Example #1
0
// 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
}
Example #2
0
// 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
}