ICD10 Mapping

Overview

Information on the ICD10 mapping project.

• ModuleId: 449080006              
• RefsetId: 447562003

Helpful Admin Commands

Remove

cd /opt/mapping-service-admin/admin/remover
// DO NOT DO THIS  mvn install -PMapRecords -D$rc -Drefset.id=447562003
mvn install -PTerminology -D$rc -Dterminology=ICD10 -Dversion=2016

Load Previous version RF2

in DB, first remove complex map refset members

DELETE from complex_map_refset_members where refsetId = 447562003; 

Note: (this should also be able to be run with this: 

Get maintenance window

cd /opt/mapping-service-admin/admin/remover  

mvn install -PMapMembers -D$rc -Drefset.id=447562003)

cd /opt/mapping-service-admin/admin/loader
set file = /home/ihtsdo/data/doc/release/20170131/icd10/der2_iisssccRefset_ExtendedMapSnapshot_INT_20170131.txt
perl -ne '@_=split/\t/; print if $_[4] eq "447562003"' $file > /tmp/x.txt
mvn install -PMapRecords -D$rc -Dinput.file=/tmp/x.txt -Dmember.flag=true -Drecord.flag=false

To validate:

select count(*) from complex_map_refset_members a, map_projects b where a.refsetId = b.refSetId and mapProjectId = $mapProjectId and 

a.terminology = b.sourceTerminology and a.terminologyVersion = b.sourceTerminologyVersion;

Compute

cd /opt/mapping-service-admin/admin/loader
mvn install -PComputeWorkflow -D$rc -Drefset.id=447562003

Release

These steps are now typically done through the Release Handling accordion in the UI on prod-mapping-release, after the clone from prod-mapping.

cd /opt/mapping-service-admin/admin/release
mvn install -PBeginRelease -D$rc -Drefset.id=447562003 -Dtest.mode.flag=true
mvn install -PRelease -D$rc -Drefset.id=447562003 -Doutput.dir=. -Dtime=20170731 -Dmodule.id=449080006 -Dtest.mode.flag=true
mvn install -PFinishRelease -D$rc -Drefset.id=447562003 (This process currently takes 36 hours. 26 of these hours is in loading the refset members at the end.)
mvn install -PBeginEditingCycle -D$rc -Drefset.id=447562003

Release with Alpha/Beta Iteration

These first steps of reloading snomed are now typically done on the prod-mapping server. Skip steps 2 - 5 on the first iteration.
1.) Take server down.  supervisorctl stop mapping-rest

2.) cd /opt/mapping-admin/remover
3.) mvn install -PTerminology -Drun.config=/opt/mapping-rest/config.properties -Dterminology=SNOMEDCT -Dversion=latest
4.) cd /opt/mapping-admin/loader
5.) mvn install -PRF2-snapshot -Drun.config=/opt/mapping-rest/config.properties -Dterminology=SNOMEDCT -Dinput.dir=/home/ihstdo/data/xSnomedCT_InternationalRF2_ALPHA_20170731T120000Z/Snapshot

6.) DELETE from complex_map_refset_members where refsetId = 447562003; 
7.) cd /opt/mapping-admin/loader
8.) set file = /home/ihtsdo/data/doc/release/20170131/icd10/der2_iisssccRefset_ExtendedMapActiveSnapshot_INT_20200731.txt

perl -ne '@_=split/\t/; print if $_[4] eq "447562003"' $file > /tmp/icd10.20200731.txt
mvn install -PMapRecords -Drun.config=/opt/mapping-rest/config.properties -Dinput.file=/tmp/icd10.20200731.txt -Dmember.flag=true -Drecord.flag=false

Note: this step requires the ActiveSnapshot file.  If you have the plain Snapshot file, you'll need to remove inactive content as follows: awk '$3 == "1" { print $_ }' icd10.txt > icd10active.txt

8a.) Bring server back up.

9.) rerun compute workflow to ensure that there aren't any new concepts in scope that need to be mapped, begin, and process release steps (these steps happen through the UI)

Loading "Human Readable" View

TBD

Updating Published Project

# Remove old records
cd /opt/mapping-admin/remover
mvn install -PMapRecords -Drun.config=/opt/mapping-rest/config.properties -Drefset.id=P447562003

# Add updated records
cd /opt/mapping-admin/loader
/bin/rm -f x.txt
perl -ne 's/447562003/P447562003/; @_=split/\t/;print if $_[4] eq "P447562003"; ' /opt/mapping-data/doc/release/SNOMEDCT_to_ICD10_447562003/20200731/der2_iisssccRefset_ExtendedMapActiveSnapshot_INT_20200731.txt > x.txt
mvn install -PMapRecords -Drun.config=/opt/mapping-rest/config.properties -Dinput.file=x.txt -Dmember.flag=false -Drecord.flag=true

Remove old reports

service tomcat7 stop

References/Links

• n/a