@quiltdata/benchling-webhook 0.4.13 → 0.5.0-20251029T180511Z

package/dist/lib/utils/stack-inference.js

@@ -0,0 +1,410 @@
+"use strict";
+/**
+ * Stack inference utilities for discovering CloudFormation stacks
+ * and extracting configuration from Quilt catalogs
+ */
+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;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fetchJson = fetchJson;
+exports.extractBucketName = extractBucketName;
+exports.findStackByResource = findStackByResource;
+exports.searchStacksByPattern = searchStacksByPattern;
+exports.getStackDetails = getStackDetails;
+exports.getAwsAccountId = getAwsAccountId;
+exports.extractApiGatewayId = extractApiGatewayId;
+exports.inferStackPrefix = inferStackPrefix;
+exports.findStack = findStack;
+exports.buildInferredConfig = buildInferredConfig;
+exports.inferStackConfig = inferStackConfig;
+const child_process_1 = require("child_process");
+/**
+ * Fetch JSON from a URL using native Node.js modules
+ */
+async function fetchJson(url) {
+    const https = await Promise.resolve().then(() => __importStar(require("https")));
+    const http = await Promise.resolve().then(() => __importStar(require("http")));
+    return new Promise((resolve, reject) => {
+        const parsedUrl = new URL(url);
+        const client = parsedUrl.protocol === "https:" ? https : http;
+        const options = {
+            headers: {
+                "User-Agent": "benchling-webhook-config-tool/1.0",
+                Accept: "application/json",
+            },
+        };
+        client
+            .get(url, options, (res) => {
+            let data = "";
+            if (res.statusCode !== 200) {
+                reject(new Error(`HTTP ${res.statusCode}: ${res.statusMessage}`));
+                return;
+            }
+            res.on("data", (chunk) => {
+                data += chunk.toString();
+            });
+            res.on("end", () => {
+                try {
+                    resolve(JSON.parse(data));
+                }
+                catch (e) {
+                    const error = e;
+                    reject(new Error(`Failed to parse JSON: ${error.message}`));
+                }
+            });
+        })
+            .on("error", reject);
+    });
+}
+/**
+ * Extract bucket name from S3 ARN or bucket name string
+ */
+function extractBucketName(bucketString) {
+    if (bucketString.startsWith("arn:aws:s3:::")) {
+        return bucketString.replace("arn:aws:s3:::", "").split("/")[0];
+    }
+    return bucketString.split("/")[0];
+}
+/**
+ * Try to find CloudFormation stack by searching for resource
+ */
+function findStackByResource(region, resourceId) {
+    try {
+        const result = (0, child_process_1.execSync)(`aws cloudformation describe-stack-resources --region ${region} --physical-resource-id "${resourceId}" --query "StackResources[0].StackName" --output text 2>/dev/null`, { encoding: "utf-8" });
+        const stackName = result.trim();
+        return stackName && stackName !== "None" ? stackName : null;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Search for stacks by name pattern
+ */
+function searchStacksByPattern(region, pattern) {
+    try {
+        const result = (0, child_process_1.execSync)(`aws cloudformation list-stacks --region ${region} --stack-status-filter CREATE_COMPLETE UPDATE_COMPLETE UPDATE_ROLLBACK_COMPLETE --query "StackSummaries[?contains(StackName, '${pattern}')].StackName" --output json`, { encoding: "utf-8" });
+        return JSON.parse(result);
+    }
+    catch {
+        return [];
+    }
+}
+/**
+ * Get stack outputs and parameters
+ */
+function getStackDetails(region, stackName) {
+    try {
+        const outputsResult = (0, child_process_1.execSync)(`aws cloudformation describe-stacks --region ${region} --stack-name "${stackName}" --query "Stacks[0].Outputs" --output json`, { encoding: "utf-8" });
+        const paramsResult = (0, child_process_1.execSync)(`aws cloudformation describe-stacks --region ${region} --stack-name "${stackName}" --query "Stacks[0].Parameters" --output json`, { encoding: "utf-8" });
+        return {
+            outputs: JSON.parse(outputsResult) || [],
+            parameters: JSON.parse(paramsResult) || [],
+        };
+    }
+    catch (error) {
+        console.error(`Warning: Could not get stack details: ${error.message}`);
+        return { outputs: [], parameters: [] };
+    }
+}
+/**
+ * Get AWS account ID
+ */
+function getAwsAccountId() {
+    try {
+        const result = (0, child_process_1.execSync)("aws sts get-caller-identity --query Account --output text", {
+            encoding: "utf-8",
+        });
+        return result.trim();
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Extract API Gateway ID from endpoint URL
+ */
+function extractApiGatewayId(endpoint) {
+    const match = endpoint.match(/https:\/\/([a-z0-9]+)\.execute-api/);
+    return match ? match[1] : null;
+}
+/**
+ * Extract stack name prefix from bucket names
+ */
+function inferStackPrefix(analyticsBucket, serviceBucket) {
+    const patterns = [analyticsBucket, serviceBucket]
+        .filter(Boolean)
+        .map((bucket) => {
+        const parts = bucket.split("-");
+        if (parts.length >= 3) {
+            return parts.slice(0, 2).join("-");
+        }
+        return parts[0];
+    });
+    return patterns[0] || "quilt";
+}
+/**
+ * Find CloudFormation stack using multiple search strategies
+ */
+function findStack(region, apiGatewayId, analyticsBucket, serviceBucket, stackPrefix, verbose = true) {
+    let stackName = null;
+    // Method 1: Search by API Gateway ID
+    if (apiGatewayId) {
+        if (verbose)
+            console.log(`Searching by API Gateway ID: ${apiGatewayId}...`);
+        stackName = findStackByResource(region, apiGatewayId);
+        if (stackName && verbose) {
+            console.log(`✓ Found stack by API Gateway: ${stackName}`);
+        }
+    }
+    // Method 2: Search by Analytics Bucket
+    if (!stackName && analyticsBucket) {
+        if (verbose)
+            console.log(`Searching by Analytics Bucket: ${analyticsBucket}...`);
+        stackName = findStackByResource(region, analyticsBucket);
+        if (stackName && verbose) {
+            console.log(`✓ Found stack by Analytics Bucket: ${stackName}`);
+        }
+    }
+    // Method 3: Search by Service Bucket
+    if (!stackName && serviceBucket) {
+        if (verbose)
+            console.log(`Searching by Service Bucket: ${serviceBucket}...`);
+        stackName = findStackByResource(region, serviceBucket);
+        if (stackName && verbose) {
+            console.log(`✓ Found stack by Service Bucket: ${stackName}`);
+        }
+    }
+    // Method 4: Search by name pattern
+    if (!stackName && stackPrefix) {
+        if (verbose)
+            console.log(`Searching by stack name pattern: *${stackPrefix}*...`);
+        const stacks = searchStacksByPattern(region, stackPrefix);
+        if (stacks.length > 0) {
+            if (verbose) {
+                console.log(`✓ Found ${stacks.length} potential stack(s):`);
+                stacks.forEach((name, i) => console.log(`  ${i + 1}. ${name}`));
+            }
+            if (stacks.length === 1) {
+                stackName = stacks[0];
+                if (verbose)
+                    console.log(`  Using: ${stackName}`);
+            }
+            else {
+                if (verbose) {
+                    console.log("");
+                    console.log("⚠️  Multiple stacks found. Using first match: " + stacks[0]);
+                    console.log("   If this is incorrect, manually verify the stack name.");
+                }
+                stackName = stacks[0];
+            }
+        }
+    }
+    return stackName;
+}
+/**
+ * Build inferred configuration from stack details
+ */
+function buildInferredConfig(config, stackName, stackDetails, region, accountId, catalogDomain) {
+    const vars = {};
+    // Extract catalog domain
+    const catalogMatch = catalogDomain.match(/https?:\/\/([^/]+)/);
+    const catalog = catalogMatch ? catalogMatch[1] : "";
+    // AWS Configuration
+    if (accountId) {
+        vars.CDK_DEFAULT_ACCOUNT = accountId;
+    }
+    vars.CDK_DEFAULT_REGION = region;
+    vars.AWS_REGION = region;
+    // Quilt Configuration
+    if (catalog) {
+        vars.QUILT_CATALOG = catalog;
+    }
+    // Try to infer bucket and database from stack or config
+    const serviceBucket = extractBucketName(config.serviceBucket);
+    // Find data bucket from stack outputs or use service bucket as fallback
+    const bucketOutput = stackDetails.outputs.find((o) => o.OutputKey === "Bucket" || o.OutputKey === "DataBucket");
+    const dataBucket = bucketOutput?.OutputValue || serviceBucket;
+    if (dataBucket) {
+        vars.QUILT_USER_BUCKET = `${dataBucket} # Verify this is YOUR data bucket`;
+    }
+    // Try to find database name from stack
+    const databaseOutput = stackDetails.outputs.find((o) => o.OutputKey === "Database" ||
+        o.OutputKey === "AthenaDatabase" ||
+        o.OutputKey === "UserAthenaDatabase");
+    if (databaseOutput) {
+        vars.QUILT_DATABASE = databaseOutput.OutputValue;
+    }
+    else if (catalog) {
+        // Infer database name from catalog (common pattern)
+        const dbGuess = catalog.replace(/[.-]/g, "_") + "_db";
+        vars.QUILT_DATABASE = `${dbGuess} # VERIFY THIS - inferred from catalog name`;
+    }
+    // SQS Queue
+    const queueOutput = stackDetails.outputs.find((o) => o.OutputKey === "PackagerQueue" || o.OutputKey.includes("Queue"));
+    if (queueOutput) {
+        const queueValue = queueOutput.OutputValue;
+        // Parse queue name from ARN or URL
+        let queueName;
+        if (queueValue.startsWith("arn:aws:sqs:")) {
+            // ARN format: arn:aws:sqs:region:account:queue-name
+            queueName = queueValue.split(":").pop();
+        }
+        else if (queueValue.includes("sqs.")) {
+            // URL format: https://sqs.region.amazonaws.com/account/queue-name
+            queueName = queueValue.split("/").pop();
+        }
+        else {
+            // Assume it's just the queue name
+            queueName = queueValue;
+        }
+        vars.QUEUE_NAME = queueName;
+        // Build SQS URL
+        if (accountId && region && queueName) {
+            vars.SQS_QUEUE_URL = `https://sqs.${region}.amazonaws.com/${accountId}/${queueName}`;
+        }
+    }
+    else if (stackName) {
+        vars.QUEUE_NAME = `${stackName}-PackagerQueue-XXXXX # VERIFY THIS - not found in outputs`;
+    }
+    // Additional useful info
+    if (stackName) {
+        vars["# CloudFormation Stack"] = stackName;
+    }
+    if (config.stackVersion) {
+        vars["# Stack Version"] = config.stackVersion;
+    }
+    vars["# API Gateway Endpoint"] = config.apiGatewayEndpoint;
+    return vars;
+}
+/**
+ * Parse config.json and infer stack information
+ */
+async function inferStackConfig(catalogUrl, verbose = true) {
+    if (verbose) {
+        console.log(`Fetching config from: ${catalogUrl}`);
+        console.log("");
+    }
+    // Normalize URL and construct config.json URL
+    let configUrl = catalogUrl.replace(/\/$/, "");
+    if (!configUrl.endsWith("/config.json")) {
+        configUrl += "/config.json";
+    }
+    // Fetch config.json
+    let config;
+    try {
+        config = (await fetchJson(configUrl));
+    }
+    catch (error) {
+        // If direct fetch fails, try with just /config.json path
+        const err = error;
+        if (err.message.includes("403") || err.message.includes("404")) {
+            const baseUrl = catalogUrl.match(/https?:\/\/[^/]+/)?.[0];
+            if (baseUrl) {
+                if (verbose)
+                    console.log(`Direct fetch failed, trying: ${baseUrl}/config.json`);
+                config = (await fetchJson(`${baseUrl}/config.json`));
+            }
+            else {
+                throw error;
+            }
+        }
+        else {
+            throw error;
+        }
+    }
+    if (verbose) {
+        console.log("✓ Successfully fetched config.json");
+        console.log("");
+        console.log("Configuration Summary:");
+        console.log("=".repeat(80));
+        console.log(`Region:           ${config.region}`);
+        console.log(`API Gateway:      ${config.apiGatewayEndpoint}`);
+        console.log(`Analytics Bucket: ${config.analyticsBucket}`);
+        console.log(`Service Bucket:   ${config.serviceBucket}`);
+        console.log(`Stack Version:    ${config.stackVersion}`);
+        console.log("=".repeat(80));
+        console.log("");
+    }
+    // Extract identifiable resources
+    const region = config.region;
+    const apiGatewayId = extractApiGatewayId(config.apiGatewayEndpoint);
+    const analyticsBucket = extractBucketName(config.analyticsBucket);
+    const serviceBucket = extractBucketName(config.serviceBucket);
+    const stackPrefix = inferStackPrefix(analyticsBucket, serviceBucket);
+    if (verbose) {
+        console.log("Searching for CloudFormation stack...");
+        console.log(`  Region: ${region}`);
+        console.log(`  API Gateway ID: ${apiGatewayId || "not found"}`);
+        console.log(`  Inferred stack prefix: ${stackPrefix}`);
+        console.log("");
+    }
+    // Try to find the stack
+    const stackName = findStack(region, apiGatewayId, analyticsBucket, serviceBucket, stackPrefix, verbose);
+    if (verbose) {
+        console.log("");
+        if (!stackName) {
+            console.log("⚠️  Could not automatically find CloudFormation stack.");
+            console.log("   You may need to manually specify stack resources.");
+            console.log("");
+        }
+    }
+    // Get stack details if found
+    let stackDetails = { outputs: [], parameters: [] };
+    if (stackName) {
+        if (verbose) {
+            console.log(`Fetching stack details for: ${stackName}...`);
+        }
+        stackDetails = getStackDetails(region, stackName);
+        if (verbose) {
+            console.log(`✓ Retrieved ${stackDetails.outputs.length} outputs and ${stackDetails.parameters.length} parameters`);
+            console.log("");
+        }
+    }
+    // Get AWS account ID
+    const accountId = getAwsAccountId();
+    if (accountId && verbose) {
+        console.log(`✓ AWS Account ID: ${accountId}`);
+        console.log("");
+    }
+    // Build inferred environment variables
+    const inferredVars = buildInferredConfig(config, stackName, stackDetails, region, accountId, catalogUrl.replace(/\/config\.json$/, ""));
+    return {
+        config,
+        stackName,
+        stackDetails,
+        inferredVars,
+    };
+}
+//# sourceMappingURL=stack-inference.js.map

package/dist/lib/utils/stack-inference.js.map

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package/dist/package.json

@@ -0,0 +1,90 @@
+{
+    "name": "@quiltdata/benchling-webhook",
+    "version": "0.5.0-20251029T180511Z",
+    "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",
+    "files": [
+        "dist/",
+        "README.md",
+        "LICENSE",
+        "env.template"
+    ],
+    "bin": {
+        "benchling-webhook": "./dist/bin/cli.js"
+    },
+    "scripts": {
+        "clean": "rm -rf cdk.out */{*.js,*.d.ts}",
+        "test": "NODE_ENV=test TMPDIR=./.tmp node --max-old-space-size=4096 ./node_modules/.bin/jest",
+        "cdk": "npm run test && npx cdk deploy --require-approval never",
+        "lint": "eslint . --ext .ts --fix",
+        "build": "tsc",
+        "prebuild": "rm -rf dist",
+        "postbuild": "chmod +x dist/bin/cli.js && cp bin/*.js dist/bin/ 2>/dev/null || true",
+        "synth": "npx cdk synth",
+        "logs": "node bin/check-logs.js",
+        "event": "node bin/send-event.js",
+        "check": "npm run cdk && npm run event && sleep 45 && npm run logs",
+        "docker:test": "make -C docker test",
+        "docker-push": "make -C docker push-local",
+        "docker-check": "make -C docker docker-validate",
+        "release": "npm run test && node bin/release.js",
+        "release:dev": "npm run test && node bin/release.js dev",
+        "notes": "bin/release-notes.sh \"$(jq -r .version package.json)\" \"712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:$(jq -r .version package.json)\" \"false\" \"$(jq -r .name package.json)\"",
+        "version": "node bin/version.js patch",
+        "version:patch": "npm run version -- patch",
+        "prepublishOnly": "npm run build"
+    },
+    "keywords": [
+        "benchling",
+        "webhook",
+        "aws",
+        "cdk",
+        "fargate",
+        "docker",
+        "quilt",
+        "cli",
+        "npx"
+    ],
+    "author": "Quilt Data",
+    "license": "Apache-2.0",
+    "repository": {
+        "type": "git",
+        "url": "git+https://github.com/quiltdata/benchling-webhook.git"
+    },
+    "devDependencies": {
+        "@eslint/js": "^9.22.0",
+        "@types/adm-zip": "^0.5.7",
+        "@types/aws-lambda": "^8.10.156",
+        "@types/jest": "^30.0.0",
+        "@types/node": "^24.0.0",
+        "@typescript-eslint/eslint-plugin": "^8.26.1",
+        "@typescript-eslint/parser": "^8.26.1",
+        "aws-cdk": "2.1031.0",
+        "dotenv": "^17.2.3",
+        "esbuild": "0.25.11",
+        "eslint": "^9.22.0",
+        "globals": "^16.0.0",
+        "jest": "^30.0.0",
+        "ts-jest": "^29.2.5",
+        "ts-node": "^10.9.2",
+        "typescript": "~5.9.0"
+    },
+    "dependencies": {
+        "@aws-sdk/client-s3": "^3.758.0",
+        "adm-zip": "^0.5.10",
+        "aws-cdk-lib": "2.221.0",
+        "aws-sdk": "^2.1574.0",
+        "boxen": "^5.1.2",
+        "chalk": "^4.1.2",
+        "commander": "^14.0.2",
+        "constructs": "^10.0.0",
+        "dotenv-expand": "^12.0.3",
+        "enquirer": "^2.4.1",
+        "ora": "^5.4.1"
+    },
+    "engines": {
+        "node": ">=18.0.0",
+        "npm": ">=9.0.0"
+    }
+}

package/package.json

@@ -1,36 +1,39 @@
 {
   "name": "@quiltdata/benchling-webhook",
-  "version": "0.4.13",
-  "description": "AWS CDK deployment for Benchling webhook processing using Fargate",
-  "main": "lib/index.ts",
+  "version": "0.5.0-20251029T180511Z",
+  "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",
+  "files": [
+    "dist/",
+    "README.md",
+    "LICENSE",
+    "env.template"
+  ],
   "bin": {
-    "benchling-webhook": "bin/benchling-webhook.ts"
+    "benchling-webhook": "./dist/bin/cli.js"
   },
   "scripts": {
-    "sync-version": "node bin/sync-version.js",
     "clean": "rm -rf cdk.out */{*.js,*.d.ts}",
     "test": "NODE_ENV=test TMPDIR=./.tmp node --max-old-space-size=4096 ./node_modules/.bin/jest",
     "cdk": "npm run test && npx cdk deploy --require-approval never",
     "lint": "eslint . --ext .ts --fix",
-    "build": "tsc --noEmit",
-    "watch": "tsc --noEmit -w",
+    "build": "tsc",
+    "prebuild": "rm -rf dist",
+    "postbuild": "chmod +x dist/bin/cli.js && cp bin/*.js dist/bin/ 2>/dev/null || true",
     "synth": "npx cdk synth",
-    "diff": "npx cdk diff",
     "logs": "node bin/check-logs.js",
     "event": "node bin/send-event.js",
     "check": "npm run cdk && npm run event && sleep 45 && npm run logs",
-    "get-env": "node bin/get-env.js",
-    "dev": "npm run build && npm run docker:test && npm run lint",
     "docker:test": "make -C docker test",
     "docker-push": "make -C docker push-local",
     "docker-check": "make -C docker docker-validate",
-    "release": "node bin/release.js",
-    "release:dev": "node bin/release.js dev",
-    "version:major": "node bin/version.js major",
-    "version:minor": "node bin/version.js minor",
-    "version:patch": "node bin/version.js patch",
-    "version:dev": "node bin/version.js dev",
-    "publish:manual": "node bin/publish-manual.js"
+    "release": "npm run test && node bin/release.js",
+    "release:dev": "npm run test && node bin/release.js dev",
+    "notes": "bin/release-notes.sh \"$(jq -r .version package.json)\" \"712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:$(jq -r .version package.json)\" \"false\" \"$(jq -r .name package.json)\"",
+    "version": "node bin/version.js patch",
+    "version:patch": "npm run version -- patch",
+    "prepublishOnly": "npm run build"
   },
   "keywords": [
     "benchling",
@@ -39,13 +42,15 @@
     "cdk",
     "fargate",
     "docker",
-    "quilt"
+    "quilt",
+    "cli",
+    "npx"
   ],
   "author": "Quilt Data",
   "license": "Apache-2.0",
   "repository": {
     "type": "git",
-    "url": "https://github.com/quiltdata/benchling-webhook.git"
+    "url": "git+https://github.com/quiltdata/benchling-webhook.git"
   },
   "devDependencies": {
     "@eslint/js": "^9.22.0",
@@ -70,7 +75,13 @@
     "adm-zip": "^0.5.10",
     "aws-cdk-lib": "2.221.0",
     "aws-sdk": "^2.1574.0",
-    "constructs": "^10.0.0"
+    "boxen": "^5.1.2",
+    "chalk": "^4.1.2",
+    "commander": "^14.0.2",
+    "constructs": "^10.0.0",
+    "dotenv-expand": "^12.0.3",
+    "enquirer": "^2.4.1",
+    "ora": "^5.4.1"
   },
   "engines": {
     "node": ">=18.0.0",