Merge pull request #298 from teharrison/master

several minor added features and bug fixes

RELEASE_NOTES.txt

@@ -1,4 +1,13 @@
+# v0.9.13
+
+- added option to copy attributes when doing node copy
+- added version_parts map to returned node
+- test mongo connection with short timeout on startup
+- add admin flag when creating new admin user
+- skip version updates on start if node collection is empty
+
 # v0.9.12
+
 - Fix to occasional deadlock with parts node locking
 
 # v0.9.11

VERSION

@@ -1 +1 @@
-0.9.12
+0.9.13

shock-server/conf/conf.go

@@ -20,6 +20,7 @@ var (
 	// Admin
 	ADMIN_EMAIL = ""
 	ADMIN_USERS = ""
+	AdminUsers  []string
 
 	// Permissions for anonymous user
 	ANON_READ   = true
@@ -97,6 +98,11 @@ func Initialize() {
 	// Admin
 	ADMIN_EMAIL, _ = c.String("Admin", "email")
 	ADMIN_USERS, _ = c.String("Admin", "users")
+	if ADMIN_USERS != "" {
+		for _, name := range strings.Split(ADMIN_USERS, ",") {
+			AdminUsers = append(AdminUsers, strings.TrimSpace(name))
+		}
+	}
 
 	// Access-Control
 	ANON_READ, _ = c.Bool("Anonymous", "read")

shock-server/db/db.go

@@ -10,7 +10,9 @@ import (
 )
 
 const (
-	DbTimeout = time.Duration(time.Second * 1200)
+	DbTimeout    = time.Duration(time.Second * 1200)
+	DialTimeout  = time.Duration(time.Second * 10)
+	DialAttempts = 3
 )
 
 var (
@@ -27,10 +29,25 @@ type connection struct {
 
 func Initialize() (err error) {
 	c := connection{}
+
+	// test connection
+	canDial := false
+	for i := 0; i < DialAttempts; i++ {
+		s, err := mgo.DialWithTimeout(conf.MONGODB_HOSTS, DialTimeout)
+		if err == nil {
+			s.Close()
+			canDial = true
+			break
+		}
+	}
+	if !canDial {
+		return errors.New(fmt.Sprintf("no reachable mongodb server(s) at %s", conf.MONGODB_HOSTS))
+	}
+
+	// get handle
 	s, err := mgo.DialWithTimeout(conf.MONGODB_HOSTS, DbTimeout)
 	if err != nil {
-		e := errors.New(fmt.Sprintf("no reachable mongodb server(s) at %s", conf.MONGODB_HOSTS))
-		return e
+		return errors.New(fmt.Sprintf("no reachable mongodb server(s) at %s", conf.MONGODB_HOSTS))
 	}
 	c.Session = s
 	c.DB = c.Session.DB(conf.MONGODB_DATABASE)

shock-server/node/node.go

@@ -25,7 +25,7 @@ type Node struct {
 	Attributes   interface{}       `bson:"attributes" json:"attributes"`
 	Indexes      Indexes           `bson:"indexes" json:"indexes"`
 	Acl          acl.Acl           `bson:"acl" json:"-"`
-	VersionParts map[string]string `bson:"version_parts" json:"-"`
+	VersionParts map[string]string `bson:"version_parts" json:"version_parts"`
 	Tags         []string          `bson:"tags" json:"tags"`
 	Revisions    []Node            `bson:"revisions" json:"-"`
 	Linkages     []linkage         `bson:"linkage" json:"linkage"`

shock-server/node/update.go

@@ -209,6 +209,11 @@ func (node *Node) Update(params map[string]string, files FormFiles) (err error)
 			node.Type = "copy"
 		}
 
+		// Copy node attributes
+		if _, copyAttributes := params["copy_attributes"]; copyAttributes {
+			node.Attributes = n.Attributes
+		}
+
 		// Copy node indexes
 		if _, copyIndex := params["copy_indexes"]; copyIndex && (len(n.Indexes) > 0) {
 			// loop through parent indexes

shock-server/user/user.go

@@ -6,7 +6,6 @@ import (
 	"github.com/MG-RAST/Shock/vendor/github.com/MG-RAST/golib/go-uuid/uuid"
 	mgo "github.com/MG-RAST/Shock/vendor/gopkg.in/mgo.v2"
 	"github.com/MG-RAST/Shock/vendor/gopkg.in/mgo.v2/bson"
-	"strings"
 )
 
 // Array of User
@@ -42,17 +41,12 @@ func Initialize() (err error) {
 	}
 
 	// This config parameter contains a string that should be a comma-separated list of users that are Admins.
-	adminUsers := strings.Split(conf.ADMIN_USERS, ",")
-	for _, v := range adminUsers {
+	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 {
 				return err
 			} else if info.Updated == 0 {
-				u, err := New(v, "", true)
-				if err != nil {
-					return err
-				}
-				if err := u.Save(); err != nil {
+				if _, err := New(v, "", true); err != nil {
 					return err
 				}
 			}
@@ -63,7 +57,8 @@ func Initialize() (err error) {
 
 func New(username string, password string, isAdmin bool) (u *User, err error) {
 	u = &User{Uuid: uuid.New(), Username: username, Password: password, Admin: isAdmin}
-	if err = u.Save(); err != nil {
+	err = u.Save()
+	if err != nil {
 		u = nil
 	}
 	return
@@ -105,7 +100,15 @@ func (u *User) SetMongoInfo() (err error) {
 		u.Admin = admin
 		return nil
 	} else {
+		// this is a new user
 		u.Uuid = uuid.New()
+		// check if user is on admin list, if so set as true
+		for _, v := range conf.AdminUsers {
+			if v == u.Username {
+				u.Admin = true
+				break
+			}
+		}
 		if err := u.Save(); err != nil {
 			return err
 		}

shock-server/util/util.go

@@ -15,7 +15,7 @@ const chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890"
 
 // Arrays to check for valid param and file form names for node creation and updating, and also acl modification.
 // Note: indexing and querying do not use functions that use these arrays and thus we don't have to include those field names.
-var validParams = []string{"action", "all", "archive_format", "attributes_str", "copy_data", "copy_indexes", "compression", "delete", "expiration", "file_name", "format", "ids", "index_name", "linkage", "operation", "owner", "parent_index", "parent_node", "parts", "path", "preserve_acls", "read", "remove_expiration", "source", "tags", "type", "unpack_node", "users", "write"}
+var validParams = []string{"action", "all", "archive_format", "attributes_str", "copy_attributes", "copy_data", "copy_indexes", "compression", "delete", "expiration", "file_name", "format", "ids", "index_name", "linkage", "operation", "owner", "parent_index", "parent_node", "parts", "path", "preserve_acls", "read", "remove_expiration", "source", "tags", "type", "unpack_node", "users", "write"}
 var validFiles = []string{"attributes", "subset_indices", "upload", "gzip", "bzip2"}
 var ValidUpload = []string{"upload", "gzip", "bzip2"}
 

shock-server/versions/versions.go

@@ -70,6 +70,18 @@ func RunVersionUpdates() (err error) {
 	confVersionACL, ok1 := conf.VERSIONS["ACL"]
 	dbVersionACL, ok2 := VersionMap["ACL"]
 
+	// skip version updates if database is empty / new shock deploy
+	session := db.Connection.Session.Copy()
+	c := session.DB(conf.MONGODB_DATABASE).C("Nodes")
+	num, err := c.Count()
+	session.Close()
+	if err != nil {
+		return err
+	}
+	if num == 0 {
+		return nil
+	}
+
 	// Upgrading databases with ACL schema before version 2
 	if (ok1 && confVersionACL >= 2) && (!ok2 || (ok2 && dbVersionACL < 2)) {
 		consoleReader := bufio.NewReader(os.Stdin)