research-article.js

Polymer({
  attached: function() {
    this.url = window.location.href;
    this.doi = $('head > meta[name=citation_doi]').attr('content');
    this.github = $('[rel=source][data-github]').data('github');

    this.async(this.references);
    this.async(this.figures);
    this.async(this.orcid);
    this.async(this.mathjax);
    this.async(this.releases);
  },
  references: function() {
    var referencesList = $('#references > ul');
    var references = referencesList.find('li');

    // build an index of URLs in the reference list
    var referenceLinks = {};
    references.each(function(i) {
        $(this).find('a[href]').each(function() {
            referenceLinks[this.href] = i;
        });
    });

    // start from the bottom, so the reference list gets re-ordered correctly
    var links = $('section a').get().reverse();

    // move each reference to the top of the list
    $(links).each(function() {
        var referenceIndex = referenceLinks[this.href];

        if (typeof referenceIndex === 'undefined') {
          references.eq(referenceIndex).prependTo(referencesList);
        }
    });

    // add a popover to each link in the article
    $(links).each(function() {
      $(this).popover({
        trigger: 'hover',
        delay: {
             show: 250,
             hide: 100
        },
        placement: 'right',
        container: 'body',
        html: true,
        title: this.getAttribute('title'),
        content: function() {
          var referenceIndex = referenceLinks[this.href];

          if (typeof referenceIndex !== 'undefined') {
            return references.eq(referenceIndex).html();
          }

          var node = document.createElement('article-reference');
          node.originalTitle = this.getAttribute('data-original-title');
          node.originalText = this.getAttribute('data-original-text');
          node.url = this.href;

          return node.go() ? node : '';
        }
      });
    });

    // update numbered references
    var inlineCitations = $('section a').filter(function() {
      if (['👍', '👎'].indexOf(this.textContent) !== -1) {
        return true;
      }

      if (/^cito:/.test(this.textContent)) {
        return true;
      }

      return false;
    });

    var citedURLs = [];

    inlineCitations.each(function() {
      var url = this.href;
      var text = this.textContent.trim();

      var index = citedURLs.indexOf(url);

      if (index === -1) {
        citedURLs.push(url);
        index = citedURLs.length;
      }

      $(this).attr('data-original-text', text).text(index).addClass('citation');
    });
  },
  figures: function() {
    var modal = $('<div id="figure-modal" class="modal fade" tabindex="-1" role="dialog" aria-hidden="true" hidden-print><div class="modal-dialog modal-lg"><div class="modal-content"></div></div></div>');

    modal.appendTo(document.body).modal({ show: false });

    var content = modal.find('.modal-content').text('Loading…');

    modal.on('hidden.bs.modal', function() {
        content.html('Loading…');
    });

    $(this).on('click', 'a.figure-link', function() {
        modal.modal('show');
        content.load(this.href + ' figure');
        return false;
    });
  },
  orcid: function() {
    var modal = $('<div id="orcid-modal" class="modal fade" tabindex="-1" role="dialog" aria-hidden="true" hidden-print><div class="modal-dialog modal-lg"><div class="modal-content"></div></div></div>');

    modal.appendTo(document.body).modal({ show: false });

    var content = modal.find('.modal-content').text('Loading…');

    modal.on('hidden.bs.modal', function() {
        content.html('Loading…');
    });

    $('a[data-orcid]').tooltip({
      placement: 'bottom'
    }).on('click', function() {
        modal.modal('show');
        var element = $('<orcid-profile/>').attr('orcid', $(this).data('orcid'));
        content.html(element);
        return false;
    });
  },
  releases: function() {
    var link = $('[rel=source][data-github]');

    if (!link.length) {
      return;
    }

    var container = link.parent();
    var url = this.url;

    var button = $('<button/>', {
      type: 'button',
      html: '&darr; show version history'
    });

    var showVersionHistory = function() {
      var node = document.createElement('version-history');
      node.github = link.data('github');
      node.url = url;

      container.append(node);
      $(this).remove();
    };

    button.addClass('btn btn-link btn-mini').on('click', showVersionHistory).appendTo(container);
  },
  mathjax: function() {
    window.MathJax = {
      messageStyle: 'none',
      'HTML-CSS': {
          linebreaks: { automatic: true },
          scale: 80
      },
      menuSettings: {
          zoom: 'Click'
      },
      elements: this.children
    };

    this.addScript('https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML,Safe');
  },
  addScript: function(src) {
    var script = document.createElement('script');
    script.src = src;
    document.querySelector('head').appendChild(script);
  }
});