// Validate validates that a taxon is valid in the database, and set some
// canonical values. It returns an error if the taxon is not valid.
func (t *taxonomy) validate(tax *jdh.Taxon) error {
tax.Id = strings.TrimSpace(tax.Id)
tax.Name = strings.Join(strings.Fields(tax.Name), " ")
if (len(tax.Id) == 0) || (len(tax.Name) == 0) {
return errors.New("taxon without identification")
}
if _, ok := t.ids[tax.Id]; ok {
return fmt.Errorf("taxon id %s already in use", tax.Id)
}
p := t.root
if tax.Rank > jdh.Species {
tax.Rank = jdh.Unranked
}
if len(tax.Parent) > 0 {
var ok bool
if p, ok = t.ids[tax.Parent]; !ok {
return fmt.Errorf("taxon %s parent [%s] not in database", tax.Name, tax.Parent)
}
}
if p == t.root {
if !tax.IsValid {
return fmt.Errorf("taxon %s is a synonym without a parent", tax.Name)
}
} else if !p.data.IsValid {
return fmt.Errorf("taxon %s parent [%s] is a synonym", tax.Name, p.data.Name)
}
if !p.isDescValid(tax.Rank, tax.IsValid) {
return fmt.Errorf("taxon %s rank incompatible with database hierarchy", tax.Name)
}
ext := tax.Extern
tax.Extern = nil
for _, e := range ext {
serv, id, err := jdh.ParseExtern(e)
if err != nil {
continue
}
if len(id) == 0 {
continue
}
add := true
for _, ex := range tax.Extern {
if strings.HasPrefix(ex, serv) {
add = false
break
}
}
if !add {
continue
}
if _, ok := t.ids[e]; !ok {
tax.Extern = append(tax.Extern, e)
}
}
return nil
}
// Add adds a new taxon to the database.
func (t *taxonomy) add(tax *jdh.Taxon) (string, error) {
id := strconv.FormatInt(t.next, 10)
tax.Id = id
if err := t.validate(tax); err != nil {
return "", err
}
t.addTaxon(tax)
t.next++
t.changed = true
return id, nil
}
