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)
}
}
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 raMkFetch(c *cmdapp.Command, spDB jdh.DB, tax *jdh.Taxon, prevRank, rank jdh.Rank, size float64) {
r := tax.Rank
if r == jdh.Unranked {
r = prevRank
}
defer func() {
l := getTaxDesc(c, localDB, tax.Id, true)
raMkNav(c, l, spDB, r, rank, size)
}()
if len(tax.Id) == 0 {
return
}
if r < rank {
return
}
vals := new(jdh.Values)
if spDB != localDB {
eid := searchExtern(extDBFlag, tax.Extern)
if len(eid) == 0 {
return
}
vals.Add(jdh.SpeTaxonParent, eid)
} else {
vals.Add(jdh.SpeTaxonParent, tax.Id)
}
vals.Add(jdh.SpeGeoref, "true")
inDB := true
ras := raMkGetRas(c, tax.Id, size)
if len(ras.Id) == 0 {
inDB = false
ras = &jdh.Raster{
Taxon: tax.Id,
Cols: uint(360 / size),
Source: jdh.ExplicitPoints,
}
}
l := speList(c, spDB, 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 !spe.Georef.IsValid() {
continue
}
if validFlag && (len(spe.Georef.Validation) == 0) {
continue
}
azm, inc := spe.Georef.Point.Lon+180, 90-spe.Georef.Point.Lat
x, y := int(azm/size), int(inc/size)
if inDB {
vals.Reset()
vals.Add(jdh.KeyId, ras.Id)
vals.Add(jdh.RasPixel, fmt.Sprintf("%d,%d,1", x, y))
localDB.Exec(jdh.Set, jdh.RasDistros, vals)
continue
}
if ras.Raster == nil {
ras.Raster = pixlist.NewPixList()
}
pt := image.Pt(x, y)
ras.Raster.Set(pt, 1)
}
if inDB || (ras.Raster == nil) {
return
}
localDB.Exec(jdh.Add, jdh.RasDistros, ras)
}
// TxSyncMatch implements the match option of tx.sync.
func txSyncMatch(c *cmdapp.Command, tax *jdh.Taxon) {
defer func() {
l := getTaxDesc(c, localDB, tax.Id, true)
txSyncMatchNav(c, l)
l = getTaxDesc(c, localDB, tax.Id, false)
txSyncMatchNav(c, l)
}()
if len(tax.Id) == 0 {
return
}
eid := searchExtern(extDBFlag, tax.Extern)
if len(eid) > 0 {
return
}
var pEids []string
args := new(jdh.Values)
args.Add(jdh.TaxParents, tax.Id)
pl, err := localDB.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
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)
}
pe := searchExtern(extDBFlag, p.Extern)
if len(pEids) == 0 {
continue
}
pEids = append(pEids, pe)
}
args.Reset()
args.Add(jdh.TaxName, tax.Name)
l, err := extDB.List(jdh.Taxonomy, args)
if err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
var extTax *jdh.Taxon
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)
}
if len(pEids) > 0 {
if !isInParentList(c, extDB, et.Id, pEids) {
continue
}
}
if (len(tax.Authority) > 0) && (len(et.Authority) > 0) {
if tax.Authority != et.Authority {
continue
}
}
if extTax == nil {
extTax = et
continue
}
// The name is ambiguous
fmt.Fprintf(os.Stderr, "taxon name %s is ambiguous in %s\n", tax.Name, extDBFlag)
l.Close()
return
}
if extTax == nil {
return
}
args.Reset()
args.Add(jdh.KeyId, tax.Id)
args.Add(jdh.KeyExtern, extDBFlag+":"+extTax.Id)
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
}
func txDelRun(c *cmdapp.Command, args []string) {
openLocal(c)
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 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong taxon name or id"))
c.Usage()
}
vals := new(jdh.Values)
if colpFlag {
if len(tax.Parent) > 0 {
vals.Add(jdh.KeyId, tax.Id)
vals.Add(jdh.TaxSynonym, "")
if _, err := localDB.Exec(jdh.Set, jdh.Taxonomy, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
} else {
l := getTaxDesc(c, localDB, tax.Id, true)
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)
}
vals.Reset()
vals.Add(jdh.KeyId, desc.Id)
vals.Add(jdh.TaxParent, "")
if _, err := localDB.Exec(jdh.Set, jdh.Taxonomy, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
}
}
}
vals.Reset()
vals.Add(jdh.KeyId, tax.Id)
if _, err := localDB.Exec(jdh.Delete, jdh.Taxonomy, vals); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
localDB.Exec(jdh.Commit, "", nil)
}