Institute of Cardiovascular Regeneration Webtool Repository

Missing Database Connection

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

Stack Trace

CORE/Cake/Model/Datasource/DboSource.php line 260 → Mysql->connect()

            ));
        }
        if ($autoConnect) {
            $this->connect();
        }

CORE/Cake/Model/ConnectionManager.php line 105 → DboSource->__construct(array)

                '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
)

CORE/Cake/Model/Model.php line 3524 → ConnectionManager::getDataSource(string)

            $this->useDbConfig = $dataSource;
        }

        $db = ConnectionManager::getDataSource($this->useDbConfig);
        if (!empty($oldConfig) && isset($db->config['prefix'])) {

'default'

CORE/Cake/Model/Model.php line 1136 → Model->setDataSource(string)

 * @return void
 */
    public function setSource($tableName) {
        $this->setDataSource($this->useDbConfig);
        $db = ConnectionManager::getDataSource($this->useDbConfig);

'default'

CORE/Cake/Model/Model.php line 3551 → Model->setSource(string)

    public function getDataSource() {
        if (!$this->_sourceConfigured && $this->useTable !== false) {
            $this->_sourceConfigured = true;
            $this->setSource($this->useTable);
        }

'transcripts'

CORE/Cake/Model/Model.php line 808 → Model->getDataSource()

            return $result;
        }

        return $this->getDataSource()->query($method, $params, $this);
    }

APP/Controller/TranscriptController.php line 319 → Model->__call(string, array)

        $longest_tissue_len = 0;
        $all_tissue_title_arr = array();

        $transcript_data = $this->Transcript->findByid($this->params->accession);

'findByid'
array(
	(int) 0 => 'ENST00000510637'
)

APP/Controller/TranscriptController.php line 319 → Transcript->findByid(string)

        $longest_tissue_len = 0;
        $all_tissue_title_arr = array();

        $transcript_data = $this->Transcript->findByid($this->params->accession);

'ENST00000510637'

[internal function] → TranscriptController->show()

CORE/Cake/Controller/Controller.php line 490 → ReflectionMethod->invokeArgs(TranscriptController, array)

                    'action' => $request->params['action']
                ));
            }
            return $method->invokeArgs($this, $request->params['pass']);

object(TranscriptController) {
	helpers => array(
		[maximum depth reached]
	)
	components => array(
		[maximum depth reached]
	)
	page_size_choices => array(
		[maximum depth reached]
	)
	default_choice => '10'
	UCSC_links => array(
		[maximum depth reached]
	)
	accession_map => array(
		[maximum depth reached]
	)
	sci_name_map => array(
		[maximum depth reached]
	)
	expression_types => array(
		[maximum depth reached]
	)
	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]
	)
	[private] parenthesis => array(
		[maximum depth reached]
	)
}
array()

CORE/Cake/Routing/Dispatcher.php line 191 → Controller->invokeAction(CakeRequest)


        $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/ENST00000510637'
	base => ''
	webroot => '/'
	here => '/transcript/ENST00000510637'
	[protected] _detectors => array(
		[maximum depth reached]
	)
	[protected] _input => ''
}

CORE/Cake/Routing/Dispatcher.php line 165 → Dispatcher->_invoke(TranscriptController, CakeRequest)

            ));
        }

        $response = $this->_invoke($controller, $request);
        if (isset($request->params['return'])) {

object(TranscriptController) {
	helpers => array(
		[maximum depth reached]
	)
	components => array(
		[maximum depth reached]
	)
	page_size_choices => array(
		[maximum depth reached]
	)
	default_choice => '10'
	UCSC_links => array(
		[maximum depth reached]
	)
	accession_map => array(
		[maximum depth reached]
	)
	sci_name_map => array(
		[maximum depth reached]
	)
	expression_types => array(
		[maximum depth reached]
	)
	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]
	)
	[private] parenthesis => array(
		[maximum depth reached]
	)
}
object(CakeRequest) {
	params => array(
		[maximum depth reached]
	)
	data => array([maximum depth reached])
	query => array([maximum depth reached])
	url => 'transcript/ENST00000510637'
	base => ''
	webroot => '/'
	here => '/transcript/ENST00000510637'
	[protected] _detectors => array(
		[maximum depth reached]
	)
	[protected] _input => ''
}

APP/webroot/index.php line 108 → Dispatcher->dispatch(CakeRequest, CakeResponse)

$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/ENST00000510637'
	base => ''
	webroot => '/'
	here => '/transcript/ENST00000510637'
	[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])
}

C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Missing Database Connection

Stack Trace

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