@larsgw/formica 0.9.2 → 0.10.0

package/src/resources/parse-name.ts

@@ -1,392 +0,0 @@
-export class RecoverableSyntaxError<Result> extends SyntaxError {
-    result: Result
-
-    constructor (message: string, result: Result) {
-        super(message)
-        this.result = result
-    }
-}
-
-export const RANKS: Rank[] = [
-    'phylum',
-    'subphylum',
-    'class',
-    'subclass',
-    'infraclass',
-    'superorder',
-    'order',
-    'suborder',
-    'infraorder',
-    'superfamily',
-    'family',
-    'subfamily',
-    'tribe',
-    'subtribe',
-    'genus',
-    'subgenus',
-    'section', // not ICZN
-    'subsection', // not ICZN
-    'series', // not ICZN
-    'group',
-    'subgroup', // ...
-    'aggregate', // not ICZN
-    'complex', // not ICZN
-    'species',
-    'subspecies',
-    'variety',
-    'form',
-    'aberration', // not ICZN
-    'race', // not ICZN
-    'stirps' // not ICZN
-]
-
-const TAXONOMIC_STATUS: Record<string, TaxonStatus> = {
-    '>': 'incorrect',
-    '+': 'proparte synonym',
-    '=': 'synonym'
-}
-
-const RANK_LABELS: Record<Rank, string> = {
-    'subspecies': 'subsp.',
-    'variety': 'var.',
-    'form': 'f.',
-    'aberration': 'ab.',
-    'race': 'r.',
-    'stirps': 'st.'
-}
-
-const RANK_LABELS_REVERSE: Record<string, Rank> = {
-    'st': 'stirps',
-    'r': 'race',
-    'ab': 'aberration',
-    'f': 'form',
-    'var': 'variety',
-    'ssp': 'subspecies',
-    'subsp': 'subspecies'
-}
-
-const HYBRID_SIGN = '\u00D7'
-
-/**
- *   1. Any number of
- *      - capitalized words
- *      - "&"
- *      - " in "
- *      - " ex "
- *      - lowercase name particles
- *   2. Followed by a capitalized word
- *   3. Optionally, followed by "et al."
- */
-const LOWERCASE_NAME_PARTICLES = ['y', 'der', 'den', 'de', 'van', 'von'].join('|')
-const SIMPLE_AUTHOR_PATTERN = '(?:(?:\\p{Lu}\\S*|&|in|ex|' + LOWERCASE_NAME_PARTICLES + ')\\s*)*\\p{Lu}\\S+(?:\\s+et\\s+al\\.)?'
-
-const NAME_PATTERN = new RegExp(
-    '^' +
-        // $1 main name part
-        '(\\S+)' +
-        // $2 optional author citation
-        '(?: ' +
-            // but not auct(t)., etc.
-            '(?!auctt?\\.|(?:syn|comb|sp|spec|nom|gen|subgen)\\. n(?:ov)?\\.|s(?:ens[.u]|\\.)|in part|partim)' +
-        '(' +
-            // $2.1 anything in parentheses, followed by optional revising author(s)
-            '\\(.+?\\)(?:\\s+' + SIMPLE_AUTHOR_PATTERN + ')?' +
-        '|' +
-            // $2.2 anything followed by a year
-            '.+?\\d{4}\\)?' +
-        '|' +
-            // $2.3 author(s)
-            SIMPLE_AUTHOR_PATTERN +
-        '))?' +
-        // $3 optional notes
-        '(?:,? (.+))?' +
-    '$',
-    'u'
-)
-
-/**
- * Structure
- *   $1 genus: ((?:x )?[A-Z]\S+)
- *   $2 subgenus: (?:\(([A-Z]\S+?)\) )?
- */
-const SUBGENUS_PATTERN = /^([A-Z]\S+) (?:\(([A-Z]\S+?)\))(?= |$)/
-
-/**
- * Structure
- *   $1 genus+subgenus (+ trailing space): (?:([A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?
- *     $1.1 genus: ((?:x )?[A-Z]\S+)
- *     $1.2 subgenus: (?:\(([A-Z]\S+?)\) )?
- *   $2 species: (x [a-z-]+|[a-z-][^\s.]+(?: x [a-z-]+)?|[A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+)
- *     $2a: x [a-z-]+
- *     $2b hybrid: [a-z-][^\s.]+(?: x [a-z-]+)?
- *     $2c intergeneric hybrid: [A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+
- */
-const BINAME_PATTERN = /^(?:((?:x )?[A-Z]\S+) (?:\(([A-Z]\S+?)\) )?)?(x [a-z-]+|[a-z-][^\s.]+(?: x [a-z-]+)?|[A-Z][a-z]+_[a-z-]+ x [A-Z][a-z]+_[a-z-]+)(?= |$)/
-
-const CLUSTER_PATTERN = /^\[(_|\d+)\] /
-
-function compareRanks (a: Rank, b: Rank): number {
-    return RANKS.indexOf(a) - RANKS.indexOf(b)
-}
-
-function capitalize (name: string): string {
-    return name[0].toUpperCase() + name.slice(1).toLowerCase()
-}
-
-function capitalizeGenericName (name: string): string {
-    if (name[0] === HYBRID_SIGN) {
-        return HYBRID_SIGN + capitalize(name.slice(1))
-    }
-
-    return capitalize(name)
-}
-
-function isUpperCase (name: string): boolean {
-    return name === name.toUpperCase()
-}
-
-function getSynonymRank (name: string, rank: Rank): Rank {
-    const rest = name.replace(BINAME_PATTERN, '')
-    const rankPrefix = rest.match(/^(?: |^)(st|r|ab|f|var|ssp|subsp)\. /)
-    if (rankPrefix) {
-        return RANK_LABELS_REVERSE[rankPrefix[1]] as string
-    } else if (!BINAME_PATTERN.test(name)) {
-        return SUBGENUS_PATTERN.test(name) ? 'subgenus' : rank
-    } else if (/^ (?!sensu)[a-z0-9-]+($| )/.test(rest)) {
-        return 'subspecies'
-    } else {
-        return 'species'
-    }
-}
-
-function capitalizeAuthors (authors: string): string {
-    return authors
-        .replace(
-            /[^\x00-\x40\x5B-\x60\x7B-\x7F]+/g, // eslint-disable-line no-control-regex
-            name => isUpperCase(name) ? capitalize(name) : name
-        )
-        .replace(/ Y /g, ' y ')
-}
-
-export function parseName (name: string, rank: Rank, parent: WorkingTaxon): WorkingTaxon {
-    const item = {} as WorkingTaxon
-
-    // Synonyms have the accepted name usage as 'parent'.
-    const isSynonym = /^[+=>] /.test(name)
-    if (isSynonym) {
-        item.taxonomicStatus = TAXONOMIC_STATUS[name[0]]
-        name = name.slice(2)
-        if (/^\? ?/.test(name)) {
-            item.dynamicProperties = '{"synonymUncertain":true}'
-            name = name.replace(/^\? ?/, '')
-        }
-        rank = getSynonymRank(name, parent.taxonRank as Rank)
-    } else {
-        item.taxonomicStatus = 'accepted'
-    }
-
-    // Clusters
-    if (CLUSTER_PATTERN.test(name)) {
-        const [match, cluster] = name.match(CLUSTER_PATTERN) as string[]
-        item.cluster = cluster
-        name = name.slice(match.length)
-    }
-
-    // Set verbatim identification after subsequent syntax is removed.
-    item.verbatimIdentification = name.replace(/(?<=^| )x(?=$| )/g, HYBRID_SIGN).replace(/_/g, ' ')
-
-    // Parent context is used for parsing and formatting binomial names.
-    // For formatting, it needs to match external databases (i.e. be correct).
-    // For parsing, it needs to match the current file. If relevant parents
-    // (i.e. genus, species) had mistakes that were corrected, the uncorrected
-    // genus and species names need to be used.
-    const parentContext = {
-        genus: parent.genus,
-        subgenus: parent.subgenus,
-        specificEpithet: parent.specificEpithet,
-        incorrect: {
-            genus: parent.incorrect && parent.incorrect.genus,
-            specificEpithet: parent.incorrect && parent.incorrect.specificEpithet
-        }
-    }
-
-    // Both contexts should be amended in the two cases where binomial names
-    // are fully used: (1) synonyms and (2) multinomial taxa without parents to
-    // provide parts of the name (e.g. bare species without a genus parent, or
-    // even subspecies without a species or genus parent).
-    if (isSynonym || !parentContext.genus || (compareRanks('species', rank) < 0 && !parentContext.specificEpithet)) {
-        const [, genus, subgenus, species] = name.match(BINAME_PATTERN) ?? name.match(SUBGENUS_PATTERN) ?? []
-        if (genus) {
-            parentContext.incorrect.genus = genus
-            parentContext.genus = capitalizeGenericName(genus.replace(/(^| )x /, HYBRID_SIGN))
-        }
-        if (subgenus) {
-            parentContext.subgenus = capitalize(subgenus)
-        } else if (genus) {
-            // If a genus is given but no subgenus, remove any existing subgenus
-            // from the parent context.
-            delete parentContext.subgenus
-        }
-        if (species && compareRanks('species', rank) < 0) {
-            parentContext.incorrect.specificEpithet = species
-            parentContext.specificEpithet = species.replace(/(^| )x /, HYBRID_SIGN)
-        }
-    }
-
-    // In taxa of group, species or lower, the name should just contain the
-    // (infra)specific epithet and the author information & remarks when processing
-    // further.
-    if (compareRanks('group', rank) <= 0) {
-        // Remove genus
-        const genus = parentContext.incorrect.genus || parentContext.genus || ''
-        if (name[0] === genus[0] && name.toLowerCase().startsWith(genus.toLowerCase() + ' ')) {
-            name = name.slice(genus.length + 1)
-        }
-
-        // Remove subgenus
-        name = name.replace(/^\(.*?\) /, '')
-
-        // Infraspecific taxa
-        if (compareRanks('species', rank) < 0) {
-            // Remove specific epithet
-            const species = parentContext.incorrect.specificEpithet || parentContext.specificEpithet || ''
-            if (name.startsWith(species + ' ')) {
-                name = name.slice(species.length + 1)
-            }
-
-            // Remove rank abbreviations
-            name = name.replace(/^(st|r|ab|f|var|ssp|subsp)\. /, '')
-        }
-    } else if (compareRanks('genus', rank) <= 0) {
-        // Remove genus
-        const genus = parentContext.incorrect.genus || parentContext.genus || ''
-        if (name[0] === genus[0] && name.toLowerCase().startsWith(genus.toLowerCase() + ' (')) {
-            name = name.slice(genus.length + 1)
-        }
-
-        // Remove subgenus parentheses
-        name = name.replace(/^\((.*?)\)/, '$1')
-    }
-
-    // Hybrids
-    if (rank === 'genus' && name.startsWith('x ')) {
-        name = HYBRID_SIGN + name.slice(2)
-    }
-
-    if (rank === 'species' && /(^| )x /.test(name)) {
-        name = name.replace(/(^| )x /, HYBRID_SIGN)
-    }
-
-    // Divide the name into the main scientific name (only the epithet for taxa
-    // lower than genus), the authorship information, and optionally remarks
-    const nameParts = name.match(NAME_PATTERN)
-    if (!nameParts) {
-        throw new Error(`Taxon "${name}" could not be parsed`)
-    }
-
-    // To encode old names with spaces (e.g. "Orsillus pini canariensis Lindberg, 1953")
-    // underscores are used, which are replaced here. This is also used for undescribed
-    // species (e.g. "Leiobunum species A") and intergeneric hybrids (e.g. "×Festulpia
-    // Festuca rubra × Vulpia bromoides")
-    if (nameParts[1].includes('_')) {
-        nameParts[1] = nameParts[1].replace(/_/g, ' ')
-    }
-
-    const [_, taxon, citation = '', notes] = nameParts
-    item.scientificNameAuthorship = capitalizeAuthors(citation)
-    item.taxonRemarks = notes
-    item.taxonRank = rank
-    item.genericName = undefined
-    item.infragenericEpithet = undefined
-    item.specificEpithet = undefined
-    item.infraspecificEpithet = undefined
-
-    if (/[^\p{L}0-9\u{00D7}\- ]/u.test(taxon)) {
-        throw new RecoverableSyntaxError(`Taxon name contains unexpected characters: "${taxon}"`, item)
-    }
-
-    // Validate names and recompose binomial and trinomial names
-    if (compareRanks('genus', rank) > 0) {
-        item.scientificName = capitalize(taxon)
-        if (taxon[0].toUpperCase() !== taxon[0]) {
-            throw new RecoverableSyntaxError(`Taxon name (${rank}) should be capitalized: "${taxon}"`, item)
-        }
-    } else if (rank === 'genus') {
-        item.scientificName = capitalizeGenericName(taxon)
-        if (taxon[0].toUpperCase() !== taxon[0] || (taxon[0] === HYBRID_SIGN && taxon[1].toUpperCase() !== taxon[1])) {
-            throw new RecoverableSyntaxError(`Generic epithet should be capitalized: "${taxon}"`, item)
-        }
-    } else if (compareRanks('group', rank) > 0) {
-        item.genericName = parentContext.genus
-        item.infragenericEpithet = parentContext.subgenus
-        item.scientificName = capitalize(taxon)
-        if (taxon[0].toUpperCase() !== taxon[0]) {
-            throw new RecoverableSyntaxError(`Infrageneric epithet should be capitalized: "${taxon}"`, item)
-        }
-    } else if (rank === 'group') {
-        item.genericName = parentContext.genus
-        item.infragenericEpithet = parentContext.subgenus
-        const specificEpithet = taxon.toLowerCase().replace(/(-group)?$/, '')
-        item.scientificName = `${item.genericName} ${specificEpithet}-group`
-        if (taxon.toLowerCase() !== taxon) {
-            throw new RecoverableSyntaxError(`Group name should be lowercase: "${taxon}"`, item)
-        }
-    } else if (rank === 'subgroup') {
-        item.genericName = parentContext.genus
-        item.infragenericEpithet = parentContext.subgenus
-        const specificEpithet = taxon.toLowerCase().replace(/(-subgroup)?$/, '')
-        item.scientificName = `${item.genericName} ${specificEpithet}-subgroup`
-        if (taxon.toLowerCase() !== taxon) {
-            throw new RecoverableSyntaxError(`Subgroup name should be lowercase: "${taxon}"`, item)
-        }
-    } else if (compareRanks('species', rank) > 0) {
-        item.genericName = parentContext.genus
-        item.infragenericEpithet = parentContext.subgenus
-        const specificEpithet = taxon.toLowerCase()
-        item.scientificName = `${item.genericName} ${specificEpithet}`
-        if (specificEpithet !== taxon) {
-            throw new RecoverableSyntaxError(`Taxon name should be lowercase: "${taxon}"`, item)
-        }
-    } else if (rank === 'species') {
-        item.genericName = parentContext.genus
-        item.infragenericEpithet = parentContext.subgenus
-        if (taxon.toLowerCase() !== taxon && !/^[A-Z][a-z]+ [a-z]+\xD7[A-Z][a-z]+ [a-z]+$/.test(taxon)) {
-            throw new RecoverableSyntaxError(`Specific epithet should be lowercase: "${taxon}"`, item)
-        }
-        item.specificEpithet = taxon
-        item.scientificName = `${item.genericName} ${item.specificEpithet}`
-    } else if (compareRanks('species', rank) < 0) {
-        item.genericName = parentContext.genus
-        item.infragenericEpithet = parentContext.subgenus
-        item.specificEpithet = parentContext.specificEpithet
-        item.infraspecificEpithet = taxon.toLowerCase()
-
-        // If possible, names below species should have abbreviations for ranks,
-        // like "subsp."
-        const nameParts = [
-            item.genericName,
-            item.specificEpithet,
-            item.infraspecificEpithet
-        ]
-        if (item.taxonRank in RANK_LABELS) {
-            nameParts.splice(2, 0, RANK_LABELS[item.taxonRank])
-        }
-        item.scientificName = nameParts.join(' ')
-
-        if (item.infraspecificEpithet !== taxon) {
-            throw new RecoverableSyntaxError(`Infraspecific epithet should be lowercase: "${taxon}"`, item)
-        }
-    }
-
-    // Re-add authorship information
-    item.scientificNameOnly = item.scientificName
-    if (item.scientificNameAuthorship) {
-        item.scientificName += ` ${item.scientificNameAuthorship}`
-    }
-
-    if (isSynonym && /^auctt?\./.test(item.taxonRemarks)) {
-        item.taxonomicStatus = 'misapplied'
-    }
-
-    return item
-}