@quiltdata/benchling-webhook 0.21.2 → 0.21.3

package/README.md

@@ -45,7 +45,7 @@ To put each scientist's notebook packages in the same namespace as their raw-dat
 
 #### Package Metadata
 
-The package metadata is the package's `entry.json`. Besides the entry's IDs, name, creator, authors, and timestamps, it includes the entry's schema `fields` and `customFields`. Benchling keys these by display name, so the webhook re-keys them in snake_case: "Experiment Type" becomes `experiment_type` and "ELN-ID #" becomes `eln_id`. Each field keeps its display name as `name`; its other values are exactly what Benchling returns. Both keys are always present, as `{}` when the entry has none. The package's `entry_data.json` keeps the raw entry.
+The package metadata is the package's `entry.json`. Besides the entry's IDs, name, creator, authors, and timestamps, it includes the entry's schema `fields` and `customFields`. Benchling keys these by display name, so the webhook re-keys them in snake_case: "Experiment Type" becomes `experiment_type` and "ELN-ID #" becomes `eln_id`. Each key maps to the field's `value` as Benchling returns it. Both keys are always present, as `{}` when the entry has none. The package's `entry_data.json` keeps the raw entry, with each field's display name, `displayValue`, `type`, and so on.
 
 ```json
 {
@@ -53,11 +53,11 @@ The package metadata is the package's `entry.json`. Besides the entry's IDs, nam
   "display_id": "EXP26000025",
   "name": "HPLC run 3",
   "fields": {
-    "project": {"name": "Project", "value": "VIR-0001", "displayValue": "VIR-0001", "type": "text", "isMulti": false, "textValue": "VIR-0001"},
-    "experiment_type": {"name": "Experiment Type", "value": "Assay", "displayValue": "Assay", "type": "dropdown", "isMulti": false, "textValue": "Assay"}
+    "project": "VIR-0001",
+    "experiment_type": "Assay"
   },
   "customFields": {
-    "instrument": {"name": "Instrument", "value": "HPLC-02"}
+    "instrument": "HPLC-02"
   }
 }
 ```
@@ -73,7 +73,7 @@ A bucket's [Quilt workflow](https://docs.quilt.bio/advanced-features/workflows)
     "fields": {
       "type": "object",
       "properties": {
-        "project": {"properties": {"value": {"type": "string", "pattern": "^VIR-"}}}
+        "project": {"type": "string", "pattern": "^VIR-"}
       }
     }
   }

package/dist/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@quiltdata/benchling-webhook",
-    "version": "0.21.2",
+    "version": "0.21.3",
     "description": "AWS CDK deployment for Benchling webhook processing using Fargate - Deploy directly with npx",
     "main": "dist/lib/index.js",
     "types": "dist/lib/index.d.ts",
@@ -54,10 +54,13 @@
         "test:prod": "make -C docker test-deployed-prod PROFILE=default",
         "test:python": "make -C docker test-unit",
         "test:ts": "cross-env NODE_ENV=test NODE_OPTIONS='--experimental-vm-modules' jest --maxWorkers=50%",
+        "release:context": "ts-node scripts/version.ts release-context",
+        "release:publish": "ts-node scripts/npm-publish.ts",
         "version": "ts-node scripts/version.ts",
         "version:dev": "ts-node scripts/get-dev-version.ts",
         "version:verify": "ts-node scripts/version.ts verify-clean-git",
         "version:tag": "npm run version:verify && npm test && ts-node scripts/version.ts tag",
+        "version:tag:auto": "ts-node scripts/version.ts auto-tag",
         "version:tag:dev": "npm run version:verify && npm test && ts-node scripts/version.ts tag dev",
         "test:integration": "cross-env NODE_ENV=test NODE_OPTIONS='--experimental-vm-modules' jest --config jest.integration.config.js --testMatch='**/test/integration/**/*.test.ts' --runInBand",
         "test:integration:verbose": "npm run test:integration -- --verbose"

package/dist/scripts/npm-publish.d.ts

@@ -0,0 +1,37 @@
+#!/usr/bin/env node
+/**
+ * Retry-safe npm publication with monotonic shared dist-tags.
+ *
+ * npm trusted publishing (OIDC) authorizes only `npm publish`; `npm dist-tag`
+ * needs a registry token. Promotion therefore happens atomically inside
+ * `npm publish --tag <channel>`, and stale candidates are parked under a
+ * per-version tag so a shared channel never moves backward.
+ */
+export interface NpmRegistry {
+    versions(packageName: string): string[];
+    distTags(packageName: string): Record<string, string>;
+    publish(tag: string): void;
+}
+export interface PublishResult {
+    immutableCreated: boolean;
+    channel: "latest" | "dev";
+    promotion: "initialized" | "promoted" | "current" | "stale";
+}
+export interface NpmCommandResult {
+    status: number;
+    stdout: string;
+    stderr: string;
+}
+export type NpmCommandRunner = (args: readonly string[], inherit?: boolean) => NpmCommandResult;
+export declare const defaultNpmRunner: NpmCommandRunner;
+export declare class CliNpmRegistry implements NpmRegistry {
+    private readonly runner;
+    constructor(runner?: NpmCommandRunner);
+    versions(packageName: string): string[];
+    distTags(packageName: string): Record<string, string>;
+    publish(tag: string): void;
+}
+export declare function parkingDistTag(version: string): string;
+export declare function publishRelease(registry: NpmRegistry, packageName: string, version: string, packageVersion: string): PublishResult;
+export declare function main(args?: string[]): number;
+//# sourceMappingURL=npm-publish.d.ts.map

package/dist/scripts/npm-publish.d.ts.map

@@ -0,0 +1 @@
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package/dist/scripts/npm-publish.js

@@ -0,0 +1,186 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Retry-safe npm publication with monotonic shared dist-tags.
+ *
+ * npm trusted publishing (OIDC) authorizes only `npm publish`; `npm dist-tag`
+ * needs a registry token. Promotion therefore happens atomically inside
+ * `npm publish --tag <channel>`, and stale candidates are parked under a
+ * per-version tag so a shared channel never moves backward.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CliNpmRegistry = exports.defaultNpmRunner = void 0;
+exports.parkingDistTag = parkingDistTag;
+exports.publishRelease = publishRelease;
+exports.main = main;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const child_process_1 = require("child_process");
+const version_1 = require("./version");
+function npmError(args, result) {
+    const detail = result.stderr.trim() || result.stdout.trim() || `exit status ${result.status}`;
+    return new Error(`npm ${args.join(" ")} failed: ${detail}`);
+}
+const defaultNpmRunner = (args, inherit = false) => {
+    const result = (0, child_process_1.spawnSync)("npm", [...args], {
+        encoding: "utf8",
+        stdio: inherit ? "inherit" : "pipe",
+    });
+    return {
+        status: result.status ?? 127,
+        stdout: result.stdout?.toString() ?? "",
+        stderr: [result.stderr?.toString(), result.error?.message].filter(Boolean).join("\n"),
+    };
+};
+exports.defaultNpmRunner = defaultNpmRunner;
+function parseJson(value, label) {
+    try {
+        return JSON.parse(value);
+    }
+    catch (error) {
+        throw new Error(`Malformed npm ${label} response: ${error instanceof Error ? error.message : String(error)}`);
+    }
+}
+class CliNpmRegistry {
+    constructor(runner = exports.defaultNpmRunner) {
+        this.runner = runner;
+    }
+    versions(packageName) {
+        const args = ["view", packageName, "versions", "--json"];
+        const result = this.runner(args);
+        if (result.status !== 0) {
+            throw npmError(args, result);
+        }
+        const parsed = parseJson(result.stdout, "versions");
+        const versions = typeof parsed === "string" ? [parsed] : parsed;
+        if (!Array.isArray(versions) || !versions.every((version) => typeof version === "string")) {
+            throw new Error("Malformed npm versions response: expected a string array");
+        }
+        return versions;
+    }
+    distTags(packageName) {
+        const args = ["view", packageName, "dist-tags", "--json"];
+        const result = this.runner(args);
+        if (result.status !== 0) {
+            throw npmError(args, result);
+        }
+        const parsed = parseJson(result.stdout, "dist-tags");
+        if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+            throw new Error("Malformed npm dist-tags response: expected an object");
+        }
+        for (const value of Object.values(parsed)) {
+            if (typeof value !== "string") {
+                throw new Error("Malformed npm dist-tags response: expected string versions");
+            }
+        }
+        return parsed;
+    }
+    publish(tag) {
+        const args = ["publish", "--provenance", "--access", "public", "--tag", tag];
+        const result = this.runner(args, true);
+        if (result.status !== 0) {
+            throw npmError(args, result);
+        }
+    }
+}
+exports.CliNpmRegistry = CliNpmRegistry;
+function parkingDistTag(version) {
+    return `release-${version.replace(/[^0-9A-Za-z-]/g, "-")}`;
+}
+function promotionDecision(candidate, current) {
+    if (!current) {
+        return "initialized";
+    }
+    const comparison = (0, version_1.compareReleaseVersions)(candidate, current);
+    if (comparison > 0) {
+        return "promoted";
+    }
+    return comparison === 0 ? "current" : "stale";
+}
+function publishRelease(registry, packageName, version, packageVersion) {
+    const release = (0, version_1.parseReleaseVersion)(version);
+    if (packageVersion !== version) {
+        throw new Error(`package.json version ${packageVersion} does not match release ${version}`);
+    }
+    const channel = release.prerelease ? "dev" : "latest";
+    const immutableCreated = !registry.versions(packageName).includes(version);
+    const current = registry.distTags(packageName)[channel];
+    if (current) {
+        const currentRelease = (0, version_1.parseReleaseVersion)(current);
+        if (!release.prerelease && currentRelease.prerelease) {
+            throw new Error(`npm latest must point to a plain semantic version, found ${current}`);
+        }
+    }
+    const promotion = promotionDecision(version, current);
+    const advancesChannel = promotion === "initialized" || promotion === "promoted";
+    if (immutableCreated) {
+        registry.publish(advancesChannel ? channel : parkingDistTag(version));
+    }
+    else if (advancesChannel) {
+        throw new Error(`${packageName}@${version} is already published but npm ${channel} is ${current ?? "unset"}; ` +
+            `trusted publishing cannot move dist-tags, so run: npm dist-tag add ${packageName}@${version} ${channel}`);
+    }
+    return {
+        immutableCreated,
+        channel,
+        promotion,
+    };
+}
+function readPackageJson() {
+    const packagePath = path.join(__dirname, "..", "package.json");
+    const parsed = JSON.parse(fs.readFileSync(packagePath, "utf8"));
+    if (typeof parsed.name !== "string" || typeof parsed.version !== "string") {
+        throw new Error("package.json must contain string name and version fields");
+    }
+    return parsed;
+}
+function main(args = process.argv.slice(2)) {
+    try {
+        const pkg = readPackageJson();
+        const version = args[0] ?? process.env.RELEASE_VERSION ?? pkg.version;
+        const result = publishRelease(new CliNpmRegistry(), pkg.name, version, pkg.version);
+        console.log(`npm ${result.channel}: immutable=${result.immutableCreated}, promotion=${result.promotion}`);
+        return 0;
+    }
+    catch (error) {
+        console.error(`❌ ${error instanceof Error ? error.message : String(error)}`);
+        return 1;
+    }
+}
+if (require.main === module) {
+    process.exitCode = main();
+}
+//# sourceMappingURL=npm-publish.js.map

package/dist/scripts/npm-publish.js.map

@@ -0,0 +1 @@
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package/dist/scripts/version.d.ts

@@ -1,15 +1,102 @@
 #!/usr/bin/env node
 /**
- * Version management script - bumps version numbers and creates release tags
+ * Version management and release-tag tooling.
  *
- * Usage:
- *   node bin/version.ts          # Show all three version files
- *   node bin/version.ts patch    # 0.4.7 -> 0.4.8
- *   node bin/version.ts minor    # 0.4.7 -> 0.5.0
- *   node bin/version.ts major    # 0.4.7 -> 1.0.0
- *   node bin/version.ts sync     # Force TOML and YAML to match JSON version
- *   node bin/version.ts tag      # Create and push production release tag
- *   node bin/version.ts tag dev  # Create and push dev release tag
+ * Version bumps remain explicit commands. Release commands share tag construction,
+ * local/remote target verification, and annotated-tag creation semantics.
  */
+interface VersionParts {
+    major: number;
+    minor: number;
+    patch: number;
+}
+export interface ReleaseVersion extends VersionParts {
+    raw: string;
+    prerelease: boolean;
+    timestamp?: string;
+}
+export interface CommandResult {
+    status: number;
+    stdout: string;
+    stderr: string;
+}
+export interface CommandOptions {
+    cwd: string;
+    inherit?: boolean;
+}
+export type CommandRunner = (command: string, args: readonly string[], options: CommandOptions) => CommandResult;
+export type AutoTagOutcome = "no-version-change" | "non-production-version" | "verified-existing-tag" | "verified-recovered-tag" | "created" | "verified-race";
+export interface AutoTagResult {
+    outcome: AutoTagOutcome;
+    releaseRequired: boolean;
+    verified: boolean;
+    tag: string;
+    targetSha: string;
+}
+export interface ReleaseContext {
+    verified: boolean;
+    tag: string;
+    version: string;
+    baseVersion: string;
+    targetSha: string;
+    isPrerelease: boolean;
+}
+export interface TagAnnotation {
+    message: string;
+    taggerName: string;
+    taggerEmail: string;
+}
+export interface RemoteReleaseTag {
+    targetSha: string;
+    annotation: TagAnnotation | null;
+}
+export interface ReleaseRepository {
+    resolveCommit(ref: string): string;
+    commitExists(ref: string): boolean;
+    readFileAtCommit(commit: string, file: string): string;
+    localTagTarget(tag: string): string | null;
+    remoteTag(tag: string): RemoteReleaseTag | null;
+    createAnnotatedTag(tag: string, message: string, targetSha: string): void;
+    pushTag(tag: string): boolean;
+    isClean(): boolean;
+}
+export interface AutomaticReleaseOptions {
+    repository: ReleaseRepository;
+    currentVersion: string;
+    beforeSha?: string;
+    githubSha: string;
+    runProductionGate: () => void;
+}
+export declare const AUTOMATIC_RELEASE_TAGGER_NAME = "github-actions[bot]";
+export declare const AUTOMATIC_RELEASE_TAGGER_EMAIL = "41898282+github-actions[bot]@users.noreply.github.com";
+export declare const defaultCommandRunner: CommandRunner;
+export declare function isSemanticVersion(version: string): boolean;
+export declare function parseReleaseVersion(version: string): ReleaseVersion;
+export declare function compareReleaseVersions(left: string, right: string): number;
+export declare function productionTag(version: string): string;
+export declare function devTag(version: string, now?: Date): string;
+export declare function annotatedTagMessage(tag: string): string;
+export declare function parseTag(tag: string): Omit<ReleaseContext, "verified" | "targetSha">;
+export declare class GitReleaseRepository implements ReleaseRepository {
+    private readonly cwd;
+    private readonly runner;
+    constructor(cwd: string, runner?: CommandRunner);
+    private git;
+    resolveCommit(ref: string): string;
+    commitExists(ref: string): boolean;
+    readFileAtCommit(commit: string, file: string): string;
+    localTagTarget(tag: string): string | null;
+    private fetchedTagAnnotation;
+    remoteTag(tag: string): RemoteReleaseTag | null;
+    remoteTagTarget(tag: string): string | null;
+    createAnnotatedTag(tag: string, message: string, targetSha: string): void;
+    pushTag(tag: string): boolean;
+    isClean(): boolean;
+}
+export declare function isAutomaticReleaseTag(tag: string, remote: RemoteReleaseTag): boolean;
+export declare function runAutomaticRelease(options: AutomaticReleaseOptions): AutoTagResult;
+export declare function validateReleaseContext(repository: ReleaseRepository, tag: string, packageVersion: string, githubSha: string): ReleaseContext;
+export declare function runProductionGate(repository: ReleaseRepository, cwd?: string, runner?: CommandRunner): void;
+export declare function main(args?: string[]): number;
 export {};
 //# sourceMappingURL=version.d.ts.map

package/dist/scripts/version.d.ts.map

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