move skate-verify to skate-reduce

1 files changed, 144 insertions, 0 deletions

diff --git a/skate/cmd/skate-reduce/main.go b/skate/cmd/skate-reduce/main.go
new file mode 100644
index 0000000..df72ef4
--- /dev/null
+++ b/skate/cmd/skate-reduce/main.go
@@ -0,0 +1,144 @@
+// 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 the biblioref schema.
+//
+// Support various modes.
+//
+// * exact: takes (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 (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")
+	// Each mode may work on one or two files, and may need extra args.
+	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)
+		}
+	}
+}