ICD11 Mapping

#!/bin/csh -f

set rc = run.config=/opt/mapping-service/conf/config.properties
if ($#argv != 1) then
  echo "usage: $0 <refsetId>"
  echo "  icd11RefsetId"
  echo "  icd11RefsetId-b"
  exit 1
endif
#set refsetId = icd11RefsetId-b
set refsetId = $1
if ($refsetId != "icd11RefsetId" && $refsetId != "icd11RefsetId-b") then
    echo "ERROR: unexpected value for refsetId: $refsetId"
    exit 1
endif

set adminDir = /opt/mapping-service-admin/admin

echo "---------------------------------------------------"
echo "Starting ...`/bin/date`"
echo "---------------------------------------------------"
echo "refsetId: $refsetId"
echo ""

curl "https://prod-mapping-icd11.ihtsdotools.org/" | grep 'Bad Gateway' > /tmp/x.$$
if ($status == 0 && `cat /tmp/x.$$ | wc -l` == 0) then
    echo "STOP the server before running this (as root)"
    echo "    supervisorctl stop mapping-service"
    exit 1
endif

# Stop server
#sudo supervisorctl stop mapping-service

echo "  Extract icd11Map.txt into LOW, MED, HIGH"
grep 'FINAL CATEGORY LOW' icd11MapNotes.txt | cut -f 6 | sort -u -o low.txt
grep 'FINAL CATEGORY MEDIUM' icd11MapNotes.txt | cut -f 6 | sort -u -o medium.txt
grep 'FINAL CATEGORY HIGH' icd11MapNotes.txt | cut -f 6 | sort -u -o high.txt
grep 'FINAL CATEGORY NO MAP' icd11MapNotes.txt | cut -f 6 | sort -u >> high.txt

/bin/rm -f icd11Map.{low,medium,high}.txt
perl -ne 'BEGIN {open(I,"low.txt"); while(<I>){chop; $m{$_}=1;} close(I);} @_=split/\t/; print if $m{$_[5]}; ' icd11Map.txt > icd11Map.low.txt
perl -ne 'BEGIN {open(I,"medium.txt"); while(<I>){chop; $m{$_}=1;} close(I);} @_=split/\t/; print if $m{$_[5]}; ' icd11Map.txt > icd11Map.medium.txt
perl -ne 'BEGIN {open(I,"high.txt"); while(<I>){chop; $m{$_}=1;} close(I);} @_=split/\t/; print if $m{$_[5]}; ' icd11Map.txt > icd11Map.high.txt

/bin/rm -f icd11MapNotes.{low,medium,high}.txt
perl -ne 'BEGIN {open(I,"low.txt"); while(<I>){chop; $m{$_}=1;} close(I);} @_=split/\t/; print if $m{$_[5]}; ' icd11MapNotes.txt > icd11MapNotes.low.txt
perl -ne 'BEGIN {open(I,"medium.txt"); while(<I>){chop; $m{$_}=1;} close(I);} @_=split/\t/; print if $m{$_[5]}; ' icd11MapNotes.txt > icd11MapNotes.medium.txt
perl -ne 'BEGIN {open(I,"high.txt"); while(<I>){chop; $m{$_}=1;} close(I);} @_=split/\t/; print if $m{$_[5]}; ' icd11MapNotes.txt > icd11MapNotes.high.txt

echo "  Replace notes for maps ...`/bin/date`"
perl -ne 'BEGIN {open(I,"icd11MapNotes.txt"); while(<I>){@_=split/\t/; $m{$_[5]}=1;} close(I);} @_=split/\t/; print unless $m{$_[5]}; ' notes/icd11MapNotes.txt > fix
/bin/mv -f fix notes/icd11MapNotes.txt
cat icd11MapNotes.txt >> notes/icd11MapNotes.txt

# map remover augmented to remove map records for concept ids in a specified input file
echo "  Removing old maps ...`/bin/date`"
cd $adminDir/remover
mvn install -PMapRecords -D$rc -Drefset.id=$refsetId -Dinput.file=/opt/mapping-data/ICD11/icd11Map.txt >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR removing map records"
    exit 1
endif

echo "  Adding new maps and notes ...`/bin/date`"

echo "    add MEDIUM records as EDITING_DONE ...`/bin/date`"
cd $adminDir/loader
mvn install -PMapRecords -D$rc -Dinput.file=/opt/mapping-data/ICD11/icd11Map.medium.txt \
  -Dmember.flag=false -Drecord.flag=true -Dworkflow.status=EDITING_DONE >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR installing maps"
    exit 1
endif
echo "    add MEDIUM notes ...`/bin/date`"
cd $adminDir/loader
mvn install -PMapNotes -D$rc -Dinput.file=/opt/mapping-data/ICD11/icd11MapNotes.medium.txt >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR installing map notes"
    exit 1
endif

echo "    add HIGH as PUBLISHED ...`/bin/date`"
cd $adminDir/loader
mvn install -PMapRecords -D$rc -Dinput.file=/opt/mapping-data/ICD11/icd11Map.high.txt \
  -Dmember.flag=false -Drecord.flag=true >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR installing maps"
    exit 1
endif
echo "    add HIGH notes ...`/bin/date`"
cd $adminDir/loader
mvn install -PMapNotes -D$rc -Dinput.file=/opt/mapping-data/ICD11/icd11MapNotes.high.txt >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR installing map notes"
    exit 1
endif

# before doing workflow stuff with HIGH, compute workflow
echo "  Compute workflow ...`/bin/date`"
cd $adminDir/loader
mvn install -PComputeWorkflow -D$rc -Drefset.id=$refsetId >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR running compute workflow"
    exit 1
endif

echo "    convert HIGH to QA ...`/bin/date`"
cd $adminDir/loader
mvn install -PAdHoc -D$rc -Drefset.id=$refsetId -Dmode=icd11 -Dinput.file=/opt/mapping-data/ICD11/icd11Map.high.txt >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR running adhoc step"
    exit 1
endif

# compute workflow again when finished assigning to QA
echo "  Compute workflow ...`/bin/date`"
cd $adminDir/loader
mvn install -PComputeWorkflow -D$rc -Drefset.id=$refsetId >&! /tmp/mvn.log
if ($status != 0) then
    cat /tmp/mvn.log | sed 's/^/     /'
    echo "ERROR running compute workflow"
    exit 1
endif


# Start server -
#sudo supervisorctl start mapping-service

echo "---------------------------------------------------"
echo "Finished ...`/bin/date`"
echo "---------------------------------------------------"
echo ""
echo "REMEMBER to restart the server = supervisorctl start mapping-service"