C-It-Loci: A knowledge database for tissue-enriched loci.
Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main
Warning (512): _cake_core_ cache was unable to write 'cake_dev_eng' to File cache [CORE/Cake/Cache/Cache.php, line 323]Code Context),E_USER_WARNING);$key = 'cake_dev_eng' $value = array( 'LC_MESSAGES' => array() ) $config = '_cake_core_' $settings = array( 'prefix' => '*****', 'engine' => 'File', 'path' => '/var/www/c-it-loci/app/tmp/cache/persistent/', 'serialize' => true, 'duration' => (int) 10, 'lock' => true, 'isWindows' => false, 'mask' => (int) 436, 'probability' => (int) 100, 'groups' => array() ) $success = falseCache::write() - CORE/Cake/Cache/Cache.php, line 323 I18n::translate() - CORE/Cake/I18n/I18n.php, line 237 __d - CORE/Cake/basics.php, line 617 CakeException::__construct() - CORE/Cake/Error/exceptions.php, line 236 MissingConnectionException::__construct() - CORE/Cake/Error/exceptions.php, line 391 Mysql::connect() - CORE/Cake/Model/Datasource/Database/Mysql.php, line 194 DboSource::__construct() - CORE/Cake/Model/Datasource/DboSource.php, line 260 ConnectionManager::getDataSource() - CORE/Cake/Model/ConnectionManager.php, line 105 Model::setDataSource() - CORE/Cake/Model/Model.php, line 3524 Model::setSource() - CORE/Cake/Model/Model.php, line 1136 Model::getDataSource() - CORE/Cake/Model/Model.php, line 3551 Model::__call() - CORE/Cake/Model/Model.php, line 808 Transcript::findByid() - APP/Controller/TranscriptController.php, line 319 TranscriptController::show() - APP/Controller/TranscriptController.php, line 319 ReflectionMethod::invokeArgs() - [internal], line ?? Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 490 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 191
Warning (2): file_put_contents() [function.file-put-contents]: Only 0 of 1592 bytes written, possibly out of free disk space [CORE/Cake/Log/Engine/FileLog.php, line 142]Code Context$pathname = $this->_path . $filename;if (empty($this->_config['mask'])) {return file_put_contents($pathname, $output, FILE_APPEND);$type = 'error' $message = '[MissingConnectionException] Database connection "Mysql" is missing, or could not be created. Exception Attributes: array ( 'class' => 'Mysql', 'message' => 'SQLSTATE[HY000] [2002] Connection refused', 'enabled' => true, ) Request URL: /transcript/ENST00000336034 Stack Trace: #0 /var/www/c-it-loci/lib/Cake/Model/Datasource/DboSource.php(260): Mysql->connect() #1 /var/www/c-it-loci/lib/Cake/Model/ConnectionManager.php(105): DboSource->__construct(Array) #2 /var/www/c-it-loci/lib/Cake/Model/Model.php(3524): ConnectionManager::getDataSource('default') #3 /var/www/c-it-loci/lib/Cake/Model/Model.php(1136): Model->setDataSource('default') #4 /var/www/c-it-loci/lib/Cake/Model/Model.php(3551): Model->setSource('transcripts') #5 /var/www/c-it-loci/lib/Cake/Model/Model.php(808): Model->getDataSource() #6 /var/www/c-it-loci/app/Controller/TranscriptController.php(319): Model->__call('findByid', Array) #7 /var/www/c-it-loci/app/Controller/TranscriptController.php(319): Transcript->findByid('ENST00000336034') #8 [internal function]: TranscriptController->show() #9 /var/www/c-it-loci/lib/Cake/Controller/Controller.php(490): ReflectionMethod->invokeArgs(Object(TranscriptController), Array) #10 /var/www/c-it-loci/lib/Cake/Routing/Dispatcher.php(191): Controller->invokeAction(Object(CakeRequest)) #11 /var/www/c-it-loci/lib/Cake/Routing/Dispatcher.php(165): Dispatcher->_invoke(Object(TranscriptController), Object(CakeRequest)) #12 /var/www/c-it-loci/app/webroot/index.php(108): Dispatcher->dispatch(Object(CakeRequest), Object(CakeResponse)) #13 {main}' $output = '2026-01-06 23:35:31 Error: [MissingConnectionException] Database connection "Mysql" is missing, or could not be created. Exception Attributes: array ( 'class' => 'Mysql', 'message' => 'SQLSTATE[HY000] [2002] Connection refused', 'enabled' => true, ) Request URL: /transcript/ENST00000336034 Stack Trace: #0 /var/www/c-it-loci/lib/Cake/Model/Datasource/DboSource.php(260): Mysql->connect() #1 /var/www/c-it-loci/lib/Cake/Model/ConnectionManager.php(105): DboSource->__construct(Array) #2 /var/www/c-it-loci/lib/Cake/Model/Model.php(3524): ConnectionManager::getDataSource('default') #3 /var/www/c-it-loci/lib/Cake/Model/Model.php(1136): Model->setDataSource('default') #4 /var/www/c-it-loci/lib/Cake/Model/Model.php(3551): Model->setSource('transcripts') #5 /var/www/c-it-loci/lib/Cake/Model/Model.php(808): Model->getDataSource() #6 /var/www/c-it-loci/app/Controller/TranscriptController.php(319): Model->__call('findByid', Array) #7 /var/www/c-it-loci/app/Controller/TranscriptController.php(319): Transcript->findByid('ENST00000336034') #8 [internal function]: TranscriptController->show() #9 /var/www/c-it-loci/lib/Cake/Controller/Controller.php(490): ReflectionMethod->invokeArgs(Object(TranscriptController), Array) #10 /var/www/c-it-loci/lib/Cake/Routing/Dispatcher.php(191): Controller->invokeAction(Object(CakeRequest)) #11 /var/www/c-it-loci/lib/Cake/Routing/Dispatcher.php(165): Dispatcher->_invoke(Object(TranscriptController), Object(CakeRequest)) #12 /var/www/c-it-loci/app/webroot/index.php(108): Dispatcher->dispatch(Object(CakeRequest), Object(CakeResponse)) #13 {main} ' $filename = 'error.log' $pathname = '/var/www/c-it-loci/app/tmp/logs/error.log'file_put_contents - [internal], line ?? FileLog::write() - CORE/Cake/Log/Engine/FileLog.php, line 142 CakeLog::write() - CORE/Cake/Log/CakeLog.php, line 442 ErrorHandler::_log() - CORE/Cake/Error/ErrorHandler.php, line 178 ErrorHandler::handleException() - CORE/Cake/Error/ErrorHandler.php, line 110 [main] - [internal], line ??
Error:
A Database connection using "Mysql" was missing or unable to connect.
The database server returned this error: SQLSTATE[HY000] [2002] Connection refused
Notice: If you want to customize this error message, create app/View/Errors/missing_connection.ctp
));}if ($autoConnect) {$this->connect();}
'message' => 'Datasource is not found in Model/Datasource package.'));}self::$_dataSources[$name] = new $class(self::$config->{$name});self::$_dataSources[$name]->configKeyName = $name;
array( 'password' => '*****', 'login' => '*****', 'host' => '*****', 'database' => '*****', 'prefix' => '*****', 'datasource' => 'Database/Mysql', 'persistent' => false )
$this->useDbConfig = $dataSource;}$db = ConnectionManager::getDataSource($this->useDbConfig);if (!empty($oldConfig) && isset($db->config['prefix'])) {
'default'
* @return void*/public function setSource($tableName) {$this->setDataSource($this->useDbConfig);$db = ConnectionManager::getDataSource($this->useDbConfig);
'default'
public function getDataSource() {if (!$this->_sourceConfigured && $this->useTable !== false) {$this->_sourceConfigured = true;$this->setSource($this->useTable);}
'transcripts'
return $result;}return $this->getDataSource()->query($method, $params, $this);}
$longest_tissue_len = 0;$all_tissue_title_arr = array();$transcript_data = $this->Transcript->findByid($this->params->accession);
'findByid' array( (int) 0 => 'ENST00000336034' )
$longest_tissue_len = 0;$all_tissue_title_arr = array();$transcript_data = $this->Transcript->findByid($this->params->accession);
'ENST00000336034'
'action' => $request->params['action']));}return $method->invokeArgs($this, $request->params['pass']);
object(TranscriptController) {
helpers => array(
[maximum depth reached]
)
components => array(
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)
page_size_choices => array(
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UCSC_links => array(
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)
sci_name_map => array(
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)
expression_types => array(
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)
expression_type_none => 'none'
expression_type_default => 'Enriched'
geneviewer => array(
[maximum depth reached]
)
name => 'Transcript'
uses => array(
[maximum depth reached]
)
request => object(CakeRequest) {}
response => object(CakeResponse) {}
viewPath => 'Transcript'
layoutPath => null
viewVars => array([maximum depth reached])
view => 'show'
layout => 'default'
autoRender => true
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Components => object(ComponentCollection) {}
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View => null
ext => '.ctp'
plugin => null
cacheAction => false
passedArgs => array([maximum depth reached])
scaffold => false
methods => array(
[maximum depth reached]
)
modelClass => 'Transcript'
modelKey => 'transcript'
validationErrors => null
Session => object(SessionComponent) {}
RequestHandler => object(RequestHandlerComponent) {}
Transcript => object(Transcript) {}
[protected] _responseClass => 'CakeResponse'
[protected] _mergeParent => 'AppController'
[protected] _eventManager => object(CakeEventManager) {}
[private] operators => array(
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)
[private] num_operands => array(
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[private] parenthesis => array(
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}
array()$response = $controller->response;$render = true;$result = $controller->invokeAction($request);if ($result instanceof CakeResponse) {
object(CakeRequest) {
params => array(
[maximum depth reached]
)
data => array([maximum depth reached])
query => array([maximum depth reached])
url => 'transcript/ENST00000336034'
base => ''
webroot => '/'
here => '/transcript/ENST00000336034'
[protected] _detectors => array(
[maximum depth reached]
)
[protected] _input => ''
}));}$response = $this->_invoke($controller, $request);if (isset($request->params['return'])) {
object(TranscriptController) {
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[maximum depth reached]
)
components => array(
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page_size_choices => array(
[maximum depth reached]
)
default_choice => '10'
UCSC_links => array(
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sci_name_map => array(
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expression_types => array(
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expression_type_none => 'none'
expression_type_default => 'Enriched'
geneviewer => array(
[maximum depth reached]
)
name => 'Transcript'
uses => array(
[maximum depth reached]
)
request => object(CakeRequest) {}
response => object(CakeResponse) {}
viewPath => 'Transcript'
layoutPath => null
viewVars => array([maximum depth reached])
view => 'show'
layout => 'default'
autoRender => true
autoLayout => true
Components => object(ComponentCollection) {}
viewClass => 'View'
View => null
ext => '.ctp'
plugin => null
cacheAction => false
passedArgs => array([maximum depth reached])
scaffold => false
methods => array(
[maximum depth reached]
)
modelClass => 'Transcript'
modelKey => 'transcript'
validationErrors => null
Session => object(SessionComponent) {}
RequestHandler => object(RequestHandlerComponent) {}
Transcript => object(Transcript) {}
[protected] _responseClass => 'CakeResponse'
[protected] _mergeParent => 'AppController'
[protected] _eventManager => object(CakeEventManager) {}
[private] operators => array(
[maximum depth reached]
)
[private] num_operands => array(
[maximum depth reached]
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[private] parenthesis => array(
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}
object(CakeRequest) {
params => array(
[maximum depth reached]
)
data => array([maximum depth reached])
query => array([maximum depth reached])
url => 'transcript/ENST00000336034'
base => ''
webroot => '/'
here => '/transcript/ENST00000336034'
[protected] _detectors => array(
[maximum depth reached]
)
[protected] _input => ''
}$Dispatcher->dispatch(new CakeRequest(),new CakeResponse());
object(CakeRequest) {
params => array(
[maximum depth reached]
)
data => array([maximum depth reached])
query => array([maximum depth reached])
url => 'transcript/ENST00000336034'
base => ''
webroot => '/'
here => '/transcript/ENST00000336034'
[protected] _detectors => array(
[maximum depth reached]
)
[protected] _input => ''
}
object(CakeResponse) {
[protected] _statusCodes => array(
[maximum depth reached]
)
[protected] _mimeTypes => array(
[maximum depth reached]
)
[protected] _protocol => 'HTTP/1.1'
[protected] _status => (int) 200
[protected] _contentType => 'text/html'
[protected] _headers => array([maximum depth reached])
[protected] _body => null
[protected] _file => null
[protected] _fileRange => null
[protected] _charset => 'UTF-8'
[protected] _cacheDirectives => array([maximum depth reached])
[protected] _cookies => array([maximum depth reached])
}
Warning (512): _cake_core_ cache was unable to write 'file_map' to File cache [CORE/Cake/Cache/Cache.php, line 323]Code Context),E_USER_WARNING);$key = 'file_map' $value = array( 'Configure' => '/var/www/c-it-loci/lib/Cake/Core/Configure.php', 'Hash' => '/var/www/c-it-loci/lib/Cake/Utility/Hash.php', 'Cache' => '/var/www/c-it-loci/lib/Cake/Cache/Cache.php', 'FileEngine' => '/var/www/c-it-loci/lib/Cake/Cache/Engine/FileEngine.php', 'CacheEngine' => '/var/www/c-it-loci/lib/Cake/Cache/CacheEngine.php', 'Inflector' => '/var/www/c-it-loci/lib/Cake/Utility/Inflector.php', 'ErrorHandler' => '/var/www/c-it-loci/lib/Cake/Error/ErrorHandler.php', 'CakePlugin' => '/var/www/c-it-loci/lib/Cake/Core/CakePlugin.php', 'CakeLog' => '/var/www/c-it-loci/lib/Cake/Log/CakeLog.php', 'LogEngineCollection' => '/var/www/c-it-loci/lib/Cake/Log/LogEngineCollection.php', 'ObjectCollection' => '/var/www/c-it-loci/lib/Cake/Utility/ObjectCollection.php', 'FileLog' => '/var/www/c-it-loci/lib/Cake/Log/Engine/FileLog.php', 'BaseLog' => '/var/www/c-it-loci/lib/Cake/Log/Engine/BaseLog.php', 'CakeLogInterface' => '/var/www/c-it-loci/lib/Cake/Log/CakeLogInterface.php', 'Debugger' => '/var/www/c-it-loci/lib/Cake/Utility/Debugger.php', 'String' => '/var/www/c-it-loci/lib/Cake/Utility/String.php', 'Dispatcher' => '/var/www/c-it-loci/lib/Cake/Routing/Dispatcher.php', 'CakeEventListener' => '/var/www/c-it-loci/lib/Cake/Event/CakeEventListener.php', 'CakeRequest' => '/var/www/c-it-loci/lib/Cake/Network/CakeRequest.php', 'CakeResponse' => '/var/www/c-it-loci/lib/Cake/Network/CakeResponse.php', 'CakeEvent' => '/var/www/c-it-loci/lib/Cake/Event/CakeEvent.php', 'CakeEventManager' => '/var/www/c-it-loci/lib/Cake/Event/CakeEventManager.php', 'AssetDispatcher' => '/var/www/c-it-loci/lib/Cake/Routing/Filter/AssetDispatcher.php', 'DispatcherFilter' => '/var/www/c-it-loci/lib/Cake/Routing/DispatcherFilter.php', 'CacheDispatcher' => '/var/www/c-it-loci/lib/Cake/Routing/Filter/CacheDispatcher.php', 'Router' => '/var/www/c-it-loci/lib/Cake/Routing/Router.php', 'CakeRoute' => '/var/www/c-it-loci/lib/Cake/Routing/Route/CakeRoute.php', 'PluginShortRoute' => '/var/www/c-it-loci/lib/Cake/Routing/Route/PluginShortRoute.php', 'TranscriptController' => '/var/www/c-it-loci/app/Controller/TranscriptController.php', 'AppController' => '/var/www/c-it-loci/app/Controller/AppController.php', 'Controller' => '/var/www/c-it-loci/lib/Cake/Controller/Controller.php', 'Object' => '/var/www/c-it-loci/lib/Cake/Core/Object.php', 'ComponentCollection' => '/var/www/c-it-loci/lib/Cake/Controller/ComponentCollection.php', 'SessionComponent' => '/var/www/c-it-loci/lib/Cake/Controller/Component/SessionComponent.php', 'Component' => '/var/www/c-it-loci/lib/Cake/Controller/Component.php', 'RequestHandlerComponent' => '/var/www/c-it-loci/lib/Cake/Controller/Component/RequestHandlerComponent.php', 'ClassRegistry' => '/var/www/c-it-loci/lib/Cake/Utility/ClassRegistry.php', 'Transcript' => '/var/www/c-it-loci/app/Model/Transcript.php', 'AppModel' => '/var/www/c-it-loci/app/Model/AppModel.php', 'Model' => '/var/www/c-it-loci/lib/Cake/Model/Model.php', 'BehaviorCollection' => '/var/www/c-it-loci/lib/Cake/Model/BehaviorCollection.php', 'ConnectionManager' => '/var/www/c-it-loci/lib/Cake/Model/ConnectionManager.php', 'Mysql' => '/var/www/c-it-loci/lib/Cake/Model/Datasource/Database/Mysql.php', 'DboSource' => '/var/www/c-it-loci/lib/Cake/Model/Datasource/DboSource.php', 'DataSource' => '/var/www/c-it-loci/lib/Cake/Model/Datasource/DataSource.php', 'I18n' => '/var/www/c-it-loci/lib/Cake/I18n/I18n.php', 'L10n' => '/var/www/c-it-loci/lib/Cake/I18n/L10n.php', 'CakeSession' => '/var/www/c-it-loci/lib/Cake/Model/Datasource/CakeSession.php', 'ExceptionRenderer' => '/var/www/c-it-loci/lib/Cake/Error/ExceptionRenderer.php', 'CakeErrorController' => '/var/www/c-it-loci/lib/Cake/Controller/CakeErrorController.php', 'View' => '/var/www/c-it-loci/lib/Cake/View/View.php', 'HelperCollection' => '/var/www/c-it-loci/lib/Cake/View/HelperCollection.php', 'ViewBlock' => '/var/www/c-it-loci/lib/Cake/View/ViewBlock.php', 'SessionHelper' => '/var/www/c-it-loci/lib/Cake/View/Helper/SessionHelper.php', 'AppHelper' => '/var/www/c-it-loci/app/View/Helper/AppHelper.php', 'Helper' => '/var/www/c-it-loci/lib/Cake/View/Helper.php' ) $config = '_cake_core_' $settings = array( 'prefix' => '*****', 'engine' => 'File', 'path' => '/var/www/c-it-loci/app/tmp/cache/persistent/', 'serialize' => true, 'duration' => (int) 10, 'lock' => true, 'isWindows' => false, 'mask' => (int) 436, 'probability' => (int) 100, 'groups' => array() ) $success = falseCache::write() - CORE/Cake/Cache/Cache.php, line 323 App::shutdown() - CORE/Cake/Core/App.php, line 899 [main] - [internal], line ??