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delphine |
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<?php
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//declare(encoding='UTF-8');
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/**
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* Exemple de lancement du script : :
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aurelien |
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* /opt/lampp/bin/php cli.php lbf -a chargerTous
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delphine |
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*
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* @category php 5.2
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* @package eFlore/Scripts
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aurelien |
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* @author Delphine Cauquil <delphine@tela-botanica.org>
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* @author Aurélien PERONNET <aurelien@tela-botanica.org>
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* @copyright Copyright (c) 2014, Tela Botanica (accueil@tela-botanica.org)
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delphine |
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* @license http://www.cecill.info/licences/Licence_CeCILL_V2-fr.txt Licence CECILL
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* @license http://www.gnu.org/licenses/gpl.html Licence GNU-GPL
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* @version $Id$
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*/
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aurelien |
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class Lbf extends EfloreScript {
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delphine |
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private $table = null;
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private $pasInsertion = 1000;
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private $departInsertion = 0;
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protected $parametres_autorises = array(
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'-t' => array(false, false, 'Permet de tester le script sur un jeu réduit de données (indiquer le nombre de lignes).'));
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public function executer() {
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try {
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aurelien |
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$this->initialiserProjet('lbf');
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delphine |
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// Lancement de l'action demandée
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$cmd = $this->getParametre('a');
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switch ($cmd) {
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case 'chargerTous' :
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$this->chargerStructureSql();
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aurelien |
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$this->chargerlbf();
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delphine |
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$this->genererChpNomSciHtml();
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$this->genererChpFamille();
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//$this->genererChpHierarchie();
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break;
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case 'chargerStructureSql' :
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$this->chargerStructureSql();
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break;
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aurelien |
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case 'chargerlbf' :
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$this->chargerlbf();
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delphine |
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break;
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case 'genererNomSciHtml' :
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$this->genererChpNomSciHtml();
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break;
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case 'genererChpFamille' :
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$this->genererChpFamille();
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break;
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case 'supprimerTous' :
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$this->supprimerTous();
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break;
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default :
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throw new Exception("Erreur : la commande '$cmd' n'existe pas!");
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}
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} catch (Exception $e) {
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$this->traiterErreur($e->getMessage());
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}
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}
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aurelien |
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private function chargerlbf() {
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$chemin = Config::get('chemins.lbf');
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$table = Config::get('tables.lbf');
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delphine |
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$requete = "LOAD DATA INFILE '$chemin' ".
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"REPLACE INTO TABLE $table ".
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'CHARACTER SET utf8 '.
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'FIELDS '.
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" TERMINATED BY '\t' ".
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" ENCLOSED BY '' ".
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" ESCAPED BY '\\\' ".
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'IGNORE 1 LINES';
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$this->getBdd()->requeter($requete);
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}
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private function genererChpNomSciHtml() {
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpNomSciHtml();
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$generateur = new GenerateurNomSciHtml();
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$nbreTotal = $this->recupererNbTotalTuples();
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$erreurs = array();
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$this->departInsertion = 0;
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while ($this->departInsertion < $nbreTotal) {
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$resultat = $this->recupererTuplesPrChpNomSciHtml();
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try {
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$nomsSciEnHtml = $generateur->generer($resultat);
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} catch (Exception $e) {
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$erreurs[] = $e->getMessage();
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}
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$this->remplirChpNomSciHtm($nomsSciEnHtml);
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$this->departInsertion += $this->pasInsertion;
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$this->afficherAvancement("Insertion des noms scientifique au format HTML dans la base par paquet de {$this->pasInsertion} en cours");
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if ($this->stopperLaBoucle($this->getParametre('t'))) break;
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}
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echo "\n";
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$this->creerFichierLog('Erreurs lors de la génération HTML des noms scientifiques', $erreurs, 'erreurs_noms_sci_html');
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}
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private function initialiserGenerationChamps() {
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aurelien |
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$this->table = Config::get('tables.lbf');
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delphine |
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}
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private function preparerTablePrChpNomSciHtml() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'nom_sci_html' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD nom_sci_html VARCHAR( 500 ) '.
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'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
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$this->getBdd()->requeter($requete);
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}
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}
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private function recupererNbTotalTuples(){
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$requete = "SELECT count(*) AS nb FROM {$this->table} ";
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$resultat = $this->getBdd()->recuperer($requete);
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return $resultat['nb'];
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}
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private function recupererTuplesPrChpNomSciHtml() {
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$requete = 'SELECT num_nom, rang, nom_sci, nom_supra_generique, genre, epithete_infra_generique, '.
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' epithete_sp, type_epithete, epithete_infra_sp,cultivar_groupe, '.
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' nom_commercial, cultivar '.
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"FROM {$this->table} ".
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"LIMIT {$this->departInsertion},{$this->pasInsertion} ";
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$resultat = $this->getBdd()->recupererTous($requete);
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return $resultat;
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}
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private function remplirChpNomSciHtm($nomsSciHtm) {
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foreach ($nomsSciHtm as $id => $html) {
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$html = $this->getBdd()->proteger($html);
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$requete = "UPDATE {$this->table} SET nom_sci_html = $html WHERE num_nom = $id ";
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$resultat = $this->getBdd()->requeter($requete);
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if ($resultat === false) {
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throw new Exception("Erreur d'insertion pour le tuple $id");
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}
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}
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}
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private function traiterResultatsFamille(&$resultats, &$noms, &$introuvables, &$introuvablesSyno) {
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foreach ($resultats as $id => $nom) {
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$nn = $nom['num_nom'];
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$nnr = $nom['num_nom_retenu'];
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$nts = $nom['num_tax_sup'];
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$rg = $nom['rang'];
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if ($nnr != '') {
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if ($rg == '180') {
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$noms[$nn] = $nom['nom_sci'];
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} else {
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if ($nn == $nnr) {// nom retenu
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if (isset($noms[$nts])) {
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// signifie que recupererTuplesPrChpFamille() devrait
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// récupérer ce record *avant*
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$noms[$nn] = $noms[$nts];
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} else {
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$introuvables[] = $nn;
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}
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} else {// nom synonyme
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if (isset($noms[$nnr])) {
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// signifie que recupererTuplesPrChpFamille() devrait
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// récupérer ce record *avant*
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$noms[$nn] = $noms[$nnr];
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} else {
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$introuvablesSyno[] = $nom;
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}
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}
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}
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}
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unset($resultats[$id]);
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$this->afficherAvancement("Attribution de leur famille aux noms en cours");
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if ($this->stopperLaBoucle($this->getParametre('t'))) break;
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}
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}
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private function genererChpFamille() {
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpFamille();
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$resultats = $this->recupererTuplesPrChpFamille();
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$noms = array();
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$introuvables = array();
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$introuvablesSyno = array();
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$i = 1;
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while(true) {
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printf("passe n°%d:\n", $i);
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$this->traiterResultatsFamille($resultats, $noms, $introuvables, $introuvablesSyno);
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echo "\n\n";
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// printf("noms: %d, introuvables: %d, introuvablesSyno: %d\n", count($noms), count($introuvables), count($introuvablesSyno));
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// XXX, au 22/07/2013, 3 passes sont suffisantes
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// TODO: MySQL procédure stockée !
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if($i++ == 3) break;
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$resultats = array_merge($resultats, $introuvables, $introuvablesSyno);
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$introuvables = $introuvablesSyno = array();
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}
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foreach ($introuvablesSyno as $id => $nom) {
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$nn = $nom['num_nom'];
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$nnr = $nom['num_nom_retenu'];
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if (isset($noms[$nnr])) {
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$noms[$nn] = $noms[$nnr];
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} else {
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$introuvables[] = $nn;
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}
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unset($introuvablesSyno[$id]);
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$this->afficherAvancement("Attribution de leur famille aux synonymes en cours");
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}
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echo "\n";
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$msg = 'Plusieurs familles sont introuvables';
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$this->creerFichierLog($msg, $introuvables, 'famille_introuvable');
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$this->remplirChpFamille($noms);
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}
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private function preparerTablePrChpFamille() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'famille' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD famille VARCHAR(255) '.
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'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
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$this->getBdd()->requeter($requete);
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}
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}
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private function recupererTuplesPrChpFamille() {
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$requete = 'SELECT num_nom, num_nom_retenu, num_tax_sup, rang, nom_sci '.
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"FROM {$this->table} ".
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"WHERE rang >= 180 ".
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"ORDER BY rang ASC, num_tax_sup ASC, num_nom_retenu DESC ";
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$resultat = $this->getBdd()->recupererTous($requete);
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return $resultat;
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}
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private function remplirChpFamille($noms) {
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foreach ($noms as $id => $famille) {
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$famille = $this->getBdd()->proteger($famille);
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$requete = "UPDATE {$this->table} SET famille = $famille WHERE num_nom = $id ";
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$resultat = $this->getBdd()->requeter($requete);
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if ($resultat === false) {
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throw new Exception("Erreur d'insertion pour le tuple $id");
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}
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$this->afficherAvancement("Insertion des noms de famille dans la base en cours");
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}
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echo "\n";
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}
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private function genererChpHierarchie() {
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpHierarchie();
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aurelien |
255 |
$table = Config::get('tables.lbf');
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delphine |
256 |
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$requete = "UPDATE $table SET hierarchie = NULL ";
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$mise_a_jour = $this->getBdd()->requeter($requete);
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$requete_hierarchie = "SELECT num_nom, num_nom_retenu, num_tax_sup FROM ".$table." ORDER BY rang DESC";
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$resultat = $this->getBdd()->recupererTous($requete_hierarchie);
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$num_nom_a_num_sup = array();
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foreach($resultat as &$taxon) {
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$num_nom_a_num_sup[$taxon['num_nom']] = $taxon['num_tax_sup'];
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}
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$chemin_taxo = "";
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foreach($resultat as &$taxon) {
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$chemin_taxo = $this->traiterHierarchieNumTaxSup($taxon['num_nom_retenu'], $num_nom_a_num_sup).'-';
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$requete = "UPDATE $table SET hierarchie = ".$this->getBdd()->proteger($chemin_taxo)." WHERE num_nom = ".$taxon['num_nom']." ";
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$mise_a_jour = $this->getBdd()->requeter($requete);
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$this->afficherAvancement("Insertion de la hierarchie taxonomique en cours");
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}
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echo "\n";
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}
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private function traiterHierarchieNumTaxSup($num_nom_retenu, &$num_nom_a_num_sup) {
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$chaine_hierarchie = "";
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if(isset($num_nom_a_num_sup[$num_nom_retenu])) {
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$num_tax_sup = $num_nom_a_num_sup[$num_nom_retenu];
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$chaine_hierarchie = '-'.$num_tax_sup;
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if($num_tax_sup != 0 && $num_tax_sup != '') {
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$chaine_hierarchie = $this->traiterHierarchieNumTaxSup($num_tax_sup, $num_nom_a_num_sup).$chaine_hierarchie;
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}
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}
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return $chaine_hierarchie;
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}
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private function preparerTablePrChpHierarchie() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'hierarchie' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD hierarchie VARCHAR(1000) '.
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'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
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$this->getBdd()->requeter($requete);
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}
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}
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300 |
private function genererDonneesTestMultiVersion() {
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301 |
$contenuSql = $this->recupererContenu(Config::get('chemins.structureSqlTest'));
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302 |
$this->executerScripSql($contenuSql);
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303 |
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| 1146 |
aurelien |
304 |
$table = Config::get('tables.lbf');
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305 |
$tableTest = Config::get('tables.lbfTest');
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| 1144 |
delphine |
306 |
$requete = "INSERT INTO $tableTest SELECT * FROM $table";
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307 |
$this->getBdd()->requeter($requete);
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308 |
}
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309 |
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310 |
private function supprimerDonneesTestMultiVersion() {
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| 1146 |
aurelien |
311 |
$tableMeta = Config::get('tables.lbfMeta');
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312 |
$requete = "DELETE FROM $tableMeta WHERE guid = 'urn:lsid:tela-botanica.org:lbf:1.02'";
|
| 1144 |
delphine |
313 |
$this->getBdd()->requeter($requete);
|
|
|
314 |
|
| 1146 |
aurelien |
315 |
$tableTest = Config::get('tables.lbfTest');
|
| 1144 |
delphine |
316 |
$requete = "DROP TABLE IF EXISTS $tableTest";
|
|
|
317 |
$this->getBdd()->requeter($requete);
|
|
|
318 |
}
|
|
|
319 |
|
|
|
320 |
private function supprimerTous() {
|
| 1146 |
aurelien |
321 |
$requete = "DROP TABLE IF EXISTS lbf_meta, lbf_v1_00";
|
| 1144 |
delphine |
322 |
$this->getBdd()->requeter($requete);
|
|
|
323 |
}
|
|
|
324 |
|
|
|
325 |
private function creerFichierLog($message, $lignes, $nomFichier) {
|
|
|
326 |
$lignesNbre = count($lignes);
|
|
|
327 |
if ($lignesNbre != 0) {
|
|
|
328 |
echo "$message. Voir le log de $lignesNbre lignes :\n";
|
|
|
329 |
|
|
|
330 |
$logContenu = implode(", \n", $lignes);
|
|
|
331 |
$logFichier = realpath(dirname(__FILE__))."/log/$nomFichier.log";
|
|
|
332 |
echo $logFichier."\n";
|
|
|
333 |
file_put_contents($logFichier, $logContenu);
|
|
|
334 |
}
|
|
|
335 |
}
|
|
|
336 |
}
|
|
|
337 |
?>
|