@hongmaple0820/med-scale-research-os 0.43.0

package/dist/knowledge/CerebrumManager.js

@@ -0,0 +1,127 @@
+// SCALE Engine 鈥?Cerebrum Manager
+// Manages Do-Not-Repeat rules and user preferences via the Knowledge Base.
+// Inspired by OpenWolf's cerebrum system.
+export class CerebrumManager {
+    constructor(kb) {
+        this.kb = kb;
+        this.entries = [];
+    }
+    async addDoNotRepeat(pattern, description) {
+        const kbEntry = await this.kb.add({
+            type: 'do_not_repeat',
+            title: pattern,
+            tags: ['cerebrum', 'do_not_repeat'],
+            contentRef: description,
+            verified: true,
+            verifiedBy: 'cerebrum',
+            verifiedAt: Date.now(),
+        });
+        const entry = {
+            id: kbEntry.id,
+            type: 'do_not_repeat',
+            pattern,
+            description,
+            createdAt: kbEntry.createdAt,
+            hitCount: 0,
+        };
+        this.entries.push(entry);
+        return entry;
+    }
+    async addPreference(description, tags = []) {
+        const kbEntry = await this.kb.add({
+            type: 'preference',
+            title: description,
+            tags: ['cerebrum', 'preference', ...tags],
+            contentRef: description,
+            verified: true,
+            verifiedBy: 'cerebrum',
+            verifiedAt: Date.now(),
+        });
+        const entry = {
+            id: kbEntry.id,
+            type: 'preference',
+            pattern: description,
+            description,
+            createdAt: kbEntry.createdAt,
+            hitCount: 0,
+        };
+        this.entries.push(entry);
+        return entry;
+    }
+    check(content) {
+        const hits = [];
+        const contentTokens = tokenize(content);
+        for (const entry of this.entries) {
+            if (entry.type !== 'do_not_repeat')
+                continue;
+            const patternTokens = tokenize(entry.pattern);
+            const overlap = contentTokens.filter(w => patternTokens.includes(w));
+            if (overlap.length > 0 && overlap.length >= Math.ceil(patternTokens.length * 0.4)) {
+                entry.hitCount++;
+                hits.push({ entry, matchedWords: overlap });
+            }
+        }
+        return hits;
+    }
+    async loadAll() {
+        const doNotRepeat = await this.kb.recall({ type: 'do_not_repeat', limit: 200 });
+        const preferences = await this.kb.recall({ type: 'preference', limit: 200 });
+        this.entries = [
+            ...doNotRepeat.map(e => this.fromKbEntry(e, 'do_not_repeat')),
+            ...preferences.map(e => this.fromKbEntry(e, 'preference')),
+        ];
+        return this.entries;
+    }
+    toMarkdown() {
+        const lines = [
+            '# cerebrum.md',
+            '',
+            `> Auto-maintained by SCALE Engine. Last updated: ${new Date().toISOString()}`,
+            '',
+        ];
+        const dnr = this.entries.filter(e => e.type === 'do_not_repeat');
+        const prefs = this.entries.filter(e => e.type === 'preference');
+        if (dnr.length > 0) {
+            lines.push('## Do Not Repeat');
+            lines.push('');
+            for (const e of dnr) {
+                lines.push(`- **${e.pattern}** - ${e.description} (hits: ${e.hitCount})`);
+            }
+            lines.push('');
+        }
+        if (prefs.length > 0) {
+            lines.push('## Preferences');
+            lines.push('');
+            for (const e of prefs) {
+                lines.push(`- ${e.description}`);
+            }
+            lines.push('');
+        }
+        if (dnr.length === 0 && prefs.length === 0) {
+            lines.push('_No entries yet._');
+            lines.push('');
+        }
+        return lines.join('\n');
+    }
+    getEntries() {
+        return this.entries;
+    }
+    fromKbEntry(kb, type) {
+        return {
+            id: kb.id,
+            type,
+            pattern: kb.title,
+            description: kb.contentRef || kb.title,
+            createdAt: kb.createdAt,
+            hitCount: kb.accessCount,
+        };
+    }
+}
+function tokenize(text) {
+    return text
+        .toLowerCase()
+        .replace(/[^\p{L}\p{N}_]+/gu, ' ')
+        .split(/\s+/)
+        .filter(w => w.length > 2);
+}
+//# sourceMappingURL=CerebrumManager.js.map

package/dist/knowledge/CerebrumManager.js.map

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package/dist/knowledge/GraphifyKnowledgeBase.d.ts

@@ -0,0 +1,38 @@
+import type { KnowledgeEntry, KnowledgeQuery } from '../artifact/types.js';
+import type { IEventBus } from '../core/eventBus.js';
+import type { IKnowledgeBase } from './KnowledgeBase.js';
+interface GraphifyKnowledgeBaseOptions {
+    projectDir?: string;
+    scaleDir?: string;
+    graphPath?: string;
+    reportPath?: string;
+    entriesDir?: string;
+}
+export declare class GraphifyKnowledgeBase implements IKnowledgeBase {
+    private eventBus;
+    private projectDir;
+    private scaleRoot;
+    private graphPath;
+    private reportPath;
+    private entriesDir;
+    private indexPath;
+    private seq;
+    constructor(eventBus: IEventBus, options?: GraphifyKnowledgeBaseOptions);
+    add(input: Omit<KnowledgeEntry, 'id' | 'createdAt' | 'accessCount' | 'relevance'>): Promise<KnowledgeEntry>;
+    recall(query: KnowledgeQuery): Promise<KnowledgeEntry[]>;
+    recallByVector(text: string, topK: number): Promise<KnowledgeEntry[]>;
+    markHelpful(id: string, sessionId: string): Promise<void>;
+    markUseless(id: string, sessionId: string): Promise<void>;
+    verify(id: string, verifiedBy: string): Promise<void>;
+    decay(): Promise<void>;
+    private searchOverlay;
+    private searchGraph;
+    private searchGraphWithCli;
+    private graphEntries;
+    private loadGraphDocument;
+    private loadOverlayEntries;
+    private loadOverlayRecords;
+    private writeOverlayRecords;
+    private generateId;
+}
+export {};

package/dist/knowledge/GraphifyKnowledgeBase.js

@@ -0,0 +1,409 @@
+import { existsSync, mkdirSync, readFileSync, readdirSync, writeFileSync } from 'node:fs';
+import { dirname, isAbsolute, join, resolve } from 'node:path';
+import { externalCommandExists, runExternalCommandSync } from '../core/ExternalCommand.js';
+export class GraphifyKnowledgeBase {
+    constructor(eventBus, options = {}) {
+        this.eventBus = eventBus;
+        this.seq = 0;
+        this.projectDir = resolve(options.projectDir ?? process.cwd());
+        this.scaleRoot = resolveScaleRoot(this.projectDir, options.scaleDir);
+        this.graphPath = resolveProjectPath(this.projectDir, options.graphPath ?? join('graphify-out', 'graph.json'));
+        this.reportPath = resolveProjectPath(this.projectDir, options.reportPath ?? join('graphify-out', 'GRAPH_REPORT.md'));
+        this.entriesDir = resolveProjectPath(this.projectDir, options.entriesDir ?? join(this.scaleRoot, 'graphify-knowledge', 'entries'));
+        this.indexPath = join(dirname(this.entriesDir), 'index.json');
+        this.seq = this.loadOverlayEntries().length;
+    }
+    async add(input) {
+        const entry = {
+            ...input,
+            id: this.generateId(),
+            createdAt: Date.now(),
+            accessCount: 0,
+            relevance: 0.5,
+        };
+        const record = {
+            entry,
+            notePath: join(this.entriesDir, `${entry.id}.md`),
+        };
+        const records = this.loadOverlayRecords();
+        records.push(record);
+        this.writeOverlayRecords(records);
+        this.eventBus.emit('lesson.proposed', { lessonId: entry.id }, { artifactId: input.sourceArtifact });
+        return entry;
+    }
+    async recall(query) {
+        const records = this.loadOverlayRecords()
+            .map(record => record.entry)
+            .filter(entry => matchesKnowledgeQuery(entry, query))
+            .sort((a, b) => b.relevance - a.relevance || b.createdAt - a.createdAt);
+        if (records.length > 0)
+            return records.slice(0, query.limit ?? 10);
+        const graphEntries = this.graphEntries(query.limit ?? 10)
+            .filter(entry => matchesKnowledgeQuery(entry, query))
+            .sort((a, b) => b.relevance - a.relevance);
+        return graphEntries.slice(0, query.limit ?? 10);
+    }
+    async recallByVector(text, topK) {
+        const overlayHits = this.searchOverlay(text, topK);
+        const graphHits = this.searchGraph(text, topK);
+        const merged = dedupeKnowledgeEntries([...overlayHits, ...graphHits])
+            .sort((a, b) => b.relevance - a.relevance || b.accessCount - a.accessCount)
+            .slice(0, topK);
+        if (merged.length > 0)
+            return merged;
+        return this.recall({ verifiedOnly: true, limit: topK });
+    }
+    async markHelpful(id, sessionId) {
+        const records = this.loadOverlayRecords();
+        const record = records.find(item => item.entry.id === id);
+        if (!record)
+            return;
+        record.entry.relevance = Math.min(1, record.entry.relevance + 0.05);
+        record.entry.accessCount += 1;
+        record.entry.lastAccessed = Date.now();
+        this.writeOverlayRecords(records);
+        this.eventBus.emit('lesson.helpful', { lessonId: id }, { sessionId });
+    }
+    async markUseless(id, sessionId) {
+        const records = this.loadOverlayRecords();
+        const record = records.find(item => item.entry.id === id);
+        if (!record)
+            return;
+        record.entry.relevance = Math.max(0.05, record.entry.relevance - 0.1);
+        this.writeOverlayRecords(records);
+        this.eventBus.emit('lesson.useless', { lessonId: id }, { sessionId });
+    }
+    async verify(id, verifiedBy) {
+        const records = this.loadOverlayRecords();
+        const record = records.find(item => item.entry.id === id);
+        if (!record)
+            return;
+        record.entry.verified = true;
+        record.entry.verifiedBy = verifiedBy;
+        record.entry.verifiedAt = Date.now();
+        this.writeOverlayRecords(records);
+        this.eventBus.emit('lesson.approved', { lessonId: id, verifiedBy });
+    }
+    async decay() {
+        const DAY = 24 * 60 * 60 * 1000;
+        const now = Date.now();
+        const records = this.loadOverlayRecords();
+        for (const record of records) {
+            const days = record.entry.lastAccessed ? (now - record.entry.lastAccessed) / DAY : 90;
+            const recency = Math.exp(-days / 30);
+            record.entry.relevance = Math.max(0.05, record.entry.relevance * 0.95 + recency * 0.05);
+        }
+        this.writeOverlayRecords(records);
+    }
+    searchOverlay(text, topK) {
+        const tokens = tokenize(text);
+        if (tokens.length === 0)
+            return [];
+        return this.loadOverlayRecords()
+            .map(record => {
+            const corpus = [
+                record.entry.title,
+                record.entry.tags.join(' '),
+                record.entry.contentRef,
+                previewText(record.notePath),
+            ].join(' ');
+            return {
+                entry: record.entry,
+                score: scoreText(tokens, corpus),
+            };
+        })
+            .filter(item => item.score > 0)
+            .sort((a, b) => b.score - a.score || b.entry.relevance - a.entry.relevance)
+            .slice(0, topK)
+            .map(item => ({
+            ...item.entry,
+            relevance: Math.min(1, Math.max(item.entry.relevance, item.score)),
+        }));
+    }
+    searchGraph(text, topK) {
+        const cliHits = this.searchGraphWithCli(text, topK);
+        if (cliHits.length > 0)
+            return cliHits;
+        const graph = this.loadGraphDocument();
+        const nodes = graphNodes(graph);
+        const tokens = tokenize(text);
+        return nodes
+            .map(node => {
+            const corpus = nodeCorpus(node);
+            return {
+                node,
+                score: scoreText(tokens, corpus),
+            };
+        })
+            .filter(item => item.score > 0)
+            .sort((a, b) => b.score - a.score)
+            .slice(0, topK)
+            .map((item, index) => nodeToKnowledgeEntry(item.node, index, item.score));
+    }
+    searchGraphWithCli(text, topK) {
+        if (!commandExists('graphify') || !existsSync(this.graphPath))
+            return [];
+        try {
+            const output = runExternalCommandSync('graphify', ['query', text, '--graph', this.graphPath], {
+                encoding: 'utf-8',
+                timeout: 5_000,
+                stdio: ['ignore', 'pipe', 'pipe'],
+            });
+            const lines = String(output).split(/\r?\n/).map((line) => line.trim()).filter(Boolean);
+            return lines.slice(0, topK).map((line, index) => ({
+                id: `GRAPHIFY-CLI-${index + 1}`,
+                type: 'reference',
+                title: truncate(line, 140),
+                tags: ['graphify', 'cli-query'],
+                contentRef: normalizeProjectPath(this.projectDir, this.graphPath),
+                relevance: Math.max(0.55, 0.95 - index * 0.05),
+                accessCount: 0,
+                verified: true,
+                verifiedBy: 'graphify',
+                verifiedAt: Date.now(),
+                createdAt: Date.now(),
+            }));
+        }
+        catch {
+            return [];
+        }
+    }
+    graphEntries(limit) {
+        const nodes = graphNodes(this.loadGraphDocument())
+            .slice(0, limit)
+            .map((node, index) => nodeToKnowledgeEntry(node, index, 0.5));
+        if (nodes.length > 0)
+            return nodes;
+        if (!existsSync(this.reportPath))
+            return [];
+        return [{
+                id: 'GRAPHIFY-REPORT-1',
+                type: 'reference',
+                title: 'Graphify project report',
+                tags: ['graphify', 'report'],
+                contentRef: normalizeProjectPath(this.projectDir, this.reportPath),
+                relevance: 0.5,
+                accessCount: 0,
+                verified: true,
+                verifiedBy: 'graphify',
+                verifiedAt: Date.now(),
+                createdAt: Date.now(),
+            }];
+    }
+    loadGraphDocument() {
+        if (!existsSync(this.graphPath))
+            return null;
+        try {
+            return JSON.parse(readFileSync(this.graphPath, 'utf-8'));
+        }
+        catch {
+            return null;
+        }
+    }
+    loadOverlayEntries() {
+        return this.loadOverlayRecords().map(record => record.entry);
+    }
+    loadOverlayRecords() {
+        if (!existsSync(this.indexPath))
+            return [];
+        try {
+            const parsed = JSON.parse(readFileSync(this.indexPath, 'utf-8'));
+            if (!Array.isArray(parsed))
+                return [];
+            return parsed
+                .map(item => ({
+                entry: item.entry,
+                notePath: String(item.notePath ?? ''),
+            }))
+                .filter(item => item.entry?.id && item.notePath);
+        }
+        catch {
+            return [];
+        }
+    }
+    writeOverlayRecords(records) {
+        mkdirSync(this.entriesDir, { recursive: true });
+        writeFileSync(this.indexPath, JSON.stringify(records, null, 2), 'utf-8');
+        for (const record of records) {
+            writeFileSync(record.notePath, renderKnowledgeNote(record.entry), 'utf-8');
+        }
+        const existing = existsSync(this.entriesDir) ? readdirSync(this.entriesDir) : [];
+        for (const file of existing) {
+            if (!file.endsWith('.md'))
+                continue;
+            const absolute = join(this.entriesDir, file);
+            if (!records.some(record => record.notePath === absolute)) {
+                try {
+                    writeFileSync(absolute, '', 'utf-8');
+                }
+                catch {
+                    // ignore stale note cleanup failures
+                }
+            }
+        }
+    }
+    generateId() {
+        this.seq = (this.seq + 1) % 10000;
+        return `KB-${Date.now()}-${this.seq.toString().padStart(4, '0')}`;
+    }
+}
+function graphNodes(document) {
+    if (!document || typeof document !== 'object')
+        return [];
+    const record = document;
+    const direct = Array.isArray(record.nodes) ? record.nodes : [];
+    if (direct.length > 0)
+        return direct.filter(isRecord);
+    const graph = isRecord(record.graph) && Array.isArray(record.graph.nodes) ? record.graph.nodes : [];
+    if (graph.length > 0)
+        return graph.filter(isRecord);
+    const elements = isRecord(record.elements) && Array.isArray(record.elements.nodes) ? record.elements.nodes : [];
+    return elements.filter(isRecord);
+}
+function nodeToKnowledgeEntry(node, index, score) {
+    const now = Date.now();
+    const title = firstString(node.title, node.label, node.name, nestedValue(node, ['data', 'title']), nestedValue(node, ['data', 'label']), nestedValue(node, ['data', 'name'])) ?? `Graphify node ${index + 1}`;
+    const contentRef = normalizePath(firstString(node.file, node.path, nestedValue(node, ['source', 'path']), nestedValue(node, ['source', 'file']), nestedValue(node, ['data', 'file']), nestedValue(node, ['data', 'path'])) ?? 'graphify-out/graph.json');
+    const tags = dedupeStrings([
+        'graphify',
+        firstString(node.type, node.kind, nestedValue(node, ['data', 'type']), nestedValue(node, ['data', 'kind'])),
+    ]);
+    return {
+        id: firstString(node.id, nestedValue(node, ['data', 'id'])) ?? `GRAPHIFY-${index + 1}`,
+        type: 'reference',
+        title: truncate(title, 140),
+        tags,
+        contentRef,
+        relevance: Math.min(1, Math.max(0.45, score)),
+        accessCount: 0,
+        verified: true,
+        verifiedBy: 'graphify',
+        verifiedAt: now,
+        createdAt: now,
+    };
+}
+function nodeCorpus(node) {
+    return [
+        firstString(node.title, node.label, node.name, node.text, node.summary, nestedValue(node, ['data', 'title']), nestedValue(node, ['data', 'label']), nestedValue(node, ['data', 'name']), nestedValue(node, ['data', 'text']), nestedValue(node, ['data', 'summary'])) ?? '',
+        firstString(node.file, node.path, nestedValue(node, ['source', 'path']), nestedValue(node, ['source', 'file']), nestedValue(node, ['data', 'file']), nestedValue(node, ['data', 'path'])) ?? '',
+        dedupeStrings([
+            firstString(node.type, node.kind, nestedValue(node, ['data', 'type']), nestedValue(node, ['data', 'kind'])),
+        ]).join(' '),
+    ].join(' ');
+}
+function matchesKnowledgeQuery(entry, query) {
+    if (query.type) {
+        const types = Array.isArray(query.type) ? query.type : [query.type];
+        if (!types.includes(entry.type))
+            return false;
+    }
+    if (query.tags && query.tags.some(tag => !entry.tags.includes(tag)))
+        return false;
+    if (query.minRelevance !== undefined && entry.relevance < query.minRelevance)
+        return false;
+    if (query.verifiedOnly && !entry.verified)
+        return false;
+    return true;
+}
+function scoreText(tokens, corpus) {
+    if (tokens.length === 0)
+        return 0;
+    const haystack = corpus.toLowerCase();
+    let hits = 0;
+    for (const token of tokens) {
+        if (haystack.includes(token))
+            hits += 1;
+    }
+    return hits === 0 ? 0 : Math.min(0.98, hits / tokens.length);
+}
+function previewText(path) {
+    if (!existsSync(path))
+        return '';
+    try {
+        return readFileSync(path, 'utf-8').slice(0, 800);
+    }
+    catch {
+        return '';
+    }
+}
+function renderKnowledgeNote(entry) {
+    const lines = [
+        '---',
+        `id: ${entry.id}`,
+        `type: ${entry.type}`,
+        `verified: ${entry.verified}`,
+        `relevance: ${entry.relevance}`,
+        `createdAt: ${entry.createdAt}`,
+        `contentRef: ${entry.contentRef}`,
+        'tags:',
+        ...entry.tags.map(tag => `  - ${tag}`),
+        '---',
+        '',
+        `# ${entry.title}`,
+        '',
+        `- Source Artifact: ${entry.sourceArtifact ?? 'n/a'}`,
+        `- Verified By: ${entry.verifiedBy ?? 'n/a'}`,
+        '',
+        '## Notes',
+        '',
+        entry.contentRef || 'No additional notes recorded.',
+        '',
+    ];
+    return lines.join('\n');
+}
+function dedupeKnowledgeEntries(entries) {
+    const seen = new Map();
+    for (const entry of entries) {
+        const key = `${entry.id}::${entry.contentRef}`;
+        const existing = seen.get(key);
+        if (!existing || existing.relevance < entry.relevance)
+            seen.set(key, entry);
+    }
+    return [...seen.values()];
+}
+function tokenize(text) {
+    return text
+        .toLowerCase()
+        .replace(/[^\p{L}\p{N}_]+/gu, ' ')
+        .split(/\s+/)
+        .filter(token => token.length > 2);
+}
+function truncate(value, maxChars) {
+    return value.length > maxChars ? `${value.slice(0, maxChars - 3)}...` : value;
+}
+function dedupeStrings(values) {
+    return [...new Set(values.filter((value) => Boolean(value && value.trim())).map(value => value.trim()))];
+}
+function firstString(...values) {
+    return values.map(value => typeof value === 'string' ? value.trim() : '').find(Boolean);
+}
+function nestedValue(record, path) {
+    let cursor = record;
+    for (const segment of path) {
+        if (!isRecord(cursor))
+            return undefined;
+        cursor = cursor[segment];
+    }
+    return cursor;
+}
+function normalizePath(value) {
+    return value.replace(/\\/g, '/');
+}
+function normalizeProjectPath(projectDir, targetPath) {
+    const absolute = isAbsolute(targetPath) ? targetPath : resolve(projectDir, targetPath);
+    const relativePath = normalizePath(absolute.startsWith(projectDir) ? absolute.slice(projectDir.length).replace(/^[/\\]+/, '') : targetPath);
+    return relativePath || normalizePath(targetPath);
+}
+function resolveScaleRoot(projectDir, scaleDir) {
+    return isAbsolute(scaleDir ?? '') ? String(scaleDir) : join(projectDir, scaleDir ?? '.scale');
+}
+function resolveProjectPath(projectDir, targetPath) {
+    return isAbsolute(targetPath) ? targetPath : resolve(projectDir, targetPath);
+}
+function isRecord(value) {
+    return Boolean(value) && typeof value === 'object' && !Array.isArray(value);
+}
+function commandExists(command) {
+    return externalCommandExists(command);
+}
+//# sourceMappingURL=GraphifyKnowledgeBase.js.map

package/dist/knowledge/GraphifyKnowledgeBase.js.map

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package/dist/knowledge/KnowledgeBase.d.ts

@@ -0,0 +1,51 @@
+import type { KnowledgeEntry, KnowledgeQuery } from '../artifact/types.js';
+import type { IEventBus } from '../core/eventBus.js';
+export interface IKnowledgeBase {
+    add(entry: Omit<KnowledgeEntry, 'id' | 'createdAt' | 'accessCount' | 'relevance'>): Promise<KnowledgeEntry>;
+    recall(query: KnowledgeQuery): Promise<KnowledgeEntry[]>;
+    recallByVector(text: string, topK: number): Promise<KnowledgeEntry[]>;
+    markHelpful(id: string, sessionId: string): Promise<void>;
+    markUseless(id: string, sessionId: string): Promise<void>;
+    verify(id: string, verifiedBy: string): Promise<void>;
+    decay(): Promise<void>;
+}
+export declare class KnowledgeBase implements IKnowledgeBase {
+    private eventBus;
+    private entries;
+    private seq;
+    private documentFrequencies;
+    private totalDocuments;
+    constructor(eventBus: IEventBus);
+    add(input: Omit<KnowledgeEntry, 'id' | 'createdAt' | 'accessCount' | 'relevance'>): Promise<KnowledgeEntry>;
+    recall(query: KnowledgeQuery): Promise<KnowledgeEntry[]>;
+    recallByVector(text: string, topK: number): Promise<KnowledgeEntry[]>;
+    /**
+     * Tokenize text into lowercase terms (simple word splitting)
+     */
+    private tokenize;
+    /**
+     * Calculate term frequency (TF) for a term in a document
+     */
+    private termFrequency;
+    /**
+     * Calculate inverse document frequency (IDF) for a term
+     */
+    private inverseDocumentFrequency;
+    /**
+     * Rebuild document frequency cache
+     */
+    private rebuildDocumentFrequencies;
+    /**
+     * Calculate TF-IDF vector for a document
+     */
+    private tfidfVector;
+    /**
+     * Calculate cosine similarity between two term sets
+     */
+    private cosineSimilarity;
+    markHelpful(id: string, sessionId: string): Promise<void>;
+    markUseless(id: string, sessionId: string): Promise<void>;
+    verify(id: string, verifiedBy: string): Promise<void>;
+    decay(): Promise<void>;
+    private generateId;
+}