Add periodic SQLite database backups with compression and encryption by Copilot · Pull Request #3154 · PelicanPlatform/pelican

Copilot · 2026-02-21T02:11:25Z

Original prompt

This section details on the original issue you should resolve

<issue_title>Have Pelican make periodic sqlite dumps of it databases</issue_title>
<issue_description>In order to backup the Sqlite databases of Pelican components, we either need to shutdown the service to copy the database file (to ensure to writes are occurring), or have sqlite make an atomic dump of the contents. Other methods of copying a live database and introduce corruption caused by a write operation occurring in the middle of a filesystem (non-sql) read of the file.

Could Pelican create a dumpfile of it's database ~once a day (in a configurable location) to facilitate automatic backups?</issue_description>

<agent_instructions>- Make sure to add tests.

Use the Go sqlite library to do the backup.

Have a parameter that determines the location of the sqlite backup.

Have a parameter for sqlite backup frequency.

Have a parameter controlling the count of backups to keep.

Compress and encrypt the database backups based on server private key (there are multiple keys; provide a copy of the encryption key encrypted with each).

Restore from backup automatically if the primary database is missing but a backup is present.

Background goroutines must be managed by an errgroup and cancellable by a context.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

Fixes Have Pelican make periodic sqlite dumps of it databases #3152

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- Add parameters: Server.DatabaseBackup.Location, Server.DatabaseBackup.Frequency, Server.DatabaseBackup.MaxCount - Create database/backup.go with backup/restore logic using VACUUM INTO - Compress backups with gzip, encrypt with NaCl box using all issuer keys - Auto-restore from backup if primary database is missing - Background backup goroutine managed by errgroup with context cancellation - Export GetEncryptionKeyPair from config package for reuse - Add comprehensive tests in database/backup_test.go Co-authored-by: bbockelm <1093447+bbockelm@users.noreply.github.com>

Co-authored-by: bbockelm <1093447+bbockelm@users.noreply.github.com>

- Add CLI. Auto-restore is clever but otherwise denies the ability to do things like manually snapshot the files - Avoid buffering the DB in memory. Split it into chunks and write them out - Have a more readable, PEM-encoded format - Calculate when the first backup should be made from what backups exist, not based on server startup. Plus other small fixes.

cmd/server_database_backup.go

database/backup.go

h2zh

@copilot Address these comments

h2zh · 2026-02-24T22:05:28Z

cmd/server_database_backup.go

+	if err := config.InitServer(ctx, server_structs.OriginType); err == nil {
+		return nil
+	}
+	return errors.New("failed to initialize server configuration; ensure a valid pelican.yaml is present")


Suggested change

return errors.New("failed to initialize server configuration; ensure a valid pelican.yaml is present")

return errors.Wrap(err, "failed to initialize server configuration")

Fixed in 8dde278 — now uses errors.Wrap(err, ...) to preserve the underlying error.

h2zh · 2026-02-24T22:34:32Z

database/backup.go

+	decoder := newPEMStreamDecoder(backupFile)
+
+	// Phase 1: read ENCRYPTED BACKUP KEY blocks and attempt to decrypt DEK.
+	var dek [32]byte


To reduce the window for memory-dump attacks, this variable should be cleared after use.

Fixed in 8dde278 — added a defer that zeros out all bytes of the dek array after restoreFromSingleBackup returns.

h2zh · 2026-02-24T22:52:41Z

database/backup.go

+	if err := restoredTmp.Close(); err != nil {
+		return false, errors.Wrap(err, "failed to close restored database file")
+	}
+


After decrypting and decompressing, it should verify that the result is actually a valid SQLite database. A simple check like trying to open it with database/sql and running PRAGMA integrity_check would prevent corrupted restores.

Fixed in 8dde278 — added verifySQLiteIntegrity() which opens the restored file via database/sql and runs PRAGMA integrity_check before renaming it into place.

h2zh · 2026-02-24T23:18:02Z

cmd/server_database_backup.go

+
+	// We need the database open for VACUUM INTO.
+	if database.ServerDatabase == nil {
+		if err := database.InitServerDatabase(0); err != nil {


Given the existing struct and function signature:

const ( CacheType ServerType = 1 << iota OriginType DirectorType RegistryType BrokerType LocalCacheType ) func InitServerDatabase(serverType server_structs.ServerType) error {}

For this DB backup CLI command, passing 0 might be an intentional shortcut meaning "just open the database, don't bother with type-specific schema setup." It would be nice to leave a comment to elaborate this point.

Fixed in 8dde278 — added a comment explaining that passing 0 opens the database without running type-specific migrations, which is appropriate for backup commands that only need read access.

h2zh · 2026-02-24T23:27:09Z

database/backup.go

+	}
+
+	// Atomically move the temporary file to the final backup path.
+	timestamp := time.Now().UTC().Format(backupTimestampFormat)


The metadata timestamp and filename timestamp are generated at different times. If the backup takes a while (large DB), they could diverge by seconds or more. The timestamp should be captured once and reused for both.

Fixed in 8dde278 — backupTime is now captured once at the start of createBackup and passed to both collectBackupMetadata and the filename formatter.

h2zh

@copilot Address these comments

…integrity check, timestamp consistency, and server type comment Co-authored-by: h2zh <61568048+h2zh@users.noreply.github.com>

Copilot · 2026-02-25T00:15:02Z

@copilot Address these comments

All five review comments addressed in 8dde278.

h2zh · 2026-02-27T22:49:24Z

@copilot fix the failed CIs: rebase on main and fix the linter issues (suggestion: run pre-commit run --all-files)

Co-authored-by: h2zh <61568048+h2zh@users.noreply.github.com>

Copilot · 2026-02-27T22:53:14Z

@copilot fix the failed CIs: rebase on main and fix the linter issues (suggestion: run pre-commit run --all-files)

Fixed the goimports lint issue in a23997d — moved _ "github.com/glebarez/sqlite" blank import into the third-party imports group where it belongs.

For the rebase on main: I'm unable to perform git rebase operations in my environment. Could you rebase the branch on main?

Initial plan

962e807

Copilot AI assigned Copilot and bbockelm Feb 21, 2026

Copilot started work on behalf of bbockelm February 21, 2026 02:11 View session

Copilot AI and others added 2 commits February 21, 2026 02:30

Use secretbox instead of box for symmetric data encryption in backups

09e25c1

Co-authored-by: bbockelm <1093447+bbockelm@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add periodic sqlite dumps for Pelican databases~~ Add periodic SQLite database backups with compression and encryption Feb 21, 2026

Copilot AI requested a review from bbockelm February 21, 2026 02:35

Copilot finished work on behalf of bbockelm February 21, 2026 02:35

bbockelm added 2 commits February 21, 2026 09:26

Add 'info' sub-command and backup metadata

4d4a203

bbockelm added enhancement New feature or request client Issue affecting the OSDF client user-request labels Feb 21, 2026

github-advanced-security bot found potential problems Feb 21, 2026

View reviewed changes

A third attempt at cleaning up Windows ordering issues

85afc3e

bbockelm requested a review from h2zh February 21, 2026 16:23

bbockelm marked this pull request as ready for review February 21, 2026 16:23

h2zh assigned h2zh and unassigned bbockelm, h2zh and Copilot Feb 23, 2026

h2zh requested changes Feb 25, 2026

View reviewed changes

Copilot started work on behalf of h2zh February 25, 2026 00:09 View session

Address PR review feedback: wrap init error, add DEK zeroing, SQLite …

8dde278

…integrity check, timestamp consistency, and server type comment Co-authored-by: h2zh <61568048+h2zh@users.noreply.github.com>

Copilot AI requested a review from h2zh February 25, 2026 00:15

Copilot finished work on behalf of h2zh February 25, 2026 00:15

Copilot started work on behalf of h2zh February 25, 2026 00:15 View session

Copilot finished work on behalf of h2zh February 25, 2026 00:16

Copilot started work on behalf of h2zh February 27, 2026 22:49 View session

Fix goimports lint: move blank sqlite import to third-party group

a23997d

Co-authored-by: h2zh <61568048+h2zh@users.noreply.github.com>

Copilot finished work on behalf of h2zh February 27, 2026 22:53

	return errors.New("failed to initialize server configuration; ensure a valid pelican.yaml is present")
	return errors.Wrap(err, "failed to initialize server configuration")

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Copilot AI commented Feb 21, 2026 •

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