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<?php
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// Encodage : UTF-8
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// +-------------------------------------------------------------------------------------------------------------------+
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/**
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* Importation d'un fichier ref-tax dans une bdnt
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*
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* Description : classe permettant de versionner les référentiels selon le manuel technique
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* Utilisation : php script.php comparaison -r bdnff -a tout -f fichier.txt
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*
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//Auteur original :
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* @author Jean-Pascal MILCENT <jpm@tela-botanica.org>
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* @copyright Tela-Botanica 1999-2010
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* @link http://www.tela-botanica.org/wikini/RTaxMethodo/wakka.php?wiki=MaNuel
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* @licence GPL v3 & CeCILL v2
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* @version $Id$
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*/
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// +-------------------------------------------------------------------------------------------------------------------+
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class Importation extends ScriptCommande {
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const SCRIPT_NOM = 'importation';
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const MANUEL_VERSION = '4.3';
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private $referentiel = null;
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/*public $parametres = array(
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'-r' => array(true, true, 'referentiel de base'),
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'-f' => array(true, true, 'fichier à comparer'));*/
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private $noms_supprimes = null;
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private $noms_colonnes = array();
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private $rangs_bdnt_taxref = null;
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private $statuts_bdnt_taxref = null;
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private $correspondance_colonnes = array("CD_NOM" => "", "CD_SUP" => "", "CD_REF" => "",
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"RANG" => "rang", "LB_NOM" => "nom_sci", "LB_AUTEUR" => array("auteur","annee"),
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"FR" => "presence",
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"FR-FRA" => "presence_Ga", "FR-COR" => "presence_Co", "REU" => "presence",
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"GUA" => "presence_Guadeloupe", "SMSB" => array("presence_Saint_Martin", "presence_Saint_Barthelemy"),
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"SM" => "presence_Saint_Martin", "SB" => "presence_Saint_Barthelemy", "MAR" => "presence_Martinique",
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"GF" => "presence", "MAY" => "presence_Mayotte", "TAAF" => "presence_Taaf",
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"SPM" => "presence_Guadeloupe", "PF" => "presence_Polynesie", "NC" => "presence_Nouvelle_Caledonie",
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"BIBLIO" => "biblio_origine", "BDNGM" => "num_nom", "NUM_NOM" => "num_nom", "NOM_VERN" => "nom_francais");
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private $sans_correspondance = array(
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"FG_VALIDITE", "habitat", "WF", "CLI", "EPA",
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"EU", "WLD", "ORACLE",
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"DATE_CREA", "ORIGINE_CREA",
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"NOM_COMPLET", "NOM_COMPLET_HTML",
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"GENRE", "ESPECE", "SOUS_ESPECE", "ANNEE");
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/*public function executer() {
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$this->referentiel = $this->getParam('r');
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// Lancement du test demandé
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$fichier = $this->getParam('f');
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if (file_exists($fichier)) {
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$manuel_chemin = Config::get('chemin_appli').DS.'..'.DS.'configurations'.DS;
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$manuel_config_nom = 'referentiel_v'.self::MANUEL_VERSION.'.ini';
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$this->manuel = parse_ini_file($manuel_chemin.$manuel_config_nom);
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$this->creerCorrespondanceRangBdntTaxref();
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$donnees = $this->traiterFichierTaxref($fichier);
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Debug::printr("Fin du traitement du fichier.");
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$this->connecterPDO();
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$this->creerTableTaxref();
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$this->ajouterColonneCDNOM();
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Debug::printr("Fin de la création de la table.");
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$this->ajouterDonneesTaxRef($donnees);
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Debug::printr("Fin de l'insertion des données.");
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$this->creerTableComparaison();
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Debug::printr("Fin de la création de la table comparaison.");
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}
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}*/
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public function executer() {
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// Récupération du dernier traitement demandé
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$this->traitementDao = new TraitementDao();
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$this->traitement = $this->traitementDao->getDernierTraitement('tout', self::SCRIPT_NOM);
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if (isset($this->traitement)) {
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$this->referentiel = $this->traitement['referentiel_code']; // Récupération du nom de projet
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$fichier = $this->traitement['script_parametres'];
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if (file_exists($fichier)) {
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Debug::printr('Debute:'.$this->traitementDao->debuterTraitement($this->traitement['id_traitement']));
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// Nettoyage des traitements obsolètes
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$traitements_obsoletes = $this->traitementDao->getTraitementsObsoletes($this->referentiel, self::SCRIPT_NOM);
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if (isset($traitements_obsoletes)) {
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Debug::printr('Supp. obsoletes:'.$this->traitementDao->supprimer($traitements_obsoletes));
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}
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Debug::printr("Début du traitement du fichier.");
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$manuel_chemin = Config::get('chemin_appli').DS.'..'.DS.'configurations'.DS;
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$manuel_config_nom = 'referentiel_v'.self::MANUEL_VERSION.'.ini';
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$this->manuel = parse_ini_file($manuel_chemin.$manuel_config_nom);
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$this->creerCorrespondanceRangBdntTaxref();
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$donnees = $this->traiterFichierTaxref($fichier);
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Debug::printr("Fin du traitement du fichier.");
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$this->connecterPDO();
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$this->creerTableTaxref();
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$this->ajouterColonneCDNOM();
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Debug::printr("Fin de la création de la table.");
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$this->ajouterDonneesTaxRef($donnees);
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Debug::printr("Fin de l'insertion des données.");
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$this->decouperNomSciTaxRef();
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$this->creerTableComparaison();
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Debug::printr("Fin de la création de la table comparaison.");
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Debug::printr('Termine:'.$this->traitementDao->terminerTraitement($this->traitement['id_traitement']));
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} else {
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Debug::printr("Fichier introuvable".$fichier);
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Debug::printr('Termine:'.$this->traitementDao->terminerTraitement($this->traitement['id_traitement']));
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}
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} else {
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Debug::printr("Pas de traitement");
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}
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}
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// +-------------------------------------------------------------------------------------------------------------------+
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private function creerTableTaxref() {
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$requete = "DROP TABLE IF EXISTS {$this->referentiel}_taxref; ".
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"CREATE TABLE {$this->referentiel}_taxref AS SELECT * FROM {$this->referentiel};".
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"ALTER TABLE {$this->referentiel}_taxref ADD PRIMARY KEY (num_nom);";
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$resultat = $this->executerRequeter($requete);
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}
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private function ajouterColonneCDNOM() {
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$requete = "ALTER TABLE {$this->referentiel}_taxref ADD ".
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"`CD_NOM` INT( 15 ) NULL DEFAULT NULL COMMENT 'numéro correspondant dans la base taxref.';";
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$resultat = $this->executerRequeter($requete);
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}
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private function ajouterDonneesTaxRef($liste_noms) {
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$i = 0; $j = 0; $requete = "";
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foreach ($liste_noms as $nom) { $i++;
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$requete .= "UPDATE {$this->referentiel}_taxref SET ".implode(' , ', $nom).
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" WHERE {$nom['num_nom']} ;";//echo $requete;
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if ($i == 1000 || ($j*1000+$i) == count($liste_noms) ) { $j++;
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$resultat = $this->executerRequeter($requete.'commit;');
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if ($resultat == null) {
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$resultat = $this->executerRequeter($requete.'commit;');
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}
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$i = 0; $requete = "";
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}
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}
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}
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private function creerTableComparaison() {
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foreach ($this->noms_colonnes as $colonne) {
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if (isset($this->correspondance_colonnes[$colonne]) && $this->correspondance_colonnes[$colonne] != "") {
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$nom_champ = $this->correspondance_colonnes[$colonne];
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if (is_array($nom_champ)) {
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foreach ($nom_champ as $nom) {
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$champs_tax[] = "t.{$nom} AS tax_{$nom}";
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$champs_tax[] = "b.{$nom} AS {$nom}";
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$concat[] = "IF(t.{$nom} != b.{$nom}, '{$nom}, ', '')";
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}
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} else {
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$champs_tax[] = "t.{$nom_champ} AS tax_{$nom_champ}";
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$champs_tax[] = "b.{$nom_champ} AS {$nom_champ}";
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$concat[] = "IF(t.{$nom_champ} != b.{$nom_champ}, '{$nom_champ}, ', '')";
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}
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}
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}
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date_default_timezone_set('Europe/London');
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$requete = "CREATE TABLE {$this->referentiel}_comparaison_".date("Y_m_d_H_i_s")." AS".
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" SELECT CONCAT(".implode(', ', $concat).") AS difference, ".implode(', ', $champs_tax).
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" FROM {$this->referentiel} b, {$this->referentiel}_taxref t".
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" WHERE b.num_nom = t.num_nom AND (b.nom_sci != t.nom_sci or b.auteur != t.auteur or b.annee != t.annee);";
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//echo $requete;
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$resultat = $this->executerRequeter($requete);
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}
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// +-------------------------------------------------------------------------------------------------------------------+
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private function traiterFichierTaxref($fichier) {
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$donnees = array();
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if (($pointeur = fopen($fichier, "r")) !== FALSE) {
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$this->noms_colonnes = fgetcsv($pointeur, 1000, chr(9));
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$num_nom = 0;//print_r($this->noms_colonnes);
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while (($ligne = fgetcsv($pointeur, 1000, chr(9))) !== FALSE) {
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$nombreChamps = count($ligne);
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$taxref[$ligne[0]] = $ligne;//print_r($ligne);
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for ($c=0; $c < $nombreChamps; $c++) {
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if (isset($this->correspondance_colonnes[$this->noms_colonnes[$c]])) {
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if (is_array($this->correspondance_colonnes[$this->noms_colonnes[$c]])) {
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if ($this->noms_colonnes[$c] == 'LB_AUTEUR') {
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if (preg_match('/(.*), +([0-9]{4})/', utf8_encode($ligne[$c]), $matches) == 1) {
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$nom['auteur'] = 'auteur="'.$matches[1].'"';
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$nom['annee'] = 'annee="'.trim($matches[2]).'"';
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} else {
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$nom['auteur'] = 'auteur="'.utf8_encode($ligne[$c]).'"';
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$nom['annee'] = 'annee=""';
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}
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} else {
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foreach ($this->correspondance_colonnes[$this->noms_colonnes[$c]] as $a=>$nom_colonne) {
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$nom[$nom_colonne] = $nom_colonne.'="'.$ligne[$c].'"';
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}
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}
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} elseif ($this->correspondance_colonnes[$this->noms_colonnes[$c]] == "") {
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$nom[$this->noms_colonnes[$c]] = $ligne[$c];
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} else {
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if ($this->correspondance_colonnes[$this->noms_colonnes[$c]] == "rang") {
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$rang = $this->rangs_bdnt_taxref[$ligne[$c]];
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// à remettre si on décide de prendre les rangs taxref
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//$nom[$this->correspondance_colonnes[$this->noms_colonnes[$c]]] =
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//$this->correspondance_colonnes[$this->noms_colonnes[$c]].'="'.$this->rangs_bdnt_taxref[$ligne[$c]].'"';
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delphine |
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} elseif ($this->correspondance_colonnes[$this->noms_colonnes[$c]] == "num_nom") {
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$num_nom = $ligne[$c];
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$nom[$this->correspondance_colonnes[$this->noms_colonnes[$c]]] =
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$this->correspondance_colonnes[$this->noms_colonnes[$c]].'="'.$ligne[$c].'"';
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delphine |
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} elseif ($this->correspondance_colonnes[$this->noms_colonnes[$c]] == "nom_sci") {
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$nom_sci = $ligne[$c];
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$nom[$this->correspondance_colonnes[$this->noms_colonnes[$c]]] =
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$this->correspondance_colonnes[$this->noms_colonnes[$c]].'="'.trim($ligne[$c]).'"';
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delphine |
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} else {
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$nom[$this->correspondance_colonnes[$this->noms_colonnes[$c]]] =
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$this->correspondance_colonnes[$this->noms_colonnes[$c]].'="'.trim(utf8_encode($ligne[$c])).'"';
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delphine |
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}
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}
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}
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}
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$nom['exclure_taxref'] = 'exclure_taxref="0"';
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$donnees[$num_nom] = $nom;
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$correspondance_taxref_bdnt[$nom['CD_NOM']] = $num_nom;
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}
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fclose($pointeur);
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$donnees = $this->changerNumerotation($donnees, $correspondance_taxref_bdnt, $taxref);
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}
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return $donnees;
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}
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private function changerNumerotation($donnees, $correspondance, $taxref) {
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$i=0;$j=0;$k=0;
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foreach ($donnees as $num_nom=>$infos) {
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if (isset($correspondance[$infos['CD_SUP']])) {
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$donnees[$num_nom]['num_tax_sup'] = "num_tax_sup=".$correspondance[$infos['CD_SUP']];
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$i++;
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} elseif ($infos['CD_SUP'] != '') {
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$donnees[$num_nom]['num_tax_sup'] = "num_tax_sup=''";
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delphine |
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//$sup[$infos['CD_NOM']] = $taxref[$infos['CD_NOM']];
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$sup[$infos['CD_SUP']] = $infos['CD_SUP'];
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delphine |
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}
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unset($donnees[$num_nom]['CD_SUP']);
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if (isset($correspondance[$infos['CD_REF']])) {
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$donnees[$num_nom]['num_nom_retenu'] = "num_nom_retenu=".$correspondance[$infos['CD_REF']];
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$j++;
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} elseif ($infos['CD_REF'] != '') {$k++;
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$donnees[$num_nom]['num_nom_retenu'] = "num_nom_retenu=''";
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delphine |
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//$ref[$infos['CD_NOM']] = $taxref[$infos['CD_NOM']];
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$ref[$infos['CD_REF']] = $infos['CD_REF'];
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delphine |
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} else {
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Debug::printr($infos['CD_NOM']."n'a pas de valeur pour CD_REF");
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}
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unset($donnees[$num_nom]['CD_REF']);
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delphine |
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$donnees[$num_nom]['CD_NOM'] = 'CD_NOM='.$donnees[$num_nom]['CD_NOM'];
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delphine |
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}echo "les ".count($sup)." taxons supérieurs manquants :".implode(" ,", $sup)." \nles "."retenus ".implode(" ,", $ref);
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delphine |
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//$this->ecrireFichierCsv($ref, './retenu_absent.csv');
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delphine |
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//$this->ajouterTaxonAbsent($abs);
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delphine |
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//$this->ecrireFichierCsv($sup, './superieur_absent.csv');
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delphine |
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echo "$j correspondance pour nom retenu $i correspondance pour nom sup $k non pas de correspondance retenu";
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return $donnees;
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}
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delphine |
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// rechercher dans reftax les numéros absent dans la base
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// modifier les tableaux ref et sup pour modifier $donnees (ajout + modif)
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private function ajouterTaxonAbsent($abs) {
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$requete = "SELECT ".implode(",", $this->noms_colonnes)." FROM taxref_v5 where CD_NOM IN (".implode(",", $abs).")";
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260 |
echo $requete;
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261 |
}
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262 |
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263 |
private function creerCorrespondanceRangBdntTaxref() {
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264 |
$rangs = explode(',', $this->manuel['rangs_bdnt_taxref']);
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265 |
foreach ($rangs as $rang) {
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266 |
list($id_bdnt, $code_taxref) = explode(':', trim($rang));
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|
267 |
$this->rangs_bdnt_taxref[$code_taxref] = $id_bdnt;
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268 |
}
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269 |
}
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270 |
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271 |
// +-------------------------------------------------------------------------------------------------------------------+
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272 |
private function decouperNomSciTaxRef() {
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273 |
$requete = "SELECT num_nom, nom_sci, rang, type_epithete FROM {$this->referentiel}_taxref WHERE CD_NOM != ''";
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274 |
$resultats = $this->executerRequeter($requete);
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275 |
foreach ($resultats as $nom) {
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276 |
extract($nom);
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277 |
$nomen =array('nom_supra_generique' => 'nom_supra_generique=""', 'genre' => 'genre=""',
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278 |
'epithete_infra_generique' => 'epithete_infra_generique=""', 'epithete_sp' => 'epithete_sp=""',
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279 |
'type_epithete' => 'type_epithete=""', 'epithete_infra_sp' => 'epithete_infra_sp=""',
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280 |
'cultivar_groupe' => 'cultivar_groupe=""', 'cultivar' => 'cultivar=""', 'nom_commercial' => 'nom_commercial=""');
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281 |
$parties_noms = explode(' ', $nom_sci);
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282 |
if ($rang < 220) {
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|
283 |
$nomen['nom_supra_generique'] = 'nom_supra_generique="'.$nom_sci.'"';
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284 |
} elseif ($rang == 220) {
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285 |
$nomen['genre'] = 'genre="'.trim($nom_sci).'"';
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|
286 |
} elseif ($rang < 290) {
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|
287 |
$nomen['genre'] = 'genre="'.$parties_noms[0].'"';
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|
288 |
$nomen['epithete_infra_generique'] = 'epithete_infra_generique="'.$parties_noms[1].'"';
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289 |
} else {
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|
290 |
$nomen = array_merge($nomen, $this->decouperEspece($parties_noms));
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|
291 |
$hybride = $this->etreHybride($parties_noms);
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|
292 |
if (isset($parties_noms[2]) && ($hybride === false || $hybride > 2)) {
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|
|
293 |
$nomen = array_merge($nomen, $this->decouperSousEspece($parties_noms));
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|
294 |
}
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|
295 |
}
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|
|
296 |
$update = "UPDATE {$this->referentiel}_taxref SET ".implode(' , ', $nomen)." WHERE num_nom = ".$num_nom;
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|
|
297 |
$resultat = $this->executerRequeter($update);
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|
|
298 |
}
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|
|
299 |
return $nomen;
|
|
|
300 |
}
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|
|
301 |
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|
|
302 |
private function decouperSousEspece($parties_noms) {
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|
|
303 |
if ($this->etreTypeSousEpithete($parties_noms[2]) == true) {
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|
|
304 |
$nomen['type_epithete'] = 'type_epithete="'.$parties_noms[2].'"';
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|
|
305 |
$nomen['epithete_infra_sp'] = 'epithete_infra_sp="'.$parties_noms[3].'"';
|
|
|
306 |
} elseif (strpos($parties_noms[2], '(') === 0) {
|
|
|
307 |
$nomen['cultivar_groupe'] = 'cultivar_groupe="'.trim($parties_noms[2], "(").'"';
|
|
|
308 |
} elseif (strpos($parties_noms[2], "'") === 0) {
|
|
|
309 |
$nomen['cultivar'] = 'cultivar="'.trim($parties_noms[2], "'").'"';
|
|
|
310 |
} elseif (ctype_upper($parties_noms[2]) === true) {
|
|
|
311 |
$nomen['nom_commercial'] = 'nom_commercial="'.$parties_noms[2].'"';
|
|
|
312 |
} else {
|
|
|
313 |
$nomen['epithete_infra_sp'] = 'epithete_infra_sp="'.$parties_noms[2].'"';
|
|
|
314 |
}
|
|
|
315 |
return $nomen;
|
|
|
316 |
}
|
|
|
317 |
|
|
|
318 |
private function etreTypeSousEpithete($chaine) {
|
|
|
319 |
$type = false;
|
|
|
320 |
$types_epithete = array('subsp.', 'infra-sp.', 'var.', 'subvar.', 'f.', 'subf.', 'f. sp.', 'race', 'proles');
|
|
|
321 |
if (in_array(utf8_encode($chaine), $types_epithete)) {
|
|
|
322 |
$type = true;
|
|
|
323 |
}
|
|
|
324 |
return $type;
|
|
|
325 |
}
|
|
|
326 |
|
|
|
327 |
private function decouperEspece($parties_noms) {
|
|
|
328 |
$nomen['genre'] = 'genre="'.$parties_noms[0].'"';
|
|
|
329 |
$nomen['epithete_sp'] = 'epithete_sp="'.$parties_noms[1].'"';
|
|
|
330 |
$hybride = $this->etreHybride($parties_noms);
|
|
|
331 |
$chimere = array_search('+', $parties_noms);
|
|
|
332 |
if ($hybride != false || $hybride===0) {
|
|
|
333 |
$nomen = $this->decouperEspeceHybride($hybride, $parties_noms);
|
|
|
334 |
}
|
|
|
335 |
return $nomen;
|
|
|
336 |
}
|
|
|
337 |
|
|
|
338 |
private function etreHybride($parties_noms) {
|
|
|
339 |
$hybride = array_search('x', $parties_noms);
|
|
|
340 |
return $hybride;
|
|
|
341 |
}
|
|
|
342 |
|
|
|
343 |
private function decouperEspeceHybride($hybride, $parties_noms) {
|
|
|
344 |
if ($hybride == 0) {
|
|
|
345 |
$nomen['genre'] = 'genre="'.$parties_noms[0].' '.$parties_noms[1].'"';
|
|
|
346 |
$nomen['epithete_sp'] = 'epithete_sp="'.$parties_noms[2].'"';
|
|
|
347 |
} elseif ($hybride == 1 && count($parties_noms) == 4) {
|
|
|
348 |
$nomen['genre'] = 'genre="'.$parties_noms[0].' '.$parties_noms[1].' '.$parties_noms[2].'"';
|
|
|
349 |
$nomen['epithete_sp'] = 'epithete_sp="'.$parties_noms[3].'"';
|
|
|
350 |
} elseif ($hybride == 1 && count($parties_noms) == 3) {
|
|
|
351 |
$nomen['genre'] = 'genre="'.$parties_noms[0].'"';
|
|
|
352 |
$nomen['epithete_sp'] = 'epithete_sp="'.$parties_noms[1].' '.$parties_noms[2].'"';
|
|
|
353 |
} elseif ($hybride == 2) {
|
|
|
354 |
$nomen['genre'] = 'genre="'.$parties_noms[0].'"';
|
|
|
355 |
$nomen['epithete_sp'] = 'epithete_sp="'.$parties_noms[1].' '.$parties_noms[2].' '.$parties_noms[3].'"';
|
|
|
356 |
}
|
|
|
357 |
return $nomen;
|
|
|
358 |
}
|
|
|
359 |
|
|
|
360 |
// +-------------------------------------------------------------------------------------------------------------------+
|
| 267 |
delphine |
361 |
private function ecrireFichierCsv(&$contenu, $fichier) {
|
|
|
362 |
$retour = true;
|
|
|
363 |
$fichier = fopen($fichier, "w");
|
|
|
364 |
fputcsv($fichier, $this->noms_colonnes, chr('9'));
|
|
|
365 |
foreach ($contenu as $ligne) {
|
|
|
366 |
if (fputcsv($fichier, $ligne, chr('9')) == false) {
|
|
|
367 |
$e = "Une erreur est survenu lors de l'écriture du fichier : $fichier";
|
|
|
368 |
Debug::printr($e);
|
|
|
369 |
$retour = false;
|
|
|
370 |
}
|
|
|
371 |
}
|
|
|
372 |
$contenu = null;
|
|
|
373 |
return $retour;
|
|
|
374 |
}
|
|
|
375 |
|
|
|
376 |
|
|
|
377 |
private function connecterPDO() {
|
|
|
378 |
Config::charger('./configurations/bdd.ini');
|
|
|
379 |
try {
|
| 269 |
delphine |
380 |
$dsn = Config::get('bdd_type').':dbname='.Config::get('bdd_nom').';host='.
|
|
|
381 |
Config::get('bdd_hote');
|
| 273 |
delphine |
382 |
//$dsn = "mysql:dbname=referentiels;host=localhost";
|
| 269 |
delphine |
383 |
$this->bdd = new PDO($dsn, Config::get('bdd_utilisateur'), Config::get('bdd_mot_de_passe'));
|
| 267 |
delphine |
384 |
} catch (PDOException $e) {
|
|
|
385 |
print_r($e);
|
|
|
386 |
echo 'La connexion à la base de donnée via PDO a échouée : ' . $e->getMessage();
|
|
|
387 |
}
|
|
|
388 |
// Passe en UTF-8 la connexion à la BDD
|
|
|
389 |
$this->bdd->exec("SET NAMES 'utf8'");
|
|
|
390 |
// Affiche les erreurs détectées par PDO (sinon mode silencieux => aucune erreur affiché)
|
|
|
391 |
$this->bdd->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
|
|
|
392 |
}
|
|
|
393 |
|
|
|
394 |
protected function executerRequeter($requete) {
|
|
|
395 |
$infos = null;
|
|
|
396 |
try {
|
|
|
397 |
$infos = $this->bdd->query($requete);
|
|
|
398 |
if ($infos === false) {
|
|
|
399 |
echo $requete;
|
|
|
400 |
}
|
|
|
401 |
} catch (PDOException $e) {
|
| 273 |
delphine |
402 |
echo sprintf($e->getFile(), $e->getLine(), $e->getMessage(), $e->getCode(), $requete);
|
| 267 |
delphine |
403 |
}
|
|
|
404 |
return $infos;
|
|
|
405 |
}
|
|
|
406 |
}
|
|
|
407 |
?>
|