283 flatten

ent/parsed/flatten.go

@@ -0,0 +1,345 @@
+package parsed
+
+import "strings"
+
+// ParsedFlat is the result of a scientific name-string parsing flattened
+// for the convenience.
+type ParsedFlat struct {
+	// Parsed is false if parsing did not succeed.
+	Parsed bool `json:"parsed"`
+
+	// NomCode modifies parsing rules according to provided nomenclatural code.
+	NomCode string `json:"nomenclaturalCode,omitempty"`
+
+	// ParseQuality is a number that represents the quality of the
+	// parsing.
+	//
+	//  0 - name-string is not parseable
+	//  1 - no parsing problems encountered
+	//  2 - small parsing problems
+	//  3 - serious parsing problems
+	//  4 - severe problems, name could not be parsed completely
+	//
+	// The ParseQuality is equal to the quality of the most
+	// severe warning (see qualityWarnings). If no problems
+	// are encountered, and the parsing succeeded, the parseQuality
+	// is set to 1. If parsing failed, the parseQuality is 0.
+	ParseQuality int `json:"quality"`
+
+	// Verbatim is input name-string without modifications.
+	Verbatim string `json:"verbatim"`
+
+	// Normalized is a normalized version of the input name-string.
+	Normalized string `json:"normalized,omitempty"`
+
+	// CanonicalSimple is a simplified version of a name where some elements like ranks,
+	// or hybrid signs "×" are omitted (hybrid signs are present for hybrid
+	// formulas).
+	//
+	// It is most useful to match names in general.
+	CanonicalSimple string `json:"canonicalSimple,omitempty"`
+
+	// CanonicalFull is a canonical form that keeps hybrid signs "×" for named
+	// hybrids and shows infra-specific ranks.
+	//
+	// It is most useful for detection of the best matches from
+	// multiple results. It is also recommended for displaying
+	// canonical forms of botanical names.
+	CanonicalFull string `json:"canonicalFull,omitempty"`
+
+	// CanonicalStemmed is the most "normalized" and simplified version of the name.
+	// Species epithets are stripped of suffixes, "j" character converted to "i",
+	// "v" character converted to "u" according to "Schinke R, Greengrass M,
+	// Robertson AM and Willett P (1996)"
+	//
+	// It is most useful to match names when a variability in suffixes is
+	// possible.
+	CanonicalStemmed string `json:"canonicalStemmed,omitempty"`
+
+	// Cardinality allows to sort, partition names according to number of
+	// elements in their canonical forms.
+	//
+	// 0 - cardinality cannot be calculated
+	// 1 - uninomial
+	// 2 - binomial
+	// 3 - trinomial
+	// 4 - quadrinomial
+	Cardinality int `json:"cardinality"`
+
+	// Rank provides information about the rank of the name. It is not
+	// always possible to infer rank correctly, so this field will be
+	// omitted when the data for it does not exist.
+	Rank string `json:"rank,omitempty"`
+
+	// Authorship is the verbatim authorship of the name.
+	Authorship string `json:"authorship,omitempty"`
+
+	// Bacteria is not nil if the input name has a genus
+	// that is registered as bacterial. Possible
+	// values are "maybe" - if the genus has homonyms in other groups
+	// and "yes" if GNparser dictionary does not detect any homonyms
+	//
+	// The bacterial names often contain strain information which are
+	// not parseable and are placed into the "tail" field.
+	Bacteria string `json:"bacteria,omitempty"`
+
+	// Candidatus indicates that the parsed string is a candidatus bacterial name.
+	Candidatus bool `json:"candidatus,omitempty"`
+
+	// Virus is set to true in case if name is not parsed, and probably
+	// belongs to a wide variety of sub-cellular entities like
+	//
+	// - viruses
+	// - plasmids
+	// - prions
+	// - RNA
+	// - DNA
+	//
+	// Viruses are the vast majority in this group of names,
+	// as a result they gave (very imprecise) name to
+	// the field.
+	//
+	// We do plan to create a parser for viruses at some point,
+	// which will expand this group into more precise categories.
+	Virus bool `json:"virus,omitempty"`
+
+	// Cultivar is true if a name was parsed as a cultivar.
+	Cultivar bool `json:"cultivar,omitempty"`
+
+	// DaggerChar if true if a name-string includes '†' rune.
+	// This rune might mean a fossil, or be indication of the clade extinction.
+	DaggerChar bool `json:"daggerChar,omitempty"`
+
+	// Hybrid is a string representation of a hybrid type.
+	//
+	// - a non-categorized hybrid
+	// - named hybrid
+	// - notho- hybrid
+	// - hybrid formula
+	Hybrid string `json:"hybrid,omitempty"`
+
+	// GraftChimera is a string representation of graft chimera.
+	//
+	// - a non-categorized graft chimera
+	// - named graft chimera
+	// - graft chimera formula
+	GraftChimera string `json:"graftchimera,omitempty"`
+
+	// Surrogate is a string repsresentation of a surrogate type.
+
+	// - a non-categorized surrogates
+	// - surrogate names from BOLD project
+	// - comparisons (Homo cf. sapiens)
+	// - approximations (names for specimen that not fully identified)
+	Surrogate string `json:"surrogate,omitempty"`
+
+	// Tail is an unparseable tail of a name. It might contain "junk",
+	// annotations, malformed parts of a scientific name, taxonomic concept
+	// indications, bacterial strains etc.  If there is an unparseable tail, the
+	// quality of the name-parsing is set to the worst category.
+	Tail string `json:"tail,omitempty"`
+
+	// Uninomial represents the single name used for uninomial nomenclature,
+	// typically applied to higher taxonomic ranks (e.g., family or order names
+	// like "Asteraceae"). This field is populated only for uninomial names and
+	// omitted otherwise.
+	Uninomial string `json:"uninomial,omitempty"`
+
+	// Genus specifies the genus part of a binomial or trinomial scientific name
+	// (e.g., "Quercus" in "Quercus robur"). This field is empty if the name is
+	// uninomial.
+	Genus string `json:"genus,omitempty"`
+
+	// Subgenus indicates the infrageneric epithet when present.
+	// This field is omitted if not applicable.
+	Subgenus string `json:"infragenericEpithet,omitempty"`
+
+	// Species is the specific epithet of a binomial or trinomial.
+	Species string `json:"specificEpithet,omitempty"`
+
+	// Infraspecies is the infraspecificEpither of trinomials (names with
+	// cardinality 3). We do not provide details for names with higher
+	// cardinality.
+	Infraspecies string `json:"infraspecificEpithet,omitempty"`
+
+	// CultivarEpithet contains the cultivar name for cultivated plant varieties
+	// (e.g., "Golden Delicious" in "Malus domestica 'Golden Delicious'"). This
+	// field is populated only for names that include a cultivar designation.
+	CultivarEpithet string `json:"cultivarEpithet,omitempty"`
+
+	// Notho denotes the hybrid status of a name, indicating whether it is a
+	// hybrid (e.g., "nothosubsp." or "nothovar." in "Salvia × sylvestris"). This
+	// field is empty if not given.
+	Notho string `json:"notho,omitempty"`
+
+	// CombinationAuthorship provides the authorship for the current combination
+	// of the name, typically the authors who transferred the species to a new
+	// genus. (e.g., "K." in "Aus bus (L.) K."). This field is
+	// omitted if no combination authorship is specified.
+	CombinationAuthorship string `json:"combinationAuthorship,omitempty"`
+
+	// CombinationExAuthorship captures the "ex" part of the combination
+	// authorship (e.g., "ex DC." in "Quercus robur L. ex DC."). This field is
+	// empty if no "ex" authorship exists.
+	CombinationExAuthorship string `json:"combinationExAuthorship,omitempty"`
+
+	// CombinationAuthorshipYear records the year associated with the combination
+	// authorship, if provided (e.g., "1754" in "Homo sapiens (L.) K. 1753").
+	// This field is omitted if the year is not specified.
+	CombinationAuthorshipYear string `json:"combinationAuthorshipYear,omitempty"`
+
+	// BasionymAuthorship identifies the authorship of the original combination
+	// of the name (e.g., "Mill." in "Quercus robur (Mill.) L." where Mill. is
+	// the original author). This field is populated only if basionym authorship
+	// is present.
+	BasionymAuthorship string `json:"basionymAuthorship,omitempty"`
+
+	// BasionymExAuthorship specifies the "ex" part of the basionym authorship,
+	// if applicable (e.g., "ex Torr." in "Pinus ponderosa Douglas ex Torr.").
+	// This field is empty when no "ex" basionym authorship is provided.
+	BasionymExAuthorship string `json:"basionymExAuthorship,omitempty"`
+
+	// BasionymAuthorshipYear indicates the year tied to the basionym authorship
+	// (e.g., "1820" in "Pinus ponderosa Douglas, 1820"). This field is included
+	// only when the basionym year is explicitly stated.
+	BasionymAuthorshipYear string `json:"basionymAuthorshipYear,omitempty"`
+
+	// VerbatimID is a UUID v5 generated from the verbatim value of the
+	// input name-string. Every unique string always generates the same
+	// UUID.
+	VerbatimID string `json:"id"`
+
+	// ParserVersion is the version number of the GNparser.
+	ParserVersion string `json:"parserVersion"`
+}
+
+// Flatten converts a Parsed struct into a ParsedFlat struct, which is a
+// flattened representation of the parsed data.
+func (p Parsed) Flatten() ParsedFlat {
+	var bact string
+	if p.Bacteria != nil && p.Bacteria.Valid {
+		switch p.Bacteria.Value {
+		case 0:
+			bact = "maybe"
+		case 1:
+			bact = "yes"
+		default:
+			bact = "no"
+		}
+	}
+	var hybrid string
+	if p.Hybrid != nil {
+		hybrid = p.Hybrid.String()
+	}
+	var graft string
+	if p.GraftChimera != nil {
+		graft = p.GraftChimera.String()
+	}
+	var surrogate string
+	if p.Surrogate != nil {
+		surrogate = p.Surrogate.String()
+	}
+
+	res := ParsedFlat{
+		Parsed:        p.Parsed,
+		NomCode:       p.NomCode,
+		ParseQuality:  p.ParseQuality,
+		Verbatim:      p.Verbatim,
+		Normalized:    p.Normalized,
+		Cardinality:   p.Cardinality,
+		Rank:          p.Rank,
+		Bacteria:      bact,
+		Candidatus:    p.Candidatus,
+		Virus:         p.Virus,
+		Cultivar:      p.Cultivar,
+		DaggerChar:    p.DaggerChar,
+		Hybrid:        hybrid,
+		GraftChimera:  graft,
+		Surrogate:     surrogate,
+		Tail:          p.Tail,
+		VerbatimID:    p.VerbatimID,
+		ParserVersion: p.ParserVersion,
+	}
+	if !p.Parsed {
+		return res
+	}
+
+	res.CanonicalSimple = p.Canonical.Simple
+	res.CanonicalFull = p.Canonical.Full
+	res.CanonicalStemmed = p.Canonical.Stemmed
+
+	if p.Authorship != nil {
+		au := p.Authorship
+		res.Authorship = au.Verbatim
+
+		if au.Original != nil {
+			res.BasionymAuthorship = authorship(au.Original)
+			res.BasionymExAuthorship = exAuthorship(au.Original)
+			res.BasionymAuthorshipYear = year(au.Original)
+		}
+
+		if au.Combination != nil {
+			res.CombinationAuthorship = authorship(au.Combination)
+			res.CombinationExAuthorship = exAuthorship(au.Combination)
+			res.CombinationAuthorshipYear = year(au.Combination)
+		}
+	}
+
+	switch detail := p.Details.(type) {
+	case DetailsUninomial:
+		res.Uninomial = detail.Uninomial.Value
+	case DetailsSpecies:
+		res.Genus = detail.Species.Genus
+		res.Subgenus = detail.Species.Subgenus
+		res.Species = detail.Species.Species
+	case DetailsInfraspecies:
+		if len(detail.Infraspecies.Infraspecies) == 1 {
+			res.Genus = detail.Infraspecies.Genus
+			res.Species = detail.Infraspecies.Species.Species
+			res.Rank = detail.Infraspecies.Infraspecies[0].Rank
+			res.Infraspecies = detail.Infraspecies.Infraspecies[0].Value
+		}
+		res.BasionymAuthorshipYear = year(detail.Infraspecies.Authorship.Original)
+	}
+	return res
+}
+
+func authorship(ag *AuthGroup) string {
+	if ag == nil {
+		return ""
+	}
+	return joinAuthors(ag.Authors)
+}
+
+func joinAuthors(aus []string) string {
+	var res string
+	switch len(aus) {
+	case 0:
+		res = ""
+	case 1:
+		res = aus[0]
+	case 2:
+		res = strings.Join(aus, " & ")
+	default:
+		res = strings.Join(aus[0:len(aus)-1], ", ")
+		res = res + " & " + aus[len(aus)-1]
+	}
+	return res
+}
+
+func exAuthorship(ag *AuthGroup) string {
+	if ag == nil || ag.ExAuthors == nil {
+		return ""
+	}
+	return joinAuthors(ag.ExAuthors.Authors)
+}
+
+func year(ag *AuthGroup) string {
+	if ag == nil || ag.Year == nil {
+		return ""
+	}
+	if ag.Year.IsApproximate {
+		return "(" + ag.Year.Value + ")"
+	}
+	return ag.Year.Value
+}