Merge pull request #7 from umccr/refactor/toml

refactor: remove TOML config and related changes

.pre-commit-config.yaml

@@ -9,10 +9,19 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: pretty-format-json
-        args: ["--autofix"]
   - repo: https://github.com/Yelp/detect-secrets
     rev: v1.5.0
     hooks:
       - id: detect-secrets
         args: ["--baseline", ".secrets.baseline"]
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.4.2
+    hooks:
+      - id: prettier
+        exclude: pnpm-lock.yaml
+  - repo: https://github.com/pre-commit/mirrors-eslint
+    rev: v9.18.0
+    hooks:
+      - id: eslint
+        files: \.[jt]sx?$
+        types: [file]

README.md

@@ -1,43 +1,94 @@
-# Quickstart
+# htsget-deploy
 
-Here's how to deploy [htsget-rs's htsget-lambda](https://github.com/umccr/htsget-rs) to AWS:
+Deploy a cloud-based implementation of [htsget-rs]. This project contains a reusable CDK construct that deploys
+[htsget-lambda] using an AWS [API Gateway][aws-api-gateway] function and an example CDK stack.
+
+## Quickstart
 
-1. Authenticate to your AWS account (preferably using SSO).
-2. Modify the `bin/settings.ts`, according to your preferences.
-3. Modify `config/<YOUR_TOML_FILE>.toml` pointed by `bin/settings.ts` accordingly.
-4. Run `cdk deploy`.
+Here's how to deploy [htsget-rs's htsget-lambda](https://github.com/umccr/htsget-rs) to AWS:
 
-If the above guidance is insufficient, please refer to the [DEPLOY.md](DEPLOY.md) document for a more in-depth
-walkthrough settings and operations.
+1. Install packages by running `npm install` or `pnpm install`.
+2. Authenticate to your AWS account (preferably using SSO).
+3. Modify the [`bin/settings.ts`][htsget-settings], according to your preferences. All options are documented at [`docs/CONFIG.md`][docs-config].
+4. Run `npx cdk deploy`.
 
-## Does it work?
+### Does it work?
 
 A simple `curl` command should be able to determine that:
 
 ```sh
-curl "https://htsget-demo.ga4gh-demo.org/reads/service-info"
+curl "https://htsget.ga4gh-demo.org/reads/service-info"
 ```
 
-Should return a response similar to the following one (some fields elided for brevity):
+Should return a response similar to the following:
 
 ```json
 {
-  "name": "umccr-htsget-rs",
-  "version": "0.1",
+  "id": "htsget-lambda/0.5.2",
+  "createdAt": "2025-01-22T23:29:34.423733522+00:00",
+  "name": "htsget-lambda",
+  "version": "0.5.2",
+  "updatedAt": "2025-01-22T23:29:34.423735886+00:00",
+  "description": "A cloud-based instance of htsget-rs using AWS Lambda, which serves data according to the htsget protocol.",
   "organization": {
-    "name": "UMCCR",
-    "url": "https://umccr.org/"
+    "name": "",
+    "url": ""
+  },
+  "documentationUrl": "https://github.com/umccr/htsget-rs",
+  "type": {
+    "group": "org.ga4gh",
+    "artifact": "htsget",
+    "version": "1.3.0"
   },
   "htsget": {
     "datatype": "reads",
     "formats": [
       "BAM",
       "CRAM"
-    ]
-  },
-  "contactUrl": "https://umccr.org/",
-  "documentationUrl": "https://github.com/umccr/htsget-rs",
+    ],
+    "fieldsParametersEffective": false,
+    "tagsParametersEffective": false
+  }
 }
 ```
 
-Please note that the example above assumes a publicly accessible endpoint. If you have an authz'd deployment, please use `-H "Authorization: $JWT_TOKEN"` flags added to your `curl` command.
+Please note that the example above assumes a publicly accessible endpoint. If you have an authz'd deployment, please add `-H "Authorization: $JWT_TOKEN"` flags to your `curl` command.
+
+## Library
+
+The `HtsgetConstruct` is [published][htsget-npm] as an NPM package so that it can be used as construct in other projects.
+
+## Local development
+
+This project uses pnpm as the preferred package manager. To install and update the lock file, run:
+
+```sh
+pnpm install
+```
+
+To generate the [config docs][docs-config], run:
+
+```sh
+npx typedoc
+```
+
+[htsget-npm]: https://www.npmjs.com/package/htsget-lambda
+[docs-config]: docs/CONFIG.md
+[htsget-settings]: bin/settings.ts
+[cargo-lambda]: https://github.com/cargo-lambda/cargo-lambda
+[htsget-rs]: https://github.com/umccr/htsget-rs
+[aws-cdk]: https://docs.aws.amazon.com/cdk/v2/guide/getting_started.html
+[cdk-context]: https://docs.aws.amazon.com/cdk/v2/guide/context.html
+[cdk-lookup-value]: https://docs.aws.amazon.com/cdk/api/v2/docs/aws-cdk-lib.aws_ssm.StringParameter.html#static-valuewbrfromwbrlookupscope-parametername
+[cdk-json]: cdk.json
+[aws-ssm]: https://docs.aws.amazon.com/systems-manager/latest/userguide/systems-manager-parameter-store.html
+[aws-api-gateway]: https://docs.aws.amazon.com/apigateway/latest/developerguide/http-api-develop-integrations-lambda.html
+[aws-cognito]: https://docs.aws.amazon.com/cognito/latest/developerguide/cognito-user-identity-pools.html
+[jwt-authorizer]: https://docs.aws.amazon.com/apigateway/latest/developerguide/http-api-jwt-authorizer.html
+[jwt-audience]: https://docs.aws.amazon.com/apigatewayv2/latest/api-reference/apis-apiid-authorizers-authorizerid.html#apis-apiid-authorizers-authorizerid-model-jwtconfiguration
+[route-53]: https://docs.aws.amazon.com/Route53/latest/DeveloperGuide/Welcome.html
+[rust-function]: https://www.npmjs.com/package/rust.aws-cdk-lambda
+[aws-cdk]: https://docs.aws.amazon.com/cdk/v2/guide/getting_started.html
+[aws-cli]: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html
+[npm]: https://docs.npmjs.com/downloading-and-installing-node-js-and-npm
+[rust]: https://www.rust-lang.org/tools/install

bin/htsget-stack.ts

@@ -0,0 +1,31 @@
+import * as cdk from "aws-cdk-lib";
+import { Construct } from "constructs";
+import { HtsgetLambdaProps } from "../index";
+import { SETTINGS } from "./settings";
+import { HtsgetLambda } from "../lib/htsget-lambda";
+
+export class HtsgetStack extends cdk.Stack {
+  constructor(
+    scope: Construct,
+    id: string,
+    settings: HtsgetLambdaProps,
+    props?: cdk.StackProps,
+  ) {
+    super(scope, id, props);
+
+    new HtsgetLambda(this, "HtsgetLambda", settings);
+  }
+}
+
+const app = new cdk.App();
+new HtsgetStack(app, "HtsgetLambdaStack", SETTINGS, {
+  stackName: "HtsgetLambdaStack",
+  description: "A stack deploying htsget-rs with API gateway.",
+  tags: {
+    Stack: "HtsgetLambdaStack",
+  },
+  env: {
+    account: process.env.CDK_DEFAULT_ACCOUNT,
+    region: process.env.CDK_DEFAULT_REGION,
+  },
+});

bin/settings.ts

@@ -1,26 +1,9 @@
-import { HtsgetStatelessSettings } from "../lib/htsget-lambda-construct";
-import { HtsgetStatefulSettings } from "../lib/htsget-lambda-construct";
+import { HtsgetLambdaProps } from "../index";
 
 /**
  * Settings to use for the htsget deployment.
  */
-export const SETTINGS: HtsgetStatelessSettings & HtsgetStatefulSettings = {
-  config: "config/example_deploy.toml",
-  domain: "demo.umccr.org",
-  subDomain: "htsget",
-  s3BucketResources: [],
-  lookupHostedZone: true,
-  createS3Bucket: true,
+export const SETTINGS: HtsgetLambdaProps = {
+  domain: "ga4gh.org",
   copyTestData: true,
-  copyExampleKeys: true,
-  // Override the bucket name.
-  // bucketName: "bucket",
-  jwtAuthorizer: {
-    // Set this to false if you want a private instance.
-    public: true,
-    cogUserPoolId: "", // i.e: ap-southeast-2_iWOHnsurL
-    jwtAudience: [""], // Should match your cognito client id, i.e: 3jgmc7kqaaf8mqbv2sgmujslrp
-  },
-  // Enable additional features for compiling htsget-rs. `s3-storage` is always enabled.
-  features: ["experimental", "aws"], // i.e: Enables Crypt4Gh+htsget functionality
 };

cdk.json

@@ -1,5 +1,5 @@
 {
-  "app": "npx ts-node --prefer-ts-exts bin/htsget-lambda.ts",
+  "app": "npx ts-node --prefer-ts-exts bin/htsget-stack.ts",
   "context": {
     "@aws-cdk-containers/ecs-service-extensions:enableDefaultLogDriver": true,
     "@aws-cdk/aws-apigateway:usagePlanKeyOrderInsensitiveId": true,
@@ -10,10 +10,7 @@
     "@aws-cdk/aws-rds:lowercaseDbIdentifier": true,
     "@aws-cdk/core:checkSecretUsage": true,
     "@aws-cdk/core:stackRelativeExports": true,
-    "@aws-cdk/core:target-partitions": [
-      "aws",
-      "aws-cn"
-    ]
+    "@aws-cdk/core:target-partitions": ["aws", "aws-cn"]
   },
   "watch": {
     "exclude": [
@@ -27,8 +24,6 @@
       "node_modules",
       "test"
     ],
-    "include": [
-      "**"
-    ]
+    "include": ["**"]
   }
 }