cgraphx 1.4.3 → 2.0.1

package/dist/core/markdown/indexer.js

@@ -0,0 +1,256 @@
+"use strict";
+/**
+ * MarkdownIndexer — cover-the-table full rebuild.
+ *
+ * Flow (spec §6.1):
+ *   1. Open shared cgraphx DB; ensure markdown schema.
+ *   2. Scan <projectRoot>/docs/knowledge/ recursively (skip symlinks + dot-dirs).
+ *   3. Extract each .md/.mdx via `extractFromFile`.
+ *   4. In ONE transaction: wipeAll → insert documents/vocabularies/edges →
+ *      resolve document_references → rebuild FTS5.
+ *   5. Return IndexReport.
+ *
+ * Failure handling: any throw inside the transaction triggers ROLLBACK;
+ * the prior index is preserved untouched. The function itself only throws
+ * for unrecoverable problems (DB not initialized, scan dir absolutely
+ * unreadable).
+ *
+ * Not integrated: .gitignore filtering (YAGNI — docs/knowledge/ is a curated
+ * knowledge dir, not a vendor payload). Can be added later if needed.
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.indexMarkdownKnowledgeBase = indexMarkdownKnowledgeBase;
+const node_crypto_1 = __importDefault(require("node:crypto"));
+const node_fs_1 = __importDefault(require("node:fs"));
+const node_path_1 = __importDefault(require("node:path"));
+const constants_1 = require("./constants");
+const extractor_1 = require("./extractor");
+const store_1 = require("./store");
+const schema_bootstrap_1 = require("./schema-bootstrap");
+const EMPTY_SKIP_BREAKDOWN = {
+    no_frontmatter: 0,
+    frontmatter_unclosed: 0,
+    frontmatter_parse_error: 0,
+    field_type_error: 0,
+    missing_required_field: 0,
+    invalid_enum_value: 0,
+    read_error: 0,
+    dangling_reference: 0,
+};
+/**
+ * Index the markdown knowledge base under <projectRoot>/docs/knowledge/.
+ *
+ * Re-uses the shared `.cgraphx/cgraphx.db` (must already exist via
+ * `cgraphx init`). The markdown schema is auto-applied on first call.
+ *
+ * Errors thrown: only for unrecoverable problems. User-data problems
+ * (bad frontmatter, missing fields) are returned via `report.skipBreakdown`.
+ */
+async function indexMarkdownKnowledgeBase(projectRoot, options = {}) {
+    const startedAt = Date.now();
+    const runId = node_crypto_1.default
+        .createHash('sha256')
+        .update(`${projectRoot}:${startedAt}`)
+        .digest('hex')
+        .slice(0, 16);
+    const knowledgeDir = node_path_1.default.join(projectRoot, constants_1.KNOWLEDGE_DIR);
+    if (!node_fs_1.default.existsSync(knowledgeDir)) {
+        return {
+            runId,
+            startedAt,
+            finishedAt: Date.now(),
+            durationMs: 0,
+            scannedFiles: 0,
+            indexedDocuments: 0,
+            skippedFiles: 0,
+            skipBreakdown: { ...EMPTY_SKIP_BREAKDOWN },
+            conceptsCreated: 0,
+            domainsCreated: 0,
+            tagsCreated: 0,
+            referencesCreated: 0,
+            danglingReferences: 0,
+            conflictPaths: [],
+            error: `${constants_1.KNOWLEDGE_DIR}/ not found at ${knowledgeDir}`,
+        };
+    }
+    // Phase 1: scan
+    const filePaths = collectMarkdownFiles(knowledgeDir);
+    options.onProgress?.(`Found ${filePaths.length} file(s) under ${constants_1.KNOWLEDGE_DIR}/`);
+    // Phase 2: extract
+    const parsedFiles = [];
+    const skipLog = [];
+    for (const absPath of filePaths) {
+        const result = (0, extractor_1.extractFromFile)(absPath, projectRoot);
+        if (result.ok) {
+            parsedFiles.push(result.parsed);
+        }
+        else {
+            skipLog.push(result.skip);
+        }
+    }
+    options.onProgress?.(`Extracted ${parsedFiles.length} valid document(s); ${skipLog.length} skipped`);
+    // Phase 3: transactional rebuild
+    const connection = (0, schema_bootstrap_1.openMarkdownDb)(projectRoot);
+    const store = new store_1.MarkdownStore(connection.getDb());
+    let report;
+    try {
+        report = store.transaction(() => {
+            // Wipe (cover-the-table)
+            store.wipeAll();
+            // Insert documents
+            for (const file of parsedFiles) {
+                store.upsertDocument(file.document);
+            }
+            // Insert vocabulary (deduped via UNIQUE + ON CONFLICT DO NOTHING)
+            const conceptSet = new Set();
+            const domainSet = new Set();
+            const tagSet = new Set();
+            for (const file of parsedFiles) {
+                for (const c of file.concepts)
+                    conceptSet.add(c);
+                for (const d of file.domains)
+                    domainSet.add(d);
+                for (const t of file.tags)
+                    tagSet.add(t);
+            }
+            for (const name of conceptSet)
+                store.upsertVocab('markdown_concepts', name);
+            for (const name of domainSet)
+                store.upsertVocab('markdown_domains', name);
+            for (const name of tagSet)
+                store.upsertVocab('markdown_tags', name);
+            // Link edges
+            for (const file of parsedFiles) {
+                const docId = file.document.id;
+                for (const c of file.concepts) {
+                    store.linkDocumentConcept(docId, (0, store_1.vocabIdFromName)(c));
+                }
+                for (const d of file.domains) {
+                    store.linkDocumentDomain(docId, (0, store_1.vocabIdFromName)(d));
+                }
+                for (const t of file.tags) {
+                    store.linkDocumentTag(docId, (0, store_1.vocabIdFromName)(t));
+                }
+            }
+            // Resolve references (two-phase: documents all inserted above)
+            let referencesCreated = 0;
+            const dangling = [];
+            for (const file of parsedFiles) {
+                const sourceId = file.document.id;
+                const sourceDir = node_path_1.default.dirname(file.document.path);
+                for (const rawRef of file.relatedDocumentsRaw) {
+                    // Support BOTH conventions: many authors write `related_documents`
+                    // as project-root-relative (`docs/knowledge/x.md`), others write
+                    // them as source-document-relative (`./x.md`, `../y.md`). Try
+                    // source-relative first (markdown-link convention), then
+                    // root-relative (project-overview convention).
+                    const fromSource = resolveRefPath(rawRef, sourceDir, projectRoot);
+                    const fromRoot = resolveRefPath(rawRef, '', projectRoot);
+                    const targetFromSource = store.getDocumentByPath(fromSource);
+                    const target = targetFromSource ?? store.getDocumentByPath(fromRoot);
+                    if (target) {
+                        store.linkDocumentReference(sourceId, target.id, rawRef);
+                        referencesCreated++;
+                    }
+                    else {
+                        dangling.push({
+                            path: file.document.path,
+                            reason: 'dangling_reference',
+                            detail: `unresolved ref "${rawRef}" (tried ${fromSource}, ${fromRoot})`,
+                        });
+                    }
+                }
+            }
+            // Rebuild keyword index: with LIKE-based search (see schema.sql note),
+            // there's no separate FTS table to refresh — title/summary_text live in
+            // markdown_documents, which the upsert loop above already populated.
+            // Write skip log
+            for (const entry of skipLog) {
+                store.insertSkipLog(runId, entry);
+            }
+            for (const entry of dangling) {
+                store.insertSkipLog(runId, entry);
+            }
+            // Compose report
+            const skipBreakdown = { ...EMPTY_SKIP_BREAKDOWN };
+            for (const entry of skipLog) {
+                skipBreakdown[entry.reason]++;
+            }
+            skipBreakdown.dangling_reference = dangling.length;
+            return {
+                runId,
+                startedAt,
+                finishedAt: Date.now(),
+                durationMs: Date.now() - startedAt,
+                scannedFiles: filePaths.length,
+                indexedDocuments: parsedFiles.length,
+                skippedFiles: skipLog.length,
+                skipBreakdown,
+                conceptsCreated: conceptSet.size,
+                domainsCreated: domainSet.size,
+                tagsCreated: tagSet.size,
+                referencesCreated,
+                danglingReferences: dangling.length,
+                conflictPaths: [],
+            };
+        });
+    }
+    finally {
+        connection.close();
+    }
+    options.onProgress?.(`Done: ${report.indexedDocuments} docs, ${report.conceptsCreated} concepts, ${report.durationMs}ms`);
+    return report;
+}
+/**
+ * Walk a directory and collect markdown files.
+ *
+ * - Skip dot-directories (e.g. `.git/`, `.drafts/`).
+ * - Skip symlinks (prevents cycles + security).
+ * - Accept only .md / .mdx extensions (case-sensitive — README.MD is rejected).
+ */
+function collectMarkdownFiles(rootDir) {
+    const results = [];
+    function walk(dir) {
+        let entries;
+        try {
+            entries = node_fs_1.default.readdirSync(dir, { withFileTypes: true });
+        }
+        catch {
+            return;
+        }
+        for (const entry of entries) {
+            if (entry.name.startsWith('.'))
+                continue;
+            const fullPath = node_path_1.default.join(dir, entry.name);
+            // Symlinks: lstat via Dirent.isSymbolicLink() catches them
+            if (entry.isSymbolicLink())
+                continue;
+            if (entry.isDirectory()) {
+                walk(fullPath);
+            }
+            else if (entry.isFile()) {
+                if (constants_1.ACCEPTED_EXTENSIONS.some(ext => entry.name.endsWith(ext))) {
+                    results.push(fullPath);
+                }
+            }
+        }
+    }
+    walk(rootDir);
+    results.sort(); // deterministic order across runs
+    return results;
+}
+/**
+ * Resolve a `related_documents` reference to a project-relative path.
+ *
+ * Reference is relative to the SOURCE document's directory (not the project
+ * root). Output is normalized to POSIX for `markdown_documents.path` lookup.
+ */
+function resolveRefPath(rawRef, sourceDocDir, projectRoot) {
+    const absolute = node_path_1.default.resolve(projectRoot, sourceDocDir, rawRef);
+    const rel = node_path_1.default.relative(projectRoot, absolute);
+    return rel.split(node_path_1.default.sep).join('/');
+}
+//# sourceMappingURL=indexer.js.map

package/dist/core/markdown/indexer.js.map

@@ -0,0 +1 @@
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package/dist/core/markdown/query-dedup.d.ts

@@ -0,0 +1,23 @@
+/**
+ * checkConceptDedup(Layer 2 概念去重)的实现体。
+ *
+ * 从 query.ts 整体搬出(原 MarkdownQuery.checkConceptDedup 私有语义),
+ * 逻辑未改写,仅把 `this.db` 参数化为显式 `db` 入参;供 query.ts 薄委托。
+ * 不进入子系统门面,模块内导出。
+ */
+import type { SqliteDatabase } from '../db';
+import type { DedupResponse } from './types';
+/**
+ * Check candidate names against the indexed vocabulary.
+ *
+ * Two match modes, exact first:
+ *   - exact: normalize(candidate) === normalize(concept.name)
+ *   - alias: normalize(candidate) === normalize(document.aliases[i])
+ *     (matched_concept is then the document's primary concept name,
+ *      resolved through markdown_document_concepts)
+ *
+ * All concepts + all document aliases are pulled in two batch queries
+ * (no per-candidate SQL, no SQLite JSON1 — aliases are JSON.parse'd in TS).
+ */
+export declare function runConceptDedupCheck(db: SqliteDatabase, names: string[]): DedupResponse;
+//# sourceMappingURL=query-dedup.d.ts.map

package/dist/core/markdown/query-dedup.d.ts.map

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package/dist/core/markdown/query-dedup.js

@@ -0,0 +1,141 @@
+"use strict";
+/**
+ * checkConceptDedup(Layer 2 概念去重)的实现体。
+ *
+ * 从 query.ts 整体搬出(原 MarkdownQuery.checkConceptDedup 私有语义),
+ * 逻辑未改写,仅把 `this.db` 参数化为显式 `db` 入参;供 query.ts 薄委托。
+ * 不进入子系统门面,模块内导出。
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runConceptDedupCheck = runConceptDedupCheck;
+const dedup_1 = require("./dedup");
+/**
+ * Check candidate names against the indexed vocabulary.
+ *
+ * Two match modes, exact first:
+ *   - exact: normalize(candidate) === normalize(concept.name)
+ *   - alias: normalize(candidate) === normalize(document.aliases[i])
+ *     (matched_concept is then the document's primary concept name,
+ *      resolved through markdown_document_concepts)
+ *
+ * All concepts + all document aliases are pulled in two batch queries
+ * (no per-candidate SQL, no SQLite JSON1 — aliases are JSON.parse'd in TS).
+ */
+function runConceptDedupCheck(db, names) {
+    const warnings = [];
+    const results = [];
+    // Phase 1: normalize candidates, filtering empty normalized forms to warnings.
+    const candidates = [];
+    for (const name of names) {
+        const normalized = (0, dedup_1.normalizeName)(name);
+        if (normalized.length === 0) {
+            warnings.push(`empty normalized form: '${name}'`);
+            continue;
+        }
+        candidates.push({ original: name, normalized });
+    }
+    // Phase 2: batch-load all concepts → Map<normalized_name, concept_name>
+    const conceptRows = db
+        .prepare('SELECT name FROM markdown_concepts')
+        .all();
+    const exactIndex = new Map(); // normalized → concept.name
+    for (const r of conceptRows) {
+        const n = (0, dedup_1.normalizeName)(r.name);
+        if (n.length === 0)
+            continue; // skip degenerate concept names already in DB
+        // First-write-wins on collision (deterministic by row order)
+        if (!exactIndex.has(n))
+            exactIndex.set(n, r.name);
+    }
+    // Phase 3: batch-load all (document_id, aliases) pairs with non-empty aliases,
+    // JSON.parse in TS, and build:
+    //   aliasIndex: Map<normalized_alias, { originalAlias, docId }>
+    //   primaryConceptByDoc: Map<doc_id, concept_name>  (joined via doc_concepts)
+    const docAliasRows = db
+        .prepare(`SELECT id, aliases FROM markdown_documents WHERE aliases != '[]'`)
+        .all();
+    const aliasIndex = new Map();
+    const docIdsWithAliases = new Set();
+    for (const r of docAliasRows) {
+        let aliases = [];
+        try {
+            const parsed = JSON.parse(r.aliases);
+            if (Array.isArray(parsed)) {
+                aliases = parsed.filter((x) => typeof x === 'string');
+            }
+        }
+        catch {
+            continue; // malformed aliases JSON — skip this doc
+        }
+        if (aliases.length === 0)
+            continue;
+        docIdsWithAliases.add(r.id);
+        for (const alias of aliases) {
+            const n = (0, dedup_1.normalizeName)(alias);
+            if (n.length === 0)
+                continue;
+            // First-write-wins on collision (deterministic by row order)
+            if (!aliasIndex.has(n)) {
+                aliasIndex.set(n, { originalAlias: alias, docId: r.id });
+            }
+        }
+    }
+    // Resolve primary concept name for every doc that contributed an alias.
+    // One batched IN-clause query, then take the first concept per doc.
+    const primaryConceptByDoc = new Map();
+    if (docIdsWithAliases.size > 0) {
+        const docIds = [...docIdsWithAliases];
+        const placeholders = docIds.map(() => '?').join(',');
+        const rows = db
+            .prepare(`SELECT dc.document_id, c.name
+         FROM markdown_document_concepts dc
+         JOIN markdown_concepts c ON c.id = dc.concept_id
+         WHERE dc.document_id IN (${placeholders})
+         ORDER BY dc.document_id ASC, c.name ASC`)
+            .all(...docIds);
+        for (const r of rows) {
+            // First-write-wins preserves "first concept alphabetically" per doc
+            if (!primaryConceptByDoc.has(r.document_id)) {
+                primaryConceptByDoc.set(r.document_id, r.name);
+            }
+        }
+    }
+    // Phase 4: evaluate each candidate (exact first, then alias).
+    for (const { original, normalized } of candidates) {
+        const exactMatch = exactIndex.get(normalized);
+        if (exactMatch !== undefined) {
+            results.push({
+                name: original,
+                normalized,
+                is_duplicate: true,
+                matched_concept: exactMatch,
+                matched_alias: null,
+                matched_via: 'exact',
+            });
+            continue;
+        }
+        const aliasMatch = aliasIndex.get(normalized);
+        if (aliasMatch !== undefined) {
+            const primaryConcept = primaryConceptByDoc.get(aliasMatch.docId) ?? null;
+            results.push({
+                name: original,
+                normalized,
+                is_duplicate: true,
+                matched_concept: primaryConcept,
+                matched_alias: aliasMatch.originalAlias,
+                matched_via: 'alias',
+            });
+            continue;
+        }
+        results.push({
+            name: original,
+            normalized,
+            is_duplicate: false,
+            matched_concept: null,
+            matched_alias: null,
+            matched_via: null,
+        });
+    }
+    return { results, warnings };
+}
+//# sourceMappingURL=query-dedup.js.map

package/dist/core/markdown/query-dedup.js.map

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package/dist/core/markdown/query-helpers.d.ts

@@ -0,0 +1,66 @@
+/**
+ * query.ts 的私有助手模块:find / findPaged 共用的查询管线,以及
+ * getReferences / getDocumentDetail 依赖的行解析与组装逻辑。
+ *
+ * 本模块不进入子系统门面(index.ts 不导出),仅供同目录 query.ts 内部
+ * 委托调用 —— 拆分目的纯粹是把膨胀的 query.ts 压回 600 行以内,逻辑是
+ * 原私有方法的纯搬运:方法体逐字保留,`this.db` 参数化为显式 `db` 入参。
+ *
+ * 全部为纯函数:接收 SqliteDatabase 等显式参数,不持有任何状态。
+ */
+import type { SqliteDatabase } from '../db';
+import type { MarkdownDocumentRow } from './store';
+import type { DocumentDescriptor, DocumentDetail, FindFilter } from './types';
+/** JSON 字符串列(owners/aliases/related_code)→ string[];非法/非数组 → []。 */
+export declare function parseJsonArray(s: string): string[];
+/**
+ * 关联到给定词表名(concept/domain/tag)的文档 id 列表。
+ * 名字先解析为词表 id;不在词表中则解析不到,返回 []。
+ */
+export declare function docIdsForVocab(db: SqliteDatabase, name: string, targetColumn: 'concept_id' | 'domain_id' | 'tag_id', table: 'markdown_document_concepts' | 'markdown_document_domains' | 'markdown_document_tags'): string[];
+/**
+ * docIdsForVocab 的批量版:一次 IN 查询解析名字 → id,再一次 IN 查询
+ * 取文档 id(维度内 OR,即多个名字的候选集并集;沿用 checkConceptDedup
+ * 的批量 IN 占位符模式)。名字不在词表中则解析不到 id,自然不产出候选。
+ */
+export declare function docIdsForVocabMany(db: SqliteDatabase, names: string[], targetColumn: 'concept_id' | 'domain_id' | 'tag_id', table: 'markdown_document_concepts' | 'markdown_document_domains' | 'markdown_document_tags'): string[];
+/**
+ * Phase 1:按过滤维度收集候选文档 id 集合。
+ *
+ * 每个维度产出至多两个候选集:单值字段一个、复数字段一个(同维度两者
+ * 共存 = 两个约束在 Phase 2 取交)。复数维度内为 OR(一条 IN 查询);
+ * 空数组视为未施加约束(不产出候选集)。
+ *
+ * @returns 候选集数组;含非法枚举值时返回 null(该维度候选集为空 ⇒
+ *   交集必为空 ⇒ 调用方直接返回空结果,与现有单值非法枚举返回 [] 一致)。
+ */
+export declare function collectCandidateSets(db: SqliteDatabase, filter: FindFilter): string[][] | null;
+/**
+ * Phase 2:候选集求交(维度间 AND)+ 全量排序(不切片,切片由调用方做)。
+ *
+ * 无候选集(无任何过滤维度)→ 全表按选定顺序输出;
+ * sort:'relevance' 但无 q → 降级为 recency(相关度无查询词可依)。
+ */
+export declare function orderCandidates(db: SqliteDatabase, candidateSets: string[][], opts: {
+    q?: string;
+    sort: 'recency' | 'relevance' | 'title';
+}): string[];
+/**
+ * 当页文档的引用计数(出向 + 入向)。
+ *
+ * 一条 IN 聚合查询(UNION ALL 出向/入向两侧后 GROUP BY),避免 N+1;
+ * 自引用文档两侧各计一次,与 getReferences 的出/入双列语义一致。
+ * 无引用的文档不在返回 Map 中(调用方 ?? 0)。
+ */
+export declare function referenceCountsForDocs(db: SqliteDatabase, ids: string[]): Map<string, number>;
+/** 按 ID 或项目相对路径解析文档(找不到返回 null)。 */
+export declare function resolveDocument(db: SqliteDatabase, docIdOrPath: string): MarkdownDocumentRow | null;
+/**
+ * 按 id 取行并组装描述符(find 使用)。
+ */
+export declare function hydrateDescriptor(db: SqliteDatabase, id: string, q?: string): DocumentDescriptor;
+/** 从已持有的行记录组装描述符(find 与 findPaged 共用,输出形状一致)。 */
+export declare function hydrateDescriptorFromRow(db: SqliteDatabase, doc: MarkdownDocumentRow, q?: string): DocumentDescriptor;
+/** getDocumentDetail 的详情组装(描述符 + owners/aliases/relatedCode/时间戳)。 */
+export declare function hydrateDetail(db: SqliteDatabase, doc: MarkdownDocumentRow): DocumentDetail;
+//# sourceMappingURL=query-helpers.d.ts.map

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