| ( ! ) Fatal error: Uncaught FatalErrorException: [CakeSessionException] Unable to configure the session, setting session.use_trans_sid failed.
#0 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(619): CakeSession::_configureSession()
#1 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(632): CakeSession::_cookieName()
#2 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(248): CakeSession::_hasSession()
#3 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/Helper/SessionHelper.php(134): CakeSession::check()
#4 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Console/Templates/skel/View/Layouts/error.ctp(35): SessionHelper->flash()
#5 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/View.php(971): include('/www/bioinforma...')
#6 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/View.php(933): View->_evaluate()
#7 /www/ in /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php on line 138 |
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| Call Stack |
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| # | Time | Memory | Function | Location |
|---|
| 1 | 0.0025 | 434592 | {main}( ) | .../index.php:0 |
| 2 | 0.0837 | 1903776 | Dispatcher->dispatch( $request = class CakeRequest { public $params = ['plugin' => NULL, 'controller' => 'orthologs', 'action' => 'explore', 'named' => [...], 'pass' => [...]]; public $data = []; public $query = []; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = ['get' => [...], 'patch' => [...], 'post' => [...], 'put' => [...], 'delete' => [...], 'head' => [...], 'options' => [...], 'ssl' => [...], 'ajax' => [...], 'flash' => [...], 'mobile' => [...], 'requested' => [...], 'json' => [...], 'xml' => [...]]; protected $_input = '' }, $response = class CakeResponse { protected $_statusCodes = [100 => 'Continue', 101 => 'Switching Protocols', 200 => 'OK', 201 => 'Created', 202 => 'Accepted', 203 => 'Non-Authoritative Information', 204 => 'No Content', 205 => 'Reset Content', 206 => 'Partial Content', 300 => 'Multiple Choices', 301 => 'Moved Permanently', 302 => 'Found', 303 => 'See Other', 304 => 'Not Modified', 305 => 'Use Proxy', 307 => 'Temporary Redirect', 400 => 'Bad Request', 401 => 'Unauthorized', 402 => 'Payment Required', 403 => 'Forbidden', 404 => 'Not Found', 405 => 'Method Not Allowed', 406 => 'Not Acceptable', 407 => 'Proxy Authentication Required', 408 => 'Request Time-out', 409 => 'Conflict', 410 => 'Gone', 411 => 'Length Required', 412 => 'Precondition Failed', 413 => 'Request Entity Too Large', 414 => 'Request-URI Too Large', 415 => 'Unsupported Media Type', 416 => 'Requested range not satisfiable', 417 => 'Expectation Failed', 429 => 'Too Many Requests', 500 => 'Internal Server Error', 501 => 'Not Implemented', 502 => 'Bad Gateway', 503 => 'Service Unavailable', 504 => 'Gateway Time-out', 505 => 'Unsupported Version']; protected $_mimeTypes = ['html' => [...], 'json' => 'application/json', 'xml' => [...], 'rss' => 'application/rss+xml', 'ai' => 'application/postscript', 'bcpio' => 'application/x-bcpio', 'bin' => 'application/octet-stream', 'ccad' => 'application/clariscad', 'cdf' => 'application/x-netcdf', 'class' => 'application/octet-stream', 'cpio' => 'application/x-cpio', 'cpt' => 'application/mac-compactpro', 'csh' => 'application/x-csh', 'csv' => [...], 'dcr' => 'application/x-director', 'dir' => 'application/x-director', 'dms' => 'application/octet-stream', 'doc' => 'application/msword', 'docx' => 'application/vnd.openxmlformats-officedocument.wordprocessingml.document', 'drw' => 'application/drafting', 'dvi' => 'application/x-dvi', 'dwg' => 'application/acad', 'dxf' => 'application/dxf', 'dxr' => 'application/x-director', 'eot' => 'application/vnd.ms-fontobject', 'eps' => 'application/postscript', 'exe' => 'application/octet-stream', 'ez' => 'application/andrew-inset', 'flv' => 'video/x-flv', 'gtar' => 'application/x-gtar', 'gz' => 'application/x-gzip', 'bz2' => 'application/x-bzip', '7z' => 'application/x-7z-compressed', 'hdf' => 'application/x-hdf', 'hqx' => 'application/mac-binhex40', 'ico' => 'image/x-icon', 'ips' => 'application/x-ipscript', 'ipx' => 'application/x-ipix', 'js' => 'application/javascript', 'jsonapi' => 'application/vnd.api+json', 'latex' => 'application/x-latex', 'lha' => 'application/octet-stream', 'lsp' => 'application/x-lisp', 'lzh' => 'application/octet-stream', 'man' => 'application/x-troff-man', 'me' => 'application/x-troff-me', 'mif' => 'application/vnd.mif', 'ms' => 'application/x-troff-ms', 'nc' => 'application/x-netcdf', 'oda' => 'application/oda', 'otf' => 'font/otf', 'pdf' => 'application/pdf', 'pgn' => 'application/x-chess-pgn', 'pot' => 'application/vnd.ms-powerpoint', 'pps' => 'application/vnd.ms-powerpoint', 'ppt' => 'application/vnd.ms-powerpoint', 'pptx' => 'application/vnd.openxmlformats-officedocument.presentationml.presentation', 'ppz' => 'application/vnd.ms-powerpoint', 'pre' => 'application/x-freelance', 'prt' => 'application/pro_eng', 'ps' => 'application/postscript', 'roff' => 'application/x-troff', 'scm' => 'application/x-lotusscreencam', 'set' => 'application/set', 'sh' => 'application/x-sh', 'shar' => 'application/x-shar', 'sit' => 'application/x-stuffit', 'skd' => 'application/x-koan', 'skm' => 'application/x-koan', 'skp' => 'application/x-koan', 'skt' => 'application/x-koan', 'smi' => 'application/smil', 'smil' => 'application/smil', 'sol' => 'application/solids', 'spl' => 'application/x-futuresplash', 'src' => 'application/x-wais-source', 'step' => 'application/STEP', 'stl' => 'application/SLA', 'stp' => 'application/STEP', 'sv4cpio' => 'application/x-sv4cpio', 'sv4crc' => 'application/x-sv4crc', 'svg' => 'image/svg+xml', 'svgz' => 'image/svg+xml', 'swf' => 'application/x-shockwave-flash', 't' => 'application/x-troff', 'tar' => 'application/x-tar', 'tcl' => 'application/x-tcl', 'tex' => 'application/x-tex', 'texi' => 'application/x-texinfo', 'texinfo' => 'application/x-texinfo', 'tr' => 'application/x-troff', 'tsp' => 'application/dsptype', 'ttc' => 'font/ttf', 'ttf' => 'font/ttf', 'unv' => 'application/i-deas', 'ustar' => 'application/x-ustar', 'vcd' => 'application/x-cdlink', 'vda' => 'application/vda', 'xlc' => 'application/vnd.ms-excel', 'xll' => 'application/vnd.ms-excel', 'xlm' => 'application/vnd.ms-excel', 'xls' => 'application/vnd.ms-excel', 'xlsx' => 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet', 'xlw' => 'application/vnd.ms-excel', 'zip' => 'application/zip', 'aif' => 'audio/x-aiff', 'aifc' => 'audio/x-aiff', 'aiff' => 'audio/x-aiff', 'au' => 'audio/basic', 'kar' => 'audio/midi', 'mid' => 'audio/midi', 'midi' => 'audio/midi', 'mp2' => 'audio/mpeg', 'mp3' => 'audio/mpeg', 'mpga' => 'audio/mpeg', 'ogg' => 'audio/ogg', 'oga' => 'audio/ogg', 'spx' => 'audio/ogg', 'ra' => 'audio/x-realaudio', 'ram' => 'audio/x-pn-realaudio', 'rm' => 'audio/x-pn-realaudio', 'rpm' => 'audio/x-pn-realaudio-plugin', 'snd' => 'audio/basic', 'tsi' => 'audio/TSP-audio', 'wav' => 'audio/x-wav', 'aac' => 'audio/aac', 'asc' => 'text/plain', 'c' => 'text/plain', ...]; protected $_protocol = 'HTTP/1.1'; protected $_status = 200; protected $_contentType = 'text/html'; protected $_headers = []; protected $_body = NULL; protected $_file = NULL; protected $_fileRange = NULL; protected $_charset = 'UTF-8'; protected $_cacheDirectives = []; protected $_cookies = [] }, $additionalParams = ??? ) | .../index.php:151 |
| 3 | 0.1309 | 2712280 | Dispatcher->_invoke( $controller = class OrthologsController { public $name = 'Orthologs'; public $helpers = ['Session' => NULL, 'Html' => NULL, 'Form' => NULL, 'Cache' => NULL]; public $uses = [0 => 'Annotation', 1 => 'AnnotSource', 2 => 'Configuration', 3 => 'DnaMotifsCns', 4 => 'GfDatum', 5 => 'Msa', 6 => 'Orthologs', 7 => 'Similarities', 8 => 'Trees', 9 => 'AdExperiments', 10 => 'FunctionalClustersExperiments']; public $components = ['Session' => NULL, 'DataUtils' => NULL, 'FunctionalAnnotationUtils' => NULL, 'GeneFamilies' => NULL, 'Organism' => NULL, 'WorkbenchUtils' => NULL, 'Orthology' => NULL]; public $request = class CakeRequest { public $params = [...]; public $data = [...]; public $query = [...]; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = [...]; protected $_input = '' }; public $response = class CakeResponse { protected $_statusCodes = [...]; protected $_mimeTypes = [...]; protected $_protocol = 'HTTP/1.1'; protected $_status = 200; protected $_contentType = 'text/html'; protected $_headers = [...]; protected $_body = NULL; protected $_file = NULL; protected $_fileRange = NULL; protected $_charset = 'UTF-8'; protected $_cacheDirectives = [...]; protected $_cookies = [...] }; protected $_responseClass = 'CakeResponse'; public $viewPath = 'Orthologs'; public $layoutPath = NULL; public $viewVars = ['supporting_types' => [...], 'ortholog_types' => [...], 'all_organisms' => [...], 'target_species' => 'cme', 'query_species' => 'spe', 'query_gene' => 'Sopen11g022860', 'title_for_layout' => 'Dicots PLAZA 5.0 : Integrative Orthology']; public $view = 'explore'; public $layout = 'default'; public $autoRender = TRUE; public $autoLayout = TRUE; public $Components = class ComponentCollection { protected $_Controller = ...; protected $_enabled = [...]; protected $_loaded = [...]; public $defaultPriority = 10 }; public $viewClass = 'View'; public $View = NULL; public $ext = '.ctp'; public $plugin = NULL; public $cacheAction = FALSE; public $passedArgs = [0 => 'Sopen11g022860', 1 => 'cme']; public $scaffold = FALSE; public $methods = [1 => 'overview', 2 => 'explore', 3 => 'get_orthologs_type_data', 4 => 'get_supporting_data', 5 => 'get_supporting_type_data', 6 => 'get_orthologs_data']; public $modelClass = 'Annotation'; public $modelKey = 'ortholog'; public $validationErrors = NULL; protected $_mergeParent = 'AppController'; protected $_eventManager = class CakeEventManager { protected $_listeners = [...]; protected $_isGlobal = FALSE }; public $Session = class SessionComponent { protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $DataUtils = class DataUtilsComponent { public $name = 'DataUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $FunctionalAnnotationUtils = class FunctionalAnnotationUtilsComponent { public $name = 'FunctionalAnnotationUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $GeneFamilies = class GeneFamiliesComponent { public $name = 'GeneFamilies'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Organism = class OrganismComponent { public $name = 'Organism'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $WorkbenchUtils = class WorkbenchUtilsComponent { public $name = 'WorkbenchUtils'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $Orthology = class OrthologyComponent { public $name = 'Orthology'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Annotation = class Annotation { public $name = 'Annotation'; public $useTable = 'annotation'; public $primaryKey = 'gene_id'; public $cacheQueries = FALSE; public $cacheSources = FALSE; public $belongsTo = [...]; public $hasMany = [...]; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annotation'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Annotation'; public $tableToModel = [...]; public $hasOne = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $AnnotSource = class AnnotSource { public $name = 'AnnotSource'; public $useTable = 'annot_sources'; public $primaryKey = 'species'; public $displayField = 'common_name'; public $useDbConfig = 'default'; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annot_sources'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'AnnotSource'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Configuration = class Configuration { public $name = 'Configuration'; public $useTable = 'configuration'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'configuration'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Configuration'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'first'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Orthologs = class Orthologs { public $name = 'Orthologs'; public $useTable = 'orthologs'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'orthologs'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Orthologs'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'all'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL } }, $request = class CakeRequest { public $params = ['plugin' => NULL, 'controller' => 'orthologs', 'action' => 'explore', 'named' => [...], 'pass' => [...]]; public $data = []; public $query = []; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = ['get' => [...], 'patch' => [...], 'post' => [...], 'put' => [...], 'delete' => [...], 'head' => [...], 'options' => [...], 'ssl' => [...], 'ajax' => [...], 'flash' => [...], 'mobile' => [...], 'requested' => [...], 'json' => [...], 'xml' => [...]]; protected $_input = '' } ) | .../Dispatcher.php:167 |
| 4 | 0.1571 | 3124200 | Controller->invokeAction( $request = class CakeRequest { public $params = ['plugin' => NULL, 'controller' => 'orthologs', 'action' => 'explore', 'named' => [...], 'pass' => [...]]; public $data = []; public $query = []; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = ['get' => [...], 'patch' => [...], 'post' => [...], 'put' => [...], 'delete' => [...], 'head' => [...], 'options' => [...], 'ssl' => [...], 'ajax' => [...], 'flash' => [...], 'mobile' => [...], 'requested' => [...], 'json' => [...], 'xml' => [...]]; protected $_input = '' } ) | .../Dispatcher.php:193 |
| 5 | 0.1572 | 3124312 | invokeArgs( $object = class OrthologsController { public $name = 'Orthologs'; public $helpers = ['Session' => NULL, 'Html' => NULL, 'Form' => NULL, 'Cache' => NULL]; public $uses = [0 => 'Annotation', 1 => 'AnnotSource', 2 => 'Configuration', 3 => 'DnaMotifsCns', 4 => 'GfDatum', 5 => 'Msa', 6 => 'Orthologs', 7 => 'Similarities', 8 => 'Trees', 9 => 'AdExperiments', 10 => 'FunctionalClustersExperiments']; public $components = ['Session' => NULL, 'DataUtils' => NULL, 'FunctionalAnnotationUtils' => NULL, 'GeneFamilies' => NULL, 'Organism' => NULL, 'WorkbenchUtils' => NULL, 'Orthology' => NULL]; public $request = class CakeRequest { public $params = [...]; public $data = [...]; public $query = [...]; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = [...]; protected $_input = '' }; public $response = class CakeResponse { protected $_statusCodes = [...]; protected $_mimeTypes = [...]; protected $_protocol = 'HTTP/1.1'; protected $_status = 200; protected $_contentType = 'text/html'; protected $_headers = [...]; protected $_body = NULL; protected $_file = NULL; protected $_fileRange = NULL; protected $_charset = 'UTF-8'; protected $_cacheDirectives = [...]; protected $_cookies = [...] }; protected $_responseClass = 'CakeResponse'; public $viewPath = 'Orthologs'; public $layoutPath = NULL; public $viewVars = ['supporting_types' => [...], 'ortholog_types' => [...], 'all_organisms' => [...], 'target_species' => 'cme', 'query_species' => 'spe', 'query_gene' => 'Sopen11g022860', 'title_for_layout' => 'Dicots PLAZA 5.0 : Integrative Orthology']; public $view = 'explore'; public $layout = 'default'; public $autoRender = TRUE; public $autoLayout = TRUE; public $Components = class ComponentCollection { protected $_Controller = ...; protected $_enabled = [...]; protected $_loaded = [...]; public $defaultPriority = 10 }; public $viewClass = 'View'; public $View = NULL; public $ext = '.ctp'; public $plugin = NULL; public $cacheAction = FALSE; public $passedArgs = [0 => 'Sopen11g022860', 1 => 'cme']; public $scaffold = FALSE; public $methods = [1 => 'overview', 2 => 'explore', 3 => 'get_orthologs_type_data', 4 => 'get_supporting_data', 5 => 'get_supporting_type_data', 6 => 'get_orthologs_data']; public $modelClass = 'Annotation'; public $modelKey = 'ortholog'; public $validationErrors = NULL; protected $_mergeParent = 'AppController'; protected $_eventManager = class CakeEventManager { protected $_listeners = [...]; protected $_isGlobal = FALSE }; public $Session = class SessionComponent { protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $DataUtils = class DataUtilsComponent { public $name = 'DataUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $FunctionalAnnotationUtils = class FunctionalAnnotationUtilsComponent { public $name = 'FunctionalAnnotationUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $GeneFamilies = class GeneFamiliesComponent { public $name = 'GeneFamilies'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Organism = class OrganismComponent { public $name = 'Organism'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $WorkbenchUtils = class WorkbenchUtilsComponent { public $name = 'WorkbenchUtils'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $Orthology = class OrthologyComponent { public $name = 'Orthology'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Annotation = class Annotation { public $name = 'Annotation'; public $useTable = 'annotation'; public $primaryKey = 'gene_id'; public $cacheQueries = FALSE; public $cacheSources = FALSE; public $belongsTo = [...]; public $hasMany = [...]; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annotation'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Annotation'; public $tableToModel = [...]; public $hasOne = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $AnnotSource = class AnnotSource { public $name = 'AnnotSource'; public $useTable = 'annot_sources'; public $primaryKey = 'species'; public $displayField = 'common_name'; public $useDbConfig = 'default'; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annot_sources'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'AnnotSource'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Configuration = class Configuration { public $name = 'Configuration'; public $useTable = 'configuration'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'configuration'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Configuration'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'first'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Orthologs = class Orthologs { public $name = 'Orthologs'; public $useTable = 'orthologs'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'orthologs'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Orthologs'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'all'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL } }, $args = [0 => 'Sopen11g022860', 1 => 'cme'] ) | .../Controller.php:491 |
| 6 | 0.1572 | 3124408 | OrthologsController->explore( $query_gene = 'Sopen11g022860', $target_species = 'cme' ) | .../Controller.php:491 |
| 7 | 0.2455 | 5324264 | Orthologs->getOrthologsMappingData( $gene_id = 'Sopen11g022860', $query_species = 'spe', $target_species = 'cme' ) | .../OrthologsController.php:133 |
| 8 | 0.2455 | 5324264 | Orthologs->getOrthologs( $gene_ids = 'Sopen11g022860', $query_species = 'spe', $target_species = 'cme', $evidence_types = NULL, $required_num_evidences = NULL, $orthologous_relationship_types = NULL, $include_non_query_paralogs = TRUE ) | .../Orthologs.php:490 |
| 9 | 0.2606 | 7750552 | Model->find( $type = 'all', $query = ['conditions' => ['gene_id' => [...]]] ) | .../Orthologs.php:275 |
| 10 | 0.2607 | 7751248 | Model->_readDataSource( $type = 'all', $query = ['conditions' => ['gene_id' => [...]], 'fields' => NULL, 'joins' => [], 'limit' => NULL, 'offset' => NULL, 'order' => [], 'page' => 1, 'group' => NULL, 'callbacks' => TRUE] ) | .../Model.php:3013 |
| 11 | 0.2607 | 7751248 | CustomMysql->read( $Model = class Orthologs { public $name = 'Orthologs'; public $useTable = 'orthologs'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = []; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'orthologs'; public $primaryKey = 'id'; protected $_schema = ['gene_id' => [...], 'species' => [...], 'type' => [...], 'gene_content' => [...], 'comment' => [...]]; public $validate = []; public $validationErrors = []; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Orthologs'; public $tableToModel = ['orthologs' => 'Orthologs']; public $cacheQueries = FALSE; public $belongsTo = []; public $hasOne = []; public $hasMany = []; public $hasAndBelongsToMany = []; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { public $modelName = 'Orthologs'; protected $_methods = [...]; protected $_mappedMethods = [...]; protected $_enabled = [...]; protected $_loaded = [...]; public $defaultPriority = 10 }; public $whitelist = []; public $cacheSources = TRUE; public $findQueryType = 'all'; public $recursive = 1; public $order = NULL; public $virtualFields = []; protected $_associationKeys = ['belongsTo' => [...], 'hasOne' => [...], 'hasMany' => [...], 'hasAndBelongsToMany' => [...]]; protected $_associations = [0 => 'belongsTo', 1 => 'hasOne', 2 => 'hasMany', 3 => 'hasAndBelongsToMany']; public $__backAssociation = []; public $__backInnerAssociation = []; public $__backOriginalAssociation = []; public $__backContainableAssociation = []; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = ['all' => TRUE, 'first' => TRUE, 'count' => TRUE, 'neighbors' => TRUE, 'list' => TRUE, 'threaded' => TRUE]; protected $_eventManager = class CakeEventManager { protected $_listeners = [...]; protected $_isGlobal = FALSE }; protected $_validator = NULL }, $queryData = ['conditions' => ['gene_id' => [...]], 'fields' => NULL, 'joins' => [], 'limit' => NULL, 'offset' => NULL, 'order' => [], 'page' => 1, 'group' => NULL, 'callbacks' => TRUE], $recursive = ??? ) | .../Model.php:3041 |
| 12 | 0.2690 | 7826152 | DboSource->fetchAll( $sql = 'SELECT `Orthologs`.`gene_id`, `Orthologs`.`species`, `Orthologs`.`type`, `Orthologs`.`gene_content`, `Orthologs`.`comment` FROM `db_plaza_public_dicots_05`.`orthologs` AS `Orthologs` WHERE `gene_id` IN (\'Sopen11g022860\', \'Sopen05g025490\', \'Sopen05g020930\', \'Sopen12g012660\', \'Sopen06g010510\', \'Sopen10g021970\', \'Sopen03g018910\', \'Sopen12g013980\', \'Sopen09g017840\', \'Sopen08g011030\', \'Sopen02g004340\', \'Sopen08g012280\', \'Sopen09g013870\', \'Sopen01g010020\', \'Sopen02g009130\', \'Sopen12g017670\', \'Sopen03g035150\', '..., $params = FALSE, $options = ??? ) | .../CustomMysql.php:1129 |
| 13 | 0.2690 | 7826528 | DboSource->execute( $sql = 'SELECT `Orthologs`.`gene_id`, `Orthologs`.`species`, `Orthologs`.`type`, `Orthologs`.`gene_content`, `Orthologs`.`comment` FROM `db_plaza_public_dicots_05`.`orthologs` AS `Orthologs` WHERE `gene_id` IN (\'Sopen11g022860\', \'Sopen05g025490\', \'Sopen05g020930\', \'Sopen12g012660\', \'Sopen06g010510\', \'Sopen10g021970\', \'Sopen03g018910\', \'Sopen12g013980\', \'Sopen09g017840\', \'Sopen08g011030\', \'Sopen02g004340\', \'Sopen08g012280\', \'Sopen09g013870\', \'Sopen01g010020\', \'Sopen02g009130\', \'Sopen12g017670\', \'Sopen03g035150\', '..., $options = [], $params = [] ) | .../DboSource.php:702 |
| 14 | 0.2690 | 7826904 | DboSource->_execute( $sql = 'SELECT `Orthologs`.`gene_id`, `Orthologs`.`species`, `Orthologs`.`type`, `Orthologs`.`gene_content`, `Orthologs`.`comment` FROM `db_plaza_public_dicots_05`.`orthologs` AS `Orthologs` WHERE `gene_id` IN (\'Sopen11g022860\', \'Sopen05g025490\', \'Sopen05g020930\', \'Sopen12g012660\', \'Sopen06g010510\', \'Sopen10g021970\', \'Sopen03g018910\', \'Sopen12g013980\', \'Sopen09g017840\', \'Sopen08g011030\', \'Sopen02g004340\', \'Sopen08g012280\', \'Sopen09g013870\', \'Sopen01g010020\', \'Sopen02g009130\', \'Sopen12g017670\', \'Sopen03g035150\', '..., $params = [], $prepareOptions = ??? ) | .../DboSource.php:455 |
| 15 | 0.2690 | 7974872 | execute( $bound_input_params = [] ) | .../DboSource.php:489 |
| ( ! ) FatalErrorException: [CakeSessionException] Unable to configure the session, setting session.use_trans_sid failed.
#0 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(619): CakeSession::_configureSession()
#1 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(632): CakeSession::_cookieName()
#2 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(248): CakeSession::_hasSession()
#3 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/Helper/SessionHelper.php(134): CakeSession::check()
#4 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Console/Templates/skel/View/Layouts/error.ctp(35): SessionHelper->flash()
#5 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/View.php(971): include('/www/bioinforma...')
#6 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/View.php(933): View->_evaluate()
#7 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/View.php(546): View->_render()
#8 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/View/View.php(481): View->renderLayout()
#9 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ExceptionRenderer.php(328): View->render()
#10 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ExceptionRenderer.php(309): ExceptionRenderer->_outputMessageSafe()
#11 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ExceptionRenderer.php(213): ExceptionRenderer->_outputMessage()
#12 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ExceptionRenderer.php(190): ExceptionRenderer->_cakeError()
#13 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php(127): ExceptionRenderer->render()
#14 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php(269): ErrorHandler::handleException()
#15 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php(212): ErrorHandler::handleFatalError()
#16 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Core/App.php(970): ErrorHandler::handleError()
#17 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Core/App.php(943): App::_checkFatalError()
#18 [internal function]: App::shutdown()
#19 {main} in /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php on line 138 |
|---|
| Call Stack |
|---|
| # | Time | Memory | Function | Location |
|---|
| 1 | 0.0025 | 434592 | {main}( ) | .../index.php:0 |
| 2 | 0.0837 | 1903776 | Dispatcher->dispatch( $request = class CakeRequest { public $params = ['plugin' => NULL, 'controller' => 'orthologs', 'action' => 'explore', 'named' => [...], 'pass' => [...]]; public $data = []; public $query = []; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = ['get' => [...], 'patch' => [...], 'post' => [...], 'put' => [...], 'delete' => [...], 'head' => [...], 'options' => [...], 'ssl' => [...], 'ajax' => [...], 'flash' => [...], 'mobile' => [...], 'requested' => [...], 'json' => [...], 'xml' => [...]]; protected $_input = '' }, $response = class CakeResponse { protected $_statusCodes = [100 => 'Continue', 101 => 'Switching Protocols', 200 => 'OK', 201 => 'Created', 202 => 'Accepted', 203 => 'Non-Authoritative Information', 204 => 'No Content', 205 => 'Reset Content', 206 => 'Partial Content', 300 => 'Multiple Choices', 301 => 'Moved Permanently', 302 => 'Found', 303 => 'See Other', 304 => 'Not Modified', 305 => 'Use Proxy', 307 => 'Temporary Redirect', 400 => 'Bad Request', 401 => 'Unauthorized', 402 => 'Payment Required', 403 => 'Forbidden', 404 => 'Not Found', 405 => 'Method Not Allowed', 406 => 'Not Acceptable', 407 => 'Proxy Authentication Required', 408 => 'Request Time-out', 409 => 'Conflict', 410 => 'Gone', 411 => 'Length Required', 412 => 'Precondition Failed', 413 => 'Request Entity Too Large', 414 => 'Request-URI Too Large', 415 => 'Unsupported Media Type', 416 => 'Requested range not satisfiable', 417 => 'Expectation Failed', 429 => 'Too Many Requests', 500 => 'Internal Server Error', 501 => 'Not Implemented', 502 => 'Bad Gateway', 503 => 'Service Unavailable', 504 => 'Gateway Time-out', 505 => 'Unsupported Version']; protected $_mimeTypes = ['html' => [...], 'json' => 'application/json', 'xml' => [...], 'rss' => 'application/rss+xml', 'ai' => 'application/postscript', 'bcpio' => 'application/x-bcpio', 'bin' => 'application/octet-stream', 'ccad' => 'application/clariscad', 'cdf' => 'application/x-netcdf', 'class' => 'application/octet-stream', 'cpio' => 'application/x-cpio', 'cpt' => 'application/mac-compactpro', 'csh' => 'application/x-csh', 'csv' => [...], 'dcr' => 'application/x-director', 'dir' => 'application/x-director', 'dms' => 'application/octet-stream', 'doc' => 'application/msword', 'docx' => 'application/vnd.openxmlformats-officedocument.wordprocessingml.document', 'drw' => 'application/drafting', 'dvi' => 'application/x-dvi', 'dwg' => 'application/acad', 'dxf' => 'application/dxf', 'dxr' => 'application/x-director', 'eot' => 'application/vnd.ms-fontobject', 'eps' => 'application/postscript', 'exe' => 'application/octet-stream', 'ez' => 'application/andrew-inset', 'flv' => 'video/x-flv', 'gtar' => 'application/x-gtar', 'gz' => 'application/x-gzip', 'bz2' => 'application/x-bzip', '7z' => 'application/x-7z-compressed', 'hdf' => 'application/x-hdf', 'hqx' => 'application/mac-binhex40', 'ico' => 'image/x-icon', 'ips' => 'application/x-ipscript', 'ipx' => 'application/x-ipix', 'js' => 'application/javascript', 'jsonapi' => 'application/vnd.api+json', 'latex' => 'application/x-latex', 'lha' => 'application/octet-stream', 'lsp' => 'application/x-lisp', 'lzh' => 'application/octet-stream', 'man' => 'application/x-troff-man', 'me' => 'application/x-troff-me', 'mif' => 'application/vnd.mif', 'ms' => 'application/x-troff-ms', 'nc' => 'application/x-netcdf', 'oda' => 'application/oda', 'otf' => 'font/otf', 'pdf' => 'application/pdf', 'pgn' => 'application/x-chess-pgn', 'pot' => 'application/vnd.ms-powerpoint', 'pps' => 'application/vnd.ms-powerpoint', 'ppt' => 'application/vnd.ms-powerpoint', 'pptx' => 'application/vnd.openxmlformats-officedocument.presentationml.presentation', 'ppz' => 'application/vnd.ms-powerpoint', 'pre' => 'application/x-freelance', 'prt' => 'application/pro_eng', 'ps' => 'application/postscript', 'roff' => 'application/x-troff', 'scm' => 'application/x-lotusscreencam', 'set' => 'application/set', 'sh' => 'application/x-sh', 'shar' => 'application/x-shar', 'sit' => 'application/x-stuffit', 'skd' => 'application/x-koan', 'skm' => 'application/x-koan', 'skp' => 'application/x-koan', 'skt' => 'application/x-koan', 'smi' => 'application/smil', 'smil' => 'application/smil', 'sol' => 'application/solids', 'spl' => 'application/x-futuresplash', 'src' => 'application/x-wais-source', 'step' => 'application/STEP', 'stl' => 'application/SLA', 'stp' => 'application/STEP', 'sv4cpio' => 'application/x-sv4cpio', 'sv4crc' => 'application/x-sv4crc', 'svg' => 'image/svg+xml', 'svgz' => 'image/svg+xml', 'swf' => 'application/x-shockwave-flash', 't' => 'application/x-troff', 'tar' => 'application/x-tar', 'tcl' => 'application/x-tcl', 'tex' => 'application/x-tex', 'texi' => 'application/x-texinfo', 'texinfo' => 'application/x-texinfo', 'tr' => 'application/x-troff', 'tsp' => 'application/dsptype', 'ttc' => 'font/ttf', 'ttf' => 'font/ttf', 'unv' => 'application/i-deas', 'ustar' => 'application/x-ustar', 'vcd' => 'application/x-cdlink', 'vda' => 'application/vda', 'xlc' => 'application/vnd.ms-excel', 'xll' => 'application/vnd.ms-excel', 'xlm' => 'application/vnd.ms-excel', 'xls' => 'application/vnd.ms-excel', 'xlsx' => 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet', 'xlw' => 'application/vnd.ms-excel', 'zip' => 'application/zip', 'aif' => 'audio/x-aiff', 'aifc' => 'audio/x-aiff', 'aiff' => 'audio/x-aiff', 'au' => 'audio/basic', 'kar' => 'audio/midi', 'mid' => 'audio/midi', 'midi' => 'audio/midi', 'mp2' => 'audio/mpeg', 'mp3' => 'audio/mpeg', 'mpga' => 'audio/mpeg', 'ogg' => 'audio/ogg', 'oga' => 'audio/ogg', 'spx' => 'audio/ogg', 'ra' => 'audio/x-realaudio', 'ram' => 'audio/x-pn-realaudio', 'rm' => 'audio/x-pn-realaudio', 'rpm' => 'audio/x-pn-realaudio-plugin', 'snd' => 'audio/basic', 'tsi' => 'audio/TSP-audio', 'wav' => 'audio/x-wav', 'aac' => 'audio/aac', 'asc' => 'text/plain', 'c' => 'text/plain', ...]; protected $_protocol = 'HTTP/1.1'; protected $_status = 200; protected $_contentType = 'text/html'; protected $_headers = []; protected $_body = NULL; protected $_file = NULL; protected $_fileRange = NULL; protected $_charset = 'UTF-8'; protected $_cacheDirectives = []; protected $_cookies = [] }, $additionalParams = ??? ) | .../index.php:151 |
| 3 | 0.1309 | 2712280 | Dispatcher->_invoke( $controller = class OrthologsController { public $name = 'Orthologs'; public $helpers = ['Session' => NULL, 'Html' => NULL, 'Form' => NULL, 'Cache' => NULL]; public $uses = [0 => 'Annotation', 1 => 'AnnotSource', 2 => 'Configuration', 3 => 'DnaMotifsCns', 4 => 'GfDatum', 5 => 'Msa', 6 => 'Orthologs', 7 => 'Similarities', 8 => 'Trees', 9 => 'AdExperiments', 10 => 'FunctionalClustersExperiments']; public $components = ['Session' => NULL, 'DataUtils' => NULL, 'FunctionalAnnotationUtils' => NULL, 'GeneFamilies' => NULL, 'Organism' => NULL, 'WorkbenchUtils' => NULL, 'Orthology' => NULL]; public $request = class CakeRequest { public $params = [...]; public $data = [...]; public $query = [...]; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = [...]; protected $_input = '' }; public $response = class CakeResponse { protected $_statusCodes = [...]; protected $_mimeTypes = [...]; protected $_protocol = 'HTTP/1.1'; protected $_status = 200; protected $_contentType = 'text/html'; protected $_headers = [...]; protected $_body = NULL; protected $_file = NULL; protected $_fileRange = NULL; protected $_charset = 'UTF-8'; protected $_cacheDirectives = [...]; protected $_cookies = [...] }; protected $_responseClass = 'CakeResponse'; public $viewPath = 'Orthologs'; public $layoutPath = NULL; public $viewVars = ['supporting_types' => [...], 'ortholog_types' => [...], 'all_organisms' => [...], 'target_species' => 'cme', 'query_species' => 'spe', 'query_gene' => 'Sopen11g022860', 'title_for_layout' => 'Dicots PLAZA 5.0 : Integrative Orthology']; public $view = 'explore'; public $layout = 'default'; public $autoRender = TRUE; public $autoLayout = TRUE; public $Components = class ComponentCollection { protected $_Controller = ...; protected $_enabled = [...]; protected $_loaded = [...]; public $defaultPriority = 10 }; public $viewClass = 'View'; public $View = NULL; public $ext = '.ctp'; public $plugin = NULL; public $cacheAction = FALSE; public $passedArgs = [0 => 'Sopen11g022860', 1 => 'cme']; public $scaffold = FALSE; public $methods = [1 => 'overview', 2 => 'explore', 3 => 'get_orthologs_type_data', 4 => 'get_supporting_data', 5 => 'get_supporting_type_data', 6 => 'get_orthologs_data']; public $modelClass = 'Annotation'; public $modelKey = 'ortholog'; public $validationErrors = NULL; protected $_mergeParent = 'AppController'; protected $_eventManager = class CakeEventManager { protected $_listeners = [...]; protected $_isGlobal = FALSE }; public $Session = class SessionComponent { protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $DataUtils = class DataUtilsComponent { public $name = 'DataUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $FunctionalAnnotationUtils = class FunctionalAnnotationUtilsComponent { public $name = 'FunctionalAnnotationUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $GeneFamilies = class GeneFamiliesComponent { public $name = 'GeneFamilies'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Organism = class OrganismComponent { public $name = 'Organism'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $WorkbenchUtils = class WorkbenchUtilsComponent { public $name = 'WorkbenchUtils'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $Orthology = class OrthologyComponent { public $name = 'Orthology'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Annotation = class Annotation { public $name = 'Annotation'; public $useTable = 'annotation'; public $primaryKey = 'gene_id'; public $cacheQueries = FALSE; public $cacheSources = FALSE; public $belongsTo = [...]; public $hasMany = [...]; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annotation'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Annotation'; public $tableToModel = [...]; public $hasOne = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $AnnotSource = class AnnotSource { public $name = 'AnnotSource'; public $useTable = 'annot_sources'; public $primaryKey = 'species'; public $displayField = 'common_name'; public $useDbConfig = 'default'; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annot_sources'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'AnnotSource'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Configuration = class Configuration { public $name = 'Configuration'; public $useTable = 'configuration'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'configuration'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Configuration'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'first'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Orthologs = class Orthologs { public $name = 'Orthologs'; public $useTable = 'orthologs'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'orthologs'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Orthologs'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'all'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL } }, $request = class CakeRequest { public $params = ['plugin' => NULL, 'controller' => 'orthologs', 'action' => 'explore', 'named' => [...], 'pass' => [...]]; public $data = []; public $query = []; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = ['get' => [...], 'patch' => [...], 'post' => [...], 'put' => [...], 'delete' => [...], 'head' => [...], 'options' => [...], 'ssl' => [...], 'ajax' => [...], 'flash' => [...], 'mobile' => [...], 'requested' => [...], 'json' => [...], 'xml' => [...]]; protected $_input = '' } ) | .../Dispatcher.php:167 |
| 4 | 0.1571 | 3124200 | Controller->invokeAction( $request = class CakeRequest { public $params = ['plugin' => NULL, 'controller' => 'orthologs', 'action' => 'explore', 'named' => [...], 'pass' => [...]]; public $data = []; public $query = []; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = ['get' => [...], 'patch' => [...], 'post' => [...], 'put' => [...], 'delete' => [...], 'head' => [...], 'options' => [...], 'ssl' => [...], 'ajax' => [...], 'flash' => [...], 'mobile' => [...], 'requested' => [...], 'json' => [...], 'xml' => [...]]; protected $_input = '' } ) | .../Dispatcher.php:193 |
| 5 | 0.1572 | 3124312 | invokeArgs( $object = class OrthologsController { public $name = 'Orthologs'; public $helpers = ['Session' => NULL, 'Html' => NULL, 'Form' => NULL, 'Cache' => NULL]; public $uses = [0 => 'Annotation', 1 => 'AnnotSource', 2 => 'Configuration', 3 => 'DnaMotifsCns', 4 => 'GfDatum', 5 => 'Msa', 6 => 'Orthologs', 7 => 'Similarities', 8 => 'Trees', 9 => 'AdExperiments', 10 => 'FunctionalClustersExperiments']; public $components = ['Session' => NULL, 'DataUtils' => NULL, 'FunctionalAnnotationUtils' => NULL, 'GeneFamilies' => NULL, 'Organism' => NULL, 'WorkbenchUtils' => NULL, 'Orthology' => NULL]; public $request = class CakeRequest { public $params = [...]; public $data = [...]; public $query = [...]; public $url = 'orthologs/explore/Sopen11g022860/cme'; public $base = '/plaza.dev/_dev_instances/feedback'; public $webroot = '/plaza.dev/_dev_instances/feedback/'; public $here = '/plaza.dev/_dev_instances/feedback/orthologs/explore/Sopen11g022860/cme'; protected $_detectors = [...]; protected $_input = '' }; public $response = class CakeResponse { protected $_statusCodes = [...]; protected $_mimeTypes = [...]; protected $_protocol = 'HTTP/1.1'; protected $_status = 200; protected $_contentType = 'text/html'; protected $_headers = [...]; protected $_body = NULL; protected $_file = NULL; protected $_fileRange = NULL; protected $_charset = 'UTF-8'; protected $_cacheDirectives = [...]; protected $_cookies = [...] }; protected $_responseClass = 'CakeResponse'; public $viewPath = 'Orthologs'; public $layoutPath = NULL; public $viewVars = ['supporting_types' => [...], 'ortholog_types' => [...], 'all_organisms' => [...], 'target_species' => 'cme', 'query_species' => 'spe', 'query_gene' => 'Sopen11g022860', 'title_for_layout' => 'Dicots PLAZA 5.0 : Integrative Orthology']; public $view = 'explore'; public $layout = 'default'; public $autoRender = TRUE; public $autoLayout = TRUE; public $Components = class ComponentCollection { protected $_Controller = ...; protected $_enabled = [...]; protected $_loaded = [...]; public $defaultPriority = 10 }; public $viewClass = 'View'; public $View = NULL; public $ext = '.ctp'; public $plugin = NULL; public $cacheAction = FALSE; public $passedArgs = [0 => 'Sopen11g022860', 1 => 'cme']; public $scaffold = FALSE; public $methods = [1 => 'overview', 2 => 'explore', 3 => 'get_orthologs_type_data', 4 => 'get_supporting_data', 5 => 'get_supporting_type_data', 6 => 'get_orthologs_data']; public $modelClass = 'Annotation'; public $modelKey = 'ortholog'; public $validationErrors = NULL; protected $_mergeParent = 'AppController'; protected $_eventManager = class CakeEventManager { protected $_listeners = [...]; protected $_isGlobal = FALSE }; public $Session = class SessionComponent { protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $DataUtils = class DataUtilsComponent { public $name = 'DataUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $FunctionalAnnotationUtils = class FunctionalAnnotationUtilsComponent { public $name = 'FunctionalAnnotationUtils'; public $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $GeneFamilies = class GeneFamiliesComponent { public $name = 'GeneFamilies'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Organism = class OrganismComponent { public $name = 'Organism'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $WorkbenchUtils = class WorkbenchUtilsComponent { public $name = 'WorkbenchUtils'; private $controller = ...; public $components = [...]; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; protected $_componentMap = [...] }; public $Orthology = class OrthologyComponent { public $name = 'Orthology'; private $controller = ...; protected $_Collection = class ComponentCollection { ... }; public $settings = [...]; public $components = [...]; protected $_componentMap = [...] }; public $Annotation = class Annotation { public $name = 'Annotation'; public $useTable = 'annotation'; public $primaryKey = 'gene_id'; public $cacheQueries = FALSE; public $cacheSources = FALSE; public $belongsTo = [...]; public $hasMany = [...]; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annotation'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Annotation'; public $tableToModel = [...]; public $hasOne = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $AnnotSource = class AnnotSource { public $name = 'AnnotSource'; public $useTable = 'annot_sources'; public $primaryKey = 'species'; public $displayField = 'common_name'; public $useDbConfig = 'default'; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'annot_sources'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'AnnotSource'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = NULL; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Configuration = class Configuration { public $name = 'Configuration'; public $useTable = 'configuration'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'configuration'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Configuration'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'first'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL }; public $Orthologs = class Orthologs { public $name = 'Orthologs'; public $useTable = 'orthologs'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = [...]; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'orthologs'; public $primaryKey = 'id'; protected $_schema = [...]; public $validate = [...]; public $validationErrors = [...]; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Orthologs'; public $tableToModel = [...]; public $cacheQueries = FALSE; public $belongsTo = [...]; public $hasOne = [...]; public $hasMany = [...]; public $hasAndBelongsToMany = [...]; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { ... }; public $whitelist = [...]; public $cacheSources = TRUE; public $findQueryType = 'all'; public $recursive = 1; public $order = NULL; public $virtualFields = [...]; protected $_associationKeys = [...]; protected $_associations = [...]; public $__backAssociation = [...]; public $__backInnerAssociation = [...]; public $__backOriginalAssociation = [...]; public $__backContainableAssociation = [...]; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = [...]; protected $_eventManager = class CakeEventManager { ... }; protected $_validator = NULL } }, $args = [0 => 'Sopen11g022860', 1 => 'cme'] ) | .../Controller.php:491 |
| 6 | 0.1572 | 3124408 | OrthologsController->explore( $query_gene = 'Sopen11g022860', $target_species = 'cme' ) | .../Controller.php:491 |
| 7 | 0.2455 | 5324264 | Orthologs->getOrthologsMappingData( $gene_id = 'Sopen11g022860', $query_species = 'spe', $target_species = 'cme' ) | .../OrthologsController.php:133 |
| 8 | 0.2455 | 5324264 | Orthologs->getOrthologs( $gene_ids = 'Sopen11g022860', $query_species = 'spe', $target_species = 'cme', $evidence_types = NULL, $required_num_evidences = NULL, $orthologous_relationship_types = NULL, $include_non_query_paralogs = TRUE ) | .../Orthologs.php:490 |
| 9 | 0.2606 | 7750552 | Model->find( $type = 'all', $query = ['conditions' => ['gene_id' => [...]]] ) | .../Orthologs.php:275 |
| 10 | 0.2607 | 7751248 | Model->_readDataSource( $type = 'all', $query = ['conditions' => ['gene_id' => [...]], 'fields' => NULL, 'joins' => [], 'limit' => NULL, 'offset' => NULL, 'order' => [], 'page' => 1, 'group' => NULL, 'callbacks' => TRUE] ) | .../Model.php:3013 |
| 11 | 0.2607 | 7751248 | CustomMysql->read( $Model = class Orthologs { public $name = 'Orthologs'; public $useTable = 'orthologs'; public $useDbConfig = 'default'; public $displayField = *uninitialized*; public $id = FALSE; public $data = []; public $schemaName = 'db_plaza_public_dicots_05'; public $table = 'orthologs'; public $primaryKey = 'id'; protected $_schema = ['gene_id' => [...], 'species' => [...], 'type' => [...], 'gene_content' => [...], 'comment' => [...]]; public $validate = []; public $validationErrors = []; public $validationDomain = NULL; public $tablePrefix = ''; public $plugin = NULL; public $alias = 'Orthologs'; public $tableToModel = ['orthologs' => 'Orthologs']; public $cacheQueries = FALSE; public $belongsTo = []; public $hasOne = []; public $hasMany = []; public $hasAndBelongsToMany = []; public $actsAs = NULL; public $Behaviors = class BehaviorCollection { public $modelName = 'Orthologs'; protected $_methods = [...]; protected $_mappedMethods = [...]; protected $_enabled = [...]; protected $_loaded = [...]; public $defaultPriority = 10 }; public $whitelist = []; public $cacheSources = TRUE; public $findQueryType = 'all'; public $recursive = 1; public $order = NULL; public $virtualFields = []; protected $_associationKeys = ['belongsTo' => [...], 'hasOne' => [...], 'hasMany' => [...], 'hasAndBelongsToMany' => [...]]; protected $_associations = [0 => 'belongsTo', 1 => 'hasOne', 2 => 'hasMany', 3 => 'hasAndBelongsToMany']; public $__backAssociation = []; public $__backInnerAssociation = []; public $__backOriginalAssociation = []; public $__backContainableAssociation = []; public $__safeUpdateMode = FALSE; public $useConsistentAfterFind = TRUE; protected $_insertID = NULL; protected $_sourceConfigured = TRUE; public $findMethods = ['all' => TRUE, 'first' => TRUE, 'count' => TRUE, 'neighbors' => TRUE, 'list' => TRUE, 'threaded' => TRUE]; protected $_eventManager = class CakeEventManager { protected $_listeners = [...]; protected $_isGlobal = FALSE }; protected $_validator = NULL }, $queryData = ['conditions' => ['gene_id' => [...]], 'fields' => NULL, 'joins' => [], 'limit' => NULL, 'offset' => NULL, 'order' => [], 'page' => 1, 'group' => NULL, 'callbacks' => TRUE], $recursive = ??? ) | .../Model.php:3041 |
| 12 | 0.2690 | 7826152 | DboSource->fetchAll( $sql = 'SELECT `Orthologs`.`gene_id`, `Orthologs`.`species`, `Orthologs`.`type`, `Orthologs`.`gene_content`, `Orthologs`.`comment` FROM `db_plaza_public_dicots_05`.`orthologs` AS `Orthologs` WHERE `gene_id` IN (\'Sopen11g022860\', \'Sopen05g025490\', \'Sopen05g020930\', \'Sopen12g012660\', \'Sopen06g010510\', \'Sopen10g021970\', \'Sopen03g018910\', \'Sopen12g013980\', \'Sopen09g017840\', \'Sopen08g011030\', \'Sopen02g004340\', \'Sopen08g012280\', \'Sopen09g013870\', \'Sopen01g010020\', \'Sopen02g009130\', \'Sopen12g017670\', \'Sopen03g035150\', '..., $params = FALSE, $options = ??? ) | .../CustomMysql.php:1129 |
| 13 | 0.2690 | 7826528 | DboSource->execute( $sql = 'SELECT `Orthologs`.`gene_id`, `Orthologs`.`species`, `Orthologs`.`type`, `Orthologs`.`gene_content`, `Orthologs`.`comment` FROM `db_plaza_public_dicots_05`.`orthologs` AS `Orthologs` WHERE `gene_id` IN (\'Sopen11g022860\', \'Sopen05g025490\', \'Sopen05g020930\', \'Sopen12g012660\', \'Sopen06g010510\', \'Sopen10g021970\', \'Sopen03g018910\', \'Sopen12g013980\', \'Sopen09g017840\', \'Sopen08g011030\', \'Sopen02g004340\', \'Sopen08g012280\', \'Sopen09g013870\', \'Sopen01g010020\', \'Sopen02g009130\', \'Sopen12g017670\', \'Sopen03g035150\', '..., $options = [], $params = [] ) | .../DboSource.php:702 |
| 14 | 0.2690 | 7826904 | DboSource->_execute( $sql = 'SELECT `Orthologs`.`gene_id`, `Orthologs`.`species`, `Orthologs`.`type`, `Orthologs`.`gene_content`, `Orthologs`.`comment` FROM `db_plaza_public_dicots_05`.`orthologs` AS `Orthologs` WHERE `gene_id` IN (\'Sopen11g022860\', \'Sopen05g025490\', \'Sopen05g020930\', \'Sopen12g012660\', \'Sopen06g010510\', \'Sopen10g021970\', \'Sopen03g018910\', \'Sopen12g013980\', \'Sopen09g017840\', \'Sopen08g011030\', \'Sopen02g004340\', \'Sopen08g012280\', \'Sopen09g013870\', \'Sopen01g010020\', \'Sopen02g009130\', \'Sopen12g017670\', \'Sopen03g035150\', '..., $params = [], $prepareOptions = ??? ) | .../DboSource.php:455 |
| 15 | 0.2690 | 7974872 | execute( $bound_input_params = [] ) | .../DboSource.php:489 |
| 16 | 2.1024 | 397612832 | App::shutdown( ) | .../App.php:0 |
| 17 | 2.1025 | 397612864 | App::_checkFatalError( ) | .../App.php:943 |
| 18 | 2.1025 | 397613608 | ErrorHandler::handleError( $code = 1, $description = 'Allowed memory size of 402653184 bytes exhausted (tried to allocate 204800 bytes)', $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/DboSource.php', $line = 489, $context = [] ) | .../App.php:970 |
| 19 | 2.1025 | 397613608 | ErrorHandler::handleFatalError( $code = 1, $description = 'Allowed memory size of 402653184 bytes exhausted (tried to allocate 204800 bytes)', $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/DboSource.php', $line = 489 ) | .../ErrorHandler.php:212 |
| 20 | 2.1080 | 397566808 | ErrorHandler::handleException( $exception = class FatalErrorException { protected $_attributes = []; protected $_messageTemplate = ''; protected $_responseHeaders = NULL; protected $message = 'Allowed memory size of 402653184 bytes exhausted (tried to allocate 204800 bytes)'; private ${Exception}string = ''; protected $code = 500; protected $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/DboSource.php'; protected $line = 489; private ${Exception}trace = [0 => [...], 1 => [...], 2 => [...], 3 => [...]]; private ${Exception}previous = NULL } ) | .../ErrorHandler.php:269 |
| 21 | 2.2746 | 399123208 | trigger_error( $message = '[CakeSessionException] Unable to configure the session, setting session.use_trans_sid failed.\n#0 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(619): CakeSession::_configureSession()\n#1 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(632): CakeSession::_cookieName()\n#2 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(248): CakeSession::_hasSession()\n#3 /www/bioin'..., $error_type = 256 ) | .../ErrorHandler.php:138 |
| 22 | 2.2746 | 399128824 | ErrorHandler::handleError( $code = 256, $description = '[CakeSessionException] Unable to configure the session, setting session.use_trans_sid failed.\n#0 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(619): CakeSession::_configureSession()\n#1 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(632): CakeSession::_cookieName()\n#2 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(248): CakeSession::_hasSession()\n#3 /www/bioin'..., $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php', $line = 138, $context = ['exception' => class FatalErrorException { protected $_attributes = [...]; protected $_messageTemplate = ''; protected $_responseHeaders = NULL; protected $message = 'Allowed memory size of 402653184 bytes exhausted (tried to allocate 204800 bytes)'; private ${Exception}string = ''; protected $code = 500; protected $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/DboSource.php'; protected $line = 489; private ${Exception}trace = [...]; private ${Exception}previous = NULL }, 'config' => ['handler' => 'ErrorHandler::handleException', 'renderer' => 'ExceptionRenderer', 'log' => TRUE], 'renderer' => 'ExceptionRenderer', 'error' => class ExceptionRenderer { public $controller = class CakeErrorController { ... }; public $template = 'fatalError'; public $method = '_cakeError'; public $error = class FatalErrorException { ... } }, 'e' => class CakeSessionException { protected $_attributes = [...]; protected $_messageTemplate = ''; protected $_responseHeaders = NULL; protected $message = 'Unable to configure the session, setting session.use_trans_sid failed.'; private ${Exception}string = ''; protected $code = 500; protected $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php'; protected $line = 582; private ${Exception}trace = [...]; private ${Exception}previous = NULL; public $xdebug_message = '<tr><th align=\'left\' bgcolor=\'#f57900\' colspan="5"><span style=\'background-color: #cc0000; color: #fce94f; font-size: x-large;\'>( ! )</span> CakeSessionException: Unable to configure the session, setting session.use_trans_sid failed. in /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php on line <i>582</i></th></tr>\n<tr><th align=\'left\' bgcolor=\'#e9b96e\' colspan=\'5\'>Call Stack</th></tr>\n<tr><th align=\'center\' bgcolor=\'#eeeeec\'>#</th><th align=\'left\' bgcolor=\'#eee'... }, 'message' => '[CakeSessionException] Unable to configure the session, setting session.use_trans_sid failed.\n#0 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(619): CakeSession::_configureSession()\n#1 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(632): CakeSession::_cookieName()\n#2 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(248): CakeSession::_hasSession()\n#3 /www/bioin'...] ) | .../ErrorHandler.php:138 |
| 23 | 2.2746 | 399128824 | ErrorHandler::handleFatalError( $code = 256, $description = '[CakeSessionException] Unable to configure the session, setting session.use_trans_sid failed.\n#0 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(619): CakeSession::_configureSession()\n#1 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(632): CakeSession::_cookieName()\n#2 /www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Model/Datasource/CakeSession.php(248): CakeSession::_hasSession()\n#3 /www/bioin'..., $file = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib/Cake/Error/ErrorHandler.php', $line = 138 ) | .../ErrorHandler.php:212 |