Update README.md

README.md

@@ -106,7 +106,118 @@ conda env create -f environment.yaml
 
 ## BigDataServer
 
-TODO
+Description: Client -> Nginx proxy tcp/80 -> Java application tcp/8020
+
+Start or stop the application
+```
+systemctl start/stop/restart bigdata-0.2.0
+systemctl start/stop/restart nginx
+```
+
+Monitor logs
+```
+tail /var/log/bigdata.log /var/log/nginx/error.log
+```
+
+- Add user
+```
+useradd --shell /sbin/nologin bigdata
+cat /etc/passwd |grep bigdata:
+bigdata:x:1000:1000::/home/bigdata:/sbin/nologin
+```
+
+- Configure Nginx (/etc/nginx/conf.d/cbb-bigdatra01.conf)
+```
+server {
+  listen       80;
+  server_name  cbb-bigdata01.embl.de;
+
+  location /0.2.0 {
+    proxy_pass       http://cbb-bigdata01.embl.de:8020/0.2.0;
+    proxy_set_header X-Real-IP $remote_addr;
+    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    proxy_set_header Host $http_host;
+  }
+
+  location /0.2.1 {
+    proxy_pass       http://cbb-bigdata01.embl.de:8021/0.2.1;
+    proxy_set_header X-Real-IP $remote_addr;
+    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    proxy_set_header Host $http_host;
+  }
+
+# Allow only GET, HEAD 
+if ($request_method !~ ^(GET|HEAD)$ )
+{
+       return 405;
+}
+
+# Allow only requests for published applications
+if ($request_uri !~ ^/0.2.0/.*|^0.2.1/.*) {return 403;}
+
+server_tokens off;
+
+large_client_header_buffers 4 32k;
+}
+```
+
+- Copy the application to /opt/bigdata/ and set permissions
+```
+chown -R bigdata.bigdata /opt/bigdata/*
+touch /var/log/bigdata.log
+chown bigdata.bigdata /var/log/bigdata.log
+```
+
+- Create Java application startup script (/opt/bigdata/bigdata.sh)
+```
+#!/bin/sh
+
+# Check	that the parameter is given for	the version
+if [ -z "$1" ]
+  then
+    echo "No instance version supplied"
+    exit 1
+fi
+
+# Create the listening port from the version
+port=$(echo "8" $1 |sed 's/[^0-9]//g')
+
+# Mount the network drive if not mounted
+if  [ ! -f /data/s3 ]; then echo "S3 not mounted, mounting"; 
+goofys --endpoint https://s3.embl.de --uid=1000 --gid=1000 --dir-mode=0777 --file-mode=0666 --profile embl  cbb-bigdata /data;
+fi
+
+echo "Starting the server"
+cd /data/platy-browser-data/data/$1/misc/
+java -Xmx4G -jar /opt/bigdata/bigdataserver.jar -d /data/platy-browser-data/data/$1/misc/bdv_server.txt -s cbb-bigdata01.embl.de -p 80 -b $port -P /0.2.1 -t /var/thumb  &>/var/log/bigdata.log &
+```
+
+- Create Systemd for Java application (/etc/systemd/system/bigdata-0.2.0.service)
+```
+[Unit]
+Description=Bigdata Platy image server 0.2.0
+After=network.target
+
+[Service]
+User=bigdata
+Group=bigdata
+Type=forking
+ExecStart=/opt/bigdata/bigdata.sh 0.2.0
+ExecReload=/bin/kill -s HUP $MAINPID
+ExecStop=/bin/kill -s QUIT $MAINPID
+
+[Install]
+WantedBy=multi-user.targe
+```
+
+- Enable and start the services
+```
+systemctl daemon-reload
+systemctl enable bigdata-0.2.0
+systemctl restart bigdata-0.2.0
+systemctl restart nginx
+```
+
 
 
 ## Data generation