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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 biblioref schema stream.
//
// 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
//
// * verify: takes two (key, doc) TSV files (one for release, one for refs),
// runs verification within a group and will emit biblioref.
//
// $ skate-reduce -m verify -F a.tsv -L b.tsv
//
// * ref: takes a single file with clusters containing releases and refs and
// will emit verification results.
//
// $ skate-reduce -m ref < a.ndj
//
// * bref: same as ref, but generate a biblioref file as output
//
// $ skate-reduce -m bref < a.ndj
//
// * wiki: zippy mode for releases and wikipedia inputs.
//
// $ skate-reduce -m wiki -L a.ndj -W b.ndj
//
package main
import (
"bufio"
"flag"
"log"
"os"
"runtime"
"runtime/pprof"
"git.archive.org/martin/cgraph/skate"
"git.archive.org/martin/cgraph/skate/parallel"
"git.archive.org/martin/cgraph/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, verify, ref, bref, wiki")
cpuProfile = flag.String("cpuprofile", "", "write cpu profile to file")
memProfile = flag.String("memprofile", "", "write heap profile to file (go tool pprof -png --alloc_objects program mem.pprof > mem.png)")
// Possible inputs -- we could switch to a subcommand cli parser?
refs = flag.String("F", "", "path to refs input")
releases = flag.String("L", "", "path to release input")
wiki = flag.String("W", "", "path to wiki input")
// 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},
}
)
func main() {
flag.Parse()
if *cpuProfile != "" {
file, err := os.Create(*cpuProfile)
if err != nil {
log.Fatal(err)
}
pprof.StartCPUProfile(file)
defer pprof.StopCPUProfile()
}
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 "verify":
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)
}
default:
log.Fatalf("invalid mode")
}
if *memProfile != "" {
f, err := os.Create(*memProfile)
if err != nil {
log.Fatal("could not create memory profile: ", err)
}
defer f.Close()
runtime.GC()
if err := pprof.WriteHeapProfile(f); err != nil {
log.Fatal(err)
}
}
}
|
