Dependencies Update && Support Samplesheet V2

README.md

@@ -1,6 +1,6 @@
 # samplesheet-check-frontend
 
-This is the front end code for UMCCR samplesheet check.
+This is the frontend code for UMCCR samplesheet check.
 
 The directories:
 - *deploy* - It will contain the AWS cdk cloud infrastructrure. 

buildspec.yml

@@ -2,7 +2,7 @@ version: 0.2
 phases:
   install:
     runtime-versions:
-      nodejs: 14
+      nodejs: 18
     commands:
       - npm i react-scripts
   build:

deploy/README.md

@@ -1,7 +1,6 @@
 # UMCCR client CDK for Samplesheet Check
 
-This cdk will build an AWS cloud infrastructure for the UMCCR samplesheet check. 
-
+This cdk will build an AWS cloud infrastructure for the UMCCR samplesheet check.
 
 The directories:
 - *cdkpipeline* - Contain the stack for the pipeline.
@@ -17,18 +16,17 @@ The directories:
     Setup DNS for the samplesheet check for cloudfront
 
 # Setting up
+It is recommended to create a virtual environment for the app.
 
-It is recomended to create a virtual environment for the app.
-
-To do so please follow the instruction below.
+To do so please follow the instructions below.
 
 Change your directory to the root of this readme file.
 ```
 $ cd deploy
 ```
 Create a virtual environment for the app.
 ```
-$ python3 -m venv .venv
+$ virtualenv .venv --python=python3.11
 ```
 
 After the init process completes and the virtualenv is created, you can use the following
@@ -38,11 +36,6 @@ step to activate your virtualenv.
 $ source .venv/bin/activate
 ```
 
-If you are a Windows platform, you might try this:
-
-```
-% .venv\Scripts\activate.bat
-```
 Once the virtualenv is activated, you can install the required dependencies.
 
 ```

deploy/app.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 import os
 
-from aws_cdk import core as cdk
+from aws_cdk import App
 
 # Import cdk pipeline stack
 from stacks.pipeline_stack import PipelineStack
@@ -42,7 +42,7 @@
     }
 }
 
-app = cdk.App(
+app = App(
     context={
         "app_stage": app_stage,
         "props": props

deploy/cdk.json

@@ -2,18 +2,10 @@
   "app": "python3 app.py",
   "context": {
     "@aws-cdk/aws-apigateway:usagePlanKeyOrderInsensitiveId": true,
-    "@aws-cdk/core:enableStackNameDuplicates": "true",
-    "aws-cdk:enableDiffNoFail": "true",
     "@aws-cdk/core:stackRelativeExports": "true",
-    "@aws-cdk/aws-ecr-assets:dockerIgnoreSupport": true,
-    "@aws-cdk/aws-secretsmanager:parseOwnedSecretName": true,
-    "@aws-cdk/aws-kms:defaultKeyPolicies": true,
-    "@aws-cdk/aws-s3:grantWriteWithoutAcl": true,
     "@aws-cdk/aws-ecs-patterns:removeDefaultDesiredCount": true,
     "@aws-cdk/aws-rds:lowercaseDbIdentifier": true,
-    "@aws-cdk/aws-efs:defaultEncryptionAtRest": true,
     "@aws-cdk/aws-lambda:recognizeVersionProps": true,
-    "@aws-cdk/aws-cloudfront:defaultSecurityPolicyTLSv1.2_2021": true,
     "@aws-cdk/core:newStyleStackSynthesis": true
   }
 }

deploy/requirements.txt

@@ -1,16 +1,2 @@
-aws-cdk.core==1.122.0
-aws-cdk.aws-lambda==1.122.0
-aws-cdk.aws-apigateway==1.122.0
-aws-cdk.aws-cognito==1.122.0
-aws-cdk.aws-route53-targets==1.122.0
-aws-cdk.pipelines==1.122.0
-aws-cdk.aws-ssm==1.122.0
-aws-cdk.aws-codepipeline==1.122.0
-aws-cdk.aws-codepipeline_actions==1.122.0
-aws-cdk.aws-codebuild==1.122.0
-aws-cdk.aws-route53==1.122.0
-aws-cdk.aws-certificatemanager==1.122.0
-aws-cdk.aws-s3==1.122.0
-aws-cdk.aws-iam==1.122.0
-aws-cdk.aws-cloudfront==1.122.0
-aws-cdk.aws-sns==1.122.0
+aws-cdk-lib==2.114.1
+constructs>=10.0.0

deploy/stacks/pipeline_stack.py

@@ -1,9 +1,13 @@
 # importing modules
+from constructs import Construct
 import os
 from aws_cdk import (
+    Stack,
+    Stage,
+    Duration,
+    RemovalPolicy,
     aws_ssm as ssm,
     pipelines,
-    core as cdk,
     aws_codepipeline as codepipeline,
     aws_s3 as s3,
     aws_codepipeline_actions as codepipeline_actions,
@@ -15,8 +19,8 @@
 from stacks.sscheck_front_end_stack import SampleSheetCheckFrontEndStack
 
 
-class SampleSheetCheckFrontEndStage(cdk.Stage):
-    def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
+class SampleSheetCheckFrontEndStage(Stage):
+    def __init__(self, scope: Construct, construct_id: str, **kwargs) -> None:
         super().__init__(scope, construct_id, **kwargs)
 
         app_stage = self.node.try_get_context("app_stage")
@@ -39,9 +43,9 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
 # Class for the CDK pipeline stack
 
 
-class PipelineStack(cdk.Stack):
+class PipelineStack(Stack):
 
-    def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
+    def __init__(self, scope: Construct, construct_id: str, **kwargs) -> None:
         super().__init__(scope, construct_id, **kwargs)
 
         # Defining app stage
@@ -61,7 +65,7 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
             "sscheck-front-end-artifact-bucket",
             bucket_name=props["pipeline_artifact_bucket_name"][app_stage],
             auto_delete_objects=True,
-            removal_policy=cdk.RemovalPolicy.DESTROY,
+            removal_policy=RemovalPolicy.DESTROY,
             block_public_access=s3.BlockPublicAccess.BLOCK_ALL
         )
 
@@ -99,14 +103,10 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
                 input=code_pipeline_source,
                 commands=[
                     "cdk synth",
-                    "mkdir ./cfnnag_output",
-                    "for template in $(find ./cdk.out -type f -maxdepth 2 -name '*.template.json'); do cp $template ./cfnnag_output; done",
-                    "cfn_nag_scan --input-path ./cfnnag_output"
                 ],
                 install_commands=[
                     "cd deploy",
                     "npm install -g aws-cdk",
-                    "gem install cfn-nag",
                     "pip install -r requirements.txt"
                 ],
                 primary_output_directory="deploy/cdk.out"
@@ -137,7 +137,7 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
             description="The project from codebuild to build react project.",
             project_name="SSCheckFrontEndReactBuild",
             environment=codebuild.BuildEnvironment(
-                build_image=codebuild.LinuxBuildImage.STANDARD_5_0
+                build_image=codebuild.LinuxArmBuildImage.AMAZON_LINUX_2_STANDARD_3_0
             )
         )
 
@@ -146,8 +146,10 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
                 actions=["ssm:GetParameter"],
                 effect=iam.Effect.ALLOW,
                 resources=[
-                    "arn:aws:ssm:%s:%s:parameter/sscheck/*" % (self.region, self.account),
-                    "arn:aws:ssm:%s:%s:parameter/data_portal/client/*" % (self.region, self.account)
+                    "arn:aws:ssm:%s:%s:parameter/sscheck/*" % (
+                        self.region, self.account),
+                    "arn:aws:ssm:%s:%s:parameter/data_portal/client/*" % (
+                        self.region, self.account)
                 ]
             )
         )
@@ -229,7 +231,7 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
             project_name="InvalidateSSCheckCDNCache",
             check_secrets_in_plain_text_env_variables=False,
             environment=codebuild.BuildEnvironment(
-                build_image=codebuild.LinuxBuildImage.STANDARD_5_0
+                build_image=codebuild.LinuxArmBuildImage.AMAZON_LINUX_2_STANDARD_3_0
             ),
             build_spec=codebuild.BuildSpec.from_object({
                 "version": "0.2",
@@ -247,8 +249,8 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
                     }
                 }
             }),
-            timeout=cdk.Duration.minutes(5),
-            queued_timeout=cdk.Duration.minutes(5)
+            timeout=Duration.minutes(5),
+            queued_timeout=Duration.minutes(5)
         )
 
         # Add invalidate CDN role

deploy/stacks/sscheck_front_end_stack.py

@@ -1,6 +1,9 @@
 import os
+from constructs import Construct
 from aws_cdk import (
-    core as cdk,
+    Stack,
+    RemovalPolicy,
+    CfnOutput,
     aws_s3 as s3,
     aws_cloudfront as cloudfront,
     aws_ssm as ssm,
@@ -12,9 +15,9 @@
 )
 
 
-class SampleSheetCheckFrontEndStack(cdk.Stack):
+class SampleSheetCheckFrontEndStack(Stack):
 
-    def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
+    def __init__(self, scope: Construct, construct_id: str, **kwargs) -> None:
         super().__init__(scope, construct_id, **kwargs)
 
         # Defining app constants
@@ -64,7 +67,7 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
             "umccr-samplesheet-script",
             bucket_name=bucket_name,
             auto_delete_objects=True,
-            removal_policy=cdk.RemovalPolicy.DESTROY,
+            removal_policy=RemovalPolicy.DESTROY,
             website_index_document="index.html",
             website_error_document="index.html",
             block_public_access=s3.BlockPublicAccess.BLOCK_ALL
@@ -127,7 +130,7 @@ def __init__(self, scope: cdk.Construct, construct_id: str, **kwargs) -> None:
         )
 
         # Cloudformation Distribution_id
-        cdk.CfnOutput(
+        CfnOutput(
             self,
             'CfnOutputCloudFrontDistributionId',
             value=sscheck_cloudfront.distribution_id

get_env.sh

@@ -66,11 +66,10 @@ oauth_redirect_in=$(aws ssm get-parameter --name '/data_portal/client/oauth_redi
 oauth_redirect_out=$(aws ssm get-parameter --name '/data_portal/client/oauth_redirect_out_local' | jq -r .Parameter.Value)
 
 lambda_api_domain=$(aws ssm get-parameter --name '/sscheck/lambda-api-domain' | jq -r .Parameter.Value)
-bucket_name=$(aws ssm get-parameter --name '/sscheck/bucket_name' | jq -r .Parameter.Value)
 
 data_portal_api_domain=$(aws ssm get-parameter --name '/data_portal/backend/api_domain_name' | jq -r .Parameter.Value)
 
-export REACT_APP_BUCKET_NAME=$bucket_name
+export REACT_APP_BUCKET_NAME=org.umccr.dev.sscheck
 export REACT_APP_LAMBDA_API_DOMAIN=$lambda_api_domain
 export REACT_APP_REGION=ap-southeast-2