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mathilde |
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<?php
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/** Exemple lancement:
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* /opt/lampp/bin/php -d memory_limit=3500M ~/web/eflore-projets/scripts/cli.php baseflor -a chargerTous
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*/
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class Baseflor extends EfloreScript {
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private $table = null;
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private $nb_erreurs;
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private $erreurs_ligne;
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private $ligne_num;
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private $colonne_valeur;
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private $colonne_num;
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private $type_bio = array(
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"A","a","B","b","C","c","Cfru","cfru","Csuf","csuf","Ccou","ccou","H","h","Heri",
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"heri","Hsto","hsto","Hces","hces","Hros","hros","Hrub","hrub","Hbis","hbis","G",
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"g","Gbul","gbul","Gtub","gtub","Grhi","grhi","T","t","Tver","tver","Test","test");
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private $ss_type_bio = array("aqua", "lia", "épi", "hpar", "par", "suc", "semp", "cad", "car");
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//les deux suivants basés sur valeurs trouvées (--> pas de légende !)
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private $signes_seuls = array("?", "x", "x~", "x=","xb","xB","-");
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private $signes_nn_seuls = array("~", "=","b","B");
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//paramètres pour lancement de fonctions sur colonnes
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private $verifierIntervalle = array(23 => array(1,9), 24 => array(1,9), 25 => array(1,9),
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26 => array(1,9), 27 => array(1,12), 28 => array(1,9), 29 => array(1,9), 30 => array(0,9),
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31 => array(1,9), 32 => array(1,9), 33 => array(1,9), 34 => array(1,9), 35 => array(1,9),
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36 => array(1,12), 37 => array(1,9), 38 => array(1,9), 39 => array(0,9),);
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private $verifierColonnesBasiques = array(1 =>"/(^[0-9]*\/)|(inconnu)/", 2 => "/(^[AB]?[0-9]+$)|(^nc$)/",
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3 => "/(^[AB]?[0-9]+$)|(^nc$)/", 4 => "/[^0-9]+/", 5 => "/[^0-9]+/", 6 => "/[^0-9]+/", 7 => "/[^0-9]+/",
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8 => "/[^0-9]+/", 9 => "/[^0-9]+/", 10 => "/[^0-9]+/", 11 => "/[^0-9]+/", 12 => "/[^0-9]+/",
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13 => "/[^0-9]+/", 14 => "/^([1-9]|1[0-2])(\-([1-9]|1[0-2]))*$/", 16 => "/[^0-9]+/", 19 => "/[^0-9]+/",
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20 => "/[^0-9]+/", 21 => "/[^0-9]+/", 22 => "/[^0-9]+/", 40 => "/[^0-9]+/",
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41 => "/[^0-9]+/", 42 => "/[^0-9]+/", 43 => "/[^0-9]+/", 44 => "/[^0-9]+/", 45 => "/[^0-9]+/",
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46 => "/[^0-9]+/", 47 => "/[^0-9]+/", 48 => "/[^0-9]+/", 49 => "/[^0-9]+/", 50 => "/[^0-9]+/",
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51 => "/[^0-9]+/", 52 => "/[^0-9]+/", 53 => "/[^0-9]+/", 54 => "/[^0-9]+/", 55 => "/[^0-9]+/"
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);
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public function executer() {
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// Lancement de l'action demandée
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try {
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$this->initialiserProjet('baseflor');
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$cmd = $this->getParametre('a');
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switch ($cmd) {
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case 'chargerStructureSql' :
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$this->chargerStructureSql();
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break;
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case 'chargerDonnees' :
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$this->verifFichier();
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if($this->nb_erreurs == 0){
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$this->chargerDonnees();
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} else {
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echo "je ne peux pas charger les données car le fichier comporte des erreurs.
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Voir le fichier baseflor_verif.txt\n";
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}
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break;
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case 'supprimerTous' :
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$this->supprimerTous();
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break;
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case 'chargerOntologies' :
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$this->chargerOntologies();
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break;
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case 'verifierDonnees' :
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$this->verifFichier();
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break;
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case 'genererChamps' :
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$this->genererChpsBDNT();
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$this->genererChpsNumTaxon();
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$this->genererChpsNumNomen();
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break;
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case 'chargerMetadonnees':
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$this->chargerMetadonnees();
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break;
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default :
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throw new Exception("Erreur : la commande '$cmd' n'existe pas!");
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}
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} catch (Exception $e) {
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$this->traiterErreur($e->getMessage());
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}
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}
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//-- génération de champs --//
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private function genererChamps(){
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$this->genererChpsBDNT();
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$this->genererChpsNumTaxon();
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$this->genererChpsNumNomen();
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}
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private function genererChpsBDNT(){
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpsBDNT();
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$resultats = $this->recupererTuplesNumsOriginels();
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$bdnt = array();
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foreach ($resultats as $chps => $res) {
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$cle = $res['cle'];
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$nno = $res['num_nomen_originel'];
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$nto = $res['num_taxon_originel'];
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if ( (preg_match("/^([AB])[0-9]+$/", $nno, $retour)) || (preg_match("/^([AB])[0-9]+$/", $nto, $retour)) ){
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if($retour[1]=='A'){
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$bdnt[$cle]= "BDAFX";
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}else{
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$bdnt[$cle]= "BDBFX";
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}
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}elseif(($nno == 'nc') && ($nto == 'nc')){
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$bdnt[$cle]= "nc";
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}else{
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$bdnt[$cle]= "BDTFX";
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}
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}
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$this->remplirChamps($bdnt, "BDNT");
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}
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private function genererChpsNumTaxon(){
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpsNumTaxon();
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$resultats = $this->recupererTuplesNumsOriginels();
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$num_taxon= array();
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foreach ($resultats as $chps => $res) {
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$cle = $res['cle'];
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$nto = $res['num_taxon_originel'];
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if (preg_match("/^[AB]([0-9]+)$/", $nto, $retour)){
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$num_taxon[$cle]= intval($retour[1]);
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}elseif($nto == 'nc'){
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$num_taxon[$cle]= 0;
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}else{
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$num_taxon[$cle]= intval($nto);
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}
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}
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$this->remplirChamps($num_taxon, "num_taxon");
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}
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private function genererChpsNumNomen(){
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$this->initialiserGenerationChamps();
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$this->preparerTablePrChpsNumNomen();
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$resultats = $this->recupererTuplesNumsOriginels();
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$num_nomen= array();
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foreach ($resultats as $chps => $res) {
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$cle = $res['cle'];
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$nno = $res['num_nomen_originel'];
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if (preg_match("/^[AB]([0-9]+)$/", $nno, $retour)){
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$num_nomen[$cle]= intval($retour[1]);
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}elseif($nno == 'nc'){
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$num_nomen[$cle]= 0;
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}else{
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$num_nomen[$cle]=intval($nno);
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}
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}
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$this->remplirChamps($num_nomen, "num_nomen");
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}
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private function remplirChamps($champs, $nom_colonne) {
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foreach ($champs as $cle => $val) {
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$val = $this->getBdd()->proteger($val);
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$requete = "UPDATE {$this->table} SET $nom_colonne = $val WHERE cle = $cle ";
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$resultat = $this->getBdd()->requeter($requete);
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if ($resultat === false) {
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throw new Exception("Erreur d'insertion pour le tuple clé = ".$cle);
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}
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$this->afficherAvancement("Insertion des valeurs pour ".$nom_colonne." 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 initialiserGenerationChamps() {
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$this->table = Config::get('tables.donnees');
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}
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private function preparerTablePrChpsBDNT() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'BDNT' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD BDNT VARCHAR( 6 ) '.
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'CHARACTER SET utf8 COLLATE utf8_general_ci'.
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' NOT NULL AFTER catminat_code ';
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$this->getBdd()->requeter($requete);
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}
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}
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private function preparerTablePrChpsNumTaxon() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'num_taxon' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD num_taxon INT( 10 ) NOT NULL'.
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' AFTER catminat_code';
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$this->getBdd()->requeter($requete);
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}
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}
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private function preparerTablePrChpsNumNomen() {
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$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'num_nomen' ";
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$resultat = $this->getBdd()->recuperer($requete);
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if ($resultat === false) {
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$requete = "ALTER TABLE {$this->table} ".
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'ADD num_nomen INT( 10 ) NOT NULL'.
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' AFTER catminat_code';
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$this->getBdd()->requeter($requete);
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}
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}
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private function recupererTuplesNumsOriginels(){
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$requete = 'SELECT cle, num_taxon_originel, num_nomen_originel '.
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"FROM {$this->table} ";
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$resultat = $this->getBdd()->recupererTous($requete);
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return $resultat;
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}
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//-- chargements, suppression, exécution --//
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protected function chargerMetadonnees() {
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$contenuSql = $this->recupererContenu(Config::get('chemins.metadonnees'));
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$this->executerScripSql($contenuSql);
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}
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private function chargerOntologies() {
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$chemin = Config::get('chemins.ontologies');
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$table = Config::get('tables.ontologies');
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$requete = "LOAD DATA INFILE '$chemin' ".
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"REPLACE INTO TABLE $table ".
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'CHARACTER SET utf8 '.
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'FIELDS '.
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" TERMINATED BY '\t' ".
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" ENCLOSED BY '' ".
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" ESCAPED BY '\\\' "
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;
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$this->getBdd()->requeter($requete);
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}
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protected function chargerStructureSql() {
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$contenuSql = $this->recupererContenu(Config::get('chemins.structureSql'));
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$this->executerScripSql($contenuSql);
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}
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protected function executerScripSql($sql) {
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$requetes = Outils::extraireRequetes($sql);
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foreach ($requetes as $requete) {
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$this->getBdd()->requeter($requete);
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}
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}
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private function chargerDonnees() {
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$table = Config::get('tables.donnees');
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$requete = "LOAD DATA INFILE '".Config::get('chemins.donnees')."' ".
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"REPLACE INTO TABLE $table ".
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'CHARACTER SET utf8 '.
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'FIELDS '.
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" TERMINATED BY '\t' ".
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" ENCLOSED BY '' ".
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" ESCAPED BY '\\\'";
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$this->getBdd()->requeter($requete);
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}
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private function supprimerTous() {
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$requete = "DROP TABLE IF EXISTS baseflor_meta, baseflor_ontologies, baseflor_v2012_03_19";
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mathilde |
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$this->getBdd()->requeter($requete);
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}
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//-- vérifications de données --//
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private function verifierSiVide(){
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$bool=false;
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if ( $this->colonne_valeur == "" ){
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$bool=true;
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}
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return $bool;
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}
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private function verifierIntervallesTous($valeur){
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$intervalle=$this->verifierIntervalle[$this->colonne_num];
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$this->verifierIntervalleChiffres($intervalle[0], $intervalle[1],$valeur);
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}
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private function verifierIntervalleChiffres($mini, $max, $valeur){
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if (( ($valeur < $mini) || ($valeur > $max) ) && ($valeur != "")){
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$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
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$this->nb_erreurs++;
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}
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}
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291 |
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private function verifierValeursIndic(){
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if (( preg_match("/^([^0-9])*([0-9]+)([^0-9])*$/", $this->colonne_valeur,$retour) == 1 )){
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$this->verifierIntervallesTous($retour[2]);
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if((isset($retour[3]))&&(!(in_array($retour[3], $this->signes_nn_seuls))) ){
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$this->erreurs_ligne[$this->colonne_num] =$this->colonne_valeur;
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$this->nb_erreurs++;
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}
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if(($retour[1] != "-")&&($retour[1]!="") ){
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$this->erreurs_ligne[$this->colonne_num] =$this->colonne_valeur;
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$this->nb_erreurs++;
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303 |
if($this->ligne_num==3){
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}
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}
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}elseif(!(in_array( $this->colonne_valeur, $this->signes_seuls))&& !($this->verifierSiVide())) {
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307 |
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
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308 |
$this->nb_erreurs++;
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309 |
}
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310 |
}
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311 |
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312 |
private function verifierTypeBio(){
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313 |
if (( preg_match("/(.+)\((.+)\)$/", $this->colonne_valeur,$retour) == 1 )){
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314 |
$this->verifType_SsType($retour[1]);
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315 |
$this->verifType_SsType($retour[2]);
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316 |
}else{
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|
|
317 |
$this->verifType_SsType($this->colonne_valeur);
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|
|
318 |
}
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|
319 |
}
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320 |
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321 |
private function verifType_SsType($chaine_a_verif){
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|
|
322 |
//verifie type
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|
323 |
if(( preg_match("/^([a-zA-Zé]+)\-(.+)$|^([a-zA-Zé]+[^\-])$/", $chaine_a_verif, $retour) == 1 )){
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|
|
324 |
$type=$retour[1];
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|
325 |
if(isset($retour[3])){
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|
|
326 |
$type=$retour[3];
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|
|
327 |
}
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|
|
328 |
if(!(in_array($type, $this->type_bio))) {
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|
|
329 |
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
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|
|
330 |
$this->nb_erreurs++;
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|
|
331 |
}
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|
|
332 |
//verifie sous_type(s)
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|
|
333 |
if ($retour[2]!=""){
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|
|
334 |
$ss_type[0]=$retour[2];
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|
|
335 |
if (( preg_match("/\-/", $ss_type[0])) == 1 ){
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|
|
336 |
$ss_type = preg_split("/\-/", $retour[2]);
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|
|
337 |
}
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|
|
338 |
foreach($ss_type as $sst){
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|
|
339 |
if(!(in_array($sst, $this->ss_type_bio))) {
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|
|
340 |
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
|
|
|
341 |
$this->nb_erreurs++;
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|
|
342 |
}
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|
|
343 |
}
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|
|
344 |
}
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|
|
345 |
}
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|
|
346 |
}
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|
|
347 |
|
|
|
348 |
private function verifierColonne($chaine){
|
|
|
349 |
if ( ( preg_match($chaine, $this->colonne_valeur) == 0 ) && !($this->verifierSiVide()) ){
|
|
|
350 |
$this->erreurs_ligne[$this->colonne_num]=$this->colonne_valeur;
|
|
|
351 |
$this->nb_erreurs++;
|
|
|
352 |
}
|
|
|
353 |
}
|
|
|
354 |
|
|
|
355 |
//vérifie par colonnes les erreurs d'une ligne
|
|
|
356 |
private function verifErreursLignes($colonne_array){
|
|
|
357 |
$this->erreurs_ligne=array();
|
|
|
358 |
for ($this->colonne_num = 0; $this->colonne_num < count($colonne_array); $this->colonne_num++){
|
|
|
359 |
if ( isset($colonne_array) ){
|
|
|
360 |
$this->colonne_valeur = $colonne_array[$this->colonne_num];
|
|
|
361 |
if ( (( ($this->colonne_num > 0) && ($this->colonne_num < 15) ) || ( $this->colonne_num == 16 )
|
|
|
362 |
|| (($this->colonne_num > 18 ) && ( $this->colonne_num < 23 ) )
|
|
|
363 |
|| ( $this->colonne_num > 39 )) ){
|
|
|
364 |
$motif = $this->verifierColonnesBasiques[$this->colonne_num];
|
|
|
365 |
$this->verifierColonne($motif);
|
|
|
366 |
}elseif ( $this->colonne_num == 15 ){
|
|
|
367 |
$this->verifierTypeBio();
|
|
|
368 |
} elseif (($this->colonne_num > 22 ) && ( $this->colonne_num < 33 )){
|
|
|
369 |
$this->verifierIntervallesTous($this->colonne_valeur);
|
|
|
370 |
}elseif (( $this->colonne_num > 32) && ( $this->colonne_num < 41)){
|
|
|
371 |
$this->verifierValeursIndic();
|
|
|
372 |
}
|
|
|
373 |
} else {
|
|
|
374 |
echo "ligne ".$this->ligne_num.": pas de tabulation \n ";
|
|
|
375 |
}
|
|
|
376 |
}
|
|
|
377 |
|
|
|
378 |
}
|
|
|
379 |
|
|
|
380 |
//verifie la cohérence des valeurs des colonnes
|
|
|
381 |
private function verifFichier(){
|
| 383 |
mathilde |
382 |
$dernier_nb_erreur = 0;
|
| 373 |
mathilde |
383 |
if (file_exists(Config::get('chemins.donnees_verif'))) {
|
|
|
384 |
unlink(Config::get('chemins.donnees_verif'));
|
|
|
385 |
}
|
| 370 |
mathilde |
386 |
$fichier = fopen(Config::get('chemins.donnees'), "r");
|
|
|
387 |
$fichier2 = fopen(Config::get('chemins.donnees_verif'), "w");
|
|
|
388 |
$this->valeurs=array();
|
|
|
389 |
$this->nb_erreurs=0;
|
|
|
390 |
if ( ($fichier != false) && ($fichier2 != false) ){
|
| 383 |
mathilde |
391 |
$this->ligne_num=0;
|
| 370 |
mathilde |
392 |
while ( !feof($fichier) ) {
|
| 383 |
mathilde |
393 |
if ($this->ligne_num == 0){
|
| 370 |
mathilde |
394 |
fputs($fichier2," !!! REGARDEZ LES COLONNES DANS NUMERO_COLONNES_IMPORTANT.TXT.\n");
|
|
|
395 |
}
|
|
|
396 |
$this->ligne_num++;
|
|
|
397 |
$ligne = fgets($fichier);
|
|
|
398 |
$col = preg_split("/ /", $ligne);
|
|
|
399 |
$this->verifErreursLignes($col);
|
|
|
400 |
//rédaction du fichier de vérif
|
|
|
401 |
if(count($this->nb_erreurs)!= 0){
|
|
|
402 |
if($dernier_nb_erreur != $this->nb_erreurs){
|
|
|
403 |
$dernier_nb_erreur = $this->nb_erreurs;
|
|
|
404 |
fputs($fichier2," \n erreurs sur la ligne".$this->ligne_num."\n");
|
|
|
405 |
foreach ($this->erreurs_ligne as $cle => $v){
|
|
|
406 |
fputs($fichier2,"colonne ".$cle." : ".$v." - ");
|
|
|
407 |
}
|
|
|
408 |
}
|
|
|
409 |
}
|
|
|
410 |
}
|
|
|
411 |
}
|
|
|
412 |
if ($this->nb_erreurs == 0){
|
|
|
413 |
fputs($fichier2,"/n il n'y a pas d'erreurs./n");
|
|
|
414 |
}
|
|
|
415 |
echo $this->nb_erreurs."erreurs";
|
|
|
416 |
fclose($fichier);
|
|
|
417 |
fclose($fichier2);
|
|
|
418 |
}
|
|
|
419 |
|
|
|
420 |
|
|
|
421 |
|
|
|
422 |
}
|
|
|
423 |
|
|
|
424 |
?>
|