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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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* 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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* 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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* 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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*
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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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* @param string $render_path
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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 $renderPath.
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* @return array
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* An associative array, the render template
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*/
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function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {
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static $default_render_templates = NULL;
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static $split_render_templates = NULL;
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if (!isset($default_render_templates)) {
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$default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
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}
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if($split_render_templates == NULL) {
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$render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
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// needs to be converted to an array
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$render_templates = (object_to_array($render_templates));
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// separate render templates which are combined with a comma
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$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] = $template;
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}
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}
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}
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// get the base element of the renderPath
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if (($separatorPos = strpos($render_path, '.')) > 0) {
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$renderPath_base = substr($render_path, 0, $separatorPos);
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} else {
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$renderPath_base = $render_path;
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}
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$template = NULL;
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// 1. try to find a template using the render path base element
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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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}
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// 2. Find best matching default RenderTemplate
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// by stripping the dot separated render path element by element
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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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foreach ($split_render_templates as $path => $t) {
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if ($path == $render_path) {
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$template = $t;
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break;
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}
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}
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// shorten by one element
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$render_path = substr($render_path, strrpos($render_path, '.') + 1, strlen($render_path));
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}
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// 3. Otherwise get default RenderTemplate from theme.
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if (!is_array($template)) {
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$template = $split_render_templates['#DEFAULT'];
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}
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// --- set the link uris to the according template fields if they exist
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if(isset($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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* @param object $taxonNameType
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* A cdm TaxonNameType entity
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*
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*/
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function get_partDefinition($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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$part_definitions = object_to_array(variable_get(CDM_PART_DEFINITIONS, $default_part_definitions));
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}
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$dtype = nameTypeToDTYPE($taxonNameType);
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if (array_key_exists($taxonNameType, $part_definitions)) {
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return $part_definitions[$taxonNameType];
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} else if (array_key_exists($dtype, $part_definitions)) {
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return $part_definitions[$dtype];
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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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* cdm TaxonName instance
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* @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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* @param $is_invalid
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* Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
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* This is useful when rendering taxon relation ships.
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*
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* @return string
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* The markup for a taxon name.
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*
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*/
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function render_taxon_or_name($taxon_name_or_taxon_base, $nameLink = NULL, $refenceLink = NULL,
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$show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {
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$is_doubtful = false;
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if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){
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$taxonName = $taxon_name_or_taxon_base->name;
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$is_doubtful = $taxon_name_or_taxon_base->doubtful;
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// use the TaxonBase.tagged_title so we have the secRef
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$tagged_title = $taxon_name_or_taxon_base->taggedTitle;
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} else {
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// assuming this is a TaxonName
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$taxonName = $taxon_name_or_taxon_base;
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if(isset($taxonName->taggedFullTitle)){
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$tagged_title = $taxon_name_or_taxon_base->taggedFullTitle;
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} else {
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$tagged_title = $taxon_name_or_taxon_base->taggedName;
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}
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}
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$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
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$partDefinition = get_partDefinition($taxonName->nameType);
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// Apply definitions to template.
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foreach ($renderTemplate as $part => $uri) {
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if (isset($partDefinition[$part])) {
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$renderTemplate[$part] = $partDefinition[$part];
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}
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if (is_array($uri) && isset($uri['#uri'])) {
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$renderTemplate[$part]['#uri'] = $uri['#uri'];
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}
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}
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$secref_tagged_text = tagged_text_extract_reference_and_detail($tagged_title);
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// taxon names will have the nomenclatural reference in the tagged full title:
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$nomref_tagged_text = tagged_text_extract_reference($tagged_title);
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$nom_status_tagged_text = tagged_text_extract_nomstatus($tagged_title);
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$appended_phrase_tagged_text = array(); // this is filled later
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normalize_tagged_text($tagged_title);
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$is_valid_tagged_title =
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isset($tagged_title)
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&& is_array($tagged_title)
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&& isset($tagged_title[0]->text)
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&& is_string($tagged_title[0]->text)
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&& $tagged_title[0]->text != ''
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&& isset($tagged_title[0]->type);
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$lastAuthorElementString = FALSE;
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$name_encasement = $is_invalid ? '"' : '';
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$doubtful_marker = $is_doubtful ? '? ' : ''; //   = NARROW NO-BREAK SPACE
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$doubtful_marker_markup = '';
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if($doubtful_marker){
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$doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
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if($tagged_title[0]->text == '?' ){
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// remove the first tagged text element
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unset($tagged_title[0]);
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}
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}
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// split off all appendedPhrase item from the end of the array (usually there only should be one)
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while($tagged_title[count($tagged_title)-1]->type == "appendedPhrase"){
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$appended_phrase_tagged_text[] = array_pop($tagged_title);
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}
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// Got to use second entry as first one, see ToDo comment below ...
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if ($is_valid_tagged_title) {
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$taggedName = $tagged_title;
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$hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
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350
|
$hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
|
|
351
|
|
|
352
|
|
|
353
|
if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
|
|
354
|
// Find author and split off from name.
|
|
355
|
// TODO expecting to find the author as the last element.
|
|
356
|
/*
|
|
357
|
if($taggedName[count($taggedName)- 1]->type == 'authors'){
|
|
358
|
$authorTeam = $taggedName[count($taggedName)- 1]->text;
|
|
359
|
unset($taggedName[count($taggedName)- 1]);
|
|
360
|
}
|
|
361
|
*/
|
|
362
|
|
|
363
|
// Remove all authors.
|
|
364
|
$taggedNameNew = array();
|
|
365
|
foreach ($taggedName as $element) {
|
|
366
|
if ($element->type != 'authors') {
|
|
367
|
$taggedNameNew[] = $element;
|
|
368
|
}
|
|
369
|
else {
|
|
370
|
$lastAuthorElementString = $element->text;
|
|
371
|
}
|
|
372
|
}
|
|
373
|
$taggedName = $taggedNameNew;
|
|
374
|
unset($taggedNameNew);
|
|
375
|
}
|
|
376
|
$name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
|
|
377
|
}
|
|
378
|
else {
|
|
379
|
// use titleCache instead
|
|
380
|
$name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
|
|
381
|
}
|
|
382
|
|
|
383
|
|
|
384
|
if(isset($appended_phrase_tagged_text[0])){
|
|
385
|
$name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
|
|
386
|
}
|
|
387
|
|
|
388
|
// Fill name into $renderTemplate.
|
|
389
|
array_setr('name', $name , $renderTemplate);
|
|
390
|
|
|
391
|
// Fill with authorTeam.
|
|
392
|
/*
|
|
393
|
if($authorTeam){
|
|
394
|
$authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
|
|
395
|
array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
|
|
396
|
}
|
|
397
|
*/
|
|
398
|
|
|
399
|
// Fill with reference.
|
|
400
|
if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
|
|
401
|
|
|
402
|
$registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
|
|
403
|
$registration_markup = render_registrations($registrations);
|
|
404
|
|
|
405
|
// default separator
|
|
406
|
$separator = '';
|
|
407
|
|
|
408
|
// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
|
|
409
|
// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
|
|
410
|
if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {
|
|
411
|
$microreference = NULL;
|
|
412
|
if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
|
|
413
|
$microreference = $taxonName->nomenclaturalMicroReference;
|
|
414
|
}
|
|
415
|
if(count($nomref_tagged_text) == 0){
|
|
416
|
$citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
|
|
417
|
// Find preceding element of the reference.
|
|
418
|
$precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
|
|
419
|
if (str_beginsWith($citation, ", in")) {
|
|
420
|
$citation = substr($citation, 2);
|
|
421
|
$separator = ' ';
|
|
422
|
}
|
|
423
|
elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
|
|
424
|
$separator = ', ';
|
|
425
|
} else {
|
|
426
|
$separator = ' ';
|
|
427
|
}
|
|
428
|
$referenceArray['#separator'] = $separator;
|
|
429
|
$referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
|
|
430
|
} else {
|
|
431
|
// this ist the case for taxon names
|
|
432
|
$referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);
|
|
433
|
}
|
|
434
|
|
|
435
|
|
|
436
|
array_setr('reference', $referenceArray, $renderTemplate);
|
|
437
|
}
|
|
438
|
|
|
439
|
// If authors have been removed from the name part the last named authorteam
|
|
440
|
// should be added to the reference citation, otherwise, keep the separator
|
|
441
|
// out of the reference.
|
|
442
|
if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
|
|
443
|
// If the nomenclaturalReference citation is not included in the
|
|
444
|
// reference part but display of the microreference
|
|
445
|
// is wanted, append the microreference to the authorTeam.
|
|
446
|
$citation = '';
|
|
447
|
if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
|
|
448
|
$separator = ": ";
|
|
449
|
$citation = $taxonName->nomenclaturalMicroReference;
|
|
450
|
}
|
|
451
|
$referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
|
|
452
|
array_setr('authors', $referenceArray, $renderTemplate);
|
|
453
|
}
|
|
454
|
}
|
|
455
|
|
|
456
|
$is_reference_year = false;
|
|
457
|
if (isset($renderTemplate['referenceYearPart']['reference.year'])) {
|
|
458
|
if(isset($taxonName->nomenclaturalReference->datePublished)){
|
|
459
|
$referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalReference->datePublished) . '</span>';
|
|
460
|
array_setr('reference.year', $referenceArray, $renderTemplate);
|
|
461
|
$is_reference_year = true;
|
|
462
|
}
|
|
463
|
}
|
|
464
|
|
|
465
|
// Fill with status.
|
|
466
|
if(isset($renderTemplate['statusPart']['status'])){
|
|
467
|
if (isset($nom_status_tagged_text[0])) {
|
|
468
|
$tt_to_markup_options = array('html' => false);
|
|
469
|
foreach ($nom_status_tagged_text as &$tt){
|
|
470
|
if($tt->type == 'nomStatus'&& isset($tt->entityReference)) {
|
|
471
|
$nom_status = cdm_ws_get(CDM_WS_NOMENCLATURALSTATUS, array($tt->entityReference->uuid));
|
|
472
|
$nom_status_fkey = nomenclatural_status_footnote_markup($nom_status);
|
|
473
|
$tt->text .= $nom_status_fkey;
|
|
474
|
$tt_to_markup_options['html'] = true;
|
|
475
|
}
|
|
476
|
}
|
|
477
|
array_setr(
|
|
478
|
'status',
|
|
479
|
'<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator'), 'span', $tt_to_markup_options) . '</span>', $renderTemplate);
|
|
480
|
}
|
|
481
|
}
|
|
482
|
|
|
483
|
if (isset($renderTemplate['secReferencePart'])){
|
|
484
|
if(isset($secref_tagged_text[1])){
|
|
485
|
$post_separator_markup = $is_reference_year ? '.': '';
|
|
486
|
if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type == 'postSeparator')){
|
|
487
|
$post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
|
|
488
|
};
|
|
489
|
array_setr('secReference',
|
|
490
|
$post_separator_markup
|
|
491
|
. ' <span class="sec_reference">'
|
|
492
|
. join('', cdm_tagged_text_values($secref_tagged_text))
|
|
493
|
. '</span>', $renderTemplate);
|
|
494
|
}
|
|
495
|
}
|
|
496
|
|
|
497
|
// Fill with protologues etc...
|
|
498
|
$descriptionHtml = '';
|
|
499
|
if (array_setr('description', TRUE, $renderTemplate)) {
|
|
500
|
$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
|
|
501
|
foreach ($descriptions as $description) {
|
|
502
|
if (!empty($description)) {
|
|
503
|
foreach ($description->elements as $description_element) {
|
|
504
|
$second_citation = '';
|
|
505
|
if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
|
|
506
|
$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
|
|
507
|
}
|
|
508
|
$descriptionHtml .= $second_citation;
|
|
509
|
$descriptionHtml .= cdm_description_element_media(
|
|
510
|
$description_element,
|
|
511
|
array(
|
|
512
|
'application/pdf',
|
|
513
|
'image/png',
|
|
514
|
'image/jpeg',
|
|
515
|
'image/gif',
|
|
516
|
'text/html',
|
|
517
|
)
|
|
518
|
);
|
|
519
|
|
|
520
|
}
|
|
521
|
}
|
|
522
|
}
|
|
523
|
array_setr('description', $descriptionHtml, $renderTemplate);
|
|
524
|
}
|
|
525
|
|
|
526
|
// Render.
|
|
527
|
$out = '';
|
|
528
|
if(isset($_REQUEST['RENDER_PATH'])){
|
|
529
|
// developer option to show the render path with each taxon name
|
|
530
|
$out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
|
|
531
|
}
|
|
532
|
$out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
|
|
533
|
. '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
|
|
534
|
|
|
535
|
foreach ($renderTemplate as $partName => $part) {
|
|
536
|
$separator = '';
|
|
537
|
$partHtml = '';
|
|
538
|
$uri = FALSE;
|
|
539
|
if (!is_array($part)) {
|
|
540
|
continue;
|
|
541
|
}
|
|
542
|
if (isset($part['#uri']) && is_string($part['#uri'])) {
|
|
543
|
$uri = $part['#uri'];
|
|
544
|
unset($part['#uri']);
|
|
545
|
}
|
|
546
|
foreach ($part as $key => $content) {
|
|
547
|
$html = '';
|
|
548
|
if (is_array($content)) {
|
|
549
|
$html = $content['#html'];
|
|
550
|
if(isset($content['#separator'])) {
|
|
551
|
$separator = $content['#separator'];
|
|
552
|
}
|
|
553
|
}
|
|
554
|
elseif (is_string($content)) {
|
|
555
|
$html = $content;
|
|
556
|
}
|
|
557
|
$partHtml .= '<span class="' . $key . '">' . $html . '</span>';
|
|
558
|
}
|
|
559
|
if ($uri) {
|
|
560
|
// cannot use l() here since the #uri aleady should have been processed through uri() at this point
|
|
561
|
$out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
|
|
562
|
|
|
563
|
}
|
|
564
|
else {
|
|
565
|
$out .= $separator . $partHtml;
|
|
566
|
}
|
|
567
|
}
|
|
568
|
$out .= '</span>';
|
|
569
|
if ($show_annotations) {
|
|
570
|
// $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
|
|
571
|
}
|
|
572
|
return $out;
|
|
573
|
}
|
|
574
|
|
|
575
|
|
|
576
|
|
|
577
|
/**
|
|
578
|
* Composes information for a registration from a dto object.
|
|
579
|
*
|
|
580
|
* Registrations which are not yet published are suppressed.
|
|
581
|
*
|
|
582
|
* @param $registration_dto
|
|
583
|
* @param $with_citation
|
|
584
|
* Whether to show the citation.
|
|
585
|
*
|
|
586
|
* @return array
|
|
587
|
* A drupal render array with the elements:
|
|
588
|
* - 'name'
|
|
589
|
* - 'name-relations'
|
|
590
|
* - 'specimen_type_designations'
|
|
591
|
* - 'name_type_designations'
|
|
592
|
* - 'citation'
|
|
593
|
* - 'registration_date_and_institute'
|
|
594
|
* @ingroup compose
|
|
595
|
*/
|
|
596
|
function compose_registration_dto_full($registration_dto, $with_citation = true)
|
|
597
|
{
|
|
598
|
$render_array = array(
|
|
599
|
'#prefix' => '<div class="registration">',
|
|
600
|
'#suffix' => '</div>'
|
|
601
|
);
|
|
602
|
|
|
603
|
if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
|
|
604
|
return $render_array;
|
|
605
|
}
|
|
606
|
|
|
607
|
$render_array['sub_headline'] = markup_to_render_array(join(", ", registration_types($registration_dto)),-10, '<h3 class="registration_type">' . t('Event: '), '</h3>' );
|
|
608
|
$render_array['nomenclatural_act'] = array(
|
|
609
|
'#weight' => 0,
|
|
610
|
'#prefix' => '<div class="nomenclatural_act">',
|
|
611
|
|
|
612
|
'#suffix' => '</div>'
|
|
613
|
);
|
|
614
|
|
|
615
|
// name
|
|
616
|
if($registration_dto->nameRef){
|
|
617
|
$name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
|
|
618
|
cdm_load_tagged_full_title($name);
|
|
619
|
$render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
|
|
620
|
$name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
|
|
621
|
$render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
|
|
622
|
$render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
|
|
623
|
} else {
|
|
624
|
// in this case the registration must have a
|
|
625
|
$name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
|
|
626
|
$render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
|
|
627
|
}
|
|
628
|
// typedesignation in detail
|
|
629
|
if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
|
|
630
|
$field_unit_uuids = array();
|
|
631
|
$specimen_type_designation_refs = array();
|
|
632
|
$name_type_designation_refs = array();
|
|
633
|
foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
|
|
634
|
$tokens = explode("#", $workingset_ref);
|
|
635
|
$types_in_fieldunit = get_object_vars($obj); // convert into associative array
|
|
636
|
|
|
637
|
if ($tokens[0] == 'NameTypeDesignation') {
|
|
638
|
foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
|
|
639
|
if(!isset($name_type_designation_refs[$type_status])){
|
|
640
|
$name_type_designation_refs[$type_status] = $entity_reference_list;
|
|
641
|
} else {
|
|
642
|
array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);
|
|
643
|
}
|
|
644
|
}
|
|
645
|
} else if ($tokens[0] == 'FieldUnit'){
|
|
646
|
$field_unit_uuids[] = $tokens[1];
|
|
647
|
foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
|
|
648
|
if(!isset($specimen_type_designation_refs[$type_status])){
|
|
649
|
$specimen_type_designation_refs[$type_status] = $entity_reference_list;
|
|
650
|
} else {
|
|
651
|
array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);
|
|
652
|
}
|
|
653
|
}
|
|
654
|
} else {
|
|
655
|
drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
|
|
656
|
}
|
|
657
|
}
|
|
658
|
// type designations wich are in this nomenclatural act.
|
|
659
|
if (count($name_type_designation_refs) > 0) {
|
|
660
|
$render_array['nomenclatural_act']['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
|
|
661
|
$render_array['nomenclatural_act']['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
|
|
662
|
$render_array['nomenclatural_act']['name_type_designations']['#suffix'] = '</p>';
|
|
663
|
$render_array['nomenclatural_act']['name_type_designations']['#weight'] = 20;
|
|
664
|
}
|
|
665
|
if (count($field_unit_uuids) > 0) {
|
|
666
|
$specimen_type_designations_array = compose_specimen_type_designations($specimen_type_designation_refs, true);
|
|
667
|
$render_array['nomenclatural_act']['specimen_type_designations'] = $specimen_type_designations_array['type_designations'];
|
|
668
|
$render_array['map'] = $specimen_type_designations_array['map'];
|
|
669
|
$render_array['map']['#weight'] = $render_array['nomenclatural_act']['#weight'] + 20;
|
|
670
|
}
|
|
671
|
}
|
|
672
|
|
|
673
|
// citation
|
|
674
|
if ($with_citation) {
|
|
675
|
$render_array['citation'] = markup_to_render_array(
|
|
676
|
"<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
|
|
677
|
. "<span class=\"label\">published in: </span>"
|
|
678
|
. $registration_dto->bibliographicInRefCitationString
|
|
679
|
. l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))
|
|
680
|
. "</div>",
|
|
681
|
$render_array['nomenclatural_act']['#weight'] + 10 );
|
|
682
|
}
|
|
683
|
|
|
684
|
// registration date and office
|
|
685
|
$registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
|
|
686
|
if($registration_date_insitute_markup){
|
|
687
|
$render_array['registration_date_and_institute'] = markup_to_render_array(
|
|
688
|
$registration_date_insitute_markup . '</p>',
|
|
689
|
100);
|
|
690
|
}
|
|
691
|
|
|
692
|
return $render_array;
|
|
693
|
}
|
|
694
|
|
|
695
|
|
|
696
|
/**
|
|
697
|
* Composes a compact representation for a registrationDTO object
|
|
698
|
*
|
|
699
|
* Registrations which are not yet published are suppressed.
|
|
700
|
*
|
|
701
|
* @param $registration_dto
|
|
702
|
* @param $style string
|
|
703
|
* The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
|
|
704
|
* - 'citation': Similar to the arrearance of nomenclatural acts in print media
|
|
705
|
* - 'list-item' : style suitable for result lists etc
|
|
706
|
*
|
|
707
|
* @return array
|
|
708
|
* A drupal render array with the elements:
|
|
709
|
* - 'registration-metadata' when $style == 'list-item'
|
|
710
|
* - 'summary'
|
|
711
|
* @ingroup compose
|
|
712
|
*/
|
|
713
|
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
|
|
714
|
{
|
|
715
|
$render_array = array();
|
|
716
|
$media_link_map = array();
|
|
717
|
|
|
718
|
if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
|
|
719
|
return $render_array;
|
|
720
|
}
|
|
721
|
|
|
722
|
$registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
|
|
723
|
$itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
|
|
724
|
|
|
725
|
$tagged_text_options = array();
|
|
726
|
if(isset($registration_dto->nameRef)){
|
|
727
|
$tagged_text_options[] = array(
|
|
728
|
'filter-type' => 'name',
|
|
729
|
'prefix' => '<span class="registered_name">',
|
|
730
|
'suffix' => '</span>',
|
|
731
|
);
|
|
732
|
} else {
|
|
733
|
$tagged_text_options[] = array(
|
|
734
|
'filter-type' => 'name',
|
|
735
|
'prefix' => '<span class="referenced_typified_name">',
|
|
736
|
'suffix' => '</span>',
|
|
737
|
);
|
|
738
|
}
|
|
739
|
cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
|
|
740
|
$taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
|
|
741
|
foreach ($taggged_text_expanded as $tagged_text){
|
|
742
|
if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
|
|
743
|
$mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
|
|
744
|
if(isset($mediaDTOs[0]->uri)){
|
|
745
|
$media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
|
|
746
|
$tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
|
|
747
|
$media_link_map[$media_url_key] = cdm_external_uri($mediaDTOs[0]->uri, true);
|
|
748
|
}
|
|
749
|
}
|
|
750
|
}
|
|
751
|
$registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
|
|
752
|
foreach($media_link_map as $media_url_key => $link){
|
|
753
|
$registation_markup = str_replace($media_url_key, $link, $registation_markup);
|
|
754
|
}
|
|
755
|
if($style == 'citation') {
|
|
756
|
$registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
|
|
757
|
} else {
|
|
758
|
$render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
|
|
759
|
}
|
|
760
|
$render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
|
|
761
|
|
|
762
|
return $render_array;
|
|
763
|
}
|
|
764
|
|
|
765
|
|
|
766
|
/**
|
|
767
|
* Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
|
|
768
|
*
|
|
769
|
* @param $registration_dto
|
|
770
|
* @return string
|
|
771
|
* The markup or an empty string
|
|
772
|
*/
|
|
773
|
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
|
|
774
|
$registration_date_institute_markup = '';
|
|
775
|
if ($registration_dto->registrationDate) {
|
|
776
|
$date_string = format_datetime($registration_dto->registrationDate);
|
|
777
|
if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
|
|
778
|
$registration_date_institute_markup =
|
|
779
|
t("Registration on @date in @institution", array(
|
|
780
|
'@date' => $date_string,
|
|
781
|
'@institution' => $registration_dto->institutionTitleCache,
|
|
782
|
));
|
|
783
|
} else {
|
|
784
|
$registration_date_institute_markup =
|
|
785
|
t("Registration on @date", array(
|
|
786
|
'@date' => $date_string
|
|
787
|
));
|
|
788
|
}
|
|
789
|
$registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
|
|
790
|
}
|
|
791
|
return $registration_date_institute_markup;
|
|
792
|
}
|
|
793
|
|
|
794
|
|
|
795
|
/**
|
|
796
|
* @param $registrations
|
|
797
|
* @return string
|
|
798
|
*/
|
|
799
|
function render_registrations($registrations)
|
|
800
|
{
|
|
801
|
$registration_markup = '';
|
|
802
|
$registration_markup_array = array();
|
|
803
|
if ($registrations) {
|
|
804
|
foreach ($registrations as $reg) {
|
|
805
|
$registration_markup_array[] = render_registration($reg);
|
|
806
|
}
|
|
807
|
$registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
|
|
808
|
. join(', ', $registration_markup_array);
|
|
809
|
}
|
|
810
|
return $registration_markup;
|
|
811
|
}
|
|
812
|
|
|
813
|
|
|
814
|
/**
|
|
815
|
* Renders a registration
|
|
816
|
*
|
|
817
|
* TODO replace by compose_registration_dto_compact
|
|
818
|
* @param $registration
|
|
819
|
*/
|
|
820
|
function render_registration($registration){
|
|
821
|
$markup = '';
|
|
822
|
|
|
823
|
if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
|
|
824
|
$office_class_attribute = '';
|
|
825
|
if(isset($registration->institution->titleCache)){
|
|
826
|
$office_class_attribute = registration_intitute_class_attribute($registration);
|
|
827
|
}
|
|
828
|
$markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
|
|
829
|
. preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
|
|
830
|
. '</span>';
|
|
831
|
}
|
|
832
|
return $markup;
|
|
833
|
}
|
|
834
|
|
|
835
|
/**
|
|
836
|
* @param $registration
|
|
837
|
* @return string
|
|
838
|
*/
|
|
839
|
function registration_intitute_class_attribute($registration_dto)
|
|
840
|
{
|
|
841
|
if(isset($registration_dto->institutionTitleCache)){
|
|
842
|
$institutionTitleCache = $registration_dto->institutionTitleCache;
|
|
843
|
} else {
|
|
844
|
// fall back option to also support cdm entities
|
|
845
|
$institutionTitleCache = @$registration_dto->institution->titleCache;
|
|
846
|
}
|
|
847
|
return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
|
|
848
|
}
|
|
849
|
|
|
850
|
|
|
851
|
/**
|
|
852
|
* Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
|
|
853
|
*
|
|
854
|
* @param $taxon_name_uuid
|
|
855
|
* @param $show_specimen_details
|
|
856
|
* @return array
|
|
857
|
* A drupal render array with the following elements:
|
|
858
|
* - 'type_designations'
|
|
859
|
* - 'map'
|
|
860
|
* - 'specimens'
|
|
861
|
*
|
|
862
|
* @ingroup compose
|
|
863
|
*/
|
|
864
|
function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
|
|
865
|
{
|
|
866
|
$render_array = array(
|
|
867
|
'type_designations' => array(),
|
|
868
|
'map' => array(),
|
|
869
|
);
|
|
870
|
$type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
|
|
871
|
if ($type_designations) {
|
|
872
|
usort($type_designations, 'compare_specimen_type_designation');
|
|
873
|
$render_array['type_designations'] = markup_to_render_array(
|
|
874
|
theme('cdm_typedesignations', array('typeDesignations' => $type_designations, 'enclosing_tag' => 'div', 'element_tag' => 'div'))
|
|
875
|
);
|
|
876
|
|
|
877
|
$render_array['map'] = compose_type_designations_map($type_designations);
|
|
878
|
}
|
|
879
|
return $render_array;
|
|
880
|
}
|
|
881
|
|
|
882
|
/**
|
|
883
|
* Composes a map with the location points of the passed $type_designations.
|
|
884
|
*
|
|
885
|
* @param $type_designations
|
|
886
|
*
|
|
887
|
* @return array
|
|
888
|
* A drupal render array or an empty array in case there are no point to show.
|
|
889
|
*
|
|
890
|
* @ingroup compose
|
|
891
|
*/
|
|
892
|
function compose_type_designations_map($type_designations)
|
|
893
|
{
|
|
894
|
$points = array();
|
|
895
|
$map_render_array = array();
|
|
896
|
foreach ($type_designations as $td) {
|
|
897
|
if ($td->class == "SpecimenTypeDesignation") {
|
|
898
|
$derived_unit_facade = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, array($td->typeSpecimen->uuid));
|
|
899
|
if (isset($derived_unit_facade->exactLocation)) {
|
|
900
|
$points[] = $derived_unit_facade->exactLocation->latitude . ',' . $derived_unit_facade->exactLocation->longitude;
|
|
901
|
}
|
|
902
|
}
|
|
903
|
}
|
|
904
|
|
|
905
|
if (count($points) > 0) {
|
|
906
|
// os=1:c/ff0000/10/noLabel&od=1:52.52079,13.57781|-43.46333333333333,172.60355&legend=0
|
|
907
|
$occurrence_query = 'os=1:c/ff0000/10/noLabel&od=1:' . join('|', $points) . '&legend=0';
|
|
908
|
// $occurrence_query = 'os=1:c/ff0000/10/noLabel&od=1:52.52079,13.57781|-43.46333333333333,172.60355&legend=0';
|
|
909
|
$legend_format_query = null;
|
|
910
|
$distribution_query = NULL;
|
|
911
|
$map_render_array = compose_map('specimens', $occurrence_query, $distribution_query, $legend_format_query, array());
|
|
912
|
}
|
|
913
|
return $map_render_array;
|
|
914
|
}
|
|
915
|
|
|
916
|
/**
|
|
917
|
* Composes the TypedEntityReference to name type designations passed as associatve array.
|
|
918
|
*
|
|
919
|
* @param $$type_entity_refs array
|
|
920
|
* an associative array of name type type => TypedEntityReference for name type designations as
|
|
921
|
* produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
|
|
922
|
*
|
|
923
|
* @ingroup compose
|
|
924
|
*/
|
|
925
|
function compose_name_type_designations($type_entity_refs){
|
|
926
|
$render_array = array();
|
|
927
|
$preferredStableUri = '';
|
|
928
|
foreach($type_entity_refs as $type_status => $name_types){
|
|
929
|
foreach ($name_types as $name_type){
|
|
930
|
$type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
|
|
931
|
if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
|
|
932
|
$preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
|
|
933
|
}
|
|
934
|
$render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type) . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
|
|
935
|
. $name_type->label
|
|
936
|
. ($preferredStableUri ? " ". l($preferredStableUri, $preferredStableUri) : '')
|
|
937
|
. '</div>');
|
|
938
|
}
|
|
939
|
}
|
|
940
|
return $render_array;
|
|
941
|
}
|
|
942
|
|
|
943
|
/**
|
|
944
|
* Composes the specimen type designations with map from the the $type_entity_refs
|
|
945
|
*
|
|
946
|
* @param $type_entity_refs array
|
|
947
|
* an associative array of specimen type type => TypedEntityReference for specimen type designations as
|
|
948
|
* produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
|
|
949
|
*
|
|
950
|
* @param $show_media_specimen
|
|
951
|
* @return array
|
|
952
|
* A drupal render array with the following elements:
|
|
953
|
* - 'type_designations'
|
|
954
|
* - 'map'
|
|
955
|
*
|
|
956
|
* @ingroup compose
|
|
957
|
*
|
|
958
|
*/
|
|
959
|
function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
|
|
960
|
|
|
961
|
$render_array = array();
|
|
962
|
|
|
963
|
$type_designation_list = array();
|
|
964
|
uksort($type_entity_refs, "compare_type_designation_status_labels");
|
|
965
|
foreach($type_entity_refs as $type_status => $specimen_types){
|
|
966
|
foreach($specimen_types as $specimen_type){
|
|
967
|
|
|
968
|
$type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($specimen_type->uuid));
|
|
969
|
$type_designation_list[] = $type_designation; // collect for the map
|
|
970
|
|
|
971
|
$derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
|
|
972
|
// the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately
|
|
973
|
$mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
|
|
974
|
|
|
975
|
|
|
976
|
$preferredStableUri = '';
|
|
977
|
$citation_markup = '';
|
|
978
|
$media = '';
|
|
979
|
|
|
980
|
// preferredStableUri
|
|
981
|
if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
|
|
982
|
$preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
|
|
983
|
}
|
|
984
|
|
|
985
|
if($show_media_specimen && $mediaSpecimen){
|
|
986
|
// compose output
|
|
987
|
// mediaURI
|
|
988
|
if(isset($mediaSpecimen->representations[0])) {
|
|
989
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
|
990
|
$captionElements = array(
|
|
991
|
'#uri' => t('open media'),
|
|
992
|
'elements' => array('-none-'),
|
|
993
|
'sources_as_content' => true
|
|
994
|
);
|
|
995
|
$media = compose_cdm_media_gallerie(array(
|
|
996
|
'mediaList' => array($mediaSpecimen),
|
|
997
|
'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
|
|
998
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
|
999
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
|
1000
|
'captionElements' => $captionElements,
|
|
1001
|
));
|
|
1002
|
}
|
|
1003
|
// citation and detail
|
|
1004
|
$annotations_and_sources = handle_annotations_and_sources(
|
|
1005
|
$mediaSpecimen,
|
|
1006
|
array(
|
|
1007
|
'sources_as_content' => true,
|
|
1008
|
'link_to_name_used_in_source' => false,
|
|
1009
|
'link_to_reference' => true,
|
|
1010
|
'add_footnote_keys' => false,
|
|
1011
|
'bibliography_aware' => false),
|
|
1012
|
'',
|
|
1013
|
null
|
|
1014
|
);
|
|
1015
|
if(is_array( $annotations_and_sources['source_references'])){
|
|
1016
|
$citation_markup = join(', ', $annotations_and_sources['source_references']);
|
|
1017
|
}
|
|
1018
|
}
|
|
1019
|
|
|
1020
|
$specimen_markup = $derivedUnitFacadeInstance->titleCache;
|
|
1021
|
if(isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
|
|
1022
|
$specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);
|
|
1023
|
}
|
|
1024
|
|
|
1025
|
$type_designation_render_array = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type) . '">
|
|
1026
|
<span class="type-status">' . ucfirst($type_status) . "</span>: "
|
|
1027
|
. $specimen_markup
|
|
1028
|
. ($citation_markup ? ' '. $citation_markup : '')
|
|
1029
|
. ($preferredStableUri ? " ". l($preferredStableUri, $preferredStableUri) : '')
|
|
1030
|
. $media
|
|
1031
|
. '</div>');
|
|
1032
|
|
|
1033
|
$render_array['type_designations'][] = $type_designation_render_array;
|
|
1034
|
}
|
|
1035
|
}
|
|
1036
|
if(count($type_designation_list) > 0 ){
|
|
1037
|
$render_array['map'] = compose_type_designations_map($type_designation_list);
|
|
1038
|
} else {
|
|
1039
|
$render_array['map'] = array();
|
|
1040
|
}
|
|
1041
|
return $render_array;
|
|
1042
|
}
|
|
1043
|
|
|
1044
|
/**
|
|
1045
|
* @param $name_rel
|
|
1046
|
* @param $current_name_uuid
|
|
1047
|
* @param $current_taxon_uuid
|
|
1048
|
* @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
|
|
1049
|
* @param $show_name_cache_only
|
|
1050
|
* The nameCache will be shown instead of the titleCache if this parameter is true.
|
|
1051
|
* @return null|string
|
|
1052
|
*/
|
|
1053
|
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
|
|
1054
|
|
|
1055
|
$relationship_markup = null;
|
|
1056
|
|
|
1057
|
$current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
|
|
1058
|
|
|
1059
|
if($current_name_is_toName){
|
|
1060
|
$name = $name_rel->fromName;
|
|
1061
|
} else {
|
|
1062
|
$name = $name_rel->toName;
|
|
1063
|
}
|
|
1064
|
|
|
1065
|
cdm_load_tagged_full_title($name);
|
|
1066
|
|
|
1067
|
$highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
|
|
1068
|
if(!$show_name_cache_only){
|
|
1069
|
$relationship_markup = render_taxon_or_name($name,
|
|
1070
|
url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
|
|
1071
|
);
|
|
1072
|
} else {
|
|
1073
|
$relationship_markup = l(
|
|
1074
|
'<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
|
|
1075
|
path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
|
|
1076
|
array('html' => true)
|
|
1077
|
);
|
|
1078
|
}
|
|
1079
|
|
|
1080
|
return $relationship_markup;
|
|
1081
|
}
|
|
1082
|
|
|
1083
|
|
|
1084
|
/**
|
|
1085
|
* Composes an inline representation of selected name relationships
|
|
1086
|
*
|
|
1087
|
* The output of this function will be usually appended to taxon name representations.
|
|
1088
|
* Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
|
|
1089
|
*
|
|
1090
|
* LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
|
|
1091
|
* non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
|
|
1092
|
* are ordered alphabetically.
|
|
1093
|
*
|
|
1094
|
* ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
|
|
1095
|
*
|
|
1096
|
* Related issues:
|
|
1097
|
* - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
|
|
1098
|
* - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
|
|
1099
|
* - https://dev.e-taxonomy.eu/redmine/issues/5857
|
|
1100
|
* - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
|
|
1101
|
*
|
|
1102
|
* @param $name_relations
|
|
1103
|
* The list of CDM NameRelationsips
|
|
1104
|
* @param $current_name_uuid
|
|
1105
|
* The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
|
|
1106
|
* rendering the relation an only the other name is shown. Parameter is REQUIRED.
|
|
1107
|
* @param $suppress_if_current_name_is_source
|
|
1108
|
* The display of the relation will be
|
|
1109
|
* suppressed is the current name is on the source of the relation edge.
|
|
1110
|
* That is if it is on the from side of the relation. Except for 'blocking name for' which is
|
|
1111
|
* an inverse relation. For this relation type the toName is taken in to account.
|
|
1112
|
* @param $current_taxon_uuid
|
|
1113
|
* The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
|
|
1114
|
* @return array
|
|
1115
|
* A drupal render array
|
|
1116
|
*
|
|
1117
|
* @ingroup Compose
|
|
1118
|
*/
|
|
1119
|
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
|
|
1120
|
|
|
1121
|
RenderHints::pushToRenderStack('homonym');
|
|
1122
|
// the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
|
|
1123
|
|
|
1124
|
$selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
|
|
1125
|
$name_rel_type_filter = array('direct' => array(), 'inverse' => array());
|
|
1126
|
foreach ($selected_name_rel_uuids as $uuid){
|
|
1127
|
$name_rel_type_filter['direct'][$uuid] = $uuid;
|
|
1128
|
if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
|
|
1129
|
$name_rel_type_filter['inverse'][$uuid] = $uuid;
|
|
1130
|
}
|
|
1131
|
}
|
|
1132
|
|
|
1133
|
$list_prefix = '<span class="name_relationships">[';
|
|
1134
|
$list_suffix = ']</span>';
|
|
1135
|
$item_prefix = '<span class="item">';
|
|
1136
|
$item_suffix = '</span> ';
|
|
1137
|
$render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
|
|
1138
|
|
|
1139
|
// remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
|
|
1140
|
$items_ctn = count($render_array['list']['items']);
|
|
1141
|
if($items_ctn){
|
|
1142
|
$render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
|
|
1143
|
}
|
|
1144
|
|
|
1145
|
RenderHints::popFromRenderStack();
|
|
1146
|
return $render_array;
|
|
1147
|
}
|
|
1148
|
|
|
1149
|
/**
|
|
1150
|
* Composes an list representation of the name relationships.
|
|
1151
|
*
|
|
1152
|
* The output of this function will be usually appended to taxon name representations.
|
|
1153
|
*
|
|
1154
|
* Related issues:
|
|
1155
|
* - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
|
|
1156
|
* - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
|
|
1157
|
* - https://dev.e-taxonomy.eu/redmine/issues/5857
|
|
1158
|
*
|
|
1159
|
* @param $name_relations
|
|
1160
|
* The list of CDM NameRelationsips
|
|
1161
|
* @param $current_name_uuid
|
|
1162
|
* The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
|
|
1163
|
* rendering the relation an only the other name is shown. Parameter is REQUIRED.
|
|
1164
|
* @param $current_taxon_uuid
|
|
1165
|
* The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
|
|
1166
|
* @return array
|
|
1167
|
* A drupal render array
|
|
1168
|
*
|
|
1169
|
* @ingroup Compose
|
|
1170
|
*/
|
|
1171
|
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
|
|
1172
|
|
|
1173
|
// $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
|
|
1174
|
|
|
1175
|
$key = 'name_relationships';
|
|
1176
|
RenderHints::pushToRenderStack($key);
|
|
1177
|
if(!RenderHints::getFootnoteListKey()){
|
|
1178
|
RenderHints::setFootnoteListKey($key);
|
|
1179
|
}
|
|
1180
|
// the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
|
|
1181
|
|
|
1182
|
$selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
|
|
1183
|
$name_rel_type_filter = array('direct' => array(), 'inverse' => array());
|
|
1184
|
foreach ($selected_name_rel_uuids as $uuid){
|
|
1185
|
$name_rel_type_filter['direct'][$uuid] = $uuid;
|
|
1186
|
$name_rel_type_filter['inverse'][$uuid] = $uuid;
|
|
1187
|
}
|
|
1188
|
|
|
1189
|
$list_prefix = '<div class="relationships_list name_relationships">';
|
|
1190
|
$list_suffix = '</div>';
|
|
1191
|
$item_prefix = '<div class="item">';
|
|
1192
|
$item_suffix = '</div>';
|
|
1193
|
|
|
1194
|
$render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
|
|
1195
|
|
|
1196
|
RenderHints::popFromRenderStack();
|
|
1197
|
$render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
|
|
1198
|
if(RenderHints::getFootnoteListKey() == $key) {
|
|
1199
|
RenderHints::clearFootnoteListKey();
|
|
1200
|
}
|
|
1201
|
return $render_array;
|
|
1202
|
}
|
|
1203
|
|
|
1204
|
/**
|
|
1205
|
* @param $name_relations
|
|
1206
|
* @param $name_rel_type_filter
|
|
1207
|
* Associative array with two keys:
|
|
1208
|
* - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
|
|
1209
|
* - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
|
|
1210
|
* @param $current_name_uuid
|
|
1211
|
* @param $current_taxon_uuid
|
|
1212
|
* @param $list_prefix
|
|
1213
|
* @param $list_suffix
|
|
1214
|
* @param $item_prefix
|
|
1215
|
* @param $item_suffix
|
|
1216
|
* @return array
|
|
1217
|
*
|
|
1218
|
* @ingroup Compose
|
|
1219
|
*/
|
|
1220
|
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
|
|
1221
|
$list_prefix, $list_suffix, $item_prefix, $item_suffix)
|
|
1222
|
{
|
|
1223
|
$non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
|
|
1224
|
UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
|
|
1225
|
UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
|
|
1226
|
UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
|
|
1227
|
UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
|
|
1228
|
|
|
1229
|
$render_array = array(
|
|
1230
|
'list' => array(
|
|
1231
|
'#prefix' => $list_prefix,
|
|
1232
|
'#suffix' => $list_suffix,
|
|
1233
|
'items' => array()
|
|
1234
|
),
|
|
1235
|
'footnotes' => array()
|
|
1236
|
);
|
|
1237
|
|
|
1238
|
if ($name_relations) {
|
|
1239
|
|
|
1240
|
// remove all relations which are not selected in the settings and
|
|
1241
|
// separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
|
|
1242
|
// for special handling
|
|
1243
|
$filtered_name_rels = array();
|
|
1244
|
$non_nec_name_rels = array();
|
|
1245
|
$orthographic_variants = array();
|
|
1246
|
foreach ($name_relations as $name_rel) {
|
|
1247
|
$rel_type_uuid = $name_rel->type->uuid;
|
|
1248
|
$is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
|
|
1249
|
if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
|
|
1250
|
||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
|
|
1251
|
|
|
1252
|
if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
|
|
1253
|
$current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
|
|
1254
|
|| $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
|
|
1255
|
)
|
|
1256
|
){
|
|
1257
|
$non_nec_name_rels[] = $name_rel;
|
|
1258
|
} else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
|
|
1259
|
$orthographic_variants[] = $name_rel;
|
|
1260
|
} else {
|
|
1261
|
|
|
1262
|
$filtered_name_rels[] = $name_rel;
|
|
1263
|
}
|
|
1264
|
}
|
|
1265
|
}
|
|
1266
|
$name_relations = $filtered_name_rels;
|
|
1267
|
|
|
1268
|
usort($name_relations, 'compare_name_relations_by_term_order_index');
|
|
1269
|
|
|
1270
|
// compose
|
|
1271
|
foreach ($name_relations as $name_rel) {
|
|
1272
|
|
|
1273
|
$is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
|
|
1274
|
|
|
1275
|
$rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
|
|
1276
|
$relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
|
|
1277
|
|
|
1278
|
$label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
|
|
1279
|
$symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
|
|
1280
|
$symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
|
|
1281
|
$relationship_markup = $symbol_markup . $relationship_markup;
|
|
1282
|
if ($relationship_markup) {
|
|
1283
|
$render_array['list']['items'][] = markup_to_render_array($relationship_markup,
|
|
1284
|
null,
|
|
1285
|
$item_prefix,
|
|
1286
|
$item_suffix);
|
|
1287
|
}
|
|
1288
|
}
|
|
1289
|
|
|
1290
|
// name relationships to be displayed as non nec
|
|
1291
|
if (count($non_nec_name_rels) > 0) {
|
|
1292
|
$non_nec_markup = '';
|
|
1293
|
foreach ($non_nec_name_rels as $name_rel) {
|
|
1294
|
$is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
|
|
1295
|
$rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
|
|
1296
|
$relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
|
|
1297
|
$label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
|
|
1298
|
$symbol = $non_nec_markup ? ' nec ' : 'non';
|
|
1299
|
$symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
|
|
1300
|
$non_nec_markup .= $symbol_markup . $relationship_markup;
|
|
1301
|
}
|
|
1302
|
if ($non_nec_markup) {
|
|
1303
|
$render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
|
|
1304
|
null,
|
|
1305
|
$item_prefix,
|
|
1306
|
$item_suffix);
|
|
1307
|
}
|
|
1308
|
}
|
|
1309
|
|
|
1310
|
// orthographic variants
|
|
1311
|
if (count($orthographic_variants) > 0) {
|
|
1312
|
foreach ($orthographic_variants as $name_rel) {
|
|
1313
|
|
|
1314
|
$is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
|
|
1315
|
$rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
|
|
1316
|
$relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
|
|
1317
|
$nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
|
|
1318
|
$label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
|
|
1319
|
$symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
|
|
1320
|
$symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
|
|
1321
|
$relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
|
|
1322
|
}
|
|
1323
|
if ($relationship_markup) {
|
|
1324
|
$render_array['list']['items'][] = markup_to_render_array($relationship_markup,
|
|
1325
|
null,
|
|
1326
|
$item_prefix,
|
|
1327
|
$item_suffix);
|
|
1328
|
}
|
|
1329
|
}
|
|
1330
|
}
|
|
1331
|
return $render_array;
|
|
1332
|
}
|
|
1333
|
|
|
1334
|
/**
|
|
1335
|
* @param $name_rel
|
|
1336
|
* @return string
|
|
1337
|
*/
|
|
1338
|
function name_relationship_footnote_markup($name_rel)
|
|
1339
|
{
|
|
1340
|
$footnote_markup = '';
|
|
1341
|
$footnote_key_markup = '';
|
|
1342
|
if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
|
|
1343
|
$footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
|
|
1344
|
}
|
|
1345
|
if (isset($name_rel->citation)) {
|
|
1346
|
$footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
|
|
1347
|
}
|
|
1348
|
if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
|
|
1349
|
$footnote_markup .= (isset($name_rel->citation) ? ':' : '') . '<span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
|
|
1350
|
}
|
|
1351
|
if ($footnote_markup) {
|
|
1352
|
$fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
|
|
1353
|
$footnote_key_markup = theme('cdm_footnote_key', array(
|
|
1354
|
'footnoteKey' => $fnkey,
|
|
1355
|
'separator' => ',',
|
|
1356
|
'highlightable' => TRUE,
|
|
1357
|
'separator_off' => TRUE,
|
|
1358
|
));
|
|
1359
|
}
|
|
1360
|
return $footnote_key_markup;
|
|
1361
|
}
|
|
1362
|
|
|
1363
|
/**
|
|
1364
|
* @param $nom_status
|
|
1365
|
* @return string
|
|
1366
|
*/
|
|
1367
|
function nomenclatural_status_footnote_markup($nom_status)
|
|
1368
|
{
|
|
1369
|
// NomenclaturalStatus is a subclass of ReferencedEntityBase
|
|
1370
|
// and has the same structure as TaxonNameRelationship
|
|
1371
|
return name_relationship_footnote_markup($nom_status);
|
|
1372
|
}
|
|
1373
|
|
|
1374
|
/**
|
|
1375
|
* @param $name
|
|
1376
|
* @return string
|
|
1377
|
*/
|
|
1378
|
function nomenclatural_reference_footnote_key_markup($name)
|
|
1379
|
{
|
|
1380
|
$footnote_markup = '';
|
|
1381
|
$footnote_key_markup = '';
|
|
1382
|
if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
|
|
1383
|
$footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
|
|
1384
|
}
|
|
1385
|
if (isset($name->nomenclaturalMicroReference)) {
|
|
1386
|
$footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
|
|
1387
|
}
|
|
1388
|
if ($footnote_markup) {
|
|
1389
|
$fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
|
|
1390
|
$footnote_key_markup = theme('cdm_footnote_key', array(
|
|
1391
|
'footnoteKey' => $fnkey,
|
|
1392
|
'separator' => ',',
|
|
1393
|
'highlightable' => TRUE,
|
|
1394
|
'separator_off' => TRUE,
|
|
1395
|
));
|
|
1396
|
}
|
|
1397
|
return $footnote_key_markup;
|
|
1398
|
}
|
|
1399
|
|
|
1400
|
|
|
1401
|
/**
|
|
1402
|
* @param $taxon
|
|
1403
|
* @return array
|
|
1404
|
*/
|
|
1405
|
function cdm_name_relationships_for_taxon($taxon)
|
|
1406
|
{
|
|
1407
|
$from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
|
|
1408
|
$to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
|
|
1409
|
$name_relations = array_merge($from_name_relations, $to_name_relations);
|
|
1410
|
return $name_relations;
|
|
1411
|
}
|
|
1412
|
|
|
1413
|
|
|
1414
|
/**
|
|
1415
|
* Recursively searches the array for the $key and sets the given value.
|
|
1416
|
*
|
|
1417
|
* @param mixed $key
|
|
1418
|
* Key to search for.
|
|
1419
|
* @param mixed $value
|
|
1420
|
* Value to set.'
|
|
1421
|
* @param array $array
|
|
1422
|
* Array to search in.
|
|
1423
|
*
|
|
1424
|
* @return bool
|
|
1425
|
* True if the key has been found.
|
|
1426
|
*/
|
|
1427
|
function &array_setr($key, $value, array &$array) {
|
|
1428
|
$res = NULL;
|
|
1429
|
foreach ($array as $k => &$v) {
|
|
1430
|
if ($key == $k) {
|
|
1431
|
$v = $value;
|
|
1432
|
return $array;
|
|
1433
|
}
|
|
1434
|
elseif (is_array($v)) {
|
|
1435
|
$innerArray = array_setr($key, $value, $v);
|
|
1436
|
if ($innerArray) {
|
|
1437
|
return $array;
|
|
1438
|
}
|
|
1439
|
}
|
|
1440
|
}
|
|
1441
|
return $res;
|
|
1442
|
}
|
|
1443
|
|
|
1444
|
/**
|
|
1445
|
* @todo Please document this function.
|
|
1446
|
* @see http://drupal.org/node/1354
|
|
1447
|
*/
|
|
1448
|
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
|
|
1449
|
$res = NULL;
|
|
1450
|
$precedingElement = NULL;
|
|
1451
|
foreach ($renderTemplate as &$part) {
|
|
1452
|
foreach ($part as $key => &$element) {
|
|
1453
|
if ($key == $contentElementKey) {
|
|
1454
|
return $precedingElement;
|
|
1455
|
}
|
|
1456
|
$precedingElement = $element;
|
|
1457
|
}
|
|
1458
|
}
|
|
1459
|
return $res;
|
|
1460
|
}
|
|
1461
|
|
|
1462
|
/**
|
|
1463
|
* @todo Please document this function.
|
|
1464
|
* @see http://drupal.org/node/1354
|
|
1465
|
*/
|
|
1466
|
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
|
|
1467
|
$res = NULL;
|
|
1468
|
$precedingKey = NULL;
|
|
1469
|
foreach ($renderTemplate as &$part) {
|
|
1470
|
if (is_array($part)) {
|
|
1471
|
foreach ($part as $key => &$element) {
|
|
1472
|
if ($key == $contentElementKey) {
|
|
1473
|
return $precedingKey;
|
|
1474
|
}
|
|
1475
|
if (!str_beginsWith($key, '#')) {
|
|
1476
|
$precedingKey = $key;
|
|
1477
|
}
|
|
1478
|
}
|
|
1479
|
}
|
|
1480
|
}
|
|
1481
|
return $res;
|
|
1482
|
}
|
|
1483
|
|
|
1484
|
function nameTypeToDTYPE($dtype){
|
|
1485
|
static $nameTypeLabelMap = array(
|
|
1486
|
"ICNB" => "BacterialName",
|
|
1487
|
"ICNAFP" => "BotanicalName",
|
|
1488
|
"ICNCP" => "CultivarPlantName",
|
|
1489
|
"ICZN" => "ZoologicalName",
|
|
1490
|
"ICVCN" => "ViralName",
|
|
1491
|
"Any taxon name" => "TaxonName",
|
|
1492
|
"NonViral" => "TaxonName",
|
|
1493
|
"Fungus" => "BotanicalName",
|
|
1494
|
"Plant" => "BotanicalName",
|
|
1495
|
"Algae" => "BotanicalName",
|
|
1496
|
);
|
|
1497
|
return $nameTypeLabelMap[$dtype];
|
|
1498
|
|
|
1499
|
}
|
|
1500
|
|
|
1501
|
|
|
1502
|
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
|
|
1503
|
return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
|
|
1504
|
}
|
|
1505
|
|
|
1506
|
/**
|
|
1507
|
* Provides an array with the different registration types covered by the passed registration.
|
|
1508
|
*
|
|
1509
|
* The labels in the returned array are translatable.
|
|
1510
|
*
|
|
1511
|
* See also https://dev.e-taxonomy.eu/redmine/issues/8016
|
|
1512
|
*
|
|
1513
|
* @param $registration_dto
|
|
1514
|
* @return array
|
|
1515
|
* An array of the labels describing the different registration types covered by the passed registration.
|
|
1516
|
*/
|
|
1517
|
function registration_types($registration_dto){
|
|
1518
|
$reg_type_labels = array();
|
|
1519
|
if(isset($registration_dto->nameRef)){
|
|
1520
|
$reg_type_labels["name"] = t("new name");
|
|
1521
|
$reg_type_labels["taxon"] = t("new taxon");
|
|
1522
|
$name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
|
|
1523
|
$is_new_combination = true;
|
|
1524
|
foreach($name_relations as $name_rel){
|
|
1525
|
if(isset($name_rel->type->uuid)){
|
|
1526
|
$name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
|
|
1527
|
switch($name_rel->type->uuid) {
|
|
1528
|
case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
|
|
1529
|
if(!$name_is_from_name){
|
|
1530
|
$reg_type_labels["basionym"] = t("new combination");
|
|
1531
|
$is_new_combination = true;
|
|
1532
|
}
|
|
1533
|
break;
|
|
1534
|
case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
|
|
1535
|
if(!$name_is_from_name) {
|
|
1536
|
$is_new_combination = true;
|
|
1537
|
}
|
|
1538
|
break;
|
|
1539
|
case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
|
|
1540
|
if(!$name_is_from_name) {
|
|
1541
|
$reg_type_labels["validation"] = t("validation");
|
|
1542
|
}
|
|
1543
|
break;
|
|
1544
|
case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
|
|
1545
|
if(!$name_is_from_name) {
|
|
1546
|
$reg_type_labels["orth_var"] = t("orthographical correction");
|
|
1547
|
}break;
|
|
1548
|
default:
|
|
1549
|
// NOTHING
|
|
1550
|
}
|
|
1551
|
}
|
|
1552
|
}
|
|
1553
|
if($is_new_combination){
|
|
1554
|
unset($reg_type_labels["taxon"]);
|
|
1555
|
}
|
|
1556
|
}
|
|
1557
|
if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
|
|
1558
|
$reg_type_labels[] = t("new nomenclatural type");
|
|
1559
|
}
|
|
1560
|
return $reg_type_labels;
|
|
1561
|
}
|
|
1562
|
|
|
1563
|
/**
|
|
1564
|
* Collects and deduplicates the type designations associated with the passes synonyms.
|
|
1565
|
*
|
|
1566
|
* @param $synonymy_group
|
|
1567
|
* An array containing a homotypic or heterotypic group of names.
|
|
1568
|
* @param $accepted_taxon_name_uuid
|
|
1569
|
* The uuid of the accepted taxon name. Optional parameter which is required when composing
|
|
1570
|
* the information for the homotypic group. In this case the accepted taxon is not included
|
|
1571
|
* in the $synonymy_group and must therefor passed in this second parameter.
|
|
1572
|
*
|
|
1573
|
* @return array
|
|
1574
|
* The type designations
|
|
1575
|
*/
|
|
1576
|
function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
|
|
1577
|
{
|
|
1578
|
if (count($synonymy_group) > 0) {
|
|
1579
|
$name_uuid = array_pop($synonymy_group)->name->uuid;
|
|
1580
|
} else {
|
|
1581
|
$name_uuid = $accepted_taxon_name_uuid;
|
|
1582
|
}
|
|
1583
|
if ($name_uuid) {
|
|
1584
|
$type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
|
|
1585
|
if ($type_designations) {
|
|
1586
|
return $type_designations;
|
|
1587
|
}
|
|
1588
|
}
|
|
1589
|
|
|
1590
|
return array();
|
|
1591
|
}
|
|
1592
|
|
|
1593
|
|
|
1594
|
/**
|
|
1595
|
* Compares the status of two SpecimenTypeDesignations
|
|
1596
|
*
|
|
1597
|
* @param object $a
|
|
1598
|
* A SpecimenTypeDesignation.
|
|
1599
|
* @param object $b
|
|
1600
|
* SpecimenTypeDesignation.
|
|
1601
|
*/
|
|
1602
|
function compare_specimen_type_designation($a, $b) {
|
|
1603
|
|
|
1604
|
$type_status_order = type_status_order();
|
|
1605
|
|
|
1606
|
|
|
1607
|
$aQuantifier = FALSE;
|
|
1608
|
$bQuantifier = FALSE;
|
|
1609
|
if (isset($a->typeStatus->titleCache) && isset($b->typeStatus->titleCache)) {
|
|
1610
|
$aQuantifier = array_search($a->typeStatus->titleCache, $type_status_order);
|
|
1611
|
$bQuantifier = array_search($b->typeStatus->titleCache, $type_status_order);
|
|
1612
|
}
|
|
1613
|
if ($aQuantifier == $bQuantifier) {
|
|
1614
|
// Sort alphabetically.
|
|
1615
|
$a_text = isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
|
|
1616
|
$b_text = isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
|
|
1617
|
return strcasecmp($a_text, $b_text);
|
|
1618
|
}
|
|
1619
|
return ($aQuantifier < $bQuantifier) ? -1 : 1;
|
|
1620
|
}
|
|
1621
|
|
|
1622
|
/**
|
|
1623
|
* Compares the status of two SpecimenTypeDesignations
|
|
1624
|
*
|
|
1625
|
* @param object $a
|
|
1626
|
* A TypeDesignationStatusBase.
|
|
1627
|
* @param object $b
|
|
1628
|
* TypeDesignationStatusBase.
|
|
1629
|
*/
|
|
1630
|
function compare_type_designation_status($a, $b) {
|
|
1631
|
|
|
1632
|
$type_status_order = type_status_order();
|
|
1633
|
|
|
1634
|
|
|
1635
|
$aQuantifier = FALSE;
|
|
1636
|
$bQuantifier = FALSE;
|
|
1637
|
if (isset($a->label) && isset($b->label)) {
|
|
1638
|
$aQuantifier = array_search($a->label, $type_status_order);
|
|
1639
|
$bQuantifier = array_search($b->label, $type_status_order);
|
|
1640
|
}
|
|
1641
|
return ($aQuantifier < $bQuantifier) ? -1 : 1;
|
|
1642
|
}
|
|
1643
|
|
|
1644
|
|
|
1645
|
/**
|
|
1646
|
* Compares two SpecimenTypeDesignation status labels
|
|
1647
|
*
|
|
1648
|
* @param string $a
|
|
1649
|
* A TypeDesignationStatus label.
|
|
1650
|
* @param string $b
|
|
1651
|
* A TypeDesignationStatus label.
|
|
1652
|
*/
|
|
1653
|
function compare_type_designation_status_labels($a, $b) {
|
|
1654
|
|
|
1655
|
$type_status_order = type_status_order();
|
|
1656
|
|
|
1657
|
|
|
1658
|
$aQuantifier = FALSE;
|
|
1659
|
$bQuantifier = FALSE;
|
|
1660
|
if (isset($a) && isset($b)) {
|
|
1661
|
$aQuantifier = array_search($a, $type_status_order);
|
|
1662
|
$bQuantifier = array_search($b, $type_status_order);
|
|
1663
|
}
|
|
1664
|
return ($aQuantifier < $bQuantifier) ? -1 : 1;
|
|
1665
|
}
|
|
1666
|
|
|
1667
|
/**
|
|
1668
|
* @return array
|
|
1669
|
*/
|
|
1670
|
function type_status_order()
|
|
1671
|
{
|
|
1672
|
/*
|
|
1673
|
This is the desired sort order as of now: Holotype Isotype Lectotype
|
|
1674
|
Isolectotype Syntype.
|
|
1675
|
TODO Basically, what we are trying to do is, we define
|
|
1676
|
an ordered array of TypeDesignation-states and use the index of this array
|
|
1677
|
for comparison. This array has to be filled with the cdm- TypeDesignation
|
|
1678
|
states and the order should be parameterisable inside the dataportal.
|
|
1679
|
*/
|
|
1680
|
// Make that static for now.
|
|
1681
|
$type_status_order = array(
|
|
1682
|
'Epitype',
|
|
1683
|
'Holotype',
|
|
1684
|
'Isotype',
|
|
1685
|
'Lectotype',
|
|
1686
|
'Isolectotype',
|
|
1687
|
'Syntype',
|
|
1688
|
'Paratype'
|
|
1689
|
);
|
|
1690
|
return $type_status_order;
|
|
1691
|
}
|