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chg: [galaxyCluster] Centralized permission checks and code refactoring

pull/6120/head
mokaddem 2020-06-18 15:26:03 +02:00
parent d4b1ecb088
commit 7590408dc3
No known key found for this signature in database
GPG Key ID: 164C473F627A06FA
4 changed files with 124 additions and 269 deletions
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1
app/Controller/Component/ACLComponent.php
View File

@ -265,7 +265,6 @@ class ACLComponent extends Component
'edit' => array('perm_galaxy_editor'),
'index' => array('*'),
'view' => array('*'),
'fetchClustersFromRelation' => array('*'),
),
'galaxyElements' => array(
'index' => array('*')

58
app/Controller/GalaxyClusterRelationsController.php
View File

@ -122,14 +122,12 @@ class GalaxyClusterRelationsController extends AppController
$relation['GalaxyClusterRelation']['sharing_group_id'] = null;
}
$clusters = $this->fetchClustersFromRelation($relation);
$clusterSource = $clusters['clusterSource'];
$clusterTarget = $clusters['clusterTarget'];
$clusterSource = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $relation['GalaxyClusterRelation']['galaxy_cluster_uuid'], array('edit', 'publish'), $throwErrors=false, $full=false);
if (isset($clusterSource['authorized']) && !$clusterSource['authorized']) {
$errors = array($clusterSource['error']);
}
$errors = array();
if (!$this->Auth->user()['Role']['perm_galaxy_editor']) {
$errors = array(__('Invalid permssions'));
}
if (!empty($relation['GalaxyClusterRelation']['tags'])) {
$tags = explode(',', $relation['GalaxyClusterRelation']['tags']);
@ -139,11 +137,7 @@ class GalaxyClusterRelationsController extends AppController
$relation['GalaxyClusterRelation' ]['tags'] = array();
}
if ($this->Auth->user()['Role']['perm_site_admin'] || $clusterSource['SourceCluster']['org_id'] == $this->Auth->user()['org_id']) {
$errors = $this->GalaxyClusterRelation->saveRelation($this->Auth->user(), $clusterSource['SourceCluster'], $relation);
} else {
$errors = array(__('Only the owner organisation of the source cluster can use it as a source'));
}
$errors = $this->GalaxyClusterRelation->saveRelation($this->Auth->user(), $clusterSource['SourceCluster'], $relation);
if (empty($errors)) {
$message = __('Relationship added.');
@ -219,13 +213,7 @@ class GalaxyClusterRelationsController extends AppController
$relation['GalaxyClusterRelation']['sharing_group_id'] = null;
}
$clusters = $this->fetchClustersFromRelation($relation);
$clusterSource = $clusters['clusterSource'];
$errors = array();
if (!$this->Auth->user()['Role']['perm_galaxy_editor']) {
$errors = array(__('Invalid permssions'));
}
$clusterSource = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $relation['GalaxyClusterRelation']['galaxy_cluster_uuid'], array('edit', 'publish'), $throwErrors=false, $full=false);
if (!empty($relation['GalaxyClusterRelation']['tags'])) {
$tags = explode(',', $relation['GalaxyClusterRelation']['tags']);
@ -235,11 +223,7 @@ class GalaxyClusterRelationsController extends AppController
$relation['GalaxyClusterRelation' ]['tags'] = array();
}
if ($this->Auth->user()['Role']['perm_site_admin'] || $clusterSource['SourceCluster']['org_id'] == $this->Auth->user()['org_id']) {
$errors = $this->GalaxyClusterRelation->editRelation($this->Auth->user(), $relation);
} else {
$errors = array(__('Only the owner organisation of the source cluster can use it as a source'));
}
$errors = $this->GalaxyClusterRelation->editRelation($this->Auth->user(), $relation);
if (empty($errors)) {
$message = __('Relationship added.');
@ -278,8 +262,9 @@ class GalaxyClusterRelationsController extends AppController
if ($this->request->is('post')) {
$relation = $this->GalaxyClusterRelation->fetchRelations($this->Auth->user(), array('conditions' => array('id' => $id)));
if (empty($relation)) {
throw new NotFoundException(__('Target cluster not found.'));
throw new NotFoundException(__('Relation not found.'));
}
$clusterSource = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $relation['GalaxyClusterRelation']['galaxy_cluster_uuid'], array('edit', 'publish'), $throwErrors=true, $full=false);
$result = $this->GalaxyClusterRelation->delete($id, true);
if ($result) {
$this->GalaxyClusterRelation->SourceCluster->unpublish($clusterSource['SourceCluster']['id']);
@ -301,29 +286,4 @@ class GalaxyClusterRelationsController extends AppController
}
}
}
public function fetchClustersFromRelation($relation)
{
// Fetch cluster source and adapt IDs
$conditions = array();
$conditions['uuid'] = $relation['GalaxyClusterRelation']['galaxy_cluster_uuid'];
$clusterSource = $this->GalaxyClusterRelation->SourceCluster->fetchGalaxyClusters($this->Auth->user(), array('conditions' => $conditions), false);
if (empty($clusterSource)) {
throw new NotFoundException(__('Source cluster not found.'));
}
$clusterSource = $clusterSource[0];
// Fetch cluster target and adapt IDs
$conditions['uuid'] = $relation['GalaxyClusterRelation']['referenced_galaxy_cluster_uuid'];
$clusterTarget = $this->GalaxyClusterRelation->TargetCluster->fetchGalaxyClusters($this->Auth->user(), array('conditions' => $conditions), false);
if (empty($clusterTarget)) {
throw new NotFoundException(__('Target cluster not found.'));
}
$clusterTarget = $clusterTarget[0];
return array(
'clusterSource' => $clusterSource,
'clusterTarget' => $clusterTarget,
'relation' => $relation,
);
}
}

123
app/Controller/GalaxyClustersController.php
View File

@ -347,25 +347,7 @@ class GalaxyClustersController extends AppController
public function edit($id)
{
if (Validation::uuid($id)) {
$temp = $this->GalaxyCluster->find('first', array(
'recursive' => -1,
'fields' => array('GalaxyCluster.id', 'GalaxyCluster.uuid'),
'conditions' => array('GalaxyCluster.uuid' => $id)
));
if ($temp === null) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$id = $temp['GalaxyCluster']['id'];
} elseif (!is_numeric($id)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$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 = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $id, 'edit', $throwErrors=true, $full=true);
if ($cluster['GalaxyCluster']['default']) {
throw new MethodNotAllowedException('Default galaxy cluster cannot be edited');
}
@ -382,16 +364,20 @@ class GalaxyClustersController extends AppController
$this->loadModel('SharingGroup');
$sgs = $this->SharingGroup->fetchAllAuthorised($this->Auth->user(), 'name', 1);
$origCluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), array(
'conditions' => array('uuid' => $cluster['GalaxyCluster']['extends_uuid']),
), false);
if (!empty($cluster['GalaxyCluster']['extends_uuid'])) {
$forkedCluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), array(
'conditions' => array('uuid' => $cluster['GalaxyCluster']['extends_uuid']),
), false);
} else {
$forkedCluster = array();
}
if (!empty($origCluster)) {
$origCluster = $origCluster[0];
if (!empty($forkedCluster)) {
$forkedCluster = $forkedCluster[0];
$this->set('forkUuid', $cluster['GalaxyCluster']['extends_uuid']);
$origClusterMeta = $origCluster['GalaxyCluster'];
$this->set('origCluster', $origCluster);
$this->set('origClusterMeta', $origClusterMeta);
$forkedClusterMeta = $forkedCluster['GalaxyCluster'];
$this->set('origCluster', $forkedCluster);
$this->set('origClusterMeta', $forkedClusterMeta);
}
if ($this->request->is('post') || $this->request->is('put')) {
$cluster = $this->request->data;
@ -476,32 +462,11 @@ class GalaxyClustersController extends AppController
$this->render('add');
}
public function publish($cluster_id)
public function publish($clusterId)
{
if (Validation::uuid($cluster_id)) {
$temp = $this->GalaxyCluster->find('first', array(
'recursive' => -1,
'fields' => array('GalaxyCluster.id', 'GalaxyCluster.uuid'),
'conditions' => array('GalaxyCluster.uuid' => $cluster_id)
));
if ($temp === null) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$cluster_id = $temp['GalaxyCluster']['id'];
} elseif (!is_numeric($cluster_id)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$conditions = array('conditions' => array('GalaxyCluster.id' => $cluster_id));
$cluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), $conditions, false);
if (empty($cluster)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$cluster = $cluster[0];
if ($cluster['GalaxyCluster']['orgc_id'] != $this->Auth->user('org_id')) {
throw new MethodNotAllowedException(__('You don\'t have the permission to do that.'));
}
$cluster = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $clusterId, 'publish', $throwErrors=true, $full=false);
if ($cluster['GalaxyCluster']['published']) {
throw new MethodNotAllowedException(__('You can\'t publish an galaxy cluster that is already published'));
throw new MethodNotAllowedException(__('You can\'t publish a galaxy cluster that is already published'));
}
if ($cluster['GalaxyCluster']['default']) {
throw new MethodNotAllowedException(__('Default galaxy cluster cannot be published'));
@ -532,32 +497,11 @@ class GalaxyClustersController extends AppController
}
}
public function unpublish($cluster_id)
public function unpublish($clusterId)
{
if (Validation::uuid($cluster_id)) {
$temp = $this->GalaxyCluster->find('first', array(
'recursive' => -1,
'fields' => array('GalaxyCluster.id', 'GalaxyCluster.uuid'),
'conditions' => array('GalaxyCluster.uuid' => $cluster_id)
));
if ($temp === null) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$cluster_id = $temp['GalaxyCluster']['id'];
} elseif (!is_numeric($cluster_id)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$conditions = array('conditions' => array('GalaxyCluster.id' => $cluster_id));
$cluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), $conditions, false);
if (empty($cluster)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$cluster = $cluster[0];
if ($cluster['GalaxyCluster']['orgc_id'] != $this->Auth->user('org_id')) {
throw new MethodNotAllowedException(__('You don\'t have the permission to do that.'));
}
$cluster = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $clusterId, 'publish', $throwErrors=true, $full=false);
if (!$cluster['GalaxyCluster']['published']) {
throw new MethodNotAllowedException(__('You can\'t unpublish an galaxy cluster that is already published'));
throw new MethodNotAllowedException(__('You can\'t unpublish a galaxy cluster that is not published'));
}
if ($cluster['GalaxyCluster']['default']) {
throw new MethodNotAllowedException(__('Default galaxy cluster cannot be unpublished'));
@ -752,10 +696,10 @@ class GalaxyClustersController extends AppController
{
if ($this->request->is('post')) {
$result = false;
$galaxy_cluster = $this->GalaxyCluster->isAuthorizedTo($user, $id, 'edit');
if (!empty($galaxy_cluster)) {
$cluster = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $id, 'delete', $throwErrors=true, $full=false);
if (!empty($cluster)) {
$result = $this->GalaxyCluster->delete($id, true);
$galaxy_id = $galaxy_cluster['GalaxyCluster']['galaxy_id'];
$galaxy_id = $cluster['GalaxyCluster']['galaxy_id'];
}
if ($result) {
$message = 'Galaxy cluster successfuly deleted.';
@ -904,25 +848,7 @@ class GalaxyClustersController extends AppController
public function updateCluster($clusterId)
{
if (Validation::uuid($clusterId)) {
$temp = $this->GalaxyCluster->find('first', array(
'recursive' => -1,
'fields' => array('GalaxyCluster.id', 'GalaxyCluster.uuid'),
'conditions' => array('GalaxyCluster.uuid' => $clusterId)
));
if ($temp === null) {
throw new NotFoundException('Invalid galaxy cluster');
}
$clusterId = $temp['GalaxyCluster']['id'];
} elseif (!is_numeric($clusterId)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$conditions = array('conditions' => array('GalaxyCluster.id' => $clusterId));
$cluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), $conditions, true);
if (empty($cluster)) {
throw new NotFoundException('Invalid galaxy cluster');
}
$cluster = $cluster[0];
$cluster = $this->GalaxyCluster->checkAuthorization($this->Auth->user(), $clusterId, 'edit', $throwErrors=true, $full=false);
if ($cluster['GalaxyCluster']['default']) {
throw new MethodNotAllowedException(__('Default galaxy cluster cannot be updated'));
}
@ -950,7 +876,8 @@ class GalaxyClustersController extends AppController
}
$cluster['GalaxyCluster']['elements'] = $elements;
$cluster['GalaxyCluster']['extends_version'] = $parentVersion;
$errors = $this->GalaxyCluster->editCluster($this->Auth->user(), $cluster, $fromPull=false, $fieldList=array('extends_version'), $deleteOldElements=false);
$cluster['GalaxyCluster']['published'] = false;
$errors = $this->GalaxyCluster->editCluster($this->Auth->user(), $cluster, $fromPull=false, $fieldList=array('extends_version', 'published'), $deleteOldElements=false);
if (!empty($errors)) {
$flashErrorMessage = implode(', ', $errors);
$this->Flash->error($flashErrorMessage);

211
app/Model/GalaxyCluster.php
View File

@ -229,14 +229,6 @@ class GalaxyCluster extends AppModel
}
$cluster['GalaxyCluster']['org_id'] = $user['Organisation']['id'];
$cluster['GalaxyCluster']['orgc_id'] = $user['Organisation']['id'];
// if (!isset($cluster['GalaxyCluster']['orgc_id'])) {
// if (isset($cluster['Orgc']['uuid'])) {
// $orgc_id = $this->Orgc->find('first', array('conditions' => array('Orgc.uuid' => $cluster['Orgc']['uuid']), 'fields' => array('Orgc.id'), 'recursive' => -1));
// } else {
// $orgc_id = $user['org_id'];
// }
// $cluster['GalaxyCluster']['orgc_id'] = $orgc_id;
// }
if ($user['Role']['perm_sync']) {
if (isset($cluster['GalaxyCluster']['distribution']) && $cluster['GalaxyCluster']['distribution'] == 4 && !$this->SharingGroup->checkIfAuthorised($user, $cluster['GalaxyCluster']['sharing_group_id'])) {
@ -539,59 +531,6 @@ class GalaxyCluster extends AppModel
return $cluster;
}
// receive a full galaxy and add all new clusters, update existing ones contained in the new galaxy, cull old clusters that are removed from the galaxy
public function update($id, $galaxy)
{
$existingClusters = $this->find('all', array(
'conditions' => array('GalaxyCluster.galaxy_id' => $id),
'recursive' => -1,
));
foreach ($galaxy['values'] as $cluster) {
$oldCluster = false;
if (!empty($existingClusters)) {
foreach ($existingClusters as $k => $existingCluster) {
if ($existingCluster['GalaxyCluster']['value'] == $cluster['value']) {
$oldCluster = true;
if ($cluster['description'] != $existingCluster['GalaxyCluster']['description']) {
$existingCluster['GalaxyCluster']['description'] = $cluster['description'];
$this->GalaxyElement->deleteAll('galaxy_cluster_id' == $existingCluster['GalaxyCluster']['id']);
$this->save($existingCluster);
$template = array('galaxy_cluster_id' => $this->id);
$toSave = array();
foreach ($cluster as $key => $value) {
if (in_array($key, array('value', 'description'))) {
continue;
}
$tosave[] = array_merge($template, array('key' => $key, 'value' => $value));
}
$this->GalaxyElement->saveMany($toSave);
}
unset($existingClusters[$k]);
}
}
}
if (!$oldCluster) {
$newCluster = array_intersect_key($cluster, array_flip(array('value', 'description')));
$newCluster['galaxy_id'] = $id;
$newCluster['type'] = $galaxy['type'];
$newCluster['collection_uuid'] = $newCluster['uuid'];
$toSave[] = $newCluster;
}
$final = array();
if (!empty($existingCluster)) {
$fieldsToUpdate = array('description', '');
$final = $existingCluster;
}
}
$this->saveMany($toSave);
// Let's retrieve the full list of clusters we have for the given galaxy and pass it to the element system
$existingClusters = $this->find('all', array(
'conditions' => array('GalaxyCluster.galaxy_id'),
'contain' => array('GalaxyElement'/*, 'GalaxyReference'*/)
));
$this->GalaxyElement->update($id, $existingClusters, $galaxy['values']);
}
/* Return a list of all tags associated with the cluster specific cluster within the galaxy (or all clusters if $clusterValue is false)
* The counts are restricted to the event IDs that the user is allowed to see.
*/
@ -628,17 +567,16 @@ class GalaxyCluster extends AppModel
if (isset($this->__clusterCache[$name])) {
return $this->__clusterCache[$name];
}
$conditions = $this->buildConditions($user);
$conditions = array();
if (is_numeric($name)) {
$conditions['AND'] = array('GalaxyCluster.id' => $name);
$conditions[] = array('GalaxyCluster.id' => $name);
} else {
$conditions['AND'] = array('LOWER(GalaxyCluster.tag_name)' => strtolower($name));
$conditions[] = array('LOWER(GalaxyCluster.tag_name)' => strtolower($name));
}
$cluster = $this->find('first', array(
$cluster = $this->fetchGalaxyClusters($user, array(
'conditions' => $conditions,
'contain' => array('Galaxy', 'GalaxyElement')
));
'first' => true
), true);
if (!empty($cluster)) {
$cluster = $this->postprocess($cluster);
@ -651,21 +589,20 @@ class GalaxyCluster extends AppModel
public function getClusters($names, $user, $postProcess=true)
{
$conditions = $this->buildConditions($user);
$conditions = array();
if (count(array_filter($names, 'is_numeric' )) === count($names)) { // all elements are numeric
$conditions['AND'] = array('GalaxyCluster.id' => $names);
$conditions[] = array('GalaxyCluster.id' => $names);
} else {
$names = array_map('strtolower', $names);
$conditions['AND'] = array('LOWER(GalaxyCluster.tag_name)' => $names);
$conditions[] = array('LOWER(GalaxyCluster.tag_name)' => array_map('strtolower', $names));
}
$clusters = $this->find('all', array(
$clusters = $this->fetchGalaxyClusters($user, array(
'conditions' => $conditions,
'contain' => array('Galaxy', 'GalaxyElement')
));
), true);
if (!empty($clusters) && $postProcess) {
$clusters = $this->postprocess($clusters);
foreach ($clusters as $k => $cluster) {
$clusters[$k] = $this->postprocess($cluster);
}
}
return $clusters;
@ -941,40 +878,75 @@ class GalaxyCluster extends AppModel
return $conditions;
}
public function isAuthorizedTo($user, $cluster_id, $authorization)
public function fetchClusterById($user, $clusterId, $full=false)
{
$possibleAuthorization = array('view', 'edit');
if (!in_array($authorization, $possibleAuthorization)) {
throw new NotFoundException(__('Invalid authorization requested'));
}
if (Validation::uuid($cluster_id)) {
$temp = $this->GalaxyCluster->find('first', array(
if (Validation::uuid($clusterId)) {
$temp = $this->find('first', array(
'recursive' => -1,
'fields' => array('GalaxyCluster.id', 'GalaxyCluster.uuid'),
'conditions' => array('GalaxyCluster.uuid' => $cluster_id)
'conditions' => array('GalaxyCluster.uuid' => $clusterId)
));
if ($temp === null) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$cluster_id = $temp['GalaxyCluster']['id'];
} elseif (!is_numeric($cluster_id)) {
$clusterId = $temp['GalaxyCluster']['id'];
} elseif (!is_numeric($clusterId)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
}
$conditions = array('conditions' => array('GalaxyCluster.id' => $cluster_id));
$cluster = $this->GalaxyCluster->fetchGalaxyClusters($this->Auth->user(), $conditions, false);
if (empty($cluster)) {
throw new NotFoundException(__('Invalid galaxy cluster'));
$conditions = array('conditions' => array('GalaxyCluster.id' => $clusterId));
$cluster = $this->fetchGalaxyClusters($user, $conditions, $full);
return $cluster;
}
public function checkAuthorization($user, $cluster, $authorizations, $throwErrors=true, $full=false)
{
$authorizations = is_array($authorizations) ? $authorizations : array($authorizations);
$possibleAuthorizations = array('view', 'edit', 'delete', 'publish');
if (!empty(array_diff($authorizations, $possibleAuthorizations))) {
throw new NotFoundException(__('Invalid authorization requested'));
}
if (!isset($cluster['GalaxyCluster']['uuid'])) {
$cluster = $this->fetchClusterById($user, $cluster, $full=$full);
if (empty($cluster)) {
$message = __('Invalid galaxy cluster');
if ($throwErrors) {
throw new NotFoundException($message);
}
return array('authorized' => false, 'error' => $message);
}
}
$cluster = $cluster[0];
if ($authorization == 'view') {
if ($user['Role']['perm_site_admin']) {
return $cluster;
}
if (in_array('view', $authorizations) && count($authorizations) == 1) {
return $cluster;
} else {
if (!$user['Role']['perm_galaxy_editor'] && !$user['Role']['perm_site_admin']) {
throw new MethodNotAllowedException(__('You don\'t have the permission to do that.'));
if (!$user['Role']['perm_galaxy_editor']) {
$message = __('You don\'t have the permission to do that.');
if ($throwErrors) {
throw new MethodNotAllowedException($message);
}
return array('authorized' => false, 'error' => $message);
}
if ($authorization == 'edit') {
if (!$user['Role']['perm_site_admin'] && $cluster['GalaxyCluster']['orgc_id'] != $this->Auth->user('org_id')) {
throw new MethodNotAllowedException(__('You can\'t modify galaxy cluster where you are not part of the creator organisation.'));
if (in_array('edit', $authorizations) || in_array('delete', $authorizations)) {
if ($cluster['GalaxyCluster']['orgc_id'] != $this->Auth->user('org_id')) {
$message = __('Only the creator organisation can modify the galaxy cluster');
if ($throwErrors) {
throw new MethodNotAllowedException($message);
}
return array('authorized' => false, 'error' => $message);
}
}
if (in_array('publish', $authorizations)) {
if ($cluster['GalaxyCluster']['orgc_id'] != $this->Auth->user('org_id')) {
$message = __('Only the creator organisation can publish the galaxy cluster');
if ($throwErrors) {
throw new MethodNotAllowedException($message);
}
return array('authorized' => false, 'error' => $message);
}
}
return $cluster;
@ -1032,16 +1004,20 @@ class GalaxyCluster extends AppModel
$cluster['GalaxyCluster']['Galaxy'] = $cluster['Galaxy'];
unset($cluster['Galaxy']);
}
if (isset($cluster['GalaxyElement'])) {
$cluster['GalaxyCluster']['GalaxyElement'] = $cluster['GalaxyElement'];
unset($cluster['GalaxyElement']);
}
$elements = array();
foreach ($cluster['GalaxyElement'] as $element) {
foreach ($cluster['GalaxyCluster']['GalaxyElement'] as $element) {
if (!isset($elements[$element['key']])) {
$elements[$element['key']] = array($element['value']);
} else {
$elements[$element['key']][] = $element['value'];
}
}
unset($cluster['GalaxyElement']);
unset($cluster['GalaxyCluster']['GalaxyElement']);
$cluster['GalaxyCluster']['meta'] = $elements;
if ($tagId) {
@ -1073,8 +1049,8 @@ class GalaxyCluster extends AppModel
foreach ($galaxyElements as $galaxyElementKey => $galaxyElementValue) {
$tmpResults[] = array_values($this->GalaxyElement->find('list', array(
'conditions' => array(
'key' => $galaxyElementKey,
'value' => $galaxyElementValue,
'LOWER(GalaxyElement.key)' => strtolower($galaxyElementKey),
'LOWER(GalaxyElement.value)' => strtolower($galaxyElementValue),
),
'fields' => array('galaxy_cluster_id'),
'recursive' => -1
@ -1088,13 +1064,11 @@ class GalaxyCluster extends AppModel
foreach ($tmpResults as $tmpResult) {
$matchingClusters = array_intersect($matchingClusters, $tmpResult);
}
$clusterTags = $this->find('list', array(
$clusterTags = $this->fetchGalaxyClusters($user, array(
'conditions' => array('id' => $matchingClusters),
'fields' => array('GalaxyCluster.tag_name'),
'recursive' => -1
));
// TODO: Apply ACL
'list' => true,
), $full=false);
}
return array_values($clusterTags);
}
@ -1104,32 +1078,27 @@ class GalaxyCluster extends AppModel
$options = array(
'conditions' => array(
'GalaxyCluster.default' => 0,
'GalaxyCluster.published' => 1,
),
'fields' => array('uuid', 'version')
'fields' => array('uuid', 'version'),
'list' => true,
);
$clusters = $this->fetchGalaxyClusters($user, $options, $full=false);
$clusterUuids = array();
foreach($clusters as $cluster) {
$clusterUuids[$cluster['GalaxyCluster']['uuid']] = $cluster['GalaxyCluster']['version'];
}
return $clusterUuids;
return $clusters;
}
public function getElligibleClustersToPull($user)
public function getElligibleLocalClustersToUpdate($user)
{
$options = array(
'conditions' => array(
'GalaxyCluster.default' => 0,
'GalaxyCluster.locked' => 1,
),
'fields' => array('uuid', 'version')
'fields' => array('uuid', 'version'),
'list' => true,
);
$clusters = $this->fetchGalaxyClusters($user, $options, $full=false);
$clusterUuids = array();
foreach($clusters as $cluster) {
$clusterUuids[$cluster['GalaxyCluster']['uuid']] = $cluster['GalaxyCluster']['version'];
}
return $clusterUuids;
return $clusters;
}
public function uploadClusterToServer($cluster, $server, $HttpSocket, $user)
@ -1405,8 +1374,8 @@ class GalaxyCluster extends AppModel
{
$this->Server = ClassRegistry::init('Server');
if ("update" === $technique) {
$elligibleClusters = $this->GalaxyCluster->getElligibleClustersToPull($user);
$clusterIds = $this->Server->getClusterIdsFromServer($server, $HttpSocket=null, $performLocalDelta=true, $elligibleClusters=$elligibleClusters);
$localClustersToUpdate = $this->GalaxyCluster->getElligibleLocalClustersToUpdate($user);
$clusterIds = $this->Server->getClusterIdsFromServer($server, $HttpSocket=null, $performLocalDelta=true, $elligibleClusters=$localClustersToUpdate);
if ($clusterIds === 403) {
return array('error' => array(1, null));
} elseif (is_string($clusterIds)) {