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// magrefs turns MAG references into a doi-to-doi version
// PaperReferences.txt is a two column file: PaperId, PaperReferenceId.
//
// Use in memory lookup table.
package main
import (
"bufio"
"flag"
"fmt"
"io"
"log"
"os"
"strconv"
"strings"
"sync/atomic"
_ "github.com/mattn/go-sqlite3"
"github.com/miku/parallel"
)
var (
mappingFile = flag.String("f", "", "two column TSV with key and value")
cache = make(map[int]string)
edgeMissingDOI int64 // number of edges that have one or zero DOI, but not both
)
func populateCache(r io.Reader, cache map[int]string) error {
var (
br = bufio.NewReader(r)
i int
)
for {
line, err := br.ReadString('\n')
if err == io.EOF {
break
}
if err != nil {
return err
}
fields := strings.Split(line, "\t")
if len(fields) < 2 {
continue
}
a, b := strings.TrimSpace(fields[0]), strings.TrimSpace(fields[1])
id, err := strconv.Atoi(a)
if err != nil {
log.Println("skipping invalid id: %s", line)
continue
}
cache[id] = b
i++
if i%1000000 == 0 {
log.Printf("%d", i)
}
}
return nil
}
func main() {
flag.Parse()
if *mappingFile == "" {
log.Fatal("mapping file required")
}
f, err := os.Open(*mappingFile)
if err != nil {
log.Fatal(err)
}
defer f.Close()
if err := populateCache(f, cache); err != nil {
log.Fatal(err)
}
pp := parallel.NewProcessor(os.Stdin, os.Stdout, func(p []byte) ([]byte, error) {
var (
s, t, v, w string
source, target int
err error
ok bool
complete = true
fields = strings.Split(string(p), "\t")
)
if len(fields) < 2 {
return nil, nil
}
s, t = strings.TrimSpace(fields[0]), strings.TrimSpace(fields[1])
if source, err = strconv.Atoi(s); err != nil {
log.Printf("skipping invalid source id: %s (%v)", s, err)
return nil, nil
}
if target, err = strconv.Atoi(t); err != nil {
log.Printf("skipping invalid target id: %s (%v)", t, err)
return nil, nil
}
if v, ok = cache[source]; !ok {
complete = false
}
if w, ok = cache[target]; !ok {
complete = false
}
if !complete {
atomic.AddInt64(&edgeMissingDOI, 1)
return nil, nil
}
line := fmt.Sprintf("%s\t%s\n", v, w)
return []byte(line), nil
})
if err := pp.Run(); err != nil {
log.Fatal(err)
}
log.Printf("edges without DOI: %d", edgeMissingDOI)
}
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