// searchExtern searches an extern id.
func searchExtern(serv string, extern []string) string {
seid := serv + ":"
for _, e := range extern {
sv, id, _ := jdh.ParseExtern(e)
if sv == seid {
return id
}
}
return ""
}
// 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
}
// Validate validates that a raster is valid in the database, and set some
// canonical values. It returns an error if the raster is not valid.
func (d *distros) validate(ras *jdh.Raster) error {
ras.Id = strings.TrimSpace(ras.Id)
ras.Taxon = strings.TrimSpace(ras.Taxon)
if (len(ras.Id) == 0) || (len(ras.Taxon) == 0) {
return errors.New("raster without identification")
}
if _, ok := d.ids[ras.Id]; ok {
return fmt.Errorf("raster id %s already in use", ras.Id)
}
if !d.db.t.isInDB(ras.Taxon) {
return fmt.Errorf("taxon %s [associated with raster %s] not in dabtase", ras.Taxon, ras.Id)
}
if ras.Cols == 0 {
return fmt.Errorf("raster %s with an invalid number of cols: 0", ras.Id)
}
if ras.Raster == nil {
return fmt.Errorf("raster %s without rasterized data", ras.Id)
}
if ras.Source > jdh.MachineModel {
ras.Source = jdh.UnknownRaster
}
ras.Reference = strings.TrimSpace(ras.Reference)
ext := ras.Extern
ras.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 ras.Extern {
if strings.HasPrefix(ex, serv) {
add = false
break
}
}
if !add {
continue
}
if _, ok := d.ids[e]; !ok {
ras.Extern = append(ras.Extern, e)
}
}
return nil
}
// Validates that a dataset is valid in the database. When posible canonical
// values will be set. If the dataset is invalid it will return an error.
func (d *datasets) validate(set *jdh.Dataset) error {
set.Id = strings.TrimSpace(set.Id)
set.Title = strings.Join(strings.Fields(set.Title), " ")
if (len(set.Id) == 0) || (len(set.Title) == 0) {
return errors.New("dataset without identification")
}
if _, ok := d.ids[set.Id]; ok {
return fmt.Errorf("dataset id %s already in use", set.Id)
}
set.Citation = strings.Join(strings.Fields(set.Citation), " ")
set.License = strings.Join(strings.Fields(set.License), " ")
if u, err := url.Parse(set.Url); err != nil {
set.Url = ""
} else {
set.Url = u.String()
}
ext := set.Extern
set.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 set.Extern {
if strings.HasPrefix(ex, serv) {
add = false
break
}
}
if !add {
continue
}
if _, ok := d.ids[e]; !ok {
set.Extern = append(set.Extern, e)
}
}
return nil
}
// AddExtern adds an extern id to an specimen.
func (tr *trees) addExtern(ph *phylogeny, extern string) error {
serv, id, err := jdh.ParseExtern(extern)
if err != nil {
return err
}
if len(id) == 0 {
return nil
}
if or, ok := tr.ids[extern]; ok {
return fmt.Errorf("extern id %s of %s alredy in use by %s", extern, ph.data.Id, or.data.Id)
}
// the service is already assigned, then overwrite
for i, e := range ph.data.Extern {
if strings.HasPrefix(e, serv) {
delete(tr.ids, e)
ph.data.Extern[i] = extern
tr.ids[extern] = ph
return nil
}
}
ph.data.Extern = append(ph.data.Extern, extern)
tr.ids[extern] = ph
return nil
}
// ValPhy validates that a tree is valid in the database, and set some
// canonical values. It returns an error if the tree is not valid.
func (tr *trees) valPhy(phy *jdh.Phylogeny) error {
phy.Id = strings.TrimSpace(phy.Id)
if len(phy.Id) == 0 {
return errors.New("phylogeny without identification")
}
if _, ok := tr.ids[phy.Id]; ok {
return fmt.Errorf("phylogeny id %s alredy in use", phy.Id)
}
phy.Name = strings.Join(strings.Fields(phy.Name), " ")
phy.Root = ""
ext := phy.Extern
phy.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 phy.Extern {
if strings.HasPrefix(ex, serv) {
add = false
break
}
}
if !add {
continue
}
if _, ok := tr.ids[e]; !ok {
phy.Extern = append(phy.Extern, e)
}
}
return nil
}
// AddExtern adds an extern id to an specimen.
func (d *distros) addExtern(rd *raster, extern string) error {
serv, id, err := jdh.ParseExtern(extern)
if err != nil {
return err
}
if len(id) == 0 {
return nil
}
if or, ok := d.ids[extern]; ok {
return fmt.Errorf("extern id %s of %s alredy in use by %s", extern, rd.data.Id, or.data.Id)
}
// the service is already assigned, then overwrite
for i, e := range rd.data.Extern {
if strings.HasPrefix(e, serv) {
delete(d.ids, e)
rd.data.Extern[i] = extern
d.ids[extern] = rd
return nil
}
}
rd.data.Extern = append(rd.data.Extern, extern)
d.ids[extern] = rd
return nil
}
// AddExtern adds an extern id to a taxon.
func (t *taxonomy) addExtern(tx *taxon, extern string) error {
serv, id, err := jdh.ParseExtern(extern)
if err != nil {
return err
}
if len(id) == 0 {
return nil
}
if ot, ok := t.ids[extern]; ok {
return fmt.Errorf("extern id %s of %s alredy in use by %s", extern, tx.data.Name, ot.data.Name)
}
// the service is already assigned, then overwrite
for i, e := range tx.data.Extern {
if strings.HasPrefix(e, serv) {
delete(t.ids, e)
tx.data.Extern[i] = extern
t.ids[extern] = tx
return nil
}
}
tx.data.Extern = append(tx.data.Extern, extern)
t.ids[extern] = tx
return nil
}
// AddExtern adds an extern id to a dataset.
func (d *datasets) addExtern(sd *setData, extern string) error {
serv, id, err := jdh.ParseExtern(extern)
if err != nil {
return err
}
if len(id) == 0 {
return nil
}
if ot, ok := d.ids[extern]; ok {
return fmt.Errorf("extern id %s of %s alredy in use by %s", extern, sd.data.Id, ot.data.Id)
}
// the service is already assigned, then overwrite
for i, e := range sd.data.Extern {
if strings.HasPrefix(e, serv) {
delete(d.ids, e)
sd.data.Extern[i] = extern
d.ids[extern] = sd
return nil
}
}
sd.data.Extern = append(sd.data.Extern, extern)
d.ids[extern] = sd
return nil
}
// AddExtern adds an extern id to an specimen.
func (s *specimens) addExtern(sp *specimen, extern string) error {
serv, id, err := jdh.ParseExtern(extern)
if err != nil {
return err
}
if len(id) == 0 {
return nil
}
if or, ok := s.ids[extern]; ok {
return fmt.Errorf("extern id %s of %s alredy in use by %s", extern, sp.data.Id, or.data.Id)
}
// the service is already assigned, then overwrite
for i, e := range sp.data.Extern {
if strings.HasPrefix(e, serv) {
delete(s.ids, e)
sp.data.Extern[i] = extern
s.ids[extern] = sp
return nil
}
}
sp.data.Extern = append(sp.data.Extern, extern)
s.ids[extern] = sp
return nil
}
// SetTree sets a value of a tree in the database.
func (tr *trees) setTree(vals []jdh.KeyValue) error {
id := ""
for _, kv := range vals {
if len(kv.Value) == 0 {
continue
}
if kv.Key == jdh.KeyId {
id = kv.Value[0]
break
}
}
if len(id) == 0 {
return errors.New("tree without identification")
}
ph, ok := tr.ids[id]
if !ok {
return nil
}
phy := ph.data
for _, kv := range vals {
switch kv.Key {
case jdh.TreName:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if phy.Name == v {
continue
}
phy.Name = v
case jdh.KeyComment:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if phy.Comment == v {
continue
}
phy.Comment = v
case jdh.KeyExtern:
ok := false
for _, v := range kv.Value {
v = strings.TrimSpace(v)
if len(v) == 0 {
continue
}
serv, ext, err := jdh.ParseExtern(v)
if err != nil {
return err
}
if len(ext) == 0 {
if !tr.delExtern(ph, serv) {
continue
}
ok = true
continue
}
if tr.addExtern(ph, v) != nil {
continue
}
ok = true
}
if !ok {
continue
}
default:
continue
}
tr.changed = true
}
return nil
}
// Set sets a value of a raster in the database.
func (d *distros) set(vals []jdh.KeyValue) error {
id := ""
for _, kv := range vals {
if len(kv.Value) == 0 {
continue
}
if kv.Key == jdh.KeyId {
id = kv.Value[0]
break
}
}
if len(id) == 0 {
return errors.New("raster without identification")
}
rd, ok := d.ids[id]
if !ok {
return nil
}
ras := rd.data
for _, kv := range vals {
switch kv.Key {
case jdh.RasPixel:
if len(kv.Value) == 0 {
continue
}
v := strings.TrimSpace(kv.Value[0])
if len(v) == 0 {
continue
}
coor := strings.Split(v, ",")
if len(coor) != 3 {
return errors.New("invalid raster pixel reference: " + v)
}
x64, err := strconv.ParseInt(coor[0], 10, 0)
if err != nil {
return err
}
y64, err := strconv.ParseInt(coor[1], 10, 0)
if err != nil {
return err
}
p64, err := strconv.ParseInt(coor[2], 10, 0)
if err != nil {
return err
}
pt, px := image.Pt(int(x64), int(y64)), int(p64)
if ras.Raster.At(pt) == px {
continue
}
ras.Raster.Set(pt, px)
case jdh.RDisSource:
v := jdh.UnknownRaster
if len(kv.Value) > 0 {
v = jdh.GetRasterSource(strings.TrimSpace(kv.Value[0]))
}
if ras.Source == v {
continue
}
case jdh.RDisTaxon:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if len(v) == 0 {
continue
}
if ras.Taxon == v {
continue
}
tax, ok := d.taxId[v]
if !ok {
if !d.db.t.isInDB(v) {
continue
}
tax = &rasTaxon{
id: v,
rsLs: list.New(),
}
tax.elem = d.taxLs.PushBack(tax)
d.taxId[tax.id] = tax
}
oldtax := rd.taxon
oldtax.rsLs.Remove(rd.elem)
rd.elem = tax.rsLs.PushBack(rd)
rd.taxon = tax
rd.data.Taxon = tax.id
if oldtax.rsLs.Len() == 0 {
oldtax.rsLs = nil
d.taxLs.Remove(oldtax.elem)
oldtax.elem = nil
delete(d.taxId, oldtax.id)
}
case jdh.KeyComment:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if ras.Comment == v {
continue
}
ras.Comment = v
case jdh.KeyExtern:
ok := false
for _, v := range kv.Value {
v = strings.TrimSpace(v)
if len(v) == 0 {
continue
}
serv, ext, err := jdh.ParseExtern(v)
if err != nil {
return err
}
if len(ext) == 0 {
if !d.delExtern(rd, serv) {
continue
}
ok = true
continue
}
if d.addExtern(rd, v) != nil {
continue
}
ok = true
}
if !ok {
continue
}
case jdh.KeyReference:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if ras.Reference == v {
continue
}
ras.Reference = v
default:
continue
}
d.changed = true
}
return nil
}
// Set sets a value of a taxon in the taxonomy.
func (t *taxonomy) set(vals []jdh.KeyValue) error {
id := ""
for _, kv := range vals {
if len(kv.Value) == 0 {
continue
}
if kv.Key == jdh.KeyId {
id = kv.Value[0]
break
}
}
if len(id) == 0 {
return errors.New("taxon without identification")
}
tx, ok := t.ids[id]
if !ok {
return nil
}
tax := tx.data
for _, kv := range vals {
switch kv.Key {
case jdh.KeyComment:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if tax.Comment == v {
continue
}
tax.Comment = v
case jdh.KeyExtern:
ok := false
for _, v := range kv.Value {
v := strings.TrimSpace(v)
if len(v) == 0 {
continue
}
serv, ext, err := jdh.ParseExtern(v)
if err != nil {
continue
}
if len(ext) == 0 {
if !t.delExtern(tx, serv) {
continue
}
ok = true
continue
}
if t.addExtern(tx, v) != nil {
continue
}
ok = true
}
if !ok {
continue
}
case jdh.TaxAuthority:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if tax.Authority == v {
continue
}
tax.Authority = v
case jdh.TaxName:
nm := ""
if len(kv.Value) > 0 {
nm = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if len(nm) == 0 {
return fmt.Errorf("new name for %s undefined", tx.data.Name)
}
if tax.Name == nm {
continue
}
// remove the old name
nmLow := strings.ToLower(tax.Name)
v := t.names.Lookup(nmLow).([]*taxon)
v = delTaxFromList(v, tx)
if len(v) > 0 {
t.names.Set(nmLow, v)
} else {
t.names.Delete(nmLow)
}
tax.Name = nm
// add the new name
nmLow = strings.ToLower(tax.Name)
vi := t.names.Lookup(nmLow)
var txLs []*taxon
if vi == nil {
txLs = []*taxon{tx}
} else {
txLs = append(vi.([]*taxon), tx)
}
t.names.Set(nmLow, txLs)
case jdh.TaxParent:
p := t.root
if len(kv.Value) > 0 {
v := strings.TrimSpace(kv.Value[0])
if len(v) == 0 {
continue
}
var ok bool
p, ok = t.ids[v]
if !ok {
return fmt.Errorf("new parent [%s] for taxon %s not in database", kv.Value, tax.Name)
}
}
if tx.parent == p {
continue
}
if (!tax.IsValid) && (p == t.root) {
return fmt.Errorf("taxon %s is a synonym, it requires a parent", tax.Name)
}
if (p != t.root) && (!p.data.IsValid) {
return fmt.Errorf("new parent [%s] for taxon %s is a synonym", p.data.Name, tax.Name)
}
if !p.isDescValid(tax.Rank, tax.IsValid) {
return fmt.Errorf("taxon %s rank incompatible with new parent [%s] hierarchy", tax.Name, p.data.Name)
}
tx.parent.childs = delTaxFromList(tx.parent.childs, tx)
p.childs = append(p.childs, tx)
tx.parent = p
if p == t.root {
tax.Parent = ""
} else {
tax.Parent = p.data.Id
}
case jdh.TaxRank:
v := jdh.Unranked
if len(kv.Value) > 0 {
v = jdh.GetRank(strings.TrimSpace(kv.Value[0]))
}
if tax.Rank == v {
continue
}
if !tx.parent.isDescValid(v, tax.IsValid) {
return fmt.Errorf("new rank [%s] for taxon %s incompatible with taxonomy hierarchy", v, tax.Name)
}
tax.Rank = v
case jdh.TaxSynonym:
p := tx.parent
if len(kv.Value) > 0 {
v := strings.TrimSpace(kv.Value[0])
if len(v) == 0 {
continue
}
var ok bool
p, ok = t.ids[v]
if !ok {
return fmt.Errorf("new parent [%s] for taxon %s not in database", kv.Value, tax.Name)
}
}
if (p == tx.parent) && (!tax.IsValid) {
continue
}
if p == t.root {
return fmt.Errorf("taxon %s can not be a synonym: no new parent defined", tax.Name)
}
if p != tx.parent {
if !p.isDescValid(tax.Rank, false) {
return fmt.Errorf("taxon %s rank incompatible with new parent [%s] hierarchy", tax.Name, p.data.Name)
}
tx.parent.childs = delTaxFromList(tx.parent.childs, tx)
tx.parent = p
tax.Parent = p.data.Id
p.childs = append(p.childs, tx)
}
for _, d := range tx.childs {
d.parent = p
d.data.Parent = p.data.Id
p.childs = append(p.childs, d)
}
tx.childs = nil
tax.IsValid = false
case jdh.TaxValid:
if tax.IsValid {
continue
}
tx.parent.childs = delTaxFromList(tx.parent.childs, tx)
tx.parent = tx.parent.parent
tx.data.Parent = tx.parent.data.Id
tx.parent.childs = append(tx.parent.childs, tx)
tax.IsValid = true
default:
continue
}
t.changed = true
}
return nil
}
// Set sets one or more values of a dataset element.
func (d *datasets) set(vals []jdh.KeyValue) error {
id := ""
for _, kv := range vals {
if len(kv.Value) == 0 {
continue
}
if kv.Key == jdh.KeyId {
id = kv.Value[0]
break
}
}
if len(id) == 0 {
return errors.New("dataset without identification")
}
sd, ok := d.ids[id]
if !ok {
return nil
}
set := sd.data
for _, kv := range vals {
switch kv.Key {
case jdh.KeyComment:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if set.Comment == v {
continue
}
set.Comment = v
case jdh.KeyExtern:
ok := false
for _, v := range kv.Value {
v = strings.TrimSpace(v)
if len(v) == 0 {
continue
}
serv, ext, err := jdh.ParseExtern(v)
if err != nil {
continue
}
if len(ext) == 0 {
if !d.delExtern(sd, serv) {
continue
}
ok = true
continue
}
if d.addExtern(sd, v) != nil {
continue
}
ok = true
}
if !ok {
continue
}
case jdh.DataCitation:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if set.Citation == v {
continue
}
set.Citation = v
case jdh.DataLicense:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if set.License == v {
continue
}
set.License = v
case jdh.DataTitle:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if set.Title == v {
continue
}
set.Title = v
case jdh.DataUrl:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if len(v) == 0 {
if len(set.Url) == 0 {
continue
}
set.Url = ""
break
}
u, err := url.Parse(v)
if err != nil {
continue
}
if set.Url == u.String() {
continue
}
set.Url = u.String()
}
d.changed = true
}
return 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
}
// Set sets a value of an specimen in the database.
func (s *specimens) set(vals []jdh.KeyValue) error {
id := ""
for _, kv := range vals {
if len(kv.Value) == 0 {
continue
}
if kv.Key == jdh.KeyId {
id = kv.Value[0]
break
}
}
if len(id) == 0 {
return errors.New("specimen without identification")
}
sp, ok := s.ids[id]
if !ok {
return nil
}
spe := sp.data
for _, kv := range vals {
switch kv.Key {
case jdh.SpeBasis:
v := jdh.UnknownBasis
if len(kv.Value) > 0 {
v = jdh.GetBasisOfRecord(strings.TrimSpace(kv.Value[0]))
}
if spe.Basis == v {
continue
}
spe.Basis = v
case jdh.SpeCatalog:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if spe.Catalog == v {
continue
}
if len(v) > 0 {
if _, ok := s.ids[v]; ok {
return fmt.Errorf("specimen catalog code %s already in use", kv.Value)
}
}
if len(spe.Catalog) > 0 {
delete(s.ids, spe.Catalog)
}
spe.Catalog = v
if len(v) > 0 {
s.ids[v] = sp
}
case jdh.SpeCollector:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Collector == v {
continue
}
spe.Collector = v
case jdh.SpeDataset:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if spe.Dataset == v {
continue
}
if len(v) > 0 {
if !s.db.d.isInDB(v) {
continue
}
}
spe.Dataset = v
case jdh.SpeDate:
if len(kv.Value) > 0 {
v := strings.TrimSpace(kv.Value[0])
t, err := time.Parse(jdh.Iso8601, v)
if err != nil {
return err
}
if spe.Date.Equal(t) {
continue
}
spe.Date = t
break
}
if spe.Date.IsZero() {
continue
}
spe.Date = time.Time{}
case jdh.SpeDeterminer:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Determiner == v {
continue
}
spe.Determiner = v
case jdh.SpeLocality:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Locality == v {
continue
}
spe.Locality = v
case jdh.SpeTaxon:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if len(v) == 0 {
continue
}
if spe.Taxon == v {
continue
}
tax, ok := s.taxId[v]
if !ok {
if !s.db.t.isInDB(v) {
continue
}
tax = &speTaxon{
id: v,
specs: list.New(),
}
tax.elem = s.taxLs.PushBack(tax)
s.taxId[tax.id] = tax
}
oldtax := sp.taxon
oldtax.specs.Remove(sp.elem)
sp.elem = tax.specs.PushBack(sp)
sp.taxon = tax
sp.data.Taxon = tax.id
if oldtax.specs.Len() == 0 {
oldtax.specs = nil
s.taxLs.Remove(oldtax.elem)
oldtax.elem = nil
delete(s.taxId, oldtax.id)
}
case jdh.GeoCountry:
v := geography.Country("")
if len(kv.Value) > 0 {
v = geography.GetCountry(strings.Join(strings.Fields(kv.Value[0]), " "))
}
if spe.Geography.Country == v {
continue
}
spe.Geography.Country = v
case jdh.GeoCounty:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Geography.County == v {
continue
}
spe.Geography.County = v
case jdh.GeoLonLat:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if len(v) == 0 {
if !spe.Georef.IsValid() {
continue
}
spe.Georef = geography.InvalidGeoref()
break
}
coor := strings.Split(v, ",")
if len(coor) != 2 {
return errors.New("invalid geographic coordinate values")
}
lon, err := strconv.ParseFloat(coor[0], 64)
if err != nil {
return err
}
lat, err := strconv.ParseFloat(coor[1], 64)
if err != nil {
return err
}
if (lon == 0) || (lon == 1) || (lat == 0) || (lat == 1) {
return errors.New("invalid geographic coordinate values")
}
if (!geography.IsLon(lon)) || (!geography.IsLat(lat)) {
return errors.New("invalid geographic coordinate values")
}
spe.Georef.Point = geography.Point{Lon: lon, Lat: lat}
case jdh.GeoSource:
if !spe.Georef.IsValid() {
continue
}
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Georef.Source == v {
continue
}
spe.Georef.Source = v
case jdh.GeoState:
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Geography.State == v {
continue
}
spe.Geography.State = v
case jdh.GeoUncertainty:
if !spe.Georef.IsValid() {
continue
}
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
un64, err := strconv.ParseUint(v, 10, 0)
if err != nil {
return err
}
un := uint(un64)
if un == spe.Georef.Uncertainty {
continue
}
spe.Georef.Uncertainty = un
case jdh.GeoValidation:
if !spe.Georef.IsValid() {
continue
}
v := ""
if len(kv.Value) > 0 {
v = strings.Join(strings.Fields(kv.Value[0]), " ")
}
if spe.Georef.Validation == v {
continue
}
spe.Georef.Validation = v
case jdh.KeyComment:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if spe.Comment == v {
continue
}
spe.Comment = v
case jdh.KeyExtern:
ok := false
for _, v := range kv.Value {
v = strings.TrimSpace(v)
if len(v) == 0 {
continue
}
serv, ext, err := jdh.ParseExtern(v)
if err != nil {
return err
}
if len(ext) == 0 {
if !s.delExtern(sp, serv) {
continue
}
ok = true
continue
}
if s.addExtern(sp, v) != nil {
continue
}
ok = true
}
if !ok {
continue
}
case jdh.KeyReference:
v := ""
if len(kv.Value) > 0 {
v = strings.TrimSpace(kv.Value[0])
}
if spe.Reference == v {
continue
}
spe.Reference = v
default:
continue
}
s.changed = true
}
return nil
}
