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dockerbits.sh
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dockerbits.sh
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set -e
apt-get update
apt-get install -y --no-install-recommends wget software-properties-common gnupg2 unixodbc
## Team RabbitMQ's main signing key
apt-key adv --keyserver "hkps://keys.openpgp.org" --recv-keys "0x0A9AF2115F4687BD29803A206B73A36E6026DFCA"
## Cloudsmith: modern Erlang repository
wget -qO- https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-erlang/gpg.E495BB49CC4BBE5B.key | apt-key add -
## Cloudsmith: RabbitMQ repository
wget -qO- https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-server/gpg.9F4587F226208342.key | apt-key add -
apt-key add <<EOK
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Version: GnuPG v1.4.7 (GNU/Linux)
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-----END PGP PUBLIC KEY BLOCK-----
-----BEGIN PGP PUBLIC KEY BLOCK-----
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-----END PGP PUBLIC KEY BLOCK-----
-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: GnuPG v1
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-----END PGP PUBLIC KEY BLOCK-----
EOK
add-apt-repository -u "deb [arch=amd64] https://packages.microsoft.com/ubuntu/18.04/prod bionic main"
echo "deb http://repo.mongodb.org/apt/debian buster/mongodb-org/4.4 main" > /etc/apt/sources.list.d/mongodb-org-4.4.list
## Add apt repositories maintained by Team RabbitMQ
tee /etc/apt/sources.list.d/rabbitmq.list <<EOF
## Provides modern Erlang/OTP releases
##
deb https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-erlang/deb/ubuntu bionic main
deb-src https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-erlang/deb/ubuntu bionic main
## Provides RabbitMQ
##
deb https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-server/deb/ubuntu bionic main
deb-src https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-server/deb/ubuntu bionic main
EOF
add-apt-repository "deb [arch=amd64] https://packages.microsoft.com/ubuntu/18.04/prod bionic main"
add-apt-repository -u "deb [arch=amd64] https://packages.microsoft.com/ubuntu/18.04/mssql-server-2019 bionic main"
apt-get update
ACCEPT_EULA=Y apt-get install -y --no-install-recommends libtinfo5 rabbitmq-server mssql-tools mariadb-server default-jre-headless mongodb-org redis-server
apt-get install -y --no-install-recommends mssql-server
MSSQL_SA_PASSWORD="YourStrong\!Passw0rd" /opt/mssql/bin/sqlservr --pid 3 --setup --reset-sa-password --accept-eula
/opt/mssql/bin/sqlservr &
sleep 10
# Disable irrelenvant .Net L16n to avoid extra dependencies or a coredump from RDMP
cat > /rdmp-cli/rdmp.runtimeconfig.json <<EOJ
{
"runtimeOptions": {
"configProperties": {
"System.Globalization.Invariant": true
},
"tfm": "net5.0",
"includedFrameworks": [
{
"name": "Microsoft.NETCore.App",
"version": "5.0.3"
}
]
}
}
EOJ
ln -f /rdmp-cli/rdmp.runtimeconfig.json /smi/smi.runtimeconfig.json
./rdmp-cli/rdmp install localhost TEST_ -u sa -p "YourStrong\!Passw0rd"
kill -TERM `jobs -p`
mkdir -p /data/db
echo -e '\nreplication:\n replSetName: rs0' >> /etc/mongodb.conf
mongod -f /etc/mongodb.conf &
sleep 10
mongo --eval 'rs.initiate()'
kill -TERM `jobs -p`
echo "NODENAME=rabbit@localhost" > /etc/rabbitmq/rabbitmq-env.conf
mkdir -p /var/lib/rabbitmq
chown -R rabbitmq:rabbitmq /var/lib/rabbitmq
rabbitmq-server &
sleep 15
rabbitmq-plugins enable rabbitmq_management < /dev/null
wget -O/bin/rabbitmqadmin http://127.0.0.1:15672/cli/rabbitmqadmin
chmod +x /bin/rabbitmqadmin
# RABBITGOESHERE
kill -TERM `jobs -p`
cat > /smi.yaml <<EOY
jobs:
- "/opt/mssql/bin/sqlservr"
- "/usr/bin/mongod"
- "/usr/bin/redis-server"
- "/usr/sbin/mysqld"
- "/usr/sbin/rabbitmq-server"
- "wait"
- "/usr/bin/java -jar /smi/smi-nerd-v3.0.2.jar"
- "/usr/bin/java -jar /smi/CTPAnonymiser-portable-1.0.0.jar -a /smi/ctp-whitelist.script -y /smi.yaml"
- "/smi/smi dicom-relational-mapper -y /smi.yaml"
- "/smi/smi is-identifiable service -y /smi.yaml"
- "/smi/smi cohort-extractor -y /smi.yaml"
- "/smi/smi dicom-tag-reader -y /smi.yaml"
- "/smi/smi mongodb-populator -y /smi.yaml"
- "/smi/smi cohort-packager -y /smi.yaml"
- "/smi/smi file-copier -y /smi.yaml"
- "/smi/smi identifier-mapper -y /smi.yaml"
- "/smi/smi update-values -y /smi.yaml"
EOY
sed -e 's/c:\\temp/\/tmp/gi' /smi/default.yaml | tail -n +2 >> /smi.yaml