From cedef349990c12747efdbe10f692c57436dc5c91 Mon Sep 17 00:00:00 2001 From: Martin Czygan Date: Wed, 31 Mar 2021 23:35:34 +0200 Subject: remote skate-biblioref --- skate/Makefile | 2 +- skate/README.md | 17 ++++- skate/cmd/skate-biblioref/main.go | 139 -------------------------------------- 3 files changed, 17 insertions(+), 141 deletions(-) delete mode 100644 skate/cmd/skate-biblioref/main.go (limited to 'skate') diff --git a/skate/Makefile b/skate/Makefile index 3574f4d..ccfbe9e 100644 --- a/skate/Makefile +++ b/skate/Makefile @@ -1,5 +1,5 @@ SHELL := /bin/bash -TARGETS := skate-ref-to-release skate-derive-key skate-cluster skate-biblioref skate-cluster-stats skate-verify skate-to-doi skate-bref-id skate-from-unstructured skate-biblioref-from-wikipedia +TARGETS := skate-ref-to-release skate-derive-key skate-cluster skate-cluster-stats skate-verify skate-to-doi skate-bref-id skate-from-unstructured skate-biblioref-from-wikipedia PKGNAME := skate .PHONY: test diff --git a/skate/README.md b/skate/README.md index 2892190..6c39717 100644 --- a/skate/README.md +++ b/skate/README.md @@ -1,6 +1,21 @@ # skate -Key extractors and zipping tools. +The skate suite of command line tools have been written for various parts of the +citation graph pipeline. + +## Tools + +### skate-biblioref +### skate-biblioref-from-wikipedia +### skate-bref-id +### skate-cluster +### skate-cluster-stats +### skate-derive-key +### skate-from-unstructured +### skate-ref-to-release +### skate-to-doi +### skate-verify + Goal: make key extraction and comparisons fast for billions of records on a single machine to support deduplication work for [fatcat](https://fatcat.wiki) diff --git a/skate/cmd/skate-biblioref/main.go b/skate/cmd/skate-biblioref/main.go deleted file mode 100644 index d16c99b..0000000 --- a/skate/cmd/skate-biblioref/main.go +++ /dev/null @@ -1,139 +0,0 @@ -// Experimental: Turn the minimal cluster result (key, target, source) into an -// indexable biblio ref (10eb30251f89806cb7a0f147f427c5ea7e5f9941). -// -// Supports multiple input styles transparently, for the moment. -// -// "id style" -// -// ---- id, title, ... --- ---- target -------------- ---- source -------------- -// -// 10.1001/2012.jama.11164 zhscs2mjlvcdte2i3j44ibgzae icg7bkoeqvfqnc5t5ot4evto6a -// 10.1001/2012.jama.11164 zhscs2mjlvcdte2i3j44ibgzae ichuaiowbvbx5ajae5ing27lka -// 10.1001/2012.jama.11164 zhscs2mjlvcdte2i3j44ibgzae io6b76ow6ngxnilc24qsf5kw6i -// -// "verify style" -// -// ---- target ------------------------------------------ ---- source ------------------------------------------ -- match ---- ---- match reason ------------------ -// -// https://fatcat.wiki/release/a6xucdggk5h7bcmbxidvqt7hxe https://fatcat.wiki/release/amnpvj5ma5dxlc2a3x2bm2zbnq Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH -// https://fatcat.wiki/release/vyppsuuh2bhapdwcqzln5momta https://fatcat.wiki/release/6gd53yl5yzakrlr72xeojamchi Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY -// https://fatcat.wiki/release/hazousx6wna5bn5e27s5mrljzq https://fatcat.wiki/release/iajt2xam5nbc3ichkxxuhqaqw4 Status.DIFFERENT Reason.YEAR -// -// Input might change, so we keep this short. -package main - -import ( - "flag" - "fmt" - "io/ioutil" - "log" - "os" - "runtime" - "strconv" - "strings" - "time" - - "git.archive.org/martin/cgraph/skate" - "git.archive.org/martin/cgraph/skate/parallel" - "github.com/dgraph-io/ristretto" - jsoniter "github.com/json-iterator/go" - "github.com/sethgrid/pester" -) - -var ( - numWorkers = flag.Int("w", runtime.NumCPU(), "number of workers") - batchSize = flag.Int("b", 100000, "batch size") - extended = flag.Bool("E", false, "fetch data from fatcat API") - - json = jsoniter.ConfigCompatibleWithStandardLibrary - bytesNewline = []byte("\n") - cache *ristretto.Cache - err error -) - -func main() { - flag.Parse() - cache, err = ristretto.NewCache(&ristretto.Config{ - NumCounters: 1e7, // number of keys to track frequency of (10M). - MaxCost: 1 << 30, // maximum cost of cache (1GB). - BufferItems: 64, // number of keys per Get buffer. - }) - if err != nil { - log.Fatal(err) - } - pp := parallel.NewProcessor(os.Stdin, os.Stdout, func(p []byte) ([]byte, error) { - var ( - fields = strings.Fields(string(p)) - target, source, matchStatus, matchReason, matchProvenance string - ) - switch len(fields) { - case 3: - // Some join output. - source = fields[2] - target = fields[1] - matchProvenance = "join" - case 4: - source = strings.ReplaceAll(fields[1], "https://fatcat.wiki/release/", "") - target = strings.ReplaceAll(fields[0], "https://fatcat.wiki/release/", "") - matchProvenance = "fuzzycat/ebee2de" - matchStatus = strings.ReplaceAll(fields[2], "Status.", "") - matchReason = strings.ReplaceAll(fields[3], "Reason.", "") - } - if source == target { - return nil, nil - } - br := skate.BiblioRef{ - IndexedTs: time.Now().Unix(), - SourceReleaseIdent: source, - TargetReleaseIdent: target, - MatchStatus: matchStatus, - MatchReason: matchReason, - MatchProvenance: matchProvenance, - } - if *extended { - var release skate.Release - if err := FetchRelease(source, &release); err != nil { - log.Fatal(err) - } - br.SourceReleaseStage = release.ReleaseStage - br.SourceWorkIdent = release.WorkID - br.SourceYear = strconv.Itoa(release.ReleaseYear()) - if err := FetchRelease(target, &release); err != nil { - log.Fatal(err) - } - br.TargetWorkIdent = release.WorkID - } - b, err := json.Marshal(br) - b = append(b, bytesNewline...) - return b, err - }) - pp.NumWorkers = *numWorkers - pp.BatchSize = *batchSize - if err := pp.Run(); err != nil { - log.Fatal(err) - } -} - -func FetchRelease(ident string, release *skate.Release) error { - v, found := cache.Get(ident) - if !found { - link := fmt.Sprintf("https://api.fatcat.wiki/v0/release/%s", ident) - resp, err := pester.Get(link) - if err != nil { - return err - } - defer resp.Body.Close() - b, err := ioutil.ReadAll(resp.Body) - if err != nil { - return err - } - cache.Set(ident, string(b), 1) - return json.Unmarshal(b, release) - } else { - s, ok := v.(string) - if !ok { - return fmt.Errorf("invalid cache value") - } - return json.Unmarshal([]byte(s), release) - } -} -- cgit v1.2.3