tripal_jbrowse/tripal_jbrowse_page/tripal_jbrowse_page.module

<?php

// API.
require_once 'includes/tripal_jbrowse_page.api.inc';

// Include files.
require_once 'includes/tripal_jbrowse_page.listing.inc';

/**
 * Implements hook_menu().
 */
function tripal_jbrowse_page_menu() {
  $items = [];

  $items['jbrowse'] = [
    'title' => 'JBrowse',
    'description' => 'A listing of available JBrowse instances.',
    'page callback' => 'tripal_jbrowse_page_listing_page',
    'access arguments' => ['access content'],
    'type' => MENU_NORMAL_ITEM,
  ];

  $instances = tripal_jbrowse_mgmt_get_instances();
  foreach ($instances as $instance) {

    $path = 'jbrowse/'.$instance->organism->genus . '/' . $instance->organism->species;
    $items[$path] = [
      'title' => $instance->title,
      'description' => $instance->description,
      'page callback' => 'tripal_jbrowse_page_page',
      'page arguments' => [1, 2],
      'access arguments' => ['access content'],
      'type' => MENU_NORMAL_ITEM,
    ];
  }

  return $items;
}

/**
 * Implements hook_theme().
 */
function tripal_jbrowse_page_theme($existing, $type, $theme, $path) {

  $items = array(
    'jbrowse_instance_public_listing' => array(
      // Don't specify the path in the template name.
      // Unless you have your template inside a directory within this module.
      'template' =>  'theme/jbrowse-instance--public-listing',
      'variables' => array('instances' => []),
    ),
  );

  return $items;
}

/**
 * Redirect to the JBrowse Instance.
 */
function tripal_jbrowse_page_page($genus, $species) {

  $instance = tripal_jbrowse_page_get_instance_id([
    'genus' => $genus,
    'species' => $species
  ],
  ['load_instance' => TRUE]);

  $query_params = tripal_jbrowse_mgmt_build_http_query($instance);
  $settings = tripal_jbrowse_mgmt_get_settings();

  $url = url($settings['link'],['query' => $query_params]);
  drupal_goto($url, array('external' => TRUE));

  return '';
}