Merge pull request #619 from KeyboardNerd/sidac/rm_layer

database: Remove LayerWithContent from interface

api/v3/clairpb/convert.go

@@ -123,7 +123,7 @@ func VulnerabilityWithFixedInFromDatabaseModel(dbVuln database.VulnerabilityWith
 }
 
 // LayerFromDatabaseModel converts database layer to api layer.
-func LayerFromDatabaseModel(dbLayer database.Layer) *Layer {
+func LayerFromDatabaseModel(dbLayer database.LayerMetadata) *Layer {
 	layer := Layer{Hash: dbLayer.Hash}
 	return &layer
 }

database/database.go

@@ -120,22 +120,16 @@ type Session interface {
 	// PersistNamespaces inserts a set of namespaces if not in the database.
 	PersistNamespaces([]Namespace) error
 
-	// PersistLayer creates a layer using the blob Sum hash.
-	PersistLayer(hash string) error
-
-	// PersistLayerContent persists a layer's content in the database. The given
+	// PersistLayer persists a layer's content in the database. The given
 	// namespaces and features can be partial content of this layer.
 	//
 	// The layer, namespaces and features are expected to be already existing
 	// in the database.
-	PersistLayerContent(hash string, namespaces []Namespace, features []Feature, processedBy Processors) error
-
-	// FindLayer retrieves the metadata of a layer.
-	FindLayer(hash string) (layer Layer, found bool, err error)
+	PersistLayer(hash string, namespaces []Namespace, features []Feature, processedBy Processors) error
 
-	// FindLayerWithContent returns a layer with all detected features and
+	// FindLayer returns a layer with all detected features and
 	// namespaces.
-	FindLayerWithContent(hash string) (layer LayerWithContent, found bool, err error)
+	FindLayer(hash string) (layer Layer, found bool, err error)
 
 	// InsertVulnerabilities inserts a set of UNIQUE vulnerabilities with
 	// affected features into database, assuming that all vulnerabilities
@@ -167,9 +161,9 @@ type Session interface {
 	// always considered first page.
 	FindVulnerabilityNotification(name string, limit int, oldVulnerabilityPage pagination.Token, newVulnerabilityPage pagination.Token) (noti VulnerabilityNotificationWithVulnerable, found bool, err error)
 
-	// MarkNotificationNotified marks a Notification as notified now, assuming
+	// MarkNotificationAsRead marks a Notification as notified now, assuming
 	// the requested notification is in the database.
-	MarkNotificationNotified(name string) error
+	MarkNotificationAsRead(name string) error
 
 	// DeleteNotification removes a Notification in the database.
 	DeleteNotification(name string) error

database/mock.go

@@ -32,10 +32,8 @@ type MockSession struct {
 	FctPersistFeatures                  func([]Feature) error
 	FctPersistNamespacedFeatures        func([]NamespacedFeature) error
 	FctCacheAffectedNamespacedFeatures  func([]NamespacedFeature) error
-	FctPersistLayer                     func(hash string) error
-	FctPersistLayerContent              func(hash string, namespaces []Namespace, features []Feature, processedBy Processors) error
+	FctPersistLayer                     func(hash string, namespaces []Namespace, features []Feature, processedBy Processors) error
 	FctFindLayer                        func(name string) (Layer, bool, error)
-	FctFindLayerWithContent             func(name string) (LayerWithContent, bool, error)
 	FctInsertVulnerabilities            func([]VulnerabilityWithAffected) error
 	FctFindVulnerabilities              func([]VulnerabilityID) ([]NullableVulnerability, error)
 	FctDeleteVulnerabilities            func([]VulnerabilityID) error
@@ -43,7 +41,7 @@ type MockSession struct {
 	FctFindNewNotification              func(lastNotified time.Time) (NotificationHook, bool, error)
 	FctFindVulnerabilityNotification    func(name string, limit int, oldPage pagination.Token, newPage pagination.Token) (
 		vuln VulnerabilityNotificationWithVulnerable, ok bool, err error)
-	FctMarkNotificationNotified func(name string) error
+	FctMarkNotificationAsRead func(name string) error
 	FctDeleteNotification     func(name string) error
 	FctUpdateKeyValue         func(key, value string) error
 	FctFindKeyValue           func(key string) (string, bool, error)
@@ -115,16 +113,9 @@ func (ms *MockSession) CacheAffectedNamespacedFeatures(namespacedFeatures []Name
 	panic("required mock function not implemented")
 }
 
-func (ms *MockSession) PersistLayer(layer string) error {
+func (ms *MockSession) PersistLayer(hash string, namespaces []Namespace, features []Feature, processedBy Processors) error {
 	if ms.FctPersistLayer != nil {
-		return ms.FctPersistLayer(layer)
-	}
-	panic("required mock function not implemented")
-}
-
-func (ms *MockSession) PersistLayerContent(hash string, namespaces []Namespace, features []Feature, processedBy Processors) error {
-	if ms.FctPersistLayerContent != nil {
-		return ms.FctPersistLayerContent(hash, namespaces, features, processedBy)
+		return ms.FctPersistLayer(hash, namespaces, features, processedBy)
 	}
 	panic("required mock function not implemented")
 }
@@ -136,13 +127,6 @@ func (ms *MockSession) FindLayer(name string) (Layer, bool, error) {
 	panic("required mock function not implemented")
 }
 
-func (ms *MockSession) FindLayerWithContent(name string) (LayerWithContent, bool, error) {
-	if ms.FctFindLayerWithContent != nil {
-		return ms.FctFindLayerWithContent(name)
-	}
-	panic("required mock function not implemented")
-}
-
 func (ms *MockSession) InsertVulnerabilities(vulnerabilities []VulnerabilityWithAffected) error {
 	if ms.FctInsertVulnerabilities != nil {
 		return ms.FctInsertVulnerabilities(vulnerabilities)
@@ -186,9 +170,9 @@ func (ms *MockSession) FindVulnerabilityNotification(name string, limit int, old
 	panic("required mock function not implemented")
 }
 
-func (ms *MockSession) MarkNotificationNotified(name string) error {
-	if ms.FctMarkNotificationNotified != nil {
-		return ms.FctMarkNotificationNotified(name)
+func (ms *MockSession) MarkNotificationAsRead(name string) error {
+	if ms.FctMarkNotificationAsRead != nil {
+		return ms.FctMarkNotificationAsRead(name)
 	}
 	panic("required mock function not implemented")
 }

database/models.go

@@ -41,25 +41,25 @@ type Ancestry struct {
 
 // AncestryLayer is a layer with all detected namespaced features.
 type AncestryLayer struct {
-	Layer
+	LayerMetadata
 
 	// DetectedFeatures are the features introduced by this layer when it was
 	// processed.
 	DetectedFeatures []NamespacedFeature
 }
 
-// Layer contains the metadata of a layer.
-type Layer struct {
+// LayerMetadata contains the metadata of a layer.
+type LayerMetadata struct {
 	// Hash is content hash of the layer.
 	Hash string
 	// ProcessedBy contains the processors that processed this layer.
 	ProcessedBy Processors
 }
 
-// LayerWithContent is a layer with its detected namespaces and features by
+// Layer is a layer with its detected namespaces and features by
 // ProcessedBy.
-type LayerWithContent struct {
-	Layer
+type Layer struct {
+	LayerMetadata
 
 	Namespaces []Namespace
 	Features   []Feature

database/pgsql/ancestry.go

@@ -170,7 +170,7 @@ func (tx *pgSession) findAncestryLayers(id int64) ([]database.AncestryLayer, err
 		}
 
 		if !index.Valid || !id.Valid {
-			return nil, commonerr.ErrNotFound
+			panic("null ancestry ID or ancestry index violates database constraints")
 		}
 
 		if _, ok := layers[index.Int64]; ok {

database/pgsql/ancestry_test.go

@@ -30,7 +30,7 @@ func TestUpsertAncestry(t *testing.T) {
 		Name: "a1",
 		Layers: []database.AncestryLayer{
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-N",
 				},
 			},
@@ -43,7 +43,7 @@ func TestUpsertAncestry(t *testing.T) {
 		Name: "a",
 		Layers: []database.AncestryLayer{
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-0",
 				},
 			},
@@ -54,7 +54,7 @@ func TestUpsertAncestry(t *testing.T) {
 		Name: "a",
 		Layers: []database.AncestryLayer{
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-1",
 				},
 			},
@@ -137,7 +137,7 @@ func assertAncestryEqual(t *testing.T, expected database.Ancestry, actual databa
 }
 
 func assertAncestryLayerEqual(t *testing.T, expected database.AncestryLayer, actual database.AncestryLayer) bool {
-	return assertLayerEqual(t, expected.Layer, actual.Layer) &&
+	return assertLayerEqual(t, expected.LayerMetadata, actual.LayerMetadata) &&
 		assertNamespacedFeatureEqual(t, expected.DetectedFeatures, actual.DetectedFeatures)
 }
 
@@ -159,7 +159,7 @@ func TestFindAncestry(t *testing.T) {
 		},
 		Layers: []database.AncestryLayer{
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-0",
 				},
 				DetectedFeatures: []database.NamespacedFeature{
@@ -188,17 +188,17 @@ func TestFindAncestry(t *testing.T) {
 				},
 			},
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-1",
 				},
 			},
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-2",
 				},
 			},
 			{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: "layer-3b",
 				},
 			},

database/pgsql/layer.go

@@ -23,19 +23,14 @@ import (
 )
 
 func (tx *pgSession) FindLayer(hash string) (database.Layer, bool, error) {
-	layer, _, ok, err := tx.findLayer(hash)
-	return layer, ok, err
-}
-
-func (tx *pgSession) FindLayerWithContent(hash string) (database.LayerWithContent, bool, error) {
 	var (
-		layer   database.LayerWithContent
+		layer   database.Layer
 		layerID int64
 		ok      bool
 		err     error
 	)
 
-	layer.Layer, layerID, ok, err = tx.findLayer(hash)
+	layer.LayerMetadata, layerID, ok, err = tx.findLayer(hash)
 	if err != nil {
 		return layer, false, err
 	}
@@ -49,46 +44,53 @@ func (tx *pgSession) FindLayerWithContent(hash string) (database.LayerWithConten
 	return layer, true, nil
 }
 
-func (tx *pgSession) PersistLayer(hash string) error {
+func (tx *pgSession) persistLayer(hash string) (int64, error) {
 	if hash == "" {
-		return commonerr.NewBadRequestError("Empty Layer Hash is not allowed")
+		return -1, commonerr.NewBadRequestError("Empty Layer Hash is not allowed")
 	}
 
-	_, err := tx.Exec(queryPersistLayer(1), hash)
-	if err != nil {
-		return handleError("queryPersistLayer", err)
+	id := sql.NullInt64{}
+	if err := tx.QueryRow(soiLayer, hash).Scan(&id); err != nil {
+		return -1, handleError("queryPersistLayer", err)
 	}
 
-	return nil
+	if !id.Valid {
+		panic("null layer.id violates database constraint")
+	}
+
+	return id.Int64, nil
 }
 
-// PersistLayerContent relates layer identified by hash with namespaces,
+// PersistLayer relates layer identified by hash with namespaces,
 // features and processors provided. If the layer, namespaces, features are not
 // in database, the function returns an error.
-func (tx *pgSession) PersistLayerContent(hash string, namespaces []database.Namespace, features []database.Feature, processedBy database.Processors) error {
+func (tx *pgSession) PersistLayer(hash string, namespaces []database.Namespace, features []database.Feature, processedBy database.Processors) error {
 	if hash == "" {
 		return commonerr.NewBadRequestError("Empty layer hash is not allowed")
 	}
 
-	var layerID int64
-	err := tx.QueryRow(searchLayer, hash).Scan(&layerID)
-	if err != nil {
+	var (
+		err error
+		id  int64
+	)
+
+	if id, err = tx.persistLayer(hash); err != nil {
 		return err
 	}
 
-	if err = tx.persistLayerNamespace(layerID, namespaces); err != nil {
+	if err = tx.persistLayerNamespace(id, namespaces); err != nil {
 		return err
 	}
 
-	if err = tx.persistLayerFeatures(layerID, features); err != nil {
+	if err = tx.persistLayerFeatures(id, features); err != nil {
 		return err
 	}
 
-	if err = tx.persistLayerDetectors(layerID, processedBy.Detectors); err != nil {
+	if err = tx.persistLayerDetectors(id, processedBy.Detectors); err != nil {
 		return err
 	}
 
-	if err = tx.persistLayerListers(layerID, processedBy.Listers); err != nil {
+	if err = tx.persistLayerListers(id, processedBy.Listers); err != nil {
 		return err
 	}
 
@@ -275,10 +277,10 @@ func (tx *pgSession) findLayerFeatures(layerID int64) ([]database.Feature, error
 	return features, nil
 }
 
-func (tx *pgSession) findLayer(hash string) (database.Layer, int64, bool, error) {
+func (tx *pgSession) findLayer(hash string) (database.LayerMetadata, int64, bool, error) {
 	var (
 		layerID int64
-		layer   = database.Layer{Hash: hash, ProcessedBy: database.Processors{}}
+		layer   = database.LayerMetadata{Hash: hash, ProcessedBy: database.Processors{}}
 	)
 
 	if hash == "" {

database/pgsql/layer_test.go

@@ -26,65 +26,72 @@ func TestPersistLayer(t *testing.T) {
 	datastore, tx := openSessionForTest(t, "PersistLayer", false)
 	defer closeTest(t, datastore, tx)
 
-	l1 := ""
-	l2 := "HESOYAM"
-
 	// invalid
-	assert.NotNil(t, tx.PersistLayer(l1))
-	// valid
-	assert.Nil(t, tx.PersistLayer(l2))
-	// duplicated
-	assert.Nil(t, tx.PersistLayer(l2))
-}
+	assert.NotNil(t, tx.PersistLayer("", nil, nil, database.Processors{}))
+	// insert namespaces + features to
+	namespaces := []database.Namespace{
+		{
+			Name:          "sushi shop",
+			VersionFormat: "apk",
+		},
+	}
 
-func TestPersistLayerProcessors(t *testing.T) {
-	datastore, tx := openSessionForTest(t, "PersistLayerProcessors", true)
-	defer closeTest(t, datastore, tx)
+	features := []database.Feature{
+		{
+			Name:          "blue fin sashimi",
+			Version:       "v1.0",
+			VersionFormat: "apk",
+		},
+	}
 
-	// invalid
-	assert.NotNil(t, tx.PersistLayerContent("hash", []database.Namespace{}, []database.Feature{}, database.Processors{}))
-	// valid
-	assert.Nil(t, tx.PersistLayerContent("layer-4", []database.Namespace{}, []database.Feature{}, database.Processors{Detectors: []string{"new detector!"}}))
-}
+	processors := database.Processors{
+		Listers:   []string{"release"},
+		Detectors: []string{"apk"},
+	}
 
-func TestFindLayer(t *testing.T) {
-	datastore, tx := openSessionForTest(t, "FindLayer", true)
-	defer closeTest(t, datastore, tx)
+	assert.Nil(t, tx.PersistNamespaces(namespaces))
+	assert.Nil(t, tx.PersistFeatures(features))
 
-	expected := database.Layer{
-		Hash: "layer-4",
-		ProcessedBy: database.Processors{
-			Detectors: []string{"os-release", "apt-sources"},
-			Listers:   []string{"dpkg", "rpm"},
-		},
-	}
+	// Valid
+	assert.Nil(t, tx.PersistLayer("RANDOM_FOREST", namespaces, features, processors))
 
-	// invalid
-	_, _, err := tx.FindLayer("")
-	assert.NotNil(t, err)
-	_, ok, err := tx.FindLayer("layer-non")
+	nonExistingFeature := []database.Feature{{Name: "lobster sushi", Version: "v0.1", VersionFormat: "apk"}}
+	// Invalid:
+	assert.NotNil(t, tx.PersistLayer("RANDOM_FOREST", namespaces, nonExistingFeature, processors))
+
+	assert.Nil(t, tx.PersistFeatures(nonExistingFeature))
+	// Update the layer
+	assert.Nil(t, tx.PersistLayer("RANDOM_FOREST", namespaces, nonExistingFeature, processors))
+
+	// confirm update
+	layer, ok, err := tx.FindLayer("RANDOM_FOREST")
 	assert.Nil(t, err)
-	assert.False(t, ok)
+	assert.True(t, ok)
 
-	// valid
-	layer, ok2, err := tx.FindLayer("layer-4")
-	if assert.Nil(t, err) && assert.True(t, ok2) {
-		assertLayerEqual(t, expected, layer)
+	expectedLayer := database.Layer{
+		LayerMetadata: database.LayerMetadata{
+			Hash:        "RANDOM_FOREST",
+			ProcessedBy: processors,
+		},
+		Features:   append(features, nonExistingFeature...),
+		Namespaces: namespaces,
 	}
+
+	assertLayerWithContentEqual(t, expectedLayer, layer)
 }
 
-func TestFindLayerWithContent(t *testing.T) {
-	datastore, tx := openSessionForTest(t, "FindLayerWithContent", true)
+func TestFindLayer(t *testing.T) {
+	datastore, tx := openSessionForTest(t, "FindLayer", true)
 	defer closeTest(t, datastore, tx)
 
-	_, _, err := tx.FindLayerWithContent("")
+	_, _, err := tx.FindLayer("")
 	assert.NotNil(t, err)
-	_, ok, err := tx.FindLayerWithContent("layer-non")
+	_, ok, err := tx.FindLayer("layer-non")
 	assert.Nil(t, err)
 	assert.False(t, ok)
 
-	expectedL := database.LayerWithContent{
-		Layer: database.Layer{
+	expectedL := database.Layer{
+		LayerMetadata: database.LayerMetadata{
 			Hash: "layer-4",
 			ProcessedBy: database.Processors{
 				Detectors: []string{"os-release", "apt-sources"},
@@ -101,19 +108,19 @@ func TestFindLayerWithContent(t *testing.T) {
 		},
 	}
 
-	layer, ok2, err := tx.FindLayerWithContent("layer-4")
+	layer, ok2, err := tx.FindLayer("layer-4")
 	if assert.Nil(t, err) && assert.True(t, ok2) {
 		assertLayerWithContentEqual(t, expectedL, layer)
 	}
 }
 
-func assertLayerWithContentEqual(t *testing.T, expected database.LayerWithContent, actual database.LayerWithContent) bool {
-	return assertLayerEqual(t, expected.Layer, actual.Layer) &&
+func assertLayerWithContentEqual(t *testing.T, expected database.Layer, actual database.Layer) bool {
+	return assertLayerEqual(t, expected.LayerMetadata, actual.LayerMetadata) &&
 		assertFeaturesEqual(t, expected.Features, actual.Features) &&
 		assertNamespacesEqual(t, expected.Namespaces, actual.Namespaces)
 }
 
-func assertLayerEqual(t *testing.T, expected database.Layer, actual database.Layer) bool {
+func assertLayerEqual(t *testing.T, expected database.LayerMetadata, actual database.LayerMetadata) bool {
 	return assertProcessorsEqual(t, expected.ProcessedBy, actual.ProcessedBy) &&
 		assert.Equal(t, expected.Hash, actual.Hash)
 }

database/pgsql/notification.go

@@ -289,23 +289,23 @@ func (tx *pgSession) FindVulnerabilityNotification(name string, limit int, oldPa
 	return noti, true, nil
 }
 
-func (tx *pgSession) MarkNotificationNotified(name string) error {
+func (tx *pgSession) MarkNotificationAsRead(name string) error {
 	if name == "" {
 		return commonerr.NewBadRequestError("Empty notification name is not allowed")
 	}
 
-	r, err := tx.Exec(updatedNotificationNotified, name)
+	r, err := tx.Exec(updatedNotificationAsRead, name)
 	if err != nil {
-		return handleError("updatedNotificationNotified", err)
+		return handleError("updatedNotificationAsRead", err)
 	}
 
 	affected, err := r.RowsAffected()
 	if err != nil {
-		return handleError("updatedNotificationNotified", err)
+		return handleError("updatedNotificationAsRead", err)
 	}
 
 	if affected <= 0 {
-		return handleError("updatedNotificationNotified", errNotificationNotFound)
+		return handleError("updatedNotificationAsRead", errNotificationNotFound)
 	}
 	return nil
 }

database/pgsql/notification_test.go

@@ -200,7 +200,7 @@ func TestFindNewNotification(t *testing.T) {
 	}
 
 	// can't find the notified
-	assert.Nil(t, tx.MarkNotificationNotified("test"))
+	assert.Nil(t, tx.MarkNotificationAsRead("test"))
 	// if the notified time is before
 	noti, ok, err = tx.FindNewNotification(time.Now().Add(-time.Duration(10 * time.Second)))
 	assert.Nil(t, err)
@@ -225,16 +225,16 @@ func TestFindNewNotification(t *testing.T) {
 	assert.False(t, ok)
 }
 
-func TestMarkNotificationNotified(t *testing.T) {
-	datastore, tx := openSessionForTest(t, "MarkNotificationNotified", true)
+func TestMarkNotificationAsRead(t *testing.T) {
+	datastore, tx := openSessionForTest(t, "MarkNotificationAsRead", true)
 	defer closeTest(t, datastore, tx)
 
 	// invalid case: notification doesn't exist
-	assert.NotNil(t, tx.MarkNotificationNotified("non-existing"))
+	assert.NotNil(t, tx.MarkNotificationAsRead("non-existing"))
 	// valid case
-	assert.Nil(t, tx.MarkNotificationNotified("test"))
+	assert.Nil(t, tx.MarkNotificationAsRead("test"))
 	// valid case
-	assert.Nil(t, tx.MarkNotificationNotified("test"))
+	assert.Nil(t, tx.MarkNotificationAsRead("test"))
 }
 
 func TestDeleteNotification(t *testing.T) {

database/pgsql/queries.go

@@ -73,7 +73,16 @@ const (
 			AND v.deleted_at IS NULL`
 
 	// layer.go
-	searchLayerIDs = `SELECT id, hash FROM layer WHERE hash = ANY($1);`
+	soiLayer = `
+		WITH new_layer AS (
+			INSERT INTO layer (hash)
+			SELECT CAST ($1 AS VARCHAR)
+			WHERE NOT EXISTS (SELECT id FROM layer WHERE hash = $1)
+			RETURNING id
+		)
+		SELECT id FROM new_Layer
+		UNION
+		SELECT id FROM layer WHERE hash = $1`
 
 	searchLayerFeatures = `
 		SELECT feature.Name, feature.Version, feature.version_format 
@@ -168,7 +177,7 @@ const (
 		INSERT INTO Vulnerability_Notification(name, created_at, old_vulnerability_id, new_vulnerability_id)
 		VALUES ($1, $2, $3, $4)`
 
-	updatedNotificationNotified = `
+	updatedNotificationAsRead = `
 		UPDATE Vulnerability_Notification
 		SET notified_at = CURRENT_TIMESTAMP
 		WHERE name = $1`

database/pgsql/vulnerability.go

@@ -16,7 +16,6 @@ package pgsql
 
 import (
 	"database/sql"
-	"encoding/json"
 	"errors"
 	"time"
 
@@ -220,17 +219,6 @@ func (tx *pgSession) insertVulnerabilities(vulnerabilities []database.Vulnerabil
 	return vulnIDs, nil
 }
 
-// castMetadata marshals the given database.MetadataMap and unmarshals it again to make sure that
-// everything has the interface{} type.
-// It is required when comparing crafted MetadataMap against MetadataMap that we get from the
-// database.
-func castMetadata(m database.MetadataMap) database.MetadataMap {
-	c := make(database.MetadataMap)
-	j, _ := json.Marshal(m)
-	json.Unmarshal(j, &c)
-	return c
-}
-
 func (tx *pgSession) lockFeatureVulnerabilityCache() error {
 	_, err := tx.Exec(lockVulnerabilityAffects)
 	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 := markNotificationNotified(datastore, notification.Name)
+				err := markNotificationAsRead(datastore, notification.Name)
 				if err != nil {
 					log.WithError(err).Error("Failed to mark notification notified")
 				}
@@ -196,14 +196,14 @@ func findNewNotification(datastore database.Datastore, renotifyInterval time.Dur
 	return tx.FindNewNotification(time.Now().Add(-renotifyInterval))
 }
 
-func markNotificationNotified(datastore database.Datastore, name string) error {
+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.MarkNotificationNotified(name); err != nil {
+	if err := tx.MarkNotificationAsRead(name); err != nil {
 		return err
 	}
 	return tx.Commit()

worker.go

@@ -1,4 +1,4 @@
-// Copyright 2017 clair authors
+// Copyright 2018 clair authors
 //
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
@@ -146,32 +146,29 @@ func processRequests(imageFormat string, toDetect []processRequest) ([]database.
 	return namespaces, features, updates, nil
 }
 
-func getLayer(datastore database.Datastore, req LayerRequest) (layer database.LayerWithContent, preq *processRequest, err error) {
-	var ok bool
-	tx, err := datastore.Begin()
-	if err != nil {
+func getLayer(datastore database.Datastore, req LayerRequest) (layer database.Layer, preq *processRequest, err error) {
+	var (
+		tx database.Session
+		ok bool
+	)
+
+	if tx, err = datastore.Begin(); err != nil {
 		return
 	}
+
 	defer tx.Rollback()
 
-	layer, ok, err = tx.FindLayerWithContent(req.Hash)
-	if err != nil {
+	if layer, ok, err = tx.FindLayer(req.Hash); err != nil {
 		return
 	}
 
 	if !ok {
-		err = tx.PersistLayer(req.Hash)
-		if err != nil {
-			return
-		}
-
-		if err = tx.Commit(); err != nil {
-			return
+		layer = database.Layer{
+			LayerMetadata: database.LayerMetadata{
+				Hash: req.Hash,
+			},
 		}
 
-		layer = database.LayerWithContent{}
-		layer.Hash = req.Hash
-
 		preq = &processRequest{
 			request:        req,
 			notProcessedBy: Processors,
@@ -185,15 +182,16 @@ func getLayer(datastore database.Datastore, req LayerRequest) (layer database.La
 			}
 		}
 	}
+
 	return
 }
 
 // processLayers processes a set of post layer requests, stores layers and
 // returns an ordered list of processed layers with detected features and
 // namespaces.
-func processLayers(datastore database.Datastore, imageFormat string, requests []LayerRequest) ([]database.LayerWithContent, error) {
+func processLayers(datastore database.Datastore, imageFormat string, requests []LayerRequest) ([]database.Layer, error) {
 	toDetect := []processRequest{}
-	layers := map[string]database.LayerWithContent{}
+	layers := map[string]database.Layer{}
 	for _, req := range requests {
 		if _, ok := layers[req.Hash]; ok {
 			continue
@@ -208,7 +206,7 @@ func processLayers(datastore database.Datastore, imageFormat string, requests []
 		}
 	}
 
-	namespaces, features, partialRes, err := processRequests(imageFormat, toDetect)
+	namespaces, features, partialLayers, err := processRequests(imageFormat, toDetect)
 	if err != nil {
 		return nil, err
 	}
@@ -222,10 +220,18 @@ func processLayers(datastore database.Datastore, imageFormat string, requests []
 		return nil, err
 	}
 
-	for _, res := range partialRes {
-		if err := persistPartialLayer(datastore, res); err != nil {
+	for _, layer := range partialLayers {
+		if err := persistPartialLayer(datastore, layer); err != nil {
 			return nil, err
 		}
+
+		log.WithFields(log.Fields{
+			"Hash":                layer.hash,
+			"namespace count":     len(layer.namespaces),
+			"feature count":       len(layer.features),
+			"namespace detectors": layer.processedBy.Detectors,
+			"feature listers":     layer.processedBy.Listers,
+		}).Debug("saved layer")
 	}
 
 	// NOTE(Sida): The full layers are computed using partially
@@ -233,9 +239,9 @@ func processLayers(datastore database.Datastore, imageFormat string, requests []
 	// Clair are changing some layers in this set of layers, it might generate
 	// different results especially when the other Clair is with different
 	// processors.
-	completeLayers := []database.LayerWithContent{}
+	completeLayers := []database.Layer{}
 	for _, req := range requests {
-		if partialLayer, ok := partialRes[req.Hash]; ok {
+		if partialLayer, ok := partialLayers[req.Hash]; ok {
 			completeLayers = append(completeLayers, combineLayers(layers[req.Hash], partialLayer))
 		} else {
 			completeLayers = append(completeLayers, layers[req.Hash])
@@ -252,9 +258,10 @@ func persistPartialLayer(datastore database.Datastore, layer partialLayer) error
 	}
 	defer tx.Rollback()
 
-	if err := tx.PersistLayerContent(layer.hash, layer.namespaces, layer.features, layer.processedBy); err != nil {
+	if err := tx.PersistLayer(layer.hash, layer.namespaces, layer.features, layer.processedBy); err != nil {
 		return err
 	}
+
 	return tx.Commit()
 }
 
@@ -286,7 +293,7 @@ func persistNamespaces(datastore database.Datastore, namespaces []database.Names
 }
 
 // combineLayers merges `layer` and `partial` without duplicated content.
-func combineLayers(layer database.LayerWithContent, partial partialLayer) database.LayerWithContent {
+func combineLayers(layer database.Layer, partial partialLayer) database.Layer {
 	mapF := map[database.Feature]struct{}{}
 	mapNS := map[database.Namespace]struct{}{}
 	for _, f := range layer.Features {
@@ -312,8 +319,8 @@ func combineLayers(layer database.LayerWithContent, partial partialLayer) databa
 
 	layer.ProcessedBy.Detectors = append(layer.ProcessedBy.Detectors, strutil.CompareStringLists(partial.processedBy.Detectors, layer.ProcessedBy.Detectors)...)
 	layer.ProcessedBy.Listers = append(layer.ProcessedBy.Listers, strutil.CompareStringLists(partial.processedBy.Listers, layer.ProcessedBy.Listers)...)
-	return database.LayerWithContent{
-		Layer: database.Layer{
+	return database.Layer{
+		LayerMetadata: database.LayerMetadata{
 			Hash:        layer.Hash,
 			ProcessedBy: layer.ProcessedBy,
 		},
@@ -346,7 +353,7 @@ func ProcessAncestry(datastore database.Datastore, imageFormat, name string, lay
 	var (
 		err              error
 		ok               bool
-		layers           []database.LayerWithContent
+		layers           []database.Layer
 		commonProcessors database.Processors
 	)
 
@@ -361,7 +368,7 @@ func ProcessAncestry(datastore database.Datastore, imageFormat, name string, lay
 	if ok, err = isAncestryProcessed(datastore, name); err != nil {
 		return err
 	} else if ok {
-		log.WithField("ancestry", name).Debug("Ancestry is processed")
+		log.WithField("name", name).Debug("ancestry is already processed")
 		return nil
 	}
 
@@ -386,7 +393,7 @@ func getNamespacedFeatures(layers []database.AncestryLayer) []database.Namespace
 	return features
 }
 
-func processAncestry(datastore database.Datastore, name string, layers []database.LayerWithContent, commonProcessors database.Processors) error {
+func processAncestry(datastore database.Datastore, name string, layers []database.Layer, commonProcessors database.Processors) error {
 	var (
 		ancestry database.Ancestry
 		err      error
@@ -458,7 +465,7 @@ func persistNamespacedFeatures(datastore database.Datastore, features []database
 }
 
 // getProcessors retrieves common subset of the processors of each layer.
-func getProcessors(layers []database.LayerWithContent) (database.Processors, error) {
+func getProcessors(layers []database.Layer) (database.Processors, error) {
 	if len(layers) == 0 {
 		return database.Processors{}, nil
 	}
@@ -495,7 +502,7 @@ type introducedFeature struct {
 
 // computeAncestryLayers computes ancestry's layers along with what features are
 // introduced.
-func computeAncestryLayers(layers []database.LayerWithContent, commonProcessors database.Processors) ([]database.AncestryLayer, error) {
+func computeAncestryLayers(layers []database.Layer, commonProcessors database.Processors) ([]database.AncestryLayer, error) {
 	// TODO(sidchen): Once the features are linked to specific processor, we
 	// will use commonProcessors to filter out the features for this ancestry.
 
@@ -506,7 +513,7 @@ func computeAncestryLayers(layers []database.LayerWithContent, commonProcessors
 	ancestryLayers := []database.AncestryLayer{}
 	for index, layer := range layers {
 		// Initialize the ancestry Layer
-		initializedLayer := database.AncestryLayer{Layer: layer.Layer, DetectedFeatures: []database.NamespacedFeature{}}
+		initializedLayer := database.AncestryLayer{LayerMetadata: layer.LayerMetadata, DetectedFeatures: []database.NamespacedFeature{}}
 		ancestryLayers = append(ancestryLayers, initializedLayer)
 
 		// Precondition: namespaces and features contain the result from union

worker_test.go

@@ -40,7 +40,7 @@ import (
 type mockDatastore struct {
 	database.MockDatastore
 
-	layers             map[string]database.LayerWithContent
+	layers             map[string]database.Layer
 	ancestry           map[string]database.Ancestry
 	namespaces         map[string]database.Namespace
 	features           map[string]database.Feature
@@ -56,14 +56,14 @@ type mockSession struct {
 }
 
 func copyDatastore(md *mockDatastore) mockDatastore {
-	layers := map[string]database.LayerWithContent{}
+	layers := map[string]database.Layer{}
 	for k, l := range md.layers {
 		features := append([]database.Feature(nil), l.Features...)
 		namespaces := append([]database.Namespace(nil), l.Namespaces...)
 		listers := append([]string(nil), l.ProcessedBy.Listers...)
 		detectors := append([]string(nil), l.ProcessedBy.Detectors...)
-		layers[k] = database.LayerWithContent{
-			Layer: database.Layer{
+		layers[k] = database.Layer{
+			LayerMetadata: database.LayerMetadata{
 				Hash: l.Hash,
 				ProcessedBy: database.Processors{
 					Listers:   listers,
@@ -78,23 +78,23 @@ func copyDatastore(md *mockDatastore) mockDatastore {
 	ancestry := map[string]database.Ancestry{}
 	for k, a := range md.ancestry {
 		ancestryLayers := []database.AncestryLayer{}
-		layers := []database.Layer{}
+		layers := []database.LayerMetadata{}
 
 		for _, layer := range a.Layers {
-			layers = append(layers, database.Layer{
+			layers = append(layers, database.LayerMetadata{
 				Hash: layer.Hash,
 				ProcessedBy: database.Processors{
-					Detectors: append([]string(nil), layer.Layer.ProcessedBy.Detectors...),
-					Listers:   append([]string(nil), layer.Layer.ProcessedBy.Listers...),
+					Detectors: append([]string(nil), layer.LayerMetadata.ProcessedBy.Detectors...),
+					Listers:   append([]string(nil), layer.LayerMetadata.ProcessedBy.Listers...),
 				},
 			})
 
 			ancestryLayers = append(ancestryLayers, database.AncestryLayer{
-				Layer: database.Layer{
+				LayerMetadata: database.LayerMetadata{
 					Hash: layer.Hash,
 					ProcessedBy: database.Processors{
-						Detectors: append([]string(nil), layer.Layer.ProcessedBy.Detectors...),
-						Listers:   append([]string(nil), layer.Layer.ProcessedBy.Listers...),
+						Detectors: append([]string(nil), layer.LayerMetadata.ProcessedBy.Detectors...),
+						Listers:   append([]string(nil), layer.LayerMetadata.ProcessedBy.Listers...),
 					},
 				},
 				DetectedFeatures: append([]database.NamespacedFeature(nil), layer.DetectedFeatures...),
@@ -137,7 +137,7 @@ func copyDatastore(md *mockDatastore) mockDatastore {
 func newMockDatastore() *mockDatastore {
 	errSessionDone := errors.New("Session Done")
 	md := &mockDatastore{
-		layers:             make(map[string]database.LayerWithContent),
+		layers:             make(map[string]database.Layer),
 		ancestry:           make(map[string]database.Ancestry),
 		namespaces:         make(map[string]database.Namespace),
 		features:           make(map[string]database.Feature),
@@ -186,27 +186,9 @@ func newMockDatastore() *mockDatastore {
 				return database.Layer{}, false, errSessionDone
 			}
 			layer, ok := session.copy.layers[name]
-			return layer.Layer, ok, nil
-		}
-
-		session.FctFindLayerWithContent = func(name string) (database.LayerWithContent, bool, error) {
-			if session.terminated {
-				return database.LayerWithContent{}, false, errSessionDone
-			}
-			layer, ok := session.copy.layers[name]
 			return layer, ok, nil
 		}
 
-		session.FctPersistLayer = func(hash string) error {
-			if session.terminated {
-				return errSessionDone
-			}
-			if _, ok := session.copy.layers[hash]; !ok {
-				session.copy.layers[hash] = database.LayerWithContent{Layer: database.Layer{Hash: hash}}
-			}
-			return nil
-		}
-
 		session.FctPersistNamespaces = func(ns []database.Namespace) error {
 			if session.terminated {
 				return errSessionDone
@@ -234,15 +216,20 @@ func newMockDatastore() *mockDatastore {
 			return nil
 		}
 
-		session.FctPersistLayerContent = func(hash string, namespaces []database.Namespace, features []database.Feature, processedBy database.Processors) error {
+		session.FctPersistLayer = func(hash string, namespaces []database.Namespace, features []database.Feature, processedBy database.Processors) error {
 			if session.terminated {
 				return errSessionDone
 			}
 
 			// update the layer
+			_, ok := session.copy.layers[hash]
+			if !ok {
+				session.copy.layers[hash] = database.Layer{}
+			}
+
 			layer, ok := session.copy.layers[hash]
 			if !ok {
-				return errors.New("layer not found")
+				return errors.New("Failed to insert layer")
 			}
 
 			layerFeatures := map[string]database.Feature{}
@@ -381,7 +368,7 @@ func TestProcessAncestryWithDistUpgrade(t *testing.T) {
 		}
 	}
 
-	assert.Equal(t, []database.Layer{
+	assert.Equal(t, []database.LayerMetadata{
 		{Hash: "blank"},
 		{Hash: "wheezy"},
 		{Hash: "jessie"},
@@ -571,32 +558,32 @@ func TestComputeAncestryFeatures(t *testing.T) {
 	// Suppose Clair is watching two files for namespaces one containing ns1
 	// changes e.g. os-release and the other one containing ns2 changes e.g.
 	// node.
-	blank := database.LayerWithContent{Layer: database.Layer{Hash: "blank"}}
-	initNS1a := database.LayerWithContent{
-		Layer:      database.Layer{Hash: "init ns1a"},
+	blank := database.Layer{LayerMetadata: database.LayerMetadata{Hash: "blank"}}
+	initNS1a := database.Layer{
+		LayerMetadata: database.LayerMetadata{Hash: "init ns1a"},
 		Namespaces:    []database.Namespace{ns1a},
 		Features:      []database.Feature{f1, f2},
 	}
 
-	upgradeNS2b := database.LayerWithContent{
-		Layer:      database.Layer{Hash: "upgrade ns2b"},
+	upgradeNS2b := database.Layer{
+		LayerMetadata: database.LayerMetadata{Hash: "upgrade ns2b"},
 		Namespaces:    []database.Namespace{ns2b},
 	}
 
-	upgradeNS1b := database.LayerWithContent{
-		Layer:      database.Layer{Hash: "upgrade ns1b"},
+	upgradeNS1b := database.Layer{
+		LayerMetadata: database.LayerMetadata{Hash: "upgrade ns1b"},
 		Namespaces:    []database.Namespace{ns1b},
 		Features:      []database.Feature{f1, f2},
 	}
 
-	initNS2a := database.LayerWithContent{
-		Layer:      database.Layer{Hash: "init ns2a"},
+	initNS2a := database.Layer{
+		LayerMetadata: database.LayerMetadata{Hash: "init ns2a"},
 		Namespaces:    []database.Namespace{ns2a},
 		Features:      []database.Feature{f3, f4},
 	}
 
-	removeF2 := database.LayerWithContent{
-		Layer:    database.Layer{Hash: "remove f2"},
+	removeF2 := database.Layer{
+		LayerMetadata: database.LayerMetadata{Hash: "remove f2"},
 		Features:      []database.Feature{f1},
 	}
 
@@ -609,7 +596,7 @@ func TestComputeAncestryFeatures(t *testing.T) {
 	// -> f1 (remove f2)
 	// -> blank (empty)
 
-	layers := []database.LayerWithContent{
+	layers := []database.Layer{
 		blank,
 		initNS1a,
 		removeF2,