/**
* {@inheritDoc}
*/
public function removeGene(Gene $gene, $recurse = true)
{
$this->genes->removeElement($gene);
if ($recurse === true) {
$gene->removeExon($this, false);
}
}
/**
* Set groups
*
* @param SimpleXMLElement $xml
* @return void
*/
private function setGroups(\SimpleXMLElement $xml)
{
$this->groups = new \Doctrine\Common\Collections\ArrayCollection();
foreach ($xml->children() as $groupXml) {
$this->groups->add(Group::createFromXml($groupXml));
}
}
/**
* {@inheritDoc}
*/
public function removemRNA(mRNA $mRNA, $recurse = true)
{
$this->mRNAs->removeElement($mRNA);
if ($recurse === true) {
$mRNA->removeUTR3($mRNA, false);
}
}
/**
* Set remote content
*
* @param SimpleXMLElement $xml
* @return void
*/
private function setRemoteContent(\SimpleXMLElement $xml)
{
$this->remoteContent = new \Doctrine\Common\Collections\ArrayCollection();
foreach ($xml->children() as $remoteContentXml) {
$this->remoteContent->add(RemoteContent::createFromXml($remoteContentXml));
}
}
/**
* Remove tag
*
* @param VIB\Bundle\BioBundle\Entity\DNA\Abstracts\FeatureTag $tag
* @param boolean $recurse
*/
public function removeTag(FeatureTag $tag, $recurse = true)
{
$this->tags->removeElement($tag);
if ($recurse === true) {
$tag->setFeature(null, false);
}
}
/**
* Remove intron
*
* @param VIB\Bundle\BioBundle\Entity\DNA\Feature\Gene\Intron $intron
* @param boolean $recurse
*/
public function removeIntron(Intron $intron, $recurse = true)
{
$this->introns->removeElement($intron);
if ($recurse === true) {
$intron->removeGene($this, false);
}
}
/**
* Set subjects
*
* @param SimpleXMLElement $xml
* @return void
*/
protected function setSubjects(\SimpleXMLElement $xml)
{
$this->subjects = new \Doctrine\Common\Collections\ArrayCollection();
foreach ($xml->subject as $subjectXml) {
$this->subjects->add(Subject::createFromXml($subjectXml));
}
}
/**
* Remove feature
*
* @param VIB\Bundle\BioBundle\Entity\DNA\Abstracts\Feature $feature
* @param boolean $recurse
*/
public function removeFeature(Feature $feature, $recurse = true)
{
$this->features->removeElement($feature);
if ($recurse === true) {
$feature->setSequence(null, false);
}
}
/**
* Set catalog refs
*
* @param SimpleXMLElement $xml
* @return void
*/
public function setCatalogRefs(\SimpleXMLElement $xml)
{
$this->catalogRefs = new \Doctrine\Common\Collections\ArrayCollection();
foreach ($xml->catalogRef as $catalogRefXml) {
$this->catalogRefs->add(new CatalogRef($catalogRefXml['href']));
}
}
/**
* Set refs
*
* @param SimpleXMLElement $xml
* @return void
*/
public function setRefs($xml)
{
$this->refs = new \Doctrine\Common\Collections\ArrayCollection();
foreach ($xml->children() as $refXml) {
if ($refXml->getName() === 'groupRef') {
$this->refs->add(new GroupRef($refXml['idref']));
} else {
if ($refXml->getName() === 'itemRef') {
$this->refs->add(ItemRef::createFromXml($refXml));
} else {
throw new \InvalidArgumentException("Expected group or item ref, got '{$refXml->getName()}'");
}
}
}
}
/**
* Add item for this participant
*
* @param Doctrine\Common\Collections\Collection $items
* @return Participant
*/
public function addItems(Item $item)
{
if (!$this->items->contains($item)) {
$this->items->add($item);
}
return $this;
}
/**
* @param string $value
* @param Doctrine\Common\Collections\Collection $collection
*/
public function reverseTransform($value, $collection)
{
if (strlen(trim($value)) == 0) {
// don't check for collection count, a straight clear doesnt initialize the collection
$collection->clear();
return $collection;
}
$className = $this->getOption('className');
$values = explode($this->getOption('separator'), $value);
if ($this->getOption('trim') === true) {
$values = array_map('trim', $values);
}
/* @var $em Doctrine\ORM\EntityManager */
$em = $this->getOption('em');
$reflField = $em->getClassMetadata($className)->getReflectionProperty($this->getOption('fieldName'));
// 1. removing elements that are not yet present anymore
foreach ($collection as $object) {
$uniqueIdent = $reflField->getValue($object);
$key = \array_search($uniqueIdent, $values);
if ($key === false) {
$collection->removeElement($object);
} else {
// found in the collection, no need to do anything with it so remove it
unset($values[$key]);
}
}
// 2. add elements that are known to the EntityManager but newly connected, query them from the repository
if (count($values)) {
$dql = "SELECT o FROM " . $className . " o WHERE o." . $this->getOption('fieldName') . " IN (";
$query = $em->createQuery();
$needles = array();
$i = 0;
foreach ($values as $val) {
$query->setParameter(++$i, $val);
$needles[] = "?" . $i;
}
$dql .= implode(",", $needles) . ")";
$query->setDql($dql);
$newElements = $query->getResult();
foreach ($newElements as $object) {
$collection->add($object);
$uniqueIdent = $reflField->getValue($object);
$key = \array_search($uniqueIdent, $values);
unset($values[$key]);
}
}
// 3. new elements that are not in the repository have to be created and persisted then attached:
if (count($values)) {
$callback = $this->getOption('createInstanceCallback');
if (!$callback || !\is_callable($callback)) {
throw new TransformationFailedException("Cannot transform list of identifiers, because a new " . "element was detected and it is unknown how to create an instance of this element.");
}
foreach ($values as $newValue) {
$newInstance = \call_user_func($callback, $newValue);
if (!$newInstance instanceof $className) {
throw new TransformationFailedException("Error while trying to create a new instance for " . "the identifier '" . $newValue . "'. No new instance was created.");
}
$collection->add($newInstance);
$em->persist($newInstance);
}
}
return $collection;
}
/**
* Remove detailIndicateurs
*
* @param \AppBundle\Entity\DetailIndicateur $detailIndicateurs
*/
public function removeDetailIndicateur(\AppBundle\Entity\DetailIndicateur $detailIndicateurs)
{
$this->detailIndicateurs->removeElement($detailIndicateurs);
}
/**
* Get view.
*
* @return object
*/
public function getView()
{
try {
$view = new ArticleView(array('number' => $this->number, 'language' => $this->language->getCode(), 'languageId' => $this->language->getId(), 'title' => $this->name, 'updated' => $this->updated, 'published' => $this->published, 'indexed' => $this->indexed, 'onFrontPage' => $this->onFrontPage, 'onSection' => $this->onSection, 'type' => $this->type, 'webcode' => $this->getWebcode(), 'publication_number' => $this->publication ? $this->publication->getId() : null, 'issue_number' => $this->issue ? $this->issue->getNumber() : null, 'section_number' => $this->section ? $this->section->getNumber() : null, 'keywords' => array_filter(explode(',', $this->keywords))));
} catch (EntityNotFoundException $e) {
return new ArticleView();
}
$view->authors = $this->authors->map(function ($author) {
return $author->getView()->name;
})->toArray();
$view->topics = $this->topics->map(function ($topic) {
return $topic->getView()->name;
})->toArray();
$this->addFields($view);
return $view;
}
/**
* Add ban of a champion for this game
*
* @param Doctrine\Common\Collections\Collection $bans
* @return Game
*/
public function addBans(Champion $ban)
{
if (!$this->bans->contains($ban)) {
$this->bans->add($ban);
}
return $this;
}
/**
* (non-PHPdoc)
* @see \Rizza\CalendarBundle\Model\CalendarInterface::removeEvent()
*/
public function removeEvent(EventInterface $event)
{
if ($this->events->contains($event)) {
$this->events->removeElement($event);
}
}
/**
* Is polycistronic
*
* @return boolean
*/
public function isPolycistronic()
{
return $this->genes->count() > 1 ? true : false;
}
/**
* Remove users
*
* @param Nmpolo\RestBundle\Entity\User $users
*/
public function removeUser(\Nmpolo\RestBundle\Entity\User $users)
{
$this->users->removeElement($users);
}
