func txSetRun(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) && (strings.Index(args[0], "=") < 0) {
name := args[0]
pName := ""
args = args[1:]
if (len(args) > 0) && (strings.Index(args[0], "=") < 0) {
pName = args[0]
args = args[1:]
}
tax = pickTaxName(c, localDB, name, pName)
if len(tax.Id) == 0 {
return
}
} else {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong taxon name or id"))
c.Usage()
}
vals := valsFromArgs(tax.Id, args)
localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
localDB.Exec(jdh.Commit, "", nil)
}
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 dsSetRun(c *cmdapp.Command, args []string) {
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong dataset id"))
c.Usage()
}
openLocal(c)
set := dataset(c, localDB, idFlag)
if len(set.Id) == 0 {
return
}
vals := valsFromArgs(set.Id, args)
localDB.Exec(jdh.Set, jdh.Datasets, vals)
localDB.Exec(jdh.Commit, "", nil)
}
func raSetRun(c *cmdapp.Command, args []string) {
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong specimen id"))
c.Usage()
}
openLocal(c)
ras := raster(c, localDB, idFlag)
if len(ras.Id) == 0 {
return
}
vals := valsFromArgs(ras.Id, args)
localDB.Exec(jdh.Set, jdh.RasDistros, vals)
localDB.Exec(jdh.Commit, "", nil)
}
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 trSetRun(c *cmdapp.Command, args []string) {
openLocal(c)
if len(nodeFlag) > 0 {
trSetNode(c, args)
return
}
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong tree or node id"))
c.Usage()
}
phy := phylogeny(c, localDB, idFlag)
if len(phy.Id) == 0 {
return
}
vals := valsFromArgs(phy.Id, args)
localDB.Exec(jdh.Set, jdh.Trees, vals)
localDB.Exec(jdh.Commit, "", nil)
}
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 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)
}
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)
}
func raInfoRun(c *cmdapp.Command, args []string) {
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong raster id"))
c.Usage()
}
openLocal(c)
ras := raster(c, localDB, idFlag)
if len(ras.Id) == 0 {
return
}
if machineFlag {
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.RDisTaxon, ras.Taxon)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.RDisSource, ras.Source)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyReference, ras.Reference)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.RDisCols, ras.Cols)
for _, e := range ras.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, ras.Comment)
return
}
switch jdh.Key(keyFlag) {
case jdh.RDisTaxon:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.RDisTaxon, ras.Taxon)
case jdh.RDisSource:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.RDisSource, ras.Source)
case jdh.RDisCols:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.RDisCols, ras.Cols)
case jdh.KeyExtern:
for _, e := range ras.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, ras.Comment)
case jdh.KeyReference:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyReference, ras.Reference)
}
return
}
if len(keyFlag) == 0 {
tax := taxon(c, localDB, ras.Taxon)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Id:", ras.Id)
fmt.Fprintf(os.Stdout, "%-16s %s %s [id: %s]\n", "Taxon:", tax.Name, tax.Authority, ras.Taxon)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Source:", ras.Source)
fmt.Fprintf(os.Stdout, "%-16s %dx%d\n", "Dimensions:", ras.Cols, ras.Cols/2)
if len(ras.Reference) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Reference:", ras.Reference)
}
if len(ras.Extern) > 0 {
fmt.Fprintf(os.Stdout, "Extern ids:\n")
for _, e := range ras.Extern {
fmt.Fprintf(os.Stdout, "\t%s\n", e)
}
}
if len(ras.Comment) > 0 {
fmt.Fprintf(os.Stdout, "Comments:\n%s\n", ras.Comment)
}
return
}
switch jdh.Key(keyFlag) {
case jdh.RDisTaxon:
fmt.Fprintf(os.Stdout, "%s\n", ras.Taxon)
case jdh.RDisSource:
fmt.Fprintf(os.Stdout, "%s\n", ras.Source)
case jdh.RDisCols:
fmt.Fprintf(os.Stdout, "%s\n", ras.Cols)
case jdh.KeyExtern:
for _, e := range ras.Extern {
fmt.Fprintf(os.Stdout, "%s\n", e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s\n", ras.Comment)
case jdh.KeyReference:
fmt.Fprintf(os.Stdout, "%s\n", ras.Reference)
}
}
func txInfoRun(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
}
} else {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong taxon name or id"))
c.Usage()
}
if machineFlag {
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxName, tax.Name)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxAuthority, tax.Authority)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxRank, tax.Rank)
if tax.IsValid {
fmt.Fprintf(os.Stdout, "%s=true\n", jdh.TaxValid)
} else {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxSynonym, tax.Parent)
}
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxParent, tax.Parent)
for _, e := range tax.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, tax.Comment)
return
}
switch jdh.Key(keyFlag) {
case jdh.TaxName:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxName, tax.Name)
case jdh.TaxAuthority:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxAuthority, tax.Authority)
case jdh.TaxRank:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxRank, tax.Rank)
case jdh.TaxValid, jdh.TaxSynonym:
if tax.IsValid {
fmt.Fprintf(os.Stdout, "%s=true\n", jdh.TaxValid)
} else {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxSynonym, tax.Parent)
}
case jdh.TaxParent:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TaxParent, tax.Parent)
case jdh.KeyExtern:
for _, e := range tax.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, tax.Comment)
}
return
}
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Id:", tax.Id)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Name:", tax.Name)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Authority:", tax.Authority)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Rank:", tax.Rank)
if tax.IsValid {
fmt.Fprintf(os.Stdout, "%-16s true\n", "Valid:")
} else {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Synonym of:", tax.Parent)
}
if len(tax.Parent) > 0 {
p := taxon(c, db, tax.Parent)
fmt.Fprintf(os.Stdout, "%-16s %s %s [id: %s]\n", "Parent:", p.Name, p.Authority, p.Id)
}
if len(tax.Extern) > 0 {
fmt.Fprintf(os.Stdout, "Extern ids:\n")
for _, e := range tax.Extern {
fmt.Fprintf(os.Stdout, "\t%s\n", e)
}
}
if len(tax.Comment) > 0 {
fmt.Fprintf(os.Stdout, "Comments:\n%s\n", tax.Comment)
}
txInfoList(c, db, tax.Id, true)
txInfoList(c, db, tax.Id, false)
return
}
switch jdh.Key(keyFlag) {
case jdh.TaxName:
fmt.Fprintf(os.Stdout, "%s\n", tax.Name)
case jdh.TaxAuthority:
fmt.Fprintf(os.Stdout, "%s\n", tax.Authority)
case jdh.TaxRank:
fmt.Fprintf(os.Stdout, "%s\n", tax.Rank)
case jdh.TaxValid, jdh.TaxSynonym:
if tax.IsValid {
fmt.Fprintf(os.Stdout, "true\n")
} else {
fmt.Fprintf(os.Stdout, "synonym of %s\n", tax.Parent)
}
case jdh.TaxParent:
fmt.Fprintf(os.Stdout, "%s\n", tax.Parent)
case jdh.KeyExtern:
for _, e := range tax.Extern {
fmt.Fprintf(os.Stdout, "%s\n", e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s\n", tax.Comment)
}
}
func spLsRun(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(taxonFlag) > 0 {
tax = taxon(c, db, 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, db, 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.SpeTaxonParent, tax.Id)
} else {
vals.Add(jdh.SpeTaxon, tax.Id)
}
if len(countryFlag) > 0 {
vals.Add(jdh.GeoCountry, countryFlag)
}
if geoRefFlag {
vals.Add(jdh.SpeGeoref, "true")
} else if noRefFlag {
vals.Add(jdh.SpeGeoref, "false")
}
l := speList(c, db, vals)
defer l.Close()
ct := tax
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 machineFlag {
fmt.Fprintf(os.Stdout, "%s\n", spe.Id)
continue
}
if spe.Taxon != ct.Id {
ct = taxon(c, db, spe.Taxon)
}
if verboseFlag {
fmt.Fprintf(os.Stdout, "%s %s %s\t%s %s", ct.Id, ct.Name, ct.Authority, spe.Id, spe.Catalog)
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "\t%.5f %.5f %d", spe.Georef.Point.Lon, spe.Georef.Point.Lat, spe.Georef.Uncertainty)
}
fmt.Fprintf(os.Stdout, "\n")
continue
}
fmt.Fprintf(os.Stdout, "%s\t%s", ct.Name, spe.Catalog)
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "\t%.5f %.5f", spe.Georef.Point.Lon, spe.Georef.Point.Lat)
}
fmt.Fprintf(os.Stdout, "\n")
}
}
func trInfoRun(c *cmdapp.Command, args []string) {
openLocal(c)
if len(nodeFlag) > 0 {
trInfoNode(c)
return
}
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong tree or node id"))
c.Usage()
}
phy := phylogeny(c, localDB, idFlag)
if len(phy.Id) == 0 {
return
}
if machineFlag {
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TreName, phy.Name)
for _, e := range phy.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, phy.Comment)
return
}
switch jdh.Key(keyFlag) {
case jdh.TreName:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.TreName, phy.Name)
case jdh.KeyExtern:
for _, e := range phy.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, phy.Comment)
}
return
}
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Id:", phy.Id)
if len(phy.Name) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Name:", phy.Name)
}
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Root:", phy.Root)
if len(phy.Extern) > 0 {
fmt.Fprintf(os.Stdout, "Extern ids:\n")
for _, e := range phy.Extern {
fmt.Fprintf(os.Stdout, "\t%s\n", e)
}
}
if len(phy.Comment) > 0 {
fmt.Fprintf(os.Stdout, "Comments:\n%s\n", phy.Comment)
}
return
}
switch jdh.Key(keyFlag) {
case jdh.TreName:
fmt.Fprintf(os.Stdout, "%s\n", phy.Name)
case jdh.KeyExtern:
for _, e := range phy.Extern {
fmt.Fprintf(os.Stdout, "%s\n", e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s\n", phy.Comment)
}
}
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()
}
}
func spInfoRun(c *cmdapp.Command, args []string) {
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong specimen id"))
c.Usage()
}
var db jdh.DB
if len(extDBFlag) != 0 {
openExt(c, extDBFlag, "")
db = extDB
} else {
openLocal(c)
db = localDB
}
spe := specimen(c, db, idFlag)
if len(spe.Id) == 0 {
return
}
if machineFlag {
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeTaxon, spe.Taxon)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeBasis, spe.Basis)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyReference, spe.Reference)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeDataset, spe.Dataset)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeCatalog, spe.Catalog)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeDeterminer, spe.Determiner)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeCollector, spe.Collector)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeDate, spe.Date.Format(jdh.Iso8601))
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoCountry, spe.Geography.Country)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoState, spe.Geography.State)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoCounty, spe.Geography.County)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeLocality, spe.Locality)
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s=%.8f,%.8f\n", jdh.GeoLonLat, spe.Georef.Point.Lon, spe.Georef.Point.Lat)
fmt.Fprintf(os.Stdout, "%s=%d\n", jdh.GeoUncertainty, spe.Georef.Uncertainty)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoSource, spe.Georef.Source)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoValidation, spe.Georef.Validation)
} else {
fmt.Fprintf(os.Stdout, "%s=\n", jdh.GeoLonLat)
fmt.Fprintf(os.Stdout, "%s=0\n", jdh.GeoUncertainty)
fmt.Fprintf(os.Stdout, "%s=\n", jdh.GeoSource)
fmt.Fprintf(os.Stdout, "%s=\n", jdh.GeoValidation)
}
for _, e := range spe.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, spe.Comment)
return
}
switch jdh.Key(keyFlag) {
case jdh.SpeTaxon:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeTaxon, spe.Taxon)
case jdh.SpeBasis:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeBasis, spe.Basis)
case jdh.SpeDataset:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeDataset, spe.Dataset)
case jdh.SpeCatalog:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeCatalog, spe.Catalog)
case jdh.SpeDeterminer:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeDeterminer, spe.Determiner)
case jdh.SpeCollector:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeCollector, spe.Collector)
case jdh.SpeDate:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeDate, spe.Date.Format(jdh.Iso8601))
case jdh.GeoCountry:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoCountry, spe.Geography.Country)
case jdh.GeoState:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoState, spe.Geography.State)
case jdh.GeoCounty:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoCounty, spe.Geography.County)
case jdh.SpeLocality:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.SpeLocality, spe.Locality)
case jdh.GeoLonLat:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s=%.8f,%.8f\n", jdh.GeoLonLat, spe.Georef.Point.Lon, spe.Georef.Point.Lat)
} else {
fmt.Fprintf(os.Stdout, "%s=\n", jdh.GeoLonLat)
}
case jdh.GeoUncertainty:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s=%d\n", jdh.GeoUncertainty, spe.Georef.Uncertainty)
} else {
fmt.Fprintf(os.Stdout, "%s=0\n", jdh.GeoUncertainty)
}
case jdh.GeoSource:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoSource, spe.Georef.Source)
} else {
fmt.Fprintf(os.Stdout, "%s=\n", jdh.GeoSource)
}
case jdh.GeoValidation:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.GeoValidation, spe.Georef.Validation)
} else {
fmt.Fprintf(os.Stdout, "%s=\n", jdh.GeoValidation)
}
case jdh.KeyExtern:
for _, e := range spe.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, spe.Comment)
case jdh.KeyReference:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyReference, spe.Reference)
}
return
}
if len(keyFlag) == 0 {
tax := taxon(c, db, spe.Taxon)
var set *jdh.Dataset
if len(spe.Dataset) > 0 {
set = dataset(c, db, spe.Dataset)
}
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Id:", spe.Id)
fmt.Fprintf(os.Stdout, "%-16s %s %s [id: %s]\n", "Taxon:", tax.Name, tax.Authority, spe.Taxon)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Basis:", spe.Basis)
if len(spe.Reference) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Reference:", spe.Reference)
}
if set != nil {
fmt.Fprintf(os.Stdout, "%-16s [id: %s]\n%s\n", "Dataset:", set.Id, set.Title)
}
if len(spe.Catalog) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Catalog:", spe.Catalog)
}
if len(spe.Determiner) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Determiner:", spe.Determiner)
}
if len(spe.Collector) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Collector:", spe.Collector)
}
if !spe.Date.IsZero() {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Date:", spe.Date.Format(jdh.Iso8601))
}
if len(spe.Geography.Country) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Country:", spe.Geography.Country.Name())
}
if len(spe.Geography.State) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "State:", spe.Geography.State)
}
if len(spe.Geography.County) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "County:", spe.Geography.County)
}
if len(spe.Locality) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Locality:", spe.Locality)
}
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%-16s %.8f, %.8f\n", "LonLat:", spe.Georef.Point.Lon, spe.Georef.Point.Lat)
if spe.Georef.Uncertainty != 0 {
fmt.Fprintf(os.Stdout, "%-16s %d\n", "Uncertainty:", spe.Georef.Uncertainty)
}
if len(spe.Georef.Source) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Source:", spe.Georef.Source)
}
if len(spe.Georef.Validation) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Validation:", spe.Georef.Validation)
}
}
if len(spe.Extern) > 0 {
fmt.Fprintf(os.Stdout, "Extern ids:\n")
for _, e := range spe.Extern {
fmt.Fprintf(os.Stdout, "\t%s\n", e)
}
}
if len(spe.Comment) > 0 {
fmt.Fprintf(os.Stdout, "Comments:\n%s\n", spe.Comment)
}
if set != nil {
if len(set.Citation) > 0 {
fmt.Fprintf(os.Stdout, "Citation:\n%s\n", set.Citation)
}
if len(set.License) > 0 {
fmt.Fprintf(os.Stdout, "License:\n%s\n", set.License)
}
}
return
}
switch jdh.Key(keyFlag) {
case jdh.SpeTaxon:
fmt.Fprintf(os.Stdout, "%s\n", spe.Taxon)
case jdh.SpeBasis:
fmt.Fprintf(os.Stdout, "%s\n", spe.Basis)
case jdh.SpeDataset:
fmt.Fprintf(os.Stdout, "%s\n", spe.Dataset)
case jdh.SpeCatalog:
fmt.Fprintf(os.Stdout, "%s\n", spe.Catalog)
case jdh.SpeDeterminer:
fmt.Fprintf(os.Stdout, "%s\n", spe.Determiner)
case jdh.SpeCollector:
fmt.Fprintf(os.Stdout, "%s\n", spe.Collector)
case jdh.SpeDate:
fmt.Fprintf(os.Stdout, "%s\n", spe.Date.Format(jdh.Iso8601))
case jdh.GeoCountry:
fmt.Fprintf(os.Stdout, "%s\n", spe.Geography.Country)
case jdh.GeoState:
fmt.Fprintf(os.Stdout, "%s\n", spe.Geography.State)
case jdh.GeoCounty:
fmt.Fprintf(os.Stdout, "%s\n", spe.Geography.County)
case jdh.SpeLocality:
fmt.Fprintf(os.Stdout, "%s\n", spe.Locality)
case jdh.GeoLonLat:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%.8f\t%.8f\n", spe.Georef.Point.Lon, spe.Georef.Point.Lat)
} else {
fmt.Fprintf(os.Stdout, "\n")
}
case jdh.GeoUncertainty:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%d\n", spe.Georef.Uncertainty)
} else {
fmt.Fprintf(os.Stdout, "\n")
}
case jdh.GeoSource:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s\n", spe.Georef.Source)
} else {
fmt.Fprintf(os.Stdout, "\n")
}
case jdh.GeoValidation:
if spe.Georef.IsValid() {
fmt.Fprintf(os.Stdout, "%s\n", spe.Georef.Validation)
} else {
fmt.Fprintf(os.Stdout, "\n")
}
case jdh.KeyExtern:
for _, e := range spe.Extern {
fmt.Fprintf(os.Stdout, "%s\n", e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s\n", spe.Comment)
case jdh.KeyReference:
fmt.Fprintf(os.Stdout, "%s\n", spe.Reference)
}
}
func dsInfoRun(c *cmdapp.Command, args []string) {
if len(idFlag) == 0 {
fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong dataset id"))
c.Usage()
}
var db jdh.DB
if len(extDBFlag) != 0 {
openExt(c, extDBFlag, "")
db = extDB
} else {
openLocal(c)
db = localDB
}
set := dataset(c, db, idFlag)
if len(set.Id) == 0 {
return
}
if machineFlag {
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataTitle, set.Title)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataCitation, set.Citation)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataLicense, set.License)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataUrl, set.Url)
for _, e := range set.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, set.Comment)
return
}
switch jdh.Key(keyFlag) {
case jdh.DataTitle:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataTitle, set.Title)
case jdh.DataCitation:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataCitation, set.Citation)
case jdh.DataLicense:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataLicense, set.License)
case jdh.DataUrl:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.DataUrl, set.Url)
case jdh.KeyExtern:
for _, e := range set.Extern {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyExtern, e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, set.Comment)
}
return
}
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Id:", set.Id)
fmt.Fprintf(os.Stdout, "Title:\n%s\n", set.Title)
if len(set.Url) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Url:", set.Url)
}
if len(set.Citation) > 0 {
fmt.Fprintf(os.Stdout, "Citation:\n%s\n", set.Citation)
}
if len(set.License) > 0 {
fmt.Fprintf(os.Stdout, "License:\n%s\n", set.License)
}
if len(set.Extern) > 0 {
fmt.Fprintf(os.Stdout, "Extern ids:\n")
for _, e := range set.Extern {
fmt.Fprintf(os.Stdout, "\t%s\n", e)
}
}
if len(set.Comment) > 0 {
fmt.Fprintf(os.Stdout, "Comments:\n%s\n", set.Comment)
}
return
}
switch jdh.Key(keyFlag) {
case jdh.DataTitle:
fmt.Fprintf(os.Stdout, "%s\n", set.Title)
case jdh.DataCitation:
fmt.Fprintf(os.Stdout, "%s\n", set.Citation)
case jdh.DataLicense:
fmt.Fprintf(os.Stdout, "%s\n", set.License)
case jdh.DataUrl:
fmt.Fprintf(os.Stdout, "%s\n", set.Url)
case jdh.KeyExtern:
for _, e := range set.Extern {
fmt.Fprintf(os.Stdout, "%s\n", e)
}
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s\n", set.Comment)
}
}
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)
}