/
trackManager.go
196 lines (183 loc) · 4.63 KB
/
trackManager.go
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package data
import (
"encoding/json"
"errors"
"io"
"net/http"
"strings"
"github.com/gorilla/mux"
"github.com/nimezhu/indexed"
)
type TrackManager struct {
id string
uriMap map[string]string
formatMap map[string]string
managers map[string]Manager
root string
}
func NewTrackManager(uri string, dbname string, root string) *TrackManager {
m := InitTrackManager(dbname, root)
uriMap := loadURI(uri)
for k, v := range uriMap {
m.AddURI(v, k)
}
return m
}
func InitTrackManager(dbname string, root string) *TrackManager {
uriMap := make(map[string]string)
formatMap := make(map[string]string)
dataMap := make(map[string]Manager)
m := TrackManager{
dbname,
uriMap,
formatMap,
dataMap,
root,
}
return &m
}
func _newManager(prefix string, format string, root string) Manager {
if format == "bigwig" {
return InitBigWigManager(prefix+".bigwig", root)
}
if format == "bigbed" {
return InitBigBedManager(prefix+".bigbed", root)
}
if format == "bigbedLarge" {
return InitBigBedManager(prefix+".bigbedLarge", root)
}
if format == "hic" {
return InitHicManager(prefix + ".hic")
}
/* obsoleted
if format == "image" {
return InitTabixImageManager(prefix + ".image")
}
*/
return nil
}
func (m *TrackManager) SetAttr(key string, values map[string]interface{}) error {
if v, ok := m.managers[m.formatMap[key]]; ok {
return v.SetAttr(key, values)
}
return errors.New("not found manager")
}
func (m *TrackManager) GetAttr(key string) (map[string]interface{}, bool) {
if _, ok := m.formatMap[key]; !ok {
return nil, false
}
return m.managers[m.formatMap[key]].GetAttr(key)
}
func (m *TrackManager) Add(key string, reader io.ReadSeeker, uri string) error {
format, _ := indexed.MagicReadSeeker(reader)
if format == "hic" || format == "bigwig" || format == "bigbed" {
reader.Seek(0, 0)
if _, ok := m.managers[format]; !ok {
m.managers[format] = _newManager(m.id, format, m.root)
}
m.managers[format].Add(key, reader, uri)
m.formatMap[key] = format
m.uriMap[key] = uri
}
return nil
}
func (m *TrackManager) AddURI(uri string, key string) error {
format, _ := indexed.Magic(uri)
//HANDLE binindex in mem
if format == "binindex" {
m.uriMap[key] = strings.Replace(uri, "_format_:binindex:", "", 1)
return nil
}
if _, ok := m.managers[format]; !ok {
if _m := _newManager(m.id, format, m.root); _m != nil {
m.managers[format] = _m
m.managers[format].AddURI(uri, key)
} else {
return errors.New("format not support yet")
}
} else {
m.managers[format].AddURI(uri, key)
}
m.formatMap[key] = format
m.uriMap[key] = uri
return nil
}
func (m *TrackManager) Del(k string) error {
if uri, ok := m.uriMap[k]; ok {
format, _ := indexed.Magic(uri)
//TODO binindex
delete(m.uriMap, k)
return m.managers[format].Del(k)
}
return errors.New("key not found")
}
func (m *TrackManager) ServeTo(router *mux.Router) {
for _, v := range m.managers {
v.ServeTo(router)
}
prefix := "/" + m.id
sub := router.PathPrefix(prefix).Subrouter()
sub.HandleFunc("/ls", func(w http.ResponseWriter, r *http.Request) {
attr, ok := r.URL.Query()["attr"]
if !ok || len(attr) < 1 || !(attr[0] == "1" || attr[0] == "true") {
jsonHic, _ := json.Marshal(m.uriMap)
w.Write(jsonHic)
} else {
//TODO PRECOMPUTING ??
retv := make(map[string]map[string]interface{})
for _, m0 := range m.managers {
for _, k := range m0.List() {
retv[k], _ = m0.GetAttr(k)
}
}
jsonAttr, _ := json.Marshal(retv)
w.Write(jsonAttr)
}
})
sub.HandleFunc("/list", func(w http.ResponseWriter, r *http.Request) {
a := make([]map[string]string, 0)
//TODO fix this for trackAgent
attr, ok := r.URL.Query()["attr"]
sign := true
if !ok || len(attr) < 1 || !(attr[0] == "1" || attr[0] == "true") {
sign = false
}
for k, _ := range m.uriMap {
a = append(a, map[string]string{"id": k, "format": m.formatMap[k]})
if sign {
if attrs, ok := m.managers[m.formatMap[k]].GetAttr(k); ok {
for k0, v0 := range attrs {
switch v0.(type) {
case string:
a[len(a)-1][k0] = v0.(string)
default:
}
}
}
}
}
jsonHic, _ := json.Marshal(a)
w.Write(jsonHic)
})
}
func (m *TrackManager) List() []string {
s := make([]string, 0)
for k, _ := range m.uriMap {
s = append(s, k)
}
return s
}
func (m *TrackManager) Get(key string) (string, bool) {
v, ok := m.uriMap[key]
return v, ok
}
func (m *TrackManager) Move(key1 string, key2 string) bool { //TODO
if v, ok := m.uriMap[key1]; ok {
m.uriMap[key2] = v
delete(m.uriMap, key1)
format, _ := indexed.Magic(v) // TODO Fix this with ReadSeeker.
m.managers[format].Move(key1, key2)
return true
}
return false
}