add exeptions to annotations (close #53)

CHANGELOG.md

@@ -2,9 +2,13 @@
 
 ## Unreleased
 
-## [v1.3.1]
+## [v1.3.2]
 
 - Add [#182]: support `Do`, `Oo`, `Nu` 2-letter genera.
+- Add [#53]: exceptions to annotations (`Bottaria nudum` for example).
+
+## [v1.3.1]
+
 - Add [#180]: Zenodo DOI.
 
 ## [v1.3.0]

ent/internal/preprocess/preprocess.go

@@ -13,6 +13,57 @@ import (
 var hybridCharRe1 = regexp.MustCompile(`(^)[Xx](\p{Lu})`)
 var hybridCharRe2 = regexp.MustCompile(`(\s|^)[Xx](\s|$)`)
 
+var VirusException = map[string]string{
+	"Aspilota":      "vector",
+	"Bembidion":     "satellites",
+	"Bolivina":      "prion",
+	"Ceylonesmus":   "vector",
+	"Cryptops":      "vector",
+	"Culex":         "vector",
+	"Dasyproctus":   "cevirus",
+	"Desmoxytes":    "vector",
+	"Dicathais":     "vector",
+	"Erateina":      "satellites",
+	"Euragallia":    "prion",
+	"Exochus":       "virus",
+	"Hilara":        "vector",
+	"Ithomeis":      "satellites",
+	"Microgoneplax": "prion",
+	"Neoaemula":     "vector",
+	"Nephodia":      "satellites",
+	"Ophion":        "virus",
+	"Psenulus":      "trevirus",
+	"Tidabius":      "vector",
+}
+
+var AnnotationException = map[string]string{
+	"Acrostichum":      "nudum",
+	"Adiantum":         "nudum",
+	"Africanthion":     "nudum",
+	"Agathidium":       "nudum",
+	"Aphaniosoma":      "nudum",
+	"Aspidium":         "nudum",
+	"Athyrium":         "nudum",
+	"Blechnum":         "nudum",
+	"Bottaria":         "nudum",
+	"Gnathopleustes":   "den",
+	"Lycopodium":       "nudum",
+	"Nephrodium":       "nudum",
+	"Paralvinella":     "dela",
+	"Polypodium":       "nudum",
+	"Polystichum":      "nudum",
+	"Psilotum":         "nudum",
+	"Ruteloryctes":     "bis",
+	"Selenops":         "ab",
+	"Tortolena":        "dela",
+	"Trachyphloeosoma": "nudum",
+	"Zodarion":         "van",
+}
+
+var NoParseException = map[string]string{
+	"Navicula": "bacterium",
+}
+
 var notesRe = regexp.MustCompile(
 	`(?i)\s+(environmental|samples|species\s+group|species\s+complex|clade|group|author)\b.*$`,
 )
@@ -68,14 +119,17 @@ func Preprocess(bs []byte) *Preprocessor {
 	}
 	i := len(bs)
 	name := string(bs)
-	if !VirusLikeName(name) {
+	if !IsException(name, VirusException) {
 		pr.Virus = IsVirus(bs[0:i])
 	}
 	if pr.Virus {
 		pr.NoParse = true
 		return pr
 	}
 	pr.NoParse = NoParse(bs[0:i])
+	if IsException(name, NoParseException) {
+		pr.NoParse = false
+	}
 	if pr.NoParse {
 		return pr
 	}
@@ -96,50 +150,14 @@ func Preprocess(bs []byte) *Preprocessor {
 	return pr
 }
 
-// LikeVirus takes a string and checks it against known species that can
-// easily be mistaken for viruses. If the string belongs to one of such species
-// returns true.
-// The following names are covered:
-//    Aspilota vector Belokobylskij, 2007
-//    Ceylonesmus vector Chamberlin, 1941
-//    Cryptops (Cryptops) vector Chamberlin, 1939
-//    Culex vector Dyar & Knab, 1906
-//    Dasyproctus cevirus Leclercq, 1963
-//    Desmoxytes vector (Chamberlin, 1941)
-//    Dicathais vector Thornley, 1952
-//    Euragallia prion Kramer, 1976
-//    Exochus virus Gauld & Sithole, 2002
-//    Hilara vector Miller, 1923
-//    Microgoneplax prion Castro, 2007
-//    Neoaemula vector Mackinnon, Hiller, Long & Marshall, 2008
-//    Ophion virus Gauld & Mitchell, 1981
-//    Psenulus trevirus Leclercq, 1961
-//    Tidabius vector Chamberlin, 1931
-func VirusLikeName(name string) bool {
-	names := map[string]string{
-		"Aspilota":      "vector",
-		"Ceylonesmus":   "vector",
-		"Cryptops":      "vector",
-		"Culex":         "vector",
-		"Dasyproctus":   "cevirus",
-		"Desmoxytes":    "vector",
-		"Dicathais":     "vector",
-		"Euragallia":    "prion",
-		"Exochus":       "virus",
-		"Hilara":        "vector",
-		"Microgoneplax": "prion",
-		"Neoaemula":     "vector",
-		"Ophion":        "virus",
-		"Psenulus":      "trevirus",
-		"Tidabius":      "vector",
-	}
+func IsException(name string, names map[string]string) bool {
 	words := strings.Fields(name)
 	if len(words) < 2 {
 		return false
 	}
 	if epithet, ok := names[words[0]]; ok {
 		for _, w := range words[1:] {
-			if strings.HasPrefix(w, epithet) {
+			if w == epithet {
 				return true
 			}
 		}
@@ -161,6 +179,9 @@ func NormalizeHybridChar(bs []byte) []byte {
 // input.
 func Annotation(bs []byte) int {
 	i := len(bs)
+	if IsException(string(bs), AnnotationException) {
+		return i
+	}
 	regexps := []*regexp.Regexp{
 		notesRe, taxonConceptsRe1, taxonConceptsRe2, taxonConceptsRe3,
 		nomenConceptsRe, lastWordJunkRe, stopWordsRe,
@@ -178,8 +199,8 @@ func Annotation(bs []byte) int {
 	// `Anthurium Trustees of the British Museum` should not.
 	cultivarRankLoc := cultivarRankRe.FindIndex(bs[0:i])
 	ofLoc := ofWordRe.FindIndex(bs[0:i])
-	if(	len(ofLoc) > 0 && ofLoc[0] < i &&
-			(len(cultivarRankLoc) == 0 || cultivarRankLoc[0] > ofLoc[0])) {
+	if len(ofLoc) > 0 && ofLoc[0] < i &&
+		(len(cultivarRankLoc) == 0 || cultivarRankLoc[0] > ofLoc[0]) {
 		i = ofLoc[0]
 	}
 

ent/internal/preprocess/preprocess_test.go

@@ -113,6 +113,50 @@ func TestPreprocess(t *testing.T) {
 				[]byte(v.out), v.msg)
 		}
 	})
+	t.Run("NoParseLikeName", func(t *testing.T) {
+		data := []struct {
+			msg            string
+			name           string
+			likeAnnotation bool
+		}{
+			{"name", "Navicula bacterium", true},
+		}
+		for _, v := range data {
+			assert.Equal(t, ppr.IsException(v.name, ppr.NoParseException), v.likeAnnotation, v.msg)
+		}
+	})
+	t.Run("AnnotationLikeName", func(t *testing.T) {
+		data := []struct {
+			msg            string
+			name           string
+			likeAnnotation bool
+		}{
+			{"name", "Acrostichum nudum", true},
+			{"name", "Adiantum nudum", true},
+			{"name", "Africanthion nudum", true},
+			{"name", "Agathidium nudum", true},
+			{"name", "Aphaniosoma nudum", true},
+			{"name", "Aspidium nudum", true},
+			{"name", "Athyrium nudum", true},
+			{"name", "Blechnum nudum", true},
+			{"name", "Bottaria nudum", true},
+			{"name", "Gnathopleustes den", true},
+			{"name", "Lycopodium nudum", true},
+			{"name", "Nephrodium nudum", true},
+			{"name", "Paralvinella dela", true},
+			{"name", "Polypodium nudum", true},
+			{"name", "Polystichum nudum", true},
+			{"name", "Psilotum nudum", true},
+			{"name", "Ruteloryctes bis", true},
+			{"name", "Selenops ab", true},
+			{"name", "Tortolena dela", true},
+			{"name", "Trachyphloeosoma nudum", true},
+			{"name", "Zodarion van", true},
+		}
+		for _, v := range data {
+			assert.Equal(t, ppr.IsException(v.name, ppr.AnnotationException), v.likeAnnotation, v.msg)
+		}
+	})
 
 	t.Run("VirusLikeName", func(t *testing.T) {
 		data := []struct {
@@ -139,7 +183,7 @@ func TestPreprocess(t *testing.T) {
 			{"name17", "Homo sapiens coronavirus", false},
 		}
 		for _, v := range data {
-			assert.Equal(t, ppr.VirusLikeName(v.name), v.likeVirus, v.msg)
+			assert.Equal(t, ppr.IsException(v.name, ppr.VirusException), v.likeVirus, v.msg)
 		}
 	})
 

ent/parser/grammar.peg

@@ -59,7 +59,7 @@ CultivarApostrophe <- '\'' / '‘' / '’' / '"' / '“' / '”'
 
 SpeciesEpithet <- !(AuthorEx) Word (_? Authorship)?
 
-Comparison <- 'cf' '.'?
+Comparison <- 'cf' '.'? &(SpaceCharEOI)
 
 Rank <- (RankForma / RankVar / RankSsp / RankOther / RankOtherUncommon /
   RankAgamo / RankNotho) (_? LowerGreek ('.' / &(SpaceCharEOI)))?