// returns a copy of a taxon
func (tx *taxon) copy() *jdh.Taxon {
tax := &jdh.Taxon{
Id: strings.TrimSpace(tx.id),
Name: strings.Join(strings.Fields(tx.name), " "),
Rank: jdh.GetRank(strings.TrimSpace(tx.rank)),
}
return tax
}
func spInRun(c *cmdapp.Command, args []string) {
openLocal(c)
pId := ""
if len(ancFlag) > 0 {
p := taxon(c, localDB, ancFlag)
if !p.IsValid {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("taxon "+p.Name+" a synonym, can ot be a parent"))
os.Exit(1)
}
pId = p.Id
}
var set *jdh.Dataset
if len(dsetFlag) > 0 {
set = dataset(c, localDB, dsetFlag)
} else {
set = &jdh.Dataset{}
}
rank := jdh.Unranked
if len(rankFlag) > 0 {
rank = jdh.GetRank(rankFlag)
}
format := "txt"
if len(formatFlag) > 0 {
format = formatFlag
}
if len(args) > 0 {
switch format {
case "txt":
for _, fname := range args {
spInTxt(c, fname, pId, rank, set)
}
case "ndm":
for _, fname := range args {
spInNdm(c, fname, pId, rank, set)
}
default:
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("format "+format+" unknown"))
os.Exit(1)
}
} else {
switch format {
case "txt":
spInTxt(c, "", pId, rank, set)
case "ndm":
spInNdm(c, "", pId, rank, set)
default:
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("format "+format+" unknown"))
os.Exit(1)
}
}
localDB.Exec(jdh.Commit, "", nil)
}
// TrInPickTax returns the id of a given taxon name. If there are more taxons
// fullfilling the name, then it will print a list of the potential
// names and finish the program.
func trInPickTax(name, parent string) (string, error) {
vals := new(jdh.Values)
vals.Add(jdh.TaxName, name)
if len(parent) != 0 {
vals.Add(jdh.TaxParent, parent)
}
rank := jdh.Unranked
if len(rankFlag) > 0 {
rank = jdh.GetRank(rankFlag)
if rank != jdh.Unranked {
vals.Add(jdh.TaxRank, rankFlag)
}
}
l, err := localDB.List(jdh.Taxonomy, vals)
if err != nil {
return "", err
}
var tax *jdh.Taxon
mult := ""
for {
ot := &jdh.Taxon{}
if err := l.Scan(ot); err != nil {
if err == io.EOF {
break
}
return "", err
}
if tax == nil {
tax = ot
continue
}
if len(mult) == 0 {
mult = fmt.Sprintf("ambiguos taxon name\n")
mult += fmt.Sprintf("%s\t%s\n", tax.Id, tax.Name)
}
mult += fmt.Sprintf("%s\t%s\n", ot.Id, ot.Name)
}
if len(mult) > 0 {
return "", errors.New(mult)
}
if tax == nil {
tax = &jdh.Taxon{
Name: name,
IsValid: true,
Parent: parent,
Rank: rank,
}
return localDB.Exec(jdh.Add, jdh.Taxonomy, tax)
}
return tax.Id, nil
}
func raMkRun(c *cmdapp.Command, args []string) {
openLocal(c)
var spDB jdh.DB
if len(extDBFlag) > 0 {
openExt(c, extDBFlag, "")
spDB = extDB
} else {
spDB = localDB
}
var tax *jdh.Taxon
if len(taxonFlag) > 0 {
tax = taxon(c, localDB, taxonFlag)
if len(tax.Id) == 0 {
return
}
} else if len(args) > 0 {
if len(args) > 2 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("too many arguments"))
os.Exit(1)
}
pName := ""
if len(args) > 1 {
pName = args[1]
}
tax = pickTaxName(c, localDB, args[0], pName)
if len(tax.Id) == 0 {
return
}
} else {
tax = &jdh.Taxon{}
}
rank := jdh.Kingdom
if len(rankFlag) > 0 {
rank = jdh.GetRank(rankFlag)
if rank == jdh.Unranked {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("invalid rank"))
os.Exit(1)
}
}
if (sizeFlag <= 0) || (sizeFlag >= 360) {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("invalid size option"))
os.Exit(1)
}
cols := uint(360 / sizeFlag)
if int(float64(cols)*sizeFlag) < 360 {
cols++
}
size := 360 / float64(cols)
raMkFetch(c, spDB, tax, jdh.Kingdom, rank, size)
localDB.Exec(jdh.Commit, "", nil)
}
func txInRun(c *cmdapp.Command, args []string) {
openLocal(c)
pId := ""
if len(ancFlag) > 0 {
p := taxon(c, localDB, ancFlag)
if !p.IsValid {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("taxon "+p.Name+" a synonym, can ot be a parent"))
os.Exit(1)
}
pId = p.Id
}
valid := true
if synonymFlag {
if len(pId) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("synonym without defined parent"))
os.Exit(2)
}
valid = false
}
rank := jdh.Unranked
if len(rankFlag) > 0 {
rank = jdh.GetRank(rankFlag)
}
format := "txt"
if len(formatFlag) > 0 {
format = formatFlag
}
if len(args) > 0 {
switch format {
case "txt":
for _, fn := range args {
txInTxt(c, fn, pId, rank, valid)
}
default:
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("format "+format+" unknown"))
os.Exit(1)
}
} else {
switch format {
case "txt":
txInTxt(c, "", pId, rank, valid)
default:
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("format "+format+" unknown"))
os.Exit(1)
}
}
localDB.Exec(jdh.Commit, "", nil)
}
// returns a copy of species
func (sp *species) copy() *jdh.Taxon {
if sp.Key == 0 {
return &jdh.Taxon{}
}
rank := jdh.GetRank(strings.TrimSpace(sp.Rank))
tax := &jdh.Taxon{
Id: strconv.FormatInt(sp.Key, 10),
Name: strings.Join(strings.Fields(sp.CanonicalName), " "),
Authority: strings.Join(strings.Fields(sp.Authorship), " "),
Rank: rank,
IsValid: !sp.Synonym,
Comment: strings.Join(strings.Fields(sp.AccordingTo), " "),
}
if sp.Synonym {
tax.Parent = strconv.FormatInt(sp.AcceptedKey, 10)
} else if sp.ParentKey > 0 {
tax.Parent = strconv.FormatInt(sp.ParentKey, 10)
}
return tax
}
func spPopRun(c *cmdapp.Command, args []string) {
if len(extDBFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong '--extdb' option"))
c.Usage()
}
openLocal(c)
openExt(c, extDBFlag, "")
var tax *jdh.Taxon
if len(taxonFlag) > 0 {
tax = taxon(c, localDB, taxonFlag)
if len(tax.Id) == 0 {
return
}
} else if len(args) > 0 {
if len(args) > 2 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("too many arguments"))
os.Exit(1)
}
pName := ""
if len(args) > 1 {
pName = args[1]
}
tax = pickTaxName(c, localDB, args[0], pName)
if len(tax.Id) == 0 {
return
}
} else {
tax = &jdh.Taxon{}
}
rank := jdh.Kingdom
if len(rankFlag) > 0 {
rank = jdh.GetRank(rankFlag)
if rank == jdh.Unranked {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("invalid rank"))
os.Exit(1)
}
}
spPopFetch(c, tax, jdh.Kingdom, rank)
localDB.Exec(jdh.Commit, "", nil)
}
// searchTaxon searchs for taxon name in gbif.
func (db *DB) searchTaxon(l *listScanner, name string, kvs []jdh.KeyValue) {
nm := strings.Join(strings.Fields(name), " ")
if i := strings.Index(nm, "*"); i > 0 {
l.setErr(errors.New("current gbif api does not support partial lookups"))
return
}
var pId int64
var pName string
var rank jdh.Rank
for _, kv := range kvs {
if len(kv.Value) == 0 {
continue
}
switch kv.Key {
case jdh.TaxParent:
pId, _ = strconv.ParseInt(kv.Value[0], 10, 64)
case jdh.TaxRank:
rank = jdh.GetRank(kv.Value[0])
case jdh.TaxParentName:
pName = strings.ToLower(strings.Join(strings.Fields(kv.Value[0]), " "))
}
}
vals := url.Values{}
vals.Add("name", nm)
for off := int64(0); ; {
if off > 0 {
vals.Set("offset", strconv.FormatInt(off, 10))
}
request := wsHead + "species?" + vals.Encode()
an := new(spAnswer)
if err := db.listRequest(request, an); err != nil {
l.setErr(err)
return
}
for _, sp := range an.Results {
if sp.Key != sp.NubKey {
continue
}
if pId != 0 {
if !sp.isDesc(pId) {
continue
}
}
if rank != jdh.Unranked {
if rank != jdh.GetRank(strings.TrimSpace(sp.Rank)) {
continue
}
}
if len(pName) > 0 {
if !sp.hasParentName(pName) {
continue
}
}
select {
case l.c <- sp.copy():
case <-l.end:
return
}
}
if an.EndOfRecords {
break
}
off += an.Limit
}
select {
case l.c <- nil:
case <-l.end:
}
}
func readTaxon(id string) (*taxon, error) {
if (len(id) == 0) || (id == "0") {
return nil, errors.New("taxon without identification")
}
request := emblHead + "Taxon:" + id + "&display=xml"
answer, err := http.Get(request)
if err != nil {
return nil, err
}
defer answer.Body.Close()
dec := xml.NewDecoder(answer.Body)
tx := &taxon{
tax: &jdh.Taxon{},
}
for tk, err := dec.Token(); err != io.EOF; tk, err = dec.Token() {
if err != nil {
return nil, err
}
switch t := tk.(type) {
case xml.StartElement:
switch t.Name.Local {
case "taxon":
for _, at := range t.Attr {
switch at.Name.Local {
case "scientificName":
tx.tax.Name = at.Value
tx.tax.IsValid = true
case "taxId":
tx.tax.Id = at.Value
case "parentTaxId":
tx.tax.Parent = at.Value
case "rank":
tx.tax.Rank = jdh.GetRank(at.Value)
}
}
case "lineage":
if err = readTaxonLineage(dec, tx); err != nil {
return nil, err
}
case "children":
skip(dec, t.Name.Local)
case "synonym":
nm := ""
isSyn := false
for _, at := range t.Attr {
switch at.Name.Local {
case "type":
if at.Value == "synonym" {
isSyn = true
}
case "name":
nm = at.Value
}
}
if isSyn {
tx.syn = append(tx.syn, nm)
}
}
}
}
return tx, nil
}
// SearchTaxon search for a taxon name in iNaturalist.
func (db *DB) searchTaxon(l *listScanner, name string, kvs []jdh.KeyValue) {
nm := strings.Join(strings.Fields(name), " ")
i := strings.Index(nm, "*")
prefix := ""
if i == 0 {
l.setErr(errors.New("taxon without identification"))
return
}
if i > 0 {
prefix = nm[:i]
nm = nm[:i]
}
pId := ""
var rank jdh.Rank
pName := ""
for _, kv := range kvs {
if len(kv.Value) == 0 {
continue
}
switch kv.Key {
case jdh.TaxParent:
pId = kv.Value[0]
case jdh.TaxRank:
rank = jdh.GetRank(kv.Value[0])
case jdh.TaxParentName:
pName = strings.Join(strings.Fields(kv.Value[0]), " ")
}
}
vals := url.Values{}
vals.Add("q", name)
vals.Add("utf8", "✓")
for next := 1; ; next++ {
if next > 1 {
vals.Set("page", strconv.FormatInt(int64(next), 10))
}
ls, nx, err := db.txSearch(inatHead + "taxa/search?" + vals.Encode())
if err != nil {
l.setErr(err)
return
}
for _, tx := range ls {
tax := tx.copy()
if len(prefix) > 0 {
if strings.HasPrefix(tax.Name, prefix) {
if len(pId) > 0 {
pl, err := db.txList(tx.id)
if err != nil {
l.setErr(err)
return
}
isP := false
for _, pt := range pl {
if pt.id == tx.id {
break
}
if pt.id == pId {
isP = true
break
}
}
if !isP {
continue
}
}
if len(pName) > 0 {
pl, err := db.txList(tx.id)
if err != nil {
l.setErr(err)
return
}
isP := false
for _, pt := range pl {
if pt.id == tx.id {
break
}
if strings.Join(strings.Fields(pt.name), " ") == pName {
isP = true
break
}
}
if !isP {
continue
}
}
if rank != jdh.Unranked {
if rank != tax.Rank {
continue
}
}
select {
case l.c <- tax:
case <-l.end:
return
}
}
continue
}
if tax.Name == nm {
if len(pId) > 0 {
pl, err := db.txList(tx.id)
if err != nil {
l.setErr(err)
return
}
isP := false
for _, pt := range pl {
if pt.id == tx.id {
break
}
if pt.id == pId {
isP = true
break
}
}
if !isP {
continue
}
}
if len(pName) > 0 {
pl, err := db.txList(tx.id)
if err != nil {
l.setErr(err)
return
}
isP := false
for _, pt := range pl {
if pt.id == tx.id {
break
}
if strings.Join(strings.Fields(pt.name), " ") == pName {
isP = true
break
}
}
if !isP {
continue
}
}
if rank != jdh.Unranked {
if rank != tax.Rank {
continue
}
}
select {
case l.c <- tax:
case <-l.end:
return
}
}
}
if !nx {
break
}
}
select {
case l.c <- nil:
case <-l.end:
}
}
// SearchTaxon search for a taxon name in ncbi.
func (db *DB) searchTaxon(l *listScanner, name string, kvs []jdh.KeyValue) {
nm := strings.Join(strings.Fields(name), " ")
i := strings.Index(nm, "*")
prefix := ""
if i == 0 {
l.setErr(errors.New("taxon without identification"))
return
}
if i > 0 {
prefix = nm[:i]
nm = nm[:i]
}
pId := ""
var rank jdh.Rank
pName := ""
for _, kv := range kvs {
if len(kv.Value) == 0 {
continue
}
switch kv.Key {
case jdh.TaxParent:
pId = kv.Value[0]
case jdh.TaxRank:
rank = jdh.GetRank(kv.Value[0])
case jdh.TaxParentName:
pName = strings.Join(strings.Fields(kv.Value[0]), " ")
}
}
vals := url.Values{}
vals.Add("db", "taxonomy")
vals.Add("term", nm)
for next := 0; ; {
if next > 0 {
vals.Set("RetStart", strconv.FormatInt(int64(next), 10))
}
request := ncbiHead + "esearch.fcgi?" + vals.Encode()
nl, nx, err := db.search(request)
if err != nil {
l.setErr(err)
return
}
for _, id := range nl {
tx, err := readTaxon(id)
if err != nil {
l.setErr(err)
return
}
if len(prefix) > 0 {
if strings.HasPrefix(tx.tax.Name, prefix) {
if len(pId) > 0 {
isP := false
for _, p := range tx.par {
if pId == p {
isP = true
break
}
}
if !isP {
continue
}
}
if rank != jdh.Unranked {
if rank != tx.tax.Rank {
continue
}
}
if len(pName) > 0 {
isP := false
for _, p := range tx.lin {
if pName == p {
isP = true
break
}
}
if !isP {
continue
}
}
select {
case l.c <- tx.tax:
case <-l.end:
return
}
continue
}
for i, s := range tx.syn {
if strings.HasPrefix(s, prefix) {
if len(pId) > 0 {
isP := false
for _, p := range tx.par {
if pId == p {
isP = true
break
}
}
if !isP {
continue
}
}
if rank != jdh.Unranked {
if rank != tx.tax.Rank {
continue
}
}
if len(pName) > 0 {
isP := false
for _, p := range tx.lin {
if pName == p {
isP = true
break
}
}
if !isP {
continue
}
}
st := &jdh.Taxon{
Id: tx.tax.Id + "." + strconv.FormatInt(int64(i)+1, 10),
Name: s,
IsValid: false,
Parent: tx.tax.Id,
Rank: tx.tax.Rank,
}
select {
case l.c <- st:
case <-l.end:
return
}
break
}
}
continue
}
if tx.tax.Name == nm {
if len(pId) > 0 {
isP := false
for _, p := range tx.par {
if pId == p {
isP = true
break
}
}
if !isP {
continue
}
}
if rank != jdh.Unranked {
if rank != tx.tax.Rank {
continue
}
}
if len(pName) > 0 {
isP := false
for _, p := range tx.lin {
if pName == p {
isP = true
break
}
}
if !isP {
continue
}
}
select {
case l.c <- tx.tax:
case <-l.end:
return
}
continue
}
for i, s := range tx.syn {
if s == nm {
if len(pId) > 0 {
isP := false
for _, p := range tx.par {
if pId == p {
isP = true
break
}
}
if !isP {
continue
}
}
if rank != jdh.Unranked {
if rank != tx.tax.Rank {
continue
}
}
st := &jdh.Taxon{
Id: tx.tax.Id + "." + strconv.FormatInt(int64(i)+1, 10),
Name: s,
IsValid: false,
Parent: tx.tax.Id,
Rank: tx.tax.Rank,
}
select {
case l.c <- st:
case <-l.end:
return
}
break
}
}
}
if nx == 0 {
break
}
next = nx
}
select {
case l.c <- nil:
case <-l.end:
}
}
func txLsRun(c *cmdapp.Command, args []string) {
var db jdh.DB
if len(extDBFlag) != 0 {
openExt(c, extDBFlag, "")
db = extDB
} else {
openLocal(c)
db = localDB
}
var tax *jdh.Taxon
if len(idFlag) > 0 {
tax = taxon(c, db, idFlag)
if len(tax.Id) == 0 {
return
}
} else if len(args) > 0 {
if len(args) > 2 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("too many arguments"))
os.Exit(1)
}
pName := ""
if len(args) > 1 {
pName = args[1]
}
tax = pickTaxName(c, db, args[0], pName)
if len(tax.Id) == 0 {
return
}
}
if ancsFlag {
if tax == nil {
os.Exit(0)
}
vals := new(jdh.Values)
vals.Add(jdh.TaxParents, tax.Id)
l, err := db.List(jdh.Taxonomy, vals)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
txLsProc(c, l)
return
}
if len(rankFlag) > 0 {
rank := jdh.GetRank(rankFlag)
if (rank == jdh.Unranked) && (strings.ToLower(rankFlag) != rank.String()) {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("unknown rank"))
os.Exit(1)
}
txLsRank(c, db, tax, rank)
return
}
if synonymFlag {
if tax == nil {
os.Exit(0)
}
l := getTaxDesc(c, db, tax.Id, false)
txLsProc(c, l)
return
}
id := ""
if tax != nil {
id = tax.Id
}
l := getTaxDesc(c, db, id, true)
txLsProc(c, l)
}
func txSyncRun(c *cmdapp.Command, args []string) {
if len(extDBFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong '--extdb' option"))
c.Usage()
}
openLocal(c)
openExt(c, extDBFlag, "")
var tax *jdh.Taxon
if len(idFlag) > 0 {
tax = taxon(c, localDB, idFlag)
if len(tax.Id) == 0 {
return
}
} else if len(args) > 0 {
if len(args) > 2 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("too many arguments"))
os.Exit(1)
}
pName := ""
if len(args) > 1 {
pName = args[1]
}
tax = pickTaxName(c, localDB, args[0], pName)
if len(tax.Id) == 0 {
return
}
} else {
tax = &jdh.Taxon{}
}
noFlag := true
if matchFlag {
txSyncMatch(c, tax)
localDB.Exec(jdh.Commit, "", nil)
noFlag = false
}
if updateFlag || validFlag {
txSyncUpdate(c, tax)
localDB.Exec(jdh.Commit, "", nil)
noFlag = false
}
if len(rankFlag) > 0 {
rank := jdh.GetRank(rankFlag)
if rank == jdh.Unranked {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("invalid rank"))
os.Exit(1)
}
txSyncRank(c, tax, rank)
localDB.Exec(jdh.Commit, "", nil)
noFlag = false
}
if len(popFlag) > 0 {
rank := jdh.GetRank(popFlag)
if rank == jdh.Unranked {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("invalid rank"))
os.Exit(1)
}
prev := tax.Rank
if prev == jdh.Unranked {
prev = jdh.Kingdom
}
txSyncPop(c, tax, prev, rank)
localDB.Exec(jdh.Commit, "", nil)
noFlag = false
}
if noFlag {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("undefined action"))
c.Usage()
}
}
// 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
}
// List returns a list of taxons.
func (t *taxonomy) list(vals []jdh.KeyValue) (*list.List, error) {
l := list.New()
nameList := false
noVal := true
// creates the list
for _, kv := range vals {
switch kv.Key {
case jdh.TaxChildren:
tx := t.root
if len(kv.Value) > 0 {
v := strings.TrimSpace(kv.Value[0])
if len(v) > 0 {
var ok bool
if tx, ok = t.ids[v]; !ok {
return nil, fmt.Errorf("taxon %s not in database", kv.Value)
}
}
}
for _, d := range tx.childs {
if d.data.IsValid {
l.PushBack(d.data)
}
}
noVal = false
case jdh.TaxSynonyms:
if len(kv.Value) == 0 {
return l, nil
}
tx := t.root
v := strings.TrimSpace(kv.Value[0])
if len(v) == 0 {
return l, nil
}
var ok bool
if tx, ok = t.ids[v]; !ok {
return nil, fmt.Errorf("taxon %s not in database", kv.Value)
}
for _, d := range tx.childs {
if !d.data.IsValid {
l.PushBack(d.data)
}
}
noVal = false
case jdh.TaxParents:
if len(kv.Value) == 0 {
return l, nil
}
v := strings.TrimSpace(kv.Value[0])
if len(v) == 0 {
return l, nil
}
tx, ok := t.ids[v]
if !ok {
return nil, fmt.Errorf("taxon %s not in database", kv.Value)
}
for p := tx.parent; p != t.root; p = p.parent {
l.PushBack(p.data)
}
noVal = false
case jdh.TaxName:
if len(kv.Value) == 0 {
return nil, errors.New("taxon without identification")
}
nm := strings.ToLower(strings.Join(strings.Fields(kv.Value[0]), " "))
if len(nm) == 0 {
return nil, errors.New("taxon without identification")
}
i := strings.Index(nm, "*")
if i == 0 {
return nil, errors.New("taxon without identification")
}
var ls *list.List
if i > 0 {
prefix := nm[:i]
ls = t.names.Prefix(prefix)
} else {
ls = list.New()
if v := t.names.Lookup(nm); v != nil {
ls.PushBack(v)
}
}
for e := ls.Front(); e != nil; e = e.Next() {
tl := e.Value.([]*taxon)
for _, tx := range tl {
l.PushBack(tx.data)
}
}
noVal = false
nameList = true
}
if !noVal {
break
}
}
if noVal {
return nil, errors.New("taxon without identification")
}
if !nameList {
return l, nil
}
// filters of the list.
for _, kv := range vals {
if l.Len() == 0 {
break
}
if len(kv.Value) == 0 {
continue
}
switch kv.Key {
case jdh.TaxParent:
pId := strings.TrimSpace(kv.Value[0])
if len(pId) == 0 {
continue
}
for e := l.Front(); e != nil; {
nx := e.Next()
tax := e.Value.(*jdh.Taxon)
if !t.isDesc(tax.Id, pId) {
l.Remove(e)
}
e = nx
}
case jdh.TaxParentName:
p := strings.Join(strings.Fields(kv.Value[0]), " ")
if len(p) == 0 {
continue
}
for e := l.Front(); e != nil; {
nx := e.Next()
tax := e.Value.(*jdh.Taxon)
if !t.hasParentName(tax.Id, p) {
l.Remove(e)
}
e = nx
}
case jdh.TaxRank:
rank := jdh.GetRank(strings.TrimSpace(kv.Value[0]))
for e := l.Front(); e != nil; {
nx := e.Next()
tax := e.Value.(*jdh.Taxon)
if tax.Rank != rank {
l.Remove(e)
}
e = nx
}
}
}
return l, nil
}
