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// Filter to parse out a correctly looking DOI from a field.
//
// $ echo "1,xxx 10.123/12312 xxx,3" | skate-to-doi -d , -f 2
// 1,10.123/12312,3
//
// We can use this to sanitize DOI-like fields in the reference dataset.
package main
import (
"flag"
"fmt"
"log"
"os"
"regexp"
"runtime"
"strings"
"git.archive.org/martin/cgraph/skate/parallel"
)
var (
numWorkers = flag.Int("w", runtime.NumCPU(), "number of workers")
batchSize = flag.Int("b", 100000, "batch size")
delimiter = flag.String("d", "\t", "delimiter")
index = flag.Int("f", 1, "one field to cleanup up a doi, 1-indexed")
bestEffort = flag.Bool("B", false, "only log errors, but do not stop")
skipNonMatches = flag.Bool("S", false, "do not emit a line for non-matches")
PatDOI = regexp.MustCompile(`10[.][0-9]{1,8}/[^ ]*[\w]`)
)
func main() {
flag.Parse()
pp := parallel.NewProcessor(os.Stdin, os.Stdout, func(p []byte) ([]byte, error) {
parts := strings.Split(string(p), *delimiter)
if len(parts) < *index {
msg := fmt.Sprintf("warn: line has too few fields (%d): %s", len(parts), string(p))
if *bestEffort {
log.Println(msg)
return nil, nil
} else {
return nil, fmt.Errorf(msg)
}
}
result := PatDOI.FindString(parts[*index-1])
if len(result) == 0 && *skipNonMatches {
return nil, nil
}
parts[*index-1] = result
return []byte(strings.Join(parts, *delimiter)), nil
})
pp.NumWorkers = *numWorkers
pp.BatchSize = *batchSize
if err := pp.Run(); err != nil {
log.Fatal(err)
}
}
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