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cd ~/code/admin/remover
mvn install -PMapRecords -D$rc -Drefset.id=446608001
mvn install -PTerminology -D$rc -Dterminology=ICDO -Dversion=16_1
Load
Get maintenance windowcd ~/code/admin/loader
mvn install -PICDO -Dinput.dir=/home/ihtsdo/data/ICDO -Dterminology=ICDO -Dversion=16_1 -D$rc
cd ~/code/admin/loader
set file = /home/ihtsdo/data/ICDO/der2_sRefset_IcdoMorphSimpleMapSnapshot_INT_20170131.txt
/bin/rm -f /tmp/x.txt
# Keep only morphology codes (with '/')
perl -ne '@_=split/\t/; print if $_[4] eq "446608001"' $file | grep '/' > /tmp/x.txt
mvn install -PSimpleMapRecords -D$rc -Dinput.file=/tmp/x.txt -Dmember.flag=true -Drecord.flag=false
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Release with Alpha/Beta Iteration
Reloading Snomed is typically being done on prod-mapping now before the clone-over, so steps 2-5 should be skipped on alpha iteration.
1.)
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Take server
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down. Check RAM allocated to MAVEN_OPTS with export command. Adjust server size and RAM allocated with this command if necessary:
export MAVEN_OPTS="-XX:MaxPermSize=512m -Xmx3000M -Xmx7000M"
2.)
...
cd
...
~/code/admin/remover
...
3.)
...
mvn
...
install
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-PTerminology
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-Drun.config=/home/ihtsdo/config/config.properties
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-Dterminology=SNOMEDCT
...
-Dversion=latest
...
4.)
...
cd
...
~/code/admin/loader
...
5.)
...
mvn
...
install
...
-PRF2-snapshot
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-Drun.config=/home/ihtsdo/config/config.properties
...
-Dterminology=SNOMEDCT
...
-Dinput.dir=/home/ihstdo/data/xSnomedCT_InternationalRF2_ALPHA_20170731T120000Z/Snapshot
...
6.)
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DELETE
...
from
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simple_map_refset_members
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where
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refsetId
...
=
...
446608001;
...
...
7.)
...
set
...
file
...
=
...
/home/ihtsdo/data/ICDO/der2_sRefset_SimpleMapSnapshot_INT_20170131.txt
#
...
Keep
...
only
...
morphology
...
codes
...
(with
...
'/')
perl
...
-ne
...
'@_=split/\t/;
...
...
if
...
$_[4]
...
eq
...
"446608001"'
...
$file
...
|
...
grep
...
'/'
...
>
...
/tmp/
...
icdo.txt
mvn
...
install
...
-PSimpleMapRecords
...
-Drun.config=/opt/mapping-rest/config.properties -Dinput.file=/tmp/
...
icdo.txt -Dmember.flag=true
...
-Drecord.flag=false
8.) bring server back up
9.)
...
rerun
...
compute
...
workflow,
...
begin,
...
and
...
process
...
release
...
steps
Loading "Human Readable" View
...
Similar approach to ICD10 but using the "simple" map loader. e.g.
cd ~/codeopt/mapping-admin/remover
mvn install -PMapRecords -D$rc-Drun.config=/opt/mapping-rest/config.properties -Drefset.id=P446608001
cd ~/codeopt/mapping-admin/loader setgrep file = ~/446608001 /opt/mapping-data/doc/release/20170131/icdo/*ActiveSnapshot*txt grep 446608001 $fileSNOMEDCT_to_ICDO_446608001/20200731/der2_sRefset_SimpleMapActiveSnapshot_INT_20200731.txt | perl -pe 's/446608001/P446608001/;' > x.txt mvn install -PSimpleMapRecords -Drun.config=/home/ihtsdo/configopt/mapping-rest/config.properties -Dinput.file=x.txt -Dmember.flag=false -Drecord.flag=true >&! mvn.log
...
- in the /home/ihtsdo/data/ICDO directory (on PROD or UAT) are the files containing just morphology code data.
icdo3.txt (see format below)
Code Block Code|Level|Term|Note|Code reference|obs|See also|See note|Includes|Excludes|Other text|comment_April_Fritz |1|MORPHOLOGY||||||||| 800|2|Neoplasms, NOS||||||||| 801-804|2|Epithelial neoplasms, NOS|||||||||
chdPar.txt (sample entries below, it's a child → parent code list).
Code Block 800|MORPHOLOGY 801-804|MORPHOLOGY 805-808|MORPHOLOGY 809-811|MORPHOLOGY
- The same directory has a conversion script (icdo3.pl) that produces a valid ClaML representation of the morphology codes (icdo-3-1.xml).
- This file can be loaded using the standard ClaML loader.
- In the same directory is a subset of the ICDO mapping file containing just the morphology entries.
- der2_sRefset_IcdoMorphSimpleMapSnapshot_INT_20160131.txt
- The mapping tool is loaded with just morphology terminology and just morphology mappings. Thus, RF2 release output from the tool can be simply applied to the previous full as it will only indicate modifications to morphology codes. Thus, it is not necessary to load all of ICD-O in order to make this work.
...
At such time as official files are obtained from WHO and are in a different format, work will be done (as part of warranty/maintenance) to either convert that format into suitable ClaML or a new loader will be created for the native data format.
...