wp-duckbehaviorjournal/functions.php

<?php
function duck_behavior_journal_setup()
{
    add_theme_support('post-thumbnails');
    add_theme_support('title-tag');
    register_nav_menus(array(
        'primary' => __('Primary Menu', 'duck-behavior-journal'),
        'footer'  => __('Footer Menu', 'duck-behavior-journal'),
    ));

    add_theme_support('custom-logo');

    add_theme_support('custom-header', array(
        'default-image' => get_template_directory_uri() . '/assets/img/hero.png',
        'width'         => 1920,
        'height'        => 1080,
        'flex-height'   => true,
        'flex-width'    => true,
    ));

    add_theme_support('pagination');
}
add_action('after_setup_theme', 'duck_behavior_journal_setup');

function duck_behavior_journal_scripts()
{
    wp_enqueue_style('bootstrap-css', get_template_directory_uri() . '/assets/dist/css/bootstrap.min.css');
    wp_enqueue_style('mathjax-css', get_template_directory_uri() . '/assets/dist/css/mathjax.css');
    wp_enqueue_style('theme-style', get_stylesheet_uri());
    wp_enqueue_script('jquery', get_template_directory_uri() . '/assets/dist/js/jquery-3.7.1.min.js', array(), null, true);
    wp_enqueue_script('bootstrap-js', get_template_directory_uri() . '/assets/dist/js/bootstrap.bundle.min.js', array(), null, true);
    wp_enqueue_script('lightbox', get_template_directory_uri() . '/assets/js/lightbox.js', array(), null, true);
}
add_action('wp_enqueue_scripts', 'duck_behavior_journal_scripts');

require_once get_template_directory() . '/classes/navwalker.php';

function duck_behavior_journal_customizer($wp_customize)
{
    // Hero Image Section
    $wp_customize->add_section('hero_image_section', array(
        'title'    => __('Hero Section', 'duck-behavior-journal'),
        'priority' => 30,
    ));

    // Hero Image Setting
    $wp_customize->add_setting('hero_image', array(
        'default'   => get_template_directory_uri() . '/assets/img/hero.png',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control(new WP_Customize_Image_Control($wp_customize, 'hero_image_control', array(
        'label'    => __('Hero Image', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_image',
    )));

    // Hero Title Setting
    $wp_customize->add_setting('hero_title', array(
        'default'   => 'Advancing the Understanding of Duck Behavior',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('hero_title_control', array(
        'label'    => __('Hero Title', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_title',
        'type'     => 'text',
    ));

    // Hero Subtitle Setting
    $wp_customize->add_setting('hero_subtitle', array(
        'default'   => 'Through Rigorous Scientific Research',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('hero_subtitle_control', array(
        'label'    => __('Hero Subtitle', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_subtitle',
        'type'     => 'text',
    ));

    // Hero Primary Button Text Setting
    $wp_customize->add_setting('hero_primary_button_text', array(
        'default'   => 'Submit Your Research',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('hero_primary_button_text_control', array(
        'label'    => __('Hero Primary Button Text', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_primary_button_text',
        'type'     => 'text',
    ));

    // Hero Primary Button URL Setting
    $wp_customize->add_setting('hero_primary_button_url', array(
        'default'   => '#',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('hero_primary_button_url_control', array(
        'label'    => __('Hero Primary Button URL', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_primary_button_url',
        'type'     => 'url',
    ));

    // Hero Secondary Button Text Setting
    $wp_customize->add_setting('hero_secondary_button_text', array(
        'default'   => 'Subscribe to the Journal',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('hero_secondary_button_text_control', array(
        'label'    => __('Hero Secondary Button Text', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_secondary_button_text',
        'type'     => 'text',
    ));

    // Hero Secondary Button URL Setting
    $wp_customize->add_setting('hero_secondary_button_url', array(
        'default'   => '#',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('hero_secondary_button_url_control', array(
        'label'    => __('Hero Secondary Button URL', 'duck-behavior-journal'),
        'section'  => 'hero_image_section',
        'settings' => 'hero_secondary_button_url',
        'type'     => 'url',
    ));

    // Footer Section
    $wp_customize->add_section('footer_section', array(
        'title'    => __('Footer', 'duck-behavior-journal'),
        'priority' => 40,
    ));

    // Footer Text Setting
    $wp_customize->add_setting('footer_text', array(
        'default'   => '&copy; ' . date('Y') . ' Duck Behavior Journal. All rights reserved.',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('footer_text_control', array(
        'label'    => __('Footer Text', 'duck-behavior-journal'),
        'section'  => 'footer_section',
        'settings' => 'footer_text',
        'type'     => 'textarea',
    ));

    // Footer Social Media Links
    $social_media = array('facebook', 'twitter', 'linkedin');

    foreach ($social_media as $platform) {
        $wp_customize->add_setting("footer_{$platform}_link", array(
            'default'   => '#',
            'transport' => 'refresh',
        ));

        $wp_customize->add_control("footer_{$platform}_link_control", array(
            'label'    => __(ucfirst($platform) . ' URL', 'duck-behavior-journal'),
            'section'  => 'footer_section',
            'settings' => "footer_{$platform}_link",
            'type'     => 'url',
        ));
    }

    // DOI Prefix Section
    $wp_customize->add_section('doi_prefix_section', array(
        'title'    => __('DOI Prefix', 'duck-behavior-journal'),
        'priority' => 50,
    ));

    $wp_customize->add_setting('doi_prefix', array(
        'default'   => '22.2222/DBJ/',
        'transport' => 'refresh',
    ));

    $wp_customize->add_control('doi_prefix_control', array(
        'label'    => __('DOI Prefix', 'duck-behavior-journal'),
        'section'  => 'doi_prefix_section',
        'settings' => 'doi_prefix',
        'type'     => 'text',
    ));
}
add_action('customize_register', 'duck_behavior_journal_customizer');

function create_article_post_type()
{
    $labels = array(
        'name'                  => _x('Articles', 'Post type general name', 'duck-behavior-journal'),
        'singular_name'         => _x('Article', 'Post type singular name', 'duck-behavior-journal'),
        'menu_name'             => _x('Articles', 'Admin Menu text', 'duck-behavior-journal'),
        'name_admin_bar'        => _x('Article', 'Add New on Toolbar', 'duck-behavior-journal'),
        'add_new'               => __('Add New', 'duck-behavior-journal'),
        'add_new_item'          => __('Add New Article', 'duck-behavior-journal'),
        'new_item'              => __('New Article', 'duck-behavior-journal'),
        'edit_item'             => __('Edit Article', 'duck-behavior-journal'),
        'view_item'             => __('View Article', 'duck-behavior-journal'),
        'all_items'             => __('All Articles', 'duck-behavior-journal'),
        'search_items'          => __('Search Articles', 'duck-behavior-journal'),
        'parent_item_colon'     => __('Parent Articles:', 'duck-behavior-journal'),
        'not_found'             => __('No articles found.', 'duck-behavior-journal'),
        'not_found_in_trash'    => __('No articles found in Trash.', 'duck-behavior-journal'),
        'featured_image'        => _x('Featured Image', 'Overrides the “Featured Image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'set_featured_image'    => _x('Set featured image', 'Overrides the “Set featured image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'remove_featured_image' => _x('Remove featured image', 'Overrides the “Remove featured image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'use_featured_image'    => _x('Use as featured image', 'Overrides the “Use as featured image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'archives'              => _x('Article archives', 'The post type archive label used in nav menus. Default “Post Archives”. Added in 4.4', 'duck-behavior-journal'),
        'insert_into_item'      => _x('Insert into article', 'Overrides the “Insert into post”/”Insert into page” phrase (used when inserting media into a post). Added in 4.4', 'duck-behavior-journal'),
        'uploaded_to_this_item' => _x('Uploaded to this article', 'Overrides the “Uploaded to this post”/”Uploaded to this page” phrase (used when viewing media attached to a post). Added in 4.4', 'duck-behavior-journal'),
        'filter_items_list'     => _x('Filter articles list', 'Screen reader text for the filter links heading on the post type listing screen. Default “Filter posts list”/”Filter pages list”. Added in 4.4', 'duck-behavior-journal'),
        'items_list_navigation' => _x('Articles list navigation', 'Screen reader text for the pagination heading on the post type listing screen. Default “Posts list navigation”/”Pages list navigation”. Added in 4.4', 'duck-behavior-journal'),
        'items_list'            => _x('Articles list', 'Screen reader text for the items list heading on the post type listing screen. Default “Posts list”/”Pages list”. Added in 4.4', 'duck-behavior-journal'),
    );

    $args = array(
        'labels'             => $labels,
        'public'             => true,
        'publicly_queryable' => true,
        'show_ui'            => true,
        'show_in_menu'       => true,
        'query_var'          => true,
        'rewrite'            => array('slug' => 'article'),
        'capability_type'    => 'post',
        'has_archive'        => true,
        'hierarchical'       => false,
        'menu_position'      => null,
        'supports'           => array('title', 'editor', 'author', 'thumbnail', 'excerpt', 'comments'),
    );

    register_post_type('article', $args);
}
add_action('init', 'create_article_post_type');

function create_publication_status_taxonomy()
{
    $labels = array(
        'name'              => _x('Publication Statuses', 'taxonomy general name', 'duck-behavior-journal'),
        'singular_name'     => _x('Publication Status', 'taxonomy singular name', 'duck-behavior-journal'),
        'search_items'      => __('Search Publication Statuses', 'duck-behavior-journal'),
        'all_items'         => __('All Publication Statuses', 'duck-behavior-journal'),
        'parent_item'       => __('Parent Publication Status', 'duck-behavior-journal'),
        'parent_item_colon' => __('Parent Publication Status:', 'duck-behavior-journal'),
        'edit_item'         => __('Edit Publication Status', 'duck-behavior-journal'),
        'update_item'       => __('Update Publication Status', 'duck-behavior-journal'),
        'add_new_item'      => __('Add New Publication Status', 'duck-behavior-journal'),
        'new_item_name'     => __('New Publication Status Name', 'duck-behavior-journal'),
        'menu_name'         => __('Publication Status', 'duck-behavior-journal'),
    );

    $args = array(
        'hierarchical'      => true,
        'labels'            => $labels,
        'show_ui'           => true,
        'show_admin_column' => true,
        'query_var'         => true,
        'rewrite'           => array('slug' => 'publication-status'),
    );

    register_taxonomy('publication_status', array('article'), $args);
}

add_action('init', 'create_publication_status_taxonomy', 0);

// Add color picker to publication status taxonomy
function add_publication_status_color_field($term)
{
    $color = get_term_meta($term->term_id, 'publication_status_color', true);
?>
    <tr class="form-field">
        <th scope="row" valign="top">
            <label for="publication_status_color"><?php _e('Color', 'duck-behavior-journal'); ?></label>
        </th>
        <td>
            <input type="text" name="publication_status_color" id="publication_status_color" value="<?php echo esc_attr($color) ? esc_attr($color) : '#ffffff'; ?>" class="color-field" />
            <p class="description"><?php _e('Choose a color for this publication status.', 'duck-behavior-journal'); ?></p>
        </td>
    </tr>
<?php
}

add_action('publication_status_edit_form_fields', 'add_publication_status_color_field', 10, 2);

// Add color picker to add new term screen
function add_publication_status_color_field_new($term)
{
?>
    <div class="form-field">
        <label for="publication_status_color"><?php _e('Color', 'duck-behavior-journal'); ?></label>
        <input type="text" name="publication_status_color" id="publication_status_color" value="#ffffff" class="color-field" />
        <p class="description"><?php _e('Choose a color for this publication status.', 'duck-behavior-journal'); ?></p>
    </div>
<?php
}

add_action('publication_status_add_form_fields', 'add_publication_status_color_field_new', 10, 2);

// Save the color meta data
function save_publication_status_color_meta($term_id)
{
    if (isset($_POST['publication_status_color']) && !empty($_POST['publication_status_color'])) {
        update_term_meta($term_id, 'publication_status_color', sanitize_hex_color($_POST['publication_status_color']));
    } else {
        delete_term_meta($term_id, 'publication_status_color');
    }
}

add_action('edited_publication_status', 'save_publication_status_color_meta', 10, 2);
add_action('create_publication_status', 'save_publication_status_color_meta', 10, 2);

// Enqueue the color picker script
function enqueue_color_picker($hook_suffix)
{
    // Load only on the term edit page
    if (strpos($hook_suffix, 'edit-tags.php') === false) {
        return;
    }

    wp_enqueue_style('wp-color-picker');
    wp_enqueue_script('custom-color-picker', get_template_directory_uri() . '/assets/js/custom-color-picker.js', array('wp-color-picker'), false, true);
}

add_action('admin_enqueue_scripts', 'enqueue_color_picker');

function display_publication_status_terms($post_id)
{
    $terms = get_the_terms($post_id, 'publication_status');
    if (!empty($terms) && !is_wp_error($terms)) {
        foreach ($terms as $term) {
            $color = get_term_meta($term->term_id, 'publication_status_color', true);
            $color_style = $color ? ' style="color:' . esc_attr($color) . ';"' : '';
            echo '<span' . $color_style . '>' . esc_html($term->name) . '</span> ';
        }
    }
}

function add_article_meta_boxes()
{
    add_meta_box(
        'article_authors',
        __('Article Authors', 'duck-behavior-journal'),
        'render_article_authors_meta_box',
        'article',
        'side',
        'default'
    );

    add_meta_box(
        'article_doi',
        __('Article DOI', 'duck-behavior-journal'),
        'render_article_doi_meta_box',
        'article',
        'side',
        'default'
    );

    add_meta_box(
        'article_attachment',
        __('File Attachment', 'duck-behavior-journal'),
        'render_article_attachment_meta_box',
        'article',
        'side',
        'default'
    );

    add_meta_box(
        'article_open_access',
        __('Open Access', 'duck-behavior-journal'),
        'render_article_open_access_meta_box',
        'article',
        'side',
        'default'
    );
}
add_action('add_meta_boxes', 'add_article_meta_boxes');

function render_article_authors_meta_box($post)
{
    $authors = get_post_meta($post->ID, 'article_authors', true);
?>
    <div id="article-authors">
        <div id="article-authors-list">
            <?php
            if (!empty($authors)) {
                foreach ($authors as $index => $author) {
            ?>
                    <p>
                        <input type="text" name="article_authors[]" value="<?php echo esc_attr($author); ?>" />
                        <button type="button" class="button remove-author-button" data-index="<?php echo $index; ?>"><?php _e('Remove', 'duck-behavior-journal'); ?></button>
                    </p>
                <?php
                }
            } else {
                ?>
                <p><input type="text" name="article_authors[]" value="" /></p>
            <?php
            }
            ?>
        </div>
        <button type="button" id="add-author-button" class="button"><?php _e('Add Author', 'duck-behavior-journal'); ?></button>
    </div>
    <script>
        jQuery(document).ready(function($) {
            $('#add-author-button').on('click', function() {
                $('#article-authors-list').append('<p><input type="text" name="article_authors[]" value="" /><button type="button" class="button remove-author-button"><?php _e('Remove', 'duck-behavior-journal'); ?></button></p>');
            });

            $(document).on('click', '.remove-author-button', function() {
                $(this).parent().remove();
            });
        });
    </script>
<?php
}

function render_article_doi_meta_box($post)
{
    $doi = get_post_meta($post->ID, 'article_doi', true);
    $doi_prefix = get_theme_mod('doi_prefix', '22.2222/DBJ/');
?>
    <div id="article-doi">
        <p>
            <input type="text" name="article_doi" value="<?php echo esc_attr($doi); ?>" />
            <button type="button" id="generate-doi-button" class="button"><?php _e('Generate DOI', 'duck-behavior-journal'); ?></button>
        </p>
    </div>
    <script>
        function generateRandomDOI(prefix) {
            const randomString = Math.random().toString(36).substring(2, 10);
            return prefix + randomString;
        }

        jQuery(document).ready(function($) {
            $('#generate-doi-button').on('click', function() {
                const doiPrefix = '<?php echo esc_js($doi_prefix); ?>';
                const doi = generateRandomDOI(doiPrefix);
                $('input[name="article_doi"]').val(doi);
            });
        });
    </script>
<?php
}

function render_article_attachment_meta_box($post)
{
    $attachment_id = get_post_meta($post->ID, 'article_attachment_id', true);
    $attachment_url = $attachment_id ? wp_get_attachment_url($attachment_id) : '';
?>
    <div id="article-attachment">
        <p>
            <input type="hidden" name="article_attachment_id" id="article_attachment_id" value="<?php echo esc_attr($attachment_id); ?>" />
            <input type="url" name="article_attachment_url" id="article_attachment_url" value="<?php echo esc_url($attachment_url); ?>" readonly />
            <button type="button" id="upload-attachment-button" class="button"><?php _e('Upload Attachment', 'duck-behavior-journal'); ?></button>
            <button type="button" id="remove-attachment-button" class="button" <?php echo $attachment_id ? '' : 'style="display:none;"'; ?>><?php _e('Remove Attachment', 'duck-behavior-journal'); ?></button>
        </p>
    </div>
    <script>
        jQuery(document).ready(function($) {
            var file_frame;

            $('#upload-attachment-button').on('click', function(event) {
                event.preventDefault();

                if (file_frame) {
                    file_frame.open();
                    return;
                }

                file_frame = wp.media.frames.file_frame = wp.media({
                    title: '<?php _e('Select Attachment', 'duck-behavior-journal'); ?>',
                    button: {
                        text: '<?php _e('Use this file', 'duck-behavior-journal'); ?>',
                    },
                    multiple: false
                });

                file_frame.on('select', function() {
                    var attachment = file_frame.state().get('selection').first().toJSON();
                    $('#article_attachment_id').val(attachment.id);
                    $('#article_attachment_url').val(attachment.url);
                    $('#remove-attachment-button').show();
                });

                file_frame.open();
            });

            $('#remove-attachment-button').on('click', function(event) {
                event.preventDefault();
                $('#article_attachment_id').val('');
                $('#article_attachment_url').val('');
                $(this).hide();
            });
        });
    </script>
<?php
}

function render_article_open_access_meta_box($post)
{
    $open_access = get_post_meta($post->ID, 'article_open_access', true);
?>
    <div id="article-open-access">
        <p>
            <label for="article_open_access">
                <input type="checkbox" name="article_open_access" id="article_open_access" value="1" <?php checked($open_access, '1'); ?> />
                <?php _e('This article is Open Access', 'duck-behavior-journal'); ?>
            </label>
        </p>
    </div>
<?php
}

function add_keywords_meta_box()
{
    add_meta_box(
        'article_keywords',
        __('Article Keywords', 'duck-behavior-journal'),
        'render_keywords_meta_box',
        'article',
        'side',
        'default'
    );
}

add_action('add_meta_boxes', 'add_keywords_meta_box');

function render_keywords_meta_box($post)
{
    $keywords = get_post_meta($post->ID, 'article_keywords', true);
    ?>
    <div id="article-keywords">
        <div id="article-keywords-list">
            <?php
            if (!empty($keywords)) {
                foreach ($keywords as $index => $keyword) {
                    ?>
                    <p>
                        <input type="text" name="article_keywords[]" value="<?php echo esc_attr($keyword); ?>" />
                        <button type="button" class="button remove-keyword-button" data-index="<?php echo $index; ?>"><?php _e('Remove', 'duck-behavior-journal'); ?></button>
                    </p>
                <?php
                }
            } else {
                ?>
                <p><input type="text" name="article_keywords[]" value="" /></p>
            <?php
            }
            ?>
        </div>
        <button type="button" id="add-keyword-button" class="button"><?php _e('Add Keyword', 'duck-behavior-journal'); ?></button>
    </div>
    <script>
        jQuery(document).ready(function($) {
            $('#add-keyword-button').on('click', function() {
                $('#article-keywords-list').append('<p><input type="text" name="article_keywords[]" value="" /><button type="button" class="button remove-keyword-button"><?php _e('Remove', 'duck-behavior-journal'); ?></button></p>');
            });

            $(document).on('click', '.remove-keyword-button', function() {
                $(this).parent().remove();
            });
        });
    </script>
    <?php
}

function save_article_meta_boxes($post_id)
{
    if (defined('DOING_AUTOSAVE') && DOING_AUTOSAVE) return;
    if (!isset($_POST['article_authors'])) return;

    $authors = array_map('sanitize_text_field', $_POST['article_authors']);
    update_post_meta($post_id, 'article_authors', $authors);

    if (isset($_POST['article_doi'])) {
        $doi = sanitize_text_field($_POST['article_doi']);
        update_post_meta($post_id, 'article_doi', $doi);
    }

    if (isset($_POST['article_attachment_id'])) {
        $attachment_id = sanitize_text_field($_POST['article_attachment_id']);
        update_post_meta($post_id, 'article_attachment_id', $attachment_id);
    }

    if (isset($_POST['article_keywords'])) {
        $keywords = array_map('sanitize_text_field', $_POST['article_keywords']);
        update_post_meta($post_id, 'article_keywords', $keywords);
    }

    $open_access = isset($_POST['article_open_access']) ? '1' : '0';
    update_post_meta($post_id, 'article_open_access', $open_access);
}

add_action('save_post', 'save_article_meta_boxes');

function add_doi_rewrite_rule()
{
    add_rewrite_rule('^([0-9]{2})\.([0-9]{4,})/([a-zA-Z0-9_\-\/]+)?$', 'index.php?doi=$matches[1].$matches[2]/$matches[3]', 'top');
}

add_action('init', 'add_doi_rewrite_rule');

function add_doi_query_var($vars)
{
    $vars[] = 'doi';
    return $vars;
}

add_filter('query_vars', 'add_doi_query_var');

function redirect_doi_to_article($query)
{
    if (isset($query->query_vars['doi'])) {
        $doi = $query->query_vars['doi'];
        $args = array(
            'post_type' => 'article',
            'meta_query' => array(
                array(
                    'key' => 'article_doi',
                    'value' => $doi,
                    'compare' => '='
                )
            )
        );
        $articles = new WP_Query($args);
        if ($articles->have_posts()) {
            $articles->the_post();
            wp_redirect(get_permalink(), 301);
            exit;
        }
    }
}

add_action('parse_query', 'redirect_doi_to_article');

function create_letter_post_type()
{
    $labels = array(
        'name'                  => _x('Letters to the Editor', 'Post type general name', 'duck-behavior-journal'),
        'singular_name'         => _x('Letter to the Editor', 'Post type singular name', 'duck-behavior-journal'),
        'menu_name'             => _x('Letters to the Editor', 'Admin Menu text', 'duck-behavior-journal'),
        'name_admin_bar'        => _x('Letter to the Editor', 'Add New on Toolbar', 'duck-behavior-journal'),
        'add_new'               => __('Add New', 'duck-behavior-journal'),
        'add_new_item'          => __('Add New Letter', 'duck-behavior-journal'),
        'new_item'              => __('New Letter', 'duck-behavior-journal'),
        'edit_item'             => __('Edit Letter', 'duck-behavior-journal'),
        'view_item'             => __('View Letter', 'duck-behavior-journal'),
        'all_items'             => __('All Letters', 'duck-behavior-journal'),
        'search_items'          => __('Search Letters', 'duck-behavior-journal'),
        'parent_item_colon'     => __('Parent Letters:', 'duck-behavior-journal'),
        'not_found'             => __('No letters found.', 'duck-behavior-journal'),
        'not_found_in_trash'    => __('No letters found in Trash.', 'duck-behavior-journal'),
        'featured_image'        => _x('Featured Image', 'Overrides the “Featured Image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'set_featured_image'    => _x('Set featured image', 'Overrides the “Set featured image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'remove_featured_image' => _x('Remove featured image', 'Overrides the “Remove featured image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'use_featured_image'    => _x('Use as featured image', 'Overrides the “Use as featured image” phrase for this post type. Added in 4.3', 'duck-behavior-journal'),
        'archives'              => _x('Letter archives', 'The post type archive label used in nav menus. Default “Post Archives”. Added in 4.4', 'duck-behavior-journal'),
        'insert_into_item'      => _x('Insert into letter', 'Overrides the “Insert into post”/”Insert into page” phrase (used when inserting media into a post). Added in 4.4', 'duck-behavior-journal'),
        'uploaded_to_this_item' => _x('Uploaded to this letter', 'Overrides the “Uploaded to this post”/”Uploaded to this page” phrase (used when viewing media attached to a post). Added in 4.4', 'duck-behavior-journal'),
        'filter_items_list'     => _x('Filter letters list', 'Screen reader text for the filter links heading on the post type listing screen. Default “Filter posts list”/”Filter pages list”. Added in 4.4', 'duck-behavior-journal'),
        'items_list_navigation' => _x('Letters list navigation', 'Screen reader text for the pagination heading on the post type listing screen. Default “Posts list navigation”/”Pages list navigation”. Added in 4.4', 'duck-behavior-journal'),
        'items_list'            => _x('Letters list', 'Screen reader text for the items list heading on the post type listing screen. Default “Posts list”/”Pages list”. Added in 4.4', 'duck-behavior-journal'),
    );

    $args = array(
        'labels'             => $labels,
        'public'             => true,
        'publicly_queryable' => true,
        'show_ui'            => true,
        'show_in_menu'       => true,
        'query_var'          => true,
        'rewrite'            => array('slug' => 'letter'),
        'capability_type'    => 'post',
        'has_archive'        => true,
        'hierarchical'       => false,
        'menu_position'      => null,
        'supports'           => array('title', 'editor', 'author', 'thumbnail', 'excerpt', 'comments'),
    );

    register_post_type('letter', $args);
}

add_action('init', 'create_letter_post_type');

function add_letter_meta_boxes()
{
    add_meta_box(
        'article_authors',
        __('Authors', 'duck-behavior-journal'),
        'render_article_authors_meta_box',
        array('letter'),
        'side',
        'default'
    );
}

add_action('add_meta_boxes', 'add_letter_meta_boxes');

function disable_comments_post_types_support()
{
    $post_types = get_post_types();
    foreach ($post_types as $post_type) {
        if (post_type_supports($post_type, 'comments')) {
            remove_post_type_support($post_type, 'comments');
            remove_post_type_support($post_type, 'trackbacks');
        }
    }
}

add_action('admin_init', 'disable_comments_post_types_support');

function disable_comments_status()
{
    return false;
}

add_filter('comments_open', 'disable_comments_status', 20, 2);
add_filter('pings_open', 'disable_comments_status', 20, 2);

function disable_comments_hide_existing_comments($comments)
{
    $comments = array();
    return $comments;
}

add_filter('comments_array', 'disable_comments_hide_existing_comments', 10, 2);

function disable_comments_admin_menu()
{
    remove_menu_page('edit-comments.php');
}

add_action('admin_menu', 'disable_comments_admin_menu');

function disable_comments_admin_menu_redirect()
{
    global $pagenow;
    if ($pagenow === 'edit-comments.php') {
        wp_redirect(admin_url());
        exit;
    }
}

add_action('admin_init', 'disable_comments_admin_menu_redirect');

function disable_comments_dashboard()
{
    remove_meta_box('dashboard_recent_comments', 'dashboard', 'normal');
}

add_action('admin_init', 'disable_comments_dashboard');

function disable_comments_admin_bar()
{
    if (is_admin_bar_showing()) {
        remove_action('admin_bar_menu', 'wp_admin_bar_comments_menu', 60);
    }
}

add_action('init', 'disable_comments_admin_bar');

function rename_excerpt_to_abstract($translated)
{
    $translated = str_ireplace('Excerpt', 'Abstract', $translated);
    return $translated;
}

add_filter('gettext', 'rename_excerpt_to_abstract');

function add_custom_download_endpoint()
{
    add_rewrite_rule('^download/([0-9]+)/?', 'index.php?download_file=$matches[1]', 'top');
}

add_action('init', 'add_custom_download_endpoint');

function add_download_query_var($vars)
{
    $vars[] = 'download_file';
    return $vars;
}

add_filter('query_vars', 'add_download_query_var');

function handle_file_download()
{
    $file_id = get_query_var('download_file');

    if ($file_id && is_numeric($file_id)) {
        if (!is_user_logged_in()) {
            wp_redirect(wp_login_url());
            exit;
        }

        $file_path = get_attached_file($file_id);

        if (file_exists($file_path)) {
            $file_url = wp_get_attachment_url($file_id);
            $file_info = pathinfo($file_url);
            $file_name = $file_info['basename'];

            header('Content-Description: File Transfer');
            header('Content-Type: application/octet-stream');
            header('Content-Disposition: attachment; filename=' . basename($file_name));
            header('Expires: 0');
            header('Cache-Control: must-revalidate');
            header('Pragma: public');
            header('Content-Length: ' . filesize($file_path));

            readfile($file_path);
            exit;
        }
    }
}

add_action('template_redirect', 'handle_file_download');

function custom_login_logo()
{
    $custom_logo_id = get_theme_mod('custom_logo');
    $logo_url = wp_get_attachment_image_url($custom_logo_id, 'full');
?>
    <style type="text/css">
        #login h1 a,
        .login h1 a {
            background-image: url(<?php echo esc_url($logo_url); ?>);
            height: 65px;
            width: auto;
            background-size: contain;
            background-repeat: no-repeat;
            padding-bottom: 30px;
        }
    </style>
<?php
}

add_action('login_enqueue_scripts', 'custom_login_logo');

function custom_login_logo_url()
{
    return home_url();
}

add_filter('login_headerurl', 'custom_login_logo_url');

function custom_login_logo_url_title()
{
    return get_bloginfo('name');
}

add_filter('login_headertext', 'custom_login_logo_url_title');

// Check if TCPDF is available
function is_tcpdf_available()
{
    if (is_autoloader_available()) {
        require_once get_template_directory() . '/vendor/autoload.php';
    }
    return class_exists('TCPDF');
}

// Check if the Composer autoloader is available
function is_autoloader_available()
{
    return file_exists(get_template_directory() . '/vendor/autoload.php');
}

// Display admin notice if TCPDF or autoloader is missing
function tcpdf_missing_notice()
{
    if (!is_autoloader_available()) {
        echo '<div class="notice notice-error"><p>';
        _e('Composer autoloader is missing. Please run "composer install" to install the required dependencies.', 'duck-behavior-journal');
        echo '</p></div>';
    } elseif (!is_tcpdf_available()) {
        echo '<div class="notice notice-error"><p>';
        _e('TCPDF library is missing. Please install it via Composer to enable the PDF download feature.', 'duck-behavior-journal');
        echo '</p></div>';
    }
}

add_action('admin_notices', 'tcpdf_missing_notice');

// Add custom endpoint for PDF download
function add_pdf_download_endpoint()
{
    add_rewrite_rule('^download-pdf/([0-9]+)/?', 'index.php?download_pdf=$matches[1]', 'top');
}

add_action('init', 'add_pdf_download_endpoint');

// Add query vars for PDF download
function add_pdf_query_vars($vars)
{
    $vars[] = 'download_pdf';
    return $vars;
}

add_filter('query_vars', 'add_pdf_query_vars');

// Handle PDF download
function handle_pdf_download()
{
    if (is_autoloader_available()) {
        require_once get_template_directory() . '/vendor/autoload.php';
    }

    if (is_tcpdf_available()) {
        require_once get_template_directory() . '/classes/paperpdf.php';

        $post_id = get_query_var('download_pdf');

        if ($post_id && is_numeric($post_id)) {
            $post = get_post($post_id);

            if ($post && $post->post_type == 'article') {
                // Create new PDF document
                $pdf = new PaperPDF(PDF_PAGE_ORIENTATION, PDF_UNIT, PDF_PAGE_FORMAT, true, 'UTF-8', false);

                // Set document information
                $pdf->SetCreator(PDF_CREATOR);
                $pdf->SetAuthor(get_bloginfo('name'));
                $pdf->SetTitle($post->post_title);
                $pdf->SetSubject('Scientific Paper');
                $pdf->SetMargins(PDF_MARGIN_LEFT, 50, PDF_MARGIN_RIGHT);

                // Add a page
                $pdf->AddPage();

                // Set title
                $pdf->SetFont('helvetica', 'B', 20);
                $pdf->writeHTML('<h1>' . $post->post_title . '</h1>', true, false, false, false, 'C');

                // Set authors
                $pdf->SetFont('helvetica', '', 12);
                $authors = get_post_meta($post_id, 'article_authors', true);
                if (!empty($authors)) {
                    $pdf->Cell(0, 10, implode(', ', array_map('esc_html', $authors)), 0, 1, 'C');
                }

                // Set abstract
                if ($post->post_excerpt) {
                    $pdf->Ln(10);
                    $pdf->SetFont('helvetica', '', 12);
                    $pdf->setTextColor(128);
                    $pdf->writeHTML("<b>Abstract:</b> " . $post->post_excerpt);
                }

                // Set keywords
                $keywords = get_post_meta($post_id, 'article_keywords', true);
                if (!empty($keywords)) {
                    $pdf->Ln(10);
                    $pdf->SetFont('helvetica', 'I', 12);
                    $pdf->writeHTML('<b>Keywords:</b> ' . implode(', ', array_map('esc_html', $keywords)));
                }

                // Set content
                $pdf->setTextColor(0);
                $pdf->Ln(10);
                $pdf->SetFont('helvetica', '', 12);

                $content = apply_filters('the_content', $post->post_content);

                $mathjax_css = file_get_contents(get_template_directory() . '/assets/dist/css/mathjax.css');
                $content = "<style>$mathjax_css</style>$content";

                $pdf->writeHTML($content);

                // Output PDF document
                $pdf->Output(sanitize_title($post->post_title) . '.pdf', 'D');
                exit;
            }
        }
    }
}

add_action('template_redirect', 'handle_pdf_download');

function allow_more_uploads($mime_types)
{
    $mime_types['py'] = 'text/x-python';
    return $mime_types;
}

add_filter('upload_mimes', 'allow_more_uploads');

function disable_real_mime_check($data, $file, $filename, $mimes)
{
    $wp_filetype = wp_check_filetype($filename, $mimes);
    $ext = $wp_filetype['ext'];
    $type = $wp_filetype['type'];
    $proper_filename = $data['proper_filename'];

    return compact('ext', 'type', 'proper_filename');
}

add_filter('wp_check_filetype_and_ext', 'disable_real_mime_check', 10, 4);

function custom_articles_per_page($query)
{
    if (!is_admin() && $query->is_main_query()) {
        if (is_post_type_archive('article')) {
            $query->set('posts_per_page', 9);
        }
    }
}

add_action('pre_get_posts', 'custom_articles_per_page');

function mathjax_customizer_settings($wp_customize)
{
    // Add a section for MathJax settings
    $wp_customize->add_section('mathjax_settings', [
        'title' => __('MathJax Settings', 'duck-behavior-journal'),
        'priority' => 30,
        'description' => __('Specify the URL of your MathJax-node server application. The required server application can be found at <a href="https://git.private.coffee/privatecoffee/mathjax-server" target="_blank">https://git.private.coffee/privatecoffee/mathjax-server</a>.', 'duck-behavior-journal'),
    ]);

    // Add a setting for the MathJax-node server URL
    $wp_customize->add_setting('mathjax_server_url', [
        'default' => '',
        'sanitize_callback' => 'esc_url_raw',
    ]);

    // Add a control for the MathJax-node server URL
    $wp_customize->add_control('mathjax_server_url', [
        'label' => __('MathJax-node Server URL', 'duck-behavior-journal'),
        'section' => 'mathjax_settings',
        'type' => 'url',
    ]);
}

add_action('customize_register', 'mathjax_customizer_settings');

function renderMathJax($latex)
{
    $url = get_theme_mod('mathjax_server_url', '');
    if (empty($url)) {
        return '<span class="error">' . htmlspecialchars($latex) . '</span>';
    }

    $data = json_encode(['tex' => $latex]);

    $options = [
        'http' => [
            'header'  => "Content-Type: application/json\r\n" .
                "Content-Length: " . strlen($data) . "\r\n",
            'method'  => 'POST',
            'content' => $data,
        ],
    ];

    $context  = stream_context_create($options);
    $result = file_get_contents($url, false, $context);

    if ($result === FALSE) {
        return '<span class="error">Error rendering LaTeX</span>';
    }

    $response = json_decode($result, true);

    if (isset($response['error'])) {
        return '<span class="error">Error rendering LaTeX: ' . implode(', ', $response['error']) . '</span>';
    }

    return $response['html'];
}

function convertMathJaxInHTML($html)
{
    $url = get_theme_mod('mathjax_server_url', '');
    if (empty($url)) {
        return $html;  // If the URL is not specified, return the original HTML
    }

    // Use a regular expression to find LaTeX expressions within the HTML
    $pattern = '/\$\$(.*?)\$\$/';
    $callback = function ($matches) {
        $latex = $matches[1];
        try {
            // Render the LaTeX to HTML using the MathJax-node server
            $rendered = renderMathJax($latex);
            return $rendered;
        } catch (Exception $e) {
            // Handle rendering errors
            return '<span class="error">' . htmlspecialchars($latex) . '</span>';
        }
    };

    // Replace all LaTeX expressions in the HTML with rendered HTML
    $convertedHtml = preg_replace_callback($pattern, $callback, $html);

    return $convertedHtml;
}

function preprocess_mathjax_content($content)
{
    return convertMathJaxInHTML($content);
}

add_filter('the_content', 'preprocess_mathjax_content');

function customize_register($wp_customize)
{
    // Add setting to disable posts
    $wp_customize->add_setting('disable_posts', array(
        'default'   => false,
        'transport' => 'refresh',
    ));

    // Add control for the setting
    $wp_customize->add_control('disable_posts_control', array(
        'label'     => __('Disable Post content type', 'duck_behavior_journal'),
        'section'   => 'title_tagline',
        'settings'  => 'disable_posts',
        'type'      => 'checkbox',
    ));
}

add_action('customize_register', 'customize_register');

function process_unregister_post_type()
{
    // Get the customizer setting
    $disable_posts = get_theme_mod('disable_posts', false);

    // If the setting is enabled, unregister the post type
    if ($disable_posts) {
        unregister_post_type('post');
    }
}

add_action('init', 'process_unregister_post_type', 20);

function remove_post_menu_item()
{
    $disable_posts = get_theme_mod('disable_posts', false);
    if ($disable_posts) {
        remove_menu_page('edit.php');
    }
}

add_action('admin_menu', 'remove_post_menu_item');

function exclude_posts_from_queries($query)
{
    if (!is_admin() && $query->is_main_query()) {
        $disable_posts = get_theme_mod('disable_posts', false);
        if ($disable_posts && $query->get('post_type') === 'post') {
            $query->set('post_type', 'page');
        }
    }
}

add_action('pre_get_posts', 'exclude_posts_from_queries');

function remove_posts_from_toolbar($wp_admin_bar)
{
    $disable_posts = get_theme_mod('disable_posts', false);

    if ($disable_posts) {
        $wp_admin_bar->remove_node('new-post');
    }
}

add_action('admin_bar_menu', 'remove_posts_from_toolbar', 999);

function duck_behavior_journal_redirect_post_new()
{
    global $pagenow;

    $disable_posts = get_theme_mod('disable_posts', false);

    if ($disable_posts) {
        // Check if the current page is 'post-new.php' and 'post_type' parameter is missing
        if ($pagenow == 'post-new.php' && !isset($_GET['post_type'])) {
            wp_redirect(admin_url('post-new.php?post_type=article'));
            exit;
        }
    }
}

add_action('admin_init', 'duck_behavior_journal_redirect_post_new');

// Add custom columns to the articles admin list view
function add_article_columns($columns)
{
    // Add a new column for the lead author
    $columns['lead_author'] = __('Lead Author', 'duck-behavior-journal');

    // Remove the default author column
    unset($columns['author']);

    return $columns;
}
add_filter('manage_article_posts_columns', 'add_article_columns');

// Populate the custom columns for articles
function custom_article_column($column, $post_id)
{
    if ($column == 'lead_author') {
        $authors = get_post_meta($post_id, 'article_authors', true);
        if (!empty($authors) && is_array($authors) && !empty($authors[0])) {
            echo esc_html($authors[0]);
        } else {
            echo __('Unknown', 'duck-behavior-journal');
        }
    }
}
add_action('manage_article_posts_custom_column', 'custom_article_column', 10, 2);

// Add custom columns to the letters admin list view
function add_letter_columns($columns)
{
    // Add a new column for the lead author
    $columns['lead_author'] = __('Lead Author', 'duck-behavior-journal');

    // Remove the default author column
    unset($columns['author']);

    return $columns;
}
add_filter('manage_letter_posts_columns', 'add_letter_columns');

// Populate the custom columns for letters
function custom_letter_column($column, $post_id)
{
    if ($column == 'lead_author') {
        $authors = get_post_meta($post_id, 'article_authors', true);
        if (!empty($authors) && is_array($authors) && !empty($authors[0])) {
            echo esc_html($authors[0]);
        } else {
            echo __('Unknown', 'duck-behavior-journal');
        }
    }
}
add_action('manage_letter_posts_custom_column', 'custom_letter_column', 10, 2);