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Information on building and deploying UMLS.

Steps

  1. Download UMLS and unpack into a local directory.
    1. https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html

  2. Run MetamorphoSys and install the Level 0+SNOMED configuration but make sure to exclude NCBI as well (it is very large).
    1. Note the "META" directory of the output.
    2. Alter the MRHIER.RRF to keep only rows for SAB=MSH or SAB=USPMG, all other hierarchies will be computed.

  3. Configure a c:/umlsserver/config/config-rrf.properties file based on the config.properties from the prod config project.
    1. Make sure database info and paths are configured properly for your environment (so as to not overwrite data from other builds).
    2. See this sample
  4. Run an eclipse process to load the entire UMLS RRF


  5. Run the server in dev mode through eclipse to test,

  6. Export the mysql database → snomedct.sql, then zip it as snomedct-sql.zip and put into S3
    1. https://s3.amazonaws.com/wci1/TermServer/umls.sql.gz 
  7. Log into a.terminology.tools and become the ec2-tomcat user (need sudo priveleges for "sudo -u ec2-tomcat -i")

  8. Update the landing page (e.g. "UMLS-Terminology-Server\config\prod\src\main\resources\app\page\general\landingContent.html") to update the references to the latest version, e.g. 2016AA → 2017AA
    1. Repeat for the "loginContent.html" page too.

  9. Update and rebuild the code (master branch) - **Note: this may require merging from "develop"

    cd ~/snomed/code
git pull
mvn -Drun.config.label=ts -Dconfig.artifactId=term-server-config-prod-snomedct clean install

  10. Go to ~/snomed and look at README.txt.  See the "RELOADING DATA" section, e.g.

    RELOADING DATA

* Undeploy and start maintenance page
/bin/rm -rf /var/lib/tomcat8/work/Catalina/localhost/snomed-server-rest
/bin/rm -rf /var/lib/tomcat8/webapps/snomed-server-rest
/bin/rm -rf /var/lib/tomcat8/webapps/snomed-server-rest.war
/opt/maint/getMaintHtml.sh start snomed

# deploy data - ~30 min
cd ~/snomed/data
wget https://wci1.s3.amazonaws.com/TermServer/snomedct-sql.zip
### NOTE: if this step gets stuck (should take < 1 min) it means tomcat session has "Locked" the DB
### you're best bet is to log in as root and bounce tomcat with "service tomcat8 restart" 
mysqls < ~/snomed/code/admin/mojo/src/main/resources/truncate_all.sql
unzip -p snomedct-sql.zip "snomedct.sql" | mysqls &
wait
mysqls < ~/fixWindowsExportData.sql
/bin/rm ~/snomed/data/snomed-sql.zip

# recompute indexes (make sure latest code is built) - ~40 min
/bin/rm -rf /var/lib/tomcat8/indexes/snomedct/*
cd ~/snomed/code/admin/lucene
mvn install -PReindex  -Drun.config.umls=/home/ec2-tomcat/snomed/config/config.properties >&! mvn.log &

# Deploy and remove maintenance page
/bin/cp -f ~/snomed/code/rest/target/umls-server-rest*war /var/lib/tomcat8/webapps/snomed-server-rest.war
/opt/maint/getMaintHtml.sh stop snomed

# Remember to remove snomed.sql when finished (it takes a lot of space)



  11. Laucnch https://snomed.terminology.tools and verify that it's up and running and loaded with data you expect (E.g. search for a SNOMED concept new in the latest version)

  12. Consider announcements new version
    1. UMLS Users List Template
    2. Twitter Template
    3. LinkedIn (see past post - may be a reply to a message on the SNOMED group)
    4. Update WCI resources.html - http://westcoastinformatics.com/resources.html

 

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