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<?php
//declare(encoding='UTF-8');
/**
 * Exemple de lancement du script : :
 * /opt/lampp/bin/php cli.php taxref -a chargerTous
 *
 * @category    php 5.2
 * @package             eFlore/Scripts
 * @author              Jean-Pascal MILCENT <jpm@tela-botanica.org>
 * @copyright   Copyright (c) 2012, Tela Botanica (accueil@tela-botanica.org)
 * @license             http://www.cecill.info/licences/Licence_CeCILL_V2-fr.txt Licence CECILL
 * @license             http://www.gnu.org/licenses/gpl.html Licence GNU-GPL
 * @version             $Id$
 */
class Taxref extends EfloreScript {

        private $table = null;
        private $pasInsertion = 1000;
        private $departInsertion = 0;

        protected $parametres_autorises = array(
                '-t' => array(false, false, 'Permet de tester le script sur un jeu réduit de données (indiquer le nombre de lignes).'));

        public function executer() {
                try {
                        $this->initialiserProjet('taxref');

                        // Lancement de l'action demandée
                        $cmd = $this->getParametre('a');
                        switch ($cmd) {
                                case 'chargerTous' :
                                        $this->chargerStructureSql();
                                        $this->chargertaxref();
                                        $this->genererChpNumTax();
                                        $this->genererChpNomSciHtml();
                                        $this->genererChpFamille();
                                        $this->genererChpNomComplet();
                                        $this->genererChpHierarchie();
                                        break;
                                case 'chargerStructureSql' :
                                        $this->chargerStructureSql();
                                        break;
                                case 'chargerTaxref' :
                                        $this->chargerTaxref();
                                        break;
                                case 'genererChpNumTax' :
                                        $this->genererChpNumTax();
                                        break;
                                case 'genererChpNomSciHtml' :
                                        $this->genererChpNomSciHtml();
                                        break;
                                case 'genererChpNomComplet' :
                                        $this->initialiserGenerationChamps();
                                        $this->genererChpNomComplet();
                                        break;
                                case 'genererChpFamille' :
                                        $this->genererChpFamille();
                                        break;
                                case 'genererChpHierarchie' :
                                        $this->genererChpHierarchie();
                                        break;
                                case 'supprimerTous' :
                                        $this->supprimerTous();
                                        break;
                                default :
                                        throw new Exception("Erreur : la commande '$cmd' n'existe pas!");
                        }
                } catch (Exception $e) {
                        $this->traiterErreur($e->getMessage());
                }
        }

        private function chargerTaxref() {
                $chemin = Config::get('chemins.bdt');
                $table = Config::get('tables.taxref');
                $requete = "LOAD DATA INFILE '$chemin' ".
                                "REPLACE INTO TABLE $table ".
                                'CHARACTER SET utf8 '.
                                'FIELDS '.
                                "       TERMINATED BY '\t' ".
                                "       ENCLOSED BY '' ".
                                "       ESCAPED BY '\\\' ".
                                'IGNORE 1 LINES';
                $this->getBdd()->requeter($requete);
        }
        
        private function genererChpNumTax() {
                $this->initialiserGenerationChamps();
                $this->preparerTablePrChpNumTax();
                $erreurs = array();
                $this->departInsertion = 0;
                $dernier_num_tax = 0;
                
                $requete = 'SELECT num_nom '.
                                        'FROM '.$this->table.' '.
                                        'WHERE num_nom = num_nom_retenu AND num_nom_retenu != 0 '.
                                        'ORDER by num_nom_retenu ASC ';

                $resultat = $this->getBdd()->recupererTous($requete);
                foreach ($resultat as $taxon) {
                        $dernier_num_tax++;
                        $requete_maj = 'UPDATE '.$this->table.' '.
                                                        'SET num_taxonomique = '.$dernier_num_tax.' '.
                                                        'WHERE num_nom_retenu = '.$taxon['num_nom'];
                        $this->getBdd()->requeter($requete_maj);
                        $this->pasInsertion++;
                        $this->afficherAvancement("Insertion des num tax, ".count($resultat)." num tax a traiter");
                }
                echo "\n";
                $this->creerFichierLog('Erreurs lors de la génération des numéros taxonomiques', $erreurs, 'erreurs_num_tax');
        }
        
        private function preparerTablePrChpNumTax() {
                $requete = "SHOW COLUMNS FROM {$this->table} LIKE 'num_taxonomique' ";
                $resultat = $this->getBdd()->recuperer($requete);
                if ($resultat === false) {
                        $requete =      "ALTER TABLE {$this->table} ".
                                                'ADD num_taxonomique INT( 9 ) ';
                        $this->getBdd()->requeter($requete);
                }
        }

        private function genererChpNomSciHtml() {
                $this->initialiserGenerationChamps();
                $this->preparerTablePrChpNomSciHtml();
                $generateur = new GenerateurNomSciHtml();
                $nbreTotal = $this->recupererNbTotalTuples();
                $erreurs = array();
                $this->departInsertion = 0;
                while ($this->departInsertion < $nbreTotal) {
                        $resultat = $this->recupererTuplesPrChpNomSciHtml();

                        try {
                                $nomsSciEnHtml = $generateur->generer($resultat);
                        } catch (Exception $e) {
                                $erreurs[] = $e->getMessage();
                        }

                        $this->remplirChpNomSciHtm($nomsSciEnHtml);
                        $this->departInsertion += $this->pasInsertion;
                        $this->afficherAvancement("Insertion des noms scientifique au format HTML dans la base par paquet de {$this->pasInsertion} en cours");
                        if ($this->stopperLaBoucle($this->getParametre('t'))) break;
                }
                echo "\n";

                $this->creerFichierLog('Erreurs lors de la génération HTML des noms scientifiques', $erreurs, 'erreurs_noms_sci_html');
        }

        private function initialiserGenerationChamps() {
                $this->table = Config::get('tables.taxref');
        }

        private function preparerTablePrChpNomSciHtml() {
                $requete = "SHOW COLUMNS FROM {$this->table} LIKE 'nom_sci_html' ";
                $resultat = $this->getBdd()->recuperer($requete);
                if ($resultat === false) {
                        $requete =      "ALTER TABLE {$this->table} ".
                                        'ADD nom_sci_html VARCHAR( 500 ) '.
                                        'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
                        $this->getBdd()->requeter($requete);
                }
        }

        private function recupererNbTotalTuples(){
                $requete = "SELECT count(*) AS nb FROM {$this->table} ";
                $resultat = $this->getBdd()->recuperer($requete);
                return $resultat['nb'];
        }

        private function recupererTuplesPrChpNomSciHtml() {
                $requete = 'SELECT      num_nom, rang, genre, '.
                                '       epithete_sp, type_epithete, epithete_infra_sp '.
                                "FROM {$this->table} ".
                                "LIMIT {$this->departInsertion},{$this->pasInsertion} ";
                $resultat = $this->getBdd()->recupererTous($requete);
                return $resultat;
        }

        private function remplirChpNomSciHtm($nomsSciHtm) {
                foreach ($nomsSciHtm as $id => $html) {
                        $html = $this->getBdd()->proteger($html);
                        $requete = "UPDATE {$this->table} SET nom_sci_html = $html WHERE num_nom = $id ";
                        $resultat = $this->getBdd()->requeter($requete);
                        if ($resultat === false) {
                                throw new Exception("Erreur d'insertion pour le tuple $id");
                        }
                }
        }

        private function genererChpNomComplet() {
                $this->preparerTablePrChpNomComplet();
                $this->remplirChpNomComplet();
        }

        private function preparerTablePrChpNomComplet() {
                $requete = "SHOW COLUMNS FROM {$this->table} LIKE 'nom_complet' ";
                $resultat = $this->getBdd()->recuperer($requete);
                if ($resultat === false) {
                        $requete =      "ALTER TABLE {$this->table} ".
                                                'ADD nom_complet VARCHAR( 500 ) '.
                                                'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
                        $this->getBdd()->requeter($requete);
                }
        }

        private function remplirChpNomComplet() {
                echo "Attribution du champ nom complet au taxons : ";
                $requete = "UPDATE {$this->table} SET nom_complet = CONCAT(nom_sci,' ',auteur)";
                $resultat = $this->getBdd()->requeter($requete);
                if ($resultat === false) {
                        echo "KO\n";
                        throw new Exception("Erreur de génération du champ nom complet");
                } else {
                        echo "OK\n";
                }
        }

        private function genererChpFamille() {
                $this->initialiserGenerationChamps();
                $this->preparerTablePrChpFamille();
                $resultats = $this->recupererTuplesPrChpFamille();
                $noms = array();
                $introuvables = array();
                $introuvablesSyno = array();
                foreach ($resultats as $id => $nom) {
                        $nn = $nom['num_nom'];
                        $nnr = $nom['num_nom_retenu'];
                        $nts = $nom['num_tax_sup'];
                        $rg = $nom['rang'];
                        if ($nnr != '') {
                                if ($rg == '180') {
                                        $noms[$nn] = $nom['nom_sci'];
                                } else {
                                        if ($nn == $nnr) {// nom retenu
                                                if (isset($noms[$nts])) {
                                                        $noms[$nn] = $noms[$nts];
                                                } else {
                                                        $introuvables[] = $nn;
                                                }
                                        } else {// nom synonyme
                                                if (isset($noms[$nnr])) {
                                                        $noms[$nn] = $noms[$nnr];
                                                } else {
                                                        $introuvablesSyno[] = $nom;
                                                }
                                        }
                                }
                        }
                        unset($resultats[$id]);
                        $this->afficherAvancement("Attribution de leur famille aux noms en cours");
                        if ($this->stopperLaBoucle($this->getParametre('t'))) break;
                }
                echo "\n";

                foreach ($introuvablesSyno as $id => $nom) {
                        $nn = $nom['num_nom'];
                        $nnr = $nom['num_nom_retenu'];
                        if (isset($noms[$nnr])) {
                                $noms[$nn] = $noms[$nnr];
                        } else {
                                $introuvables[] = $nn;
                        }
                        unset($introuvablesSyno[$id]);
                        $this->afficherAvancement("Attribution de leur famille aux synonymes en cours");
                }
                echo "\n";

                $msg = 'Plusieurs familles sont introuvables';
                $this->creerFichierLog($msg, $introuvables, 'famille_introuvable');

                $this->remplirChpFamille($noms);
        }

        private function preparerTablePrChpFamille() {
                $requete = "SHOW COLUMNS FROM {$this->table} LIKE 'famille' ";
                $resultat = $this->getBdd()->recuperer($requete);
                if ($resultat === false) {
                        $requete =      "ALTER TABLE {$this->table} ".
                                'ADD famille VARCHAR(255) '.
                                'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
                        $this->getBdd()->requeter($requete);
                }
        }

        private function recupererTuplesPrChpFamille() {
                $requete = 'SELECT num_nom, num_nom_retenu, num_tax_sup, rang, nom_sci '.
                        "FROM {$this->table} ".
                        "WHERE rang >= 180 ".
                        "ORDER BY rang ASC, num_tax_sup ASC, num_nom_retenu DESC ";
                $resultat = $this->getBdd()->recupererTous($requete);
                return $resultat;
        }

        private function remplirChpFamille($noms) {
                foreach ($noms as $id => $famille) {
                        $famille = $this->getBdd()->proteger($famille);
                        $requete = "UPDATE {$this->table} SET famille = $famille WHERE num_nom = $id ";
                        $resultat = $this->getBdd()->requeter($requete);
                        if ($resultat === false) {
                                throw new Exception("Erreur d'insertion pour le tuple $id");
                        }
                        $this->afficherAvancement("Insertion des noms de famille dans la base en cours");
                }
                echo "\n";
        }
        
        private function genererChpHierarchie() {
                $this->initialiserGenerationChamps();
                $this->preparerTablePrChpHierarchie();
                $table = Config::get('tables.taxref');
        
                $requete = "UPDATE $table SET hierarchie = NULL ";
                $mise_a_jour = $this->getBdd()->requeter($requete);
        
                $requete_hierarchie = "SELECT num_nom, num_nom_retenu, num_tax_sup FROM ".$table." ORDER BY rang DESC";
        
                $resultat = $this->getBdd()->recupererTous($requete_hierarchie);
                $num_nom_a_num_sup = array();
                foreach($resultat as &$taxon) {
                        $num_nom_a_num_sup[$taxon['num_nom']] = $taxon['num_tax_sup'];
                }
                $chemin_taxo = "";
                foreach($resultat as &$taxon) {
                        $chemin_taxo = $this->traiterHierarchieNumTaxSup($taxon['num_nom_retenu'], $num_nom_a_num_sup).'-';
                        $requete = "UPDATE $table SET hierarchie = ".$this->getBdd()->proteger($chemin_taxo)." WHERE num_nom = ".$taxon['num_nom']." ";
                        $mise_a_jour = $this->getBdd()->requeter($requete);
                        $this->afficherAvancement("Insertion de la hierarchie taxonomique en cours");
                }
                echo "\n";
        }
        
        private function traiterHierarchieNumTaxSup($num_nom_retenu, &$num_nom_a_num_sup) {
                $chaine_hierarchie = "";
                if(isset($num_nom_a_num_sup[$num_nom_retenu])) {
                        $num_tax_sup = $num_nom_a_num_sup[$num_nom_retenu];
                        $chaine_hierarchie = '-'.$num_tax_sup;
                        if($num_tax_sup != 0 && $num_tax_sup != '') {
                                $chaine_hierarchie = $this->traiterHierarchieNumTaxSup($num_tax_sup, $num_nom_a_num_sup).$chaine_hierarchie;
                        }
                }
                return $chaine_hierarchie;
        }
        
        private function preparerTablePrChpHierarchie() {
                $requete = "SHOW COLUMNS FROM {$this->table} LIKE 'hierarchie' ";
                $resultat = $this->getBdd()->recuperer($requete);
                if ($resultat === false) {
                        $requete =      "ALTER TABLE {$this->table} ".
                                                'ADD hierarchie VARCHAR(1000) '.
                                                'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
                        $this->getBdd()->requeter($requete);
                }
        }
        
        private function genererDonneesTestMultiVersion() {
                $contenuSql = $this->recupererContenu(Config::get('chemins.structureSqlTest'));
                $this->executerScripSql($contenuSql);

                $table = Config::get('tables.taxref');
                $tableTest = Config::get('tables.taxrefTest');
                $requete = "INSERT INTO $tableTest SELECT * FROM $table";
                $this->getBdd()->requeter($requete);
        }

        private function supprimerDonneesTestMultiVersion() {
                $tableMeta = Config::get('tables.taxrefMeta');
                $requete = "DELETE FROM $tableMeta WHERE guid = 'urn:lsid:tela-botanica.org:taxref:1.00'";
                $this->getBdd()->requeter($requete);

                $tableTest = Config::get('tables.taxrefTest');
                $requete = "DROP TABLE IF EXISTS $tableTest";
                $this->getBdd()->requeter($requete);
        }
        private function supprimerTous() {
                $requete = "DROP TABLE IF EXISTS taxref_meta, taxref_v0_01, taxref_v1_00";
                $this->getBdd()->requeter($requete);
        }

        private function creerFichierLog($message, $lignes, $nomFichier) {
                $lignesNbre = count($lignes);
                if ($lignesNbre != 0) {
                        echo "$message. Voir le log de $lignesNbre lignes :\n";

                        $logContenu = implode(", \n", $lignes);
                        $logFichier = realpath(dirname(__FILE__))."/log/$nomFichier.log";
                        echo $logFichier."\n";
                        file_put_contents($logFichier, $logContenu);
                }
        }
}
?>