backport fixes from bbip

templates/page--front.tpl.php

@@ -157,7 +157,7 @@
                         <?php if (getenv('ENABLE_JBROWSE')): ?>
                             <?php
                                 if (getenv('ENABLE_JBROWSE') == "1")
-                                    $url = '/jbrowse';
+                                    $url = '/jbrowse/';
                                 else
                                     $url = getenv('ENABLE_JBROWSE');
                             ?>

templates/page.tpl.php

@@ -168,7 +168,7 @@ if (isset($node) && $node->type == "chado_feature") {
                         <?php if (getenv('ENABLE_JBROWSE')): ?>
                             <?php
                                 if (getenv('ENABLE_JBROWSE') == "1")
-                                    $url = '/jbrowse';
+                                    $url = '/jbrowse/';
                                 else
                                     $url = getenv('ENABLE_JBROWSE');
                             ?>

templates/tripal_feature_alignments.tpl.php

@@ -72,6 +72,17 @@ if(count($alignments) > 0){ ?>
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
 
+  if (getenv('ENABLE_APOLLO') == "1")
+      $url_apollo_base = $GLOBALS['base_url'] . '/apollo/annotator/loadLink?';
+  else {
+      // Some url was given
+      $url_apollo_base = getenv('ENABLE_APOLLO');
+      if (strpos($url_apollo_base, '?') !== false)
+          $url_apollo_base .= '&';
+      else
+          $url_apollo_base .= 'annotator/loadLink?';
+  }
+
   foreach ($alignments as $alignment){
     $feature_name = $alignment->name;
     if (property_exists($alignment, 'nid')) {
@@ -111,7 +122,7 @@ if(count($alignments) > 0){ ?>
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
                 if ($cur_org === $d[0] || substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
-                    $url = "/jbrowse?data=data/".$d[1]."&";
+                    $url = "/jbrowse/?data=data/".$d[1]."&";
                     $found_link = true;
                     break;
                 }
@@ -120,7 +131,7 @@ if(count($alignments) > 0){ ?>
 
         if (!$found_link) {
             if (getenv('ENABLE_JBROWSE') == "1")
-                $url = '/jbrowse?';
+                $url = '/jbrowse/?';
             else {
                 // Some url was given
                 $url = getenv('ENABLE_JBROWSE');
@@ -145,7 +156,7 @@ if(count($alignments) > 0){ ?>
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
                 if ($cur_org === $d[0] || substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
-                    $url = "/apollo/annotator/loadLink?organism=".$d[1]."&";
+                    $url = $url_apollo_base."organism=".$d[1]."&";
                     $found_link = true;
                     break;
                 }
@@ -153,21 +164,12 @@ if(count($alignments) > 0){ ?>
         }
 
         if (!$found_link) {
-            if (getenv('ENABLE_APOLLO') == "1")
-                $url = $GLOBALS['base_url'] . '/apollo/annotator/loadLink?';
-            else {
-                // Some url was given
-                $url = getenv('ENABLE_APOLLO');
-                if (strpos($url, '?') !== false)
-                    $url .= '&';
-                else
-                    $url .= 'annotator/loadLink?';
-            }
             $org_name = $feature->organism_id->genus . ' ' . $feature->organism_id->species;
             $apollo_org = "&organism=" . $org_name;
             if (array_key_exists($feature->organism_id->organism_id, $genome_versions)) {
               $apollo_org .= ' ' . $genome_versions[$feature->organism_id->organism_id]->version;
             }
+            $url = $url_apollo_base.$apollo_org;
         }
 
         $feature_loc .= " &nbsp;&nbsp; View in <a href='".$url."loc=".$alignment->name."%3A".($alignment->fmin + 1)."..".$alignment->fmax.$apollo_org."'>Apollo</a>";