// parses keyValue argument. It returns the key and the value.
func parseKeyValArg(arg string) (jdh.Key, string) {
arg = strings.Join(strings.Fields(arg), " ")
if len(arg) == 0 {
return "", ""
}
p := strings.Split(arg, "=")
key := p[0]
if len(key) == 0 {
return "", ""
}
p = p[1:]
var val string
if len(p) > 1 {
val = strings.Join(p, "=")
} else {
val = p[0]
}
return jdh.Key(key), val
}
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 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 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 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 trInfoNode(c *cmdapp.Command) {
nod := phyloNode(c, localDB, nodeFlag)
if len(nod.Id) == 0 {
return
}
if machineFlag {
if len(keyFlag) == 0 {
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.NodTaxon, nod.Taxon)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.NodLength, nod.Len)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.NodAge, nod.Age)
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, nod.Comment)
return
}
switch jdh.Key(keyFlag) {
case jdh.NodTaxon:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.NodTaxon, nod.Taxon)
case jdh.NodLength:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.NodLength, nod.Len)
case jdh.NodAge:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.NodAge, nod.Age)
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s=%s\n", jdh.KeyComment, nod.Comment)
}
return
}
if len(keyFlag) == 0 {
var tax *jdh.Taxon
if len(nod.Taxon) > 0 {
tax = taxon(c, localDB, nod.Taxon)
}
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Id:", nod.Id)
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Tree:", nod.Tree)
if tax != nil {
fmt.Fprintf(os.Stdout, "%-16s %s %s [id: %s]\n", "Taxon:", tax.Name, tax.Authority, tax.Id)
}
if len(nod.Parent) > 0 {
fmt.Fprintf(os.Stdout, "%-16s %s\n", "Parent:", nod.Parent)
} else {
fmt.Fprintf(os.Stdout, "Root node\n")
}
if nod.Len > 0 {
fmt.Fprintf(os.Stdout, "%-16s %d\n", "Length:", nod.Len)
}
if nod.Age > 0 {
fmt.Fprintf(os.Stdout, "%-16s %d\n", "Age:", nod.Age)
}
if len(nod.Comment) > 0 {
fmt.Fprintf(os.Stdout, "Comments:\n%s\n", nod.Comment)
}
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)
}
first := true
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)
}
if first {
fmt.Fprintf(os.Stdout, "Children nodes:\n")
first = false
}
fmt.Fprintf(os.Stdout, "\t%s", desc.Id)
if len(desc.Taxon) > 0 {
tax := taxon(c, localDB, desc.Taxon)
fmt.Fprintf(os.Stdout, "\t[%s [id: %s]]", tax.Name, tax.Id)
}
fmt.Fprintf(os.Stdout, "\n")
}
return
}
switch jdh.Key(keyFlag) {
case jdh.NodTaxon:
fmt.Fprintf(os.Stdout, "%s\n", nod.Taxon)
case jdh.NodLength:
fmt.Fprintf(os.Stdout, "%s\n", nod.Len)
case jdh.NodAge:
fmt.Fprintf(os.Stdout, "%s\n", nod.Age)
case jdh.KeyComment:
fmt.Fprintf(os.Stdout, "%s\n", nod.Comment)
}
}
