@rbalchii/anchor-engine 4.7.0

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

@@ -0,0 +1,316 @@
+export function setupGitRoutes(app) {
+    // GitHub Repository Ingestion Endpoints (Standard 115)
+    // POST /v1/github/repos - Register new repo and trigger initial ingestion
+    app.post('/v1/github/repos', async (req, res) => {
+        try {
+            const body = req.body;
+            const url = body.url;
+            const bucket = body.bucket;
+            const includeHistory = body.include_history === true;
+            if (!url || !bucket) {
+                res.status(400).json({ error: 'url and bucket are required' });
+                return;
+            }
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            // Register repo
+            const repo = await service.registerRepo(url, bucket);
+            // Start async ingestion (don't wait for completion)
+            (async () => {
+                try {
+                    await service.syncRepo(repo.id);
+                    if (includeHistory) {
+                        const token = process.env.GITHUB_TOKEN;
+                        await service.ingestGitHistory(repo.owner, repo.repo, repo.branch, bucket, token);
+                        console.log(`[API] Git history ingested for ${repo.owner}/${repo.repo}`);
+                    }
+                }
+                catch (error) {
+                    console.error(`[API] Background sync/history failed for ${repo.id}:`, error);
+                }
+            })();
+            res.status(202).json({
+                id: repo.id,
+                status: 'ingesting',
+                include_history: includeHistory,
+                message: `Started ingestion for ${repo.owner}/${repo.repo}${includeHistory ? ' (with full commit history)' : ''}`,
+            });
+        }
+        catch (error) {
+            console.error('[API] GitHub repo registration error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // GET /v1/github/repos - List all registered repos
+    app.get('/v1/github/repos', async (_req, res) => {
+        try {
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            const repos = await service.listRepos();
+            res.status(200).json(repos);
+        }
+        catch (error) {
+            console.error('[API] GitHub repo list error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // POST /v1/github/repos/:id/sync - Manual sync trigger
+    app.post('/v1/github/repos/:id/sync', async (req, res) => {
+        try {
+            const id = req.params.id;
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            // Start async sync
+            service.syncRepo(id).catch((error) => {
+                console.error(`[API] Background sync failed for ${id}:`, error);
+            });
+            res.status(202).json({
+                id,
+                status: 'syncing',
+                message: 'Sync started',
+            });
+        }
+        catch (error) {
+            console.error('[API] GitHub sync trigger error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // DELETE /v1/github/repos/:id - Remove repo
+    app.delete('/v1/github/repos/:id', async (req, res) => {
+        try {
+            const id = req.params.id;
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            const quarantinedCount = await service.removeRepo(id);
+            res.status(200).json({
+                status: 'removed',
+                quarantined_atoms: quarantinedCount,
+            });
+        }
+        catch (error) {
+            console.error('[API] GitHub repo removal error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // GET /v1/github/rate-limit - Check GitHub API rate limit status
+    app.get('/v1/github/rate-limit', async (_req, res) => {
+        try {
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            const rateLimit = await service.getRateLimitStatus();
+            res.status(200).json(rateLimit);
+        }
+        catch (error) {
+            console.error('[API] GitHub rate limit check error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // GET /v1/github/credentials - Check for stored GitHub credentials
+    app.get('/v1/github/credentials', async (_req, res) => {
+        try {
+            const fs = await import('fs');
+            const path = await import('path');
+            const os = await import('os');
+            let token = null;
+            let source = null;
+            let username = null;
+            // 1. Check environment variable
+            if (process.env.GITHUB_TOKEN) {
+                token = process.env.GITHUB_TOKEN;
+                source = 'GITHUB_TOKEN environment variable';
+            }
+            // 2. Check .netrc file
+            if (!token) {
+                const netrcPath = path.join(os.homedir(), '.netrc');
+                if (fs.existsSync(netrcPath)) {
+                    const netrcContent = fs.readFileSync(netrcPath, 'utf8');
+                    const netrcMatch = netrcContent.match(/machine\s+github\.com\s+login\s+(\S+)\s+password\s+(\S+)/);
+                    if (netrcMatch) {
+                        username = netrcMatch[1];
+                        token = netrcMatch[2];
+                        source = '.netrc file';
+                    }
+                }
+            }
+            // 3. Check git config for credential helper
+            if (!token) {
+                const { exec } = await import('child_process');
+                const util = await import('util');
+                const execPromise = util.promisify(exec);
+                try {
+                    // Try to get credential helper status
+                    const { stdout } = await execPromise('git config --global credential.helper', {
+                        timeout: 5000
+                    });
+                    if (stdout.trim()) {
+                        source = `git credential.helper: ${stdout.trim()}`;
+                        // Note: We can't directly read credentials from git credential-store
+                        // without invoking the credential helper, which is complex.
+                        // We just inform the user that a helper is configured.
+                    }
+                }
+                catch {
+                    // Git not available or no credential helper
+                }
+            }
+            // If we have a token, validate it and get user info
+            let userInfo = null;
+            let tokenValid = false;
+            let tokenScopes = [];
+            if (token) {
+                try {
+                    const response = await fetch('https://api.github.com/user', {
+                        headers: {
+                            'Authorization': `token ${token}`,
+                            'Accept': 'application/vnd.github.v3+json',
+                            'User-Agent': 'anchor-engine-node',
+                        }
+                    });
+                    if (response.ok) {
+                        const data = await response.json();
+                        userInfo = { login: data.login, name: data.name };
+                        tokenValid = true;
+                        // Get scopes from headers
+                        const scopesHeader = response.headers.get('x-oauth-scopes');
+                        if (scopesHeader) {
+                            tokenScopes = scopesHeader.split(',').map(s => s.trim());
+                        }
+                    }
+                }
+                catch (error) {
+                    console.error('[API] GitHub token validation error:', error.message);
+                }
+            }
+            const hasCredentials = !!token;
+            const canAccessPrivateRepos = tokenValid && (tokenScopes.includes('repo') || tokenScopes.includes('public_repo'));
+            res.status(200).json({
+                has_credentials: hasCredentials,
+                credential_source: source,
+                username: username || userInfo?.login || null,
+                user_info: userInfo,
+                token_valid: tokenValid,
+                scopes: tokenScopes,
+                can_access_private_repos: canAccessPrivateRepos,
+                message: hasCredentials
+                    ? (canAccessPrivateRepos
+                        ? 'GitHub credentials found. You can access both public and private repositories.'
+                        : 'GitHub credentials found but may be limited to public repositories only.')
+                    : 'No GitHub credentials found. You can only access public repositories.',
+            });
+        }
+        catch (error) {
+            console.error('[API] GitHub credentials check error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // Helper to discover allowed git repositories
+    const getDiscoveredRepos = async () => {
+        const path = await import('path');
+        const fs = await import('fs');
+        const { pathManager } = await import('../../utils/path-manager.js');
+        const { PROJECT_ROOT } = await import('../../config/paths.js');
+        const potentialRepos = [];
+        const basePath = pathManager.getBasePath();
+        const checkDirs = [
+            basePath,
+            path.join(basePath, '..'),
+            path.join(basePath, '..', '..'),
+            PROJECT_ROOT
+        ];
+        for (const dir of checkDirs) {
+            if (!dir)
+                continue;
+            try {
+                const entries = fs.readdirSync(dir, { withFileTypes: true });
+                for (const entry of entries) {
+                    if (entry.isDirectory()) {
+                        const repoPath = path.join(dir, entry.name);
+                        const gitPath = path.join(repoPath, '.git');
+                        // Resolve to absolute path to prevent traversal evasion
+                        const absoluteRepoPath = path.resolve(repoPath);
+                        if (fs.existsSync(gitPath) && !potentialRepos.includes(absoluteRepoPath)) {
+                            potentialRepos.push(absoluteRepoPath);
+                        }
+                    }
+                }
+            }
+            catch {
+                // Skip if directory doesn't exist or can't be read
+            }
+        }
+        return potentialRepos;
+    };
+    // GET /v1/git/repos - List available git repositories
+    app.get('/v1/git/repos', async (_req, res) => {
+        try {
+            const repos = await getDiscoveredRepos();
+            res.status(200).json(repos);
+        }
+        catch (error) {
+            console.error('[API] Git repos list error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    // POST /v1/git/run - Execute git command
+    app.post('/v1/git/run', async (req, res) => {
+        try {
+            const { command, working_dir } = req.body;
+            if (!command || !working_dir) {
+                return res.status(400).json({ error: 'command and working_dir are required' });
+            }
+            const { execFile } = await import('child_process');
+            const util = await import('util');
+            const path = await import('path');
+            const execFilePromise = util.promisify(execFile);
+            // Security: Resolve requested directory to absolute path and verify it's a discovered repository
+            const absoluteRequestedDir = path.resolve(working_dir);
+            const allowedRepos = await getDiscoveredRepos();
+            if (!allowedRepos.includes(absoluteRequestedDir)) {
+                console.warn(`[Git] Rejected unauthorized directory access: ${working_dir} (resolved: ${absoluteRequestedDir})`);
+                return res.status(403).json({ error: 'Directory not authorized for git commands' });
+            }
+            // Security: Strict whitelist of allowed git commands and their arguments
+            const allowedCommands = {
+                'status': ['status'],
+                'log --oneline -20': ['log', '--oneline', '-20'],
+                'log --graph --oneline -15': ['log', '--graph', '--oneline', '-15'],
+                'diff': ['diff'],
+                'diff --cached': ['diff', '--cached'],
+                'branch -a': ['branch', '-a'],
+                'remote -v': ['remote', '-v']
+            };
+            if (!(command in allowedCommands)) {
+                console.warn(`[Git] Rejected unauthorized command: ${command} in ${absoluteRequestedDir}`);
+                return res.status(400).json({ error: 'Command not allowed for security reasons' });
+            }
+            const args = allowedCommands[command];
+            console.log(`[Git] Running: git ${args.join(' ')} in ${absoluteRequestedDir}`);
+            try {
+                const { stdout, stderr } = await execFilePromise('git', args, {
+                    cwd: absoluteRequestedDir,
+                    encoding: 'utf8',
+                    timeout: 30000 // 30 second timeout
+                });
+                res.status(200).json({
+                    command,
+                    output: stdout || stderr,
+                    success: true
+                });
+            }
+            catch (execError) {
+                // Git command failed - return error output
+                res.status(200).json({
+                    command,
+                    output: execError.stdout || '',
+                    error: execError.stderr || execError.message,
+                    success: false
+                });
+            }
+        }
+        catch (error) {
+            console.error('[API] Git command execution error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+}
+//# sourceMappingURL=git.js.map

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

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

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

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

@@ -0,0 +1 @@
+{"version":3,"file":"ingest.d.ts","sourceRoot":"","sources":["../../../src/routes/v1/ingest.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAqB,MAAM,SAAS,CAAC;AAMzD,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,WAAW,QA2EjD"}

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

@@ -0,0 +1,66 @@
+import { validate, schemas } from '../../middleware/validate.js';
+import { StructuredLogger } from '../../utils/structured-logger.js';
+import { AtomizerService } from '../../services/ingest/atomizer-service.js';
+import { AtomicIngestService } from '../../services/ingest/ingest-atomic.js';
+export function setupIngestRoutes(app) {
+    // Ingestion endpoint (Atomic Architecture)
+    app.post('/v1/ingest', validate(schemas.ingest), async (req, res) => {
+        const startTime = Date.now();
+        try {
+            const { content, source, type, bucket, buckets = [], tags = [] } = req.body;
+            if (!content) {
+                StructuredLogger.warn('INGEST_INVALID_REQUEST', { error: 'Content is required' });
+                res.status(400).json({ error: 'Content is required' });
+                return;
+            }
+            StructuredLogger.info('INGEST_REQUEST', {
+                source: source || 'api_upload',
+                content_length: content.length,
+                buckets: buckets.length > 0 ? buckets : [bucket || 'notebook']
+            });
+            // Use legacy Atomizer pipeline for performance
+            const atomizer = new AtomizerService();
+            const atomicIngest = new AtomicIngestService();
+            const provenance = (source && (source.includes('external') || source.includes('web'))) ? 'external' : 'internal';
+            const atomizeResult = await atomizer.atomize(content, source || 'api_upload', provenance);
+            // Skip ingestion if transient data was detected
+            if (!atomizeResult) {
+                const result = {
+                    status: 'skipped',
+                    message: 'Content skipped (transient data detected)',
+                    id: null,
+                    duration_ms: Date.now() - startTime
+                };
+                return res.json(result);
+            }
+            const { compound, molecules, atoms } = atomizeResult;
+            // Ingest result
+            const targetBuckets = buckets.length > 0 ? buckets : [bucket || 'notebook'];
+            await atomicIngest.ingestResult(compound, molecules, atoms, targetBuckets);
+            const duration = Date.now() - startTime;
+            StructuredLogger.ingestion('success', {
+                source: source || 'api_upload',
+                compound_id: compound.id,
+                atoms_count: atoms.length,
+                molecules_count: molecules.length,
+                buckets: targetBuckets,
+                duration_ms: duration
+            });
+            const result = {
+                status: 'success',
+                message: `Ingested ${atoms.length} atoms and ${molecules.length} molecules`,
+                id: compound.id,
+                duration_ms: duration
+            };
+            res.status(200).json(result);
+        }
+        catch (e) {
+            const duration = Date.now() - startTime;
+            StructuredLogger.error('INGEST_ERROR', e, {
+                duration_ms: duration
+            });
+            res.status(500).json({ error: e.message });
+        }
+    });
+}
+//# sourceMappingURL=ingest.js.map

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

@@ -0,0 +1 @@
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package/engine/dist/routes/v1/memory.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Memory routes — explore / illuminate endpoint
+ *
+ * POST /v1/memory/explore
+ *   BFS graph traversal from seed concepts.
+ *   Returns the connected subgraph as structural corpus compression.
+ *
+ * POST /v1/memory/distill
+ *   Standard 133: Radial Distillation
+ *   Line-level deduplication with radial inflation.
+ */
+import { Application } from 'express';
+export declare function setupMemoryRoutes(app: Application): void;
+//# sourceMappingURL=memory.d.ts.map

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

@@ -0,0 +1 @@
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package/engine/dist/routes/v1/memory.js

@@ -0,0 +1,87 @@
+/**
+ * Memory routes — explore / illuminate endpoint
+ *
+ * POST /v1/memory/explore
+ *   BFS graph traversal from seed concepts.
+ *   Returns the connected subgraph as structural corpus compression.
+ *
+ * POST /v1/memory/distill
+ *   Standard 133: Radial Distillation
+ *   Line-level deduplication with radial inflation.
+ */
+import { StructuredLogger } from '../../utils/structured-logger.js';
+import { exploreMemory } from '../../services/search/explore.js';
+import { radialDistill } from '../../services/distillation/radial-distiller.js';
+export function setupMemoryRoutes(app) {
+    app.post('/v1/memory/explore', async (req, res) => {
+        const startTime = Date.now();
+        StructuredLogger.info('EXPLORE_REQUEST', { endpoint: '/v1/memory/explore' });
+        try {
+            const body = req.body;
+            if (!body?.seed || (!body.seed.global && !body.seed.query && !body.seed.atom_ids?.length)) {
+                res.status(400).json({ error: 'seed.query, seed.atom_ids, or seed.global:true is required' });
+                return;
+            }
+            const result = await exploreMemory(body);
+            const duration = Date.now() - startTime;
+            StructuredLogger.info('EXPLORE_COMPLETE', {
+                nodes: result.stats.nodes_count,
+                strategy: result.stats.strategy,
+                duration_ms: duration
+            });
+            // Normalise to a consistent shape regardless of flat/graph format
+            if (result.nodes !== undefined && !('results' in result)) {
+                // graph or flat — return as-is but also expose `results` alias for MCP compatibility
+                res.json({
+                    ...result,
+                    results: result.nodes.map(n => ({
+                        id: n.id,
+                        content: n.content,
+                        source: n.source,
+                        tags: n.tags,
+                        score: 1
+                    })),
+                    duration_ms: duration
+                });
+            }
+            else {
+                res.json({ ...result, duration_ms: duration });
+            }
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            StructuredLogger.error('EXPLORE_ERROR', err instanceof Error ? err : new Error(msg), { error: msg });
+            res.status(500).json({ error: msg });
+        }
+    });
+    app.post('/v1/memory/distill', async (req, res) => {
+        const startTime = Date.now();
+        StructuredLogger.info('DISTILL_REQUEST', {
+            endpoint: '/v1/memory/distill',
+            mode: 'radial'
+        });
+        try {
+            // Standard 133: Radial Distillation (only mode supported)
+            const body = req.body;
+            const result = await radialDistill(body);
+            const duration = Date.now() - startTime;
+            StructuredLogger.info('RADIAL_DISTILL_COMPLETE', {
+                compounds_processed: result.stats.compounds_processed,
+                lines_total: result.stats.lines_total,
+                lines_unique: result.stats.lines_unique,
+                compression_ratio: result.stats.compression_ratio,
+                duration_ms: duration
+            });
+            res.json({
+                ...result,
+                duration_ms: duration
+            });
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            StructuredLogger.error('DISTILL_ERROR', err instanceof Error ? err : new Error(msg), { error: msg });
+            res.status(500).json({ error: msg });
+        }
+    });
+}
+//# sourceMappingURL=memory.js.map

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

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

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

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

@@ -0,0 +1 @@
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package/engine/dist/routes/v1/research.js

@@ -0,0 +1,109 @@
+import path from 'path';
+import fs from 'fs';
+import { validate, schemas } from '../../middleware/validate.js';
+import { fetchAndProcess, searchWeb } from '../../services/research/researcher.js';
+import { ENGINE_PLUGINS } from '../../config/paths.js';
+export function setupResearchRoutes(app) {
+    // Research Plugin Endpoint
+    app.post('/v1/research/scrape', validate(schemas.researchScrape), async (req, res) => {
+        try {
+            const { url, category } = req.body;
+            if (!url) {
+                res.status(400).json({ error: 'URL required' });
+                return;
+            }
+            const result = await fetchAndProcess(url, category || 'article');
+            if (result.success) {
+                res.status(200).json(result);
+            }
+            else {
+                res.status(500).json(result);
+            }
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // POST /v1/research/upload-raw - Save raw content as file
+    app.post('/v1/research/upload-raw', async (req, res) => {
+        try {
+            const { content, filename } = req.body;
+            if (!content || !filename) {
+                res.status(400).json({ error: 'Content and filename required' });
+                return;
+            }
+            // Route to: engine/plugins/articles
+            const targetDir = path.join(ENGINE_PLUGINS, 'articles');
+            if (!fs.existsSync(targetDir))
+                fs.mkdirSync(targetDir, { recursive: true });
+            // Fix for Arbitrary File Write via Path Traversal
+            // Ensure filename does not contain directory traversal characters
+            const safeFilename = path.basename(filename);
+            const filePath = path.join(targetDir, safeFilename);
+            await fs.promises.writeFile(filePath, content, 'utf8');
+            console.log(`[Research] Manual upload saved: ${filePath}`);
+            res.status(200).json({ success: true, filePath });
+        }
+        catch (e) {
+            console.error('[Research] Upload failed:', e.message);
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // Web Search Endpoint
+    app.get('/v1/research/web-search', async (req, res) => {
+        try {
+            const q = req.query['q'];
+            if (!q) {
+                res.status(400).json({ error: 'Query required' });
+                return;
+            }
+            const results = await searchWeb(q);
+            res.status(200).json(results);
+        }
+        catch (e) {
+            res.status(500).json({ error: e.message });
+        }
+    });
+    // Compatibility: /v1/research/github -> proxy to /v1/github/repos
+    app.get('/v1/research/github', async (_req, res) => {
+        try {
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            const repos = await service.listRepos();
+            res.status(200).json(repos);
+        }
+        catch (error) {
+            console.error('[API] GitHub repo list error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+    app.post('/v1/research/github', async (req, res) => {
+        try {
+            const body = req.body;
+            // UI sends 'repo', but we also support 'url' for compatibility
+            const repoUrl = body.repo || body.url;
+            const bucket = body.bucket || 'code';
+            const branch = body.branch || 'main';
+            if (!repoUrl) {
+                res.status(400).json({ error: 'repo (or url) and bucket are required' });
+                return;
+            }
+            const { GitHubIngestService } = await import('../../services/ingest/github-ingest-service.js');
+            const service = new GitHubIngestService();
+            const repo = await service.registerRepo(repoUrl, bucket);
+            service.syncRepo(repo.id).catch((error) => {
+                console.error(`[API] Background sync failed for ${repo.id}:`, error);
+            });
+            res.status(202).json({
+                id: repo.id,
+                status: 'ingesting',
+                message: `Started ingestion for ${repo.owner}/${repo.repo}`,
+            });
+        }
+        catch (error) {
+            console.error('[API] GitHub repo registration error:', error);
+            res.status(500).json({ error: error.message });
+        }
+    });
+}
+//# sourceMappingURL=research.js.map