Deploy Instructions

Overview

Describes how to set up and deploy the application to the WCI term-server.com server.

Diagram

Details

Log into the server 10.230.174.16
1. You'll need to be able to sudo su - to root and ec2-tomcat.
Install and configure software as root (nginx, tomcat7 (and webapps), mysql-server-5.5 (and client), Java/jdk (including devel), maven, git, svn, etc.
1. Edit the /etc/init.d script to comment out the top part that forces running as root
2. Edit the /etc/init.d script to use this so the ec2-user can write the pid file:
```
CATALINA_PID="/var/lib/tomcat7/$NAME.pid"

# also change all instances of /var/run to /var/lib/tomcat7 
```
3. Set permissions of the tomcat installation to the "ec2-tomcat"user
```
# for each linked directory in /usr/share/tomcat7 d
chown -R ec2-tomcat $dir
chgrp -R ec2-user $dir


Edit /etc/init.d/tomcat7 to use the following
* TOMCAT_USER=ec2-tomcat
* TOMCAT_GROUP=ec2-user


Also edit /etc/tomcat7.conf
* CATALINA_PID=/var/lib/tomcat7/tomcat7.pid
* TOMCAT_USER=ec2-tomcat
* TOMCAT_GROUP=ec2-user


Make sure all the "chown" commands in the script change to group to $TOMCAT_USER
```
  NOTE: the tomcat user can start/stop the server with "/usr/sbin/tomcat7 start/stop".
  HOWEVER: if the process was started by root, it will likely have to be killed by root first.. we're working on this.
Tomcat must be configured to pass "run.config" environment variable to the application
1. One way to do this is to invoke the java command with -Drun.config=/home/ihtsdo/data/config.properties
  (e.g. edit this in /usr/share/tomcat7/conf/tomcat7.conf and add to JAVA_OPTS)
2. Also add -Xmx2500M to JAVA_OPTS in the tomcat startup script.
3. NOTE: development environments must also be configured as such
Tomcat must be configured to support POST requests of size > 2MB
1. Edit server.xml and add maxPostSize="50000000" to each <Connector> element.
Tomcat must be configured to support following of links. Make sure any Context tags in the configuration contain allowLinking="true".
1. Edit context.xml to add this parameter to the Context tag.

To enable tomcat manager, add this to tomcat-users.xml file.

<role rolename="manager-gui" />
<user name="tomcat" password="********" roles="manager-gui" />
<role rolename="protected" />

Make sure you have MAVEN_OPTS set
1. e.g. -XX:MaxPermSize=512m -Xmx5000m
Nginx Configuration
1. Install the SSL keys as root in the appropriate places (if SSH needed)
2. Add a file "snomed.term-server.com.conf" to /etc/nginx/conf.d
3. Add a Valve to tomcat to handle proxy headers.
```
        <Valve className="org.apache.catalina.valves.RemoteIpValve"
               remoteIpHeader="x-forwarded-for"
               remoteIpProxiesHeader="x-forwarded-by"
               protocolHeader="x-forwarded-proto"/>
```
4. Edit /etc/nginx/nginx.conf and add "client_max_body_size 50M;" to the "http" context.
5. /etc/nginx/nginx.conf contains the master configuration - see for details
6. For more info click here
MySQL Configuration
1. When configuring the database URL in config.properties, use ?autoconnect=true to avoid connection issues
2. Also (as root) edit the my.cnf file for your platform and add this to the mysqld section.
```
[mysqld]
...
wait_timeout = 230400
interactive_timeout = 230400
```

As the MySQL root user, create an OTF user with the mysql client

CREATE USER 'otf'@'localhost' IDENTIFIED BY 'otfpwd';
GRANT ALL privileges ON *.* TO 'otf'@'localhost';

As the MySQL root user, create a database in the mysql client

CREATE DATABASE tsdb
  DEFAULT CHARACTER SET utf8
  DEFAULT COLLATE utf8_general_ci;
CREATE DATABASE tsdbtest
  DEFAULT CHARACTER SET utf8
  DEFAULT COLLATE utf8_general_ci;
GRANT ALL ON tsdb.* TO 'otf';
GRANT ALL ON tsdbtest.* TO 'otf';

Get code

cd
mkdir code
cd code
git clone https://github.com/WestCoastInformatics/SNOMED-Terminology-Server.git .
 
# switch to dev branch - for UAT
git checkout develop
 
# switch to dev branch - for PROD
git checkout master

Prepare the environment (set your shell up with these ENV variables):

JAVA_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64
MAVEN_OPTS=-Xmx3000M
SERVER_HOME=/home/ec2-tomcat/code
SERVER_CONFIG=/home/ec2-tomcat/config/config.properties
SERVER_CONFIG_TEST=/home/ec2-tomcat/config/config.properties.test

The sample data lives in the "config" project. Install in the ~/data directory
```
cd
mkdir data
cp -r code/config/src/main/resources/* data
```

Prepare a config file

cd
mkdir config
cp -r code/config/src/main/resources/config.properties.prod ~/config/config.properties
# edit as needed
# in particular, set base.url to the base URL for this environment - needed by Swagger. e.g.
#   base.url=http://snomed.terminology.tools

Build the environment using the prepared configuration as the build.config
```
cd
cd code
mvn -Dbuild.config=~/config/config.properties clean install
```

Prepare the tomcat indexes location

# To clean up the indexes do this (as root)
/bin/rm -rf /var/lib/tomcat7/indexes
mkdir /var/lib/tomcat7/indexes
chmod -R ga+rwx /var/lib/tomcat7/indexes
chown -R ec2-tomcat:ec2-user /var/lib/tomcat7/indexes
 
# Ensure the config.properties file used to run the application has this setting
hibernate.search.default.indexBase=/var/lib/tomcat7/indexes/

Create and Load the data

cd
mkdir bin
cp ~/code/admin/loader/scripts/* bin
chmod 775 bin/*
cd bin
./load.csh >&! load.log

Stop tomcat, clear cache,and remove the currently deployed .war files (and associated folders).

# Stop the tomcat7 server
service tomcat7 stop
/bin/rm -rf /var/lib/tomcat7/work/Catalina/localhost/term-server-rest
/bin/rm -rf /var/lib/tomcat7/webapps/term-server-rest
/bin/rm -rf /var/lib/tomcat7/webapps/term-server-rest.war

Update the database (this needs to go into the reload page):

mvn clean install -Drun.config=/home/ihtsdo/config/config.properties -Dhibernate.hbm2ddl.auto=update

Update file modification date to prevent caching issues.

cd ~/code
set date = `date +%Y%m%d%H%M`
touch -t $date `find . -name "*"`

Build Rest and deploy war

cd ~/code/rest
mvn -Drun.config=$SERVER_CONFIG -Dbase.url=http://snomed.terminology.tools clean install
/bin/cp -f target/term-server-rest*war /var/lib/tomcat7/webapps/term-server-rest.war

Start service
```
service tomcat7 start
```

Run the integration tests.

cd
cd code/integration-test
mvn -DskipTests=false -Drun.config.test=$SERVER_CONFIG_TEST test

References/Links

n/a