database: Move db logic to dbutil

Move all transaction related logic to dbutil to simplify and later unify
the db interface.

api/v3/rpc.go

@@ -15,8 +15,6 @@
 package v3
 
 import (
-	"fmt"
-
 	"golang.org/x/net/context"
 	"google.golang.org/grpc/codes"
 	"google.golang.org/grpc/status"
@@ -25,7 +23,6 @@ import (
 	pb "github.com/coreos/clair/api/v3/clairpb"
 	"github.com/coreos/clair/database"
 	"github.com/coreos/clair/ext/imagefmt"
-	"github.com/coreos/clair/pkg/commonerr"
 	"github.com/coreos/clair/pkg/pagination"
 )
 
@@ -128,20 +125,13 @@ func (s *AncestryServer) GetAncestry(ctx context.Context, req *pb.GetAncestryReq
 		return nil, status.Errorf(codes.InvalidArgument, "ancestry name should not be empty")
 	}
 
-	tx, err := s.Store.Begin()
+	ancestry, ok, err := database.FindAncestryAndRollback(s.Store, name)
 	if err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
+		return nil, newRPCErrorWithClairError(codes.Internal, err)
-	}
-
-	defer tx.Rollback()
-
-	ancestry, ok, err := tx.FindAncestry(name)
-	if err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
 	}
 
 	if !ok {
-		return nil, status.Error(codes.NotFound, fmt.Sprintf("requested ancestry '%s' is not found", req.GetAncestryName()))
+		return nil, status.Errorf(codes.NotFound, "requested ancestry '%s' is not found", req.GetAncestryName())
 	}
 
 	pbAncestry := &pb.GetAncestryResponse_Ancestry{
@@ -150,7 +140,7 @@ func (s *AncestryServer) GetAncestry(ctx context.Context, req *pb.GetAncestryReq
 	}
 
 	for _, layer := range ancestry.Layers {
-		pbLayer, err := GetPbAncestryLayer(tx, layer)
+		pbLayer, err := s.GetPbAncestryLayer(layer)
 		if err != nil {
 			return nil, err
 		}
@@ -180,13 +170,8 @@ func (s *NotificationServer) GetNotification(ctx context.Context, req *pb.GetNot
 		return nil, status.Error(codes.InvalidArgument, "notification page limit should not be empty or less than 1")
 	}
 
-	tx, err := s.Store.Begin()
+	dbNotification, ok, err := database.FindVulnerabilityNotificationAndRollback(
-	if err != nil {
+		s.Store,
-		return nil, status.Error(codes.Internal, err.Error())
-	}
-	defer tx.Rollback()
-
-	dbNotification, ok, err := tx.FindVulnerabilityNotification(
 		req.GetName(),
 		int(req.GetLimit()),
 		pagination.Token(req.GetOldVulnerabilityPage()),
@@ -194,11 +179,11 @@ func (s *NotificationServer) GetNotification(ctx context.Context, req *pb.GetNot
 	)
 
 	if err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
+		return nil, newRPCErrorWithClairError(codes.Internal, err)
 	}
 
 	if !ok {
-		return nil, status.Error(codes.NotFound, fmt.Sprintf("requested notification '%s' is not found", req.GetName()))
+		return nil, status.Errorf(codes.NotFound, "requested notification '%s' is not found", req.GetName())
 	}
 
 	notification, err := pb.NotificationFromDatabaseModel(dbNotification)
@@ -216,21 +201,13 @@ func (s *NotificationServer) MarkNotificationAsRead(ctx context.Context, req *pb
 		return nil, status.Error(codes.InvalidArgument, "notification name should not be empty")
 	}
 
-	tx, err := s.Store.Begin()
+	found, err := database.MarkNotificationAsReadAndCommit(s.Store, req.GetName())
 	if err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
+		return nil, newRPCErrorWithClairError(codes.Internal, err)
 	}
 
-	defer tx.Rollback()
+	if !found {
-	err = tx.DeleteNotification(req.GetName())
+		return nil, status.Errorf(codes.NotFound, "requested notification '%s' is not found", req.GetName())
-	if err == commonerr.ErrNotFound {
-		return nil, status.Error(codes.NotFound, "requested notification \""+req.GetName()+"\" is not found")
-	} else if err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
-	}
-
-	if err := tx.Commit(); err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
 	}
 
 	return &pb.MarkNotificationAsReadResponse{}, nil

api/v3/util.go

@@ -33,7 +33,7 @@ func GetClairStatus(store database.Datastore) (*pb.ClairStatus, error) {
 
 // GetPbAncestryLayer retrieves an ancestry layer with vulnerabilities and
 // features in an ancestry based on the provided database layer.
-func GetPbAncestryLayer(tx database.Session, layer database.AncestryLayer) (*pb.GetAncestryResponse_AncestryLayer, error) {
+func (s *AncestryServer) GetPbAncestryLayer(layer database.AncestryLayer) (*pb.GetAncestryResponse_AncestryLayer, error) {
 	pbLayer := &pb.GetAncestryResponse_AncestryLayer{
 		Layer: &pb.Layer{
 			Hash: layer.Hash,
@@ -41,18 +41,14 @@ func GetPbAncestryLayer(tx database.Session, layer database.AncestryLayer) (*pb.
 	}
 
 	features := layer.GetFeatures()
-	affectedFeatures, err := tx.FindAffectedNamespacedFeatures(features)
+	affectedFeatures, err := database.FindAffectedNamespacedFeaturesAndRollback(s.Store, features)
 	if err != nil {
-		return nil, status.Error(codes.Internal, err.Error())
+		return nil, newRPCErrorWithClairError(codes.Internal, err)
 	}
 
-	// NOTE(sidac): It's quite inefficient, but the easiest way to implement
-	// this feature for now, we should refactor the implementation if there's
-	// any performance issue. It's expected that the number of features is less
-	// than 1000.
 	for _, feature := range affectedFeatures {
 		if !feature.Valid {
-			return nil, status.Error(codes.Internal, "ancestry feature is not found")
+			panic("feature is missing in the database, it indicates the database is corrupted.")
 		}
 
 		for _, detectedFeature := range layer.Features {

database/dbutil.go

@@ -20,6 +20,8 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"github.com/coreos/clair/pkg/commonerr"
+	"github.com/coreos/clair/pkg/pagination"
 	"github.com/deckarep/golang-set"
 )
 
@@ -400,3 +402,125 @@ func PersistDetectorsAndCommit(store Datastore, detectors []Detector) error {
 
 	return nil
 }
+
+// MarkNotificationAsReadAndCommit marks a notification as read.
+func MarkNotificationAsReadAndCommit(store Datastore, name string) (bool, error) {
+	tx, err := store.Begin()
+	if err != nil {
+		return false, err
+	}
+
+	defer tx.Rollback()
+	err = tx.DeleteNotification(name)
+	if err == commonerr.ErrNotFound {
+		return false, nil
+	} else if err != nil {
+		return false, err
+	}
+
+	if err := tx.Commit(); err != nil {
+		return false, err
+	}
+
+	return true, nil
+}
+
+// FindAffectedNamespacedFeaturesAndRollback finds the vulnerabilities on each
+// feature.
+func FindAffectedNamespacedFeaturesAndRollback(store Datastore, features []NamespacedFeature) ([]NullableAffectedNamespacedFeature, error) {
+	tx, err := store.Begin()
+	if err != nil {
+		return nil, err
+	}
+
+	defer tx.Rollback()
+	nullableFeatures, err := tx.FindAffectedNamespacedFeatures(features)
+	if err != nil {
+		return nil, err
+	}
+
+	return nullableFeatures, nil
+}
+
+// FindVulnerabilityNotificationAndRollback finds the vulnerability notification
+// and rollback.
+func FindVulnerabilityNotificationAndRollback(store Datastore, name string, limit int, oldVulnerabilityPage pagination.Token, newVulnerabilityPage pagination.Token) (VulnerabilityNotificationWithVulnerable, bool, error) {
+	tx, err := store.Begin()
+	if err != nil {
+		return VulnerabilityNotificationWithVulnerable{}, false, err
+	}
+
+	defer tx.Rollback()
+	return tx.FindVulnerabilityNotification(name, limit, oldVulnerabilityPage, newVulnerabilityPage)
+}
+
+// FindNewNotification finds notifications either never notified or notified
+// before the given time.
+func FindNewNotification(store Datastore, notifiedBefore time.Time) (NotificationHook, bool, error) {
+	tx, err := store.Begin()
+	if err != nil {
+		return NotificationHook{}, false, err
+	}
+
+	defer tx.Rollback()
+	return tx.FindNewNotification(notifiedBefore)
+}
+
+// UpdateKeyValueAndCommit stores the key value to storage.
+func UpdateKeyValueAndCommit(store Datastore, key, value string) error {
+	tx, err := store.Begin()
+	if err != nil {
+		return err
+	}
+
+	defer tx.Rollback()
+	if err = tx.UpdateKeyValue(key, value); err != nil {
+		return err
+	}
+
+	return tx.Commit()
+}
+
+// InsertVulnerabilityNotificationsAndCommit inserts the notifications into db
+// and commit.
+func InsertVulnerabilityNotificationsAndCommit(store Datastore, notifications []VulnerabilityNotification) error {
+	tx, err := store.Begin()
+	if err != nil {
+		return err
+	}
+	defer tx.Rollback()
+
+	if err := tx.InsertVulnerabilityNotifications(notifications); err != nil {
+		return err
+	}
+
+	return tx.Commit()
+}
+
+// FindVulnerabilitiesAndRollback finds the vulnerabilities based on given ids.
+func FindVulnerabilitiesAndRollback(store Datastore, ids []VulnerabilityID) ([]NullableVulnerability, error) {
+	tx, err := store.Begin()
+	if err != nil {
+		return nil, err
+	}
+
+	defer tx.Rollback()
+	return tx.FindVulnerabilities(ids)
+}
+
+func UpdateVulnerabilitiesAndCommit(store Datastore, toRemove []VulnerabilityID, toAdd []VulnerabilityWithAffected) error {
+	tx, err := store.Begin()
+	if err != nil {
+		return err
+	}
+
+	if err := tx.DeleteVulnerabilities(toRemove); err != nil {
+		return err
+	}
+
+	if err := tx.InsertVulnerabilities(toAdd); err != nil {
+		return err
+	}
+
+	return tx.Commit()
+}

ext/vulnsrc/suse/suse.go

@@ -127,16 +127,10 @@ func init() {
 func (u *updater) Update(datastore database.Datastore) (resp vulnsrc.UpdateResponse, err error) {
 	log.WithField("package", u.Name).Info("Start fetching vulnerabilities")
 
-	tx, err := datastore.Begin()
-	if err != nil {
-		return resp, err
-	}
-	defer tx.Rollback()
-
 	// openSUSE and SUSE have one single xml file for all the products, there are no incremental
 	// xml files. We store into the database the value of the generation timestamp
 	// of the latest file we parsed.
-	flagValue, ok, err := tx.FindKeyValue(u.UpdaterFlag)
+	flagValue, ok, err := database.FindKeyValueAndRollback(datastore, u.UpdaterFlag)
 	if err != nil {
 		return resp, err
 	}

ext/vulnsrc/ubuntu/ubuntu.go

@@ -94,13 +94,6 @@ func (u *updater) Update(db database.Datastore) (resp vulnsrc.UpdateResponse, er
 		return resp, err
 	}
 
-	// Open a database transaction.
-	tx, err := db.Begin()
-	if err != nil {
-		return resp, err
-	}
-	defer tx.Rollback()
-
 	// Ask the database for the latest commit we successfully applied.
 	dbCommit, ok, err := database.FindKeyValueAndRollback(db, updaterFlag)
 	if err != nil {

notifier.go

@@ -93,7 +93,7 @@ func RunNotifier(config *notification.Config, datastore database.Datastore, stop
 		go func() {
 			success, interrupted := handleTask(*notification, stopper, config.Attempts)
 			if success {
-				err := markNotificationAsRead(datastore, notification.Name)
+				_, err := database.MarkNotificationAsReadAndCommit(datastore, notification.Name)
 				if err != nil {
 					log.WithError(err).Error("Failed to mark notification notified")
 				}
@@ -126,7 +126,7 @@ func RunNotifier(config *notification.Config, datastore database.Datastore, stop
 
 func findTask(datastore database.Datastore, renotifyInterval time.Duration, whoAmI string, stopper *stopper.Stopper) *database.NotificationHook {
 	for {
-		notification, ok, err := findNewNotification(datastore, renotifyInterval)
+		notification, ok, err := database.FindNewNotification(datastore, time.Now().Add(-renotifyInterval))
 		if err != nil || !ok {
 			if !ok {
 				log.WithError(err).Warning("could not get notification to send")
@@ -186,25 +186,3 @@ func handleTask(n database.NotificationHook, st *stopper.Stopper, maxAttempts in
 	log.WithField(logNotiName, n.Name).Info("successfully sent notification")
 	return true, false
 }
-
-func findNewNotification(datastore database.Datastore, renotifyInterval time.Duration) (database.NotificationHook, bool, error) {
-	tx, err := datastore.Begin()
-	if err != nil {
-		return database.NotificationHook{}, false, err
-	}
-	defer tx.Rollback()
-	return tx.FindNewNotification(time.Now().Add(-renotifyInterval))
-}
-
-func markNotificationAsRead(datastore database.Datastore, name string) error {
-	tx, err := datastore.Begin()
-	if err != nil {
-		log.WithError(err).Error("an error happens when beginning database transaction")
-	}
-	defer tx.Rollback()
-
-	if err := tx.MarkNotificationAsRead(name); err != nil {
-		return err
-	}
-	return tx.Commit()
-}

updater.go

@@ -431,13 +431,7 @@ func addMetadata(ctx context.Context, datastore database.Datastore, vulnerabilit
 // GetLastUpdateTime retrieves the latest successful time of update and whether
 // or not it's the first update.
 func GetLastUpdateTime(datastore database.Datastore) (time.Time, bool, error) {
-	tx, err := datastore.Begin()
+	lastUpdateTSS, ok, err := database.FindKeyValueAndRollback(datastore, updaterLastFlagName)
-	if err != nil {
-		return time.Time{}, false, err
-	}
-	defer tx.Rollback()
-
-	lastUpdateTSS, ok, err := tx.FindKeyValue(updaterLastFlagName)
 	if err != nil {
 		return time.Time{}, false, err
 	}
@@ -449,7 +443,7 @@ func GetLastUpdateTime(datastore database.Datastore) (time.Time, bool, error) {
 
 	lastUpdateTS, err := strconv.ParseInt(lastUpdateTSS, 10, 64)
 	if err != nil {
-		return time.Time{}, false, err
+		panic(err)
 	}
 
 	return time.Unix(lastUpdateTS, 0).UTC(), false, nil
@@ -539,40 +533,19 @@ func doVulnerabilitiesNamespacing(vulnerabilities []database.VulnerabilityWithAf
 	return response
 }
 
-// updateUpdaterFlags updates the flags specified by updaters, every transaction
-// is independent of each other.
 func updateUpdaterFlags(datastore database.Datastore, flags map[string]string) error {
 	for key, value := range flags {
-		tx, err := datastore.Begin()
+		if err := database.UpdateKeyValueAndCommit(datastore, key, value); err != nil {
-		if err != nil {
-			return err
-		}
-		defer tx.Rollback()
-
-		err = tx.UpdateKeyValue(key, value)
-		if err != nil {
-			return err
-		}
-		if err = tx.Commit(); err != nil {
 			return err
 		}
 	}
+
 	return nil
 }
 
 // setLastUpdateTime records the last successful date time in database.
 func setLastUpdateTime(datastore database.Datastore) error {
-	tx, err := datastore.Begin()
+	return database.UpdateKeyValueAndCommit(datastore, updaterLastFlagName, strconv.FormatInt(time.Now().UTC().Unix(), 10))
-	if err != nil {
-		return err
-	}
-	defer tx.Rollback()
-
-	err = tx.UpdateKeyValue(updaterLastFlagName, strconv.FormatInt(time.Now().UTC().Unix(), 10))
-	if err != nil {
-		return err
-	}
-	return tx.Commit()
 }
 
 // isVulnerabilityChange compares two vulnerabilities by their severity and
@@ -648,12 +621,6 @@ func createVulnerabilityNotifications(datastore database.Datastore, changes []vu
 		return nil
 	}
 
-	tx, err := datastore.Begin()
-	if err != nil {
-		return err
-	}
-	defer tx.Rollback()
-
 	notifications := make([]database.VulnerabilityNotification, 0, len(changes))
 	for _, change := range changes {
 		var oldVuln, newVuln *database.Vulnerability
@@ -675,11 +642,7 @@ func createVulnerabilityNotifications(datastore database.Datastore, changes []vu
 		})
 	}
 
-	if err := tx.InsertVulnerabilityNotifications(notifications); err != nil {
+	return database.InsertVulnerabilityNotificationsAndCommit(datastore, notifications)
-		return err
-	}
-
-	return tx.Commit()
 }
 
 // updateVulnerabilities upserts unique vulnerabilities into the database and
@@ -698,13 +661,7 @@ func updateVulnerabilities(ctx context.Context, datastore database.Datastore, vu
 		})
 	}
 
-	tx, err := datastore.Begin()
+	oldVulnNullable, err := database.FindVulnerabilitiesAndRollback(datastore, ids)
-	if err != nil {
-		return nil, err
-	}
-	defer tx.Rollback()
-
-	oldVulnNullable, err := tx.FindVulnerabilities(ids)
 	if err != nil {
 		return nil, err
 	}
@@ -748,21 +705,8 @@ func updateVulnerabilities(ctx context.Context, datastore database.Datastore, vu
 		}
 	}
 
-	log.WithField("count", len(toRemove)).Debug("marking vulnerabilities as outdated")
+	log.Debugf("there are %d vulnerability changes", len(changes))
-	if err := tx.DeleteVulnerabilities(toRemove); err != nil {
+	return changes, database.UpdateVulnerabilitiesAndCommit(datastore, toRemove, toAdd)
-		return nil, err
-	}
-
-	log.WithField("count", len(toAdd)).Debug("inserting new vulnerabilities")
-	if err := tx.InsertVulnerabilities(toAdd); err != nil {
-		return nil, err
-	}
-
-	if err := tx.Commit(); err != nil {
-		return nil, err
-	}
-
-	return changes, nil
 }
 
 func updaterEnabled(updaterName string) bool {