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1. Log into the server mapping.ihtsdotools.org
   
   1. Ensure there is an "ihtsdo" user - everything will run as this user
      
      
2. Install and configure software as root (nginx, tomcat7, libapache2_mod_jk, mysql-server-5.5, maven, git, etc)
   
   1. You'll need the root user password

   2. Set up your maven settings.xml according to Settings.xml Page.

   3. Edit the /etc/init.d/tomcat7 script to comment out the top part that forces running as root

      Code Block
      #if [ `id -u` -ne 0 ]; then # echo "You need root privileges to run this script" # exit 1 #fi

   4. Edit the /etc/init.d/tomcat7 script to use this:

      Code Block
      CATALINA_PID="/var/lib/tomcat7/$NAME.pid"

   5. Set permissions of the tomcat installation to the "ihtsdo" user:

      Code Block

      ** This must be done while tomcat is NOT running. 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 /etc/init.d/tomcat7 to use the following * TOMCAT7_USER=ihtsdo * TOMCAT7_GROUP=ihtsdo Edit /etc/default/tomcat7 * TOMCAT7_USER=ihtsdo * TOMCAT7_GROUP=ihtsdo

   6. See ~root/README.txt [file not present]
      
      

3. 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=~/opt/mapping-service/conf/config/config.properties
      (e.g. edit this in /etc/init.d/tomcat7 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
      
      
4. Tomcat must be configured to support POST requests of size > 2MB
   1. Edit /var/lib/tomcat7/conf/server.xml and add  maxPostSize="50000000" to each <Connector> element.
      
      
5. Tomcat must be configured to support following of links.  Make sure any Context tags in the configuration contain  allowLinking="true".
   1. Edit /var/lib/tomcat7/conf/context.xml to add this parameter to the Context tag.
      
      
6. Make sure you have MAVEN_OPTS set
   
   1. e.g. -XX:MaxPermSize=512m -Xmx3072m
      
      
7. 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
   4. Add a Valve to tomcat to handle proxy headers.
   5. Edit /etc/nginx/nginx.conf and , edit or add "client_max_body_size 50M;" to the "http" context.
   6. See the attachment for more details
      
      

8. 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:

      Code Block
      [mysqld] ... wait_timeout = 1048576 interactive_timeout = 1048576

   3. It may also be worth considering using the innodb table per file option

      Code Block
      [mysqld] ... innodb_file_per_table

      This is useful to better manage the overall size of the database because individual tables can then be optimized rather than having to dump/reload the entire database.

   4. Consider other optimizations to mysql parameters (e.g. http://www.percona.com/blog/2014/01/28/10-mysql-settings-to-tune-after-installation/)

   5. Restart MySQL for the changes to take effect. 

      Code Block
      /etc/init.d/mysql restart

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

   Code Block
   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:

    Code Block
    CREATE DATABASE mappingservicedb DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_bin; GRANT ALL ON mappingservicedb.* TO 'otf';

11. Create "code", "config", and "data" directories

    1. ~/code - for the code

    2. ~/data - for the data files (only needed on initial load)

    3. ~/opt/mapping-service/config - for the configuration files and configurable admin scripts:

       Code Block
       cd mkdir code mkdir data mkdir config [may already exist in /opt/mapping-service/]

12. Get code:

    Code Block
    cd ~/code git clone https://github.com/IHTSDO/OTF-Mapping-Service.git . # switch to dev branch - for UAT git checkout develop # switch to dev branch - for PROD git checkout master

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

    Code Block
    JAVA_HOME=/path/to/java MAVEN_OPTS=-Xmx3000M

14. Build all of the code, making sure to choose the correct "config.artifactId" for your environment.  Shown is "prod" configuration:

    Code Block
    cd ~/code mvn -Dconfig.artifactId=mapping-config-prod clean install

15. If have a new project go to 16 to get the data, otherwise jump to 17.
    
    

16. Get data:

    Code Block
    cd ~/data git clone https://git.ihtsdotools.org/ihtsdo/ihtsdo-mapping-tool-data.git data # set up doc directories, for uploading mapping handbook files mkdir data/doc mkdir data/doc/archive chmod -R ga+rwx data/doc

17. Prepare indexes to be maintainable by ihtsdo user:

    Code Block
    # 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:ihtsdo /var/lib/tomcat7/indexes

    
    
    

18. Unpack the config artifact corresponding to your environment The example shown below is for "prod":

    Code Block
    cd ~/config unzip ~/code/config/prod/target/mapping-config-prod.*.zip

19. Edit the configuration file and scripts.

    1. Edit config.properties and replace the "EDIT_THIS" entries with real values (mostly passwords, etc).

    2. Edit the mail notification settings to list email addresses of those admins or maintenance staff that should be notified of errors and/or automation outcomes.

    3. Edit the scripts in bin/ as needed for this environment (default setup requires no changes).
       
       

20. Edit the load script for your environment. Run it to load the data:

    Code Block
    cd ~/config/bin ./load.csh >&! load.log

21. Deploy war files:

    Code Block
    /bin/cp -f ~/code/rest/target/mapping-rest*war /var/lib/tomcat7/webapps/mapping-rest.war

22. Start service and link "doc" directory:

    Code Block
    service tomcat7 start # wait for deploy to create the ROOT directory sleep 10 # link doc directory cd /var/lib/tomcat7/webapps/mapping-rest ln -s ~/data/doc

23. Setup cron jobs for nightly/weekly automations.  For example,

    Code Block

    # * * * * * command to execute # ? ? ? ? ? # ? ? ? ? ? # ? ? ? ? ?????? day of week (0 - 6) (0 to 6 are Sunday to Saturday, or use names; 7 is Sunday, the same as 0) # ? ? ? ??????????? month (1 - 12) # ? ? ???????????????? day of month (1 - 31) # ? ????????????????????? hour (0 - 23) # ?????????????????????????? min (0 - 59)   0 23 * * 4 csh /home/ihtsdo/config/bin/loadDelta.csh > /home/ihtsdo/logs/loadDelta.log 2>&1 0 0 * * 0,1,2,4,5,6 csh /home/ihtsdo/config/bin/qaCron.csh > /home/ihtsdo/logs/qaCron.log 2>&1 0 0 * * 0,1,2,4,5,6 csh /home/ihtsdo/config/bin/dailyReports.csh > /home/ihtsdo/logs/dailyReports.log 2>&1

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