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tabixManager.go
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tabixManager.go
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package data
import (
"encoding/json"
"fmt"
"io"
"log"
"net/http"
"strconv"
"github.com/brentp/bix"
"github.com/gorilla/mux"
)
type TabixManager struct {
uriMap map[string]string
dataMap map[string]*bix.Bix
dbname string
valueMap map[string]map[string]interface{} //LONG LABELS
}
type loc struct {
chrom string
start int
end int
}
func (s loc) Chrom() string {
return s.chrom
}
func (s loc) Start() uint32 {
return uint32(s.start)
}
func (s loc) End() uint32 {
return uint32(s.end)
}
func (m *TabixManager) SetAttr(key string, value map[string]interface{}) error {
m.valueMap[key] = value
return nil
}
func (m *TabixManager) GetAttr(key string) (map[string]interface{}, bool) {
v, ok := m.valueMap[key]
return v, ok
}
func (T *TabixManager) AddURI(uri string, key string) error {
b, err := bix.New(uri) //path to file now; not working for http
if err != nil {
return err
}
T.uriMap[key] = uri
T.dataMap[key] = b
log.Println(" Loading entry", key)
return nil
}
func (m *TabixManager) Del(key string) error {
delete(m.uriMap, key)
delete(m.dataMap, key)
return nil
}
func (m *TabixManager) Get(key string) (string, bool) {
v, ok := m.uriMap[key]
return v, ok
}
func (m *TabixManager) Move(key1 string, key2 string) bool {
v, ok1 := m.uriMap[key1]
d, ok2 := m.dataMap[key1]
if ok1 && ok2 {
m.uriMap[key2] = v
m.dataMap[key2] = d
delete(m.uriMap, key1)
delete(m.dataMap, key1)
}
return ok1 && ok2
}
func (m *TabixManager) List() []string {
keys := []string{}
for k, _ := range m.uriMap {
keys = append(keys, k)
}
return keys
}
func (T *TabixManager) ServeTo(router *mux.Router) {
prefix := "/" + T.dbname
router.HandleFunc(prefix+"/list", func(w http.ResponseWriter, r *http.Request) {
a := make([]map[string]string, 0)
attr, ok := r.URL.Query()["attr"]
if !ok || len(attr) < 1 || !(attr[0] == "1" || attr[0] == "true") {
keys := []string{}
for key, _ := range T.uriMap {
keys = append(keys, key)
}
jsonHic, _ := json.Marshal(keys)
w.Write(jsonHic)
} else {
for k, _ := range T.uriMap {
a = append(a, map[string]string{"id": k, "format": "tabix"})
if attrs, ok := T.GetAttr(k); ok {
i := len(a) - 1
for k0, v0 := range attrs {
switch v0.(type) {
case string:
a[i][k0] = v0.(string)
default:
}
}
}
}
jsonHic, _ := json.Marshal(a)
w.Write(jsonHic)
}
})
router.HandleFunc(prefix+"/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(T.uriMap)
w.Write(jsonHic)
} else {
jsonAttr, _ := json.Marshal(T.valueMap)
w.Write(jsonAttr)
}
})
router.HandleFunc(prefix+"/{id}/list", func(w http.ResponseWriter, r *http.Request) {
params := mux.Vars(r)
id := params["id"]
if _, ok := T.dataMap[id]; ok {
//jsonChr, _ := json.Marshal(a.Names()) //TODO FIX
//w.Write(jsonChr)
w.Write([]byte("TODO CHRS"))
} else {
fmt.Println("can not find id", id)
}
})
router.HandleFunc(prefix+"/{id}/get/{chr}:{start}-{end}", func(w http.ResponseWriter, r *http.Request) {
params := mux.Vars(r)
id := params["id"]
chrom := params["chr"]
s, _ := strconv.Atoi(params["start"])
e, _ := strconv.Atoi(params["end"])
vals, _ := T.dataMap[id].Query(loc{chrom, s, e})
i := 0
for {
v, err := vals.Next()
if err != nil {
break
}
//fmt.Println(v)
i++
io.WriteString(w, fmt.Sprint(v))
io.WriteString(w, "\n")
}
})
}
func NewTabixManager(uri string, dbname string) *TabixManager {
uriMap := loadURI(uri)
dataMap := make(map[string]*bix.Bix)
valueMap := make(map[string]map[string]interface{})
for k, v := range uriMap {
b, err := bix.New(v)
if err == nil {
dataMap[k] = b
fmt.Println("loading ", k)
} else {
panic(err)
}
}
m := TabixManager{
uriMap,
dataMap,
dbname,
valueMap,
}
//m.ServeTo(router)
return &m
}
func InitTabixManager(dbname string) *TabixManager {
uriMap := make(map[string]string)
dataMap := make(map[string]*bix.Bix)
valueMap := make(map[string]map[string]interface{})
m := TabixManager{
uriMap,
dataMap,
dbname,
valueMap,
}
return &m
}