I have following entities with many to many relation: User

 /**
 * @ORM\ManyToMany(targetEntity = "Role", mappedBy = "users")
 *
 * @var ArrayCollection $roles;
 */
 private $roles;

Role

 /**
 * @ORM\ManyToMany(targetEntity = "User", inversedBy = "roles")
 * 
 * @var ArrayCollection $users
 */
 protected $users;

Doctrine generated 3 tables: user role user_role

Then I added data fixture:

class FixtureLoader implements FixtureInterface {
 public function load(ObjectManager $manager) {
 $role = new Role();
 $role->setName('Администратор');
 $role->setRole('ROLE_ADMIN');
 $manager->persist($role);
 $user = new User();
 $user->setUsername('ahmed');
 $user->setEmail('[email protected]');
 $user->setSalt(md5(time()));
 $user->setIsActive(false);
 $encoder = new MessageDigestPasswordEncoder('sha512',true,10);
 $password = $encoder->encodePassword('admin', $user->getSalt());
 $user->setPassword($password);
 //$user->getUserRoles()->add($role);
 $user->addRole($role);
 $manager->persist($user);
 $manager->flush(); 
 }
}

When I load it using console, only 2 tables populated with data, but user_role table, which keep manytomany relations is empty.

How to solve this? Or I need to populate it myself?

/**
 * Umahanov\UserBundle\Entity\User
 *
 * @ORM\Entity
 * @ORM\Table(name="user")
 */
class User implements UserInterface, \Serializable {
 /**
 * @var integer
 *
 * @ORM\Column(name="id", type="integer")
 * @ORM\Id
 * @ORM\GeneratedValue(strategy="AUTO")
 */
 private $id;
 /**
 * @ORM\ManyToMany(targetEntity = "Role", mappedBy = "users")
 * @ORM\JoinTable(name="user_role",
 * joinColumns={@ORM\JoinColumn(name="user_id", referencedColumnName="id")},
 * inverseJoinColumns={@ORM\JoinColumn(name="role_id", referencedColumnName="id")}
 * )
 * @var ArrayCollection $roles;
 */
 private $roles;
 /**
 * @var string
 *
 * @ORM\Column(name="username", type="string", length=25, unique=true)
 */
 private $username;
 /**
 * @var string
 *
 * @ORM\Column(name="salt", type="string", length=32)
 */
 private $salt;
 /**
 * @var string
 *
 * @ORM\Column(name="password", type="string", length=88)
 */
 private $password;
 /**
 * @var string
 *
 * @ORM\Column(name="email", type="string", length=60, unique=true)
 */
 private $email;
 /**
 * @var boolean
 *
 * @ORM\Column(name="is_active", type="boolean")
 */
 private $isActive;
 public function __construct() {
 $this->isActive = false;
 $this->salt = md5(uniqid(null, true));
 $this->roles = new ArrayCollection();
 }
 /**
 * Get roles (array)
 *
 * @return array
 */
 public function getRoles() {
 return $this->roles->toArray();
 }
 /**
 * @inheritDoc
 */
 public function eraseCredentials() {
 }
 /**
 * @see \Serializable::serialize()
 */
 public function serialize() {
 return serialize(array(
 $this->id,
 ));
 }
 /**
 * @see \Serializable::unserialize()
 */
 public function unserialize($serialized) {
 list (
 $this->id,
 ) = unserialize($serialized);
 }
 /**
 * Get id
 *
 * @return integer
 */
 public function getId() {
 return $this->id;
 }
 /**
 * Set username
 *
 * @param string $username
 * @return User
 */
 public function setUsername($username) {
 $this->username = $username;
 return $this;
 }
 /**
 * Get username
 *
 * @return string
 */
 public function getUsername() {
 return $this->username;
 }
 /**
 * Set salt
 *
 * @param string $salt
 * @return User
 */
 public function setSalt($salt) {
 $this->salt = $salt;
 return $this;
 }
 /**
 * Get salt
 *
 * @return string
 */
 public function getSalt() {
 return $this->salt;
 }
 /**
 * Set password
 *
 * @param string $password
 * @return User
 */
 public function setPassword($password) {
 $this->password = $password;
 return $this;
 }
 /**
 * Get password
 *
 * @return string
 */
 public function getPassword() {
 return $this->password;
 }
 /**
 * Set email
 *
 * @param string $email
 * @return User
 */
 public function setEmail($email) {
 $this->email = $email;
 return $this;
 }
 /**
 * Get email
 *
 * @return string
 */
 public function getEmail() {
 return $this->email;
 }
 /**
 * Set is_active
 *
 * @param boolean $isActive
 * @return User
 */
 public function setIsActive($isActive) {
 $this->isActive = $isActive;
 return $this;
 }
 /**
 * Get is_active
 *
 * @return boolean
 */
 public function getIsActive() {
 return $this->isActive;
 }
 /**
 * Сравнивает пользователя с другим пользователем и определяет
 * один и тот же ли это человек.
 * 
 * @param UserInterface $user The user
 * @return boolean True if equal, false othwerwise.
 */
 public function equals(UserInterface $user) {
 return md5($this->getUsername()) == md5($user->getUsername());
 }
 /**
 * Add roles
 *
 * @param \Umahanov\UserBundle\Entity\Role $roles
 * @return User
 */
 public function addRole(\Umahanov\UserBundle\Entity\Role $roles) {
 $this->roles[] = $roles;
 return $this;
 }
 /**
 * Remove roles
 *
 * @param \Umahanov\UserBundle\Entity\Role $roles
 */
 public function removeRole(\Umahanov\UserBundle\Entity\Role $roles) {
 $this->roles->removeElement($roles);
 }
}

And here is role:

/**
 * @ORM\Entity
 * @ORM\Table(name="role")
 */
class Role implements RoleInterface {
 /**
 * @ORM\Id
 * @ORM\Column(type="integer")
 * @ORM\GeneratedValue(strategy="AUTO")
 * 
 * @var integer $id
 */
 protected $id;
 /**
 * @ORM\Column(type="string", length=255)
 * 
 * @var string $name
 */
 protected $name;
 /**
 * @ORM\Column(type="string", length=255)
 * 
 * @var string $role
 */
 protected $role; 
 /**
 * @ORM\Column(type="datetime", name="created_at")
 *
 * @var DateTime $createdAt;
 */
 protected $createdAt;
 public function getRole() {
 return $this->role;
 }
 /**
 * @ORM\ManyToMany(targetEntity = "User", inversedBy = "roles")
 * 
 * @var ArrayCollection $users
 */
 protected $users;
 public function getCreatedAt() {
 return $this->createdAt;
 }
 public function __construct() {
 $this->createdAt = new \DateTime();
 $this->users = new ArrayCollection();
 }
 /**
 * Get id
 *
 * @return integer 
 */
 public function getId()
 {
 return $this->id;
 }
 /**
 * Set name
 *
 * @param string $name
 * @return Role
 */
 public function setName($name)
 {
 $this->name = $name;
 return $this;
 }
 /**
 * Get name
 *
 * @return string 
 */
 public function getName()
 {
 return $this->name;
 }
 /**
 * Set role
 *
 * @param string $role
 * @return Role
 */
 public function setRole($role)
 {
 $this->role = $role;
 return $this;
 }
 /**
 * Set createdAt
 *
 * @param \DateTime $createdAt
 * @return Role
 */
 public function setCreatedAt($createdAt)
 {
 $this->createdAt = $createdAt;
 return $this;
 }
 /**
 * Add users
 *
 * @param \Umahanov\UserBundle\Entity\User $users
 * @return Role
 */
 public function addUser(\Umahanov\UserBundle\Entity\User $users)
 {
 $this->users[] = $users;
 return $this;
 }
 /**
 * Remove users
 *
 * @param \Umahanov\UserBundle\Entity\User $users
 */
 public function removeUser(\Umahanov\UserBundle\Entity\User $users)
 {
 $this->users->removeElement($users);
 }
 /**
 * Get users
 *
 * @return \Doctrine\Common\Collections\Collection 
 */
 public function getUsers()
 {
 return $this->users;
 }
}