diff --git a/release/get_db.sh b/release/get_db.sh new file mode 100644 index 0000000000000000000000000000000000000000..8bfe0896ac60e5f75cff1c901b8ebb3c162e2e3e --- /dev/null +++ b/release/get_db.sh @@ -0,0 +1,22 @@ +mountpoint=/media/disk1 + +# get compressed graph db from S3 +echo "Getting compressed graph db from S3 - START" +date +aws s3 --region=us-east-2 cp s3://ebi-pdbe/neo4j/graph_data/next/graph.db.bz2 $mountpoint/ +date +echo "Getting compressed graph db from S3 - END" + +mv $mountpoint/graph.db.bz2 $mountpoint/neo4j_data/databases/graph.db/ + +# uncompress graph data +echo "Uncompress graph db - START" +cd $mountpoint/neo4j_data/databases/graph.db +date +pbzip2 -dc graph.db.bz2 | tar x +date +rm graph.db.bz2 +echo "Uncompress graph db - END" + +# echo "Starting Neo4J" +$NEO4J_HOME/bin/neo4j start diff --git a/release/neo4j.conf b/release/neo4j.conf new file mode 100644 index 0000000000000000000000000000000000000000..a14772572aa9244418f617b9fe1f53993da353b8 --- /dev/null +++ b/release/neo4j.conf @@ -0,0 +1,7 @@ +dbms.security.auth_enabled=false +dbms.connectors.default_listen_address=0.0.0.0 +dbms.read_only=false +dbms.security.procedures.unrestricted=apoc.*,org.pdbe.* +dbms.memory.heap.initial_size=110g +dbms.memory.heap.max_size=110g +dbms.memory.pagecache.size=10g diff --git a/release/startup.sh b/release/startup.sh new file mode 100644 index 0000000000000000000000000000000000000000..56dbeddb7e05ca02ba736b887f2f636643a1eb8e --- /dev/null +++ b/release/startup.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +# update yum +yum update -y + +# get the SSD device name +device=$(lsblk | grep xvdb | cut -d' ' -f1) + +# create an ext4 partition on the disk +mkfs.ext4 -E nodiscard -m0 /dev/$device + +# create a mount point +mountpoint=/media/disk1 +sudo mkdir -p $mountpoint + +# mount the device +mount -o discard /dev/$device $mountpoint + +# create directories for neo4j data +mkdir -p $mountpoint/neo4j_data/databases/graph.db +mkdir -p $mountpoint/neo4j_data/dbms + +# provide ownership to ec2-user user +chown -R ec2-user:ec2-user $mountpoint + +# get pdbe graph extensions +aws s3 cp s3://ebi-pdbe/neo4j/pdbe-extensions-1.0.2-SNAPSHOT.jar . +mv pdbe-extensions-1.0.2-SNAPSHOT.jar $NEO4J_HOME/plugins/ diff --git a/release/userdata_script b/release/userdata_script new file mode 100644 index 0000000000000000000000000000000000000000..b3f328bdc568c44f27fe0253f0dd7537c0d93296 --- /dev/null +++ b/release/userdata_script @@ -0,0 +1,10 @@ +#!/bin/bash + +yum update -y +yum install git -y + +git clone https://gitlab.ebi.ac.uk/sreenath/pdbe-neo4j-aws.git +cd pdbe-neo4j-aws +chmod -R 755 . +./setup.sh release + diff --git a/setup.sh b/setup.sh index f24260cb588bd975d3bf76a6dd0e369e9e965d33..5fd491a614df9a6f7393742c3dfd85b071c5db39 100755 --- a/setup.sh +++ b/setup.sh @@ -1,7 +1,7 @@ env=$1 -[[ $env != "highspec" && $env != "playground" ]] && echo "Usage: bash setup.sh <env (highspec or playground)>" && exit 1 +[[ $env != "highspec" && $env != "playground" && $env != "release" ]] && echo "Usage: bash setup.sh <env (highspec, playground or release)>" && exit 1 echo "Setting up $env machine"