Page Comparison

...

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

Details

1. Log into the server 162server 10.243230.215174.7616
   
   1. You'll need the ihtsdo user password (uat3#Map for UAT, prod3#Map for prod)to be able to sudo su - to root and ec2-tomcat.
      
      
2. Install and configure software as root (nginx,tomcat7, libapache2_mod_jk, mysql-server-5.5, maven, git, svn, etc)
   
3. You'll need the root user password
.

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:

    

   Code Block
   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 "ihtsdoec2-tomcat"user

    

    

   chown -R ihtsdo /var/log/tomcat7

   chgrp -R ihtsdo /var/log/tomcat7

   chown -R ihtsdo /var/cache/tomcat7

   chgrp -R ihtsdo /var/cache/tomcat7

   chown -R ihtsdo  /var/lib/tomcat7

   chgrp -R ihtsdo  /var/lib/tomcat7

    

   Edit

   Code Block
   # 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

   *

   TOMCAT7

   TOMCAT_USER=

   ihtsdo

   * TOMCAT7_GROUP=ihtsdo

    

   Edit /etc/default/tomcat7

   * TOMCAT7_USER=ihtsdo

   * TOMCAT7_GROUP=ihtsdo

   ** This must be done while tomcat is NOT running.
   See ~root/README.txt

   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. 

    

4. 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 /etc/init.dusr/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
      
      
5. Tomcat must be configured to support POST requests of size > 2MB
   1. Edit server.xml and add  maxPostSize="50000000" to each <Connector> element.
      
      
6. 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.
      
      
7. Make sure you have MAVEN_OPTS set 
   
   1. e.g. -XX:MaxPermSize=512m -Xmx3072m
8. Nginx Configuration
   
   1. Install the SSL keys as root in the appropriate places
   2. Edit /etc/nginx/sites-available/mapping.ihtsdotools.org (see the webapp/src/main/nginx directory for configurations).
   3. Link /etc/nginx/sites-enabled/mapping.ihtsdotools.org to the file above(if SSH needed)
   4. Add a file "snomed.term-server.com.conf" to /etc/nginx/conf.d

   5. Add a Valve to tomcat to handle proxy headers.
      

      Code Block
      <Valve className="org.apache.catalina.valves.RemoteIpValve" remoteIpHeader="x-forwarded-for" remoteIpProxiesHeader="x-forwarded-by" protocolHeader="x-forwarded-proto"/>

   6. Edit /etc/nginx/nginx.conf and add "client_max_body_size 50M;" to the "http" context.
   7. See the attachment for more details/etc/nginx/nginx.conf contains the master configuration - see for details
   8. For more info click here
       

9. 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';

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

     

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

11. Get code

     

    cd mkdir code cd code git clone https://github.com/WestCoastInformatics/OTF-Mapping-Service.git .   # switch to dev branch - for UAT git checkout develop   # switch to dev branch - for PROD git checkout master   mvn -DskipTests=false clean install

12. Get data.

     

    cd mkdir data git clone ssh://csfe.aceworkspace.net:29418/mapping data mkdir data/doc mkdir data/doc/archive chmod -R ga+rwx data/doc

13. 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 mkdir /var/lib/tomcat7/indexes/lucene mkdir /var/lib/tomcat7/indexes/lucene/indexes chmod -R ga+rwx /var/lib/tomcat7/indexes chown -R ihtsdo /var/lib/tomcat7/indexes chgrp -R ihtsdo /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/lucene/indexes

     

    
    
    

14. Create and Load the data

     

    cd ~/code/admin/loader/scripts load_prod.csh >&! load_prod.log

     

    Note also that TreePositions will be automatically calculated when loading a terminology.  To recompute SNOMED tree positions without reloading terminology, use:

     

    cd ~/code/admin/loader mvn -Drun.config=prod -P SNOMEDCT-treepos

15. 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/mapping-rest /bin/rm -rf /var/lib/tomcat7/webapps/mapping-rest /bin/rm -rf /var/lib/tomcat7/webapps/ROOT /bin/rm -rf /var/lib/tomcat7/webapps/mapping-rest.war /bin/rm -rf /var/lib/tomcat7/webapps/ROOT.war

16. 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

17. Update file modification date to prevent caching issues.

     

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

18. Build Rest and deploy war

     

    cd ~/code/rest mvn -Drun.config=$OTF_MAPPING_CONFIG clean install /bin/cp -f target/mapping-rest*war /var/lib/tomcat7/webapps/mapping-rest.war

19. Build Webapp war

     

    cd ~/code/webapp mvn -Drun.config=$OTF_MAPPING_CONFIG clean install /bin/cp -f target/mapping-webapp*war /var/lib/tomcat7/webapps/ROOT.war

20. Start service and link "doc" directory.

     

    service tomcat7 start   # wait for deploy to create the ROOT directory sleep 5 # link doc directory cd /var/lib/tomcat7/webapps/ROOT ln -s /home/ihtsdo/data/doc

21. NOW, if deploying to PROD, create a github pull request.
    
    

22. Wire tomcat to redirect to the home URL.  In the webapp root find the ROOT application and replace the index.html page. e.g.
    NOTE:  DO NOT do this step anymore as the application is now deployed as the root war

     

    <?xml version="1.0" encoding="ISO-8859-1"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head>     <meta http-equiv="refresh" content="0; url=/mapping-webapp/app/index.html#/" />     <title>IHTSDO Mapping Tool - redirect</title> </head> <Body> </body> </html>

...