Gnu/Unix Scripts

1. Renaming annotations

Here are two scripts to rename one annotation type named 'Old' to 'New'.
Note that it will do the renaming for all annotation sets.
It will create *.renamed files for all *.xml files in the current directory and below.

# GATE format
for file in `find . -name '*.xml'`; do
 sed -r -e 's/<Annotation (.*) Type="Old" (.*)>/<Annotation \1 Type="New" \2>/g' $file > $file.renamed
done

# Inline XML format
for file in `find . -name '*.xml'`; do
 sed -r -e 's!<(/?)Old( |>|$)!<\1New\2!g' $file > $file.renamed
done

2. Output GATE XML text content

#! /bin/sh

# keep only the document content part
# remove XML tags
# remove empty lines
# remove spaces starting a line
# remove spaces ending a line

cat "$1" |
tr '\n\r' ' ' |
sed -r \
 -e 's/^.*<TextWithNodes>//g' \
 -e 's/<\/TextWithNodes>.*$//g' |
sed -r \
 -e 's/<[^>]+>//g' \
 -e '/^\s*$/d' \
 -e 's/^\s+//g'\
 -e 's/\s+$//g'

3. Extract annotation statistics from a Gate XML document file.

#! /bin/sh

if [ "$1" = "" -o "$2" = "" -o "$1" = "--help" -o "$2" = "--help" ]; then
  cat << eof

  Extract annotation statistics from a Gate XML document file.

  Usage: $0 gate_document.xml annotation_set_name [feature_name]

  To run on a directory use:
  for f in \`ls directory\`; do
    sh $0 directory/\$f annotation_set_name;
  done > results.txt

eof
  exit
fi

file=`basename $1`

# keep only the document content part
# remove XML tags
# remove empty lines
# remove spaces starting a line
# remove spaces ending a line
# calculate number of lines, words and characters
# format the result

cat "$1" |
tr '\n\r' ' ' |
sed -r \
 -e 's/^.*<TextWithNodes>//g' \
 -e 's/<\/TextWithNodes>.*$//g' |
sed -r \
 -e 's/<[^>]+>//g' \
 -e '/^\s*$/d' \
 -e 's/^\s+//g'\
 -e 's/\s+$//g' |
wc --lines --words --chars |
sed -r -e 's/^\s*([0-9]+)\s+([0-9]+)\s+([0-9]+)$/'$file' _Lines_ \1\n'$file' _Words_ \2\n'$file' _Characters_ \3/'

echo $file _AnnotationSet_ $2

# keep only the annotation set given in second parameter
# put one annotation type per line
# optionnaly get the name of the feature given in third parameter
# remove all other XML tag
# sort lines
# count each annotation type [and feature]
# format the result
cat "$1" |
tr '\n\r' ' ' |
sed -r \
 -e 's/^.*<AnnotationSet Name="'$2'">//g' \
 -e 's/<\/AnnotationSet>.*$//g' \
 -e 's/<Annotation [^>]+Type="([^"]+)" [^>]+>/\n\1/g' |
sed -r \
 -e 's/\s+<Feature>.+<Name [^>]+>('$3')<\/Name>\s+<Value [^>]+>([^<]+).+$/ \1=\2/g' \
 -e 's/\s+<Feature>.+$//g' \
 -e 's/\s+<\/Annotation>\s+//g' \
 -e 's/^<\?xml .+$/This annotation set do not exist !!!/g' \
 -e '/^\s*$/d' |
sort --field-separator=' ' --key=1,1 --key=2,2 |
uniq --count |
sort --reverse --numeric-sort |
sed -r -e 's/^\s*([0-9]+)\s+(.+)$/'$file' \2 \1/g'