@quiltdata/benchling-webhook 0.6.3-20251104T182406Z → 0.7.2-20251106T010445Z

package/dist/bin/cli.js

@@ -12,6 +12,8 @@ const validate_1 = require("./commands/validate");
 const test_1 = require("./commands/test");
 const manifest_1 = require("./commands/manifest");
 const setup_wizard_1 = require("./commands/setup-wizard");
+const setup_profile_1 = require("./commands/setup-profile");
+const health_check_1 = require("./commands/health-check");
 // Load package.json for version
 // eslint-disable-next-line @typescript-eslint/no-require-imports
 const pkg = require("../package.json");
@@ -20,7 +22,17 @@ program
     .name("benchling-webhook")
     .description("Benchling Webhook Integration for Quilt - Deploy lab notebook integration to AWS")
     .version(pkg.version, "-v, --version", "Display version number")
-    .helpOption("-h, --help", "Display help for command");
+    .helpOption("-h, --help", "Display help for command")
+    .addHelpText("after", `
+
+v0.7.0 Changes:
+  - New unified configuration architecture with profile support
+  - Profile-based deployment tracking (~/.config/benchling-webhook/{profile}/)
+  - Independent --profile and --stage options for flexible deployments
+  - Profile inheritance support for environment hierarchies
+
+For upgrade instructions: https://github.com/quiltdata/benchling-webhook/blob/main/MIGRATION.md
+`);
 // Deploy command (default)
 program
     .command("deploy", { isDefault: true })
@@ -28,23 +40,29 @@ program
     .option("--quilt-stack-arn <arn>", "ARN of Quilt CloudFormation stack")
     .option("--benchling-secret <name>", "Name or ARN of Benchling secret in Secrets Manager")
     .option("--env-file <path>", "Path to .env file", ".env")
+    // Multi-environment options (v0.7.0)
+    .option("--profile <name>", "Configuration profile to use (default: default)")
+    .option("--stage <name>", "API Gateway stage: dev or prod (default: prod)")
     // Common options
     .option("--no-bootstrap-check", "Skip CDK bootstrap verification")
     .option("--require-approval <level>", "CDK approval level", "never")
-    .option("--profile <name>", "AWS profile to use")
     .option("--region <region>", "AWS region to deploy to")
     .option("--image-tag <tag>", "Docker image tag to deploy (default: latest)")
     .option("--yes", "Skip confirmation prompts")
     .addHelpText("after", `
+
 Examples:
-  Deploy with default secret name:
+  Deploy to production with default profile:
     $ npx @quiltdata/benchling-webhook deploy \\
         --quilt-stack-arn "arn:aws:cloudformation:us-east-1:123456789012:stack/QuiltStack/abc123"
 
-  Deploy with custom secret name:
+  Deploy to dev stage with dev profile:
     $ npx @quiltdata/benchling-webhook deploy \\
-        --quilt-stack-arn "arn:aws:cloudformation:us-east-1:123456789012:stack/QuiltStack/abc123" \\
-        --benchling-secret "my-benchling-credentials"
+        --profile dev --stage dev
+
+  Deploy to prod with custom image tag:
+    $ npx @quiltdata/benchling-webhook deploy \\
+        --stage prod --image-tag "0.7.0"
 
 For more information: https://github.com/quiltdata/benchling-webhook#deployment
 `)
@@ -117,9 +135,79 @@ program
         process.exit(1);
     }
 });
+// Setup profile command (v0.7.0)
+program
+    .command("setup-profile <name>")
+    .description("Create a new configuration profile with optional inheritance")
+    .option("--inherit-from <profile>", "Base profile to inherit from", "default")
+    .option("--force", "Overwrite existing profile without prompting")
+    .addHelpText("after", `
+
+Examples:
+  Create dev profile inheriting from default:
+    $ npx @quiltdata/benchling-webhook setup-profile dev
+
+  Create staging profile inheriting from prod:
+    $ npx @quiltdata/benchling-webhook setup-profile staging --inherit-from prod
+
+Profile inheritance allows you to:
+  - Reuse common settings across environments
+  - Override only environment-specific values
+  - Maintain a single source of truth for shared configuration
+
+For more information: https://github.com/quiltdata/benchling-webhook#multi-environment-setup
+`)
+    .action(async (name, options) => {
+    try {
+        await (0, setup_profile_1.setupProfileCommand)(name, options);
+    }
+    catch (error) {
+        console.error(chalk_1.default.red(error.message));
+        process.exit(1);
+    }
+});
+// Health check command
+program
+    .command("health-check")
+    .description("Check configuration health and secrets sync status")
+    .option("--profile <name>", "Configuration profile to check", "default")
+    .option("--json", "Output in JSON format")
+    .action(async (options) => {
+    try {
+        await (0, health_check_1.healthCheckCommand)(options);
+    }
+    catch (error) {
+        console.error(chalk_1.default.red(error.message));
+        process.exit(1);
+    }
+});
 // Run setup wizard when no command provided
-if (!process.argv.slice(2).length) {
-    (0, setup_wizard_1.setupWizardCommand)()
+if (!process.argv.slice(2).length || (process.argv.slice(2).length > 0 && process.argv[2].startsWith("--"))) {
+    // Parse options for setup wizard
+    const args = process.argv.slice(2);
+    const options = {};
+    for (let i = 0; i < args.length; i++) {
+        if (args[i] === "--yes" || args[i] === "-y") {
+            options.nonInteractive = true;
+        }
+        else if (args[i] === "--profile" && i + 1 < args.length) {
+            options.profile = args[i + 1];
+            i++;
+        }
+        else if (args[i] === "--inherit-from" && i + 1 < args.length) {
+            options.inheritFrom = args[i + 1];
+            i++;
+        }
+        else if (args[i] === "--region" && i + 1 < args.length) {
+            options.awsRegion = args[i + 1];
+            i++;
+        }
+        else if (args[i] === "--aws-profile" && i + 1 < args.length) {
+            options.awsProfile = args[i + 1];
+            i++;
+        }
+    }
+    (0, setup_wizard_1.setupWizardCommand)(options)
         .then(() => process.exit(0))
         .catch((error) => {
         console.error(chalk_1.default.red(error.message));

package/dist/bin/cli.js.map

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package/dist/bin/{config-profiles.d.ts → commands/config-profiles.d.ts}

@@ -2,6 +2,11 @@
 /**
  * Configuration Profile Management CLI
  *
+ * WARNING: This file needs refactoring for v0.7.0
+ * TODO: Update to use ProfileConfig instead of UserConfig/DerivedConfig/DeploymentConfig
+ * TODO: Remove references to BaseConfig and loadProfile
+ * TODO: Update to use new readProfile API
+ *
  * Provides commands for creating, listing, and managing configuration profiles.
  * Supports AWS profile integration and profile validation.
  *
@@ -13,7 +18,7 @@
  *
  * @module bin/config-profiles
  */
-import { ProfileName } from "../lib/types/config";
+import { ProfileName } from "../../lib/types/config";
 /**
  * Profile Manager
  *
@@ -30,12 +35,8 @@ declare class ProfileManager {
      * Creates a new profile
      *
      * @param profileName - Name of the profile to create
-     * @param options - Creation options
      */
-    createProfile(profileName: ProfileName, options?: {
-        awsProfile?: string;
-        description?: string;
-    }): void;
+    createProfile(profileName: ProfileName): void;
     /**
      * Shows detailed information about a profile
      *
@@ -49,11 +50,11 @@ declare class ProfileManager {
      */
     validateProfile(profileName: ProfileName): void;
     /**
-     * Prints configuration object in a readable format
+     * Prints a configuration section in a readable format
      *
-     * @param config - Configuration object to print
+     * @param section - Configuration section to print
      */
-    private printConfig;
+    private printSection;
 }
 export { ProfileManager };
 //# sourceMappingURL=config-profiles.d.ts.map

package/dist/bin/commands/config-profiles.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"config-profiles.d.ts","sourceRoot":"","sources":["../../../bin/commands/config-profiles.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;GAkBG;AAGH,OAAO,EAAE,WAAW,EAAiB,MAAM,wBAAwB,CAAC;AAGpE;;;;GAIG;AACH,cAAM,cAAc;IAChB,OAAO,CAAC,SAAS,CAAY;;IAM7B;;OAEG;IACI,YAAY,IAAI,IAAI;IAwC3B;;;;OAIG;IACI,aAAa,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI;IAiDpD;;;;OAIG;IACI,WAAW,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI;IA2ClD;;;;OAIG;IACI,eAAe,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI;IAsCtD;;;;OAIG;IACH,OAAO,CAAC,YAAY;CAwBvB;AA6DD,OAAO,EAAE,cAAc,EAAE,CAAC"}

package/dist/bin/{config-profiles.js → commands/config-profiles.js}

@@ -3,6 +3,11 @@
 /**
  * Configuration Profile Management CLI
  *
+ * WARNING: This file needs refactoring for v0.7.0
+ * TODO: Update to use ProfileConfig instead of UserConfig/DerivedConfig/DeploymentConfig
+ * TODO: Remove references to BaseConfig and loadProfile
+ * TODO: Update to use new readProfile API
+ *
  * Provides commands for creating, listing, and managing configuration profiles.
  * Supports AWS profile integration and profile validation.
  *
@@ -16,7 +21,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ProfileManager = void 0;
-const xdg_config_1 = require("../lib/xdg-config");
+const xdg_config_1 = require("../../lib/xdg-config");
 const commander_1 = require("commander");
 /**
  * Profile Manager
@@ -45,13 +50,23 @@ class ProfileManager {
             console.log(`  ${status} ${profileName}${marker}`);
             // Show configuration status
             if (exists) {
-                const profile = this.xdgConfig.loadProfile(profileName);
-                const hasUser = profile.user ? "user" : "";
-                const hasDerived = profile.derived ? "derived" : "";
-                const hasDeploy = profile.deploy ? "deploy" : "";
-                const configs = [hasUser, hasDerived, hasDeploy].filter(Boolean).join(", ");
-                if (configs) {
-                    console.log(`    Configs: ${configs}`);
+                try {
+                    const profile = this.xdgConfig.readProfile(profileName);
+                    const sections = [];
+                    if (profile.quilt)
+                        sections.push("quilt");
+                    if (profile.benchling)
+                        sections.push("benchling");
+                    if (profile.packages)
+                        sections.push("packages");
+                    if (profile.deployment)
+                        sections.push("deployment");
+                    if (sections.length > 0) {
+                        console.log(`    Sections: ${sections.join(", ")}`);
+                    }
+                }
+                catch (error) {
+                    console.log(`    Error reading profile: ${error.message}`);
                 }
             }
         });
@@ -61,34 +76,49 @@ class ProfileManager {
      * Creates a new profile
      *
      * @param profileName - Name of the profile to create
-     * @param options - Creation options
      */
-    createProfile(profileName, options = {}) {
+    createProfile(profileName) {
         console.log(`Creating profile: ${profileName}\n`);
         // Check if profile already exists
         if (this.xdgConfig.profileExists(profileName)) {
             console.error(`Error: Profile '${profileName}' already exists.`);
             process.exit(1);
         }
-        // Ensure directories exist
-        this.xdgConfig.ensureProfileDirectories(profileName);
-        // Create initial user configuration
-        const userConfig = {
-            awsProfile: options.awsProfile,
+        // Create minimal valid ProfileConfig
+        const config = {
+            quilt: {
+                stackArn: "arn:aws:cloudformation:us-east-1:123456789012:stack/placeholder/placeholder",
+                catalog: "https://placeholder.quilt.com",
+                bucket: "placeholder-bucket",
+                database: "placeholder_db",
+                queueArn: "arn:aws:sqs:us-east-1:123456789012:placeholder",
+                region: "us-east-1",
+            },
+            benchling: {
+                tenant: "placeholder",
+                clientId: "placeholder",
+                appDefinitionId: "placeholder",
+            },
+            packages: {
+                bucket: "placeholder-bucket",
+                prefix: "benchling",
+                metadataKey: "experiment_id",
+            },
+            deployment: {
+                region: "us-east-1",
+            },
             _metadata: {
-                savedAt: new Date().toISOString(),
+                version: "0.7.0",
+                createdAt: new Date().toISOString(),
+                updatedAt: new Date().toISOString(),
                 source: "cli",
-                version: "0.6.0",
             },
         };
-        // Write user configuration
-        this.xdgConfig.writeProfileConfig("user", userConfig, profileName);
-        const paths = this.xdgConfig.getProfilePaths(profileName);
+        // Write profile configuration
+        this.xdgConfig.writeProfile(profileName, config);
         console.log(`Profile '${profileName}' created successfully!`);
-        console.log("\nConfiguration files:");
-        console.log(`  User config:   ${paths.userConfig}`);
-        console.log(`  Derived config: ${paths.derivedConfig}`);
-        console.log(`  Deploy config:  ${paths.deployConfig}`);
+        console.log(`\nConfiguration file: ~/.config/benchling-webhook/${profileName}/config.json`);
+        console.log("\nEdit the config file to add your actual configuration values.");
         console.log();
     }
     /**
@@ -102,31 +132,32 @@ class ProfileManager {
             process.exit(1);
         }
         console.log(`Profile: ${profileName}\n`);
-        const profile = this.xdgConfig.loadProfile(profileName);
-        const paths = this.xdgConfig.getProfilePaths(profileName);
-        // Show paths
-        console.log("Configuration files:");
-        console.log(`  User config:   ${paths.userConfig}`);
-        console.log(`  Derived config: ${paths.derivedConfig}`);
-        console.log(`  Deploy config:  ${paths.deployConfig}`);
-        console.log();
-        // Show user configuration
-        if (profile.user) {
-            console.log("User Configuration:");
-            this.printConfig(profile.user);
-            console.log();
-        }
-        // Show derived configuration
-        if (profile.derived) {
-            console.log("Derived Configuration:");
-            this.printConfig(profile.derived);
+        try {
+            const profile = this.xdgConfig.readProfile(profileName);
+            console.log("Configuration:");
+            console.log("\nQuilt:");
+            this.printSection(profile.quilt);
+            console.log("\nBenchling:");
+            this.printSection(profile.benchling);
+            console.log("\nPackages:");
+            this.printSection(profile.packages);
+            console.log("\nDeployment:");
+            this.printSection(profile.deployment);
+            if (profile.logging) {
+                console.log("\nLogging:");
+                this.printSection(profile.logging);
+            }
+            if (profile.security) {
+                console.log("\nSecurity:");
+                this.printSection(profile.security);
+            }
+            console.log("\nMetadata:");
+            this.printSection(profile._metadata);
             console.log();
         }
-        // Show deployment configuration
-        if (profile.deploy) {
-            console.log("Deployment Configuration:");
-            this.printConfig(profile.deploy);
-            console.log();
+        catch (error) {
+            console.error(`Error reading profile: ${error.message}`);
+            process.exit(1);
         }
     }
     /**
@@ -140,66 +171,43 @@ class ProfileManager {
             console.error(`Error: Profile '${profileName}' does not exist.`);
             process.exit(1);
         }
-        const profile = this.xdgConfig.loadProfile(profileName);
-        const errors = [];
-        const warnings = [];
-        // Validate user configuration
-        if (!profile.user) {
-            errors.push("Missing user configuration");
-        }
-        else {
-            // Check required fields
-            const required = [
-                "benchlingTenant",
-                "benchlingClientId",
-                "quiltCatalog",
-                "quiltUserBucket",
-            ];
-            required.forEach((field) => {
-                if (!profile.user[field]) {
-                    errors.push(`Missing required field in user config: ${field}`);
-                }
-            });
-            // Check AWS profile
-            if (!profile.user.awsProfile) {
-                warnings.push("No AWS profile specified");
+        try {
+            const profile = this.xdgConfig.readProfile(profileName);
+            const validation = this.xdgConfig.validateProfile(profile);
+            if (validation.isValid) {
+                console.log("✓ Profile validation passed!");
+                return;
             }
-        }
-        // Validate derived configuration
-        if (profile.derived) {
-            if (!profile.derived.catalogUrl) {
-                warnings.push("Derived config missing catalogUrl");
+            if (validation.errors.length > 0) {
+                console.log("Errors:");
+                validation.errors.forEach((error) => console.log(`  ✗ ${error}`));
+                console.log();
+            }
+            if (validation.warnings && validation.warnings.length > 0) {
+                console.log("Warnings:");
+                validation.warnings.forEach((warning) => console.log(`  ⚠ ${warning}`));
+                console.log();
+            }
+            if (validation.errors.length > 0) {
+                process.exit(1);
             }
         }
-        else {
-            warnings.push("No derived configuration found");
-        }
-        // Report results
-        if (errors.length === 0 && warnings.length === 0) {
-            console.log("✓ Profile validation passed!");
-            return;
-        }
-        if (errors.length > 0) {
-            console.log("Errors:");
-            errors.forEach((error) => console.log(`  ✗ ${error}`));
-            console.log();
-        }
-        if (warnings.length > 0) {
-            console.log("Warnings:");
-            warnings.forEach((warning) => console.log(`  ⚠ ${warning}`));
-            console.log();
-        }
-        if (errors.length > 0) {
+        catch (error) {
+            console.error(`Validation failed: ${error.message}`);
             process.exit(1);
         }
     }
     /**
-     * Prints configuration object in a readable format
+     * Prints a configuration section in a readable format
      *
-     * @param config - Configuration object to print
+     * @param section - Configuration section to print
      */
-    printConfig(config) {
-        const entries = Object.entries(config).filter(([key]) => key !== "_metadata");
+    printSection(section) {
+        if (!section || typeof section !== "object") {
+            console.log("  (empty)");
+            return;
+        }
+        const entries = Object.entries(section);
         if (entries.length === 0) {
             console.log("  (empty)");
             return;
@@ -209,7 +217,7 @@ class ProfileManager {
                 // Mask secrets
                 console.log(`  ${key}: ${value.substring(0, 4)}****`);
             }
-            else if (typeof value === "object") {
+            else if (typeof value === "object" && value !== null) {
                 console.log(`  ${key}: ${JSON.stringify(value, null, 2)}`);
             }
             else {
@@ -228,7 +236,7 @@ function main() {
     program
         .name("config-profiles")
         .description("Configuration Profile Management for Benchling Webhook")
-        .version("0.6.0");
+        .version("0.7.0");
     // List command
     program
         .command("list")
@@ -242,8 +250,8 @@ function main() {
         .description("Create a new configuration profile")
         .option("--aws-profile <profile>", "AWS profile to associate with this configuration")
         .option("--description <text>", "Profile description")
-        .action((profileName, options) => {
-        manager.createProfile(profileName, options);
+        .action((profileName) => {
+        manager.createProfile(profileName);
     });
     // Show command
     program

package/dist/bin/commands/config-profiles.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"create-secret.d.ts","sourceRoot":"","sources":["../../../bin/commands/create-secret.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;;;;;;;;;;;;GAqBG"}

package/dist/bin/commands/create-secret.js.map

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

@@ -1,7 +1,18 @@
+/**
+ * Deploy command for v0.7.0 configuration architecture
+ *
+ * Uses new profile-based configuration with deployment tracking.
+ * Supports independent --profile and --stage options.
+ *
+ * @module commands/deploy
+ * @version 0.7.0
+ */
 export declare function deployCommand(options: {
     yes?: boolean;
     bootstrapCheck?: boolean;
     requireApproval?: string;
+    profile?: string;
+    stage?: "dev" | "prod";
     quiltStackArn?: string;
     benchlingSecret?: string;
     imageTag?: string;

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

@@ -1 +1 @@
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+{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../../bin/commands/deploy.ts"],"names":[],"mappings":"AAeA;;;;;;;;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,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;CACpB,GAAG,OAAO,CAAC,IAAI,CAAC,CAqEhB"}