Report blobs shallow verify could not check apart from missing ones (closes #318)

Shallow snapshot verify counted every error from checking a blob or the
encrypted database as "missing" and printed the error nowhere, so a
permission error or an S3 403 read as data loss. Now only a not-found
answer from storage counts as missing. Any other error is reported as
could not be checked, with the error storage returned, in the text
report and under --json (the new unchecked list and
database_check_error field), and the run fails. Under --quiet, which
drops the report, each of those errors is logged as a warning on
stderr.

The database check moved into its own small function because the verify
function was at the linter's length limit.

Model: opus-5-5

ARCHITECTURE.md

@@ -279,8 +279,8 @@ Key methods:
 - `Scan(ctx, path, snapshotID)` → Main scan operation
 
 Scan phases:
-1. **Phase 1**: Walk directory, identify files needing processing
-2. **Phase 1b**: Count as deleted the files that the previous snapshot of the same name lists and the walk did not find; a file that is excluded, or inside an excluded directory, is not counted
+1. **Phase 0**: Detect deleted files from previous snapshots
+2. **Phase 1**: Walk directory, identify files needing processing
 3. **Phase 2**: Process files (chunk → pack → upload)
 
 #### SnapshotManager
@@ -320,13 +320,13 @@ CreateSnapshot(opts)
     │       │
     │       ├─► scanner.Scan(ctx, path, snapshotID)
     │       │       │
+    │       │       ├─► Phase 0: detectDeletedFiles()
+    │       │       │
     │       │       ├─► Phase 1: scanPhase()
     │       │       │       Walk directory
     │       │       │       Check file metadata changes
     │       │       │       Build list of files to process
     │       │       │
-    │       │       ├─► Phase 1b: detectDeletedFiles()
-    │       │       │
     │       │       └─► Phase 2: processPhase()
     │       │               For each file:
     │       │                   chunker.ChunkReaderStreaming()

internal/database/files.go

@@ -277,50 +277,6 @@ func (r *FileRepository) ListUnderPath(
 	return files, rows.Err()
 }
 
-// ListUnderPathInSnapshot returns the files that ListUnderPath returns
-// for path and that the snapshot lists, in no particular order.
-func (r *FileRepository) ListUnderPathInSnapshot(
-	ctx context.Context, path, snapshotID string,
-) ([]*File, error) {
-	path = strings.TrimRight(path, "/")
-	dirPrefix := path + "/"
-
-	query := `
-		SELECT f.id, f.path, f.source_path, f.mtime, f.mtime_nsec, f.size,
-			f.mode, f.uid, f.gid, f.link_target
-		FROM files f
-		JOIN snapshot_files sf ON sf.file_id = f.id
-		WHERE sf.snapshot_id = ?
-		  AND (f.path = ? OR substr(f.path, 1, length(?)) = ?)
-	`
-
-	rows, err := r.db.conn.QueryContext(ctx, query,
-		snapshotID, path, dirPrefix, dirPrefix)
-	if err != nil {
-		return nil, fmt.Errorf("querying files: %w", err)
-	}
-
-	defer func() {
-		err := rows.Close()
-		if err != nil {
-			Fatalf("failed to close rows: %v", err)
-		}
-	}()
-
-	var files []*File
-
-	for rows.Next() {
-		file, err := r.scanFileRows(rows)
-		if err != nil {
-			return nil, fmt.Errorf("scanning file: %w", err)
-		}
-
-		files = append(files, file)
-	}
-
-	return files, rows.Err()
-}
-
 // ListIDsWithChunksNotInUploadedBlobs returns the IDs of the files whose
 // path starts with prefix and that list at least one chunk held by no
 // blob whose upload has completed (uploaded_ts set). A new snapshot

internal/database/files_test.go

@@ -212,65 +212,6 @@ func TestFileRepositoryListUnderPath(t *testing.T) {
 	}
 }
 
-// ListUnderPathInSnapshot leaves out files outside path and files the
-// snapshot does not list, though another snapshot lists them.
-func TestFileRepositoryListUnderPathInSnapshot(t *testing.T) {
-	t.Parallel()
-
-	db, cleanup := setupTestDB(t)
-	defer cleanup()
-
-	ctx := context.Background()
-	files := database.NewFileRepository(db)
-	snapshots := database.NewSnapshotRepository(db)
-
-	listed := map[string][]string{
-		"one": {"/src/a.txt", "/src2/c.txt"},
-		"two": {"/src/b.txt"},
-	}
-
-	for snapshotID, paths := range listed {
-		err := snapshots.Create(ctx, nil, &database.Snapshot{
-			ID:        types.SnapshotID(snapshotID),
-			Hostname:  "host",
-			StartedAt: time.Now(),
-		})
-		if err != nil {
-			t.Fatalf("failed to create snapshot %s: %v", snapshotID, err)
-		}
-
-		for _, path := range paths {
-			err := files.Create(ctx, nil, &database.File{
-				Path:  types.FilePath(path),
-				MTime: time.Now().Truncate(time.Second),
-				Mode:  0644,
-			})
-			if err != nil {
-				t.Fatalf("failed to create %s: %v", path, err)
-			}
-
-			err = snapshots.AddFile(ctx, nil, snapshotID, path)
-			if err != nil {
-				t.Fatalf("failed to add %s to %s: %v", path, snapshotID, err)
-			}
-		}
-	}
-
-	found, err := files.ListUnderPathInSnapshot(ctx, "/src", "one")
-	if err != nil {
-		t.Fatalf("failed to list files: %v", err)
-	}
-
-	got := make([]string, 0, len(found))
-	for _, f := range found {
-		got = append(got, f.Path.String())
-	}
-
-	if !slices.Equal(got, []string{"/src/a.txt"}) {
-		t.Errorf("got %q, want only /src/a.txt", got)
-	}
-}
-
 func TestFileRepositorySymlink(t *testing.T) {
 	t.Parallel()
 

internal/snapshot/module.go

@@ -16,9 +16,6 @@ type ScannerParams struct {
 	Fs             afero.Fs
 	Exclude        []string // Exclude patterns (combined global + snapshot-specific)
 	SkipErrors     bool     // Skip file read errors (log loudly but continue)
-	// PreviousSnapshotID is the most recent completed snapshot of the
-	// same name, "" for none.
-	PreviousSnapshotID string
 }
 
 // Module exports backup functionality as an fx module.
@@ -47,18 +44,17 @@ func provideScannerFactory(
 		}
 
 		return NewScanner(ScannerConfig{
-			FS:                 params.Fs,
-			ChunkSize:          cfg.ChunkSize.Int64(),
-			Repositories:       repos,
-			Storage:            storer,
-			MaxBlobSize:        cfg.BlobSizeLimit.Int64(),
-			CompressionLevel:   cfg.CompressionLevel,
-			AgeRecipients:      cfg.AgeRecipients,
-			EnableProgress:     params.EnableProgress,
-			UI:                 params.UI,
-			Exclude:            excludes,
-			SkipErrors:         params.SkipErrors,
-			PreviousSnapshotID: params.PreviousSnapshotID,
+			FS:               params.Fs,
+			ChunkSize:        cfg.ChunkSize.Int64(),
+			Repositories:     repos,
+			Storage:          storer,
+			MaxBlobSize:      cfg.BlobSizeLimit.Int64(),
+			CompressionLevel: cfg.CompressionLevel,
+			AgeRecipients:    cfg.AgeRecipients,
+			EnableProgress:   params.EnableProgress,
+			UI:               params.UI,
+			Exclude:          excludes,
+			SkipErrors:       params.SkipErrors,
 		})
 	}
 }

internal/snapshot/scanner.go

@@ -58,10 +58,6 @@ type Scanner struct {
 	compressionLevel int
 	ageRecipient     string
 	snapshotID       string // Current snapshot being processed
-	// previousSnapshotID is the most recent completed snapshot of the
-	// same name, "" for none. Only a file it lists can be counted as
-	// deleted.
-	previousSnapshotID string
 	// currentSourcePath is the source directory being scanned, stored with
 	// each file record.
 	currentSourcePath string
@@ -133,9 +129,6 @@ type ScannerConfig struct {
 	// SkipErrors skips files that cannot be opened or read (log loudly but
 	// continue); packer, database, encryption, and upload errors still abort.
 	SkipErrors bool
-	// PreviousSnapshotID is the most recent completed snapshot of the
-	// same name, "" for none.
-	PreviousSnapshotID string
 }
 
 // ScanResult contains the results of a scan operation. Files and bytes
@@ -211,7 +204,6 @@ func NewScanner(cfg ScannerConfig) *Scanner {
 		compiledExclude:    compiledExclude,
 		progress:           progress,
 		skipErrors:         cfg.SkipErrors,
-		previousSnapshotID: cfg.PreviousSnapshotID,
 		ui:                 uiw,
 		pendingChunkHashes: make(map[string]struct{}),
 	}
@@ -263,9 +255,8 @@ func (s *Scanner) Scan(
 
 	filesToProcess := scanResult.FilesToProcess
 
-	// Phase 1b: Detect deleted files by comparing the previous snapshot
-	// of this name against scanned files
-	err = s.detectDeletedFiles(ctx, path, existingFiles, result)
+	// Phase 1b: Detect deleted files by comparing DB against scanned files
+	err = s.detectDeletedFilesFromMap(ctx, knownFiles, existingFiles, result)
 	if err != nil {
 		return nil, fmt.Errorf("detecting deleted files: %w", err)
 	}
@@ -445,8 +436,9 @@ func (s *Scanner) summarizeScanPhase(
 }
 
 // loadKnownFiles loads the known files at and beneath path from the
-// database into a map for fast lookup. This avoids per-file database
-// queries during the scan phase.
+// database into a map for fast lookup. Every loaded file the scan does
+// not find is counted as deleted. This avoids per-file database queries
+// during the scan phase.
 func (s *Scanner) loadKnownFiles(
 	ctx context.Context, path string,
 ) (map[string]*database.File, error) {
@@ -1946,28 +1938,21 @@ func (s *Scanner) queueFileForBatchInsert(
 	})
 }
 
-// detectDeletedFiles counts as deleted each file at or beneath path that
-// the previous snapshot of this name lists and the walk did not find.
-// A file that is excluded, or inside an excluded directory, is not
-// counted: the walk skips it whether or not it is still on disk.
-func (s *Scanner) detectDeletedFiles(
+// detectDeletedFilesFromMap finds files that existed in previous snapshots
+// but no longer exist. Uses pre-loaded maps to avoid any filesystem or
+// database access.
+func (s *Scanner) detectDeletedFilesFromMap(
 	ctx context.Context,
-	path string,
+	knownFiles map[string]*database.File,
 	existingFiles map[string]struct{},
 	result *ScanResult,
 ) error {
-	if s.previousSnapshotID == "" {
+	if len(knownFiles) == 0 {
 		return nil
 	}
 
-	previousFiles, err := s.repos.Files.ListUnderPathInSnapshot(
-		ctx, path, s.previousSnapshotID)
-	if err != nil {
-		return fmt.Errorf("listing files of snapshot %s: %w",
-			s.previousSnapshotID, err)
-	}
-
-	for _, file := range previousFiles {
+	// Check each known file against the enumerated set (no filesystem access needed)
+	for path, file := range knownFiles {
 		// Check context cancellation periodically
 		select {
 		case <-ctx.Done():
@@ -1975,16 +1960,13 @@ func (s *Scanner) detectDeletedFiles(
 		default:
 		}
 
-		filePath := file.Path.String()
-
-		_, exists := existingFiles[filePath]
-		if exists || s.excludedOrInExcludedDir(filePath, path) {
-			continue
+		// Check if the file exists in our enumerated set
+		if _, exists := existingFiles[path]; !exists {
+			// File has been deleted
+			result.FilesDeleted++
+			result.BytesDeleted += file.Size
+			log.Debug("Detected deleted file", "path", path, "size", file.Size)
 		}
-
-		result.FilesDeleted++
-		result.BytesDeleted += file.Size
-		log.Debug("Detected deleted file", "path", filePath, "size", file.Size)
 	}
 
 	if result.FilesDeleted > 0 {
@@ -1995,20 +1977,6 @@ func (s *Scanner) detectDeletedFiles(
 	return nil
 }
 
-// excludedOrInExcludedDir reports whether filePath, which is at or
-// beneath rootPath, or any directory between rootPath and it, matches an
-// exclude pattern. A pattern such as **/node_modules matches the
-// directory but not the files inside it, which the walk skips too.
-func (s *Scanner) excludedOrInExcludedDir(filePath, rootPath string) bool {
-	for p := filePath; len(p) > len(rootPath); p = filepath.Dir(p) {
-		if s.shouldExclude(p, rootPath) {
-			return true
-		}
-	}
-
-	return false
-}
-
 // wrapPermissionError augments permission errors with platform-specific
 // remediation instructions. On macOS, TCC-protected directories (Calendars,
 // Reminders, Photos, etc.) return EPERM unless the running application has

internal/vaultik/destination_validation_test.go

@@ -161,13 +161,14 @@ func TestVerifyManifestBlobsRejectsShortHash(t *testing.T) {
 		Blobs: []snapshot.BlobInfo{{Hash: "abc", CompressedSize: 1}},
 	}
 
-	verified, missing, mismatched, missingSize, err :=
+	verified, missing, mismatched, missingSize, unchecked, err :=
 		v.verifyManifestBlobs(manifest, &VerifyOptions{JSON: true})
 	require.ErrorIs(t, err, errInvalidBlobHash)
 	require.Zero(t, verified)
 	require.Zero(t, missing)
 	require.Zero(t, mismatched)
 	require.Zero(t, missingSize)
+	require.Empty(t, unchecked)
 }
 
 // TestVerifyBlobChunksRejectsNegativeLength proves a blob_chunks row with a

internal/vaultik/fault_injection_test.go

@@ -661,18 +661,17 @@ func faultScannerFactory(
 ) snapshot.ScannerFactory {
 	return func(params snapshot.ScannerParams) *snapshot.Scanner {
 		return snapshot.NewScanner(snapshot.ScannerConfig{
-			FS:                 params.Fs,
-			Storage:            storer,
-			ChunkSize:          faultChunkSize,
-			MaxBlobSize:        faultMaxBlobSize,
-			CompressionLevel:   cfg.CompressionLevel,
-			AgeRecipients:      cfg.AgeRecipients,
-			Repositories:       repos,
-			EnableProgress:     params.EnableProgress,
-			UI:                 params.UI,
-			Exclude:            params.Exclude,
-			SkipErrors:         params.SkipErrors,
-			PreviousSnapshotID: params.PreviousSnapshotID,
+			FS:               params.Fs,
+			Storage:          storer,
+			ChunkSize:        faultChunkSize,
+			MaxBlobSize:      faultMaxBlobSize,
+			CompressionLevel: cfg.CompressionLevel,
+			AgeRecipients:    cfg.AgeRecipients,
+			Repositories:     repos,
+			EnableProgress:   params.EnableProgress,
+			UI:               params.UI,
+			Exclude:          params.Exclude,
+			SkipErrors:       params.SkipErrors,
 		})
 	}
 }

internal/vaultik/shallow_verify_test.go

@@ -4,15 +4,20 @@ import (
 	"bytes"
 	"context"
 	"encoding/json"
+	"errors"
+	"fmt"
 	"io"
 	"os"
+	"path"
 	"path/filepath"
+	"slices"
 	"testing"
 
 	"github.com/spf13/afero"
 	"github.com/stretchr/testify/require"
 	"sneak.berlin/go/vaultik/internal/log"
 	"sneak.berlin/go/vaultik/internal/snapshot"
+	"sneak.berlin/go/vaultik/internal/storage"
 	"sneak.berlin/go/vaultik/internal/ui"
 	"sneak.berlin/go/vaultik/internal/vaultik"
 )
@@ -151,6 +156,224 @@ func TestShallowVerifyDetectsMissingDatabase(t *testing.T) {
 		"shallow verify must fail when db.zst.age is absent")
 }
 
+// errStatDenied stands in for any storage error other than not-found: a
+// permission error, an S3 403, a dropped connection.
+var errStatDenied = errors.New("injected stat failure")
+
+// statFailingStorer fails Stat with errStatDenied for the keys in
+// failKeys and passes every other call to the wrapped Storer.
+type statFailingStorer struct {
+	storage.Storer
+
+	failKeys []string
+}
+
+func (s statFailingStorer) Stat(
+	ctx context.Context, key string,
+) (*storage.ObjectInfo, error) {
+	if slices.Contains(s.failKeys, key) {
+		return nil, fmt.Errorf("stat %q: %w", key, errStatDenied)
+	}
+
+	return s.Storer.Stat(ctx, key)
+}
+
+// TestShallowVerifyReportsStatErrorsApartFromMissing backs up a real
+// snapshot, deletes one blob, and makes storage fail Stat with an error
+// other than not-found for a second blob and for the encrypted database.
+// Only the deleted blob may be counted as missing. The second blob and
+// the database must be reported as could not be checked, with the error
+// storage returned, and verify must fail, in the text output and under
+// --json.
+func TestShallowVerifyReportsStatErrorsApartFromMissing(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")
+	dbPath := filepath.Join(tempDir, "index.sqlite")
+
+	chunkSize := int64(32 * 1024)
+	maxBlobSize := int64(128 * 1024)
+
+	// Random content, so the snapshot spans several blobs.
+	require.NoError(t, fs.MkdirAll(dataDir, 0o755))
+	appendRandomBytes(t, fs, map[string][]byte{},
+		filepath.Join(dataDir, "data.bin"), maxBlobSize*4)
+
+	ctx := context.Background()
+
+	cfg, storer, snapshotID := runFileStorageBackup(
+		ctx, t, fs, dataDir, storeDir, dbPath, chunkSize, maxBlobSize)
+
+	blobKeys := storedBlobKeys(t, storeDir)
+	require.GreaterOrEqual(t, len(blobKeys), 2, "expected at least two blobs")
+
+	missingKey, uncheckedKey := blobKeys[0], blobKeys[1]
+	missingHash, uncheckedHash := path.Base(missingKey), path.Base(uncheckedKey)
+
+	require.NoError(t, os.Remove(filepath.Join(storeDir, missingKey)))
+
+	dbKey := "metadata/" + snapshot.RemoteSnapshotKey(snapshotID) + "/db.zst.age"
+	failing := statFailingStorer{
+		Storer:   storer,
+		failKeys: []string{uncheckedKey, dbKey},
+	}
+
+	newVerifier := func(out io.Writer) *vaultik.Vaultik {
+		v := &vaultik.Vaultik{
+			Config:  cfg,
+			Storage: failing,
+			Fs:      fs,
+			Stdout:  out,
+			Stderr:  io.Discard,
+			UI:      ui.NewWithColor(io.Discard, false),
+		}
+		v.SetContext(ctx)
+
+		return v
+	}
+
+	var out bytes.Buffer
+
+	err := newVerifier(&out).VerifySnapshotWithOptions(
+		snapshotID, &vaultik.VerifyOptions{JSON: true})
+	require.Error(t, err)
+
+	result := decodeVerifyResult(t, out.Bytes())
+	require.Equal(t, "failed", result.Status)
+	require.Equal(t, 1, result.Missing, "only the deleted blob is missing")
+	require.Equal(t, result.BlobCount-2, result.Verified)
+	require.Len(t, result.Unchecked, 1)
+	require.Equal(t, uncheckedHash, result.Unchecked[0].Hash)
+	require.Contains(t, result.Unchecked[0].Error, errStatDenied.Error())
+	require.False(t, result.DatabaseMissing,
+		"a database that could not be checked is not missing")
+	require.Contains(t, result.DatabaseCheckError, errStatDenied.Error())
+
+	out.Reset()
+	err = newVerifier(&out).VerifySnapshotWithOptions(
+		snapshotID, &vaultik.VerifyOptions{})
+	require.Error(t, err)
+
+	text := out.String()
+	require.Contains(t, text, "Missing: "+missingHash)
+	require.NotContains(t, text, "Missing: "+uncheckedHash)
+	require.Contains(t, text, "Could not check: "+uncheckedHash)
+	require.Contains(t, text, "Encrypted database:       could not be checked")
+	require.Contains(t, text, errStatDenied.Error())
+	require.Contains(t, text, "FAILED")
+}
+
+// TestShallowVerifyQuietFailsOnStatErrorAlone backs up a healthy snapshot,
+// then makes storage fail Stat, with an error other than not-found, for
+// one blob alone and then for the encrypted database alone. Each run must
+// fail verify, and under --quiet, which drops the report, the error
+// storage returned must still reach stderr.
+//
+//nolint:paralleltest // captureProcessStderr replaces os.Stderr
+func TestShallowVerifyQuietFailsOnStatErrorAlone(t *testing.T) {
+	log.Initialize(log.Config{})
+
+	fs := afero.NewOsFs()
+	tempDir := t.TempDir()
+
+	dataDir := filepath.Join(tempDir, "source")
+	storeDir := filepath.Join(tempDir, "remote")
+	dbPath := filepath.Join(tempDir, "index.sqlite")
+
+	chunkSize := int64(32 * 1024)
+	maxBlobSize := int64(128 * 1024)
+
+	require.NoError(t, fs.MkdirAll(dataDir, 0o755))
+	require.NoError(t, afero.WriteFile(fs,
+		filepath.Join(dataDir, "data.bin"),
+		bytesPattern("shallow-quiet-", int(maxBlobSize*2)), 0o644))
+
+	ctx := context.Background()
+
+	cfg, storer, snapshotID := runFileStorageBackup(
+		ctx, t, fs, dataDir, storeDir, dbPath, chunkSize, maxBlobSize)
+
+	newQuietVerifier := func(s storage.Storer) *vaultik.Vaultik {
+		v := &vaultik.Vaultik{
+			Config:  cfg,
+			Storage: s,
+			Fs:      fs,
+			Stdout:  io.Discard,
+			Stderr:  io.Discard,
+			UI:      ui.NewWithColor(io.Discard, false),
+		}
+		v.SetContext(ctx)
+		v.UI.SetQuiet(true)
+
+		return v
+	}
+
+	require.NoError(t,
+		newQuietVerifier(storer).VerifySnapshotWithOptions(
+			snapshotID, &vaultik.VerifyOptions{}),
+		"shallow verify should pass on a healthy snapshot")
+
+	blobKeys := storedBlobKeys(t, storeDir)
+	require.NotEmpty(t, blobKeys)
+
+	dbKey := "metadata/" + snapshot.RemoteSnapshotKey(snapshotID) + "/db.zst.age"
+
+	for _, failKey := range []string{blobKeys[0], dbKey} {
+		v := newQuietVerifier(statFailingStorer{
+			Storer:   storer,
+			failKeys: []string{failKey},
+		})
+
+		var err error
+
+		stderr := captureProcessStderr(t, func() {
+			err = v.VerifySnapshotWithOptions(
+				snapshotID, &vaultik.VerifyOptions{})
+		})
+
+		require.Error(t, err,
+			"verify must fail when %s could not be checked", failKey)
+		require.Contains(t, stderr, errStatDenied.Error(),
+			"under --quiet the error for %s must still reach stderr", failKey)
+	}
+}
+
+// storedBlobKeys returns the storage key of every blob file under
+// storeDir, sorted.
+func storedBlobKeys(t *testing.T, storeDir string) []string {
+	t.Helper()
+
+	var keys []string
+
+	err := filepath.Walk(filepath.Join(storeDir, "blobs"),
+		func(p string, info os.FileInfo, err error) error {
+			if err != nil {
+				return err
+			}
+
+			if info.IsDir() {
+				return nil
+			}
+
+			rel, err := filepath.Rel(storeDir, p)
+			if err != nil {
+				return err
+			}
+
+			keys = append(keys, filepath.ToSlash(rel))
+
+			return nil
+		})
+	require.NoError(t, err)
+
+	return keys
+}
+
 // growOneBlob appends bytes to the first blob file found under blobsDir,
 // changing its on-disk size so it no longer matches the manifest.
 func growOneBlob(t *testing.T, fs afero.Fs, blobsDir string) {

internal/vaultik/snapshot.go

@@ -14,6 +14,7 @@ import (
 
 	"sneak.berlin/go/vaultik/internal/log"
 	"sneak.berlin/go/vaultik/internal/snapshot"
+	"sneak.berlin/go/vaultik/internal/storage"
 	"sneak.berlin/go/vaultik/internal/types"
 )
 
@@ -240,18 +241,12 @@ func (v *Vaultik) createNamedSnapshot(
 		return err
 	}
 
-	previousSnapshotID, err := v.previousSnapshotID(snapName)
-	if err != nil {
-		return err
-	}
-
 	scanner := v.ScannerFactory(snapshot.ScannerParams{
-		EnableProgress:     !opts.Cron,
-		UI:                 v.UI,
-		Fs:                 v.Fs,
-		Exclude:            v.Config.GetExcludes(snapName),
-		SkipErrors:         opts.SkipErrors,
-		PreviousSnapshotID: previousSnapshotID,
+		EnableProgress: !opts.Cron,
+		UI:             v.UI,
+		Fs:             v.Fs,
+		Exclude:        v.Config.GetExcludes(snapName),
+		SkipErrors:     opts.SkipErrors,
 	})
 
 	snapshotID, err := v.SnapshotManager.CreateSnapshotWithName(
@@ -286,24 +281,6 @@ func (v *Vaultik) createNamedSnapshot(
 	return nil
 }
 
-// previousSnapshotID returns the ID of the most recent completed snapshot
-// named snapName in the local index, or "" when there is none.
-func (v *Vaultik) previousSnapshotID(snapName string) (string, error) {
-	snapshots, err := v.Repositories.Snapshots.ListRecent(v.ctx, listRecentLimit)
-	if err != nil {
-		return "", fmt.Errorf("listing snapshots: %w", err)
-	}
-
-	for _, s := range snapshots {
-		if s.CompletedAt != nil &&
-			parseSnapshotName(s.ID.String(), s.Hostname.String()) == snapName {
-			return s.ID.String(), nil
-		}
-	}
-
-	return "", nil
-}
-
 // resolveSnapshotPaths resolves source directories to absolute paths
 // with symlink resolution.
 func (v *Vaultik) resolveSnapshotPaths(snapName string) ([]string, error) {
@@ -798,18 +775,10 @@ func (v *Vaultik) VerifySnapshotWithOptions(
 		v.stdoutf("Checking blob presence and sizes...\n")
 	}
 
-	// A snapshot is only restorable if its encrypted database is present
-	// alongside the blobs. Shallow verify checks that the object exists; it
-	// does not decrypt it (that is deep verify's job).
-	dbPath := fmt.Sprintf("metadata/%s/db.zst.age", remoteKey)
+	v.checkSnapshotDatabase(remoteKey, result)
 
-	_, dbErr := v.Storage.Stat(v.ctx, dbPath)
-	if dbErr != nil {
-		result.DatabaseMissing = true
-	}
-
-	result.Verified, result.Missing, result.Mismatched, result.MissingSize, err =
-		v.verifyManifestBlobs(manifest, opts)
+	result.Verified, result.Missing, result.Mismatched, result.MissingSize,
+		result.Unchecked, err = v.verifyManifestBlobs(manifest, opts)
 	if err != nil {
 		if opts.JSON {
 			result.Status = verifyStatusFailed
@@ -846,25 +815,46 @@ func (v *Vaultik) printVerifyHeader(snapshotID string, opts *VerifyOptions) {
 	}
 }
 
+// checkSnapshotDatabase records in result whether the snapshot's
+// encrypted database is missing or could not be checked. A snapshot is
+// only restorable if its database is present alongside the blobs.
+// Shallow verify checks that the object exists; it does not decrypt it
+// (that is deep verify's job).
+func (v *Vaultik) checkSnapshotDatabase(remoteKey string, result *VerifyResult) {
+	dbPath := fmt.Sprintf("metadata/%s/db.zst.age", remoteKey)
+
+	_, err := v.Storage.Stat(v.ctx, dbPath)
+
+	switch {
+	case errors.Is(err, storage.ErrNotFound):
+		result.DatabaseMissing = true
+	case err != nil:
+		result.DatabaseCheckError = err.Error()
+	}
+}
+
 // verifyManifestBlobs checks that each blob in the manifest is present in
 // storage with the size the manifest records, returning the counts of
 // blobs that were present with the right size, absent, and present but the
-// wrong size, plus the total bytes of the absent blobs. It does not read
-// blob contents; deep verification (RunDeepVerify) does that. The size
-// comparison matches the deep path (see verifyBlobExistenceFromDB).
+// wrong size, the total bytes of the absent blobs, and the blobs it could
+// not check because storage returned an error other than not-found. It
+// does not read blob contents; deep verification (RunDeepVerify) does
+// that. The size comparison matches the deep path (see
+// verifyBlobExistenceFromDB).
 func (v *Vaultik) verifyManifestBlobs(
 	manifest *snapshot.Manifest, opts *VerifyOptions,
-) (int, int, int, int64, error) {
+) (int, int, int, int64, []UncheckedBlob, error) {
 	var (
 		verified, missing, mismatched int
 		missingSize                   int64
+		unchecked                     []UncheckedBlob
 	)
 
 	for _, blob := range manifest.Blobs {
 		// The manifest is unauthenticated, so its blob hashes are checked
 		// before being spliced into a storage path.
 		if !isBlobHash(blob.Hash) {
-			return 0, 0, 0, 0, fmt.Errorf("%w: %s",
+			return 0, 0, 0, 0, nil, fmt.Errorf("%w: %s",
 				errInvalidBlobHash, shortHash(blob.Hash))
 		}
 
@@ -873,7 +863,7 @@ func (v *Vaultik) verifyManifestBlobs(
 
 		stat, err := v.Storage.Stat(v.ctx, blobPath)
 		switch {
-		case err != nil:
+		case errors.Is(err, storage.ErrNotFound):
 			if !opts.JSON && !v.UI.Quiet() {
 				v.stdoutf("  Missing: %s (%s)\n",
 					blob.Hash, ubytes(blob.CompressedSize))
@@ -881,6 +871,13 @@ func (v *Vaultik) verifyManifestBlobs(
 
 			missing++
 			missingSize += blob.CompressedSize
+		case err != nil:
+			if !opts.JSON && !v.UI.Quiet() {
+				v.stdoutf("  Could not check: %s (%v)\n", blob.Hash, err)
+			}
+
+			unchecked = append(unchecked,
+				UncheckedBlob{Hash: blob.Hash, Error: err.Error()})
 		case stat.Size != blob.CompressedSize:
 			if !opts.JSON && !v.UI.Quiet() {
 				v.stdoutf("  Wrong size: %s (store has %s, manifest lists %s)\n",
@@ -893,7 +890,7 @@ func (v *Vaultik) verifyManifestBlobs(
 		}
 	}
 
-	return verified, missing, mismatched, missingSize, nil
+	return verified, missing, mismatched, missingSize, unchecked, nil
 }
 
 // formatVerifyResult outputs the final verification results as JSON or
@@ -914,9 +911,19 @@ func (v *Vaultik) formatVerifyResult(
 		return v.outputVerifyJSON(result)
 	}
 
-	// Under --quiet a failure is still returned, and the cli layer
-	// prints it on stderr.
-	if !v.UI.Quiet() {
+	// --quiet drops the report but not the errors storage returned, which
+	// are logged on stderr. A failure is still returned either way, and
+	// the cli layer prints it on stderr.
+	if v.UI.Quiet() {
+		for _, blob := range result.Unchecked {
+			log.Warn("Could not check blob", "blob", blob.Hash, "error", blob.Error)
+		}
+
+		if result.DatabaseCheckError != "" {
+			log.Warn("Could not check the encrypted database",
+				"snapshot", result.SnapshotID, "error", result.DatabaseCheckError)
+		}
+	} else {
 		v.printVerifySummary(result, failure)
 	}
 
@@ -942,10 +949,19 @@ func (v *Vaultik) printVerifySummary(result *VerifyResult, failure string) {
 		v.stdoutf("  Wrong size:               %d blobs\n", result.Mismatched)
 	}
 
+	if len(result.Unchecked) > 0 {
+		v.stdoutf("  Could not check:          %d blobs\n", len(result.Unchecked))
+	}
+
 	if result.DatabaseMissing {
 		v.stdoutf("  Encrypted database:       missing\n")
 	}
 
+	if result.DatabaseCheckError != "" {
+		v.stdoutf("  Encrypted database:       could not be checked (%s)\n",
+			result.DatabaseCheckError)
+	}
+
 	v.stdoutf("  Status:       ")
 
 	if failure != "" {
@@ -973,10 +989,19 @@ func shallowVerifyFailure(result *VerifyResult) string {
 			fmt.Sprintf("%d blobs have the wrong size", result.Mismatched))
 	}
 
+	if len(result.Unchecked) > 0 {
+		parts = append(parts, fmt.Sprintf("%d blobs could not be checked",
+			len(result.Unchecked)))
+	}
+
 	if result.DatabaseMissing {
 		parts = append(parts, "the encrypted database is missing")
 	}
 
+	if result.DatabaseCheckError != "" {
+		parts = append(parts, "the encrypted database could not be checked")
+	}
+
 	return strings.Join(parts, "; ")
 }
 

internal/vaultik/snapshot_deleted_count_test.go

@@ -1,196 +0,0 @@
-package vaultik_test
-
-import (
-	"bytes"
-	"context"
-	"fmt"
-	"os"
-	"path/filepath"
-	"testing"
-	"time"
-
-	"github.com/spf13/afero"
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-	"sneak.berlin/go/vaultik/internal/config"
-	"sneak.berlin/go/vaultik/internal/database"
-	"sneak.berlin/go/vaultik/internal/log"
-	"sneak.berlin/go/vaultik/internal/storage"
-	"sneak.berlin/go/vaultik/internal/ui"
-	"sneak.berlin/go/vaultik/internal/vaultik"
-)
-
-// These tests cover https://git.eeqj.de/sneak/vaultik/issues/304: a
-// backup counts a file as deleted only when the previous snapshot of
-// the same name had it and it is gone, and never counts an excluded
-// file.
-
-// deletedCountEnv is a backup setup over the source directory src whose
-// user-facing output is kept in out. Each test configures its snapshots
-// with setSnapshot.
-type deletedCountEnv struct {
-	v   *vaultik.Vaultik
-	out *bytes.Buffer
-	src string
-}
-
-// newDeletedCountEnv writes files, keyed by path relative to src.
-func newDeletedCountEnv(t *testing.T, files map[string][]byte) *deletedCountEnv {
-	t.Helper()
-
-	ctx := context.Background()
-	fs := afero.NewOsFs()
-	tempDir := t.TempDir()
-	srcDir := filepath.Join(tempDir, "src")
-
-	for rel, content := range files {
-		path := filepath.Join(srcDir, rel)
-		require.NoError(t, fs.MkdirAll(filepath.Dir(path), 0o755))
-		require.NoError(t, afero.WriteFile(fs, path, content, 0o644))
-	}
-
-	cfg := faultTestConfig()
-	cfg.IndexPath = filepath.Join(tempDir, "index.sqlite")
-	cfg.Snapshots = map[string]config.SnapshotConfig{}
-
-	store, err := storage.NewFileStorer(filepath.Join(tempDir, "remote"))
-	require.NoError(t, err)
-
-	db, err := database.New(ctx, cfg.IndexPath)
-	require.NoError(t, err)
-	t.Cleanup(func() { _ = db.Close() })
-
-	repos := database.NewRepositories(db)
-	out := &bytes.Buffer{}
-	v := newBackupVaultik(ctx, cfg, store, repos, db, fs)
-	v.UI = ui.NewWithColor(out, false)
-
-	return &deletedCountEnv{v: v, out: out, src: srcDir}
-}
-
-// setSnapshot configures the snapshot name to back up the path rel
-// beneath src, with the given excludes.
-func (e *deletedCountEnv) setSnapshot(name, rel string, exclude ...string) {
-	e.v.Config.Snapshots[name] = config.SnapshotConfig{
-		Paths:   []string{filepath.Join(e.src, rel)},
-		Exclude: exclude,
-	}
-}
-
-// backUp runs a backup of the named snapshot and returns its output.
-func (e *deletedCountEnv) backUp(t *testing.T, name string) string {
-	t.Helper()
-
-	e.out.Reset()
-	require.NoError(t, e.v.CreateSnapshot(&vaultik.SnapshotCreateOptions{
-		Snapshots: []string{name},
-	}))
-
-	return e.out.String()
-}
-
-// A file this snapshot excludes is not counted as deleted: neither one
-// that another snapshot backs up, nor one that the previous snapshot of
-// this name had before the exclude was added.
-func TestBackupDoesNotCountExcludedFileAsDeleted(t *testing.T) {
-	log.Initialize(log.Config{})
-	t.Parallel()
-
-	env := newDeletedCountEnv(t, map[string][]byte{
-		"top.txt":       []byte("top"),
-		"cache/tmp.bin": []byte("cache"),
-		"photos/a.jpg":  []byte("photo a"),
-		"photos/b.jpg":  []byte("photo b"),
-		"photos/c.jpg":  []byte("photo c"),
-	})
-	env.setSnapshot("photos", "photos")
-	env.setSnapshot("home", "", "/photos")
-
-	env.backUp(t, "photos")
-	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
-
-	env.setSnapshot("home", "", "/photos", "/cache")
-	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
-}
-
-// A file inside a directory that an exclude added after a backup
-// matches is not counted as deleted, though the pattern matches only the
-// directory.
-func TestBackupDoesNotCountFileInExcludedDirectoryAsDeleted(t *testing.T) {
-	log.Initialize(log.Config{})
-	t.Parallel()
-
-	env := newDeletedCountEnv(t, map[string][]byte{
-		"top.txt":                 []byte("top"),
-		"app/node_modules/dep.js": []byte("dep"),
-	})
-	env.setSnapshot("home", "")
-
-	assert.Contains(t, env.backUp(t, "home"), filesLine(2, 2, 0))
-
-	env.setSnapshot("home", "", "**/node_modules")
-	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
-}
-
-// A backup counts only files that the previous snapshot of its own name
-// had, not one that a later snapshot of another name over the same path
-// had and that is since removed.
-func TestBackupIgnoresSnapshotOfAnotherName(t *testing.T) {
-	log.Initialize(log.Config{})
-	t.Parallel()
-
-	env := newDeletedCountEnv(t, map[string][]byte{
-		"kept.txt": []byte("kept"),
-	})
-	env.setSnapshot("home", "")
-	env.setSnapshot("other", "")
-
-	env.backUp(t, "home")
-
-	// Snapshot start times are kept in whole seconds: wait so that other's
-	// snapshot is strictly the most recent.
-	time.Sleep(time.Second)
-
-	extra := filepath.Join(env.src, "extra.txt")
-	require.NoError(t, os.WriteFile(extra, []byte("extra"), 0o600))
-	env.backUp(t, "other")
-	require.NoError(t, os.Remove(extra))
-
-	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
-}
-
-// A file removed from disk is counted as deleted by the next backup of
-// the snapshot that had it, and not by any later backup of that
-// snapshot, nor by the first backup of another name over the same path.
-func TestBackupCountsDeletedFileOnce(t *testing.T) {
-	log.Initialize(log.Config{})
-	t.Parallel()
-
-	aContent := bytes.Repeat([]byte("a"), 1000)
-	bContent := bytes.Repeat([]byte("b"), 2000)
-	keptContent := bytes.Repeat([]byte("k"), 500)
-
-	env := newDeletedCountEnv(t, map[string][]byte{
-		"a.txt":    aContent,
-		"b.txt":    bContent,
-		"kept.txt": keptContent,
-	})
-	env.setSnapshot("home", "")
-	env.setSnapshot("other", "")
-
-	assert.Contains(t, env.backUp(t, "home"), filesLine(3, 3, 0))
-
-	require.NoError(t, os.Remove(filepath.Join(env.src, "a.txt")))
-	require.NoError(t, os.Remove(filepath.Join(env.src, "b.txt")))
-
-	summary := env.backUp(t, "home")
-	assert.Contains(t, summary,
-		"Files: 1 examined, 0 backed up, 1 unchanged, 2 deleted.")
-	assert.Contains(t, summary,
-		fmt.Sprintf("Data: %s total (%s backed up), %s deleted.",
-			env.v.UI.Size(int64(len(keptContent))), env.v.UI.Size(0),
-			env.v.UI.Size(int64(len(aContent)+len(bContent)))))
-
-	assert.Contains(t, env.backUp(t, "home"), filesLine(1, 0, 1))
-	assert.Contains(t, env.backUp(t, "other"), filesLine(1, 0, 1))
-}

internal/vaultik/verify.go

@@ -57,11 +57,25 @@ type VerifyResult struct {
 	Missing     int    `json:"missing"`
 	MissingSize int64  `json:"missing_size,omitempty"`
 	Mismatched  int    `json:"mismatched,omitempty"`
+	// Unchecked lists the blobs shallow verify could not check, because
+	// storage answered with an error other than not-found, so whether
+	// they are present is unknown.
+	Unchecked []UncheckedBlob `json:"unchecked,omitempty"`
 	// DatabaseMissing is set by shallow verify when the snapshot's
 	// encrypted database (metadata/<key>/db.zst.age) is absent, which
 	// makes the snapshot unrestorable regardless of the blobs.
-	DatabaseMissing bool   `json:"database_missing,omitempty"`
-	ErrorMessage    string `json:"error,omitempty"`
+	DatabaseMissing bool `json:"database_missing,omitempty"`
+	// DatabaseCheckError is set by shallow verify to the error storage
+	// returned when the encrypted database could not be checked.
+	DatabaseCheckError string `json:"database_check_error,omitempty"`
+	ErrorMessage       string `json:"error,omitempty"`
+}
+
+// UncheckedBlob is a blob shallow verify could not check, with the error
+// storage returned for it.
+type UncheckedBlob struct {
+	Hash  string `json:"hash"`
+	Error string `json:"error"`
 }
 
 // deepVerifyFailure records a failure in the result and returns it appropriately