fix apollo urls

README.md

@@ -23,6 +23,6 @@ services:
       ENABLE_GO: 1 # 1 to add links to GO summary, some/url to specify the path (relative to tripal BASE_URL_PATH), 0 to disable it
       JBROWSE_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and jbrowse dataset id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
       # By default APOLLO_LINKS == JBROWSE_LINKS
-      APOLLO_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and apollo dataset id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
+      APOLLO_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and apollo organism id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
     [...]
 ```

templates/tripal_feature_alignments.tpl.php

@@ -144,7 +144,7 @@ if(count($alignments) > 0){ ?>
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
                 if (substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
-                    $url = "/apollo/jbrowse?data=data/".$d[1]."&";
+                    $url = "/apollo/annotator/loadLink?organism=".$d[1]."&";
                     $found_link = true;
                     break;
                 }
@@ -153,7 +153,7 @@ if(count($alignments) > 0){ ?>
 
         if (!$found_link) {
             if (getenv('ENABLE_JBROWSE') == "1")
-                $url = '/apollo/jbrowse?';
+                $url = '/apollo/annotator/loadLink?';
             else {
                 // Some url was given
                 $url = getenv('ENABLE_JBROWSE');