Merge pull request #336 from teharrison/master

updates

shock-server/auth/auth.go

@@ -3,7 +3,6 @@ package auth
 
 import (
 	"errors"
-	//"github.com/MG-RAST/Shock/shock-server/auth/basic"
 	"github.com/MG-RAST/Shock/shock-server/auth/globus"
 	"github.com/MG-RAST/Shock/shock-server/auth/oauth"
 	"github.com/MG-RAST/Shock/shock-server/conf"

shock-server/auth/globus/globus.go

@@ -8,7 +8,6 @@ import (
 	"github.com/MG-RAST/Shock/shock-server/auth/basic"
 	"github.com/MG-RAST/Shock/shock-server/conf"
 	e "github.com/MG-RAST/Shock/shock-server/errors"
-	"github.com/MG-RAST/Shock/shock-server/logger"
 	"github.com/MG-RAST/Shock/shock-server/user"
 	"io/ioutil"
 	"net/http"
@@ -94,13 +93,14 @@ func fetchProfile(t string) (u *user.User, err error) {
 	client := &http.Client{
 		Transport: &http.Transport{TLSClientConfig: &tls.Config{InsecureSkipVerify: true}},
 	}
-	//logger.Error("got here")
-	req, err := http.NewRequest("GET", conf.AUTH_GLOBUS_PROFILE_URL+"/"+clientId(t), nil)
-	//logger.Error("URL: " + conf.AUTH_GLOBUS_PROFILE_URL+"/"+clientId(t))
+	cid, err := clientId(t)
+	if err != nil {
+		return nil, err
+	}
+	req, err := http.NewRequest("GET", conf.AUTH_GLOBUS_PROFILE_URL+"/"+cid, nil)
 	if err != nil {
 		return nil, errors.New("HTTP GET: " + err.Error())
 	}
-	//req.Header.Add("Authorization", t)
 	req.Header.Add("Authorization", "Globus-Goauthtoken "+t)
 	if resp, err := client.Do(req); err == nil {
 		defer resp.Body.Close()
@@ -129,10 +129,11 @@ func fetchProfile(t string) (u *user.User, err error) {
 	return
 }
 
-func clientId(t string) string {
+func clientId(t string) (c string, err error) {
+	// test for old format first
 	for _, part := range strings.Split(t, "|") {
 		if kv := strings.Split(part, "="); kv[0] == "client_id" {
-			return kv[1]
+			return kv[1], nil
 		}
 	}
 	//if we get here then we have a new style token and need to make a call to look up the
@@ -141,38 +142,28 @@ func clientId(t string) string {
 		Transport: &http.Transport{TLSClientConfig: &tls.Config{InsecureSkipVerify: true}},
 	}
 	req, err := http.NewRequest("GET", conf.AUTH_GLOBUS_TOKEN_URL, nil)
-	//logger.Error("URL: " + conf.AUTH_GLOBUS_TOKEN_URL)
-
 	if err != nil {
-		logger.Error("Failed contact with auth server")
-		return ""
+		return "", errors.New("HTTP GET: " + err.Error())
 	}
 	req.Header.Add("X-Globus-Goauthtoken", t)
 	if resp, err := client.Do(req); err == nil {
-		//logger.Error("resp: " + resp.Status)
 		defer resp.Body.Close()
 		if resp.StatusCode == http.StatusCreated || resp.StatusCode == http.StatusOK {
 			if body, err := ioutil.ReadAll(resp.Body); err == nil {
 				var dat map[string]interface{}
 				if err = json.Unmarshal(body, &dat); err != nil {
-					logger.Error("Unable to parse response from auth server")
-					return ""
+					return "", errors.New("JSON Unmarshal: " + err.Error())
 				} else {
-					return dat["client_id"].(string)
+					return dat["client_id"].(string), nil
 				}
 			}
 		} else if resp.StatusCode == http.StatusForbidden {
-			logger.Error("Auth request rejected as Forbidden")
-			return ""
+			return "", errors.New(e.InvalidAuth)
 		} else {
-			err_str := "Authentication failed in clientID: Unexpected response status: " + resp.Status
-			logger.Error(err_str)
-			return ""
+			return "", errors.New("Authentication failed: Unexpected response status: " + resp.Status)
 		}
 	} else {
-		logger.Error("Undefined auth error 1")
-		return ""
+		return "", err
 	}
-	logger.Error("Undefined auth error 2")
-	return ""
+	return
 }

shock-server/conf/conf.go

@@ -2,11 +2,11 @@
 package conf
 
 import (
-	//"flag"
 	"errors"
 	"fmt"
 	"github.com/MG-RAST/golib/goconfig/config"
 	"os"
+	"path/filepath"
 	"strconv"
 	"strings"
 )
@@ -19,6 +19,12 @@ type idxOpts struct {
 
 const VERSION string = "[% VERSION %]"
 
+var VERSIONS = map[string]int{
+	"ACL":  2,
+	"Auth": 1,
+	"Node": 4,
+}
+
 var LOG_OUTPUTS = [3]string{"file", "console", "both"}
 
 var (
@@ -88,9 +94,6 @@ var (
 	SSL_KEY  string
 	SSL_CERT string
 
-	// Versions
-	VERSIONS = make(map[string]int)
-
 	PRINT_HELP   bool // full usage
 	SHOW_HELP    bool // simple usage
 	SHOW_VERSION bool
@@ -207,11 +210,6 @@ func getConfiguration(c *config.Config) (c_store *Config_store, err error) {
 	// Admin
 	c_store.AddString(&ADMIN_EMAIL, "", "Admin", "email", "", "")
 	c_store.AddString(&ADMIN_USERS, "", "Admin", "users", "", "")
-	if ADMIN_USERS != "" {
-		for _, name := range strings.Split(ADMIN_USERS, ",") {
-			AdminUsers = append(AdminUsers, strings.TrimSpace(name))
-		}
-	}
 
 	// Access-Control
 	c_store.AddBool(&ANON_READ, true, "Anonymous", "read", "", "")
@@ -290,10 +288,8 @@ func getConfiguration(c *config.Config) (c_store *Config_store, err error) {
 
 	// SSL
 	c_store.AddBool(&SSL, false, "SSL", "enable", "", "")
-	if SSL {
-		c_store.AddString(&SSL_KEY, "", "SSL", "key", "", "")
-		c_store.AddString(&SSL_CERT, "", "SSL", "cert", "", "")
-	}
+	c_store.AddString(&SSL_KEY, "", "SSL", "key", "", "")
+	c_store.AddString(&SSL_CERT, "", "SSL", "cert", "", "")
 
 	// Other - thses option are CLI only
 	c_store.AddString(&RELOAD, "", "Other", "reload", "path or url to shock data. WARNING this will drop all current data.", "")
@@ -303,16 +299,18 @@ func getConfiguration(c *config.Config) (c_store *Config_store, err error) {
 	c_store.AddBool(&PRINT_HELP, false, "Other", "fullhelp", "show detailed usage without \"--\"-prefixes", "")
 	c_store.AddBool(&SHOW_HELP, false, "Other", "help", "show usage", "")
 
-	VERSIONS["ACL"] = 2
-	VERSIONS["Auth"] = 1
-	VERSIONS["Node"] = 4
-
 	c_store.Parse()
-
 	return
 }
 
 func parseConfiguration() (err error) {
+	// get admin users
+	if ADMIN_USERS != "" {
+		for _, name := range strings.Split(ADMIN_USERS, ",") {
+			AdminUsers = append(AdminUsers, strings.TrimSpace(name))
+		}
+	}
+
 	// parse OAuth settings if used
 	if AUTH_OAUTH_URL_STR != "" && AUTH_OAUTH_BEARER_STR != "" {
 		ou := strings.Split(AUTH_OAUTH_URL_STR, ",")
@@ -325,6 +323,7 @@ func parseConfiguration() (err error) {
 		}
 		OAUTH_DEFAULT = ou[0] // first url is default for "oauth" bearer token
 	}
+
 	// validate LOG_OUTPUT
 	vaildLogout := false
 	for _, logout := range LOG_OUTPUTS {
@@ -335,5 +334,20 @@ func parseConfiguration() (err error) {
 	if !vaildLogout {
 		return errors.New("invalid option for logoutput, use one of: file, console, both")
 	}
+
+	// clean paths
+	PATH_SITE = cleanPath(PATH_SITE)
+	PATH_DATA = cleanPath(PATH_DATA)
+	PATH_LOGS = cleanPath(PATH_LOGS)
+	PATH_LOCAL = cleanPath(PATH_LOCAL)
+	PATH_PIDFILE = cleanPath(PATH_PIDFILE)
+
 	return
 }
+
+func cleanPath(p string) string {
+	if p != "" {
+		p, _ = filepath.Abs(p)
+	}
+	return p
+}

shock-server/user/user.go

@@ -40,15 +40,15 @@ func Initialize() (err error) {
 		return err
 	}
 
-	// This config parameter contains a string that should be a comma-separated list of users that are Admins.
+	// process list of amin users from config, create those that are missing
 	for _, v := range conf.AdminUsers {
-		if info, err := c.UpdateAll(bson.M{"username": v}, bson.M{"$set": bson.M{"shock_admin": true}}); err != nil {
-			if err != nil {
+		info, err := c.UpdateAll(bson.M{"username": v}, bson.M{"$set": bson.M{"shock_admin": true}})
+		if err != nil {
+			return err
+		}
+		if info.Updated == 0 {
+			if _, err := New(v, "", true); err != nil {
 				return err
-			} else if info.Updated == 0 {
-				if _, err := New(v, "", true); err != nil {
-					return err
-				}
 			}
 		}
 	}