Move SQLite datastore to its own package/folder

This layout is closer to the PostrgeSQL datastore layout in claircore
and easier to navigate.

Author: evgenyz

cmd/cvetool/scan.go

@@ -24,8 +24,10 @@ import (
 	"github.com/urfave/cli/v2"
 
 	datastore "github.com/ComplianceAsCode/cvetool/datastore"
+	ds_sqlite "github.com/ComplianceAsCode/cvetool/datastore/sqlite"
 	image "github.com/ComplianceAsCode/cvetool/image"
 	output "github.com/ComplianceAsCode/cvetool/output"
+	"github.com/ComplianceAsCode/cvetool/util"
 )
 
 type EnumValue struct {
@@ -159,7 +161,7 @@ func scan(c *cli.Context) error {
 	case dbPath != "":
 	case dbURL != "":
 		var err error
-		err = datastore.DownloadDB(ctx, dbURL, "")
+		err = util.DownloadDB(ctx, dbURL, "")
 		if err != nil {
 			return fmt.Errorf("could not download database: %v", err)
 		}
@@ -175,7 +177,7 @@ func scan(c *cli.Context) error {
 		return fmt.Errorf("unable to get database path")
 	}
 
-	matcherStore, err := datastore.NewSQLiteMatcherStore(dbPath, true)
+	matcherStore, err := ds_sqlite.NewSQLiteMatcherStore(dbPath, true)
 	if err != nil {
 		return fmt.Errorf("error creating sqlite backend: %v", err)
 	}

cmd/cvetool/update.go

@@ -7,7 +7,7 @@ import (
 	"path/filepath"
 	"time"
 
-	"github.com/ComplianceAsCode/cvetool/datastore"
+	ds_sqlite "github.com/ComplianceAsCode/cvetool/datastore/sqlite"
 	"github.com/quay/claircore/libvuln"
 	_ "github.com/quay/claircore/updater/defaults"
 	"github.com/urfave/cli/v2"
@@ -44,7 +44,7 @@ func update(c *cli.Context) error {
 			}
 		}
 	}
-	matcherStore, err := datastore.NewSQLiteMatcherStore(dbPath, true)
+	matcherStore, err := ds_sqlite.NewSQLiteMatcherStore(dbPath, true)
 	if err != nil {
 		return fmt.Errorf("error creating sqlite backend: %v", err)
 	}

datastore/indexer_store.go

@@ -1,4 +1,4 @@
-package datastore
+package sqlite
 
 import (
 	"bytes"
@@ -21,6 +21,7 @@ type localStore struct {
 	lock      *sync.RWMutex
 }
 
+// compile check datastore.IndexerStore implementation
 var _ indexer.Indexer = (*LocalIndexerStore)(nil)
 
 // LocalIndexerStore is an implementation of indexer.Indexer.

datastore/sqlite/gc.go

@@ -0,0 +1,200 @@
+package sqlite
+
+import (
+	"context"
+	"database/sql"
+	"encoding/json"
+	"fmt"
+
+	"github.com/google/uuid"
+	"github.com/quay/claircore/libvuln/driver"
+	"github.com/quay/zlog"
+)
+
+// GC will delete any update operations for an updater which exceeds the provided keep
+// value.
+//
+// Implementations may throttle the GC process for datastore efficiency reasons.
+//
+// The returned int64 value indicates the remaining number of update operations needing GC.
+// Running this method till the returned value is 0 accomplishes a full GC of the vulnstore.
+func (ms *sqliteMatcherStore) GC(ctx context.Context, count int) (int64, error) {
+	ctx = zlog.ContextWithValues(ctx, "component", "datastore/sqlite/GC")
+
+	// obtain update operations which need deletin'
+	ops, totalOps, err := eligibleUpdateOpts(ctx, ms.conn, count)
+	if err != nil {
+		return 0, err
+	}
+
+	deletedOps, err := ms.DeleteUpdateOperations(ctx, ops...)
+	if err != nil {
+		zlog.Error(ctx).Err(err).Msg("DeleteUpdateOperations")
+		return totalOps - deletedOps, err
+	}
+
+	// get all updaters we know about.
+	updaters, err := distinctUpdaters(ctx, ms.conn)
+	if err != nil {
+		return totalOps - deletedOps, err
+	}
+
+	for kind, us := range updaters {
+		var cleanup cleanupFunc
+		switch kind {
+		case driver.VulnerabilityKind:
+			cleanup = vulnCleanup
+		case driver.EnrichmentKind:
+			cleanup = enrichmentCleanup
+		default:
+			zlog.Error(ctx).Str("kind", string(kind)).Msg("unknown updater kind; skipping cleanup")
+			continue
+		}
+		for _, u := range us {
+			err := cleanup(ctx, ms.conn, u)
+			if err != nil {
+				return totalOps - deletedOps, err
+			}
+		}
+	}
+
+	return totalOps - deletedOps, nil
+}
+
+// distinctUpdaters returns all updaters which have registered an update
+// operation.
+func distinctUpdaters(ctx context.Context, conn *sql.DB) (map[driver.UpdateKind][]string, error) {
+	const (
+		// will always contain at least two update operations
+		selectUpdaters = `SELECT DISTINCT(updater), kind FROM update_operation;`
+	)
+	rows, err := conn.QueryContext(ctx, selectUpdaters)
+	if err != nil {
+		return nil, fmt.Errorf("error selecting distinct updaters: %v", err)
+	}
+	defer rows.Close()
+
+	updaters := make(map[driver.UpdateKind][]string)
+	for rows.Next() {
+		var (
+			updater string
+			kind    driver.UpdateKind
+		)
+		err := rows.Scan(&updater, &kind)
+		switch err {
+		case nil:
+			// hop out
+		default:
+			return nil, fmt.Errorf("error scanning updater: %v", err)
+		}
+		updaters[kind] = append(updaters[kind], updater)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	return updaters, nil
+}
+
+// eligibleUpdateOpts returns a list of update operation refs which exceed the specified
+// keep value.
+func eligibleUpdateOpts(ctx context.Context, conn *sql.DB, keep int) ([]uuid.UUID, int64, error) {
+	const (
+		// this query will return rows of UUID arrays.
+		updateOps = `SELECT updater, json_group_array(ref ORDER BY date desc) FROM update_operation GROUP BY updater;`
+	)
+
+	// gather any update operations exceeding our keep value.
+	// keep+1 is used because PG's array slicing is inclusive,
+	// we want to grab all items once after our keep value.
+	m := []uuid.UUID{}
+
+	rows, err := conn.QueryContext(ctx, updateOps)
+	switch err {
+	case nil:
+	default:
+		return nil, 0, fmt.Errorf("error querying for update operations: %v", err)
+	}
+
+	defer rows.Close()
+	for rows.Next() {
+		var uuids_json string
+		var updater string
+		err := rows.Scan(&updater, &uuids_json)
+		if err != nil {
+			return nil, 0, fmt.Errorf("error scanning update operations: %w", err)
+		}
+		var uuids []uuid.UUID
+		json.Unmarshal([]byte(uuids_json), &uuids)
+		m = append(m, uuids[keep:]...)
+	}
+	if rows.Err() != nil {
+		return nil, 0, rows.Err()
+	}
+
+	return m, int64(len(m)), nil
+}
+
+type cleanupFunc func(context.Context, *sql.DB, string) error
+
+func vulnCleanup(ctx context.Context, conn *sql.DB, updater string) error {
+	const (
+		deleteOrphanedVulns = `
+		DELETE FROM vuln
+			WHERE id IN (
+    	SELECT v2.id
+     	FROM vuln v2
+      	LEFT JOIN uo_vuln uvl
+        	ON v2.id = uvl.vuln
+        WHERE uvl.vuln IS NULL
+        AND v2.updater = $1
+    );
+`
+	)
+
+	ctx = zlog.ContextWithValues(ctx, "updater", updater)
+	zlog.Debug(ctx).
+		Msg("starting vuln clean up")
+	res, err := conn.ExecContext(ctx, deleteOrphanedVulns, updater)
+	if err != nil {
+		return fmt.Errorf("failed while exec'ing vuln delete: %w", err)
+	}
+	rows, err := res.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed while exec'ing vuln delete (affected): %w", err)
+	}
+	zlog.Debug(ctx).Int64("rows affected", rows).Msg("vulns deleted")
+
+	return nil
+}
+
+func enrichmentCleanup(ctx context.Context, conn *sql.DB, updater string) error {
+	const (
+		deleteOrphanedEnrichments = `
+		DELETE FROM enrichment
+			WHERE id IN (
+    	SELECT e2.id
+     	FROM enrichment e2
+      	LEFT JOIN uo_enrich uen
+        	ON e2.id = uen.enrich
+        WHERE uen.enrich IS NULL
+        AND e2.updater = $1
+    );
+`
+	)
+
+	ctx = zlog.ContextWithValues(ctx, "updater", updater)
+	zlog.Debug(ctx).
+		Msg("starting enrichment clean up")
+	res, err := conn.ExecContext(ctx, deleteOrphanedEnrichments, updater)
+	if err != nil {
+		return fmt.Errorf("failed while exec'ing enrichment delete: %w", err)
+	}
+	rows, err := res.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed while exec'ing enrichment delete (affected): %w", err)
+	}
+	zlog.Debug(ctx).Int64("rows affected", rows).Msg("enrichments deleted")
+
+	return nil
+}