render ( 'search', array ( 'model' => $model, 'selectionLists' => $this->selectionLists, 'submitURL' => $this->submitURL ) ); } catch (\yii\base\ErrorException $e) { Yii::$app->mailer->compose() ->setFrom('errorggbn@bgbm.org') ->setTo('p.kelbert@bgbm.org') ->setSubject('Error occured') ->setTextBody($e) ->send(); return $this->render('site/error', ["name"=>"Oooops", "message"=>"Something went wrong.","exception"=>$e]); } } public function actionBold() { $att = Yii::$app->request->get (); foreach ( $att as $k => $v ) { if (! empty ( $k )) ExploreManager::getBOLDRecord ( $k ); } } public function actionGbif() { $att = Yii::$app->request->get (); foreach ( $att as $k => $v ) { if (! empty ( $k )) ExploreManager::getGBIFRecord ( $k ); } } public function actionNcbi() { $att = Yii::$app->request->get (); foreach ( $att as $k => $v ) { if (! empty ( $k )) ExploreManager::getNCBIRecord( $k ); } } public function actionTree($id, $name, $rank, $kingdom, $phylum, $classis, $ordo, $family, $genus,$institution) { $elts = Yii::$app->request->get (); // $connection = new \yii\db\Connection ( Yii::$app->db ); // $connection->open (); $x = ""; // the child rank $y = $rank; // the current rank for SOLR switch ($rank) { case "kingdom" : $x = $z = "phylum"; break; case "phylum" : $x = $z = "classis"; $z = "class"; break; case "class" : $x = "ordo"; $y = "classis"; $z = "order"; break; case "order" : $x = $z = "family"; $y = "ordo"; break; case "family" : $x = $z = "genus"; break; case "genus" : $x = "name"; $z = "species"; break; case "species" : $x = "name"; $z = "species"; break; default : $sep = "   "; break; } $config = SOLRQueryManager::getConfigColTree (); $queryTree = SOLRQueryManager::createSearchQuery ( $config ); $q = "parent_id:" . $id; $fq = null; // $fq="{!join from=parent_id to=taxonID fromIndex=colTree}"; $raw_responseTree = SOLRQueryManager::fillAndExecuteQuery ( $queryTree, $q, $fq, [ ], False ); $docsTree = $raw_responseTree->getDocuments (); // $tree = "

"; $tree2 = "
"; $connection = new \yii\db\Connection ( Yii::$app->db ); $connection->open (); foreach ( $docsTree as $docTree ) { // $tree2.="search ".$docTree->name." and rank ".$rank."
"; if (! empty ( $x )) { $sql = "select count(distinct fullscientificname) as nbChildren, count(distinct occurrenceid) as nbOccurrences, FIELDS from treeoflife where kingdom='" . $kingdom . "'"; $groupby = [ ]; $selectFields = [ ]; if ($rank == "kingdom") $sql .= " AND phylum='" . $docTree->name . "'"; if ($rank == "phylum") $sql .= " AND classis='" . $docTree->name . "'"; if ($rank == "class") $sql .= " AND ordo='" . $docTree->name . "'"; if ($rank == "order") $sql .= " AND family='" . $docTree->name . "'"; if ($rank == "family") $sql .= " AND genus='" . $docTree->name . "'"; if ($rank == "genus") $sql .= " AND canonicalNameChecklist='" . $docTree->name . "'"; // $config = SOLRQueryManager::getConfigBackbone (); // $query = SOLRQueryManager::createSearchQuery ( $config ); $value = $this->getValue ( $docTree->name, $x ); $q = $value . " AND rank:" . strtoupper ( $z ); if (! empty ( $kingdom ) && $kingdom != "null") { $q .= " AND " . $this->getValue ( $kingdom, "kingdom" ); $groupby = [ "kingdom", "phylum" ]; } if (! empty ( $phylum ) && $phylum != "null") { $q .= " AND " . $this->getValue ( $phylum, "phylum" ); $sql .= " AND " . $this->getSQLValue ( $phylum, "phylum" ); $groupby = [ "kingdom", "phylum", "classis" ]; } if (! empty ( $classis ) && $classis != "null") { $q .= " AND " . $this->getValue ( $classis, "classis" ); $sql .= " AND " . $this->getSQLValue ( $classis, "classis" ); $groupby = [ "kingdom", "phylum", "classis", "ordo" ]; } if (! empty ( $ordo ) && $ordo != "null") { $q .= " AND " . $this->getValue ( $ordo, "ordo" ); $sql .= " AND " . $this->getSQLValue ( $ordo, "ordo" ); $groupby = [ "kingdom", "phylum", "classis", "ordo", "family" ]; } if (! empty ( $family ) && $family != "null") { $q .= " AND " . $this->getValue ( $family, "family" ); $sql .= " AND " . $this->getSQLValue ( $family, "family" ); $groupby = [ "kingdom", "phylum", "classis", "ordo", "family", "genus" ]; } if (! empty ( $genus ) && $genus != "null") { $q .= " AND " . $this->getValue ( $genus, "genus" ); $sql .= " AND " . $this->getSQLValue ( $genus, "genus" ); $groupby = [ "kingdom", "phylum", "classis", "ordo", "family", "genus", "fullscientificname" ]; } if(isset($institution) && $institution!="---") $sql .=" AND institution='".$institution."'"; $sql .= " group by " . implode ( ", ", $groupby ); $inst=""; if(isset ($institution) && !empty($institution)) $inst="&institution=".str_ireplace("---", "", $institution); $fields = [ ]; foreach ( $groupby as $f ) { $fields [] = " IFNULL (" . $f . ", 'Not assigned' ) as " . $f; } $sql = str_ireplace ( "FIELDS", implode ( ", ", $fields ), $sql ); // echo $sql . "
"; // $tree2.=$sql; $command = $connection->createCommand ( $sql ); $dataReader = $command->queryAll (); $ok = false; foreach ( $dataReader as $row ) { $ok = true; $nbOccurrences = $row ['nbOccurrences']; $nbTaxChildren = $row ['nbChildren']; $mykingdom = $row ['kingdom']; if (isset ( $row ['phylum'] )) $myphylum = $row ['phylum']; else $myphylum = ""; if (isset ( $row ['ordo'] )) $myordo = $row ['ordo']; else $myordo = ""; if (isset ( $row ['classis'] )) $myclassis = $row ['classis']; else $myclassis = ""; if (isset ( $row ['family'] )) $myfamily = $row ['family']; else $myfamily = ""; if (isset ( $row ['phylum'] )) $myphylum = $row ['phylum']; else $myphylum = ""; if (isset ( $row ['genus'] )) $mygenus = $row ['genus']; else $mygenus = ""; $currentName = $docTree->name; $cl = "col_absent"; $butterfly = ""; if ($docTree->total_species_extant == 0) { if ($nbOccurrences > 0) { $cl = "col_present"; $butterfly = ""; } $tree2 .= "
• " . $docTree->name . "" . $butterfly . "
"; } else { if ($nbOccurrences > 0) { $cl = "col_present"; $butterfly = ""; } $tree2 .= "
• " . $docTree->name . " (" . $nbTaxChildren . " / " . $nbOccurrences . " )" . $butterfly . "
"; } } if (! $ok) { $cl = "col_absent"; $butterfly = ""; if ($docTree->total_species_extant == 0) { $tree2 .= "
• " . $docTree->name . "
"; } else $tree2 .= "
• " . $docTree->name . " (0 / 0)
"; } Yii::$app->db->close (); // $fq = null; // $raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, $q, $fq, [ ], False ); // $nbHits = $raw_response->getNumFound (); // $docs = $raw_response->getDocuments (); // $nbOccurrences = 0; // $nbTaxChildren = 0; // if ($nbHits > 0) { // foreach ( $docs as $doc ) { // $nbOccurrences = 0; // $nbTaxChildren = 0; // $nbOccurrences = $doc->occurrenceCount; // if (empty ( $nbOccurrences )) // $nbOccurrences = 0; // $nbTaxChildren = $doc->childrenCount; // if (empty ( $nbTaxChildren )) // $nbTaxChildren = 0; // $cl = "col_absent"; // $butterfly = ""; // if ($docTree->total_species_extant == 0) { // if ($nbOccurrences > 0) { // $cl = "col_present"; // $butterfly = ""; // } // $tree .= "
• " . $docTree->name . "" . $butterfly . "
"; // } else { // if ($nbOccurrences > 0) { // $cl = "col_present"; // $butterfly = ""; // } // $tree .= "
• " . $docTree->name . " (" . $nbTaxChildren . " / " . $nbOccurrences . " )" . $butterfly . "
"; // } // } // } else { // $cl = "col_absent"; // $butterfly = ""; // if ($docTree->total_species_extant == 0) { // $tree .= "
• " . $docTree->name . "
"; // } else // $tree .= "
• " . $docTree->name . " (0 / 0)
"; // } } } Yii::$app->db->close (); // $tree .= "
"; $tree2 .= "

"; echo $tree2; } private function getValue($value, $field) { $valuep = str_replace ( " ", "\ ", $value ); if ($value == "Not assigned") { $valuep = " ( " . $field . ":" . $valuep . " OR " . $field . ":N/A OR " . $field . ":null ) "; } else $valuep = $field . ':' . $valuep; return $valuep; } private function getSQLValue($value, $field) { if ($value == "Not assigned") { $value = " ( " . $field . "='" . $value . "' OR " . $field . "='N/A' OR " . $field . " is null ) "; } else $value = $field . "='" . $value . "'"; return $value; } }