Updated custom linkouts to return an already rendered link. This avoids a potential url-encoding bug

includes/blast_ui.linkouts.inc

@@ -32,7 +32,7 @@
 
     // Do some simple steps to generate the suffix based on the $hit.
 
-    return $url_prefix . $url_postfix;
+    return l('url name', $url_prefix . $url_postfix);
   }
  * @endcode
  *
@@ -146,12 +146,17 @@ function blast_ui_blast_linkout_info() {
  *   supported by this particular link-out type.
  *
  * @return
- *   The URL string to be linked to.
+ *   An html link.
  */
 function tripal_blast_generate_linkout_link($url_prefix, $hit, $info, $options = array()) {
 
   if (isset($hit->{'linkout_id'})) {
-    return $url_prefix . $hit->{'linkout_id'};
+    $hit_url = $url_prefix . $hit->{'linkout_id'};
+    return l(
+      $hit->{'linkout_id'},
+      $hit_url,
+      array('attributes' => array('target' => '_blank'))
+    );
   }
   else {
     return FALSE;
@@ -181,7 +186,7 @@ function tripal_blast_generate_linkout_link($url_prefix, $hit, $info, $options =
  *   supported by this particular link-out type.
  *
  * @return
- *   The URL string to be linked to.
+ *   An html link.
  */
 function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $options = array()) {
 
@@ -209,13 +214,13 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
   // Now we are finally ready to build the URL.
   // First lets set the location of the hit so the GBrowse focuses in on the correct region.
   $query = array();
-  $query['ref'] = 'ref=' . $hit->{'linkout_id'};
-  $query['start'] = 'start=' . $min;
-  $query['stop'] = 'stop=' . $max;
-  
+  $query['ref'] = $hit->{'linkout_id'};
+  $query['start'] = $min;
+  $query['stop'] = $max;
+
   // Next we want to add our BLAST hit to the GBrowse.
   $query['add'] = format_string(
-    'add=!ref+!trackname+!featurename+!hspcoords',
+    '!ref !trackname !featurename !hspcoords',
     array(
       '!ref' => $hit->{'linkout_id'},
       '!trackname' => 'BLAST',
@@ -225,14 +230,24 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
   );
   
   // Highlight our newly added feature.
-  $query['highlight'] = format_string(
-    'h_feat=!featurename',
-    array('!featurename' => 'BlastHit')
+  $query['h_feat'] = 'BlastHit';
+
+  $hit_url = $url_prefix; //. $url_postfix;
+  $url = l(
+    $hit->{'linkout_id'},
+    $hit_url,
+    array( 
+      'query' => $query,
+      'attributes' => array('target' => '_blank')
+    )
   );
   
-  $url_postfix = implode(';', $query);
+  // For some reason GBrowse expects semi-colons (;) to delineate query paramters 
+  // whereas Drupal throws ampherstands (&) in. This is to fix that.
+  $url = str_replace('&',';', $url);
+  
+  return $url;
 
-  return $url_prefix . $url_postfix;
 }
 
 /**
@@ -271,7 +286,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
  *   supported by this particular link-out type.
  *
  * @return
- *   The URL string to be linked to.
+ *   An html link.
  */
 function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $options = array()) {
 
@@ -351,5 +366,10 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
 
   $url_postfix = implode('&', $jbrowse_query);
 
-  return $url_prefix . $url_postfix;
+  $hit_url = $url_prefix . $url_postfix;
+  return l(
+    $hit->{'linkout_id'},
+    $hit_url,
+    array('attributes' => array('target' => '_blank'))
+  );
 }

theme/blast_report.tpl.php

@@ -240,7 +240,7 @@ and click the <em>target name </em> to get more information about the target hit
             
               // Allow custom functions to determine the URL to support more complicated
               // link-outs rather than just using the tripal database prefix.
-              $hit_url = call_user_func(
+              $hit_name = call_user_func(
                 $url_function,
                 $linkout_urlprefix,
                 $hit,
@@ -252,21 +252,6 @@ and click the <em>target name </em> to get more information about the target hit
                   'Target'     => $blast_job->blastdb->db_name,
                 )
               );
-
-              // Create Link.
-              if ($hit_url) {
-                // It is important to url-encode links, especially in this case,
-                // since jbrowse links have double quotes in them which result in
-                // truncated links due to <a href="yoururl"></a> (notice the double quotes).
-                $hit_name = l(
-                  $hit->{'linkout_id'},
-                  $hit_url,
-                  array('attributes' => array('target' => '_blank'))
-                );
-                
-                //HACK: change '%3F' to '?' to work around a Drupal bug"
-                $hit_name = str_replace('%3F', '?', $hit_name);
-              }
             }
                         
             // Replace the target name with the link.