Subversion Repositories eFlore/Projets.eflore-projets

Compare Revisions

Ignore whitespace Rev 405 → Rev 406

/trunk/scripts/modules/bdtxa/bdtxa.ini
New file
0,0 → 1,17
code="bdtxa"
version="1_00"
dossierTsv = "{ref:dossierDonneesEflore}{ref:code}/1.00/"
dossierSql = "{ref:dossierTsv}"
 
[tables]
bdtMeta = "{ref:code}_meta"
bdt = "{ref:code}_v{ref:version}"
 
 
[fichiers]
structureSql = "{ref:code}_v{ref:version}.sql"
bdt = "{ref:code}_v{ref:version}_ref.txt"
 
[chemins]
structureSql = "{ref:dossierSql}{ref:fichiers.structureSql}"
bdt = "{ref:dossierTsv}{ref:fichiers.bdt}"
/trunk/scripts/modules/bdtxa/Bdtxa.php
New file
0,0 → 1,233
<?php
//declare(encoding='UTF-8');
/**
* Exemple de lancement du script : :
* /opt/lampp/bin/php cli.php bdtxa -a chargerTous
*
* @category php 5.2
* @package eFlore/Scripts
* @author Jean-Pascal MILCENT <jpm@tela-botanica.org>
* @copyright Copyright (c) 2012, Tela Botanica (accueil@tela-botanica.org)
* @license http://www.cecill.info/licences/Licence_CeCILL_V2-fr.txt Licence CECILL
* @license http://www.gnu.org/licenses/gpl.html Licence GNU-GPL
* @version $Id$
*/
class Bdtxa 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('bdtxa');
 
// Lancement de l'action demandée
$cmd = $this->getParametre('a');
switch ($cmd) {
case 'chargerTous' :
$this->chargerStructureSql();
$this->chargerBdtxa();
$this->genererChpNomSciHtml();
$this->genererChpFamille();
break;
case 'chargerStructureSql' :
$this->chargerStructureSql();
break;
case 'chargerBdtxa' :
$this->chargerBdtxa();
break;
case 'genererNomSciHtml' :
$this->genererChpNomSciHtml();
break;
case 'genererChpFamille' :
$this->genererChpFamille();
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 chargerBdtxa() {
$chemin = Config::get('chemins.bdt');
$table = Config::get('tables.bdt');
$requete = "LOAD DATA INFILE '$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();
$this->departInsertion = 0;
while ($this->departInsertion < $nbreTotal) {
$resultat = $this->recupererTuplesPrChpNomSciHtml();
$nomsSciEnHtml = $generateur->generer($resultat);
$this->remplirChpNomSciHtm($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";
}
 
private function initialiserGenerationChamps() {
$this->table = Config::get('tables.bdt');
}
 
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";
 
if (count($introuvables) != 0) {
$introuvablesNbre = count($introuvables);
echo "Famille introuvable pour $introuvablesNbre noms ! Voir le log.\n";
 
$logContenu = implode(", \n", $introuvables);
$logFichier = realpath(dirname(__FILE__)).'/log/famille_introuvable.log';
echo $logFichier."\n";
file_put_contents($logFichier, $logContenu);
}
$this->remplirChpFamille($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 supprimerTous() {
$requete = "DROP TABLE IF EXISTS bdtxa_meta, bdtxa_v0_01";
$this->getBdd()->requeter($requete);
}
}
?>