@quiltdata/benchling-webhook 0.11.0 → 0.11.2

package/dist/lib/wizard/profile-config-builder.js

@@ -0,0 +1,162 @@
+"use strict";
+/**
+ * Profile configuration builders for setup wizard flows.
+ *
+ * @module wizard/profile-config-builder
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.buildProfileConfigFromParameters = buildProfileConfigFromParameters;
+exports.buildProfileConfigFromExisting = buildProfileConfigFromExisting;
+const package_json_1 = __importDefault(require("../../package.json"));
+function createMetadata(existingConfig) {
+    const now = new Date().toISOString();
+    return {
+        version: package_json_1.default.version,
+        createdAt: existingConfig?._metadata?.createdAt || now,
+        updatedAt: now,
+        source: "wizard",
+    };
+}
+function applyDiscoveredResources(config, stackQuery) {
+    if (stackQuery.athenaUserWorkgroup) {
+        config.quilt.athenaUserWorkgroup = stackQuery.athenaUserWorkgroup;
+    }
+    if (stackQuery.bucketWritePolicyArn) {
+        config.quilt.bucketWritePolicyArn = stackQuery.bucketWritePolicyArn;
+    }
+    if (stackQuery.athenaUserPolicyArn) {
+        config.quilt.athenaUserPolicyArn = stackQuery.athenaUserPolicyArn;
+    }
+}
+/**
+ * Build profile config from collected parameters.
+ */
+function buildProfileConfigFromParameters(input) {
+    const { stackQuery, parameters, benchlingSecretArn, catalogDns, integratedStack } = input;
+    const config = {
+        quilt: {
+            stackArn: stackQuery.stackArn,
+            catalog: catalogDns,
+            database: stackQuery.database,
+            queueUrl: stackQuery.queueUrl,
+            region: stackQuery.region,
+        },
+        benchling: {
+            tenant: parameters.benchling.tenant,
+            clientId: parameters.benchling.clientId,
+            clientSecret: parameters.benchling.clientSecret,
+            appDefinitionId: parameters.benchling.appDefinitionId,
+            ...(benchlingSecretArn ? { secretArn: benchlingSecretArn } : {}),
+        },
+        packages: {
+            bucket: parameters.packages.bucket,
+            prefix: parameters.packages.prefix,
+            metadataKey: parameters.packages.metadataKey,
+        },
+        deployment: {
+            region: parameters.deployment.region,
+            account: parameters.deployment.account,
+            vpc: parameters.deployment.vpc,
+        },
+        integratedStack,
+        logging: {
+            level: parameters.logging.level,
+        },
+        security: {
+            enableVerification: parameters.security.enableVerification,
+            webhookAllowList: parameters.security.webhookAllowList,
+        },
+        _metadata: createMetadata(),
+    };
+    applyDiscoveredResources(config, stackQuery);
+    return config;
+}
+/**
+ * Build profile config from existing config or secret details (no prompts).
+ */
+function buildProfileConfigFromExisting(input) {
+    const { stackQuery, existingConfig, secretDetails, benchlingSecretArn, catalogDns, integratedStack } = input;
+    const benchling = {
+        tenant: existingConfig?.benchling?.tenant ?? secretDetails?.tenant,
+        clientId: existingConfig?.benchling?.clientId ?? secretDetails?.clientId,
+        clientSecret: existingConfig?.benchling?.clientSecret ?? secretDetails?.clientSecret,
+        appDefinitionId: existingConfig?.benchling?.appDefinitionId ?? secretDetails?.appDefinitionId,
+        secretArn: benchlingSecretArn ?? existingConfig?.benchling?.secretArn,
+    };
+    const packages = {
+        bucket: existingConfig?.packages?.bucket ?? secretDetails?.userBucket,
+        prefix: existingConfig?.packages?.prefix ?? secretDetails?.pkgPrefix ?? "benchling",
+        metadataKey: existingConfig?.packages?.metadataKey ?? secretDetails?.pkgKey ?? "experiment_id",
+    };
+    if (!benchling.tenant || !benchling.clientId || !benchling.clientSecret || !benchling.appDefinitionId) {
+        throw new Error("Missing Benchling credentials in existing configuration or secret");
+    }
+    if (!packages.bucket) {
+        throw new Error("Missing package bucket in existing configuration or secret");
+    }
+    const vpcFromStack = stackQuery.discoveredVpc?.isValid
+        ? {
+            vpcId: stackQuery.discoveredVpc.vpcId,
+            privateSubnetIds: stackQuery.discoveredVpc.privateSubnetIds,
+            publicSubnetIds: stackQuery.discoveredVpc.publicSubnetIds,
+            availabilityZones: stackQuery.discoveredVpc.availabilityZones,
+            vpcCidrBlock: stackQuery.discoveredVpc.cidrBlock,
+        }
+        : undefined;
+    const benchlingConfig = {
+        tenant: benchling.tenant,
+        clientId: benchling.clientId,
+        clientSecret: benchling.clientSecret,
+        appDefinitionId: benchling.appDefinitionId,
+        secretArn: benchling.secretArn,
+    };
+    const packagesConfig = {
+        bucket: packages.bucket,
+        prefix: packages.prefix,
+        metadataKey: packages.metadataKey,
+    };
+    const config = {
+        quilt: {
+            stackArn: stackQuery.stackArn,
+            catalog: catalogDns,
+            database: stackQuery.database,
+            queueUrl: stackQuery.queueUrl,
+            region: stackQuery.region,
+            athenaUserWorkgroup: existingConfig?.quilt?.athenaUserWorkgroup,
+            bucketWritePolicyArn: existingConfig?.quilt?.bucketWritePolicyArn,
+            athenaUserPolicyArn: existingConfig?.quilt?.athenaUserPolicyArn,
+        },
+        benchling: benchlingConfig,
+        packages: packagesConfig,
+        deployment: {
+            region: stackQuery.region,
+            account: stackQuery.account,
+            vpc: vpcFromStack ?? existingConfig?.deployment?.vpc,
+            imageTag: existingConfig?.deployment?.imageTag,
+        },
+        integratedStack,
+        logging: {
+            level: (existingConfig?.logging?.level ||
+                secretDetails?.logLevel ||
+                "INFO"),
+        },
+        security: {
+            enableVerification: existingConfig?.security?.enableVerification ??
+                secretDetails?.enableVerification ??
+                true,
+            webhookAllowList: existingConfig?.security?.webhookAllowList ??
+                secretDetails?.webhookAllowList ??
+                "",
+        },
+        _metadata: createMetadata(existingConfig),
+    };
+    if (benchlingSecretArn) {
+        config.benchling.secretArn = benchlingSecretArn;
+    }
+    applyDiscoveredResources(config, stackQuery);
+    return config;
+}
+//# sourceMappingURL=profile-config-builder.js.map

package/dist/lib/wizard/profile-config-builder.js.map

@@ -0,0 +1 @@
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package/dist/lib/wizard/stack-waiter.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Stack polling helpers for setup wizard flow.
+ *
+ * @module wizard/stack-waiter
+ */
+interface StackPollOptions {
+    stackArn: string;
+    region: string;
+    awsProfile?: string;
+    timeoutMs?: number;
+    intervalMs?: number;
+}
+/**
+ * Poll stack status until it reaches a terminal state or times out.
+ */
+export declare function pollStackStatus(options: StackPollOptions): Promise<void>;
+/**
+ * Wait for Benchling secret ARN to appear in stack outputs.
+ */
+export declare function waitForBenchlingSecretArn(options: StackPollOptions): Promise<string>;
+export {};
+//# sourceMappingURL=stack-waiter.d.ts.map

package/dist/lib/wizard/stack-waiter.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/wizard/stack-waiter.js

@@ -0,0 +1,77 @@
+"use strict";
+/**
+ * Stack polling helpers for setup wizard flow.
+ *
+ * @module wizard/stack-waiter
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pollStackStatus = pollStackStatus;
+exports.waitForBenchlingSecretArn = waitForBenchlingSecretArn;
+const chalk_1 = __importDefault(require("chalk"));
+const client_cloudformation_1 = require("@aws-sdk/client-cloudformation");
+const credential_providers_1 = require("@aws-sdk/credential-providers");
+const TERMINAL_STATUSES = new Set([
+    "CREATE_COMPLETE",
+    "UPDATE_COMPLETE",
+    "UPDATE_ROLLBACK_COMPLETE",
+    "ROLLBACK_COMPLETE",
+    "CREATE_FAILED",
+    "UPDATE_FAILED",
+]);
+function sleep(ms) {
+    return new Promise((resolve) => setTimeout(resolve, ms));
+}
+/**
+ * Poll stack status until it reaches a terminal state or times out.
+ */
+async function pollStackStatus(options) {
+    const { stackArn, region, awsProfile, timeoutMs = 5 * 60 * 1000, intervalMs = 15000 } = options;
+    const clientConfig = { region };
+    if (awsProfile) {
+        clientConfig.credentials = (0, credential_providers_1.fromIni)({ profile: awsProfile });
+    }
+    const client = new client_cloudformation_1.CloudFormationClient(clientConfig);
+    const startedAt = Date.now();
+    let lastStatus;
+    while (Date.now() - startedAt < timeoutMs) {
+        const response = await client.send(new client_cloudformation_1.DescribeStacksCommand({ StackName: stackArn }));
+        const stack = response.Stacks?.[0];
+        const status = stack?.StackStatus;
+        if (status && status !== lastStatus) {
+            console.log(chalk_1.default.dim(`  Stack status: ${status}`));
+            lastStatus = status;
+        }
+        if (status && TERMINAL_STATUSES.has(status)) {
+            return;
+        }
+        await sleep(intervalMs);
+    }
+    console.warn(chalk_1.default.yellow("⚠️  Timed out waiting for stack update to complete"));
+}
+/**
+ * Wait for Benchling secret ARN to appear in stack outputs.
+ */
+async function waitForBenchlingSecretArn(options) {
+    const { stackArn, region, awsProfile, timeoutMs = 5 * 60 * 1000, intervalMs = 15000 } = options;
+    const clientConfig = { region };
+    if (awsProfile) {
+        clientConfig.credentials = (0, credential_providers_1.fromIni)({ profile: awsProfile });
+    }
+    const client = new client_cloudformation_1.CloudFormationClient(clientConfig);
+    const startedAt = Date.now();
+    while (Date.now() - startedAt < timeoutMs) {
+        const response = await client.send(new client_cloudformation_1.DescribeStacksCommand({ StackName: stackArn }));
+        const stack = response.Stacks?.[0];
+        const outputs = stack?.Outputs || [];
+        const secretArn = outputs.find((output) => ["BenchlingSecretArn", "BenchlingClientSecretArn", "SecretArn"].includes(output.OutputKey || ""))?.OutputValue;
+        if (secretArn) {
+            return secretArn;
+        }
+        await sleep(intervalMs);
+    }
+    throw new Error("Timed out waiting for BenchlingSecret creation");
+}
+//# sourceMappingURL=stack-waiter.js.map

package/dist/lib/wizard/stack-waiter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"stack-waiter.js","sourceRoot":"","sources":["../../../lib/wizard/stack-waiter.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;;;AA8BH,0CA8BC;AAKD,8DA2BC;AA1FD,kDAA0B;AAC1B,0EAA6F;AAC7F,wEAAwD;AAUxD,MAAM,iBAAiB,GAAG,IAAI,GAAG,CAAC;IAC9B,iBAAiB;IACjB,iBAAiB;IACjB,0BAA0B;IAC1B,mBAAmB;IACnB,eAAe;IACf,eAAe;CAClB,CAAC,CAAC;AAEH,SAAS,KAAK,CAAC,EAAU;IACrB,OAAO,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAC;AAC7D,CAAC;AAED;;GAEG;AACI,KAAK,UAAU,eAAe,CAAC,OAAyB;IAC3D,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,SAAS,GAAG,CAAC,GAAG,EAAE,GAAG,IAAI,EAAE,UAAU,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEhG,MAAM,YAAY,GAAiE,EAAE,MAAM,EAAE,CAAC;IAC9F,IAAI,UAAU,EAAE,CAAC;QACb,YAAY,CAAC,WAAW,GAAG,IAAA,8BAAO,EAAC,EAAE,OAAO,EAAE,UAAU,EAAE,CAAC,CAAC;IAChE,CAAC;IACD,MAAM,MAAM,GAAG,IAAI,4CAAoB,CAAC,YAAY,CAAC,CAAC;IAEtD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;IAC7B,IAAI,UAA8B,CAAC;IAEnC,OAAO,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS,GAAG,SAAS,EAAE,CAAC;QACxC,MAAM,QAAQ,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,IAAI,6CAAqB,CAAC,EAAE,SAAS,EAAE,QAAQ,EAAE,CAAC,CAAC,CAAC;QACvF,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC;QACnC,MAAM,MAAM,GAAG,KAAK,EAAE,WAAW,CAAC;QAElC,IAAI,MAAM,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;YAClC,OAAO,CAAC,GAAG,CAAC,eAAK,CAAC,GAAG,CAAC,mBAAmB,MAAM,EAAE,CAAC,CAAC,CAAC;YACpD,UAAU,GAAG,MAAM,CAAC;QACxB,CAAC;QAED,IAAI,MAAM,IAAI,iBAAiB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;YAC1C,OAAO;QACX,CAAC;QAED,MAAM,KAAK,CAAC,UAAU,CAAC,CAAC;IAC5B,CAAC;IAED,OAAO,CAAC,IAAI,CAAC,eAAK,CAAC,MAAM,CAAC,oDAAoD,CAAC,CAAC,CAAC;AACrF,CAAC;AAED;;GAEG;AACI,KAAK,UAAU,yBAAyB,CAAC,OAAyB;IACrE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,SAAS,GAAG,CAAC,GAAG,EAAE,GAAG,IAAI,EAAE,UAAU,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEhG,MAAM,YAAY,GAAiE,EAAE,MAAM,EAAE,CAAC;IAC9F,IAAI,UAAU,EAAE,CAAC;QACb,YAAY,CAAC,WAAW,GAAG,IAAA,8BAAO,EAAC,EAAE,OAAO,EAAE,UAAU,EAAE,CAAC,CAAC;IAChE,CAAC;IACD,MAAM,MAAM,GAAG,IAAI,4CAAoB,CAAC,YAAY,CAAC,CAAC;IAEtD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;IAE7B,OAAO,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS,GAAG,SAAS,EAAE,CAAC;QACxC,MAAM,QAAQ,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,IAAI,6CAAqB,CAAC,EAAE,SAAS,EAAE,QAAQ,EAAE,CAAC,CAAC,CAAC;QACvF,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC;QACnC,MAAM,OAAO,GAAG,KAAK,EAAE,OAAO,IAAI,EAAE,CAAC;QACrC,MAAM,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CACtC,CAAC,oBAAoB,EAAE,0BAA0B,EAAE,WAAW,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,IAAI,EAAE,CAAC,CACnG,EAAE,WAAW,CAAC;QAEf,IAAI,SAAS,EAAE,CAAC;YACZ,OAAO,SAAS,CAAC;QACrB,CAAC;QAED,MAAM,KAAK,CAAC,UAAU,CAAC,CAAC;IAC5B,CAAC;IAED,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;AACtE,CAAC"}

package/dist/lib/wizard/types.d.ts

@@ -75,6 +75,21 @@ export interface StackQueryResult {
     /** Discovered VPC from Quilt stack (optional) */
     discoveredVpc?: DiscoveredVpcInfo;
 }
+/**
+ * Benchling secret details (optional context data)
+ */
+export interface BenchlingSecretDetails {
+    tenant?: string;
+    clientId?: string;
+    clientSecret?: string;
+    appDefinitionId?: string;
+    userBucket?: string;
+    pkgPrefix?: string;
+    pkgKey?: string;
+    logLevel?: string;
+    webhookAllowList?: string;
+    enableVerification?: boolean;
+}
 /**
  * Phase 3: Parameter Collection Input
  */
@@ -164,6 +179,31 @@ export interface ModeDecisionResult {
     /** BenchlingSecret ARN (for integrated mode) */
     benchlingSecretArn?: string;
 }
+/**
+ * Unified flow action choices
+ */
+export type UnifiedFlowAction = "update-integration-secret" | "review-only" | "disable-integration" | "switch-standalone" | "enable-integration" | "deploy-standalone" | "update-standalone-redeploy" | "update-standalone-secret" | "exit";
+/**
+ * Unified flow decision input
+ */
+export interface UnifiedFlowDecisionInput {
+    stackQuery: StackQueryResult;
+    existingConfig?: ProfileConfig | null;
+    configStorage: XDGBase;
+    profile: string;
+    yes?: boolean;
+    awsProfile?: string;
+}
+/**
+ * Unified flow decision result
+ */
+export interface UnifiedFlowDecisionResult {
+    action: UnifiedFlowAction;
+    flow: "integration-running" | "integration-disabled" | "integration-missing" | "standalone-existing";
+    benchlingSecretArn?: string;
+    secretDetails?: BenchlingSecretDetails | null;
+    hasStandaloneDeployment: boolean;
+}
 /**
  * Phase 6: Integrated Mode Input
  */

package/dist/lib/wizard/types.d.ts.map

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package/dist/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@quiltdata/benchling-webhook",
-    "version": "0.11.0",
+    "version": "0.11.2",
     "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",
@@ -58,7 +58,7 @@
         "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: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 --testMatch='**/test/integration/**/*.test.ts' --runInBand",
+        "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"
     },
     "keywords": [

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@quiltdata/benchling-webhook",
-  "version": "0.11.0",
+  "version": "0.11.2",
   "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",
@@ -58,7 +58,7 @@
     "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: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 --testMatch='**/test/integration/**/*.test.ts' --runInBand",
+    "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"
   },
   "keywords": [