merge_pdbml_nextgen_worker.sh

#!/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 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 $pdbml_gz_file -noatom.xml.gz`
  pdbml_nextgen_gz_file=$NEXTGEN/${pdb_id:1:2}/$NEXTGEN_FILE_PREFIX$pdb_id/$NEXTGEN_FILE_PREFIX$pdb_id$NEXTGEN_FILE_SUFFIX.xml.gz
  pdbml_sifts_file=$WORK_DIR/$pdb_id-noatom-sifts.xml
  div_dir=$WORK_DIR/${pdb_id:1:2}
  err_file=$WORK_DIR/merge_pdbml_nextgen_$pdb_id.err
  lock_file=$WORK_DIR/$pdb_id.lock

  if [ ! -e $pdbml_nextgen_gz_file ] ; then

   if [ ! -e $div_dir/$pdb_id-noatom-sifts.xml.gz ] ; then

    mk_div_dir $div_dir
    cp $pdbml_gz_file $div_dir/$pdb_id-noatom-sifts.xml.gz

   fi

  elif [ ! -e $lock_file ] && ( ( [ ! -e $pdbml_sifts_file ] && [ ! -e $div_dir/`basename $pdbml_sifts_file`.gz ] ) || [ -e $err_file ] ) ; then

   touch $lock_file

   pdbml_file=${pdbml_gz_file%.*} # remove the last '.gz'
   gunzip -c $pdbml_gz_file > $pdbml_file || exit 1
   pdbml_nextgen_file=${pdbml_nextgen_gz_file%.*} # remove the last '.gz'
   gunzip -c $pdbml_nextgen_gz_file > $pdbml_nextgen_file || exit 1

   xsltproc -o $pdbml_sifts_file --stringparam nextgen_file ../$pdbml_nextgen_file $MERGE_PDBML_NEXTGEN_XSL $pdbml_file 2> $err_file && rm -f $err_file $pdbml_file $pdbml_nextgen_file || ( rm -f $pdbml_file $pdbml_nextgen_file $pdbml_sifts_file $sifts_xml_file ; cat $err_file )
   #java -jar $SAXON -s:$pdbml_file -xsl:$MERGE_PDBML_NEXTGEN_XSL -o:$pdbml_sifts_file nextgen_file=../$pdbml_nextgen_file 2> $err_file && rm -f $err_file $pdbml_file $pdbml_nextgen_file || ( rm -f $pdbml_file $pdbml_nextgen_file $pdbml_sifts_file $sifts_xml_file ; cat $err_file )

   if [ -e $pdbml_sifts_file ] ; then

    xml_pretty $pdbml_sifts_file

    mk_div_dir $div_dir

    if [ $VALIDATE = 'true' ] ; then

     java -classpath $XSD2PGSCHEMA xmlvalidator --xsd $PDBML_XSD --xml $pdbml_sifts_file > /dev/null 2> $err_file

     if [ $? = 0 ] && [ -s $pdbml_sifts_file ] ; then
      rm -f $err_file
      gzip_in_div_dir $pdbml_sifts_file $div_dir
     else
      cat $err_file
     fi

    elif [ -s $pdbml_sifts_file ] ; then
     gzip_in_div_dir $pdbml_sifts_file $div_dir
    fi

   else
    mk_div_dir $div_dir
    cp $pdbml_gz_file $div_dir/$pdb_id-noatom-sifts.xml.gz
   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 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 $pdbml_gz_file -noatom.xml.gz`
  pdbml_nextgen_gz_file=$NEXTGEN/${pdb_id:1:2}/$NEXTGEN_FILE_PREFIX$pdb_id/$NEXTGEN_FILE_PREFIX$pdb_id$NEXTGEN_FILE_SUFFIX.xml.gz
  pdbml_sifts_file=$WORK_DIR/$pdb_id-noatom-sifts.xml
  div_dir=$WORK_DIR/${pdb_id:1:2}
  err_file=$WORK_DIR/merge_pdbml_nextgen_$pdb_id.err
  lock_file=$WORK_DIR/$pdb_id.lock

  if [ ! -e $pdbml_nextgen_gz_file ] ; then

   if [ ! -e $div_dir/$pdb_id-noatom-sifts.xml.gz ] ; then

    mk_div_dir $div_dir
    cp $pdbml_gz_file $div_dir/$pdb_id-noatom-sifts.xml.gz

   fi

  elif [ -e $lock_file ] && ( ( [ ! -e $pdbml_sifts_file ] && [ ! -e $div_dir/`basename $pdbml_sifts_file`.gz ] ) || [ -e $err_file ] ) ; then

   touch $lock_file

   pdbml_file=${pdbml_gz_file%.*} # remove the last '.gz'
   gunzip -c $pdbml_gz_file > $pdbml_file || exit 1
   pdbml_nextgen_file=${pdbml_nextgen_gz_file%.*} # remove the last '.gz'
   gunzip -c $pdbml_nextgen_gz_file > $pdbml_nextgen_file || exit 1

   xsltproc -o $pdbml_sifts_file --stringparam nextgen_file ../$pdbml_nextgen_file $MERGE_PDBML_NEXTGEN_XSL $pdbml_file 2> $err_file && rm -f $err_file $pdbml_file $pdbml_nextgen_file || ( rm -f $pdbml_file $pdbml_nextgen_file $pdbml_sifts_file $sifts_xml_file ; cat $err_file )
   #java -jar $SAXON -s:$pdbml_file -xsl:$MERGE_PDBML_NEXTGEN_XSL -o:$pdbml_sifts_file nextgen_file=../$pdbml_nextgen_file 2> $err_file && rm -f $err_file $pdbml_file $pdbml_nextgen_file || ( rm -f $pdbml_file $pdbml_nextgen_file $pdbml_sifts_file $sifts_xml_file ; cat $err_file )

   if [ -e $pdbml_sifts_file ] ; then

    xml_pretty $pdbml_sifts_file

    mk_div_dir $div_dir

    if [ $VALIDATE = 'true' ] ; then

     java -classpath $XSD2PGSCHEMA xmlvalidator --xsd $PDBML_XSD --xml $pdbml_sifts_file > /dev/null 2> $err_file

     if [ $? = 0 ] && [ -s $pdbml_sifts_file ] ; then
      rm -f $err_file
      gzip_in_div_dir $pdbml_sifts_file $div_dir
     else
      cat $err_file
     fi

    elif [ -s $pdbml_sifts_file ] ; then
     gzip_in_div_dir $pdbml_sifts_file $div_dir
    fi

   else
    mk_div_dir $div_dir
    cp $pdbml_gz_file $div_dir/$pdb_id-noatom-sifts.xml.gz
   fi

   rm -f $lock_file

  fi

 fi

 let proc_id++

done < $FILE_LIST~