new files

00. DOCUMENTATION/01. Interactions Bipartites/README.md

+Exemple réseau socio-semantique:
+
+	États possibles:
+	- - - - - - - - - 
+	• SOC: Projection social, niveau global                 (voir  00_Bipartite-Components.png ,  [fig. b] )
+	• SEM: Projection semantique, niveau global             (voir  00_Bipartite-Components.png ,  [fig. c] )
+	• soc: Projection social, niveau local.
+	• sem: Projection semantique, niveau local.
+	• socsem: Projection socio-semantique, niveau local.    (voir  00_Bipartite-Components.png ,  [fig. a] )
+		L'asterisk dans un état représente une selection des nœuds active.
+
+
+	Actions possibles:
+	- - - - - - - - - 
+	• Sel: L'utilisateur sélectionne 1..* nœuds
+	• ctype: L'utilisateur clique sur le boutton "Change Type".
+	• clevel: L'utilisateur clique sur le boutton "Change Level".
+

LOCALDB/DirScan_main.php

+<?php
+
+header('Content-Type: application/json');
+
+include("DirectoryScanner.php");
+$projectFolderPat = dirname(dirname(getcwd())) . "/";
+$instance = new scanTree($projectFolderPat);
+$instance->getDirectoryTree("data");
+
+//pr(var_dump($instance->folders));
+$output = array();
+$output["folders"] = $instance->folders;
+$output["gexf_idfolder"] = $instance->gexf_folder;
+echo json_encode($output);
+
+// ** Debug Functions: **
+function br() {
+    echo "----------<br>";
+}
+
+function pr($msg) {
+    echo $msg . "<br>";
+}
+
+?>

LOCALDB/DirectoryScanner.php

+<?php
+
+class scanTree {
+
+    public $root;
+    public $folders = array();
+    public $gexf_folder = array();
+
+    public function __construct($rootpath = "") {
+        $this->root = $rootpath;
+    }
+
+    public function getDirectoryTree($dir) {
+        $folder = array();
+        $dbs = array();
+        $gexfs = array();
+        $dataFolder = $this->root . $dir;
+        $files = scandir($dataFolder);
+        foreach ($files as $f) {
+            if ($f != "." and $f != ".." and $f[strlen($f) - 1] != "~") {
+                if (is_dir($dataFolder . "/" . $f)) {
+                    //pr("Dir: ".$f);
+                    $subfolder = $f;
+                    $this->getDirectoryTree($dir . "/" . $subfolder);
+                } else {
+                    //pr("File: ".$f);
+                    if ((strpos($f, '.gexf')))
+                        array_push($gexfs, $f);
+                    if ((strpos($f, '.db')) or (strpos($f, '.sqlite')) or (strpos($f, '.sqlite3')))
+                        array_push($dbs, $f);
+                    if (!$folder[$dir]["gexf"] or !$folder[$dir]["dbs"])
+                        $folder[$dir] = array();
+                    $folder[$dir]["gexf"] = $gexfs;
+                    $folder[$dir]["dbs"] = $dbs;
+                    if ((strpos($f, '.gexf'))) {
+                        $this->gexf_folder[$dir . "/" . $f] = "";
+                    }
+                }
+            }
+        }
+        if ($folder[$dir]["gexf"]) {
+            foreach ($folder[$dir]["gexf"] as $g) {
+                $this->gexf_folder[$dir . "/" . $g] = count($this->folders);
+            }
+        }
+        array_push($this->folders, $folder);
+    }
+
+}
+
+?>

LOCALDB/clear_favorites.php

+<?php
+
+echo 'toto';
+?>
\ No newline at end of file

LOCALDB/default_div.php

+<?php
+
+// default informations	
+$thedb = $graphdb;
+$gexf=$_GET["gexf"];
+$max_item_displayed=6;
+$type = $_GET["type"];
+$TITLE="ISITITLE";
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$elems = json_decode($query);
+
+
+
+$table = "";
+$column = "";
+$id="";
+$twjs="API_CNRS/"; // submod path of TinaWebJS
+
+if($type=="social"){
+  $table = "ISIAUTHOR";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;// factor for normalisation of stars
+}
+
+if($type=="semantic"){
+  $table = $_GET["index"];//"ISItermsfirstindexing";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;
+}
+$restriction='';
+$factor=10;
+
+$sql="";
+//////////
+if (count($elems)==1){// un seul mot est sélectionné, on compte les mots multiples
+	$sql = 'SELECT count(*),'.$id.'
+	FROM '.$table.' where (';
+        	foreach($elems as $elem){
+              	$sql.=' '.$column.'="'.$elem.'" OR ';
+        	}
+	#$querynotparsed=$sql;#####
+    $sql = substr($sql, 0, -3);
+    $sql = str_replace( ' & ', '" OR '.$column.'="', $sql );
+    $sql.=')'.$restriction.'
+	GROUP BY '.$id.'
+	ORDER BY count('.$id.') DESC
+	LIMIT 1000';
+}else{// on compte une seule fois un mot dans un article
+	$factor=ceil(count($elems)/5); //les scores sont moins haut
+	$sql='';
+	foreach($elems as $elem){
+          	$sql.=' '.$column.'="'.$elem.'" OR ';
+        }
+    $sql=substr($sql, 0, -3);
+    $sql='SELECT count(*),id,data FROM (SELECT *
+	FROM '.$table.' where ('.$sql.')'.$restriction.'
+	 group by id,data) GROUP BY '.$id.'
+	ORDER BY count('.$id.') DESC
+	LIMIT 1000';
+
+}
+
+$wos_ids = array();
+$sum=0;
+
+// echo "<br>";
+// echo "$sql";
+
+
+//The final query!
+// array of all relevant documents with score
+
+foreach ($base->query($sql) as $row) {        
+        // on pondère le score par le nombre de termes mentionnés par l'article
+        
+        //$num_rows = $result->numRows();
+        $wos_ids[$row[$id]] = $row["count(*)"];
+        $sum = $row["count(*)"] +$sum;
+}
+
+
+// /// nombre de document associés $related
+$total_count=0;
+$count_max=500;	
+$number_doc=count($wos_ids);
+$count=0;
+
+$all_terms_from_selected_projects=array();// list of terms for the top 6 project selected
+
+// to filter under some conditions
+$to_display=true; 
+$count=0;
+foreach ($wos_ids as $id => $score) {	
+	if ($total_count<$count_max) {
+		// retrieve publication year
+		
+		if ($to_display){
+			$total_count+=1;
+
+			if ($count<=$max_item_displayed){
+				$count+=1;
+
+				$sql = 'SELECT data FROM ISITITLE WHERE id='.$id.' group by data';
+
+				foreach ($base->query($sql) as $row) {
+					$external_link="<a href=http://google.com/webhp?#q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=15px src="'.$twjs.'img/google.png"></a>';	
+					$output.="<li title='".$score."'>";
+					$output.=$external_link.imagestar($score,$factor,$twjs).' ';	
+					$output.='<a href="JavaScript:newPopup(\''.$twjs.'default_doc_details.php?gexf='.urlencode($gexf).'&index='.$table.'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.'	\')">'.$row['data']." </a> ";
+					// echo '<a href="JavaScript:newPopup(\''.$twjs.'default_doc_details.php?gexf='.urlencode($gexf).'&index='.$table.'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.'	\')">'.$row['data']." </a> ";
+				}
+
+				// get the authors
+				$sql = 'SELECT data FROM ISIAUTHOR WHERE id='.$id;
+				foreach ($base->query($sql) as $row) {
+					$output.=($row['data']).', ';
+				}
+				$output = rtrim($output, ", ");
+				$output.="</li><br>";	
+
+			}
+		}
+
+	} else{
+		continue;
+	}
+}
+if ($total_count<$count_max){
+	$related .= $total_count;
+}else{
+	$related .= ">".$count_max;
+}
+
+$output .= "</ul>"; #####
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+// // if (($project_folder=='nci')&&(count($elems)<$max_selection_size)){
+// // 	// for NCI we compare the impact and novelty score making the difference if there are more than 4 terms selected
+// // 	$news='';//new terms
+// // 	$terms_from_selected_projects=array_unique($all_terms_from_selected_projects); 
+// // 	if(count($terms_from_selected_projects)>3){
+// // 	$diff=array();
+// // 	foreach ($terms_from_selected_projects as $key => $term) {
+// // 		$sql=	"select  count(*),ISIterms.id, ISIterms.data from ISIterms join ISIpubdate on (ISIterms.id=ISIpubdate.id AND ISIpubdate.data=2011 AND ISIterms.data='".$term."') group by ISIterms.data";
+// // 		$nov=0;
+// // 		foreach ($corporadb->query($sql) as $row) {
+// // 			$nov=$row['count(*)'];
+// // 		}
+// // 		$sql=	"select  count(*),ISIterms.id, ISIterms.data from ISIterms join ISIpubdate on (ISIterms.id=ISIpubdate.id AND ISIpubdate.data=2012 AND ISIterms.data='".$term."') group by ISIterms.data";
+// // 		$imp=0;
+// // 		foreach ($corporadb->query($sql) as  $row) {
+// // 			$imp=$row['count(*)'];
+// // 		}
+// // 		$diff[$term]=info($nov,$imp); //positive si c'est un term novelty, negatif si c'est un terme impact.
+// // 		//echo $term.'-nov: '.$nov.'- imp:'.$imp.'<br/>';//'-info'.$diff[$term].
+// // 	}	
+
+// // if (true){
+// // 	arsort($diff);
+// // 	$res=array_keys($diff);
+// // 	//echo implode(', ', $res);
+// // 	$nov_string='';
+// // 	for ($i=0;$i<$top_displayed;$i++){
+
+// // 		// on récupère les titres du document qui a le plus for impact
+// // 		$sql="SELECT ISIterms.id,ISIC1_1.data,count(*) from ISIterms,ISIpubdate,ISIC1_1 where ISIterms.data='".$res[$i]."' AND  ISIterms.id=ISIpubdate.id AND ISIterms.id=ISIC1_1.id AND ISIpubdate.data='2011' group by ISIterms.id ORDER BY RANDOM()  limit 1";	
+
+// // 		//on récupère les id associés.
+// // 		foreach ($corporadb->query($sql) as $row){
+// // 			$sql2='SELECT ISIpubdate.id,ISIC1_1.data from ISIpubdate,ISIC1_1 where ISIC1_1.data="'.$row['data'].'" AND  ISIpubdate.id=ISIC1_1.id AND ISIpubdate.data="2013"  limit 1';
+// // 			//echo $sql2;
+// // 			foreach ($corporadb->query($sql2) as $row2){
+// // 				$nov_string.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($graphdb).'&gexf='.urlencode($gexf).'&query='.urlencode('["'.$res[$i].'"]').'&type='.urlencode($_GET["type"]).'&id='.$row2['id'].'	\')">'.$res[$i]."</a>, ";	
+// // 			}		
+// // 		}
+// // 	}	
+
+// // 	$news.='<br/><b><font color="#FF0066">Top '.$top_displayed.' Novelty related terms </font></b>'.$nov_string.'<br/>';
+// // 	asort($diff);	
+// // 	$res=array_keys($diff);	
+// // 	$res_string='';
+// // 	for ($i=0;$i<$top_displayed;$i++){
+
+// // 		// on récupère les titres du document qui a le plus for impact
+// // 		$sql="SELECT ISIterms.id,ISIC1_1.data,count(*) from ISIterms,ISIpubdate,ISIC1_1 where ISIterms.data='".$res[$i]."' AND  ISIterms.id=ISIpubdate.id AND ISIterms.id=ISIC1_1.id AND ISIpubdate.data='2012' group by ISIterms.id ORDER BY RANDOM()limit 1";	
+
+// // 		//on récupère les id associés.
+// // 		foreach ($corporadb->query($sql) as $row){
+// // 			$sql2='SELECT ISIpubdate.id,ISIC1_1.data from ISIpubdate,ISIC1_1 where ISIC1_1.data="'.$row['data'].'" AND  ISIpubdate.id=ISIC1_1.id AND ISIpubdate.data="2013"  limit 1';
+// // 			//echo $sql2;
+// // 			foreach ($corporadb->query($sql2) as $row2){
+// // 				$res_string.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($graphdb).'&gexf='.urlencode($gexf).'&query='.urlencode('["'.$res[$i].'"]').'&type='.urlencode($_GET["type"]).'&id='.$row2['id'].'	\')">'.$res[$i]."</a>, ";	
+// // 			}		
+// // 		}
+// // 	}
+// // 	$news.='<br/><b><font color="#CF5300">Top '.$top_displayed.' Impact related terms: </font></b>'.$res_string.'<br/>';	
+// // }
+// // }	
+// // }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+// // display the most occuring terms when only one is selected.
+// //elseif (count($elems)==1) {// on affiche les voisins
+// //	$terms_array=array();
+// //	$id_sql='SELECT ISIterms.id FROM ISIterms where ISIterms.data="'.$elems[0].'" group by id';
+// //	foreach ($base->query($id_sql) as $row_id) {			
+// //			$sql2='SELECT ISIterms.data FROM ISIterms where ISIterms.id='.$row_id['id'];
+// //			foreach ($base->query($sql2) as $row_terms) {				
+// //				if ($terms_array[$row_terms['data']]>0){
+// //					$terms_array[$row_terms['data']]=$terms_array[$row_terms['data']]+1;	
+// //				}else{
+// //					$terms_array[$row_terms['data']]=1;		
+// //				}				
+// //			}			
+// //		}
+// //		natsort($terms_array);			
+// //		$terms_list=array_keys(array_slice($terms_array,-11,-1));
+// //		foreach ($terms_list as $first_term) {
+// //			$related_terms.=$first_term.', ';
+// //		}															
+// //	$news.='<br/><b><font color="#CF5300">Related terms: </font></b>'.$related_terms.'<br/>';
+// //}
+
+   // calculate binomial coefficient
+ function binomial_coeff($n, $k) {
+
+      $j = $res = 1;
+
+      if($k < 0 || $k > $n)
+         return 0;
+      if(($n - $k) < $k)
+         $k = $n - $k;
+
+      while($j <= $k) {
+         $res *= $n--;
+         $res /= $j++;
+      }
+
+      return $res;
+
+   }
+
+
+
+
+function imagestar($score,$factor,$twjs) {
+// produit le html des images de score
+	$star_image = '';
+	if ($score > .5) {
+		$star_image = '';
+		for ($s = 0; $s < min(5,$score/$factor); $s++) {
+			$star_image.='<img src="'.$twjs.'img/star.gif" border="0" >';
+		}
+	} else {
+		$star_image.='<img src="'.$twjs.'img/stargrey.gif" border="0">';
+	}
+	return $star_image;
+}
+if($max_item_displayed>$related) $max_item_displayed=$related;
+echo $news.'<br/><h4><font color="#0000FF"> Full text of top '.$max_item_displayed.'/'.$related.' related publications:</font></h4>'.$output;
+//pt - 301 ; 15.30
+?>

LOCALDB/default_doc_details.php

+<?php
+include('parameters_details.php');
+$db = $gexf_db[$gexf];
+
+$base = new PDO("sqlite:../" .$db);
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$terms_of_query = json_decode($query);
+
+// echo "mainpath: ".$mainpath."<br>";
+// echo "thedb: ".$db."<br>";
+// echo "thequery: ".var_dump($terms_of_query);
+
+echo '
+<html>
+        <head>
+  <meta charset="utf-8" />
+  <title>Document details</title>
+  <link rel="stylesheet" href="js/jquery-ui.css" />
+  <script src="js/jquery-1.9.1.js"></script>
+  <script src="js/jquery-ui.js"></script>
+  
+  <script>
+  $(function() {
+    $( "#tabs" ).tabs({
+      collapsible: true
+    });
+  });
+  </script>
+</head>
+          
+    <body>
+    <div id="tabs">
+  <ul>
+    <li><a href="#tabs-1">Selected Document</a></li>
+    <li><a href="full_doc_list.php?'.'gexf='.urlencode($gexf).'&query='.urlencode($_GET["query"]).'&type='.urlencode($_GET["type"]).'">Full list</a></li>';    
+  echo '</ul>';
+
+echo '<div id="tabs-1">';
+
+
+
+$id=$_GET["id"];
+// //$elems = json_decode($query);
+//   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
+//         foreach ($base->query($sql) as $row) {
+//           $country=$CC[strtoupper($row['data'])];         
+//         }
+
+	$sql = 'SELECT data FROM ISITITLE WHERE id='.$id.' group by data';
+
+	foreach ($base->query($sql) as $row) {
+		$output.='<h2>'.$row['data'].'</h2>';
+		$find.="<br/><a href=http://google.com/webhp?q=".urlencode('"'.$row['data'].'"')." target='blank'>[ Search on the web ] </a>";		
+	}
+
+
+  // get the authors
+  $sql = 'SELECT data FROM ISIAUTHOR WHERE id='.$id;
+  foreach ($base->query($sql) as $row) {
+    $output.='<i>'.($row['data']).'</i>, ';
+  }
+  $output = rtrim($output, ", ");
+// //  // get the company
+// //  $sql = 'SELECT data FROM ISIC1_1 WHERE id='.$id;
+// //  foreach ($base->query($sql) as $row) {
+//     //$output.=' - '.substr($row['data'],3,strlen(  $row['data'])).' ';
+//   //}
+
+  // get the date
+  $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
+  foreach ($base->query($sql) as $row) {
+    $output.=' ('.$row['data'].') ';
+  }
+
+// // get the country
+//   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
+//   foreach ($base->query($sql) as $row) {
+//     $country=$CC[strtoupper($row['data'])];
+  
+//     $output.=strtoupper($country).'<br/>   ';
+//   }
+
+//   // get the date
+  if(strpos($_GET["index"],'terms') ) $sql = 'SELECT data FROM '.$_GET["index"].' WHERE id='.$id;
+  else $sql = 'SELECT data FROM ISItermsListV1 WHERE id='.$id;
+  $output.='<br/><b>Keywords: </b>';
+  $terms=array();
+  foreach ($base->query($sql) as $row) {
+    $terms[]=$row['data'];
+  }
+  natsort($terms);
+  $terms=array_unique($terms); // liste des termes de l'article
+  $keywords='';
+  foreach ($terms as $key => $value) {
+    $keywords.=$value.', ';
+  }
+
+  foreach ($terms_of_query as $key => $value) {
+      $keywords=str_replace($value,'<font color="green"><b> '.$value.'</b></font>',$keywords);
+    }
+    foreach (array_diff($terms,$terms_of_query) as $key => $value) {
+      $keywords=str_ireplace($value,'<font color="#800000"> '.$value.'</font>',$keywords);
+    }
+
+  $output.='<p align="justify">'.$keywords.'</p>';
+
+
+//   // get the website
+  $sql = 'SELECT data FROM ISISO WHERE id='.$id;
+  foreach ($base->query($sql) as $row) {
+    $output.='<b>Journal: </b>'.$row['data'].'<br/> ';
+  }
+
+	$sql = 'SELECT data FROM ISIABSTRACT WHERE id='.$id;
+  // echo $output."<br>";
+  $abs="";
+	foreach ($base->query($sql) as $row) {
+    $abs.=". ".$row['data'];
+	}
+  $abs=str_replace('ISSUES:'  ,'<br/><br/><b>Issues:</b>',$abs);
+  $abs=str_replace('INTENDED IMPACT:'  ,'<br/><br/><b>Intended impact:</b>',$abs);    
+  $abs=str_replace('IMPACT:'  ,'<br/><br/><b>Impact:</b>',$abs);
+  $abs=str_replace('NOVELTY:'  ,'<br/><br/><b>Novelty:</b>',$abs);
+  $abs=str_replace('BOLD INNOVATION:'  ,'<br/><br/><b>Bold innovation:</b>',$abs);
+  $abs=str_replace('SOCIAL PROBLEM:'  ,'<br/><br/><b>Social problem:</b>',$abs);
+
+  // solving encoding pb
+  $abs=str_replace('―', ' ', $abs);
+  $abs=str_replace('‟‟', ' ', $abs);
+  $abs=str_replace('„‟', ' ', $abs);
+  $abs=str_replace('_x000D_', ' ', $abs);
+  $abs=str_replace('•', ' ', $abs);
+  $abs=str_replace('’', '\'', $abs);
+  
+  foreach ($terms_of_query as $key => $value) {
+    $abs=str_ireplace($value,'<font color="green"><b> '.$value.'</b></font>',$abs);
+  }
+  foreach (array_diff($terms,$terms_of_query) as $key => $value) {
+    $abs=str_ireplace($value,'<font color="#800000"> '.$value.'</font>',$abs);
+  }
+
+  $output.='<br/><p align="justify"><b>Abstract : </b><i>'.$abs.' </i></p>';
+  $output.="<br>"; 
+
+
+
+echo $output.$find;
+echo '</div>';
+//echo '<div id="tabs-2">
+//    <p><strong>Click this tab again to close the content pane.</strong></p>
+//    <p>Morbi tincidunt, dui sit amet facilisis feugiat, odio metus gravida ante, ut pharetra massa metus id nunc. Duis scelerisque molestie turpis. Sed fringilla, massa eget luctus malesuada, metus eros molestie lectus, ut tempus eros massa ut dolor. Aenean aliquet fringilla sem. Suspendisse sed ligula in ligula suscipit aliquam. Praesent in eros vestibulum mi adipiscing adipiscing. Morbi facilisis. Curabitur ornare consequat nunc. Aenean vel metus. Ut posuere viverra nulla. Aliquam erat volutpat. Pellentesque convallis. Maecenas feugiat, tellus pellentesque pretium posuere, felis lorem euismod felis, eu ornare leo nisi vel felis. Mauris consectetur tortor et purus.</p>
+//  </div>';
+
+
+echo '</div>';
+
+function pt($string){
+    // juste pour afficher avec retour à la ligne
+echo $string."<br/>";
+}
+
+function pta($array){
+    print_r($array);
+    echo '<br/>';
+}
+
+
+?>

LOCALDB/default_doc_details2.php

+<?php
+include('parameters_details.php');
+$db = $gexf_db[$gexf];
+
+$base = new PDO("sqlite:../" ."data/terrorism/data.db");
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$terms_of_query = json_decode($query);
+
+// echo "mainpath: ".$mainpath."<br>";
+// echo "thedb: ".$db."<br>";
+// echo "thequery: ".var_dump($terms_of_query);
+
+echo '
+<html>
+        <head>
+  <meta charset="utf-8" />
+  <title>Document details</title>
+  <link rel="stylesheet" href="js/jquery-ui.css" />
+  <script src="js/jquery-1.9.1.js"></script>
+  <script src="js/jquery-ui.js"></script>
+  
+  <script>
+  $(function() {
+    $( "#tabs" ).tabs({
+      collapsible: true
+    });
+  });
+  </script>
+</head>
+          
+    <body>
+    <div id="tabs">
+  <ul>
+    <li><a href="#tabs-1">Selected Document</a></li>
+    <li><a href="full_doc_list2.php?'.'gexf='.urlencode($gexf).'&query='.urlencode($_GET["query"]).'&type='.urlencode($_GET["type"]).'">Full list</a></li>';    
+  echo '</ul>';
+
+echo '<div id="tabs-1">';
+
+
+
+$id=$_GET["id"];
+// //$elems = json_decode($query);
+//   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
+//         foreach ($base->query($sql) as $row) {
+//           $country=$CC[strtoupper($row['data'])];         
+//         }
+
+
+  $sql = 'SELECT data FROM ID WHERE id='.$id.' group by data';
+
+  foreach ($base->query($sql) as $row) {
+    $output.='<h2>Project Identification: '.$row['data'].'</h2>';
+  }
+
+
+
+	$sql = 'SELECT data FROM TI WHERE id='.$id.' group by data';
+
+	foreach ($base->query($sql) as $row) {
+		$output.='<h2>'.$row['data'].'</h2>';
+		$find.="<br/><a href=http://google.com/webhp?q=".urlencode('"'.$row['data'].'"')." target='blank'>[ Search on the web ] </a>";		
+	}
+
+
+  // get the authors
+  $sql = 'SELECT data FROM PI WHERE id='.$id;
+  foreach ($base->query($sql) as $row) {
+    $output.='<i>'.($row['data']).'</i>, ';
+  }
+  $output = rtrim($output, ", ");
+// //  // get the company
+// //  $sql = 'SELECT data FROM ISIC1_1 WHERE id='.$id;
+// //  foreach ($base->query($sql) as $row) {
+//     //$output.=' - '.substr($row['data'],3,strlen(  $row['data'])).' ';
+//   //}
+
+
+    $output.=' (2014) ';
+ 
+
+// // get the country
+//   $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
+//   foreach ($base->query($sql) as $row) {
+//     $country=$CC[strtoupper($row['data'])];
+  
+//     $output.=strtoupper($country).'<br/>   ';
+//   }
+
+//   // get the date
+  // $sql = 'SELECT data FROM '."ISItermsBigWL".' WHERE id='.$id;
+  $sql = 'SELECT data FROM ISItermsfirstindexing WHERE id='.$id;
+  $output.='<br/><b>Keywords: </b>';
+  $terms=array();
+  foreach ($base->query($sql) as $row) {
+    $terms[]=$row['data'];
+  }
+  natsort($terms);
+  $terms=array_unique($terms); // liste des termes de l'article
+  $keywords='';
+  foreach ($terms as $key => $value) {
+    $keywords.=$value.', ';
+  }
+
+  foreach ($terms_of_query as $key => $value) {
+      $keywords=str_replace($value,'<font color="green"><b> '.$value.'</b></font>',$keywords);
+    }
+    foreach (array_diff($terms,$terms_of_query) as $key => $value) {
+      $keywords=str_ireplace($value,'<font color="#800000"> '.$value.'</font>',$keywords);
+    }
+
+  $output.='<p align="justify">'.$keywords.'</p>';
+
+
+//   // get the website
+  $sql = 'SELECT data FROM AG1 WHERE id='.$id;
+  foreach ($base->query($sql) as $row) {
+    $output.='<b>Agency: </b>'.$row['data'].'<br/> ';
+  }
+
+	$sql = 'SELECT data FROM ABS WHERE id='.$id;
+  // echo $output."<br>";
+  $abs="";
+	foreach ($base->query($sql) as $row) {
+    $abs.=". ".$row['data'];
+	}
+  $abs=str_replace('ISSUES:'  ,'<br/><br/><b>Issues:</b>',$abs);
+  $abs=str_replace('INTENDED IMPACT:'  ,'<br/><br/><b>Intended impact:</b>',$abs);    
+  $abs=str_replace('IMPACT:'  ,'<br/><br/><b>Impact:</b>',$abs);
+  $abs=str_replace('NOVELTY:'  ,'<br/><br/><b>Novelty:</b>',$abs);
+  $abs=str_replace('BOLD INNOVATION:'  ,'<br/><br/><b>Bold innovation:</b>',$abs);
+  $abs=str_replace('SOCIAL PROBLEM:'  ,'<br/><br/><b>Social problem:</b>',$abs);
+
+  // solving encoding pb
+  $abs=str_replace('―', ' ', $abs);
+  $abs=str_replace('‟‟', ' ', $abs);
+  $abs=str_replace('„‟', ' ', $abs);
+  $abs=str_replace('_x000D_', ' ', $abs);
+  $abs=str_replace('•', ' ', $abs);
+  $abs=str_replace('’', '\'', $abs);
+  
+  foreach ($terms_of_query as $key => $value) {
+    $abs=str_ireplace($value,'<font color="green"><b> '.$value.'</b></font>',$abs);
+  }
+  foreach (array_diff($terms,$terms_of_query) as $key => $value) {
+    $abs=str_ireplace($value,'<font color="#800000"> '.$value.'</font>',$abs);
+  }
+
+  $output.='<br/><p align="justify"><b>Abstract : </b><i>'.$abs.' </i></p>';
+  $output.="<br>"; 
+
+
+
+echo $output.$find;
+echo '</div>';
+//echo '<div id="tabs-2">
+//    <p><strong>Click this tab again to close the content pane.</strong></p>
+//    <p>Morbi tincidunt, dui sit amet facilisis feugiat, odio metus gravida ante, ut pharetra massa metus id nunc. Duis scelerisque molestie turpis. Sed fringilla, massa eget luctus malesuada, metus eros molestie lectus, ut tempus eros massa ut dolor. Aenean aliquet fringilla sem. Suspendisse sed ligula in ligula suscipit aliquam. Praesent in eros vestibulum mi adipiscing adipiscing. Morbi facilisis. Curabitur ornare consequat nunc. Aenean vel metus. Ut posuere viverra nulla. Aliquam erat volutpat. Pellentesque convallis. Maecenas feugiat, tellus pellentesque pretium posuere, felis lorem euismod felis, eu ornare leo nisi vel felis. Mauris consectetur tortor et purus.</p>
+//  </div>';
+
+
+echo '</div>';
+
+function pt($string){
+    // juste pour afficher avec retour à la ligne
+echo $string."<br/>";
+}
+
+function pta($array){
+    print_r($array);
+    echo '<br/>';
+}
+
+
+?>

LOCALDB/favorite.php

+<?php
+$db= $_GET["db"];//I receive the specific database as string!
+$terms_of_query=json_decode($_GET["query"]);
+include('parameters_details.php');
+$base = new PDO("sqlite:" .$mainpath.$db);
+$query=$_GET["query"];
+$gexf=$_GET["gexf"];
+$max_tag_could_size=15;
+$output = "<ul>"; // string sent to the javascript for display
+$type = $_GET["type"];
+
+$sql='SELECT id from favorites';
+$wos_ids=array(); // favorite list
+$num_favorite=0;
+$count=0;
+foreach ($base->query($sql) as $row){
+        $wos_ids[$row['id']] = 1;
+        $num_favorite+=1;
+}
+
+$favorite_keywords=array();
+
+foreach ($wos_ids as $id => $score) { 
+  if ($count<1000){
+    // retrieve publication year
+    $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
+    foreach ($base->query($sql) as $row) {
+      $pubdate=$row['data'];
+    }
+
+      $count+=1;
+      $output.="<li >";
+
+      $sql = 'SELECT data FROM ISItermsListV1 WHERE id='.$id;
+      foreach ($base->query($sql) as $row) {
+        if (array_key_exists($row['data'], $favorite_keywords)){
+          $favorite_keywords[$row['data']]=$favorite_keywords[$row['data']]+1;
+        }else{
+          $favorite_keywords[$row['data']]=1;
+        }
+      }  
+      
+
+
+      $sql = 'SELECT data FROM ISITITLE WHERE id='.$id;
+      foreach ($base->query($sql) as $row) {
+         $output.='<a href="default_doc_details.php?db='.urlencode($db).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+
+                        //this should be the command:
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+
+                        //the old one:  
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>'; 
+        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+      }
+
+  // get the authors
+      $sql = 'SELECT data FROM ISIAUTHOR WHERE id='.$id;
+      foreach ($base->query($sql) as $row) {
+        $output.=strtoupper($row['data']).', ';
+      }
+
+      if($project_folder!='nci'){
+        
+        $output.='('.$pubdate.') ';
+
+      }else {
+        $output.='(2013) ';
+      }
+
+// get the country
+  $sql = 'SELECT data FROM ISIkeyword WHERE id='.$id;
+  foreach ($base->query($sql) as $row) {
+    $country=$CC[strtoupper($row['data'])];
+  
+    $output.=strtoupper($country).'  ';
+  }
+
+
+  //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
+
+      $output.=$external_link."</li><br>";      
+    
+
+  }else{
+    continue;
+  }
+}
+
+
+
+arsort($favorite_keywords);
+$tag_coud_size=0;
+$tag_could='';
+foreach ($favorite_keywords as $key => $value) {
+  if ($tag_coud_size<$max_tag_could_size){
+      $tag_coud_size+=1;
+      $tag_could.='<font size="'.(3+log($value)).'">'.$key.', </font>';
+  }else{
+    continue;
+  } # code...
+}
+
+
+$output= '<h3>'.$num_favorite.' favorite items </h3>'.$tag_could.'<br/>'.$output;
+
+
+echo $output;                
+
+function imagestar($score,$factor,$twjs) {
+// produit le html des images de score
+  $star_image = '';
+  if ($score > .5) {
+    $star_image = '';
+    for ($s = 0; $s < min(5,$score/$factor); $s++) {
+      $star_image.='<img src="img/star.gif" border="0" >';
+    }
+  } else {
+    $star_image.='<img src="img/stargrey.gif" border="0">';
+  }
+  return $star_image;
+}
+        
+        
+
+?>

LOCALDB/full_doc_list.php

+<?php
+include('parameters_details.php');
+$db = $gexf_db[$gexf];
+
+$base = new PDO("sqlite:../" .$db);
+
+
+$output = "<ul>"; // string sent to the javascript for display
+#http://localhost/branch_ademe/php/test.php?type=social&query=[%22marwah,%20m%22]
+
+
+$type = $_GET["type"];
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$terms_of_query=json_decode($_GET["query"]);
+$elems = json_decode($query);
+
+// nombre d'item dans les tables 
+$sql='SELECT COUNT(*) FROM ISIABSTRACT';
+foreach ($base->query($sql) as $row) {
+  $table_size=$row['COUNT(*)'];
+}
+
+$table = "";
+$column = "";
+$id="";
+$twjs="API_CNRS/"; // submod path of TinaWebJS
+
+if($type=="social"){
+  $table = "ISIAUTHOR";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;// factor for normalisation of stars
+}
+
+if($type=="semantic"){
+  $table = "ISItermsListV1";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;
+}
+
+
+$sql = 'SELECT count(*),'.$id.'
+FROM '.$table.' where (';
+        foreach($elems as $elem){
+                $sql.=' '.$column.'="'.$elem.'" OR ';
+        }
+#$querynotparsed=$sql;#####
+        $sql = substr($sql, 0, -3);
+        $sql = str_replace( ' & ', '" OR '.$column.'="', $sql );
+
+        $sql.=')'.$restriction.'
+GROUP BY '.$id.'
+ORDER BY count('.$id.') DESC
+LIMIT 1000';
+
+#$queryparsed=$sql;#####
+
+$wos_ids = array();
+$sum=0;
+
+//The final query!
+// array of all relevant documents with score
+
+foreach ($base->query($sql) as $row) {        
+        // on pondère le score par le nombre de termes mentionnés par l'article
+        
+        //$num_rows = $result->numRows();
+        $wos_ids[$row[$id]] = $row["count(*)"];
+        $sum = $row["count(*)"] +$sum;
+}
+
+
+//arsort($wos_ids);
+
+$number_doc=ceil(count($wos_ids)/3);
+$count=0;
+foreach ($wos_ids as $id => $score) { 
+  if ($count<1000){
+    // retrieve publication year
+    $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
+    foreach ($base->query($sql) as $row) {
+      $pubdate=$row['data'];
+    }
+
+    // to filter under some conditions
+    $to_display=true; 
+    if ($to_display){
+      $count+=1;
+      $output.="<li title='".$score."'>";
+      $output.=imagestar($score,$factor,$twjs).' '; 
+      $sql = 'SELECT data FROM ISITITLE WHERE id='.$id." group by data";
+
+      foreach ($base->query($sql) as $row) {
+         $output.='<a href="default_doc_details.php?gexf='.urlencode($gexf).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+
+                        //this should be the command:
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+
+                        //the old one:  
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>'; 
+        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+      }
+
+  // get the authors
+      $sql = 'SELECT data FROM ISIAUTHOR WHERE id='.$id;
+      foreach ($base->query($sql) as $row) {
+        $output.=strtoupper($row['data']).', ';
+      }
+
+  //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
+
+      $output.=$external_link."</li><br>";      
+    }
+
+  }else{
+    continue;
+  }
+}
+
+$output= '<h3>'.$count.' items related to: '.implode(' OR ', $elems).'</h3>'.$output;
+
+
+
+echo $output;
+
+
+function imagestar($score,$factor,$twjs) {
+// produit le html des images de score
+  $star_image = '';
+  if ($score > .5) {
+    $star_image = '';
+    for ($s = 0; $s < min(5,$score/$factor); $s++) {
+      $star_image.='<img src="img/star.gif" border="0" >';
+    }
+  } else {
+    $star_image.='<img src="img/stargrey.gif" border="0">';
+  }
+  return $star_image;
+}
+
+?>
+
+

LOCALDB/full_doc_list2.php

+<?php
+include('parameters_details.php');
+$db = $gexf_db[$gexf];
+
+$base = new PDO("sqlite:../" ."data/terrorism/data.db");
+
+echo "sqlite:../" ."data/terrorism/data.db";
+$output = "<ul>"; // string sent to the javascript for display
+#http://localhost/branch_ademe/php/test.php?type=social&query=[%22marwah,%20m%22]
+
+
+$type = $_GET["type"];
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$terms_of_query=json_decode($_GET["query"]);
+$elems = json_decode($query);
+
+// nombre d'item dans les tables 
+$sql='SELECT COUNT(*) FROM ISIABSTRACT';
+foreach ($base->query($sql) as $row) {
+  $table_size=$row['COUNT(*)'];
+}
+
+$table = "";
+$column = "";
+$id="";
+$twjs="pasteurapi/"; // submod path of TinaWebJS
+
+if($type=="social"){
+  $table = "ISIAUTHOR";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;// factor for normalisation of stars
+}
+
+if($type=="semantic"){
+  $table = "ISItermsListV1";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;
+}
+
+
+$sql = 'SELECT count(*),'.$id.'
+FROM '.$table.' where (';
+        foreach($elems as $elem){
+                $sql.=' '.$column.'="'.$elem.'" OR ';
+        }
+#$querynotparsed=$sql;#####
+        $sql = substr($sql, 0, -3);
+        $sql = str_replace( ' & ', '" OR '.$column.'="', $sql );
+
+        $sql.=')'.$restriction.'
+GROUP BY '.$id.'
+ORDER BY count('.$id.') DESC
+LIMIT 1000';
+
+#$queryparsed=$sql;#####
+
+$wos_ids = array();
+$sum=0;
+
+//The final query!
+// array of all relevant documents with score
+
+foreach ($base->query($sql) as $row) {        
+        // on pondère le score par le nombre de termes mentionnés par l'article
+        
+        //$num_rows = $result->numRows();
+        $wos_ids[$row[$id]] = $row["count(*)"];
+        $sum = $row["count(*)"] +$sum;
+}
+
+
+//arsort($wos_ids);
+
+$number_doc=ceil(count($wos_ids)/3);
+$count=0;
+foreach ($wos_ids as $id => $score) { 
+  if ($count<1000){
+    // retrieve publication year
+    $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
+    foreach ($base->query($sql) as $row) {
+      $pubdate="2014";
+    }
+
+    // to filter under some conditions
+    $to_display=true; 
+    if ($to_display){
+      $count+=1;
+      $output.="<li title='".$score."'>";
+      $output.=imagestar($score,$factor,$twjs).' '; 
+      $sql = 'SELECT data FROM ISITITLE WHERE id='.$id." group by data";
+
+      foreach ($base->query($sql) as $row) {
+         $output.='<a href="default_doc_details2.php?gexf='.urlencode($gexf).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+
+                        //this should be the command:
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+
+                        //the old one:  
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>'; 
+        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+      }
+
+  // get the authors
+      $sql = 'SELECT data FROM ISIAUTHOR WHERE id='.$id;
+      foreach ($base->query($sql) as $row) {
+        $output.=strtoupper($row['data']).', ';
+      }
+
+  //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
+
+      $output.=$external_link."</li><br>";      
+    }
+
+  }else{
+    continue;
+  }
+}
+
+$output= '<h3>'.$count.' items related to: '.implode(' OR ', $elems).'</h3>'.$output;
+
+
+
+echo $output;
+
+
+function imagestar($score,$factor,$twjs) {
+// produit le html des images de score
+  $star_image = '';
+  if ($score > .5) {
+    $star_image = '';
+    for ($s = 0; $s < min(5,$score/$factor); $s++) {
+      $star_image.='<img src="img/star.gif" border="0" >';
+    }
+  } else {
+    $star_image.='<img src="img/stargrey.gif" border="0">';
+  }
+  return $star_image;
+}
+
+?>
+
+

LOCALDB/full_doc_list_tidf.php

+<?php
+include('parameters_details.php');
+  
+$db= $_GET["db"];//I receive the specific database as string!
+$query=$_GET["query"];
+$gexf=$_GET["gexf"];
+
+$base = new PDO("sqlite:" .$mainpath.$db);
+
+$temp=explode('/',$db);
+$project_folder=$temp[1];
+$corpora=$temp[count($temp)-2];
+$corporadb = new PDO("sqlite:" .$mainpath.'data/'.$corpora.'/'.$corpora.'.sqlite'); //data base with complementary data
+
+
+$output = "<ul>"; // string sent to the javascript for display
+
+#http://localhost/branch_ademe/php/test.php?type=social&query=[%22marwah,%20m%22]
+
+
+$type = $_GET["type"];
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$elems = json_decode($query);
+// nombre d'item dans les tables 
+$sql='SELECT COUNT(*) FROM ISIABSTRACT';
+foreach ($base->query($sql) as $row) {
+  $table_size=$row['COUNT(*)'];
+}
+
+///// Specific to rock //////////
+// Other restrictions
+// extracting the project folder and the year
+if (strpos($gexf,'2013')>0){
+  $year='2013'; 
+  $year_filter=true;
+}elseif (strpos($gexf,'2012')>0){
+  $year='2012';
+  $year_filter=true;
+}else{
+  $year_filter=false;
+}
+
+// identification d'une année pour echoing
+if($project_folder=='nci'){
+  $year_filter=true;  
+  
+}
+
+$table = "";
+$column = "";
+$id="";
+$twjs="tinawebJS/"; // submod path of TinaWebJS
+
+if($type=="social"){
+  $table = "ISIAUTHOR";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;// factor for normalisation of stars
+}
+
+if($type=="semantic"){
+  $table = "ISItermsListV1";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;
+}
+
+// identification d'une année pour echoing
+if($project_folder=='nci'){
+  $restriction.=" AND ISIpubdate='2013'";
+}
+
+$sql = 'SELECT sum(tfidf),id
+FROM tfidf where (';
+  foreach($elems as $elem){
+    $sql.=' term="'.$elem.'" OR ';
+  }
+#$querynotparsed=$sql;#####
+  $sql = substr($sql, 0, -3);
+  $sql = str_replace( ' & ', '" OR term="', $sql );
+
+  $sql.=')'.//$restriction.
+'GROUP BY '.$id.'
+ORDER BY sum(tfidf) DESC
+LIMIT 1000';
+
+//echo $sql;
+#$queryparsed=$sql;#####
+
+$wos_ids = array();
+$sum=0;
+
+//echo $sql;//The final query!
+// array of all relevant documents with score
+$count=0;
+foreach ($corporadb ->query($sql) as $row) {  
+  //if ($count<4*$max_item_displayed){
+    $wos_ids[$row[$id]] = $row['sum(tfidf)'];//$row["count(*)"];
+    $sum = $row["count(*)"] +$sum;
+  //}else{
+  //  continue;
+  //}
+}
+
+
+//arsort($wos_ids);
+
+$number_doc=ceil(count($wos_ids)/3);
+$count=0;
+foreach ($wos_ids as $id => $score) { 
+  if ($count<1000){
+    // retrieve publication year
+    $sql = 'SELECT data FROM ISIpubdate WHERE id='.$id;
+    foreach ($base->query($sql) as $row) {
+      $pubdate=$row['data'];
+    }
+
+    // to filter under some conditions
+    $to_display=true; 
+    if ($project_folder=='echoing'){
+      if ($year_filter){
+        if ($pubdate!=$year){
+          $to_display=false;
+        }
+      }     
+    }elseif($project_folder=='nci'){
+      if ($year_filter){
+        if ($pubdate!='2013'){
+          $to_display=false;
+        }
+      } 
+    }
+
+    if ($to_display){
+      $count+=1;
+      $output.="<li title='".$score."'>";
+      $output.=imagestar($score,$factor,$twjs).' '; 
+      $sql = 'SELECT data FROM ISITITLE WHERE id='.$id;
+
+      foreach ($base->query($sql) as $row) {
+         $output.='<a href="default_doc_details.php?db='.urlencode($db).'&type='.urlencode($_GET["type"]).'&query='.urlencode($query).'&id='.$id.'">'.$row['data']." </a> ";
+
+                        //this should be the command:
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?db='.urlencode($datadb).'&id='.$id.'  \')">'.$row['data']." </a> "; 
+
+                        //the old one:  
+      //$output.='<a href="JavaScript:newPopup(\''.$twjs.'php/default_doc_details.php?id='.$id.'  \')">'.$row['data']." </a> ";   
+        $external_link="<a href=http://scholar.google.com/scholar?q=".urlencode('"'.$row['data'].'"')." target=blank>".' <img width=20px src="img/gs.png"></a>'; 
+        //$output.='<a href="JavaScript:newPopup(''php/doc_details.php?id='.$id.''')"> Link</a>'; 
+      }
+
+  // get the authors
+      $sql = 'SELECT data FROM ISIAUTHOR WHERE id='.$id;
+      foreach ($base->query($sql) as $row) {
+        $output.=strtoupper($row['data']).', ';
+      }
+
+      if($project_folder!='nci'){
+        
+        $output.='('.$pubdate.') ';
+
+      }else {
+        $output.='(2013) ';
+      }
+
+
+
+  //<a href="JavaScript:newPopup('http://www.quackit.com/html/html_help.cfm');">Open a popup window</a>'
+
+      $output.=$external_link."</li><br>";      
+    }
+
+  }else{
+    continue;
+  }
+}
+
+$output= '<h3>'.$count.' items related to: '.implode(' OR ', $elems).'</h3>'.$output;
+
+
+
+echo $output;
+
+
+function imagestar($score,$factor,$twjs) {
+// produit le html des images de score
+  $star_image = '';
+  if ($score > .5) {
+    $star_image = '';
+    for ($s = 0; $s < min(5,$score/$factor); $s++) {
+      $star_image.='<img src="img/star.gif" border="0" >';
+    }
+  } else {
+    $star_image.='<img src="img/stargrey.gif" border="0">';
+  }
+  return $star_image;
+}
+
+?>
+
+

LOCALDB/info_div.php

+<?php
+// manage the dynamical additional information in the left panel.
+
+// ini_set('display_errors',1);
+// ini_set('display_startup_errors',1);
+// error_reporting(-1);
+
+include('parameters_details.php');
+
+$max_item_displayed=6;
+$base = new PDO("sqlite:../" .$graphdb);
+
+include('default_div.php');
+
+
+/*
+ * This function gets the first db name in the data folder
+ * IT'S NOT SCALABLE! (If you want to use several db's)
+ */
+function getDB ($directory)  {
+    //$results = array();
+    $result = "";
+    $handler = opendir($directory);
+    while ($file = readdir($handler)) {
+      if ($file != "." && $file != ".." 
+              && 
+        ((strpos($file,'.db~'))==false && (strpos($file,'.db'))==true )
+              || 
+        ((strpos($file,'.sqlite~'))==false && (strpos($file,'.sqlite'))==true)
+      ) {
+            //$results[] = $file;
+            $result = $file;
+            break;
+      }
+    }
+    closedir($handler);
+    //return $results;
+    return $result;
+}
+
+?>

LOCALDB/info_div2.php

+<?php
+// manage the dynamical additional information in the left panel.
+// include('parameters_details.php');
+
+$gexf= str_replace('"','',$_GET["gexf"]);
+
+$max_item_displayed=6;
+$type = $_GET["type"];
+$TITLE="ISITITLE";
+$query = str_replace( '__and__', '&', $_GET["query"] );
+$elems = json_decode($query);
+
+$table = "";
+$column = "";
+$id="";
+$twjs="API_CNRS/"; // submod path of TinaWebJS
+
+
+if($type=="semantic"){
+  $table = "ISItermsListV1";
+  $column = "data";
+  $id = "id";
+  $restriction='';
+  $factor=10;
+}
+$restriction='';
+$factor=10;
+
+
+$sql="";
+if (count($elems)==1){// un seul mot est sélectionné, on compte les mots multiples
+  $sql = 'SELECT count(*),'.$id.'
+  FROM '.$table.' where (';
+          foreach($elems as $elem){
+                $sql.=' '.$column.'="'.$elem.'" OR ';
+          }
+  #$querynotparsed=$sql;#####
+    $sql = substr($sql, 0, -3);
+    $sql = str_replace( ' & ', '" OR '.$column.'="', $sql );
+    $sql.=')'.$restriction.'
+  GROUP BY '.$id.'
+  ORDER BY count('.$id.') DESC
+  LIMIT 1000';
+}else{// on compte une seule fois un mot dans un article
+  $factor=ceil(count($elems)/5); //les scores sont moins haut
+  $sql='';
+  foreach($elems as $elem){
+            $sql.=' '.$column.'="'.$elem.'" OR ';
+        }
+    $sql=substr($sql, 0, -3);
+    $sql='SELECT count(*),id,data FROM (SELECT *
+  FROM '.$table.' where ('.$sql.')'.$restriction.'
+   group by id,data) GROUP BY '.$id.'
+  ORDER BY count('.$id.') DESC
+  LIMIT 1000  COLLATE NOCASE';
+
+}
+
+// echo $sql."<br>";
+
+$base = new PDO("sqlite:../data/terrorism/data.db");
+$wos_ids = array();
+$sum=0;
+
+//The final query!
+// array of all relevant documents with score
+
+foreach ($base->query($sql) as $row) {        
+        // on pondère le score par le nombre de termes mentionnés par l'article
+        
+        //$num_rows = $result->numRows();
+        $wos_ids[$row[$id]] = $row["count(*)"];
+        $sum = $row["count(*)"] +$sum;
+}
+
+
+// /// nombre de document associés $related
+$total_count=0;
+$count_max=500; 
+$number_doc=count($wos_ids);
+$count=0;
+
+$all_terms_from_selected_projects=array();// list of terms for the top 6 project selected
+
+// to filter under some conditions
+$to_display=true; 
+$count=0;
+
+
+foreach ($wos_ids as $id => $score) { 
+  if ($total_count<$count_max) {
+    // retrieve publication year
+    
+    if ($to_display){
+      $total_count+=1;
+
+      if ($count<=$max_item_displayed){
+        $count+=1;
+
+        $sql = 'SELECT data FROM ISITITLE WHERE id='.$id.' group by data';
+        foreach ($base->query($sql) as $row) {
+          $external_link="<a href=http://google.com/webhp?#q=".urlencode('"'.utf8_decode($row['data']).'"')." target=blank>".' <img width=15px src="'.$twjs.'img/google.png"></a>';  
+          $output.="<li title='".$score."'>";
+          $output.=$external_link.imagestar($score,$factor,$twjs).' '; 
+          $output.='<a href="JavaScript:newPopup(\''.$twjs.'default_doc_details2.php?gexf='.urlencode($gexf).'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.' \')">'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
+          // $output.='<a>'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
+          
+        }
+
+        $sql = 'SELECT data FROM ISIDOI WHERE id='.$id.' group by data';
+        foreach ($base->query($sql) as $row) {
+          $output.=$external_link.imagestar($score,$factor,$twjs).' ';  
+          $output.='<a href="JavaScript:newPopup(\''.$twjs.'default_doc_details2.php?gexf='.urlencode($gexf).'&query='.urlencode($query).'&type='.urlencode($_GET["type"]).'&id='.$id.' \')">'.htmlentities($row['data'], ENT_QUOTES, "UTF-8")." </a> ";
+          
+        }        // get the authors
+        $sql2 = 'SELECT data FROM ISIAUTHOR WHERE id='.$id. ' group by data';
+        foreach ($base->query($sql2) as $row2) {
+          $output.=(str_replace("\r", "", $row2['data'])).', ';
+          
+        }
+        $output = rtrim($output, ", ");
+        $output.="</li><br>"; 
+
+      }
+    }
+
+  } else{
+    continue;
+  }
+}
+if ($total_count<$count_max){
+  $related .= $total_count;
+}else{
+  $related .= ">".$count_max;
+}
+
+$output .= "</ul>"; #####
+
+// echo $output."<br>";
+
+
+
+if($max_item_displayed>$related) $max_item_displayed=$related;
+echo $news.'<br/><h4><font color="#0000FF"> Full text of top '.$max_item_displayed.'/'.$related.' related grant proposals:</font></h4>'.$output;
+//pt - 301 ; 15.30
+
+
+/*
+ * This function gets the first db name in the data folder
+ * IT'S NOT SCALABLE! (If you want to use several db's)
+ */
+function getDB ($directory)  {
+    //$results = array();
+    $result = "";
+    $handler = opendir($directory);
+    while ($file = readdir($handler)) {
+      if ($file != "." && $file != ".." 
+              && 
+        ((strpos($file,'.db~'))==false && (strpos($file,'.db'))==true )
+              || 
+        ((strpos($file,'.sqlite~'))==false && (strpos($file,'.sqlite'))==true)
+      ) {
+            //$results[] = $file;
+            $result = $file;
+            break;
+      }
+    }
+    closedir($handler);
+    //return $results;
+    return $result;
+}
+
+
+function imagestar($score,$factor,$twjs) {
+// produit le html des images de score
+  $star_image = '';
+  if ($score > .5) {
+    $star_image = '';
+    for ($s = 0; $s < min(5,$score/$factor); $s++) {
+      $star_image.='<img src="'.$twjs.'img/star.gif" border="0" >';
+    }
+  } else {
+    $star_image.='<img src="'.$twjs.'img/stargrey.gif" border="0">';
+  }
+  return $star_image;
+}
+
+?>

LOCALDB/listFiles.php

+<?php
+header ("Content-Type:application/json"); 
+//$string = getcwd();
+//$string = str_replace("/php","",$string);
+
+$string=dirname(dirname(getcwd())); // ProjectExplorer folder name: /var/www/ademe
+
+//$files = getDirectoryList($string."/data");
+include("DirectoryScanner.php");
+$projectFolderPat = dirname(dirname(getcwd())) . "/";
+$instance = new scanTree($projectFolderPat);
+$instance->getDirectoryTree("data");
+$gexfs=$instance->gexf_folder;
+$files=array();
+foreach($gexfs as $key => $value){
+    array_push($files,$key);
+}
+$filesSorted=array();
+foreach($files as $file){
+    array_push($filesSorted,$file);
+}
+sort($filesSorted);
+
+echo json_encode($filesSorted);
+
+function getDirectoryList ($directory)  {
+    $results = array();
+    $handler = opendir($directory);
+    while ($file = readdir($handler)) {
+      if ($file != "." && $file != ".." && 
+         (strpos($file,'.gexf~'))==false && 
+         (strpos($file,'.gexf'))==true) {
+        $results[] = $file;
+      }
+    }
+    closedir($handler);
+    return $results;
+}
+
+?>
+

LOCALDB/parameters_details.php

+<?php
+
+
+$gexf_db = array();
+$gexf_db["data/medq1/20141208_MED_01_bi.gexf"] = "data/medq1/01_medline-query1.db";
+
+$gexf_db["data/medq2/20141128_MED_02_bi.gexf"] = "data/medq2/02_medline-query2.db";
+$gexf_db["data/medq2/20141128_MED_03_bi.gexf"] = "data/medq2/02_medline-query2.db";
+$gexf_db["data/medq2/20141208_MED_Author_name-ISItermsjulien_index.gexf"] = "data/medq2/02_medline-query2.db";
+$gexf_db["data/20141128_GPs_03_bi.gexf"] = "data/00_grantproposals.db";
+$gexf_db["data/20141215_GPs_04.gexf"] = "data/00_grantproposals.db";
+
+# new stuff
+$gexf_db["data/terrorism/terrorism_mono.gexf"] = "data/terrorism/data.db";
+$gexf_db["data/terrorism/terrorism_bi.gexf"] = "data/terrorism/data.db";
+
+# new stuff2
+$gexf_db["data/ClimateChange/hnetwork-2014_2015hhn-wosclimatechange2014_2015top509-ISItermsListV3bis-ISItermsListV3bis-distributionalcooc-99999-oT0.36-20-louTrue.gexf"] = "data/ClimateChange/wosclimatechange-61715-1-wosclimatechange-db(2).db";
+$gexf_db["data/ClimateChange/ClimateChangeV1.gexf"] = "data/ClimateChange/wosclimatechange-61715-1-wosclimatechange-db(2).db";
+$gexf_db["data/ClimateChange/hnetwork-2014_2015hn-wosclimatechange2014_2015top509-ISItermsListV3bis-ISItermsListV3bis-distributionalcooc-99999-oT0.36-20-louTrue.gexf"] = "data/ClimateChange/wosclimatechange-61715-1-wosclimatechange-db(2).db";
+
+$gexf= str_replace('"','',$_GET["gexf"]);
+
+$mainpath=dirname(getcwd())."/";
+$graphdb = $gexf_db[$gexf];
+
+
+?>

LOCALDB/tfidf.php

+<?php
+echo '<meta http-equiv="Content-type" content="text/html; charset=UTF-8"/>';
+// compute the tfidf score for each terms for each document for cortext like databases and store them in a specific table
+//include('parameters_details.php');
+$db = new PDO("sqlite:graph.db");
+
+$database_name='echoing.sqlite';
+$project_base = new PDO("sqlite:" .$database_name);
+
+// Table creation
+// efface la base existante
+$project_base->exec("DROP TABLE IF EXIST tfidf");
+pt("creation of tfidf table");
+//on crée un table pour les infos de clusters 
+$project_base->exec("CREATE TABLE tfidf (id NUMERIC,term TEXT,tfidf NUMERIC)");
+
+//generating number of mention of terms in the corpora
+$terms_freq=array();	
+pt('processing terms frequency');
+$sql='SELECT count(*),data FROM ISItermsListV1 group by data';
+foreach ($db->query($sql) as $term) {
+	$terms_freq[$term['data']]=$term['count(*)'];	
+}
+pt('processing number of doc');
+
+// nombre d'iterator_apply(iterator, function)em dans les tables 
+$sql='SELECT COUNT(*) FROM ISIABSTRACT';
+foreach ($db->query($sql) as $row) {
+	$table_size=$row['COUNT(*)'];
+}
+pt($table_size.' documents in database');	
+// select all the doc
+$sql='SELECT * FROM ISIABSTRACT';
+foreach ($db->query($sql) as $doc) {
+	$id=$doc['id'];
+	pt($id);
+	//select all the terms of that document with their occurrences
+	$sql2="SELECT count(*),data FROM ISItermsListV1 where id='".$id."' group by data";
+	// for each term we compute the tfidf
+	foreach ($db->query($sql2) as $term_data) {
+		$term=$term_data['data'];
+		$term_occ_in_doc=$term_data['count(*)'];
+		$terms_tfidf=log(1+$term_occ_in_doc)*log($table_size/$terms_freq[$term]);
+		$query='INSERT INTO tfidf  (id,term,tfidf) VALUES ('.$id.',"'.$term.'",'.$terms_tfidf.')';
+		$project_base->query($query);		
+	}
+}
+
+function pt ($string)  {
+	echo $string.'<br/>';
+}
+?>

db.json

+{
+	"data/ClimateChange": {
+		"dbname":"wosclimatechange-61490-1-wosclimatechange-db.db",
+		"title":"ISITITLE",
+		"date":"ISIpubdate",
+		"abstract":"ISIABSTRACT",
+		"gexfs": {
+			"hnetwork-2014_2015hn-wosclimatechange2014_2015top509-ISItermsListV3bis-ISItermsListV3bis-distributionalcooc-99999-oT0.36-20-louTrue.gexf": {
+				"social": { "table":"ISIAUTHOR" , "textCol":"data","forkeyCol":"id"},
+				"semantic": { "table":"ISItermsListV3bis" , "textCol":"data","forkeyCol":"id"}
+			},
+			"ClimateChangeV1.gexf": {
+				"social": { "table":"ISIAUTHOR" , "textCol":"data","forkeyCol":"id"},
+				"semantic": { "table":"ISItermsListV3bis" , "textCol":"data","forkeyCol":"id"}
+			}
+		}
+	},"data/terrorism": {
+		"dbname":"data.db",
+		"title":"ISITITLE",
+		"date":"ISIpubdate",
+		"abstract":"ISIABSTRACT",
+		"gexfs": {
+			"terrorism_bi.gexf": {
+				"social": { "table":"ISIAUTHOR" , "textCol":"data","forkeyCol":"id"},
+				"semantic": { "table":"ISItermsListV1" , "textCol":"data","forkeyCol":"id"}
+			},
+			"terrorism_mono.gexf":{
+				"semantic": { "table":"ISItermsListV1" , "textCol":"data","forkeyCol":"id"}
+			}
+		}
+	},
+	"data/medq2/": {
+		"dbname":"02_medline-query2.db",
+		"title":"ArticleTitle",
+		"date":"ISIpubdate",
+		"abstract":"Abstract",
+		"gexfs": {
+			"20141208_MED_Author_name-ISItermsjulien_index.gexf": {
+				"social": { "table":"Author_name" , "textCol":"data","forkeyCol":"id"},
+				"semantic": { "table":"ISItermsBigWL" , "textCol":"data","forkeyCol":"id"}
+			}
+		}
+	}
+}

libs/bootstrap/js/bootstrap-hover-dropdown.min.js

+/**
+ * @preserve
+ * Project: Bootstrap Hover Dropdown
+ * Author: Cameron Spear
+ * Version: v2.0.10
+ * Contributors: Mattia Larentis
+ * Dependencies: Bootstrap's Dropdown plugin, jQuery
+ * Description: A simple plugin to enable Bootstrap dropdowns to active on hover and provide a nice user experience.
+ * License: MIT
+ * Homepage: http://cameronspear.com/blog/bootstrap-dropdown-on-hover-plugin/
+ */
+!function($,n,e){var o=$();$.fn.dropdownHover=function(e){return"ontouchstart"in document?this:(o=o.add(this.parent()),this.each(function(){function t(e){o.find(":focus").blur(),h.instantlyCloseOthers===!0&&o.removeClass("open"),n.clearTimeout(c),i.addClass("open"),r.trigger(a)}var r=$(this),i=r.parent(),d={delay:500,instantlyCloseOthers:!0},s={delay:$(this).data("delay"),instantlyCloseOthers:$(this).data("close-others")},a="show.bs.dropdown",u="hide.bs.dropdown",h=$.extend(!0,{},d,e,s),c;i.hover(function(n){return i.hasClass("open")||r.is(n.target)?void t(n):!0},function(){c=n.setTimeout(function(){i.removeClass("open"),r.trigger(u)},h.delay)}),r.hover(function(n){return i.hasClass("open")||i.is(n.target)?void t(n):!0}),i.find(".dropdown-submenu").each(function(){var e=$(this),o;e.hover(function(){n.clearTimeout(o),e.children(".dropdown-menu").show(),e.siblings().children(".dropdown-menu").hide()},function(){var t=e.children(".dropdown-menu");o=n.setTimeout(function(){t.hide()},h.delay)})})}))},$(document).ready(function(){$('[data-hover="dropdown"]').dropdownHover()})}(jQuery,this);
\ No newline at end of file