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
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
|
// skate-reduce takes prepared inputs (e.g. from skate-map) and applies various
// verification and conversion functions. The output will often be a stream of
// biblioref schema docs.
//
// Support various "modes", e.g. exact, verify, ref, bref, wiki. Each mode may
// work on one or two files, and may need extra args.
//
// * exact | takes two (key, doc) TSV files (one for releases, one for refs) and
// | will emit biblioref docs relating *one* element from releases with *all*
// | elements from ref; this is for "doi", "pmid" and other id matches, where no
// | further checks are necessary. The match reason, e.g. "doi" needs to be
// | supplied
// |
// | $ skate-reduce -m exact -r doi -F a.tsv -L b.tsv
// |
// |
// * fuzzy | takes two (key, doc) TSV files (one for release, one for refs),
// | runs verification within a group and will emit biblioref
// |
// | $ skate-reduce -m fuzzy -F a.tsv -L b.tsv
// |
// |
// * wiki | zippy mode for releases and wikipedia inputs
// |
// | $ skate-reduce -m wiki -L a.ndj -W b.ndj
// |
// |
// * oledt | zippy mode for releases and OL inputs, dumps table for debugging
// |
// | $ skate-reduce -m oled -F a.ndj -O b.ndj
// |
// |
// * oled | zippy mode for releases and OL inputs, emit biblioref
// |
// | $ skate-reduce -m oled -F a.ndj -O b.ndj
// |
// |
// * rere | zippy mode for OL release and ref (as release) inputs, emit biblioref
// |
// | $ skate-reduce -m rere -O a.ndj -F b.ndj
// |
// |
// * unmatched | join matched and unmatched reference data; deduplicate on the fly
// |
// | $ skate-reduce -m unmatched -B a.ndj -F b.ndj
// |
// |
// * wb | join raw refs with urls with ad-hoc wayback json schema noting last timestamp
// |
// | $ skate-reduce -m wb -F a.ndj -C b.ndj
//
package main
import (
"bufio"
"flag"
"fmt"
"io/ioutil"
"log"
"os"
"runtime"
gzip "github.com/klauspost/compress/gzip"
"gitlab.com/internetarchive/refcat/skate"
"gitlab.com/internetarchive/refcat/skate/xio"
)
var (
numWorkers = flag.Int("w", runtime.NumCPU(), "number of workers")
batchSize = flag.Int("b", 10000, "batch size")
mode = flag.String("m", "ref", "mode, e.g. exact, fuzzy, ref, bref, wiki, oled, oledt, unmatched")
quite = flag.Bool("q", false, "be quiet")
logFile = flag.String("log", "", "log filename (stderr, if empty; logfile will be gzip compressed)")
// Possible inputs -- we could switch to a subcommand cli parser?
bref = flag.String("B", "", "path to bref file")
refs = flag.String("F", "", "path to refs input")
releases = flag.String("L", "", "path to release input")
wiki = flag.String("W", "", "path to wiki input")
openLibrary = flag.String("O", "", "path to open library input") // XXX: Too generic name.
cdxAdhoc = flag.String("C", "", "path to cdx adhoc schema")
// Extra args.
matchResult = flag.String("r", "", "reason for match: doi, pmid, pmcid, arxiv, unknown")
matchResultMap = map[string]skate.MatchResult{
"doi": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonDOI},
"pmid": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonPMID},
"pmcid": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonPMCID},
"arxiv": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonArxiv},
"unknown": skate.MatchResult{Status: skate.StatusUnknown, Reason: skate.ReasonUnknown},
"isbn": skate.MatchResult{Status: skate.StatusExact, Reason: skate.ReasonISBN},
}
help = `Reduce modes
TODO: table of modes and inputs, or specific link to docs
`
)
func main() {
flag.Usage = func() {
fmt.Fprintf(flag.CommandLine.Output(), "Usage of %s:\n", os.Args[0])
flag.PrintDefaults()
fmt.Println()
fmt.Println(help)
}
flag.Parse()
if *logFile != "" {
f, err := os.OpenFile(*logFile, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0644)
if err != nil {
log.Fatal(err)
}
gzw := gzip.NewWriter(f)
defer gzw.Flush()
defer f.Close()
log.SetOutput(gzw)
}
if *quite {
log.SetOutput(ioutil.Discard)
}
var (
bw = bufio.NewWriter(os.Stdout)
l, f, w, o, b, c *os.File
r skate.MatchResult
ok bool
err error
)
defer bw.Flush()
switch *mode {
case "exact":
if l, f, err = xio.OpenTwo(*releases, *refs); err != nil {
log.Fatal(err)
}
if r, ok = matchResultMap[*matchResult]; !ok {
log.Fatalf("unknown reason: %v", *matchResult)
}
if err := skate.ZippyExact(l, f, r, bw); err != nil {
log.Fatal(err)
}
case "fuzzy":
if l, f, err = xio.OpenTwo(*releases, *refs); err != nil {
log.Fatal(err)
}
if err := skate.ZippyVerifyRefs(l, f, bw); err != nil {
log.Fatal(err)
}
case "wiki":
if l, w, err = xio.OpenTwo(*releases, *wiki); err != nil {
log.Fatal(err)
}
if err := skate.ZippyExactWiki(l, w, matchResultMap["doi"], bw); err != nil {
log.Fatal(err)
}
case "oledt":
if o, f, err = xio.OpenTwo(*openLibrary, *refs); err != nil {
log.Fatal(err)
}
if err := skate.ZippyVerifyRefsOpenLibraryTable(o, f, bw); err != nil {
log.Fatal(err)
}
case "oled":
if o, f, err = xio.OpenTwo(*openLibrary, *refs); err != nil {
log.Fatal(err)
}
if err := skate.ZippyVerifyRefsOpenLibrary(o, f, bw); err != nil {
log.Fatal(err)
}
case "rere":
if o, f, err = xio.OpenTwo(*releases, *refs); err != nil {
log.Fatal(err)
}
if r, ok = matchResultMap[*matchResult]; !ok {
log.Fatalf("unknown reason: %v", *matchResult)
}
if err := skate.ZippyExactReleases(o, f, r, bw); err != nil {
log.Fatal(err)
}
case "unmatched":
if b, f, err = xio.OpenTwo(*bref, *refs); err != nil {
log.Fatal(err)
}
if err := skate.ZippyBrefAugment(b, f, bw); err != nil {
log.Fatal(err)
}
case "wb":
if f, c, err = xio.OpenTwo(*refs, *cdxAdhoc); err != nil {
log.Fatal(err)
}
if err := skate.ZippyWayback(f, c, bw); err != nil {
log.Fatal(err)
}
default:
log.Fatalf("invalid mode")
}
}
|
