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| Original file line number | Diff line number | Diff line change |
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| AWSTemplateFormatVersion: 2010-09-09 | ||
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| Description: Sets up an Synthea on Amazon EC2 Instance | ||
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| Parameters: | ||
| InstanceType: | ||
| Type: String | ||
| Description: Instance type for Synth. Default is t2.micro. | ||
| AllowedValues: | ||
| - t3.small | ||
| - t3.medium | ||
| - t3.large | ||
| - t3.xlarge | ||
| - t3.2xlarge | ||
| - m4.large | ||
| - m4.xlarge | ||
| - m4.2xlarge | ||
| - m4.4xlarge | ||
| - m4.10xlarge | ||
| - m4.16xlarge | ||
| - c4.large | ||
| - c4.xlarge | ||
| - c4.2xlarge | ||
| - c4.4xlarge | ||
| - c4.8xlarge | ||
| - r4.large | ||
| - r4.xlarge | ||
| - r4.2xlarge | ||
| - r4.4xlarge | ||
| - r4.8xlarge | ||
| - r4.16xlarge | ||
| - g2.2xlarge | ||
| - g2.8xlarge | ||
| - p2.xlarge | ||
| - p2.8xlarge | ||
| - p2.16xlarge | ||
| - g3.4xlarge | ||
| - g3.8xlarge | ||
| - g3.16xlarge | ||
| ConstraintDescription: Valid instance type in the t23 m4, c4, r4, g2, p2, and g3 families | ||
| Default: t3.large | ||
| LatestAmiId: | ||
| Type: 'AWS::SSM::Parameter::Value<AWS::EC2::Image::Id>' | ||
| Default: '/aws/service/ami-amazon-linux-latest/al2023-ami-kernel-default-x86_64' | ||
| VpcId: | ||
| Type: AWS::EC2::VPC::Id | ||
| Description: VPC this server will reside in | ||
| MyIp: | ||
| Type: String | ||
| Description: Provide your Public IP (you can find your ip address by visiting - https://whatismyipaddress.com/) | ||
| Default: 0.0.0.0/0 | ||
| KeyPair: | ||
| Type: "AWS::EC2::KeyPair::KeyName" | ||
| Description: Amazon EC2 Key Pair | ||
| SubnetId: | ||
| Type: "AWS::EC2::Subnet::Id" | ||
| Description: Subnet ID your instance will launch in. | ||
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| Resources: | ||
| SyntheOutPutS3Bucket: | ||
| Type: 'AWS::S3::Bucket' | ||
| Properties: | ||
| BucketName: !Join | ||
| - '-' | ||
| - - synthea-output | ||
| - !Ref 'AWS::AccountId' | ||
| PublicAccessBlockConfiguration: | ||
| BlockPublicAcls: true | ||
| BlockPublicPolicy: true | ||
| IgnorePublicAcls: true | ||
| RestrictPublicBuckets: true | ||
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| SyntheaInstanceProfile: | ||
| Type: AWS::IAM::InstanceProfile | ||
| Properties: | ||
| Path: / | ||
| Roles: | ||
| - !Ref SyntheaRole | ||
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| SyntheaRole: | ||
| Type: AWS::IAM::Role | ||
| Properties: | ||
| AssumeRolePolicyDocument: | ||
| Version: 2012-10-17 | ||
| Statement: | ||
| - Effect: Allow | ||
| Principal: | ||
| Service: | ||
| - "ec2.amazonaws.com" | ||
| Action: | ||
| - "sts:AssumeRole" | ||
| Policies: | ||
| - PolicyName: "S3InlinePolicy" | ||
| PolicyDocument: | ||
| Version: "2012-10-17" | ||
| Statement: | ||
| - Effect: "Allow" | ||
| Action: ["s3:ListBucket","s3:GetObject","s3:PutObject","s3:DeleteObject"] | ||
| Resource: | ||
| - "arn:aws:s3:::synthea-output*" | ||
| ManagedPolicyArns: | ||
| - "arn:aws:iam::aws:policy/AmazonSSMManagedInstanceCore" | ||
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| SyntheaEC2SecurityGroup: | ||
| Type: AWS::EC2::SecurityGroup | ||
| Properties: | ||
| GroupDescription: Synthea Security Group | ||
| VpcId: !Ref VpcId | ||
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| SecurityGroupIngressMySSH: | ||
| Type: AWS::EC2::SecurityGroupIngress | ||
| Properties: | ||
| Description: "Allow SSH connections from MyIp" | ||
| GroupId: !Ref SyntheaEC2SecurityGroup | ||
| CidrIp: !Sub "${MyIp}" | ||
| IpProtocol: tcp | ||
| FromPort: 22 | ||
| ToPort: 22 | ||
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| SyntheaNetworkInterface: | ||
| Type: AWS::EC2::NetworkInterface | ||
| Properties: | ||
| SubnetId: !Ref SubnetId | ||
| Description: Interface for the Connection | ||
| GroupSet: | ||
| - !Ref SyntheaEC2SecurityGroup | ||
| SourceDestCheck: true | ||
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| SyntheaEC2Instance: | ||
| Type: AWS::EC2::Instance | ||
| Metadata: | ||
| 'AWS::CloudFormation::Init': | ||
| config: | ||
| files: | ||
| /tmp/test.txt: | ||
| content: Hello world! | ||
| mode: '000755' | ||
| owner: root | ||
| group: root | ||
| Properties: | ||
| ImageId: !Ref LatestAmiId | ||
| InstanceType: !Ref InstanceType | ||
| KeyName: !Ref KeyPair | ||
| IamInstanceProfile: !Ref SyntheaInstanceProfile | ||
| NetworkInterfaces: | ||
| - NetworkInterfaceId: !Ref SyntheaNetworkInterface | ||
| DeviceIndex: 0 | ||
| Tags: | ||
| - Key: Name | ||
| Value: Synthea | ||
| UserData: | ||
| Fn::Base64: | | ||
| #!/bin/bash | ||
| cd /home/ec2-user/ | ||
| sudo yum -y install java-17-amazon-corretto-headless | ||
| wget https://github.com/synthetichealth/synthea/releases/download/master-branch-latest/synthea-with-dependencies.jar | ||
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| Outputs: | ||
| PublicIp: | ||
| Value: !GetAtt SyntheaEC2Instance.PublicIp |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| #!/bin/bash | ||
| # This script generates 100 sample patients in the most common output formats | ||
| # and zips them up by type in the ./samples/ subdirectory | ||
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| ./run_synthea -p 100 \ | ||
| --exporter.ccda.export=true \ | ||
| --exporter.fhir.export=true \ | ||
| --exporter.fhir_stu3.export=true \ | ||
| --exporter.fhir_dstu2.export=true \ | ||
| --exporter.csv.export=true \ | ||
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| mkdir samples | ||
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| for type in ccda fhir fhir_stu3 fhir_dstu2 csv | ||
| do | ||
| zip -jr samples/synthea_sample_data_${type}_latest.zip output/${type}/ | ||
| done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| distributionBase=GRADLE_USER_HOME | ||
| distributionPath=wrapper/dists | ||
| distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip | ||
| distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip | ||
| zipStoreBase=GRADLE_USER_HOME | ||
| zipStorePath=wrapper/dists |
Empty file.
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,18 @@ | ||
| #!/usr/bin/env sh | ||
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| ############################################################################## | ||
| ## | ||
| ## Flexporter launcher for UN*X | ||
| ## | ||
| ############################################################################## | ||
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| ARGS= | ||
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| for arg in "$@" | ||
| do | ||
| ARGS=$ARGS\'$arg\', | ||
| # Trailing comma ok, don't need to remove it | ||
| done | ||
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| ./gradlew flexporter -Params="[$ARGS]" | ||
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