Information on the GMDN mapping project.
The following steps were used to create the projects:
* 20 * * 0,1,2,3,4,5,6 csh /home/ihtsdo/config/bin/pullGmdn.csh > /home/ihtsdo/logs/pullGmdn.log 2>&1 |
% ls -lt /home/ihtsdo/data/GMDN/17_1 total 93700 -rw-rw-r-- 1 ihtsdo ihtsdo 58681302 Jan 3 12:02 termcollectiveterm17_1.xml -rw-rw-r-- 1 ihtsdo ihtsdo 34357440 Jan 3 11:57 term17_1.xml -rw-rw-r-- 1 ihtsdo ihtsdo 1889072 Jan 3 11:56 collectiveterm17_1.xml -rw-rw-r-- 1 ihtsdo ihtsdo 1003824 Jan 3 11:56 cttreenode17_1.xml |
As a separate (and currently manual process), the GMDN version should be loaded (the server must be taken down for this process). NOTE: if there are any problems, download the GMDN version (e.g. zip and copy to the "doc" folder and the file should be accessible, e.g. https://mapping.ihtsdotools.org/doc/17_1.zip) and try loading it into a local dev environment to track down the errors. The loader assumes the structure of the .xml files is constant - if it changes that may cause problems.
# This process takes about 15 min service tomcat7 stop cd ~/code/admin/loader mvn install -PGMDN -Dinput.dir=/home/ihtsdo/data/GMDN/17_1 \ -Dterminology=GMDN -Dversion=17_1 -Drun.config=/home/ihtsdo/config/config.properties |
Determine the older version(s) of GMDN
mysql> select distinct destinationTerminologyVersion from map_projects where destinationTerminology='GMDN'; +-------------------------------+ | destinationTerminologyVersion | +-------------------------------+ | 16_10 | +-------------------------------+ |
Remove the older version, then restart the server
# This process takes under 5 min cd ~/code/admin/remover mvn install -PTerminology -Dterminology=GMDN -Dversion=16_10 -Drun.config=/home/ihtsdo/config/config.properties service tomcat7 start |
Remove
cd ~/code/admin/remover
mvn install -PMapRecords -D$rc -Drefset.id=467614008
mvn install -PTerminology -D$rc -Dterminology=GMDN -Dversion=latest
Load
Get maintenance window
cd ~/code/admin/loader
mvn install -PGMDN -Dinput.dir=/home/ihtsdo/data/GMDN/16_10 -Dterminology=GMDN -Dversion=17_1 -D$rc
cd ~/code/admin/loader
set file = /home/ihtsdo/data/doc/release/20160731/gmdn/der2_sRefset_SimpleMapSnapshot_INT_20160731.txt
/bin/rm -f /tmp/x.txt
perl -ne '@_=split/\t/; print if $_[4] eq "467614008"' $file > /tmp/x.txt
mvn install -PSimpleMapRecords -D$rc -Dinput.file=/tmp/x.txt -Dmember.flag=true -Drecord.flag=false
Compute
cd ~/code/admin/loader
mvn install -PComputeWorkflow -D$rc -Drefset.id=467614008
Release
cd ~/code/admin/release
mvn install -PBeginRelease -D$rc -Drefset.id=467614008 -Dtest.mode.flag=true
mvn install -PRelease -D$rc -Drefset.id=467614008 -Doutput.dir=. -Dtime=20170131 -Dmodule.id=466707005 -Dtest.mode.flag=true
mvn install -PFinishRelease -D$rc -Drefset.id=467614008
mvn install -PBeginEditingCycle -D$rc -Drefset.id=467614008
Similar approach to ICD10 but using the "simple" map loader. e.g.
cd ~/code/admin/loader set file = ~/data/GMDN/*2016*txt grep -v 900000000000207008 $file | perl -pe 's/467614008/P467614008/;' >! x.txt mvn install -PSimpleMapRecords -Drun.config=/home/ihtsdo/config/config.properties -Dinput.file=x.txt -Dmember.flag=false -Drecord.flag=true >&! mvn.log
On release server, stop the server (Get a maintenance window FIRST)
supervisorctl stop mapping-service |
On release server, remove simple map refset members with GMDN refsetId.
//in DB, first remove simplemap refset members DELETE from simple_map_refset_members where refsetId = 467614008; |
On release server, load previous release simple map refset members with GMDN refsetId from previous (e.g.20170131) release. Andrew will provide this file, or it should be on server in previous release file.
cd /opt/mapping-service-admin/admin/loader perl -ne '@_=split/\t/; print if $_[4] eq "467614008"' /home/ihtsdo/data/doc/release/20170131/gmdn/der2_sRefset_SimpleMapActiveSnapshot_INT_20170131.txt > /tmp/x.txt mvn install -PSimpleMapRecords -Drun.config=/opt/mapping-service/conf/config.properties -Dinput.file=/tmp/x.txt -Dmember.flag=true -Drecord.flag=false |
Remove SNOMEDCT 20170131.
Add SNOMEDCT 20170731 (this took 2 1/2 hours on the release server)
cd /opt/mapping-service-admin/admin/loader mvn install -PRF2-snapshot -Drun.config=/opt/mapping-service/conf/config.properties -Dterminology=SNOMEDCT -Dversion=20170731 -Dinput.dir=/home/ihtsdo/data/SNOMEDCT/SnomedCT_InternationalRF2_PRODUCTION_20170731T120000Z/Snapshot > /opt/mapping-service/logs/loadSnomed20170731.log |
Add GMDN 17_05. (OK if later versions remain in the db as long as the project references the correct release version)
cd /opt/mapping-service-admin/admin/loader mvn install -PGMDN -Dinput.dir=/home/ihtsdo/data/GMDN/17_5 \ -Dterminology=GMDN -Dversion=17_5 -Drun.config=/opt/mapping-service/conf/config.properties > /opt/mapping-service/logs/loadGmdn17_05.log |
Reindex (is this necessary?)
cd /opt/mapping-service-admin/admin/lucene mvn install -PReindex -Drun.config=/opt/mapping-service/conf/config.properties > /opt/mapping-service/logs/reindex.log |
Start the server
supervisorctl start mapping-service |
NOTE: No need to create 'Published SNOMED to GMDN'. GMDN project is private.