@quiltdata/benchling-webhook 0.9.7-20251218T232525Z → 0.9.7

package/dist/bin/cli.js

@@ -51,6 +51,7 @@ const config_show_1 = require("./commands/config-show");
 const install_1 = require("./commands/install");
 const status_1 = require("./commands/status");
 const logs_1 = require("./commands/logs");
+const clean_1 = require("./commands/clean");
 const package_json_1 = __importDefault(require("../package.json"));
 const DEFAULT_LOG_LIMIT = 5; // Number of log entries to show per log group (health checks dominate, so keep this small)
 const program = new commander_1.Command();
@@ -416,6 +417,41 @@ program
         process.exit(1);
     }
 });
+// Clean command
+program
+    .command("clean")
+    .description("Remove a configuration profile (does not destroy AWS resources)")
+    .option("--profile <name>", "Configuration profile to delete (default: default)")
+    .option("--yes", "Skip confirmation prompt")
+    .addHelpText("after", `
+
+Examples:
+  Remove the default profile:
+    $ npx @quiltdata/benchling-webhook clean
+
+  Remove a specific profile:
+    $ npx @quiltdata/benchling-webhook clean --profile dev
+
+  Remove without confirmation:
+    $ npx @quiltdata/benchling-webhook clean --profile dev --yes
+
+Important Notes:
+  - This command only removes local configuration files
+  - AWS resources (CloudFormation stacks) are NOT destroyed
+  - To destroy AWS resources, use the 'destroy' command first
+  - If you have active deployments, you should destroy them before cleaning
+
+For more information: https://github.com/quiltdata/benchling-webhook#configuration
+`)
+    .action(async (options) => {
+    try {
+        await (0, clean_1.cleanCommand)(options);
+    }
+    catch (error) {
+        console.error(chalk_1.default.red(error.message));
+        process.exit(1);
+    }
+});
 // Run install command when no command provided (but not for help/version flags)
 const args = process.argv.slice(2);
 const isHelpOrVersion = args.some((arg) => arg === "--help" || arg === "-h" || arg === "--version" || arg === "-v");

package/dist/bin/cli.js.map

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package/dist/bin/commands/clean.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Clean Command - Remove Configuration Profile
+ *
+ * Deletes a configuration profile and all associated data including:
+ * - Profile configuration (~/.config/benchling-webhook/{profile}/config.json)
+ * - Deployment tracking (~/.config/benchling-webhook/{profile}/deployments.json)
+ * - Profile directory
+ *
+ * IMPORTANT: This command does NOT destroy AWS resources. To destroy the deployed
+ * CloudFormation stack, use the 'destroy' command first.
+ *
+ * @module bin/commands/clean
+ */
+import type { XDGBase } from "../../lib/xdg-base";
+interface CleanOptions {
+    profile?: string;
+    yes?: boolean;
+    xdg?: XDGBase;
+}
+/**
+ * Clean command: Remove a configuration profile
+ *
+ * @param options - Command options
+ */
+export declare function cleanCommand(options: CleanOptions): Promise<void>;
+export {};
+//# sourceMappingURL=clean.d.ts.map

package/dist/bin/commands/clean.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"clean.d.ts","sourceRoot":"","sources":["../../../bin/commands/clean.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAIH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAGlD,UAAU,YAAY;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,GAAG,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;;;GAIG;AACH,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CA0FvE"}

package/dist/bin/commands/clean.js

@@ -0,0 +1,114 @@
+"use strict";
+/**
+ * Clean Command - Remove Configuration Profile
+ *
+ * Deletes a configuration profile and all associated data including:
+ * - Profile configuration (~/.config/benchling-webhook/{profile}/config.json)
+ * - Deployment tracking (~/.config/benchling-webhook/{profile}/deployments.json)
+ * - Profile directory
+ *
+ * IMPORTANT: This command does NOT destroy AWS resources. To destroy the deployed
+ * CloudFormation stack, use the 'destroy' command first.
+ *
+ * @module bin/commands/clean
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.cleanCommand = cleanCommand;
+const chalk_1 = __importDefault(require("chalk"));
+const xdg_config_1 = require("../../lib/xdg-config");
+const inquirer_1 = __importDefault(require("inquirer"));
+/**
+ * Clean command: Remove a configuration profile
+ *
+ * @param options - Command options
+ */
+async function cleanCommand(options) {
+    const xdg = options.xdg || new xdg_config_1.XDGConfig();
+    const profile = options.profile || "default";
+    // Check if profile exists
+    if (!xdg.profileExists(profile)) {
+        console.log(chalk_1.default.yellow(`Profile '${profile}' does not exist.`));
+        console.log();
+        console.log(chalk_1.default.dim("Available profiles:"));
+        const profiles = xdg.listProfiles();
+        if (profiles.length === 0) {
+            console.log(chalk_1.default.dim("  (none)"));
+        }
+        else {
+            profiles.forEach((p) => {
+                console.log(chalk_1.default.dim(`  - ${p}`));
+            });
+        }
+        return;
+    }
+    // Load profile to check for active deployments
+    let hasDeployments = false;
+    let activeStages = [];
+    try {
+        xdg.readProfile(profile); // Verify profile can be read
+        const deployments = xdg.getDeployments(profile);
+        if (deployments && deployments.active) {
+            activeStages = Object.keys(deployments.active);
+            hasDeployments = activeStages.length > 0;
+        }
+    }
+    catch (error) {
+        console.log(chalk_1.default.yellow(`Warning: Could not read profile '${profile}' details: ${error.message}`));
+    }
+    // Show warning about active deployments
+    if (hasDeployments) {
+        console.log();
+        console.log(chalk_1.default.yellow.bold("⚠️  WARNING: Active Deployments Detected"));
+        console.log();
+        console.log(chalk_1.default.yellow(`The profile '${profile}' has active deployments for the following stages:`));
+        activeStages.forEach((stage) => {
+            console.log(chalk_1.default.yellow(`  - ${stage}`));
+        });
+        console.log();
+        console.log(chalk_1.default.yellow("This command will ONLY remove the local configuration."));
+        console.log(chalk_1.default.yellow("AWS resources (CloudFormation stacks, etc.) will NOT be destroyed."));
+        console.log();
+        console.log(chalk_1.default.cyan("To destroy AWS resources first, run:"));
+        activeStages.forEach((stage) => {
+            console.log(chalk_1.default.cyan(`  npx @quiltdata/benchling-webhook destroy --profile ${profile} --stage ${stage}`));
+        });
+        console.log();
+    }
+    // Confirm deletion
+    if (!options.yes) {
+        console.log();
+        console.log(chalk_1.default.bold(`About to delete profile: ${profile}`));
+        console.log();
+        console.log(chalk_1.default.dim("This will remove:"));
+        console.log(chalk_1.default.dim(`  - Configuration: ~/.config/benchling-webhook/${profile}/config.json`));
+        console.log(chalk_1.default.dim(`  - Deployment tracking: ~/.config/benchling-webhook/${profile}/deployments.json`));
+        console.log(chalk_1.default.dim(`  - Profile directory: ~/.config/benchling-webhook/${profile}/`));
+        console.log();
+        const response = await inquirer_1.default.prompt([
+            {
+                type: "confirm",
+                name: "confirmed",
+                message: `Are you sure you want to delete profile '${profile}'?`,
+                default: false,
+            },
+        ]);
+        if (!response.confirmed) {
+            console.log(chalk_1.default.yellow("Operation cancelled."));
+            return;
+        }
+    }
+    // Delete the profile
+    try {
+        xdg.deleteProfile(profile);
+        console.log();
+        console.log(chalk_1.default.green(`✓ Profile '${profile}' deleted successfully.`));
+        console.log();
+    }
+    catch (error) {
+        throw new Error(`Failed to delete profile '${profile}': ${error.message}`);
+    }
+}
+//# sourceMappingURL=clean.js.map

package/dist/bin/commands/clean.js.map

@@ -0,0 +1 @@
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package/dist/bin/commands/deploy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../../bin/commands/deploy.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,aAAa,EAAgB,MAAM,wBAAwB,CAAC;AA6GrE;;;;;;;;GAQG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE;IACzC,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,KAAK,GAAG,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB,GAAG,OAAO,CAAC,IAAI,CAAC,CA8FhB;AAED;;GAEG;AACH,wBAAsB,MAAM,CACxB,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EACvB,MAAM,EAAE,aAAa,EACrB,OAAO,EAAE;IACL,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB,GACF,OAAO,CAAC,IAAI,CAAC,CA8gBf"}
+{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../../bin/commands/deploy.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,aAAa,EAAgB,MAAM,wBAAwB,CAAC;AAuNrE;;;;;;;;GAQG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE;IACzC,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,KAAK,GAAG,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB,GAAG,OAAO,CAAC,IAAI,CAAC,CA8FhB;AAED;;GAEG;AACH,wBAAsB,MAAM,CACxB,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EACvB,MAAM,EAAE,aAAa,EACrB,OAAO,EAAE;IACL,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB,GACF,OAAO,CAAC,IAAI,CAAC,CAuhBf"}

package/dist/bin/commands/deploy.js

@@ -61,6 +61,93 @@ function suggestSetup(profileName, message) {
     console.log(chalk_1.default.cyan(`  npm run setup -- --profile ${profileName}`));
     console.log();
 }
+/**
+ * Build CDK app path
+ */
+function getCdkAppPath() {
+    let moduleDir;
+    if (__dirname.includes("/dist/")) {
+        moduleDir = path.resolve(__dirname, "../../..");
+    }
+    else {
+        moduleDir = path.resolve(__dirname, "../..");
+    }
+    const tsSourcePath = path.join(moduleDir, "bin/benchling-webhook.ts");
+    const jsDistPath = path.join(moduleDir, "dist/bin/benchling-webhook.js");
+    if (fs.existsSync(tsSourcePath)) {
+        return `npx ts-node --prefer-ts-exts "${tsSourcePath}"`;
+    }
+    else if (fs.existsSync(jsDistPath)) {
+        return `node "${jsDistPath}"`;
+    }
+    return "";
+}
+/**
+ * Build CDK environment variables from config
+ */
+function buildCdkEnv(config, options) {
+    const env = {
+        ...process.env,
+        CDK_DEFAULT_ACCOUNT: options.deployAccount,
+        CDK_DEFAULT_REGION: options.deployRegion,
+        QUILT_STACK_ARN: options.stackArn,
+        BENCHLING_SECRET: options.benchlingSecret,
+        PROFILE: options.profileName,
+        STACK_NAME: options.stackName,
+        QUILT_CATALOG: config.quilt.catalog,
+        QUILT_DATABASE: config.quilt.database,
+        QUEUE_URL: config.quilt.queueUrl,
+        QUILT_USER_BUCKET: config.packages.bucket,
+        PKG_PREFIX: config.packages.prefix || "benchling",
+        PKG_KEY: config.packages.metadataKey || "experiment_id",
+        BENCHLING_TENANT: config.benchling.tenant,
+        BENCHLING_CLIENT_ID: config.benchling.clientId || "",
+        BENCHLING_APP_DEFINITION_ID: config.benchling.appDefinitionId || "",
+        LOG_LEVEL: config.logging?.level || "INFO",
+        IMAGE_TAG: options.imageTag,
+    };
+    // Add optional Quilt fields if present
+    if (config.quilt.icebergDatabase) {
+        env.ICEBERG_DATABASE = config.quilt.icebergDatabase;
+    }
+    if (config.quilt.icebergWorkgroup) {
+        env.ICEBERG_WORKGROUP = config.quilt.icebergWorkgroup;
+    }
+    if (config.quilt.athenaUserWorkgroup) {
+        env.ATHENA_USER_WORKGROUP = config.quilt.athenaUserWorkgroup;
+    }
+    if (config.quilt.athenaResultsBucket) {
+        env.ATHENA_RESULTS_BUCKET = config.quilt.athenaResultsBucket;
+    }
+    // Pass VPC configuration if specified in profile
+    if (config.deployment.vpc?.vpcId) {
+        env.VPC_ID = config.deployment.vpc.vpcId;
+        if (config.deployment.vpc.privateSubnetIds) {
+            env.VPC_PRIVATE_SUBNET_IDS = JSON.stringify(config.deployment.vpc.privateSubnetIds);
+        }
+        if (config.deployment.vpc.publicSubnetIds) {
+            env.VPC_PUBLIC_SUBNET_IDS = JSON.stringify(config.deployment.vpc.publicSubnetIds);
+        }
+        if (config.deployment.vpc.availabilityZones) {
+            env.VPC_AVAILABILITY_ZONES = JSON.stringify(config.deployment.vpc.availabilityZones);
+        }
+        if (config.deployment.vpc.vpcCidrBlock) {
+            env.VPC_CIDR_BLOCK = config.deployment.vpc.vpcCidrBlock;
+        }
+    }
+    // Pass security configuration if specified in profile
+    if (config.security?.webhookAllowList) {
+        env.WEBHOOK_ALLOW_LIST = config.security.webhookAllowList;
+    }
+    if (config.security?.enableVerification !== undefined) {
+        env.ENABLE_WEBHOOK_VERIFICATION = config.security.enableVerification.toString();
+    }
+    // Pass ECR repository if specified
+    if (config.deployment.ecrRepository) {
+        env.ECR_REPOSITORY_NAME = config.deployment.ecrRepository;
+    }
+    return env;
+}
 /**
  * Check if the existing stack is in a problematic state (active rollback, failed, etc.)
  *
@@ -365,6 +452,64 @@ async function deploy(stackArn, benchlingSecret, config, options) {
     // Check for rollback or failed state
     spinner.start("Checking stack status...");
     const stackCheck = await checkStackStatus(deployRegion, stackName);
+    // REVIEW_IN_PROGRESS is unrecoverable - must destroy and recreate
+    if (stackCheck.stackExists && stackCheck.stackStatus === "REVIEW_IN_PROGRESS") {
+        spinner.fail("Stack in unrecoverable state (REVIEW_IN_PROGRESS)");
+        console.log();
+        console.log((0, boxen_1.default)(`${chalk_1.default.red.bold("Stack in Unrecoverable State")}\n\n` +
+            `The stack ${chalk_1.default.cyan(stackName)} is in ${chalk_1.default.yellow("REVIEW_IN_PROGRESS")} state.\n` +
+            "This means a CloudFormation change set failed during creation.\n\n" +
+            `${chalk_1.default.bold("This stack must be destroyed and recreated.")}\n`, { padding: 1, borderColor: "red", borderStyle: "round" }));
+        console.log();
+        const { shouldDestroy } = await (0, enquirer_1.prompt)([
+            {
+                type: "confirm",
+                name: "shouldDestroy",
+                message: "Destroy this stack and recreate? (Only option to proceed)",
+                initial: true,
+            },
+        ]);
+        if (!shouldDestroy) {
+            console.log(chalk_1.default.yellow("Deployment cancelled"));
+            process.exit(1);
+        }
+        // Destroy the stack
+        console.log();
+        spinner.start("Destroying stuck stack...");
+        try {
+            // REVIEW_IN_PROGRESS stacks require special handling:
+            // 1. Delete the failed changeset first
+            // 2. Then delete the stack directly (CDK destroy won't work)
+            // Step 1: Delete the failed changeset
+            spinner.text = "Deleting failed changeset...";
+            try {
+                (0, child_process_1.execSync)(`aws cloudformation delete-change-set --change-set-name cdk-deploy-change-set --stack-name ${stackName} --region ${deployRegion}`, { encoding: "utf-8" });
+            }
+            catch (_changesetError) {
+                // Changeset might not exist, which is fine - continue with stack deletion
+            }
+            // Step 2: Delete the stack directly using AWS CLI
+            spinner.text = "Deleting stack...";
+            (0, child_process_1.execSync)(`aws cloudformation delete-stack --stack-name ${stackName} --region ${deployRegion}`, { encoding: "utf-8" });
+            // Step 3: Wait for deletion to complete
+            spinner.text = "Waiting for stack deletion to complete...";
+            (0, child_process_1.execSync)(`aws cloudformation wait stack-delete-complete --stack-name ${stackName} --region ${deployRegion}`, { encoding: "utf-8", timeout: 300000 });
+            spinner.succeed("Stack destroyed");
+            console.log(chalk_1.default.blue("Proceeding with fresh deployment..."));
+            console.log();
+        }
+        catch (error) {
+            spinner.fail("Failed to destroy stack");
+            console.log();
+            console.error(chalk_1.default.red(error.message));
+            console.log();
+            console.log(chalk_1.default.yellow("You may need to manually delete the stack:"));
+            console.log(chalk_1.default.cyan(`  aws cloudformation delete-change-set --change-set-name cdk-deploy-change-set --stack-name ${stackName} --region ${deployRegion}`));
+            console.log(chalk_1.default.cyan(`  aws cloudformation delete-stack --stack-name ${stackName} --region ${deployRegion}`));
+            console.log();
+            process.exit(1);
+        }
+    }
     const needsAttention = ["in_progress", "failed", "rolled_back"].includes(stackCheck.statusCategory);
     if (needsAttention) {
         const isActiveRollback = stackCheck.statusCategory === "in_progress";
@@ -521,6 +666,9 @@ async function deploy(stackArn, benchlingSecret, config, options) {
     console.log();
     console.log(chalk_1.default.blue.bold("▶ Starting deployment..."));
     console.log();
+    // Track deployment success - we'll verify actual stack status even if CDK command fails
+    let deploymentSucceeded = false;
+    let cdkError = null;
     try {
         // Build CloudFormation parameters
         // Parameter names must match the CfnParameter IDs in BenchlingWebhookStack
@@ -542,111 +690,48 @@ async function deploy(stackArn, benchlingSecret, config, options) {
             `LogLevel=${config.logging?.level || "INFO"}`,
         ];
         const parametersArg = parameters.map(p => `--parameters ${p}`).join(" ");
-        // Determine the CDK app entry point
-        // The path needs to be absolute to work from any cwd
-        // Find the package root directory
-        // When compiled: __dirname is dist/bin/commands, so go up 3 levels
-        // When source: __dirname is bin/commands, so go up 2 levels
-        let moduleDir;
-        if (__dirname.includes("/dist/")) {
-            // Compiled: dist/bin/commands -> ../../../
-            moduleDir = path.resolve(__dirname, "../../..");
-        }
-        else {
-            // Source: bin/commands -> ../../
-            moduleDir = path.resolve(__dirname, "../..");
-        }
-        let appPath;
-        const tsSourcePath = path.join(moduleDir, "bin/benchling-webhook.ts");
-        const jsDistPath = path.join(moduleDir, "dist/bin/benchling-webhook.js");
-        if (fs.existsSync(tsSourcePath)) {
-            // Development mode: TypeScript source exists, use it directly
-            appPath = `npx ts-node --prefer-ts-exts "${tsSourcePath}"`;
-        }
-        else if (fs.existsSync(jsDistPath)) {
-            // Production mode: use compiled JavaScript
-            appPath = `node "${jsDistPath}"`;
-        }
-        else {
-            // Fallback: rely on cdk.json (should not happen)
-            console.warn(chalk_1.default.yellow("⚠️  Could not find CDK app entry point, relying on cdk.json"));
-            appPath = "";
-        }
+        const appPath = getCdkAppPath();
         const appArg = appPath ? `--app "${appPath}"` : "";
-        const cdkCommand = `npx cdk deploy ${appArg} --require-approval ${options.requireApproval || "never"} ${parametersArg}`;
+        // Use --method=direct to skip changeset creation (avoids REVIEW_IN_PROGRESS state for new stacks)
+        const cdkCommand = `npx cdk deploy ${appArg} --require-approval ${options.requireApproval || "never"} --method=direct ${parametersArg}`;
         // Build environment variables for CDK synthesis
-        const env = {
-            ...process.env,
-            CDK_DEFAULT_ACCOUNT: deployAccount,
-            CDK_DEFAULT_REGION: deployRegion,
-            QUILT_STACK_ARN: stackArn,
-            BENCHLING_SECRET: benchlingSecret,
-            // Pass profile and stack name for multi-stack support
-            PROFILE: options.profileName,
-            STACK_NAME: stackName,
-            // Pass Quilt configuration (required by A07 validation)
-            QUILT_CATALOG: config.quilt.catalog,
-            QUILT_DATABASE: config.quilt.database,
-            QUEUE_URL: config.quilt.queueUrl,
-            // Pass optional Quilt fields if present
-            ...(config.quilt.icebergDatabase && {
-                ICEBERG_DATABASE: config.quilt.icebergDatabase,
-            }),
-            ...(config.quilt.icebergWorkgroup && {
-                ICEBERG_WORKGROUP: config.quilt.icebergWorkgroup,
-            }),
-            ...(config.quilt.athenaUserWorkgroup && {
-                ATHENA_USER_WORKGROUP: config.quilt.athenaUserWorkgroup,
-            }),
-            ...(config.quilt.athenaResultsBucket && {
-                ATHENA_RESULTS_BUCKET: config.quilt.athenaResultsBucket,
-            }),
-            // Pass package configuration
-            QUILT_USER_BUCKET: config.packages.bucket,
-            PKG_PREFIX: config.packages.prefix || "benchling",
-            PKG_KEY: config.packages.metadataKey || "experiment_id",
-            // Pass Benchling configuration
-            BENCHLING_TENANT: config.benchling.tenant,
-            BENCHLING_CLIENT_ID: config.benchling.clientId || "",
-            BENCHLING_APP_DEFINITION_ID: config.benchling.appDefinitionId || "",
-            // Pass logging configuration
-            LOG_LEVEL: config.logging?.level || "INFO",
-            // Pass image configuration
-            IMAGE_TAG: options.imageTag,
-            ...(config.deployment.ecrRepository && {
-                ECR_REPOSITORY_NAME: config.deployment.ecrRepository,
-            }),
-        };
-        // Pass VPC configuration if specified in profile
-        if (config.deployment.vpc?.vpcId) {
-            env.VPC_ID = config.deployment.vpc.vpcId;
-            // Serialize subnet arrays as JSON for environment variables
-            if (config.deployment.vpc.privateSubnetIds) {
-                env.VPC_PRIVATE_SUBNET_IDS = JSON.stringify(config.deployment.vpc.privateSubnetIds);
-            }
-            if (config.deployment.vpc.publicSubnetIds) {
-                env.VPC_PUBLIC_SUBNET_IDS = JSON.stringify(config.deployment.vpc.publicSubnetIds);
-            }
-            if (config.deployment.vpc.availabilityZones) {
-                env.VPC_AVAILABILITY_ZONES = JSON.stringify(config.deployment.vpc.availabilityZones);
-            }
-            if (config.deployment.vpc.vpcCidrBlock) {
-                env.VPC_CIDR_BLOCK = config.deployment.vpc.vpcCidrBlock;
-            }
-        }
-        // Pass security configuration if specified in profile
-        if (config.security?.webhookAllowList) {
-            env.WEBHOOK_ALLOW_LIST = config.security.webhookAllowList;
-        }
-        if (config.security?.enableVerification !== undefined) {
-            env.ENABLE_WEBHOOK_VERIFICATION = config.security.enableVerification.toString();
-        }
+        const env = buildCdkEnv(config, {
+            stackArn,
+            benchlingSecret,
+            profileName: options.profileName,
+            stackName,
+            imageTag: options.imageTag,
+            deployAccount,
+            deployRegion,
+        });
         (0, child_process_1.execSync)(cdkCommand, {
             stdio: "inherit",
             env,
         });
+        deploymentSucceeded = true;
         console.log();
         spinner.succeed("Stack deployed successfully");
+    }
+    catch (error) {
+        // CDK command failed, but the stack might have actually deployed successfully
+        // Check actual stack status before failing
+        cdkError = error;
+        console.log();
+        console.log(chalk_1.default.yellow("CDK command exited with error, checking actual stack status..."));
+        const finalCheck = await checkStackStatus(deployRegion, stackName);
+        if (finalCheck.stackExists &&
+            (finalCheck.stackStatus === "CREATE_COMPLETE" || finalCheck.stackStatus === "UPDATE_COMPLETE")) {
+            console.log(chalk_1.default.green(`✓ Stack deployment succeeded despite CDK error (${finalCheck.stackStatus})`));
+            deploymentSucceeded = true;
+            spinner.succeed("Stack deployed successfully");
+        }
+        else {
+            deploymentSucceeded = false;
+            spinner.fail("Deployment failed");
+        }
+    }
+    // Record deployment endpoint if stack deployed successfully
+    if (deploymentSucceeded) {
         // After successful deployment, store endpoint and run tests
         console.log();
         console.log("Retrieving deployment endpoint...");
@@ -701,10 +786,10 @@ async function deploy(stackArn, benchlingSecret, config, options) {
             console.warn("   Deployment succeeded but endpoint could not be recorded");
         }
     }
-    catch (error) {
-        spinner.fail("Deployment failed");
-        console.error();
-        console.error(chalk_1.default.red(error.message));
+    else {
+        // Deployment failed - report the error
+        console.log();
+        console.error(chalk_1.default.red(cdkError.message));
         process.exit(1);
     }
 }