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<?php
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/**
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* @file
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* functions for annotation and sources handling which are to be rendered as
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* footnotes.
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*
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* @copyright
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* (C) 2007-2020 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this module are subject to the Mozilla
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* Public License Version 1.1.
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* @see http://www.mozilla.org/MPL/MPL-1.1.html
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*
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* @author
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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*/
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const MEMBER_OF_FOOTNOTES = ' member-of-footnotes-';
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/**
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* Creates the footnotes for the given CDM instance.
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*
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* Footnotes are created for annotations and original sources whereas the resulting footnote keys depend on the
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* parameters $footnote_list_key and $is_bibliography_aware, see parameter $footnote_list_key
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* for more details.
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*
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* possible keys for annotation and source footnotes:
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* - $footnote_list_key
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* - RenderHints::getFootnoteListKey()
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* - original source footnotes
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* - "BIBLIOGRAPHY" (when !$is_bibliography_aware && bibliography_settings['enabled'] == 1 )
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* - "BIBLIOGRAPHY-$footnote_list_key" (when !$is_bibliography_aware && bibliography_settings['enabled'] == 0 )
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* - $footnote_list_key (when $is_bibliography_aware)
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*
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* @param $cdm_entity
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* A CDM entity
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* @param $footnote_list_key string
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* Optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined by the nested
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* method calls by calling RenderHints::getFootnoteListKey().
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* For original sources the $footnote_list_key will be overwritten by bibliography_footnote_list_key() when
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* $is_bibliography_aware is set TRUE.
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* @param bool $do_link_to_reference
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* Create a link to the reference pages for sources when TRUE.
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* @param bool $do_link_to_name_used_in_source
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* Create a link to the name pages for name in source when TRUE.
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* @param bool $is_bibliography_aware
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* Put source references into the bibliography when this param is TRUE.
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* For original sources the $footnote_list_key will be overwritten
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* by bibliography_footnote_list_key() when
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* $is_bibliography_aware is set TRUE.
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* @return array
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* An array of the footnote keys for the supplied cdm entity
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*
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* NOTE: Only used in @see handle_annotations_and_sources()
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*/
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function cdm_entity_footnotes(
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$cdm_entity,
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$footnote_list_key = NULL,
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$do_link_to_reference = FALSE,
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$do_link_to_name_used_in_source = FALSE,
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$is_bibliography_aware = FALSE
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){
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$sources = cdm_entity_sources_sorted($cdm_entity);
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if (!isset($footnote_list_key) || !$footnote_list_key) {
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$footnote_list_key = RenderHints::getFootnoteListKey();
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}
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// Annotations as footnotes.
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$footnote_keys = cdm_entity_annotations_as_footnote_keys($cdm_entity, $footnote_list_key);
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// Source references as footnotes.
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if($is_bibliography_aware){
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$bibliography_settings = get_bibliography_settings();
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$sources_footnote_list_key = bibliography_footnote_list_key($footnote_list_key);
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$original_source_footnote_tag = $bibliography_settings['enabled'] == 1 ? 'div' : null; // null will cause bibliography_footnote_list_key to use the default
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} else {
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$sources_footnote_list_key = $footnote_list_key;
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$original_source_footnote_tag = NULL;
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}
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foreach ($sources as $source) {
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if (_is_original_source_type($source)) {
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$fn_key = FootnoteManager::addNewFootnote(
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$sources_footnote_list_key,
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render_original_source(
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$source,
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$do_link_to_reference,
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$do_link_to_name_used_in_source
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),
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$original_source_footnote_tag
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);
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// Ensure uniqueness of the footnote keys.
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if(array_search($fn_key, $footnote_keys)=== false) {
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$footnote_keys[] = $fn_key;
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}
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}
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}
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// Sort and render footnote keys.
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asort($footnote_keys);
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return $footnote_keys;
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}
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/**
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* Fetches the list of visible annotations for the cdm entity or for the comparable
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* object and returns the footnote keys.
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*
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* The footnotes are passed to the FootnoteManager in order to store the
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* annotations and to create the footnote keys.
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* @param stdClass $cdm_entity
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* A single CdmBase instance ore comparable object.
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* @param $footnote_list_key string
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* optional parameter. If this parameter is left empty (null, 0, "") the
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* footnote key will be set to RenderHints::getFootnoteListKey()
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* otherwise the supplied $footnote_list_key will be used.
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* @return array of footnote keys
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*
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* @see cdm_fetch_visible_annotations()
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*/
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function cdm_entity_annotations_as_footnote_keys(stdClass $cdm_entity, $footnote_list_key = NULL) {
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$foot_note_keys = [];
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if (!isset($footnote_list_key) || !$footnote_list_key) {
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$footnote_list_key = RenderHints::getFootnoteListKey();
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}
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// Adding the footnotes keys.
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$annotations = cdm_fetch_visible_annotations($cdm_entity);
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if (is_array($annotations)) {
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foreach ($annotations as $annotation) {
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$foot_note_keys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
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}
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}
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return $foot_note_keys;
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}
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/**
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* Creates markup for an array of foot note keys
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*
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* @param array $footnote_keys
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* @param string $separator
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*
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* @return string
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*/
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function render_footnote_keys(array $footnote_keys, $separator) {
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$footnotes_markup = '';
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foreach ($footnote_keys as $foot_note_key) {
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try {
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$footnotes_markup .= render_footnote_key($foot_note_key, ($footnotes_markup ? $separator : ''));
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} catch (Exception $e) {
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drupal_set_message("Exception: " . $e->getMessage(), 'error');
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}
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}
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return $footnotes_markup;
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}
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/**
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* Creates markup for a foot note key
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*
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* @param null $footnoteKey
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* @param string $separator
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* @param bool $separator_off
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*
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* @return string
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* The footnote key markup
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*/
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function render_footnote_key($footnoteKey = null, $separator = '', $separator_off = false) {
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if (!is_object($footnoteKey) or !isset($footnoteKey->footnoteListKey)) {
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return '';
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}
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if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)) {
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return '';
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}
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if ($separator_off) {
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$separator = '';
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}
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$out = '<span class="footnote-key footnote-key-' . $footnoteKey->keyStr . MEMBER_OF_FOOTNOTES . $footnoteKey->footnoteListKey . '">'
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. $separator . '<a href="#footnote-' . $footnoteKey->keyStr . '">' . $footnoteKey->keyStr . '</a>' . '</span>';
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return $out;
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}
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/**
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* Create the markup for a footnote. This method is used in {@link Footnote::doRender()}
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* @param null $footnoteKey
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* @param null $footnoteText
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* @param string $enclosing_tag
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* default is 'span'
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*
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* @return string
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*
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*/
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function render_footnote($footnoteKey = null, $footnoteText = null, $enclosing_tag = 'span', $footnote_list_key = null) {
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_add_js_footnotes();
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if($enclosing_tag == null){
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$enclosing_tag = 'span';
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}
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$class_attribute_member_of = '';
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if($footnote_list_key){
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$class_attribute_member_of = MEMBER_OF_FOOTNOTES . $footnote_list_key;
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}
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return '<' . $enclosing_tag . ' class="footnote footnote-' . $footnoteKey . $class_attribute_member_of . '">'
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. '<a name="footnote-' . $footnoteKey . '"></a>'
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. '<span class="footnote-anchor">' . $footnoteKey . '.</span> ' . $footnoteText
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. '</' . $enclosing_tag . '>';
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}
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/**
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* Create markup for the footnotes mapped to the $footnoteListKey.
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*
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* @param null $footnote_list_key
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* The footnote list key, see RenderHints::getFootnoteListKey()
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* @param $element_tag
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* The tag for the footnote element
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*
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* @return string
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* The markup
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*/
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function render_footnotes($footnote_list_key = null, $element_tag = 'span') {
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if (variable_get('cdm_dataportal_all_footnotes', CDM_DATAPORTAL_ALL_FOOTNOTES)) {
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return '';
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}
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if (!isset($footnote_list_key) || !$footnote_list_key) {
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$footnote_list_key = RenderHints::getFootnoteListKey();
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}
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$out = '<' . $element_tag . ' class="footnotes footnotes-' . $footnote_list_key . ' ">'
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. FootnoteManager::renderFootnoteList($footnote_list_key)
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. '</' . $element_tag . '>';
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FootnoteManager::removeFootnoteList($footnote_list_key);
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return $out;
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}
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/**
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* This method determines the footnote key for original sources to be shown in the bibliography block
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*
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* The footnote key depends on the value of the 'enabled' value of the bibliography_settings
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* - enabled == 1 -> "BIBLIOGRAPHY"
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* - enabled == 0 -> "BIBLIOGRAPHY-$key_suggestion"
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*
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* @see get_bibliography_settings() and @see constant BIBLIOGRAPHY_FOOTNOTE_KEY
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*
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* @param $key_suggestion string
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* optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be retrieved by
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* calling RenderHints::getFootnoteListKey().
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*
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* @return string
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* the footnote_list_key
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*/
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function bibliography_footnote_list_key($key_suggestion = null) {
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if(!$key_suggestion){
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$key_suggestion = RenderHints::getFootnoteListKey();
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}
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$bibliography_settings = get_bibliography_settings();
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$footnote_list_key = $bibliography_settings['enabled'] == 1 ? BIBLIOGRAPHY_FOOTNOTE_KEY : BIBLIOGRAPHY_FOOTNOTE_KEY . '-' . $key_suggestion;
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return $footnote_list_key;
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}
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/**
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* Creates footnote markup for the name relationship and
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* registers it in the {@link \FootnoteManager}. The resulting foonote
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* key is returned as markup.
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*
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* @param $name_rel
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* The cdm name relationship
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* @return \FootnoteKey
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* The FootnoteKey
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*/
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function handle_name_relationship_as_footnote($name_rel)
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{
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$footnote_markup = '';
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$fnkey = null;
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if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
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$footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
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}
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if (isset($name_rel->source->citation)) {
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$footnote_markup .= '<span class="reference">' . $name_rel->source->citation->titleCache . '</span>';
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}
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if (isset($name_rel->source->citationMicroReference) && $name_rel->source->citationMicroReference) {
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$footnote_markup .= (isset($name_rel->source->citation) ? ':' : '') . ' <span class="reference_detail">' . $name_rel->source->citationMicroReference . '</span>';
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}
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if ($footnote_markup) {
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$fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
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}
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return $fnkey;
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}
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/**
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* Creates footnote markup for nomenclatural status and
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* registers it in the {@link \FootnoteManager}. The resulting foonote
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* key is returned as markup.
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*
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* @param $nom_status
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* @return \FootnoteKey
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* The FootnoteKey
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*/
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311
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function handle_nomenclatural_status_as_footnote($nom_status)
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312
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{
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// NomenclaturalStatus is a subclass of ReferencedEntityBase
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// and has the same structure as TaxonNameRelationship
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return handle_name_relationship_as_footnote($nom_status);
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}
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/**
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* Creates footnote markup for nomenclatural reference of the name and
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* registers it in the {@link \FootnoteManager}. The resulting foonote
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* key is returned as markup.
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*
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* @param $name
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* The name whose nomenclatural reference is to be shown as footnote
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* @return \FootnoteKey
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* The FootnoteKey
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*/
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function handle_nomenclatural_reference_as_footnote($name)
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{
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$footnote_markup = '';
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$footnote_key_markup = '';
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if (isset($name->nomenclaturalSource->citation) && $name->nomenclaturalSource->citation) {
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$footnote_markup .= '<span class="reference">' . $name->nomenclaturalSource->citation->titleCache . '</span>';
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}
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if (isset($name->nomenclaturalSource->citationMicroReference)) {
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$footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalSource->citationMicroReference . '</span>';
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}
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$fnkey = null;
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if ($footnote_markup) {
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$fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
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}
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return $fnkey;
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}
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345
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/* ============ annotations_and_sources handling =================== */
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346
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347
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const ANNOTATIONS_AND_SOURCE_CONFIG_DEFAULT = [
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'sources_as_content' => FALSE,
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'link_to_name_used_in_source' => TRUE,
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350
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'link_to_reference' => TRUE,
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'add_footnote_keys' => TRUE,
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'bibliography_aware' => FALSE
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];
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354
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355
|
/**
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356
|
* Provides the default configuration for handle_annotations_and_sources() in the
|
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357
|
* synonymy.
|
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358
|
*
|
|
359
|
* @return bool[]
|
|
360
|
*/
|
|
361
|
function synonymy_annotations_and_source_config() {
|
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362
|
static $annotations_and_sources_config = null;
|
|
363
|
if(!$annotations_and_sources_config){
|
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364
|
$bibliography_settings = get_bibliography_settings();
|
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365
|
$annotations_and_sources_config = [
|
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366
|
'sources_as_content' => FALSE,
|
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367
|
'link_to_name_used_in_source' => TRUE,
|
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368
|
'link_to_reference' => TRUE,
|
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369
|
'add_footnote_keys' => TRUE,
|
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370
|
'bibliography_aware' => $bibliography_settings['enabled'] == 1
|
|
371
|
];
|
|
372
|
}
|
|
373
|
return $annotations_and_sources_config;
|
|
374
|
}
|
|
375
|
|
|
376
|
/**
|
|
377
|
* Provides the default configuration for typedesignations which
|
|
378
|
* are passed to the handle_annotations_and_sources()
|
|
379
|
* function:
|
|
380
|
* - 'sources_as_content' => TRUE,
|
|
381
|
* - 'link_to_name_used_in_source' => FALSE,
|
|
382
|
* - 'link_to_reference' => TRUE,
|
|
383
|
* - 'add_footnote_keys' => FALSE,
|
|
384
|
* - 'bibliography_aware' => FALSE
|
|
385
|
*
|
|
386
|
* @return array
|
|
387
|
*/
|
|
388
|
function annotations_and_sources_config_typedesignations() {
|
|
389
|
static $annotations_and_sources_config = [
|
|
390
|
'sources_as_content' => TRUE,
|
|
391
|
'link_to_name_used_in_source' => FALSE,
|
|
392
|
'link_to_reference' => TRUE,
|
|
393
|
'add_footnote_keys' => FALSE,
|
|
394
|
'bibliography_aware' => FALSE
|
|
395
|
];
|
|
396
|
return $annotations_and_sources_config;
|
|
397
|
}
|
|
398
|
|
|
399
|
/**
|
|
400
|
* Provides the default configuration for occurrences which
|
|
401
|
* are passed to the handle_annotations_and_sources()
|
|
402
|
* function:
|
|
403
|
* - 'sources_as_content' => TRUE,
|
|
404
|
* - 'link_to_name_used_in_source' => TRUE,
|
|
405
|
* - 'link_to_reference' => FALSE,
|
|
406
|
* - 'add_footnote_keys' => FALSE,
|
|
407
|
* - 'bibliography_aware' => FALSE
|
|
408
|
*
|
|
409
|
* @return array
|
|
410
|
*/
|
|
411
|
function annotations_and_sources_config_occurrences() {
|
|
412
|
static $annotations_and_sources_config = [
|
|
413
|
'sources_as_content' => TRUE,
|
|
414
|
'link_to_name_used_in_source' => TRUE,
|
|
415
|
'link_to_reference' => FALSE,
|
|
416
|
'add_footnote_keys' => FALSE,
|
|
417
|
'bibliography_aware' => FALSE
|
|
418
|
];
|
|
419
|
return $annotations_and_sources_config;
|
|
420
|
}
|
|
421
|
|
|
422
|
function annotation_and_source_config_taxon_node() {
|
|
423
|
static $conf = null;
|
|
424
|
if(!$conf){
|
|
425
|
$bibliography_settings = get_bibliography_settings();
|
|
426
|
$conf = [
|
|
427
|
'sources_as_content' => false,
|
|
428
|
'link_to_name_used_in_source' => false,
|
|
429
|
'link_to_reference' => true,
|
|
430
|
'add_footnote_keys' => true,
|
|
431
|
'bibliography_aware' => $bibliography_settings['enabled'] == 1
|
|
432
|
];
|
|
433
|
}
|
|
434
|
return $conf;
|
|
435
|
}
|
|
436
|
|
|
437
|
/**
|
|
438
|
* Creates a handle_annotations_and_sources configuration array from feature_block_settings.
|
|
439
|
*
|
|
440
|
* The handle_annotations_and_sources configuration array is meant to be used for the
|
|
441
|
* method handle_annotations_and_sources().
|
|
442
|
*
|
|
443
|
* @param $feature_block_settings array
|
|
444
|
*
|
|
445
|
* @return array
|
|
446
|
* The configuration array for handle_annotations_and_sources()
|
|
447
|
*/
|
|
448
|
function handle_annotations_and_sources_config($feature_block_settings){
|
|
449
|
|
|
450
|
$config = [
|
|
451
|
'sources_as_content' => $feature_block_settings['sources_as_content'] == 1,
|
|
452
|
'link_to_name_used_in_source' => $feature_block_settings['link_to_name_used_in_source'] == 1,
|
|
453
|
'link_to_reference' => $feature_block_settings['link_to_reference'] == 1,
|
|
454
|
'add_footnote_keys' => (
|
|
455
|
$feature_block_settings['sources_as_content'] !== 1 ||
|
|
456
|
$feature_block_settings['sources_as_content_to_bibliography'] == 1
|
|
457
|
),
|
|
458
|
'bibliography_aware' => TRUE // FIXME shouldn't this be retrieved from the settings?
|
|
459
|
];
|
|
460
|
return $config;
|
|
461
|
}
|
|
462
|
|
|
463
|
/**
|
|
464
|
* @param $entity
|
|
465
|
* The cdm entity for which the annotations and sources are to be handled.
|
|
466
|
* @param $inline_text_prefix
|
|
467
|
* Only used to decide if the source references should be enclosed in
|
|
468
|
* brackets or not when displayed inline. This text will not be included into
|
|
469
|
* the response.
|
|
470
|
* @param $footnote_list_key_suggestion string
|
|
471
|
* Optional parameter. If this parameter is left empty (null, 0, "") the
|
|
472
|
* footnote key will be determined by the nested method calls by calling
|
|
473
|
* RenderHints::getFootnoteListKey().
|
|
474
|
*
|
|
475
|
* @return AnnotationsAndSources
|
|
476
|
* an object with the following elements:
|
|
477
|
* - foot_note_keys: all footnote keys as markup
|
|
478
|
* - source_references: an array of the source references citations
|
|
479
|
* - names used in source: an associative array of the names in source,
|
|
480
|
* the name in source strings are de-duplicated
|
|
481
|
* !!!NOTE!!!!: this field will most probably be removed soon (TODO)
|
|
482
|
*/
|
|
483
|
function handle_annotations_and_sources($entity, $inline_text_prefix = null, $footnote_list_key_suggestion = null, AnnotationsAndSources $annotationsAndSources = null) {
|
|
484
|
|
|
485
|
if($annotationsAndSources == null){
|
|
486
|
$annotationsAndSources = new AnnotationsAndSources();
|
|
487
|
}
|
|
488
|
|
|
489
|
// some entity types only have single sources:
|
|
490
|
$sources = cdm_entity_sources_sorted($entity);
|
|
491
|
|
|
492
|
$config = RenderHints::getAnnotationsAndSourceConfig();
|
|
493
|
|
|
494
|
if ($config['sources_as_content']) {
|
|
495
|
foreach ($sources as $source) {
|
|
496
|
if (_is_original_source_type($source)) {
|
|
497
|
$reference_citation = render_original_source(
|
|
498
|
$source,
|
|
499
|
$config['link_to_reference'],
|
|
500
|
$config['link_to_name_used_in_source']
|
|
501
|
);
|
|
502
|
|
|
503
|
if ($reference_citation) {
|
|
504
|
if (empty($inline_text_prefix)) {
|
|
505
|
$annotationsAndSources->addSourceReferencesCitation($reference_citation);
|
|
506
|
} else {
|
|
507
|
$annotationsAndSources->addSourceReferencesCitation(' (' . $reference_citation . ')');
|
|
508
|
}
|
|
509
|
}
|
|
510
|
|
|
511
|
// also put the name in source into the array, these are already included in the $reference_citation but are
|
|
512
|
// still required to be available separately in some contexts.
|
|
513
|
$name_in_source_render_array = compose_name_in_source(
|
|
514
|
$source,
|
|
515
|
$config['link_to_name_used_in_source']
|
|
516
|
);
|
|
517
|
|
|
518
|
if (!empty($name_in_source_render_array)) {
|
|
519
|
$annotationsAndSources->putNamesUsedInSource($name_in_source_render_array['#_plaintext'], drupal_render($name_in_source_render_array));
|
|
520
|
}
|
|
521
|
}
|
|
522
|
} // END of loop over sources
|
|
523
|
|
|
524
|
// annotations footnotes separate from sources
|
|
525
|
$footnote_keys = cdm_entity_annotations_as_footnote_keys($entity, $footnote_list_key_suggestion);
|
|
526
|
$annotationsAndSources->addAllFootNoteKeys($footnote_keys);
|
|
527
|
|
|
528
|
} // END of references inline
|
|
529
|
|
|
530
|
// footnotes for sources and annotations or put into into bibliography if requested ...
|
|
531
|
if ($config['add_footnote_keys']) {
|
|
532
|
$annotationsAndSources->addAllFootNoteKeys(cdm_entity_footnotes(
|
|
533
|
$entity,
|
|
534
|
$footnote_list_key_suggestion,
|
|
535
|
$config['link_to_reference'],
|
|
536
|
$config['link_to_name_used_in_source'],
|
|
537
|
(!empty($config['bibliography_aware']) ? $config['bibliography_aware'] : FALSE)
|
|
538
|
));
|
|
539
|
}
|
|
540
|
return $annotationsAndSources;
|
|
541
|
}
|
|
542
|
|
|
543
|
/**
|
|
544
|
* Get the source or the sources from a cdm entity and return them ordered by see compare_original_sources()
|
|
545
|
* (Some entity types only have single sources)
|
|
546
|
* @param $entity
|
|
547
|
*
|
|
548
|
* @return array
|
|
549
|
*/
|
|
550
|
function cdm_entity_sources_sorted($entity) {
|
|
551
|
if (isset($entity->source) && is_object($entity->source)) {
|
|
552
|
$sources = [$entity->source];
|
|
553
|
}
|
|
554
|
else if (isset($entity->sources)) {
|
|
555
|
$sources = $entity->sources;
|
|
556
|
}
|
|
557
|
else {
|
|
558
|
// try to load the sources
|
|
559
|
if(isset_not_empty($entity->uuid)){
|
|
560
|
$sources = cdm_ws_fetch_all(cdm_compose_ws_url('portal/' . cdm_ws_base_uri($entity->class), [ $entity->uuid, 'sources']));
|
|
561
|
} else {
|
|
562
|
// this may happen with DerivedUnitFaced, also with others?
|
|
563
|
$sources = [];
|
|
564
|
}
|
|
565
|
}
|
|
566
|
usort($sources, 'compare_original_sources');
|
|
567
|
return $sources;
|
|
568
|
}
|
|
569
|
|
|
570
|
/**
|
|
571
|
* Compare two different footnotes objects.
|
|
572
|
*
|
|
573
|
* The comparison is based on the footnote key. The one which is
|
|
574
|
* displayed as footnote number.
|
|
575
|
*
|
|
576
|
* @param mixed $a
|
|
577
|
* Footnote object $a.
|
|
578
|
* @param mixed $b
|
|
579
|
* Footnote object $b.
|
|
580
|
*
|
|
581
|
* @return int
|
|
582
|
*
|
|
583
|
* @deprecated seems to be unused: TODO remove!
|
|
584
|
*/
|
|
585
|
function footnotes_key_compare($a, $b) {
|
|
586
|
$res = 0;
|
|
587
|
if (empty($a) || empty($b)) {
|
|
588
|
return $res;
|
|
589
|
}
|
|
590
|
if ($a->keyStr < $b->keyStr) {
|
|
591
|
$res = -1;
|
|
592
|
}
|
|
593
|
elseif ($a->keyStr > $b->keyStr) {
|
|
594
|
$res = 1;
|
|
595
|
}
|
|
596
|
return $res;
|
|
597
|
}
|
|
598
|
|
|
599
|
|