@optave/codegraph 3.6.0 → 3.8.0

package/dist/domain/graph/builder/pipeline.js

@@ -32,18 +32,27 @@ function initializeEngine(ctx) {
         dataflow: ctx.opts.dataflow !== false,
         ast: ctx.opts.ast !== false,
         nativeDb: ctx.nativeDb,
-        // WAL checkpoint callbacks for dual-connection WAL guard (#696).
+        // WAL checkpoint callbacks for dual-connection WAL guard (#696, #715).
         // Feature modules (ast, cfg, complexity, dataflow) receive `db` as a
         // parameter and cannot tolerate close/reopen (stale reference). Instead,
-        // checkpoint the WAL so native writes start with a clean slate. Features
-        // return early on native success and never read native-written WAL data
-        // through the JS connection, so a post-write checkpoint is unnecessary.
+        // checkpoint the WAL so native writes start with a clean slate.
+        // After native writes, resumeJsDb checkpoints through rusqlite so
+        // better-sqlite3 never reads WAL frames from a different SQLite library.
         suspendJsDb: ctx.nativeDb
             ? () => {
                 ctx.db.pragma('wal_checkpoint(TRUNCATE)');
             }
             : undefined,
-        resumeJsDb: ctx.nativeDb ? () => { } : undefined,
+        resumeJsDb: ctx.nativeDb
+            ? () => {
+                try {
+                    ctx.nativeDb?.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+                }
+                catch {
+                    /* ignore — nativeDb may already be closed */
+                }
+            }
+            : undefined,
     };
     const { name: engineName, version: engineVersion } = getActiveEngine(ctx.engineOpts);
     ctx.engineName = engineName;
@@ -105,9 +114,18 @@ function setupPipeline(ctx) {
         try {
             ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
             ctx.nativeDb.initSchema();
+            // Checkpoint WAL through rusqlite so better-sqlite3 sees a clean DB
+            // with no cross-library WAL frames (#715, #717).
+            ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
         }
         catch (err) {
-            warn(`NativeDatabase init failed, falling back to JS: ${err.message}`);
+            warn(`NativeDatabase setup failed, falling back to JS: ${err.message}`);
+            try {
+                ctx.nativeDb?.close();
+            }
+            catch {
+                /* ignore close errors */
+            }
             ctx.nativeDb = undefined;
         }
         // Always run JS initSchema so better-sqlite3 sees the schema —
@@ -159,6 +177,16 @@ async function runPipelineStages(ctx) {
     // that use suspendJsDb/resumeJsDb WAL checkpoint pattern (#696).
     const hadNativeDb = !!ctx.nativeDb;
     if (ctx.db && ctx.nativeDb) {
+        // Checkpoint WAL through rusqlite before closing so better-sqlite3 never
+        // needs to apply WAL frames written by a different SQLite library (#715, #717).
+        // Separate try/catch blocks ensure close() always runs even if checkpoint throws,
+        // preventing a live rusqlite connection from lingering until GC.
+        try {
+            ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+        }
+        catch {
+            /* ignore checkpoint errors */
+        }
         try {
             ctx.nativeDb.close();
         }
@@ -177,7 +205,51 @@ async function runPipelineStages(ctx) {
     if (ctx.earlyExit)
         return;
     await parseFiles(ctx);
+    // Temporarily reopen nativeDb for insertNodes — it uses the WAL checkpoint
+    // guard internally (same pattern as feature modules). Closed again before
+    // resolveImports/buildEdges which don't yet have the guard (#709).
+    if (hadNativeDb && ctx.engineName === 'native') {
+        const native = loadNative();
+        if (native?.NativeDatabase) {
+            try {
+                ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
+            }
+            catch {
+                ctx.nativeDb = undefined;
+            }
+        }
+    }
     await insertNodes(ctx);
+    // Close nativeDb after insertNodes — remaining pipeline stages use JS paths.
+    if (ctx.nativeDb && ctx.db) {
+        // Checkpoint WAL through rusqlite before closing so better-sqlite3 never
+        // needs to apply WAL frames written by a different SQLite library (#715, #717).
+        try {
+            ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+        }
+        catch {
+            /* ignore checkpoint errors */
+        }
+        try {
+            ctx.nativeDb.close();
+        }
+        catch {
+            /* ignore close errors */
+        }
+        ctx.nativeDb = undefined;
+        // Reopen better-sqlite3 connection to get a fresh page cache.
+        // After rusqlite truncates the WAL, better-sqlite3's internal WAL index
+        // (shared-memory mapping) may reference frames that no longer exist,
+        // causing SQLITE_CORRUPT on the next read. Closing and reopening
+        // forces a clean slate — the only reliable cross-library handoff (#715, #736).
+        try {
+            ctx.db.close();
+        }
+        catch {
+            /* ignore close errors */
+        }
+        ctx.db = openDb(ctx.dbPath);
+    }
     await resolveImports(ctx);
     await buildEdges(ctx);
     await buildStructure(ctx);
@@ -204,6 +276,15 @@ async function runPipelineStages(ctx) {
     // Close nativeDb after analyses — finalize uses JS paths for setBuildMeta
     // and closeDbPair handles cleanup. Avoids dual-connection during finalize.
     if (ctx.nativeDb) {
+        // Checkpoint WAL through rusqlite before closing so better-sqlite3 never
+        // needs to apply WAL frames written by a different SQLite library (#715, #717).
+        // Separate try/catch blocks ensure close() always runs even if checkpoint throws.
+        try {
+            ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+        }
+        catch {
+            /* ignore checkpoint errors */
+        }
         try {
             ctx.nativeDb.close();
         }
@@ -227,6 +308,47 @@ export async function buildGraph(rootDir, opts = {}) {
     ctx.rootDir = rootDir;
     try {
         setupPipeline(ctx);
+        // ── Rust orchestrator fast path (#695) ────────────────────────────
+        // When available, run the entire build pipeline in Rust with zero
+        // napi crossings (eliminates WAL dual-connection dance). Falls back
+        // to the JS pipeline on failure or when native is unavailable.
+        const forceJs = process.env.CODEGRAPH_FORCE_JS_PIPELINE === '1';
+        if (!forceJs && ctx.nativeDb?.buildGraph) {
+            try {
+                const resultJson = ctx.nativeDb.buildGraph(ctx.rootDir, JSON.stringify(ctx.config), JSON.stringify(ctx.aliases), JSON.stringify(opts));
+                const result = JSON.parse(resultJson);
+                if (result.earlyExit) {
+                    closeDbPair({ db: ctx.db, nativeDb: ctx.nativeDb });
+                    return;
+                }
+                // Map Rust timing fields to the JS BuildResult format.
+                // Rust handles collect+detect+parse+insert+resolve+edges+structure+roles.
+                // AST/complexity/CFG/dataflow analyses are not yet ported to Rust.
+                const p = result.phases;
+                closeDbPair({ db: ctx.db, nativeDb: ctx.nativeDb });
+                info(`Native build orchestrator completed: ${result.nodeCount ?? 0} nodes, ${result.edgeCount ?? 0} edges, ${result.fileCount ?? 0} files`);
+                return {
+                    phases: {
+                        setupMs: +((p.setupMs ?? 0) + (p.collectMs ?? 0) + (p.detectMs ?? 0)).toFixed(1),
+                        parseMs: +(p.parseMs ?? 0).toFixed(1),
+                        insertMs: +(p.insertMs ?? 0).toFixed(1),
+                        resolveMs: +(p.resolveMs ?? 0).toFixed(1),
+                        edgesMs: +(p.edgesMs ?? 0).toFixed(1),
+                        structureMs: +(p.structureMs ?? 0).toFixed(1),
+                        rolesMs: +(p.rolesMs ?? 0).toFixed(1),
+                        astMs: 0,
+                        complexityMs: 0,
+                        cfgMs: 0,
+                        dataflowMs: 0,
+                        finalizeMs: +(p.finalizeMs ?? 0).toFixed(1),
+                    },
+                };
+            }
+            catch (err) {
+                warn(`Native build orchestrator failed, falling back to JS pipeline: ${err.message}`);
+                // Fall through to JS pipeline
+            }
+        }
         await runPipelineStages(ctx);
     }
     catch (err) {

package/dist/domain/graph/builder/pipeline.js.map

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package/dist/domain/graph/builder/stages/build-edges.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"build-edges.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-edges.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAiiBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAqEpE"}
+{"version":3,"file":"build-edges.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-edges.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAsrBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA6EpE"}

package/dist/domain/graph/builder/stages/build-edges.js

@@ -86,6 +86,98 @@ function buildBarrelEdges(ctx, imp, resolvedPath, fileNodeId, edgeKind, getNodeI
         }
     }
 }
+// ── Import edges (native engine) ────────────────────────────────────────
+function buildImportEdgesNative(ctx, getNodeIdStmt, allEdgeRows, native) {
+    const { fileSymbols, barrelOnlyFiles, rootDir } = ctx;
+    // 1. Build per-file input data
+    const files = [];
+    // Collect all file node IDs we'll need (sources + targets)
+    const fileNodeIds = [];
+    const seenNodeFiles = new Set();
+    const addFileNodeId = (relPath) => {
+        if (seenNodeFiles.has(relPath))
+            return fileNodeRowCache.get(relPath);
+        const row = getNodeIdStmt.get(relPath, 'file', relPath, 0);
+        if (row) {
+            seenNodeFiles.add(relPath);
+            fileNodeIds.push({ file: relPath, nodeId: row.id });
+            fileNodeRowCache.set(relPath, row);
+        }
+        return row;
+    };
+    const fileNodeRowCache = new Map();
+    // 2. Pre-resolve all imports and collect supplemental resolved entries
+    const supplementalResolved = [];
+    for (const [relPath, symbols] of fileSymbols) {
+        const fileNodeRow = addFileNodeId(relPath);
+        if (!fileNodeRow)
+            continue;
+        const importInfos = [];
+        for (const imp of symbols.imports) {
+            // Pre-resolve and register target file node
+            const resolvedPath = getResolved(ctx, path.join(rootDir, relPath), imp.source);
+            addFileNodeId(resolvedPath);
+            // Check if this resolution is in batchResolved; if not, add supplemental
+            const resolveKey = `${path.join(rootDir, relPath)}|${imp.source}`;
+            if (!ctx.batchResolved?.has(resolveKey)) {
+                supplementalResolved.push({ key: resolveKey, resolvedPath });
+            }
+            importInfos.push({
+                source: imp.source,
+                names: imp.names,
+                reexport: !!imp.reexport,
+                typeOnly: !!imp.typeOnly,
+                dynamicImport: !!imp.dynamicImport,
+                wildcardReexport: !!imp.wildcardReexport,
+            });
+        }
+        files.push({
+            file: relPath,
+            fileNodeId: fileNodeRow.id,
+            isBarrelOnly: barrelOnlyFiles.has(relPath),
+            imports: importInfos,
+            definitionNames: symbols.definitions.map((d) => d.name),
+        });
+    }
+    // 3. Flatten batchResolved + supplemental into resolved imports array
+    const resolvedImports = [];
+    if (ctx.batchResolved) {
+        for (const [key, resolvedPath] of ctx.batchResolved) {
+            resolvedImports.push({ key, resolvedPath });
+        }
+    }
+    for (const entry of supplementalResolved) {
+        resolvedImports.push(entry);
+    }
+    // 4. Flatten reexportMap
+    const fileReexports = [];
+    if (ctx.reexportMap) {
+        for (const [file, entries] of ctx.reexportMap) {
+            const reexports = entries.map((re) => ({
+                source: re.source,
+                names: re.names,
+                wildcardReexport: !!re.wildcardReexport,
+            }));
+            fileReexports.push({ file, reexports });
+            // Register reexport target files for node ID lookup
+            for (const re of reexports) {
+                addFileNodeId(re.source);
+            }
+        }
+    }
+    // 5. Compute barrel file list
+    const barrelFiles = [];
+    for (const [relPath] of fileSymbols) {
+        if (isBarrelFile(ctx, relPath)) {
+            barrelFiles.push(relPath);
+        }
+    }
+    // 6. Call native
+    const nativeEdges = native.buildImportEdges(files, resolvedImports, fileReexports, fileNodeIds, barrelFiles, rootDir);
+    for (const e of nativeEdges) {
+        allEdgeRows.push([e.sourceId, e.targetId, e.kind, e.confidence, e.dynamic]);
+    }
+}
 // ── Call edges (native engine) ──────────────────────────────────────────
 function buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodes, native) {
     const { fileSymbols, barrelOnlyFiles, rootDir } = ctx;
@@ -395,7 +487,15 @@ export async function buildEdges(ctx) {
                 deleteOutgoingEdges.run(relPath);
             }
         }
-        buildImportEdges(ctx, getNodeIdStmt, allEdgeRows);
+        // Skip native import-edge path for small incremental builds (≤3 files):
+        // napi-rs marshaling overhead exceeds computation savings.
+        const useNativeImportEdges = native?.buildImportEdges && (ctx.isFullBuild || ctx.fileSymbols.size > 3);
+        if (useNativeImportEdges) {
+            buildImportEdgesNative(ctx, getNodeIdStmt, allEdgeRows, native);
+        }
+        else {
+            buildImportEdges(ctx, getNodeIdStmt, allEdgeRows);
+        }
         // Skip native call-edge path for small incremental builds (≤3 files):
         // napi-rs marshaling overhead for allNodes exceeds computation savings.
         const useNativeCallEdges = native?.buildCallEdges && (ctx.isFullBuild || ctx.fileSymbols.size > 3);

package/dist/domain/graph/builder/stages/build-edges.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/stages/collect-files.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"collect-files.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/collect-files.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAgErD,wBAAsB,YAAY,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0CtE"}
+{"version":3,"file":"collect-files.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/collect-files.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA2ErD,wBAAsB,YAAY,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0CtE"}

package/dist/domain/graph/builder/stages/collect-files.js

@@ -17,13 +17,23 @@ import { collectFiles as collectFilesUtil } from '../helpers.js';
  */
 function tryFastCollect(ctx) {
     const { db, rootDir } = ctx;
+    const useNative = ctx.engineName === 'native' && !!ctx.nativeDb?.getCollectFilesData;
     // 1. Check that file_hashes table exists and has entries
     let dbFileCount;
-    try {
-        dbFileCount = db.prepare('SELECT COUNT(*) as c FROM file_hashes').get().c;
+    let dbFiles;
+    if (useNative) {
+        const data = ctx.nativeDb.getCollectFilesData();
+        dbFileCount = data.count;
+        dbFiles = data.files;
     }
-    catch {
-        return null;
+    else {
+        try {
+            dbFileCount = db.prepare('SELECT COUNT(*) as c FROM file_hashes').get().c;
+        }
+        catch {
+            return null;
+        }
+        dbFiles = []; // deferred — loaded below only if needed
     }
     if (dbFileCount === 0)
         return null;
@@ -38,7 +48,9 @@ function tryFastCollect(ctx) {
     if (!hasEntries)
         return null;
     // 3. Load existing file list from file_hashes (relative paths)
-    const dbFiles = db.prepare('SELECT file FROM file_hashes').all().map((r) => r.file);
+    if (!useNative) {
+        dbFiles = db.prepare('SELECT file FROM file_hashes').all().map((r) => r.file);
+    }
     // 4. Apply journal deltas: remove deleted files, add new/changed files
     const fileSet = new Set(dbFiles);
     if (journal.removed) {

package/dist/domain/graph/builder/stages/collect-files.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/stages/detect-changes.d.ts.map

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