Add default taxonomy

cmd/obitools/obifind/main.go

@@ -5,6 +5,7 @@ import (
 	"os"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
 )
 
@@ -23,12 +24,8 @@ func main() {
 
 	switch {
 	case obifind.CLIRequestsPathForTaxid() != "NA":
-		taxonomy, err := obifind.CLILoadSelectedTaxonomy()
-		if err != nil {
-			fmt.Printf("%+v", err)
-		}
 
-		taxon := taxonomy.Taxon(obifind.CLIRequestsPathForTaxid())
+		taxon := obitax.DefaultTaxonomy().Taxon(obifind.CLIRequestsPathForTaxid())
 
 		if taxon == nil {
 			fmt.Printf("%+v", err)
@@ -44,11 +41,7 @@ func main() {
 			fmt.Sprintf("path:%s", taxon.String()))
 
 	case len(args) == 0:
-		taxonomy, err := obifind.CLILoadSelectedTaxonomy()
-		if err != nil {
-			fmt.Printf("%+v", err)
-		}
-
+		taxonomy := obitax.DefaultTaxonomy()
 		obifind.TaxonWriter(restrictions(taxonomy.Iterator()), "")
 
 	default:

pkg/obioptions/options.go

@@ -1,10 +1,13 @@
 package obioptions
 
 import (
+	"errors"
 	"fmt"
 	"os"
 	"runtime"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	log "github.com/sirupsen/logrus"
 
 	"github.com/DavidGamba/go-getoptions"
@@ -28,6 +31,9 @@ var _PprofGoroutine = 6060
 var _Quality_Shift_Input = byte(33)
 var _Quality_Shift_Output = byte(33)
 
+var __taxdump__ = ""
+var __alternative_name__ = false
+
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
 
 func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser {
@@ -124,6 +130,14 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 			log.Info("  go tool pprof -http=127.0.0.1:8080 'http://localhost:6060/debug/pprof/block'")
 		}
 
+		if options.Called("taxdump") {
+			taxonomy, err := ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(),
+				!CLIAreAlternativeNamesSelected())
+			if err != nil {
+				log.Fatalf("Loading taxonomy error: %v", err)
+			}
+			taxonomy.SetAsDefault()
+		}
 		// Handle user errors
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err)
@@ -169,6 +183,24 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 	}
 }
 
+func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bool) {
+	if required {
+		options.StringVar(&__taxdump__, "taxdump", "",
+			options.Alias("t"),
+			options.Required(),
+			options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
+	} else {
+		options.StringVar(&__taxdump__, "taxdump", "",
+			options.Alias("t"),
+			options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
+	}
+	if alternatiive {
+		options.BoolVar(&__alternative_name__, "alternative-names", false,
+			options.Alias("a"),
+			options.Description("Enable the search on all alternative names and not only scientific names."))
+	}
+}
+
 // CLIIsDebugMode returns whether the CLI is in debug mode.
 //
 // The debug mode is activated by the command line option --debug or
@@ -420,3 +452,33 @@ func ParallelFilesRead() int {
 func SetParallelFilesRead(n int) {
 	_ParallelFilesRead = n
 }
+
+func CLISelectedNCBITaxDump() string {
+	return __taxdump__
+}
+
+func CLIHasSelectedTaxonomy() bool {
+	return __taxdump__ != ""
+}
+
+func CLIAreAlternativeNamesSelected() bool {
+	return __alternative_name__
+}
+
+func CLILoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
+	if obitax.IsDefaultTaxonomyDefined() {
+		return obitax.DefaultTaxonomy(), nil
+	}
+
+	if CLISelectedNCBITaxDump() != "" {
+		taxonomy, err := ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(),
+			!CLIAreAlternativeNamesSelected())
+		if err != nil {
+			return nil, err
+		}
+		taxonomy.SetAsDefault()
+		return taxonomy, nil
+	}
+
+	return nil, errors.New("no NCBI taxdump selected using option -t|--taxdump")
+}

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "9471fed"
+var _Commit = "7633fc4"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.