Fix a bug for parsing keg files. When there is a single quote ' in the value (e.g. 3'-deoxyribose), the SQL insertion to analysisprop fails. Single quote was replaced by html code (') before executing the SQL statement. Also, tabs in the code are replaced by spaces for proper formatting.

tripal_analysis_kegg/tripal_analysis_kegg.module

@@ -642,12 +642,13 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
    }
    $dir_handle = @opendir($hierdir) or die("Unable to open $hierdir");
    $total_files = count(glob($hierdir . '/*.*'));
+   print "There are $total_files keg file(s).\n";
    $interval = intval($total_files * 0.01);
    $no_file = 0;
    while ($file = readdir($dir_handle)) {
 
       if(preg_match("/^.*\.keg/",$file)){
-      	// Update the progress
+         // Update the progress
          if ($no_file % $interval == 0) {
             $percentage = (int) ($no_file / $total_files * 100);
             tripal_job_set_progress($job_id, $percentage);
@@ -655,7 +656,7 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
          }
          $no_file ++;
          
-         # print "Parsing $hierdir/$file\n";
+         # $type variable will be set in tripal_analysis_kegg_parse_keg_file()
          $content = tripal_analysis_kegg_parse_keg_file("$hierdir/$file",$type,$analysis_id, $base_path);
 
          # add the item to the database
@@ -665,7 +666,8 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
             //------------------------------------------------------
             // Make sure the same value doesn't exist before inserting into chado
             $sql = "SELECT value
-                    FROM {analysisprop}                     WHERE analysis_id = %d
+                    FROM {analysisprop}
+                    WHERE analysis_id = %d
                     AND type_id = (SELECT cvterm_id 
                                    FROM {cvterm} CVT 
                                    INNER JOIN CV ON CVT.cv_id = CV.cv_id
@@ -675,18 +677,27 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
             $previous_db = db_set_active('chado');
             $oldvalue = db_result(db_query($sql, $analysis_id, $type));
             db_set_active($previous_db);
+            
+            // Insert the content
             if ($oldvalue != $content) {
-               $sql = "
-	             INSERT INTO {analysisprop} (analysis_id, type_id, value) VALUES
-	             (%d,
-	              (SELECT cvterm_id 
-	               FROM {cvterm} CVT 
-	               INNER JOIN CV ON CVT.cv_id = CV.cv_id
-	               WHERE CV.name = 'tripal' AND CVT.name = '%s'),
-	              '%s')";   
-               $previous_db = db_set_active('chado');
-               db_query($sql,$analysis_id,$type,$content);
-               db_set_active($previous_db);
+            	
+            	$previous_db = db_set_active('chado'); // Use chado database
+            	// Get type_id for the BRITE term
+            	$sql = "SELECT cvterm_id 
+                       FROM {cvterm} CVT 
+                       INNER JOIN CV ON CVT.cv_id = CV.cv_id
+                       WHERE CV.name = 'tripal' AND CVT.name = '%s'";
+            	$brite_cvterm_id = db_result(db_query($sql, $type)); 
+
+            	// Replace all single quote as HTML code before insert
+            	$content = preg_replace("/\'/", "'", $content);
+            	
+            	// Insert the value
+               $sql = "INSERT INTO {analysisprop} (analysis_id, type_id, value) 
+                       VALUES (%d, %d,'$content')";   
+               
+               db_query($sql, $analysis_id, $brite_cvterm_id);
+               db_set_active($previous_db); // Use drupal database
             }
             
          }
@@ -703,7 +714,10 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
    return;
 }
 /*******************************************************************************
- *
+ * Parse *.keg files. 
+ * Each file has a definition line. BRITE term is extracted * from this line 
+ * and added to chado as a cvterm. Tree structure for this cvterm is then 
+ * generated and saved to analysisfeature and analysisfeatureprop tables.
  */
 function tripal_analysis_kegg_parse_keg_file ($file,&$type,$analysis_id, $base_path){
    $handle = fopen($file,'r');
@@ -762,7 +776,7 @@ function tripal_analysis_kegg_parse_keg_file ($file,&$type,$analysis_id, $base_p
       // add id to <a> tags so we can link kegg.gif to it in tripal_analysis_kegg.css
       $matches[2] = preg_replace("/<a href=\"/i","<a id=\"tripal_kegg_brite_links\" target=\"_blank\" href=\"",$matches[2]);
 
-      // extract the features that have been mapped to the various KEGG IDs
+      // extract the features that have been mapped to the KEGG IDs
       if(preg_match("/^(.*?);\s*(\<a.+)/",$matches[2],$mat)){
          // Find cvterm_id for 'kegg_brite_data'
          $sql = "SELECT cvterm_id 
@@ -857,10 +871,10 @@ function tripal_analysis_kegg_nodeapi(&$node, $op, $teaser, $page) {
 
          // Abort if this node is not one of the types we should show.
          if (!in_array($node->type, $types_to_show, TRUE)) {
-         	// Turn the menu off if it's on
+            // Turn the menu off if it's on
             $box_status = variable_get("tripal_analysis_kegg-box-results","menu_off");
             if (strcmp($box_status,"menu_on")==0 && $node->type =='chado_organism'){
-            	variable_set("tripal_analysis_kegg-box-results","menu_off");
+               variable_set("tripal_analysis_kegg-box-results","menu_off");
             }
             break;
          }
@@ -870,13 +884,13 @@ function tripal_analysis_kegg_nodeapi(&$node, $op, $teaser, $page) {
             // add the library to the organism/feature search indexing
             if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
                $node->content['tripal_analysis_kegg_search_index'] = array(
-						'#value' => theme('tripal_analysis_kegg_search_index',$node),
-						'#weight' => 6,
+                  '#value' => theme('tripal_analysis_kegg_search_index',$node),
+                  '#weight' => 6,
                );
             } else if ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
                $node->content['tripal_analysis_kegg_search_result'] = array(
-						'#value' => theme('tripal_analysis_kegg_search_result',$node),
-						'#weight' => 6,
+                  '#value' => theme('tripal_analysis_kegg_search_result',$node),
+                  '#weight' => 6,
                );
             } else {
                // Show KEGG BRITE on an analysis page OR KEGG info box on a feature page
@@ -1145,8 +1159,8 @@ function tripal_analysis_kegg_organism_add($node) {
       $content .= "
       <div class=\"tripal_kegg_summary-info-box\">
         <div class=\"tripal_expandableBox\">
-	       <h3>KEGG Analysis Results</h3>
-	     </div>
+          <h3>KEGG Analysis Results</h3>
+        </div>
         <div class=\"tripal_expandableBoxContent\">
       ";
    } 
@@ -1164,7 +1178,7 @@ function tripal_analysis_kegg_organism_add($node) {
 
    if(user_access('access administrative pages')){
       $link = url("tripal_toggle_box_menu/tripal_analysis_kegg/results/$node->nid");
-   	if(strcmp($box_status,"menu_off")==0){
+      if(strcmp($box_status,"menu_off")==0){
          $content .= "<br><a href=\"$link\">Show on menu</a>";
       } else {
          $content .= "<br><a href=\"$link\">Remove from menu</a>";