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11 jpm 1 
<?php
121 jpm 2 
//declare(encoding='UTF-8');
11 jpm 3 
/**
4 
 * Exemple de lancement du script : :
121 jpm 5 
 * /opt/lampp/bin/php cli.php bdtfx -a chargerTous
6 
 *
11 jpm 7 
 * @category	php 5.2
121 jpm 8 
 * @package		eFlore/Scripts
11 jpm 9 
 * @author		Jennifer DHÉ <jennifer@tela-botanica.org>
10 
 * @author		Jean-Pascal MILCENT <jpm@tela-botanica.org>
11 
 * @copyright	Copyright (c) 2011, Tela Botanica (accueil@tela-botanica.org)
12 
 * @license		http://www.cecill.info/licences/Licence_CeCILL_V2-fr.txt Licence CECILL
13 
 * @license		http://www.gnu.org/licenses/gpl.html Licence GNU-GPL
14 
 * @version		$Id$
15 
 */
68 jpm 16 
class Bdtfx extends EfloreScript {
46 jpm 17 
 
68 jpm 18 
	private $table = null;
19 
	private $pasInsertion = 1000;
20 
	private $departInsertion = 0;
11 jpm 21 
 
22 
	protected $parametres_autorises = array(
369 mathilde 23 
		'-t' => array(false, false, 'Permet de tester le script sur un jeu réduit de données (indiquer le nombre de lignes).'));
11 jpm 24 
 
25 
	public function executer() {
46 jpm 26 
		try {
68 jpm 27 
			$this->initialiserProjet('bdtfx');
46 jpm 28 
 
29 
			// Lancement de l'action demandée
30 
			$cmd = $this->getParametre('a');
31 
			switch ($cmd) {
32 
				case 'chargerTous' :
33 
					$this->chargerStructureSql();
34 
					$this->chargerBdtfx();
340 jpm 35 
					$this->genererChpNomSciHtml();
36 
					$this->genererChpFamille();
103 jpm 37 
					$this->genererDonneesTestMultiVersion();
699 aurelien 38 
					$this->genererChpHierarchie();
46 jpm 39 
					break;
40 
				case 'chargerStructureSql' :
41 
					$this->chargerStructureSql();
42 
					break;
43 
				case 'chargerBdtfx' :
44 
					$this->chargerBdtfx();
45 
					break;
46 
				case 'genererNomSciHtml' :
340 jpm 47 
					$this->genererChpNomSciHtml();
46 jpm 48 
					break;
335 jpm 49 
				case 'genererChpFamille' :
50 
					$this->genererChpFamille();
51 
					break;
699 aurelien 52 
				case 'genererChpHierarchie' :
53 
					$this->genererChpHierarchie();
54 
					break;
103 jpm 55 
				case 'genererDonneesTestMultiVersion' :
56 
					$this->genererDonneesTestMultiVersion();
57 
					break;
58 
				case 'supprimerDonneesTestMultiVersion' :
59 
					$this->supprimerDonneesTestMultiVersion();
60 
					break;
130 jpm 61 
				case 'supprimerTous' :
62 
					$this->supprimerTous();
63 
					break;
46 jpm 64 
				default :
65 
					throw new Exception("Erreur : la commande '$cmd' n'existe pas!");
66 
			}
67 
		} catch (Exception $e) {
68 
			$this->traiterErreur($e->getMessage());
11 jpm 69 
		}
46 jpm 70 
	}
11 jpm 71 
 
46 jpm 72 
	private function chargerBdtfx() {
73 
		$chemin = Config::get('chemins.bdtfx');
74 
		$table = Config::get('tables.bdtfx');
75 
		$requete = "LOAD DATA INFILE '$chemin' ".
76 
				"REPLACE INTO TABLE $table ".
77 
				'CHARACTER SET utf8 '.
78 
				'FIELDS '.
79 
				"	TERMINATED BY '\t' ".
80 
				"	ENCLOSED BY '' ".
81 
				"	ESCAPED BY '\\\' ".
82 
				'IGNORE 1 LINES';
68 jpm 83 
		$this->getBdd()->requeter($requete);
46 jpm 84 
	}
85 
 
340 jpm 86 
	private function genererChpNomSciHtml() {
335 jpm 87 
		$this->initialiserGenerationChamps();
88 
		$this->preparerTablePrChpNomSciHtml();
46 jpm 89 
		$generateur = new GenerateurNomSciHtml();
90 
		$nbreTotal = $this->recupererNbTotalTuples();
661 jpm 91 
		$erreurs = array();
335 jpm 92 
		$this->departInsertion = 0;
46 jpm 93 
		while ($this->departInsertion < $nbreTotal) {
340 jpm 94 
			$resultat = $this->recupererTuplesPrChpNomSciHtml();
661 jpm 95 
 
96 
			try {
97 
				$nomsSciEnHtml = $generateur->generer($resultat);
98 
			} catch (Exception $e) {
99 
				$erreurs[] = $e->getMessage();
100 
			}
101 
 
340 jpm 102 
			$this->remplirChpNomSciHtm($nomsSciEnHtml);
46 jpm 103 
			$this->departInsertion += $this->pasInsertion;
104 
			$this->afficherAvancement("Insertion des noms scientifique au format HTML dans la base par paquet de {$this->pasInsertion} en cours");
68 jpm 105 
			if ($this->stopperLaBoucle($this->getParametre('t'))) break;
11 jpm 106 
		}
107 
		echo "\n";
661 jpm 108 
 
109 
		$this->creerFichierLog('Erreurs lors de la génération HTML des noms scientifiques', $erreurs, 'erreurs_noms_sci_html');
11 jpm 110 
	}
111 
 
335 jpm 112 
	private function initialiserGenerationChamps() {
46 jpm 113 
		$this->table = Config::get('tables.bdtfx');
11 jpm 114 
	}
115 
 
335 jpm 116 
	private function preparerTablePrChpNomSciHtml() {
11 jpm 117 
		$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'nom_sci_html' ";
68 jpm 118 
		$resultat = $this->getBdd()->recuperer($requete);
11 jpm 119 
		if ($resultat === false) {
120 
			$requete = 	"ALTER TABLE {$this->table} ".
335 jpm 121 
				'ADD nom_sci_html VARCHAR( 500 ) '.
122 
				'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
68 jpm 123 
			$this->getBdd()->requeter($requete);
11 jpm 124 
		}
125 
	}
126 
 
127 
	private function recupererNbTotalTuples(){
46 jpm 128 
		$requete = "SELECT count(*) AS nb FROM {$this->table} ";
68 jpm 129 
		$resultat = $this->getBdd()->recuperer($requete);
46 jpm 130 
		return $resultat['nb'];
11 jpm 131 
	}
132 
 
340 jpm 133 
	private function recupererTuplesPrChpNomSciHtml() {
11 jpm 134 
		$requete = 'SELECT 	num_nom, rang, nom_supra_generique, genre, epithete_infra_generique, '.
335 jpm 135 
			'	epithete_sp, type_epithete, epithete_infra_sp,cultivar_groupe, '.
136 
			'	nom_commercial, cultivar '.
137 
			"FROM {$this->table} ".
138 
			"LIMIT {$this->departInsertion},{$this->pasInsertion} ";
68 jpm 139 
		$resultat = $this->getBdd()->recupererTous($requete);
11 jpm 140 
		return $resultat;
141 
	}
142 
 
340 jpm 143 
	private function remplirChpNomSciHtm($nomsSciHtm) {
46 jpm 144 
		foreach ($nomsSciHtm as $id => $html) {
68 jpm 145 
			$html = $this->getBdd()->proteger($html);
340 jpm 146 
			$requete = "UPDATE {$this->table} SET nom_sci_html = $html WHERE num_nom = $id ";
68 jpm 147 
			$resultat = $this->getBdd()->requeter($requete);
46 jpm 148 
			if ($resultat === false) {
149 
				throw new Exception("Erreur d'insertion pour le tuple $id");
11 jpm 150 
			}
151 
		}
152 
	}
339 jpm 153 
 
335 jpm 154 
	private function genererChpFamille() {
155 
		$this->initialiserGenerationChamps();
156 
		$this->preparerTablePrChpFamille();
336 jpm 157 
		$resultats = $this->recupererTuplesPrChpFamille();
158 
		$noms = array();
159 
		$introuvables = array();
339 jpm 160 
		$introuvablesSyno = array();
161 
		foreach ($resultats as $id => $nom) {
336 jpm 162 
			$nn = $nom['num_nom'];
339 jpm 163 
			$nnr = $nom['num_nom_retenu'];
336 jpm 164 
			$nts = $nom['num_tax_sup'];
165 
			$rg = $nom['rang'];
339 jpm 166 
			if ($nnr != '') {
167 
				if ($rg == '180') {
340 jpm 168 
					$noms[$nn] = $nom['nom_sci'];
336 jpm 169 
				} else {
339 jpm 170 
					if ($nn == $nnr) {// nom retenu
171 
						if (isset($noms[$nts])) {
172 
							$noms[$nn] = $noms[$nts];
173 
						} else {
174 
							$introuvables[] = $nn;
175 
						}
176 
					} else {// nom synonyme
177 
						if (isset($noms[$nnr])) {
178 
							$noms[$nn] = $noms[$nnr];
179 
						} else {
180 
							$introuvablesSyno[] = $nom;
181 
						}
182 
					}
336 jpm 183 
				}
184 
			}
339 jpm 185 
			unset($resultats[$id]);
336 jpm 186 
			$this->afficherAvancement("Attribution de leur famille aux noms en cours");
335 jpm 187 
			if ($this->stopperLaBoucle($this->getParametre('t'))) break;
188 
		}
336 jpm 189 
		echo "\n";
339 jpm 190 
 
191 
		foreach ($introuvablesSyno as $id => $nom) {
192 
			$nn = $nom['num_nom'];
193 
			$nnr = $nom['num_nom_retenu'];
194 
			if (isset($noms[$nnr])) {
195 
				$noms[$nn] = $noms[$nnr];
196 
			} else {
197 
				$introuvables[] = $nn;
198 
			}
199 
			unset($introuvablesSyno[$id]);
200 
			$this->afficherAvancement("Attribution de leur famille aux synonymes en cours");
336 jpm 201 
		}
339 jpm 202 
		echo "\n";
203 
 
661 jpm 204 
		$msg = 'Plusieurs familles sont introuvables';
205 
		$this->creerFichierLog($msg, $introuvables, 'famille_introuvable');
339 jpm 206 
 
340 jpm 207 
		$this->remplirChpFamille($noms);
335 jpm 208 
	}
699 aurelien 209 
 
335 jpm 210 
	private function preparerTablePrChpFamille() {
211 
		$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'famille' ";
212 
		$resultat = $this->getBdd()->recuperer($requete);
213 
		if ($resultat === false) {
214 
			$requete = 	"ALTER TABLE {$this->table} ".
215 
				'ADD famille VARCHAR(255) '.
216 
				'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
217 
			$this->getBdd()->requeter($requete);
218 
		}
219 
	}
339 jpm 220 
 
335 jpm 221 
	private function recupererTuplesPrChpFamille() {
339 jpm 222 
		$requete = 'SELECT num_nom, num_nom_retenu, num_tax_sup, rang, nom_sci '.
335 jpm 223 
				"FROM {$this->table} ".
224 
				"WHERE rang >= 180 ".
340 jpm 225 
				"ORDER BY rang ASC, num_tax_sup ASC, num_nom_retenu DESC ";
335 jpm 226 
		$resultat = $this->getBdd()->recupererTous($requete);
227 
		return $resultat;
228 
	}
339 jpm 229 
 
340 jpm 230 
	private function remplirChpFamille($noms) {
336 jpm 231 
		foreach ($noms as $id => $famille) {
232 
			$famille = $this->getBdd()->proteger($famille);
340 jpm 233 
			$requete = "UPDATE {$this->table} SET famille = $famille WHERE num_nom = $id ";
336 jpm 234 
			$resultat = $this->getBdd()->requeter($requete);
235 
			if ($resultat === false) {
236 
				throw new Exception("Erreur d'insertion pour le tuple $id");
237 
			}
238 
			$this->afficherAvancement("Insertion des noms de famille dans la base en cours");
239 
		}
240 
		echo "\n";
241 
	}
699 aurelien 242 
 
243 
	private function genererChpHierarchie() {
244 
		$this->initialiserGenerationChamps();
245 
		$this->preparerTablePrChpHierarchie();
246 
		$table = Config::get('tables.bdtfx');
247 
 
248 
		$requete = "UPDATE $table SET hierarchie = NULL ";
249 
		$mise_a_jour = $this->getBdd()->requeter($requete);
250 
 
251 
		$requete_hierarchie = "SELECT num_nom, num_nom_retenu, num_tax_sup FROM ".$table." ORDER BY rang DESC";
252 
 
253 
		$resultat = $this->getBdd()->recupererTous($requete_hierarchie);
254 
		$num_nom_a_num_sup = array();
255 
		foreach($resultat as &$taxon) {
256 
			$num_nom_a_num_sup[$taxon['num_nom']] = $taxon['num_tax_sup'];
257 
		}
258 
		$chemin_taxo = "";
259 
		foreach($resultat as &$taxon) {
260 
			$chemin_taxo = $this->traiterHierarchieNumTaxSup($taxon['num_nom_retenu'], $num_nom_a_num_sup).'-';
261 
			$requete = "UPDATE $table SET hierarchie = ".$this->getBdd()->proteger($chemin_taxo)." WHERE num_nom = ".$taxon['num_nom']." ";
262 
			$mise_a_jour = $this->getBdd()->requeter($requete);
263 
			$this->afficherAvancement("Insertion de la hierarchie taxonomique en cours");
264 
		}
265 
		echo "\n";
266 
	}
267 
 
268 
	private function traiterHierarchieNumTaxSup($num_nom_retenu, &$num_nom_a_num_sup) {
269 
		$chaine_hierarchie = "";
270 
		if(isset($num_nom_a_num_sup[$num_nom_retenu])) {
271 
			$num_tax_sup = $num_nom_a_num_sup[$num_nom_retenu];
272 
			$chaine_hierarchie = '-'.$num_tax_sup;
273 
			if($num_tax_sup != 0 && $num_tax_sup != '') {
274 
				$chaine_hierarchie = $this->traiterHierarchieNumTaxSup($num_tax_sup, $num_nom_a_num_sup).$chaine_hierarchie;
275 
			}
276 
		}
277 
		return $chaine_hierarchie;
278 
	}
279 
 
280 
	private function preparerTablePrChpHierarchie() {
281 
		$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'hierarchie' ";
282 
		$resultat = $this->getBdd()->recuperer($requete);
283 
		if ($resultat === false) {
284 
			$requete = 	"ALTER TABLE {$this->table} ".
285 
					'ADD hierarchie VARCHAR(1000) '.
286 
					'CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ';
287 
			$this->getBdd()->requeter($requete);
288 
		}
289 
	}
11 jpm 290 
 
103 jpm 291 
	private function genererDonneesTestMultiVersion() {
292 
		$contenuSql = $this->recupererContenu(Config::get('chemins.structureSqlTest'));
293 
		$this->executerScripSql($contenuSql);
68 jpm 294 
 
103 jpm 295 
		$table = Config::get('tables.bdtfx');
296 
		$tableTest = Config::get('tables.bdtfxTest');
297 
		$requete = "INSERT INTO $tableTest SELECT * FROM $table";
298 
		$this->getBdd()->requeter($requete);
299 
	}
300 
 
301 
	private function supprimerDonneesTestMultiVersion() {
302 
		$tableMeta = Config::get('tables.bdtfxMeta');
303 
		$requete = "DELETE FROM $tableMeta WHERE guid = 'urn:lsid:tela-botanica.org:bdtfx:1.02'";
304 
		$this->getBdd()->requeter($requete);
305 
 
306 
		$tableTest = Config::get('tables.bdtfxTest');
342 jpm 307 
		$requete = "DROP TABLE IF EXISTS $tableTest";
103 jpm 308 
		$this->getBdd()->requeter($requete);
309 
	}
130 jpm 310 
 
311 
	private function supprimerTous() {
342 jpm 312 
		$requete = "DROP TABLE IF EXISTS bdtfx_meta, bdtfx_v1_01, bdtfx_v1_02";
130 jpm 313 
		$this->getBdd()->requeter($requete);
314 
	}
661 jpm 315 
 
316 
	private function creerFichierLog($message, $lignes, $nomFichier) {
317 
		$lignesNbre = count($lignes);
318 
		if ($lignesNbre != 0) {
319 
			echo "$message. Voir le log de $lignesNbre lignes :\n";
320 
 
321 
			$logContenu = implode(", \n", $lignes);
322 
			$logFichier = realpath(dirname(__FILE__))."/log/$nomFichier.log";
323 
			echo $logFichier."\n";
324 
					file_put_contents($logFichier, $logContenu);
325 
		}
326 
	}
11 jpm 327 
}
328 
?>