First attempt at full embed -not working yet.

tripal_jbrowse/theme/node--jbrowse-instance.tpl.php

@@ -2,98 +2,16 @@
 
 /**
  * @file
- * Bartik's theme implementation to display a node.
+ * JBrowse Instance page
  *
  * Available variables:
- * - $title: the (sanitized) title of the node.
- * - $content: An array of node items. Use render($content) to print them all,
- *   or print a subset such as render($content['field_example']). Use
- *   hide($content['field_example']) to temporarily suppress the printing of a
- *   given element.
- * - $user_picture: The node author's picture from user-picture.tpl.php.
- * - $date: Formatted creation date. Preprocess functions can reformat it by
- *   calling format_date() with the desired parameters on the $created variable.
- * - $name: Themed username of node author output from theme_username().
- * - $node_url: Direct URL of the current node.
- * - $display_submitted: Whether submission information should be displayed.
- * - $submitted: Submission information created from $name and $date during
- *   template_preprocess_node().
- * - $classes: String of classes that can be used to style contextually through
- *   CSS. It can be manipulated through the variable $classes_array from
- *   preprocess functions. The default values can be one or more of the
- *   following:
- *   - node: The current template type; for example, "theming hook".
- *   - node-[type]: The current node type. For example, if the node is a
- *     "Blog entry" it would result in "node-blog". Note that the machine
- *     name will often be in a short form of the human readable label.
- *   - node-teaser: Nodes in teaser form.
- *   - node-preview: Nodes in preview mode.
- *   The following are controlled through the node publishing options.
- *   - node-promoted: Nodes promoted to the front page.
- *   - node-sticky: Nodes ordered above other non-sticky nodes in teaser
- *     listings.
- *   - node-unpublished: Unpublished nodes visible only to administrators.
- * - $title_prefix (array): An array containing additional output populated by
- *   modules, intended to be displayed in front of the main title tag that
- *   appears in the template.
- * - $title_suffix (array): An array containing additional output populated by
- *   modules, intended to be displayed after the main title tag that appears in
- *   the template.
- *
- * Other variables:
- * - $node: Full node object. Contains data that may not be safe.
- * - $type: Node type; for example, story, page, blog, etc.
- * - $comment_count: Number of comments attached to the node.
- * - $uid: User ID of the node author.
- * - $created: Time the node was published formatted in Unix timestamp.
- * - $classes_array: Array of html class attribute values. It is flattened
- *   into a string within the variable $classes.
- * - $zebra: Outputs either "even" or "odd". Useful for zebra striping in
- *   teaser listings.
- * - $id: Position of the node. Increments each time it's output.
- *
- * Node status variables:
- * - $view_mode: View mode; for example, "full", "teaser".
- * - $teaser: Flag for the teaser state (shortcut for $view_mode == 'teaser').
- * - $page: Flag for the full page state.
- * - $promote: Flag for front page promotion state.
- * - $sticky: Flags for sticky post setting.
- * - $status: Flag for published status.
- * - $comment: State of comment settings for the node.
- * - $readmore: Flags true if the teaser content of the node cannot hold the
- *   main body content.
- * - $is_front: Flags true when presented in the front page.
- * - $logged_in: Flags true when the current user is a logged-in member.
- * - $is_admin: Flags true when the current user is an administrator.
- *
- * Field variables: for each field instance attached to the node a corresponding
- * variable is defined; for example, $node->body becomes $body. When needing to
- * access a field's raw values, developers/themers are strongly encouraged to
- * use these variables. Otherwise they will have to explicitly specify the
- * desired field language; for example, $node->body['en'], thus overriding any
- * language negotiation rule that was previously applied.
- *
- * @see template_preprocess()
- * @see template_preprocess_node()
- * @see template_process()
+ *  - url_prefix: the URL without parameters for the JBrowse to be embedded.
+ *  - location: the location to display by default
+ *  - tracks: a comma-separated list of tracks to display by default
+ *  - url: the full URL for the JBrowse you would like to embed
  */
 ?>
 
-<?php
-  // Determine the URL of the JBrowse based on the node properties
-  $url = $node->field_jburl['und'][0]['url'];
-  $location = (!empty($node->field_jbloc)) ? $node->field_jbloc['und'][0]['safe_value'] : '';
-  $tracks = (!empty($node->field_jbtracks)) ? $node->field_jbtracks['und'][0]['safe_value'] : '';
-
-  $url = "$url/?q=loc=$location&tracks=$tracks";
-?>
-
-<style>
-iframe {
-  min-height: 600px;
-}
-</style>
-
 <div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
 
   <?php if (!$page): ?>
@@ -104,10 +22,12 @@ iframe {
   <?php print render($title_suffix); ?>
 
   <div class="content clearfix"<?php print $content_attributes; ?>>
-    <div id="JBrowseInstance">
-      <iframe src="<?php print $url;?>" width="100%" height="100%">
-      </iframe>
+    <div class="jbrowse" id="GenomeBrowser">
+      <div id="LoadingScreen" style="padding: 50px;">
+        <h1>Loading...</h1>
+      </div>
     </div>
+    <div style="display: none">JBrowseDefaultMainPage</div>
   </div>
 
 </div>

tripal_jbrowse/tripal_jbrowse.module

@@ -19,4 +19,38 @@ function tripal_jbrowse_theme($existing, $type, $theme, $path) {
   );
 
   return $items;
+}
+
+/**
+ * Implements node preprocess hook.
+ */
+function tripal_jbrowse_preprocess_node(&$vars) {
+
+  if ($vars['node']->type == 'jbrowse_instance') {
+
+    $node = $vars['node'];
+
+    // Determine the URL of the JBrowse based on the node properties
+    $vars['url_prefix'] = $node->field_jburl['und'][0]['url'];
+    $vars['location'] = (!empty($node->field_jbloc)) ? $node->field_jbloc['und'][0]['safe_value'] : '';
+    $vars['tracks'] = (!empty($node->field_jbtracks)) ? $node->field_jbtracks['und'][0]['safe_value'] : '';
+    $vars['url'] = $vars['url_prefix'] . "/?q=loc=" . $vars['location'] . "&tracks=" . $vars['tracks'];
+
+    // Add inline JS for jbrowse to display an error.
+    drupal_add_js('
+      window.onerror=function(msg){
+          if( document.body )
+              document.body.setAttribute("JSError",msg);
+      }
+      if(window.process&&process.versions&&process.versions.electron) {
+          window.electronRequire = require;
+          delete window.require;
+      }', 'inline');
+
+    // Currently hardcoding the path just to get it working ;-)
+    // My JBrowse is just unpacked in the files directory as you can see below.
+    // @error failing to load chunks. Look into how to set root path for webpack?
+    drupal_add_js('sites/default/files/JBrowse-1.14.1/dist/main.bundle.js');
+
+  }
 }