@quiltdata/benchling-webhook 0.5.4 → 0.6.0

package/dist/scripts/infer-quilt-config.js

@@ -0,0 +1,353 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Quilt Catalog Auto-Inference
+ *
+ * Automatically infers Quilt catalog configuration from:
+ * 1. quilt3 CLI command (`quilt3 config`)
+ * 2. AWS CloudFormation stack inspection
+ * 3. Interactive catalog selection (if multiple catalogs available)
+ *
+ * @module scripts/infer-quilt-config
+ */
+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.inferQuiltConfig = inferQuiltConfig;
+exports.inferenceResultToDerivedConfig = inferenceResultToDerivedConfig;
+const child_process_1 = require("child_process");
+const readline = __importStar(require("readline"));
+const client_cloudformation_1 = require("@aws-sdk/client-cloudformation");
+/**
+ * Executes quilt3 config command to get current catalog URL
+ *
+ * @returns Catalog URL from quilt3 CLI or null if command fails
+ */
+function getQuilt3Catalog() {
+    try {
+        const output = (0, child_process_1.execSync)("quilt3 config", { encoding: "utf-8", stdio: ["pipe", "pipe", "ignore"] });
+        const catalogUrl = output.trim();
+        if (catalogUrl && catalogUrl.startsWith("http")) {
+            console.log(`Found quilt3 CLI configuration: ${catalogUrl}`);
+            return { catalogUrl };
+        }
+        return null;
+    }
+    catch {
+        // quilt3 command not available or failed
+        return null;
+    }
+}
+/**
+ * Finds Quilt CloudFormation stacks in AWS account
+ *
+ * @param region - AWS region to search (defaults to us-east-1)
+ * @param profile - AWS profile to use
+ * @returns Array of Quilt stack information
+ */
+async function findQuiltStacks(region = "us-east-1", profile) {
+    try {
+        const clientConfig = { region };
+        if (profile) {
+            // Load AWS profile credentials
+            const { fromIni } = await Promise.resolve().then(() => __importStar(require("@aws-sdk/credential-providers")));
+            clientConfig.credentials = fromIni({ profile });
+        }
+        const client = new client_cloudformation_1.CloudFormationClient(clientConfig);
+        // List all stacks
+        const listCommand = new client_cloudformation_1.ListStacksCommand({
+            StackStatusFilter: ["CREATE_COMPLETE", "UPDATE_COMPLETE"],
+        });
+        const listResponse = await client.send(listCommand);
+        const stacks = listResponse.StackSummaries || [];
+        // Filter for Quilt stacks (containing "quilt" in the name)
+        const quiltStacks = stacks.filter((stack) => stack.StackName?.toLowerCase().includes("quilt") ||
+            stack.StackName?.toLowerCase().includes("catalog"));
+        // Get detailed information for each stack
+        const stackInfos = [];
+        for (const stack of quiltStacks) {
+            if (!stack.StackName)
+                continue;
+            try {
+                const describeCommand = new client_cloudformation_1.DescribeStacksCommand({
+                    StackName: stack.StackName,
+                });
+                const describeResponse = await client.send(describeCommand);
+                const stackDetail = describeResponse.Stacks?.[0];
+                if (!stackDetail)
+                    continue;
+                const outputs = stackDetail.Outputs || [];
+                const stackInfo = {
+                    stackName: stack.StackName,
+                    stackArn: stackDetail.StackId || "",
+                    region: region,
+                };
+                // Extract outputs
+                for (const output of outputs) {
+                    const key = output.OutputKey || "";
+                    const value = output.OutputValue || "";
+                    if (key === "QuiltWebHost") {
+                        stackInfo.catalogUrl = value;
+                    }
+                    else if (key.includes("ucket")) {
+                        stackInfo.bucket = value;
+                    }
+                    else if (key === "UserAthenaDatabaseName" || key.includes("Database")) {
+                        stackInfo.database = value;
+                    }
+                    else if (key.includes("Queue")) {
+                        stackInfo.queueArn = value;
+                    }
+                }
+                stackInfos.push(stackInfo);
+            }
+            catch (describeError) {
+                console.error(`Warning: Failed to describe stack ${stack.StackName}: ${describeError.message}`);
+            }
+        }
+        return stackInfos;
+    }
+    catch (error) {
+        console.error(`Warning: Failed to list CloudFormation stacks: ${error.message}`);
+        return [];
+    }
+}
+/**
+ * Prompts user to select from multiple catalog options
+ *
+ * @param options - Array of catalog options
+ * @returns Selected catalog index
+ */
+async function promptCatalogSelection(options) {
+    console.log("\nMultiple Quilt catalog configurations found:");
+    options.forEach((opt, idx) => {
+        console.log(`  ${idx + 1}. ${opt}`);
+    });
+    const rl = readline.createInterface({
+        input: process.stdin,
+        output: process.stdout,
+    });
+    return new Promise((resolve) => {
+        rl.question(`\nSelect catalog (1-${options.length}): `, (answer) => {
+            rl.close();
+            const selection = parseInt(answer.trim(), 10);
+            if (isNaN(selection) || selection < 1 || selection > options.length) {
+                console.log("Invalid selection, using first option.");
+                resolve(0);
+            }
+            else {
+                resolve(selection - 1);
+            }
+        });
+    });
+}
+/**
+ * Infers Quilt configuration from multiple sources
+ *
+ * Priority order:
+ * 1. quilt3 CLI command (`quilt3 config`)
+ * 2. CloudFormation stack inspection
+ * 3. Interactive selection if multiple options
+ *
+ * @param options - Inference options
+ * @returns Inferred configuration
+ */
+async function inferQuiltConfig(options) {
+    const { region = "us-east-1", profile, interactive = true } = options;
+    const result = {
+        source: "none",
+    };
+    // Step 1: Try quilt3 CLI command
+    console.log("Checking quilt3 CLI configuration...");
+    const quilt3Config = getQuilt3Catalog();
+    if (quilt3Config?.catalogUrl) {
+        result.catalogUrl = quilt3Config.catalogUrl;
+        result.source = "quilt3-cli";
+    }
+    else {
+        console.log("No quilt3 CLI configuration found.");
+    }
+    // Step 2: Search for CloudFormation stacks
+    console.log("\nSearching for Quilt CloudFormation stacks...");
+    const stacks = await findQuiltStacks(region, profile);
+    if (stacks.length === 0) {
+        console.log("No Quilt CloudFormation stacks found.");
+        return result;
+    }
+    console.log(`Found ${stacks.length} Quilt stack(s):\n`);
+    let selectedStack;
+    // If we have a catalog URL from quilt3, try to find matching stack
+    if (result.catalogUrl && stacks.length > 1) {
+        // Normalize URLs for comparison (remove protocol and trailing slashes)
+        const normalizeUrl = (url) => url.replace(/^https?:\/\//, "").replace(/\/$/, "");
+        const targetUrl = normalizeUrl(result.catalogUrl);
+        const matchingStack = stacks.find((s) => s.catalogUrl && normalizeUrl(s.catalogUrl) === targetUrl);
+        if (matchingStack) {
+            selectedStack = matchingStack;
+            console.log(`Auto-selected stack matching catalog URL: ${selectedStack.stackName}`);
+        }
+        else {
+            // No match found, prompt user
+            console.log(`No stack found matching catalog URL: ${result.catalogUrl}`);
+            if (interactive) {
+                const options = stacks.map((s) => `${s.stackName} (${s.region})`);
+                const selectedIndex = await promptCatalogSelection(options);
+                selectedStack = stacks[selectedIndex];
+                console.log(`\nSelected: ${selectedStack.stackName}`);
+            }
+            else {
+                selectedStack = stacks[0];
+                console.log(`Using first stack: ${selectedStack.stackName}`);
+            }
+        }
+    }
+    else if (stacks.length === 1) {
+        selectedStack = stacks[0];
+        console.log(`Using stack: ${selectedStack.stackName}`);
+    }
+    else if (interactive) {
+        const options = stacks.map((s) => `${s.stackName} (${s.region})`);
+        const selectedIndex = await promptCatalogSelection(options);
+        selectedStack = stacks[selectedIndex];
+        console.log(`\nSelected: ${selectedStack.stackName}`);
+    }
+    else {
+        selectedStack = stacks[0];
+        console.log(`Using first stack: ${selectedStack.stackName}`);
+    }
+    // Populate result from selected stack
+    if (selectedStack.stackArn) {
+        result.quiltStackArn = selectedStack.stackArn;
+    }
+    if (selectedStack.bucket) {
+        result.quiltUserBucket = selectedStack.bucket;
+    }
+    if (selectedStack.queueArn) {
+        result.queueArn = selectedStack.queueArn;
+    }
+    if (selectedStack.catalogUrl && !result.catalogUrl) {
+        result.catalogUrl = selectedStack.catalogUrl;
+    }
+    if (selectedStack.region) {
+        result.quiltRegion = selectedStack.region;
+    }
+    if (result.source === "quilt3-cli") {
+        result.source = "quilt3-cli+cloudformation";
+    }
+    else {
+        result.source = "cloudformation";
+    }
+    return result;
+}
+/**
+ * Converts inference result to DerivedConfig
+ *
+ * @param result - Inference result
+ * @returns DerivedConfig object
+ */
+function inferenceResultToDerivedConfig(result) {
+    const config = {
+        _metadata: {
+            inferredAt: new Date().toISOString(),
+            inferredFrom: result.source,
+            source: "infer-quilt-config",
+            version: "0.6.0",
+        },
+    };
+    if (result.catalogUrl) {
+        config.catalogUrl = result.catalogUrl;
+        config.quiltCatalog = result.catalogUrl;
+    }
+    if (result.quiltUserBucket) {
+        config.quiltUserBucket = result.quiltUserBucket;
+    }
+    if (result.quiltStackArn) {
+        config.quiltStackArn = result.quiltStackArn;
+    }
+    if (result.quiltRegion) {
+        config.quiltRegion = result.quiltRegion;
+    }
+    if (result.queueArn) {
+        config.queueArn = result.queueArn;
+    }
+    return config;
+}
+/**
+ * Main execution for CLI usage
+ */
+async function main() {
+    const args = process.argv.slice(2);
+    const options = {
+        interactive: true,
+    };
+    // Parse command line arguments
+    for (let i = 0; i < args.length; i++) {
+        if (args[i] === "--region" && i + 1 < args.length) {
+            options.region = args[i + 1];
+            i++;
+        }
+        else if (args[i] === "--profile" && i + 1 < args.length) {
+            options.profile = args[i + 1];
+            i++;
+        }
+        else if (args[i] === "--non-interactive") {
+            options.interactive = false;
+        }
+    }
+    console.log("Quilt Catalog Auto-Inference\n");
+    const result = await inferQuiltConfig(options);
+    console.log("\n=== Inference Results ===");
+    console.log(`Source: ${result.source}`);
+    if (result.catalogUrl)
+        console.log(`Catalog URL: ${result.catalogUrl}`);
+    if (result.quiltUserBucket)
+        console.log(`User Bucket: ${result.quiltUserBucket}`);
+    if (result.quiltStackArn)
+        console.log(`Stack ARN: ${result.quiltStackArn}`);
+    if (result.quiltRegion)
+        console.log(`Region: ${result.quiltRegion}`);
+    if (result.queueArn)
+        console.log(`Queue ARN: ${result.queueArn}`);
+    const derivedConfig = inferenceResultToDerivedConfig(result);
+    console.log("\n=== Derived Configuration ===");
+    console.log(JSON.stringify(derivedConfig, null, 4));
+}
+// Run main if executed directly
+if (require.main === module) {
+    main().catch((error) => {
+        console.error("Error:", error.message);
+        process.exit(1);
+    });
+}
+//# sourceMappingURL=infer-quilt-config.js.map

package/dist/scripts/infer-quilt-config.js.map

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package/dist/scripts/install-wizard.d.ts

@@ -0,0 +1,34 @@
+#!/usr/bin/env node
+/**
+ * Interactive Configuration Wizard
+ *
+ * Guided configuration setup with comprehensive validation:
+ * - Benchling tenant and OAuth credentials
+ * - S3 bucket access verification
+ * - Quilt API connectivity testing
+ * - AWS Secrets Manager integration
+ *
+ * Supports both interactive and non-interactive (CI/CD) modes.
+ *
+ * @module scripts/install-wizard
+ */
+import { UserConfig, ProfileName } from "../lib/types/config";
+/**
+ * Wizard configuration options
+ */
+interface WizardOptions {
+    profile?: ProfileName;
+    nonInteractive?: boolean;
+    skipValidation?: boolean;
+    awsProfile?: string;
+    awsRegion?: string;
+}
+/**
+ * Runs the interactive configuration wizard
+ *
+ * @param options - Wizard options
+ * @returns Completed user configuration
+ */
+export declare function runInstallWizard(options?: WizardOptions): Promise<UserConfig>;
+export {};
+//# sourceMappingURL=install-wizard.d.ts.map

package/dist/scripts/install-wizard.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"install-wizard.d.ts","sourceRoot":"","sources":["../../scripts/install-wizard.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;GAYG;AAOH,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAO9D;;GAEG;AACH,UAAU,aAAa;IACnB,OAAO,CAAC,EAAE,WAAW,CAAC;IACtB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,CAAC;CACtB;AA6RD;;;;;GAKG;AACH,wBAAsB,gBAAgB,CAAC,OAAO,GAAE,aAAkB,GAAG,OAAO,CAAC,UAAU,CAAC,CA2ZvF"}