Squashed commit of the following:

commit fe06f739545d0b9f3204f8ee3aee6a55e3520023
Author: Alexander O'Neill <aoneill@upei.ca>
Date:   Tue Oct 30 15:16:19 2018 -0300

    Add sorting options for references list.

    Support parenthetical citations.

bibcite_footnotes.module

@@ -9,8 +9,9 @@ use Drupal\Core\Form\FormStateInterface;
 use Drupal\Core\Routing\RouteMatchInterface;
 use Drupal\Core\Url;
 use Drupal\Core\Link;
+use Drupal\bibcite_footnotes\CitationTools;
 
-/**
+/**_bibcite_foot
  * Implements hook_help().
  */
 function bibcite_footnotes_help($route_name, RouteMatchInterface $route_match) {
@@ -57,9 +58,9 @@ function bibcite_footnotes_preprocess_footnote_list(&$variables) {
 
   ];
   $references['#attached']['library'][] = 'bibcite_footnotes/reference_footnote';
-
+  $dont_show_backlink_text = $config->get('filters.filter_reference_footnotes.settings.reference_dont_show_backlink_text');
-  $serializer = \Drupal::service('serializer');
+  $sort_references_by = $config->get('filters.filter_reference_footnotes.settings.reference_sort_by');
-
+  $citation_tools = new CitationTools();
   foreach ($footnotes as $fn) {
     $item = [
       '#id' => $fn['fn_id'],
@@ -68,12 +69,14 @@ function bibcite_footnotes_preprocess_footnote_list(&$variables) {
       ],
     ];
     $build = [];
+    $reference_entity_id = _bibcite_footnotes_get_reference_entity_id_from_bibcite_footnote($fn['text']);
+
     if (!is_array($fn['ref_id'])) {
       // Output normal footnote.
 
 
       $url = Url::fromUserInput('#' . $fn['ref_id'], ['attributes' => ['id' => $fn['fn_id'], 'class' => 'footnote-link']]);
-      $link = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
+      $link = Link::fromTextAndUrl(($dont_show_backlink_text && $reference_entity_id ? '^' : $fn['value']), $url)->toRenderable();
       $build[] = $link;
     }
     else {
@@ -95,16 +98,12 @@ function bibcite_footnotes_preprocess_footnote_list(&$variables) {
 
     }
 
-    preg_match('/\[bibcite_reference:(\d*)\]/', $fn['text'], $matches);
-    $reference_entity_id = $matches[1];
     if (!empty($reference_entity_id)) {
-      $reference_storage = \Drupal::entityTypeManager()
+      $citation_build = $citation_tools->getRenderableReference($reference_entity_id);
-        ->getStorage('bibcite_reference')
+      $build[] = $citation_build;
-        ->load($reference_entity_id);
-      $data = $serializer->normalize($reference_storage, 'csl');
-      $build[] = ['#theme' => 'bibcite_citation', '#data' => $data];
       $render = render($build);
       $item['#markup'] = $render;
+      $item['sort'] = trim(strip_tags(render($citation_build)));
       $references['#items'][] = $item;
 
     }
@@ -119,7 +118,41 @@ function bibcite_footnotes_preprocess_footnote_list(&$variables) {
 
   $variables['notes'] = $notes;
 
+  if ($sort_references_by == 'alphabetical') {
+    usort($references['#items'], '_bibcite_footnotes_reference_array_cmp');
+  }
   $variables['references'] = $references;
+}
+
+/**
+ * @param $text The text of the bibcite reference placeholder.
+ * @return Entity id of the Reference.
+ */
+function _bibcite_footnotes_get_reference_entity_id_from_bibcite_footnote($text){
+  preg_match('/\[bibcite_reference:(\d*)\]/', $text, $matches);
+  return $matches[1];
+}
+
+function _bibcite_footnotes_reference_array_cmp($a, $b) {
+  $a1 = (!empty($a['sort']) ? strtolower($a['sort']) : '');
+  $b1 = (!empty($b['sort']) ? strtolower($b['sort']) : '');
+  return strcmp($a1, $b1);
+}
+
+function bibcite_footnotes_preprocess_footnote_link(&$variables) {
+//  $variables['fn']['fn']['#type'] = 'markeup';
+//  $variables['fn']['fn']['#markup'] = '<h2>Hello!</h2>';
+  $fn = $variables['fn']['fn'];
+  // TODO: Make a more formal way to denote inline citations.
+  $citation_is_inline = ($fn['value'][0] == '(' && $fn['value'][strlen($fn['value']) - 1] == ')') ? '-inline' : '';
+  $class = 'see-footnote' . $citation_is_inline;
+  // Generate the hover text
+  $citation_tools = new CitationTools();
+  $citation_entity_id = _bibcite_footnotes_get_reference_entity_id_from_bibcite_footnote($fn['text']);
+  $title = trim(strip_tags(render($citation_tools->getRenderableReference($citation_entity_id))));
+  $url = Url::fromUserInput('#' . $fn['fn_id'], ['attributes' => ['id' => $fn['ref_id'], 'class' => $class, 'title' => $title]]);
+  $link = Link::fromTextAndUrl($fn['value'], $url)->toRenderable();
+  $variables['fn']['fn'][] = $link;
 
 }
 
@@ -136,69 +169,14 @@ function bibcite_footnotes_theme() {
 
 function bibcite_footnotes_theme_registry_alter(&$theme_registry) {
   unset($theme_registry['footnote_list']['function']);
-//  $theme_registry['footnote_list']['function'] = 'bibcite_footnotes_theme_footnote_list';
   $theme_registry['footnote_list']['path'] = drupal_get_path('module', 'bibcite_footnotes') . '/templates';
   $theme_registry['footnote_list']['template'] = 'footnote-list';
   $theme_registry['footnote_list']['variables']['notes'] = [];
   $theme_registry['footnote_list']['variables']['references'] = [];
   $theme_registry['footnote_list']['variables']['footnotes'] = [];
-}
-
-function bibcite_footnotes_theme_footnote_list($footnotes) {
-  // @todo: change this ugly array for arguments in the function.
-  $footnotes = $footnotes['footnotes']['#footnotes'];
-
-  $notes = [
-    '#theme' => 'item_list',
-    '#list_type' => 'ul',
-    '#title' => 'Notes',
-    '#attributes' => ['class' => ''],
-    '#wrapper_attributes' => ['class' => 'container'],
-  ];
-
-//  return drupal_render($content);
-  $str = '<ul class="footnotes">';
-  // Drupal 7 requires we use "render element" which just introduces a wrapper
-  // around the old array.
-  // $footnotes = $footnotes['footnotes'];
-  // loop through the footnotes.
-  $view_builder = \Drupal::entityTypeManager()->getViewBuilder('bibcite_reference');
-  foreach ($footnotes as $fn) {
-    if (!is_array($fn['ref_id'])) {
-      // Output normal footnote.
-      $str .= '<li class="footnote" id="' . $fn['fn_id'] . '"><a class="footnote-label" href="#' . $fn['ref_id'] . '">' . $fn['value'] . '.</a> ';
-      preg_match('/\[bibcite_reference:(\d*)\]/', $fn['text'], $matches);
-      $reference_entity_id = $matches[1];
-      if (!empty($reference_entity_id)) {
-        $reference_storage = \Drupal::entityTypeManager()
-          ->getStorage('bibcite_reference')
-          ->load($reference_entity_id);
-
-        $build = $view_builder->view($reference_storage, 'citation');
-        $render = render($build);
-
-        $str .= $render . "</li>\n";
-      }
-      else {
-        $str .= $fn['text'] . "</li>\n";
-      }
-    }
-    else {
-      // Output footnote that has more than one reference to it in the body.
-      // The only difference is to insert backlinks to all references.
-      // Helper: we need to enumerate a, b, c...
-      $abc = str_split("abcdefghijklmnopqrstuvwxyz");
-      $i = 0;
-
-      $str .= '<li class="footnote" id="' . $fn['fn_id'] . '"><a href="#' . $fn['ref_id'][0] . '" class="footnote-label">' . $fn['value'] . '.</a> ';
-      foreach ($fn['ref_id'] as $ref) {
-        $str .= '<a class="footnote-multi" href="#' . $ref . '">' . $abc[$i] . '.</a> ';
-        $i++;
-      }
-      $str .= $fn['text'] . "</li>\n";
-    }
-  }
-
-  return $str;
 
+  unset($theme_registry['footnote_link']['function']);
+  $theme_registry['footnote_link']['path'] = drupal_get_path('module', 'bibcite_footnotes') . '/templates';
+  $theme_registry['footnote_link']['template'] = 'footnote-link';
 }
+

js/plugins/reference_footnotes/dialogs/footnotes.js

@@ -26,8 +26,12 @@
                             type: 'textarea',
                             label: Drupal.t('Or add free-form footnote text :'),
                             setup: function (element) {
-                              if (isEdit)
+                                if (isEdit) {
-                                this.setValue(element.getText());
+                                    var text = element.getText();
+                                    if (!text.match(/\[bibcite_reference:(\d*)\]/)) {
+                                        this.setValue(text);
+                                    }
+                                }
                             }
                           },
                             {

src/CitationTools.php

@@ -0,0 +1,22 @@
+<?php
+/**
+ * Created by PhpStorm.
+ * User: aoneill
+ * Date: 2018-10-30
+ * Time: 2:36 PM
+ */
+
+namespace Drupal\bibcite_footnotes;
+
+
+class CitationTools {
+
+  public function getRenderableReference($reference_entity_id) {
+    $reference_storage = \Drupal::entityTypeManager()
+      ->getStorage('bibcite_reference')
+      ->load($reference_entity_id);
+    $serializer = \Drupal::service('serializer');
+    $data = $serializer->normalize($reference_storage, 'csl');
+    return ['#theme' => 'bibcite_citation', '#data' => $data];
+  }
+}

src/Plugin/Filter/ReferenceFootnotesFilter.php

@@ -78,7 +78,22 @@ class ReferenceFootnotesFilter extends FootnotesFilter {
       '#type' => 'textfield',
       '#title' => $this->t('References section label'),
       '#description' => $this->t('E.g., "Works Cited" for MLA style.'),
-      '#default_value' =>  $this->settings['references_section_label'],
+      '#default_value' => $this->settings['references_section_label'],
+    ];
+    $settings['reference_dont_show_backlink_text'] = [
+      '#type' => 'checkbox',
+      '#title' => $this->t("Don't show note 'value' text in reference list."),
+      '#description' => $this->t("Suitable for MLA-style citations, like (Smith, 33-22)"),
+      '#default_value' => $this->settings['reference_dont_show_backlink_text'],
+    ];
+    $settings['reference_sort_by'] = [
+      '#type' => 'select',
+      '#title' => $this->t("Sort references list by"),
+      '#options' => [
+        'order' => $this->t("Order in text"),
+        'alphabetical' => $this->t("Alphabetical"),
+      ],
+      '#default_value' => $this->settings['reference_sort_by'],
     ];
     return $settings;
   }

templates/footnote-link.html.twig

@@ -0,0 +1,16 @@
+{#
+/**
+ * @file footnote-link.html.twig
+ * Default theme implementation to present an inline reference footnote link.
+ *
+ * Available variables:
+ * - fn: Components of the footnote
+ * - link: Rendered link.
+ * - attributes: HTML attributes for the container element.
+ *
+ * @see template_preprocess_footnote_link().
+ *
+ * @ingroup themeable
+ */
+#}
+{{ fn }}

templates/footnote-list.html.twig

@@ -17,5 +17,5 @@
 
 <div{{ attributes.addClass('footnote-list') }}>
     {{ notes }}
-    {{  references }}
+    {{ references }}
 </div>