@elaraai/e3-core 1.0.17 → 1.0.18

package/dist/src/storage/local/LocalRefStore.js

@@ -7,6 +7,7 @@ import * as path from 'path';
 import { decodeBeast2For, encodeBeast2For } from '@elaraai/east';
 import { ExecutionStatusType, DataflowRunType } from '@elaraai/e3-types';
 import { isNotFoundError, ExecutionCorruptError } from '../../errors.js';
+import { atomicWriteFile } from './localHelpers.js';
 /**
  * Local filesystem implementation of RefStore.
  *
@@ -27,6 +28,10 @@ export class LocalRefStore {
                 if (stat.isDirectory()) {
                     const versions = await fs.readdir(nameDir);
                     for (const version of versions) {
+                        // Skip in-flight / crash-orphaned atomic-write staging files
+                        // (packageWrite stages `<version>.<rand>.partial` siblings here).
+                        if (version.includes('.partial'))
+                            continue;
                         packages.push({ name, version });
                     }
                 }
@@ -54,10 +59,8 @@ export class LocalRefStore {
         }
     }
     async packageWrite(repo, name, version, hash) {
-        const refDir = path.join(repo, 'packages', name);
-        await fs.mkdir(refDir, { recursive: true });
-        const refPath = path.join(refDir, version);
-        await fs.writeFile(refPath, hash + '\n');
+        const refPath = path.join(repo, 'packages', name, version);
+        await atomicWriteFile(refPath, hash + '\n');
     }
     async packageRemove(repo, name, version) {
         const refPath = path.join(repo, 'packages', name, version);
@@ -114,14 +117,10 @@ export class LocalRefStore {
         }
     }
     async workspaceWrite(repo, name, state) {
-        const wsDir = path.join(repo, 'workspaces');
-        const stateFile = path.join(wsDir, `${name}.beast2`);
-        await fs.mkdir(wsDir, { recursive: true });
-        // Write atomically: write to temp file, then rename
-        const randomSuffix = Math.random().toString(36).slice(2, 10);
-        const tempPath = path.join(wsDir, `.${name}.${Date.now()}.${randomSuffix}.tmp`);
-        await fs.writeFile(tempPath, state);
-        await fs.rename(tempPath, stateFile);
+        const stateFile = path.join(repo, 'workspaces', `${name}.beast2`);
+        // Atomic stage-and-rename: a concurrent reader sees the old or new complete
+        // state, never a 0-byte truncation window.
+        await atomicWriteFile(stateFile, state);
     }
     async workspaceRemove(repo, name) {
         const stateFile = path.join(repo, 'workspaces', `${name}.beast2`);
@@ -173,12 +172,17 @@ export class LocalRefStore {
     }
     async executionWrite(repo, taskHash, inputsHash, executionId, status) {
         const execDir = this.executionDir(repo, taskHash, inputsHash, executionId);
-        await fs.mkdir(execDir, { recursive: true });
+        // A single execution rewrites status.beast2 several times over its lifetime
+        // (running → success/failed). A bare overwrite truncates the file to 0 bytes
+        // mid-write, which a concurrent reader (e.g. a workspace-status poll calling
+        // executionGet) decodes as "Data too short for Beast2 format". Stage-and-
+        // rename makes each update atomic, so a reader only ever sees a complete
+        // status object.
         const encoder = encodeBeast2For(ExecutionStatusType);
-        await fs.writeFile(path.join(execDir, 'status.beast2'), encoder(status));
+        await atomicWriteFile(path.join(execDir, 'status.beast2'), encoder(status));
         // Also write output hash for success status
         if (status.type === 'success') {
-            await fs.writeFile(path.join(execDir, 'output'), status.value.outputHash + '\n');
+            await atomicWriteFile(path.join(execDir, 'output'), status.value.outputHash + '\n');
         }
     }
     async executionListIds(repo, taskHash, inputsHash) {
@@ -301,11 +305,12 @@ export class LocalRefStore {
         return decoder(data);
     }
     async dataflowRunWrite(repo, workspace, run) {
-        const dir = this.dataflowDir(repo, workspace);
-        await fs.mkdir(dir, { recursive: true });
+        // A run record is rewritten in place as the run progresses (initial →
+        // cancelled/final); stage-and-rename so a concurrent dataflowRunGet never
+        // observes a 0-byte truncation window.
         const encoder = encodeBeast2For(DataflowRunType);
         const runPath = this.dataflowRunPath(repo, workspace, run.runId);
-        await fs.writeFile(runPath, encoder(run));
+        await atomicWriteFile(runPath, encoder(run));
     }
     async dataflowRunList(repo, workspace) {
         const dir = this.dataflowDir(repo, workspace);

package/dist/src/storage/local/LocalRefStore.js.map

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package/dist/src/storage/local/LocalRefStore.spec.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Copyright (c) 2025 Elara AI Pty Ltd
+ * Licensed under BSL 1.1. See LICENSE for details.
+ */
+export {};
+//# sourceMappingURL=LocalRefStore.spec.d.ts.map

package/dist/src/storage/local/LocalRefStore.spec.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LocalRefStore.spec.d.ts","sourceRoot":"","sources":["../../../../src/storage/local/LocalRefStore.spec.ts"],"names":[],"mappings":"AAAA;;;GAGG"}

package/dist/src/storage/local/LocalRefStore.spec.js

@@ -0,0 +1,159 @@
+/**
+ * Copyright (c) 2025 Elara AI Pty Ltd
+ * Licensed under BSL 1.1. See LICENSE for details.
+ */
+/**
+ * Concurrency regression tests for LocalRefStore execution status.
+ *
+ * A single execution rewrites executions/<task>/<inputs>/<id>/status.beast2
+ * several times over its lifetime (running → success/failed). The dataflow
+ * orchestrator does this while a workspace-status poll concurrently reads the
+ * same file via executionGet. A non-atomic overwrite truncates the file to 0
+ * bytes mid-write, which the reader decodes as "Data too short for Beast2
+ * format: 0 bytes" → ExecutionCorruptError → API "internal" — the macOS CI
+ * flake in the "dataflowStart triggers execution (non-blocking)" suite.
+ */
+import { describe, it, beforeEach, afterEach } from 'node:test';
+import assert from 'node:assert';
+import * as fs from 'node:fs/promises';
+import { join } from 'node:path';
+import { variant, some, none } from '@elaraai/east';
+import { LocalRefStore } from './LocalRefStore.js';
+import { createTestRepo, removeTestRepo } from '../../test-helpers.js';
+describe('LocalRefStore execution status (concurrent read/write)', () => {
+    let repo;
+    beforeEach(() => { repo = createTestRepo(); });
+    afterEach(() => { removeTestRepo(repo); });
+    const taskHash = 'a'.repeat(64);
+    const inputsHash = 'b'.repeat(64);
+    const executionId = '0190a0b0-0000-7000-8000-000000000000';
+    // Thousands of input hashes so the encoded status spans many write() chunks:
+    // this is what turns a non-atomic overwrite into an observable truncation
+    // window. A bare fs.writeFile makes the read-side throw reliably here.
+    const bigInputs = Array.from({ length: 3000 }, (_, i) => i.toString(16).padStart(64, '0'));
+    // variant() is constructed inline (not via a shared helper) so the East
+    // diagnostics don't read these as authoring-time macros.
+    const running = variant('running', {
+        executionId,
+        inputHashes: bigInputs,
+        startedAt: new Date(0),
+        pid: 1234n,
+        pidStartTime: 5678n,
+        bootId: 'boot-id',
+    });
+    const success = variant('success', {
+        executionId,
+        inputHashes: bigInputs,
+        outputHash: 'c'.repeat(64),
+        startedAt: new Date(0),
+        completedAt: new Date(1000),
+    });
+    it('executionGet never tears while executionWrite overwrites status in place', async () => {
+        const store = new LocalRefStore();
+        await store.executionWrite(repo, taskHash, inputsHash, executionId, running); // seed
+        let stop = false;
+        const reader = (async () => {
+            const errors = [];
+            while (!stop) {
+                try {
+                    const s = await store.executionGet(repo, taskHash, inputsHash, executionId);
+                    assert.ok(s !== null, 'the seeded status is always present');
+                }
+                catch (err) {
+                    errors.push(err.message);
+                }
+                // Yield: a tight read loop would hold the file open ~continuously and on
+                // Windows starve the writer's rename (EPERM). A real status poll is periodic.
+                await new Promise((r) => setTimeout(r, 1));
+            }
+            return errors;
+        })();
+        try {
+            for (let i = 0; i < 250; i++) {
+                await store.executionWrite(repo, taskHash, inputsHash, executionId, i % 2 === 0 ? success : running);
+            }
+        }
+        finally {
+            stop = true; // always release the reader, even if a write throws, or it spins forever
+        }
+        const errors = await reader;
+        assert.deepStrictEqual(errors, [], `executionGet must never observe a torn write; saw: ${errors.slice(0, 3).join(' | ')}`);
+    });
+});
+describe('LocalRefStore dataflow run (concurrent read/write)', () => {
+    let repo;
+    beforeEach(() => { repo = createTestRepo(); });
+    afterEach(() => { removeTestRepo(repo); });
+    const workspace = 'main';
+    const runId = '0190a0b0-1111-7000-8000-000000000000';
+    // A large inputVersions map so the encoded run spans many write() chunks — the
+    // same widening that makes a non-atomic overwrite tear a concurrent read.
+    // dataflowRunGet decodes Beast2 with no corruption wrapper, so a torn read
+    // would surface a raw "Data too short for Beast2 format" error here.
+    const bigVersions = new Map(Array.from({ length: 3000 }, (_, i) => [`inputs/p${i}`, i.toString(16).padStart(64, '0')]));
+    const summary = { total: 0n, completed: 0n, cached: 0n, failed: 0n, skipped: 0n, reexecuted: 0n };
+    const runningRun = {
+        runId,
+        workspaceName: workspace,
+        packageRef: 'pkg@1.0.0',
+        startedAt: new Date(0),
+        completedAt: none,
+        status: variant('running', {}),
+        inputVersions: bigVersions,
+        outputVersions: none,
+        taskExecutions: new Map(),
+        summary,
+    };
+    const completedRun = {
+        ...runningRun,
+        completedAt: some(new Date(1000)),
+        status: variant('completed', {}),
+        outputVersions: some(bigVersions),
+    };
+    it('dataflowRunGet never tears while dataflowRunWrite overwrites the run in place', async () => {
+        const store = new LocalRefStore();
+        await store.dataflowRunWrite(repo, workspace, runningRun); // seed
+        let stop = false;
+        const reader = (async () => {
+            const errors = [];
+            while (!stop) {
+                try {
+                    const run = await store.dataflowRunGet(repo, workspace, runId);
+                    assert.ok(run !== null, 'the seeded run is always present');
+                }
+                catch (err) {
+                    errors.push(err.message);
+                }
+                // Yield: a tight read loop would hold the file open ~continuously and on
+                // Windows starve the writer's rename (EPERM). A real status poll is periodic.
+                await new Promise((r) => setTimeout(r, 1));
+            }
+            return errors;
+        })();
+        try {
+            for (let i = 0; i < 250; i++) {
+                await store.dataflowRunWrite(repo, workspace, i % 2 === 0 ? completedRun : runningRun);
+            }
+        }
+        finally {
+            stop = true; // always release the reader, even if a write throws, or it spins forever
+        }
+        const errors = await reader;
+        assert.deepStrictEqual(errors, [], `dataflowRunGet must never observe a torn write; saw: ${errors.slice(0, 3).join(' | ')}`);
+    });
+});
+describe('LocalRefStore packageList', () => {
+    let repo;
+    beforeEach(() => { repo = createTestRepo(); });
+    afterEach(() => { removeTestRepo(repo); });
+    it('ignores atomic-write .partial staging siblings (no phantom versions)', async () => {
+        const store = new LocalRefStore();
+        await store.packageWrite(repo, 'pkg', '1.0.0', 'a'.repeat(64));
+        // Simulate a crash-orphaned staging file left next to the version ref.
+        const nameDir = join(repo, 'packages', 'pkg');
+        await fs.writeFile(join(nameDir, '1.0.0.abc12345.partial'), 'b'.repeat(64) + '\n');
+        const pkgs = await store.packageList(repo);
+        assert.deepStrictEqual(pkgs, [{ name: 'pkg', version: '1.0.0' }], 'the .partial sibling must not surface as a phantom version');
+    });
+});
+//# sourceMappingURL=LocalRefStore.spec.js.map

package/dist/src/storage/local/LocalRefStore.spec.js.map

@@ -0,0 +1 @@
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package/dist/src/storage/local/gc.d.ts.map

@@ -1 +1 @@
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package/dist/src/storage/local/gc.js

@@ -356,6 +356,20 @@ export async function repoGc(storage, repo, options = {}) {
     catch {
         // Not a fatal error
     }
+    // Step 4b: Sweep orphaned .partial staging files left by atomicWriteFile in
+    // the ref trees (packages/, workspaces/ incl. nested dataset refs,
+    // executions/, dataflows/) — cleanupPartials above only covers objects/.
+    const partialNow = Date.now();
+    for (const refRoot of ['packages', 'workspaces', 'executions', 'dataflows']) {
+        try {
+            const result = await cleanupRefTreePartials(path.join(repo, refRoot), partialNow, minAge, dryRun);
+            deletedPartials += result.deleted;
+            partialSkippedYoung += result.skippedYoung;
+        }
+        catch {
+            // Not a fatal error
+        }
+    }
     // Step 5: Clean up orphaned transfer staging files
     try {
         const transferResult = await cleanupTransferStaging(minAge, dryRun);
@@ -424,6 +438,54 @@ async function cleanupPartials(repoPath, minAge, dryRun) {
     }
     return { deleted, skippedYoung };
 }
+/**
+ * Recursively unlink aged `.partial` staging files under a ref-tree root.
+ *
+ * `atomicWriteFile` stages bytes in a sibling `<dest>.<rand>.partial` file
+ * before renaming it over the destination; that staging file survives only if a
+ * writer crashed between the write and the rename. This sweeps those orphans
+ * from the ref trees (packages/, workspaces/ — including nested dataset refs —,
+ * executions/, dataflows/), which the objects-only {@link cleanupPartials} does
+ * not cover. The age gate ensures a live, in-flight staging file is never raced.
+ *
+ * @param rootDir - Ref-tree root directory to walk
+ * @param now - Reference timestamp for the age gate
+ * @param minAge - Minimum age (ms) before a staging file is eligible for removal
+ * @param dryRun - When true, count but do not delete
+ * @returns Counts of deleted and too-young-to-delete staging files
+ */
+async function cleanupRefTreePartials(rootDir, now, minAge, dryRun) {
+    let deleted = 0;
+    let skippedYoung = 0;
+    const entries = await fs.readdir(rootDir, { withFileTypes: true }).catch(() => null);
+    if (!entries)
+        return { deleted, skippedYoung }; // Root directory doesn't exist
+    for (const entry of entries) {
+        const full = path.join(rootDir, entry.name);
+        if (entry.isDirectory()) {
+            const sub = await cleanupRefTreePartials(full, now, minAge, dryRun);
+            deleted += sub.deleted;
+            skippedYoung += sub.skippedYoung;
+        }
+        else if (entry.name.endsWith('.partial')) {
+            try {
+                const fileStat = await fs.stat(full);
+                if (minAge > 0 && now - fileStat.mtimeMs < minAge) {
+                    skippedYoung++;
+                    continue;
+                }
+                if (!dryRun) {
+                    await fs.unlink(full);
+                }
+                deleted++;
+            }
+            catch {
+                // Skip files we can't stat or delete
+            }
+        }
+    }
+    return { deleted, skippedYoung };
+}
 /**
  * Clean up orphaned transfer staging files from the OS temp directory.
  * These are created by the transfer upload flow and should be cleaned up

package/dist/src/storage/local/gc.js.map

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package/dist/src/storage/local/localHelpers.d.ts

@@ -22,4 +22,44 @@ export declare function objectPath(repoPath: string, hash: string): string;
  * @returns Minimum unambiguous prefix length
  */
 export declare function objectAbbrev(repoPath: string, hash: string, minLength?: number): Promise<number>;
+/**
+ * Rename `from` over `to`, retrying on Windows sharing-violation errors.
+ *
+ * POSIX rename-over-existing is atomic even while another process holds the
+ * destination open for read, so the first attempt always succeeds there.
+ * Windows refuses the rename (EPERM/EACCES/EBUSY) while a reader holds the
+ * destination open — Node/libuv never opens files with FILE_SHARE_DELETE and
+ * exposes no way to set the share mode — so, like graceful-fs / npm, we retry
+ * with a bounded exponential backoff. A realistic reader holds the handle only
+ * for the brief duration of its read, so the lock clears almost immediately
+ * (usually the first or second attempt); the attempt count is generous so that
+ * even bursty concurrent reads on a loaded Windows host clear well before the
+ * bound, while a genuine permission error still surfaces promptly. A no-op on
+ * POSIX, where the first attempt always succeeds.
+ *
+ * @param from - Staging path to rename from
+ * @param to - Destination path to atomically replace
+ * @param maxAttempts - Upper bound on retries (≈1.9s total over the default 25)
+ */
+export declare function renameWithRetry(from: string, to: string, maxAttempts?: number): Promise<void>;
+/**
+ * Atomically (over)write a file: stage the bytes in a unique sibling
+ * `.partial` file, then rename it over the destination.
+ *
+ * A bare `fs.writeFile` to an existing path opens it `O_TRUNC` — the file is
+ * momentarily 0 bytes, so a concurrent reader can observe an empty/truncated
+ * file and fail to decode it (e.g. "Data too short for Beast2 format: 0 bytes").
+ * The stage-and-rename makes the replacement atomic: a reader sees either the
+ * old complete file or the new complete file, never a partial one. Use this for
+ * every mutable ref/state file a reader may read while a writer overwrites it
+ * (execution status, dataflow runs, workspace state, dataset refs).
+ *
+ * Staging files use a `.partial` extension so the directory-listing helpers
+ * (which filter `.partial`) never mistake them for real entries, and orphaned
+ * stages from a crashed writer are swept by `gc` (see cleanupPartials).
+ *
+ * @param filePath - Destination path to atomically (over)write
+ * @param data - Bytes (or string) to write
+ */
+export declare function atomicWriteFile(filePath: string, data: Uint8Array | string): Promise<void>;
 //# sourceMappingURL=localHelpers.d.ts.map

package/dist/src/storage/local/localHelpers.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"localHelpers.d.ts","sourceRoot":"","sources":["../../../../src/storage/local/localHelpers.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH;;;;;;GAMG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,CAIjE;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,YAAY,CAChC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,SAAS,GAAE,MAAU,GACpB,OAAO,CAAC,MAAM,CAAC,CAwCjB;AAOD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAsB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,WAAW,SAAK,GAAG,OAAO,CAAC,IAAI,CAAC,CAY/F;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAsB,eAAe,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,UAAU,GAAG,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAehG"}

package/dist/src/storage/local/localHelpers.js

@@ -66,4 +66,81 @@ export async function objectAbbrev(repoPath, hash, minLength = 4) {
     }
     return hash.length;
 }
+// Transient Windows errors raised when renaming over a file another handle
+// currently has open (sharing violation), or when the destination briefly
+// resists replacement. POSIX never raises these on rename-over-existing.
+const WIN_RENAME_RETRYABLE = new Set(['EPERM', 'EACCES', 'EBUSY', 'EEXIST']);
+/**
+ * Rename `from` over `to`, retrying on Windows sharing-violation errors.
+ *
+ * POSIX rename-over-existing is atomic even while another process holds the
+ * destination open for read, so the first attempt always succeeds there.
+ * Windows refuses the rename (EPERM/EACCES/EBUSY) while a reader holds the
+ * destination open — Node/libuv never opens files with FILE_SHARE_DELETE and
+ * exposes no way to set the share mode — so, like graceful-fs / npm, we retry
+ * with a bounded exponential backoff. A realistic reader holds the handle only
+ * for the brief duration of its read, so the lock clears almost immediately
+ * (usually the first or second attempt); the attempt count is generous so that
+ * even bursty concurrent reads on a loaded Windows host clear well before the
+ * bound, while a genuine permission error still surfaces promptly. A no-op on
+ * POSIX, where the first attempt always succeeds.
+ *
+ * @param from - Staging path to rename from
+ * @param to - Destination path to atomically replace
+ * @param maxAttempts - Upper bound on retries (≈1.9s total over the default 25)
+ */
+export async function renameWithRetry(from, to, maxAttempts = 25) {
+    for (let attempt = 0;; attempt++) {
+        try {
+            await fs.rename(from, to);
+            return;
+        }
+        catch (err) {
+            const code = err.code ?? '';
+            if (attempt >= maxAttempts - 1 || !WIN_RENAME_RETRYABLE.has(code))
+                throw err;
+            // 1, 2, 4, … ms, capped at 100ms (≈1.9s total over 25 attempts).
+            await new Promise((resolve) => setTimeout(resolve, Math.min(2 ** attempt, 100)));
+        }
+    }
+}
+/**
+ * Atomically (over)write a file: stage the bytes in a unique sibling
+ * `.partial` file, then rename it over the destination.
+ *
+ * A bare `fs.writeFile` to an existing path opens it `O_TRUNC` — the file is
+ * momentarily 0 bytes, so a concurrent reader can observe an empty/truncated
+ * file and fail to decode it (e.g. "Data too short for Beast2 format: 0 bytes").
+ * The stage-and-rename makes the replacement atomic: a reader sees either the
+ * old complete file or the new complete file, never a partial one. Use this for
+ * every mutable ref/state file a reader may read while a writer overwrites it
+ * (execution status, dataflow runs, workspace state, dataset refs).
+ *
+ * Staging files use a `.partial` extension so the directory-listing helpers
+ * (which filter `.partial`) never mistake them for real entries, and orphaned
+ * stages from a crashed writer are swept by `gc` (see cleanupPartials).
+ *
+ * @param filePath - Destination path to atomically (over)write
+ * @param data - Bytes (or string) to write
+ */
+export async function atomicWriteFile(filePath, data) {
+    await fs.mkdir(path.dirname(filePath), { recursive: true });
+    // A short random suffix so concurrent writers to the same destination never
+    // collide on the staging path. Kept short (no timestamp) to minimise the
+    // extra length added over the destination — the staging path is always
+    // longer than the final path, which matters near the Windows MAX_PATH limit.
+    const randomSuffix = Math.random().toString(36).slice(2, 10);
+    const stagingPath = `${filePath}.${randomSuffix}.partial`;
+    await fs.writeFile(stagingPath, data);
+    try {
+        await renameWithRetry(stagingPath, filePath);
+    }
+    catch (err) {
+        try {
+            await fs.unlink(stagingPath);
+        }
+        catch { /* ignore cleanup failure */ }
+        throw err;
+    }
+}
 //# sourceMappingURL=localHelpers.js.map

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