rods

#!/bin/bash -e
####################################################################
# Maintained by Jaakko Lappalainen. jaakko@torroja.dmt.upm.es - 2012
####################################################################
METAPOS_FILE=3
_HOME='/home/rodsadmin'
OUT_FILES_PATH=$_HOME'/out_files'
SORT_FILES_PATH=$_HOME'/sort_files'
INPUT_FILES_PATH=$_HOME'/input_files'
IFS='
'

for file in `ls $INPUT_FILES_PATH`;do
	rm -rf $INPUT_FILES_PATH/$file
done

for file in `ls $SORT_FILES_PATH`;do
        rm -rf $SORT_FILES_PATH/$file
done

/home/rodsadmin/iRODS/clients/icommands/bin/iinit rods_*1234

for file in `ls $OUT_FILES_PATH`;do
	while read line;do
		file_block=`echo $line | cut -d '|' -f $METAPOS_FILE`
		metadata_block=`echo $line | cut --complement -d '|' -f $METAPOS_FILE`
		if [ "$file_block" '!=' "- " ]; then
			dir=`dirname "$file_block"`
		fi
		if [ "$dir" '==' "." ]; then
			file=`basename $file_block`
                	echo $metadata_block"|"$file >> $SORT_FILES_PATH/$machine/$input/$target_file
		else
			machine=`echo $dir | cut -d '/' -f 1`
                	input=`echo $dir | cut -d '/' -f 2`
			target_file=`echo $dir | sed -e "s/\///g"`
			mkdir -p $SORT_FILES_PATH/$machine/$input
			echo $metadata_block"|"$file_block > $SORT_FILES_PATH/$machine/$input/$target_file
		fi	
	done < $OUT_FILES_PATH/$file &
done
wait
cd $SORT_FILES_PATH
for dir in `ls $SORT_FILES_PATH`;do
	for file in `find $dir -type f`;do
		file_dir=`dirname $file`
		mkdir -p $INPUT_FILES_PATH/$file_dir
		cat -n $file|sort -k2,2 -u |sort -k1,1 -n|nawk ' { $1=""; gsub("^ ",""); print $0 } ' > $INPUT_FILES_PATH/$file
	done
done
wait
for dir in `ls $INPUT_FILES_PATH`;do
	for root in `ls $INPUT_FILES_PATH/$dir`;do
		for file in `ls $INPUT_FILES_PATH/$dir/$root`;do
			/home/rodsadmin/syncgen2 $INPUT_FILES_PATH/$dir/$root/$file
		done
	done &
done
wait