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repere2SNER.sh
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repere2SNER.sh
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#!/bin/bash
JCP="bin:lib/jsafran.jar:lib/mallet.jar:lib/mallet-deps.jar:lib/trove.jar:lib/org.annolab.tt4j-1.0.12.jar:build/classes::lib/anna.jar"
#allens="pers fonc org loc prod time amount"
# debug
allens="pers"
dest2="/home/rojasbar/development/contnomina/corpus/ESTER2ftp/package_scoring_ESTER2-v1.7/information_extraction_task"
export PATH=$PATH:$dest2/tools
if [ "1" == "0" ]; then
echo "conversion du train en .xml"
mkdir reptrain
for i in /global/rojasbar/nasdata1/TALC/ExternalResources/NEW_RESOURCES/REPERE/data/reference/train/*.trs
do
j=`echo $i | sed 's,/, ,g;s,trs$,,g' | awk '{print $NF}'`"xml"
echo "convert train to xml "$i" "$j
echo $i > tmp.trsl
java -cp "$JCP" repere.REPERE2EN -trs2xml tmp.trsl
mv output.xml oo2.xml
java -cp "$JCP" jsafran.ponctuation.UttSegmenter oo2.xml
mv -f output.xml /tmp/
pushd .
cd ../jsafran
java -cp "$JCP" jsafran.JSafran -retag /tmp/output.xml
mv -f output_treetagged.xml /tmp/
popd
mv /tmp/output_treetagged.xml reptrain/$j
done
fi
#NO PARSING
#if [ "1" == "0" ]; then
#echo "parsing du train et du test"
#cp -f ../jsafran/mate.mods.FTBfull ./mate.mods
#mkdir train
#for i in reptrain/*.xml
#do
# java -Xmx20g -cp "$JCP" jsafran.MateParser -parse $i
# mv output.xml $i
#done
#ls reptest/*.xml | grep -v -e merged > test.xmll
#for i in `cat test.xmll`
#do
# java -Xmx20g -cp "$JCP" jsafran.MateParser -parse $i
# mv output.xml $i
#done
#fi
if [ "1" == "0" ]; then
echo "create training files for CRF"
#echo "no syntax"
ls reptrain/*.xml > train.xmll
for i in pers
do
echo $i
# merge toutes les ENs qui commencent par $i en un seul fichier groups.$i.tab
# laisse le champs syntaxique vide
java -Xmx1g -cp "$JCP" ester2.ESTER2EN -saveNER train.xmll $i
cp -f groups.$i.tab.crf groups.$i.tab.train
done
fi
if [ "0" == "0" ]; then
echo "train CRF"
for en in pers
#unk
do
sed 's,trainFile=synfeats0.tab,trainFile=groups.'$en'.tab.train,g' syn.props > tmp.props
java -Xmx20g -cp ../stanfordNLP/stanford-ner-2014-01-04/stanford-ner-2014-01-04.jar edu.stanford.nlp.ie.crf.CRFClassifier -prop tmp.props
mv kiki.mods en.$en.mods
done
fi
###############################################################
if [ "1" == "0" ]; then
echo "create the graphs.xml files from the gold test TRS"
rm -rf reptest
mkdir reptest
touch reptest/trs2xml.list
for i in /global/rojasbar/nasdata1/TALC/ExternalResources/NEW_RESOURCES/REPERE/data/reference/test/*.trs
do
j=`echo $i | sed 's,/, ,g;s,\.trs$,,g' | awk '{print $NF}'`
echo $i" "$j".xml"
echo $i > tmp.trsl
java -cp "$JCP" repere.REPERE2EN -trs2xml tmp.trsl
grep -v -e '^<group> ' output.xml > oo2.xml
java -cp "$JCP" jsafran.ponctuation.UttSegmenter oo2.xml
mv -f output.xml /tmp/
pushd .
cd ../jsafran
java -cp "$JCP" jsafran.JSafran -retag /tmp/output.xml
mv -f output_treetagged.xml /tmp/
popd
mv /tmp/output_treetagged.xml reptest/$j".xml"
echo $i" reptest/"$j".xml" >> reptest/trs2xml.list
done
fi
if [ "1" == "0" ]; then
echo "conversion du test en .xml, similar to train"
rm -rf reptest
mkdir reptest
for i in /global/rojasbar/nasdata1/TALC/ExternalResources/NEW_RESOURCES/REPERE/data/reference/test/*.trs
do
j=`echo $i | sed 's,/, ,g;s,trs$,,g' | awk '{print $NF}'`"xml"
echo "convert test to xml "$i" "$j
echo $i > tmp.trsl
java -cp "$JCP" repere.REPERE2EN -trs2xml tmp.trsl
mv output.xml oo2.xml
java -cp "$JCP" jsafran.ponctuation.UttSegmenter oo2.xml
mv -f output.xml /tmp/
pushd .
cd ../jsafran
java -cp "$JCP" jsafran.JSafran -retag /tmp/output.xml
mv -f output_treetagged.xml /tmp/
popd
mv /tmp/output_treetagged.xml reptest/$j
echo $i" reptest/"$j >> reptest/trs2xml.list
done
fi
if [ "1" == "0" ]; then
echo "create the TAB files from the groups in the graphs.xml files"
ls reptest/*.xml | grep -v -e merged > test.xmll
for i in $allens
do
echo $i
# merge toutes les ENs qui commencent par $i en un seul fichier groups.$i.tab
java -Xmx1g -cp "$JCP" ester2.ESTER2EN -saveNER test.xmll $i
cp -f groups.$i.tab.crf groups.$i.tab.test
done
fi
if [ "0" == "0" ]; then
for en in $allens
do
echo "test the CRF for $en"
# I use a compiled version instead of the jar because I put verbose=2 so that to see all samples from Gibbs, and not just the best one
java -Xmx1g -cp ../stanfordNLP/stanford-ner-2014-01-04/stanford-ner-2014-01-04.jar edu.stanford.nlp.ie.crf.CRFClassifier -loadClassifier en.$en.mods -testFile groups.$en.tab.test > test.$en.log
done
fi
#exit
# eval chaque EN individuellement
if [ "1" == "0" ]; then
for en in $allens
do
echo "evals individuelles baseline for $en $allens"
./conlleval.pl -d '\t' -o NO < test.$en.log > res.log
#./conlleval.pl -d '\t' -o NO < test.$en.log | grep $en >> res.log
done
fi
# merge les res dans un seul stmne
if [ "1" == "0" ]; then
echo "put all CRF outputs into a single xml file"
ls reptest/*.xml | grep -v -e merged > train.xmll
java -cp "$JCP" ester2.REPERE2EN -mergeens train.xmll $allens
echo "convert the graph.xml into a .stm-ne file"
nl=`wc -l reptest/trs2xml.list | cut -d' ' -f1`
for (( c=1; c<=$nl; c++ ))
do
echo " c = $c "
trs=`awk '{if (NR=='$c') print $1}' reptest/trs2xml.list`
grs=`awk '{if (NR=='$c') print $2}' reptest/trs2xml.list | sed 's,\.xml,.xml.merged.xml,g'`
out=`echo $grs | sed 's,\.xml\.merged\.xml,,g'`".stm-ne"
echo "build stmne from $trs $grs $out"
java -Xmx1g -cp "$JCP" ester2.STMNEParser -project2stmne $grs $trs $out
done
fi
# eval selon protocole ESTER2
if [ "1" == "0" ]; then
score-ne -rd $dest2/../../EN/test/ -cfg $dest2/example/ref/NE-ESTER2.cfg -dic $dest2/tools/ESTER1-dictionnary-v1.9.1.dic reptest/*.stm-ne
fi