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agent_build.yaml
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AWSTemplateFormatVersion: '2010-09-09'
Description: Creates a Bedrock Agent and action group
Parameters:
BedrockModelId:
Type: String
Description: The ID of the Foundation Model to use for the Agent
Default: anthropic.claude-3-sonnet-20240229-v1:0
EnvironmentName:
Type: String
Description: The name of the agent environment, used to differentiate agent application. Must be lowercase, contain one number, and be no more than 5 characters long.
Default: env1
MaxLength: 5
AllowedPattern: ^[a-z]{1,4}[0-9]$
ConstraintDescription: Must be lowercase, contain one number at the end, and be no more than 5 characters long.
GitRepoURL:
Type: String
Default: 'https://github.com/aws-samples/amazon-bedrock-agents-cancer-biomarker-discovery.git'
Description: Git repository URL where the code files are stored
ImageTag:
Type: String
Default: latest
Description: Tag for the Docker image
VectorStoreName:
Type: String
Default: nmcicollection
Description: Name of the vector store/collection
IndexName:
Type: String
Default: vector-index
Description: Name of the vector index to be created
GitBranch:
Type: String
Description: 'The github branch to clone, change only for dev testing'
Default: 'main'
Mappings:
RegionMap:
us-east-1:
PandasLayer: 'arn:aws:lambda:us-east-1:336392948345:layer:AWSSDKPandas-Python312:12'
us-east-2:
PandasLayer: 'arn:aws:lambda:us-east-2:336392948345:layer:AWSSDKPandas-Python312:12'
us-west-1:
PandasLayer: 'arn:aws:lambda:us-west-1:336392948345:layer:AWSSDKPandas-Python312:12'
us-west-2:
PandasLayer: 'arn:aws:lambda:us-west-2:336392948345:layer:AWSSDKPandas-Python312:12'
Resources:
# Create ECR repository
ECRRepository:
Type: AWS::ECR::Repository
Properties:
RepositoryName: lifelines-lambda-sample
EnsureECRImagePushed:
Type: Custom::EnsureECRImagePushed
DependsOn:
- TriggerBuildCustomResource
- TriggerImagingDockerBuild
Properties:
ServiceToken: !GetAtt TriggerBuildLambda.Arn
ECRRepository: !Ref ECRRepository
ImageTag: !Ref ImageTag
EnsureImagingDockerImagePushed:
Type: Custom::EnsureECRImagePushed
DependsOn:
- TriggerBuildCustomResource
- TriggerImagingDockerBuild
Properties:
ServiceToken: !GetAtt TriggerBuildLambda.Arn
ECRRepository: !Ref ImagingECRRepository
ImageTag: !Ref ImageTag
CleanupLambdaFunction:
Type: AWS::Lambda::Function
Properties:
Handler: index.handler
Role: !GetAtt CleanupLambdaRole.Arn
Code:
ZipFile: |
import boto3
import cfnresponse
def delete_ecr_images(repository_name):
ecr = boto3.client('ecr')
paginator = ecr.get_paginator('list_images')
try:
for page in paginator.paginate(repositoryName=repository_name):
if 'imageIds' in page:
ecr.batch_delete_image(
repositoryName=repository_name,
imageIds=page['imageIds']
)
print(f"All images deleted from repository: {repository_name}")
except Exception as e:
print(f"Error deleting images from repository {repository_name}: {str(e)}")
raise
def handler(event, context):
if event['RequestType'] == 'Delete':
try:
# Clean up ECR
ecr = boto3.client('ecr')
for repo_name in [event['ResourceProperties']['ECRRepositoryName'], 'medical-image-processing-smstudio']:
try:
delete_ecr_images(repo_name)
ecr.delete_repository(repositoryName=repo_name)
print(f"Repository {repo_name} deleted successfully")
except ecr.exceptions.RepositoryNotFoundException:
print(f"Repository {repo_name} not found, skipping deletion")
except Exception as e:
print(f"Error deleting repository {repo_name}: {str(e)}")
# Continue with other cleanup tasks even if ECR deletion fails
# Clean up S3
s3 = boto3.resource('s3')
bucket = s3.Bucket(event['ResourceProperties']['S3BucketName'])
bucket.objects.all().delete()
logbucket = s3.Bucket(event['ResourceProperties']['LogBucketName'])
logbucket.objects.all().delete()
cfnresponse.send(event, context, cfnresponse.SUCCESS, {})
except Exception as e:
print(e)
cfnresponse.send(event, context, cfnresponse.FAILED, {})
else:
cfnresponse.send(event, context, cfnresponse.SUCCESS, {})
Runtime: python3.12
Timeout: 300
CleanupLambdaRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: lambda.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: CleanupPolicy
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- 's3:ListBucket'
- 's3:DeleteObject'
Resource:
- !Sub 'arn:aws:s3:::${S3Bucket}'
- !Sub 'arn:aws:s3:::${S3Bucket}/*'
- !Sub 'arn:aws:s3:::${LogBucket}'
- !Sub 'arn:aws:s3:::${LogBucket}/*'
- Effect: Allow
Action:
- 'ecr:ListImages'
- 'ecr:BatchDeleteImage'
- 'ecr:DeleteRepository'
- 'ecr:DescribeRepositories'
Resource:
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/${ECRRepository}'
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/medical-image-processing-smstudio'
- Effect: Allow
Action:
- 'logs:CreateLogGroup'
- 'logs:CreateLogStream'
- 'logs:PutLogEvents'
Resource: !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/lambda/*'
CleanupCustomResource:
Type: Custom::Cleanup
DependsOn:
- S3Bucket
- ECRRepository
Properties:
ServiceToken: !GetAtt CleanupLambdaFunction.Arn
ECRRepositoryName: !Ref ECRRepository
S3BucketName: !Ref S3Bucket
LogBucketName: !Ref LogBucket
S3Bucket:
Type: AWS::S3::Bucket
Properties:
BucketName: !Sub '${EnvironmentName}-${AWS::AccountId}-${AWS::Region}-agent-build-bucket'
BucketEncryption:
ServerSideEncryptionConfiguration:
- ServerSideEncryptionByDefault:
SSEAlgorithm: AES256
LoggingConfiguration:
DestinationBucketName: !Ref LogBucket
LogFilePrefix: 'access-logs/'
#Forces SSL/TLS encryption for all S3 operations on the S3 Bucket
S3BucketPolicy:
Type: AWS::S3::BucketPolicy
Properties:
Bucket: !Ref S3Bucket
PolicyDocument:
Version: '2012-10-17'
Statement:
- Sid: ForceSSLOnlyAccess
Effect: Deny
Principal: '*'
Action: 's3:*'
Resource:
- !Sub '${S3Bucket.Arn}'
- !Sub '${S3Bucket.Arn}/*'
Condition:
Bool:
'aws:SecureTransport': false
LogBucket:
Type: AWS::S3::Bucket
Properties:
BucketName: !Sub '${EnvironmentName}-${AWS::AccountId}-${AWS::Region}-log-bucket'
LogBucketPolicy:
Type: AWS::S3::BucketPolicy
Properties:
Bucket: !Ref LogBucket
PolicyDocument:
Version: '2012-10-17'
Statement:
- Sid: AllowLogDeliveryWrite
Effect: Allow
Principal:
Service: logging.s3.amazonaws.com
Action:
- s3:PutObject
Resource: !Sub '${LogBucket.Arn}/*'
# Create CloudWatch Log Group
CodeBuildLogGroup:
Type: AWS::Logs::LogGroup
Properties:
LogGroupName: !Sub '/aws/codebuild/${AWS::StackName}-DockerPushProject'
RetentionInDays: 14
#Gather Assets for pubmed lambda function, knowledgebase and survival data processing lambda
DataRetrievalLogic:
Type: AWS::CodeBuild::Project
Properties:
Name: DataRetrievalLogic
ServiceRole: !GetAtt DataRetrievalRole.Arn
Artifacts:
Type: NO_ARTIFACTS
LogsConfig:
CloudWatchLogs:
Status: ENABLED
GroupName: !Ref CodeBuildLogGroup
Environment:
Type: LINUX_CONTAINER
ComputeType: BUILD_GENERAL1_SMALL
Image: aws/codebuild/amazonlinux2-x86_64-standard:5.0
PrivilegedMode: true
Source:
Type: GITHUB
Location: !Ref GitRepoURL
BuildSpec: !Sub |
version: 0.2
phases:
pre_build:
commands:
- echo "downloading Ncbi article for KB ingestion"
- yum install -y wget
build:
commands:
- echo "Starting build phase"
- echo "Downloading NCBI article..."
- wget --user-agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749594/pdf/radiol.2017161845.pdf -O ncbi_article.pdf
- echo "Uploading NCBI article to S3..."
- aws s3 cp ncbi_article.pdf s3://${S3Bucket}/ncbi_article.pdf
- echo "NCBI article uploaded to S3"
- echo "Cloning Git repository..."
- git clone -b ${GitBranch} --single-branch ${GitRepoURL} repo
- echo "Zipping Lambda function..."
- cd ActionGroups/matplotbarchartlambda
- echo "Creating list of items to zip..."
- items_to_zip=$(ls -A | tr '\n' ' ')
- zip -r matplotbarchartlambda.zip $items_to_zip
- cd ../..
- echo "Moving zip file to project root..."
- mv ActionGroups/matplotbarchartlambda/matplotbarchartlambda.zip .
- aws s3 cp matplotbarchartlambda.zip s3://${S3Bucket}/matplotbarchartlambda.zip
- cd repo/ActionGroups/pubmed-lambda-function
- echo "Creating list of items to zip..."
- items_to_zip=$(ls -A | tr '\n' ' ')
- echo "Creating zip pubmed lambda file..."
- zip -r pubmed-lambda-function.zip $items_to_zip
- echo "Lambda function zipped"
- cd ../..
- echo "Moving zip file to project root..."
- mv ActionGroups/pubmed-lambda-function/pubmed-lambda-function.zip .
- aws s3 cp pubmed-lambda-function.zip s3://${S3Bucket}/pubmed-lambda-function.zip
- cd ActionGroups/querydatabaselambda
- echo "Creating list of items to zip..."
- items_to_zip=$(ls -A | tr '\n' ' ')
- zip -r querydatabaselambda.zip $items_to_zip
- cd ../..
- echo "Moving zip file to project root..."
- mv ActionGroups/querydatabaselambda/querydatabaselambda.zip .
- aws s3 cp querydatabaselambda.zip s3://${S3Bucket}/querydatabaselambda.zip
- cd ActionGroups/survivaldataprocessinglambda
- echo "Creating list of items to zip..."
- items_to_zip=$(ls -A | tr '\n' ' ')
- zip -r survivaldataprocessinglambda.zip $items_to_zip
- cd ../..
- echo "Moving zip file to project root..."
- mv ActionGroups/survivaldataprocessinglambda/survivaldataprocessinglambda.zip .
- aws s3 cp survivaldataprocessinglambda.zip s3://${S3Bucket}/survivaldataprocessinglambda.zip
- echo "Build phase completed"
- echo "lambda layer preperation phase starts"
- mkdir -p python
- pip install -r lambdalayers/requirements.txt -t python
- zip -r9 lambda-layer.zip python
- aws s3 cp lambda-layer.zip s3://${S3Bucket}/lambda-layer.zip
TimeoutInMinutes: 10
# Log into ECR and push scientific-plots-with-lifelines Docker image
DockerPushLogic:
Type: AWS::CodeBuild::Project
Properties:
Name: DockerPushProject
ServiceRole: !GetAtt DockerPushRole.Arn
Artifacts:
Type: NO_ARTIFACTS
LogsConfig:
CloudWatchLogs:
Status: ENABLED
GroupName: !Ref CodeBuildLogGroup
Environment:
Type: LINUX_CONTAINER
ComputeType: BUILD_GENERAL1_SMALL
Image: aws/codebuild/amazonlinux2-x86_64-standard:5.0
PrivilegedMode: true
Source:
Type: GITHUB
Location: !Ref GitRepoURL
BuildSpec: !Sub |
version: 0.2
phases:
pre_build:
commands:
- echo "Starting pre_build phase"
- echo "Logging into Amazon ECR..."
- aws ecr get-login-password --region ${AWS::Region} | docker login --username AWS --password-stdin ${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com
- echo "ECR login complete"
build:
commands:
- echo "Starting build phase"
- echo "Cloning Git repository..."
- git clone -b ${GitBranch} --single-branch ${GitRepoURL} repo
- cd repo/ActionGroups/scientific-plots-with-lifelines
- echo "Building Docker image..."
- docker build -t lifelines-python3.12-v2 .
- echo "Tagging Docker image..."
- docker tag lifelines-python3.12-v2:latest ${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/${ECRRepository}:${ImageTag}
- echo "Docker image tagged"
post_build:
commands:
- echo "Starting post_build phase"
- echo "Pushing Docker image to ECR..."
- docker push ${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/${ECRRepository}:${ImageTag}
- echo "Docker image pushed to ECR"
- echo "Displaying Docker images"
- docker images
- echo "Displaying ECR repository contents"
- aws ecr list-images --repository-name ${ECRRepository}
TimeoutInMinutes: 10
ImagingECRRepository:
Type: AWS::ECR::Repository
Properties:
RepositoryName: medical-image-processing-smstudio
ImagingDockerBuildProject:
Type: AWS::CodeBuild::Project
Properties:
Artifacts:
Type: NO_ARTIFACTS
Environment:
ComputeType: BUILD_GENERAL1_SMALL
Image: aws/codebuild/amazonlinux2-x86_64-standard:3.0
Type: LINUX_CONTAINER
PrivilegedMode: true
ServiceRole: !GetAtt ImagingDockerBuildRole.Arn
Source:
Type: GITHUB
Location: !Ref GitRepoURL
BuildSpec: !Sub |
version: 0.2
phases:
pre_build:
commands:
- echo Logging in to Amazon ECR...
- aws ecr get-login-password --region ${AWS::Region} | docker login --username AWS --password-stdin ${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com
- echo Cloning the repository...
- git clone -b ${GitBranch} --single-branch ${GitRepoURL} repo
- cd repo/ActionGroups/imaging-biomarker
- echo Checking for required files...
- ls -la
- if [ ! -f requirements.txt ] || [ ! -f dcm2nifti_processing.py ] || [ ! -f radiomics_utils.py ]; then echo "Missing required files"; exit 1; fi
- zip -r Imaginglambdafunction.zip dummy_lambda.py
- echo Copying lambda function
- aws s3 cp Imaginglambdafunction.zip s3://${S3Bucket}/Imaginglambdafunction.zip
build:
commands:
- echo Build started on `date`
- echo Building the Docker image...
- docker build -t ${ImagingECRRepository}:${ImageTag} .
- docker tag ${ImagingECRRepository}:${ImageTag} ${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/${ImagingECRRepository}:${ImageTag}
post_build:
commands:
- echo Build completed on `date`
- echo Pushing the Docker image...
- docker push ${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/${ImagingECRRepository}:${ImageTag}
SourceVersion: main
ImagingStateMachine:
Type: AWS::StepFunctions::StateMachine
Properties:
RoleArn: !GetAtt StepFunctionsExecutionRole.Arn
DefinitionString: !Sub
- |
{
"StartAt": "iterate_over_subjects",
"States": {
"iterate_over_subjects": {
"ItemsPath": "$.Subject",
"MaxConcurrency": 50,
"Type": "Map",
"Next": "Finish",
"Iterator": {
"StartAt": "DICOM/NIfTI Conversion and Radiomic Feature Extraction",
"States": {
"Fallback": {
"Type": "Pass",
"Result": "This iteration failed for some reason",
"End": true
},
"DICOM/NIfTI Conversion and Radiomic Feature Extraction": {
"Type": "Task",
"OutputPath": "$.ProcessingJobArn",
"Resource": "arn:aws:states:::sagemaker:createProcessingJob.sync",
"Retry": [
{
"ErrorEquals": [
"SageMaker.AmazonSageMakerException"
],
"IntervalSeconds": 15,
"MaxAttempts": 8,
"BackoffRate": 1.5
}
],
"Catch": [
{
"ErrorEquals": [
"States.TaskFailed"
],
"Next": "Fallback"
}
],
"Parameters": {
"ProcessingJobName.$": "States.Format('{}-{}', $$.Execution.Input['PreprocessingJobName'], $)",
"ProcessingInputs": [
{
"InputName": "DICOM",
"AppManaged": false,
"S3Input": {
"S3Uri.$": "States.Format('s3://sagemaker-solutions-prod-${AWS::Region}/sagemaker-lung-cancer-survival-prediction/1.1.0/data/nsclc_radiogenomics/{}' , $)",
"LocalPath": "/opt/ml/processing/input",
"S3DataType": "S3Prefix",
"S3InputMode": "File",
"S3DataDistributionType": "FullyReplicated",
"S3CompressionType": "None"
}
}
],
"ProcessingOutputConfig": {
"Outputs": [
{
"OutputName": "CT-Nifti",
"AppManaged": false,
"S3Output": {
"S3Uri": "${S3Bucket}/nsclc_radiogenomics/CT-Nifti",
"LocalPath": "/opt/ml/processing/output/CT-Nifti",
"S3UploadMode": "EndOfJob"
}
},
{
"OutputName": "CT-SEG",
"AppManaged": false,
"S3Output": {
"S3Uri": "${S3Bucket}/nsclc_radiogenomics/CT-SEG",
"LocalPath": "/opt/ml/processing/output/CT-SEG",
"S3UploadMode": "EndOfJob"
}
},
{
"OutputName": "PNG",
"AppManaged": false,
"S3Output": {
"S3Uri": "${S3Bucket}/nsclc_radiogenomics/PNG",
"LocalPath": "/opt/ml/processing/output/PNG",
"S3UploadMode": "EndOfJob"
}
},
{
"OutputName": "CSV",
"AppManaged": false,
"S3Output": {
"S3Uri": "${S3Bucket}/nsclc_radiogenomics/CSV",
"LocalPath": "/opt/ml/processing/output/CSV",
"S3UploadMode": "EndOfJob"
}
}
]
},
"AppSpecification": {
"ImageUri": "${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/${ImagingECRRepository}:${ImageTag}",
"ContainerArguments.$": "States.Array('--subject', $)",
"ContainerEntrypoint": [
"python3",
"/opt/dcm2nifti_processing.py"
]
},
"RoleArn": "${SageMakerExecutionRoleArn}",
"ProcessingResources": {
"ClusterConfig": {
"InstanceCount": 1,
"InstanceType": "ml.m5.xlarge",
"VolumeSizeInGB": 5
}
}
},
"End": true
}
}
}
},
"Finish": {
"Type": "Succeed"
}
}
}
- {
S3Bucket: !Sub "s3://${S3Bucket}",
SageMakerExecutionRoleArn: !GetAtt SageMakerExecutionRole.Arn
}
DataRetrievalRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: codebuild.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: S3Access
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- s3:PutObject
- s3:GetObject
Resource:
- !GetAtt S3Bucket.Arn
- !Sub "${S3Bucket.Arn}/*"
- PolicyName: CloudWatchLogs
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- logs:CreateLogGroup
- logs:CreateLogStream
- logs:PutLogEvents
Resource:
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/codebuild/*'
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/codebuild/*:*'
DockerPushRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: codebuild.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: ECRAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- ecr:GetAuthorizationToken
Resource: '*' # This action requires resource '*'
- Effect: Allow
Action:
- ecr:ListImages
- ecr:BatchCheckLayerAvailability
- ecr:GetDownloadUrlForLayer
- ecr:BatchGetImage
- ecr:InitiateLayerUpload
- ecr:UploadLayerPart
- ecr:CompleteLayerUpload
- ecr:PutImage
Resource:
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/${ECRRepository}'
- PolicyName: CloudWatchLogs
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- logs:CreateLogGroup
- logs:CreateLogStream
- logs:PutLogEvents
Resource:
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/codebuild/*'
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/codebuild/*:*'
- PolicyName: GitCloneAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- codecommit:GitPull
Resource: !Sub 'arn:aws:codecommit:${AWS::Region}:${AWS::AccountId}:${GitRepoURL}'
ImagingDockerBuildRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: codebuild.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: ECRAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- ecr:GetAuthorizationToken
Resource: '*'
- Effect: Allow
Action:
- ecr:ListImages
- ecr:BatchCheckLayerAvailability
- ecr:GetDownloadUrlForLayer
- ecr:BatchGetImage
- ecr:InitiateLayerUpload
- ecr:UploadLayerPart
- ecr:CompleteLayerUpload
- ecr:PutImage
Resource:
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/medical-image-processing-smstudio'
- PolicyName: S3Access
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- s3:PutObject
Resource:
- !Sub "${S3Bucket.Arn}/Imaginglambdafunction.zip"
- PolicyName: CloudWatchLogs
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- logs:CreateLogGroup
- logs:CreateLogStream
- logs:PutLogEvents
Resource:
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/codebuild/*'
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/codebuild/*:*'
StepFunctionsExecutionRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: states.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: StepFunctionsExecutionPolicy
PolicyDocument:
Version: '2012-10-17'
Statement:
# SageMaker permissions
- Effect: Allow
Action:
- 'sagemaker:CreateProcessingJob'
- 'sagemaker:DescribeProcessingJob'
- 'sagemaker:StopProcessingJob'
- 'sagemaker:ListTags'
- 'sagemaker:AddTags'
Resource: !Sub 'arn:aws:sagemaker:${AWS::Region}:${AWS::AccountId}:processing-job/dcm-nifti-*'
# IAM permissions
- Effect: Allow
Action:
- 'iam:PassRole'
Resource: !GetAtt SageMakerExecutionRole.Arn
# Step Functions Map state permissions
- Effect: Allow
Action:
- 'events:PutTargets'
- 'events:PutRule'
- 'events:DescribeRule'
- 'events:DeleteRule'
- 'events:DisableRule'
- 'events:EnableRule'
- 'events:RemoveTargets'
Resource:
- !Sub 'arn:aws:events:${AWS::Region}:${AWS::AccountId}:rule/StepFunctions-Map-*'
- !Sub 'arn:aws:events:${AWS::Region}:${AWS::AccountId}:rule/StepFunctions-*'
# States permissions for Map state
- Effect: Allow
Action:
- 'states:StartExecution'
- 'states:StopExecution'
- 'states:DescribeExecution'
- 'states:CreateStateMachine'
- 'states:DeleteStateMachine'
- 'states:UpdateStateMachine'
- 'states:DescribeStateMachine'
- 'states:DescribeStateMachineForExecution'
- 'states:ListExecutions'
Resource:
- !Sub 'arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:*'
- !Sub 'arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:*:*'
# CloudWatch Logs permissions
- Effect: Allow
Action:
- 'logs:CreateLogDelivery'
- 'logs:GetLogDelivery'
- 'logs:UpdateLogDelivery'
- 'logs:DeleteLogDelivery'
- 'logs:ListLogDeliveries'
- 'logs:PutLogEvents'
- 'logs:PutResourcePolicy'
- 'logs:DescribeResourcePolicies'
- 'logs:DescribeLogGroups'
Resource:
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:*'
- Effect: Allow
Action:
- 'lambda:InvokeFunction'
Resource: !Sub 'arn:aws:lambda:${AWS::Region}:${AWS::AccountId}:function:*'
- PolicyName: EventsPolicy
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- 'events:PutTargets'
- 'events:PutRule'
- 'events:DescribeRule'
Resource:
- !Sub 'arn:aws:events:${AWS::Region}:${AWS::AccountId}:rule/*'
SageMakerExecutionRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: sagemaker.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: SageMakerProcessingAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
# Processing Job Permissions
- Effect: Allow
Action:
- 'sagemaker:CreateProcessingJob'
- 'sagemaker:DescribeProcessingJob'
- 'sagemaker:StopProcessingJob'
- 'sagemaker:ListProcessingJobs'
Resource: !Sub 'arn:aws:sagemaker:${AWS::Region}:${AWS::AccountId}:processing-job/*'
# ECR Access for Container
- Effect: Allow
Action:
- 'ecr:GetAuthorizationToken'
Resource: '*'
- Effect: Allow
Action:
- 'ecr:BatchCheckLayerAvailability'
- 'ecr:GetDownloadUrlForLayer'
- 'ecr:BatchGetImage'
Resource:
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/${ImagingECRRepository}'
- PolicyName: S3Access
PolicyDocument:
Version: '2012-10-17'
Statement:
# Input data access
- Effect: Allow
Action:
- 's3:GetObject'
- 's3:ListBucket'
Resource:
- 'arn:aws:s3:::sagemaker-solutions-prod-*'
- 'arn:aws:s3:::sagemaker-solutions-prod-*/sagemaker-lung-cancer-survival-prediction/*'
# Output data access
- Effect: Allow
Action:
- 's3:PutObject'
- 's3:GetObject'
- 's3:ListBucket'
Resource:
- !Sub 'arn:aws:s3:::${S3Bucket}'
- !Sub 'arn:aws:s3:::${S3Bucket}/nsclc_radiogenomics/*'
- PolicyName: CloudWatchLogsAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- 'logs:CreateLogGroup'
- 'logs:CreateLogStream'
- 'logs:PutLogEvents'
- 'logs:DescribeLogStreams'
Resource:
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/sagemaker/ProcessingJobs:*'
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/sagemaker/ProcessingJobs:log-stream:*'
- PolicyName: KMSAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- 'kms:Decrypt'
- 'kms:GenerateDataKey'
Resource: !Sub 'arn:aws:kms:${AWS::Region}:${AWS::AccountId}:key/*'
Condition:
StringEquals:
'kms:ViaService': !Sub 'sagemaker.${AWS::Region}.amazonaws.com'
- PolicyName: NetworkAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- 'ec2:CreateNetworkInterface'
- 'ec2:CreateNetworkInterfacePermission'
- 'ec2:DeleteNetworkInterface'
- 'ec2:DeleteNetworkInterfacePermission'
- 'ec2:DescribeNetworkInterfaces'
- 'ec2:DescribeVpcs'
- 'ec2:DescribeDhcpOptions'
- 'ec2:DescribeSubnets'
- 'ec2:DescribeSecurityGroups'
Resource: '*'
Condition:
StringEquals:
'aws:RequestedRegion': !Ref 'AWS::Region'
TriggerBuildLambda:
Type: AWS::Lambda::Function
Properties:
Handler: index.handler
Role: !GetAtt TriggerBuildLambdaRole.Arn
Code:
ZipFile: |
import boto3
import cfnresponse
import time
def handler(event, context):
if event['RequestType'] in ['Create', 'Update']:
try:
codebuild = boto3.client('codebuild')
ecr = boto3.client('ecr')
if 'ProjectName' in event['ResourceProperties']:
# This is for TriggerBuildCustomResource
project_name = event['ResourceProperties']['ProjectName']
response = codebuild.start_build(projectName=project_name)
build_id = response['build']['id']
print(f"Build started: {build_id}")
# Wait for build to complete
while True:
build_status = codebuild.batch_get_builds(ids=[build_id])['builds'][0]['buildStatus']
if build_status == 'SUCCEEDED':
print("Build completed successfully")
break
elif build_status in ['FAILED', 'STOPPED', 'TIMED_OUT']:
print(f"Build failed with status: {build_status}")
cfnresponse.send(event, context, cfnresponse.FAILED, {"Error": f"Build failed with status: {build_status}"})
return
time.sleep(10) # Wait for 10 seconds before checking again
cfnresponse.send(event, context, cfnresponse.SUCCESS, {"BuildId": build_id})
elif 'ECRRepository' in event['ResourceProperties']:
# This is for EnsureECRImagePushed
repository_name = event['ResourceProperties']['ECRRepository']
image_tag = event['ResourceProperties']['ImageTag']
# Wait for image to be available in ECR
max_attempts = 30 # Maximum number of attempts
for attempt in range(max_attempts):
try:
ecr.describe_images(repositoryName=repository_name, imageIds=[{'imageTag': image_tag}])
print(f"Image {repository_name}:{image_tag} exists in ECR")
cfnresponse.send(event, context, cfnresponse.SUCCESS, {})
return
except ecr.exceptions.ImageNotFoundException:
if attempt == max_attempts - 1:
print(f"Image {repository_name}:{image_tag} not found in ECR after {max_attempts} attempts")
cfnresponse.send(event, context, cfnresponse.FAILED, {"Error": "Image not found in ECR after maximum attempts"})
return
time.sleep(10) # Wait for 10 seconds before trying again
else:
cfnresponse.send(event, context, cfnresponse.FAILED, {"Error": "Invalid ResourceProperties"})
except Exception as e:
print(f"Error: {str(e)}")
cfnresponse.send(event, context, cfnresponse.FAILED, {"Error": str(e)})
else:
cfnresponse.send(event, context, cfnresponse.SUCCESS, {})
Runtime: python3.8
Timeout: 900
TriggerBuildLambdaRole:
Type: AWS::IAM::Role
Properties:
AssumeRolePolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Principal:
Service: lambda.amazonaws.com
Action: sts:AssumeRole
Policies:
- PolicyName: CodeBuildAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- codebuild:StartBuild
- codebuild:BatchGetBuilds
Resource:
- !GetAtt DockerPushLogic.Arn
- !GetAtt DataRetrievalLogic.Arn
- !Sub 'arn:aws:codebuild:${AWS::Region}:${AWS::AccountId}:project/ImagingDockerBuildProject-*'
- PolicyName: CloudWatchLogs
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action:
- logs:CreateLogGroup
- logs:CreateLogStream
- logs:PutLogEvents
Resource:
- !Sub 'arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/aws/lambda/${AWS::StackName}-TriggerBuildLambda-*'
- PolicyName: ECRDescribeAccess
PolicyDocument:
Version: '2012-10-17'
Statement:
- Effect: Allow
Action: ecr:DescribeImages
Resource:
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/${ECRRepository}'
- !Sub 'arn:aws:ecr:${AWS::Region}:${AWS::AccountId}:repository/medical-image-processing-smstudio'
TriggerBuildCustomResource:
Type: Custom::TriggerBuild