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upgrade_atlas_webapi.yaml
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# Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You may not use this file except in compliance with the License.
# A copy of the License is located at
# http://aws.amazon.com/apache2.0/
# or in the "license" file accompanying this file. This file is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
# either express or implied. See the License for the specific language governing permissions and limitations under the License.
AWSTemplateFormatVersion: '2010-09-09'
Description: This CloudFormation Template deploys a complete OHDSI environment. It
depends on the OHDSI-VPC CloudFormation Template.
Metadata:
AWS::CloudFormation::Interface:
ParameterGroups:
- Label:
default: General AWS
Parameters:
- EC2KeyName
- Label:
default: New Atlas and WebAPI Versions
Parameters:
- Atlasv
- WebAPIv
- Label:
default: Existing Elastic Beanstalk Configuration
Parameters:
- SubnetAppA
- SGApp
- EBBucket
- EBEndpoint
- EBEnvironmentId
- Label:
default: DNS and SSL
Parameters:
- UseRoute53Boolean
- UseACMBoolean
- HostedZoneId
- HostedZoneName
- DomainName
- Label:
default: Database Tier
Parameters:
- DatabaseMasterPassword
- RDSEndpoint
- RedshiftEndpoint
ParameterLabels:
EC2KeyName:
default: EC2 Key Pair
AccessCidr:
default: Limit access to IP address range?
EBEndpoint:
default: Elastic Beanstalk Endpoint Name
UseRoute53Boolean:
default: Use Route 53?
UseACMBoolean:
default: Use AWS Certificate Manager?
HostedZoneId:
default: Route53 Hosted Zone ID
HostedZoneName:
default: Hosted Zone
DomainName:
default: Site Domain
DatabaseMasterPassword:
default: 'Aurora Postgres and Redshift master password'
Atlasv:
default: Atlas Version
WebAPIv:
default: WebAPI Version
SubnetAppA:
default: An existing Elastic Beanstalk Atlas / WebAPI subnet
SGApp:
default: The existing Elastic Beanstalk Atlas / WebAPI Security Group
Parameters:
EBEndpoint:
Description: "The unique name to use for your Elastic Beanstalk URL (will be rendered http://(EBEndpoint).(region).elasticbeanstalk.com)"
Type: String
UseRoute53Boolean:
AllowedValues:
- true
- false
Default: false
Description: Specifies whether a record set should be created in Route 53 for your REDCap domain name. If not, you will recieve a default Elastic Beanstalk DNS name (e.g. redcap.us-east-1.elasticbeanstalk.com).
Type: String
UseACMBoolean:
AllowedValues:
- true
- false
Default: false
Description: Specifies whether an SSL certificate should be generated for your domain name using AWS Certificate Manager (ACM). If one is not generated, HTTP will be used and an SSL certificate can be applied after deployment.
Type: String
HostedZoneName:
Type: String
Description: "The hosted zone that will be used by your application. If using the Elastic Beanstalk provided hosted zone in us-east-1, just accept the default value."
DomainName:
AllowedPattern: ^$|(([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9\-]*[a-zA-Z0-9])\.)*([A-Za-z0-9]|[A-Za-z0-9][A-Za-z0-9\-]*[A-Za-z0-9])$
Description: '[ Optional, only if using Route53 ] The sub-domain name of the Project REDCap site. This sub-domain will be prepended your specified Hosted Zone (e.g. redcap in redcap.example.edu).'
Type: String
DatabaseMasterPassword:
Description: Must be letters (upper or lower), numbers, spaces, and these special characters `~#$%^&*()_+,-
Type: String
NoEcho: true
AllowedPattern: ^([a-zA-Z0-9`~#$%^&*()_+,\\-])*$
ConstraintDescription: The Amazon RDS master password. Letters, numbers, spaces, and these special characters `~#$%^&*()_+,-
Atlasv:
Description: The OHDSI Atlas GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v2.6.0'
WebAPIv:
Description: OHDSI WebAPI GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v2.6.0'
EC2KeyName:
Description: The EC2 Key Pair to use for the Atlas/WebAPI EC2 Instances.
Type: AWS::EC2::KeyPair::KeyName
SubnetAppA:
Type: AWS::EC2::Subnet::Id
SGApp:
Type: AWS::EC2::SecurityGroup::Id
RDSEndpoint:
Type: String
RedshiftEndpoint:
Type: String
EBBucket:
Type: String
Description: 'S3 Bucket used to store the application package for Elastic Beanstalk.'
EBEnvironmentId:
Type: String
Description: 'ID of the Atlas/WebAPI Elastic Beanstalk environment to upgrade. (ex. e-jsvxakmis5)'
#Mapping to find the Amazon Linux AMI in each region. This AMI is used for the temporary EC2 server.
Mappings:
RegionMap:
us-east-1:
AMI: ami-cfe4b2b0
us-east-2:
AMI: ami-40142d25
us-west-1:
AMI: ami-0e86606d
us-west-2:
AMI: ami-0ad99772
ca-central-1:
AMI: ami-03e86a67
eu-west-1:
AMI: ami-e4515e0e
eu-west-2:
AMI: ami-b2b55cd5
eu-west-3:
AMI: ami-d50bbaa8
eu-central-1:
AMI: ami-a058674b
sa-east-1:
AMI: ami-83d58fef
ap-south-1:
AMI: ami-5a8da735
ap-southeast-1:
AMI: ami-ed838091
ap-southeast-2:
AMI: ami-33f92051
ap-northeast-1:
AMI: ami-9c9443e3
ap-northeast-2:
AMI: ami-ebc47185
ap-northeast-3:
AMI: ami-09b8b674
Conditions:
DeployRoute53:
!Equals [ true, !Ref UseRoute53Boolean ]
DeployACM: !And
- !Equals [ true, !Ref UseACMBoolean ]
- !Condition DeployRoute53
NotDeployACM: !Or
- !Equals [ false, !Ref UseACMBoolean ]
- !Equals [ false, !Ref UseRoute53Boolean ]
Resources:
#IAM Roles for the temporary EC2 server to compile Atlas and WebAPI, apply the database DDLs, load the sample data, and run Achilles
EC2Role:
Type: AWS::IAM::Role
Properties:
ManagedPolicyArns:
- "arn:aws:iam::aws:policy/service-role/AmazonEC2RoleforSSM"
AssumeRolePolicyDocument:
Statement:
- Effect: Allow
Principal:
Service:
- ec2.amazonaws.com
Action:
- sts:AssumeRole
Path: /
EC2RolePolicies:
Type: AWS::IAM::Policy
Properties:
PolicyName: root
PolicyDocument:
Statement:
- Effect: Allow
Action:
- "s3:*"
Resource:
- !Join [ "", [ 'arn:aws:s3:::', !Ref "EBBucket" ] ]
- !Join [ "", [ 'arn:aws:s3:::', !Ref "EBBucket", '/*' ] ]
- !Join
- ''
- - 'arn:aws'
- ':s3:::elasticbeanstalk-*-'
- !Ref 'AWS::AccountId'
- !Join
- ''
- - 'arn:aws'
- ':s3:::elasticbeanstalk-*-'
- !Ref 'AWS::AccountId'
- /*
- !Join
- ''
- - 'arn:aws'
- ':s3:::elasticbeanstalk-*-'
- !Ref 'AWS::AccountId'
- '-*'
- !Join
- ''
- - 'arn:aws'
- ':s3:::elasticbeanstalk-*-'
- !Ref 'AWS::AccountId'
- '-*/*'
- Effect: Allow
Action:
- "elasticbeanstalk:RestartAppServer"
- "elasticbeanstalk:ListAvailableSolutionStacks"
- "elasticbeanstalk:DescribeEnvironmentResources"
- "elasticloadbalancing:RegisterTargets"
- "elasticloadbalancing:DescribeTargetGroups"
- "elasticloadbalancing:DescribeLoadBalancers"
- "elasticloadbalancing:DescribeListeners"
- "elasticloadbalancing:CreateRule"
- "elasticloadbalancing:DescribeRules"
- "autoscaling:DescribeAutoScalingGroups"
- "cloudformation:DescribeStackResources"
- "cloudformation:DescribeStackResource"
Resource:
- '*'
- Effect: Allow
Action:
- 'logs:CreateLogGroup'
- 'logs:CreateLogStream'
- 'logs:PutLogEvents'
- 'logs:DescribeLogStreams'
Resource: 'arn:aws:logs:*:*:*'
- Sid: CreateNewEBVersion
Action:
- 'elasticbeanstalk:RetrieveEnvironmentInfo'
- "elasticbeanstalk:DescribeEnvironments"
- "elasticbeanstalk:DescribeEvents"
- "elasticbeanstalk:DescribeConfigurationOptions"
- "elasticbeanstalk:DescribeInstancesHealth"
- "elasticbeanstalk:DescribeApplicationVersions"
- "elasticbeanstalk:DescribeEnvironmentHealth"
- "elasticbeanstalk:DescribeApplications"
- "elasticbeanstalk:ListPlatformVersions"
- "elasticbeanstalk:DescribeEnvironmentResources"
- "elasticbeanstalk:DescribeEnvironmentManagedActions"
- "elasticbeanstalk:RequestEnvironmentInfo"
- "elasticbeanstalk:DescribeEnvironmentManagedActionHistory"
- "elasticbeanstalk:CreateApplicationVersion"
- "elasticbeanstalk:ValidateConfigurationSettings"
- "elasticbeanstalk:DescribeConfigurationSettings"
- "elasticbeanstalk:CheckDNSAvailability"
- "elasticbeanstalk:ListAvailableSolutionStacks"
- "elasticbeanstalk:DescribePlatformVersion"
- "elasticbeanstalk:UpdateEnvironment"
- "cloudformation:GetTemplate"
- 'cloudformation:DescribeStackResources'
- 'cloudformation:DescribeStackResource'
- "autoscaling:DescribeAutoScalingGroups"
- "autoscaling:SuspendProcesses"
- "autoscaling:DescribeScalingActivities"
- "autoscaling:ResumeProcesses"
- "elasticloadbalancing:DescribeTargetGroups"
- "elasticloadbalancing:RegisterTargets"
Effect: Allow
Resource: '*'
Roles:
- !Ref 'EC2Role'
EC2InstanceProfile:
Type: AWS::IAM::InstanceProfile
Properties:
Path: /
Roles:
- !Ref 'EC2Role'
# This is a temporary EC2 server used to add the necessary Elastic Beanstalk scripts to the Project REDCap source code zip file.
TempEC2Instance:
Type: AWS::EC2::Instance
Metadata:
AWS::CloudFormation::Init:
config:
files:
/etc/awslogs/awslogs.conf:
content: !Sub |
[general]
state_file = /var/lib/awslogs/agent-state
[ohdsi-build-log]
file = /tmp/log.txt
log_group_name = ohdsi-temporary-ec2-instnace-build-log
log_stream_name = ${EBEndpoint}-${AWS::StackName}-build-log
mode: 000664
owner: root
group: root
/etc/awslogs/awscli.conf:
content: !Sub |
[plugins]
cwlogs = cwlogs
[default]
region = ${AWS::Region}
mode: 000664
owner: root
group: root
/tmp/upgrade_ohdsi.sh:
content: !Sub |
# This script configures the CFN deployed environment for OHDSI WebAPI and Atlas
#
# Requirements:
# $RDS_ENDPOINT must contain the endpoint of the Postgres Aurora RDS environment to be used to store the WebAPI application data
# $EB_ENDPOINT must contain the endpoint of the Elastic Beanstalk Tomcat environment
# $REDSHIFT_ENDPOINT must contain the endpoint of the Redshift Cluster used for OMOP CDM and Vocabulary
# $BUCKET_NAME must contain the s3 bucket name in which Elastic Beanstalk will look for the ohdsi-webapi-atlas.zip file
# $DATABASE_PASSWORD must contain the password that was used for the master accounts for Redshift and RDS Aurora Postgres
echo "RDS_ENDPOINT=" $RDS_ENDPOINT
echo "EB_ENDPOINT=" $EB_ENDPOINT
echo "REDSHIFT_ENDPOINT=" $REDSHIFT_ENDPOINT
echo "BUCKET_NAME=" $BUCKET_NAME
echo "DATABASE_PASSWORD=" $DATABASE_PASSWORD
export APPLICATION_NAME=$(aws elasticbeanstalk describe-environments --region $REGION --environment-ids $ENVIRONMENT_ID --query 'Environments[0].ApplicationName' --output text)
#Download build tools and compile WebAPI
curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.32.0/install.sh | bash
export NVM_DIR="/root/.nvm"
[ -s "$NVM_DIR/nvm.sh" ] && . "$NVM_DIR/nvm.sh"
nvm install 11.11.0
sudo wget http://repos.fedorapeople.org/repos/dchen/apache-maven/epel-apache-maven.repo -O /etc/yum.repos.d/epel-apache-maven.repo
sudo sed -i s/\$releasever/6/g /etc/yum.repos.d/epel-apache-maven.repo
sudo yum install -y apache-maven
sudo yum install -y java-1.8.0
sudo yum install -y java-1.8.0-openjdk-devel
export JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk
mv settings.xml ./WebAPI/
cd WebAPI
mvn clean package -s settings.xml -P webapi-postgresql -DskipTests=true
cd ..
cp ./WebAPI/target/WebAPI.war .
#Build Atlas "war" file to put at the root URL of the Tomcat server
mv config-local.js ./Atlas/js/
cd Atlas
npm config set strict-ssl false
npm run build
zip -r ../ROOT.war *
cd ..
zip -r ohdsi-webapi-atlas-${Atlasv}.zip ROOT.war WebAPI.war .ebextensions
aws s3 cp ohdsi-webapi-atlas-${Atlasv}.zip s3://$BUCKET_NAME
aws elasticbeanstalk create-application-version --region $REGION --application-name $APPLICATION_NAME --version-label ohdsi-webapi-atlas-${Atlasv}-${AWS::StackName} --source-bundle S3Bucket=$BUCKET_NAME,S3Key=ohdsi-webapi-atlas-${Atlasv}.zip
aws elasticbeanstalk update-environment --region $REGION --environment-id $ENVIRONMENT_ID --version-label ohdsi-webapi-atlas-${Atlasv}-${AWS::StackName}
mode: 000777
owner: root
group: root
/tmp/settings.xml:
content: !Sub |
<settings>
<profiles>
<profile>
<id>webapi-postgresql</id>
<properties>
<datasource.driverClassName>org.postgresql.Driver</datasource.driverClassName>
<datasource.url>jdbc:postgresql://${RDSEndpoint}:5432/OHDSI?ssl=true&sslfactory=org.postgresql.ssl.NonValidatingFactory</datasource.url>
<datasource.username>ohdsi_app_user</datasource.username>
<datasource.password>app1</datasource.password>
<datasource.dialect>postgresql</datasource.dialect>
<datasource.ohdsi.schema>webapi</datasource.ohdsi.schema>
<flyway.datasource.driverClassName>${!datasource.driverClassName}</flyway.datasource.driverClassName>
<flyway.datasource.url>${!datasource.url}</flyway.datasource.url>
<flyway.datasource.username>ohdsi_admin_user</flyway.datasource.username>
<flyway.datasource.password>admin1</flyway.datasource.password>
<flyway.locations>classpath:db/migration/postgresql</flyway.locations>
<security.enabled>false</security.enabled>
<security.token.expiration>43200</security.token.expiration>
<security.origin>*</security.origin>
<security.ssl.enabled>false</security.ssl.enabled>
<security.oauth.callback.ui>http://localhost/atlas/#/welcome</security.oauth.callback.ui>
<security.oauth.callback.api>http://localhost:8080/WebAPI/user/oauth/callback</security.oauth.callback.api>
<security.oauth.google.apiKey></security.oauth.google.apiKey>
<security.oauth.google.apiSecret></security.oauth.google.apiSecret>
<security.oauth.facebook.apiKey></security.oauth.facebook.apiKey>
<security.oauth.facebook.apiSecret></security.oauth.facebook.apiSecret>
</properties>
</profile>
</profiles>
</settings>
mode: 000664
owner: root
group: root
/tmp/config-local.js:
content: !Sub
- |
define([], function () {
var configLocal = {};
configLocal.api = {
name: 'My Organization Name',
url: '${Protocol}${RCDomainName}.${HostedZone}/WebAPI/'
};
return configLocal;
});
- { Protocol: !If [ DeployACM, 'https://', 'http://' ], RCDomainName: !If [DeployRoute53, !Ref DomainName, !Ref EBEndpoint], HostedZone: !If [DeployRoute53, !Ref HostedZoneName, !Join ['.', [!Ref 'AWS::Region', 'elasticbeanstalk.com']]] }
mode: 000664
owner: root
group: root
/tmp/.ebextensions/httpd/conf.d/ssl.conf:
content: |
LoadModule ssl_module modules/mod_ssl.so
Listen 443
<VirtualHost *:443>
<Proxy *>
Require all granted
</Proxy>
SSLEngine on
SSLCertificateFile "/etc/pki/tls/certs/server.crt"
SSLCertificateKeyFile "/etc/pki/tls/certs/server.key"
SSLCipherSuite EECDH+AESGCM:EDH+AESGCM:AES256+EECDH:AES256+EDH
SSLProtocol All -SSLv2 -SSLv3
SSLHonorCipherOrder On
SSLSessionTickets Off
Header always set Strict-Transport-Security "max-age=63072000; includeSubdomains; preload"
Header always set X-Content-Type-Options nosniff
ProxyPass / http://localhost:80/ retry=0
ProxyPassReverse / http://localhost:80/
ProxyPreserveHost on
RequestHeader set X-Forwarded-Proto "https" early
</VirtualHost>
mode: 000500
owner: root
group: root
/tmp/.ebextensions/00HIPAA.config:
content: |
packages:
yum:
mod24_ssl : []
commands:
00mountencrypted:
command: |
#Create an encrypted EBS volume and mount it to store the HTTPD access_log and error_log. Just in case PHI is written to these logs in error messages.
mount='/var/log/tomcat8'
if grep -qs "$mount" /proc/mounts; then
echo "encrypted volume already mounted ..."
else
awszone=$(curl -s http://169.254.169.254/latest/meta-data/placement/availability-zone)
awsregion=${awszone::-1}
device='/dev/sdh'
instanceId=$(curl -s http://169.254.169.254/latest/meta-data/instance-id)
createJson=$(aws ec2 create-volume --size 4 --region $awsregion --availability-zone $awszone --volume-type standard --encrypted)
volumeId=$(echo $createJson | sed -n 's/.*"VolumeId": "\(.*\)",/\1/p' | cut -d '"' -f 1)
aws ec2 wait volume-available --region $awsregion --volume-ids $volumeId
aws ec2 attach-volume --volume-id $volumeId --instance-id $instanceId --device $device --region $awsregion
aws ec2 wait volume-in-use --region $awsregion --volume-ids $volumeId
aws ec2 modify-instance-attribute --instance-id $instanceId --block-device-mappings DeviceName=$device,Ebs={DeleteOnTermination=true} --region $awsregion
while [ `stat ${device} 2>/dev/null 1>&2; echo $?` -ne 0 ]; do
sleep 1
done
mkfs -t ext3 $device
mkdir /tmp/mnt
cp -a $mount /tmp/mnt
mount $device $mount
cp -a /tmp/mnt $mount
chown tomcat.tomcat /var/log/tomcat8
fi
ignoreErrors: false
01SelfSignedSSL:
command: |
#Generate a self-signed cert to be used between the AWS ALB and the Apache PHP servers.
if [ ! -f /etc/pki/tls/certs/server.key ]; then
openssl genrsa 2048 > server.key
openssl req -new -key server.key -out csr.pem -subj "/C=US/ST=WA/L=Seattle/O=anon/OU=anon/CN=none/emailAddress=none"
openssl x509 -req -days 365 -in csr.pem -signkey server.key -out server.crt
cp server.crt server.key /etc/pki/tls/certs/
rm -f server.crt server.key csr.pem
else
echo "Already have a self-signed private key. This must be an application redeployment"
fi
02InstallSSMClient:
command: |
# Install SSM client
yum install -y https://s3.amazonaws.com/ec2-downloads-windows/SSMAgent/latest/linux_amd64/amazon-ssm-agent.rpm
restart amazon-ssm-agent
mode: 000500
owner: root
group: root
Properties:
InstanceInitiatedShutdownBehavior: 'terminate'
InstanceType: 't2.medium'
KeyName: !Ref 'EC2KeyName'
ImageId: !FindInMap
- RegionMap
- !Ref 'AWS::Region'
- AMI
IamInstanceProfile: !Ref EC2InstanceProfile
SecurityGroupIds:
- !Ref SGApp
SubnetId: !Ref SubnetAppA
UserData:
Fn::Base64: !Sub |
#!/bin/bash
export RDS_ENDPOINT=${RDSEndpoint}
export EB_ENDPOINT=${EBEndpoint}.${AWS::Region}.elasticbeanstalk.com
export REDSHIFT_ENDPOINT=${RedshiftEndpoint}
export BUCKET_NAME=${EBBucket}
export DATABASE_PASSWORD=${DatabaseMasterPassword}
export AWS_DEFAULT_REGION=${AWS::Region}
export REGION=${AWS::Region}
export ENVIRONMENT_ID=${EBEnvironmentId}
yum update -y aws-cli
yum install -y awslogs git
yum install -y https://s3.amazonaws.com/ec2-downloads-windows/SSMAgent/latest/linux_amd64/amazon-ssm-agent.rpm
restart amazon-ssm-agent
#Use cfn-init to grab and apply the files specified in the above UserData
/opt/aws/bin/cfn-init --verbose --stack ${AWS::StackName} --resource TempEC2Instance --region ${AWS::Region}
cd /tmp
git clone -b ${Atlasv} https://github.com/OHDSI/Atlas
git clone -b ${WebAPIv} https://github.com/OHDSI/WebAPI
sudo service awslogs start
aws s3 mb s3://${EBBucket}
sudo -E bash ./upgrade_ohdsi.sh &>> log.txt
aws s3 cp log.txt s3://$BUCKET_NAME
#Shutdown and terminate this temporary instance
sleep 20
#shutdown -h now