@quiltdata/benchling-webhook 0.6.1-20251104T053146Z → 0.6.1

package/dist/bin/check-logs.d.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * Check CloudWatch logs for the deployed Benchling webhook ECS service
+ * Uses CloudFormation stack outputs to find the correct log group
+ */
+import "dotenv/config";
+//# sourceMappingURL=check-logs.d.ts.map

package/dist/bin/check-logs.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"check-logs.d.ts","sourceRoot":"","sources":["../../bin/check-logs.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,eAAe,CAAC"}

package/dist/bin/check-logs.js

@@ -1,63 +1,58 @@
 #!/usr/bin/env node
+"use strict";
 /**
  * Check CloudWatch logs for the deployed Benchling webhook ECS service
  * Uses CloudFormation stack outputs to find the correct log group
  */
-
+Object.defineProperty(exports, "__esModule", { value: true });
 require("dotenv/config");
-const { execSync } = require("child_process");
-
+const child_process_1 = require("child_process");
 const STACK_NAME = "BenchlingWebhookStack";
-
 // Validate required environment variables
 if (!process.env.CDK_DEFAULT_REGION) {
     console.error("Error: CDK_DEFAULT_REGION is not set in .env file");
     console.error("Please set CDK_DEFAULT_REGION in your .env file");
     process.exit(1);
 }
-
 const AWS_REGION = process.env.CDK_DEFAULT_REGION;
-
 function getStackOutputs() {
     try {
-        const output = execSync(
-            `aws cloudformation describe-stacks --stack-name ${STACK_NAME} --region ${AWS_REGION} --query 'Stacks[0].Outputs' --output json`,
-            { encoding: "utf-8" },
-        );
+        const output = (0, child_process_1.execSync)(`aws cloudformation describe-stacks --stack-name ${STACK_NAME} --region ${AWS_REGION} --query 'Stacks[0].Outputs' --output json`, { encoding: "utf-8" });
         return JSON.parse(output);
-    } catch (error) {
+    }
+    catch (_error) {
         console.error(`Error: Could not get stack outputs for ${STACK_NAME}`);
         console.error("Make sure the stack is deployed and AWS credentials are configured.");
         process.exit(1);
     }
 }
-
 function getLogGroupFromOutputs(outputs, logType) {
     let outputKey;
     if (logType === "ecs") {
         outputKey = "EcsLogGroup";
-    } else if (logType === "api") {
+    }
+    else if (logType === "api") {
         outputKey = "ApiGatewayLogGroup";
-    } else if (logType === "api-exec") {
+    }
+    else if (logType === "api-exec") {
         outputKey = "ApiGatewayExecutionLogGroup";
     }
-
+    else {
+        console.error(`Error: Invalid log type '${logType}'`);
+        process.exit(1);
+    }
     const logGroupOutput = outputs.find((o) => o.OutputKey === outputKey);
-
     if (!logGroupOutput) {
         console.error(`Error: Could not find ${outputKey} in stack outputs`);
         console.error("Make sure the stack has been deployed with the latest changes.");
         process.exit(1);
     }
-
     return logGroupOutput.OutputValue;
 }
-
 function printStackInfo(outputs, logGroup, logType) {
     console.log("=".repeat(80));
     console.log("Benchling Webhook Stack Information");
     console.log("=".repeat(80));
-
     const clusterName = outputs.find((o) => o.OutputKey === "FargateServiceClusterNameCD3B109F");
     const serviceName = outputs.find((o) => o.OutputKey === "FargateServiceServiceName24CFD869");
     const webhookEndpoint = outputs.find((o) => o.OutputKey === "WebhookEndpoint");
@@ -66,23 +61,27 @@ function printStackInfo(outputs, logGroup, logType) {
     const apiLogGroup = outputs.find((o) => o.OutputKey === "ApiGatewayLogGroup");
     const apiExecLogGroup = outputs.find((o) => o.OutputKey === "ApiGatewayExecutionLogGroup");
     const albDns = outputs.find((o) => o.OutputKey === "LoadBalancerDNS");
-
-    if (clusterName) console.log(`Cluster:   ${clusterName.OutputValue}`);
-    if (serviceName) console.log(`Service:   ${serviceName.OutputValue}`);
-    if (webhookEndpoint) console.log(`Endpoint:  ${webhookEndpoint.OutputValue}`);
-    if (albDns) console.log(`ALB DNS:   ${albDns.OutputValue}`);
-    if (version) console.log(`Version:   ${version.OutputValue}`);
-
+    if (clusterName)
+        console.log(`Cluster:   ${clusterName.OutputValue}`);
+    if (serviceName)
+        console.log(`Service:   ${serviceName.OutputValue}`);
+    if (webhookEndpoint)
+        console.log(`Endpoint:  ${webhookEndpoint.OutputValue}`);
+    if (albDns)
+        console.log(`ALB DNS:   ${albDns.OutputValue}`);
+    if (version)
+        console.log(`Version:   ${version.OutputValue}`);
     console.log("");
     console.log("Log Groups:");
-    if (ecsLogGroup) console.log(`  ECS:         ${ecsLogGroup.OutputValue}${logType === "ecs" ? " (viewing)" : ""}`);
-    if (apiLogGroup) console.log(`  API Access:  ${apiLogGroup.OutputValue}${logType === "api" ? " (viewing)" : ""}`);
-    if (apiExecLogGroup) console.log(`  API Exec:    ${apiExecLogGroup.OutputValue}${logType === "api-exec" ? " (viewing)" : ""}`);
-
+    if (ecsLogGroup)
+        console.log(`  ECS:         ${ecsLogGroup.OutputValue}${logType === "ecs" ? " (viewing)" : ""}`);
+    if (apiLogGroup)
+        console.log(`  API Access:  ${apiLogGroup.OutputValue}${logType === "api" ? " (viewing)" : ""}`);
+    if (apiExecLogGroup)
+        console.log(`  API Exec:    ${apiExecLogGroup.OutputValue}${logType === "api-exec" ? " (viewing)" : ""}`);
     console.log("=".repeat(80));
     console.log("");
 }
-
 function main() {
     const args = process.argv.slice(2);
     const logType = args.find((arg) => arg.startsWith("--type="))?.split("=")[1] || "all";
@@ -90,27 +89,22 @@ function main() {
     const since = args.find((arg) => arg.startsWith("--since="))?.split("=")[1] || "5m";
     const follow = args.includes("--follow") || args.includes("-f");
     const tail = args.find((arg) => arg.startsWith("--tail="))?.split("=")[1] || "100";
-
     // Validate log type
     if (!["ecs", "api", "api-exec", "all"].includes(logType)) {
         console.error("Error: --type must be 'ecs', 'api', 'api-exec', or 'all'");
         process.exit(1);
     }
-
     // Get stack outputs
     const outputs = getStackOutputs();
-
     // Handle 'all' type - show all three log groups
     if (logType === "all") {
         printStackInfo(outputs, null, "all");
         console.log("Showing logs from all sources (most recent first):\n");
-
         const logGroupDefs = [
             { type: "ECS", group: outputs.find((o) => o.OutputKey === "EcsLogGroup")?.OutputValue },
             { type: "API-Access", group: outputs.find((o) => o.OutputKey === "ApiGatewayLogGroup")?.OutputValue },
             { type: "API-Exec", group: outputs.find((o) => o.OutputKey === "ApiGatewayExecutionLogGroup")?.OutputValue },
         ];
-
         // Warn about missing log groups
         const missingGroups = logGroupDefs.filter(lg => !lg.group);
         if (missingGroups.length > 0) {
@@ -120,63 +114,60 @@ function main() {
             });
             console.log("");
         }
-
         const logGroups = logGroupDefs.filter(lg => lg.group);
-
         for (const { type, group } of logGroups) {
             console.log(`\n${"=".repeat(80)}`);
             console.log(`${type}: ${group}`);
             console.log("=".repeat(80));
-
             let command = `aws logs tail "${group}"`;
             command += ` --region ${AWS_REGION}`;
             command += ` --since ${since}`;
-            command += ` --format short`;
+            command += " --format short";
             if (filterPattern) {
                 command += ` --filter-pattern "${filterPattern}"`;
             }
             command += ` 2>&1 | tail -${tail}`;
-
             try {
-                const output = execSync(command, { encoding: "utf-8", shell: "/bin/bash" });
+                const output = (0, child_process_1.execSync)(command, { encoding: "utf-8", shell: "/bin/bash" });
                 if (output.trim()) {
                     console.log(output);
-                } else {
+                }
+                else {
                     console.log(`(No logs in the last ${since})`);
                 }
-            } catch (error) {
-                console.log(`Error reading ${type} logs: ${error.message}`);
+            }
+            catch (error) {
+                const errorMessage = error instanceof Error ? error.message : String(error);
+                console.log(`Error reading ${type} logs: ${errorMessage}`);
             }
         }
         return;
     }
-
     const logGroup = getLogGroupFromOutputs(outputs, logType);
     printStackInfo(outputs, logGroup, logType);
-
     // Build AWS logs command
     let command = `aws logs tail ${logGroup}`;
     command += ` --region ${AWS_REGION}`;
     command += ` --since ${since}`;
-    command += ` --format short`;
-
+    command += " --format short";
     if (filterPattern) {
         command += ` --filter-pattern "${filterPattern}"`;
     }
-
     if (follow) {
         command += " --follow";
         console.log("Following logs (Press Ctrl+C to stop)...\n");
-    } else {
+    }
+    else {
         command += ` | tail -${tail}`;
         console.log(`Showing last ${tail} log entries from the past ${since}...\n`);
     }
-
     // Execute logs command
     try {
-        execSync(command, { stdio: "inherit" });
-    } catch (error) {
-        if (error.status !== 130) {
+        (0, child_process_1.execSync)(command, { stdio: "inherit" });
+    }
+    catch (error) {
+        const hasStatus = error && typeof error === "object" && "status" in error;
+        if (hasStatus && error.status !== 130) {
             // Ignore Ctrl+C exit (status 130)
             console.error("\nError fetching logs. Make sure:");
             console.error("1. The stack is deployed");
@@ -186,7 +177,6 @@ function main() {
         }
     }
 }
-
 function printHelp() {
     console.log("Usage: npm run logs [options]");
     console.log("");
@@ -214,18 +204,19 @@ function printHelp() {
     console.log("  npm run logs -- --type=ecs --follow            # Follow ECS logs");
     console.log("  npm run logs -- --type=api-exec --since=10m    # Last 10 min of execution logs");
 }
-
 if (require.main === module) {
     const args = process.argv.slice(2);
     if (args.includes("--help") || args.includes("-h")) {
         printHelp();
         process.exit(0);
     }
-
     try {
         main();
-    } catch (error) {
-        console.error("Error:", error.message);
+    }
+    catch (error) {
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        console.error("Error:", errorMessage);
         process.exit(1);
     }
 }
+//# sourceMappingURL=check-logs.js.map

package/dist/bin/check-logs.js.map

@@ -0,0 +1 @@
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package/dist/bin/dev-deploy.js

@@ -92,7 +92,7 @@ async function waitForWorkflow(commitSha, timeoutMinutes = 15) {
                 if (status === "completed") {
                     console.log("\n");
                     if (conclusion === "success") {
-                        console.log(`✅ CI workflow completed successfully!`);
+                        console.log("✅ CI workflow completed successfully!");
                         console.log(`   Run: ${workflowUrl}`);
                         return true;
                     }
@@ -123,10 +123,10 @@ async function waitForWorkflow(commitSha, timeoutMinutes = 15) {
         console.error(`   Check status at: ${workflowUrl}`);
     }
     else {
-        console.error(`   Check status at: https://github.com/quiltdata/benchling-webhook/actions`);
+        console.error("   Check status at: https://github.com/quiltdata/benchling-webhook/actions");
     }
     console.error("\n   Once the workflow completes, you can deploy manually with:");
-    console.error(`   npm run cli -- --image-tag <version> --yes`);
+    console.error("   npm run cli -- --image-tag <version> --yes");
     process.exit(1);
 }
 async function main() {
@@ -208,14 +208,14 @@ async function main() {
         console.log(`✅ Created git tag ${devTag}`);
         // 3. Push tag to origin (triggers CI)
         console.log("");
-        console.log(`Step 3: Pushing tag to origin (this triggers CI/CD)...`);
+        console.log("Step 3: Pushing tag to origin (this triggers CI/CD)...");
         run(`git push origin ${devTag}`);
         console.log(`✅ Pushed tag ${devTag} to origin`);
         console.log("   CI will now build Docker image for x86_64 (AWS-compatible)");
     }
     // 4. Wait for CI to complete
     console.log("");
-    console.log(`Step 4: Waiting for CI to build Docker image...`);
+    console.log("Step 4: Waiting for CI to build Docker image...");
     // Get the commit SHA for the tag (use ^{commit} to dereference annotated tags)
     const commitShaOutput = run(`git rev-parse ${devTag}^{commit}`, { silent: true });
     if (!commitShaOutput) {
@@ -226,7 +226,7 @@ async function main() {
     await waitForWorkflow(commitSha);
     // 5. Deploy CDK stack with CI-built image tag using secrets-only mode
     console.log("");
-    console.log(`Step 5: Deploying CDK stack with CI-built image (secrets-only mode)...`);
+    console.log("Step 5: Deploying CDK stack with CI-built image (secrets-only mode)...");
     process.chdir((0, path_1.join)(__dirname, ".."));
     // Use the full version with timestamp (without 'v' prefix)
     const imageTag = devTag.replace(/^v/, "");

package/dist/bin/get-env.d.ts

@@ -0,0 +1,16 @@
+#!/usr/bin/env node
+/**
+ * Get environment configuration from a Quilt catalog's config.json
+ *
+ * This script fetches config.json from a Quilt catalog URL and attempts to:
+ * 1. Parse the configuration
+ * 2. Query AWS CloudFormation to find the stack using resource identifiers
+ * 3. Extract stack outputs and parameters
+ * 4. Generate environment variables for .env
+ *
+ * Usage:
+ *   node bin/get-env.js https://quilt-catalog.yourcompany.com
+ *   node bin/get-env.js https://quilt-catalog.yourcompany.com --write
+ */
+export * from "../lib/utils/stack-inference";
+//# sourceMappingURL=get-env.d.ts.map

package/dist/bin/get-env.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"get-env.d.ts","sourceRoot":"","sources":["../../bin/get-env.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;GAYG;AA+KH,cAAc,8BAA8B,CAAC"}

package/dist/bin/get-env.js

@@ -1,4 +1,5 @@
 #!/usr/bin/env node
+"use strict";
 /**
  * Get environment configuration from a Quilt catalog's config.json
  *
@@ -12,36 +13,69 @@
  *   node bin/get-env.js https://quilt-catalog.yourcompany.com
  *   node bin/get-env.js https://quilt-catalog.yourcompany.com --write
  */
-
-const fs = require("fs");
-const path = require("path");
-
+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;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
 // Import utility functions from lib/utils
-const { inferStackConfig } = require("../lib/utils/stack-inference");
-
+const stack_inference_1 = require("../lib/utils/stack-inference");
 // Parse command line arguments (only when run directly)
-let args, catalogUrl, outputFile, writeFile;
+let args;
+let catalogUrl;
+let outputFile;
+let writeFile;
 if (require.main === module) {
     args = process.argv.slice(2);
     catalogUrl = args.find((arg) => !arg.startsWith("--"));
     outputFile = args.find((arg) => arg.startsWith("--output="))?.split("=")[1];
     writeFile = args.includes("--write");
-
     if (!catalogUrl || args.includes("--help") || args.includes("-h")) {
         printHelp();
         process.exit(catalogUrl ? 0 : 1);
     }
 }
-
 // CLI-specific functions moved to lib/utils/stack-inference.ts
 // Re-export for backward compatibility if needed
-
 /**
  * Format environment variables for output
  */
 function formatEnvVars(vars) {
     const lines = [];
-
     lines.push("# ==============================================================================");
     lines.push("# INFERRED CONFIGURATION");
     lines.push("# ==============================================================================");
@@ -52,15 +86,14 @@ function formatEnvVars(vars) {
     lines.push("#    Some values may need manual verification or completion.");
     lines.push("# ==============================================================================");
     lines.push("");
-
     for (const [key, value] of Object.entries(vars)) {
         if (key.startsWith("#")) {
             lines.push(`${key}: ${value}`);
-        } else {
+        }
+        else {
             lines.push(`${key}=${value}`);
         }
     }
-
     lines.push("");
     lines.push("# ==============================================================================");
     lines.push("# REQUIRED VALUES NOT INFERRED - Must be filled manually");
@@ -75,10 +108,8 @@ function formatEnvVars(vars) {
     lines.push("ENABLE_WEBHOOK_VERIFICATION=true");
     lines.push("BENCHLING_TEST_ENTRY=etr_123456789");
     lines.push("");
-
     return lines.join("\n");
 }
-
 /**
  * Print help
  */
@@ -111,17 +142,17 @@ function printHelp() {
     console.log("  - AWS credentials with CloudFormation read permissions");
     console.log("  - Network access to the catalog URL");
 }
-
 /**
  * Main execution
  */
 async function main() {
+    if (!catalogUrl) {
+        throw new Error("Catalog URL is required");
+    }
     try {
-        const result = await inferStackConfig(catalogUrl);
-
+        const result = await (0, stack_inference_1.inferStackConfig)(catalogUrl);
         // Format output
         const output = formatEnvVars(result.inferredVars);
-
         // Print summary
         console.log("=".repeat(80));
         console.log("INFERRED CONFIGURATION");
@@ -129,12 +160,10 @@ async function main() {
         console.log("");
         console.log(output);
         console.log("");
-
         // Write to file if requested
         const targetFile = outputFile || (writeFile ? "env.inferred" : null);
         if (targetFile) {
             const fullPath = path.resolve(targetFile);
-
             // Check if .env already exists and warn before proceeding
             const envPath = path.resolve(".env");
             if (fs.existsSync(envPath)) {
@@ -142,7 +171,6 @@ async function main() {
                 console.log(`   Writing to ${targetFile} instead to avoid overwriting your configuration.`);
                 console.log("");
             }
-
             fs.writeFileSync(fullPath, output);
             console.log("=".repeat(80));
             console.log(`✓ Configuration written to: ${fullPath}`);
@@ -154,27 +182,29 @@ async function main() {
             if (fs.existsSync(envPath)) {
                 console.log("  3. Carefully merge with your existing .env file (DO NOT overwrite!)");
                 console.log("     Compare: diff .env env.inferred");
-            } else {
+            }
+            else {
                 console.log("  3. Copy to .env when ready: cp env.inferred .env");
             }
             console.log("");
-        } else {
+        }
+        else {
             console.log("=".repeat(80));
             console.log("To save this configuration, run:");
             console.log(`  node bin/get-env.js ${catalogUrl} --write`);
             console.log("=".repeat(80));
             console.log("");
         }
-
-    } catch (error) {
-        console.error("Error:", error.message);
+    }
+    catch (error) {
+        const err = error;
+        console.error("Error:", err.message);
         process.exit(1);
     }
 }
-
 if (require.main === module) {
     main();
 }
-
 // For backward compatibility, re-export from the new location
-module.exports = require("../lib/utils/stack-inference");
+__exportStar(require("../lib/utils/stack-inference"), exports);
+//# sourceMappingURL=get-env.js.map

package/dist/bin/get-env.js.map

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package/dist/bin/publish.d.ts

@@ -0,0 +1,20 @@
+#!/usr/bin/env node
+/**
+ * NPM publish script with dev/prod modes
+ *
+ * By default, publishes with 'dev' tag (prerelease).
+ * Use --prod to publish as 'latest' (production).
+ * Use --check to view current package status without publishing.
+ *
+ * Prerequisites:
+ * 1. You must have an NPM access token with publish permissions
+ * 2. Set the token as environment variable: NPM_TOKEN=your_token_here
+ *
+ * Usage:
+ *   npm run publish                      # Publish as dev (prerelease)
+ *   npm run publish -- --prod            # Publish as latest (production)
+ *   npm run publish -- --check           # Check package status only
+ *   npm run publish -- --dry-run         # Test without publishing
+ */
+export {};
+//# sourceMappingURL=publish.d.ts.map

package/dist/bin/publish.d.ts.map

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