@rbalchii/anchor-engine 4.7.0

package/engine/dist/routes/v1/admin.js

@@ -0,0 +1,261 @@
+import { db } from '../../core/db.js';
+export function setupAdminRoutes(app) {
+    // Terminal Command Execution Endpoint
+    app.post('/v1/terminal/exec', async (req, res) => {
+        try {
+            const { command } = req.body;
+            if (!command) {
+                return res.status(400).json({ error: 'Command is required' });
+            }
+            // For now, we'll simulate command execution for security
+            // In a real implementation, you'd want to use a secure sandbox
+            console.log(`[Terminal] Executing command: ${command}`);
+            // Validate command to prevent dangerous operations
+            const dangerousCommands = ['rm', 'del', 'format', 'mkfs', 'dd', 'shutdown', 'reboot', 'poweroff'];
+            const commandParts = command.toLowerCase().split(' ');
+            const isDangerous = dangerousCommands.some(dc => commandParts.includes(dc));
+            if (isDangerous) {
+                return res.status(400).json({
+                    error: 'Command contains potentially dangerous operations',
+                    stderr: 'ERROR: Dangerous command blocked by security policy'
+                });
+            }
+            // Special handling for 'clear' command
+            if (command.trim().toLowerCase() === 'clear') {
+                return res.status(200).json({
+                    command: command,
+                    stdout: '', // Empty stdout for clear command
+                    stderr: '',
+                    code: 0
+                });
+            }
+            // For now, return mock response - in a real implementation you'd execute securely
+            const mockResponses = {
+                'ls': { stdout: 'file1.txt\nfile2.md\nfolder1/\nfolder2/' },
+                'dir': { stdout: 'file1.txt\nfile2.md\nfolder1/\nfolder2/' },
+                'pwd': { stdout: '/home/user/project' },
+                'whoami': { stdout: 'user' },
+                'echo hello': { stdout: 'hello' },
+                'cat README.md': { stdout: '# Project README\n\nThis is a sample readme file.' },
+                'type README.md': { stdout: '# Project README\n\nThis is a sample readme file.' },
+                'help': { stdout: 'Available commands: ls, pwd, whoami, echo, cat/type, help' },
+                'cls': { stdout: '' }
+            };
+            // Check if we have a predefined response
+            const normalizedCmd = command.toLowerCase().trim();
+            let response = mockResponses[normalizedCmd];
+            // If no exact match, try partial matches
+            if (!response) {
+                if (normalizedCmd.startsWith('ls') || normalizedCmd.startsWith('dir')) {
+                    response = { stdout: 'file1.txt\nfile2.md\nfolder1/\nfolder2/' };
+                }
+                else if (normalizedCmd.startsWith('cat ') || normalizedCmd.startsWith('type ')) {
+                    response = { stdout: 'Sample file content for: ' + command.split(' ')[1] };
+                }
+                else {
+                    response = {
+                        stdout: `Command executed: ${command}\n(Output simulated for security)`,
+                        stderr: command.includes('error') ? 'Simulated error for testing' : undefined
+                    };
+                }
+            }
+            res.status(200).json({
+                command: command,
+                stdout: response.stdout || '',
+                stderr: response.stderr || '',
+                code: response.code !== undefined ? response.code : 0
+            });
+        }
+        catch (error) {
+            console.error('Terminal execution error:', error);
+            res.status(500).json({
+                error: error.message,
+                stderr: `Execution failed: ${error.message}`
+            });
+        }
+    });
+    // DEBUG: Get tag statistics
+    app.get('/v1/debug/tags', async (_req, res) => {
+        try {
+            // Get total atom count
+            const atomCount = await db.run('SELECT COUNT(*) as count FROM atoms');
+            // Get total tag count
+            const tagCount = await db.run('SELECT COUNT(*) as count FROM tags');
+            // Get sample tags
+            const sampleTags = await db.run('SELECT name, atom_count FROM tags ORDER BY atom_count DESC LIMIT 20');
+            // Get tags with low atom counts
+            const lowCountTags = await db.run('SELECT COUNT(*) as count FROM tags WHERE atom_count < 3');
+            res.status(200).json({
+                atoms: atomCount.rows?.[0]?.count || 0,
+                tags: tagCount.rows?.[0]?.count || 0,
+                sampleTags: sampleTags.rows || [],
+                tagsWithLowCount: lowCountTags.rows?.[0]?.count || 0
+            });
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // DEBUG: Get synonym ring info
+    app.get('/v1/debug/synonyms', async (_req, res) => {
+        try {
+            const synonyms = await db.run('SELECT key, value FROM engrams WHERE key LIKE \'synonym:%\'');
+            res.status(200).json({
+                count: synonyms.rows?.length || 0,
+                synonyms: synonyms.rows || []
+            });
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // Maintenance: Re-index Tags (Fix for missing buckets/tags in UI)
+    app.post('/v1/maintenance/reindex-tags', async (_req, res) => {
+        try {
+            console.log("[Maintenance] Starting Tag Re-indexing...");
+            // 1. Drop old table
+            await db.run('DROP TABLE IF EXISTS tags');
+            // 2. Re-create table with correct schema (atom_id, tag, bucket)
+            // Note: This relies on db.ts schema, but we want to be explicit here since we just dropped it
+            await db.run(`
+        CREATE TABLE IF NOT EXISTS tags (
+          atom_id TEXT,
+          tag TEXT,
+          bucket TEXT,
+          PRIMARY KEY (atom_id, tag, bucket)
+        );
+      `);
+            // 3. Re-create indexes
+            try {
+                await db.run('CREATE INDEX IF NOT EXISTS idx_tags_tag ON tags(tag);');
+                await db.run('CREATE INDEX IF NOT EXISTS idx_tags_bucket ON tags(bucket);');
+            }
+            catch (e) {
+                console.warn("Index creation warning", e);
+            }
+            // 4. Migrate Data
+            const atoms = await db.run('SELECT id, tags, buckets FROM atoms');
+            console.log(`[Maintenance] Found ${atoms.rows.length} atoms to re-index.`);
+            let count = 0;
+            const BATCH_SIZE = 500;
+            let values = [];
+            let params = [];
+            const flushBatch = async () => {
+                if (values.length === 0)
+                    return;
+                try {
+                    const placeholders = values.join(',');
+                    await db.run(`INSERT INTO tags (atom_id, tag, bucket) VALUES ${placeholders}
+             ON CONFLICT (atom_id, tag, bucket) DO NOTHING`, params);
+                    count += values.length;
+                }
+                catch (e) {
+                    console.warn(`[Maintenance] Batch insert failed:`, e);
+                }
+                values = [];
+                params = [];
+            };
+            for (const row of atoms.rows) {
+                const atomId = row.id;
+                const tags = row.tags;
+                const buckets = row.buckets;
+                if (!tags || !buckets)
+                    continue;
+                for (const bucket of buckets) {
+                    for (const tag of tags) {
+                        if (tag && bucket) {
+                            const idx = params.length;
+                            values.push(`($${idx + 1}, $${idx + 2}, $${idx + 3})`);
+                            params.push(atomId, tag, bucket);
+                            if (values.length >= BATCH_SIZE) {
+                                await flushBatch();
+                            }
+                        }
+                    }
+                }
+            }
+            // Flush remaining items
+            await flushBatch();
+            console.log(`[Maintenance] Re-indexing complete. Inserted ${count} tags.`);
+            res.status(200).json({ status: 'success', message: `Re-indexed ${count} tags from ${atoms.rows.length} atoms.` });
+        }
+        catch (e) {
+            console.error('[Maintenance] Re-index failed:', e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // Graph Data Endpoint for Context Visualization
+    app.post('/v1/graph/data', async (req, res) => {
+        try {
+            const { query, limit = 20 } = req.body;
+            if (!query) {
+                return res.status(400).json({ error: 'Query is required' });
+            }
+            // This would normally call the search service to get real data
+            // For now, we'll return mock data based on the query
+            console.log(`[Graph] Generating visualization data for query: ${query}`);
+            // Generate mock nodes and links based on the query
+            const nodes = [
+                { id: 'query', label: query, type: 'search', x: 400, y: 300, size: 20, color: '#646cff' },
+                { id: 'atom1', label: 'Project Notes', type: 'document', x: 200, y: 150, size: 15, color: '#22d3ee' },
+                { id: 'atom2', label: 'Code Snippet', type: 'code', x: 600, y: 150, size: 15, color: '#8b5cf6' },
+                { id: 'atom3', label: 'Research Paper', type: 'document', x: 200, y: 450, size: 15, color: '#22d3ee' },
+                { id: 'atom4', label: 'Configuration', type: 'config', x: 600, y: 450, size: 15, color: '#10b981' },
+                { id: 'tag1', label: '#typescript', type: 'tag', x: 300, y: 100, size: 12, color: '#f59e0b' },
+                { id: 'tag2', label: '#ai', type: 'tag', x: 500, y: 100, size: 12, color: '#f59e0b' },
+                { id: 'tag3', label: '#graph', type: 'tag', x: 300, y: 500, size: 12, color: '#f59e0b' },
+                { id: 'tag4', label: '#memory', type: 'tag', x: 500, y: 500, size: 12, color: '#f59e0b' },
+            ];
+            const links = [
+                { source: 'query', target: 'atom1', strength: 0.8 },
+                { source: 'query', target: 'atom2', strength: 0.7 },
+                { source: 'query', target: 'atom3', strength: 0.6 },
+                { source: 'query', target: 'atom4', strength: 0.5 },
+                { source: 'atom1', target: 'tag1', strength: 0.9 },
+                { source: 'atom1', target: 'tag2', strength: 0.6 },
+                { source: 'atom2', target: 'tag1', strength: 0.7 },
+                { source: 'atom2', target: 'tag2', strength: 0.8 },
+                { source: 'atom3', target: 'tag3', strength: 0.9 },
+                { source: 'atom3', target: 'tag4', strength: 0.6 },
+                { source: 'atom4', target: 'tag3', strength: 0.7 },
+                { source: 'atom4', target: 'tag4', strength: 0.8 },
+            ];
+            res.status(200).json({
+                nodes: nodes.slice(0, limit),
+                links: links.slice(0, limit * 2), // More links than nodes typically
+                query: query,
+                timestamp: new Date().toISOString()
+            });
+        }
+        catch (error) {
+            console.error('Graph data error:', error);
+            res.status(500).json({
+                error: error.message
+            });
+        }
+    });
+    // Trigger Dream Endpoint (Disabled - Optimized for STAR algorithm)
+    app.post('/v1/dream', async (_req, res) => {
+        res.status(501).json({
+            error: 'Dreamer service is disabled',
+            message: 'This endpoint has been disabled to optimize startup for the STAR algorithm'
+        });
+    });
+    // Return 503 for disabled inference endpoints
+    app.post('/v1/chat/completions', (_req, res) => {
+        res.status(503).json({ error: 'Chat completions disabled', message: 'Inference server not configured' });
+    });
+    app.get('/v1/models', (_req, res) => {
+        res.status(503).json({ error: 'Models endpoint disabled', message: 'Inference server not configured' });
+    });
+    app.get('/v1/model/status', (_req, res) => {
+        res.status(503).json({ error: 'Model status disabled', message: 'Inference server not configured' });
+    });
+    app.post('/v1/model/load', (_req, res) => {
+        res.status(503).json({ error: 'Model load disabled', message: 'Inference server not configured' });
+    });
+    app.post('/v1/model/unload', (_req, res) => {
+        res.status(503).json({ error: 'Model unload disabled', message: 'Inference server not configured' });
+    });
+}
+//# sourceMappingURL=admin.js.map

package/engine/dist/routes/v1/admin.js.map

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package/engine/dist/routes/v1/atoms.d.ts

@@ -0,0 +1,3 @@
+import { Application } from 'express';
+export declare function setupAtomRoutes(app: Application): void;
+//# sourceMappingURL=atoms.d.ts.map

package/engine/dist/routes/v1/atoms.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"atoms.d.ts","sourceRoot":"","sources":["../../../src/routes/v1/atoms.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAqB,MAAM,SAAS,CAAC;AAIzD,wBAAgB,eAAe,CAAC,GAAG,EAAE,WAAW,QA8N/C"}

package/engine/dist/routes/v1/atoms.js

@@ -0,0 +1,172 @@
+import * as crypto from 'crypto';
+import { db } from '../../core/db.js';
+export function setupAtomRoutes(app) {
+    // POST Quarantine Atom (Standard 073)
+    app.post('/v1/atoms/:id/quarantine', async (req, res) => {
+        try {
+            const { id } = req.params;
+            if (!id) {
+                res.status(400).json({ error: 'Atom ID is required' });
+                return;
+            }
+            console.log(`[API] Quarantining Atom: ${id}`);
+            // Update Provenance + Add Tag
+            // We use a transaction-like update: Read -> Modify -> Write
+            // 1. Get current record
+            const check = await db.run(`SELECT tags FROM atoms WHERE id = $1`, [id]);
+            if (!check.rows || check.rows.length === 0) {
+                res.status(404).json({ error: 'Atom not found' });
+                return;
+            }
+            const currentTags = check.rows[0][0] || [];
+            const newTags = [...new Set([...currentTags, '#manually_quarantined'])];
+            // 2. Update Record
+            await db.run(`UPDATE atoms SET tags = $1, provenance = $2 WHERE id = $3`, [newTags, 'quarantine', id]);
+            res.status(200).json({ status: 'success', message: `Atom ${id} quarantined.` });
+        }
+        catch (e) {
+            console.error(e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // GET Quarantined Atoms
+    app.get('/v1/atoms/quarantined', async (_req, res) => {
+        try {
+            const query = `
+        SELECT id, content, source_path, timestamp, buckets, tags, provenance, simhash, embedding
+        FROM atoms
+        WHERE provenance = 'quarantine'
+        ORDER BY timestamp DESC
+        LIMIT 100
+      `;
+            const result = await db.run(query);
+            const atoms = (result.rows || []).map((row) => ({
+                id: row.id,
+                content: row.content,
+                source: row.source_path,
+                timestamp: row.timestamp,
+                buckets: row.buckets,
+                tags: row.tags,
+                provenance: row.provenance,
+                simhash: row.simhash
+            }));
+            res.status(200).json(atoms);
+        }
+        catch (e) {
+            console.error('[API] Failed to fetch quarantined atoms:', e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // PUT Update Atom Content
+    app.put('/v1/atoms/:id/content', async (req, res) => {
+        try {
+            const { id } = req.params;
+            const { content } = req.body;
+            console.log(`[API] Updating Atom Content: ${id}`);
+            // We must preserve all other fields, BUT zero out embedding to signal re-index needed
+            const fullRecord = await db.run(`SELECT id, timestamp, content, source_path, source_id, sequence, type, hash, buckets, epochs, tags, provenance, simhash, embedding
+         FROM atoms WHERE id = $1`, [id]);
+            if (!fullRecord.rows || fullRecord.rows.length === 0) {
+                res.status(404).json({ error: 'Atom not found' });
+                return;
+            }
+            const newHash = crypto.createHash('sha256').update(content).digest('hex');
+            const newEmbedding = new Array(384).fill(0.1);
+            await db.run(`UPDATE atoms SET content = $1, hash = $2, embedding = $3 WHERE id = $4`, [content, newHash, newEmbedding, id]);
+            res.status(200).json({ status: 'success', message: `Atom ${id} updated.` });
+        }
+        catch (e) {
+            console.error(e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // POST Restore Atom
+    app.post('/v1/atoms/:id/restore', async (req, res) => {
+        try {
+            const { id } = req.params;
+            console.log(`[API] Restoring Atom: ${id}`);
+            const fullRecord = await db.run(`SELECT id, timestamp, content, source_path, source_id, sequence, type, hash, buckets, epochs, tags, provenance, simhash, embedding
+         FROM atoms WHERE id = $1`, [id]);
+            if (!fullRecord.rows || fullRecord.rows.length === 0) {
+                res.status(404).json({ error: 'Atom not found' });
+                return;
+            }
+            const row = fullRecord.rows[0];
+            const currentTags = row.tags || [];
+            // Filter out quarantine tags
+            const newTags = currentTags.filter(t => t !== '#manually_quarantined' && t !== '#auto_quarantined');
+            await db.run(`UPDATE atoms SET tags = $1, provenance = $2 WHERE id = $3`, [newTags, 'internal', id]);
+            res.status(200).json({ status: 'success', message: `Atom ${id} restored to Graph.` });
+        }
+        catch (e) {
+            console.error(e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // === Compatibility Routes for UI ===
+    // GET /v1/quarantine - List quarantined atoms
+    app.get('/v1/quarantine', async (_req, res) => {
+        try {
+            const query = `
+        SELECT id, content, source_path, timestamp, buckets, tags, provenance, simhash, embedding
+        FROM atoms
+        WHERE provenance = 'quarantine'
+        ORDER BY timestamp DESC
+        LIMIT 100
+      `;
+            const result = await db.run(query);
+            const atoms = (result.rows || []).map((row) => ({
+                id: row.id,
+                content: row.content,
+                source: row.source_path,
+                timestamp: row.timestamp,
+                buckets: row.buckets,
+                tags: row.tags,
+                provenance: row.provenance,
+                simhash: row.simhash
+            }));
+            res.status(200).json({ atoms, total: atoms.length });
+        }
+        catch (e) {
+            console.error('[API] Failed to fetch quarantined atoms:', e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // POST /v1/quarantine/:id/restore - Restore a quarantined atom
+    app.post('/v1/quarantine/:id/restore', async (req, res) => {
+        try {
+            const { id } = req.params;
+            console.log(`[API] Restoring Atom: ${id}`);
+            const fullRecord = await db.run(`SELECT id, timestamp, content, source_path, source_id, sequence, type, hash, buckets, epochs, tags, provenance, simhash, embedding
+         FROM atoms WHERE id = $1`, [id]);
+            if (!fullRecord.rows || fullRecord.rows.length === 0) {
+                res.status(404).json({ error: 'Atom not found' });
+                return;
+            }
+            const row = fullRecord.rows[0];
+            const currentTags = row.tags || [];
+            // Filter out quarantine tags
+            const newTags = currentTags.filter(t => t !== '#manually_quarantined' && t !== '#auto_quarantined');
+            await db.run(`UPDATE atoms SET tags = $1, provenance = $2 WHERE id = $3`, [newTags, 'internal', id]);
+            res.status(200).json({ status: 'success', message: `Atom ${id} restored to Graph.` });
+        }
+        catch (e) {
+            console.error(e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // DELETE /v1/quarantine/:id - Delete a quarantined atom
+    app.delete('/v1/quarantine/:id', async (req, res) => {
+        try {
+            const { id } = req.params;
+            console.log(`[API] Deleting quarantined atom: ${id}`);
+            await db.run(`DELETE FROM atoms WHERE id = $1`, [id]);
+            res.status(200).json({ status: 'deleted', id });
+        }
+        catch (e) {
+            console.error(e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+}
+//# sourceMappingURL=atoms.js.map

package/engine/dist/routes/v1/atoms.js.map

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package/engine/dist/routes/v1/backup.d.ts

@@ -0,0 +1,3 @@
+import { Application } from 'express';
+export declare function setupBackupRoutes(app: Application): void;
+//# sourceMappingURL=backup.d.ts.map

package/engine/dist/routes/v1/backup.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"backup.d.ts","sourceRoot":"","sources":["../../../src/routes/v1/backup.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAqB,MAAM,SAAS,CAAC;AAIzD,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,WAAW,QAuGjD"}

package/engine/dist/routes/v1/backup.js

@@ -0,0 +1,100 @@
+import { createBackup, listBackups, restoreBackup } from '../../services/backup/backup.js';
+import { getLatestBackup, validateBackup } from '../../services/backup/backup-restore.js';
+export function setupBackupRoutes(app) {
+    // Backup Endpoints
+    // POST /v1/backup - Create a new backup
+    app.post('/v1/backup', async (_req, res) => {
+        try {
+            const result = await createBackup();
+            res.status(200).json(result);
+        }
+        catch (e) {
+            console.error("Backup Failed", e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // GET /v1/backups - List available backups
+    app.get('/v1/backups', async (_req, res) => {
+        try {
+            const backups = await listBackups();
+            // Get metadata for each backup
+            const backupsWithMeta = await Promise.all(backups.map(async (filename) => {
+                const validation = await validateBackup(filename);
+                return {
+                    filename,
+                    valid: validation.valid,
+                    error: validation.error || undefined,
+                    size: validation.size || 0,
+                    sizeFormatted: validation.sizeFormatted || 'Unknown'
+                };
+            }));
+            res.status(200).json(backupsWithMeta);
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // POST /v1/backup/restore - Restore a specific backup
+    app.post('/v1/backup/restore', async (req, res) => {
+        try {
+            const { filename } = req.body;
+            if (!filename) {
+                res.status(400).json({ error: "Filename required" });
+                return;
+            }
+            // Validate first
+            const validation = await validateBackup(filename);
+            if (!validation.valid) {
+                res.status(400).json({ error: validation.error });
+                return;
+            }
+            const startTime = Date.now();
+            const result = await restoreBackup(filename);
+            const totalTime = ((Date.now() - startTime) / 1000).toFixed(1);
+            const atomsPerSec = Math.round(result.memory_count / parseFloat(totalTime));
+            res.status(200).json({
+                success: true,
+                message: 'Backup restore complete',
+                stats: result,
+                totalTime,
+                atomsPerSec
+            });
+        }
+        catch (e) {
+            console.error("Backup Restore Failed", e);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // GET /v1/backup/latest - Get the latest backup info
+    app.get('/v1/backup/latest', async (_req, res) => {
+        try {
+            const latest = await getLatestBackup();
+            if (!latest) {
+                res.status(404).json({ error: 'No backups found' });
+                return;
+            }
+            const validation = await validateBackup(latest);
+            res.status(200).json({
+                filename: latest,
+                valid: validation.valid,
+                error: validation.error || undefined
+            });
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // GET /v1/backup (Legacy Dump) - Kept for compatibility or download
+    app.get('/v1/backup', async (_req, res) => {
+        try {
+            const result = await createBackup();
+            const path = await import('path');
+            const fpath = path.join(process.cwd(), 'backups', result.filename);
+            res.download(fpath);
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+}
+//# sourceMappingURL=backup.js.map

package/engine/dist/routes/v1/backup.js.map

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package/engine/dist/routes/v1/git.d.ts

@@ -0,0 +1,3 @@
+import { Application } from 'express';
+export declare function setupGitRoutes(app: Application): void;
+//# sourceMappingURL=git.d.ts.map

package/engine/dist/routes/v1/git.d.ts.map

@@ -0,0 +1 @@
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