02-rc-elasticbeanstalk.yaml

# 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 REDCap environment.  It
  depends on the REDCap-vpc CloudFormation Template.

Parameters:
  SESUsername:
    Type: String
    Description: Username to use for authentication to SES.
  SESPassword:
    Type: String
    Description: Username to use for authentication to SES.
    NoEcho: true
  SESRegion:
    Type: String
    AllowedValues:
      - us-east-2
      - us-east-1
      - us-west-1
      - us-west-2
      - af-south-1
      - ap-south-1
      - ap-northeast-1
      - ap-northeast-2
      - ap-northeast-3
      - ap-southeast-1
      - ap-southeast-2
      - ca-central-1
      - eu-central-1
      - eu-west-1
      - eu-west-2
      - eu-west-3
      - eu-north-1
      - sa-east-1
      - us-gov-west-1
    Description: Region where you configured your SES credentials.
  S3AccessKey:
    Type: String
    NoEcho: True
    Description: S3 Access Key to use to access REDCap File Repository Bucket
  S3SecretKey:
    Type: String
    NoEcho: True
    Description: S3 Access Key to use to access REDCap File Repository Bucket
  MultiAZDatabase:
    AllowedValues:
      - true
      - false
    Default: false
    Description: Specifies whether a to deploy the AWS Aurora MySQL Database in Multi-AZ configuration.
    Type: String
  DatabaseInstanceType:
    AllowedValues:
      - db.t3.small
      - db.t3.medium
      - db.t3.large
      - db.r5.large
      - db.r5.xlarge
      - db.r5.2xlarge
      - db.r5.4xlarge
      - db.r5.8xlarge
      - db.r5.16xlarge
      - db.r5.24xlarge
    ConstraintDescription: Must be a valid RDS instance class.
    Default: db.t3.small
    Description: The Amazon RDS database instance class.
    Type: String
  WebAsgMax:
    AllowedPattern: ^((?!0$)[1-2]?[0-9]|30)$
    ConstraintDescription: Must be a number between 1 and 30.
    Default: 1
    Description: Specifies the maximum number of EC2 instances in the Web Autoscaling Group.
    Type: String
  WebAsgMin:
    AllowedPattern: ^([0-0]?[0-9]|10)$
    ConstraintDescription: Must be a number between 0 and 10.
    Default: 1
    Description: Specifies the minimum number of EC2 instances in the Web Autoscaling Group.
    Type: String
  WebInstanceType:
    AllowedValues:
      - t3.nano
      - t3.micro
      - t3.small
      - t3.medium
      - t3.large
      - t3.xlarge
      - t3.2xlarge
      - m5.large 
      - m5.xlarge 
      - m5.2xlarge 
      - m5.4xlarge 
      - m5.12xlarge 
      - m5.24xlarge 
      - c5.large 
      - c5.xlarge 
      - c5.2xlarge 
      - c5.4xlarge 
      - c5.9xlarge 
      - c5.18xlarge
      - r5.large
      - r5.xlarge
      - r5.2xlarge
      - r5.4xlarge
      - r5.8xlarge
      - r5.16xlarge
      - r5.24xlarge
    ConstraintDescription: Must be a valid Amazon EC2 instance type.
    Default: t3.micro
    Description: The Amazon EC2 instance type for your web instances.
    Type: String
  PHPVersion:
    AllowedValues:
      - 7.2
      - 7.3
      - 7.4
      - 8.0
      - 8.1
    Default: 8.1
    Description: The version of PHP to use with REDCap.
    Type: String
  S3FileRepositoryBucket:
    Type: String
    Description: 'S3 Bucket Name to be used for REDCap File Repository'
  SslCertificate:
    Type: String
    Description: "AWS ARN to ACM generated SSL certificate." 
  EBEndpoint:
    Description: "The unique name to use for your Elastic Beanstalk URL (will be rendered http://(EBEndpoint).(region).elasticbeanstalk.com)"
    Type: String
    Default: myREDCapp
  UseRoute53Boolean:
    AllowedValues:
      - true
      - false
    Default: true
    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: true
    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."
    Default: us-east-1.elasticbeanstalk.com
  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
  S3orAPI:
    Description: "Download REDCap automatically or provide it in S3?"
    Type: String
    AllowedValues:
      - "Provide in S3"
      - "Download using REDCap API"  
  RedcapS3Bucket:
    Description: "S3 bucket that contains your REDCap binary file"
    Type: String
  RedcapS3Key:
    Description: "S3 Key that points to your Redcap Binary file"
    Type: String
  RedcapS3BucketRegion:
    Description: "AWS Region of the S3 bucket that contains your REDCap binary file"
    Type: String
    AllowedValues:
      - us-east-2
      - us-east-1
      - us-west-1
      - us-west-2
      - af-south-1
      - ap-south-1
      - ap-northeast-1
      - ap-northeast-2
      - ap-northeast-3
      - ap-southeast-1
      - ap-southeast-2
      - ca-central-1
      - eu-central-1
      - eu-west-1
      - eu-west-2
      - eu-west-3
      - eu-north-1
      - sa-east-1
      - us-gov-west-1
  RedcapUname:
    Description: Your REDCap Community Username (used if 'Download using REDCap API' is selected)
    Type: String
  RedcapPword:
    Description: Your REDCap Community Password (used if 'Download using REDCap API' is selected)
    Type: String
    NoEcho: true
  Redcapver:
    Description: The version of REDCap you want to install, 'latest' for latest version (used if 'Download using REDCap API' is selected)
    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 `~#$%^&*()_+,-
  EC2KeyName:
    Description: The EC2 Key Pair to use for the Atlas/WebAPI EC2 Instances.
    Type: AWS::EC2::KeyPair::KeyName
  VPCId:
    Type: AWS::EC2::VPC::Id
  SubnetPublicA:
    Type: AWS::EC2::Subnet::Id
  SubnetPublicB:
    Type: AWS::EC2::Subnet::Id
  SubnetAppA:
    Type: AWS::EC2::Subnet::Id
  SubnetAppB:
    Type: AWS::EC2::Subnet::Id
  SubnetDataA:
    Type: AWS::EC2::Subnet::Id
  SubnetDataB:
    Type: AWS::EC2::Subnet::Id
  SGPublic:
    Type: AWS::EC2::SecurityGroup::Id
  SGApp:
    Type: AWS::EC2::SecurityGroup::Id
  SGData:
    Type: AWS::EC2::SecurityGroup::Id
  EBServiceRole:
    Type: String
  EBInstanceProfile:
    Type: String
  TempEC2InstanceProfile:
    Type: String
  EBBucket:
    Type: String
    Description: 'S3 Bucket used to store the application package for Elastic Beanstalk.'
  LatestAmiId:
    Type: 'AWS::SSM::Parameter::Value<AWS::EC2::Image::Id>'
    Default: '/aws/service/ami-amazon-linux-latest/amzn2-ami-hvm-x86_64-gp2'


Conditions:
  DeployMultiAZDB: 
    !Equals [ true, !Ref MultiAZDatabase ] 
  NotDeployMultiAZDB: 
    !Equals [ false, !Ref MultiAZDatabase ]
  DeployRoute53: 
    !Equals [ true, !Ref UseRoute53Boolean ]
  DeployACM: !And 
    - !Equals [ true, !Ref UseACMBoolean ]
    - !Condition DeployRoute53
  NotDeployACM: !Or
    - !Equals [ false, !Ref UseACMBoolean ]
    - !Equals [ false, !Ref UseRoute53Boolean ]
  UseAPIDownload: !Equals
    - !Ref S3orAPI
    - "Download using REDCap API"


Resources:

# Defines the Elastic Beanstalk environment that deploys the load balancer and Project REDCap Apache/PHP servers in an auto-scaling group.
  RCAppNoMultiAZDB:
    Type: 'AWS::ElasticBeanstalk::Application'
    Condition: NotDeployMultiAZDB
    DependsOn: 
      - EC2WaitCondition
      - RDSDBInstance1   
    Properties:
      Description: Project Redcap PHP servers
 
 
  RCAppNoMultiAZDBVersion:
    Type: 'AWS::ElasticBeanstalk::ApplicationVersion'
    Condition: NotDeployMultiAZDB
    Properties:
      ApplicationName:
        Ref: RCAppNoMultiAZDB
      Description: Initial Version
      SourceBundle:
        S3Bucket: !Ref EBBucket
        S3Key: redcap-eb.zip
  
  RCAppMultiAZDB:
    Type: 'AWS::ElasticBeanstalk::Application'
    Condition: DeployMultiAZDB
    DependsOn: 
      - EC2WaitCondition
      - RDSDBInstance1
      - RDSDBInstance2
    Properties:
      Description: Project Redcap PHP servers
 
  RCAppMultiAZDBVersion:
    Type: 'AWS::ElasticBeanstalk::ApplicationVersion'
    Condition: DeployMultiAZDB
    Properties:
      ApplicationName:
        Ref: RCAppMultiAZDB
      Description: Initial Version
      SourceBundle:
        S3Bucket: !Ref EBBucket
        S3Key: redcap-eb.zip

  REDCapEnvironmentACM:
    Type: 'AWS::ElasticBeanstalk::Environment'
    Condition: DeployACM
    DependsOn: EC2WaitCondition
    Properties:
      ApplicationName: !If [ DeployMultiAZDB, !Ref 'RCAppMultiAZDB', !Ref 'RCAppNoMultiAZDB' ]
      Description: Elastic Beanstalk deployment of Project Redcap
      SolutionStackName: !Select [1, !Split ['"', !Select [0, !Split ['}', !Select [1, !Split [':', !GetAtt 'EC2WaitCondition.Data']]]]]]
      VersionLabel:  !If [ DeployMultiAZDB, !Ref 'RCAppMultiAZDBVersion', !Ref 'RCAppNoMultiAZDBVersion' ]
      EnvironmentName: !Ref EBEndpoint
      CNAMEPrefix: !Ref EBEndpoint
      Tier:
        Name: WebServer
        Type: Standard
        Version: ' '
      OptionSettings:
        - Namespace: 'aws:autoscaling:launchconfiguration'
          OptionName: IamInstanceProfile
          Value: !Ref EBInstanceProfile 
        - Namespace: 'aws:elasticbeanstalk:environment'
          OptionName: ServiceRole
          Value: !Ref EBServiceRole        
        - Namespace: aws:elasticbeanstalk:environment
          OptionName: EnvironmentType
          Value: LoadBalanced
        - Namespace: aws:elasticbeanstalk:container:php:phpini
          OptionName: document_root
          Value: '/redcap'
        - Namespace: aws:autoscaling:asg
          OptionName: MinSize
          Value: !Ref WebAsgMin
        - Namespace: aws:autoscaling:asg
          OptionName: MaxSize
          Value: !Ref WebAsgMax
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: EC2KeyName
          Value: !Ref 'EC2KeyName'
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: InstanceType
          Value: !Ref WebInstanceType
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: SecurityGroups
          Value: !Ref SGApp
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: SSHSourceRestriction
          Value: 'tcp, 22, 22, 127.0.0.1/32'
        - Namespace: aws:autoscaling:trigger
          OptionName: MeasureName
          Value: CPUUtilization
        - Namespace: aws:autoscaling:trigger
          OptionName: Unit
          Value: Percent
        - Namespace: aws:autoscaling:trigger
          OptionName: UpperThreshold
          Value: '80'
        - Namespace: aws:autoscaling:trigger
          OptionName: LowerThreshold
          Value: '20'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: MaxBatchSize
          Value: '1'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: MinInstancesInService
          Value: '0'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: RollingUpdateEnabled
          Value: 'true'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: RollingUpdateType
          Value: Health
        - Namespace: aws:ec2:vpc
          OptionName: AssociatePublicIpAddress
          Value: 'false'
        - Namespace: aws:ec2:vpc
          OptionName: ELBSubnets
          Value: !Join
            - ','
            - - !Ref SubnetPublicA
              - !Ref SubnetPublicB
        - Namespace: aws:ec2:vpc
          OptionName: Subnets
          Value: !Join
            - ','
            - - !Ref SubnetAppA
              - !Ref SubnetAppB
        - Namespace: aws:ec2:vpc
          OptionName: VPCId
          Value: !Ref VPCId
        - Namespace: aws:elasticbeanstalk:command
          OptionName: DeploymentPolicy
          Value: Rolling
        - Namespace: aws:elasticbeanstalk:environment
          OptionName: LoadBalancerType
          Value: application
        - Namespace: aws:elasticbeanstalk:healthreporting:system
          OptionName: SystemType
          Value: enhanced
        - Namespace: aws:elbv2:loadbalancer
          OptionName: SecurityGroups
          Value: !Ref SGPublic
        - Namespace: aws:elbv2:loadbalancer
          OptionName: ManagedSecurityGroup
          Value: !Ref SGPublic
        - Namespace: aws:elbv2:listener:default
          OptionName: ListenerEnabled
          Value: false
        - Namespace: aws:elbv2:listener:443
          OptionName: DefaultProcess
          Value: https
        - Namespace: aws:elbv2:listener:443
          OptionName: Protocol
          Value: HTTPS
        - Namespace: aws:elbv2:listener:443
          OptionName: SSLCertificateArns
          Value: !Ref SslCertificate
        - Namespace: aws:elasticbeanstalk:environment:process:https
          OptionName: Port
          Value: 443
        - Namespace: aws:elasticbeanstalk:environment:process:https
          OptionName: Protocol
          Value: HTTPS          
        - Namespace: aws:elasticbeanstalk:environment:process:https
          OptionName: StickinessEnabled
          Value: true  



  REDCapEnvironmentNoACM:
    Type: 'AWS::ElasticBeanstalk::Environment'
    Condition: NotDeployACM
    DependsOn: EC2WaitCondition
    Properties:
      ApplicationName: !If [ DeployMultiAZDB, !Ref 'RCAppMultiAZDB', !Ref 'RCAppNoMultiAZDB' ]
      Description: Elastic Beanstalk deployment of Project Redcap
      SolutionStackName: !Select [1, !Split ['"', !Select [0, !Split ['}', !Select [1, !Split [':', !GetAtt 'EC2WaitCondition.Data']]]]]]
      VersionLabel:  !If [ DeployMultiAZDB, !Ref 'RCAppMultiAZDBVersion', !Ref 'RCAppNoMultiAZDBVersion' ]
      EnvironmentName: !Ref EBEndpoint
      CNAMEPrefix: !Ref EBEndpoint
      Tier:
        Name: WebServer
        Type: Standard
        Version: ' '
      OptionSettings:
        - Namespace: 'aws:autoscaling:launchconfiguration'
          OptionName: IamInstanceProfile
          Value: !Ref EBInstanceProfile 
        - Namespace: 'aws:elasticbeanstalk:environment'
          OptionName: ServiceRole
          Value: !Ref EBServiceRole        
        - Namespace: aws:elasticbeanstalk:environment
          OptionName: EnvironmentType
          Value: LoadBalanced
        - Namespace: aws:elasticbeanstalk:container:php:phpini
          OptionName: document_root
          Value: '/redcap'
        - Namespace: aws:autoscaling:asg
          OptionName: MinSize
          Value: !Ref WebAsgMin
        - Namespace: aws:autoscaling:asg
          OptionName: MaxSize
          Value: !Ref WebAsgMax
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: EC2KeyName
          Value: !Ref 'EC2KeyName'
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: InstanceType
          Value: !Ref WebInstanceType
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: SecurityGroups
          Value: !Ref SGApp
        - Namespace: aws:autoscaling:launchconfiguration
          OptionName: SSHSourceRestriction
          Value: 'tcp, 22, 22, 127.0.0.1/32'
        - Namespace: aws:autoscaling:trigger
          OptionName: MeasureName
          Value: CPUUtilization
        - Namespace: aws:autoscaling:trigger
          OptionName: Unit
          Value: Percent
        - Namespace: aws:autoscaling:trigger
          OptionName: UpperThreshold
          Value: '80'
        - Namespace: aws:autoscaling:trigger
          OptionName: LowerThreshold
          Value: '20'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: MaxBatchSize
          Value: '1'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: MinInstancesInService
          Value: '0'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: RollingUpdateEnabled
          Value: 'true'
        - Namespace: aws:autoscaling:updatepolicy:rollingupdate
          OptionName: RollingUpdateType
          Value: Health
        - Namespace: aws:ec2:vpc
          OptionName: AssociatePublicIpAddress
          Value: 'false'
        - Namespace: aws:ec2:vpc
          OptionName: ELBSubnets
          Value: !Join
            - ','
            - - !Ref SubnetPublicA
              - !Ref SubnetPublicB
        - Namespace: aws:ec2:vpc
          OptionName: Subnets
          Value: !Join
            - ','
            - - !Ref SubnetAppA
              - !Ref SubnetAppB
        - Namespace: aws:ec2:vpc
          OptionName: VPCId
          Value: !Ref VPCId
        - Namespace: aws:elasticbeanstalk:command
          OptionName: DeploymentPolicy
          Value: Rolling
        - Namespace: aws:elasticbeanstalk:environment
          OptionName: LoadBalancerType
          Value: application
        - Namespace: aws:elasticbeanstalk:healthreporting:system
          OptionName: SystemType
          Value: enhanced
        - Namespace: aws:elbv2:loadbalancer
          OptionName: SecurityGroups
          Value: !Ref SGPublic
        - Namespace: aws:elbv2:loadbalancer
          OptionName: ManagedSecurityGroup
          Value: !Ref SGPublic
        - Namespace: aws:elasticbeanstalk:environment:process:default
          OptionName: StickinessEnabled
          Value: true 
        - Namespace: aws:elasticbeanstalk:environment:process:https
          OptionName: Port
          Value: 443
        - Namespace: aws:elasticbeanstalk:environment:process:https
          OptionName: Protocol
          Value: HTTPS
        - Namespace: aws:elasticbeanstalk:environment:process:https
          OptionName: StickinessEnabled
          Value: true 




# Deploys the RDS Aurora Postgres cluster used to store the application data for WebAPI.
  RDSCluster:
    Type: AWS::RDS::DBCluster
    Properties:
      MasterUsername: 'master'
      MasterUserPassword: !Ref DatabaseMasterPassword
      DatabaseName: 'redcap'
      Engine: aurora-mysql
      StorageEncrypted: 'True'
      Port: 3306
      DBSubnetGroupName:
        Ref: RDSDBSubnets
      DBClusterParameterGroupName:
        Ref: RDSDBClusterParameterGroup
      VpcSecurityGroupIds:
        - !Ref SGData
  RDSDBInstance1:
    Type: AWS::RDS::DBInstance
    Properties:
      DBSubnetGroupName:
        Ref: RDSDBSubnets
      DBParameterGroupName:
        Ref: RDSDBParameterGroup
      Engine: aurora-mysql
      DBClusterIdentifier:
        Ref: RDSCluster
      PubliclyAccessible: 'false'
      DBInstanceClass: !Ref DatabaseInstanceType
# Only create the second instance if the user specified a Multi-AZ Database  
  RDSDBInstance2:
    Condition: DeployMultiAZDB
    Type: AWS::RDS::DBInstance
    Properties:
      DBSubnetGroupName:
        Ref: RDSDBSubnets
      DBParameterGroupName:
        Ref: RDSDBParameterGroup
      Engine: aurora-mysql
      DBClusterIdentifier:
        Ref: RDSCluster
      PubliclyAccessible: 'false'
      DBInstanceClass: !Ref DatabaseInstanceType
  RDSDBClusterParameterGroup:
    Type: AWS::RDS::DBClusterParameterGroup
    Properties:
      Description: CloudFormation Sample Aurora Cluster Parameter Group
      Family: aurora-mysql5.7
      Parameters:
        time_zone: US/Eastern
  RDSDBParameterGroup:
    Type: AWS::RDS::DBParameterGroup
    Properties:
      Description: CloudFormation Sample Aurora Parameter Group
      Family: aurora-mysql5.7
      Parameters:
        sql_mode: IGNORE_SPACE
  RDSDBSubnets:
    Type: AWS::RDS::DBSubnetGroup
    Properties:
      DBSubnetGroupDescription: Subnet Group for RDS
      SubnetIds:
        - !Ref SubnetDataA
        - !Ref SubnetDataB





# 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
    DependsOn: 
      - RDSCluster
    Metadata:
      AWS::CloudFormation::Init:
        config:
          files:
              /etc/awslogs/awslogs.conf:
                content: !Sub 
                  - |
                    [general]
                    state_file = /var/lib/awslogs/agent-state        
                    
                    [REDCap-build-log]
                    file = /var/log/cloud-init-output.log
                    log_group_name = redcap-temporary-ec2-instance-log
                    log_stream_name = ${EB}-build-log
                  - { EB: !Ref EBEndpoint }
                mode: 000664
                owner: root
                group: root
              /etc/awslogs/awscli.conf:
                content: !Sub |
                  [plugins]
                  cwlogs = cwlogs
                  [default]
                  region = ${AWS::Region}
                mode: 000664
                owner: root
                group: root
              /tmp/99redcap_config.config:
                content: !Sub 
                  - |
                    container_commands:
                      leaderonly:
                        command: "touch /leaderonly"
                        leader_only: True
                    files:
                      "/create-redcap-user.sql":
                        mode: "000755"
                        owner: root
                        group: root
                        content: |
                          CREATE USER IF NOT EXISTS 'redcap_user'@'%' IDENTIFIED BY '${DBPassword}';
                          GRANT SELECT, INSERT, UPDATE, DELETE ON `redcap`.* TO 'redcap_user'@'%';
                          -- Create second MySQL user as redcap_user2 with a random password, which could possibly a randomly generated value.
                          FLUSH PRIVILEGES;
                          CREATE USER IF NOT EXISTS 'redcap_user2'@'%' IDENTIFIED BY '${DBPassword}';
                          GRANT SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, ALTER, REFERENCES ON `redcap`.* TO 'redcap_user2'@'%';
                          FLUSH PRIVILEGES;
                      "/create-initial-user.sql":
                        mode: "000755"
                        owner: root
                        group: root
                        content: |
                          UPDATE redcap_config SET value = 'table' WHERE field_name = 'auth_meth_global';
                          INSERT INTO redcap_user_information (username, user_email, user_firstname, user_lastname, super_user) VALUES ('redcap_admin', 'joe.user@projectredcap.org', 'REDCap', 'Administrator', '1');
                          INSERT INTO redcap_auth (username, password, legacy_hash, temp_pwd) VALUES ('redcap_admin', MD5('${DBPassword}'), '1', '1'); 
                          UPDATE redcap_user_information SET super_user = '0' WHERE username = 'site_admin';
                          UPDATE redcap_config set value = '2' where field_name = 'edoc_storage_option';
                          UPDATE redcap_config SET value = '${S3Bucket}' WHERE field_name = 'amazon_s3_bucket';
                          UPDATE redcap_config SET value = '${S3AccessKey}' WHERE field_name = 'amazon_s3_key';
                          UPDATE redcap_config SET value = '${S3SecretKey}' WHERE field_name = 'amazon_s3_secret'; 
                          UPDATE redcap_config SET value = '${AWS::Region}' WHERE field_name = 'amazon_s3_endpoint';     
                          -- Manually set flag to indicate that this installation is being run on AWS CloudFormation
                          REPLACE INTO redcap_config (field_name, value) VALUES ('aws_quickstart', '1'); 
                          -- Add second MySQL user with user and password in *plain text* (will be auto-encrypted by REDCap afterward)
                          REPLACE INTO redcap_config (field_name, value) VALUES
                          ('redcap_updates_user', 'redcap_user2'),
                          ('redcap_updates_password', '${DBPassword}'),
                          ('redcap_updates_password_encrypted', '0');
                          -- Translate old admin privileges for newer versions
                          update redcap_user_information set account_manager = 1, access_system_config = 1, access_system_upgrade = 1,
                            access_external_module_install = 1, admin_rights = 1, access_admin_dashboards = 1 where super_user = 1;
                  - { DBPassword: !Ref DatabaseMasterPassword, S3Bucket: !Ref S3FileRepositoryBucket }
                mode: 000500
                owner: root
                group: root
              /tmp/https.conf:
                content: |
                  server {
                      listen       443 ssl;
                      server_name  localhost;
                      
                      ssl_certificate      /etc/pki/tls/certs/server.crt;
                      ssl_certificate_key  /etc/pki/tls/certs/server.key;
                      
                      ssl_session_timeout  5m;
                      
                      ssl_protocols  TLSv1 TLSv1.1 TLSv1.2;
                      ssl_prefer_server_ciphers   on;
                      
                      location / {
                          proxy_pass  http://localhost:80;
                          proxy_set_header   Connection "";
                          proxy_http_version 1.1;
                          proxy_set_header        Host            $host;
                          proxy_set_header        X-Real-IP       $remote_addr;
                          proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;
                          proxy_set_header        X-Forwarded-Proto https;
                      }
                  }
                mode: "000644"
                owner: root
                group: root
              /tmp/99redcap_config.sh:
                content: !Sub 
                  - |
                    #!/usr/bin/env bash
                    export AWS_DEFAULT_REGION=${AWS::Region}
                    #Insert the correct environment details into the database.php file
                    sed -i "/\$hostname[ tab]\+/s/=.*/= '${RDSEndpoint}';/" /var/app/current/redcap/database.php
                    sed -i "/\$db[ tab]\+/s/=.*/= 'redcap';/" /var/app/current/redcap/database.php
                    sed -i "/\$username[ tab]\+/s/=.*/= 'redcap_user';/" /var/app/current/redcap/database.php
                    sed -i "/\$password[ tab]\+/s/=.*/= '${DBPassword}';/" /var/app/current/redcap/database.php
                    #If we don't have an established 'salt' string, generate one and store it in AWS SSM
                    if ! aws ssm get-parameter --name redcap-salt; then
                        aws ssm put-parameter --name "redcap-salt" --type "SecureString" --value `head /dev/urandom | tr -dc a-z0-9 | head -c 8 ; echo ''`
                    fi
                    #Apply 'salt' string from AWS SSM to the database.php file.  This ensures the 'salt' string is the same on every PHP server.
                    sed -i "s#\$salt = '';#\$salt = '`aws ssm get-parameter --name redcap-salt --with-decryption --query 'Parameter.Value' --output text`';#" /var/app/current/redcap/database.php
                    
                    #only do the below tasks if it's the first deployment to this server.
                    if [ ! -f /eb-configured ]; then

                    systemctl restart nginx
                    systemctl restart php-fpm

                    touch /var/log/eb-activity.log               

                    #Create the REDCap CRON entry
                    (crontab -l ; echo -e "# REDCap Cron Job (runs every minute)\n* * * * * /usr/bin/php /var/app/current/redcap/cron.php > /dev/null") | crontab

                    #Create redcap_user and redcap_user2
                    mysql -h ${RDSEndpoint} -u master -D redcap --password=${DBPassword} < /create-redcap-user.sql

                    # If this is the leader-node and if the REDCap schema hasn't already been applied, create the initial 'redcap_admin' user, grab the SQL off the install.php website and apply it.
                    if [ -e /leaderonly ]; then
                      if ! mysql -h ${RDSEndpoint} -u master -D redcap --password=${DBPassword} -e "select * from redcap_actions"; then
                              count=0  
                              while ! [ -s /curl.out ] && [ $count -ne "100" ];
                              do
                                (curl -o /curl.out -k -F redcap_csrf_token= -F superusers_only_create_project=0 -F superusers_only_move_to_prod=1 -F auto_report_stats=1 -F bioportal_api_token= -F redcap_base_url='${Protocol}${RCDomainName}.${HostedZone}/' -F enable_url_shortener=1 -F default_datetime_format='D/M/Y_12' -F default_number_format_decimal=, -F default_number_format_thousands_sep=. -F homepage_contact='REDCap Administrator (123-456-7890)' -F homepage_contact_email=email@yoursite.edu -F project_contact_name='REDCap Administrator (123-456-7890)' -F project_contact_email=email@yoursite.edu -F institution='SoAndSo University' -F site_org_type='SoAndSo Institute for Clinical and Translational Research' -F hook_functions_file='/var/app/current/redcap/hook_functions.php' ${Protocol}localhost/install.php)
                                sleep 20
                                let count+=1
                              done                               
                              sed -ni '/onclick=\x27this.select();\x27>/,/<\/textarea>/p' /curl.out 
                              sed -i -e "1d" /curl.out
                              temp=`tail -1 /curl.out | cut -d';' -f1`; sed '$d' /curl.out > /mysql-rc.sql; echo $temp';' >> /mysql-rc.sql
                              mysql -h ${RDSEndpoint} -u master -D redcap --password=${DBPassword} < /mysql-rc.sql
                              mysql -h ${RDSEndpoint} -u master -D redcap --password=${DBPassword} < /create-initial-user.sql
                      fi
                    fi
                    rm -f /curl.out /mysql.sql /mysql-rc.sql /create-redcap-user.sql /create-initial-user.sql

                    yum install -y php-ldap sendmail-cf 

                    #Apply additional PHP configuration as specified by REDCap
                    echo "max_input_vars = 100000" >> /etc/php.ini
                    sed -i "s/upload_max_filesize = 2M/upload_max_filesize = 32M/" /etc/php.ini
                    sed -i "s/post_max_size = 8M/post_max_size = 32M/" /etc/php.ini

                    if [ ${Protocol} == 'https://' ]; then
                      echo "session.cookie_secure = on" >> /etc/php.ini
                    fi

                    systemctl restart nginx
                    systemctl restart php-fpm
                    
                    #sendmail configuration to enable sending e-mails
                    sudo postconf -e "relayhost = [email-smtp.${SESReg}.amazonaws.com]:587" \
                    "smtp_sasl_auth_enable = yes" \
                    "smtp_sasl_security_options = noanonymous" \
                    "smtp_sasl_password_maps = hash:/etc/postfix/sasl_passwd" \
                    "smtp_use_tls = yes" \
                    "smtp_tls_security_level = encrypt" \
                    "smtp_tls_note_starttls_offer = yes"
                    echo "[email-smtp.${SESReg}.amazonaws.com]:587 ${SESu}:${SESpw}" >> /etc/postfix/sasl_passwd
                    sudo postmap hash:/etc/postfix/sasl_passwd
                    sudo postconf -e 'smtp_tls_CAfile = /etc/ssl/certs/ca-bundle.crt'
                    sudo postfix start
                    sudo postfix reload
                    touch /eb-configured
                    else 
                    echo "Already ran EB configuration scripts.  This must be an application redeployment"
                    fi
                  - { SESReg: !Ref SESRegion, RDSEndpoint: !GetAtt RDSCluster.Endpoint.Address, DBPassword: !Ref DatabaseMasterPassword, Protocol: !If [ DeployACM, 'https://', 'http://' ], RCDomainName: !If [DeployRoute53, !Ref DomainName, !Ref EBEndpoint], HostedZone: !If [DeployRoute53, !Ref HostedZoneName, !Join ['.', [!Ref 'AWS::Region', 'elasticbeanstalk.com']]], SESu: !Ref SESUsername, SESpw: !Ref SESPassword }
                mode: 000770
                owner: root
                group: root
              /tmp/00HIPAA.config:
                content: |
                    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/nginx'
                          if grep -qs "$mount" /proc/mounts; then
                          echo "encrypted volume already mounted ..."
                          else
                          TOKEN=$(curl -X PUT "http://169.254.169.254/latest/api/token" -H "X-aws-ec2-metadata-token-ttl-seconds: 21600") 
                          awszone=$(curl -s -H "X-aws-ec2-metadata-token: $TOKEN" http://169.254.169.254/latest/meta-data/placement/availability-zone)
                          awsregion=${awszone::-1}
                          device='/dev/sdh'
                          instanceId=$(curl -s -H "X-aws-ec2-metadata-token: $TOKEN" http://169.254.169.254/latest/meta-data/instance-id)
                          volumeId=$(aws ec2 create-volume --size 4 --region $awsregion --availability-zone $awszone --volume-type standard --encrypted --query VolumeId --output=text)
                          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/* $mount
                          fi
                        ignoreErrors: false
                      01SelfSignedSSL:
                        command: |
                          #Generate a self-signed cert to be used between the AWS ALB and the Apache PHP servers.
                          if [ ! -f /etc/pki/tls/certs/server.key ]; then
                          openssl genrsa 2048 > server.key
                          openssl req -new -key server.key -out csr.pem -subj "/C=US/ST=WA/L=Seattle/O=anon/OU=anon/CN=none/emailAddress=none"
                          openssl x509 -req -days 365 -in csr.pem -signkey server.key -out server.crt
                          cp server.crt server.key /etc/pki/tls/certs/
                          rm -f server.crt server.key csr.pem
                          systemctl restart nginx
                          else
                          echo "Already have a self-signed private key.  This must be an application redeployment"
                          fi
                mode: 000500
                owner: root
                group: root
    Properties:
      InstanceInitiatedShutdownBehavior: 'terminate'
      InstanceType: 't3.medium'
      KeyName: !Ref 'EC2KeyName'
      ImageId: !Ref LatestAmiId
      IamInstanceProfile: !Ref TempEC2InstanceProfile
      SecurityGroupIds: 
        - !Ref SGApp
      SubnetId: !Ref SubnetAppA
      UserData:
        Fn::Base64: !Sub | 
          #!/bin/bash
          export REDCAP_FILE_NAME=$(echo ${RedcapS3Key} | rev | cut -d'/' -f 1 | rev)
          export AWS_DEFAULT_REGION=${AWS::Region}
          yum update -y aws-cli 
          yum install -y awslogs

          # Install SSM client
          yum install -y https://s3.amazonaws.com/ec2-downloads-windows/SSMAgent/latest/linux_amd64/amazon-ssm-agent.rpm
          systemctl restart amazon-ssm-agent

          aws configure set metadata_service_timeout 10
          aws configure set metadata_service_num_attempts 5
          #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
          sudo systemctl start awslogsd

          if [ "${S3orAPI}" = "Provide in S3" ]; then
            #Get the REDCap source file specified by the user
            aws s3 cp s3://${RedcapS3Bucket}/${RedcapS3Key} . --region ${RedcapS3BucketRegion}
          else
            curl -o redcap.zip -d "username=${RedcapUname}&password=${RedcapPword}&version=${Redcapver}&install=1" -X POST https://redcap.vanderbilt.edu/plugins/redcap_consortium/versions.php
            export REDCAP_FILE_NAME=redcap.zip
          fi

          unzip $REDCAP_FILE_NAME -d "./redcap"
          mkdir redcap/.ebextensions/
          #Copy all of the configuration files and scripts we want Elastic Beanstalk to run into the source file
          cp *.config redcap/.ebextensions
          mkdir -p redcap/.platform/hooks/postdeploy/
          #Copy all of the configuration files and scripts we want Elastic Beanstalk to run into the source file
          cp 99redcap_config.sh redcap/.platform/hooks/postdeploy
          mkdir -p redcap/.platform/nginx/conf.d/
          cp https.conf redcap/.platform/nginx/conf.d/
          
          cd redcap
          zip -r redcap-eb.zip .
          #Put the ammended source file back in S3 so that Elastic Beanstalk can pick it up and deploy it
          aws s3 mb s3://${EBBucket}
          aws s3 cp redcap-eb.zip s3://${EBBucket}
          #Create an encrypted S3 Bucket to be the REDCap File Repository
          aws s3 mb s3://${S3FileRepositoryBucket}
          aws s3api put-bucket-encryption --bucket ${S3FileRepositoryBucket} --server-side-encryption-configuration '{ "Rules": [ { "ApplyServerSideEncryptionByDefault": { "SSEAlgorithm": "AES256" } } ] }'
          #Tell Elastic Beanstalk what the latest PHP 7 solution stack is 
          echo ${PHPVersion}
          export SOLUTION_STACK=`aws elasticbeanstalk list-available-solution-stacks --region ${AWS::Region} | grep -v "SolutionStackName" | grep "PHP ${PHPVersion}" | grep "Linux 2 " |  head -1 | cut -d \" -f2`
          echo $SOLUTION_STACK
          /opt/aws/bin/cfn-signal --stack ${AWS::StackName} --region ${AWS::Region} "${EC2WaitHandle}" -d "$SOLUTION_STACK"
          #Shutdown and terminate this temporary instance 
          sleep 600
          shutdown -h now
  EC2WaitCondition:
    Type: "AWS::CloudFormation::WaitCondition"
    DependsOn: "TempEC2Instance"
    Properties: 
      Handle: 
        Ref: "EC2WaitHandle"
      Timeout: "3600"
      Count: 1
  EC2WaitHandle:
    Type: "AWS::CloudFormation::WaitConditionHandle"

Outputs:
  PublicAlbDnsName:
    Value: !If [ DeployACM, !GetAtt 'REDCapEnvironmentACM.EndpointURL', !GetAtt 'REDCapEnvironmentNoACM.EndpointURL' ]