@jafreck/lore 0.3.3 → 0.3.5

package/dist/indexer/stages/embedding.js

@@ -3,11 +3,18 @@
  *
  * Pipeline stage: embed symbol signatures, documentation sections, and
  * commit messages into vec0 virtual tables for semantic search.
+ *
+ * Optimisations:
+ *   - **Token-aware batching**: batches are sized by estimated token budget
+ *     rather than a fixed item count, avoiding pathological padding waste
+ *     when one long signature inflates the whole batch.
+ *   - **Skip-unchanged**: in update mode, symbols whose embedding input text
+ *     has not changed (by SHA-256 hash) are skipped entirely.
+ *   - **Double-buffered I/O**: the next `embed()` call fires while the
+ *     current batch's vectors are written to SQLite.
  */
 import { setLoreMeta, createVec0Tables } from '../db.js';
-import { buildStructuralEmbeddingText } from '../embedder.js';
-/** Number of items to embed per batch. */
-const EMBED_BATCH_SIZE = 64;
+import { buildStructuralEmbeddingText, hashEmbeddingText, tokenAwareBatch } from '../embedder.js';
 /**
  * Embed symbol signatures, documentation sections, and commit messages.
  *
@@ -27,8 +34,8 @@ export class EmbeddingStage {
             // Resolve scoped file/doc IDs for incremental embedding.
             const changedFileIds = resolveFileIds(db, context.changedSourcePaths, context.branch);
             const changedDocIds = resolveDocIds(db, context.changedDocPaths, context.branch);
-            await embedStructural(db, embedder, changedFileIds);
-            await embedDocumentation(db, embedder, changedDocIds);
+            await embedStructural(db, embedder, changedFileIds, /* skipUnchanged */ true);
+            await embedDocumentation(db, embedder, changedDocIds, /* skipUnchanged */ true);
         }
         else {
             await embedStructural(db, embedder);
@@ -40,11 +47,12 @@ export class EmbeddingStage {
         context.log.indexing('embedding complete');
     }
 }
-// ─── Structural symbol embeddings ─────────────────────────────────────────────
-async function embedStructural(db, embedder, fileIds) {
+async function embedStructural(db, embedder, fileIds, skipUnchanged = false) {
     setLoreMeta(db, 'embedding_model', embedder.modelName);
     setLoreMeta(db, 'embedding_dims', String(embedder.dims));
     createVec0Tables(db, embedder.dims);
+    // Ensure the hash tracking column exists (idempotent).
+    ensureEmbeddingHashColumn(db, 'symbol_embeddings');
     const baseQuery = `SELECT id, name, signature, resolved_type_signature, resolved_return_type
      FROM symbols
      WHERE (signature IS NOT NULL
@@ -59,49 +67,46 @@ async function embedStructural(db, embedder, fileIds) {
     else {
         symbols = db.prepare(baseQuery).all();
     }
-    const insertEmbed = db.prepare('INSERT OR REPLACE INTO symbol_embeddings(rowid, embedding) VALUES (CAST(? AS INTEGER), json(?))');
-    // P4: Pipeline — start embedding the next batch while writing the current one.
-    let pendingEmbed = null;
-    let pendingBatch = [];
-    for (let i = 0; i < symbols.length; i += EMBED_BATCH_SIZE) {
-        const batch = symbols.slice(i, i + EMBED_BATCH_SIZE);
-        const texts = batch.map((symbol) => buildStructuralEmbeddingText({
-            name: symbol.name,
-            signature: symbol.signature,
-            resolvedTypeSignature: symbol.resolved_type_signature,
-            resolvedReturnType: symbol.resolved_return_type,
-        }));
-        if (pendingEmbed) {
-            const embeddings = await pendingEmbed;
-            db.transaction(() => {
-                for (let j = 0; j < pendingBatch.length; j++) {
-                    const sym = pendingBatch[j];
-                    if (sym)
-                        insertEmbed.run(sym.id, JSON.stringify(embeddings[j]));
-                }
-            })();
-        }
-        pendingEmbed = embedder.embed(texts);
-        pendingBatch = batch;
+    // Build texts and compute hashes; filter out unchanged if requested.
+    const items = [];
+    const existingHashes = skipUnchanged ? loadExistingHashes(db, 'symbol_embeddings', symbols.map(s => s.id)) : new Map();
+    for (const sym of symbols) {
+        const text = buildStructuralEmbeddingText({
+            name: sym.name,
+            signature: sym.signature,
+            resolvedTypeSignature: sym.resolved_type_signature,
+            resolvedReturnType: sym.resolved_return_type,
+        });
+        const hash = hashEmbeddingText(text);
+        if (skipUnchanged && existingHashes.get(sym.id) === hash)
+            continue;
+        items.push({ sym, text, hash });
     }
-    if (pendingEmbed) {
-        const embeddings = await pendingEmbed;
+    if (items.length === 0)
+        return;
+    const insertEmbed = db.prepare('INSERT OR REPLACE INTO symbol_embeddings(rowid, embedding) VALUES (CAST(? AS INTEGER), json(?))');
+    const insertHash = db.prepare('INSERT OR REPLACE INTO symbol_embeddings_hashes(rowid, content_hash) VALUES (?, ?)');
+    const batches = tokenAwareBatch(items, (item) => item.text);
+    await embedBatchesDoubleBuffered(batches, embedder, (item) => item.text, (batch, embeddings) => {
         db.transaction(() => {
-            for (let j = 0; j < pendingBatch.length; j++) {
-                const sym = pendingBatch[j];
-                if (sym)
-                    insertEmbed.run(sym.id, JSON.stringify(embeddings[j]));
+            for (let j = 0; j < batch.length; j++) {
+                const item = batch[j];
+                if (item) {
+                    insertEmbed.run(item.sym.id, JSON.stringify(embeddings[j]));
+                    insertHash.run(item.sym.id, item.hash);
+                }
             }
         })();
-    }
+    });
 }
 // ─── Documentation section embeddings ─────────────────────────────────────────
-async function embedDocumentation(db, embedder, docIds) {
+async function embedDocumentation(db, embedder, docIds, skipUnchanged = false) {
     db.exec(`
     CREATE VIRTUAL TABLE IF NOT EXISTS doc_section_embeddings USING vec0(
       embedding FLOAT[${embedder.dims}]
     );
   `);
+    ensureEmbeddingHashColumn(db, 'doc_section_embeddings');
     let sections;
     if (docIds && docIds.length > 0) {
         sections = db.prepare(`SELECT id, title, content
@@ -116,36 +121,32 @@ async function embedDocumentation(db, embedder, docIds) {
     }
     if (sections.length === 0)
         return;
-    const insertEmbed = db.prepare('INSERT OR REPLACE INTO doc_section_embeddings(rowid, embedding) VALUES (CAST(? AS INTEGER), json(?))');
-    // P4: Pipeline — start embedding the next batch while writing the current one.
-    let pendingEmbed = null;
-    let pendingBatch = [];
-    for (let i = 0; i < sections.length; i += EMBED_BATCH_SIZE) {
-        const batch = sections.slice(i, i + EMBED_BATCH_SIZE);
-        const texts = batch.map(section => section.content || section.title);
-        if (pendingEmbed) {
-            const embeddings = await pendingEmbed;
-            db.transaction(() => {
-                for (let j = 0; j < pendingBatch.length; j++) {
-                    const section = pendingBatch[j];
-                    if (section)
-                        insertEmbed.run(section.id, JSON.stringify(embeddings[j]));
-                }
-            })();
-        }
-        pendingEmbed = embedder.embed(texts);
-        pendingBatch = batch;
+    // Build texts, compute hashes, filter unchanged.
+    const items = [];
+    const existingHashes = skipUnchanged ? loadExistingHashes(db, 'doc_section_embeddings', sections.map(s => s.id)) : new Map();
+    for (const section of sections) {
+        const text = section.content || section.title;
+        const hash = hashEmbeddingText(text);
+        if (skipUnchanged && existingHashes.get(section.id) === hash)
+            continue;
+        items.push({ section, text, hash });
     }
-    if (pendingEmbed) {
-        const embeddings = await pendingEmbed;
+    if (items.length === 0)
+        return;
+    const insertEmbed = db.prepare('INSERT OR REPLACE INTO doc_section_embeddings(rowid, embedding) VALUES (CAST(? AS INTEGER), json(?))');
+    const insertHash = db.prepare('INSERT OR REPLACE INTO doc_section_embeddings_hashes(rowid, content_hash) VALUES (?, ?)');
+    const batches = tokenAwareBatch(items, (item) => item.text);
+    await embedBatchesDoubleBuffered(batches, embedder, (item) => item.text, (batch, embeddings) => {
         db.transaction(() => {
-            for (let j = 0; j < pendingBatch.length; j++) {
-                const section = pendingBatch[j];
-                if (section)
-                    insertEmbed.run(section.id, JSON.stringify(embeddings[j]));
+            for (let j = 0; j < batch.length; j++) {
+                const item = batch[j];
+                if (item) {
+                    insertEmbed.run(item.section.id, JSON.stringify(embeddings[j]));
+                    insertHash.run(item.section.id, item.hash);
+                }
             }
         })();
-    }
+    });
 }
 // ─── Commit message embeddings ────────────────────────────────────────────────
 async function embedCommitMessages(db, embedder) {
@@ -158,34 +159,77 @@ async function embedCommitMessages(db, embedder) {
     if (commits.length === 0)
         return;
     const insertEmbed = db.prepare('INSERT OR REPLACE INTO commit_embeddings(rowid, embedding) VALUES (CAST(? AS INTEGER), json(?))');
-    // P4: Pipeline — start embedding the next batch while writing the current one.
+    const batches = tokenAwareBatch(commits, (c) => c.message);
+    await embedBatchesDoubleBuffered(batches, embedder, (c) => c.message, (batch, embeddings) => {
+        db.transaction(() => {
+            for (let j = 0; j < batch.length; j++) {
+                const commit = batch[j];
+                if (commit)
+                    insertEmbed.run(commit.rowid, JSON.stringify(embeddings[j]));
+            }
+        })();
+    });
+}
+// ─── Double-buffered batch embedding ──────────────────────────────────────────
+/**
+ * Embeds pre-batched items using double-buffered I/O: fires the next
+ * `embed()` call while writing the current batch's results to the DB.
+ */
+async function embedBatchesDoubleBuffered(batches, embedder, getText, writeBatch) {
     let pendingEmbed = null;
     let pendingBatch = [];
-    for (let i = 0; i < commits.length; i += EMBED_BATCH_SIZE) {
-        const batch = commits.slice(i, i + EMBED_BATCH_SIZE);
+    for (const batch of batches) {
+        const texts = batch.map(getText);
+        // Write the previous batch while starting the next embed.
         if (pendingEmbed) {
             const embeddings = await pendingEmbed;
-            db.transaction(() => {
-                for (let j = 0; j < pendingBatch.length; j++) {
-                    const commit = pendingBatch[j];
-                    if (commit)
-                        insertEmbed.run(commit.rowid, JSON.stringify(embeddings[j]));
-                }
-            })();
+            writeBatch(pendingBatch, embeddings);
         }
-        pendingEmbed = embedder.embed(batch.map((commit) => commit.message));
+        pendingEmbed = embedder.embed(texts);
         pendingBatch = batch;
     }
+    // Drain the last pending batch.
     if (pendingEmbed) {
         const embeddings = await pendingEmbed;
-        db.transaction(() => {
-            for (let j = 0; j < pendingBatch.length; j++) {
-                const commit = pendingBatch[j];
-                if (commit)
-                    insertEmbed.run(commit.rowid, JSON.stringify(embeddings[j]));
-            }
-        })();
+        writeBatch(pendingBatch, embeddings);
+    }
+}
+// ─── Skip-unchanged helpers ───────────────────────────────────────────────────
+/**
+ * Idempotently add a `content_hash` column to an embedding virtual table's
+ * shadow storage.  vec0 virtual tables don't support ALTER TABLE, so we use
+ * a companion regular table for the hash.
+ */
+function ensureEmbeddingHashColumn(db, tableName) {
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS ${tableName}_hashes (
+      rowid INTEGER PRIMARY KEY,
+      content_hash TEXT NOT NULL
+    );
+  `);
+    // Migrate: if we previously stored content_hash inline in the INSERT OR REPLACE
+    // statement, the vec0 table ignores unknown columns silently, so nothing to migrate.
+}
+/**
+ * Load existing content hashes for a set of row IDs from the hash companion table.
+ */
+function loadExistingHashes(db, tableName, ids) {
+    const map = new Map();
+    if (ids.length === 0)
+        return map;
+    const hashTable = `${tableName}_hashes`;
+    const hasTable = db.prepare("SELECT 1 AS present FROM sqlite_master WHERE type = 'table' AND name = ?").get(hashTable);
+    if (!hasTable)
+        return map;
+    const CHUNK = 900;
+    for (let i = 0; i < ids.length; i += CHUNK) {
+        const chunk = ids.slice(i, i + CHUNK);
+        const rows = db.prepare(`SELECT rowid, content_hash FROM ${hashTable} WHERE rowid IN (${chunk.map(() => '?').join(', ')})`).all(...chunk);
+        for (const row of rows) {
+            map.set(row.rowid, row.content_hash);
+        }
     }
+    return map;
 }
 // ─── Update-mode helpers ──────────────────────────────────────────────────────
 function deleteSymbolEmbeddings(db, symbolIds) {

package/dist/indexer/stages/embedding.js.map

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package/dist/lore-server/db.d.ts

@@ -168,6 +168,9 @@ export interface ListResolvedEdgesOptions {
     fileId?: number;
     /** Filter by caller branch. */
     branch?: string;
+    /** Allowlist of resolution methods to include. When set, only edges whose
+     *  `resolution_method` is in this list are returned. */
+    methods?: string[];
     /** Maximum rows to return. Default: 100 000. */
     limit?: number;
 }
@@ -184,6 +187,77 @@ export interface ListResolvedEdgesOptions {
  *  - Defaults to a high limit (100 000) to avoid silent truncation
  */
 export declare function listResolvedEdges(db: Database.Database, options?: ListResolvedEdgesOptions): ResolvedEdge[];
+export interface TypeRefEdge {
+    ref_id: number;
+    symbol_id: number | null;
+    symbol_name: string | null;
+    symbol_kind: string | null;
+    symbol_file_id: number | null;
+    symbol_file_path: string | null;
+    type_id: number | null;
+    type_name: string;
+    type_name_bare: string;
+    type_kind: string | null;
+    type_file_id: number | null;
+    type_file_path: string | null;
+    ref_kind: string;
+    ref_line: number;
+    ref_character: number | null;
+    resolution_method: string;
+}
+export interface ListTypeRefsOptions {
+    /** Only include edges where `type_id` is resolved (non-NULL). Default: false. */
+    resolvedOnly?: boolean;
+    /** Restrict to edges from this file. */
+    fileId?: number;
+    /** Filter by branch. */
+    branch?: string;
+    /** Allowlist of resolution methods to include. */
+    methods?: string[];
+    /** Maximum rows to return. Default: 100 000. */
+    limit?: number;
+}
+/**
+ * Returns type-reference edges from `type_refs`, joining through
+ * `symbols` and `files` to denormalize source/target metadata.
+ */
+export declare function listTypeRefs(db: Database.Database, options?: ListTypeRefsOptions): TypeRefEdge[];
+export interface SymbolRelationshipEdge {
+    ref_id: number;
+    source_symbol_id: number | null;
+    source_name: string | null;
+    source_kind: string | null;
+    source_file_id: number | null;
+    source_file_path: string | null;
+    target_symbol_id: number | null;
+    target_symbol_name: string;
+    target_kind: string | null;
+    target_file_id: number | null;
+    target_file_path: string | null;
+    relationship_type: string;
+    line: number;
+    character: number | null;
+    resolution_method: string;
+}
+export interface ListSymbolRelationshipsOptions {
+    /** Only include edges where `target_symbol_id` is resolved (non-NULL). Default: false. */
+    resolvedOnly?: boolean;
+    /** Restrict to edges from this file. */
+    fileId?: number;
+    /** Filter by branch. */
+    branch?: string;
+    /** Filter by relationship type (e.g. 'extends', 'implements'). */
+    relationshipType?: string;
+    /** Allowlist of resolution methods to include. */
+    methods?: string[];
+    /** Maximum rows to return. Default: 100 000. */
+    limit?: number;
+}
+/**
+ * Returns symbol-relationship edges (extends, implements, etc.) from
+ * `symbol_relationships`, joining through `symbols` and `files`.
+ */
+export declare function listSymbolRelationships(db: Database.Database, options?: ListSymbolRelationshipsOptions): SymbolRelationshipEdge[];
 export interface DocRow {
     id: number;
     path: string;

package/dist/lore-server/db.d.ts.map

@@ -1 +1 @@
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package/dist/lore-server/db.js

@@ -348,6 +348,11 @@ export function listResolvedEdges(db, options = {}) {
         where.push('f_caller.branch = ?');
         params.push(options.branch);
     }
+    if (options.methods !== undefined && options.methods.length > 0) {
+        const ph = options.methods.map(() => '?').join(', ');
+        where.push(`sr.resolution_method IN (${ph})`);
+        params.push(...options.methods);
+    }
     const limit = options.limit ?? 100_000;
     params.push(limit);
     const whereClause = where.length > 0 ? `WHERE ${where.join(' AND ')}` : '';
@@ -377,6 +382,115 @@ export function listResolvedEdges(db, options = {}) {
          LIMIT ?`)
         .all(...params);
 }
+/**
+ * Returns type-reference edges from `type_refs`, joining through
+ * `symbols` and `files` to denormalize source/target metadata.
+ */
+export function listTypeRefs(db, options = {}) {
+    const where = [];
+    const params = [];
+    if (options.resolvedOnly) {
+        where.push('tr.type_id IS NOT NULL');
+    }
+    if (options.fileId !== undefined) {
+        where.push('tr.file_id = ?');
+        params.push(options.fileId);
+    }
+    if (options.branch !== undefined) {
+        where.push('f_src.branch = ?');
+        params.push(options.branch);
+    }
+    if (options.methods !== undefined && options.methods.length > 0) {
+        const ph = options.methods.map(() => '?').join(', ');
+        where.push(`tr.resolution_method IN (${ph})`);
+        params.push(...options.methods);
+    }
+    const limit = options.limit ?? 100_000;
+    params.push(limit);
+    const whereClause = where.length > 0 ? `WHERE ${where.join(' AND ')}` : '';
+    return db
+        .prepare(`SELECT tr.id           AS ref_id,
+              tr.symbol_id,
+              s_src.name      AS symbol_name,
+              s_src.kind      AS symbol_kind,
+              s_src.file_id   AS symbol_file_id,
+              f_src.path      AS symbol_file_path,
+              tr.type_id,
+              tr.type_name,
+              tr.type_name_bare,
+              s_dst.kind      AS type_kind,
+              s_dst.file_id   AS type_file_id,
+              f_dst.path      AS type_file_path,
+              tr.ref_kind,
+              tr.ref_line,
+              tr.ref_character,
+              tr.resolution_method
+         FROM type_refs tr
+         JOIN files f_src ON f_src.id = tr.file_id
+         LEFT JOIN symbols s_src ON s_src.id = tr.symbol_id
+         LEFT JOIN symbols s_dst ON s_dst.id = tr.type_id
+         LEFT JOIN files   f_dst ON f_dst.id = s_dst.file_id
+         ${whereClause}
+         ORDER BY tr.file_id ASC, tr.ref_line ASC
+         LIMIT ?`)
+        .all(...params);
+}
+/**
+ * Returns symbol-relationship edges (extends, implements, etc.) from
+ * `symbol_relationships`, joining through `symbols` and `files`.
+ */
+export function listSymbolRelationships(db, options = {}) {
+    const where = [];
+    const params = [];
+    if (options.resolvedOnly) {
+        where.push('rel.target_symbol_id IS NOT NULL');
+    }
+    if (options.fileId !== undefined) {
+        where.push('rel.file_id = ?');
+        params.push(options.fileId);
+    }
+    if (options.branch !== undefined) {
+        where.push('f_src.branch = ?');
+        params.push(options.branch);
+    }
+    if (options.relationshipType !== undefined) {
+        where.push('rel.relationship_type = ?');
+        params.push(options.relationshipType);
+    }
+    if (options.methods !== undefined && options.methods.length > 0) {
+        const ph = options.methods.map(() => '?').join(', ');
+        where.push(`rel.resolution_method IN (${ph})`);
+        params.push(...options.methods);
+    }
+    const limit = options.limit ?? 100_000;
+    params.push(limit);
+    const whereClause = where.length > 0 ? `WHERE ${where.join(' AND ')}` : '';
+    return db
+        .prepare(`SELECT rel.id               AS ref_id,
+              rel.source_symbol_id,
+              s_src.name           AS source_name,
+              s_src.kind           AS source_kind,
+              s_src.file_id        AS source_file_id,
+              f_src.path           AS source_file_path,
+              rel.target_symbol_id,
+              rel.target_symbol_name,
+              s_dst.kind           AS target_kind,
+              s_dst.file_id        AS target_file_id,
+              f_dst.path           AS target_file_path,
+              rel.relationship_type,
+              rel.line,
+              rel.character,
+              rel.resolution_method
+         FROM symbol_relationships rel
+         JOIN files f_src ON f_src.id = rel.file_id
+         LEFT JOIN symbols s_src ON s_src.id = rel.source_symbol_id
+         LEFT JOIN symbols s_dst ON s_dst.id = rel.target_symbol_id
+         LEFT JOIN files   f_dst ON f_dst.id = s_dst.file_id
+         ${whereClause}
+         ORDER BY rel.file_id ASC, rel.line ASC
+         LIMIT ?`)
+        .all(...params);
+}
 function normalizeDocKinds(kind, kinds) {
     const merged = [
         ...(kind ? [kind] : []),