npm - @quiltdata/benchling-webhook - Versions diffs - 0.9.5 → 0.9.7-20251218T192028Z - Mend

@quiltdata/benchling-webhook 0.9.5 → 0.9.7-20251218T192028Z

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (13) hide show

package/dist/bin/commands/deploy.d.ts.map +1 -1
package/dist/bin/commands/deploy.js +32 -0
package/dist/bin/commands/deploy.js.map +1 -1
package/dist/lib/benchling-webhook-stack.d.ts.map +1 -1
package/dist/lib/benchling-webhook-stack.js +28 -11
package/dist/lib/benchling-webhook-stack.js.map +1 -1
package/dist/lib/wizard/phase6-integrated-mode.d.ts.map +1 -1
package/dist/lib/wizard/phase6-integrated-mode.js +55 -6
package/dist/lib/wizard/phase6-integrated-mode.js.map +1 -1
package/dist/package.json +4 -3
package/dist/scripts/version.js +16 -2
package/dist/scripts/version.js.map +1 -1
package/package.json +4 -3

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

	@@ -1 +1 @@
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package/dist/bin/commands/deploy.js CHANGED Viewed

@@ -579,6 +579,38 @@ async function deploy(stackArn, benchlingSecret, config, options) {
             CDK_DEFAULT_REGION: deployRegion,
             QUILT_STACK_ARN: stackArn,
             BENCHLING_SECRET: benchlingSecret,
+            // 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) {

package/dist/bin/commands/deploy.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/lib/benchling-webhook-stack.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"benchling-webhook-stack.d.ts","sourceRoot":"","sources":["../../lib/benchling-webhook-stack.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,GAAG,MAAM,aAAa,CAAC;AAGnC,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAIvC,OAAO,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAG/C;;;;;GAKG;AACH,MAAM,WAAW,0BAA2B,SAAQ,GAAG,CAAC,UAAU;IAC9D;;;OAGG;IACH,QAAQ,CAAC,MAAM,EAAE,aAAa,CAAC;CAClC;AAED,qBAAa,qBAAsB,SAAQ,GAAG,CAAC,KAAK;IAChD,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAiB;IAChD,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAsB;IAC1C,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAiB;IACrC,SAAgB,eAAe,EAAE,MAAM,CAAC;gBAGpC,KAAK,EAAE,SAAS,EAChB,EAAE,EAAE,MAAM,EACV,KAAK,EAAE,0BAA0B;~~CAkUxC~~"}
1	+ {"version":3,"file":"benchling-webhook-stack.d.ts","sourceRoot":"","sources":["../../lib/benchling-webhook-stack.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,GAAG,MAAM,aAAa,CAAC;AAGnC,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAIvC,OAAO,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAG/C;;;;;GAKG;AACH,MAAM,WAAW,0BAA2B,SAAQ,GAAG,CAAC,UAAU;IAC9D;;;OAGG;IACH,QAAQ,CAAC,MAAM,EAAE,aAAa,CAAC;CAClC;AAED,qBAAa,qBAAsB,SAAQ,GAAG,CAAC,KAAK;IAChD,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAiB;IAChD,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAsB;IAC1C,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAiB;IACrC,SAAgB,eAAe,EAAE,MAAM,CAAC;gBAGpC,KAAK,EAAE,SAAS,EAChB,EAAE,EAAE,MAAM,EACV,KAAK,EAAE,0BAA0B;CAsVxC"}

package/dist/lib/benchling-webhook-stack.js CHANGED Viewed

@@ -51,10 +51,27 @@ class BenchlingWebhookStack extends cdk.Stack {
         // Validate required configuration fields
         // Skip validation if SKIP_CONFIG_VALIDATION is set (for destroy operations)
         const skipValidation = process.env.SKIP_CONFIG_VALIDATION === "true";
-        if (!skipValidation && !config.benchling.secretArn) {
-            throw new Error("Configuration validation failed. Required fields:\n" +
-                "  - config.benchling.secretArn: Secrets Manager secret ARN\n\n" +
-                "Run 'npm run setup' to configure your deployment.");
+        if (!skipValidation) {
+            const missingFields = [];
+            // Validate Benchling configuration
+            if (!config.benchling.secretArn) {
+                missingFields.push("config.benchling.secretArn: Secrets Manager secret ARN");
+            }
+            // Validate required Quilt configuration
+            if (!config.quilt.catalog) {
+                missingFields.push("config.quilt.catalog: Quilt catalog domain");
+            }
+            if (!config.quilt.database) {
+                missingFields.push("config.quilt.database: Athena/Glue database name");
+            }
+            if (!config.quilt.queueUrl) {
+                missingFields.push("config.quilt.queueUrl: SQS queue URL for package creation");
+            }
+            if (missingFields.length > 0) {
+                throw new Error("Configuration validation failed. Required fields:\n" +
+                    missingFields.map(f => `  - ${f}`).join("\n") + "\n\n" +
+                    "Run 'npm run setup' to configure your deployment.");
+            }
         }
         console.log(`Deploying with profile configuration (v${package_json_1.default.version})`);
         console.log(`  Benchling Tenant: ${config.benchling.tenant}`);
@@ -66,38 +83,38 @@ class BenchlingWebhookStack extends cdk.Stack {
         const packagerQueueUrlParam = new cdk.CfnParameter(this, "PackagerQueueUrl", {
             type: "String",
             description: "SQS queue URL for Quilt package creation jobs",
-            default: "", // Will be resolved at deployment time
+            default: config.quilt.queueUrl || "", // Use config value as default
         });
         const athenaUserDatabaseParam = new cdk.CfnParameter(this, "AthenaUserDatabase", {
             type: "String",
             description: "Athena/Glue database name for Quilt catalog metadata",
-            default: "", // Will be resolved at deployment time
+            default: config.quilt.database || "", // Use config value as default
         });
         const quiltWebHostParam = new cdk.CfnParameter(this, "QuiltWebHost", {
             type: "String",
             description: "Quilt catalog domain (without protocol or trailing slash)",
-            default: "", // Will be resolved at deployment time
+            default: config.quilt.catalog || "", // Use config value as default
         });
         const icebergDatabaseParam = new cdk.CfnParameter(this, "IcebergDatabase", {
             type: "String",
             description: "Iceberg database name (optional, leave empty if not used)",
-            default: "",
+            default: config.quilt.icebergDatabase || "", // Use config value as default
         });
         // NEW: Optional Athena resources (from Quilt stack discovery)
         const icebergWorkgroupParam = new cdk.CfnParameter(this, "IcebergWorkgroup", {
             type: "String",
             description: "Iceberg workgroup name (optional, from Quilt stack discovery)",
-            default: "",
+            default: config.quilt.icebergWorkgroup || "", // Use config value as default
         });
         const athenaUserWorkgroupParam = new cdk.CfnParameter(this, "AthenaUserWorkgroup", {
             type: "String",
             description: "Athena workgroup for user queries (optional, from Quilt stack discovery)",
-            default: "",
+            default: config.quilt.athenaUserWorkgroup || "", // Use config value as default
         });
         const athenaResultsBucketParam = new cdk.CfnParameter(this, "AthenaResultsBucket", {
             type: "String",
             description: "S3 bucket for Athena query results (optional, from Quilt stack discovery)",
-            default: "",
+            default: config.quilt.athenaResultsBucket || "", // Use config value as default
         });
         const benchlingSecretParam = new cdk.CfnParameter(this, "BenchlingSecretARN", {
             type: "String",

package/dist/lib/benchling-webhook-stack.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/lib/wizard/phase6-integrated-mode.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"phase6-integrated-mode.d.ts","sourceRoot":"","sources":["../../../lib/wizard/phase6-integrated-mode.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAMH,OAAO,EAAE,mBAAmB,EAAE,oBAAoB,EAAE,MAAM,SAAS,CAAC;AAmFpE;;;;;;;;;;;;;GAaG;AACH,wBAAsB,iBAAiB,CAAC,KAAK,EAAE,mBAAmB,GAAG,OAAO,CAAC,oBAAoB,CAAC,~~CAyLjG~~"}
1	+ {"version":3,"file":"phase6-integrated-mode.d.ts","sourceRoot":"","sources":["../../../lib/wizard/phase6-integrated-mode.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAMH,OAAO,EAAE,mBAAmB,EAAE,oBAAoB,EAAE,MAAM,SAAS,CAAC;AAmFpE;;;;;;;;;;;;;GAaG;AACH,wBAAsB,iBAAiB,CAAC,KAAK,EAAE,mBAAmB,GAAG,OAAO,CAAC,oBAAoB,CAAC,CA2OjG"}

package/dist/lib/wizard/phase6-integrated-mode.js CHANGED Viewed

@@ -218,6 +218,42 @@ async function runIntegratedMode(input) {
                 console.log(chalk_1.default.green("✓ Stack update initiated"));
                 console.log(chalk_1.default.dim("  The stack is now updating in the background\n"));
                 integrationStatusUpdated = true;
+                // Offer to monitor stack update status
+                let shouldMonitorStatus = yes;
+                if (!yes) {
+                    const { monitor } = await inquirer_1.default.prompt([
+                        {
+                            type: "confirm",
+                            name: "monitor",
+                            message: "Monitor stack update status now?",
+                            default: true,
+                        },
+                    ]);
+                    shouldMonitorStatus = monitor;
+                }
+                if (shouldMonitorStatus) {
+                    console.log(chalk_1.default.dim("\nLaunching status monitor...\n"));
+                    try {
+                        // Import and run status command
+                        const { statusCommand } = await Promise.resolve().then(() => __importStar(require("../../bin/commands/status")));
+                        await statusCommand({
+                            profile,
+                            awsProfile,
+                            configStorage,
+                            timer: 10, // 10 second refresh interval
+                            exit: true, // Exit when terminal status reached
+                        });
+                    }
+                    catch (error) {
+                        console.warn(chalk_1.default.yellow(`\n⚠️  Status monitoring failed: ${error.message}`));
+                        console.warn(chalk_1.default.yellow("   You can run status manually with:"));
+                        console.warn(chalk_1.default.cyan(`   npx @quiltdata/benchling-webhook status --profile ${profile}\n`));
+                    }
+                }
+                else {
+                    console.log(chalk_1.default.dim("  You can monitor status later with:"));
+                    console.log(chalk_1.default.cyan(`  npx @quiltdata/benchling-webhook status --profile ${profile}\n`));
+                }
             }
             else {
                 console.warn(chalk_1.default.yellow(`⚠️  Failed to enable BenchlingIntegration: ${updateResult.error}`));
@@ -291,12 +327,25 @@ async function runIntegratedMode(input) {
     console.log(chalk_1.default.dim("✓ No separate webhook deployment needed"));
     console.log(chalk_1.default.dim("✓ Quilt stack will handle webhook events\n"));
     console.log(chalk_1.default.bold("Next steps:"));
-    console.log("  1. Monitor stack update:");
-    console.log(chalk_1.default.cyan(`     npx @quiltdata/benchling-webhook@latest status --profile ${profile}`));
-    console.log("  2. Configure webhook URL in Benchling app settings");
-    console.log("     (Get the webhook URL from your Quilt stack outputs)");
-    console.log("  3. Test the webhook integration");
-    console.log("  4. Monitor logs:");
+    let stepNumber = 1;
+    // Only show status monitoring if we didn't just run it
+    if (integrationStatusUpdated && !yes) {
+        // Status was likely already shown, skip this step
+    }
+    else if (integrationStatusUpdated) {
+        // --yes mode, suggest manual monitoring
+        console.log(`  ${stepNumber++}. Monitor stack update:`);
+        console.log(chalk_1.default.cyan(`     npx @quiltdata/benchling-webhook@latest status --profile ${profile}`));
+    }
+    console.log(`  ${stepNumber++}. Configure webhook URL in Benchling app settings`);
+    if (webhookUrl) {
+        console.log(chalk_1.default.dim(`     Webhook URL: ${webhookUrl}`));
+    }
+    else {
+        console.log("     (Get the webhook URL from your Quilt stack outputs)");
+    }
+    console.log(`  ${stepNumber++}. Test the webhook integration`);
+    console.log(`  ${stepNumber++}. Monitor logs:`);
     console.log(chalk_1.default.cyan(`     npx @quiltdata/benchling-webhook@latest logs --profile ${profile}`));
     console.log("");
     return {

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package/dist/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
     "name": "@quiltdata/benchling-webhook",
-    "version": "0.9.5",
+    "version": "0.9.7-20251218T192028Z",
     "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",
@@ -54,8 +54,9 @@
         "test:ts": "cross-env NODE_ENV=test NODE_OPTIONS='--experimental-vm-modules' jest --maxWorkers=50%",
         "version": "ts-node scripts/version.ts",
         "version:dev": "ts-node scripts/get-dev-version.ts",
-        "version:tag": "npm test && ts-node scripts/version.ts tag",
-        "version:tag:dev": "npm test && ts-node scripts/version.ts tag dev",
+        "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:verbose": "npm run test:integration -- --verbose"
     },

package/dist/scripts/version.js CHANGED Viewed

@@ -213,8 +213,9 @@ function main() {
         console.log("  sync       - Force TOML and YAML to match JSON version");
         console.log("");
         console.log("Release Tagging Commands:");
-        console.log("  tag        - Create and push production release tag");
-        console.log("  tag dev    - Create and push dev release tag with timestamp");
+        console.log("  tag              - Create and push production release tag");
+        console.log("  tag dev          - Create and push dev release tag with timestamp");
+        console.log("  verify-clean-git - Check for uncommitted changes (pre-flight check)");
         console.log("");
         console.log("Options:");
         console.log("  --no-push  - Create tag but do not push to origin (tag command only)");
@@ -233,6 +234,19 @@ function main() {
         process.exit(0);
     }
     const bumpType = args[0];
+    // Verify clean git command - check for uncommitted changes
+    if (bumpType === "verify-clean-git") {
+        try {
+            (0, child_process_1.execSync)("git diff-index --quiet HEAD --", { stdio: "ignore" });
+            console.log("✅ Git working directory is clean");
+            process.exit(0);
+        }
+        catch {
+            console.error("❌ You have uncommitted changes");
+            console.error("   Commit or stash your changes before creating a release");
+            process.exit(1);
+        }
+    }
     // Sync command - force TOML and YAML to match JSON
     if (bumpType === "sync") {
         const jsonVersion = pkg.version;

package/dist/scripts/version.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@quiltdata/benchling-webhook",
-  "version": "0.9.5",
+  "version": "0.9.7-20251218T192028Z",
   "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",
@@ -54,8 +54,9 @@
     "test:ts": "cross-env NODE_ENV=test NODE_OPTIONS='--experimental-vm-modules' jest --maxWorkers=50%",
     "version": "ts-node scripts/version.ts",
     "version:dev": "ts-node scripts/get-dev-version.ts",
-    "version:tag": "npm test && ts-node scripts/version.ts tag",
-    "version:tag:dev": "npm test && ts-node scripts/version.ts tag dev",
+    "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:verbose": "npm run test:integration -- --verbose"
   },