fix(mysql): pull INVISIBLE/GIPK columns during snapshot by dtunikov · Pull Request #4553 · PeerDB-io/peerdb

dtunikov · 2026-07-08T16:21:34Z

Problem

MySQL/MariaDB QRep snapshot took a SELECT * fast path in buildSelectedColumns. Wildcard expansion omits INVISIBLE columns — including the generated invisible primary key (my_row_id) from sql_generate_invisible_primary_key. But the destination table (created from information_schema.columns) and CDC (binlog row images) both include those columns.

Result: snapshot rows keep destination defaults forever while CDC populates real values — silent divergence. Worst case is GIPK, where the invisible my_row_id is the table's only PK, so snapshot rows arrive with no key, breaking dedup/ordering.

Fix

Always build an explicit column list from the fetched table schema (drop the SELECT * fast path). The schema already contains invisible/GIPK columns, and naming them explicitly bypasses wildcard invisibility, so the snapshot pulls them — matching CDC and the destination DDL.

Tests

Unit: buildSelectedColumns never returns *; invisible/GIPK columns are listed explicitly.
E2E (clickhouse_mysql_test.go): Test_MySQL_Invisible_Column_Consistency and Test_MySQL_GIPK_Consistency compare snapshot vs CDC values (version-gated; GIPK is MySQL-only).

🤖 Generated with Claude Code

The SELECT * snapshot fast path relied on wildcard expansion, which omits INVISIBLE columns (and the generated invisible primary key, my_row_id). The destination table and CDC both include those columns, so snapshot rows kept destination defaults forever while CDC populated real values — silent divergence. For GIPK the invisible my_row_id is the only PK, so snapshot rows arrived with no key, breaking dedup/ordering. Always build an explicit column list from the fetched table schema so invisible columns are named explicitly (bypassing wildcard invisibility). Add INVISIBLE and GIPK e2e tests comparing snapshot and CDC. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

claude · 2026-07-08T16:25:46Z

Code review

No issues found. Checked for bugs and CLAUDE.md compliance.

Copilot

Pull request overview

This PR fixes MySQL/MariaDB QRep snapshot consistency by ensuring snapshots explicitly select all columns from the fetched schema (including INVISIBLE and generated invisible primary key columns), aligning snapshot output with destination DDL and CDC/binlog row images.

Changes:

Remove the SELECT * fast-path by always building an explicit column list in buildSelectedColumns.
Add MySQL/MariaDB minimum-version constants for invisible columns and MySQL GIPK.
Add/extend unit + ClickHouse E2E tests to validate snapshot vs CDC consistency for INVISIBLE and GIPK scenarios.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
`flow/pkg/mysql/validation.go`	Adds version gates for invisible columns and generated invisible primary keys used by tests.
`flow/connectors/mysql/qrep.go`	Removes the `*` selection fast-path so snapshots explicitly name columns (including INVISIBLE/GIPK).
`flow/connectors/mysql/qrep_test.go`	Updates and extends unit coverage to ensure selected columns are explicit (no `*`).
`flow/e2e/clickhouse_mysql_test.go`	Adds E2E consistency tests comparing snapshot vs CDC for INVISIBLE and GIPK columns.

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-	}
-
-	return selectedColumns
+	return strings.Join(columns, ", ")


+	require.NoError(s.t, s.source.Exec(s.t.Context(), `SET SESSION sql_generate_invisible_primary_key = ON`))
+	require.NoError(s.t, s.source.Exec(s.t.Context(), fmt.Sprintf(`
+		CREATE TABLE IF NOT EXISTS %s (
+			name VARCHAR(50) NOT NULL
+		)
+	`, srcFullName)))
+	require.NoError(s.t, s.source.Exec(s.t.Context(), `SET SESSION sql_generate_invisible_primary_key = OFF`))


github-actions · 2026-07-08T16:46:32Z

❌ Test Failure

Analysis: The new Test_MySQL_GIPK_Consistency test — which validates the exact GIPK-snapshot feature this PR adds — hangs with the mirror "stuck in snapshot" and times out in STATUS_SETUP consistently across both MySQL 6.0 and 8.0 matrix configs, indicating a real bug in the PR's snapshot logic rather than a flaky failure.
Confidence: 0.9

⚠️ This appears to be a real bug - manual intervention needed

View workflow run

ilidemi

The task will need e2e checking on how this shows up in ClickPipes UI and whether it passes validations

ilidemi · 2026-07-09T05:45:37Z

Oh CI doesn't pass, something's up

…pshot-invisible-columns

codecov · 2026-07-09T09:14:15Z

❌ 2 Tests Failed:

Tests completed	Failed	Passed	Skipped
2998	2	2996	361

View the top 3 failed test(s) by shortest run time

github.com/PeerDB-io/peerdb/flow/connectors/postgres::TestRunPipeline_DstExitsWhileSrcWriting

Stack Traces | 0.01s run time

=== RUN   TestRunPipeline_DstExitsWhileSrcWriting
    pgdump_schema_test.go:174: expected dst failure, got src failed: exit status 141
        stderr:
--- FAIL: TestRunPipeline_DstExitsWhileSrcWriting (0.01s)

github.com/PeerDB-io/peerdb/flow/e2e::TestPeerFlowE2ETestSuiteMySQL_CH_Cluster

Stack Traces | 0.01s run time

=== RUN   TestPeerFlowE2ETestSuiteMySQL_CH_Cluster
=== PAUSE TestPeerFlowE2ETestSuiteMySQL_CH_Cluster
=== CONT  TestPeerFlowE2ETestSuiteMySQL_CH_Cluster
--- FAIL: TestPeerFlowE2ETestSuiteMySQL_CH_Cluster (0.01s)
2026/07/09 09:37:18 INFO Received AWS credentials from peer for connector: ci x-peerdb-additional-metadata={Operation:FLOW_OPERATION_UNKNOWN}
2026/07/09 09:37:18 INFO fetched schema x-peerdb-additional-metadata={Operation:FLOW_OPERATION_UNKNOWN} table=e2e_test_machcl_ya1gn1nj.test_date_coercion

github.com/PeerDB-io/peerdb/flow/e2e::TestPeerFlowE2ETestSuiteMySQL_CH_Cluster/Test_MySQL_GIPK_Consistency

Stack Traces | 61.2s run time

=== RUN   TestPeerFlowE2ETestSuiteMySQL_CH_Cluster/Test_MySQL_GIPK_Consistency
=== PAUSE TestPeerFlowE2ETestSuiteMySQL_CH_Cluster/Test_MySQL_GIPK_Consistency
=== CONT  TestPeerFlowE2ETestSuiteMySQL_CH_Cluster/Test_MySQL_GIPK_Consistency
2026/07/09 09:36:17 INFO Received AWS credentials from peer for connector: ci x-peerdb-additional-metadata={Operation:FLOW_OPERATION_UNKNOWN}
2026/07/09 09:36:17 INFO fetched schema x-peerdb-additional-metadata={Operation:FLOW_OPERATION_UNKNOWN} table=e2e_test_mychcl_6vika981.test_mysql_ghost_schema
    clickhouse_mysql_test.go:2485: UNEXPECTED STATUS TIMEOUT STATUS_SETUP
--- FAIL: TestPeerFlowE2ETestSuiteMySQL_CH_Cluster/Test_MySQL_GIPK_Consistency (61.18s)

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github-actions · 2026-07-09T09:23:22Z

🔄 Flaky Test Detected

Analysis: Failures are timeout/race-based (GIPK test stuck in STATUS_SETUP past the 60s wait in both jobs, plus a SIGPIPE ordering race in TestRunPipeline_DstExitsWhileSrcWriting), all unrelated to the commit's Renovate-script change, indicating environmental flakiness rather than a real bug.
Confidence: 0.9

✅ Automatically retrying the workflow

View workflow run

github-actions · 2026-07-09T09:47:05Z

❌ Test Failure

Analysis: Both mysql-gtid jobs deterministically fail the PR's own feature test (Test_MySQL_GIPK_Consistency) with an identical STATUS_SETUP timeout, indicating the GIPK/INVISIBLE snapshot code this PR introduces hangs during setup — a real bug, not a flake.
Confidence: 0.85

⚠️ This appears to be a real bug - manual intervention needed

View workflow run

dtunikov · 2026-07-09T12:57:12Z

tested e2e with other clickpipes components, works fine

dtunikov requested a review from a team as a code owner July 8, 2026 16:21

dtunikov requested a review from Copilot July 8, 2026 16:29

Copilot started reviewing on behalf of dtunikov July 8, 2026 16:29 View session

Copilot AI reviewed Jul 8, 2026

View reviewed changes

ilidemi approved these changes Jul 9, 2026

View reviewed changes

Comment thread flow/e2e/clickhouse_mysql_test.go Outdated

dtunikov added 2 commits July 9, 2026 10:53

Merge branch 'main' of github.com:PeerDB-io/peerdb into fix/mysql-sna…

343c0ef

…pshot-invisible-columns

fail if selectedColumns == ""

ddc7c16

fix ch cluster mode tests

dfd46e6

dtunikov enabled auto-merge (squash) July 9, 2026 09:35

dtunikov disabled auto-merge July 9, 2026 09:45

dtunikov merged commit 65c76c7 into main Jul 9, 2026
20 of 21 checks passed

dtunikov deleted the fix/mysql-snapshot-invisible-columns branch July 9, 2026 10:47

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fix(mysql): pull INVISIBLE/GIPK columns during snapshot#4553

fix(mysql): pull INVISIBLE/GIPK columns during snapshot#4553
dtunikov merged 4 commits into
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fix/mysql-snapshot-invisible-columns

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dtunikov commented Jul 8, 2026

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