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<?php
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/**
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* @file
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* Module to provide a CDM Dataportal.
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*
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* @copyright
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* (C) 2007-2012 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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* - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
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*/
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module_load_include('php', 'cdm_dataportal', 'node_types');
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module_load_include('php', 'cdm_dataportal', 'settings');
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module_load_include('php', 'cdm_dataportal', 'help');
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module_load_include('php', 'cdm_dataportal', 'cdm_dataportal.search');
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module_load_include('inc', 'cdm_dataportal', 'includes/common');
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module_load_include('inc', 'cdm_dataportal', 'includes/name');
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module_load_include('inc', 'cdm_dataportal', 'includes/pages');
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module_load_include('inc', 'cdm_dataportal', 'includes/media');
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module_load_include('inc', 'cdm_dataportal', 'includes/maps');
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module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
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module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
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module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
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module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
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module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
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module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
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module_load_include('php', 'cdm_dataportal', 'classes/footnote');
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module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
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module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
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/* ============================ java script functions ============================= */
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/**
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* loads external java script files asynchronously.
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*
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* @param unknown_type $script_url
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*/
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function drupal_add_js_async($script_url, $callback){
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drupal_add_js("
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jQuery(document).ready(function() {
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jQuery.ajax({
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url: '" . $script_url . "',
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dataType: 'script',
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cache: true, // otherwise will get fresh copy every page load
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success: function() {
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" . $callback . "
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}
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});
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});"
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, 'inline');
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}
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/**
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*/
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function drupal_add_js_rowToggle($tableId){
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
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drupal_add_js('jQuery(document).ready(function(){
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addRowToggle("' . $tableId . '");
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});
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', array('type' => 'inline'));
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}
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/**
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* @param unknown_type $link_element_selector
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* @param unknown_type $progress_element_selector
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*/
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function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
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$callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
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drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
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// drupal_add_js("
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// if (Drupal.jsEnabled) {
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// $(document).ready(function() {
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// $('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
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// });
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// }", 'inline');
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_treeselector() {
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// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
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drupal_add_js("
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jQuery(document).ready(function() {
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jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
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jQuery('#cdm-taxonomictree-selector-form').submit();
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});
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});
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",
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array(
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'type' => 'inline',
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'scope' => 'footer'
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)
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);
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}
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function _add_js_openlayers() {
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$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
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$proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
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if(variable_get('cdm_js_devel_mode', FALSE)){
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// develooper mode libs
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// $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
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$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
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$proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
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}
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
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array(
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'type' => 'file',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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'preprocess' => FALSE
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)
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);
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// see https://github.com/proj4js/proj4js
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// http://openlayers.org/dev/examples/using-proj4js.html
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
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array(
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'type' => 'file',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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)
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);
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// configure the theme
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$openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
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$openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
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drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
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'type' => 'inline',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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'preprocess' => FALSE
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));
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drupal_add_css($openlayers_theme_path . 'style.tidy.css',
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array(
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'type' => 'file',
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'cache' => TRUE,
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'preprocess' => FALSE
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)
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);
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_thickbox() {
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// ---- jQuery thickbox:
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/*
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* bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
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* not triggered because of problems with compat-1.0.js' see INSTALL.txt
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*/
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// drupal_add_js(drupal_get_path('module',
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// 'cdm_dataportal').'/js/jquery.imagetool.min.js');
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//
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// Add a setting for the path to cdm_dataportal module, used to find the path
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// for the loading animation image in thickbox.
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drupal_add_js(array(
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'cdm_dataportal' => array(
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'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
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)
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),
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'setting'
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);
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
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drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_lightbox($galleryID) {
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/*
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* Important Notice: The jquery.lightbox-0.5.js has been modified in order to
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* allow using the "alt" attribute for captions instead of the "title"
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* attribute
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*/
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$lightbox_base_path = drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
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$lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
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drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
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drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
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drupal_add_js('jQuery(document).ready(function() {
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jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
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fixedNavigation: true,
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imageLoading: \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
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imageBtnPrev: \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
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imageBtnNext: \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
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imageBtnClose: \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
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imageBlank: \'' . $lightbox_image_path . 'lightbox-blank.gif\',
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adjustToWindow: true
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});
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});
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', array('type' => 'inline'));
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_footnotes() {
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_add_js_domEvent();
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_cluetip() {
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// TODO replace by
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// @see http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.min.js');
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.dimensions.js');
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.hoverIntent.js');
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if(variable_get('cdm_js_devel_mode', FALSE)){
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.js');
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}
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drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.css');
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drupal_add_js("jQuery(document).ready(function(){
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jQuery('.cluetip').css({color: '#0062C2'}).cluetip({
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splitTitle: '|',
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showTitle: true,
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activation: 'hover',
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sicky: true,
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arrows: true,
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dropShadow: false,
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cluetipClass: 'rounded'
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});
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});", array('type' => 'inline'));
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_ahah() {
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_add_js_domEvent(); // requires domEvent.js
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
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}
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/**
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* Adds the external javascript file for domEvent.js.
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*
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* @see drupal_add_js()
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*/
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function _add_js_domEvent() {
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
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}
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function _add_jquery_ui()
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{
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drupal_add_css(drupal_get_path('module',
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'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
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drupal_add_js(drupal_get_path('module',
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'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
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array(
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'type' => 'file',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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'preprocess' => FALSE
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)
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);
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}
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/**
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* Provides the markup for an font awesome icon.
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*
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* The icons is created in default size without any extra features.
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*
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* The available icons are listed here http://fontawesome.io/cheatsheet/
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* fontawesome icons have much more features than implemented here in this function,
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* for spinning icons, fixed width icons, rotation, etc please checkout the
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* examples at http://fontawesome.io/examples/
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*
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* @parameter $icon_name
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* The name of the icon which starts with 'fa-'
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*
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* @return String
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* the markup for the icon in an <i> tag
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*
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*/
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function font_awesome_icon_markup($icon_name, $attributes = array()){
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//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
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$font_awesome_css_uri=drupal_get_path('module', 'cdm_dataportal').'/font-awesome/4.2.0/css/font-awesome.min.css';
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$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css";
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drupal_add_html_head_link(
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array(
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'href' => $font_awesome_css_uri,
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'rel' => 'stylesheet'
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)
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);
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if(!isset($attributes['class'])){
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$attributes['class'] = array();
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}
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$attributes['class'][] = 'fa';
|
|
336
|
$attributes['class'][] = $icon_name;
|
|
337
|
|
|
338
|
return '<i ' . drupal_attributes($attributes) . '></i>';
|
|
339
|
}
|
|
340
|
|
|
341
|
|
|
342
|
/* ====================== hook implementations ====================== */
|
|
343
|
/**
|
|
344
|
* Implements hook_permission().
|
|
345
|
*
|
|
346
|
* Valid permissions for this module.
|
|
347
|
*
|
|
348
|
* @return array
|
|
349
|
* An array of valid permissions for the portfolio module.
|
|
350
|
*/
|
|
351
|
function cdm_dataportal_permission() {
|
|
352
|
return array(
|
|
353
|
'administer cdm_dataportal' => array(
|
|
354
|
'title' => t('administer cdm_dataportal'),
|
|
355
|
'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
|
|
356
|
),
|
|
357
|
'cdm_dataportal view notes' => array(
|
|
358
|
'title' => t('cdm_dataportal view notes'),
|
|
359
|
'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
|
|
360
|
),
|
|
361
|
// TODO Which other permissions are required?
|
|
362
|
// -> check the WP6 requirements document.
|
|
363
|
);
|
|
364
|
}
|
|
365
|
|
|
366
|
/**
|
|
367
|
* Implements hook_menu().
|
|
368
|
*/
|
|
369
|
function cdm_dataportal_menu() {
|
|
370
|
$items = array();
|
|
371
|
|
|
372
|
// @see settings.php.
|
|
373
|
cdm_dataportal_menu_admin($items);
|
|
374
|
cdm_dataportal_menu_help($items);
|
|
375
|
|
|
376
|
$items['cdm_dataportal/names'] = array(
|
|
377
|
'page callback' => 'cdm_dataportal_view_names',
|
|
378
|
'access arguments' => array('access content'),
|
|
379
|
'type' => MENU_CALLBACK,
|
|
380
|
);
|
|
381
|
|
|
382
|
// Optional callback arguments: page.
|
|
383
|
$items['cdm_dataportal/taxon'] = array(
|
|
384
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
385
|
'access arguments' => array('access content'),
|
|
386
|
'type' => MENU_CALLBACK,
|
|
387
|
// Expected callback arguments: uuid.
|
|
388
|
);
|
|
389
|
|
|
390
|
// Optional callback arguments: page.
|
|
391
|
//FIXME point to view/page method in this module
|
|
392
|
$items['cdm_dataportal/specimen'] = array(
|
|
393
|
'page callback' => 'cdm_dataportal_specimen_page_view',
|
|
394
|
'access arguments' => array('access content'),
|
|
395
|
'type' => MENU_CALLBACK,
|
|
396
|
// Expected callback arguments: uuid.
|
|
397
|
);
|
|
398
|
|
|
399
|
$items['cdm_dataportal/name'] = array(
|
|
400
|
'page callback' => 'cdm_dataportal_name_page_view',
|
|
401
|
/*
|
|
402
|
'page arguments' => array(
|
|
403
|
'taxon_name_uuid',
|
|
404
|
'taxon_to_hide_uuid',
|
|
405
|
'synonym_uuid' => NULL
|
|
406
|
),
|
|
407
|
*/
|
|
408
|
'access arguments' => array('access content'),
|
|
409
|
'type' => MENU_CALLBACK,
|
|
410
|
// Expected callback arguments: uuid.
|
|
411
|
);
|
|
412
|
|
|
413
|
$items['cdm_dataportal/reference'] = array(
|
|
414
|
'page callback' => 'cdm_dataportal_view_reference',
|
|
415
|
'access arguments' => array('access content'),
|
|
416
|
'type' => MENU_CALLBACK,
|
|
417
|
// Expected callback arguments: uuid.
|
|
418
|
);
|
|
419
|
|
|
420
|
$items['cdm_dataportal/reference/list'] = array(
|
|
421
|
'page callback' => 'cdm_dataportal_view_reference_list',
|
|
422
|
'access arguments' => array('access content'),
|
|
423
|
'type' => MENU_CALLBACK,
|
|
424
|
// Expected callback arguments: uuid.
|
|
425
|
);
|
|
426
|
|
|
427
|
$items['cdm_dataportal/media'] = array(
|
|
428
|
'page callback' => 'cdm_dataportal_view_media',
|
|
429
|
'access arguments' => array('access content'),
|
|
430
|
'type' => MENU_CALLBACK,
|
|
431
|
// Expected callback arguments:
|
|
432
|
// uuid, mediarepresentation_uuid, part_uuid or part#.
|
|
433
|
);
|
|
434
|
|
|
435
|
$items['cdm_dataportal/polytomousKey'] = array(
|
|
436
|
'page callback' => 'cdm_dataportal_view_polytomousKey',
|
|
437
|
'access arguments' => array('access content'),
|
|
438
|
'type' => MENU_CALLBACK,
|
|
439
|
// Expected callback arguments: polytomousKey->uuid.
|
|
440
|
);
|
|
441
|
|
|
442
|
$items['cdm_dataportal/search'] = array(
|
|
443
|
'page callback' => 'cdm_dataportal_view_search_advanced',
|
|
444
|
'access arguments' => array('access content'),
|
|
445
|
'type' => MENU_CALLBACK,
|
|
446
|
);
|
|
447
|
|
|
448
|
$items['cdm_dataportal/search/advanced'] = array(
|
|
449
|
'title' => 'Advanced',
|
|
450
|
'page callback' => 'cdm_dataportal_view_search_advanced',
|
|
451
|
'access arguments' => array('access content'),
|
|
452
|
'type' => MENU_DEFAULT_LOCAL_TASK,
|
|
453
|
);
|
|
454
|
|
|
455
|
$items['cdm_dataportal/search/taxon_by_description'] = array(
|
|
456
|
'title' => 'By description full text',
|
|
457
|
'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
|
|
458
|
'access arguments' => array('access content'),
|
|
459
|
'type' => MENU_LOCAL_TASK,
|
|
460
|
);
|
|
461
|
|
|
462
|
$items['cdm_dataportal/search/results/taxon'] = array(
|
|
463
|
'page callback' => 'cdm_dataportal_view_search_results_taxon',
|
|
464
|
'access arguments' => array('access content'),
|
|
465
|
'type' => MENU_CALLBACK,
|
|
466
|
);
|
|
467
|
/*
|
|
468
|
$items['cdm/xml2json'] = array(
|
|
469
|
'page callback' => 'cdm_view_xml2json',
|
|
470
|
'access arguments' => array('access content'),
|
|
471
|
'type' => MENU_CALLBACK,
|
|
472
|
);
|
|
473
|
*/
|
|
474
|
|
|
475
|
// if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
|
|
476
|
// User configuration of cdm_dataportal.
|
|
477
|
$items['user/%/cdm_dataportal'] = array(
|
|
478
|
'title' => 'cdm_dataportal',
|
|
479
|
'access arguments' => array('access content'),
|
|
480
|
'page callback' => 'drupal_get_form',
|
|
481
|
'page arguments' => array('cdm_dataportal_user_form'),
|
|
482
|
'type' => MENU_LOCAL_TASK,
|
|
483
|
'weight' => 10,
|
|
484
|
);
|
|
485
|
// }
|
|
486
|
|
|
487
|
// 'May not cache' in D5.
|
|
488
|
$items['cdm_dataportal/name/%'] = array(
|
|
489
|
// 'page callback' => 'cdm_dataportal_view_name',
|
|
490
|
'page callback' => 'cdm_dataportal_name_page_view',
|
|
491
|
'page arguments' => array(2, 3, 4),
|
|
492
|
'access arguments' => array('access content'),
|
|
493
|
'type' => MENU_CALLBACK,
|
|
494
|
);
|
|
495
|
|
|
496
|
// --- Local tasks for Taxon.
|
|
497
|
// --- tabbed taxon page
|
|
498
|
if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
|
|
499
|
$items['cdm_dataportal/taxon/%'] = array(
|
|
500
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
|
|
501
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
502
|
'access arguments' => array('access content'),
|
|
503
|
'type' => MENU_CALLBACK,
|
|
504
|
'weight' => 1,
|
|
505
|
'page arguments' => array(2, "description")
|
|
506
|
, // Expected callback arguments: taxon_uuid.
|
|
507
|
);
|
|
508
|
|
|
509
|
$items['cdm_dataportal/taxon/%/all'] = array(
|
|
510
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
|
|
511
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
512
|
'access arguments' => array('access content'),
|
|
513
|
'type' => MENU_CALLBACK,
|
|
514
|
'weight' => 2,
|
|
515
|
'page arguments' => array(2, "all")
|
|
516
|
, // Expected callback arguments: taxon_uuid.
|
|
517
|
);
|
|
518
|
|
|
519
|
$items['cdm_dataportal/taxon/%/description'] = array(
|
|
520
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
|
|
521
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
522
|
'access arguments' => array('access content'),
|
|
523
|
'type' => MENU_DEFAULT_LOCAL_TASK,
|
|
524
|
'weight' => 2,
|
|
525
|
'page arguments' => array(2, "description")
|
|
526
|
, // Expected callback arguments: taxon_uuid.
|
|
527
|
);
|
|
528
|
|
|
529
|
$items['cdm_dataportal/taxon/%/synonymy'] = array(
|
|
530
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
|
|
531
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
532
|
'access arguments' => array('access content'),
|
|
533
|
'type' => MENU_LOCAL_TASK,
|
|
534
|
'weight' => 4,
|
|
535
|
'page arguments' => array(2, "synonymy", 4)
|
|
536
|
, // Expected callback arguments: taxon_uuid and ...
|
|
537
|
);
|
|
538
|
$items['cdm_dataportal/taxon/%/images'] = array(
|
|
539
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
|
|
540
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
541
|
'access arguments' => array('access content'),
|
|
542
|
'type' => MENU_LOCAL_TASK,
|
|
543
|
'weight' => 5,
|
|
544
|
'page arguments' => array(2, "images")
|
|
545
|
, // Expected callback arguments: taxon_uuid.
|
|
546
|
);
|
|
547
|
|
|
548
|
$items['cdm_dataportal/taxon/%/specimens'] = array(
|
|
549
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
|
|
550
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
551
|
'access arguments' => array('access content'),
|
|
552
|
'type' => MENU_LOCAL_TASK,
|
|
553
|
'weight' => 6,
|
|
554
|
'page arguments' => array(2, "specimens")
|
|
555
|
, // Expected callback arguments: taxon_uuid.
|
|
556
|
);
|
|
557
|
|
|
558
|
$items['cdm_dataportal/taxon/%/keys'] = array(
|
|
559
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
|
|
560
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
561
|
'access arguments' => array('access content'),
|
|
562
|
'type' => MENU_LOCAL_TASK,
|
|
563
|
'weight' => 6,
|
|
564
|
'page arguments' => array(2, "keys")
|
|
565
|
, // Expected callback arguments: taxon_uuid.
|
|
566
|
);
|
|
567
|
|
|
568
|
$items['cdm_dataportal/taxon/%/experts'] = array(
|
|
569
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Experts')),
|
|
570
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
571
|
'access arguments' => array('access content'),
|
|
572
|
'type' => MENU_LOCAL_TASK,
|
|
573
|
'weight' => 6,
|
|
574
|
'page arguments' => array(2, "experts")
|
|
575
|
, // Expected callback arguments: taxon_uuid.
|
|
576
|
);
|
|
577
|
}
|
|
578
|
|
|
579
|
// --- refresh link for all cdmnode types
|
|
580
|
foreach (cdm_get_nodetypes() as $type=>$name) {
|
|
581
|
$items['cdm_dataportal/' . $name . '/%/refresh'] = array(
|
|
582
|
'title' => t('Refresh'),
|
|
583
|
'page callback' => 'cdm_dataportal_refresh_node',
|
|
584
|
'access arguments' => array('administer cdm_dataportal'),
|
|
585
|
'type' => MENU_LOCAL_TASK,
|
|
586
|
'weight' => 100,
|
|
587
|
'page arguments' => array($name, 2)
|
|
588
|
);
|
|
589
|
}
|
|
590
|
|
|
591
|
return $items;
|
|
592
|
}
|
|
593
|
|
|
594
|
/**
|
|
595
|
* Implements hook_init().
|
|
596
|
*
|
|
597
|
*/
|
|
598
|
function cdm_dataportal_init() {
|
|
599
|
//FIXME To add CSS or JS that should be present on all pages, modules
|
|
600
|
// should not implement this hook, but declare these files in their .info file.
|
|
601
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
|
|
602
|
// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
|
|
603
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
|
|
604
|
|
|
605
|
if(variable_get('cdm_debug_mode', FALSE)){
|
|
606
|
$file = 'temporary://drupal_debug.txt';
|
|
607
|
file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
|
|
608
|
}
|
|
609
|
|
|
610
|
$bibliography_settings = get_bibliography_settings();
|
|
611
|
$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
|
|
612
|
FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
|
|
613
|
}
|
|
614
|
|
|
615
|
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
|
|
616
|
|
|
617
|
$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
|
|
618
|
|
|
619
|
if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
|
|
620
|
// force reloading of all and notify user about this special loading
|
|
621
|
drupal_set_message(t('The level 2 cache has been cleared for all tabs of this taxon page at once, please click here to return to the tabbed page: ')
|
|
622
|
. l('Back to tabbed taxon page', $base_path));
|
|
623
|
$base_path .= '/all';
|
|
624
|
} else {
|
|
625
|
drupal_set_message(t('The level 2 cache has been cleared for this page'));
|
|
626
|
}
|
|
627
|
|
|
628
|
$parameters['cacheL2_refresh'] ='1';
|
|
629
|
|
|
630
|
|
|
631
|
drupal_goto($base_path, array('query' => $parameters));
|
|
632
|
}
|
|
633
|
|
|
634
|
/**
|
|
635
|
* The function generate form for own user cdm dataportal configurations.
|
|
636
|
*/
|
|
637
|
function cdm_dataportal_user_form($form, &$form_state) {
|
|
638
|
global $user;
|
|
639
|
$checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
|
|
640
|
|
|
641
|
$form['taxon_page_tabs'] = array(
|
|
642
|
'#type' => 'fieldset',
|
|
643
|
'#title' => t('Taxon page tabs'),
|
|
644
|
);
|
|
645
|
$form['taxon_page_tabs']['check'] = array(
|
|
646
|
'#type' => 'checkbox',
|
|
647
|
'#title' => t('Activate user default configuration'),
|
|
648
|
'#default_value' => variable_get($checkbox_value, 0),
|
|
649
|
'#description' => t('Check this if you want configure your own default tab from the below menu.'),
|
|
650
|
);
|
|
651
|
|
|
652
|
$form['taxon_page_tabs']['cdm_dataportal_user_form'] = array(
|
|
653
|
'#type' => 'select',
|
|
654
|
'#title' => t('Default tab to display'),
|
|
655
|
'#default_value' => get_default_taxon_tab(TRUE),
|
|
656
|
'#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
|
|
657
|
'#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
|
|
658
|
<strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
|
|
659
|
to be renderized will be the synonymy of the accepted taxon and not the above selected tab.'),
|
|
660
|
);
|
|
661
|
|
|
662
|
$form['submit'] = array(
|
|
663
|
'#type' => 'submit',
|
|
664
|
'#value' => t('Submit'),
|
|
665
|
);
|
|
666
|
|
|
667
|
return $form;
|
|
668
|
}
|
|
669
|
|
|
670
|
/**
|
|
671
|
* Form submission handler for user_form().
|
|
672
|
*
|
|
673
|
* Submits the user cdm dataportal configurations.
|
|
674
|
*/
|
|
675
|
function cdm_dataportal_user_form_submit($form, &$form_state) {
|
|
676
|
global $user;
|
|
677
|
$msg_type = 'status';
|
|
678
|
$username = $user->name;
|
|
679
|
$variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
|
|
680
|
|
|
681
|
// If is the right user the variables are setted.
|
|
682
|
if (arg(0) == 'user' && ($uid = arg(1)) && is_numeric($uid) && $user->uid == $uid) {
|
|
683
|
$variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
|
|
684
|
variable_set($variable_to_use . '_active', $form_state['values']['check']);
|
|
685
|
variable_set($variable_to_use, $form_state['values']['cdm_dataportal_user_form']);
|
|
686
|
if ($form_state['values']['check']) {
|
|
687
|
drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
|
|
688
|
drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
|
|
689
|
'!tab' => $variable[variable_get($variable_to_use, 0)],
|
|
690
|
'!user' => $username,
|
|
691
|
))), $msg_type);
|
|
692
|
}
|
|
693
|
else {
|
|
694
|
drupal_set_message(check_plain(t('The user default tab wont be used for
|
|
695
|
the next taxon site, check the box if you want to use the user default configuration.')));
|
|
696
|
}
|
|
697
|
// Problem with the user id => variables wont be saved.
|
|
698
|
}
|
|
699
|
else {
|
|
700
|
$msg_type = 'warning';
|
|
701
|
drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
|
|
702
|
}
|
|
703
|
}
|
|
704
|
|
|
705
|
/**
|
|
706
|
* Implements hook_block_info().
|
|
707
|
*/
|
|
708
|
function cdm_dataportal_block_info() {
|
|
709
|
|
|
710
|
// $block[0]["info"] = t("CDM DataPortal DevLinks");
|
|
711
|
// $block[1]["info"] = t("CDM DataPortal Credits");
|
|
712
|
$block["2"] = array(
|
|
713
|
"info" => t("CDM Search Taxa"),
|
|
714
|
"cache" => DRUPAL_NO_CACHE
|
|
715
|
);
|
|
716
|
// $block[3]["info"] = t("CDM Filters");
|
|
717
|
$block["4"]["info"] = t("CDM Dataportal Print");
|
|
718
|
$block["keys"]["info"] = t("CDM identification keys");
|
|
719
|
$block["fundedByEDIT"]["info"] = t('Funded by EDIT');
|
|
720
|
$block["classification_breadcrumbs"] = array(
|
|
721
|
'info' => t('Classification breadcrumbs'),
|
|
722
|
'cache' => DRUPAL_CACHE_PER_PAGE
|
|
723
|
);
|
|
724
|
|
|
725
|
return $block;
|
|
726
|
}
|
|
727
|
|
|
728
|
/**
|
|
729
|
* Implements hook_block_view().
|
|
730
|
*/
|
|
731
|
function cdm_dataportal_block_view($delta) {
|
|
732
|
// TODO Rename block deltas (e.g. '2') to readable strings.
|
|
733
|
switch ($delta) {
|
|
734
|
// case 'delta-1':
|
|
735
|
// $block['subject'] = t('Credits');
|
|
736
|
// $block['content'] = theme('cdm_credits');
|
|
737
|
// return $block;
|
|
738
|
case '2':
|
|
739
|
$block['subject'] = t('Search taxa');
|
|
740
|
$form = drupal_get_form('cdm_dataportal_search_taxon_form');
|
|
741
|
$block['content'] = drupal_render($form);
|
|
742
|
|
|
743
|
if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
|
|
744
|
$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
|
|
745
|
}
|
|
746
|
return $block;
|
|
747
|
case '4':
|
|
748
|
$block['subject'] = '';
|
|
749
|
$block['content'] = theme('cdm_print_button');
|
|
750
|
return $block;
|
|
751
|
case "keys":
|
|
752
|
$block['subject'] = t('Identification Keys');
|
|
753
|
$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
|
|
754
|
return $block;
|
|
755
|
case "fundedByEDIT":
|
|
756
|
// t('Funded by EDIT');
|
|
757
|
$text = '<none>';
|
|
758
|
$block['subject'] = $text;
|
|
759
|
$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
|
|
760
|
$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
|
|
761
|
'attributes' => array("target" => "EDIT"),
|
|
762
|
'absolute' => TRUE,
|
|
763
|
'html' => TRUE,
|
|
764
|
));
|
|
765
|
return $block;
|
|
766
|
case 'classification_breadcrumbs':
|
|
767
|
if (arg(1) == 'taxon' && is_uuid(arg(2))) {
|
|
768
|
$block['subject'] = '<none>';
|
|
769
|
$block['content'] = compose_classification_breadcrumbs(arg(2));
|
|
770
|
return $block;
|
|
771
|
}
|
|
772
|
break;
|
|
773
|
}
|
|
774
|
}
|
|
775
|
|
|
776
|
/*
|
|
777
|
function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
|
|
778
|
$_SESSION['cdm'] = NULL;
|
|
779
|
if(is_string($cdm_ws_uri_update)){
|
|
780
|
$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
|
|
781
|
}
|
|
782
|
}
|
|
783
|
|
|
784
|
function cdm_dataportal_session_validate(){
|
|
785
|
if(!isset($_SESSION['cdm']['ws_uri'])){
|
|
786
|
$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
|
|
787
|
} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
|
|
788
|
cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
|
|
789
|
}
|
|
790
|
}
|
|
791
|
*/
|
|
792
|
|
|
793
|
/**
|
|
794
|
* creates a selector form for taxonomic trees.
|
|
795
|
*
|
|
796
|
* @return a drupal form array
|
|
797
|
*/
|
|
798
|
function cdm_taxonomictree_selector() {
|
|
799
|
_add_js_treeselector();
|
|
800
|
|
|
801
|
$form = drupal_get_form('cdm_taxonomictree_selector_form');
|
|
802
|
return $form;
|
|
803
|
}
|
|
804
|
|
|
805
|
/**
|
|
806
|
* @todo Please document this function.
|
|
807
|
* @see http://drupal.org/node/1354
|
|
808
|
*/
|
|
809
|
function cdm_taxonomictree_selector_form($form, &$form_state) {
|
|
810
|
|
|
811
|
$url = url('cdm_api/setvalue/session', array('query' => NULL));
|
|
812
|
$form['#action'] = $url;
|
|
813
|
|
|
814
|
$form['var'] = array(
|
|
815
|
'#weight' => -3,
|
|
816
|
'#type' => 'hidden',
|
|
817
|
'#value' => '[cdm][taxonomictree_uuid]',
|
|
818
|
);
|
|
819
|
|
|
820
|
$destination_array = drupal_get_destination();
|
|
821
|
$destination = $destination_array['destination'];
|
|
822
|
|
|
823
|
$form['destination'] = array(
|
|
824
|
'#weight' => -3,
|
|
825
|
'#type' => 'hidden',
|
|
826
|
'#value' => $destination,
|
|
827
|
);
|
|
828
|
|
|
829
|
$options = cdm_get_taxontrees_as_options();
|
|
830
|
$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
|
|
831
|
if($taxontree_includes){
|
|
832
|
$filtered_options = array();
|
|
833
|
foreach($options as $uuid=>$label){
|
|
834
|
if(!empty($taxontree_includes[$uuid])){
|
|
835
|
$filtered_options[$uuid] = $label;
|
|
836
|
}
|
|
837
|
}
|
|
838
|
$options = $filtered_options;
|
|
839
|
}
|
|
840
|
|
|
841
|
$form['val'] = array(
|
|
842
|
'#type' => 'select',
|
|
843
|
'#title' => t('Available classifications'),
|
|
844
|
'#default_value' => get_current_classification_uuid(),
|
|
845
|
'#options' => $options,
|
|
846
|
'#attributes' => array('class' => array('highlite-first-child'))
|
|
847
|
);
|
|
848
|
|
|
849
|
return $form;
|
|
850
|
|
|
851
|
}
|
|
852
|
|
|
853
|
/* UNREACHABLE since action of form directly links to view.
|
|
854
|
function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
|
|
855
|
|
|
856
|
$_SESSION['cdm']['search'] = $form_values;
|
|
857
|
//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
|
|
858
|
return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
|
|
859
|
//$paramstr = compose_url_prameterstr($form_values);
|
|
860
|
//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
|
|
861
|
}
|
|
862
|
*/
|
|
863
|
/* ====================== menu callback functions ====================== */
|
|
864
|
/**
|
|
865
|
* @todo Please document this function.
|
|
866
|
* @see http://drupal.org/node/1354
|
|
867
|
*/
|
|
868
|
/*
|
|
869
|
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
|
|
870
|
static $comment_node_disabled = 0;
|
|
871
|
static $comment_node_read_only = 1;
|
|
872
|
static $comment_node_read_write = 2;
|
|
873
|
|
|
874
|
if ($form_id == 'node_type_form'
|
|
875
|
&& isset($form['identity']['type'])
|
|
876
|
&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
|
|
877
|
) {
|
|
878
|
$form['workflow']['comment'] = array(
|
|
879
|
'#type' => 'radios',
|
|
880
|
'#title' => t('Default comment setting'),
|
|
881
|
'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
|
|
882
|
'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
|
|
883
|
'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
|
|
884
|
);
|
|
885
|
}
|
|
886
|
}
|
|
887
|
*/
|
|
888
|
|
|
889
|
/**
|
|
890
|
* Displays a list of the known taxonomic names.
|
|
891
|
*
|
|
892
|
* When the list of taxonomic names is displayed, long lists are split up into
|
|
893
|
* multiple pages.
|
|
894
|
*
|
|
895
|
* TODO: Parameters are still preliminary.
|
|
896
|
*
|
|
897
|
* @param string $beginsWith
|
|
898
|
* @param string $page
|
|
899
|
* Page number to diplay defaults to page 1.
|
|
900
|
* @param bool $onlyAccepted
|
|
901
|
*/
|
|
902
|
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
|
|
903
|
|
|
904
|
$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
|
|
905
|
|
|
906
|
/*
|
|
907
|
// FIXME the filter for accepted names will be a form element, thus this
|
|
908
|
// widget should be generated via form api preferably as block.
|
|
909
|
$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
|
|
910
|
$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
|
|
911
|
$out .= theme('cdm_listof_taxa', $taxonPager);
|
|
912
|
return $out;
|
|
913
|
*/
|
|
914
|
}
|
|
915
|
|
|
916
|
/**
|
|
917
|
* @todo Please document this function.
|
|
918
|
* @see http://drupal.org/node/1354
|
|
919
|
*/
|
|
920
|
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
|
|
921
|
|
|
922
|
cdm_check_valid_portal_page();
|
|
923
|
|
|
924
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
|
925
|
return theme('cdm_reference_page', array('reference' => $reference));
|
|
926
|
}
|
|
927
|
|
|
928
|
/**
|
|
929
|
* Created a view on a all references contained in the portal.
|
|
930
|
*
|
|
931
|
* This function is used at the path cdm_dataportal/reference/list
|
|
932
|
*/
|
|
933
|
function cdm_dataportal_view_reference_list($pageNumber) {
|
|
934
|
$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
|
|
935
|
return theme('cdm_reference_pager', array(
|
|
936
|
'referencePager' => $referencePager,
|
|
937
|
'path' => 'cdm_dataportal/reference/list/',
|
|
938
|
));
|
|
939
|
}
|
|
940
|
|
|
941
|
/**
|
|
942
|
* @todo Please document this function.
|
|
943
|
* @see http://drupal.org/node/1354
|
|
944
|
*/
|
|
945
|
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
|
|
946
|
|
|
947
|
cdm_check_valid_portal_page();
|
|
948
|
|
|
949
|
$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
|
|
950
|
return theme('cdm_media_page', array(
|
|
951
|
'media' => $media,
|
|
952
|
'mediarepresentation_uuid' => $mediarepresentation_uuid,
|
|
953
|
'partId' => $part,
|
|
954
|
));
|
|
955
|
}
|
|
956
|
|
|
957
|
/**
|
|
958
|
* @todo Please document this function.
|
|
959
|
* @see http://drupal.org/node/1354
|
|
960
|
*/
|
|
961
|
function _load_taxonBase(&$taxonBase) {
|
|
962
|
if (isset($taxonBase->uuid)) {
|
|
963
|
$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
|
|
964
|
$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
|
|
965
|
$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
|
|
966
|
}
|
|
967
|
}
|
|
968
|
|
|
969
|
/**
|
|
970
|
* Loads the media associated to the given taxon from the cdm server.
|
|
971
|
* The aggregation settings regarding taxon relathionships and
|
|
972
|
* taxonnomic childen are taken into account.
|
|
973
|
*
|
|
974
|
* The media lists are cached in a static variable.
|
|
975
|
*
|
|
976
|
* @param Taxon $taxon
|
|
977
|
* A CDM Taxon entitiy
|
|
978
|
*
|
|
979
|
* @return array
|
|
980
|
* An array of CDM Media entities
|
|
981
|
*
|
|
982
|
*/
|
|
983
|
function _load_media_for_taxon($taxon) {
|
|
984
|
|
|
985
|
static $media = NULL;
|
|
986
|
|
|
987
|
if(!isset($media)) {
|
|
988
|
$media = array();
|
|
989
|
}
|
|
990
|
if (!isset($media[$taxon->uuid])) {
|
|
991
|
|
|
992
|
// --- GET Images --- //
|
|
993
|
$mediaQueryParameters = array(
|
|
994
|
"type" => "ImageFile",
|
|
995
|
);
|
|
996
|
|
|
997
|
$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
|
|
998
|
$mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
|
|
999
|
$mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
|
|
1000
|
|
|
1001
|
$taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
|
|
1002
|
$mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
|
|
1003
|
$mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
|
|
1004
|
$mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
|
|
1005
|
|
|
1006
|
$ws_endpoint = NULL;
|
|
1007
|
if ( variable_get('cdm_images_include_children', 0) == 0) {
|
|
1008
|
$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
|
|
1009
|
} else {
|
|
1010
|
$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
|
|
1011
|
}
|
|
1012
|
|
|
1013
|
$media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
|
|
1014
|
array(
|
|
1015
|
$taxon->uuid,
|
|
1016
|
),
|
|
1017
|
queryString($mediaQueryParameters)
|
|
1018
|
);
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
return $media[$taxon->uuid];
|
|
1022
|
}
|
|
1023
|
|
|
1024
|
/**
|
|
1025
|
*
|
|
1026
|
* @param Taxon $taxon
|
|
1027
|
* A CDM Taxon entitiy
|
|
1028
|
*
|
|
1029
|
* @return array
|
|
1030
|
* An array of CDM SpecimenOrObservation entities
|
|
1031
|
*
|
|
1032
|
function _load_occurences_for_taxon($taxon){
|
|
1033
|
|
|
1034
|
static $occurences = NULL;
|
|
1035
|
|
|
1036
|
if(!isset($occurences)) {
|
|
1037
|
$occurences = array();
|
|
1038
|
}
|
|
1039
|
|
|
1040
|
if (!isset($occurences[$taxon->uuid])){
|
|
1041
|
|
|
1042
|
$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
|
|
1043
|
$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
|
|
1044
|
$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
|
|
1045
|
|
|
1046
|
$by_associatedtaxon_query = http_build_query(array(
|
|
1047
|
'relationshipsInvers' => implode(',', $relationship_choice['invers']),
|
|
1048
|
'relationships' => implode(',', $relationship_choice['direct']),
|
|
1049
|
'pageSize' => null // all hits in one page
|
|
1050
|
)
|
|
1051
|
);
|
|
1052
|
|
|
1053
|
$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
|
|
1054
|
null,
|
|
1055
|
$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
|
|
1056
|
);
|
|
1057
|
|
|
1058
|
|
|
1059
|
if(isset($pager->records[0])){
|
|
1060
|
$occurences[$taxon->uuid] = $pager->records;
|
|
1061
|
}
|
|
1062
|
}
|
|
1063
|
return $occurences[$taxon->uuid];
|
|
1064
|
}
|
|
1065
|
*/
|
|
1066
|
|
|
1067
|
/**
|
|
1068
|
* Gets a Drupal variable, string or array and returns it.
|
|
1069
|
*
|
|
1070
|
* Similar to the variable_get() function of Drupal, except that this function
|
|
1071
|
* is able to handle arrays correctly. This function is especially useful
|
|
1072
|
* when dealing with collections of settings form elements (#tree = TRUE).
|
|
1073
|
*
|
|
1074
|
* @param string $variableKey
|
|
1075
|
* The Unique key of the Drupal variable in the Drupal variables table.
|
|
1076
|
* @param string $defaultValueString
|
|
1077
|
* A string as for example derived from a CONSTANT.
|
|
1078
|
*
|
|
1079
|
* @return mixed
|
|
1080
|
* usually an array, depending on the nature of the variable.
|
|
1081
|
*
|
|
1082
|
* TODO compare with get_array_variable_merged() duplicate functions?
|
|
1083
|
* @deprecated rather use get_array_variable_merged() since this function
|
|
1084
|
* used an array as second parameter
|
|
1085
|
*/
|
|
1086
|
function mixed_variable_get($variableKey, $defaultValueString) {
|
|
1087
|
$systemDefaults = unserialize($defaultValueString);
|
|
1088
|
$storedSettings = variable_get($variableKey, array());
|
|
1089
|
if (is_array($storedSettings)) {
|
|
1090
|
// TODO better use drupal_array_merge_deep() ?
|
|
1091
|
$settings = array_merge($systemDefaults, $storedSettings);
|
|
1092
|
}
|
|
1093
|
else {
|
|
1094
|
$settings = $systemDefaults;
|
|
1095
|
}
|
|
1096
|
return $settings;
|
|
1097
|
}
|
|
1098
|
|
|
1099
|
/**
|
|
1100
|
* Recursive function to convert an object into an array.
|
|
1101
|
* also subordinate objects will be converted.
|
|
1102
|
*
|
|
1103
|
* @param object $object
|
|
1104
|
* @return the array
|
|
1105
|
*/
|
|
1106
|
function convert_to_array($object) {
|
|
1107
|
if(is_object($object) || is_array($object)) {
|
|
1108
|
$array = (array)$object;
|
|
1109
|
foreach ($array as $key=>$value){
|
|
1110
|
$array[$key] = convert_to_array($value);
|
|
1111
|
}
|
|
1112
|
return $array;
|
|
1113
|
} else {
|
|
1114
|
return $object;
|
|
1115
|
}
|
|
1116
|
}
|
|
1117
|
|
|
1118
|
/**
|
|
1119
|
* Searches the $collection for the cdm entitiy given as $element.
|
|
1120
|
*
|
|
1121
|
* The elements are compared by their UUID.
|
|
1122
|
*
|
|
1123
|
* @param $element
|
|
1124
|
* the CDM entitiy to search for
|
|
1125
|
* @param $collection
|
|
1126
|
* the list of CDM entities to search in
|
|
1127
|
*
|
|
1128
|
* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
|
|
1129
|
*
|
|
1130
|
*/
|
|
1131
|
function contains_cdm_entitiy($element, $collection) {
|
|
1132
|
$result = FALSE;
|
|
1133
|
foreach ($collection as $a) {
|
|
1134
|
if ($a->uuid == $element->uuid) {
|
|
1135
|
$result = TRUE;
|
|
1136
|
}
|
|
1137
|
}
|
|
1138
|
return $result;
|
|
1139
|
}
|
|
1140
|
|
|
1141
|
/**
|
|
1142
|
* Fiters the array $entity_list of CDM entities by the list
|
|
1143
|
* of $excludes. Any element contained in the $excludes will be removed
|
|
1144
|
* from included int the retuned list.
|
|
1145
|
*
|
|
1146
|
* If the $entity_list is not an array the $excludes will be returned.
|
|
1147
|
*/
|
|
1148
|
function filter_cdm_entity_list($entity_list, $excludes) {
|
|
1149
|
if (is_array($entity_list)) {
|
|
1150
|
$result = $entity_list;
|
|
1151
|
if ($excludes) {
|
|
1152
|
foreach ($excludes as $exclude) {
|
|
1153
|
if (!contains_cdm_entitiy($exclude, $entity_list)) {
|
|
1154
|
$result[] = $exclude;
|
|
1155
|
}
|
|
1156
|
}
|
|
1157
|
}
|
|
1158
|
}
|
|
1159
|
else {
|
|
1160
|
$result = $excludes;
|
|
1161
|
}
|
|
1162
|
return $result;
|
|
1163
|
}
|
|
1164
|
|
|
1165
|
/**
|
|
1166
|
* Wraps the given $html string into a render array suitable for drupal_render()
|
|
1167
|
*
|
|
1168
|
* @param $html
|
|
1169
|
* the html string, see
|
|
1170
|
* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
|
|
1171
|
* @param $weight
|
|
1172
|
* A positive or negative number (integer or decimal).
|
|
1173
|
* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
|
|
1174
|
* @param $prefix
|
|
1175
|
* Optional markup for the '#prefix' element of the render array
|
|
1176
|
* @param $suffix
|
|
1177
|
* Optional markup for the '#suffix' element of the render array
|
|
1178
|
*
|
|
1179
|
* @return array
|
|
1180
|
* A render array
|
|
1181
|
*
|
|
1182
|
*/
|
|
1183
|
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
|
|
1184
|
$render_array = array(
|
|
1185
|
'#markup' => $html
|
|
1186
|
);
|
|
1187
|
if (is_numeric($weight)) {
|
|
1188
|
$render_array['#weight'] = $weight;
|
|
1189
|
}
|
|
1190
|
if($prefix){
|
|
1191
|
$render_array['#prefix'] = $prefix;
|
|
1192
|
}
|
|
1193
|
if($suffix) {
|
|
1194
|
$render_array['#suffix'] = $suffix;
|
|
1195
|
}
|
|
1196
|
return $render_array;
|
|
1197
|
}
|
|
1198
|
|
|
1199
|
/**
|
|
1200
|
* Loads the subgraph of a given PolytomousKeyNode.
|
|
1201
|
*
|
|
1202
|
* Loads the subgraph of the given PolytomousKeyNode recursively from
|
|
1203
|
* the CDM REST service.
|
|
1204
|
*
|
|
1205
|
* @param mixed $polytomousKeyNode
|
|
1206
|
* PolytomousKeyNode passed by reference.
|
|
1207
|
*
|
|
1208
|
* @return void
|
|
1209
|
*/
|
|
1210
|
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
|
|
1211
|
|
|
1212
|
if (!$polytomousKeyNode) {
|
|
1213
|
return;
|
|
1214
|
}
|
|
1215
|
if ($polytomousKeyNode->class != "PolytomousKeyNode") {
|
|
1216
|
drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
|
|
1217
|
return;
|
|
1218
|
}
|
|
1219
|
if (!is_uuid($polytomousKeyNode->uuid)) {
|
|
1220
|
drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
|
|
1221
|
return;
|
|
1222
|
}
|
|
1223
|
|
|
1224
|
$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
|
|
1225
|
|
|
1226
|
if (!$polytomousKeyNode) {
|
|
1227
|
// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
|
|
1228
|
return;
|
|
1229
|
}
|
|
1230
|
|
|
1231
|
// Load children.
|
|
1232
|
foreach ($polytomousKeyNode->children as &$childNode) {
|
|
1233
|
_load_polytomousKeySubGraph($childNode);
|
|
1234
|
}
|
|
1235
|
|
|
1236
|
// Load subkey.
|
|
1237
|
$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
|
|
1238
|
|
|
1239
|
// Load taxon.
|
|
1240
|
$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
|
|
1241
|
_load_taxonBase($polytomousKeyNode->taxon);
|
|
1242
|
return;
|
|
1243
|
}
|
|
1244
|
|
|
1245
|
/**
|
|
1246
|
* @todo Please document this function.
|
|
1247
|
* @see http://drupal.org/node/1354
|
|
1248
|
*/
|
|
1249
|
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
|
|
1250
|
|
|
1251
|
cdm_check_valid_portal_page();
|
|
1252
|
|
|
1253
|
$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
|
|
1254
|
|
|
1255
|
$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
|
|
1256
|
if (is_array($sourcePager->records)) {
|
|
1257
|
$polytomousKey->sources = $sourcePager->records;
|
|
1258
|
// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
|
|
1259
|
}
|
|
1260
|
|
|
1261
|
$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
|
|
1262
|
if (is_array($annotationPager->records)) {
|
|
1263
|
$polytomousKey->annotations = $annotationPager->records;
|
|
1264
|
}
|
|
1265
|
|
|
1266
|
_load_polytomousKeySubGraph($polytomousKey->root);
|
|
1267
|
return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
|
|
1268
|
}
|
|
1269
|
|
|
1270
|
/**
|
|
1271
|
* Creates a taxon page view or a chapter of it.
|
|
1272
|
*
|
|
1273
|
* The taxon page gives detailed information on a taxon, it shows:
|
|
1274
|
* - Taxon name.
|
|
1275
|
* - Full list of synonyms homotypic synonyms on top, followed by the
|
|
1276
|
* heterotypic and finally followed by misapplied names.
|
|
1277
|
* The list is ordered historically.
|
|
1278
|
* - All description associated with the taxon.
|
|
1279
|
*
|
|
1280
|
* @param string $uuid
|
|
1281
|
* @param string $chapter
|
|
1282
|
* Name of the part to display, valid values are:
|
|
1283
|
* 'description', 'images', 'synonymy', 'specimens', 'all'.
|
|
1284
|
*
|
|
1285
|
* @return unknown_type
|
|
1286
|
*/
|
|
1287
|
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
|
|
1288
|
|
|
1289
|
cdm_check_valid_taxon_page($chapter);
|
|
1290
|
cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
|
|
1291
|
// show a warning in case the javascript development mode is anabled
|
|
1292
|
if(variable_get('cdm_js_devel_mode', FALSE)) {
|
|
1293
|
drupal_set_message(t('The !url1 is enabled.
|
|
1294
|
WARNING: this is a performance penalty and must be turned off on production websites.', array(
|
|
1295
|
'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
|
|
1296
|
)),
|
|
1297
|
'warning'
|
|
1298
|
);
|
|
1299
|
}
|
|
1300
|
|
|
1301
|
// Display the page for the taxon defined by $uuid.
|
|
1302
|
// set_last_taxon_page_tab(arg(3));
|
|
1303
|
$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
|
|
1304
|
if (!empty($taxonpage)) {
|
|
1305
|
cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
|
|
1306
|
return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
|
|
1307
|
}
|
|
1308
|
else {
|
|
1309
|
cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
|
|
1310
|
return '';
|
|
1311
|
}
|
|
1312
|
}
|
|
1313
|
|
|
1314
|
/**
|
|
1315
|
* This function will genreate the taxon page part ($chapter) and returns a taxonpage object
|
|
1316
|
* which has two fields, one for the page title and one for the content. Later on in the
|
|
1317
|
* process chain the value contained in these fields will be passed to the cdm_node_show()
|
|
1318
|
* function as the function parameters $title and $content.
|
|
1319
|
*
|
|
1320
|
* @param string $uuid
|
|
1321
|
* the uuid of the taxon to show
|
|
1322
|
* @param string $chapter
|
|
1323
|
* Name of the part to display, valid values are:
|
|
1324
|
* 'description', 'images', 'synonymy', 'all'.
|
|
1325
|
*
|
|
1326
|
* @return taxonpage object with the following fields:
|
|
1327
|
* - title : the title of the page
|
|
1328
|
* - content: the content of the page
|
|
1329
|
*
|
|
1330
|
*/
|
|
1331
|
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
|
|
1332
|
// Taxon object.
|
|
1333
|
$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
|
|
1334
|
if (empty($taxon)) {
|
|
1335
|
drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
|
|
1336
|
return FALSE;
|
|
1337
|
}
|
|
1338
|
$taxonpage = new stdClass();
|
|
1339
|
|
|
1340
|
$taxonpage->title = theme('cdm_taxon_page_title', array(
|
|
1341
|
'taxon' => $taxon
|
|
1342
|
));
|
|
1343
|
|
|
1344
|
// Check if the taxon id contained in the currently selected tree.
|
|
1345
|
$taxon_in_current_classification = taxon_in_current_classification($uuid);
|
|
1346
|
|
|
1347
|
if (!$taxon_in_current_classification) {
|
|
1348
|
$classifications = get_classifications_for_taxon($taxon);
|
|
1349
|
if (count($classifications) == 0) {
|
|
1350
|
drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification.',
|
|
1351
|
array(
|
|
1352
|
'!taxonname' => render_taxon_or_name($taxon->name),
|
|
1353
|
)
|
|
1354
|
), 'warning');
|
|
1355
|
}
|
|
1356
|
else {
|
|
1357
|
$trees = '';
|
|
1358
|
foreach ($classifications as $classification) {
|
|
1359
|
if (isset($classification->titleCache)) {
|
|
1360
|
$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
|
|
1361
|
}
|
|
1362
|
}
|
|
1363
|
|
|
1364
|
drupal_set_message(format_plural(count($trees),
|
|
1365
|
'This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification, but in this one: !trees',
|
|
1366
|
'This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification, but in one of these: !trees',
|
|
1367
|
array('!taxonname' => render_taxon_or_name($taxon), '!trees' => $trees)
|
|
1368
|
) ,
|
|
1369
|
'warning');
|
|
1370
|
}
|
|
1371
|
}
|
|
1372
|
|
|
1373
|
// Render the taxon page.
|
|
1374
|
$render_array = compose_cdm_taxon_page($taxon, $chapter);
|
|
1375
|
$taxonpage->content = drupal_render($render_array);
|
|
1376
|
|
|
1377
|
return $taxonpage;
|
|
1378
|
}
|
|
1379
|
|
|
1380
|
/**
|
|
1381
|
* Creates a specimen page view.
|
|
1382
|
* @param string $uuid the UUID of the specimen
|
|
1383
|
* @return array|string
|
|
1384
|
*/
|
|
1385
|
function cdm_dataportal_specimen_page_view($uuid) {
|
|
1386
|
|
|
1387
|
//cdm_check_valid_taxon_page($chapter);
|
|
1388
|
//cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
|
|
1389
|
// show a warning in case the javascript development mode is anabled
|
|
1390
|
if(variable_get('cdm_js_devel_mode', FALSE)) {
|
|
1391
|
drupal_set_message(t('The !url1 is enabled.
|
|
1392
|
WARNING: this is a performance penalty and must be turned off on production websites.', array(
|
|
1393
|
'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
|
|
1394
|
)),
|
|
1395
|
'warning'
|
|
1396
|
);
|
|
1397
|
}
|
|
1398
|
|
|
1399
|
// Display the page for the specimen defined by $uuid.
|
|
1400
|
$specimenpage = cdm_dataportal_specimen_view($uuid);
|
|
1401
|
if (!empty($specimenpage)) {
|
|
1402
|
return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
|
|
1403
|
}
|
|
1404
|
else {
|
|
1405
|
return '';
|
|
1406
|
}
|
|
1407
|
}
|
|
1408
|
|
|
1409
|
/**
|
|
1410
|
*
|
|
1411
|
* Creates a specimen view.
|
|
1412
|
* @param string $uuid the UUID of the specimen
|
|
1413
|
* @return array|string
|
|
1414
|
*/
|
|
1415
|
function cdm_dataportal_specimen_view($uuid) {
|
|
1416
|
$specimen = cdm_ws_get(CDM_WS_OCCURRENCE, $uuid);
|
|
1417
|
if (empty($specimen)) {
|
|
1418
|
drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
|
|
1419
|
return FALSE;
|
|
1420
|
}
|
|
1421
|
$specimenpage = new stdClass();
|
|
1422
|
|
|
1423
|
$specimenpage->title = theme('cdm_specimen_page_title', array(
|
|
1424
|
'specimen' => $specimen
|
|
1425
|
));
|
|
1426
|
|
|
1427
|
// Render the specimen page.
|
|
1428
|
$render_array = compose_cdm_specimen_page($uuid);
|
|
1429
|
$specimenpage->content = drupal_render($render_array);
|
|
1430
|
|
|
1431
|
return $specimenpage;
|
|
1432
|
}
|
|
1433
|
|
|
1434
|
/**
|
|
1435
|
* Returns a name page as a Drupal node ready to be renderized by Drupal.
|
|
1436
|
*
|
|
1437
|
* The node page shows the taxon name title and the list of taxon related
|
|
1438
|
* with such taxon. Name on the tree already in use.
|
|
1439
|
*
|
|
1440
|
* @param UUID $taxon_name_uuid
|
|
1441
|
* The uuid of the CDM TaxonNameBase to show a name page for
|
|
1442
|
* @param UUID $taxon_to_hide_uuid
|
|
1443
|
* A taxon which should not be displayed in the taxon list
|
|
1444
|
* @param UUID $highlite_synonym_uuid
|
|
1445
|
* Optinal parameter wich takes another taxon uuid, if given the
|
|
1446
|
* target taxon pages will show the syonymy tab where the taxon
|
|
1447
|
* refenrenced by the $highlite_synonym_uuid will be highlighted
|
|
1448
|
* in case it is found on this page.
|
|
1449
|
*
|
|
1450
|
* @return mixed
|
|
1451
|
* The formatted name page as node.
|
|
1452
|
*/
|
|
1453
|
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
|
|
1454
|
|
|
1455
|
cdm_check_valid_portal_page();
|
|
1456
|
|
|
1457
|
$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
|
|
1458
|
if (!empty($taxonname_page)) {
|
|
1459
|
return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
|
|
1460
|
}
|
|
1461
|
else {
|
|
1462
|
return '';
|
|
1463
|
}
|
|
1464
|
}
|
|
1465
|
|
|
1466
|
/**
|
|
1467
|
* View function for a TaxonNameBase page.
|
|
1468
|
*
|
|
1469
|
* The name page lists all taxa for which the name specified by the
|
|
1470
|
* $taxon_name_uuid is being used. I case there is only one name the
|
|
1471
|
* page automatically redirects ti the according taxon page. Otherwise
|
|
1472
|
* the list of names is displayed.
|
|
1473
|
*
|
|
1474
|
* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
|
|
1475
|
* list of taxa. This is useful for example when referencing from a taxon
|
|
1476
|
* to the name page and the referring taxon should not be repeaded in the
|
|
1477
|
* name page.
|
|
1478
|
*
|
|
1479
|
*
|
|
1480
|
* @param UUID $taxon_name_uuid
|
|
1481
|
* The uuid of the CDM TaxonNameBase to show a name page for
|
|
1482
|
* @param UUID $taxon_to_hide_uuid
|
|
1483
|
* A taxon which should not be displayed in the taxon list
|
|
1484
|
* @param UUID $highlite_synonym_uuid
|
|
1485
|
* Optinal parameter wich takes another taxon uuid, if given the
|
|
1486
|
* target taxon pages will show the syonymy tab where the taxon
|
|
1487
|
* refenrenced by the $highlite_synonym_uuid will be highlighted
|
|
1488
|
* in case it is found on this page.
|
|
1489
|
*
|
|
1490
|
* @return object
|
|
1491
|
* An object with two fields:
|
|
1492
|
* - title: the page title
|
|
1493
|
* - content: the page content
|
|
1494
|
*/
|
|
1495
|
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
|
|
1496
|
// Getting the full taxonname object from the server.
|
|
1497
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
|
|
1498
|
if (!$taxon_name) {
|
|
1499
|
drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
|
|
1500
|
return FALSE;
|
|
1501
|
}
|
|
1502
|
// Searching for all the taxa connected with the taxon name on the tree
|
|
1503
|
// in use.
|
|
1504
|
$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
|
|
1505
|
$request_params = array();
|
|
1506
|
$request_params['query'] = $name_cache;
|
|
1507
|
$request_params['tree'] = get_current_classification_uuid();
|
|
1508
|
$request_params['doTaxa'] = 1;
|
|
1509
|
$request_params['doSynonyms'] = 1;
|
|
1510
|
$request_params['doTaxaByCommonNames'] = 0;
|
|
1511
|
$request_params['matchMode'] = "EXACT";
|
|
1512
|
$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
|
|
1513
|
|
|
1514
|
// Removing the name where we come from.
|
|
1515
|
foreach ($taxon_pager->records as $k => &$taxon) {
|
|
1516
|
if ($taxon->uuid == $taxon_to_hide_uuid) {
|
|
1517
|
unset($taxon_pager->records[$k]);
|
|
1518
|
}
|
|
1519
|
}
|
|
1520
|
// Show the taxa list or go to the singular taxon.
|
|
1521
|
if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
|
|
1522
|
$singleTaxon = array_pop($taxon_pager->records);
|
|
1523
|
if ($singleTaxon->class != "Taxon") {
|
|
1524
|
// It is a Synonym -> look for the accepted.
|
|
1525
|
$accepted_taxa = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_current_classification_uuid()));
|
|
1526
|
if (!empty($highlite_synonym_uuid)) {
|
|
1527
|
drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
|
|
1528
|
}
|
|
1529
|
else {
|
|
1530
|
drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
|
|
1531
|
}
|
|
1532
|
}
|
|
1533
|
else {
|
|
1534
|
// It is an accepted taxon.
|
|
1535
|
if (!empty($highlite_synonym_uuid)) {
|
|
1536
|
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
|
|
1537
|
}
|
|
1538
|
else {
|
|
1539
|
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
|
|
1540
|
}
|
|
1541
|
}
|
|
1542
|
}
|
|
1543
|
else {// More than one taxa case.
|
|
1544
|
$taxon_name_page = new stdClass();
|
|
1545
|
$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
|
|
1546
|
if ($taxon_pager->records) {
|
|
1547
|
$taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, FALSE);
|
|
1548
|
}
|
|
1549
|
else {
|
|
1550
|
$taxon_name_page->content = 'This name has no taxa';
|
|
1551
|
}
|
|
1552
|
return $taxon_name_page;
|
|
1553
|
}
|
|
1554
|
}
|
|
1555
|
|
|
1556
|
/**
|
|
1557
|
* Creates a page with the advance search form.
|
|
1558
|
*
|
|
1559
|
* NOTE: The advance search form allows searching for taxa.
|
|
1560
|
*/
|
|
1561
|
function cdm_dataportal_view_search_advanced() {
|
|
1562
|
drupal_set_title(t('Advanced search'), PASS_THROUGH);
|
|
1563
|
return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
|
|
1564
|
}
|
|
1565
|
|
|
1566
|
/**
|
|
1567
|
* Creates a page with the search form for searching by taxon descriptions.
|
|
1568
|
*/
|
|
1569
|
function cdm_dataportal_view_search_taxon_by_description() {
|
|
1570
|
drupal_set_title(t('Search by description full text'), PASS_THROUGH);
|
|
1571
|
return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
|
|
1572
|
}
|
|
1573
|
|
|
1574
|
/**
|
|
1575
|
* Executes the search and generates the result list of taxa.
|
|
1576
|
*/
|
|
1577
|
function cdm_dataportal_view_search_results_taxon() {
|
|
1578
|
|
|
1579
|
$taxonPager = cdm_dataportal_search_execute();
|
|
1580
|
|
|
1581
|
$showThumbnails = do_showThumbnails();
|
|
1582
|
|
|
1583
|
$setSessionUri = url('cdm_api/setvalue/session', array(
|
|
1584
|
'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
|
|
1585
|
));
|
|
1586
|
|
|
1587
|
drupal_add_js('jQuery(document).ready(function() {
|
|
1588
|
|
|
1589
|
// init
|
|
1590
|
if(' . $showThumbnails . ' == 1){
|
|
1591
|
jQuery(\'.media_gallery\').show(20);
|
|
1592
|
} else {
|
|
1593
|
jQuery(\'.media_gallery\').hide(20);
|
|
1594
|
}
|
|
1595
|
|
|
1596
|
// add change handler
|
|
1597
|
jQuery(\'#showThumbnails input.showThumbnails\').change(
|
|
1598
|
function(event){
|
|
1599
|
var state = 0;
|
|
1600
|
if(jQuery(this).is(\':checked\')){
|
|
1601
|
jQuery(\'.media_gallery\').show(20);
|
|
1602
|
state = 1;
|
|
1603
|
} else {
|
|
1604
|
jQuery(\'.media_gallery\').hide(20);
|
|
1605
|
}
|
|
1606
|
// store state in session variable
|
|
1607
|
var uri = \'' . $setSessionUri . '\' + state;
|
|
1608
|
jQuery.get(uri);
|
|
1609
|
});
|
|
1610
|
});',
|
|
1611
|
array('type' => "inline", 'scope' => JS_DEFAULT));
|
|
1612
|
|
|
1613
|
drupal_set_title(t('Search results'), PASS_THROUGH);
|
|
1614
|
|
|
1615
|
return theme('cdm_search_results', array(
|
|
1616
|
'pager' => $taxonPager,
|
|
1617
|
'path' => 'cdm_dataportal/search/results/taxon',
|
|
1618
|
));
|
|
1619
|
}
|
|
1620
|
|
|
1621
|
/**
|
|
1622
|
* Provides the standart image wich indicated a loading process
|
|
1623
|
*
|
|
1624
|
* @return string
|
|
1625
|
* The img html tag
|
|
1626
|
*/
|
|
1627
|
function loading_image_html() {
|
|
1628
|
return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
|
|
1629
|
. '/images/loading_circle_grey_16.gif" style="display:none;">';
|
|
1630
|
}
|
|
1631
|
|
|
1632
|
/**
|
|
1633
|
* Returns the state of the the showThumbnails flag set in the
|
|
1634
|
* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
|
|
1635
|
*
|
|
1636
|
* @return boolean
|
|
1637
|
* returns 1 if the flag is set
|
|
1638
|
*/
|
|
1639
|
function do_showThumbnails() {
|
|
1640
|
static $showThumbnails = null;
|
|
1641
|
|
|
1642
|
if($showThumbnails == null) {
|
|
1643
|
$showThumbnails = 0;
|
|
1644
|
if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
|
|
1645
|
$showThumbnails = 0;
|
|
1646
|
$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
|
|
1647
|
$showThumbnails = is_array($search_gallery_settings)
|
|
1648
|
&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
|
|
1649
|
&& (
|
|
1650
|
$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
|
|
1651
|
$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
|
|
1652
|
$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
|
|
1653
|
)
|
|
1654
|
? 1 : 0;
|
|
1655
|
|
|
1656
|
drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
|
|
1657
|
}
|
|
1658
|
$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
|
|
1659
|
if (!is_numeric($showThumbnails)) {
|
|
1660
|
$showThumbnails = 1;
|
|
1661
|
}
|
|
1662
|
}
|
|
1663
|
|
|
1664
|
return $showThumbnails;
|
|
1665
|
}
|
|
1666
|
|
|
1667
|
/**
|
|
1668
|
* View which transforms XML output from a given webservice endpoint into JSON.
|
|
1669
|
*/
|
|
1670
|
/*
|
|
1671
|
function cdm_view_xml2json(){
|
|
1672
|
$file = arg(2);
|
|
1673
|
$datastr = file_get_contents(variable_get('cdm_webservice_url', '').$file);
|
|
1674
|
return xml2json::transformXmlStringToJson($datastr);
|
|
1675
|
}
|
|
1676
|
*/
|
|
1677
|
|
|
1678
|
/* ====================== other functions ====================== */
|
|
1679
|
/**
|
|
1680
|
* Creates a URL to the taxon page specified by the $uuid parameter.
|
|
1681
|
*
|
|
1682
|
* The URL will be prepended with a path element to a specific taxon page tab.
|
|
1683
|
*
|
|
1684
|
* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
|
|
1685
|
* be set globally in the administrative settings or individually in the user
|
|
1686
|
* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
|
|
1687
|
* the last portal will stay on this last tab.
|
|
1688
|
*
|
|
1689
|
* A third option is offerered by the $page_tab parameter which allows overwriting this
|
|
1690
|
* internal mechanism by a specific value.
|
|
1691
|
*
|
|
1692
|
* @param string $uuid
|
|
1693
|
* The UUID of the taxon.
|
|
1694
|
* @param string $page_tab
|
|
1695
|
* Overwriting the preset mechanism by defining specific value for the
|
|
1696
|
* taxon page tab.
|
|
1697
|
*
|
|
1698
|
* @return string
|
|
1699
|
* The created URL.
|
|
1700
|
*/
|
|
1701
|
function path_to_taxon($uuid, $page_tab = FALSE) {
|
|
1702
|
|
|
1703
|
$tab = get_default_taxon_tab();
|
|
1704
|
$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
|
|
1705
|
|
|
1706
|
if (!$uuid) {
|
|
1707
|
return FALSE;
|
|
1708
|
}
|
|
1709
|
|
|
1710
|
if ($page_tab) {
|
|
1711
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
|
|
1712
|
}
|
|
1713
|
elseif (!$tab || strtolower($tab) == 'general') {
|
|
1714
|
return 'cdm_dataportal/taxon/' . $uuid;
|
|
1715
|
}
|
|
1716
|
elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
|
|
1717
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
|
|
1718
|
}
|
|
1719
|
else {
|
|
1720
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
|
|
1721
|
}
|
|
1722
|
}
|
|
1723
|
|
|
1724
|
function path_to_specimen($uuid) {
|
|
1725
|
|
|
1726
|
if (!$uuid) {
|
|
1727
|
return FALSE;
|
|
1728
|
}
|
|
1729
|
else {
|
|
1730
|
return 'cdm_dataportal/specimen/' . $uuid;
|
|
1731
|
}
|
|
1732
|
}
|
|
1733
|
|
|
1734
|
/**
|
|
1735
|
* Creates a URL to show a synonmy in the according taxon page.
|
|
1736
|
*
|
|
1737
|
* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
|
|
1738
|
* The resulting URI will include query parameters to highlight the synonym, and to optionally display
|
|
1739
|
* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
|
|
1740
|
* include the sysnonym uuid as fragment in order to let the browser scroll to the according location
|
|
1741
|
* in the page
|
|
1742
|
*
|
|
1743
|
* @param string $synonymUuid
|
|
1744
|
* The uuid of the synonym
|
|
1745
|
* @param string $acceptedUuid
|
|
1746
|
* The uuid of the according accepted taxon
|
|
1747
|
* @return string
|
|
1748
|
* The URL to show a synonmy in the according taxon page
|
|
1749
|
*/
|
|
1750
|
function uri_to_synonym($synonymUuid, $acceptedUuid) {
|
|
1751
|
$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
|
|
1752
|
return url($acceptedPath, array(
|
|
1753
|
'query' => array(
|
|
1754
|
// highlite the synony in the synonymy
|
|
1755
|
'highlite' => $synonymUuid,
|
|
1756
|
// the taxon page is refered from a synonym and the synonym can optionally be named in the page title
|
|
1757
|
// see theme_taxon_page_title()
|
|
1758
|
'acceptedFor' => $synonymUuid
|
|
1759
|
),
|
|
1760
|
'fragment' => $synonymUuid
|
|
1761
|
));
|
|
1762
|
|
|
1763
|
}
|
|
1764
|
|
|
1765
|
/**
|
|
1766
|
* Compses the drupal path to the key identified by the uuid.
|
|
1767
|
*
|
|
1768
|
* @param string $keyType
|
|
1769
|
* the key typer corresponds to the specific class of the CDM
|
|
1770
|
* IdentificationKey. Possible values are
|
|
1771
|
* -PolytomousKey
|
|
1772
|
* -MultimediaKey
|
|
1773
|
* - ...
|
|
1774
|
* @param UUID $keyUuid
|
|
1775
|
* The UUID of the key
|
|
1776
|
*/
|
|
1777
|
function path_to_key($keyType, $keyUuid) {
|
|
1778
|
if (!$keyUuid || !$keyType) {
|
|
1779
|
return FALSE;
|
|
1780
|
}
|
|
1781
|
$keyType{0} = strtolower($keyType{0});
|
|
1782
|
return "cdm_dataportal/" . $keyType . "/$keyUuid";
|
|
1783
|
}
|
|
1784
|
|
|
1785
|
/**
|
|
1786
|
* @todo Please document this function.
|
|
1787
|
* @see http://drupal.org/node/1354
|
|
1788
|
*/
|
|
1789
|
function path_to_reference($uuid) {
|
|
1790
|
if (!$uuid) {
|
|
1791
|
return FALSE;
|
|
1792
|
}
|
|
1793
|
return 'cdm_dataportal/reference/' . $uuid;
|
|
1794
|
}
|
|
1795
|
|
|
1796
|
/**
|
|
1797
|
* Creates the path to a cdm_dataportal taxon name page.
|
|
1798
|
*
|
|
1799
|
* @param UUID $taxon_name_uuid
|
|
1800
|
* The uuid of the CDM TaxonNameBase to show a name page for
|
|
1801
|
* @param UUID $taxon_to_hide_uuid
|
|
1802
|
* A taxon which should not be displayed in the taxon list
|
|
1803
|
* @param UUID $highlite_synonym_uuid
|
|
1804
|
* Optinal parameter wich takes another taxon uuid, if given the
|
|
1805
|
* target taxon pages will show the syonymy tab where the taxon
|
|
1806
|
* refenrenced by the $highlite_synonym_uuid will be highlighted
|
|
1807
|
* in case it is found on this page.
|
|
1808
|
*
|
|
1809
|
* @return a URI path element as string
|
|
1810
|
*/
|
|
1811
|
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid = NULL) {
|
|
1812
|
$res = FALSE;
|
|
1813
|
if ($name_uuid) {
|
|
1814
|
$res = 'cdm_dataportal/name/' . $name_uuid;
|
|
1815
|
}
|
|
1816
|
if($taxon_to_hide_uuid){
|
|
1817
|
$res .= '/' . $taxon_to_hide_uuid;
|
|
1818
|
if($synonym_uuid){
|
|
1819
|
$res .= '/' . $synonym_uuid;
|
|
1820
|
}
|
|
1821
|
}
|
|
1822
|
return $res;
|
|
1823
|
}
|
|
1824
|
|
|
1825
|
/**
|
|
1826
|
* @todo Please document this function.
|
|
1827
|
* @see http://drupal.org/node/1354
|
|
1828
|
*/
|
|
1829
|
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
|
|
1830
|
if (!$uuid) {
|
|
1831
|
return FALSE;
|
|
1832
|
}
|
|
1833
|
$out = 'cdm_dataportal/media/' . $uuid;
|
|
1834
|
if ($representaion_uuid) {
|
|
1835
|
$out .= '/' . $representaion_uuid;
|
|
1836
|
if ($partId !== FALSE) {
|
|
1837
|
$out .= '/' . $partId;
|
|
1838
|
}
|
|
1839
|
}
|
|
1840
|
return $out;
|
|
1841
|
}
|
|
1842
|
|
|
1843
|
/**
|
|
1844
|
* Compares thisRank with thatRank.
|
|
1845
|
*
|
|
1846
|
* Returns a negative integer, zero, or a positive integer
|
|
1847
|
* as the of thisRank is higher than, equal to, or lower than thatRank.
|
|
1848
|
* e.g:
|
|
1849
|
* <ul>
|
|
1850
|
* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
|
|
1851
|
* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
|
|
1852
|
* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
|
|
1853
|
* </ul>
|
|
1854
|
* <p>
|
|
1855
|
* This compare logic of the underlying webservice is the
|
|
1856
|
* <b>inverse logic</b> of the the one implemented in
|
|
1857
|
* java.lang.Comparable#compareTo(java.lang.Object)
|
|
1858
|
*
|
|
1859
|
* @param $thisRankUuid
|
|
1860
|
* @param $thatRankUuid
|
|
1861
|
*
|
|
1862
|
* @return int
|
|
1863
|
* A negative integer, zero, or a positive integer
|
|
1864
|
* as the thisRank is lower than, equal to, or higher than thatRank.
|
|
1865
|
*/
|
|
1866
|
function rank_compare($thisRankUuid, $thatRankUuid) {
|
|
1867
|
$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
|
|
1868
|
return $result->Integer;
|
|
1869
|
}
|
|
1870
|
|
|
1871
|
/**
|
|
1872
|
* Composes an HTML element class attribute value composed of
|
|
1873
|
* the shortname of the cdm class and the uuid of the entity.
|
|
1874
|
* This class attribute should be used whereever an cdm-entity is rendered.
|
|
1875
|
*
|
|
1876
|
* These according class selectors in css must be escaped, eg:
|
|
1877
|
* .cdm\:TextData
|
|
1878
|
*
|
|
1879
|
* @param $cdmEntity
|
|
1880
|
*/
|
|
1881
|
function html_class_attribute_ref($cdmEntity) {
|
|
1882
|
|
|
1883
|
if (is_cdm_entity($cdmEntity)) {
|
|
1884
|
return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
|
|
1885
|
}
|
|
1886
|
}
|
|
1887
|
|
|
1888
|
|
|
1889
|
/**
|
|
1890
|
* Creates a short taxonname.
|
|
1891
|
*
|
|
1892
|
* The short name is created by using the taggedTitle field of
|
|
1893
|
* NameSTO or NameTO instances.
|
|
1894
|
* If the taggedTitle if empty the fullname will be returned.
|
|
1895
|
*
|
|
1896
|
* @param unknown_type $name
|
|
1897
|
* Name or TreeNode.
|
|
1898
|
*
|
|
1899
|
* @return string
|
|
1900
|
*/
|
|
1901
|
function cdm_dataportal_shortname_of($name) {
|
|
1902
|
$nameStr = '';
|
|
1903
|
|
|
1904
|
normalize_tagged_text($name->taggedTitle);
|
|
1905
|
|
|
1906
|
// Get all tagged text tokens of the scientific name.
|
|
1907
|
foreach ($name->taggedTitle as $tagtxt) {
|
|
1908
|
if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
|
|
1909
|
$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
|
|
1910
|
}
|
|
1911
|
}
|
|
1912
|
$nameStr = trim($nameStr);
|
|
1913
|
|
|
1914
|
if ($nameStr) {
|
|
1915
|
|
|
1916
|
// Do not return short names for these.
|
|
1917
|
if ($name->unplaced || $name->excluded) {
|
|
1918
|
return $nameStr;
|
|
1919
|
}
|
|
1920
|
|
|
1921
|
/*
|
|
1922
|
1st capture group (^[a-zA-Z]): First letter of uninomial.
|
|
1923
|
Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
|
|
1924
|
Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
|
|
1925
|
but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
|
|
1926
|
OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
|
|
1927
|
*/
|
|
1928
|
$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
|
|
1929
|
if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
|
|
1930
|
return $matches[1][0] . "." . $matches[3][0];
|
|
1931
|
}
|
|
1932
|
else {
|
|
1933
|
return $nameStr;
|
|
1934
|
}
|
|
1935
|
}
|
|
1936
|
else {
|
|
1937
|
return $name->titleCache;
|
|
1938
|
}
|
|
1939
|
}
|
|
1940
|
|
|
1941
|
/**
|
|
1942
|
* Check if a taxon is accepted by the current taxonomic tree.
|
|
1943
|
*
|
|
1944
|
* @param mixed $taxon
|
|
1945
|
* The Taxon obkect to check.
|
|
1946
|
*
|
|
1947
|
* @return bool
|
|
1948
|
* Returns TRUE if $taxon is accepted, FALSE otherwise.
|
|
1949
|
*/
|
|
1950
|
function _cdm_dataportal_acceptedByCurrentView($taxon) {
|
|
1951
|
|
|
1952
|
$defaultTreeUuid = get_current_classification_uuid();
|
|
1953
|
|
|
1954
|
if (isset($taxon->taxonNodes)) {
|
|
1955
|
$taxonNodes = $taxon->taxonNodes;
|
|
1956
|
}
|
|
1957
|
else {
|
|
1958
|
$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
|
|
1959
|
}
|
|
1960
|
|
|
1961
|
if ($taxon->class == "Taxon" && isset($taxonNodes)) {
|
|
1962
|
foreach ($taxonNodes as $node) {
|
|
1963
|
if (isset($node->classification)){
|
|
1964
|
if(is_object($node->classification)) {
|
|
1965
|
if ($node->classification->uuid == $defaultTreeUuid) {
|
|
1966
|
return TRUE;
|
|
1967
|
}
|
|
1968
|
}
|
|
1969
|
else {
|
|
1970
|
if ($node->classification == $defaultTreeUuid) {
|
|
1971
|
return TRUE;
|
|
1972
|
}
|
|
1973
|
}
|
|
1974
|
}
|
|
1975
|
}
|
|
1976
|
}
|
|
1977
|
|
|
1978
|
return FALSE;
|
|
1979
|
}
|
|
1980
|
|
|
1981
|
/**
|
|
1982
|
* Checks is the source has one of the given types.
|
|
1983
|
*
|
|
1984
|
* @param object $source
|
|
1985
|
* The original source entity
|
|
1986
|
* @param array $types
|
|
1987
|
* An array of elementd of the OriginalSourceType enumeration
|
|
1988
|
* If not set the default will be used which is:
|
|
1989
|
* - Lineage
|
|
1990
|
* - PrimaryMediaSource
|
|
1991
|
* - PrimaryTaxonomicSource
|
|
1992
|
* - Unknown
|
|
1993
|
* - Other
|
|
1994
|
* @return boolean
|
|
1995
|
*/
|
|
1996
|
function _is_original_source_type($source, $types = null) {
|
|
1997
|
// this is the default
|
|
1998
|
// maybe this should also be put into the settings
|
|
1999
|
static $default = array(
|
|
2000
|
OriginalSourceType::Lineage,
|
|
2001
|
OriginalSourceType::PrimaryMediaSource,
|
|
2002
|
OriginalSourceType::PrimaryTaxonomicSource,
|
|
2003
|
OriginalSourceType::Unknown,
|
|
2004
|
OriginalSourceType::Other,
|
|
2005
|
);
|
|
2006
|
|
|
2007
|
if(!$types){
|
|
2008
|
$types = $default;
|
|
2009
|
}
|
|
2010
|
return isset($source->type) && in_array($source->type, $types);
|
|
2011
|
}
|
|
2012
|
|
|
2013
|
/**
|
|
2014
|
* @todo Please document this function.
|
|
2015
|
* @see http://drupal.org/node/1354
|
|
2016
|
*/
|
|
2017
|
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
|
|
2018
|
return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
|
|
2019
|
}
|
|
2020
|
|
|
2021
|
|
|
2022
|
/**
|
|
2023
|
* Collects all the media from a list of description elements.
|
|
2024
|
*
|
|
2025
|
* @param array $descriptionElements
|
|
2026
|
* The description elements from which to collect the media.
|
|
2027
|
*
|
|
2028
|
* @return array
|
|
2029
|
* The output with all the collected media.
|
|
2030
|
*/
|
|
2031
|
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
|
|
2032
|
|
|
2033
|
$outArrayOfMedia = array();
|
|
2034
|
|
|
2035
|
// Avoiding a warning box in Drupal for Flora Malesiana.
|
|
2036
|
if (isset($descriptionElements) && is_array($descriptionElements)) {
|
|
2037
|
foreach ($descriptionElements as $descriptionElement) {
|
|
2038
|
if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
|
|
2039
|
foreach ($descriptionElement->media as $media) {
|
|
2040
|
if (is_object($media)) {
|
|
2041
|
$outArrayOfMedia[] = $media;
|
|
2042
|
}
|
|
2043
|
}
|
|
2044
|
}
|
|
2045
|
}
|
|
2046
|
}
|
|
2047
|
return $outArrayOfMedia;
|
|
2048
|
}
|
|
2049
|
|
|
2050
|
/**
|
|
2051
|
* @todo Please document this function.
|
|
2052
|
* @see http://drupal.org/node/1354
|
|
2053
|
*
|
|
2054
|
* @param array $cdm_entities
|
|
2055
|
* An array of CdmBase instances or a single instance.
|
|
2056
|
* @param string $footnote_list_key_suggestion
|
|
2057
|
*
|
|
2058
|
* @return unknown
|
|
2059
|
*/
|
|
2060
|
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
|
|
2061
|
|
|
2062
|
static $annotations_types_filter = null;
|
|
2063
|
if(!$annotations_types_filter) {
|
|
2064
|
$annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
|
|
2065
|
}
|
|
2066
|
|
|
2067
|
$footNoteKeys = array();
|
|
2068
|
|
|
2069
|
// Is argument cdmBase an array?
|
|
2070
|
if (!is_array($cdm_entities)) {
|
|
2071
|
$cdmBase_array = array();
|
|
2072
|
$cdmBase_array[] = $cdm_entities;
|
|
2073
|
}
|
|
2074
|
else {
|
|
2075
|
$cdmBase_array = $cdm_entities;
|
|
2076
|
}
|
|
2077
|
|
|
2078
|
// Getting the key for the footnotemanager.
|
|
2079
|
if (isset($footnote_list_key_suggestion)) {
|
|
2080
|
$footnote_list_key = $footnote_list_key_suggestion;
|
|
2081
|
}
|
|
2082
|
else {
|
|
2083
|
$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
|
|
2084
|
}
|
|
2085
|
|
|
2086
|
// Adding the footnotes keys.
|
|
2087
|
foreach ($cdmBase_array as $cdmBase_element) {
|
|
2088
|
$annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
|
|
2089
|
if (is_array($annotations)) {
|
|
2090
|
foreach ($annotations as $annotation) {
|
|
2091
|
$footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
|
|
2092
|
}
|
|
2093
|
}
|
|
2094
|
}
|
|
2095
|
|
|
2096
|
return $footNoteKeys;
|
|
2097
|
}
|
|
2098
|
|
|
2099
|
|
|
2100
|
/**
|
|
2101
|
* Creates a CDM Dynabox.
|
|
2102
|
*
|
|
2103
|
* @param string $dynabox_id
|
|
2104
|
* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
|
|
2105
|
* @param string $label
|
|
2106
|
* The clickable text to show.
|
|
2107
|
* @param string $content_url
|
|
2108
|
* The cdm REST service request url wich will deliver the content to be shown
|
|
2109
|
* once the dynabox toggles open.
|
|
2110
|
* @param string $theme
|
|
2111
|
* The theme to be used for rendering the cdm REST service response with is
|
|
2112
|
* returned from the $content_url.
|
|
2113
|
* @param string $link_alt_text
|
|
2114
|
* The value for the alt attribute of the dynabox link.
|
|
2115
|
* @param array $enclosingtags
|
|
2116
|
* An array with two elements: $enclosingtags[0] will be used for the dynabox
|
|
2117
|
* element itself, $enclosingtags[1] is the tag to be used for the
|
|
2118
|
* dynabox_content (optional)
|
|
2119
|
* @param array $attributes
|
|
2120
|
* @param $content_element_selector
|
|
2121
|
* Optional jQuery selector which can be used to reference a dom element which should
|
|
2122
|
* be used as container for the content to be shown. The dynabox-<dynabox id>-content
|
|
2123
|
* element will be placed in this container.
|
|
2124
|
*
|
|
2125
|
* @param string $open_callback
|
|
2126
|
* optional javascript call back function to be triggered after toggling the box to
|
|
2127
|
* the open state.
|
|
2128
|
* @param string $close_callback
|
|
2129
|
* optional javascript call back function to be triggered after toggling the box to
|
|
2130
|
* the closed state.
|
|
2131
|
* @return string Returns HTML for a dynabox.
|
|
2132
|
* Returns HTML for a dynabox.
|
|
2133
|
*/
|
|
2134
|
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
|
|
2135
|
$enclosingtags = array('li', 'ul'), $attributes = array(),
|
|
2136
|
$content_element_selector = null,
|
|
2137
|
$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
|
|
2138
|
$out = '';
|
|
2139
|
|
|
2140
|
// check for plain class attribute string
|
|
2141
|
$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
|
|
2142
|
|
|
2143
|
if(!array_key_exists('class', $attributes)) {
|
|
2144
|
$attributes['class'] = array();
|
|
2145
|
}
|
|
2146
|
$attributes['id'][] = 'dynabox-' . $dynabox_id;
|
|
2147
|
$dynabox_attributes = drupal_attributes($attributes);
|
|
2148
|
|
|
2149
|
|
|
2150
|
_add_js_domEvent(); // requires domEvent.js
|
|
2151
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
|
|
2152
|
drupal_add_js("
|
|
2153
|
jQuery(document).ready(
|
|
2154
|
function() {
|
|
2155
|
dynabox('". $dynabox_id ."',
|
|
2156
|
{
|
|
2157
|
open_callback: " . $open_callback .",
|
|
2158
|
close_callback: " . $close_callback .
|
|
2159
|
($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
|
|
2160
|
}
|
|
2161
|
);
|
|
2162
|
}
|
|
2163
|
);",
|
|
2164
|
array(
|
|
2165
|
'type'=>'inline',
|
|
2166
|
'scope'=>'footer'
|
|
2167
|
)
|
|
2168
|
);
|
|
2169
|
|
|
2170
|
|
|
2171
|
$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
|
|
2172
|
$out .= '<!-- dynabox for ' . $content_url . ' -->';
|
|
2173
|
$out .= '<' . $enclosingtags[0] . ' ' . $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
|
|
2174
|
$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
|
|
2175
|
$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
|
|
2176
|
$out .= ' </' . $enclosingtags[1] . '>';
|
|
2177
|
$out .= ' </' . $enclosingtags[0] . '>';
|
|
2178
|
$out .= '<!-- dynabox end -->';
|
|
2179
|
return $out;
|
|
2180
|
}
|
|
2181
|
|
|
2182
|
/**
|
|
2183
|
* Checks whether a feature has any description elements.
|
|
2184
|
*
|
|
2185
|
* @param mixed $featureNode
|
|
2186
|
* A feature node as produced by the function _mergeFeatureTreeDescriptions().
|
|
2187
|
*
|
|
2188
|
* @see _mergeFeatureTreeDescriptions()
|
|
2189
|
*
|
|
2190
|
* @return bool
|
|
2191
|
* Returns TRUE if the given $featureNode or any of its subordinate nodes
|
|
2192
|
* contains at least one non empty TextData or at least one DescriptionElement
|
|
2193
|
* of an other type. A TextData element holding a multilanguageText or a
|
|
2194
|
* source reference is considered to be not empty.
|
|
2195
|
*
|
|
2196
|
* @TODO this function may have become obsolete by the new method of detecting empty blocks,
|
|
2197
|
* see $block_content_is_not_empty in compose_feature_blocks() and
|
|
2198
|
* $feature_block_has_content in compose_feature_block_items_generic
|
|
2199
|
*/
|
|
2200
|
function has_feature_node_description_elements($featureNode) {
|
|
2201
|
|
|
2202
|
if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
|
|
2203
|
if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
|
|
2204
|
foreach ($featureNode->descriptionElements as $descriptionElement) {
|
|
2205
|
if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
|
|
2206
|
&& $descriptionElement->multilanguageText_L10n->text != ''
|
|
2207
|
|| isset($descriptionElement->sources[0])
|
|
2208
|
|| isset($descriptionElement->media[0]) ) {
|
|
2209
|
return TRUE;
|
|
2210
|
}
|
|
2211
|
}
|
|
2212
|
}
|
|
2213
|
}
|
|
2214
|
else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
|
|
2215
|
foreach ($featureNode->childNodes as $child) {
|
|
2216
|
if (has_feature_node_description_elements($child)) {
|
|
2217
|
return TRUE;
|
|
2218
|
}
|
|
2219
|
}
|
|
2220
|
}
|
|
2221
|
return FALSE;
|
|
2222
|
}
|
|
2223
|
|
|
2224
|
/**
|
|
2225
|
* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
|
|
2226
|
*
|
|
2227
|
* @param $chapter
|
|
2228
|
* The taxon page chapter or part
|
|
2229
|
*/
|
|
2230
|
function cdm_check_valid_taxon_page($chapter){
|
|
2231
|
static $taxon_tabs = null;
|
|
2232
|
|
|
2233
|
cdm_check_valid_portal_page();
|
|
2234
|
|
|
2235
|
if($taxon_tabs == null){
|
|
2236
|
$taxon_tabs = array('all', 'description');
|
|
2237
|
foreach(get_taxon_tabs_list() as $tab){
|
|
2238
|
$taxon_tabs[] = strtolower($tab);
|
|
2239
|
}
|
|
2240
|
}
|
|
2241
|
|
|
2242
|
if(!in_array($chapter, $taxon_tabs)){
|
|
2243
|
// oops this is not a valid chapter name
|
|
2244
|
http_send_status(404); // 404 = Not Found
|
|
2245
|
}
|
|
2246
|
|
|
2247
|
}
|
|
2248
|
|
|
2249
|
/**
|
|
2250
|
* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise
|
|
2251
|
*
|
|
2252
|
* @param $chapter
|
|
2253
|
* The taxon page chapter or part
|
|
2254
|
*/
|
|
2255
|
function cdm_check_valid_portal_page(){
|
|
2256
|
$ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
|
|
2257
|
if(preg_match($ends_with_file_suffix_pattern, $_GET['q'])){
|
|
2258
|
// oops this urls ends with a file_suffix and thus does not refer to a portal page
|
|
2259
|
http_send_status(404); // 404 = Not Found
|
|
2260
|
exit('HTTP 404');
|
|
2261
|
}
|
|
2262
|
}
|
|
2263
|
|
|
2264
|
/**
|
|
2265
|
* Generates the diff of the texts and presents it in a HTML diff viewer.
|
|
2266
|
*
|
|
2267
|
* @param $text_a
|
|
2268
|
* @param $text_b
|
|
2269
|
* @return string
|
|
2270
|
*/
|
|
2271
|
function diff_viewer($text_a, $text_b) {
|
|
2272
|
|
|
2273
|
static $diff_viewer_count = 0;
|
|
2274
|
|
|
2275
|
$element_id = 'part_definitions_diff_' . $diff_viewer_count++;
|
|
2276
|
|
|
2277
|
// http://code.stephenmorley.org/php/diff-implementation/
|
|
2278
|
module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
|
|
2279
|
drupal_add_css(drupal_get_path('module',
|
|
2280
|
'cdm_dataportal') . '/css/diff.css');
|
|
2281
|
_add_jquery_ui();
|
|
2282
|
drupal_add_js(
|
|
2283
|
'jQuery(document).ready( function(){
|
|
2284
|
jQuery(\'#' . $element_id . '\').accordion({
|
|
2285
|
collapsible: true,
|
|
2286
|
active: false,
|
|
2287
|
fillSpace: true,
|
|
2288
|
}).children(\'div\').css({ \'height\': \'auto\' });
|
|
2289
|
jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
|
|
2290
|
});'
|
|
2291
|
, array(
|
|
2292
|
'type' => 'inline',
|
|
2293
|
'scope' => 'footer'
|
|
2294
|
));
|
|
2295
|
|
|
2296
|
$diff = Diff::compare($text_a,
|
|
2297
|
$text_b);
|
|
2298
|
$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
|
|
2299
|
. Diff::toTable($diff, '', '')
|
|
2300
|
. '</div></div>';
|
|
2301
|
return $diff_viewer_markup;
|
|
2302
|
}
|
|
2303
|
|
|
2304
|
|