1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
|
// 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"
_ "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)
)
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) {
fields := strings.Split(string(p), "\t")
if len(fields) < 2 {
return nil, nil
}
s, t := strings.TrimSpace(fields[0]), strings.TrimSpace(fields[1])
source, err := strconv.Atoi(s)
if err != nil {
log.Printf("skipping invalid source id: %s (%v)", s, err)
return nil, nil
}
target, err := strconv.Atoi(t)
if err != nil {
log.Printf("skipping invalid target id: %s (%v)", t, err)
return nil, nil
}
v, ok := cache[source]
if !ok {
return nil, nil
}
w, ok := cache[target]
if !ok {
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)
}
}
|
