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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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* /opt/lampp/bin/php cli.php taxref -a chargerTous
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*
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* @category php 5.2
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* @package eFlore/Scripts
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* @author Jean-Pascal MILCENT <jpm@tela-botanica.org>
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* @copyright Copyright (c) 2012, Tela Botanica (accueil@tela-botanica.org)
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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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class Taxref extends EfloreScript {
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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 $parametres_autorises = array(
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'-t' => array(false, false, 'Permet de tester le script sur un jeu réduit de données (indiquer le nombre de lignes).'));
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public function executer() {
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try {
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$this->initialiserProjet('vascan');
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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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$this->chargerStructureSql();
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$this->chargertaxref();
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$this->genererChpNumTax();
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$this->genererChpNomSciHtml();
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$this->genererChpFamille();
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$this->genererChpNomComplet();
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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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case 'chargerTaxref' :
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$this->chargerTaxref();
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break;
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case 'genererChpNumTax' :
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$this->genererChpNumTax();
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break;
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case 'genererChpNomSciHtml' :
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$this->genererChpNomSciHtml();
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break;
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case 'genererChpNomComplet' :
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$this->initialiserGenerationChamps();
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$this->genererChpNomComplet();
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break;
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case 'genererChpFamille' :
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$this->genererChpFamille();
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break;
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case 'genererChpHierarchie' :
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$this->genererChpHierarchie();
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break;
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case 'supprimerTous' :
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$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($e->getMessage());
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}
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}
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private function chargerTaxref() {
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$chemin = Config::get('chemins.bdt');
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$table = Config::get('tables.taxref');
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$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($requete);
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}
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private function genererChpNumTax() {
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpNumTax();
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$erreurs = array();
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$this->departInsertion = 0;
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$dernier_num_tax = 0;
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$requete = 'SELECT num_nom '.
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'FROM '.$this->table.' '.
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'WHERE num_nom = num_nom_retenu AND num_nom_retenu != 0 '.
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'ORDER by num_nom_retenu ASC ';
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$resultat = $this->getBdd()->recupererTous($requete);
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foreach ($resultat as $taxon) {
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$dernier_num_tax++;
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$requete_maj = 'UPDATE '.$this->table.' '.
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'SET num_taxonomique = '.$dernier_num_tax.' '.
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'WHERE num_nom_retenu = '.$taxon['num_nom'];
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$this->getBdd()->requeter($requete_maj);
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$this->pasInsertion++;
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$this->afficherAvancement("Insertion des num tax, ".count($resultat)." num tax a traiter");
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}
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echo "\n";
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$this->creerFichierLog('Erreurs lors de la génération des numéros taxonomiques', $erreurs, 'erreurs_num_tax');
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}
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private function preparerTablePrChpNumTax() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'num_taxonomique' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD num_taxonomique INT( 9 ) ';
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$this->getBdd()->requeter($requete);
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}
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}
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private function genererChpNomSciHtml() {
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$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', $erreurs, 'erreurs_noms_sci_html');
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}
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private function initialiserGenerationChamps() {
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$this->table = Config::get('tables.taxref');
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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, genre, '.
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' epithete_sp, type_epithete, epithete_infra_sp '.
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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 $id");
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}
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}
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}
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private function genererChpNomComplet() {
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$this->preparerTablePrChpNomComplet();
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$this->remplirChpNomComplet();
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}
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private function preparerTablePrChpNomComplet() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'nom_complet' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD nom_complet VARCHAR( 500 ) '.
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'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
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$this->getBdd()->requeter($requete);
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}
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}
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private function remplirChpNomComplet() {
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echo "Attribution du champ nom complet au taxons : ";
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$requete = "UPDATE {$this->table} SET nom_complet = CONCAT(nom_sci,' ',auteur)";
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$resultat = $this->getBdd()->requeter($requete);
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if ($resultat === false) {
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echo "KO\n";
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throw new Exception("Erreur de génération du champ nom complet");
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} else {
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echo "OK\n";
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}
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}
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private function genererChpFamille() {
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$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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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[$nts])) {
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$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[$nnr])) {
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$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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echo "\n";
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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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299 |
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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$table = Config::get('tables.taxref');
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$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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323 |
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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325 |
$requete = "UPDATE $table SET hierarchie = ".$this->getBdd()->proteger($chemin_taxo)." WHERE num_nom = ".$taxon['num_nom']." ";
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326 |
$mise_a_jour = $this->getBdd()->requeter($requete);
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327 |
$this->afficherAvancement("Insertion de la hierarchie taxonomique en cours");
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328 |
}
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329 |
echo "\n";
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|
330 |
}
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331 |
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332 |
private function traiterHierarchieNumTaxSup($num_nom_retenu, &$num_nom_a_num_sup) {
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|
333 |
$chaine_hierarchie = "";
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|
334 |
if(isset($num_nom_a_num_sup[$num_nom_retenu])) {
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|
335 |
$num_tax_sup = $num_nom_a_num_sup[$num_nom_retenu];
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|
336 |
$chaine_hierarchie = '-'.$num_tax_sup;
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|
337 |
if($num_tax_sup != 0 && $num_tax_sup != '') {
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|
338 |
$chaine_hierarchie = $this->traiterHierarchieNumTaxSup($num_tax_sup, $num_nom_a_num_sup).$chaine_hierarchie;
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|
339 |
}
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|
340 |
}
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|
341 |
return $chaine_hierarchie;
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|
|
342 |
}
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|
343 |
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|
344 |
private function preparerTablePrChpHierarchie() {
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|
345 |
$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'hierarchie' ";
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|
346 |
$resultat = $this->getBdd()->recuperer($requete);
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|
347 |
if ($resultat === false) {
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|
348 |
$requete = "ALTER TABLE {$this->table} ".
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|
349 |
'ADD hierarchie VARCHAR(1000) '.
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|
350 |
'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
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|
351 |
$this->getBdd()->requeter($requete);
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|
|
352 |
}
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|
353 |
}
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|
|
354 |
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|
|
355 |
private function genererDonneesTestMultiVersion() {
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|
|
356 |
$contenuSql = $this->recupererContenu(Config::get('chemins.structureSqlTest'));
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|
|
357 |
$this->executerScripSql($contenuSql);
|
|
|
358 |
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|
|
359 |
$table = Config::get('tables.taxref');
|
|
|
360 |
$tableTest = Config::get('tables.taxrefTest');
|
|
|
361 |
$requete = "INSERT INTO $tableTest SELECT * FROM $table";
|
|
|
362 |
$this->getBdd()->requeter($requete);
|
|
|
363 |
}
|
|
|
364 |
|
|
|
365 |
private function supprimerDonneesTestMultiVersion() {
|
|
|
366 |
$tableMeta = Config::get('tables.taxrefMeta');
|
|
|
367 |
$requete = "DELETE FROM $tableMeta WHERE guid = 'urn:lsid:tela-botanica.org:taxref:1.00'";
|
|
|
368 |
$this->getBdd()->requeter($requete);
|
|
|
369 |
|
|
|
370 |
$tableTest = Config::get('tables.taxrefTest');
|
|
|
371 |
$requete = "DROP TABLE IF EXISTS $tableTest";
|
|
|
372 |
$this->getBdd()->requeter($requete);
|
|
|
373 |
}
|
|
|
374 |
private function supprimerTous() {
|
|
|
375 |
$requete = "DROP TABLE IF EXISTS taxref_meta, taxref_v0_01, taxref_v1_00";
|
|
|
376 |
$this->getBdd()->requeter($requete);
|
|
|
377 |
}
|
|
|
378 |
|
|
|
379 |
private function creerFichierLog($message, $lignes, $nomFichier) {
|
|
|
380 |
$lignesNbre = count($lignes);
|
|
|
381 |
if ($lignesNbre != 0) {
|
|
|
382 |
echo "$message. Voir le log de $lignesNbre lignes :\n";
|
|
|
383 |
|
|
|
384 |
$logContenu = implode(", \n", $lignes);
|
|
|
385 |
$logFichier = realpath(dirname(__FILE__))."/log/$nomFichier.log";
|
|
|
386 |
echo $logFichier."\n";
|
|
|
387 |
file_put_contents($logFichier, $logContenu);
|
|
|
388 |
}
|
|
|
389 |
}
|
|
|
390 |
}
|
|
|
391 |
?>
|