memkin 0.4.0

package/dist/store/database.js

@@ -0,0 +1,113 @@
+import { SCHEMA_SQL } from "../embedded-assets.generated.js";
+import { createEngine } from "./engine-factory.js";
+import { runMigrations } from "./migrations/index.js";
+import { resyncIdSequences } from "./sequence-sync.js";
+import { fingerprintString, readMeta, writeMeta } from "./store-meta.js";
+export const DEFAULT_EMBEDDING_DIMENSIONS = 1536;
+/**
+ * Resolve the embedded base `schema.sql` template's `__EMBEDDING_DIM__` placeholder
+ * (the `vector(__EMBEDDING_DIM__)` column typemod) to a concrete dimension count.
+ *
+ * Use this anywhere a raw PGlite instance is bootstrapped from schema.sql — executing
+ * the template verbatim makes Postgres parse the placeholder as an integer and fail with
+ * `invalid input syntax for type integer: "__embedding_dim__"`.
+ */
+export function loadSchemaSql(dims = DEFAULT_EMBEDDING_DIMENSIONS) {
+    return SCHEMA_SQL.replace("__EMBEDDING_DIM__", String(dims));
+}
+export class Database {
+    executor;
+    embeddingDimensions;
+    constructor(executor, embeddingDimensions) {
+        this.executor = executor;
+        this.embeddingDimensions = embeddingDimensions;
+    }
+    static async create(dataDirOrConfig, opts) {
+        const config = typeof dataDirOrConfig === "string" || dataDirOrConfig === undefined
+            ? { store: { engine: "pglite", data_dir: dataDirOrConfig } }
+            : dataDirOrConfig;
+        const dims = opts?.embeddingDimensions ?? DEFAULT_EMBEDDING_DIMENSIONS;
+        let executor;
+        try {
+            executor = await createEngine(config);
+            const e = executor;
+            await e.bootstrap(async (conn) => {
+                await conn.exec(loadSchemaSql(dims));
+                await runMigrations(conn);
+                // Self-heal SERIAL sequences left behind by id-preserving imports —
+                // otherwise new-row INSERTs collide on the pkey (see sequence-sync.ts).
+                const repaired = await resyncIdSequences(conn);
+                if (repaired.length > 0) {
+                    // stderr: stdout may be an MCP stdio channel.
+                    console.warn(`[memoark] Repaired id sequence desync (likely an id-preserving import/restore): ` +
+                        repaired.map((r) => `${r.table} → next id ${r.maxId + 1}`).join(", "));
+                }
+                await ensureEmbeddingConsistency(conn, dims, config);
+            });
+            return new Database(e, dims);
+        }
+        catch (err) {
+            await executor?.close().catch(() => { });
+            throw err;
+        }
+    }
+    async close() {
+        await this.executor.close();
+    }
+}
+/**
+ * Migrate the embedding column dimensions if they changed.
+ * Clears all existing embeddings when the dimension count changes so they
+ * will be re-indexed with the new model.
+ */
+async function migrateEmbeddingDimensions(conn, targetDims) {
+    const result = await conn.query(`SELECT atttypmod FROM pg_attribute
+     WHERE attrelid = 'content_chunks'::regclass
+       AND attname = 'embedding'`);
+    if (result.rows.length === 0)
+        return;
+    // pgvector stores dimensions as atttypmod (the raw value equals the dimension count)
+    const currentDims = result.rows[0].atttypmod;
+    if (currentDims === targetDims)
+        return;
+    console.log(`[memkin] Embedding dimensions changed: ${currentDims} → ${targetDims}. ` +
+        "Clearing existing embeddings for re-indexing.");
+    await conn.exec(`
+    DROP INDEX IF EXISTS idx_chunks_embedding;
+    ALTER TABLE content_chunks ALTER COLUMN embedding TYPE vector(${targetDims});
+    UPDATE content_chunks SET embedding = NULL, embedded_at = NULL;
+    CREATE INDEX idx_chunks_embedding ON content_chunks
+      USING hnsw (embedding vector_cosine_ops);
+  `);
+}
+async function ensureEmbeddingConsistency(conn, targetDims, config) {
+    const fp = {
+        provider: config.embedding?.provider ?? "openai",
+        model: config.embedding?.model ?? "text-embedding-3-large",
+        dimensions: targetDims,
+    };
+    const want = fingerprintString(fp);
+    const have = await readMeta(conn, "embedding_fingerprint");
+    if (have === null) {
+        // Fresh database — migrate dimensions if needed, then record fingerprint.
+        await migrateEmbeddingDimensions(conn, targetDims);
+        await writeMeta(conn, "embedding_fingerprint", want);
+        return;
+    }
+    if (have !== want) {
+        throw new Error(`Embedding fingerprint mismatch: db="${have}" config="${want}". ` +
+            "不静默改写共享库。改回原 embedding 配置或跑显式 reindex。");
+    }
+    // Fingerprint matches — still run dimension migration guard (idempotent).
+    await migrateEmbeddingDimensions(conn, targetDims);
+}
+/**
+ * Exported for unit-testing the fingerprint logic without requiring a
+ * disk-backed PGLite instance (which would OOM in vitest fork workers).
+ *
+ * @internal — test use only.
+ */
+export async function ensureEmbeddingConsistencyForTest(conn, targetDims, config) {
+    return ensureEmbeddingConsistency(conn, targetDims, config);
+}
+//# sourceMappingURL=database.js.map

package/dist/store/database.js.map

@@ -0,0 +1 @@
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package/dist/store/embedding.d.ts

@@ -0,0 +1,23 @@
+import type { SqlConn } from "./sql-executor.js";
+export interface EmbeddingConfig {
+    provider: "openai" | "ollama";
+    model?: string;
+    dimensions?: number;
+    apiKey?: string;
+    baseUrl?: string;
+}
+export declare class EmbeddingService {
+    private pg;
+    private client;
+    private model;
+    private dimensions;
+    constructor(pg: SqlConn, config: EmbeddingConfig);
+    embedStale(opts?: {
+        limit?: number;
+    }): Promise<{
+        embedded: number;
+        errors: number;
+    }>;
+    embedText(text: string): Promise<number[]>;
+}
+//# sourceMappingURL=embedding.d.ts.map

package/dist/store/embedding.d.ts.map

@@ -0,0 +1 @@
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package/dist/store/embedding.js

@@ -0,0 +1,62 @@
+import OpenAI from "openai";
+const BATCH_SIZE = 100;
+export class EmbeddingService {
+    pg;
+    client;
+    model;
+    dimensions;
+    constructor(pg, config) {
+        this.pg = pg;
+        this.model = config.model ?? "text-embedding-3-large";
+        this.dimensions = config.dimensions ?? 1536;
+        const isOllama = config.provider === "ollama";
+        this.client = new OpenAI({
+            apiKey: isOllama ? (config.apiKey ?? "ollama") : (config.apiKey ?? ""),
+            baseURL: isOllama ? (config.baseUrl ?? "http://localhost:11434/v1") : config.baseUrl,
+        });
+    }
+    async embedStale(opts) {
+        const limit = opts?.limit;
+        let sql = "SELECT id, chunk_text FROM content_chunks WHERE embedded_at IS NULL ORDER BY id";
+        const params = [];
+        if (limit) {
+            sql += " LIMIT $1";
+            params.push(limit);
+        }
+        const stale = await this.pg.query(sql, params);
+        if (stale.rows.length === 0)
+            return { embedded: 0, errors: 0 };
+        let embedded = 0;
+        let errors = 0;
+        for (let i = 0; i < stale.rows.length; i += BATCH_SIZE) {
+            const batch = stale.rows.slice(i, i + BATCH_SIZE);
+            const texts = batch.map((r) => r.chunk_text);
+            try {
+                const response = await this.client.embeddings.create({
+                    model: this.model,
+                    input: texts,
+                    dimensions: this.dimensions,
+                });
+                for (let j = 0; j < batch.length; j++) {
+                    const vec = response.data[j].embedding;
+                    const vecStr = `[${vec.join(",")}]`;
+                    await this.pg.query(`UPDATE content_chunks SET embedding = $1::vector, model = $2, embedded_at = NOW() WHERE id = $3`, [vecStr, this.model, batch[j].id]);
+                    embedded++;
+                }
+            }
+            catch (_err) {
+                errors += batch.length;
+            }
+        }
+        return { embedded, errors };
+    }
+    async embedText(text) {
+        const response = await this.client.embeddings.create({
+            model: this.model,
+            input: text,
+            dimensions: this.dimensions,
+        });
+        return response.data[0].embedding;
+    }
+}
+//# sourceMappingURL=embedding.js.map

package/dist/store/embedding.js.map

@@ -0,0 +1 @@
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package/dist/store/engine-factory.d.ts

@@ -0,0 +1,4 @@
+import type { Config } from "../core/config.js";
+import type { SqlExecutor } from "./sql-executor.js";
+export declare function createEngine(config: Config): Promise<SqlExecutor>;
+//# sourceMappingURL=engine-factory.d.ts.map

package/dist/store/engine-factory.d.ts.map

@@ -0,0 +1 @@
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package/dist/store/engine-factory.js

@@ -0,0 +1,18 @@
+export async function createEngine(config) {
+    const engine = config.store?.engine ?? "pglite";
+    switch (engine) {
+        case "pglite": {
+            const { PgliteExecutor } = await import("./pglite-executor.js");
+            return PgliteExecutor.create(config.store?.data_dir, {});
+        }
+        case "postgres": {
+            const { PostgresExecutor } = await import("./postgres-executor.js");
+            return PostgresExecutor.create(config);
+        }
+        case "managed":
+            throw new Error('engine "managed" must be resolved via resolveDb/provisionManaged before reaching the engine factory');
+        default:
+            throw new Error(`Unknown store engine: "${engine}". Supported: pglite, postgres, managed.`);
+    }
+}
+//# sourceMappingURL=engine-factory.js.map

package/dist/store/engine-factory.js.map

@@ -0,0 +1 @@
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package/dist/store/graph.d.ts

@@ -0,0 +1,75 @@
+import type { SourceRef } from "../core/types.js";
+import type { SqlConn } from "./sql-executor.js";
+export interface LinkRow {
+    from_slug: string;
+    to_slug: string;
+    link_type: string;
+    context: string;
+    provenance?: SourceRef;
+}
+export interface EnrichedLinkRow extends LinkRow {
+    page: {
+        title: string;
+        type: string;
+        frontmatter: Record<string, unknown>;
+    };
+}
+export interface GraphNode {
+    slug: string;
+    title: string;
+    type: string;
+    depth: number;
+}
+export interface GraphEdge {
+    from_slug: string;
+    to_slug: string;
+    link_type: string;
+}
+export interface TraverseResult {
+    focus: {
+        slug: string;
+        title: string;
+        type: string;
+    };
+    nodes: GraphNode[];
+    edges: GraphEdge[];
+}
+export declare class GraphStore {
+    private pg;
+    constructor(pg: SqlConn);
+    addLink(fromSlug: string, toSlug: string, type: string, context?: string, provenance?: SourceRef, sourceHash?: string): Promise<void>;
+    removeLink(fromSlug: string, toSlug: string): Promise<void>;
+    getLinks(slug: string): Promise<LinkRow[]>;
+    getAllLinksGrouped(): Promise<Map<string, LinkRow[]>>;
+    getBacklinks(slug: string): Promise<LinkRow[]>;
+    getLinksEnriched(slug: string): Promise<EnrichedLinkRow[]>;
+    getLinksForSlugs(slugs: string[]): Promise<Map<string, LinkRow[]>>;
+    getBacklinksEnriched(slug: string): Promise<EnrichedLinkRow[]>;
+    traverse(slug: string, opts?: {
+        depth?: number;
+        direction?: "in" | "out" | "both";
+    }): Promise<TraverseResult>;
+    /**
+     * Spec 11 §三: descendants of `slug` along a relation `rel`.
+     *
+     * Children point *up* to their parent via the relation (e.g. a problem-class page
+     * carries `[[part_of:category/...]]`, so the edge is child --part_of--> parent).
+     * Descendants are therefore found by walking incoming `rel` edges (backlinks).
+     * Returns descendants in BFS order, excluding the root; deduped; depth-capped.
+     */
+    getSubtree(slug: string, rel: string, depth?: number): Promise<{
+        slug: string;
+        title: string;
+    }[]>;
+    /**
+     * Spec 11 §三: ordered chain starting at `startSlug`, following outgoing `precedes`
+     * edges (each page declares `[[precedes:next-slug]]`). Includes the start node first.
+     * Cycle-safe; returns [] when the start page does not exist.
+     */
+    getOrderedSequence(startSlug: string): Promise<{
+        slug: string;
+        title: string;
+    }[]>;
+    private pageExists;
+}
+//# sourceMappingURL=graph.d.ts.map

package/dist/store/graph.d.ts.map

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package/dist/store/graph.js

@@ -0,0 +1,276 @@
+import { compactSourceRef } from "../core/source-ref.js";
+function parseProvenance(value) {
+    if (!value)
+        return undefined;
+    if (typeof value === "string") {
+        try {
+            return JSON.parse(value);
+        }
+        catch {
+            return undefined;
+        }
+    }
+    return value;
+}
+export class GraphStore {
+    pg;
+    constructor(pg) {
+        this.pg = pg;
+    }
+    async addLink(fromSlug, toSlug, type, context, provenance, sourceHash) {
+        const result = await this.pg.query(`INSERT INTO links (from_page_id, to_page_id, link_type, context, provenance, source_hash)
+       SELECT f.id, t.id, $3, $4, $5, $6
+       FROM pages f, pages t
+       WHERE f.slug = $1 AND t.slug = $2
+       ON CONFLICT (from_page_id, to_page_id, link_type) DO UPDATE SET
+         context = EXCLUDED.context,
+         provenance = COALESCE(EXCLUDED.provenance, links.provenance),
+         source_hash = COALESCE(EXCLUDED.source_hash, links.source_hash)
+       RETURNING id`, [
+            fromSlug,
+            toSlug,
+            type,
+            context ?? "",
+            provenance ? JSON.stringify(compactSourceRef(provenance)) : null,
+            sourceHash ?? null,
+        ]);
+        if (result.rows.length === 0) {
+            const missingSlug = (await this.pageExists(fromSlug)) ? toSlug : fromSlug;
+            throw new Error(`Page not found: ${missingSlug}`);
+        }
+    }
+    async removeLink(fromSlug, toSlug) {
+        await this.pg.query(`DELETE FROM links
+       WHERE from_page_id = (SELECT id FROM pages WHERE slug = $1)
+         AND to_page_id = (SELECT id FROM pages WHERE slug = $2)`, [fromSlug, toSlug]);
+    }
+    async getLinks(slug) {
+        const result = await this.pg.query(`SELECT pf.slug AS from_slug, pt.slug AS to_slug, l.link_type, l.context, l.provenance
+       FROM links l
+       JOIN pages pf ON pf.id = l.from_page_id
+       JOIN pages pt ON pt.id = l.to_page_id
+       WHERE pf.slug = $1`, [slug]);
+        return result.rows.map((row) => ({
+            ...row,
+            provenance: parseProvenance(row.provenance),
+        }));
+    }
+    async getAllLinksGrouped() {
+        const result = await this.pg.query(`SELECT pf.slug AS from_slug, pt.slug AS to_slug, l.link_type, l.context, l.provenance
+       FROM links l
+       JOIN pages pf ON pf.id = l.from_page_id
+       JOIN pages pt ON pt.id = l.to_page_id
+       ORDER BY pf.slug, pt.slug`);
+        const grouped = new Map();
+        for (const row of result.rows) {
+            const list = grouped.get(row.from_slug);
+            if (list)
+                list.push(row);
+            else
+                grouped.set(row.from_slug, [row]);
+        }
+        return grouped;
+    }
+    async getBacklinks(slug) {
+        const result = await this.pg.query(`SELECT pf.slug AS from_slug, pt.slug AS to_slug, l.link_type, l.context, l.provenance
+       FROM links l
+       JOIN pages pf ON pf.id = l.from_page_id
+       JOIN pages pt ON pt.id = l.to_page_id
+       WHERE pt.slug = $1`, [slug]);
+        return result.rows.map((row) => ({
+            ...row,
+            provenance: parseProvenance(row.provenance),
+        }));
+    }
+    async getLinksEnriched(slug) {
+        const result = await this.pg.query(`SELECT pf.slug AS from_slug, pt.slug AS to_slug, l.link_type, l.context, l.provenance,
+              pt.title AS page_title, pt.type AS page_type, pt.frontmatter AS page_frontmatter
+       FROM links l
+       JOIN pages pf ON pf.id = l.from_page_id
+       JOIN pages pt ON pt.id = l.to_page_id
+       WHERE pf.slug = $1`, [slug]);
+        return result.rows.map((r) => {
+            const frontmatter = typeof r.page_frontmatter === "string"
+                ? JSON.parse(r.page_frontmatter)
+                : r.page_frontmatter;
+            return {
+                from_slug: r.from_slug,
+                to_slug: r.to_slug,
+                link_type: r.link_type,
+                context: r.context,
+                provenance: parseProvenance(r.provenance),
+                page: {
+                    title: r.page_title,
+                    type: r.page_type,
+                    frontmatter: frontmatter ?? {},
+                },
+            };
+        });
+    }
+    async getLinksForSlugs(slugs) {
+        if (slugs.length === 0)
+            return new Map();
+        const result = await this.pg.query(`SELECT pf.slug AS from_slug, pt.slug AS to_slug, l.link_type, l.context, l.provenance
+       FROM links l
+       JOIN pages pf ON pf.id = l.from_page_id
+       JOIN pages pt ON pt.id = l.to_page_id
+       WHERE pf.slug = ANY($1::text[])`, [slugs]);
+        const map = new Map();
+        for (const row of result.rows) {
+            const existing = map.get(row.from_slug) ?? [];
+            existing.push(row);
+            map.set(row.from_slug, existing);
+        }
+        return map;
+    }
+    async getBacklinksEnriched(slug) {
+        const result = await this.pg.query(`SELECT pf.slug AS from_slug, pt.slug AS to_slug, l.link_type, l.context, l.provenance,
+              pf.title AS page_title, pf.type AS page_type, pf.frontmatter AS page_frontmatter
+       FROM links l
+       JOIN pages pf ON pf.id = l.from_page_id
+       JOIN pages pt ON pt.id = l.to_page_id
+       WHERE pt.slug = $1`, [slug]);
+        return result.rows.map((r) => {
+            const frontmatter = typeof r.page_frontmatter === "string"
+                ? JSON.parse(r.page_frontmatter)
+                : r.page_frontmatter;
+            return {
+                from_slug: r.from_slug,
+                to_slug: r.to_slug,
+                link_type: r.link_type,
+                context: r.context,
+                provenance: parseProvenance(r.provenance),
+                page: {
+                    title: r.page_title,
+                    type: r.page_type,
+                    frontmatter: frontmatter ?? {},
+                },
+            };
+        });
+    }
+    async traverse(slug, opts) {
+        const maxDepth = Math.min(opts?.depth ?? 5, 10);
+        const direction = opts?.direction ?? "out";
+        // Query focus node
+        const focusQuery = await this.pg.query("SELECT slug, title, type FROM pages WHERE slug = $1", [slug]);
+        if (focusQuery.rows.length === 0) {
+            return {
+                focus: { slug, title: slug, type: "unknown" },
+                nodes: [],
+                edges: [],
+            };
+        }
+        const focus = focusQuery.rows[0];
+        const visited = new Set();
+        const nodes = [];
+        const edges = [];
+        let frontier = [slug];
+        visited.add(slug);
+        for (let d = 1; d <= maxDepth && frontier.length > 0; d++) {
+            const nextFrontier = [];
+            for (const current of frontier) {
+                const neighbors = [];
+                if (direction === "out" || direction === "both") {
+                    const out = await this.pg.query(`SELECT pt.slug, l.link_type FROM links l JOIN pages pt ON pt.id = l.to_page_id
+             WHERE l.from_page_id = (SELECT id FROM pages WHERE slug = $1)`, [current]);
+                    neighbors.push(...out.rows.map((r) => ({ slug: r.slug, link_type: r.link_type })));
+                    edges.push(...out.rows.map((r) => ({
+                        from_slug: current,
+                        to_slug: r.slug,
+                        link_type: r.link_type,
+                    })));
+                }
+                if (direction === "in" || direction === "both") {
+                    const inc = await this.pg.query(`SELECT pf.slug, l.link_type FROM links l JOIN pages pf ON pf.id = l.from_page_id
+             WHERE l.to_page_id = (SELECT id FROM pages WHERE slug = $1)`, [current]);
+                    neighbors.push(...inc.rows.map((r) => ({ slug: r.slug, link_type: r.link_type })));
+                    edges.push(...inc.rows.map((r) => ({
+                        from_slug: r.slug,
+                        to_slug: current,
+                        link_type: r.link_type,
+                    })));
+                }
+                for (const n of neighbors) {
+                    if (!visited.has(n.slug)) {
+                        visited.add(n.slug);
+                        nextFrontier.push(n.slug);
+                        const page = await this.pg.query("SELECT slug, title, type FROM pages WHERE slug = $1", [n.slug]);
+                        if (page.rows.length > 0) {
+                            const p = page.rows[0];
+                            nodes.push({ slug: p.slug, title: p.title, type: p.type, depth: d });
+                        }
+                    }
+                }
+            }
+            frontier = nextFrontier;
+        }
+        return {
+            focus: { slug: focus.slug, title: focus.title, type: focus.type },
+            nodes,
+            edges,
+        };
+    }
+    /**
+     * Spec 11 §三: descendants of `slug` along a relation `rel`.
+     *
+     * Children point *up* to their parent via the relation (e.g. a problem-class page
+     * carries `[[part_of:category/...]]`, so the edge is child --part_of--> parent).
+     * Descendants are therefore found by walking incoming `rel` edges (backlinks).
+     * Returns descendants in BFS order, excluding the root; deduped; depth-capped.
+     */
+    async getSubtree(slug, rel, depth = 5) {
+        const maxDepth = Math.min(depth, 10);
+        const visited = new Set([slug]);
+        const out = [];
+        let frontier = [slug];
+        for (let d = 1; d <= maxDepth && frontier.length > 0; d++) {
+            const next = [];
+            for (const current of frontier) {
+                const children = await this.pg.query(`SELECT pf.slug, pf.title, pf.type
+           FROM links l
+           JOIN pages pf ON pf.id = l.from_page_id
+           WHERE l.to_page_id = (SELECT id FROM pages WHERE slug = $1)
+             AND l.link_type = $2`, [current, rel]);
+                for (const child of children.rows) {
+                    if (visited.has(child.slug))
+                        continue;
+                    visited.add(child.slug);
+                    out.push({ slug: child.slug, title: child.title });
+                    next.push(child.slug);
+                }
+            }
+            frontier = next;
+        }
+        return out;
+    }
+    /**
+     * Spec 11 §三: ordered chain starting at `startSlug`, following outgoing `precedes`
+     * edges (each page declares `[[precedes:next-slug]]`). Includes the start node first.
+     * Cycle-safe; returns [] when the start page does not exist.
+     */
+    async getOrderedSequence(startSlug) {
+        const out = [];
+        const visited = new Set();
+        let current = startSlug;
+        while (current && !visited.has(current)) {
+            visited.add(current);
+            const page = await this.pg.query("SELECT slug, title, type FROM pages WHERE slug = $1", [current]);
+            if (page.rows.length === 0)
+                break;
+            out.push({ slug: page.rows[0].slug, title: page.rows[0].title });
+            const nextRow = await this.pg.query(`SELECT pt.slug
+         FROM links l
+         JOIN pages pt ON pt.id = l.to_page_id
+         WHERE l.from_page_id = (SELECT id FROM pages WHERE slug = $1)
+           AND l.link_type = 'precedes'
+         LIMIT 1`, [current]);
+            current = nextRow.rows[0]?.slug;
+        }
+        return out;
+    }
+    async pageExists(slug) {
+        const result = await this.pg.query("SELECT 1 FROM pages WHERE slug = $1", [slug]);
+        return result.rows.length > 0;
+    }
+}
+//# sourceMappingURL=graph.js.map

package/dist/store/graph.js.map

@@ -0,0 +1 @@
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