Stop restore --verify re-reporting files that failed to restore (closes #323)

With --skip-errors, a file that failed to restore was verified anyway,
failed again because it was never written, and was added to the same
failure list as the restore failure. restore --verify then listed it
twice and called every entry a checksum mismatch.

Verification now skips the files that failed to restore and keeps its
own failures in a separate list, so failed restores and failed
verifications are reported apart, each path once. The restore still
exits non-zero.

Model: opus-5-5

README.md

@@ -375,7 +375,9 @@ on the destination in one go, use `vaultik remote nuke --force`.
 * Optional path arguments to restore specific files/directories (default: all)
 * Preserves file permissions, timestamps, ownership (ownership requires root),
   symlinks, and empty directories
-* `--verify`: After restoring, verify every file's chunk hashes match
+* `--verify`: After restoring, verify every restored file's chunk hashes
+  match. A file skipped under `--skip-errors` is reported as failed to
+  restore and is not verified.
 
 **`prune`**: Tidy up everything that isn't needed. Runs three passes:
 (1) reconcile the local index against the destination store — any

docs/DATAMODEL.md

@@ -90,7 +90,7 @@ Stores information about packed, compressed, and encrypted blob files.
 - `created_ts` (INTEGER NOT NULL) - Creation timestamp
 - `finished_ts` (INTEGER) - Finalization timestamp (NULL if in progress)
 - `uncompressed_size` (INTEGER NOT NULL DEFAULT 0) - Total size of chunks before compression
-- `compressed_size` (INTEGER NOT NULL DEFAULT 0) - Size after compression and encryption. Once uploaded, the size of the object in storage: when the blob was already stored, under another compression level or other recipients, this can differ from the size of the local copy
+- `compressed_size` (INTEGER NOT NULL DEFAULT 0) - Size after compression and encryption
 - `uploaded_ts` (INTEGER) - Upload completion timestamp (NULL if not uploaded)
 
 **Purpose:** Tracks blob lifecycle from creation through upload. The UUID primary key allows immediate association of chunks with blobs.
@@ -183,7 +183,7 @@ Tracks blob upload metrics.
    - `UPDATE blobs SET blob_hash = ?, finished_ts = ?` - Finalize blob after packing
 
 4. **Upload**
-   - `UPDATE blobs SET uploaded_ts = ?, compressed_size = ?` - Mark blob as uploaded, with the size of the object in storage (the upload is skipped when the blob is already stored)
+   - `UPDATE blobs SET uploaded_ts = ?` - Mark blob as uploaded
    - `INSERT INTO uploads` - Record upload metrics with snapshot_id
    - `INSERT INTO snapshot_blobs` - Associate blob with snapshot
 

internal/database/blobs.go

@@ -159,16 +159,13 @@ func (r *BlobRepository) UpdateFinished(
 	return nil
 }
 
-// UpdateUploaded marks a blob as uploaded and records the size of the
-// stored object as its compressed size. That size can differ from the
-// local copy's when an identical blob was already stored with another
-// compression level or other recipients.
+// UpdateUploaded marks a blob as uploaded
 func (r *BlobRepository) UpdateUploaded(
-	ctx context.Context, tx *sql.Tx, id string, storedSize int64,
+	ctx context.Context, tx *sql.Tx, id string,
 ) error {
 	query := `
-		UPDATE blobs
-		SET uploaded_ts = ?, compressed_size = ?
+		UPDATE blobs 
+		SET uploaded_ts = ?
 		WHERE id = ?
 	`
 
@@ -176,9 +173,9 @@ func (r *BlobRepository) UpdateUploaded(
 
 	var err error
 	if tx != nil {
-		_, err = tx.ExecContext(ctx, query, now, storedSize, id)
+		_, err = tx.ExecContext(ctx, query, now, id)
 	} else {
-		_, err = r.db.ExecWithLog(ctx, query, now, storedSize, id)
+		_, err = r.db.ExecWithLog(ctx, query, now, id)
 	}
 
 	if err != nil {

internal/database/blobs_test.go

@@ -122,8 +122,8 @@ func TestBlobRepositoryUpdates(t *testing.T) {
 		t.Errorf("expected compressed size 500, got %d", updated.CompressedSize)
 	}
 
-	// Test UpdateUploaded, with a stored object larger than the local copy
-	err = repo.UpdateUploaded(ctx, nil, blob.ID.String(), 600)
+	// Test UpdateUploaded
+	err = repo.UpdateUploaded(ctx, nil, blob.ID.String())
 	if err != nil {
 		t.Fatalf("failed to update blob as uploaded: %v", err)
 	}
@@ -141,10 +141,6 @@ func TestBlobRepositoryUpdates(t *testing.T) {
 	if uploaded.UploadedTS.Before(now.Add(-1 * time.Second)) {
 		t.Error("uploaded timestamp should be around test time")
 	}
-
-	if uploaded.CompressedSize != 600 {
-		t.Errorf("expected the stored size 600, got %d", uploaded.CompressedSize)
-	}
 }
 
 func TestBlobRepositoryDuplicate(t *testing.T) {

internal/snapshot/scanner.go

@@ -1509,8 +1509,7 @@ func (s *Scanner) finalizeProcessPhase(ctx context.Context, result *ScanResult)
 			// snapshot references has uploaded_ts set, so deduplication and
 			// interrupted-run repair treat these blobs as trustworthy.
 			err = s.repos.WithTx(ctx, func(ctx context.Context, tx *sql.Tx) error {
-				err := s.repos.Blobs.UpdateUploaded(
-					ctx, tx, b.ID, b.Compressed)
+				err := s.repos.Blobs.UpdateUploaded(ctx, tx, b.ID)
 				if err != nil {
 					return fmt.Errorf("marking blob uploaded: %w", err)
 				}
@@ -1546,7 +1545,7 @@ func (s *Scanner) handleBlobReady(
 	blobPath := fmt.Sprintf("blobs/%s/%s/%s",
 		finishedBlob.Hash[:2], finishedBlob.Hash[2:4], finishedBlob.Hash)
 
-	storedSize, blobExists, err := s.uploadBlobIfNeeded(
+	blobExists, err := s.uploadBlobIfNeeded(
 		ctx, blobPath, blobWithReader, startTime, result)
 	if err != nil {
 		s.cleanupBlobTempFile(blobWithReader)
@@ -1554,8 +1553,7 @@ func (s *Scanner) handleBlobReady(
 		return fmt.Errorf("uploading blob %s: %w", finishedBlob.Hash, err)
 	}
 
-	err = s.recordBlobMetadata(
-		ctx, finishedBlob, storedSize, blobExists, startTime)
+	err = s.recordBlobMetadata(ctx, finishedBlob, blobExists, startTime)
 	if err != nil {
 		s.cleanupBlobTempFile(blobWithReader)
 
@@ -1577,22 +1575,20 @@ func (s *Scanner) handleBlobReady(
 }
 
 // uploadBlobIfNeeded uploads the blob to storage if it doesn't already
-// exist. It returns the size of the object in storage, which for an
-// existing object can differ from the local copy's, and whether it
-// already existed.
+// exist, returns whether it existed
 func (s *Scanner) uploadBlobIfNeeded(
 	ctx context.Context,
 	blobPath string,
 	blobWithReader *blob.WithReader,
 	startTime time.Time,
 	result *ScanResult,
-) (int64, bool, error) {
+) (bool, error) {
 	finishedBlob := blobWithReader.FinishedBlob
 
 	// Check if blob already exists (deduplication after restart)
 	destination := s.storage.Info().Location
 
-	stored, err := s.storage.Stat(ctx, blobPath)
+	_, err := s.storage.Stat(ctx, blobPath)
 	if err == nil {
 		log.Info("Blob already exists in storage, skipping upload",
 			"hash", finishedBlob.Hash,
@@ -1601,7 +1597,7 @@ func (s *Scanner) uploadBlobIfNeeded(
 			s.ui.Hex(finishedBlob.Hash), s.ui.Size(finishedBlob.Compressed),
 			s.ui.Path(destination))
 
-		return stored.Size, true, nil
+		return true, nil
 	}
 
 	s.ui.Beginf("Uploading blob %s (%s) to %s.",
@@ -1615,7 +1611,7 @@ func (s *Scanner) uploadBlobIfNeeded(
 	if err != nil {
 		log.Error("Failed to upload blob", "hash", finishedBlob.Hash, "error", err)
 
-		return 0, false, fmt.Errorf("uploading blob to storage: %w", err)
+		return false, fmt.Errorf("uploading blob to storage: %w", err)
 	}
 
 	uploadDuration := time.Since(startTime)
@@ -1646,7 +1642,7 @@ func (s *Scanner) uploadBlobIfNeeded(
 		stats.BytesUploaded.Add(finishedBlob.Compressed)
 	}
 
-	return finishedBlob.Compressed, false, nil
+	return false, nil
 }
 
 // makeUploadProgressCallback creates a progress callback for blob uploads.
@@ -1716,7 +1712,6 @@ func (s *Scanner) makeUploadProgressCallback(
 func (s *Scanner) recordBlobMetadata(
 	ctx context.Context,
 	finishedBlob *blob.FinishedBlob,
-	storedSize int64,
 	blobExists bool,
 	startTime time.Time,
 ) error {
@@ -1728,8 +1723,7 @@ func (s *Scanner) recordBlobMetadata(
 	uploadDuration := time.Since(startTime)
 
 	return s.repos.WithTx(ctx, func(txCtx context.Context, tx *sql.Tx) error {
-		err := s.repos.Blobs.UpdateUploaded(
-			txCtx, tx, finishedBlob.ID, storedSize)
+		err := s.repos.Blobs.UpdateUploaded(txCtx, tx, finishedBlob.ID)
 		if err != nil {
 			return fmt.Errorf("updating blob upload timestamp: %w", err)
 		}

internal/vaultik/restore.go

@@ -103,11 +103,12 @@ type RestoreResult struct {
 	BlobsDownloaded int
 	BytesDownloaded int64
 	Duration        time.Duration
+	FilesFailed     int
+	FailedFiles     []string // Paths of files that failed to restore
 	// Verification results (only populated if Verify option is set)
-	FilesVerified int
-	BytesVerified int64
-	FilesFailed   int
-	FailedFiles   []string // Paths of files that failed verification
+	FilesVerified     int
+	BytesVerified     int64
+	VerifyFailedFiles []string // Paths of restored files that failed verification
 }
 
 // Restore restores files from a snapshot to the target directory
@@ -647,20 +648,34 @@ func (v *Vaultik) handleRestoreVerification(
 	opts *RestoreOptions,
 	result *RestoreResult,
 ) error {
-	err := v.verifyRestoredFiles(v.ctx, repos, files, opts.TargetDir, result)
+	// A file that failed to restore was not written and is already
+	// reported as such, so it is not verified.
+	failedToRestore := make(map[string]bool, len(result.FailedFiles))
+	for _, path := range result.FailedFiles {
+		failedToRestore[path] = true
+	}
+
+	restored := make([]*database.File, 0, len(files))
+	for _, file := range files {
+		if !failedToRestore[file.Path.String()] {
+			restored = append(restored, file)
+		}
+	}
+
+	err := v.verifyRestoredFiles(v.ctx, repos, restored, opts.TargetDir, result)
 	if err != nil {
 		return fmt.Errorf("verification failed: %w", err)
 	}
 
-	if result.FilesFailed > 0 {
+	if len(result.VerifyFailedFiles) > 0 {
 		v.UI.Errorf("Verification failed: %s files did not match expected checksums.",
-			v.UI.Count(result.FilesFailed))
+			v.UI.Count(len(result.VerifyFailedFiles)))
 
-		for _, path := range result.FailedFiles {
+		for _, path := range result.VerifyFailedFiles {
 			v.UI.Detailf("%s", v.UI.Path(path))
 		}
 
-		return fmt.Errorf("%d %w", result.FilesFailed, errFilesFailedVerify)
+		return fmt.Errorf("%d %w", len(result.VerifyFailedFiles), errFilesFailedVerify)
 	}
 
 	v.UI.Completef("Verified %s files (%s).",
@@ -1420,8 +1435,8 @@ func (v *Vaultik) verifyRestoredFiles(
 		if err != nil {
 			log.Error("File verification failed", "path", file.Path, "error", err)
 
-			result.FilesFailed++
-			result.FailedFiles = append(result.FailedFiles, file.Path.String())
+			result.VerifyFailedFiles = append(
+				result.VerifyFailedFiles, file.Path.String())
 		}
 
 		bytesProcessed += file.Size
@@ -1437,7 +1452,7 @@ func (v *Vaultik) verifyRestoredFiles(
 	log.Info("Verification complete",
 		"files_verified", result.FilesVerified,
 		"bytes_verified", ubytes(result.BytesVerified),
-		"files_failed", result.FilesFailed,
+		"files_failed", len(result.VerifyFailedFiles),
 	)
 
 	return nil

internal/vaultik/restore_skip_errors_test.go

@@ -84,6 +84,41 @@ func TestRestoreSkipErrorsSkipsFilesOfMissingBlob(t *testing.T) {
 	}
 }
 
+// TestRestoreSkipErrorsVerifyChecksOnlyRestoredFiles restores with
+// SkipErrors and Verify after one blob of a two-blob snapshot was
+// deleted. Verification must check only the files that were written, so
+// a file of the deleted blob is reported as failed to restore and not
+// also as failing verification, and Restore must still return an error.
+func TestRestoreSkipErrorsVerifyChecksOnlyRestoredFiles(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	ctx := context.Background()
+	backup := backupThenDeleteOneBlob(ctx, t)
+
+	var out bytes.Buffer
+
+	v := newReaderVaultik(ctx, backup.cfg, backup.storer, nil, backup.fs)
+	v.UI = ui.NewWithColor(&out, false)
+
+	err := v.Restore(&vaultik.RestoreOptions{
+		SnapshotID: backup.snapshotID,
+		TargetDir:  backup.restoreDir,
+		Verify:     true,
+		SkipErrors: true,
+	})
+
+	require.Error(t, err, "restore must fail when files were skipped")
+	assert.Contains(t, err.Error(),
+		fmt.Sprintf("%d file(s) failed to restore", len(backup.lost)))
+
+	written := len(backup.files) - len(backup.lost)
+
+	assert.Contains(t, out.String(), fmt.Sprintf("Verifying %d files", written))
+	assert.Contains(t, out.String(), fmt.Sprintf("Verified %d files", written))
+	assert.NotContains(t, out.String(), "Verification failed")
+}
+
 // TestRestoreMissingBlobAbortsWithoutSkipErrors checks that a deleted blob
 // still ends the restore with an error when SkipErrors is not set.
 func TestRestoreMissingBlobAbortsWithoutSkipErrors(t *testing.T) {

internal/vaultik/reused_blob_verify_test.go

@@ -1,83 +0,0 @@
-package vaultik_test
-
-import (
-	"context"
-	"io"
-	"path/filepath"
-	"testing"
-
-	"filippo.io/age"
-	"github.com/spf13/afero"
-	"github.com/stretchr/testify/require"
-	"sneak.berlin/go/vaultik/internal/log"
-	"sneak.berlin/go/vaultik/internal/ui"
-	"sneak.berlin/go/vaultik/internal/vaultik"
-)
-
-// TestVerifyPassesWhenBackupReusesStoredBlob backs up a file, then backs it
-// up again from an empty local index, as after `database delete`, with an
-// extra age recipient. The second backup builds the same blob, finds it
-// already stored and skips the upload, but its own copy is larger, because
-// age writes a header entry for each recipient. The second snapshot must
-// record the size of the stored object, so shallow and deep verify pass.
-func TestVerifyPassesWhenBackupReusesStoredBlob(t *testing.T) {
-	log.Initialize(log.Config{})
-	t.Parallel()
-
-	fs := afero.NewOsFs()
-	tempDir := t.TempDir()
-
-	dataDir := filepath.Join(tempDir, "source")
-	storeDir := filepath.Join(tempDir, "remote")
-	secondDBPath := filepath.Join(tempDir, "second.sqlite")
-
-	chunkSize := int64(64 * 1024)
-	maxBlobSize := int64(512 * 1024)
-
-	require.NoError(t, fs.MkdirAll(dataDir, 0o755))
-	require.NoError(t, afero.WriteFile(fs,
-		filepath.Join(dataDir, "data.bin"),
-		bytesPattern("reuse-", int(chunkSize*3)), 0o644))
-
-	ctx := context.Background()
-
-	runFileStorageBackup(ctx, t, fs, dataDir, storeDir,
-		filepath.Join(tempDir, "first.sqlite"), chunkSize, maxBlobSize)
-
-	env := setupDedupBackupEnv(
-		ctx, t, fs, storeDir, secondDBPath, chunkSize, maxBlobSize)
-
-	defer func() { _ = env.db.Close() }()
-
-	extra, err := age.GenerateX25519Identity()
-	require.NoError(t, err)
-
-	env.cfg.AgeRecipients = append(env.cfg.AgeRecipients,
-		extra.Recipient().String())
-
-	snapshotID, result := runDedupSnapshot(ctx, t, env.sm, env.makeScanner(),
-		env.cfg.Hostname, "second", dataDir, secondDBPath)
-	require.Positive(t, result.BlobsCreated)
-	require.Zero(t, result.BlobsUploaded,
-		"the second backup should find every blob already stored")
-
-	require.NoError(t, env.db.Close())
-
-	verifier := &vaultik.Vaultik{
-		Config:  env.cfg,
-		Storage: env.storer,
-		Fs:      fs,
-		Stdout:  io.Discard,
-		Stderr:  io.Discard,
-		UI:      ui.NewWithColor(io.Discard, false),
-	}
-	verifier.SetContext(ctx)
-
-	require.NoError(t,
-		verifier.VerifySnapshotWithOptions(snapshotID, &vaultik.VerifyOptions{}),
-		"shallow verify should pass")
-	require.NoError(t,
-		verifier.VerifySnapshotWithOptions(snapshotID,
-			&vaultik.VerifyOptions{Deep: true}),
-		"deep verify should pass")
-}