new MySQL connectors for comex directory/filter operations

TODO_RESTORE.md

+### List of features that where deactivated
+
+During rewrite we deactivated some retrieval to match the new sql tables from registration:
+
+  - tables organizations, labs don't exist => TODO RESTORE in `directory_content.php` (and therefore empty arrays are passed to `labs_list.php` and `orga_list.php`)
+
+  - in `search_scholar.php`, column nb_keywords doesn't exist (and now keywords are never 0) => TODO RESTORE
+
+  - in `print_directory.php`, all the following columns are now ignored: 'nb_keywords', 'css_voter', 'css_member', 'keywords_ids', 'status', 'homepage', 'lab2', 'affiliation2', 'homepage', **'position'** (used in `stats_prep_from_array.php`), 'photo_url', 'address', 'city', 'postal_code', 'phone', 'mobile', 'fax', 'affiliation_acronym' => TODO RESTORE
+  - in `print_scholar_directory.php`
+    - similar changes as above
+    - additional change to keywords_ids search in old "scholars2terms" table => becomes `LIKE` search in keywords: TODO index

comex_library.php

@@ -16,14 +16,16 @@ function clean_exp($string){
     }
 }
 
-function get_value($cle_value,$table='data',$cle='cle',$valeur='valeur'){    
+
+// NB actually (2016-12) this is unused TODO use !!!
+function get_value($cle_value,$table='data',$cle='cle',$valeur='valeur'){
 // renvoie la valeur correspondant à la clé $cle dans la table data
-   
+
 $sql = 'SELECT '.$valeur.' from '.$table.' WHERE '.$cle.'="'.trim($cle_value).'"';
 $resultat=mysql_query($sql);
     while ($ligne=mysql_fetch_array($resultat)) {
         $out=$ligne[$valeur];
         }
 return $out;
-}   
+}
 ?>

parametres.php

 <?php
 
-/*
-list de parametres.
- */
+/* liste de parametres */
 
-$dbname='/home/jbilcke/databases/scholar_test_data.db';
 $dbname='community.db';
-//$dbname='scholar_test_data.db';
 
-//$scholars_db ="raw_scholars";
-$fichier = "CSSscholars20Oct2011.csv";
-$fichier = "CSSscholars2Oct2011.csv";
-$lab_csv="CSLabs13Fev2012.csv";
-$orga_csv='';
 $min_num_friends=0;// nombre minimal de voisin que doit avoir un scholar pour être affiché
-//$fichier = "Scholars13Sept2011.csv";
-//$fichier = "test2.csv";
-$drop_tables=true; // on efface les tables
-$language='english';
-$file_sep=',';
-//$scholar_filter=" where country='France' AND status='o'";
-//$scholar_filter=" where country='France' AND want_whoswho='Yes' AND css_member='Yes'";
-//$scholar_filter=" where css_member='Yes' AND want_whoswho='Yes'";
-//$scholar_filter=" where css_member='Yes' OR want_whoswho='Yes'";
-$scholar_filter="where css_member='Yes'";
-//$scholar_filter="";
-//$scholar_filter=" where country='France' AND want_whoswho='Yes'";
-//$scholar_filter=" where country='France'";
+// $compress='No';
 
-$compress='No';
 
+/* parametres externes: nom de l'hôte SQL*/
+$params = parse_ini_file("parametres_comex.ini");
+
+/* tout pour le MySQL */
+$host =  $params['SQL_HOST'];
+$db   = 'comex_shared';
+$user = 'root';
+$pass = 'very-safe-pass';
+$charset = 'utf8';
+
+$dsn = "mysql:host=$host;dbname=$db;charset=$charset";
+$opt = [
+    PDO::ATTR_ERRMODE            => PDO::ERRMODE_EXCEPTION,
+    PDO::ATTR_DEFAULT_FETCH_MODE => PDO::FETCH_ASSOC,
+    PDO::ATTR_EMULATE_PREPARES   => false,
+];
 ?>

print_scholar_directory.php

@@ -72,27 +72,33 @@ function is_utf8($string) {
 $login = $_GET['query'];
 
 
-$base = new PDO("sqlite:" . $dbname);
+// $base = new PDO("sqlite:" . $dbname);
+$base = new PDO($dsn, $user, $pass, $opt);
 
 if ($login) {
     if (sizeof($login) > 0) {
 // liste des chercheurs
-        $sql = "SELECT keywords_ids,last_name,first_name FROM scholars where unique_id='" . $login . "'";
+        $sql = "SELECT keywords,last_name,first_name FROM comex_registrations WHERE doors_uid='" . $login . "'";
         foreach ($base->query($sql) as $row) {
-            $keywords_ids = explode(',', $row['keywords_ids']);
+            $keywords = explode(',', $row['keywords']);
             $scholar_array = array();
             $target_name=$row['first_name'].' '.$row['last_name'];
-            foreach ($keywords_ids as $keywords_id) {
-
-                $sql2 = "SELECT * FROM scholars2terms where term_id=" . trim($keywords_id);
-                #pt($sql2);
-                foreach ($base->query($sql2) as $row) {
-                    if (array_key_exists($row['scholar'], $scholar_array)){
-                        $scholar_array[$row['scholar']] += 1;
-                    }else{
-                        $scholar_array[$row['scholar']] = 1;
-                    }
+            foreach ($keywords as $keyword) {
+
+                if (strlen($keyword) > 0) {
 
+                    // TODO RESTORE index keywords
+                    // $sql2 = "SELECT * FROM scholars2terms where term_id=" . trim($keywords_id);
+                    $sql2 = "SELECT doors_uid FROM comex_registrations WHERE keywords LIKE \"%" . trim($keyword)."%\"";
+                    // echo($sql2."<br/>");
+                    foreach ($base->query($sql2) as $row) {
+                        if (array_key_exists($row['doors_uid'], $scholar_array)){
+                            $scholar_array[$row['doors_uid']] += 1;
+                        }else{
+                            $scholar_array[$row['doors_uid']] = 1;
+                        }
+
+                    }
                 }
             }
         }
@@ -100,48 +106,51 @@ if ($login) {
     }
 }
 
-        // les scholars sont affichés par ordre de pertinence
-        arsort($scholar_array);
+// les scholars sont affichés par ordre de pertinence
+arsort($scholar_array);
+
+$scholar_id_array=array_keys($scholar_array);
+// echo var_dump($scholar_id_array)."<br/>" ;
 
-        $scholar_id_array=array_keys($scholar_array);
 // liste des chercheurs
 $scholars = array();
-
+//
 foreach ($scholar_id_array as $scholar_id){
-$sql = "SELECT * FROM scholars where unique_id='" . $scholar_id. "'";
-
+$sql = "SELECT * FROM comex_registrations where doors_uid='" . $scholar_id. "'";
+// echo var_dump($scholar_id)."<br/>" ;
 //$query = "SELECT * FROM scholars";
 foreach ($base->query($sql) as $row) {
     $info = array();
-    $info['unique_id'] = $row['unique_id'];
+    $info['unique_id'] = $row['doors_uid'];
     $info['first_name'] = $row['first_name'];
     $info['initials'] = $row['initials'];
     $info['last_name'] = $row['last_name'];
-    $info['nb_keywords'] = $row['nb_keywords'];
-    $info['css_voter'] = $row['css_voter'];
-    $info['css_member'] = $row['css_member'];
-    $info['keywords_ids'] = explode(',', $row['keywords_ids']);
+    // $info['nb_keywords'] = $row['nb_keywords'];
+    // $info['css_voter'] = $row['css_voter'];
+    // $info['css_member'] = $row['css_member'];
+    // $info['keywords_ids'] = explode(',', $row['keywords_ids']);
     $info['keywords'] = $row['keywords'];
-    $info['status'] = $row['status'];
+    // $info['status'] = $row['status'];
     $info['country'] = $row['country'];
-    $info['homepage'] = $row['homepage'];
-    $info['lab'] = $row['lab'];
-    $info['affiliation'] = $row['affiliation'];
-    $info['lab2'] = $row['lab2'];
-    $info['affiliation2'] = $row['affiliation2'];
-    $info['homepage'] = $row['homepage'];
-    $info['title'] = $row['title'];
-    $info['position'] = $row['position'];
-    $info['photo_url'] = $row['photo_url'];
-    $info['interests'] = $row['interests'];
-    $info['address'] = $row['address'];
-    $info['city'] = $row['city'];
-    $info['postal_code'] = $row['postal_code'];
-    $info['phone'] = $row['phone'];
-    $info['mobile'] = $row['mobile'];
-    $info['fax'] = $row['fax'];
-    $info['affiliation_acronym'] = $row['affiliation_acronym'];
-    $scholars[$row['unique_id']] = $info;
+    // $info['homepage'] = $row['homepage'];
+    $info['lab'] = $row['team_lab'];
+    $info['affiliation'] = $row['institution'];
+    // $info['lab2'] = $row['lab2'];
+    // $info['affiliation2'] = $row['affiliation2'];
+    // $info['homepage'] = $row['homepage'];
+    $info['title'] = $row['jobtitle'];
+    $info['position'] = $row['jobtitle'];
+    // $info['photo_url'] = $row['photo_url'];
+    $info['pic_file'] = $row['pic_file'];
+    $info['interests'] = $row['interests_text'];
+    // $info['address'] = $row['address'];
+    // $info['city'] = $row['city'];
+    // $info['postal_code'] = $row['postal_code'];
+    // $info['phone'] = $row['phone'];
+    // $info['mobile'] = $row['mobile'];
+    // $info['fax'] = $row['fax'];
+    // $info['affiliation_acronym'] = $row['affiliation_acronym'];
+    $scholars[$row['doors_uid']] = $info;
 }
 
 }
@@ -210,7 +219,7 @@ Contributions and ideas are welcome to improve this directory.
 
 echo $meta.' '.$stats.'</head>';
 if (count($scholars)==0){
-echo  '<h2>Sorry, '.$target_name.' did not mentioned any keywords ... we cannot process it\'s network.</h2><br/>
+echo  '<h2>Sorry, '.$target_name.' did not mention any keywords ... we cannot process its network.</h2><br/>
     If you are '.$target_name.', you can  <a href="http://main.csregistry.org/Whoswhodata"  target="_BLANK">modify your profile</a> and see your
         network in few minutes.';
 }else{

search_filter.php

 <?php
 
 /*
- * Génère le gexf des scholars à partir de la base sqlite
+ * Génère le gexf des scholars à partir de la base mysql
  */
 include("parametres.php");
 //include("../common/library/fonctions_php.php");
 include("normalize.php");
 
 
-$base = new PDO("sqlite:" . $dbname);
+$base = new PDO($dsn, $user, $pass, $opt);
 
 $category = trim(strtolower($_GET['category']));
 $term =  trim(strtolower($_GET['term']));
@@ -20,7 +20,10 @@ if ($category == 'country' || $category == 'countries') {
   $cat = "country";
   $query = 'LIKE upper(\''.strtoupper($q).'\')';
 } elseif ($category == 'organization' || $category == 'organizations') {
-  $cat = "affiliation";
+
+  // POSSIBLE: `concat(institution, ", ", IFNULL(team_lab, ""))``
+  //           (change in $cat here and in print_directory args downstream)
+  $cat = 'institution';
   $query = 'LIKE upper(\''.strtoupper($q).'\')';
 } elseif ($category == 'keyword' || $category == 'keywords') {
   $cat = "keywords";
@@ -29,7 +32,7 @@ if ($category == 'country' || $category == 'countries') {
   $cat = "tags";
   $query = 'LIKE upper(\''.strtoupper($q).'\')';
 } elseif ($category == 'labs' || $category == 'laboratories' || $category == 'laboratory') {
-  $cat = "lab";
+  $cat = "team_lab";
   $query = 'LIKE upper(\''.strtoupper($q).'\')';
 } else {
   echo ("ERROR");
@@ -41,17 +44,18 @@ $filtered = array (
 );
 function filter_word($value) {
   if ($value == null) return true;
-  return ! in_array(strtolower($value),$filtered); 
+  return ! in_array(strtolower($value),$filtered);
 }
 
-$req = "SELECT ".$cat." AS key, count(".$cat.") AS value FROM scholars WHERE ".$cat." ".$query." GROUP BY ".$cat." ORDER BY value DESC";
+$req = "SELECT ".$cat." AS clef, count(".$cat.") AS value FROM comex_registrations WHERE ".$cat." ".$query." GROUP BY ".$cat." ORDER BY value DESC";
+// echo $req;
 $results = array();
 $i = 0;
 foreach ($base->query($req) as $row) {
   $nb = $row['value'];
   if ($cat == "keywords" || $cat == "tags") {
     //echo "in keywords\n";
-     $words = explode(",", $row["key"]);
+     $words = explode(",", $row["clef"]);
     foreach ($words as $word) {
 
     $pos = strpos($word,$term);
@@ -69,9 +73,9 @@ foreach ($base->query($req) as $row) {
         }
     }
   } else {
-    $word = $row["key"];
+    $word = $row["clef"];
      if ($cat == "country") {
-        $word = normalize_country($word);  
+        $word = normalize_country($word);
     }
 
     if (filter_word($word)) {
@@ -98,7 +102,7 @@ foreach($results as $key => $value) {
         'label' => $key,
        // 'value' => $value,
        'score' => $value,
-       
+
      // F*** it, I'll put the meta data here...
        'category' => $cat,
           "term" => $term,
@@ -110,4 +114,4 @@ foreach($results as $key => $value) {
 $i = 0;
 
 echo json_encode($completion);
-?>
+?>
\ No newline at end of file

search_scholar.php

@@ -8,79 +8,114 @@ include("parametres.php");
 include("normalize.php");
 
 
-$base = new PDO("sqlite:" . $dbname);
 
-$category = trim(strtolower($_GET['category']));
-$login = trim(strtolower($_GET['login']));
-$q = "%".sanitize_input($login)."%";
+// ===================== SQL connect =====================
+$base = new PDO($dsn, $user, $pass, $opt);
+// ==================== /SQL connect =====================
 
-//echo "category: ".$category.";";
-//echo "login: ".$login.";";
-//echo "q: ".$q.";";
 
-$cat = '';
-$query = '';
-if ($category == 'login') {
-  $cat = "unique_id";
-  $query = 'unique_id LIKE upper(\''.strtoupper($q).'\')';
-} elseif ($category == 'firstname') {
-  $cat = "firstname";
-  $query = 'first_name LIKE upper(\''.strtoupper($q).'\')';
-} elseif ($category == 'lastname') {
-  $cat = "lastname";
-  $query = 'last_name LIKE upper(\''.strtoupper($q).'\')';
-} else {
-  echo ("ERROR");
-  exit();
-}
 
-$filtered = array (
-  "yes", "1", "0", "nvgfpmeilym", "no", "mr", "ms", "", " ", "   "
-);
-function filter_word($value) {
-  if ($value == null) return true;
-  return ! in_array(strtolower($value),$filtered); 
-}
+// ==================== new retrieval ======================
+$login = trim(strtolower($_GET['login']));
+$q = "%".sanitize_input($login)."%";
 
-$req = "SELECT unique_id, first_name, last_name,nb_keywords FROM scholars WHERE ".$query." GROUP BY unique_id";
-#echo "req: ".$req.";";
+$query = 'concat(first_name, " ", IFNULL(middle_name,""), " ", last_name) LIKE "%'.$q.'%"';
+
+$req = "SELECT doors_uid, email, first_name, last_name, keywords FROM comex_registrations WHERE ".$query." GROUP BY doors_uid";
+// echo "req: ".$req.";";
 $results = array();
 $i = 0;
 $res = $base->query($req);
 
-foreach ($res as $row) {
-  if ($row["nb_keywords"]==0){
-      $row["nb_keywords"]=' (no keyword to map)';
-  }  else {
-      $row["nb_keywords"]='';
-  }
-  array_push($results,$row);
-}
-
-$nbresults = sizeof($results);
-$results = array_slice($results,0,20);
-$nbresults2 = sizeof($results);
 $completion = array(
-   "results" => array()
+   "results" => array(),
+   "query" => $login
 );
 
-
-foreach($results as $row) {
+foreach($res as $row) {
      array_push($completion["results"], array(
-        'id' => $row["unique_id"],
+        'id' => $row["doors_uid"],
         'term' => $login,
         'firstname' => $row["first_name"],
-        'lastname' => $row["last_name"].$row["nb_keywords"],
-       'score' => 1,
-       
-	   // F*** it, I'll put the meta data here...
-       'category' => $cat,
-   "size" => $nbresults2,
-   "total" => $nbresults,
-   "remaining" => ($nbresults - $nbresults2)
+        'lastname' => $row["last_name"],
       ));
 }
-$i = 0;
+// ==================== /new retrieval =====================
+
+// $base = new PDO("sqlite:" . $dbname);
+//
+// $category = trim(strtolower($_GET['category']));
+// $login = trim(strtolower($_GET['login']));
+// $q = "%".sanitize_input($login)."%";
+//
+// //echo "category: ".$category.";";
+// //echo "login: ".$login.";";
+// //echo "q: ".$q.";";
+//
+// $cat = '';
+// $query = '';
+// if ($category == 'login') {
+//   $cat = "unique_id";
+//   $query = 'unique_id LIKE upper(\''.strtoupper($q).'\')';
+// } elseif ($category == 'firstname') {
+//   $cat = "firstname";
+//   $query = 'first_name LIKE upper(\''.strtoupper($q).'\')';
+// } elseif ($category == 'lastname') {
+//   $cat = "lastname";
+//   $query = 'last_name LIKE upper(\''.strtoupper($q).'\')';
+// } else {
+//   echo ("ERROR");
+//   exit();
+// }
+//
+// $filtered = array (
+//   "yes", "1", "0", "nvgfpmeilym", "no", "mr", "ms", "", " ", "   "
+// );
+// function filter_word($value) {
+//   if ($value == null) return true;
+//   return ! in_array(strtolower($value),$filtered);
+// }
+//
+// $req = "SELECT unique_id, first_name, last_name,nb_keywords FROM scholars WHERE ".$query." GROUP BY unique_id";
+// #echo "req: ".$req.";";
+// $results = array();
+// $i = 0;
+// $res = $base->query($req);
+//
+// foreach ($res as $row) {
+//   if ($row["nb_keywords"]==0){
+//       $row["nb_keywords"]=' (no keyword to map)';
+//   }  else {
+//       $row["nb_keywords"]='';
+//   }
+//   array_push($results,$row);
+// }
+//
+// $nbresults = sizeof($results);
+// $results = array_slice($results,0,20);
+// $nbresults2 = sizeof($results);
+// $completion = array(
+//    "results" => array()
+// );
+//
+//
+// foreach($results as $row) {
+//      array_push($completion["results"], array(
+//         'id' => $row["unique_id"],
+//         'term' => $login,
+//         'firstname' => $row["first_name"],
+//         'lastname' => $row["last_name"].$row["nb_keywords"],
+//        'score' => 1,
+//
+//        // TODO change: general metadata is uselessly copied x nbresults
+// 	   // F*** it, I'll put the meta data here...
+//        'category' => $cat,
+//    "size" => $nbresults2,
+//    "total" => $nbresults,
+//    "remaining" => ($nbresults - $nbresults2)
+//       ));
+// }
+// $i = 0;
 
 echo json_encode($completion);
-?>
+?>
\ No newline at end of file