#!/usr/bin/bash
# Usage: reExtract.sh 20..-.. < files...
# Input is list of paths to relative path of warc files
#  under /beegfs/common_crawl/CC-MAIN-$1

function sus () 
{ 
    sort "$@" | uniq -c | sort -k1nr,1
}

function edex () {
    echo "$1" | \
	cut -f 5 -d - | cut -f 1 -d .|sed 's/^00//' | \
	echo $(($(fgrep -n -f - ~/by11n.txt | cut -f 1 -d :) - 1))
    }

function join_by () {
    # Courtesy of https://stackoverflow.com/a/17841619/2595465
    local d=$1
    shift
    echo -n "$1"
    shift
    printf "%s" "${@/#/$d}"
}

h=/beegfs/common_crawl/CC-MAIN-$1

mkdir -p /dev/shm/rex
cd /dev/shm/rex

sed 's/\// /;s/-00/ /;s/.warc.gz//' | \
 while read s p i
 do
    printf "%s\t%s\t%s\t%s\n" $(edex $i) $s $p $i
 done > in.txt
cut -f 2,3 in.txt| sort -u | \
 while read s p
 do
    mkdir -p $s/logs
    cd $s
    # Sigh, shouldn't have used this in the extraction ...
    jobid=$(tar -tf ${h}/${s}/extract_0.tar logs/ | head -1 | \
	     cut -f 2 -d / |cut -f 1 -d _)
    for e in $(egrep "\b$s\b" ../in.txt |cut -f 1 | sort -u)
     # this could be parallel
     do
	lsf=lsl${e}.txt
	rm -f $lsf
	lff=()
	ii=()
	for i in $(egrep "^$e\\s$s\\b" ../in.txt|cut -f 4)
	 # this could be parallel
	 do
	    id=${p#CC-MAIN-*}-00$i
	    echo "$id" 1>&2
	    lf=logs/${jobid}_${i}_log
	    lff+=("${lf}") # accumulate list of log files
	    echo starting ${id} $(date) > $lf
	    unpigz -dp 1 -c ${h}/${s}/CC-MAIN-${id}.warc.gz | $HOME/lib/valhalla/bin/warc.sh ${id} application/pdf 2>> $lf
	    echo finished ${id} $(date) >> $lf
	    ls -l ${id}_* | tr -s ' ' '\011' |cut -f 5,9 >> $lsf
	    ii+=("*-00${i}_*")
	    echo "$i" "${ii[@]}" ${#ii[@]} 1>&2
	 done
	# now compare ls vs. tar
	echo "${ii[@]}"  ${#ii[@]} 1>&2
	echo lff "${lff[@]}" 1>&2
	tar -tvf ${h}/${s}/extract_${e}.tar "${ii[@]}" | \
	       tr -s ' ' '\011' |cut -f 3,6 |sort -k2.1,2.36 -k2.38,2n | diff -bw \
	    - <(sort -k2.1,2.36 -k2.38,2n $lsf) > ${e}_diff.txt
        cut -f 1 -d ' ' ${e}_diff.txt | sus > ${e}_check.txt
	ni=${#ii[@]}
	if [ $(wc -l < ${e}_check.txt) -ne $((ni + 1)) ]
	then
	    echo "extra lines in ${e}_check.txt" 1>&2
	    cd ..
	    break
	fi
	if [ $(fgrep -c a ${e}_check.txt) -ne $ni ]
	then
	    echo "non-addition lines in ${e}_check.txt" 1>&2
	    cd ..
	    break
	fi
	egrep '^> ' ${e}_diff.txt | cut -f 2 > ${e}_new.txt
	tar --delete -f ${h}/${s}/extract_${e}.tar "${lff[@]}"
	tar --append -f ${h}/${s}/extract_${e}.tar --files-from=${e}_new.txt "${lff[@]}"
     done
    cd ..
 done