// IsInParentList search an id in the list of parents of the taxon.
func isInParentList(c *cmdapp.Command, db jdh.DB, id string, pIds []string) bool {
args := new(jdh.Values)
args.Add(jdh.TaxParents, id)
pl, err := db.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
defer pl.Close()
for {
p := &jdh.Taxon{}
if err := pl.Scan(p); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
for _, pid := range pIds {
if p.Id == pid {
return true
}
}
}
return false
}
func getValidParent(c *cmdapp.Command, extId string) string {
args := new(jdh.Values)
args.Add(jdh.TaxParents, extId)
l, err := extDB.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
defer l.Close()
for {
et := &jdh.Taxon{}
if err := l.Scan(et); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
p := taxon(c, localDB, extDBFlag+":"+et.Id)
if len(p.Id) > 0 {
if p.IsValid {
return p.Id
} else {
return p.Parent
}
}
}
return ""
}
func trForceProc(c *cmdapp.Command, phy *jdh.Phylogeny) {
txLs := list.New()
vals := new(jdh.Values)
vals.Add(jdh.TreTaxon, phy.Id)
l, err := localDB.List(jdh.Trees, vals)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
for {
var tId jdh.IdElement
if err := l.Scan(&tId); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if len(tId.Id) == 0 {
continue
}
txLs.PushBack(tId.Id)
}
if txLs.Len() == 0 {
return
}
root := phyloNode(c, localDB, phy.Root)
trForceNode(c, root, txLs)
}
func txEdVal(from *jdh.Taxon) {
if from.IsValid {
return
}
vals := new(jdh.Values)
vals.Add(jdh.KeyId, from.Id)
vals.Add(jdh.TaxValid, "true")
localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
}
func raLsRun(c *cmdapp.Command, args []string) {
openLocal(c)
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 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong taxon name or id"))
c.Usage()
}
vals := new(jdh.Values)
if childFlag {
vals.Add(jdh.RDisTaxonParent, tax.Id)
} else {
vals.Add(jdh.RDisTaxon, tax.Id)
}
l := rasList(c, localDB, vals)
defer l.Close()
ct := tax
for {
ras := &jdh.Raster{}
if err := l.Scan(ras); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if machineFlag {
fmt.Fprintf(os.Stdout, "%s\n", ras.Id)
continue
}
if ras.Taxon != ct.Id {
ct = taxon(c, localDB, ras.Taxon)
}
if verboseFlag {
fmt.Fprintf(os.Stdout, "%s %s %s\t%s\t%dx%d\n", ct.Id, ct.Name, ct.Authority, ras.Id, ras.Cols, ras.Cols/2)
continue
}
fmt.Fprintf(os.Stdout, "%s\t%s\t%dx%d\n", ct.Name, ras.Id, ras.Cols, ras.Cols/2)
}
}
func spPopFetch(c *cmdapp.Command, tax *jdh.Taxon, prevRank, rank jdh.Rank) {
r := tax.Rank
if r == jdh.Unranked {
r = prevRank
}
defer func() {
l := getTaxDesc(c, localDB, tax.Id, true)
spPopNav(c, l, r, rank)
l = getTaxDesc(c, localDB, tax.Id, false)
spPopNav(c, l, r, rank)
}()
if len(tax.Id) == 0 {
return
}
if r < rank {
return
}
eid := searchExtern(extDBFlag, tax.Extern)
if len(eid) == 0 {
return
}
vals := new(jdh.Values)
vals.Add(jdh.SpeTaxon, eid)
if geoRefFlag {
vals.Add(jdh.SpeGeoref, "true")
}
l := speList(c, extDB, vals)
for {
spe := &jdh.Specimen{}
if err := l.Scan(spe); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if osp := specimen(c, localDB, extDBFlag+":"+spe.Id); len(osp.Id) > 0 {
continue
}
if len(spe.Catalog) > 0 {
if osp := specimen(c, localDB, spe.Catalog); len(osp.Id) > 0 {
exsp := searchExtern(extDBFlag, osp.Extern)
if exsp == spe.Id {
continue
}
fmt.Fprintf(os.Stderr, "specimen %s already in database as %s [duplicated in %s]\n", spe.Catalog, osp.Id, extDBFlag)
continue
}
}
addToSpecimens(c, spe, tax.Id)
}
}
func trDelNode(c *cmdapp.Command) {
vals := new(jdh.Values)
if colpFlag {
vals.Add(jdh.NodCollapse, nodeFlag)
} else {
vals.Add(jdh.KeyId, nodeFlag)
}
if _, err := localDB.Exec(jdh.Delete, jdh.Nodes, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
localDB.Exec(jdh.Commit, "", nil)
}
func setNode(nod *jdh.Node, anc *trNode, data *trData) *trNode {
trn := &trNode{
id: nod.Id,
taxon: nod.Taxon,
parent: anc,
}
data.node = append(data.node, trn)
if anc != nil {
trn.nest = anc.nest + 1
trn.minX = float32(trn.nest)
}
if len(nod.Taxon) > 0 {
tax := taxon(cmd, localDB, nod.Taxon)
trn.name.Text = tax.Name
if !tax.IsValid {
val := taxon(cmd, localDB, tax.Parent)
nm := fmt.Sprintf("[%s syn. of %s]", tax.Name, val.Name)
trn.name.Text = nm
}
}
vals := new(jdh.Values)
vals.Add(jdh.NodChildren, nod.Id)
l, err := localDB.List(jdh.Nodes, vals)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", cmd.ErrStr(err))
os.Exit(1)
}
for {
desc := &jdh.Node{}
if err := l.Scan(desc); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", cmd.ErrStr(err))
os.Exit(1)
}
d := setNode(desc, trn, data)
trn.terms += d.terms
if trn.level <= d.level {
trn.level = d.level + 1
}
trn.children = append(trn.children, d)
}
if len(trn.children) == 0 {
data.terms++
trn.terms = 1
} else {
sort.Sort(bySize(trn.children))
}
return trn
}
// GetTaxDesc return the list of descendants of a taxon.
func getTaxDesc(c *cmdapp.Command, db jdh.DB, id string, valid bool) jdh.ListScanner {
args := new(jdh.Values)
if valid {
args.Add(jdh.TaxChildren, id)
} else {
args.Add(jdh.TaxSynonyms, id)
}
l, err := db.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
return l
}
func dsDelRun(c *cmdapp.Command, args []string) {
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong dataset id"))
c.Usage()
}
openLocal(c)
vals := new(jdh.Values)
vals.Add(jdh.KeyId, idFlag)
if _, err := localDB.Exec(jdh.Delete, jdh.Datasets, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
localDB.Exec(jdh.Commit, "", nil)
}
func txEdSyn(from, to *jdh.Taxon) {
if from.Id == "0" {
return
}
if from.Id == to.Id {
return
}
if (from.Parent == to.Id) && (!from.IsValid) {
return
}
vals := new(jdh.Values)
vals.Add(jdh.KeyId, from.Id)
vals.Add(jdh.TaxSynonym, to.Id)
localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
}
func trViewMouse(tv sparta.Widget, e interface{}) bool {
dt := tv.Property(sparta.Data)
if dt == nil {
return true
}
data := dt.(*trData)
ev := e.(sparta.MouseEvent)
switch ev.Button {
case sparta.MouseRight:
if !setFlag {
return true
}
if data.sel == nil {
return true
}
sel := trViewNearestNode(ev.Loc, data.node)
if sel == nil {
return true
}
x, y, pos := data.x, data.y, data.pos
p := tv.Property(sparta.Parent).(sparta.Widget)
d := p.Property(sparta.Data).(*trList)
if sel == data.sel {
vals := new(jdh.Values)
vals.Add(jdh.NodCollapse, sel.id)
localDB.Exec(jdh.Delete, jdh.Nodes, vals)
localDB.Exec(jdh.Commit, "", nil)
} else if !sel.isValidSis(data.sel) {
return true
} else {
vals := new(jdh.Values)
vals.Add(jdh.KeyId, data.sel.id)
vals.Add(jdh.NodSister, sel.id)
localDB.Exec(jdh.Set, jdh.Nodes, vals)
localDB.Exec(jdh.Commit, "", nil)
}
rect := tv.Property(sparta.Geometry).(image.Rectangle)
data = setTree(d.phyLs[d.pos], rect)
data.x, data.y, data.pos = x, y, pos
tv.SetProperty(sparta.Data, data)
data.putOnScreen()
tv.Update()
case sparta.MouseLeft:
data.sel = trViewNearestNode(ev.Loc, data.node)
tv.Update()
case -sparta.MouseWheel:
data.pos.Y -= 5
data.putOnScreen()
tv.Update()
case sparta.MouseWheel:
data.pos.Y += 5
data.putOnScreen()
tv.Update()
}
return true
}
// TaxInDB returns true if a taxon is in the database.
func taxInDB(c *cmdapp.Command, db jdh.DB, name, parent string, rank jdh.Rank, valid bool) *jdh.Taxon {
args := new(jdh.Values)
args.Add(jdh.TaxName, name)
if len(parent) != 0 {
args.Add(jdh.TaxParent, parent)
}
if rank != jdh.Unranked {
args.Add(jdh.TaxRank, rank.String())
}
l, err := db.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
defer l.Close()
for {
tax := &jdh.Taxon{}
if err := l.Scan(tax); err != nil {
if err == io.EOF {
return nil
}
}
if len(tax.Id) > 0 {
if tax.IsValid == valid {
return tax
}
}
}
}
// ValsFromArgs adds values from an argument list or the stdin.
func valsFromArgs(id string, args []string) *jdh.Values {
vals := new(jdh.Values)
vals.Add(jdh.KeyId, id)
if len(args) == 0 {
in := bufio.NewReader(os.Stdin)
for {
tn, err := readLine(in)
if err != nil {
break
}
ln := strings.Join(tn, " ")
if strings.Index(ln, "=") < 1 {
continue
}
vals.Add(parseKeyValArg(ln))
}
} else {
for _, a := range args {
if strings.Index(a, "=") < 1 {
continue
}
vals.Add(parseKeyValArg(a))
}
}
return vals
}
func trDelRun(c *cmdapp.Command, args []string) {
openLocal(c)
if len(nodeFlag) > 0 {
trDelNode(c)
return
}
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong tree or node id"))
c.Usage()
}
vals := new(jdh.Values)
vals.Add(jdh.KeyId, idFlag)
if _, err := localDB.Exec(jdh.Delete, jdh.Trees, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
localDB.Exec(jdh.Commit, "", nil)
}
func trLsNodes(c *cmdapp.Command) {
vals := new(jdh.Values)
if ancsFlag {
vals.Add(jdh.NodParent, nodeFlag)
} else {
vals.Add(jdh.NodChildren, nodeFlag)
}
l, err := localDB.List(jdh.Nodes, vals)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
for {
nod := &jdh.Node{}
if err := l.Scan(nod); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if machineFlag {
fmt.Fprintf(os.Stdout, "%s\n", nod.Id)
continue
}
var tax *jdh.Taxon
if len(nod.Taxon) > 0 {
tax = taxon(c, localDB, nod.Taxon)
}
if verboseFlag {
fmt.Fprintf(os.Stdout, "%s\t", nod.Id)
if tax != nil {
fmt.Fprintf(os.Stdout, "%s [id:%s]", tax.Name, tax.Id)
}
fmt.Fprintf(os.Stdout, "\tlen: %d\tage: %d\n", nod.Len, nod.Age)
continue
}
fmt.Fprintf(os.Stdout, "%s\t", nod.Id)
if tax != nil {
fmt.Fprintf(os.Stdout, "%s", tax.Name)
}
fmt.Fprintf(os.Stdout, "\n")
}
}
func txSyncRankSet(c *cmdapp.Command, tax *jdh.Taxon, rank jdh.Rank) {
if len(tax.Id) == 0 {
l := getTaxDesc(c, localDB, tax.Id, true)
txSyncRankNav(c, l, rank)
l = getTaxDesc(c, localDB, tax.Id, false)
txSyncRankNav(c, l, rank)
return
}
if (tax.Rank < rank) && (tax.Rank != jdh.Unranked) {
l := getTaxDesc(c, localDB, tax.Id, true)
txSyncRankNav(c, l, rank)
l = getTaxDesc(c, localDB, tax.Id, false)
txSyncRankNav(c, l, rank)
return
} else if tax.Rank == rank {
return
}
eid := searchExtern(extDBFlag, tax.Extern)
if len(eid) == 0 {
l := getTaxDesc(c, localDB, tax.Id, true)
txSyncRankNav(c, l, rank)
l = getTaxDesc(c, localDB, tax.Id, false)
txSyncRankNav(c, l, rank)
return
}
pExt := txSyncRankedParent(c, eid, rank)
if pExt == nil {
l := getTaxDesc(c, localDB, tax.Id, true)
txSyncRankNav(c, l, rank)
l = getTaxDesc(c, localDB, tax.Id, false)
txSyncRankNav(c, l, rank)
return
}
// check if the potential parent is already in the database.
p := taxon(c, localDB, extDBFlag+":"+pExt.Id)
if len(p.Id) == 0 {
p = txSyncAddToTaxonomy(c, pExt)
}
args := new(jdh.Values)
args.Add(jdh.KeyId, tax.Id)
args.Add(jdh.TaxParent, p.Id)
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
}
func spDelRun(c *cmdapp.Command, args []string) {
openLocal(c)
vals := new(jdh.Values)
if len(idFlag) > 0 {
vals.Add(jdh.KeyId, idFlag)
if _, err := localDB.Exec(jdh.Delete, jdh.Specimens, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
localDB.Exec(jdh.Commit, "", nil)
return
}
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 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong specimen id or taxon name or id"))
c.Usage()
}
vals.Add(jdh.SpeTaxon, tax.Id)
if _, err := localDB.Exec(jdh.Delete, jdh.Specimens, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
localDB.Exec(jdh.Commit, "", nil)
}
// PickTaxName search for a unique 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 pickTaxName(c *cmdapp.Command, db jdh.DB, name, parent string) *jdh.Taxon {
args := new(jdh.Values)
args.Add(jdh.TaxName, name)
if len(parent) != 0 {
args.Add(jdh.TaxParentName, parent)
}
l, err := db.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
var tax *jdh.Taxon
mult := false
for {
ot := &jdh.Taxon{}
if err := l.Scan(ot); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if tax == nil {
tax = ot
continue
}
if !mult {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("ambiguos taxon name"))
fmt.Fprintf(os.Stderr, "%s\t%s\n", tax.Id, tax.Name)
mult = true
}
fmt.Fprintf(os.Stderr, "%s\t%s\n", ot.Id, ot.Name)
}
if mult {
os.Exit(0)
}
if tax == nil {
return &jdh.Taxon{}
}
return tax
}
func txLsRankNav(c *cmdapp.Command, db jdh.DB, id string, rank jdh.Rank) {
args := new(jdh.Values)
args.Add(jdh.TaxChildren, id)
l, err := db.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
for {
desc := &jdh.Taxon{}
if err := l.Scan(desc); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if len(desc.Id) == 0 {
continue
}
txLsRank(c, db, desc, rank)
}
}
func newSpList(tax *jdh.Taxon, db jdh.DB) *spList {
ls := &spList{
db: db,
sel: -1,
tax: tax,
}
if taxonRank(cmd, db, tax) < jdh.Species {
return ls
}
vals := new(jdh.Values)
vals.Add(jdh.SpeTaxon, tax.Id)
l, err := db.List(jdh.Specimens, vals)
if err != nil {
return ls
}
for {
spe := &jdh.Specimen{}
if err := l.Scan(spe); err != nil {
break
}
ls.spe = append(ls.spe, spe)
}
return ls
}
// 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
}
// search for a parent of the given rank.
func txSyncRankedParent(c *cmdapp.Command, id string, rank jdh.Rank) *jdh.Taxon {
args := new(jdh.Values)
args.Add(jdh.TaxParents, id)
l, err := extDB.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
defer l.Close()
for {
p := &jdh.Taxon{}
if err := l.Scan(p); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if p.Rank == rank {
return p
}
}
return nil
}
func spInSearchNmdTaxon(c *cmdapp.Command, name, parent, txNum string, rank jdh.Rank) (bool, string) {
args := new(jdh.Values)
args.Add(jdh.TaxName, name)
if len(parent) != 0 {
args.Add(jdh.TaxParent, parent)
}
if rank != jdh.Unranked {
args.Add(jdh.TaxRank, rank.String())
}
l, err := localDB.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
defer l.Close()
var tax *jdh.Taxon
mult := false
for {
ot := &jdh.Taxon{}
if err := l.Scan(ot); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if tax == nil {
tax = ot
continue
}
if !mult {
if verboseFlag {
fmt.Fprintf(os.Stdout, "WARNING:\t%s\t%s\tAmbiguos name\n", txNum)
fmt.Fprintf(os.Stdout, "%s\t%s\n", tax.Id, tax.Name)
}
mult = true
}
if verboseFlag {
fmt.Fprintf(os.Stderr, "%s\t%s\n", ot.Id, ot.Name)
}
}
if mult || (tax == nil) {
return mult, ""
}
return false, tax.Id
}
func newTxList(tax *jdh.Taxon, db jdh.DB, syns bool) *txList {
ls := &txList{
db: db,
tax: tax,
syns: syns,
}
id := ""
if tax == nil {
ls.tax = &jdh.Taxon{
Id: "0",
Name: "root",
}
} else {
id = tax.Id
}
vals := new(jdh.Values)
vals.Add(jdh.TaxChildren, id)
pl, err := db.List(jdh.Taxonomy, vals)
if err != nil {
return ls
}
for {
d := &jdh.Taxon{}
if err := pl.Scan(d); err != nil {
break
}
ls.desc = append(ls.desc, d)
}
if !syns {
return ls
}
vals.Reset()
vals.Add(jdh.TaxSynonyms, id)
pl, err = db.List(jdh.Taxonomy, vals)
if err != nil {
return ls
}
for {
s := &jdh.Taxon{}
if err := pl.Scan(s); err != nil {
break
}
ls.desc = append(ls.desc, s)
}
return ls
}
func txEdMove(from, to *jdh.Taxon) {
if from.Id == "0" {
return
}
if (from.Id == to.Id) || (from.Parent == to.Id) {
return
}
if (to.Id == "0") && (!from.IsValid) {
return
}
vals := new(jdh.Values)
vals.Add(jdh.KeyId, from.Id)
if to.Id != "0" {
vals.Add(jdh.TaxParent, to.Id)
} else {
vals.Add(jdh.TaxParent, "")
}
localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
}
func raMkGetRas(c *cmdapp.Command, id string, size float64) *jdh.Raster {
vals := new(jdh.Values)
vals.Add(jdh.RDisTaxon, id)
vals.Add(jdh.RDisCols, strconv.FormatInt(int64(360/size), 10))
vals.Add(jdh.RDisSource, jdh.ExplicitPoints.String())
l := rasList(c, localDB, vals)
defer l.Close()
for {
ras := &jdh.Raster{}
if err := l.Scan(ras); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
return ras
}
return &jdh.Raster{}
}
func trForceNode(c *cmdapp.Command, nod *jdh.Node, txLs *list.List) {
vals := new(jdh.Values)
vals.Add(jdh.NodChildren, nod.Id)
l, err := localDB.List(jdh.Nodes, vals)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
childs := 0
for {
desc := &jdh.Node{}
if err := l.Scan(desc); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
trForceNode(c, desc, txLs)
childs++
}
if childs > 1 {
return
}
if len(nod.Taxon) == 0 {
return
}
tax := taxon(c, localDB, nod.Taxon)
if tax.IsValid {
return
}
par := taxon(c, localDB, tax.Parent)
todel := false
for e := txLs.Front(); e != nil; e = e.Next() {
tId := e.Value.(string)
if tId == par.Id {
todel = true
break
}
}
if todel {
fmt.Fprintf(os.Stdout, "%s: deleted\n", tax.Name)
if !repFlag {
vals.Reset()
vals.Add(jdh.KeyId, nod.Id)
localDB.Exec(jdh.Delete, jdh.Nodes, vals)
}
return
}
fmt.Fprintf(os.Stdout, "%s: changed to: %s\n", tax.Name, par.Name)
if !repFlag {
vals.Reset()
vals.Add(jdh.KeyId, nod.Id)
vals.Add(jdh.NodTaxon, par.Id)
localDB.Exec(jdh.Set, jdh.Nodes, vals)
txLs.PushBack(par.Id)
}
}
// TrInReadTreeNode reads a tree node in parenthetical notation.
func trInReadTreeNode(in *bufio.Reader, tree, anc, pId string, taxLs map[string]string) (string, error) {
nod := &jdh.Node{
Tree: tree,
Parent: anc,
}
id, err := localDB.Exec(jdh.Add, jdh.Nodes, nod)
if err != nil {
return "", err
}
nod.Id = id
last := ""
for {
r, _, err := in.ReadRune()
if err != nil {
return "", err
}
if unicode.IsSpace(r) {
continue
}
if r == '(' {
last, err = trInReadTreeNode(in, tree, nod.Id, pId, taxLs)
if err != nil {
return "", err
}
continue
}
if r == ')' {
break
}
if r == ',' {
last = ""
continue
}
if r == ':' {
if len(last) == 0 {
return "", errors.New("unexpected ':' token")
}
v, err := trInNumber(in)
if err != nil {
return "", err
}
vals := new(jdh.Values)
vals.Add(jdh.KeyId, last)
vals.Add(jdh.NodLength, strconv.FormatUint(uint64(v), 10))
localDB.Exec(jdh.Set, jdh.Nodes, vals)
last = ""
continue
}
// a terminal
in.UnreadRune()
nm, err := trInString(in)
if err != nil {
return "", err
}
tax, ok := taxLs[nm]
if !ok {
tax, err = trInPickTax(nm, pId)
if err != nil {
return "", err
}
taxLs[nm] = tax
}
term := &jdh.Node{
Tree: tree,
Parent: nod.Id,
Taxon: tax,
}
last, err = localDB.Exec(jdh.Add, jdh.Nodes, term)
if err != nil {
return "", err
}
}
return nod.Id, nil
}
func spGrefProc(c *cmdapp.Command, tax *jdh.Taxon, gzt geography.Gazetter) {
defer func() {
l := getTaxDesc(c, localDB, tax.Id, true)
spGrefNav(c, l, gzt)
l = getTaxDesc(c, localDB, tax.Id, false)
spGrefNav(c, l, gzt)
}()
if len(tax.Id) == 0 {
return
}
vals := new(jdh.Values)
vals.Add(jdh.SpeTaxon, tax.Id)
if !addFlag {
vals.Add(jdh.SpeGeoref, "true")
}
l := speList(c, localDB, vals)
defer l.Close()
for {
spe := &jdh.Specimen{}
if err := l.Scan(spe); err != nil {
if err == io.EOF {
break
}
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
if len(spe.Georef.Validation) > 0 {
continue
}
if !spe.Geography.IsValid() {
fmt.Fprintf(os.Stdout, "%s: location without valid country\n", spe.Id)
continue
}
u := uint(uncertFlag)
if u == 0 {
if u = spe.Georef.Uncertainty; u == 0 {
// 200 km is the maximum validation
u = 200000
}
}
if !spe.Georef.IsValid() {
if !addFlag {
fmt.Fprintf(os.Stdout, "%s: invalid georeference\n", spe.Id)
continue
}
p, err := gzt.Locate(&spe.Geography, spe.Locality, uint(uncertFlag))
if err != nil {
fmt.Fprintf(os.Stdout, "%s: unable to add: %v\n", spe.Id, err)
if verboseFlag {
if err == geography.ErrAmbiguous {
pts, err := gzt.List(&spe.Geography, spe.Locality, uint(uncertFlag))
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
continue
}
for _, p := range pts {
fmt.Fprintf(os.Stderr, "\t%.5f %.5f\t%d\n", p.Point.Lon, p.Point.Lat, p.Uncertainty)
}
}
}
continue
}
vals := new(jdh.Values)
vals.Add(jdh.KeyId, spe.Id)
vals.Add(jdh.GeoLonLat, strconv.FormatFloat(p.Point.Lon, 'g', -1, 64)+","+strconv.FormatFloat(p.Point.Lat, 'g', -1, 64))
vals.Add(jdh.GeoUncertainty, strconv.FormatInt(int64(p.Uncertainty), 10))
vals.Add(jdh.GeoSource, p.Source)
vals.Add(jdh.GeoValidation, p.Validation)
localDB.Exec(jdh.Set, jdh.Specimens, vals)
continue
}
pts, err := gzt.List(&spe.Geography, spe.Locality, u)
if err != nil {
fmt.Fprintf(os.Stdout, "%s: %v\n", spe.Id, err)
continue
}
if len(pts) == 0 {
fmt.Fprintf(os.Stdout, "%s: location not found\n", spe.Id)
continue
}
lon, lat := spe.Georef.Point.Lon, spe.Georef.Point.Lat
val := false
gr := geography.Georeference{
Point: geography.InvalidPoint(),
Uncertainty: geography.EarthRadius * 10, // a distance large enough
}
for _, p := range pts {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
if (d + p.Uncertainty) < gr.Uncertainty {
gr = p
gr.Uncertainty += d
}
}
}
if val {
vals := new(jdh.Values)
vals.Add(jdh.KeyId, spe.Id)
if spe.Georef.Uncertainty == 0 {
vals.Add(jdh.GeoUncertainty, strconv.FormatInt(int64(gr.Uncertainty), 10))
}
vals.Add(jdh.GeoValidation, gr.Validation)
localDB.Exec(jdh.Set, jdh.Specimens, vals)
continue
}
if !corrFlag {
fmt.Fprintf(os.Stdout, "%s: location not found\n", spe.Id)
if verboseFlag {
fmt.Fprintf(os.Stderr, "\t%.5f %.5f\t\t[current georeference]\n", lon, lat)
for _, p := range pts {
fmt.Fprintf(os.Stderr, "\t%.5f %.5f\t%d\t%d\n", p.Point.Lon, p.Point.Lat, p.Uncertainty, p.Point.Distance(lon, lat))
}
}
continue
}
gr = geography.Georeference{
Point: geography.InvalidPoint(),
Uncertainty: geography.EarthRadius * 10, // a distance large enough
}
val = false
for _, p := range pts {
// invert lon-lat
lt, ln := lon, lat
if geography.IsLon(ln) && geography.IsLat(lt) {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
gr = p
gr.Point = geography.Point{Lon: ln, Lat: lt}
gr.Uncertainty += d
break
}
}
// lon with wrong sign
ln, lt = -lon, lat
if geography.IsLon(ln) && geography.IsLat(lt) {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
gr = p
gr.Point = geography.Point{Lon: ln, Lat: lt}
gr.Uncertainty += d
break
}
}
// lat with wrong sing
ln, lt = lon, -lat
if geography.IsLon(ln) && geography.IsLat(lt) {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
gr = p
gr.Point = geography.Point{Lon: ln, Lat: lt}
gr.Uncertainty += d
break
}
}
// invert lon-lat, wrong sings
lt, ln = -lon, -lat
if geography.IsLon(ln) && geography.IsLat(lt) {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
gr = p
gr.Point = geography.Point{Lon: ln, Lat: lt}
gr.Uncertainty += d
break
}
}
// invert lon-lat, lon with wrong sing
lt, ln = lon, -lat
if geography.IsLon(ln) && geography.IsLat(lt) {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
gr = p
gr.Point = geography.Point{Lon: ln, Lat: lt}
gr.Uncertainty += d
break
}
}
// invert lon-lat, lat with wrong sing
lt, ln = -lon, lat
if geography.IsLon(ln) && geography.IsLat(lt) {
d := p.Point.Distance(lon, lat)
if d <= u {
val = true
gr = p
gr.Point = geography.Point{Lon: ln, Lat: lt}
gr.Uncertainty += d
break
}
}
}
if val {
vals := new(jdh.Values)
vals.Add(jdh.KeyId, spe.Id)
vals.Add(jdh.GeoLonLat, strconv.FormatFloat(gr.Point.Lon, 'g', -1, 64)+","+strconv.FormatFloat(gr.Point.Lat, 'g', -1, 64))
vals.Add(jdh.GeoUncertainty, strconv.FormatInt(int64(gr.Uncertainty), 10))
vals.Add(jdh.GeoSource, gr.Source)
vals.Add(jdh.GeoValidation, gr.Validation)
localDB.Exec(jdh.Set, jdh.Specimens, vals)
continue
}
fmt.Fprintf(os.Stdout, "%s: not corrected\n", spe.Id)
if verboseFlag {
fmt.Fprintf(os.Stderr, "\t%.5f %.5f\t\t[current georeference]\n", lon, lat)
for _, p := range pts {
fmt.Fprintf(os.Stderr, "\t%.5f %.5f\t%d\t%d\n", p.Point.Lon, p.Point.Lat, p.Uncertainty, p.Point.Distance(lon, lat))
}
}
}
}