func txSyncPopDesc(c *cmdapp.Command, l jdh.ListScanner, p *jdh.Taxon) {
pId := p.Id
if !p.IsValid {
pId = p.Parent
}
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)
}
// check if the taxon is in the database
if d := taxon(c, localDB, extDBFlag+":"+desc.Id); len(d.Id) != 0 {
continue
}
// adds the new taxon
tax := &jdh.Taxon{}
*tax = *desc
tax.Id = ""
tax.Parent = pId
tax.Extern = []string{extDBFlag + ":" + desc.Id}
if _, err := localDB.Exec(jdh.Add, jdh.Taxonomy, tax); err != nil {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
os.Exit(1)
}
}
}
func spGrefNav(c *cmdapp.Command, l jdh.ListScanner, gzt geography.Gazetter) {
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)
}
spGrefProc(c, desc, gzt)
}
}
func raMkNav(c *cmdapp.Command, l jdh.ListScanner, spDB jdh.DB, prevRank, rank jdh.Rank, size float64) {
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)
}
raMkFetch(c, spDB, desc, prevRank, rank, size)
}
}
func spPopNav(c *cmdapp.Command, l jdh.ListScanner, prevRank, rank jdh.Rank) {
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)
}
spPopFetch(c, desc, prevRank, rank)
}
}
func txSyncRankNav(c *cmdapp.Command, l jdh.ListScanner, rank jdh.Rank) {
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)
}
txSyncRankSet(c, desc, rank)
}
}
func txLsProc(c *cmdapp.Command, l jdh.ListScanner) {
for {
tax := &jdh.Taxon{}
if err := l.Scan(tax); 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", tax.Id)
continue
}
if verboseFlag {
fmt.Fprintf(os.Stdout, "%s\t%s\t%s %s\t\n", tax.Id, tax.Rank, tax.Name, tax.Authority)
continue
}
fmt.Fprintf(os.Stdout, "%s %s\n", tax.Name, tax.Authority)
}
}