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2fd6da0b
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Andreas Kohlbecker
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<?php
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/**
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* @file
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* Functions for dealing with CDM entities from the package model.name
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*
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* @copyright
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* (C) 2007-2015 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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/**
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* @defgroup compose Compose functions
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* @{
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* Functions which are composing Drupal render arays
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*
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* The cdm_dataportal module needs to compose rather complex render arrays from
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* the data returned by the CDM REST service. The compose functions are
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* responsible for creating the render arrays.
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*
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* All these functions are also implementations of the compose_hook()
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* which is used in the proxy_content() function.
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* @}
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*/
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/**
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* Provides the name render template to be used within the page elements identified the the $renderPath.
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*
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a565e612
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Andreas Kohlbecker
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* The render templates arrays contains one or more name render templates to be used within the page elements identified the the
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2fd6da0b
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Andreas Kohlbecker
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* renderPath. The renderPath is the key of the subelements whereas the value is the name render template.
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*
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a565e612
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Andreas Kohlbecker
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* The render paths used for a cdm_dataportal page can be visualized by supplying the HTTP query parameter RENDER_PATH=1.
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*
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* It will be tried to find the best matching default RenderTemplate by stripping the dot separated render path
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* element by element. If no matching template is found the DEFAULT will be used:
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*
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* - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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* - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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* - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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2fd6da0b
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Andreas Kohlbecker
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*
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* A single render template can be used for multiple render paths. In this case the according key of the render templates
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* array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.
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*
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* A render template is an associative array. The keys of this array are referring to the keys as defined in the part
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* definitions array.
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* @see get_partDefinition($taxonNameType) for more information
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*
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* The value of the render template element must be set to TRUE in order to let this part being rendered.
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* The namePart, nameAuthorPart and referencePart can also hold an associative array with a single
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* element: array('#uri' => TRUE). The value of the #uri element will be replaced by the according
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* links if the parameters $nameLink or $refenceLink are set.
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*
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a565e612
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Andreas Kohlbecker
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* @param string $render_path
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2fd6da0b
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Andreas Kohlbecker
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* The render path can consist of multiple dot separated elements
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* @see RenderHints::getRenderPath()
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* @param string $nameLink
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* The link path ot URL to be used for name parts if a link is forseen in the template
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* matching the given $renderPath.
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* @param string $referenceLink
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* The link path ot URL to be used for nomenclatural reference parts if a link is forseen
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* in the template matching the given $renderPath.
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* @return array
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* An associative array, the render template
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*/
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a565e612
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Andreas Kohlbecker
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function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {
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2fd6da0b
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Andreas Kohlbecker
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static $default_render_templates = NULL;
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03f4f6f7
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Andreas Kohlbecker
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static $split_render_templates = NULL;
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2fd6da0b
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Andreas Kohlbecker
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if (!isset($default_render_templates)) {
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$default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
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}
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03f4f6f7
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Andreas Kohlbecker
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if($split_render_templates == NULL) {
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2fd6da0b
|
Andreas Kohlbecker
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$render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
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// needs to be converted to an array
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db725031
|
Andreas Kohlbecker
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$render_templates = (object_to_array($render_templates));
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03f4f6f7
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Andreas Kohlbecker
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// separate render templates which are combined with a comma
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$split_render_templates = array();
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foreach($render_templates as $key => $template){
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if(strpos($key, ',')){
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foreach(explode(',', $key) as $path){
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$split_render_templates[$path] = $template;
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}
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} else {
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$split_render_templates[$key] = $template;
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}
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}
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2fd6da0b
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Andreas Kohlbecker
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}
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// get the base element of the renderPath
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a565e612
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Andreas Kohlbecker
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if (($separatorPos = strpos($render_path, '.')) > 0) {
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$renderPath_base = substr($render_path, 0, $separatorPos);
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2fd6da0b
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Andreas Kohlbecker
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} else {
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a565e612
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Andreas Kohlbecker
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$renderPath_base = $render_path;
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2fd6da0b
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Andreas Kohlbecker
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}
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03f4f6f7
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Andreas Kohlbecker
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$template = NULL;
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2fd6da0b
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Andreas Kohlbecker
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// 1. try to find a template using the render path base element
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03f4f6f7
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Andreas Kohlbecker
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if(array_key_exists($renderPath_base, $split_render_templates)){
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$template = (array)$split_render_templates[$renderPath_base];
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2fd6da0b
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Andreas Kohlbecker
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}
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a565e612
|
Andreas Kohlbecker
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// 2. Find best matching default RenderTemplate
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2fd6da0b
|
Andreas Kohlbecker
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// by stripping the dot separated render path element by element
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a565e612
|
Andreas Kohlbecker
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// if no matching template is found the DEFAULT will be used.
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while (!is_array($template) && strlen($render_path) > 0) {
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03f4f6f7
|
Andreas Kohlbecker
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foreach ($split_render_templates as $path => $t) {
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a565e612
|
Andreas Kohlbecker
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if ($path == $render_path) {
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2fd6da0b
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Andreas Kohlbecker
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$template = $t;
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break;
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}
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}
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// shorten by one element
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a565e612
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Andreas Kohlbecker
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$render_path = substr($render_path, strrpos($render_path, '.') + 1, strlen($render_path));
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2fd6da0b
|
Andreas Kohlbecker
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}
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03f4f6f7
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Andreas Kohlbecker
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2fd6da0b
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Andreas Kohlbecker
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// 3. Otherwise get default RenderTemplate from theme.
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if (!is_array($template)) {
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03f4f6f7
|
Andreas Kohlbecker
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$template = $split_render_templates['#DEFAULT'];
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2fd6da0b
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Andreas Kohlbecker
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}
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// --- set the link uris to the according template fields if they exist
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if(isset($template['nameAuthorPart']) && isset($template['nameAuthorPart']['#uri'])) {
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if ($nameLink) {
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$template['nameAuthorPart']['#uri'] = $nameLink;
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}
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else {
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unset($template['nameAuthorPart']['#uri']);
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}
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}
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if ($nameLink && isset($template['namePart']['#uri'])) {
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$template['namePart']['#uri'] = $nameLink;
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}
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else {
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unset($template['namePart']['#uri']);
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}
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if ($referenceLink && isset($template['referencePart']['#uri'])) {
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$template['referencePart']['#uri'] = $referenceLink;
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}
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else {
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unset($template['referencePart']['#uri']);
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}
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return $template;
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}
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/**
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* The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.
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*
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* A full taxon name plus additional information can consist of the following elements:
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*
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* - name: the taxon name inclugin rank nbut without author
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* - authorTeam: The authors of a reference, also used in taxon names
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* - authors: The authors of a reference, also used in taxon names
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* - reference: the nomenclatural reference,
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* - microreference: Volume, page number etc.
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* - status: The nomenclatural status of a name
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* - description: name descriptions like protologues etc ...
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*
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* These elements are combined in the part definitions array to from the specific parts to be rendered.
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* Usually the following parts are formed:
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*
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* The name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example here:
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* - namePart: the name and rank (in example: "Lapsana communis")
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* - authorshipPart: the author (in example: "L.")
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* - nameAuthorPart: the combination of name and author part (in example: "Lapsana communis L.").
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* This is useful for zoological names where the authorshipPart belongs to the name and both should
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* be combined when a link to the taxon is rendered.
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* - referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")
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* - microreferencePart: usually the page number (in example ": 811.")
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* - statusPart: the nomenclatorical status
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* - descriptionPart:
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*
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* Each set of parts is dedicated to render a specific TaxonName type, the type names are used as keys for the
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* specific parts part definitions:
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*
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* - BotanicalName
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* - ZoologicalName
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* - #DEFAULT: covers ViralNames and general NonViralNames
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*
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* An example:
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* @code
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* array(
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* 'ZoologicalName' => array(
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* 'namePart' => array('name' => TRUE),
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* 'referencePart' => array('authorTeam' => TRUE),
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* 'microreferencePart' => array('microreference' => TRUE),
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* 'statusPart' => array('status' => TRUE),
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* 'descriptionPart' => array('description' => TRUE),
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* ),
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* 'BotanicalName' => array(
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* 'namePart' => array(
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* 'name' => TRUE,
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* 'authors' => TRUE,
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* ),
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* 'referencePart' => array(
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* 'reference' => TRUE,
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* 'microreference' => TRUE,
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* ),
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* 'statusPart' => array('status' => TRUE),
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* 'descriptionPart' => array('description' => TRUE),
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* ),
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* );
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* @endcode
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*
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219 |
828a0c8c
|
Andreas Kohlbecker
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* @param object $taxonNameType
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* A cdm TaxonNameType entity
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*
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2fd6da0b
|
Andreas Kohlbecker
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*/
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function get_partDefinition($taxonNameType) {
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static $default_part_definitions = null;
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if (!isset($default_part_definitions)) {
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$default_part_definitions= unserialize(CDM_PART_DEFINITIONS_DEFAULT);
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}
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static $part_definitions = null;
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if (!isset($part_definitions)) {
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232 |
db725031
|
Andreas Kohlbecker
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$part_definitions = object_to_array(variable_get(CDM_PART_DEFINITIONS, $default_part_definitions));
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233 |
2fd6da0b
|
Andreas Kohlbecker
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}
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c2545e1c
|
Andreas Kohlbecker
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$dtype = nameTypeToDTYPE($taxonNameType);
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2fd6da0b
|
Andreas Kohlbecker
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if (array_key_exists($taxonNameType, $part_definitions)) {
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return $part_definitions[$taxonNameType];
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c2545e1c
|
Andreas Kohlbecker
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} else if (array_key_exists($dtype, $part_definitions)) {
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return $part_definitions[$dtype];
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240 |
2fd6da0b
|
Andreas Kohlbecker
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} else {
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return $part_definitions['#DEFAULT']; // covers ViralNames and general NonViralNames
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}
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}
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/**
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* Renders the markup for a CDM TaxonName instance.
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*
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* The layout of the name representation is configured by the
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* part_definitions and render_templates (see get_partDefinition() and
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* get_nameRenderTemplate())
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*
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* @param $taxonName
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255 |
102f8c26
|
Andreas Kohlbecker
|
* cdm TaxonName instance
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256 |
2fd6da0b
|
Andreas Kohlbecker
|
* @param $nameLink
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* URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method
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* @param $refenceLink
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* URI to the reference, @see path_to_reference(), must be processed by url() before passing to this method
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* @param $show_annotations
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* turns the display of annotations on
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* @param $is_type_designation
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* To indicate that the supplied taxon name is a name type designation.
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* @param $skiptags
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* an array of name elements tags like 'name', 'rank' to skip. The name part
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* 'authors' will not ber affected by this filter. This part is managed though the render template
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* mechanism.
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268 |
c35bab7f
|
Andreas Kohlbecker
|
* @param $is_invalid
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* Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
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* This is useful when rendering taxon relation ships.
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271 |
2fd6da0b
|
Andreas Kohlbecker
|
*
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* @return string
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* The markup for a taxon name.
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*
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*/
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276 |
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function render_taxon_or_name($taxon_name_or_taxon_base, $nameLink = NULL, $refenceLink = NULL,
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277 |
c35bab7f
|
Andreas Kohlbecker
|
$show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {
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278 |
2fd6da0b
|
Andreas Kohlbecker
|
|
279 |
ea3933d7
|
Andreas Kohlbecker
|
$is_doubtful = false;
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2fd6da0b
|
Andreas Kohlbecker
|
if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){
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$taxonName = $taxon_name_or_taxon_base->name;
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283 |
ea3933d7
|
Andreas Kohlbecker
|
$is_doubtful = $taxon_name_or_taxon_base->doubtful;
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284 |
2fd6da0b
|
Andreas Kohlbecker
|
// use the TaxonBase.taggedTitle so we have the secRef
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$taggedTitle = $taxon_name_or_taxon_base->taggedTitle;
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} else {
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287 |
102f8c26
|
Andreas Kohlbecker
|
// assuming this is a TaxonName
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288 |
2fd6da0b
|
Andreas Kohlbecker
|
$taxonName = $taxon_name_or_taxon_base;
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$taggedTitle = $taxon_name_or_taxon_base->taggedName;
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}
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$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
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294 |
c2545e1c
|
Andreas Kohlbecker
|
$partDefinition = get_partDefinition($taxonName->nameType);
|
295 |
2fd6da0b
|
Andreas Kohlbecker
|
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296 |
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// Apply definitions to template.
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297 |
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foreach ($renderTemplate as $part => $uri) {
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298 |
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|
|
if (isset($partDefinition[$part])) {
|
300 |
|
|
$renderTemplate[$part] = $partDefinition[$part];
|
301 |
|
|
}
|
302 |
|
|
if (is_array($uri) && isset($uri['#uri'])) {
|
303 |
|
|
$renderTemplate[$part]['#uri'] = $uri['#uri'];
|
304 |
|
|
}
|
305 |
|
|
}
|
306 |
|
|
|
307 |
83dc60b9
|
Andreas Kohlbecker
|
$secref_tagged_text = tagged_text_extract_secref($taggedTitle);
|
308 |
|
|
$nom_status_tagged_text = tagged_text_extract_nomstatus($taggedTitle);
|
309 |
c35bab7f
|
Andreas Kohlbecker
|
$appended_phrase_tagged_text = array(); // this is filled later
|
310 |
|
|
|
311 |
e90899ac
|
Andreas Kohlbecker
|
normalize_tagged_text($taggedTitle);
|
312 |
2fd6da0b
|
Andreas Kohlbecker
|
|
313 |
|
|
$firstEntryIsValidNamePart =
|
314 |
|
|
isset($taggedTitle)
|
315 |
|
|
&& is_array($taggedTitle)
|
316 |
|
|
&& isset($taggedTitle[0]->text)
|
317 |
|
|
&& is_string($taggedTitle[0]->text)
|
318 |
|
|
&& $taggedTitle[0]->text != ''
|
319 |
|
|
&& isset($taggedTitle[0]->type)
|
320 |
|
|
&& $taggedTitle[0]->type == 'name';
|
321 |
|
|
$lastAuthorElementString = FALSE;
|
322 |
|
|
|
323 |
c35bab7f
|
Andreas Kohlbecker
|
$name_encasement = $is_invalid ? '"' : '';
|
324 |
54a3c136
|
Andreas Kohlbecker
|
$doubtful_marker = $is_doubtful ? '? ' : ''; //   = NARROW NO-BREAK SPACE
|
325 |
2330b553
|
Andreas Kohlbecker
|
$doubtful_marker_markup = '';
|
326 |
|
|
|
327 |
|
|
if($doubtful_marker){
|
328 |
|
|
$doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
|
329 |
|
|
}
|
330 |
c35bab7f
|
Andreas Kohlbecker
|
|
331 |
|
|
// split off all appendedPhrase item from the end of the array (usually there only should be one)
|
332 |
|
|
while($taggedTitle[count($taggedTitle)-1]->type == "appendedPhrase"){
|
333 |
|
|
$appended_phrase_tagged_text[] = array_pop($taggedTitle);
|
334 |
|
|
}
|
335 |
|
|
|
336 |
2fd6da0b
|
Andreas Kohlbecker
|
// Got to use second entry as first one, see ToDo comment below ...
|
337 |
|
|
if ($firstEntryIsValidNamePart) {
|
338 |
|
|
|
339 |
|
|
$taggedName = $taggedTitle;
|
340 |
|
|
$hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
|
341 |
|
|
$hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
|
342 |
|
|
|
343 |
c35bab7f
|
Andreas Kohlbecker
|
|
344 |
2fd6da0b
|
Andreas Kohlbecker
|
if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
|
345 |
|
|
// Find author and split off from name.
|
346 |
|
|
// TODO expecting to find the author as the last element.
|
347 |
|
|
/*
|
348 |
|
|
if($taggedName[count($taggedName)- 1]->type == 'authors'){
|
349 |
|
|
$authorTeam = $taggedName[count($taggedName)- 1]->text;
|
350 |
|
|
unset($taggedName[count($taggedName)- 1]);
|
351 |
|
|
}
|
352 |
|
|
*/
|
353 |
|
|
|
354 |
|
|
// Remove all authors.
|
355 |
|
|
$taggedNameNew = array();
|
356 |
|
|
foreach ($taggedName as $element) {
|
357 |
|
|
if ($element->type != 'authors') {
|
358 |
|
|
$taggedNameNew[] = $element;
|
359 |
|
|
}
|
360 |
|
|
else {
|
361 |
|
|
$lastAuthorElementString = $element->text;
|
362 |
|
|
}
|
363 |
|
|
}
|
364 |
|
|
$taggedName = $taggedNameNew;
|
365 |
e90899ac
|
Andreas Kohlbecker
|
unset($taggedNameNew);
|
366 |
2fd6da0b
|
Andreas Kohlbecker
|
}
|
367 |
0f129a6f
|
Andreas Kohlbecker
|
$name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
|
368 |
2fd6da0b
|
Andreas Kohlbecker
|
}
|
369 |
|
|
else {
|
370 |
2330b553
|
Andreas Kohlbecker
|
$name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
|
371 |
c35bab7f
|
Andreas Kohlbecker
|
}
|
372 |
|
|
|
373 |
|
|
|
374 |
|
|
if(isset($appended_phrase_tagged_text[0])){
|
375 |
54a3c136
|
Andreas Kohlbecker
|
$name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
|
376 |
2fd6da0b
|
Andreas Kohlbecker
|
}
|
377 |
|
|
|
378 |
|
|
// Fill name into $renderTemplate.
|
379 |
c35bab7f
|
Andreas Kohlbecker
|
array_setr('name', $name , $renderTemplate);
|
380 |
2fd6da0b
|
Andreas Kohlbecker
|
|
381 |
|
|
// Fill with authorTeam.
|
382 |
|
|
/*
|
383 |
|
|
if($authorTeam){
|
384 |
|
|
$authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
|
385 |
|
|
array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
|
386 |
|
|
}
|
387 |
|
|
*/
|
388 |
|
|
|
389 |
|
|
// Fill with reference.
|
390 |
|
|
if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
|
391 |
|
|
|
392 |
eaff53f7
|
Andreas Kohlbecker
|
$registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
|
393 |
|
|
$registration_markup = render_registrations($registrations);
|
394 |
|
|
|
395 |
2fd6da0b
|
Andreas Kohlbecker
|
// default separator
|
396 |
|
|
$separator = '';
|
397 |
|
|
|
398 |
|
|
// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
|
399 |
|
|
// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
|
400 |
|
|
if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {
|
401 |
|
|
$microreference = NULL;
|
402 |
|
|
if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
|
403 |
|
|
$microreference = $taxonName->nomenclaturalMicroReference;
|
404 |
|
|
}
|
405 |
|
|
$citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
|
406 |
|
|
|
407 |
|
|
// Find preceding element of the reference.
|
408 |
|
|
$precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
|
409 |
|
|
if (str_beginsWith($citation, ", in")) {
|
410 |
|
|
$citation = substr($citation, 2);
|
411 |
|
|
$separator = ' ';
|
412 |
|
|
}
|
413 |
|
|
elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
|
414 |
|
|
$separator = ', ';
|
415 |
|
|
} else {
|
416 |
|
|
$separator = ' ';
|
417 |
|
|
}
|
418 |
|
|
|
419 |
|
|
|
420 |
|
|
$referenceArray['#separator'] = $separator;
|
421 |
eaff53f7
|
Andreas Kohlbecker
|
$referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
|
422 |
2fd6da0b
|
Andreas Kohlbecker
|
array_setr('reference', $referenceArray, $renderTemplate);
|
423 |
|
|
}
|
424 |
|
|
|
425 |
|
|
// If authors have been removed from the name part the last named authorteam
|
426 |
|
|
// should be added to the reference citation, otherwise, keep the separator
|
427 |
|
|
// out of the reference.
|
428 |
|
|
if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
|
429 |
|
|
// If the nomenclaturalReference citation is not included in the
|
430 |
eaff53f7
|
Andreas Kohlbecker
|
// reference part but display of the microreference
|
431 |
2fd6da0b
|
Andreas Kohlbecker
|
// is wanted, append the microreference to the authorTeam.
|
432 |
|
|
$citation = '';
|
433 |
|
|
if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
|
434 |
|
|
$separator = ": ";
|
435 |
|
|
$citation = $taxonName->nomenclaturalMicroReference;
|
436 |
|
|
}
|
437 |
|
|
$referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
|
438 |
|
|
array_setr('authors', $referenceArray, $renderTemplate);
|
439 |
|
|
}
|
440 |
|
|
}
|
441 |
|
|
|
442 |
|
|
$is_reference_year = false;
|
443 |
|
|
if (isset($renderTemplate['referenceYearPart']['reference.year'])) {
|
444 |
|
|
if(isset($taxonName->nomenclaturalReference->datePublished)){
|
445 |
|
|
$referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalReference->datePublished) . '</span>';
|
446 |
|
|
array_setr('reference.year', $referenceArray, $renderTemplate);
|
447 |
|
|
$is_reference_year = true;
|
448 |
|
|
}
|
449 |
|
|
}
|
450 |
|
|
|
451 |
e90899ac
|
Andreas Kohlbecker
|
// Fill with status.
|
452 |
dce1dacc
|
Andreas Kohlbecker
|
if(isset($renderTemplate['statusPart']['status'])){
|
453 |
1d0407b7
|
Andreas Kohlbecker
|
if (isset($nom_status_tagged_text[0])) {
|
454 |
0f129a6f
|
Andreas Kohlbecker
|
array_setr('status', '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator')) . '</span>', $renderTemplate);
|
455 |
e90899ac
|
Andreas Kohlbecker
|
}
|
456 |
|
|
}
|
457 |
|
|
|
458 |
2fd6da0b
|
Andreas Kohlbecker
|
if (isset($renderTemplate['secReferencePart'])){
|
459 |
|
|
if(isset($secref_tagged_text[1])){
|
460 |
e90899ac
|
Andreas Kohlbecker
|
$post_separator_markup = $is_reference_year ? '.': '';
|
461 |
6aad9da8
|
Andreas Kohlbecker
|
if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type == 'postSeparator')){
|
462 |
4a1ab871
|
Andreas Kohlbecker
|
$post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
|
463 |
e90899ac
|
Andreas Kohlbecker
|
};
|
464 |
2fd6da0b
|
Andreas Kohlbecker
|
array_setr('secReference',
|
465 |
e90899ac
|
Andreas Kohlbecker
|
$post_separator_markup
|
466 |
2fd6da0b
|
Andreas Kohlbecker
|
. ' <span class="sec_reference">'
|
467 |
4bfe18f9
|
Andreas Kohlbecker
|
. join('', cdm_tagged_text_values($secref_tagged_text))
|
468 |
2fd6da0b
|
Andreas Kohlbecker
|
. '</span>', $renderTemplate);
|
469 |
|
|
}
|
470 |
|
|
}
|
471 |
|
|
|
472 |
|
|
// Fill with protologues etc...
|
473 |
|
|
$descriptionHtml = '';
|
474 |
|
|
if (array_setr('description', TRUE, $renderTemplate)) {
|
475 |
|
|
$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
|
476 |
|
|
foreach ($descriptions as $description) {
|
477 |
|
|
if (!empty($description)) {
|
478 |
|
|
foreach ($description->elements as $description_element) {
|
479 |
|
|
$second_citation = '';
|
480 |
|
|
if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
|
481 |
|
|
$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
|
482 |
|
|
}
|
483 |
|
|
$descriptionHtml .= $second_citation;
|
484 |
275b2642
|
Andreas Kohlbecker
|
$descriptionHtml .= cdm_description_element_media(
|
485 |
|
|
$description_element,
|
486 |
|
|
array(
|
487 |
2fd6da0b
|
Andreas Kohlbecker
|
'application/pdf',
|
488 |
|
|
'image/png',
|
489 |
|
|
'image/jpeg',
|
490 |
|
|
'image/gif',
|
491 |
|
|
'text/html',
|
492 |
|
|
)
|
493 |
|
|
);
|
494 |
|
|
|
495 |
|
|
}
|
496 |
|
|
}
|
497 |
|
|
}
|
498 |
|
|
array_setr('description', $descriptionHtml, $renderTemplate);
|
499 |
|
|
}
|
500 |
|
|
|
501 |
|
|
// Render.
|
502 |
f695daf4
|
Andreas Kohlbecker
|
$out = '';
|
503 |
|
|
if(isset($_REQUEST['RENDER_PATH'])){
|
504 |
|
|
// developer option to show the render path with each taxon name
|
505 |
|
|
$out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
|
506 |
|
|
}
|
507 |
|
|
$out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
|
508 |
|
|
. '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
|
509 |
2fd6da0b
|
Andreas Kohlbecker
|
|
510 |
|
|
foreach ($renderTemplate as $partName => $part) {
|
511 |
|
|
$separator = '';
|
512 |
|
|
$partHtml = '';
|
513 |
|
|
$uri = FALSE;
|
514 |
|
|
if (!is_array($part)) {
|
515 |
|
|
continue;
|
516 |
|
|
}
|
517 |
|
|
if (isset($part['#uri']) && is_string($part['#uri'])) {
|
518 |
|
|
$uri = $part['#uri'];
|
519 |
|
|
unset($part['#uri']);
|
520 |
|
|
}
|
521 |
|
|
foreach ($part as $key => $content) {
|
522 |
|
|
$html = '';
|
523 |
|
|
if (is_array($content)) {
|
524 |
|
|
$html = $content['#html'];
|
525 |
|
|
if(isset($content['#separator'])) {
|
526 |
|
|
$separator = $content['#separator'];
|
527 |
|
|
}
|
528 |
|
|
}
|
529 |
|
|
elseif (is_string($content)) {
|
530 |
|
|
$html = $content;
|
531 |
|
|
}
|
532 |
|
|
$partHtml .= '<span class="' . $key . '">' . $html . '</span>';
|
533 |
|
|
}
|
534 |
|
|
if ($uri) {
|
535 |
|
|
// cannot use l() here since the #uri aleady should have been processed through uri() at this point
|
536 |
|
|
$out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
|
537 |
|
|
|
538 |
|
|
}
|
539 |
|
|
else {
|
540 |
|
|
$out .= $separator . $partHtml;
|
541 |
|
|
}
|
542 |
|
|
}
|
543 |
|
|
$out .= '</span>';
|
544 |
|
|
if ($show_annotations) {
|
545 |
|
|
// $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
|
546 |
|
|
}
|
547 |
|
|
return $out;
|
548 |
|
|
}
|
549 |
|
|
|
550 |
7212f0bc
|
Andreas Kohlbecker
|
|
551 |
|
|
|
552 |
|
|
/**
|
553 |
26b8a1bc
|
Andreas Kohlbecker
|
* Composes information for a registration from a dto object.
|
554 |
|
|
*
|
555 |
|
|
* Registrations which are not yet published are suppressed.
|
556 |
7212f0bc
|
Andreas Kohlbecker
|
*
|
557 |
|
|
* @param $registration_dto
|
558 |
|
|
* @param $with_citation
|
559 |
|
|
* Whether to show the citation.
|
560 |
|
|
*
|
561 |
|
|
* @return array
|
562 |
|
|
* A drupal render array with the elements:
|
563 |
26b8a1bc
|
Andreas Kohlbecker
|
* - 'name'
|
564 |
|
|
* - 'name-relations'
|
565 |
|
|
* - 'specimen_type_designations'
|
566 |
|
|
* - 'name_type_designations'
|
567 |
7212f0bc
|
Andreas Kohlbecker
|
* - 'citation'
|
568 |
26b8a1bc
|
Andreas Kohlbecker
|
* - 'registration_date_and_institute'
|
569 |
7212f0bc
|
Andreas Kohlbecker
|
* @ingroup compose
|
570 |
|
|
*/
|
571 |
26b8a1bc
|
Andreas Kohlbecker
|
function compose_registration_dto_full($registration_dto, $with_citation = true)
|
572 |
7212f0bc
|
Andreas Kohlbecker
|
{
|
573 |
|
|
$render_array = array();
|
574 |
|
|
|
575 |
26b8a1bc
|
Andreas Kohlbecker
|
if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
|
576 |
|
|
return $render_array;
|
577 |
|
|
}
|
578 |
|
|
|
579 |
|
|
// name and typedesignation in detail
|
580 |
|
|
if($registration_dto->nameRef){
|
581 |
|
|
$name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
|
582 |
|
|
$render_array['name'] = markup_to_render_array('<p class="name">' . render_taxon_or_name($name) . '</p>', 0);
|
583 |
|
|
$name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
|
584 |
|
|
$render_array['name_relations'] = markup_to_render_array(render_name_relationships_of($name_relations, $registration_dto->nameRef->uuid, null, false));
|
585 |
|
|
$render_array['name_relations']['#weight'] = 10;
|
586 |
|
|
}
|
587 |
|
|
if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
|
588 |
|
|
$field_unit_uuids = array();
|
589 |
|
|
$specimen_type_designation_refs = array();
|
590 |
|
|
$name_type_designation_refs = array();
|
591 |
|
|
foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $field_unit_ref => $obj) {
|
592 |
|
|
$tokens = explode("#", $field_unit_ref);
|
593 |
|
|
foreach ($obj as $type_status => $entity_reference_list) {
|
594 |
|
|
// NOTE: there is always only one element, since we use the foreach to extract the objects field name and value
|
595 |
|
|
$entity_reference = $entity_reference_list[0];
|
596 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
597 |
26b8a1bc
|
Andreas Kohlbecker
|
if ($tokens[0] == 'NameTypeDesignation') {
|
598 |
7212f0bc
|
Andreas Kohlbecker
|
foreach ($obj as $type_status => $entity_reference_list) {
|
599 |
26b8a1bc
|
Andreas Kohlbecker
|
$name_type_designation_refs[$type_status] = $entity_reference;
|
600 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
601 |
26b8a1bc
|
Andreas Kohlbecker
|
} else if ($tokens[0] == 'FieldUnit'){
|
602 |
|
|
$field_unit_uuids[] = $tokens[1];
|
603 |
|
|
$specimen_type_designation_refs[$type_status] = $entity_reference;
|
604 |
|
|
} else {
|
605 |
|
|
drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
|
606 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
607 |
|
|
}
|
608 |
26b8a1bc
|
Andreas Kohlbecker
|
if (count($name_type_designation_refs) > 0) {
|
609 |
|
|
$render_array['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
|
610 |
|
|
$render_array['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
|
611 |
|
|
$render_array['name_type_designations']['#suffix'] = '</p>';
|
612 |
|
|
$render_array['name_type_designations']['#weight'] = 20;
|
613 |
|
|
}
|
614 |
|
|
if (count($field_unit_uuids) > 0) {
|
615 |
|
|
$render_array['specimen_type_designations'] = compose_specimen_type_designations($specimen_type_designation_refs);
|
616 |
|
|
}
|
617 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
618 |
|
|
|
619 |
|
|
// citation
|
620 |
|
|
if ($with_citation) {
|
621 |
|
|
$render_array['citation'] = markup_to_render_array(
|
622 |
|
|
"<p class=\"citation " . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
|
623 |
|
|
. l($registration_dto->bibliographicInRefCitationString, path_to_reference($registration_dto->citationUuid))
|
624 |
|
|
. "</p>",
|
625 |
|
|
50);
|
626 |
|
|
}
|
627 |
|
|
|
628 |
|
|
// registration date and office
|
629 |
26b8a1bc
|
Andreas Kohlbecker
|
$registration_date_insitute_markup = render_registration_date_and_intitute($registration_dto);
|
630 |
|
|
if($registration_date_insitute_markup){
|
631 |
|
|
$render_array['registration_date_and_institute'] = markup_to_render_array(
|
632 |
|
|
$registration_date_insitute_markup . '</p>',
|
633 |
|
|
100);
|
634 |
|
|
}
|
635 |
|
|
|
636 |
|
|
return $render_array;
|
637 |
|
|
}
|
638 |
|
|
|
639 |
|
|
|
640 |
|
|
/**
|
641 |
|
|
* Composes a compact representation for a registrationDTO object
|
642 |
|
|
*
|
643 |
|
|
* Registrations which are not yet published are suppressed.
|
644 |
|
|
*
|
645 |
|
|
* @param $registration_dto
|
646 |
|
|
* @param $style string
|
647 |
|
|
* The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
|
648 |
|
|
* - 'citation': Similar to the arrearance of nomenclatural acts in print media
|
649 |
|
|
* - 'list-item' : style suitable for result lists etc
|
650 |
|
|
*
|
651 |
|
|
* @return array
|
652 |
|
|
* A drupal render array with the elements:
|
653 |
|
|
* - 'registration-metadata' when $style == 'list-item'
|
654 |
|
|
* - 'summary'
|
655 |
|
|
* @ingroup compose
|
656 |
|
|
*/
|
657 |
|
|
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
|
658 |
|
|
{
|
659 |
|
|
$render_array = array();
|
660 |
|
|
$media_link_map = array();
|
661 |
|
|
|
662 |
|
|
if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
|
663 |
|
|
return $render_array;
|
664 |
|
|
}
|
665 |
|
|
|
666 |
|
|
$registration_date_insitute_markup = render_registration_date_and_intitute($registration_dto, 'span');
|
667 |
|
|
$itentifier_markup = l($registration_dto->identifier, $registration_dto->identifier, array('attributes' => array('class' => array('identifier'))));
|
668 |
|
|
|
669 |
|
|
$taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
|
670 |
|
|
foreach ($taggged_text_expanded as $tagged_text){
|
671 |
|
|
if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
|
672 |
|
|
$mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
|
673 |
|
|
if(isset($mediaDTOs[0]->uri)){
|
674 |
|
|
$media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
|
675 |
|
|
$tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
|
676 |
|
|
$media_link_map[$media_url_key] = cdm_external_uri($mediaDTOs[0]->uri, true);
|
677 |
|
|
}
|
678 |
|
|
}
|
679 |
|
|
}
|
680 |
|
|
$registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
|
681 |
|
|
foreach($media_link_map as $media_url_key => $link){
|
682 |
|
|
$registation_markup = str_replace($media_url_key, $link, $registation_markup);
|
683 |
|
|
}
|
684 |
|
|
if($style == 'citation') {
|
685 |
|
|
$registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
|
686 |
|
|
} else {
|
687 |
|
|
$render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
|
688 |
|
|
}
|
689 |
|
|
$render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . 'class="registration-summary">' . $registation_markup . "</' . $tag_enclosing_summary . '>", 0);
|
690 |
|
|
|
691 |
|
|
return $render_array;
|
692 |
|
|
}
|
693 |
|
|
|
694 |
|
|
|
695 |
|
|
/**
|
696 |
|
|
* Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
|
697 |
|
|
*
|
698 |
|
|
* @param $registration_dto
|
699 |
|
|
* @return string
|
700 |
|
|
* The markup or an empty string
|
701 |
|
|
*/
|
702 |
|
|
function render_registration_date_and_intitute($registration_dto, $enclosing_tag = 'p') {
|
703 |
|
|
$registration_date_insitute_markup = '';
|
704 |
|
|
if ($registration_dto->registrationDate) {
|
705 |
7212f0bc
|
Andreas Kohlbecker
|
$date_string = format_datetime($registration_dto->registrationDate);
|
706 |
26b8a1bc
|
Andreas Kohlbecker
|
if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
|
707 |
7212f0bc
|
Andreas Kohlbecker
|
$registration_date_insitute_markup =
|
708 |
|
|
t("Registration on @date in @institution", array(
|
709 |
|
|
'@date' => $date_string,
|
710 |
|
|
'@institution' => $registration_dto->institutionTitleCache,
|
711 |
|
|
));
|
712 |
|
|
} else {
|
713 |
|
|
$registration_date_insitute_markup =
|
714 |
|
|
t("Registration on @date", array(
|
715 |
|
|
'@date' => $date_string
|
716 |
|
|
));
|
717 |
|
|
}
|
718 |
26b8a1bc
|
Andreas Kohlbecker
|
$registration_date_insitute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_insitute_markup . '</' .$enclosing_tag . '>';
|
719 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
720 |
26b8a1bc
|
Andreas Kohlbecker
|
return $registration_date_insitute_markup;
|
721 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
722 |
|
|
|
723 |
|
|
|
724 |
eaff53f7
|
Andreas Kohlbecker
|
/**
|
725 |
|
|
* @param $registrations
|
726 |
|
|
* @return string
|
727 |
|
|
*/
|
728 |
|
|
function render_registrations($registrations)
|
729 |
|
|
{
|
730 |
|
|
$registration_markup = '';
|
731 |
|
|
$registration_markup_array = array();
|
732 |
|
|
if ($registrations) {
|
733 |
|
|
foreach ($registrations as $reg) {
|
734 |
|
|
$registration_markup_array[] = render_registration($reg);
|
735 |
|
|
}
|
736 |
|
|
$registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
|
737 |
|
|
. join(', ', $registration_markup_array);
|
738 |
|
|
}
|
739 |
|
|
return $registration_markup;
|
740 |
|
|
}
|
741 |
|
|
|
742 |
471192e3
|
Andreas Kohlbecker
|
|
743 |
7212f0bc
|
Andreas Kohlbecker
|
/**
|
744 |
|
|
* Renders a registration
|
745 |
|
|
*
|
746 |
26b8a1bc
|
Andreas Kohlbecker
|
* TODO replace by compose_registration_dto_compact
|
747 |
7212f0bc
|
Andreas Kohlbecker
|
* @param $registration
|
748 |
|
|
*/
|
749 |
|
|
function render_registration($registration){
|
750 |
|
|
$markup = '';
|
751 |
|
|
|
752 |
|
|
if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
|
753 |
|
|
$office_class_attribute = '';
|
754 |
|
|
if(isset($registration->institution->titleCache)){
|
755 |
26b8a1bc
|
Andreas Kohlbecker
|
$office_class_attribute = registration_intitute_class_attribute($registration);
|
756 |
7212f0bc
|
Andreas Kohlbecker
|
}
|
757 |
|
|
$markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, $registration->identifier) . ', '
|
758 |
|
|
. preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
|
759 |
|
|
. '</span>';
|
760 |
|
|
}
|
761 |
|
|
return $markup;
|
762 |
|
|
}
|
763 |
|
|
|
764 |
26b8a1bc
|
Andreas Kohlbecker
|
/**
|
765 |
|
|
* @param $registration
|
766 |
|
|
* @return string
|
767 |
|
|
*/
|
768 |
|
|
function registration_intitute_class_attribute($registration_dto)
|
769 |
|
|
{
|
770 |
|
|
if(isset($registration_dto->institutionTitleCache)){
|
771 |
|
|
$institutionTitleCache = $registration_dto->institutionTitleCache;
|
772 |
|
|
} else {
|
773 |
|
|
// fall back option to also support cdm entities
|
774 |
|
|
$institutionTitleCache = @$registration_dto->institution->titleCache;
|
775 |
|
|
}
|
776 |
|
|
return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
|
777 |
|
|
}
|
778 |
|
|
|
779 |
7212f0bc
|
Andreas Kohlbecker
|
|
780 |
471192e3
|
Andreas Kohlbecker
|
/**
|
781 |
|
|
* Composes the TypedEntityReference to name type designations passed as associatve array.
|
782 |
|
|
*
|
783 |
f5e7f68e
|
Andreas Kohlbecker
|
* @param $$type_entity_refs array
|
784 |
471192e3
|
Andreas Kohlbecker
|
* an associative array of name type type => TypedEntityReference for name type designations as
|
785 |
|
|
* produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
|
786 |
|
|
*
|
787 |
|
|
* @ingroup compose
|
788 |
|
|
*/
|
789 |
|
|
function compose_name_type_designations($type_entity_refs){
|
790 |
|
|
$render_array = array();
|
791 |
|
|
foreach($type_entity_refs as $type_status => $name_type){
|
792 |
f5e7f68e
|
Andreas Kohlbecker
|
$type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
|
793 |
|
|
if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
|
794 |
|
|
$preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
|
795 |
|
|
}
|
796 |
|
|
$render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type) . '"><span class="type_status">'. ucfirst($type_status) . "</span>: "
|
797 |
|
|
. $name_type->label
|
798 |
|
|
. ($preferredStableUri ? " ". l($preferredStableUri, $preferredStableUri) : '')
|
799 |
|
|
. '</div>');
|
800 |
|
|
}
|
801 |
|
|
return $render_array;
|
802 |
|
|
}
|
803 |
|
|
|
804 |
|
|
/**
|
805 |
|
|
* Composes the TypedEntityReference to specimen type designations passed as associatve array.
|
806 |
|
|
*
|
807 |
|
|
* @param $type_entity_refs array
|
808 |
|
|
* an associative array of specimen type type => TypedEntityReference for specimen type designations as
|
809 |
|
|
* produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
|
810 |
|
|
*
|
811 |
|
|
* @ingroup compose
|
812 |
|
|
*/
|
813 |
|
|
function compose_specimen_type_designations($type_entity_refs){
|
814 |
204e8173
|
Andreas Kohlbecker
|
|
815 |
f5e7f68e
|
Andreas Kohlbecker
|
$render_array = array();
|
816 |
204e8173
|
Andreas Kohlbecker
|
|
817 |
f5e7f68e
|
Andreas Kohlbecker
|
foreach($type_entity_refs as $type_status => $specimen_type){
|
818 |
|
|
$type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($specimen_type->uuid));
|
819 |
204e8173
|
Andreas Kohlbecker
|
|
820 |
f5e7f68e
|
Andreas Kohlbecker
|
$preferredStableUri = '';
|
821 |
204e8173
|
Andreas Kohlbecker
|
$citation_markup = '';
|
822 |
|
|
$media = '';
|
823 |
|
|
|
824 |
|
|
// preferredStableUri
|
825 |
f5e7f68e
|
Andreas Kohlbecker
|
if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
|
826 |
|
|
$preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
|
827 |
|
|
}
|
828 |
204e8173
|
Andreas Kohlbecker
|
|
829 |
|
|
$mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
|
830 |
|
|
if($mediaSpecimen){
|
831 |
|
|
// compose output
|
832 |
|
|
// mediaURI
|
833 |
|
|
if(isset($mediaSpecimen->representations[0])) {
|
834 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
835 |
|
|
$captionElements = array(
|
836 |
|
|
'#uri' => t('open media'),
|
837 |
|
|
'elements' => array('-none-'),
|
838 |
|
|
'sources_as_content' => true
|
839 |
|
|
);
|
840 |
|
|
$media = compose_cdm_media_gallerie(array(
|
841 |
|
|
'mediaList' => array($mediaSpecimen),
|
842 |
|
|
'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
|
843 |
|
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
844 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
845 |
|
|
'captionElements' => $captionElements,
|
846 |
|
|
));
|
847 |
|
|
}
|
848 |
|
|
// citation and detail
|
849 |
|
|
$annotations_and_sources = handle_annotations_and_sources(
|
850 |
|
|
$mediaSpecimen,
|
851 |
|
|
array(
|
852 |
|
|
'sources_as_content' => true,
|
853 |
|
|
'link_to_name_used_in_source' => false,
|
854 |
|
|
'link_to_reference' => true,
|
855 |
|
|
'add_footnote_keys' => false,
|
856 |
|
|
'bibliography_aware' => false),
|
857 |
|
|
'',
|
858 |
|
|
null
|
859 |
|
|
);
|
860 |
|
|
if(is_array( $annotations_and_sources['source_references'])){
|
861 |
|
|
$citation_markup = join(', ', $annotations_and_sources['source_references']);
|
862 |
|
|
}
|
863 |
|
|
}
|
864 |
|
|
|
865 |
|
|
$render_array[] = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type) . '">
|
866 |
|
|
<span class="type_status">' . ucfirst($type_status) . "</span>: "
|
867 |
f5e7f68e
|
Andreas Kohlbecker
|
. $specimen_type->label
|
868 |
204e8173
|
Andreas Kohlbecker
|
. ($citation_markup ? ' '. $citation_markup : '')
|
869 |
f5e7f68e
|
Andreas Kohlbecker
|
. ($preferredStableUri ? " ". l($preferredStableUri, $preferredStableUri) : '')
|
870 |
204e8173
|
Andreas Kohlbecker
|
. $media
|
871 |
f5e7f68e
|
Andreas Kohlbecker
|
. '</div>');
|
872 |
471192e3
|
Andreas Kohlbecker
|
}
|
873 |
|
|
return $render_array;
|
874 |
|
|
}
|
875 |
|
|
|
876 |
2fd6da0b
|
Andreas Kohlbecker
|
/**
|
877 |
d4ea0dd9
|
Andreas Kohlbecker
|
* Renders the name relationships.
|
878 |
0b7bbf68
|
Andreas Kohlbecker
|
*
|
879 |
d4ea0dd9
|
Andreas Kohlbecker
|
* @param $name_relations
|
880 |
|
|
* The list of CDM NameRelationsips
|
881 |
|
|
* @param $current_name_uuid
|
882 |
3c088da3
|
Andreas Kohlbecker
|
* The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
|
883 |
|
|
* rendering the relation an only the other name is shown. Parameter is REQUIRED.
|
884 |
|
|
* @param $suppress_if_current_name_is_source
|
885 |
|
|
* The display of the relation will be
|
886 |
|
|
* suppressed is the current name is on the source of the relation edge.
|
887 |
|
|
* That is if it is on the from side of the relation. Except for 'blocking name for' which is
|
888 |
|
|
* an inverse relation. For this relation type the toName is taken in to account.
|
889 |
d4ea0dd9
|
Andreas Kohlbecker
|
* @param $current_taxon_uuid
|
890 |
|
|
* The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
|
891 |
0b7bbf68
|
Andreas Kohlbecker
|
* @return String
|
892 |
d4ea0dd9
|
Andreas Kohlbecker
|
* The markup for the name relationships
|
893 |
0b7bbf68
|
Andreas Kohlbecker
|
*/
|
894 |
3c088da3
|
Andreas Kohlbecker
|
function render_name_relationships_of($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
|
895 |
f695daf4
|
Andreas Kohlbecker
|
|
896 |
6421984d
|
Andreas Kohlbecker
|
static $inverse_name_rels_uuids = array(UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
|
897 |
|
|
|
898 |
0b7bbf68
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('homonym');
|
899 |
|
|
// the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
|
900 |
|
|
|
901 |
6421984d
|
Andreas Kohlbecker
|
$selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_TYPES, unserialize(CDM_NAME_RELATIONSHIP_TYPES_DEFAULT));
|
902 |
|
|
|
903 |
d4ea0dd9
|
Andreas Kohlbecker
|
$relations_array = array();
|
904 |
0b7bbf68
|
Andreas Kohlbecker
|
|
905 |
|
|
if ($name_relations) {
|
906 |
d4ea0dd9
|
Andreas Kohlbecker
|
foreach ($name_relations as $name_rel) {
|
907 |
3c088da3
|
Andreas Kohlbecker
|
if (!(isset($selected_name_rel_uuids[$name_rel->type->uuid]) && $selected_name_rel_uuids[$name_rel->type->uuid])) {
|
908 |
6421984d
|
Andreas Kohlbecker
|
// skip if not selected in the settings
|
909 |
|
|
continue;
|
910 |
0b7bbf68
|
Andreas Kohlbecker
|
}
|
911 |
3c088da3
|
Andreas Kohlbecker
|
$is_inverse_relation = array_search($name_rel->type->uuid, $inverse_name_rels_uuids) !== false;
|
912 |
|
|
$is_current_name_to_name = $current_name_uuid == $name_rel->toName->uuid;
|
913 |
|
|
$is_current_name_from_name = $current_name_uuid == $name_rel->fromName->uuid;
|
914 |
d4ea0dd9
|
Andreas Kohlbecker
|
$relationship_markup = null;
|
915 |
f1c8d19a
|
Andreas Kohlbecker
|
|
916 |
3c088da3
|
Andreas Kohlbecker
|
if($is_current_name_to_name && ($suppress_if_current_name_is_source && $is_inverse_relation || !$suppress_if_current_name_is_source)){
|
917 |
|
|
$highlited_synonym_uuid = isset ($name_rel->fromName->taxonBases[0]->uuid) ? $name_rel->fromName->taxonBases[0]->uuid : '';
|
918 |
|
|
$relationship_markup = render_taxon_or_name($name_rel->fromName,
|
919 |
|
|
url(path_to_name($name_rel->fromName->uuid, $current_taxon_uuid, $highlited_synonym_uuid))
|
920 |
|
|
);
|
921 |
|
|
} else if($is_current_name_from_name && ($suppress_if_current_name_is_source && !$is_inverse_relation || !$suppress_if_current_name_is_source)){
|
922 |
d4ea0dd9
|
Andreas Kohlbecker
|
$highlited_synonym_uuid = isset ($name_rel->toName->taxonBases[0]->uuid) ? $name_rel->toName->taxonBases[0]->uuid : '';
|
923 |
3c088da3
|
Andreas Kohlbecker
|
$relationship_markup = render_taxon_or_name($name_rel->toName,
|
924 |
|
|
url(path_to_name($name_rel->toName->uuid, $current_taxon_uuid, $highlited_synonym_uuid))
|
925 |
|
|
);
|
926 |
0b7bbf68
|
Andreas Kohlbecker
|
}
|
927 |
3c088da3
|
Andreas Kohlbecker
|
|
928 |
d4ea0dd9
|
Andreas Kohlbecker
|
if($relationship_markup){
|
929 |
|
|
if (count($relations_array)) {
|
930 |
6aa5dc6a
|
Andreas Kohlbecker
|
// lat: "non nec" == german: "weder noch"
|
931 |
d4ea0dd9
|
Andreas Kohlbecker
|
$relations_array [] = 'nec ' . $relationship_markup;
|
932 |
6aa5dc6a
|
Andreas Kohlbecker
|
} else {
|
933 |
d4ea0dd9
|
Andreas Kohlbecker
|
$relations_array [] = 'non ' . $relationship_markup;
|
934 |
6aa5dc6a
|
Andreas Kohlbecker
|
}
|
935 |
6421984d
|
Andreas Kohlbecker
|
}
|
936 |
|
|
|
937 |
0b7bbf68
|
Andreas Kohlbecker
|
}
|
938 |
|
|
}
|
939 |
|
|
|
940 |
|
|
RenderHints::popFromRenderStack();
|
941 |
bbeade6a
|
Andreas Kohlbecker
|
return (count($relations_array) ?'<div class="name-relationships">[' . trim(join(" ", $relations_array)) . ']</div>' : '');
|
942 |
d4ea0dd9
|
Andreas Kohlbecker
|
}
|
943 |
|
|
|
944 |
|
|
/**
|
945 |
|
|
* @param $taxon
|
946 |
|
|
* @return array
|
947 |
|
|
*/
|
948 |
|
|
function cdm_name_relationships_for_taxon($taxon)
|
949 |
|
|
{
|
950 |
|
|
$from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
|
951 |
|
|
$to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
|
952 |
|
|
$name_relations = array_merge($from_name_relations, $to_name_relations);
|
953 |
|
|
return $name_relations;
|
954 |
0b7bbf68
|
Andreas Kohlbecker
|
}
|
955 |
|
|
|
956 |
|
|
|
957 |
d4ea0dd9
|
Andreas Kohlbecker
|
/**
|
958 |
2fd6da0b
|
Andreas Kohlbecker
|
* Recursively searches the array for the $key and sets the given value.
|
959 |
|
|
*
|
960 |
|
|
* @param mixed $key
|
961 |
|
|
* Key to search for.
|
962 |
|
|
* @param mixed $value
|
963 |
|
|
* Value to set.'
|
964 |
|
|
* @param array $array
|
965 |
|
|
* Array to search in.
|
966 |
|
|
*
|
967 |
|
|
* @return bool
|
968 |
|
|
* True if the key has been found.
|
969 |
|
|
*/
|
970 |
|
|
function &array_setr($key, $value, array &$array) {
|
971 |
|
|
$res = NULL;
|
972 |
|
|
foreach ($array as $k => &$v) {
|
973 |
|
|
if ($key == $k) {
|
974 |
|
|
$v = $value;
|
975 |
|
|
return $array;
|
976 |
|
|
}
|
977 |
|
|
elseif (is_array($v)) {
|
978 |
|
|
$innerArray = array_setr($key, $value, $v);
|
979 |
|
|
if ($innerArray) {
|
980 |
|
|
return $array;
|
981 |
|
|
}
|
982 |
|
|
}
|
983 |
|
|
}
|
984 |
|
|
return $res;
|
985 |
|
|
}
|
986 |
|
|
|
987 |
|
|
/**
|
988 |
|
|
* @todo Please document this function.
|
989 |
|
|
* @see http://drupal.org/node/1354
|
990 |
|
|
*/
|
991 |
|
|
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
|
992 |
|
|
$res = NULL;
|
993 |
|
|
$precedingElement = NULL;
|
994 |
|
|
foreach ($renderTemplate as &$part) {
|
995 |
|
|
foreach ($part as $key => &$element) {
|
996 |
|
|
if ($key == $contentElementKey) {
|
997 |
|
|
return $precedingElement;
|
998 |
|
|
}
|
999 |
|
|
$precedingElement = $element;
|
1000 |
|
|
}
|
1001 |
|
|
}
|
1002 |
|
|
return $res;
|
1003 |
|
|
}
|
1004 |
|
|
|
1005 |
|
|
/**
|
1006 |
|
|
* @todo Please document this function.
|
1007 |
|
|
* @see http://drupal.org/node/1354
|
1008 |
|
|
*/
|
1009 |
|
|
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
|
1010 |
|
|
$res = NULL;
|
1011 |
|
|
$precedingKey = NULL;
|
1012 |
|
|
foreach ($renderTemplate as &$part) {
|
1013 |
|
|
if (is_array($part)) {
|
1014 |
|
|
foreach ($part as $key => &$element) {
|
1015 |
|
|
if ($key == $contentElementKey) {
|
1016 |
|
|
return $precedingKey;
|
1017 |
|
|
}
|
1018 |
|
|
if (!str_beginsWith($key, '#')) {
|
1019 |
|
|
$precedingKey = $key;
|
1020 |
|
|
}
|
1021 |
|
|
}
|
1022 |
|
|
}
|
1023 |
|
|
}
|
1024 |
|
|
return $res;
|
1025 |
|
|
}
|
1026 |
c2545e1c
|
Andreas Kohlbecker
|
|
1027 |
|
|
function nameTypeToDTYPE($dtype){
|
1028 |
|
|
static $nameTypeLabelMap = array(
|
1029 |
|
|
"ICNB" => "BacterialName",
|
1030 |
|
|
"ICNAFP" => "BotanicalName",
|
1031 |
|
|
"ICNCP" => "CultivarPlantName",
|
1032 |
|
|
"ICZN" => "ZoologicalName",
|
1033 |
|
|
"ICVCN" => "ViralName",
|
1034 |
|
|
"Any taxon name" => "TaxonName",
|
1035 |
|
|
"NonViral" => "TaxonName",
|
1036 |
|
|
"Fungus" => "BotanicalName",
|
1037 |
|
|
"Plant" => "BotanicalName",
|
1038 |
|
|
"Algae" => "BotanicalName",
|
1039 |
|
|
);
|
1040 |
|
|
return $nameTypeLabelMap[$dtype];
|
1041 |
|
|
|
1042 |
|
|
}
|