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03-application-ohdsi.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.
Parameters:
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:
- t2.micro
- t2.small
- t2.medium
- t2.large
- t2.xlarge
- t2.2xlarge
- t3.micro
- t3.small
- t3.medium
- t3.large
- t3.xlarge
- t3.2xlarge
- m4.large
- m4.xlarge
- m4.2xlarge
- m5.large
- m5.xlarge
- m5.2xlarge
- c4.large
- c4.xlarge
- c4.2xlarge
- c5.large
- c5.xlarge
- c5.2xlarge
- r4.large
- r4.xlarge
- r5.large
- r5.xlarge
ConstraintDescription: Must be a valid Amazon EC2 instance type.
Default: t2.micro
Description: The Amazon EC2 instance type for your web instances.
Type: String
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
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 `~#$%^&*()_+,-
Sources:
Description: Comma-delimited list of OMOP CDM schema sources to load into the Redshift datawarehouse
Type: String
AllowedPattern: ^([a-zA-Z0-9,])*$
Default: CMSDESynPUF1k,CMSDESynPUF23m
SourcesBucket:
Description: S3 Bucket that contains DDL SQL files name after each 'Source'.sql that will be executed to load data into the OMOP CDM schema sources.
Type: String
AllowedPattern: ^([a-zA-Z0-9`~#$%^&*()_+,\\-])*$
Default: ohdsi-sample-data
OMOPv:
Description: The OHDSI CommonDataModel GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v5.3.1'
Atlasv:
Description: The OHDSI Atlas GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v2.3.1'
WebAPIv:
Description: OHDSI WebAPI GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v2.3.0'
Achillesv:
Description: OHDSI Achilles GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v1.5.0'
OhdsiRToolsv:
Description: OhdsiRTools GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v1.5.3'
SqlRenderv:
Description: OHDSI SqlRender GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v1.4.10'
DatabaseConnectorv:
Description: OHDSI DatabaseConnector GitHub branch you want deployed (this specifies the version)
Type: String
Default: 'v2.1.0'
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
SGPublic:
Type: AWS::EC2::SecurityGroup::Id
SGApp:
Type: AWS::EC2::SecurityGroup::Id
EBServiceRole:
Type: String
EBInstanceProfile:
Type: String
TempEC2InstanceProfile:
Type: String
RStudioTargetGroupArn:
Type: String
RDSEndpoint:
Type: String
RedshiftEndpoint:
Type: String
EBBucket:
Type: String
Description: 'S3 Bucket used to store the application package for Elastic Beanstalk.'
RSRoleArn:
Type: String
#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
tomcatconfig:
t2.micro:
Xmx: 512m
t2.small:
Xmx: 1024m
t2.medium:
Xmx: 2048m
t2.large:
Xmx: 4096m
t2.xlarge:
Xmx: 8192m
t2.2xlarge:
Xmx: 16384m
t3.micro:
Xmx: 512m
t3.small:
Xmx: 1024m
t3.medium:
Xmx: 2048m
t3.large:
Xmx: 4096m
t3.xlarge:
Xmx: 8192m
t3.2xlarge:
Xmx: 16384m
m4.large:
Xmx: 4096m
m4.xlarge:
Xmx: 8192m
m4.2xlarge:
Xmx: 16384m
m5.large:
Xmx: 4096m
m5.xlarge:
Xmx: 8192m
m5.2xlarge:
Xmx: 16384m
c4.large:
Xmx: 2048m
c4.xlarge:
Xmx: 4096m
c4.2xlarge:
Xmx: 8192m
c5.large:
Xmx: 2048m
c5.xlarge:
Xmx: 4096m
c5.2xlarge:
Xmx: 8192m
r4.large:
Xmx: 8192m
r4.xlarge:
Xmx: 16384m
r5.large:
Xmx: 8192m
r5.xlarge:
Xmx: 16384m
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:
# Defines the Elastic Beanstalk environment that deploys the load balancer and Atlas/WebAPI Tomcat servers in an auto-scaling group.
OHDSIApp:
Type: 'AWS::ElasticBeanstalk::Application'
DependsOn: EC2WaitCondition
Description: OHDSI Atlas and WebAPI
Properties:
ApplicationVersions:
- Description: Version 1.0
SourceBundle:
S3Bucket: !Ref EBBucket
S3Key: ohdsi-webapi-atlas.zip
VersionLabel: Initial Version
OHDSIEnvironmentACM:
Type: 'AWS::ElasticBeanstalk::Environment'
Condition: DeployACM
DependsOn: EC2WaitCondition
Properties:
ApplicationName: !Ref OHDSIApp
Description: Elastic Beanstalk deployment of Project Redcap
SolutionStackName: !Select [1, !Split ['"', !Select [0, !Split ['}', !Select [1, !Split [':', !GetAtt 'EC2WaitCondition.Data']]]]]]
VersionLabel: Initial Version
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: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
- Namespace: aws:elasticbeanstalk:container:tomcat:jvmoptions
OptionName: Xmx
Value: !FindInMap [tomcatconfig, !Ref WebInstanceType, Xmx]
OHDSIEnvironmentNoACM:
Type: 'AWS::ElasticBeanstalk::Environment'
Condition: NotDeployACM
DependsOn: EC2WaitCondition
Properties:
ApplicationName: !Ref OHDSIApp
Description: OHDSI Atlas and WebAPI
SolutionStackName: !Select [1, !Split ['"', !Select [0, !Split ['}', !Select [1, !Split [':', !GetAtt 'EC2WaitCondition.Data']]]]]]
VersionLabel: Initial Version
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: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
- Namespace: aws:elasticbeanstalk:container:tomcat:jvmoptions
OptionName: Xmx
Value: !FindInMap [tomcatconfig, !Ref WebInstanceType, Xmx]
# 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
[REDCap-build-log]
file = /tmp/log.txt
log_group_name = ohdsi-temporary-ec2-instnace-build-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/config_ohdsi.sh:
content: |
# 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
# $ACCT_ID must contain the AWS Account ID for the account in which this environment is being deployed
# $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 "ACCT_ID=" $ACCT_ID
echo "BUCKET_NAME=" $BUCKET_NAME
echo "DATABASE_PASSWORD=" $DATABASE_PASSWORD
export AWS_DEFAULT_REGION=$(echo $EB_ENDPOINT | cut -d . -f2)
sudo yum install -y postgresql
export PGPASSWORD=$DATABASE_PASSWORD
psql -d postgres --host=$RDS_ENDPOINT --port=5432 -U master -a -f postgres_init_master.sql
export PGPASSWORD="admin1"
psql -d postgres --host=$RDS_ENDPOINT --port=5432 -U ohdsi_admin_user -a -f postgres_init_ohdsi.sql
#Download build tools and compile WebAPI
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
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
zip -r ../ROOT.war *
cd ..
zip -r ohdsi-webapi-atlas.zip ROOT.war WebAPI.war .ebextensions
aws s3 cp ohdsi-webapi-atlas.zip s3://$BUCKET_NAME
mode: 000777
owner: root
group: root
/tmp/config_db.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
# $ACCT_ID must contain the AWS Account ID for the account in which this environment is being deployed
# $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
# $RS_ROLE_ARN must contain the role ARN that allows Redshift to read the sample data from S3.
echo "RDS_ENDPOINT=" $RDS_ENDPOINT
echo "EB_ENDPOINT=" $EB_ENDPOINT
echo "REDSHIFT_ENDPOINT=" $REDSHIFT_ENDPOINT
echo "ACCT_ID=" $ACCT_ID
echo "BUCKET_NAME=" $BUCKET_NAME
echo "DATABASE_PASSWORD=" $DATABASE_PASSWORD
echo "RS_ROLE_ARN=" $RS_ROLE_ARN
echo "RSTUDIO_TARGET_GROUP_ARN=" $RSTUDIO_TARGET_GROUP_ARN
echo "SOURCES=" $SOURCES
echo "SOURCESBUCKET= " $SOURCESBUCKET
export AWS_DEFAULT_REGION=$(echo $EB_ENDPOINT | cut -d . -f2)
#Install R and the dependencies for Achilles
sudo yum install -y xorg-x11-xauth.x86_64 xorg-x11-server-utils.x86_64 xterm libXt libX11-devel libXt-devel libcurl-devel git compat-gmp4 compat-libffi5 openssl-devel
sudo yum install R R-core R-core-devel R-devel libxml2-devel -y
if [ -f /usr/lib64/R/etc/Makeconf.rpmnew ]; then
sudo cp /usr/lib64/R/etc/Makeconf.rpmnew /usr/lib64/R/etc/Makeconf
fi
if [ -f /usr/lib64/R/etc/ldpaths.rpmnew ]; then
sudo cp /usr/lib64/R/etc/ldpaths.rpmnew /usr/lib64/R/etc/ldpaths
fi
mkdir /mnt/r-stuff
cd /mnt/r-stuff
pushd .
mkdir R-latest
cd R-latest
wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
tar -xzf R-3.5.0.tar.gz
sudo yum install -y gcc gcc-c++ gcc-gfortran readline-devel cairo-devel libpng-devel libjpeg-devel libtiff-devel
cd R-3*
./configure --with-readline=yes --enable-R-profiling=no --enable-memory-profiling=no --enable-R-shlib --with-pic --prefix=/usr --with-x --with-libpng --with-jpeglib --with-cairo --enable-R-shlib --with-recommended-packages=yes
make -j 8
sudo make install
sudo su << BASH_SCRIPT
echo 'export PATH=${!PWD}/bin:$PATH' >> /etc/profile
BASH_SCRIPT
popd
sudo sed -i 's/make/make -j 8/g' /usr/lib64/R/etc/Renviron
# set unix environment variables
sudo su << BASH_SCRIPT
echo 'export JAVA_HOME=/etc/alternatives/jre' >> /etc/profile
BASH_SCRIPT
sudo sh -c "source /etc/profile"
# fix java binding - R and packages have to be compiled with the same java version as hadoop
sudo R CMD javareconf
cd /tmp
#Deploy the OMOP CDM Schema to Redshift
export PGPASSWORD=$DATABASE_PASSWORD
export REDSHIFTDDL=`ls ./CommonDataModel/Redshift/OMOP*`
#Some of the current Vocabulary data sets from Athena do not have values for these columns
if [ "$CDM_VERSION" = "v5.3.1" ]; then
sed -i '47s/.*/ concept_name VARCHAR(255) NULL ,/' "$REDSHIFTDDL"
sed -i '52s/.*/ concept_code VARCHAR(50) NULL ,/' "$REDSHIFTDDL"
sed -i '62s/.*/ vocabulary_reference VARCHAR(255) NULL,/' "$REDSHIFTDDL"
sed -i '63s/.*/ vocabulary_version VARCHAR(255) NULL,/' "$REDSHIFTDDL"
sed -i '226s/.*/ race_source_value VARCHAR(255) NULL,/' "$REDSHIFTDDL"
sed -i '340s/.*/ procedure_source_value VARCHAR(255) NULL ,/' "$REDSHIFTDDL"
sed -i '352s/.*/ drug_exposure_start_date DATE NULL,/' "$REDSHIFTDDL"
sed -i '354s/.*/ drug_exposure_end_date DATE NULL,/' "$REDSHIFTDDL"
sed -i '411s/.*/ condition_source_value VARCHAR(255) NULL,/' "$REDSHIFTDDL"
sed -i '413s/.*/ condition_status_source_value VARCHAR(255) NULL,/' "$REDSHIFTDDL"
sed -i '437s/.*/ measurement_source_value VARCHAR(255) NULL ,/' "$REDSHIFTDDL"
sed -i '440s/.*/ value_source_value VARCHAR(255) NULL/' "$REDSHIFTDDL"
sed -i '494s/.*/ value_as_string VARCHAR(255) NULL ,/' "$REDSHIFTDDL"
sed -i '546s/.*/ place_of_service_source_value VARCHAR(255) NULL/' "$REDSHIFTDDL"
sed -i '676s/.*/ dose_era_start_date DATE NULL,/' "$REDSHIFTDDL"
sed -i '677s/.*/ dose_era_end_date DATE NULL/' "$REDSHIFTDDL"
fi
#Insert Database Credentials into the scripts
sed -i 's!REDSHIFT_ENDPOINT!'$REDSHIFT_ENDPOINT'!' postgres_init_sources.sql
sed -i 's!DATABASE_PASSWORD!'$DATABASE_PASSWORD'!' postgres_init_sources.sql
sed -i 's!REDSHIFT_ENDPOINT!'$REDSHIFT_ENDPOINT'!' /tmp/achilles.r
sed -i 's!DATABASE_PASSWORD!'$DATABASE_PASSWORD'!' /tmp/achilles.r
SOURCECOUNT=0
SOURCEDAEMONCOUNT=0
for i in $(echo $SOURCES | sed "s/,/ /g")
do
export PGPASSWORD=$DATABASE_PASSWORD
cp "$REDSHIFTDDL" "$REDSHIFTDDL-$i"
sed -i "1s/^/SET search_path to $i;\n/" "$REDSHIFTDDL-$i"
psql -d mycdm --host=$REDSHIFT_ENDPOINT --port=5439 -U master -a -c "CREATE SCHEMA $i;"
psql -d mycdm --host=$REDSHIFT_ENDPOINT --port=5439 -U master -a -f "$REDSHIFTDDL-$i"
#Deploy the DDL with the appropriate source name and run it
aws s3 cp s3://$SOURCESBUCKET/$i.sql .
sed -i 's!RS_ROLE_ARN!'$RS_ROLE_ARN'!' $i.sql
psql -d mycdm --host=$REDSHIFT_ENDPOINT --port=5439 -U master -a -f $i.sql
#Wait for the WebAPI app to be deployed by Elastic Beanstalk and populate the tables in RDS Postrgres
while [ `curl ${Protocol}${RCDomainName}.${HostedZone} 1> /dev/null 2> /dev/null; echo $?` -ne 0 ]
do
sleep 5
done
#Get the Results Schema from WebAPI and apply the Results schema
wget -q "${Protocol}${RCDomainName}.${HostedZone}/WebAPI/ddl/results?dialect=redshift&schema=${!i}results" -O results_schema.sql
psql -d mycdm --host=$REDSHIFT_ENDPOINT --port=5439 -U master -a -c "CREATE SCHEMA ${!i}results;"
psql -d mycdm --host=$REDSHIFT_ENDPOINT --port=5439 -U master -a -f results_schema.sql
#Create a WebAPI Sources DDL for this Source
cp postgres_init_sources.sql postgres_init_sources-$i.sql
let SOURCECOUNT+=1
sed -i 's!SOURCECOUNT!'$SOURCECOUNT'!' postgres_init_sources-$i.sql
let SOURCEDAEMONCOUNT+=1
sed -i 's!SOURCEDAEMONCOUNT1!'$SOURCEDAEMONCOUNT'!' postgres_init_sources-$i.sql
let SOURCEDAEMONCOUNT+=1
sed -i 's!SOURCEDAEMONCOUNT2!'$SOURCEDAEMONCOUNT'!' postgres_init_sources-$i.sql
let SOURCEDAEMONCOUNT+=1
sed -i 's!SOURCEDAEMONCOUNT3!'$SOURCEDAEMONCOUNT'!' postgres_init_sources-$i.sql
sed -i 's!SOURCENAME_PLACEHOLDER!'$i'!' postgres_init_sources-$i.sql
sed -i 's!SOURCENAME_PLACEHOLDER!'$i'!' postgres_init_sources-$i.sql
sed -i 's!CDM_PLACEHOLDER!'$i'!' postgres_init_sources-$i.sql
sed -i 's!RESULTS_PLACEHOLDER!'${!i}results'!' postgres_init_sources-$i.sql
#Load the sources reference table into the WebAPI Postgres database
export PGPASSWORD="admin1"
psql -d OHDSI --host=$RDS_ENDPOINT --port=5432 -U ohdsi_admin_user -a -f postgres_init_sources-$i.sql
aws elasticbeanstalk restart-app-server --environment-name $(echo $EB_ENDPOINT | cut -d . -f1)
#Inject source information and run Achilles R script to enabled Data Source visualization
cp /tmp/achilles.r /tmp/achilles-$i.r
sed -i 's!SOURCENAME_PLACEHOLDER!'$i'!' /tmp/achilles-$i.r
sed -i 's!CDM_PLACEHOLDER!'$i'!' /tmp/achilles-$i.r
sed -i 's!RESULTS_PLACEHOLDER!'${!i}results'!' /tmp/achilles-$i.r
Rscript /tmp/achilles-$i.r
done
#Connect R-Studio Instance to the load balancer
if [ "$RSTUDIO_TARGET_GROUP_ARN" != "none" ]; then
export EB_ENVIRONMENT=$(echo $EB_ENDPOINT | cut -d . -f1)
export EB_LB=$(aws elasticbeanstalk describe-environment-resources --environment-name $EB_ENVIRONMENT --query EnvironmentResources.LoadBalancers --output text)
export EB_LB_LISTENER=$(aws elbv2 describe-listeners --load-balancer-arn $EB_LB --query 'Listeners[0].ListenerArn' --output text)
aws elbv2 create-rule --listener-arn $EB_LB_LISTENER --priority 4 --conditions Field=host-header,Values='rstudio.*' --actions Type=forward,TargetGroupArn=$RSTUDIO_TARGET_GROUP_ARN
fi
- { Protocol: !If [ DeployACM, 'https://', 'http://' ], RCDomainName: !If [DeployRoute53, !Ref DomainName, !Ref EBEndpoint], HostedZone: !If [DeployRoute53, !Ref HostedZoneName, !Join ['.', [!Ref 'AWS::Region', 'elasticbeanstalk.com']]] }
mode: 000777
owner: root
group: root
/tmp/postgres_init_master.sql:
content: |
CREATE ROLE ohdsi_admin
CREATEDB
VALID UNTIL 'infinity';
COMMENT ON ROLE ohdsi_admin
IS 'Administration group for OHDSI applications';
CREATE ROLE ohdsi_app
VALID UNTIL 'infinity';
COMMENT ON ROLE ohdsi_app
IS 'Application groupfor OHDSI applications';
CREATE ROLE ohdsi_admin_user LOGIN ENCRYPTED PASSWORD 'md58d34c863380040dd6e1795bd088ff4a9'
VALID UNTIL 'infinity';
-- password is admin1
GRANT ohdsi_admin TO ohdsi_admin_user;
COMMENT ON ROLE ohdsi_admin_user
IS 'Admin user account for OHDSI applications';
CREATE ROLE ohdsi_app_user LOGIN ENCRYPTED PASSWORD 'md55cc9d81d14edce93a4630b7c885c6410'
VALID UNTIL 'infinity';
-- password is app1
GRANT ohdsi_app TO ohdsi_app_user;
COMMENT ON ROLE ohdsi_app_user
IS 'Application user account for OHDSI applications';
ALTER USER ohdsi_admin_user CREATEDB;
mode: 000664
owner: root
group: root
/tmp/postgres_init_ohdsi.sql:
content: |
CREATE DATABASE "OHDSI"
WITH ENCODING='UTF8'
OWNER=ohdsi_admin
CONNECTION LIMIT=-1;
COMMENT ON DATABASE "OHDSI"
IS 'OHDSI database';
GRANT ALL ON DATABASE "OHDSI" TO GROUP ohdsi_admin;
GRANT CONNECT, TEMPORARY ON DATABASE "OHDSI" TO GROUP ohdsi_app;
\c OHDSI
CREATE SCHEMA webapi
AUTHORIZATION ohdsi_admin;
COMMENT ON SCHEMA webapi
IS 'Schema containing tables to support WebAPI functionality';
GRANT USAGE ON SCHEMA webapi TO public;
GRANT ALL ON SCHEMA webapi TO GROUP ohdsi_admin;
GRANT USAGE ON SCHEMA webapi TO GROUP ohdsi_app;
ALTER DEFAULT PRIVILEGES IN SCHEMA webapi
GRANT INSERT, SELECT, UPDATE, DELETE, REFERENCES, TRIGGER ON TABLES
TO ohdsi_app;
ALTER DEFAULT PRIVILEGES IN SCHEMA webapi
GRANT SELECT, USAGE ON SEQUENCES
TO ohdsi_app;
ALTER DEFAULT PRIVILEGES IN SCHEMA webapi
GRANT EXECUTE ON FUNCTIONS
TO ohdsi_app;
ALTER DEFAULT PRIVILEGES IN SCHEMA webapi
GRANT USAGE ON TYPES
TO ohdsi_app;
mode: 000664
owner: root
group: root
/tmp/postgres_init_sources.sql:
content: |
INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect) VALUES (SOURCECOUNT, 'SOURCENAME_PLACEHOLDER', 'SOURCENAME_PLACEHOLDER', 'jdbc:redshift://REDSHIFT_ENDPOINT:5439/mycdm?user=master&password=DATABASE_PASSWORD', 'redshift');
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (SOURCEDAEMONCOUNT1,SOURCECOUNT,0, 'CDM_PLACEHOLDER', 0);
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (SOURCEDAEMONCOUNT2,SOURCECOUNT,1, 'CDM_PLACEHOLDER', 0);
INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (SOURCEDAEMONCOUNT3,SOURCECOUNT,2, 'RESULTS_PLACEHOLDER', 0);
mode: 000664
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/achilles.r:
content: !Sub |
install.packages("devtools",repos = "http://cran.us.r-project.org")
library(devtools)
devtools::install_github("ohdsi/SqlRender", ref = "${SqlRenderv}")
devtools::install_github("ohdsi/DatabaseConnector", ref = "${DatabaseConnectorv}")
devtools::install_github("ohdsi/OhdsiRTools", ref = "${OhdsiRToolsv}")
devtools::install_github("ohdsi/Achilles", ref = "${Achillesv}")
library(Achilles)
connectionDetails <- createConnectionDetails(dbms="redshift", server="REDSHIFT_ENDPOINT/mycdm", user="master",
password='DATABASE_PASSWORD', schema="CDM_PLACEHOLDER", port="5439")
achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="CDM_PLACEHOLDER",
resultsDatabaseSchema="RESULTS_PLACEHOLDER", sourceName="SOURCENAME_PLACEHOLDER",
cdmVersion = "5", vocabDatabaseSchema="CDM_PLACEHOLDER")
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