index-compiled.php

<!--<?php

ini_set( 'session.cookie_httponly', 1 );
session_start();

const SETTINGS_EXPIRATION_TIME = 2592000; // One month in seconds
const DEFAULT_SETTINGS_ARG = 'default';
const DEFAULT_SETTINGS_FILE = 'src/epiviz/default-settings.js';
$settings_file = (array_key_exists('settings', $_COOKIE)) ? $_COOKIE['settings'] : DEFAULT_SETTINGS_FILE;
$curlopt_userpwd = '';

// If the request does not contain a value for useCookie, default value will be true
$useCookie = (array_key_exists('useCookie', $_REQUEST)) ? ($_REQUEST['useCookie'] === 'true' ? true : false) : true;

if(file_exists("token.txt")){
    $myfile = fopen("token.txt", "r");
    $curlopt_userpwd = fgets($myfile);
    fclose($myfile);
}

if (array_key_exists('settings', $_REQUEST)) {
    $settings_file = $_REQUEST['settings'];
    if ($settings_file == DEFAULT_SETTINGS_ARG) {
        $settings_file = DEFAULT_SETTINGS_FILE;
    }
    if($useCookie) {
        setcookie('settings', $settings_file, time() + SETTINGS_EXPIRATION_TIME);
    }
    else {
        //If useCookie is set to false, delete/expire existing cookies set by the last instance of epiviz
        setcookie('settings', $settings_file, time() - SETTINGS_EXPIRATION_TIME);
    }

}

$settings_gist = null;
if (array_key_exists('settingsGist', $_REQUEST)) {
    $settings_gist = $_REQUEST['settingsGist'];
    // Get cURL resource
    $curl = curl_init();

    // Set some options - we are passing in a useragent too here
    curl_setopt_array($curl, array(
        CURLOPT_RETURNTRANSFER => 1,
        CURLOPT_SSL_VERIFYPEER => false,
        CURLOPT_SSL_VERIFYHOST => false,
        CURLOPT_USERAGENT => 'epiviz',
        CURLOPT_URL => 'https://api.github.com/gists/' . $settings_gist,
        CURLOPT_USERPWD => $curlopt_userpwd // TODO: Change <token> to your personal access token
    ));

    // Send the request & save response to $resp
    $resp = curl_exec($curl);

    if ($resp) {
        $json = json_decode($resp, true);
        if (array_key_exists('files', $json)) {
            foreach ($json['files'] as $filename => $details) {
                if (!array_key_exists('type', $details) ||
                    stripos($details['type'], 'javascript') === FALSE ||
                    !array_key_exists('raw_url', $details)) { continue; }
                $settings_file = 'raw.php?url=' . urlencode($details['raw_url']);
                break;
            }
        }

        if($useCookie) {
            setcookie('settings', $settings_file, time() + SETTINGS_EXPIRATION_TIME);
        }
        else {
            //If useCookie is set to false, delete/expire existing cookies set by the last instance of epiviz
            setcookie('settings', $settings_file, time() - SETTINGS_EXPIRATION_TIME);
        }

    } else {
        $settings_gist = null;
    }

    // Close request to clear up some resources
    curl_close($curl);
}

$scripts = array();
if (array_key_exists('script', $_REQUEST)) {
    $scripts = $_REQUEST['script'];
}

$gists_map = array();
if (array_key_exists('gist', $_REQUEST)) {
    $gists = $_REQUEST['gist'];

    // Get cURL resource
    $curl = curl_init();

    if (!is_array($scripts)) { $scripts = array(); }
    foreach ($gists as $i => $gist) {
        // Set some options - we are passing in a useragent too here
        curl_setopt_array($curl, array(
            CURLOPT_RETURNTRANSFER => 1,
            CURLOPT_SSL_VERIFYPEER => false,
            CURLOPT_SSL_VERIFYHOST => false,
            CURLOPT_USERAGENT => 'epiviz',
            CURLOPT_URL => 'https://api.github.com/gists/' . $gist,
            CURLOPT_USERPWD => $curlopt_userpwd // TODO: Change <token> to your personal access token
        ));

        // Send the request & save response to $resp
        if (!$resp) { continue; }

        $json = json_decode($resp, true);
        if (!array_key_exists('files', $json)) { continue; }

        foreach ($json['files'] as $filename => $details) {
            if (!array_key_exists('type', $details) ||
                stripos($details['type'], 'javascript') === FALSE ||
                !array_key_exists('raw_url', $details)) { continue; }

            $script = 'raw.php?url=' . urlencode($details['raw_url']);
            $scripts[] = $script;
            $gists_map[$script] = $gist;
        }
    }

    // Close request to clear up some resources
    curl_close($curl);
}

// Insert here settings based on $_REQUEST.
// All those settings are saved/retrieved as cookies
// TODO: Later on, in javascript, modify cookie when location or workspace are modified
$setting_names = array('ws', 'workspace', 'seqName', 'start', 'end', 'useCookie');

$settings = array(); // Used for determining configuration of EpiViz

foreach ($setting_names as $setting) {
    $val = null;

    if($setting === 'useCookie'){
        $val = $useCookie;
    }

    if (isset($_COOKIE[$setting]) && $useCookie) {
        $val = $_COOKIE[$setting];
    }
    if (isset($_REQUEST[$setting])) {
        $val = $_REQUEST[$setting];

        if($useCookie) {
            setcookie($setting, $val, time() + SETTINGS_EXPIRATION_TIME);
        }
        else {
            //If useCookie is set to false, delete/expire existing cookies set by the last instance of epiviz
            setcookie($setting, $val, time() - SETTINGS_EXPIRATION_TIME);
        }
    }
    if ($val !== null) {
        $settings[$setting] = $val;
    }
}

$user = array_key_exists('user', $_SESSION) ? $_SESSION['user'] : null;
$debug = false;
if (array_key_exists('debug', $_GET) && $_GET['debug'] == 'true') {
    $debug = true;
    $user = array(
        'id' => 0, 'email' => null, 'oauth_uid' => 0, 'oauth_provider' => 'debug', 'full_name' => 'Debugger', 'oauth_username' => null,
        'website_url' => null, 'profile_url' => null, 'photo_url' => null, 'display_name' => 'Debugger', 'description' => null,
        'first_name' => null, 'last_name' => null, 'gender' => null, 'language' => null, 'age' => null, 'birth_day' => null,
        'birth_month' => null, 'birth_year' => null, 'email_verified' => null, 'phone' => null, 'address' => null,
        'country' => null, 'region' => null, 'city' => null, 'zip' => null);
    $_SESSION['user'] = $user;
} else if (isset($_SESSION['oauth_provider']) && $_SESSION['oauth_provider'] == 'debug') {
    $debug = false;
    $user = null;
    unset($_SESSION['user']);
}

?>-->
<!DOCTYPE html>
<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
    <meta name="description" content="Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.">
    <title>EpiViz 4</title>

    <link rel="shortcut icon" href="img/epiviz_2_icon.png"/>

    <!-- CSS -->
    <link href="css/fa/css/font-awesome.css" rel="stylesheet"/>
    <!-- Icons -->
    <link href="css/icomoon/epiviz-icons.css" rel="stylesheet"/>

    <!-- JQuery UI -->
    <link href="css/theme/jquery-ui-1.8.9.custom.css" rel="stylesheet"/>
    <link href="css/theme/jquery.ui.selectmenu.css" rel="stylesheet"/>
    <link href="css/theme/ui.panel.css" rel="stylesheet"/>
    <link href="css/theme/ui.multiselect.css" rel="stylesheet"/>
    <link href="css/farbtastic-color-picker/farbtastic.css" rel="stylesheet" />
    <link href="css/DataTables-1.9.4/media/css/demo_table.css" rel="stylesheet" />
    <link href="css/DataTables-1.9.4/media/css/demo_table_jui.css" rel="stylesheet" />
    <link href="src/lib/jquery/DataTables-1.9.4/extras/TableTools/media/css/TableTools.css" rel="stylesheet" />
    <link href="css/dropdown-check-list-1.4/css/ui.dropdownchecklist.standalone.css" rel="stylesheet" />
    <!-- Future tooltip: <link href="css/qtip/jquery.qtip.min.css" rel="stylesheet" />-->

    <!-- Code editor -->
    <link rel="stylesheet" href="css/codemirror-4.5/lib/codemirror.css">

    <!-- EpiViz CSS -->
    <link rel="stylesheet" type="text/css" href="css/main.css"/>
    <link rel="stylesheet" type="text/css" href="css/svg.css"/>

    <!-- Scripts -->

    <!-- JQuery and JQuery UI scripts -->
    <script src="src/lib/jquery/jquery-1.8.2.js"></script>
    <script src="src/lib/jquery/jquery-ui-1.9.1.custom.js"></script>
    <script src="src/lib/jquery/jquery.multi-accordion-1.5.3.js"></script>
    <script src="src/lib/jquery/jquery.ui.selectmenu.js"></script>
    <script src="src/lib/jquery/ui.panel.min.js"></script>
    <script src="src/lib/jquery/ui.multiselect.js"></script>
    <script src="src/lib/jquery/jquery.watermark.min.js"></script>
    <script src="src/lib/jquery/jquery.layout-latest.js"></script>
    <script src="src/lib/jquery/jquery.activity-indicator-1.0.0.min.js"></script>
    <script src="src/lib/jquery/farbtastic-color-picker/farbtastic.js"></script>
    <script src="src/lib/jquery/DataTables-1.9.4/media/js/jquery.dataTables.js"></script>
    <script src="src/lib/jquery/DataTables-1.9.4/extras/TableTools/media/js/ZeroClipboard.js"></script>
    <script src="src/lib/jquery/DataTables-1.9.4/extras/TableTools/media/js/TableTools.js"></script>
    <script src="src/lib/jquery/DataTables-1.9.4/extras/ColumnFilter/media/js/jquery.dataTables.columnFilter.js"></script>
    <script src="src/lib/jquery/dropdown-check-list-1.4/js/ui.dropdownchecklist.js"></script>
    <!-- Future tooltip: <script src="src/lib/qtip/jquery.qtip.min.js"></script>-->

    <!--<script src="//caja.appspot.com/caja.js"></script>-->

    <!-- Google Analytics -->
    <script src="src/lib/google-analytics/google-analytics.js"></script>

    <!-- D3 -->
    <script src="src/lib/d3/d3.v3.js"></script>

    <!-- String formatting -->
    <script src="src/lib/sprintf-0.6.js"></script>
    <script src="src/lib/jquery/globalize/globalize.js"></script>

    <!-- Expression evaluation -->
    <script src="src/lib/expression-parser/parser.js"></script>

    <!-- Code editor -->
    <script src="src/lib/codemirror-4.5/lib/codemirror.js"></script>
    <script src="src/lib/codemirror-4.5/addon/edit/matchbrackets.js"></script>
    <script src="src/lib/codemirror-4.5/addon/comment/continuecomment.js"></script>
    <script src="src/lib/codemirror-4.5/addon/comment/comment.js"></script>
    <script src="src/lib/codemirror-4.5/mode/javascript/javascript.js"></script>

    <!-- File upload: src/file-upload/webtoolkit.aim.js -->

    <!-- Google Closure -->
    <script src="src/lib/closure/goog/base.js"></script>
    <!-- <script src="src/lib/closure/goog/structs/collection.js"></script> -->

    <!-- lightweight es6 promises -->
    <script src="src/lib/es6-promise/Promise.js"></script>

    <!-- canvg -->
    <script src="src/lib/canvg/rgbcolor.js"></script>
    <script src="src/lib/canvg/StackBlur.js"></script>
    <script src="src/lib/canvg/canvg.js"></script>

    <!-- html2canvas -->
    <script src="src/lib/html2canvas/html2canvas.js"></script>
    <script src="src/lib/html2canvas/html2canvas.svg.js"></script>

    <!-- jsPDF -->
    <script src="src/lib/jsPDF/BlobBuilder.js"></script>
    <script src="src/lib/jsPDF/FileSaver.js"></script>
    <script src="src/lib/jsPDF/jspdf.debug.js"></script>

    <!-- AnnoJS -->
    <link rel="stylesheet" type="text/css" href="src/lib/annojs/anno.css"/>
    <script src="src/lib/annojs/anno.js"></script>

    <script src="epiviz-compiled-jar.js"></script>
    <!-- Dynamic initializations -->


    <script src="<?php echo $settings_file; ?>"></script>
    <script src="site-settings.js"></script>
    <script>
          var items;
      <?php
          foreach ($settings as $setting => $val) {
          if (!is_array($val)) {
      ?>
          epiviz.Config.SETTINGS['<?php echo $setting; ?>'] = <?php echo json_encode($val); ?>;
      <?php
          } else {
      ?>
          items = [];
      <?php
          foreach ($val as $item) {
      ?>
          items.push(<?php echo json_encode($item); ?>);
      <?php
          }
      ?>
          epiviz.Config.SETTINGS['<?php echo $setting; ?>'] = items;
      <?php
          }
          }
      ?>

      <?php
          if ($user === null) {
      ?>
          epiviz.workspaces.UserManager.USER_STATUS = {
              loggedIn: false,
              oauthProvider: null,
              userData: null
          };
      <?php
          } else {
      ?>
          epiviz.workspaces.UserManager.USER_STATUS = {
              loggedIn: true,
              oauthProvider: '<?php echo $user['oauth_provider']; ?>',
              userData: <?php echo json_encode($user) . "\n"; ?>
          };
      <?php
          }

          foreach ($_GET as $key => $val) {
          // We'll deal with this later
          if ($key == 'script' || $key == 'settings') { continue; }
          if (is_array($val)) {
      ?>
          items = [];
      <?php
          foreach ($val as $item) {
      ?>
          items.push(<?php echo json_encode($item); ?>);
      <?php
          }
      ?>
          epiviz.ui.WebArgsManager.WEB_ARGS[<?php echo json_encode($key); ?>] = items;
      <?php
          } else {
      ?>
          epiviz.ui.WebArgsManager.WEB_ARGS[<?php echo json_encode($key); ?>] = <?php echo json_encode($val); ?>;
      <?php
          }
          }

          $settings_arg =  ($settings_file == DEFAULT_SETTINGS_FILE) ? DEFAULT_SETTINGS_ARG : $settings_file;

          if ($settings_gist != null) {
      ?>
          epiviz.ui.WebArgsManager.WEB_ARGS['settingsGist'] = <?php json_encode($settings_gist); ?>;
      <?php
          } else {
      ?>
          epiviz.ui.WebArgsManager.WEB_ARGS['settings'] = <?php echo json_encode($settings_arg); ?>;
      <?php
          }
      ?>
          epiviz.ui.WebArgsManager.WEB_ARGS['useCookie'] = <?php echo json_encode($useCookie); ?>;
      <?php
          if (is_array($scripts) && count($scripts) == 0) { $scripts = DEFAULT_SETTINGS_ARG; }
          if ($scripts != DEFAULT_SETTINGS_ARG) {
      ?>
          items = [];
          var allScripts = [];
      <?php
          foreach ($scripts as $item) {
      ?>
          allScripts.push(<?php echo json_encode($item); ?>);
      <?php
          if (strpos($item, 'raw.php') === 0 && array_key_exists($item, $gists_map)) { continue; }
      ?>
          items.push(<?php echo json_encode($item); ?>);
      <?php
          }
      ?>
          epiviz.ui.WebArgsManager.WEB_ARGS['script'] = items;
      <?php
            }
      ?>
  </script>

      <?php
          if (is_array($scripts)) {
              foreach ($scripts as $script) {
                  ?>
                  <script src="<?php echo $script; ?>"></script>
                  <?php
              }
          }
      ?>

      <script>
          // Run main once the page has loaded
          $(epiviz.main);
      </script>
  </head>
  <body>
  <div class="ui-layout-north">

      <div id="toolbar" class="toolbar-header">
          <div style="float: left; margin-top: 7px; margin-left: 7px; margin-right: 7px">
              <img src="img/epiviz_4_logo_medium.png" alt="Epiviz" width="100" height="21" />
          </div>
          <div style="float: right; font-size: small; margin-top: 7px; margin-left: 7px; margin-right: 7px">
              <?php
              if ($user === null) {
                  echo "<a id=\"login-link\" href=\"javascript:void(0)\">Login</a>";
              } else {
                  echo "Welcome, <b>".$user['display_name']."&nbsp;(@".$user['oauth_provider'].")</b>!&nbsp;";
                  echo "<a id=\"login-link\" href=\"javascript:void(0)\">logout</a>";
              }
              ?>
          </div>

          <div id="intro-navigation" class="intro-container">
              <select id="chromosome-selector"></select>
              <input id="text-location" class="ui-widget-content ui-corner-all" type="text"/>
              <button id="moveleft">Slide left</button>
              <button id="moveright">Slide right</button>

              <button id="zoomin">Zoom in</button>
              <button id="zoomout">Zoom out</button>

              <button id="location-settings">Location Settings...</button>
          </div>

          <span class="separator">|</span>

          <button id="vis-menu-button">Visualizations</button>
          <div class="dropdown-menu">
              <ul id="vis-menu"></ul>
          </div>

          <button id="computed-measurements-button">Computed Measurements</button>

          <span class="separator">|</span>

          <label for="search-box"></label>
          <input id="search-box" class="ui-widget-content ui-corner-all" type="text" />

          <span class="separator">|</span>

          <div id="intro-workspace" class="intro-container">
              <label for="save-workspace-text"></label>
              <input id="save-workspace-text" class="ui-widget-content ui-corner-all" type="text"/>
              <button id="save-workspace-button">Save Workspace</button>
              <button id="revert-workspace-button">Revert Workspace Changes</button>
              <button id="delete-workspace-button">Delete Active Workspace</button>
          </div>

          <span class="separator">|</span>

          <button id="help-button">Help</button>
          <button id="help-tutorials">Tutorials</button>
          <button id="save-page">Screenshot</button>
      </div>
  </div>

  <div id="pagemain" class="ui-layout-center">
      <div id="feature-view"></div>
      <div id="location-view"></div>
      <div id="data-structure-view"></div>
  </div>

  <div id="pagefooter" class="ui-layout-south"></div>

  <div id="dialogs">
      <div id="location-settings-dialog" title="Location Settings">
          <table>
              <tr>
                  <td><label>Zoom-in Ratio:</label></td>
                  <td><input id="zoomin-ratio-text" type="text" /></td>
              </tr>
              <tr>
                  <td><label>Zoom-out Ratio:</label></td>
                  <td><input id="zoomout-ratio-text" type="text" /></td>
              </tr>
              <tr>
                  <td><label>Navigation Step Ratio:</label></td>
                  <td><input id="navigation-step-ratio-text" type="text" /></td>
              </tr>
          </table>
      </div>
  </div>
  </body>
</html>