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OK. I've done it. In case someone will be looking for something similiar I'm putting the script.
#!/bin/sh
mkdir opf_tmp
while read id isbn ; do
echo "$id $isbn"
fetch-ebook-metadata -o OPF -i "$isbn" > ./opf_tmp/"$isbn"
calibredb set_metadata "$id" "./opf_tmp/$isbn"
done < <(calibredb list)
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