diff --git a/highspec/get_db.sh b/highspec/get_db.sh index 9d17bf25eb7c9b974028c3b9f3691ceabd23afab..bcdf19e42dc921516315abc0ff9a5d0401173501 100644 --- a/highspec/get_db.sh +++ b/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 diff --git a/highspec/startup.sh b/highspec/startup.sh index a76249de52d8a492d31459e7bd8516cf4d11da64..5c642dd136a778c88bd02ca74c5b49cefaa9315f 100644 --- a/highspec/startup.sh +++ b/highspec/startup.sh @@ -1,35 +1,5 @@ #!/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 $mountpoint diff --git a/highspec/startup.sh.old b/highspec/startup.sh.old new file mode 100644 index 0000000000000000000000000000000000000000..a76249de52d8a492d31459e7bd8516cf4d11da64 --- /dev/null +++ b/highspec/startup.sh.old @@ -0,0 +1,77 @@ +#!/bin/bash + +CURRDIR="$( 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 + diff --git a/highspec/userdata_script b/highspec/userdata_script index 0a2bff0279e53ab082545fcc30a16f93b962ef1a..0689721ca9807be87ee565483f3bfc6815ca9d60 100644 --- a/highspec/userdata_script +++ b/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 diff --git a/highspec/userdata_script.old b/highspec/userdata_script.old new file mode 100644 index 0000000000000000000000000000000000000000..0a2bff0279e53ab082545fcc30a16f93b962ef1a --- /dev/null +++ b/highspec/userdata_script.old @@ -0,0 +1,12 @@ +#!/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 +