path: root/skate/verify.go

// TODO: The various grouping and verification functions should probably be in
// a separate file and it should be obvious how to adjust or write a new one.
//
// This file contains a port of fuzzycat.verify
// (https://gitlab.com/internetarchive/fuzzycat) to Go.

//go:generate stringer -type=Status,Reason -output verify_string.go verify.go
package skate

import (
	"bytes"
	"fmt"
	"regexp"
	"strconv"
	"strings"
	"unicode/utf8"

	"git.archive.org/martin/cgraph/skate/set"
	"github.com/segmentio/encoding/json"
)

type (
	// Status represents match strength.
	Status int
	// Reason gives more context to status result.
	Reason int
)

const (
	StatusUnknown Status = iota
	StatusExact
	StatusStrong
	StatusWeak
	StatusDifferent
	StatusAmbiguous
	StatusUnmatched

	ReasonAppendix Reason = iota
	ReasonArxiv
	ReasonArxivVersion
	ReasonBlacklisted
	ReasonBlacklistedFragment
	ReasonBookChapter
	ReasonChemFormula
	ReasonComponent
	ReasonContainer
	ReasonContainerNameBlacklist
	ReasonContribIntersectionEmpty
	ReasonCustomBSISubdoc
	ReasonCustomBSIUndated
	ReasonCustomIEEEArxiv
	ReasonCustomIOPMAPattern
	ReasonCustomPrefix1014288
	ReasonCustomPrefix105860ChoiceReview
	ReasonCustomPrefix107916
	ReasonCustomVHS
	ReasonDOI
	ReasonDataciteRelatedID
	ReasonDataciteVersion
	ReasonDatasetDOI
	ReasonFigshareVersion
	ReasonISBN
	ReasonJaccardAuthors
	ReasonJstorID
	ReasonMaxClusterSizeExceeded
	ReasonNumDiff
	ReasonPMCID
	ReasonPMID
	ReasonPMIDDOIPair
	ReasonPageCount
	ReasonPreprintPublished
	ReasonPublisherBlacklist
	ReasonReleaseType
	ReasonSharedDOIPrefix
	ReasonShortTitle
	ReasonSingularCluster
	ReasonSlugTitleAuthorMatch
	ReasonSubtitle
	ReasonTitleArtifact
	ReasonTitleAuthorMatch
	ReasonTitleFilename
	ReasonTokenizedAuthors
	ReasonURLMatch
	ReasonUnknown
	ReasonVersionedDOI
	ReasonWorkID
	ReasonYear
)

var (
	PatAppendix        = regexp.MustCompile(`appendix ?[^ ]*$`)
	PatFigshareVersion = regexp.MustCompile(`[.]v[0-9]+$`)
	PatVersionedDOI    = regexp.MustCompile(`10[.].*/v[0-9]{1,}$`)
	PatArxivVersion    = regexp.MustCompile(`(.*)v[0-9]{1,2}$`)
	PatFilenameLike    = regexp.MustCompile(`.*[.][a-z]{2,3}$`)
	PatDigits          = regexp.MustCompile(`\d+`)
	PatPages           = regexp.MustCompile(`([0-9]{1,})-([0-9]{1,})`)
)

// Short name for status.
func (s Status) Short() string {
	return strings.ToLower(strings.Replace(s.String(), "Status", "", 1))
}

// Short name for reason.
func (r Reason) Short() string {
	return strings.ToLower(strings.Replace(r.String(), "Reason", "", 1))
}

// MatchResult is the result of a verification.
type MatchResult struct {
	Status Status
	Reason Reason
}

// VerificationPair groups two identifiers and their match status and
// match reason.
type MatchPair struct {
	A      string
	B      string
	Result MatchResult
}

// AsLine returns a TSV line of the match pair.
func (m *MatchPair) AsLine() string {
	return fmt.Sprintf("%s\t%s\t%s\t%s\n", m.A, m.B, m.Result.Status, m.Result.Reason)
}

// JsonMarshalNewline marshals a value as JSON and adds a newline.
func JsonMarshalNewline(v interface{}) ([]byte, error) {
	b, err := json.Marshal(v)
	if err != nil {
		return nil, err
	}
	b = append(b, []byte("\n")...)
	return b, nil
}

// Verify verifies two releases and will ignore short titles.
func Verify(a, b *Release) MatchResult {
	return VerifyMinTitleLength(a, b, 5)
}

// Verify follows the fuzzycat (Python) implementation of this function: it
// compares two release entities. The Go version can be used for large batch
// processing (where the Python version might take two or more days).
func VerifyMinTitleLength(a, b *Release, minTitleLength int) MatchResult {
	if a.ExtIDs.DOI != "" && a.ExtIDs.DOI == b.ExtIDs.DOI {
		return MatchResult{StatusExact, ReasonDOI}
	}
	if a.WorkID != "" && a.WorkID == b.WorkID {
		return MatchResult{StatusExact, ReasonWorkID}
	}
	aTitleLower := strings.ToLower(a.Title)
	bTitleLower := strings.ToLower(b.Title)
	if utf8.RuneCountInString(a.Title) < minTitleLength {
		return MatchResult{StatusAmbiguous, ReasonShortTitle}
	}
	if BlacklistTitle.Contains(aTitleLower) {
		return MatchResult{StatusAmbiguous, ReasonBlacklisted}
	}
	if BlacklistTitle.Contains(bTitleLower) {
		return MatchResult{StatusAmbiguous, ReasonBlacklisted}
	}
	for _, fragment := range BlacklistTitleFragments.Slice() {
		if strings.Contains(aTitleLower, fragment) {
			return MatchResult{StatusAmbiguous, ReasonBlacklistedFragment}
		}
	}
	if strings.Contains(aTitleLower, "subject index") && strings.Contains(bTitleLower, "subject index") {
		if a.ContainerID != "" && a.ContainerID != b.ContainerID {
			return MatchResult{StatusDifferent, ReasonContainer}
		}
	}
	if a.Title != "" && a.Title == b.Title &&
		a.Extra.DataCite.MetadataVersion > 0 && b.Extra.DataCite.MetadataVersion > 0 &&
		a.Extra.DataCite.MetadataVersion != b.Extra.DataCite.MetadataVersion {
		return MatchResult{StatusExact, ReasonDataciteVersion}
	}
	if strings.HasPrefix(a.ExtIDs.DOI, "10.14288/") && strings.HasPrefix(b.ExtIDs.DOI, "10.14288/") &&
		a.ExtIDs.DOI != b.ExtIDs.DOI {
		return MatchResult{StatusDifferent, ReasonCustomPrefix1014288}
	}
	if strings.HasPrefix(a.ExtIDs.DOI, "10.3403") && strings.HasPrefix(b.ExtIDs.DOI, "10.3403") {
		if a.ExtIDs.DOI+"u" == b.ExtIDs.DOI || b.ExtIDs.DOI+"u" == a.ExtIDs.DOI {
			return MatchResult{StatusStrong, ReasonCustomBSIUndated}
		}
		aSubtitle := a.Subtitle()
		bSubtitle := b.Subtitle()
		if a.Title != "" && a.Title == b.Title &&
			((len(aSubtitle) > 0 && aSubtitle[0] != "" && len(bSubtitle) == 0) ||
				(len(aSubtitle) == 0 && len(bSubtitle) > 0 && bSubtitle[0] != "")) {
			return MatchResult{StatusStrong, ReasonCustomBSISubdoc}
		}
	}
	if strings.HasPrefix(a.ExtIDs.DOI, "10.1149") && strings.HasPrefix(b.ExtIDs.DOI, "10.1149") {
		v := "10.1149/ma"
		if (strings.HasPrefix(a.ExtIDs.DOI, v) && !strings.HasPrefix(b.ExtIDs.DOI, v)) ||
			(!strings.HasPrefix(a.ExtIDs.DOI, v) && strings.HasPrefix(b.ExtIDs.DOI, v)) {
			return MatchResult{StatusDifferent, ReasonCustomIOPMAPattern}
		}
	}
	if strings.Contains(a.Title, "Zweckverband Volkshochschule") && a.Title != b.Title {
		return MatchResult{StatusDifferent, ReasonCustomVHS}
	}
	if PatAppendix.MatchString(a.Title) {
		return MatchResult{StatusAmbiguous, ReasonAppendix}
	}
	if strings.HasPrefix(a.ExtIDs.DOI, "10.6084/") && strings.HasPrefix(b.ExtIDs.DOI, "10.6084/") {
		av := PatFigshareVersion.ReplaceAllString(a.ExtIDs.DOI, "")
		bv := PatFigshareVersion.ReplaceAllString(b.ExtIDs.DOI, "")
		if av == bv {
			return MatchResult{StatusStrong, ReasonFigshareVersion}
		}
	}
	if PatVersionedDOI.MatchString(a.ExtIDs.DOI) && PatVersionedDOI.MatchString(b.ExtIDs.DOI) {
		return MatchResult{StatusStrong, ReasonVersionedDOI}
	}
	if looksLikeComponent(a.ExtIDs.DOI, b.ExtIDs.DOI) {
		return MatchResult{StatusStrong, ReasonVersionedDOI}
	}
	if len(a.Extra.DataCite.Relations) > 0 || len(b.Extra.DataCite.Relations) > 0 {
		getRelatedDOI := func(rel *Release) set.Set {
			ss := set.New()
			for _, rel := range rel.Extra.DataCite.Relations {
				if strings.ToLower(rel.RelatedIdentifierType) != "doi" {
					continue
				}
				ss.Add(rel.RelatedIdentifier())
			}
			return ss
		}
		aRelated := getRelatedDOI(a)
		bRelated := getRelatedDOI(b)
		if aRelated.Contains(b.ExtIDs.DOI) || bRelated.Contains(a.ExtIDs.DOI) {
			return MatchResult{StatusStrong, ReasonDataciteRelatedID}
		}
	}
	if a.ExtIDs.Arxiv != "" && b.ExtIDs.Arxiv != "" {
		aSub := PatArxivVersion.FindStringSubmatch(a.ExtIDs.Arxiv)
		bSub := PatArxivVersion.FindStringSubmatch(b.ExtIDs.Arxiv)
		if len(aSub) == 2 && len(bSub) == 2 && aSub[1] == bSub[1] {
			return MatchResult{StatusStrong, ReasonArxivVersion}
		}
	}
	if a.ReleaseType != b.ReleaseType {
		types := set.FromSlice([]string{a.ReleaseType, b.ReleaseType})
		ignoreTypes := set.FromSlice([]string{"article", "article-journal", "report", "paper-conference"})
		if types.Intersection(ignoreTypes).IsEmpty() {
			return MatchResult{StatusDifferent, ReasonReleaseType}
		}
		if types.Contains("dataset") && (types.Contains("article") || types.Contains("article-journal")) {
			return MatchResult{StatusDifferent, ReasonReleaseType}
		}
		if types.Contains("book") && (types.Contains("article") || types.Contains("article-journal")) {
			return MatchResult{StatusDifferent, ReasonReleaseType}
		}
	}
	if a.ReleaseType == "dataset" && b.ReleaseType == "dataset" && a.ExtIDs.DOI != b.ExtIDs.DOI {
		return MatchResult{StatusDifferent, ReasonDatasetDOI}
	}
	if a.ReleaseType == "chapter" && b.ReleaseType == "chapter" &&
		a.Extra.ContainerName != "" && a.Extra.ContainerName != b.Extra.ContainerName {
		return MatchResult{StatusDifferent, ReasonBookChapter}
	}
	if a.Extra.Crossref.Type == "component" && a.Title != b.Title {
		return MatchResult{StatusDifferent, ReasonComponent}
	}
	if a.ReleaseType == "component" && b.ReleaseType == "component" {
		if a.ExtIDs.DOI != "" && a.ExtIDs.DOI != b.ExtIDs.DOI {
			return MatchResult{StatusDifferent, ReasonComponent}
		}
	}
	aSlugTitle := strings.TrimSpace(strings.Replace(slugifyString(a.Title), "\n", " ", -1))
	bSlugTitle := strings.TrimSpace(strings.Replace(slugifyString(b.Title), "\n", " ", -1))

	if aSlugTitle == bSlugTitle {
		if a.ReleaseYear() != 0 && b.ReleaseYear() != 0 && absInt(a.ReleaseYear()-b.ReleaseYear()) > 40 {
			return MatchResult{StatusDifferent, ReasonYear}
		}
	}
	if aSlugTitle == bSlugTitle {
		ieeeArxivCheck := func(a, b *Release) (ok bool) {
			return doiPrefix(a.ExtIDs.DOI) == "10.1109" && b.ExtIDs.Arxiv != ""
		}
		if ieeeArxivCheck(a, b) || ieeeArxivCheck(b, a) {
			return MatchResult{StatusStrong, ReasonCustomIEEEArxiv}
		}
	}
	if aSlugTitle == bSlugTitle {
		if strings.HasPrefix(a.ExtIDs.DOI, "10.7916/") && strings.HasPrefix(b.ExtIDs.DOI, "10.7916/") {
			return MatchResult{StatusAmbiguous, ReasonCustomPrefix107916}
		}
	}
	if aSlugTitle == bSlugTitle {
		aSubtitle := a.Subtitle()
		bSubtitle := b.Subtitle()
		for _, aSub := range aSubtitle {
			for _, bSub := range bSubtitle {
				if slugifyString(aSub) != slugifyString(bSub) {
					return MatchResult{StatusDifferent, ReasonSubtitle}
				}
			}
		}
	}
	rawAuthors := func(rel *Release) (names []string) {
		for _, c := range rel.Contribs {
			name := strings.TrimSpace(c.RawName)
			if name == "" {
				continue
			}
			names = append(names, name)
		}
		return names
	}
	aAuthors := set.FromSlice(rawAuthors(a))
	bAuthors := set.FromSlice(rawAuthors(b))
	aSlugAuthors := set.FromSlice(mapString(slugifyString, aAuthors.Slice()))
	bSlugAuthors := set.FromSlice(mapString(slugifyString, bAuthors.Slice()))
	if aTitleLower == bTitleLower {
		if aAuthors.Len() > 0 && aAuthors.Equals(bAuthors) {
			if a.ReleaseYear() > 0 && b.ReleaseYear() > 0 && absInt(a.ReleaseYear()-b.ReleaseYear()) > 4 {
				return MatchResult{StatusDifferent, ReasonYear}
			}
			return MatchResult{StatusExact, ReasonTitleAuthorMatch}
		}
	}
	if looksLikeFilename(a.Title) || looksLikeFilename(b.Title) {
		if a.Title != b.Title {
			return MatchResult{StatusDifferent, ReasonTitleFilename}
		}
	}
	if a.Title != "" && a.Title == b.Title {
		if a.ReleaseYear() > 0 && b.ReleaseYear() > 0 && absInt(a.ReleaseYear()-b.ReleaseYear()) > 2 {
			return MatchResult{StatusDifferent, ReasonYear}
		}
	}
	// XXX: skipping chemical formula detection (to few cases; https://git.io/Jtdax)
	if len(aSlugTitle) < 10 && aSlugTitle != bSlugTitle {
		return MatchResult{StatusAmbiguous, ReasonShortTitle}
	}
	if PatDigits.MatchString(aSlugTitle) &&
		aSlugTitle != bSlugTitle &&
		unifyDigits(aSlugTitle) == unifyDigits(bSlugTitle) {
		return MatchResult{StatusDifferent, ReasonNumDiff}
	}
	if aSlugTitle != "" && bSlugTitle != "" &&
		strings.ReplaceAll(aSlugTitle, " ", "") == strings.ReplaceAll(bSlugTitle, " ", "") {
		if aSlugAuthors.Intersection(bSlugAuthors).Len() > 0 {
			if a.ReleaseYear() > 0 && b.ReleaseYear() > 0 && absInt(a.ReleaseYear()-b.ReleaseYear()) > 4 {
				return MatchResult{StatusDifferent, ReasonYear}
			}
			return MatchResult{StatusStrong, ReasonSlugTitleAuthorMatch}
		}
	}
	if a.ReleaseYear() > 0 && a.ReleaseYear() == b.ReleaseYear() && aTitleLower == bTitleLower {
		if (a.ExtIDs.PMID != "" && b.ExtIDs.DOI != "") || (b.ExtIDs.PMID != "" && a.ExtIDs.DOI != "") {
			return MatchResult{StatusStrong, ReasonPMIDDOIPair}
		}
	}
	if a.ExtIDs.Jstor != "" && b.ExtIDs.Jstor != "" && a.ExtIDs.Jstor != b.ExtIDs.Jstor {
		return MatchResult{StatusDifferent, ReasonJstorID}
	}
	if a.ContainerID != "" && a.ContainerID == b.ContainerID && a.ExtIDs.DOI != b.ExtIDs.DOI &&
		doiPrefix(a.ExtIDs.DOI) != "10.1126" &&
		doiPrefix(a.ExtIDs.DOI) == doiPrefix(b.ExtIDs.DOI) {
		return MatchResult{StatusDifferent, ReasonSharedDOIPrefix}
	}
	if aAuthors.Len() > 0 && aSlugAuthors.Intersection(bSlugAuthors).IsEmpty() {
		numAuthors := set.Min(aSlugAuthors, bSlugAuthors)
		score := averageScore(aSlugAuthors, bSlugAuthors)
		if (numAuthors < 3 && score > 0.9) || (numAuthors >= 3 && score > 0.5) {
			return MatchResult{StatusStrong, ReasonTokenizedAuthors}
		}
		aTok := set.FromSlice(strings.Fields(aSlugAuthors.Join(" ")))
		bTok := set.FromSlice(strings.Fields(bSlugAuthors.Join(" ")))
		aTok = set.Filter(aTok, func(s string) bool {
			return len(s) > 2
		})
		bTok = set.Filter(bTok, func(s string) bool {
			return len(s) > 2
		})
		if aTok.Len() > 0 && bTok.Len() > 0 {
			if aTok.Jaccard(bTok) > 0.35 {
				return MatchResult{StatusStrong, ReasonJaccardAuthors}
			}
		}
		return MatchResult{StatusDifferent, ReasonContribIntersectionEmpty}
	}
	if doiPrefix(a.ExtIDs.DOI) == "10.5860" || doiPrefix(b.ExtIDs.DOI) == "10.5860" {
		return MatchResult{StatusAmbiguous, ReasonCustomPrefix105860ChoiceReview}
	}
	// XXX: parse pages
	aParsedPages := parsePageString(a.Pages)
	bParsedPages := parsePageString(b.Pages)
	if aParsedPages.Err != nil && bParsedPages.Err != nil {
		if absInt(aParsedPages.Count()-bParsedPages.Count()) > 5 {
			return MatchResult{StatusDifferent, ReasonPageCount}
		}
	}
	if aAuthors.Equals(bAuthors) &&
		a.ContainerID == b.ContainerID &&
		a.ReleaseYear() == b.ReleaseYear() &&
		a.Title != b.Title &&
		(strings.Contains(a.Title, b.Title) || strings.Contains(b.Title, a.Title)) {
		return MatchResult{StatusStrong, ReasonTitleArtifact}
	}
	return MatchResult{
		StatusAmbiguous,
		ReasonUnknown,
	}
}

// generateBiblioRef generates a bibliographic schema document. XXX: This is a bit odd.
func generateBiblioRef(source, target *Release, matchResult MatchResult, provenance string) *BiblioRef {
	var bref BiblioRef
	bref.SourceReleaseIdent = source.Ident
	bref.SourceWorkIdent = source.WorkID
	bref.SourceReleaseStage = source.ReleaseStage
	if source.ReleaseYear() > 1000 {
		bref.SourceYear = source.ReleaseYearString()
	}
	bref.RefIndex = source.Extra.Skate.Ref.Index
	bref.RefKey = source.Extra.Skate.Ref.Key
	bref.TargetReleaseIdent = target.Ident
	bref.TargetWorkIdent = target.WorkID
	bref.MatchProvenance = provenance
	bref.MatchStatus = matchResult.Status.Short()
	bref.MatchReason = matchResult.Reason.Short()
	return &bref
}

type ParsedPages struct {
	Start int
	End   int
	Err   error
}

func (pp *ParsedPages) Count() int {
	return pp.End - pp.Start + 1
}

func parsePageString(s string) *ParsedPages {
	s = strings.TrimSpace(s)
	var pp = ParsedPages{}
	if len(s) == 0 {
		pp.Err = fmt.Errorf("parse pages: empty string")
		return &pp
	}
	matches := PatPages.FindStringSubmatch(s)
	if len(matches) != 3 {
		pp.Err = fmt.Errorf("parse pages: no page pattern")
		return &pp
	}
	start, end := matches[1], matches[2]
	if len(end) == 1 && len(start) > 1 && start[len(start)-1] < end[0] {
		end = fmt.Sprintf("%s%c", start[:len(start)-1], end[0])
	}
	if pp.Start, pp.Err = strconv.Atoi(start); pp.Err != nil {
		return &pp
	}
	if pp.End, pp.Err = strconv.Atoi(end); pp.Err != nil {
		return &pp
	}
	if pp.Start > pp.End {
		pp.Err = fmt.Errorf("invalid page count: %s", s)
	}
	return &pp
}

// averageScore take a limited set of authors and calculates pairwise
// similarity scores, then returns the average of the best scores; between 0
// and 1. XXX: This should be revisited and factored out; reading:
// https://github.com/djudd/human-name.
func averageScore(a, b set.Set) float64 {
	aTrimmed := a.TopK(5)
	bTrimmed := b.TopK(5)
	maxScores := make(map[string]float64) // For each a, keep the max.
	for _, pair := range aTrimmed.Product(bTrimmed) {
		a, b := pair[0], pair[1]
		score := authorSimilarityScore(a, b)
		if v, ok := maxScores[a]; !ok || score > v {
			maxScores[a] = score
		}
	}
	var sum, avg float64
	for _, v := range maxScores {
		sum += v
	}
	avg = sum / float64(len(maxScores))
	return avg
}

// authorSimilarityScore is a hacky similarity score.
func authorSimilarityScore(s, t string) float64 {
	ss := set.FromSlice(tokenNgrams(s, 2))
	ts := set.FromSlice(tokenNgrams(t, 2))
	return ss.Jaccard(ts)
}

// tokenNgrams are groups of n char-tokens per word-token in string, e.g. for
// n=2 and string "Anne K Lam", we would get ["an", "ne", "k", "la", "m"].
func tokenNgrams(s string, n int) (result []string) {
	var buf bytes.Buffer
	for _, token := range tokenizeString(s) {
		buf.Reset()
		for i, c := range token {
			if i > 0 && i%n == 0 {
				result = append(result, buf.String())
				buf.Reset()
			}
			buf.WriteRune(c) // XXX: skipping error handling
		}
		result = append(result, buf.String())
	}
	return
}

func tokenizeString(s string) []string {
	return strings.Fields(strings.ToLower(s))
}

func doiPrefix(s string) string {
	parts := strings.Split(s, "/")
	return parts[0]
}

// unifyDigits replaces all digit groups with a hopefully rare placeholder,
// e.g. "<NUM>"; This is for discovering very similar, yet different
// publications, where e.g. titles differ only by a single or few chars
// representing a year. Examples are yearly publications, e.g. "World Health
// Report 2020", "World Health Report 2021", ...  where any plain similarity
// score would yield a high number, yet publications are obviously not the
// same.
func unifyDigits(s string) string {
	return PatDigits.ReplaceAllString(s, "<NUM>")
}

// looksLikeFilename returns true, if the given string could be a filename.
func looksLikeFilename(s string) bool {
	if len(strings.Fields(s)) > 1 {
		return false
	}
	return PatFilenameLike.MatchString(s)
}

// mapString applies a function on each element of a string slice.
func mapString(f func(string) string, vs []string) (result []string) {
	for _, v := range vs {
		result = append(result, f(v))
	}
	return result
}

// absInt returns the absolute value of an int.
func absInt(v int) int {
	if v < 0 {
		return -v
	}
	return v
}

// looksLikeComponent returns true, if either a looks like a component of b, or vice versa.
func looksLikeComponent(a, b string) bool {
	ac := strings.Split(a, ".")
	bc := strings.Split(b, ".")
	if len(ac) > 1 {
		if strings.Join(ac[0:len(ac)-1], ".") == b {
			return true
		}
	}
	if len(bc) > 1 {
		if strings.Join(bc[0:len(bc)-1], ".") == a {
			return true
		}
	}
	return false
}