add the --download-ncbi option to obitaxonomy

cmd/obitools/obitaxonomy/main.go

@@ -1,13 +1,14 @@
 package main
 
 import (
-	"log"
 	"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/obitaxonomy"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+
+	log "github.com/sirupsen/logrus"
 )
 
 func main() {
@@ -19,6 +20,15 @@ func main() {
 
 	switch {
 
+	case obitaxonomy.CLIDownloadNCBI():
+		err := obitaxonomy.CLIDownloadNCBITaxdump()
+		if err != nil {
+			log.Errorf("Cannot download NCBI taxonomy: %s", err.Error())
+			os.Exit(1)
+		}
+
+		os.Exit(0)
+
 	case obitaxonomy.CLIDumpSubtaxonomy():
 		iterator = obitaxonomy.CLISubTaxonomyIterator()
 

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "67e2758"
+var _Commit = "b6b18c0"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obitaxonomy/obitaxonomy.go

@@ -1,10 +1,15 @@
 package obitaxonomy
 
 import (
+	"fmt"
+	"time"
+
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 
 	log "github.com/sirupsen/logrus"
 )
@@ -73,3 +78,18 @@ func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiitercsv.ICSVRecord {
 func CLICSVTaxaWriter(iterator *obitax.ITaxon, terminalAction bool) *obiitercsv.ICSVRecord {
 	return obicsv.CLICSVWriter(CLICSVTaxaIterator(iterator), terminalAction)
 }
+
+func CLIDownloadNCBITaxdump() error {
+	now := time.Now()
+	dateStr := now.Format("20060102") // In Go, this specific date is used as reference for formatting
+
+	filename := fmt.Sprintf("ncbitaxo_%s.tgz", dateStr)
+
+	if obiconvert.CLIOutPutFileName() != "-" {
+		filename = obiconvert.CLIOutPutFileName()
+	}
+
+	log.Infof("Downloading NCBI Taxdump to %s", filename)
+	return obiutils.DownloadFile("https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz", filename)
+
+}

pkg/obitools/obitaxonomy/options.go

@@ -22,6 +22,7 @@ var __taxid_path__ = "NA"
 var __taxid_sons__ = "NA"
 var __restrict_rank__ = ""
 var __to_dump__ = ""
+var __download_ncbi__ = false
 
 func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__rank_list__, "rank-list", false,
@@ -34,7 +35,7 @@ func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
 }
 
 func OptionSet(options *getoptions.GetOpt) {
-	obioptions.LoadTaxonomyOptionSet(options, true, true)
+	obioptions.LoadTaxonomyOptionSet(options, false, true)
 	FilterTaxonomyOptionSet(options)
 	options.BoolVar(&__fixed_pattern__, "fixed", false,
 		options.Alias("F"),
@@ -70,6 +71,10 @@ func OptionSet(options *getoptions.GetOpt) {
 		options.ArgName("TAXID"),
 		options.Description("Dump a sub-taxonomy corresponding to the precised clade"),
 	)
+	options.BoolVar(&__download_ncbi__, "download-ncbi", __download_ncbi__,
+		options.Description("Download the current NCBI taxonomy taxdump"),
+	)
+
 }
 
 func CLITaxonomicalRestrictions() (*obitax.TaxonSet, error) {
@@ -144,3 +149,7 @@ func CLIDumpSubtaxonomy() bool {
 func CLISubTaxonomyNode() string {
 	return __to_dump__
 }
+
+func CLIDownloadNCBI() bool {
+	return __download_ncbi__
+}

pkg/obiutils/download.go

@@ -0,0 +1,45 @@
+package obiutils
+
+import (
+	"fmt"
+	"io"
+	"net/http"
+	"os"
+
+	"github.com/schollz/progressbar/v3"
+)
+
+func DownloadFile(url string, filepath string) error {
+	// Get the data
+	resp, err := http.Get(url)
+	if err != nil {
+		return err
+	}
+	defer resp.Body.Close()
+
+	// Check server response
+	if resp.StatusCode != http.StatusOK {
+		return fmt.Errorf("bad status: %s", resp.Status)
+	}
+
+	// Create the file
+	out, err := os.Create(filepath)
+	if err != nil {
+		return err
+	}
+	defer out.Close()
+
+	// Create progress bar
+	bar := progressbar.DefaultBytes(
+		resp.ContentLength,
+		"downloading",
+	)
+
+	// Write the body to file while updating the progress bar
+	_, err = io.Copy(io.MultiWriter(out, bar), resp.Body)
+	if err != nil {
+		return err
+	}
+
+	return nil
+}