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<?php
//declare(encoding='UTF-8');
/**
* Exemple de lancement du script : :
* /opt/lampp/bin/php cli.php bdtfx -a chargerTous
*
* @category php 5.2
* @package eFlore/Scripts
* @author Jennifer DHÉ <jennifer@tela-botanica.org>
* @author Jean-Pascal MILCENT <jpm@tela-botanica.org>
* @copyright Copyright (c) 2011, 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 Bdtfx 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('bdtfx');
// Lancement de l'action demandée
$cmd = $this->getParametre('a');
switch ($cmd) {
case 'chargerTous' :
$this->chargerStructureSql();
$this->chargerBdtfx();
$this->genererChpNomSciHtml();
$this->genererChpFamille();
$this->genererDonneesTestMultiVersion();
break;
case 'chargerStructureSql' :
$this->chargerStructureSql();
break;
case 'chargerBdtfx' :
$this->chargerBdtfx();
break;
case 'genererNomSciHtml' :
$this->genererChpNomSciHtml();
break;
case 'genererChpFamille' :
$this->genererChpFamille();
break;
case 'genererDonneesTestMultiVersion' :
$this->genererDonneesTestMultiVersion();
break;
case 'supprimerDonneesTestMultiVersion' :
$this->supprimerDonneesTestMultiVersion();
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 chargerBdtfx() {
$chemin = Config::get('chemins.bdtfx');
$table = Config::get('tables.bdtfx');
$requete = "LOAD DATA INFILE '$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 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.bdtfx');
}
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() {
$requete = 'SELECT num_nom, rang, nom_supra_generique, genre, epithete_infra_generique, '.
' epithete_sp, type_epithete, epithete_infra_sp,cultivar_groupe, '.
' nom_commercial, cultivar '.
"FROM {$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 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 genererDonneesTestMultiVersion() {
$contenuSql = $this->recupererContenu(Config::get('chemins.structureSqlTest'));
$this->executerScripSql($contenuSql);
$table = Config::get('tables.bdtfx');
$tableTest = Config::get('tables.bdtfxTest');
$requete = "INSERT INTO $tableTest SELECT * FROM $table";
$this->getBdd()->requeter($requete);
}
private function supprimerDonneesTestMultiVersion() {
$tableMeta = Config::get('tables.bdtfxMeta');
$requete = "DELETE FROM $tableMeta WHERE guid = 'urn:lsid:tela-botanica.org:bdtfx:1.02'";
$this->getBdd()->requeter($requete);
$tableTest = Config::get('tables.bdtfxTest');
$requete = "DROP TABLE IF EXISTS $tableTest";
$this->getBdd()->requeter($requete);
}
private function supprimerTous() {
$requete = "DROP TABLE IF EXISTS bdtfx_meta, bdtfx_v1_01, bdtfx_v1_02";
$this->getBdd()->requeter($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);
}
}
}
?>