xml2claml.pl

Overview

Information on the ICD10CM mapping project.

  • ModuleId: 5991000124107
  • RefsetId: 6011000124106

Helpful Admin Commands

Setting up new ICD10CM Mapping Project

Load ICD10CM

Do xml to claml conversion to create icd10cm file to load.

 ./xml2claml.pl -episode 2018-ICD-10-Table-And-Index/icd10cm_tabular_2018.xml > icd10cm_2018.xml

Remove the following line from icd10cm_2018.xml

<!DOCTYPE ClaML SYSTEM "ClaML.dtd">


Load icd10cm_2018.xml to /home/ihtsdo/data/ICD10CM
Change owner of icd10cm_2018.xml to root
Load icd10cm data
cd /opt/mapping-service-admin/admin/loader
mvn clean install -PClaML -Drun.config=/opt/mapping-service/conf/config.properties -Dinput.file=/home/ihtsdo/data/ICD10CM/icd10cm-2018.xml -Dterminology=ICD10CM -Dversion=2018

Load SNOMEDCT_US

Pre-process the map file to clean up map relations  (see code below - examples 109006, 2217001, 2268003)

cd /opt/mapping-service-admin/admin/loader
make sure complex_map_refset_members table mapRule field is type longtext, not varchar(255)
make sure enough memory is provided (consider ~/.bash_profile): export MAVEN_OPTS="-XX:MaxPermSize=512m -Xmx3300M"
mvn clean install -PRF2-snapshot -Drun.config=/opt/mapping-service/conf/config.properties -Dinput.dir=/home/ihtsdo/data/SNOMEDCT_US/SnomedCT_USEditionRF2_Production_20170301T120000/Snapshot -Dterminology=SNOMEDCT_US -Dversion=latest

Make SNOMEDCT_US to ICD10CM project logged in as Administrator
Confirm refsetId by looking for mapping in the Terminology/..descriptions.. file in the SNOMEDCT_US release files refsetId (6011000124106)

Load Map Records from RF2
cd /opt/mapping-service-admin/admin/loader
set file = /home/ihtsdo/data/SNOMEDCT_US/SnomedCT_USEditionRF2_Production_20170301T120000/Snapshot/Refset/Map/der2_iisssccRefset_ExtendedMapSnapshot_US1000124_20170301.txt
perl -ne '@_=split/\t/; print if $_[4] eq "6011000124106"' $file > /tmp/x.txt
mvn install -PMapRecords -Drun.config=/opt/mapping-service/conf/config.properties -Dinput.file=/tmp/x.txt -Dmember.flag=false -Drecord.flag=true

Compute workflow
cd /opt/mapping-service-admin/admin/loader
mvn install -PComputeWorkflow -Drun.config=/opt/mapping-service/conf/config.properties -Drefset.id=6011000124106

Add advices, map relations, users

 

 

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