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comparison bin/preExtract.sh @ 50:5de261eb0deb

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another few log fixes
author Henry S. Thompson <ht@inf.ed.ac.uk>
date Fri, 10 Apr 2020 18:45:30 +0100
parents 18f8bcc779e8
children 427056f1784e
comparison
equal deleted inserted replaced
49:18f8bcc779e8 50:5de261eb0deb
68 fi 68 fi
69 ls -l ${id}_* | tr -s " " "\t" |cut -f 5,9 >> $lsf 69 ls -l ${id}_* | tr -s " " "\t" |cut -f 5,9 >> $lsf
70 ii+=("*-00${i}_*") 70 ii+=("*-00${i}_*")
71 echo " " "$i" "${ii[@]}" ${#ii[@]} >> log 71 echo " " "$i" "${ii[@]}" ${#ii[@]} >> log
72 done 72 done
73 echo " " extractions done 73 echo " " extractions done >> log
74 # now compare ls vs. tar 74 # now compare ls vs. tar
75 echo " " "${ii[@]}" ${#ii[@]} >> log 75 echo " " "${ii[@]}" ${#ii[@]} >> log
76 echo " " lff "${lff[@]}" >> log 76 echo " " lff "${lff[@]}" >> log
77 tar -tvf ${h}/${s}/extract_${e}.tar "${ii[@]}" | \ 77 tar -tvf ${h}/${s}/extract_${e}.tar "${ii[@]}" | \
78 tr -s " " "\t" |cut -f 3,6 |sort -k2.1,2.36 -k2.38,2n | diff -bw \ 78 tr -s " " "\t" |cut -f 3,6 |sort -k2.1,2.36 -k2.38,2n | diff -bw \
79 - <(sort -k2.1,2.36 -k2.38,2n $lsf) > ${e}_diff.txt 79 - <(sort -k2.1,2.36 -k2.38,2n $lsf) > ${e}_diff.txt
80 if [ -s ${e}_diff.txt ] 80 if [ -s ${e}_diff.txt ]
81 then 81 then
82 echo " " checking... 82 echo " " checking... >> log
83 cut -f 1 -d " " ${e}_diff.txt | sus > ${e}_check.txt 83 cut -f 1 -d " " ${e}_diff.txt | sus > ${e}_check.txt
84 ni=${#ii[@]} 84 ni=${#ii[@]}
85 if [ $(wc -l < ${e}_check.txt) -ne $((ni + 1)) ] 85 if [ $(wc -l < ${e}_check.txt) -ne $((ni + 1)) ]
86 then 86 then
87 if [[ "$(tr -s "\n\t " " " < ${e}_check.txt)" =~ \ 87 if [[ "$(tr -s "\n\t " " " < ${e}_check.txt)" =~ \
97 then 97 then
98 echo " " "non-addition lines in ${e}_check.txt" >> log 98 echo " " "non-addition lines in ${e}_check.txt" >> log
99 cd .. 99 cd ..
100 continue 100 continue
101 fi 101 fi
102 echo " " starting tar update 102 echo " " starting tar update >> log
103 egrep "^> " ${e}_diff.txt | cut -f 2 > ${e}_new.txt 103 egrep "^> " ${e}_diff.txt | cut -f 2 > ${e}_new.txt
104 tar --delete -f ${h}/${s}/extract_${e}.tar "${lff[@]}" 104 tar --delete -f ${h}/${s}/extract_${e}.tar "${lff[@]}"
105 tar --append -f ${h}/${s}/extract_${e}.tar --files-from=${e}_new.txt "${lff[@]}" 105 tar --append -f ${h}/${s}/extract_${e}.tar --files-from=${e}_new.txt "${lff[@]}"
106 else 106 else
107 echo "no diff, no update" $e >> log 107 echo "no diff, no update" $e >> log