codeseeker 1.4.0

package/dist/cli/knowledge/graph/services/graph-database-service.js

@@ -0,0 +1,593 @@
+"use strict";
+/**
+ * Graph Database Service
+ * Handles persistence and database operations for the knowledge graph
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GraphDatabaseService = void 0;
+const logger_1 = require("../../../../utils/logger");
+const factory_1 = require("../../../../database/factory");
+class GraphDatabaseService {
+    projectPath;
+    logger = logger_1.Logger.getInstance().child('GraphDatabaseService');
+    db;
+    initialized = false;
+    // Static flag to track database availability and suppress repeated errors
+    static databaseUnavailable = false;
+    static errorNotified = false;
+    constructor(projectPath) {
+        this.projectPath = projectPath;
+    }
+    /**
+     * Check if database is marked as unavailable
+     */
+    static isDatabaseUnavailable() {
+        return GraphDatabaseService.databaseUnavailable;
+    }
+    /**
+     * Reset the database unavailable flag (for retry attempts)
+     */
+    static resetAvailability() {
+        GraphDatabaseService.databaseUnavailable = false;
+        GraphDatabaseService.errorNotified = false;
+    }
+    async initializeDatabase() {
+        if (this.initialized)
+            return;
+        // Skip if database already marked as unavailable
+        if (GraphDatabaseService.databaseUnavailable) {
+            return;
+        }
+        try {
+            const config = factory_1.DatabaseFactory?.parseConfigFromEnv();
+            if (config) {
+                this.db = factory_1.DatabaseFactory?.create(config, this.logger);
+                await this.db?.initialize();
+                // NOTE: Tables should be created during setup phase, not during runtime queries
+                // The setup command handles schema creation via applyConsolidatedSchema()
+                this.initialized = true;
+                this.logger.debug('Graph database connection initialized');
+            }
+            else {
+                this.logger.warn('No database configuration found for graph storage');
+            }
+        }
+        catch (error) {
+            // Mark database as unavailable to prevent repeated error spam
+            GraphDatabaseService.databaseUnavailable = true;
+            // Only show notification once, not for every subsequent attempt
+            if (!GraphDatabaseService.errorNotified) {
+                GraphDatabaseService.errorNotified = true;
+                // Show a single user-friendly message
+                console.log('\n⚠️  Database unavailable - CodeSeeker running in local-only mode.');
+                console.log('   Database features (semantic search, knowledge graph) will be limited.');
+                console.log('   To enable full features, ensure PostgreSQL is running.\n');
+                this.logger.debug('Graph database unavailable - using fallback mode');
+            }
+            // Don't throw - allow graceful fallback
+            return;
+        }
+    }
+    /**
+     * Create database tables - should only be called during setup phase
+     */
+    async createTables() {
+        if (!this.db) {
+            this.logger.warn('Database not available for table creation');
+            return;
+        }
+        try {
+            // Create knowledge_nodes table
+            await this.db.query(`
+        CREATE TABLE IF NOT EXISTS knowledge_nodes (
+          id VARCHAR(255) PRIMARY KEY,
+          name VARCHAR(255) NOT NULL,
+          type VARCHAR(100) NOT NULL,
+          metadata JSONB,
+          created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+          updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+          project_path VARCHAR(500),
+          source_file VARCHAR(500),
+          confidence DECIMAL(3,2) DEFAULT 1.0,
+          INDEX idx_node_type (type),
+          INDEX idx_node_project (project_path),
+          INDEX idx_node_confidence (confidence)
+        )
+      `);
+            // Create knowledge_triads table
+            await this.db.query(`
+        CREATE TABLE IF NOT EXISTS knowledge_triads (
+          id VARCHAR(255) PRIMARY KEY,
+          subject VARCHAR(255) NOT NULL,
+          predicate VARCHAR(100) NOT NULL,
+          object VARCHAR(255) NOT NULL,
+          metadata JSONB,
+          evidence_type VARCHAR(100),
+          source VARCHAR(255),
+          confidence DECIMAL(3,2) DEFAULT 1.0,
+          created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+          project_path VARCHAR(500),
+          INDEX idx_triad_subject (subject),
+          INDEX idx_triad_predicate (predicate),
+          INDEX idx_triad_object (object),
+          INDEX idx_triad_project (project_path),
+          INDEX idx_triad_confidence (confidence),
+          FOREIGN KEY (subject) REFERENCES knowledge_nodes(id) ON DELETE CASCADE,
+          FOREIGN KEY (object) REFERENCES knowledge_nodes(id) ON DELETE CASCADE
+        )
+      `);
+            // Create additional indexes for performance
+            await this.db.query(`
+        CREATE INDEX IF NOT EXISTS idx_triads_subject_predicate
+        ON knowledge_triads (subject, predicate)
+      `);
+            await this.db.query(`
+        CREATE INDEX IF NOT EXISTS idx_triads_predicate_object
+        ON knowledge_triads (predicate, object)
+      `);
+            this.logger.debug('Knowledge graph database tables created');
+        }
+        catch (error) {
+            // Don't throw - table creation may fail if DB unavailable
+            this.logger.debug('Failed to create knowledge graph tables - database may be unavailable');
+        }
+    }
+    async saveNode(node) {
+        if (!this.db) {
+            this.logger.debug('Database not available, skipping node save');
+            return;
+        }
+        try {
+            // Derive name from node id or metadata
+            const nodeName = node.metadata?.name || node.id.split('_')[0] || node.id;
+            await this.db.query(`
+        INSERT INTO knowledge_nodes (
+          id, name, type, metadata, created_at, updated_at,
+          project_path, source_file, confidence
+        ) VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9)
+        ON CONFLICT (id) DO UPDATE SET
+          name = EXCLUDED.name,
+          metadata = EXCLUDED.metadata,
+          updated_at = EXCLUDED.updated_at,
+          confidence = EXCLUDED.confidence
+      `, [
+                node.id,
+                nodeName,
+                node.type,
+                JSON.stringify(node.metadata || {}),
+                node.createdAt || new Date(),
+                node.updatedAt || new Date(),
+                this.projectPath,
+                node.metadata?.sourceFile,
+                node.metadata?.confidence || 1.0
+            ]);
+        }
+        catch (error) {
+            // Don't throw - graceful fallback when DB unavailable
+            this.logger.debug(`Failed to save node ${node.id} - database may be unavailable`);
+        }
+    }
+    async saveTriad(triad) {
+        if (!this.db) {
+            this.logger.debug('Database not available, skipping triad save');
+            return;
+        }
+        try {
+            await this.db.query(`
+        INSERT INTO knowledge_triads (
+          id, subject, predicate, object, metadata,
+          evidence_type, source, confidence, created_at, project_path
+        ) VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10)
+        ON CONFLICT (id) DO UPDATE SET
+          metadata = EXCLUDED.metadata,
+          confidence = EXCLUDED.confidence,
+          evidence_type = EXCLUDED.evidence_type
+      `, [
+                triad.id,
+                triad.subject,
+                triad.predicate,
+                triad.object,
+                JSON.stringify(triad.metadata || {}),
+                triad.evidenceType,
+                triad.source,
+                triad.confidence || 1.0,
+                triad.createdAt || new Date(),
+                this.projectPath
+            ]);
+        }
+        catch (error) {
+            // Don't throw - graceful fallback when DB unavailable
+            this.logger.debug(`Failed to save triad ${triad.id} - database may be unavailable`);
+        }
+    }
+    async loadNodes() {
+        const nodes = new Map();
+        if (!this.db) {
+            this.logger.debug('Database not available, returning empty nodes map');
+            return nodes;
+        }
+        try {
+            const results = await this.db.query(`
+        SELECT * FROM knowledge_nodes
+        WHERE project_path = $1
+        ORDER BY created_at DESC
+      `, [this.projectPath]);
+            const rows = results.rows || results || [];
+            for (const row of rows) {
+                const metadata = typeof row.metadata === 'string'
+                    ? JSON.parse(row.metadata || '{}')
+                    : (row.metadata || {});
+                // Include name in metadata if present in database
+                if (row.name) {
+                    metadata.name = row.name;
+                }
+                const node = {
+                    id: row.id,
+                    type: row.type,
+                    metadata,
+                    createdAt: row.created_at,
+                    updatedAt: row.updated_at
+                };
+                nodes.set(node.id, node);
+            }
+            this.logger.debug(`Loaded ${nodes.size} knowledge nodes`);
+        }
+        catch (error) {
+            // Don't throw - return empty map when DB unavailable
+            this.logger.debug('Failed to load nodes from database - database may be unavailable');
+        }
+        return nodes;
+    }
+    async loadTriads() {
+        const triads = new Map();
+        if (!this.db) {
+            this.logger.debug('Database not available, returning empty triads map');
+            return triads;
+        }
+        try {
+            const results = await this.db.query(`
+        SELECT * FROM knowledge_triads
+        WHERE project_path = $1
+        ORDER BY created_at DESC
+      `, [this.projectPath]);
+            const rows = results.rows || results || [];
+            for (const row of rows) {
+                const triad = {
+                    id: row.id,
+                    subject: row.subject,
+                    predicate: row.predicate,
+                    object: row.object,
+                    metadata: typeof row.metadata === 'string'
+                        ? JSON.parse(row.metadata || '{}')
+                        : (row.metadata || {}),
+                    evidenceType: row.evidence_type,
+                    source: row.source,
+                    confidence: row.confidence,
+                    createdAt: row.created_at
+                };
+                triads.set(triad.id, triad);
+            }
+            this.logger.debug(`Loaded ${triads.size} knowledge triads`);
+        }
+        catch (error) {
+            // Don't throw - return empty map when DB unavailable
+            this.logger.debug('Failed to load triads from database - database may be unavailable');
+        }
+        return triads;
+    }
+    async queryNodes(query) {
+        if (!this.db) {
+            this.logger.debug('Database not available for node query');
+            return [];
+        }
+        try {
+            let sql = `SELECT * FROM knowledge_nodes WHERE project_path = $1`;
+            const params = [this.projectPath];
+            let paramIndex = 2;
+            if (query.nodeType) {
+                sql += ` AND type = $${paramIndex}`;
+                params.push(query.nodeType);
+                paramIndex++;
+            }
+            if (query.metadata) {
+                for (const [key, value] of Object.entries(query.metadata)) {
+                    sql += ` AND metadata->>'${key}' = $${paramIndex}`;
+                    params.push(value);
+                    paramIndex++;
+                }
+            }
+            if (query.confidence !== undefined) {
+                sql += ` AND confidence >= $${paramIndex}`;
+                params.push(query.confidence.toString());
+                paramIndex++;
+            }
+            sql += ` ORDER BY confidence DESC`;
+            if (query.limit) {
+                sql += ` LIMIT $${paramIndex}`;
+                params.push(query.limit.toString());
+            }
+            const results = await this.db.query(sql, params);
+            const rows = results.rows || results || [];
+            return rows.map((row) => {
+                const metadata = typeof row.metadata === 'string'
+                    ? JSON.parse(row.metadata || '{}')
+                    : (row.metadata || {});
+                if (row.name) {
+                    metadata.name = row.name;
+                }
+                return {
+                    id: row.id,
+                    type: row.type,
+                    metadata,
+                    createdAt: row.created_at,
+                    updatedAt: row.updated_at
+                };
+            });
+        }
+        catch (error) {
+            // Don't throw - return empty array when DB unavailable
+            this.logger.debug('Failed to query nodes - database may be unavailable');
+            return [];
+        }
+    }
+    async queryTriads(query) {
+        if (!this.db) {
+            this.logger.debug('Database not available for triad query');
+            return [];
+        }
+        try {
+            let sql = `SELECT * FROM knowledge_triads WHERE project_path = $1`;
+            const params = [this.projectPath];
+            let paramIndex = 2;
+            if (query.subject) {
+                sql += ` AND subject = $${paramIndex}`;
+                params.push(query.subject);
+                paramIndex++;
+            }
+            if (query.predicate) {
+                sql += ` AND predicate = $${paramIndex}`;
+                params.push(query.predicate);
+                paramIndex++;
+            }
+            if (query.object) {
+                sql += ` AND object = $${paramIndex}`;
+                params.push(query.object);
+                paramIndex++;
+            }
+            if (query.evidenceType) {
+                sql += ` AND evidence_type = $${paramIndex}`;
+                params.push(query.evidenceType);
+                paramIndex++;
+            }
+            if (query.confidence !== undefined) {
+                sql += ` AND confidence >= $${paramIndex}`;
+                params.push(query.confidence.toString());
+                paramIndex++;
+            }
+            sql += ` ORDER BY confidence DESC`;
+            if (query.limit) {
+                sql += ` LIMIT $${paramIndex}`;
+                params.push(query.limit.toString());
+            }
+            const results = await this.db.query(sql, params);
+            const rows = results.rows || results || [];
+            return rows.map((row) => ({
+                id: row.id,
+                subject: row.subject,
+                predicate: row.predicate,
+                object: row.object,
+                metadata: typeof row.metadata === 'string'
+                    ? JSON.parse(row.metadata || '{}')
+                    : (row.metadata || {}),
+                evidenceType: row.evidence_type,
+                source: row.source,
+                confidence: row.confidence,
+                createdAt: row.created_at
+            }));
+        }
+        catch (error) {
+            // Don't throw - return empty array when DB unavailable
+            this.logger.debug('Failed to query triads - database may be unavailable');
+            return [];
+        }
+    }
+    async mutateGraph(mutation) {
+        if (!this.db) {
+            this.logger.debug('Database not available for graph mutation');
+            return;
+        }
+        try {
+            // Begin transaction
+            await this.db.beginTransaction();
+            try {
+                // Add nodes
+                if (mutation.addNodes) {
+                    for (const node of mutation.addNodes) {
+                        await this.saveNode({
+                            ...node,
+                            id: node.id || this.generateNodeId(),
+                            createdAt: new Date(),
+                            updatedAt: new Date()
+                        });
+                    }
+                }
+                // Add triads
+                if (mutation.addTriads) {
+                    for (const triad of mutation.addTriads) {
+                        await this.saveTriad({
+                            ...triad,
+                            id: triad.id || this.generateTriadId(),
+                            createdAt: new Date()
+                        });
+                    }
+                }
+                // Remove nodes
+                if (mutation.removeNodes) {
+                    for (const nodeId of mutation.removeNodes) {
+                        await this.db.query(`DELETE FROM knowledge_nodes WHERE id = $1 AND project_path = $2`, [nodeId, this.projectPath]);
+                    }
+                }
+                // Remove triads
+                if (mutation.removeTriads) {
+                    for (const triadId of mutation.removeTriads) {
+                        await this.db.query(`DELETE FROM knowledge_triads WHERE id = $1 AND project_path = $2`, [triadId, this.projectPath]);
+                    }
+                }
+                // Update nodes
+                if (mutation.updateNodes) {
+                    for (const [nodeId, updates] of Object.entries(mutation.updateNodes)) {
+                        const updateFields = [];
+                        const params = [];
+                        let paramIndex = 1;
+                        if (updates.metadata) {
+                            updateFields.push(`metadata = $${paramIndex}`);
+                            params.push(JSON.stringify(updates.metadata));
+                            paramIndex++;
+                        }
+                        if (updates.confidence !== undefined) {
+                            updateFields.push(`confidence = $${paramIndex}`);
+                            params.push(updates.confidence);
+                            paramIndex++;
+                        }
+                        updateFields.push(`updated_at = $${paramIndex}`);
+                        params.push(new Date());
+                        paramIndex++;
+                        params.push(nodeId, this.projectPath);
+                        await this.db.query(`
+              UPDATE knowledge_nodes
+              SET ${updateFields.join(', ')}
+              WHERE id = $${paramIndex} AND project_path = $${paramIndex + 1}
+            `, params);
+                    }
+                }
+                // Update triads
+                if (mutation.updateTriads) {
+                    for (const [triadId, updates] of Object.entries(mutation.updateTriads)) {
+                        const updateFields = [];
+                        const params = [];
+                        let paramIndex = 1;
+                        if (updates.metadata) {
+                            updateFields.push(`metadata = $${paramIndex}`);
+                            params.push(JSON.stringify(updates.metadata));
+                            paramIndex++;
+                        }
+                        if (updates.confidence !== undefined) {
+                            updateFields.push(`confidence = $${paramIndex}`);
+                            params.push(updates.confidence);
+                            paramIndex++;
+                        }
+                        params.push(triadId, this.projectPath);
+                        await this.db.query(`
+              UPDATE knowledge_triads
+              SET ${updateFields.join(', ')}
+              WHERE id = $${paramIndex} AND project_path = $${paramIndex + 1}
+            `, params);
+                    }
+                }
+                // Commit transaction
+                await this.db.commitTransaction();
+                this.logger.debug('Graph mutation completed');
+            }
+            catch (error) {
+                try {
+                    await this.db.rollbackTransaction();
+                }
+                catch {
+                    // Ignore rollback errors
+                }
+                this.logger.debug('Failed to mutate graph - database may be unavailable');
+            }
+        }
+        catch (error) {
+            // Don't throw - graceful fallback when DB unavailable
+            this.logger.debug('Failed to mutate graph - database may be unavailable');
+        }
+    }
+    async closeConnection() {
+        if (this.db) {
+            try {
+                await this.db.close();
+                this.initialized = false;
+                this.logger.debug('Graph database connection closed');
+            }
+            catch (error) {
+                // Silently handle close errors
+                this.logger.debug('Error closing graph database connection');
+            }
+        }
+    }
+    generateNodeId() {
+        return `node_${Date.now()}_${Math.random().toString(36).substr(2, 9)}`;
+    }
+    generateTriadId() {
+        return `triad_${Date.now()}_${Math.random().toString(36).substr(2, 9)}`;
+    }
+    // Utility methods for common queries
+    async getNodesByType(nodeType, limit) {
+        return this.queryNodes({ nodeType, limit });
+    }
+    async getTriadsByPredicate(predicate, limit) {
+        return this.queryTriads({ predicate, limit });
+    }
+    async getNodeConnections(nodeId) {
+        const incoming = await this.queryTriads({ object: nodeId });
+        const outgoing = await this.queryTriads({ subject: nodeId });
+        return { incoming, outgoing };
+    }
+    async getNodeNeighbors(nodeId) {
+        const { incoming, outgoing } = await this.getNodeConnections(nodeId);
+        const neighbors = new Set();
+        incoming.forEach(triad => neighbors.add(triad.subject));
+        outgoing.forEach(triad => neighbors.add(triad.object));
+        neighbors.delete(nodeId); // Remove self
+        return Array.from(neighbors);
+    }
+    async getSubgraph(nodeIds) {
+        if (!this.db || nodeIds.length === 0) {
+            return { nodes: [], triads: [] };
+        }
+        try {
+            const nodeIdPlaceholders = nodeIds.map((_, i) => `$${i + 1}`).join(',');
+            const projectPathIndex = nodeIds.length + 1;
+            const nodes = await this.db.query(`
+        SELECT * FROM knowledge_nodes
+        WHERE id IN (${nodeIdPlaceholders}) AND project_path = $${projectPathIndex}
+      `, [...nodeIds, this.projectPath]);
+            const triadProjectPathIndex = nodeIds.length * 2 + 1;
+            const subjectPlaceholders = nodeIds.map((_, i) => `$${i + 1}`).join(',');
+            const objectPlaceholders = nodeIds.map((_, i) => `$${i + nodeIds.length + 1}`).join(',');
+            const triads = await this.db.query(`
+        SELECT * FROM knowledge_triads
+        WHERE (subject IN (${subjectPlaceholders}) OR object IN (${objectPlaceholders}))
+        AND project_path = $${triadProjectPathIndex}
+      `, [...nodeIds, ...nodeIds, this.projectPath]);
+            return {
+                nodes: nodes.map((row) => ({
+                    id: row.id,
+                    type: row.type,
+                    metadata: JSON.parse(row.metadata || '{}'),
+                    createdAt: row.created_at,
+                    updatedAt: row.updated_at
+                })),
+                triads: triads.map((row) => ({
+                    id: row.id,
+                    subject: row.subject,
+                    predicate: row.predicate,
+                    object: row.object,
+                    metadata: JSON.parse(row.metadata || '{}'),
+                    evidenceType: row.evidence_type,
+                    source: row.source,
+                    confidence: row.confidence,
+                    createdAt: row.created_at
+                }))
+            };
+        }
+        catch (error) {
+            // Don't throw - return empty result when DB unavailable
+            this.logger.debug('Failed to get subgraph - database may be unavailable');
+            return { nodes: [], triads: [] };
+        }
+    }
+}
+exports.GraphDatabaseService = GraphDatabaseService;
+//# sourceMappingURL=graph-database-service.js.map

package/dist/cli/knowledge/graph/services/graph-database-service.js.map

@@ -0,0 +1 @@
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package/dist/cli/knowledge/graph/services/graph-utility-service.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Graph Utility Service
+ * Contains helper methods and utility functions for knowledge graph operations
+ */
+import { KnowledgeNode, KnowledgeTriad, NodeType, RelationType } from '../types';
+export interface IGraphUtilityService {
+    generateNodeId(type: NodeType, name: string, namespace?: string): string;
+    generateTriadId(subject: string, predicate: RelationType, object: string): string;
+    hasConnection(nodeId1: string, nodeId2: string, triads: Map<string, KnowledgeTriad>): boolean;
+    calculateClusterCoherence(nodes: string[], triads: Map<string, KnowledgeTriad>): number;
+    calculateClusteringCoefficient(nodes: Map<string, KnowledgeNode>, triads: Map<string, KnowledgeTriad>): number;
+    groupDuplicates(duplicateTriads: KnowledgeTriad[]): string[][];
+    dfsComponent(startNode: string, nodes: Map<string, KnowledgeNode>, triads: Map<string, KnowledgeTriad>, visited: Set<string>): Promise<string[]>;
+}
+export declare class GraphUtilityService implements IGraphUtilityService {
+    private logger;
+    generateNodeId(type: NodeType, name: string, namespace?: string): string;
+    generateTriadId(subject: string, predicate: RelationType, object: string): string;
+    hasConnection(nodeId1: string, nodeId2: string, triads: Map<string, KnowledgeTriad>): boolean;
+    calculateClusterCoherence(nodes: string[], triads: Map<string, KnowledgeTriad>): number;
+    groupDuplicates(duplicateTriads: KnowledgeTriad[]): string[][];
+    dfsComponent(startNode: string, nodes: Map<string, KnowledgeNode>, triads: Map<string, KnowledgeTriad>, visited: Set<string>): Promise<string[]>;
+    /**
+     * Calculate clustering coefficient for the graph
+     */
+    calculateClusteringCoefficient(nodes: Map<string, KnowledgeNode>, triads: Map<string, KnowledgeTriad>): number;
+    /**
+     * Check if a node is semantically similar to another
+     */
+    isSemanticallySimilar(nodeId1: string, nodeId2: string, triads: Map<string, KnowledgeTriad>, threshold?: number): boolean;
+    /**
+     * Find all nodes that are semantically related to a given node
+     */
+    findSemanticNeighbors(nodeId: string, triads: Map<string, KnowledgeTriad>, semanticRelations?: RelationType[]): string[];
+    /**
+     * Calculate semantic density of a subgraph
+     */
+    calculateSemanticDensity(nodeIds: string[], triads: Map<string, KnowledgeTriad>): number;
+    private simpleHash;
+}
+//# sourceMappingURL=graph-utility-service.d.ts.map

package/dist/cli/knowledge/graph/services/graph-utility-service.d.ts.map

@@ -0,0 +1 @@
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