/*
# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# SOURCE                                                               #
# https://gitlab.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
#                                                                      #
# This R package was created for academic research and was publicly    #
# released in the hope that it will be useful, but it comes WITHOUT    #
# ANY WARRANTY OR LIABILITY.                                           #
# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
# ==================================================================== #
*/

// Add updated Font Awesome 5.8.2 library
$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css">');

// Email template for new GitLab issues
//https://stackoverflow.com/a/33190494/4575331
//incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com

$( document ).ready(function() {

  // add SurveyMonkey
  // $('body').append('<script>(function(t,e,s,o){var n,a,c;t.SMCX=t.SMCX||[],e.getElementById(o)||(n=e.getElementsByTagName(s),a=n[n.length-1],c=e.createElement(s),c.type="text/javascript",c.async=!0,c.id=o,c.src=["https:"===location.protocol?"https://":"http://","widget.surveymonkey.com/collect/website/js/tRaiETqnLgj758hTBazgd_2BrwaGaWbg59AiLjNGdPaaJiBHKqgXKIw46VauwBvZ67.js"].join(""),a.parentNode.insertBefore(c,a))})(window,document,"script","smcx-sdk");</script>');
  // add link to survey at home sidebar
  // $('.template-home #sidebar .list-unstyled:first').append('<li><strong>Please fill in our survey at</strong> <br><a href="https://www.surveymonkey.com/r/AMR_for_R" target="_blank">https://www.surveymonkey.com/r/AMR_for_R</a></li>');


  // remove version label from header
  $(".version.label").remove();

  // redirect to GitLab
  var url_old = window.location.href;
  var url_new = url_old.replace("github", "gitlab");
  if (url_old != url_new) {
    window.location.replace(url_new);
  }

  // Replace 'Value' in manual to 'Returned value'
  $(".template-reference-topic h2#value").text("Returned value");

  // PR for 'R for Data Science' on How To pages
  if ($(".template-article").length > 0) {
    $('#sidebar').prepend(
    '<div id="r4ds">' +
    '  <a target="_blank" href="https://r4ds.had.co.nz/">' +
    '    Learn R reading this great book: R for Data Science.' +
    '    <br><br>' +
    '    Click to read it online - it was published for free.' +
    '    <img src="https://gitlab.com/msberends/AMR/raw/master/docs/cover_r4ds.png" height="100px">' +
    '  </a>     ' +
    '  <hr>' +
    '</div>');
  }

  // edit footer
  $('footer').html(
    '<div>' +
      '<p>' + $('footer .copyright p').html().replace(
        "Developed by",
        '<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a>.<br>Authors:') + '</p>' +
      '<a href="https://www.rug.nl"><img src="https://gitlab.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' +
    '</div>');
  // all links should open in new tab/window
  $('footer').html($('footer').html().replace(/href/g, 'target="_blank" href'));

  // doctoral titles of authors
  function doct_tit(x) {
    if (typeof(x) != "undefined") {
      x = x.replace("Corinna", "Dr Corinna");
      x = x.replace("Alex", "Prof Dr Alex");
      x = x.replace("Bhanu", "Prof Dr Bhanu");
      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
      x = x.replace(/Authors/g, "aut_plural");
      x = x.replace(/Author, maintainer[.]?/g, "");
      x = x.replace(/Author[.]?/g, "");
      x = x.replace(/aut_plural/g, "Authors");
    }
    return(x);
  }
  $(".template-authors").html(doct_tit($(".template-authors").html()));
  $(".developers").html(doct_tit($(".developers").html()));
  $("footer").html(doct_tit($("footer").html()));

  // Edit title of manual
  $('.template-reference-index h1').text('Manual');
});

$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);  })();</script><!-- End Matomo Code -->");
