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"; |
} |
|
|
|
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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); |
} |
|
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private function verifierIntervalleChiffres($mini, $max, $valeur){ |
if (( ($valeur < $mini) || ($valeur > $max) ) && ($valeur != "")){ |
$this->erreurs_ligne[$this->colonne_num] = $this->colonne_valeur; |
$this->nb_erreurs++; |
} |
|
} |
|
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private function verifierValeursIndic(){ |
if (( preg_match("/^([^0-9])*([0-9]+)([^0-9])*$/", $this->colonne_valeur,$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); |
} |
|
|
|
} |
|
?> |