Added command to download tree images from iTOL

cmd/dlimage.go

@@ -0,0 +1,23 @@
+package cmd
+
+import (
+	"github.com/spf13/cobra"
+)
+
+var dltreeid string
+var dlformat string
+var dloutput string
+
+// dlimageCmd represents the download command
+var dlimageCmd = &cobra.Command{
+	Use:   "dlimage",
+	Short: "Download a tree image from from a server",
+	Long:  `Download a tree image from a server`,
+}
+
+func init() {
+	RootCmd.AddCommand(dlimageCmd)
+	dlimageCmd.PersistentFlags().StringVarP(&dltreeid, "tree-id", "i", "", "Tree id to download")
+	dlimageCmd.PersistentFlags().StringVarP(&dlformat, "format", "f", "pdf", "Image format (png, pdf, eps, svg)")
+	dlimageCmd.PersistentFlags().StringVarP(&dloutput, "output", "o", "", "Image output file")
+}

cmd/itoldl.go

@@ -0,0 +1,58 @@
+package cmd
+
+import (
+	"errors"
+	"io/ioutil"
+
+	"github.com/fredericlemoine/gotree/download"
+	"github.com/fredericlemoine/gotree/io"
+	"github.com/spf13/cobra"
+)
+
+var dlconfig string
+
+// dlitolCmd represents the dlitol command
+var dlitolCmd = &cobra.Command{
+	Use:   "itol",
+	Short: "Download a tree image from iTOL",
+	Long: `Download a tree image from iTOL
+
+Option -c allows to give a configuration file having tab separated key value pairs, 
+as defined here:
+http://itol.embl.de/help.cgi#bExOpt
+`,
+	Run: func(cmd *cobra.Command, args []string) {
+		if dloutput == "" {
+			io.ExitWithMessage(errors.New("Output file must be specified"))
+		}
+		if dltreeid == "" {
+			io.ExitWithMessage(errors.New("Tree id must be specified"))
+		}
+		format := download.Format(dlformat)
+		if format == download.IMGFORMAT_UNKNOWN {
+			io.ExitWithMessage(errors.New("Unkown format: " + dlformat))
+		}
+		var config map[string]string
+		if dlconfig != "" {
+			var err error
+			config, err = readMapFile(dlconfig, false)
+			if err != nil {
+				io.ExitWithMessage(err)
+			}
+		} else {
+			config = make(map[string]string)
+		}
+
+		dl := download.NewItolImageDownloader(config)
+		b, err := dl.Download(dltreeid, format)
+		if err != nil {
+			io.ExitWithMessage(err)
+		}
+		ioutil.WriteFile(dloutput, b, 0644)
+	},
+}
+
+func init() {
+	dlimageCmd.AddCommand(dlitolCmd)
+	dlitolCmd.PersistentFlags().StringVarP(&dlconfig, "config", "c", "", "Itol image config file")
+}

cmd/itol.go → cmd/itolup.go

@@ -42,7 +42,7 @@ Will store only urls in the output file
 `,
 	Run: func(cmd *cobra.Command, args []string) {
 		// args: All annotation files to add to the upload
-		upld := upload.NewItolUploader(itoluploadid, itolprojectname, args)
+		upld := upload.NewItolUploader(itoluploadid, itolprojectname, args...)
 		i := 0
 		for reftree := range readTrees(intreefile) {
 			url, response, err := upld.Upload(fmt.Sprintf("%s_%03d", itoltreename, i), reftree.Tree)

cmd/rename.go

@@ -1,59 +1,11 @@
 package cmd
 
 import (
-	"bufio"
-	"compress/gzip"
 	"errors"
-	"fmt"
 	"github.com/fredericlemoine/gotree/io"
-	"github.com/fredericlemoine/gotree/io/utils"
 	"github.com/spf13/cobra"
-	"os"
-	"strings"
 )
 
-func readMapFile(file string, revert bool) (map[string]string, error) {
-	outmap := make(map[string]string, 0)
-	var mapfile *os.File
-	var err error
-	var reader *bufio.Reader
-
-	if mapfile, err = os.Open(file); err != nil {
-		return outmap, err
-	}
-
-	if strings.HasSuffix(file, ".gz") {
-		if gr, err2 := gzip.NewReader(mapfile); err2 != nil {
-			return outmap, err2
-		} else {
-			reader = bufio.NewReader(gr)
-		}
-	} else {
-		reader = bufio.NewReader(mapfile)
-	}
-	line, e := utils.Readln(reader)
-	nl := 1
-	for e == nil {
-		cols := strings.Split(line, "\t")
-		if len(cols) != 2 {
-			return outmap, errors.New("Map file does not have 2 fields at line: " + fmt.Sprintf("%d", nl))
-		}
-		if revert {
-			outmap[cols[1]] = cols[0]
-		} else {
-			outmap[cols[0]] = cols[1]
-		}
-		line, e = utils.Readln(reader)
-		nl++
-	}
-
-	if err = mapfile.Close(); err != nil {
-		return outmap, err
-	}
-
-	return outmap, nil
-}
-
 // renameCmd represents the rename command
 var renameCmd = &cobra.Command{
 	Use:   "rename",

cmd/root.go

@@ -2,6 +2,8 @@ package cmd
 
 import (
 	"bufio"
+	"compress/gzip"
+	"errors"
 	"fmt"
 	"os"
 	"runtime"
@@ -134,3 +136,45 @@ func parseTipsFile(file string) []string {
 	f.Close()
 	return tips
 }
+
+func readMapFile(file string, revert bool) (map[string]string, error) {
+	outmap := make(map[string]string, 0)
+	var mapfile *os.File
+	var err error
+	var reader *bufio.Reader
+
+	if mapfile, err = os.Open(file); err != nil {
+		return outmap, err
+	}
+
+	if strings.HasSuffix(file, ".gz") {
+		if gr, err2 := gzip.NewReader(mapfile); err2 != nil {
+			return outmap, err2
+		} else {
+			reader = bufio.NewReader(gr)
+		}
+	} else {
+		reader = bufio.NewReader(mapfile)
+	}
+	line, e := utils.Readln(reader)
+	nl := 1
+	for e == nil {
+		cols := strings.Split(line, "\t")
+		if len(cols) != 2 {
+			return outmap, errors.New("Map file does not have 2 fields at line: " + fmt.Sprintf("%d", nl))
+		}
+		if revert {
+			outmap[cols[1]] = cols[0]
+		} else {
+			outmap[cols[0]] = cols[1]
+		}
+		line, e = utils.Readln(reader)
+		nl++
+	}
+
+	if err = mapfile.Close(); err != nil {
+		return outmap, err
+	}
+
+	return outmap, nil
+}

download/download.go

@@ -0,0 +1,5 @@
+package download
+
+type ImageDownloader interface {
+	Download(id string) ([]byte, error) // Down a tree image from a server
+}

download/format.go

@@ -0,0 +1,39 @@
+package download
+
+const (
+	IMGFORMAT_SVG     = 0
+	IMGFORMAT_PNG     = 1
+	IMGFORMAT_EPS     = 2
+	IMGFORMAT_PDF     = 3
+	IMGFORMAT_UNKNOWN = 4
+)
+
+func Format(format string) int {
+	switch format {
+	case "svg":
+		return IMGFORMAT_SVG
+	case "png":
+		return IMGFORMAT_PNG
+	case "eps":
+		return IMGFORMAT_EPS
+	case "pdf":
+		return IMGFORMAT_PDF
+	default:
+		return IMGFORMAT_UNKNOWN
+	}
+}
+
+func StrFormat(format int) string {
+	switch format {
+	case IMGFORMAT_SVG:
+		return "svg"
+	case IMGFORMAT_PNG:
+		return "png"
+	case IMGFORMAT_EPS:
+		return "eps"
+	case IMGFORMAT_PDF:
+		return "pdf"
+	default:
+		return "unknown"
+	}
+}

download/itol.go

@@ -0,0 +1,50 @@
+package download
+
+import (
+	"errors"
+	"io/ioutil"
+	"net/http"
+	"net/url"
+)
+
+type ItolImageDownloader struct {
+	config map[string]string
+}
+
+func NewItolImageDownloader(config map[string]string) *ItolImageDownloader {
+	return &ItolImageDownloader{config}
+}
+
+// Down a tree image from ITOL
+func (d *ItolImageDownloader) Download(id string, format int) ([]byte, error) {
+	posturl := "http://itol.embl.de/batch_downloader.cgi"
+	var err error
+	var postresponse *http.Response
+	var responsebody []byte
+
+	form := url.Values{}
+	form.Add("tree", id)
+
+	strformat := StrFormat(format)
+	if strformat == "unknown" {
+		return nil, errors.New("Output image format unknown")
+	}
+	form.Add("format", strformat)
+
+	for k, v := range d.config {
+		if k != "" && v != "" {
+			form.Add(k, v)
+		}
+	}
+	postresponse, err = http.PostForm(posturl, form)
+
+	defer postresponse.Body.Close()
+	if responsebody, err = ioutil.ReadAll(postresponse.Body); err != nil {
+		return nil, err
+	}
+
+	if postresponse.Header.Get("Content-Type") == "text/html" {
+		return nil, errors.New(string(responsebody))
+	}
+	return responsebody, nil
+}

upload/itol.go

@@ -24,7 +24,7 @@ type ItolUploader struct {
 // Initialize a new itoluploader
 // if uploadid=="", then tree will be public and deleted
 // after 30 days
-func NewItolUploader(uploadid, projectname string, annotationfiles []string) *ItolUploader {
+func NewItolUploader(uploadid, projectname string, annotationfiles ...string) *ItolUploader {
 	return &ItolUploader{uploadid, projectname, annotationfiles}
 }