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|
// skate-reduce takes prepared inputs (e.g. from skate-map or skate-cluster)
// 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
// |
// |
// * ref | takes a single file with clusters containing releases and refs and
// | will emit verification results (deprecated).
// |
// | $ skate-reduce -m ref < a.ndj
// |
// |
// * bref | same as ref, but generate a biblioref file as output (deprecated).
// |
// | $ skate-reduce -m bref < a.ndj
// |
// |
// * 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; do deduplicate on the fly
// |
// | $ skate-reduce -m unmatched -B a.ndj -F b.ndj
//
package main
import (
"bufio"
"flag"
"fmt"
"io/ioutil"
"log"
"os"
"runtime"
"git.archive.org/martin/cgraph/skate"
"git.archive.org/martin/cgraph/skate/parallel"
"git.archive.org/martin/cgraph/skate/xio"
gzip "github.com/klauspost/compress/gzip"
)
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.
// Extra args.
reason = flag.String("r", "", "reason for match: doi, pmid, pmcid, arxiv, unknown")
reasonMap = 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)
}
bw := bufio.NewWriter(os.Stdout)
defer bw.Flush()
switch *mode {
case "exact":
l, f, err := xio.OpenTwo(*releases, *refs)
if err != nil {
log.Fatal(err)
}
r, ok := reasonMap[*reason]
if !ok {
log.Fatalf("unknown reason: %v", *reason)
}
if err := skate.ZippyExact(l, f, r, bw); err != nil {
log.Fatal(err)
}
case "fuzzy":
l, f, err := xio.OpenTwo(*releases, *refs)
if err != nil {
log.Fatal(err)
}
if err := skate.ZippyVerifyRefs(l, f, bw); err != nil {
log.Fatal(err)
}
case "ref":
pp := parallel.NewProcessor(os.Stdin, os.Stdout, skate.RefClusterVerify)
pp.NumWorkers = *numWorkers
pp.BatchSize = *batchSize
if err := pp.Run(); err != nil {
log.Fatal(err)
}
case "bref":
pp := parallel.NewProcessor(os.Stdin, os.Stdout, skate.RefClusterToBiblioRef)
pp.NumWorkers = *numWorkers
pp.BatchSize = *batchSize
if err := pp.Run(); err != nil {
log.Fatal(err)
}
case "wiki":
l, w, err := xio.OpenTwo(*releases, *wiki)
if err != nil {
log.Fatal(err)
}
if err := skate.ZippyExactWiki(l, w, reasonMap["doi"], bw); err != nil {
log.Fatal(err)
}
case "oledt":
o, f, err := xio.OpenTwo(*openLibrary, *refs)
if err != nil {
log.Fatal(err)
}
if err := skate.ZippyVerifyRefsOpenLibraryTable(o, f, bw); err != nil {
log.Fatal(err)
}
case "oled":
o, f, err := xio.OpenTwo(*openLibrary, *refs)
if err != nil {
log.Fatal(err)
}
if err := skate.ZippyVerifyRefsOpenLibrary(o, f, bw); err != nil {
log.Fatal(err)
}
case "rere":
o, f, err := xio.OpenTwo(*releases, *refs)
if err != nil {
log.Fatal(err)
}
r, ok := reasonMap[*reason]
if !ok {
log.Fatalf("unknown reason: %v", *reason)
}
if err := skate.ZippyExactReleases(o, f, r, bw); err != nil {
log.Fatal(err)
}
case "unmatched":
b, f, err := xio.OpenTwo(*bref, *refs)
if err != nil {
log.Fatal(err)
}
if err := skate.ZippyBrefAugment(b, f, bw); err != nil {
log.Fatal(err)
}
default:
log.Fatalf("invalid mode")
}
}
|
