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