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extract_pdbml_worker.sh
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extract_pdbml_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
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 < $FILE_LIST`
proc_id=0
while read pdbml_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_gz_file ] ; then
let proc_id++
continue
fi
#pdb_id=`basename $pdbml_gz_file -noatom.xml.gz`
pdb_id=`basename $pdbml_gz_file -noatom-sifts.xml.gz`
pdbml_ext_file=$WORK_DIR/$pdb_id-noatom-ext.xml
info_gz_file=$VALID_REPORT/${pdb_id:1:2}/$pdb_id/$pdb_id"_validation.xml.gz"
err_file=$WORK_DIR/extract_pdbml_$pdb_id.err
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ -e $info_gz_file ] && ( [ ! -e $pdbml_ext_file.gz ] || [ -e $err_file ] ); then
touch $lock_file
pdbml_file=${pdbml_gz_file%.*} # remove the last '.gz'
gunzip -c $pdbml_gz_file > $pdbml_file || exit 1
info_file=${info_gz_file%.*} # remove the last '.gz'
gunzip -c $info_gz_file > $info_file || exit 1
xsltproc -o $pdbml_ext_file --stringparam info_file ../$info_file $EXT_PDBML_XSL $pdbml_file 2> $err_file && rm -f $err_file $pdbml_file $info_file || ( rm -f $pdbml_file $pdbml_ext_file $info_file ; cat $err_file ; exit 1 )
#java -jar $SAXON -s:$pdbml_file -xsl:$EXT_PDBML_XSL -o:$pdbml_ext_file info_file=../$info_file 2> $err_file && rm -f $err_file $pdbml_file $info_file || ( rm -f $pdbml_file $pdbml_ext_file $info_file ; cat $err_file ; exit 1 )
if [ $VALIDATE = 'true' ] ; then
java -classpath $XSD2PGSCHEMA xmlvalidator --xsd $PDBX_VALIDATION_XSD --xml $pdbml_ext_file > /dev/null 2> $err_file
if [ $? = 0 ] && [ -s $pdbml_ext_file ] ; then
rm -f $err_file
gzip $pdbml_ext_file
else
cat $err_file
fi
elif [ -s $pdbml_ext_file ] ; then
gzip $pdbml_ext_file
fi
fi
if [ $proc_id_mod -eq 0 ] ; then
echo -e -n "\rDone "$((proc_id + 1)) of $TOTAL ...
fi
rm -f $lock_file
fi
let proc_id++
done < $FILE_LIST
proc_id=0
while read pdbml_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_gz_file ] ; then
let proc_id++
continue
fi
#pdb_id=`basename $pdbml_gz_file -noatom.xml.gz`
pdb_id=`basename $pdbml_gz_file -noatom-sifts.xml.gz`
pdbml_ext_file=$WORK_DIR/$pdb_id-noatom-ext.xml
info_gz_file=$VALID_REPORT/${pdb_id:1:2}/$pdb_id/$pdb_id"_validation.xml.gz"
err_file=$WORK_DIR/extract_pdbml_$pdb_id.err
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ -e $info_gz_file ] && [ ! -e $pdbml_ext_file.gz ] ; then
touch $lock_file
pdbml_file=${pdbml_gz_file%.*} # remove the last '.gz'
gunzip -c $pdbml_gz_file > $pdbml_file || exit 1
info_file=${info_gz_file%.*} # remove the last '.gz'
gunzip -c $info_gz_file > $info_file || exit 1
xsltproc -o $pdbml_ext_file --stringparam info_file ../$info_file $EXT_PDBML_XSL $pdbml_file 2> $err_file && rm -f $err_file $pdbml_file $info_file || ( rm -f $pdbml_file $pdbml_ext_file $info_file ; cat $err_file ; exit 1 )
#java -jar $SAXON -s:$pdbml_file -xsl:$EXT_PDBML_XSL -o:$pdbml_ext_file info_file=../$info_file 2> $err_file && rm -f $err_file $pdbml_file $info_file || ( rm -f $pdbml_file $pdbml_ext_file $info_file ; cat $err_file ; exit 1 )
if [ $VALIDATE = 'true' ] ; then
java -classpath $XSD2PGSCHEMA xmlvalidator --xsd $PDBX_VALIDATION_XSD --xml $pdbml_ext_file > /dev/null 2> $err_file
if [ $? = 0 ] && [ -s $pdbml_ext_file ] ; then
rm -f $err_file
gzip $pdbml_ext_file
else
cat $err_file
fi
elif [ -s $pdbml_ext_file ] ; then
gzip $pdbml_ext_file
fi
rm -f $lock_file
fi
fi
let proc_id++
done < $FILE_LIST~