SNOMED International Mapping Tool

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Overview

Information on the ICD11 mapping project.

  • ModuleId: 123456789
  • RefsetId: icd11RefsetId

Regression Set

This defines concepts reviewed, the target codes they should have so that it can be used to validate against changes in the algorithm.

Deployment S erver Details

Software installed

  • csh, git, maven

Important details

  • Log in as your user (requires key to be configured)
  • User should have "sudo" rights
  • The server runs as the "mapping-service" user. 

    • For a shell as this user

      sudo su
su -s /bin/bash mapping-service
  • App details
    • star/stop server "supervisorctl start/stop mapping-service"
      • look at /etc/supervisor/conf.d/mapping-service.conf for details
    • Admin tools in: /opt/mapping-service-admin/admin (run as mapping-service user)
      • /opt/mapping-service-admin/admin/lucene/mvn install -PReindex -Drun.config=/opt/mapping-service/conf/config.properties
    • Data: in /opt/mapping-data
      • conf - configuration files
      • indexes - lucene indexes
    • Logs - /var/log/supervisor
      • mapping-service-stderr---supervisor-79oJH0.log
      • mapping-service-stdout---supervisor-6Jv0gZ.log
    • Instead of tomcat we use webapp-runner.jar which is a tomcat wrapped up. Allows us to package a known tomcat/webapp package.
    • It is installed to /opt/mapping-service with data in /opt/mapping-data and admin in /opt/mapping-admin
    • a Jenkins job exists allowing you to install wrt updating code or what ever  - see below
  • Jenkins Deploy - https://jenkins.ihtsdotools.org/view/Mapping/job/deploy-to-prod-mapping-icd11/

Details to configure:

Data files for this project are in /home/ihtsdo/data/ICD11

  • icd11Concepts.txt - faked from the "linearization" file to be oriented around "entityId" while showing the codes.
  • icd11ParChd.txt - faked from the "linearization" file to expres relationships between codes that have obvious par/chd relationships (as devined by the textual codes but not the entity codes)
  • icd11Map.txt - the computed map (from the algorithm)
  • icd11MapNotes.txt - the computed map notes (from the algorithm)

These steps were taken to set up the project

  • Manually create and configure the project as mapping admin
    • SNOMED to ICD11 Pilot - top level metadata for project
    • Map Leads selected
    • No map specialists
    • Map relations configured
    • Map age ranges configured
    • Scope concepts configured (starter set minus procedures)
  • Remake "SNOMED to ICD11" as a copy.
    • Scope definition configured (ICD10 scope, minus starter set, minus procedures)


Helpful Admin Commands

A cycle of redeploying maps involves running the algorithm to generate the "icd11Map.txt" and "icd11MapNotes.txt" files.  Assuming everything described above is already configured, the task here is simply to replace the data.  This is done with the "reload.csh" script in /home/ihtsdo/data/ICD11/reload.csh. 

#!/bin/csh -f

set rc = run.config=/home/ihtsdo/config/config.properties
echo "---------------------------------------------------"
echo "Starting ...`/bin/date`"
echo "---------------------------------------------------"
sudo service tomcat stop

echo "  Removing old maps ...`/bin/date`"
cd ~/code/admin/remover
mvn install -PMapRecords -D$rc -Drefset.id=icd11RefsetId | sed 's/^/     /'

echo "  Adding new maps ...`/bin/date`"
cd ~/code/admin/loader
mvn install -PMapRecords -D$rc -Dinput.file=/home/ihtsdo/data/ICD11/icd11Map.txt \
  -Dmember.flag=false -Drecord.flag=true
mvn install -PMapNotes -D$rc -Dinput.file=/home/ihtsdo/data/ICD11/icd11MapNotes.txt

sudo service tomcat start

echo "---------------------------------------------------"
echo "Finished ...`/bin/date`"
echo "---------------------------------------------------"