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extract_info_worker.sh
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extract_info_worker.sh
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#!/bin/bash
source ./scripts/env.sh
WORK_DIR=
FILE_LIST=
TOTAL=
VALIDATE=false
ARGV=`getopt --long -o "d:l:n:t:v" "$@"`
eval set -- "$ARGV"
while true ; do
case "$1" in
-d)
WORK_DIR=$2
shift
;;
-l)
FILE_LIST=$2
shift
;;
-n)
PROC_INFO=$2
shift
;;
-t)
TOTAL=$2
shift
;;
-v)
VALIDATE=true
;;
*)
break
;;
esac
shift
done
if ! [[ $PROC_INFO =~ .*of.* ]] ; then
echo "Invalid thread id ($PROC_INFO)."
exit 1
fi
xml_pretty() {
if [ $has_xmllint_command != "false" ] ; then
xmllint --format $1 > $1~ && mv -f $1~ $1 || rm -f $1~
fi
}
MAXPROCS=`echo $PROC_INFO | cut -d 'f' -f 2`
PROC_ID=`echo $PROC_INFO | cut -d 'o' -f 1`
PROC_ID=$(($PROC_ID - 1))
# TOTAL=`wc -l < $FILE_LIST`
proc_id=0
while read info_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $info_gz_file ] ; then
let proc_id++
continue
fi
pdb_id=`basename $info_gz_file _validation.xml.gz`
info_alt_file=$WORK_DIR/$pdb_id-validation-alt.xml
div_dir=$WORK_DIR/${pdb_id:1:2}
pdbml_ext_file=$PDBML_EXT/$pdb_id-noatom-ext.xml
err_file=$WORK_DIR/extract_info_$pdb_id.err
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ -e $pdbml_ext_file.gz ] && ( ( [ ! -e $info_alt_file ] && [ ! -e $div_dir/`basename $info_alt_file`.gz ] ) || [ -e $err_file ] ) ; then
touch $lock_file
info_file=${info_gz_file%.*} # remove the last '.gz'
gunzip -c $info_gz_file > $info_file || exit 1
gunzip -c $pdbml_ext_file.gz > $pdbml_ext_file || exit 1
complex_vrpt=`xsltproc $COMPLEX_VRPT_XSL $info_file`
if [ "$complex_vrpt" = "true" ] ; then
java -jar $SAXON -s:$info_file -xsl:$EXT_INFO_XSL -o:$info_alt_file pdbml_ext_file=../$pdbml_ext_file 2> $err_file && rm -f $err_file $info_file $pdbml_ext_file || ( rm -f $info_file $info_alt_file $pdbml_ext_file ; cat $err_file ; exit 1 )
else
# take over entries requiring ext:node-set() from xsltproc to saxon
xsltproc -o $info_alt_file --stringparam pdbml_ext_file ../$pdbml_ext_file $EXT_INFO_XSL $info_file 2> /dev/null && rm -f $err_file $info_file $pdbml_ext_file || ( java -jar $SAXON -s:$info_file -xsl:$EXT_INFO_XSL -o:$info_alt_file pdbml_ext_file=../$pdbml_ext_file 2> $err_file && rm -f $err_file $info_file $pdbml_ext_file || ( rm -f $info_file $info_alt_file $pdbml_ext_file ; cat $err_file ; exit 1 ) )
fi
xml_pretty $info_alt_file
mk_div_dir $div_dir
if [ $VALIDATE = 'true' ] ; then
java -classpath $XSD2PGSCHEMA xmlvalidator --xsd $PDBX_VALIDATION_XSD --xml $info_alt_file > /dev/null 2> $err_file
if [ $? = 0 ] && [ -s $info_alt_file ] ; then
rm -f $err_file
gzip_in_div_dir $info_alt_file $div_dir
else
cat $err_file
fi
elif [ -s $info_alt_file ] ; then
gzip_in_div_dir $info_alt_file $div_dir
fi
rm -f $lock_file
fi
if [ $proc_id_mod -eq 0 ] ; then
echo -e -n "\rDone "$((proc_id + 1)) of $TOTAL ...
fi
fi
let proc_id++
done < $FILE_LIST
proc_id=0
while read info_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $info_gz_file ] ; then
let proc_id++
continue
fi
pdb_id=`basename $info_gz_file _validation.xml.gz`
info_alt_file=$WORK_DIR/$pdb_id-validation-alt.xml
div_dir=$WORK_DIR/${pdb_id:1:2}
pdbml_ext_file=$PDBML_EXT/$pdb_id-noatom-ext.xml
err_file=$WORK_DIR/extract_info_$pdb_id.err
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ -e $pdbml_ext_file.gz ] && [ ! -e $info_alt_file ] && [ ! -e $div_dir/`basename $info_alt_file`.gz ] ; then
touch $lock_file
info_file=${info_gz_file%.*} # remove the last '.gz'
gunzip -c $info_gz_file > $info_file || exit 1
gunzip -c $pdbml_ext_file.gz > $pdbml_ext_file || exit 1
complex_vrpt=`xsltproc $COMPLEX_VRPT_XSL $info_file`
if [ "$complex_vrpt" = "true" ] ; then
java -jar $SAXON -s:$info_file -xsl:$EXT_INFO_XSL -o:$info_alt_file pdbml_ext_file=../$pdbml_ext_file 2> $err_file && rm -f $err_file $info_file $pdbml_ext_file || ( rm -f $info_file $info_alt_file $pdbml_ext_file ; cat $err_file ; exit 1 )
else
# take over entries requiring ext:node-set() from xsltproc to saxon
xsltproc -o $info_alt_file --stringparam pdbml_ext_file ../$pdbml_ext_file $EXT_INFO_XSL $info_file 2> /dev/null && rm -f $err_file $info_file $pdbml_ext_file || ( java -jar $SAXON -s:$info_file -xsl:$EXT_INFO_XSL -o:$info_alt_file pdbml_ext_file=../$pdbml_ext_file 2> $err_file && rm -f $err_file $info_file $pdbml_ext_file || ( rm -f $info_file $info_alt_file $pdbml_ext_file ; cat $err_file ; exit 1 ) )
fi
xml_pretty $info_alt_file
mk_div_dir $div_dir
if [ $VALIDATE = 'true' ] ; then
java -classpath $XSD2PGSCHEMA xmlvalidator --xsd $PDBX_VALIDATION_XSD --xml $info_alt_file > /dev/null 2> $err_file
if [ $? = 0 ] && [ -s $info_alt_file ] ; then
rm -f $err_file
gzip_in_div_dir $info_alt_file $div_dir
else
cat $err_file
fi
elif [ -s $info_alt_file ] ; then
gzip_in_div_dir $info_alt_file $div_dir
fi
rm -f $lock_file
fi
fi
let proc_id++
done < $FILE_LIST~