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chg: [galaxyClusters] Doc and code reuse

pull/6120/head
mokaddem 2020-07-07 11:43:01 +02:00
parent 8bccb07968
commit 3460af16a7
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GPG Key ID: 164C473F627A06FA
1 changed files with 43 additions and 35 deletions
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78
app/Controller/GalaxyClustersController.php
View File

@ -171,7 +171,7 @@ class GalaxyClustersController extends AppController
}
/**
* @param mixed $id ID of the cluster
* @param mixed $id ID or UUID of the cluster
*/
public function view($id)
{
@ -334,7 +334,10 @@ class GalaxyClustersController extends AppController
$this->set('sharingGroups', $sgs);
$this->set('action', 'add');
}
/**
* @param mixed $id ID or UUID of the cluster
*/
public function edit($id)
{
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'edit', $throwErrors=true, $full=true);
@ -454,9 +457,12 @@ class GalaxyClustersController extends AppController
$this->render('add');
}
public function publish($clusterId)
/**
* @param mixed $id ID or UUID of the cluster
*/
public function publish($id)
{
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $clusterId, 'publish', $throwErrors=true, $full=false);
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'publish', $throwErrors=true, $full=false);
if ($cluster['GalaxyCluster']['published']) {
throw new MethodNotAllowedException(__('You can\'t publish a galaxy cluster that is already published'));
}
@ -494,9 +500,12 @@ class GalaxyClustersController extends AppController
}
}
public function unpublish($clusterId)
/**
* @param mixed $id ID or UUID of the cluster
*/
public function unpublish($id)
{
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $clusterId, 'publish', $throwErrors=true, $full=false);
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'publish', $throwErrors=true, $full=false);
if (!$cluster['GalaxyCluster']['published']) {
throw new MethodNotAllowedException(__('You can\'t unpublish a galaxy cluster that is not published'));
}
@ -688,28 +697,28 @@ class GalaxyClustersController extends AppController
$this->redirect($this->referer());
}
// TODO: Add support for custom cluster deletion
/**
* @param mixed $id ID or UUID of the cluster
*/
public function delete($id)
{
if ($this->request->is('post')) {
$result = false;
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'delete', $throwErrors=true, $full=false);
if (!empty($cluster)) {
$result = $this->GalaxyCluster->delete($id, true);
$galaxy_id = $cluster['GalaxyCluster']['galaxy_id'];
}
$result = $this->GalaxyCluster->delete($cluster['GalaxyCluster']['id'], true);
$galaxyId = $cluster['GalaxyCluster']['galaxy_id'];
if ($result) {
$message = 'Galaxy cluster successfuly deleted.';
$message = __('Galaxy cluster successfuly deleted.');
if ($this->_isRest()) {
return $this->RestResponse->saveSuccessResponse('GalaxyCluster', 'delete', $id, $this->response->type());
return $this->RestResponse->saveSuccessResponse('GalaxyCluster', 'delete', $cluster['GalaxyCluster']['id'], $this->response->type());
} else {
$this->Flash->success($message);
$this->redirect(array('controller' => 'galaxies', 'action' => 'view', $galaxy_id));
$this->redirect(array('controller' => 'galaxies', 'action' => 'view', $galaxyId));
}
} else {
$message = 'Galaxy cluster could not be deleted.';
$message = __('Galaxy cluster could not be deleted.');
if ($this->_isRest()) {
return $this->RestResponse->saveFailResponse('GalaxyCluster', 'delete', $id, $message, $this->response->type());
return $this->RestResponse->saveFailResponse('GalaxyCluster', 'delete', $cluster['GalaxyCluster']['id'], $message, $this->response->type());
} else {
$this->Flash->error($message);
$this->redirect(array('controller' => 'taxonomies', 'action' => 'index'));
@ -717,10 +726,10 @@ class GalaxyClustersController extends AppController
}
} else {
if ($this->request->is('ajax')) {
$this->set('id', $id);
$this->set('id', $cluster['GalaxyCluster']['id']);
$this->render('ajax/galaxy_cluster_delete_confirmation');
} else {
throw new MethodNotAllowedException('This function can only be reached via AJAX.');
throw new MethodNotAllowedException(__('This function can only be reached via AJAX.'));
}
}
}
@ -848,9 +857,12 @@ class GalaxyClustersController extends AppController
$this->render('cluster_matrix');
}
public function updateCluster($clusterId)
/**
* @param mixed $id ID or UUID of the cluster
*/
public function updateCluster($id)
{
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $clusterId, 'edit', $throwErrors=true, $full=true);
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'edit', $throwErrors=true, $full=true);
if ($cluster['GalaxyCluster']['default']) {
throw new MethodNotAllowedException(__('Default galaxy cluster cannot be updated'));
}
@ -887,7 +899,7 @@ class GalaxyClustersController extends AppController
$this->Flash->error($flashErrorMessage);
} else {
$this->Flash->success(__('Cluster updated to the newer version'));
$this->redirect(array('controller' => 'galaxy_clusters', 'action' => 'view', $clusterId));
$this->redirect(array('controller' => 'galaxy_clusters', 'action' => 'view', $id));
}
}
$missingElements = array();
@ -910,23 +922,21 @@ class GalaxyClustersController extends AppController
$this->set('forkVersion', $forkVersion);
$this->set('parentVersion', $parentVersion);
$this->set('newVersionAvailable', $parentVersion > $forkVersion);
$this->set('id', $clusterId);
$this->set('id', $cluster['GalaxyCluster']['id']);
$this->set('galaxy_id', $cluster['GalaxyCluster']['galaxy_id']);
$this->set('defaultCluster', $cluster['GalaxyCluster']['default']);
$this->set('cluster', $cluster);
}
/**
* @param mixed $id ID or UUID of the cluster
*/
public function viewRelations($id)
{
if (!$this->request->is('ajax')) {
throw new MethodNotAllowedException('This function can only be reached via AJAX.');
}
$conditions = array('conditions' => array('GalaxyCluster.id' => $id));
$cluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), $conditions, true);
if (empty($cluster)) {
throw new NotFoundException('Invalid galaxy cluster');
}
$cluster = $cluster[0];
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'view', $throwErrors=true, $full=true);
$existingRelations = $this->GalaxyCluster->GalaxyClusterRelation->getExistingRelationships();
$cluster = $this->GalaxyCluster->attachClusterToRelations($this->Auth->user(), $cluster);
@ -952,14 +962,12 @@ class GalaxyClustersController extends AppController
$this->set('distributionLevels', $distributionLevels);
}
public function viewRelationTree($clusterId)
/**
* @param mixed $id ID or UUID of the cluster
*/
public function viewRelationTree($id)
{
$options = array('conditions' => array('GalaxyCluster.id' => $clusterId));
$cluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), $options, true);
if (empty($cluster)) {
throw new NotFoundException('Invalid galaxy cluster');
}
$cluster = $cluster[0];
$cluster = $this->GalaxyCluster->fetchIfAuthorized($this->Auth->user(), $id, 'view', $throwErrors=true, $full=true);
$cluster = $this->GalaxyCluster->attachClusterToRelations($this->Auth->user(), $cluster);
App::uses('ClusterRelationsTreeTool', 'Tools');
$grapher = new ClusterRelationsTreeTool();