removed pkg, added conf package, cleaned up logging of requests

Author: jaredwilkening

.gitignore

@@ -19,11 +19,9 @@ test.out
 build.out
 _obj
 
-# bin
-pkg/**/*
+# bin 
+pkg
 bin
-src/*/*/_obj
-src/cmd/shock-server/shock-server
 
 # os x files
 *.DS_Store

README.md

@@ -42,7 +42,7 @@ To build Shock:
 
 To run (additional requires mongodb=>2.0.3):
 
-    ./bin/shock-server -port=<port#> -dataroot=<path_to_data_root> -mongo=<mongo_host(s)>
+    ./bin/shock-server -port=<port to listen on> -data=<data directory to store on disk files> -mongo=<hostname(s) of mongodb>
 
 Data Types
 ----------
@@ -164,7 +164,7 @@ POST /node (multipart/form-data encoded)
 ### List nodes:
 GET /node
 
- - by adding ?offset=N you get the nodes starting at N+1 
+ - by adding ?skip=N you get the nodes starting at N+1 
  - by adding ?limit=N you get a maximum of N nodes returned 
 
 ##### querying
@@ -180,11 +180,11 @@ Multiple attributes can be selected in a single query and are treated as AND ope
 
     /node/?query&metadata.env_biome=ENVO:human-associated%20habitat&about=metagenome
 
-**Note** all special characters like a space must be url encoded.
+**Note:** all special characters like a space must be url encoded.
 
 ##### example
 
-	curl -X GET http://<shock_host>[:<port>]/node/[?offset=<offset>&limit=<count>][&query&<tag>=<value>]
+	curl -X GET http://<shock_host>[:<port>]/node/[?skip=<skip>&limit=<count>][&query&<tag>=<value>]
 		
 ##### returns
 

pkg/darwin_amd64/github.com/nu7hatch/gouuid.a

@@ -0,0 +1,16 @@
+package conf
+
+import (
+	"flag"
+)
+
+// Command line options
+var (
+	PORT     = flag.Int("port", 8000, "port to listen on")
+	DATAROOT = flag.String("data", "", "data directory to store on disk files")
+	MONGODB  = flag.String("mongodb", "localhost", "hostname(s) of mongodb")
+)
+
+func init() {
+	flag.Parse()
+}

pkg/darwin_amd64/goweb.a

@@ -1,9 +1,9 @@
 package datastore
 
 import (
-	"fmt"
 	mgo "launchpad.net/mgo"
 	bson "launchpad.net/mgo/bson"
+	conf "shock/conf"
 )
 
 type db struct {
@@ -12,8 +12,7 @@ type db struct {
 }
 
 func DBConnect() (d *db, err error) {
-	MONGODBHOST := "localhost"
-	session, err := mgo.Dial(MONGODBHOST); if err != nil { return }
+	session, err := mgo.Dial(*conf.MONGODB); if err != nil { return }
 	d = &db{Nodes: session.DB("ShockDB").C("Nodes"), Session : session}	
 	return
 }
@@ -29,7 +28,6 @@ func (d *db) FindById(id string, result *Node) (err error) {
 }
 
 func (d *db) GetAll(q bson.M, results *Nodes) (err error) {
-	fmt.Println(q)
 	err = d.Nodes.Find(q).All(results)
 	return
 } 

pkg/darwin_amd64/shock/datastore.a

@@ -11,8 +11,11 @@ import (
 	"io/ioutil"
 	"strconv"
 	bson "launchpad.net/mgo/bson"
+	conf "shock/conf"
 )
 
+func init() {}
+
 // Node array type
 type Nodes []Node
 
@@ -247,8 +250,7 @@ func (node *Node) setId() {
 }
 
 func getPath(id string) (string) {
-	DATAROOT := "/Users/jared/projects/GoShockData"
-	return fmt.Sprintf("%s/%s/%s/%s/%s", DATAROOT, id[0:2], id[2:4], id[4:6], id)
+	return fmt.Sprintf("%s/%s/%s/%s/%s", *conf.DATAROOT, id[0:2], id[2:4], id[4:6], id)
 }
 
 func (node *Node) Path() (string) {

src/shock/conf/conf.go

@@ -39,7 +39,7 @@ type NodeController struct{}
 //            multipart-form containing: data file and/or attributes (json file)
 //            empty body
 func (cr *NodeController) Create(cx *goweb.Context) {
-	fmt.Println("POST: /node")
+	logReq(cx)
 	params, files, err := ParseMultipartForm(cx.Request)
 	if err != nil {
 		if err.Error() == "request Content-Type isn't multipart/form-data" {
@@ -70,13 +70,14 @@ func (cr *NodeController) Create(cx *goweb.Context) {
 
 // DELETE: /node/{id}
 func (cr *NodeController) Delete(id string, cx *goweb.Context) {
-	fmt.Printf("DELETE: /node/%s\n", id)	
+	logReq(cx)
 	cx.ResponseWriter.Header().Set("Content-Type", "application/json")
 	fmt.Fprintf(cx.ResponseWriter, "{ \"message\" : \"delete operation currently not supported\" }")
 }
 
 // DELETE: /node
 func (cr *NodeController) DeleteMany(cx *goweb.Context) {
+	logReq(cx)
 	cx.ResponseWriter.Header().Set("Content-Type", "application/json")
 	fmt.Fprintf(cx.ResponseWriter, "{ \"message\" : \"deletemany operation currently not supported\" }")
 }
@@ -86,7 +87,7 @@ func (cr *NodeController) DeleteMany(cx *goweb.Context) {
 //                ?pipe(&{func}={funcOptions})+)
 //                ?list={indexes||functions||parts&index={index}...}
 func (cr *NodeController) Read(id string, cx *goweb.Context) {
-	fmt.Printf("GET: /node/%s\n", id)	
+	logReq(cx)	
 	query := cx.Request.URL.Query()
 	_, download := query["download"]
 	_, pipe := query["pipe"]
@@ -120,16 +121,16 @@ func (cr *NodeController) Read(id string, cx *goweb.Context) {
 //           ?paginate[&limit={limit}&offset={offset}]
 //           ?query={queryString}[&paginate[&limit={limit}&offset={offset}]]
 func (cr *NodeController) ReadMany(cx *goweb.Context) {
-	fmt.Printf("GET: /node\n")
+	logReq(cx)
 	query := cx.Request.URL.Query()
 	l, hasLimit := query["limit"]
-	o, hasOffset := query["offset"]
+	o, hasOffset := query["skip"]
 	_, hasQuery := query["query"]
 
 	q := bson.M{}
 	nodes := new(ds.Nodes)
 
-	skip := map[string]int{"limit" : 1,"offset" : 1,"query" : 1}
+	skip := map[string]int{"limit" : 1,"skip" : 1,"query" : 1}
 	if hasQuery {
 		for key, val := range query {
 			_, s := skip[key]
@@ -140,7 +141,6 @@ func (cr *NodeController) ReadMany(cx *goweb.Context) {
 	}
 	if hasLimit || hasOffset {
 		var lim, off int
-		fmt.Printf("limit: %s, offset: %s\n", l[0], o[0])
 		if !hasLimit {
 			lim = 100
 		} else {
@@ -174,8 +174,7 @@ func (cr *NodeController) ReadMany(cx *goweb.Context) {
 //                ?index={type}[&options={options}]
 //                ?file[&part={part}] 
 func (cr *NodeController) Update(id string, cx *goweb.Context) {
-	fmt.Printf("PUT: /node/%s\n", id)	
-	
+	logReq(cx)	
 	node, err := ds.LoadNode(id); if err != nil {
 		// add node not found message
 		cx.RespondWithError(http.StatusBadRequest)
@@ -208,6 +207,7 @@ func (cr *NodeController) Update(id string, cx *goweb.Context) {
 
 // PUT: /node
 func (cr *NodeController) UpdateMany(cx *goweb.Context) {
+	logReq(cx)
 	cx.ResponseWriter.Header().Set("Content-Type", "application/json")
 	fmt.Fprintf(cx.ResponseWriter, "{ \"message\" : \"updatemany operation currently not supported\" }")
 }

src/shock/datastore/db.go

@@ -1,45 +1,15 @@
 package main
 
 import (
-	"flag"
 	"fmt"
 	"goweb"
+	conf "shock/conf"
 )
 
-// Command line options
-var (
-	PORT     = flag.Int("port", 8000, "the port to listen on")
-	DATAROOT = "/Users/jared/projects/GoShockData"
-)
-
-func init() {}
-
 func main() {
-	flag.Parse()	
 	goweb.ConfigureDefaultFormatters()
 	goweb.MapRest("/node", new(NodeController))
-	fmt.Printf("Shock port:%d...starting\n", *PORT)
-	goweb.ListenAndServe(":"+fmt.Sprintf("%d", *PORT))  
+	fmt.Printf("Shock port:%d...starting\n", *conf.PORT)
+	goweb.ListenAndServe(":"+fmt.Sprintf("%d", *conf.PORT))  
 
-}
-
-/*
-n, err := ds.CreateNode("/Users/jared/ANL/Apr_Day_pf.fas", "test.json")
-if err != nil {
-	fmt.Println("hells bells: " + err.String())
-}
-err = n.Save()
-if err != nil {
-	fmt.Println("hells bells: " + err.String())
-}
-fmt.Println(n.ToJson())
-fmt.Println(n.Path())
-*/
-
-/*
-n, err = LoadNode("bf6d2f5b9611cb4ebe28d79f25cd65f4")
-if err != nil {
-	fmt.Println("hells bells: " + err.String())
-}
-fmt.Println(n.ToJson())
-*/	
+}