First panther download function

download/download.go

@@ -4,10 +4,12 @@ import (
 	"github.com/evolbioinfo/gotree/tree"
 )
 
+// ImageDownloader defines function to download an image
 type ImageDownloader interface {
 	Download(id string, format int) ([]byte, error) // Downdload a tree image from a server
 }
 
+// TreeDownloader  defines function to download an Tree
 type TreeDownloader interface {
 	Download(id string) (*tree.Tree, error) // Download a tree from a server
 }

download/panther.go

@@ -0,0 +1,166 @@
+package download
+
+import (
+	"encoding/json"
+	"errors"
+	"fmt"
+	"io/ioutil"
+	"net/http"
+
+	"github.com/evolbioinfo/gotree/tree"
+)
+
+// PantherTreeDownloader allows to download trees from Panther
+// using a family ID
+type PantherTreeDownloader struct {
+	server string
+	path   string
+}
+
+// NewPantherTreeDownloader initializes a new Panther tree downloader
+func NewPantherTreeDownloader() *PantherTreeDownloader {
+	return &PantherTreeDownloader{
+		server: "http://pantherdb.org/",
+		path:   "services/oai/pantherdb/treeinfo",
+	}
+}
+
+// Download a tree from Panther
+func (p *PantherTreeDownloader) Download(id string) (t *tree.Tree, err error) {
+	geturl := fmt.Sprintf("%s/%s?family=%s", p.server, p.path, id)
+	var getresponse *http.Response
+	var responsebody []byte
+	var answer *PantherAnswer
+
+	if getresponse, err = http.Get(geturl); err != nil {
+		return
+	}
+	defer getresponse.Body.Close()
+
+	if responsebody, err = ioutil.ReadAll(getresponse.Body); err != nil {
+		return
+	}
+
+	if err = json.Unmarshal(responsebody, answer); err != nil {
+		err = fmt.Errorf("%s (%s)", err.Error(), string(responsebody))
+		return
+	}
+
+	if answer.Error != "" {
+		err = errors.New(string(answer.Error))
+		return
+	}
+
+	if t, err = p.treeFromPantherAnswer(answer); err != nil {
+		return
+	}
+
+	return
+}
+
+// PantherAnswer is the root of Panther JSON answer
+type PantherAnswer struct {
+	Search       PantherAnswerSearch       `json:"search"`
+	TreeTopology PantherAnswerTreeTopology `json:"tree_topology"`
+	Error        string                    `json:"error"`
+	SearchType   string                    `json:"search_type"`
+}
+
+// PantherAnswerSearch defines information on answer search
+type PantherAnswerSearch struct {
+	Product    PantherAnswerProduct    `json:"product"`
+	SearchType string                  `json:"search_type"`
+	Parameters PantherAnswerParameters `json:"parameters"`
+}
+
+// PantherAnswerProduct defines information version and source of the answer
+type PantherAnswerProduct struct {
+	Source  string  `json:"source"`
+	Version float64 `json:"version"`
+}
+
+// PantherAnswerParameters defines information about family
+type PantherAnswerParameters struct {
+	Family string `json:"family"`
+}
+
+// PantherAnswerTreeTopology defines information on node
+type PantherAnswerTreeTopology struct {
+	AnnotationNode PantherAnswerAnnotationNode `json:"annotation_node"`
+}
+
+// PantherAnswerAnnotationNode defines information about the node
+type PantherAnswerAnnotationNode struct {
+	SfID           string                `json:"sf_id"`
+	PersistentID   string                `json:"persistent_id"`
+	BranchLength   float64               `json:"branch_length"`
+	PropSfID       string                `json:"prop_sf_id"`
+	EventType      string                `json:"event_type"`
+	Species        string                `json:"species"`
+	TreeNodeType   string                `json:"tree_node_type"`
+	TaxonomicRange string                `json:"taxonomic_range"`
+	SfName         string                `json:"sf_name"`
+	GeneSymbol     string                `json:"gene_symbol"`
+	NodeName       string                `json:"node_name"`
+	Organism       string                `json:"organism"`
+	Children       PantherAnswerChildren `json:"children"`
+}
+
+// PantherAnswerChildren defines the children type
+type PantherAnswerChildren struct {
+	TreeNodeType   string                        `json:"tree_node_type"`
+	TaxonomicRange string                        `json:"taxonomic_range"`
+	SfName         string                        `json:"sf_name"`
+	AnnotationNode []PantherAnswerAnnotationNode `json:"annotation_node"`
+}
+
+func (p *PantherTreeDownloader) treeFromPantherAnswer(answer *PantherAnswer) (t *tree.Tree, err error) {
+	var nedges, nnodes int = 0, 0
+
+	t = tree.NewTree()
+	err = p.annotationNodeToTree(&answer.TreeTopology.AnnotationNode, t, nil, &nedges, &nnodes)
+	return
+}
+
+func (p *PantherTreeDownloader) annotationNodeToTree(an *PantherAnswerAnnotationNode, t *tree.Tree, parent *tree.Node, nedges, nnodes *int) (err error) {
+	newNode := t.NewNode()
+	newNode.SetId(*nnodes)
+	(*nnodes)++
+	if parent == nil {
+		t.SetRoot(newNode)
+	} else {
+		e := t.ConnectNodes(parent, newNode)
+		e.SetId(*nedges)
+		(*nedges)++
+		if an.BranchLength != 0 {
+			e.SetLength(an.BranchLength)
+		}
+	}
+	if an.Species != "" {
+		newNode.SetName(an.Species)
+	}
+
+	if an.EventType != "" {
+		newNode.AddComment(an.EventType)
+	}
+
+	if an.Organism != "" {
+		newNode.AddComment(an.Organism)
+	}
+
+	if an.PersistentID != "" {
+		newNode.AddComment(an.PersistentID)
+	}
+
+	for _, cl := range an.Children.AnnotationNode {
+		if err = p.annotationNodeToTree(&cl, t, newNode, nedges, nnodes); err != nil {
+			return
+		}
+	}
+
+	if len(an.Children.AnnotationNode) == 0 && an.GeneSymbol == "" {
+		err = fmt.Errorf("One tip has no gene symbol")
+	}
+
+	return
+}