fixes

highspec/get_db.sh

@@ -19,4 +19,4 @@ rm graph.db.tgz
 echo "Uncompress graph db - END"
 
 # echo "Starting Neo4J"
-sudo -u ec2-user $NEO4J_HOME/bin/neo4j start
+$NEO4J_HOME/bin/neo4j start

highspec/startup.sh

 #!/bin/bash
 
-CURRDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-
-# update yum
-yum update -y
-
-# install dependencies
-wget $PBZIP_BASE_URL/$PBZIP_PACKAGE
-yum install $BASIC_DEPENDENCIES $PBZIP_PACKAGE -y
-rm $PBZIP_PACKAGE
-
-# get Neo4J
-wget $NEO4J_DOWNLOAD_URL
-tar -xvf artifact.php?name=$NEO4J_SETUP_FILE
-rm artifact.php?name=$NEO4J_SETUP_FILE -f
-mv $NEO4J_VERSION /var/lib/
-
-export NEO4J_HOME=/var/lib/$NEO4J_VERSION
-
-# get apoc plugin
-wget $APOC_URL
-mv $APOC_VERSION $NEO4J_HOME/plugins/
-
-### make few config changes for Neo4J
-for line in `cat $CURRDIR/neo4j.conf`; do
-    sed -i -e "1i$line\\" $NEO4J_HOME/conf/neo4j.conf
-done
-
-# provide ownership to ec2-user user
-chown -R ec2-user:ec2-user $NEO4J_HOME
-
 # get the SSD device name
 device=$(lsblk | grep nvme0n1 | cut -d' ' -f1)
 
@@ -43,35 +13,9 @@ sudo mkdir -p $mountpoint
 # mount the device
 mount -o discard /dev/$device $mountpoint
 
-# provide ownership to ec2-user user
-chown -R ec2-user:ec2-user $mountpoint
-
-# 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.db.tgz $mountpoint/
-# date
-# echo "Getting compressed graph db from S3 - END" 
-
 # create directories for neo4j data
 mkdir -p $mountpoint/neo4j_data/databases/graph.db
 mkdir -p $mountpoint/neo4j_data/dbms
-graphdb_path=$mountpoint/neo4j_data/databases/graph.db
-
-# mv $mountpoint/graph.db.tgz $mountpoint/neo4j_data/databases/graph.db/
-
-# uncompress graph data
-# echo "Uncompress graph db - START"
-# cd $mountpoint/neo4j_data/databases/graph.db
-# date
-# pbzip2 -dc graph.db.tgz | tar x
-# date
-# rm graph.db.tgz
-# echo "Uncompress graph db - END"
-
-# Change Neo4J config to pick data from new location
-sed -i -e '1idbms.directories.data='${mountpoint}'/neo4j_data\' $NEO4J_HOME/conf/neo4j.conf
-
-# echo "Starting Neo4J"
-# sudo -u ec2-user $NEO4J_HOME/bin/neo4j start
 
+# provide ownership to ec2-user user
+chown -R ec2-user:ec2-user $mountpoint

highspec/startup.sh.old

+#!/bin/bash
+
+CURRDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# update yum
+yum update -y
+
+# install dependencies
+wget $PBZIP_BASE_URL/$PBZIP_PACKAGE
+yum install $BASIC_DEPENDENCIES $PBZIP_PACKAGE -y
+rm $PBZIP_PACKAGE
+
+# get Neo4J
+wget $NEO4J_DOWNLOAD_URL
+tar -xvf artifact.php?name=$NEO4J_SETUP_FILE
+rm artifact.php?name=$NEO4J_SETUP_FILE -f
+mv $NEO4J_VERSION /var/lib/
+
+export NEO4J_HOME=/var/lib/$NEO4J_VERSION
+
+# get apoc plugin
+wget $APOC_URL
+mv $APOC_VERSION $NEO4J_HOME/plugins/
+
+### make few config changes for Neo4J
+for line in `cat $CURRDIR/neo4j.conf`; do
+    sed -i -e "1i$line\\" $NEO4J_HOME/conf/neo4j.conf
+done
+
+# provide ownership to ec2-user user
+chown -R ec2-user:ec2-user $NEO4J_HOME
+
+# get the SSD device name
+device=$(lsblk | grep nvme0n1 | 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
+
+# provide ownership to ec2-user user
+chown -R ec2-user:ec2-user $mountpoint
+
+# 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.db.tgz $mountpoint/
+# date
+# echo "Getting compressed graph db from S3 - END" 
+
+# create directories for neo4j data
+mkdir -p $mountpoint/neo4j_data/databases/graph.db
+mkdir -p $mountpoint/neo4j_data/dbms
+graphdb_path=$mountpoint/neo4j_data/databases/graph.db
+
+# mv $mountpoint/graph.db.tgz $mountpoint/neo4j_data/databases/graph.db/
+
+# uncompress graph data
+# echo "Uncompress graph db - START"
+# cd $mountpoint/neo4j_data/databases/graph.db
+# date
+# pbzip2 -dc graph.db.tgz | tar x
+# date
+# rm graph.db.tgz
+# echo "Uncompress graph db - END"
+
+# Change Neo4J config to pick data from new location
+sed -i -e '1idbms.directories.data='${mountpoint}'/neo4j_data\' $NEO4J_HOME/conf/neo4j.conf
+
+# echo "Starting Neo4J"
+# sudo -u ec2-user $NEO4J_HOME/bin/neo4j start
+

highspec/userdata_script

@@ -7,6 +7,4 @@ git clone https://gitlab.ebi.ac.uk/sreenath/pdbe-neo4j-aws.git
 cd pdbe-neo4j-aws
 chmod -R 755 .
 ./setup.sh highspec
-cp highspec/get_db.sh /usr/local/bin
-chmod 777 /usr/local/bin/get_db.sh
 

highspec/userdata_script.old

+#!/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 highspec
+cp highspec/get_db.sh /usr/local/bin
+chmod 777 /usr/local/bin/get_db.sh
+