// Add adds an specimen to the database.
func (s *specimens) add(spe *jdh.Specimen) (string, error) {
id := strconv.FormatInt(s.next, 10)
spe.Id = id
if err := s.validate(spe); err != nil {
return "", err
}
s.addSpecimen(spe)
s.next++
s.changed = true
return id, nil
}
// Validate validates that an specimen is valid in the database, and set
// some canonical values. It returns an error if the specimen is not valid.
func (s *specimens) validate(spe *jdh.Specimen) error {
spe.Id = strings.TrimSpace(spe.Id)
spe.Taxon = strings.TrimSpace(spe.Taxon)
if (len(spe.Id) == 0) || (len(spe.Taxon) == 0) {
return errors.New("specimen without identification")
}
if _, ok := s.ids[spe.Id]; ok {
return fmt.Errorf("specimen id %s already in use", spe.Id)
}
spe.Catalog = strings.TrimSpace(spe.Catalog)
if len(spe.Catalog) > 0 {
if _, ok := s.ids[spe.Catalog]; ok {
return fmt.Errorf("specimen catalog code %s already in use", spe.Catalog)
}
}
if !s.db.t.isInDB(spe.Taxon) {
return fmt.Errorf("taxon %s [associated with specimen %s] not in database", spe.Taxon, spe.Id)
}
if !spe.Geography.IsValid() {
spe.Geography = geography.Location{}
}
if !spe.Georef.IsValid() {
spe.Georef = geography.InvalidGeoref()
} else if (spe.Georef.Point.Lon == 0) || (spe.Georef.Point.Lon == 1) || (spe.Georef.Point.Lat == 0) || (spe.Georef.Point.Lat == 1) {
spe.Georef = geography.InvalidGeoref()
}
if spe.Basis > jdh.Remote {
spe.Basis = jdh.UnknownBasis
}
spe.Reference = strings.TrimSpace(spe.Reference)
spe.Determiner = strings.Join(strings.Fields(spe.Determiner), " ")
spe.Collector = strings.Join(strings.Fields(spe.Collector), " ")
spe.Dataset = strings.TrimSpace(spe.Dataset)
if len(spe.Dataset) > 0 {
if !s.db.d.isInDB(spe.Dataset) {
spe.Dataset = ""
}
}
ext := spe.Extern
spe.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 spe.Extern {
if strings.HasPrefix(ex, serv) {
add = false
break
}
}
if !add {
continue
}
if _, ok := s.ids[e]; !ok {
spe.Extern = append(spe.Extern, e)
}
}
return nil
}
