs
WHERE batched_background_migration_jobs.id = $1
LIMIT $212 0.8 ms 0.1 ms 0.1 ms 12 SELECT sum(batched_background_migration_jobs.batch_size)
FROM batched_background_migration_jobs
WHERE batched_background_migration_jobs.batched_background_migration_id = $1 AND batched_background_migration_jobs.status IN ($2)12 0.4 ms 0.1 ms 0.0 ms 12 SELECT vulnerability_reads.id
FROM vulnerability_reads
WHERE vulnerability_reads.id BETWEEN $1 AND $2
ORDER BY vulnerability_reads.id ASC
LIMIT $312 0.5 ms 0.1 ms 0.0 ms 12 SELECT batched_background_migrations.*
FROM batched_background_migrations
WHERE batched_background_migrations.id = $1
LIMIT $2Histogram of batch runtimes for BackfillIdentifierNamesOfVulnerabilityReads
Batch Runtime Count 0 seconds - 10 seconds 0 10 seconds - 1 minute 0 1 minute - 2 minutes 1 2 minutes - 3 minutes 10 3 minutes - 5 minutes 1 5 minutes + 0 Histogram across all sampled batches of BackfillIdentifierNamesOfVulnerabilityReads
Query Runtime Count 0 seconds - 0.1 seconds 235 0.1 seconds - 0.5 seconds 6953 0.5 seconds - 1 second 97 1 second - 2 seconds 6 2 seconds - 5 seconds 5 5 seconds + 8 Other information
No other migrations pending on GitLab.com
Clone details
Clone ID Clone Created At Clone Data Timestamp Expected Removal Time database-testing-3771237-15615483-main
2024-10-08T12:20:50Z 2024-10-08T08:04:10Z 2024-10-09 01:00:49 +0000 database-testing-3771237-15615483-ci
2024-10-08T12:20:50Z 2024-10-08T08:44:58Z 2024-10-09 01:00:49 +0000 Database migrations (on the ci database)
Migrations included in this change have been executed on gitlab.com data for testing purposes. For details, please see the migration testing pipeline (limited access).
Migration Type Total runtime Result DB size change 20241007115637 - QueueBackfillIdentifierNamesOfVulnerabilityReads Post deploy 7.2 s +0.00 B Runtime Histogram for all migrations
Query Runtime Count 0 seconds - 0.01 seconds 0 0.01 seconds - 0.1 seconds 2 0.1 seconds - 1 second 0 1 second - 5 seconds 0 5 seconds - 15 seconds 0 15 seconds - 5 minutes 0 5 minutes + 0 Migration: 20241007115637 - QueueBackfillIdentifierNamesOfVulnerabilityReads
- Type: Post deploy
- Duration: 7.2 s
- Database size change: +0.00 B
Calls Total Time Max Time Mean Time Rows Query 2 0.0 ms 0.0 ms 0.0 ms 2 SELECT pg_backend_pid()
Histogram for QueueBackfillIdentifierNamesOfVulnerabilityReads
Query Runtime Count 0 seconds - 0.01 seconds 0 0.01 seconds - 0.1 seconds 2 0.1 seconds - 1 second 0 1 second - 5 seconds 0 5 seconds - 15 seconds 0 15 seconds - 5 minutes 0 5 minutes + 0 Other information
No other migrations pending on GitLab.com
Clone details
Clone ID Clone Created At Clone Data Timestamp Expected Removal Time database-testing-3771237-15615483-main
2024-10-08T12:20:50Z 2024-10-08T08:04:10Z 2024-10-09 01:00:49 +0000 database-testing-3771237-15615483-ci
2024-10-08T12:20:50Z 2024-10-08T08:44:58Z 2024-10-09 01:00:49 +0000
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Edited by ****- Resolved by Bala Kumar
added database-testing-automation label
mentioned in issue #460080 (closed)
added 1 commit
- c3322e9c - Backfill migration for vulnerability_reads identifier_names
mentioned in issue #477284 (closed)
mentioned in epic gitlab-org#15036 (closed)
We probably have to modify this, and backfill as a single conjuncted string of identifiers so that we are able to create a triagram index on a text column. See: !163086 (comment 2094440994)
Edited by Bala Kumaradded 3546 commits
-
f8de0114...59cde554 - 3542 commits from branch
master
- 0e577457 - Ingest identifier_names of vulnerability_reads
- 5090a983 - Backfill migration for vulnerability_reads identifier_names
- b2373c5a - Switch to use CTE for the update query
- a1ae7943 - Change batch size
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f8de0114...59cde554 - 3542 commits from branch
changed milestone to %17.5
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mentioned in merge request !163086 (merged)
added 4993 commits
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a1ae7943...660b9abf - 4990 commits from branch
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- 3a6fc0fb - Backfill migration for vulnerability_reads identifier_names
- 406850a9 - Switch to use CTE for the update query
- 489994fc - Change batch size
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- Resolved by Bala Kumar
- Resolved by Bala Kumar
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- Resolved by Gregory Havenga
- Resolved by Gregory Havenga
requested review from @subashis
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added pipelinetier-3 pipeline:run-e2e-omnibus-once labels and removed pipelinetier-2 label
E2E Test Result Summary
allure-report-publisher
generated test report!e2e-test-on-gdk:
test report for 6d5f567cexpand test summary
+------------------------------------------------------------------+ | suites summary | +-------------+--------+--------+---------+-------+-------+--------+ | | passed | failed | skipped | flaky | total | result | +-------------+--------+--------+---------+-------+-------+--------+ | Govern | 73 | 0 | 0 | 0 | 73 | ✅ | | Package | 24 | 0 | 11 | 0 | 35 | ✅ | | Plan | 76 | 0 | 0 | 0 | 76 | ✅ | | Data Stores | 33 | 0 | 1 | 0 | 34 | ✅ | | Create | 128 | 0 | 18 | 0 | 146 | ✅ | | Manage | 1 | 0 | 1 | 0 | 2 | ✅ | | Verify | 45 | 0 | 2 | 0 | 47 | ✅ | | Monitor | 8 | 0 | 0 | 0 | 8 | ✅ | | Release | 5 | 0 | 0 | 0 | 5 | ✅ | | Fulfillment | 2 | 0 | 0 | 0 | 2 | ✅ | | Secure | 4 | 0 | 0 | 0 | 4 | ✅ | | Analytics | 2 | 0 | 0 | 0 | 2 | ✅ | +-------------+--------+--------+---------+-------+-------+--------+ | Total | 401 | 0 | 33 | 0 | 434 | ✅ | +-------------+--------+--------+---------+-------+-------+--------+
e2e-test-on-omnibus:
test report for 1079f476expand test summary
+---------------------------------------------------------------------+ | suites summary | +----------------+--------+--------+---------+-------+-------+--------+ | | passed | failed | skipped | flaky | total | result | +----------------+--------+--------+---------+-------+-------+--------+ | Monitor | 8 | 0 | 11 | 0 | 19 | ✅ | | Govern | 94 | 0 | 4 | 0 | 98 | ✅ | | Data Stores | 42 | 0 | 7 | 0 | 49 | ✅ | | Create | 526 | 0 | 79 | 0 | 605 | ✅ | | Verify | 36 | 0 | 12 | 0 | 48 | ✅ | | GitLab Metrics | 2 | 0 | 1 | 0 | 3 | ✅ | | Systems | 6 | 0 | 1 | 0 | 7 | ✅ | | Configure | 1 | 0 | 2 | 0 | 3 | ✅ | | Plan | 60 | 0 | 6 | 0 | 66 | ✅ | | Analytics | 3 | 0 | 0 | 0 | 3 | ✅ | | Fulfillment | 4 | 0 | 6 | 0 | 10 | ✅ | | Manage | 26 | 0 | 17 | 6 | 43 | ✅ | | Secure | 5 | 0 | 1 | 0 | 6 | ✅ | | Package | 30 | 0 | 10 | 0 | 40 | ✅ | | Growth | 0 | 0 | 2 | 0 | 2 | ➖ | | Ai-powered | 0 | 1 | 2 | 1 | 3 | ❌ | | Release | 5 | 0 | 1 | 0 | 6 | ✅ | | ModelOps | 0 | 0 | 1 | 0 | 1 | ➖ | +----------------+--------+--------+---------+-------+-------+--------+ | Total | 848 | 1 | 163 | 7 | 1012 | ❌ | +----------------+--------+--------+---------+-------+-------+--------+
mentioned in merge request !164883 (merged)
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aborted automatic add to merge train because the source branch was updated. Learn more.
added 1047 commits
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1079f476...027417a6 - 1044 commits from branch
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- 6fa7b6ba - Backfill migration for vulnerability_reads identifier_names
- 15c5dde8 - Switch to use CTE for the update query
- 6d5f567c - Change batch size
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mentioned in commit 6ab2c960
mentioned in incident gitlab-org/quality/engineering-productivity/master-broken-incidents#8889 (closed)
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