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Ignore whitespace Rev 369 → Rev 370

/trunk/scripts/modules/baseflor/Baseflor.php
New file
0,0 → 1,422
<?php
/** Exemple lancement:
* /opt/lampp/bin/php -d memory_limit=3500M ~/web/eflore-projets/scripts/cli.php baseflor -a chargerTous
*/
class Baseflor extends EfloreScript {
private $table = null;
private $nb_erreurs;
private $erreurs_ligne;
private $ligne_num;
private $colonne_valeur;
private $colonne_num;
private $type_bio = array(
"A","a","B","b","C","c","Cfru","cfru","Csuf","csuf","Ccou","ccou","H","h","Heri",
"heri","Hsto","hsto","Hces","hces","Hros","hros","Hrub","hrub","Hbis","hbis","G",
"g","Gbul","gbul","Gtub","gtub","Grhi","grhi","T","t","Tver","tver","Test","test");
private $ss_type_bio = array("aqua", "lia", "épi", "hpar", "par", "suc", "semp", "cad", "car");
//les deux suivants basés sur valeurs trouvées (--> pas de légende !)
private $signes_seuls = array("?", "x", "x~", "x=","xb","xB","-");
private $signes_nn_seuls = array("~", "=","b","B");
//paramètres pour lancement de fonctions sur colonnes
private $verifierIntervalle = array(23 => array(1,9), 24 => array(1,9), 25 => array(1,9),
26 => array(1,9), 27 => array(1,12), 28 => array(1,9), 29 => array(1,9), 30 => array(0,9),
31 => array(1,9), 32 => array(1,9), 33 => array(1,9), 34 => array(1,9), 35 => array(1,9),
36 => array(1,12), 37 => array(1,9), 38 => array(1,9), 39 => array(0,9),);
private $verifierColonnesBasiques = array(1 =>"/(^[0-9]*\/)|(inconnu)/", 2 => "/(^[AB]?[0-9]+$)|(^nc$)/",
3 => "/(^[AB]?[0-9]+$)|(^nc$)/", 4 => "/[^0-9]+/", 5 => "/[^0-9]+/", 6 => "/[^0-9]+/", 7 => "/[^0-9]+/",
8 => "/[^0-9]+/", 9 => "/[^0-9]+/", 10 => "/[^0-9]+/", 11 => "/[^0-9]+/", 12 => "/[^0-9]+/",
13 => "/[^0-9]+/", 14 => "/^([1-9]|1[0-2])(\-([1-9]|1[0-2]))*$/", 16 => "/[^0-9]+/", 19 => "/[^0-9]+/",
20 => "/[^0-9]+/", 21 => "/[^0-9]+/", 22 => "/[^0-9]+/", 40 => "/[^0-9]+/",
41 => "/[^0-9]+/", 42 => "/[^0-9]+/", 43 => "/[^0-9]+/", 44 => "/[^0-9]+/", 45 => "/[^0-9]+/",
46 => "/[^0-9]+/", 47 => "/[^0-9]+/", 48 => "/[^0-9]+/", 49 => "/[^0-9]+/", 50 => "/[^0-9]+/",
51 => "/[^0-9]+/", 52 => "/[^0-9]+/", 53 => "/[^0-9]+/", 54 => "/[^0-9]+/", 55 => "/[^0-9]+/"
);
public function executer() {
// Lancement de l'action demandée
try {
$this->initialiserProjet('baseflor');
$cmd = $this->getParametre('a');
switch ($cmd) {
case 'chargerTous' :
$this->supprimerTous();
$this->chargerStructureSql();
$this->chargerOntologies();
$this->verifFichier();
if ($this->$nb_erreurs == 0){
$this->chargerDonnees();
} else {
echo "je ne peux pas charger les données car le fichier comporte des erreurs.\n";
}
$This->genererChamps();
break;
case 'chargerStructureSql' :
$this->chargerStructureSql();
break;
case 'chargerDonnees' :
$this->verifFichier();
if($this->$nb_erreurs == 0){
$this->chargerDonnees();
} else {
echo "je ne peux pas charger les données car le fichier comporte des erreurs.\n";
}
break;
case 'supprimerTous' :
$this->supprimerTous();
break;
case 'chargerOntologies' :
$this->chargerOntologies();
break;
case 'verifierDonnees' :
$this->verifFichier();
break;
case 'genererChamps' :
$this->genererChpsBDNT();
$this->genererChpsNumTaxon();
$this->genererChpsNumNomen();
break;
default :
throw new Exception("Erreur : la commande '$cmd' n'existe pas!");
}
} catch (Exception $e) {
$this->traiterErreur($e->getMessage());
}
}
//-- génération de champs --//
private function genererChamps(){
$this->genererChpsBDNT();
$this->genererChpsNumTaxon();
$this->genererChpsNumNomen();
}
private function genererChpsBDNT(){
$this->initialiserGenerationChamps();
$this->preparerTablePrChpsBDNT();
$resultats = $this->recupererTuplesNumsOriginels();
$bdnt = array();
foreach ($resultats as $chps => $res) {
$cle = $res['cle'];
$nno = $res['num_nomen_originel'];
$nto = $res['num_taxon_originel'];
if ( (preg_match("/^([AB])[0-9]+$/", $nno, $retour)) || (preg_match("/^([AB])[0-9]+$/", $nto, $retour)) ){
if($retour[1]=='A'){
$bdnt[$cle]= "BDAFX";
}else{
$bdnt[$cle]= "BDBFX";
}
}elseif(($nno == 'nc') && ($nto == 'nc')){
$bdnt[$cle]= "nc";
}else{
$bdnt[$cle]= "BDTFX";
}
}
$this->remplirChamps($bdnt, "BDNT");
}
private function genererChpsNumTaxon(){
$this->initialiserGenerationChamps();
$this->preparerTablePrChpsNumTaxon();
$resultats = $this->recupererTuplesNumsOriginels();
$num_taxon= array();
foreach ($resultats as $chps => $res) {
$cle = $res['cle'];
$nto = $res['num_taxon_originel'];
if (preg_match("/^[AB]([0-9]+)$/", $nto, $retour)){
$num_taxon[$cle]= intval($retour[1]);
}elseif($nto == 'nc'){
$num_taxon[$cle]= 0;
}else{
$num_taxon[$cle]= intval($nto);
}
}
$this->remplirChamps($num_taxon, "num_taxon");
}
private function genererChpsNumNomen(){
$this->initialiserGenerationChamps();
$this->preparerTablePrChpsNumNomen();
$resultats = $this->recupererTuplesNumsOriginels();
$num_nomen= array();
foreach ($resultats as $chps => $res) {
$cle = $res['cle'];
$nno = $res['num_nomen_originel'];
if (preg_match("/^[AB]([0-9]+)$/", $nno, $retour)){
$num_nomen[$cle]= intval($retour[1]);
}elseif($nno == 'nc'){
$num_nomen[$cle]= 0;
}else{
$num_nomen[$cle]=intval($nno);
}
}
$this->remplirChamps($num_nomen, "num_nomen");
}
private function remplirChamps($champs, $nom_colonne) {
foreach ($champs as $cle => $val) {
$val = $this->getBdd()->proteger($val);
$requete = "UPDATE {$this->table} SET $nom_colonne = $val WHERE cle = $cle ";
$resultat = $this->getBdd()->requeter($requete);
if ($resultat === false) {
throw new Exception("Erreur d'insertion pour le tuple clé = ".$cle);
}
$this->afficherAvancement("Insertion des valeurs pour ".$nom_colonne." dans la base en cours");
}
echo "\n";
}
private function initialiserGenerationChamps() {
$this->table = Config::get('tables.donnees');
}
private function preparerTablePrChpsBDNT() {
$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'BDNT' ";
$resultat = $this->getBdd()->recuperer($requete);
if ($resultat === false) {
$requete = "ALTER TABLE {$this->table} ".
'ADD BDNT VARCHAR( 6 ) '.
'CHARACTER SET utf8 COLLATE utf8_general_ci'.
' NOT NULL AFTER catminat_code ';
$this->getBdd()->requeter($requete);
}
}
private function preparerTablePrChpsNumTaxon() {
$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'num_taxon' ";
$resultat = $this->getBdd()->recuperer($requete);
if ($resultat === false) {
$requete = "ALTER TABLE {$this->table} ".
'ADD num_taxon INT( 10 ) NOT NULL'.
'BEFORE num_taxon_originel';
$this->getBdd()->requeter($requete);
}
}
private function preparerTablePrChpsNumNomen() {
$requete = "SHOW COLUMNS FROM {$this->table} LIKE 'num_nomen' ";
$resultat = $this->getBdd()->recuperer($requete);
if ($resultat === false) {
$requete = "ALTER TABLE {$this->table} ".
'ADD num_nomen INT( 10 ) NOT NULL'.
'BEFORE num_taxon_originel';
$this->getBdd()->requeter($requete);
}
}
private function recupererTuplesNumsOriginels(){
$requete = 'SELECT cle, num_taxon_originel, num_nomen_originel '.
"FROM {$this->table} ";
$resultat = $this->getBdd()->recupererTous($requete);
return $resultat;
}
//-- chargements, suppression, exécution --//
private function chargerOntologies() {
$chemin = Config::get('chemins.ontologies');
$table = Config::get('tables.ontologies');
$requete = "LOAD DATA INFILE '$chemin' ".
"REPLACE INTO TABLE $table ".
'CHARACTER SET utf8 '.
'FIELDS '.
" TERMINATED BY '\t' ".
" ENCLOSED BY '' ".
" ESCAPED BY '\\\' "
;
$this->getBdd()->requeter($requete);
}
protected function chargerStructureSql() {
$contenuSql = $this->recupererContenu(Config::get('chemins.structureSql'));
$this->executerScripSql($contenuSql);
}
protected function executerScripSql($sql) {
$requetes = Outils::extraireRequetes($sql);
foreach ($requetes as $requete) {
$this->getBdd()->requeter($requete);
}
}
private function chargerDonnees() {
$table = Config::get('tables.donnees');
$requete = "LOAD DATA INFILE '".Config::get('chemins.donnees')."' ".
"REPLACE INTO TABLE $table ".
'CHARACTER SET utf8 '.
'FIELDS '.
" TERMINATED BY '\t' ".
" ENCLOSED BY '' ".
" ESCAPED BY '\\\'";
$this->getBdd()->requeter($requete);
}
private function supprimerTous() {
$requete = "DROP TABLE IF EXISTS baseflor_meta, baseflor_v2012_03_19";
$this->getBdd()->requeter($requete);
}
//-- vérifications de données --//
private function verifierSiVide(){
$bool=false;
if ( $this->colonne_valeur == "" ){
$bool=true;
}
return $bool;
}
private function verifierIntervallesTous($valeur){
$intervalle=$this->verifierIntervalle[$this->colonne_num];
$this->verifierIntervalleChiffres($intervalle[0], $intervalle[1],$valeur);
}
private function verifierIntervalleChiffres($mini, $max, $valeur){
if (( ($valeur < $mini) || ($valeur > $max) ) && ($valeur != "")){
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
$this->nb_erreurs++;
}
}
private function verifierValeursIndic(){
if (( preg_match("/^([^0-9])*([0-9]+)([^0-9])*$/", $this->colonne_valeur,$retour) == 1 )){
$this->verifierIntervallesTous($retour[2]);
if((isset($retour[3]))&&(!(in_array($retour[3], $this->signes_nn_seuls))) ){
$this->erreurs_ligne[$this->colonne_num] =$this->colonne_valeur;
$this->nb_erreurs++;
}
if(($retour[1] != "-")&&($retour[1]!="") ){
$this->erreurs_ligne[$this->colonne_num] =$this->colonne_valeur;
$this->nb_erreurs++;
if($this->ligne_num==3){
}
}
}elseif(!(in_array( $this->colonne_valeur, $this->signes_seuls))&& !($this->verifierSiVide())) {
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
$this->nb_erreurs++;
}
}
private function verifierTypeBio(){
if (( preg_match("/(.+)\((.+)\)$/", $this->colonne_valeur,$retour) == 1 )){
$this->verifType_SsType($retour[1]);
$this->verifType_SsType($retour[2]);
}else{
$this->verifType_SsType($this->colonne_valeur);
}
}
private function verifType_SsType($chaine_a_verif){
//verifie type
if(( preg_match("/^([a-zA-Zé]+)\-(.+)$|^([a-zA-Zé]+[^\-])$/", $chaine_a_verif, $retour) == 1 )){
$type=$retour[1];
if(isset($retour[3])){
$type=$retour[3];
}
if(!(in_array($type, $this->type_bio))) {
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
$this->nb_erreurs++;
}
//verifie sous_type(s)
if ($retour[2]!=""){
$ss_type[0]=$retour[2];
if (( preg_match("/\-/", $ss_type[0])) == 1 ){
$ss_type = preg_split("/\-/", $retour[2]);
}
foreach($ss_type as $sst){
if(!(in_array($sst, $this->ss_type_bio))) {
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur;
$this->nb_erreurs++;
}
}
}
}
}
private function verifierColonne($chaine){
if ( ( preg_match($chaine, $this->colonne_valeur) == 0 ) && !($this->verifierSiVide()) ){
$this->erreurs_ligne[$this->colonne_num]=$this->colonne_valeur;
$this->nb_erreurs++;
}
}
//vérifie par colonnes les erreurs d'une ligne
private function verifErreursLignes($colonne_array){
$this->erreurs_ligne=array();
for ($this->colonne_num = 0; $this->colonne_num < count($colonne_array); $this->colonne_num++){
if ( isset($colonne_array) ){
$this->colonne_valeur = $colonne_array[$this->colonne_num];
if ( (( ($this->colonne_num > 0) && ($this->colonne_num < 15) ) || ( $this->colonne_num == 16 )
|| (($this->colonne_num > 18 ) && ( $this->colonne_num < 23 ) )
|| ( $this->colonne_num > 39 )) ){
$motif = $this->verifierColonnesBasiques[$this->colonne_num];
$this->verifierColonne($motif);
}elseif ( $this->colonne_num == 15 ){
$this->verifierTypeBio();
} elseif (($this->colonne_num > 22 ) && ( $this->colonne_num < 33 )){
$this->verifierIntervallesTous($this->colonne_valeur);
}elseif (( $this->colonne_num > 32) && ( $this->colonne_num < 41)){
$this->verifierValeursIndic();
}
} else {
echo "ligne ".$this->ligne_num.": pas de tabulation \n ";
}
}
}
//verifie la cohérence des valeurs des colonnes
private function verifFichier(){
$dernier_nb_erreur =0;
unlink(Config::get('chemins.donnees_verif'));
$fichier = fopen(Config::get('chemins.donnees'), "r");
$fichier2 = fopen(Config::get('chemins.donnees_verif'), "w");
$this->valeurs=array();
$this->nb_erreurs=0;
if ( ($fichier != false) && ($fichier2 != false) ){
$this->ligne_num=1;
while ( !feof($fichier) ) {
if ($this->ligne_num == 1){
fputs($fichier2," !!! REGARDEZ LES COLONNES DANS NUMERO_COLONNES_IMPORTANT.TXT.\n");
}
$this->ligne_num++;
$ligne = fgets($fichier);
$col = preg_split("/ /", $ligne);
$this->verifErreursLignes($col);
//rédaction du fichier de vérif
if(count($this->nb_erreurs)!= 0){
if($dernier_nb_erreur != $this->nb_erreurs){
$dernier_nb_erreur = $this->nb_erreurs;
fputs($fichier2," \n erreurs sur la ligne".$this->ligne_num."\n");
foreach ($this->erreurs_ligne as $cle => $v){
fputs($fichier2,"colonne ".$cle." : ".$v." - ");
}
}
}
}
}
if ($this->nb_erreurs == 0){
fputs($fichier2,"/n il n'y a pas d'erreurs./n");
}
echo $this->nb_erreurs."erreurs";
fclose($fichier);
fclose($fichier2);
}
}
?>

/trunk/scripts/modules/baseflor/baseflor.ini
New file
0,0 → 1,19
version="2012_03_19"
dossierTsv = "{ref:dossierDonneesEflore}baseflor/2012-03-19/"
dossierSql = "{ref:dossierTsv}"
[tables]
donnees = "baseflor_v{ref:version}"
ontologies = "baseflor_ontologies"
[fichiers]
structureSql = "baseflor.sql"
donnees = "baseflor.tsv"
donnees_verif = "baseflor_verif.txt"
ontologies = "baseflor_ontologies.tsv"
[chemins]
structureSql = "{ref:dossierSql}{ref:fichiers.structureSql}"
donnees = "{ref:dossierTsv}{ref:fichiers.donnees}"
donnees_verif = "{ref:dossierTsv}{ref:fichiers.donnees_verif}"
ontologies ="{ref:dossierTsv}{ref:fichiers.ontologies}"