=') && extension_loaded('xsl')) {
if (substr(phpversion(), 0, 1) == "5") @ini_set("zend.ze1_compatibility_mode", "0");
require_once($include_path.'/xslt-php4-to-php5.inc.php');
}
require_once("pubmed_analyse_query.class.php");
/**There be komodo dragons**/
class entrez extends connector {
var $available_entrezdatabases = array("pubmed" => "PubMed");
function entrez($connector_path="") {
parent::connector($connector_path);
}
function get_id() {
return "entrez";
}
//Est-ce un entrepot ?
function is_repository() {
return 2;
}
function source_get_property_form($source_id) {
global $charset,$pmb_default_operator;
$params=$this->get_source_params($source_id);
if ($params["PARAMETERS"]) {
//Affichage du formulaire avec $params["PARAMETERS"]
$vars=unserialize($params["PARAMETERS"]);
foreach ($vars as $key=>$val) {
global $$key;
$$key=$val;
}
}
if (!isset($entrez_database))
$entrez_database = "pubmed";
if (!isset($entrez_maxresults))
$entrez_maxresults = 100;
$entrez_maxresults += 0;
if (!isset($entrez_operator))
$entrez_operator = 2;
$entrez_operator += 0;
$options = "";
foreach ($this->available_entrezdatabases as $code => $caption)
$options .= '';
$form="
";
$form="
";
$form.="
";
return $form;
}
function make_serialized_source_properties($source_id) {
global $entrez_database, $entrez_maxresults, $entrez_operator;
global $del_xsl_transform;
$t["entrez_database"]=stripslashes($entrez_database);
$t["entrez_maxresults"]=$entrez_maxresults+0;
$t["entrez_operator"]=$entrez_operator+0;
//Vérification du fichier
if (($_FILES["xslt_file"])&&(!$_FILES["xslt_file"]["error"])) {
$xslt_file_content=array();
$xslt_file_content["name"]=$_FILES["xslt_file"]["name"];
$xslt_file_content["code"]=file_get_contents($_FILES["xslt_file"]["tmp_name"]);
$t["xsl_transform"]=$xslt_file_content;
} else if ($del_xsl_transform) {
$t["xsl_transform"]="";
} else {
$oldparams=$this->get_source_params($source_id);
if ($oldparams["PARAMETERS"]) {
//Anciens paramètres
$oldvars=unserialize($oldparams["PARAMETERS"]);
}
$t["xsl_transform"] = $oldvars["xsl_transform"];
}
$this->sources[$source_id]["PARAMETERS"]=serialize($t);
}
//Récupération des proriétés globales par défaut du connecteur (timeout, retry, repository, parameters)
function fetch_default_global_values() {
$this->timeout=5;
$this->repository=2;
$this->retry=3;
$this->ttl=1800;
$this->parameters="";
}
//Formulaire des propriétés générales
function get_property_form() {
$this->fetch_global_properties();
return "";
}
function make_serialized_properties() {
$this->parameters="";
}
function apply_xsl_to_xml($xml, $xsl) {
global $charset;
$xh = xslt_create();
xslt_set_encoding($xh, $charset);
$arguments = array(
'/_xml' => $xml,
'/_xsl' => $xsl
);
$result = xslt_process($xh, 'arg:/_xml', 'arg:/_xsl', NULL, $arguments);
xslt_free($xh);
return $result;
}
//Fonction de recherche
function search($source_id,$query,$search_id) {
global $base_path;
global $pmb_default_operator;
$params=$this->get_source_params($source_id);
$this->fetch_global_properties();
if ($params["PARAMETERS"]) {
//Affichage du formulaire avec $params["PARAMETERS"]
$vars=unserialize($params["PARAMETERS"]);
foreach ($vars as $key=>$val) {
global $$key;
$$key=$val;
}
}
if (!isset($entrez_database)) {
$this->error_message = $this->msg["entrez_unconfigured"];
$this->error = 1;
return;
}
$entrez_operator = $entrez_operator+0;
$entrez_maxresults= $entrez_maxresults+0;
$unimarc_pubmed_mapping = array (
'XXX' => '',
'200$a' => '[Title]',
'7XX' => '[Author]',
'210$c' => '[Publisher]',
'210$d' => '[Publication Date]',
'461$t' => '[Journal]'
);
$pubmed_stopword = array(
"a","about","again", "all", "almost", "also", "although", "always", "among", "an", "and", "another", "any", "are", "as", "at",
"be", "because", "been", "before", "being", "between", "both","but", "by",
"can", "could",
"did", "do", "does", "done", "due", "during",
"each", "either", "enough", "especially", "etc",
"for", "found", "from", "further",
"had", "has", "have", "having", "here", "how", "however",
"i", "if", "in", "into", "is", "it", "its", "itself",
"just",
"kg", "km",
"made", "mainly", "make", "may", "mg", "might", "ml", "mm", "most", "mostly", "must",
"nearly", "neither", "no", "nor",
"obtained", "of", "often", "on", "our", "overall",
"perhaps", "pmid",
"quite",
"rather", "really", "regarding",
"seem", "seen", "several", "should", "show", "showed", "shown", "shows", "significantly", "since", "so", "some", "such",
"than", "that", "the", "their", "theirs", "them", "then", "there", "therefore", "these", "they", "this", "those", "through", "thus", "to",
"upon", "use", "used", "using",
"various", "very",
"was", "we", "were", "what", "when", "which", "while", "with", "within", "without", "would"
);
$search_query = "";
foreach($query as $aquery){
$search_querys = array();
if($entrez_operator != 2){
$operator = $pmb_default_operator;
$pmb_default_operator = $entrez_operator;
}
$field= (isset($unimarc_pubmed_mapping[$aquery->ufield]) ? $unimarc_pubmed_mapping[$aquery->ufield] : '');
$a=new pubmed_analyse_query($aquery->values[0],0,0,1,0,$field,$pubmed_stopword);
$sub_search_query =$a->show_analyse();
if($entrez_operator != 2) $pmb_default_operator=$operator;
if ($search_query) $search_query = $search_query . " " . strtoupper($aquery->inter) . " " . $sub_search_query;
else $search_query = $sub_search_query;
}
require_once 'entrez_protocol.class.php';
$entrez_client = new entrez_request($entrez_database, $search_query);
$entrez_client->get_next_idlist($entrez_maxresults);
$entrez_client->retrieve_currentidlist_notices();
$responses = $entrez_client->get_current_responses();
if($xsl_transform){
if($xsl_transform['code'])
$xsl_transform_content = $xsl_transform['code'];
else $xsl_transform_content = "";
}
if($xsl_transform_content == "")
$xsl_transform_content = file_get_contents($base_path."/admin/connecteurs/in/entrez/xslt/pubmed_to_unimarc.xsl");
$notices_pmbunimarc = array();
foreach ($responses as $aresponse) {
$anotice = $this->apply_xsl_to_xml($aresponse, $xsl_transform_content);
$notices_pmbunimarc[] = $anotice;
}
foreach($notices_pmbunimarc as $anotice)
$this->rec_records($anotice, $source_id, $search_id, $search_query);
}
function rec_records($noticesxml, $source_id, $search_id, $search_term="") {
global $charset,$base_path;
if (!trim($noticesxml))
return;
$rec_uni_dom=new xml_dom_entrez($noticesxml,$charset);
$notices=$rec_uni_dom->get_nodes("unimarc/notice");
foreach ($notices as $anotice) {
$this->rec_record($rec_uni_dom, $anotice, $source_id, $search_id, $search_term);
}
}
function rec_record($rec_uni_dom, $noticenode, $source_id, $search_id, $search_term="") {
global $charset,$base_path;
if (!$rec_uni_dom->error) {
//Initialisation
$ref="";
$ufield="";
$usubfield="";
$field_order=0;
$subfield_order=0;
$value="";
$date_import=date("Y-m-d H:i:s",time());
$fs=$rec_uni_dom->get_nodes("f", $noticenode);
$fs[] = array("NAME" => "f", "ATTRIBS" => array("c" => "1000"), 'TYPE' => 1, "CHILDS" => array(array("DATA" => $search_term, "TYPE" => 2)));
//Recherche du 001
if ($fs)
for ($i=0; $iget_datas($fs[$i]);
break;
}
}
if (!$ref) $ref = md5($record);
//Mise à jour
if ($ref) {
//Si conservation des anciennes notices, on regarde si elle existe
if (!$this->del_old) {
$requete="select count(*) from entrepot_source_".$source_id." where ref='".addslashes($ref)."'";
$rref=mysql_query($requete);
if ($rref) $ref_exists=mysql_result($rref,0,0);
}
//Si pas de conservation des anciennes notices, on supprime
if ($this->del_old) {
$requete="delete from entrepot_source_".$source_id." where ref='".addslashes($ref)."'";
mysql_query($requete);
}
$ref_exists = false;
//Si pas de conservation ou ref�rence inexistante
if (($this->del_old)||((!$this->del_old)&&(!$ref_exists))) {
//Insertion de l'ent�te
$n_header["rs"]=$rec_uni_dom->get_value("unimarc/notice/rs");
$n_header["ru"]=$rec_uni_dom->get_value("unimarc/notice/ru");
$n_header["el"]=$rec_uni_dom->get_value("unimarc/notice/el");
$n_header["bl"]=$rec_uni_dom->get_value("unimarc/notice/bl");
$n_header["hl"]=$rec_uni_dom->get_value("unimarc/notice/hl");
$n_header["dt"]=$rec_uni_dom->get_value("unimarc/notice/dt");
//R�cup�ration d'un ID
$requete="insert into external_count (recid, source_id) values('".addslashes($this->get_id()." ".$source_id." ".$ref)."', ".$source_id.")";
$rid=mysql_query($requete);
if ($rid) $recid=mysql_insert_id();
foreach($n_header as $hc=>$code) {
$requete="insert into entrepot_source_".$source_id." (connector_id,source_id,ref,date_import,ufield,usubfield,field_order,subfield_order,value,i_value,recid, search_id) values(
'".addslashes($this->get_id())."',".$source_id.",'".addslashes($ref)."','".addslashes($date_import)."',
'".$hc."','',-1,0,'".addslashes($code)."','',$recid, '$search_id')";
mysql_query($requete);
}
if ($fs)
for ($i=0; $iget_nodes("s",$fs[$i]);
if (is_array($ss)) {
for ($j=0; $jget_datas($ss[$j]);
$subfield_order=$j;
$requete="insert into entrepot_source_".$source_id." (connector_id,source_id,ref,date_import,ufield,usubfield,field_order,subfield_order,value,i_value,recid, search_id) values(
'".addslashes($this->get_id())."',".$source_id.",'".addslashes($ref)."','".addslashes($date_import)."',
'".addslashes($ufield)."','".addslashes($usubfield)."',".$field_order.",".$subfield_order.",'".addslashes($value)."',
' ".addslashes(strip_empty_words($value))." ',$recid, '$search_id')";
mysql_query($requete);
}
} else {
$value=$rec_uni_dom->get_datas($fs[$i]);
$requete="insert into entrepot_source_".$source_id." (connector_id,source_id,ref,date_import,ufield,usubfield,field_order,subfield_order,value,i_value,recid, search_id) values(
'".addslashes($this->get_id())."',".$source_id.",'".addslashes($ref)."','".addslashes($date_import)."',
'".addslashes($ufield)."','".addslashes($usubfield)."',".$field_order.",".$subfield_order.",'".addslashes($value)."',
' ".addslashes(strip_empty_words($value))." ',$recid, '$search_id')";
mysql_query($requete);
}
}
}
$this->n_recu++;
}
}
}
}
?>