Adding notebook support, commit 1

Author: EC2 Default User

DeployChemblOpenTargetsEnv.sh

@@ -4,3 +4,4 @@ cdk deploy BaselineStack --require-approval never
 cdk deploy CoreDataLake --require-approval never
 cdk deploy ChemblStack --require-approval never
 cdk deploy OpenTargetsStack --require-approval never
+cdk deploy AnalyticsStack --require-approval never

bin/aws.ts

@@ -5,6 +5,7 @@ import { BaselineStack } from '../lib/baseline-stack';
 import { DatalakeStack } from '../lib/datalake-stack';
 import { OpenTargetsStack } from '../lib/opentargets-stack';
 import { ChemblStack } from '../lib/chembl-25-stack';
+import { AnalyticsStack } from '../lib/analytics-stack.js';
 import s3 = require('@aws-cdk/aws-s3');
 
 
@@ -32,9 +33,7 @@ const openTargetsStack = new OpenTargetsStack(app, 'OpenTargetsStack', {
     dataLakeBucket: coreDataLake.DataLakeBucket
 });
 
+const analyticsStack = new AnalyticsStack(app, 'AnalyticsStack', {
+    targetVpc: baseline.Vpc
+});
 
-// new OpenTargetsStack(app, 'OpenTargetsStack', {
-//     dataLakeBucket: coreDataLake.DataLakeBucket,
-//     sourceBucket:  s3.Bucket.fromBucketName(app, 'openTargetsImportBucket', 'chembl-opentarget-blog'),
-//     sourceBucketDataPrefix: '/opentargets/sourceExports/19.11/output',
-// });

lib/analytics-stack.ts

@@ -0,0 +1,55 @@
+import * as cdk from '@aws-cdk/core';
+import ec2 = require('@aws-cdk/aws-ec2');
+import iam = require('@aws-cdk/aws-iam');
+import rds = require('@aws-cdk/aws-rds');
+import glue = require('@aws-cdk/aws-glue');
+import s3 = require('@aws-cdk/aws-s3');
+import s3assets = require('@aws-cdk/aws-s3-assets');
+import sagemaker = require('@aws-cdk/aws-sagemaker');
+
+export interface AnalyticsStackProps extends cdk.StackProps{
+    targetVpc: ec2.Vpc
+}
+
+
+export class AnalyticsStack extends cdk.Stack {
+  
+  constructor(scope: cdk.Construct, id: string, props: AnalyticsStackProps) {
+    super(scope, id, props);
+    
+    
+    const notebookSg = new ec2.SecurityGroup(this, 'notebookSg',{
+       vpc: props.targetVpc
+    });
+    
+    
+    const lifecycleCode = [
+            {"content": "echo hello" }
+        ];
+    const sageMakerIntanceLifecyclePolicy = new sagemaker.CfnNotebookInstanceLifecycleConfig(this, 'notebookLifecyclePolicy', {
+        notebookInstanceLifecycleConfigName: "Boostrap-Chembl-OpenTargets-Demo-Notebook",
+        onStart: lifecycleCode
+        
+    });
+    
+    const  sageMakerInstanceRole = new iam.Role(this, 'notebookInstanceRole', {
+        roleName: "chemblOpenTargetsNotebookRole",
+        assumedBy: new iam.ServicePrincipal('sagemaker')
+    });
+    
+    
+    new sagemaker.CfnNotebookInstance(this, 'analyticsNotebook', {
+        instanceType : 'ml.t2.medium',
+        volumeSizeInGb: 100,
+        securityGroupIds: [notebookSg.securityGroupId],
+        subnetId: props.targetVpc.selectSubnets({subnetType: ec2.SubnetType.PRIVATE}).subnetIds[0],
+        notebookInstanceName: "Chembl-OpenTargets-Demo-Notebook",
+        roleArn: sageMakerInstanceRole.roleArn,
+        directInternetAccess: 'Disabled',
+        lifecycleConfigName: sageMakerIntanceLifecyclePolicy.notebookInstanceLifecycleConfigName
+    });
+ 
+    
+  }
+}
+

lib/baseline-stack.ts

@@ -15,6 +15,7 @@ export class BaselineStack extends cdk.Stack {
     public readonly chemblDBChemblDbAccessSg: ec2.SecurityGroup;
     public readonly chemblDBSecret: rds.DatabaseSecret; 
     public readonly OpenTargetsSourceBucket: s3.Bucket; 
+    public readonly Vpc: ec2.Vpc;
 
     constructor(scope: cdk.Construct, id: string, props?: cdk.StackProps) {
 
@@ -41,6 +42,8 @@ export class BaselineStack extends cdk.Stack {
             ]
         });    
 
+        this.Vpc = baselineVpc;
+        
         const chemblAccessSG = new ec2.SecurityGroup(this, 'chemblAccessSg', {
             vpc: baselineVpc,
             allowAllOutbound: true,

lib/chembl-25-stack.ts

@@ -22,7 +22,7 @@ export class ChemblStack extends cdk.Stack{
 
 		const dataSetName = "chembl_25";
 
-	    new RDSPostgresDataSetEnrollment(this, 'chembl-25-enrollment', {
+	    const chembl25 = new RDSPostgresDataSetEnrollment(this, 'chembl-25-enrollment', {
 	    	databaseSecret: props.databaseSecret,
 	    	database: props.database,
 	    	accessSecurityGroup: props.accessSecurityGroup,
@@ -39,7 +39,6 @@ export class ChemblStack extends cdk.Stack{
 				"--DL_REGION": cdk.Stack.of(this).region,
 				"--GLUE_SRC_DATABASE": "chembl_25_src"
 			}	    	
-	    
 	    });
 	}
 }

package.json

@@ -21,11 +21,12 @@
     "typescript": "~3.7.2"
   },
   "dependencies": {
-    "@aws-cdk/aws-cloudformation": "^1.26.0",
-    "@aws-cdk/aws-ec2": "^1.26.0",
-    "@aws-cdk/aws-glue": "^1.26.0",
-    "@aws-cdk/aws-rds": "^1.26.0",
-    "@aws-cdk/core": "^1.26.0",
+    "@aws-cdk/aws-cloudformation": "^1.32.0",
+    "@aws-cdk/aws-ec2": "^1.32.0",
+    "@aws-cdk/aws-glue": "^1.32.0",
+    "@aws-cdk/aws-rds": "^1.32.0",
+    "@aws-cdk/aws-sagemaker": "^1.32.0",
+    "@aws-cdk/core": "^1.32.0",
     "source-map-support": "^0.5.16"
   }
 }