SNOMED International Mapping Tool

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Overview

Describes how to set up and deploy the mapping tool to the IHTSDO mapping.ihtsdotools.org server.

Diagram

 

Details

  1. Log into the server 162.243.215.76 (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, svn, etc)
    1. You'll need the root user password

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

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

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

    4. Set permissions of the tomcat installation to the "ihtsdo" 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 /etc/init.d/tomcat7 to use the following
* TOMCAT7_USER=ihtsdo
* TOMCAT7_GROUP=ihtsdo

Edit /etc/default/tomcat7 
* TOMCAT7_USER=ihtsdo
* TOMCAT7_GROUP=ihtsdo
** This must be done while tomcat is NOT running.

    5. See ~root/README.txt

  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=/home/ihtsdo/data/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 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 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 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.

      [mysqld]
...
wait_timeout = 230400
interactive_timeout = 230400

  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

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

    JAVA_HOME=/path/to/java
MAVEN_OPTS=-Xmx3000M
OTF_MAPPING_HOME=/home/ihtsdo/code
OTF_MAPPING_CONFIG=/home/ihtsdo/config/config.properties
OTF_MAPPING_CONFIG_TEST=/home/ihtsdo/config/config.properties.test

  13. Get data.

    # Use your collabnet username below
set username = <your collabnet username>
cd
mkdir data
git clone ssh://$username@csfe.aceworkspace.net:29418/mapping data
# set up doc directories, for uploading mapping handbook files
mkdir data/doc
mkdir data/doc/archive
chmod -R ga+rwx data/doc

  14. Prepare indexes to be maintainable by ihtsdo user.

    # 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



  15. Create a config.properties file by starting with one of those in the config project.  Edit the file as needed

    cd
mkdir config
cp -r code/config/src/main/resources/config.properties.prod ~/config/config.properties
# edit as needed
# In particular, make sure the config.properties file used to run the application has this setting
hibernate.search.default.indexBase=/var/lib/tomcat7/indexes/lucene/indexes 

  16. Build the environment using the prepared configuration as the build.config

    cd
cd code
mvn -Dbuild.config=~/config/config.properties clean install

  17. Unpack the admin scripts and do a full load - e.g. create database and load the data

    cd
unzip ~/code/admin/target/mapping-admin*zip
cd bin
load_prod.csh >&! load_prod.log

  18. 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

  19. 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

  20. Update file modification date to prevent caching issues.

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

  21. Build Rest and deploy war

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

  22. Deploy Webapp war

    /bin/cp -f ~/code/webapp/target/mapping-webapp*war /var/lib/tomcat7/webapps/ROOT.war

  23. Start service and link "doc" directory.

    service tomcat7 start

# wait for deploy to create the ROOT directory
sleep 10
# link doc directory
cd /var/lib/tomcat7/webapps/ROOT
ln -s /home/ihtsdo/data/doc

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

     

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