cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ 64cfdac1
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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/agent');
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module_load_include('inc', 'cdm_dataportal', 'includes/name');
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module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
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module_load_include('inc', 'cdm_dataportal', 'includes/taxon-node');
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module_load_include('inc', 'cdm_dataportal', 'includes/references');
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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('" . $progress_element_selector . "');
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// }); |
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// }", 'inline'); |
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} |
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/** |
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* @todo Please document this function. |
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* @see http://drupal.org/node/1354 |
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*/ |
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function _add_js_treeselector() {
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// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
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drupal_add_js("
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jQuery(document).ready(function() {
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jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
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jQuery('#cdm-taxonomictree-selector-form').submit();
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}); |
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}); |
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", |
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array( |
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'type' => 'inline', |
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'scope' => 'footer' |
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) |
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); |
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} |
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function _add_js_resizable_element($selector, $y_axis_only) {
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_add_jquery_ui(); |
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$options = ""; |
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if($y_axis_only) {
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$options = "resize: function(event, ui) {
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ui.size.width = ui.originalSize.width; |
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}, |
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handles: \"s\""; |
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} |
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drupal_add_js("
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jQuery(document).ready(function() {
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jQuery('" . $selector . "').resizable({". $options ."});
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}); |
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", |
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array( |
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'type' => 'inline', |
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'scope' => 'footer' |
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) |
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); |
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} |
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function _add_js_openlayers() {
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$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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'group' => JS_LIBRARY, |
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'weight' => 0, |
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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') . $proj4js,
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array( |
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'type' => 'file', |
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'group' => JS_LIBRARY, |
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'weight' => -1, // before open layers |
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'cache' => TRUE, |
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) |
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); |
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// configure the theme |
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$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() . $openlayers_imp_path . '";', array(
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'type' => 'inline', |
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'group' => JS_LIBRARY, |
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'weight' => 1, // after openlayers |
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'cache' => TRUE, |
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'preprocess' => FALSE |
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)); |
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drupal_add_css($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_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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* @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_taxonomic_children($jquery_selector) {
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global $base_url; |
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
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drupal_add_js('jQuery(document).ready(function() {
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jQuery(\'' . $jquery_selector . '\').taxonomic_children({
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// hoverClass: "fa-rotate-90", |
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// activeClass: "fa-rotate-90", |
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classificationUuid: "' . get_current_classification_uuid() . '", |
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taxonUuid: "' . get_current_taxon_uuid() . '", |
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cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
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proxyBaseUri: "' . $base_url . '", |
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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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* 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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function _add_js_ui_accordion(){
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_add_jquery_ui(); |
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drupal_add_js('jQuery(document).ready(function() {
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jQuery( "#accordion" ).accordion(); |
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});', |
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array('type' => 'inline')
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); |
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} |
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function _add_js_utis_client($jquery_selector){
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drupal_add_js(drupal_get_path('module',
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'cdm_dataportal') . '/js/utis-client/utis-client.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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drupal_add_js('jQuery(document).ready(function() {
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jQuery( "' . $jquery_selector . '" ).utis_client( |
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{
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spinnerIcon: \'' . font_awesome_icon_markup('fa-sync', array('class' => array('fa-3x', 'fa-spin'), 'style' => array('opacity: 0.3;'))) . '\',
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externalLinkIcon: \'' . font_awesome_icon_markup('fa-external-link-alt') . '\'
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}); |
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});', |
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array('type' => 'inline')
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); |
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} |
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function _add_js_universalviewer($jquery_selector, $manifest_uri){
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$universalviewer_path = drupal_get_path('module', 'cdm_dataportal') . '/js/universalviewer';
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drupal_add_css($universalviewer_path . '/uv/uv.css'); |
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drupal_add_css($universalviewer_path . '/uv-fix.css'); |
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// offline.js is all of these dependencies concatenated (jQuery, CoreJS, and JSViews) |
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drupal_add_js($universalviewer_path . '/uv/lib/offline.js', |
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array( |
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'type' => 'file', |
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'group' => JS_LIBRARY, |
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'cache' => TRUE, |
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'preprocess' => FALSE |
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) |
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); |
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drupal_add_js($universalviewer_path . '/uv/helpers.js', |
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array( |
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'type' => 'file', |
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'group' => 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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// from UV 3.x documentation: |
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// "root: |
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// The path to the uv directory. Use a relative path e.g. root: '../../uv' |
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// Don't start your path with a / otherwise requirejs will not append .js to |
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// dependencies and they won't load." |
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// |
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// universalviewerPath will be used to build the root config variable. |
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$iCleanUrlRequest = strpos($_SERVER['REQUEST_URI'], 'q=cdm_dataportal/') === false; |
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if($iCleanUrlRequest){
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$folders_up = preg_replace('/[^\/]+/', '..', $_GET['q']);
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$folders_up = preg_replace('/\.\.$/', '', $folders_up);
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} else {
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$folders_up = ''; |
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} |
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$basePath = base_path(); |
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$config_file = 'uv-config.json'; |
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drupal_add_js('
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console.log(\'jQuery inline: \' + jQuery.fn.jquery); |
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jQuery(window).on(\'uvLoaded\', function() {
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jQuery( "' . $jquery_selector . '" ).jqUniversalviewer( |
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{
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root: \'' . $folders_up . $universalviewer_path . '/uv\', |
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configUri: \'' . $basePath . $universalviewer_path . '/'. $config_file . '\', |
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manifestUri: \'' . $manifest_uri . '\' |
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} |
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); |
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});', |
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array( |
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'type' => 'inline', |
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'scope' => 'footer', |
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'group' => JS_DEFAULT, |
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'weight' => 0, |
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) |
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); |
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drupal_add_js($universalviewer_path . '/jq-universalviewer.js', |
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array( |
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'type' => 'file', |
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'scope' => 'footer', |
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'group' => JS_DEFAULT, |
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'weight' => 10, |
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'cache' => TRUE, |
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'preprocess' => FALSE |
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) |
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); |
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// ui.js must be last |
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drupal_add_js($universalviewer_path . '/uv/uv.js', |
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array( |
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'type' => 'file', |
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'scope' => 'footer', |
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'group' => 300, // IMPORTANT! |
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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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/** |
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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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* |
| 446 |
* The available icons are listed here http://fontawesome.io/cheatsheet/ |
| 447 |
* fontawesome icons have much more features than implemented here in this function, |
| 448 |
* for spinning icons, fixed width icons, rotation, etc please checkout the |
| 449 |
* examples at http://fontawesome.io/examples/ |
| 450 |
* |
| 451 |
* @parameter $icon_name |
| 452 |
* The name of the icon which starts with 'fa-' |
| 453 |
* |
| 454 |
* @return String |
| 455 |
* the markup for the icon in an <i> tag |
| 456 |
* |
| 457 |
*/ |
| 458 |
function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
|
| 459 |
_add_font_awesome_font(); |
| 460 |
|
| 461 |
|
| 462 |
if($icon_name){
|
| 463 |
if(!isset($attributes['class'])){
|
| 464 |
$attributes['class'] = array(); |
| 465 |
} |
| 466 |
$attributes['class'][] = 'fa'; |
| 467 |
$attributes['class'][] = $icon_name; |
| 468 |
|
| 469 |
return '<i ' . drupal_attributes($attributes) . '></i>'; |
| 470 |
} |
| 471 |
|
| 472 |
return ''; |
| 473 |
} |
| 474 |
|
| 475 |
/** |
| 476 |
* @param string $glyph_name |
| 477 |
* The name of the gloyph (e.g. 'icon-interal-link-alt-solid') for the foll list please |
| 478 |
* refer to modules/cdm_dataportal/fonts/custom-icon-font |
| 479 |
* @param array $attributes |
| 480 |
* @return string |
| 481 |
*/ |
| 482 |
function custom_icon_font_markup($glyph_name = NULL, $attributes = array()){
|
| 483 |
_add_font_custom_icon_font(); |
| 484 |
|
| 485 |
|
| 486 |
if($glyph_name){
|
| 487 |
if(!isset($attributes['class'])){
|
| 488 |
$attributes['class'] = array(); |
| 489 |
} |
| 490 |
$attributes['class'][] = $glyph_name; |
| 491 |
|
| 492 |
return '<i ' . drupal_attributes($attributes) . '></i>'; |
| 493 |
} |
| 494 |
|
| 495 |
return ''; |
| 496 |
} |
| 497 |
|
| 498 |
/** |
| 499 |
* Adds the css containing the font awesome icons to the html header. |
| 500 |
*/ |
| 501 |
function _add_font_awesome_font() |
| 502 |
{
|
| 503 |
// $fa_font_version = 'font-awesome-4.6.3/css/font-awesome.min.css'; |
| 504 |
$fa_font_version = 'fontawesome-free-5.9.0-web/css/all.css'; |
| 505 |
$font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/' . $fa_font_version;
|
| 506 |
|
| 507 |
drupal_add_html_head_link( |
| 508 |
array( |
| 509 |
'href' => $font_awesome_css_uri, |
| 510 |
'rel' => 'stylesheet' |
| 511 |
) |
| 512 |
); |
| 513 |
} |
| 514 |
|
| 515 |
/** |
| 516 |
* Adds the css containing the font awesome icons to the html header. |
| 517 |
*/ |
| 518 |
function _add_font_custom_icon_font() |
| 519 |
{
|
| 520 |
|
| 521 |
$custom_icon_font_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/custom-icon-font/style.css';
|
| 522 |
|
| 523 |
drupal_add_html_head_link( |
| 524 |
array( |
| 525 |
'href' => $custom_icon_font_css_uri, |
| 526 |
'rel' => 'stylesheet' |
| 527 |
) |
| 528 |
); |
| 529 |
} |
| 530 |
|
| 531 |
/* ====================== hook implementations ====================== */ |
| 532 |
/** |
| 533 |
* Implements hook_permission(). |
| 534 |
* |
| 535 |
* Valid permissions for this module. |
| 536 |
* |
| 537 |
* @return array |
| 538 |
* An array of valid permissions for the cdm_dataportal module. |
| 539 |
*/ |
| 540 |
function cdm_dataportal_permission() {
|
| 541 |
return array( |
| 542 |
'administer cdm_dataportal' => array( |
| 543 |
'title' => t('Administer CDM DataPortal settings'),
|
| 544 |
'description' => t("Access the settings pages specific for the cdm_dataportal module"),
|
| 545 |
), |
| 546 |
'access cdm content' => array( |
| 547 |
'title' => t('Access CDM content'),
|
| 548 |
'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
|
| 549 |
), |
| 550 |
); |
| 551 |
} |
| 552 |
|
| 553 |
/** |
| 554 |
* Implements hook_menu(). |
| 555 |
*/ |
| 556 |
function cdm_dataportal_menu() {
|
| 557 |
$items = array(); |
| 558 |
|
| 559 |
// @see settings.php. |
| 560 |
cdm_dataportal_menu_admin($items); |
| 561 |
cdm_dataportal_menu_help($items); |
| 562 |
|
| 563 |
$items['cdm_dataportal/names'] = array( |
| 564 |
'page callback' => 'cdm_dataportal_view_names', |
| 565 |
'access arguments' => array('access cdm content'),
|
| 566 |
'type' => MENU_CALLBACK, |
| 567 |
); |
| 568 |
|
| 569 |
// Optional callback arguments: page. |
| 570 |
$items['cdm_dataportal/taxon'] = array( |
| 571 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 572 |
'access arguments' => array('access cdm content'),
|
| 573 |
'type' => MENU_CALLBACK, |
| 574 |
// Expected callback arguments: uuid. |
| 575 |
); |
| 576 |
|
| 577 |
$items['cdm_dataportal/occurrence'] = array( |
| 578 |
'page callback' => 'cdm_dataportal_specimen_page_view', |
| 579 |
'access arguments' => array('access cdm content'),
|
| 580 |
'type' => MENU_CALLBACK, |
| 581 |
// Expected callback arguments: uuid. |
| 582 |
); |
| 583 |
|
| 584 |
$items['cdm_dataportal/description'] = array( |
| 585 |
'page callback' => 'cdm_dataportal_description_page_view', |
| 586 |
'access arguments' => array('access cdm content'),
|
| 587 |
'type' => MENU_CALLBACK, |
| 588 |
// Expected callback arguments: uuid. |
| 589 |
); |
| 590 |
|
| 591 |
$items['cdm_dataportal/specimen/accession_number'] = array( |
| 592 |
'page callback' => 'cdm_dataportal_specimen_by_accession_number_page_view', |
| 593 |
'access arguments' => array('access cdm content'),
|
| 594 |
'type' => MENU_CALLBACK, |
| 595 |
// Expected callback arguments: accession number. |
| 596 |
); |
| 597 |
$items['cdm_dataportal/named_area'] = array( |
| 598 |
'page callback' => 'cdm_dataportal_named_area_page_view', |
| 599 |
'access arguments' => array('access cdm content'),
|
| 600 |
'type' => MENU_CALLBACK, |
| 601 |
// Expected callback arguments: uuid. |
| 602 |
); |
| 603 |
|
| 604 |
$items['cdm_dataportal/name'] = array( |
| 605 |
'page callback' => 'cdm_dataportal_name_page_view', |
| 606 |
/* |
| 607 |
'page arguments' => array( |
| 608 |
'taxon_name_uuid', |
| 609 |
'taxon_to_hide_uuid', |
| 610 |
'synonym_uuid' => NULL |
| 611 |
), |
| 612 |
*/ |
| 613 |
'access arguments' => array('access cdm content'),
|
| 614 |
'type' => MENU_CALLBACK, |
| 615 |
// Expected callback arguments: uuid. |
| 616 |
); |
| 617 |
|
| 618 |
$items['cdm_dataportal/reference'] = array( |
| 619 |
'page callback' => 'cdm_dataportal_view_reference', |
| 620 |
'access arguments' => array('access cdm content'),
|
| 621 |
'type' => MENU_CALLBACK, |
| 622 |
// Expected callback arguments: uuid. |
| 623 |
); |
| 624 |
|
| 625 |
$items['cdm_dataportal/reference/list'] = array( |
| 626 |
'page callback' => 'cdm_dataportal_view_reference_list', |
| 627 |
'access arguments' => array('access cdm content'),
|
| 628 |
'type' => MENU_CALLBACK, |
| 629 |
// Expected callback arguments: uuid. |
| 630 |
); |
| 631 |
|
| 632 |
$items['cdm_dataportal/media'] = array( |
| 633 |
'page callback' => 'cdm_dataportal_view_media', |
| 634 |
'access arguments' => array('access cdm content'),
|
| 635 |
'type' => MENU_CALLBACK, |
| 636 |
// Expected callback arguments: |
| 637 |
// uuid, mediarepresentation_uuid, part_uuid or part#. |
| 638 |
); |
| 639 |
|
| 640 |
$items['cdm_dataportal/polytomousKey'] = array( |
| 641 |
'page callback' => 'cdm_dataportal_view_polytomousKey', |
| 642 |
'access arguments' => array('access cdm content'),
|
| 643 |
'type' => MENU_CALLBACK, |
| 644 |
// Expected callback arguments: polytomousKey->uuid. |
| 645 |
); |
| 646 |
|
| 647 |
$items['cdm_dataportal/search'] = array( |
| 648 |
'page callback' => 'cdm_dataportal_view_search_advanced', |
| 649 |
'access arguments' => array('access cdm content'),
|
| 650 |
'type' => MENU_CALLBACK, |
| 651 |
); |
| 652 |
|
| 653 |
// Optional callback arguments: page. |
| 654 |
$items['cdm_dataportal/registration'] = array( |
| 655 |
'page callback' => 'cdm_dataportal_registration_page_view', |
| 656 |
'access arguments' => array('access cdm content'),
|
| 657 |
'type' => MENU_CALLBACK, |
| 658 |
// Expected callback arguments: uuid. |
| 659 |
); |
| 660 |
|
| 661 |
// ------------ SEARCH ----------- |
| 662 |
$items['cdm_dataportal/search/advanced'] = array( |
| 663 |
'title' => 'Advanced', // will be passed through t() |
| 664 |
'page callback' => 'cdm_dataportal_view_search_advanced', |
| 665 |
'access arguments' => array('access cdm content'),
|
| 666 |
'type' => MENU_DEFAULT_LOCAL_TASK, |
| 667 |
); |
| 668 |
$items['cdm_dataportal/search/blast'] = array( |
| 669 |
'title' => 'Blast', // will be passed through t() |
| 670 |
'page callback' => 'cdm_dataportal_view_search_blast', |
| 671 |
'access arguments' => array('access cdm content'),
|
| 672 |
'type' => MENU_LOCAL_TASK, |
| 673 |
); |
| 674 |
|
| 675 |
$items['cdm_dataportal/search/taxon_by_description'] = array( |
| 676 |
'title' => 'By content category', // will be passed through t() |
| 677 |
'page callback' => 'cdm_dataportal_view_search_taxon_by_description', |
| 678 |
'access arguments' => array('access cdm content'),
|
| 679 |
'type' => MENU_LOCAL_TASK, |
| 680 |
); |
| 681 |
$items['cdm_dataportal/search/results/taxon'] = array( |
| 682 |
'page callback' => 'cdm_dataportal_view_search_results_taxon', |
| 683 |
'access arguments' => array('access cdm content'),
|
| 684 |
'type' => MENU_CALLBACK, |
| 685 |
); |
| 686 |
|
| 687 |
$items['cdm_dataportal/search/results/specimen'] = array( |
| 688 |
'page callback' => 'cdm_dataportal_view_search_results_specimen', |
| 689 |
'access arguments' => array('access cdm content'),
|
| 690 |
'type' => MENU_CALLBACK, |
| 691 |
); |
| 692 |
|
| 693 |
/* |
| 694 |
* MENU_CALLBACK at cdm_dataportal/registration-search is needed to make the |
| 695 |
* tabs in the subordinate paths work, accessing this 'page' will cause the |
| 696 |
* MENU_DEFAULT_LOCAL_TASK being displayed |
| 697 |
*/ |
| 698 |
$items['cdm_dataportal/registration-search'] = array( |
| 699 |
'title' => 'Search', // will be passed through t() |
| 700 |
'page callback' => 'cdm_dataportal_view_search_registrations_results', |
| 701 |
'page arguments' => array("filter"),
|
| 702 |
'access arguments' => array('access cdm content'),
|
| 703 |
'type' => MENU_CALLBACK, |
| 704 |
); |
| 705 |
/* |
| 706 |
* the MENU_DEFAULT_LOCAL_TASK creates a tab for the MENU_CALLBACK |
| 707 |
* defined at a higher level of the path (cdm_dataportal/registration-search) |
| 708 |
*/ |
| 709 |
$items['cdm_dataportal/registration-search/filter'] = array( |
| 710 |
'title' => 'Search', // will be passed through t() |
| 711 |
'page callback' => 'cdm_dataportal_view_search_registrations_results', |
| 712 |
'page arguments' => array("filter"),
|
| 713 |
'access arguments' => array('access cdm content'),
|
| 714 |
'type' => MENU_DEFAULT_LOCAL_TASK, |
| 715 |
); |
| 716 |
/* |
| 717 |
* the MENU_LOCAL_TASK creates another tab |
| 718 |
*/ |
| 719 |
$items['cdm_dataportal/registration-search/taxongraph'] = array( |
| 720 |
'title' => 'Taxon graph search', // will be passed through t() |
| 721 |
'page callback' => 'cdm_dataportal_view_search_registrations_results', |
| 722 |
'page arguments' => array("taxongraph"),
|
| 723 |
'access arguments' => array('access cdm content'),
|
| 724 |
'type' => MENU_LOCAL_TASK, |
| 725 |
); |
| 726 |
|
| 727 |
// Optional callback arguments: page. |
| 728 |
$items['cdm_dataportal/search/agent'] = array( |
| 729 |
'page callback' => 'cdm_dataportal_view_search_agent', |
| 730 |
'access arguments' => array('access cdm content'),
|
| 731 |
'type' => MENU_CALLBACK, |
| 732 |
// Expected callback arguments: uuid. |
| 733 |
); |
| 734 |
|
| 735 |
// ------------ menu items with variable path elements ----------- |
| 736 |
|
| 737 |
// 'May not cache' in D5. |
| 738 |
$items['cdm_dataportal/name/%'] = array( |
| 739 |
// 'page callback' => 'cdm_dataportal_view_name', |
| 740 |
'page callback' => 'cdm_dataportal_name_page_view', |
| 741 |
'page arguments' => array(2, 3, 4, 5), |
| 742 |
'access arguments' => array('access cdm content'),
|
| 743 |
'type' => MENU_CALLBACK, |
| 744 |
); |
| 745 |
|
| 746 |
// --- Local tasks for Taxon. |
| 747 |
// --- tabbed taxon page |
| 748 |
if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
|
| 749 |
$items['cdm_dataportal/taxon/%'] = array( |
| 750 |
'title' => cdm_taxonpage_tab_label('General'),
|
| 751 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 752 |
'access arguments' => array('access cdm content'),
|
| 753 |
'type' => MENU_CALLBACK, |
| 754 |
'weight' => 1, |
| 755 |
'page arguments' => array(2, "description") |
| 756 |
, // Expected callback arguments: taxon_uuid. |
| 757 |
); |
| 758 |
|
| 759 |
$items['cdm_dataportal/taxon/%/all'] = array( |
| 760 |
'title' => cdm_taxonpage_tab_label('General'),
|
| 761 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 762 |
'access arguments' => array('access cdm content'),
|
| 763 |
'type' => MENU_CALLBACK, |
| 764 |
'weight' => 2, |
| 765 |
'page arguments' => array(2, "all") |
| 766 |
, // Expected callback arguments: taxon_uuid. |
| 767 |
); |
| 768 |
|
| 769 |
$items['cdm_dataportal/taxon/%/description'] = array( |
| 770 |
'title' => cdm_taxonpage_tab_label('General'),
|
| 771 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 772 |
'access arguments' => array('access cdm content'),
|
| 773 |
'type' => MENU_DEFAULT_LOCAL_TASK, |
| 774 |
'weight' => 2, |
| 775 |
'page arguments' => array(2, "description") |
| 776 |
, // Expected callback arguments: taxon_uuid. |
| 777 |
); |
| 778 |
|
| 779 |
$items['cdm_dataportal/taxon/%/synonymy'] = array( |
| 780 |
'title' => cdm_taxonpage_tab_label('Synonymy'),
|
| 781 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 782 |
'access arguments' => array('access cdm content'),
|
| 783 |
'type' => MENU_LOCAL_TASK, |
| 784 |
'weight' => 4, |
| 785 |
'page arguments' => array(2, "synonymy", 4) |
| 786 |
, // Expected callback arguments: taxon_uuid and ... |
| 787 |
); |
| 788 |
$items['cdm_dataportal/taxon/%/images'] = array( // Images |
| 789 |
'title' => cdm_taxonpage_tab_label('Images'),
|
| 790 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 791 |
'access arguments' => array('access cdm content'),
|
| 792 |
'type' => MENU_LOCAL_TASK, |
| 793 |
'weight' => 5, |
| 794 |
'page arguments' => array(2, "images") |
| 795 |
, // Expected callback arguments: taxon_uuid. |
| 796 |
); |
| 797 |
|
| 798 |
$items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens |
| 799 |
'title' => cdm_taxonpage_tab_label('Specimens'),
|
| 800 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 801 |
'access arguments' => array('access cdm content'),
|
| 802 |
'type' => MENU_LOCAL_TASK, |
| 803 |
'weight' => 6, |
| 804 |
'page arguments' => array(2, "specimens") |
| 805 |
, // Expected callback arguments: taxon_uuid. |
| 806 |
); |
| 807 |
|
| 808 |
$items['cdm_dataportal/taxon/%/keys'] = array( // Keys |
| 809 |
'title' => cdm_taxonpage_tab_label('Keys'),
|
| 810 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 811 |
'access arguments' => array('access cdm content'),
|
| 812 |
'type' => MENU_LOCAL_TASK, |
| 813 |
'weight' => 6, |
| 814 |
'page arguments' => array(2, "keys") |
| 815 |
, // Expected callback arguments: taxon_uuid. |
| 816 |
); |
| 817 |
|
| 818 |
$items['cdm_dataportal/taxon/%/experts'] = array( // Experts |
| 819 |
'title' => cdm_taxonpage_tab_label('Experts'),
|
| 820 |
'page callback' => 'cdm_dataportal_taxon_page_view', |
| 821 |
'access arguments' => array('access cdm content'),
|
| 822 |
'type' => MENU_LOCAL_TASK, |
| 823 |
'weight' => 6, |
| 824 |
'page arguments' => array(2, "experts") |
| 825 |
, // Expected callback arguments: taxon_uuid. |
| 826 |
); |
| 827 |
|
| 828 |
$items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array( |
| 829 |
'page callback' => 'cdm_dataportal_taxon_autosuggest', |
| 830 |
'access arguments' => array('access cdm content'),
|
| 831 |
'page arguments' => array(3,4,5), |
| 832 |
'type' => MENU_CALLBACK |
| 833 |
); |
| 834 |
} |
| 835 |
|
| 836 |
// --- refresh link for all cdmnode types |
| 837 |
foreach (cdm_get_nodetypes() as $type=>$name) {
|
| 838 |
$items['cdm_dataportal/' . $name . '/%/refresh'] = array( |
| 839 |
'title' => 'Refresh', |
| 840 |
'page callback' => 'cdm_dataportal_refresh_node', |
| 841 |
'access arguments' => array('administer cdm_dataportal'),
|
| 842 |
'type' => MENU_LOCAL_TASK, |
| 843 |
'weight' => 100, |
| 844 |
'page arguments' => array($name, 2) |
| 845 |
); |
| 846 |
} |
| 847 |
|
| 848 |
return $items; |
| 849 |
} |
| 850 |
|
| 851 |
/** |
| 852 |
* Implements hook_init(). |
| 853 |
* |
| 854 |
*/ |
| 855 |
function cdm_dataportal_init() {
|
| 856 |
if (!path_is_admin(current_path())) {
|
| 857 |
//FIXME To add CSS or JS that should be present on all pages, modules |
| 858 |
// should not implement this hook, but declare these files in their .info file. |
| 859 |
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
|
| 860 |
// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
|
| 861 |
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
|
| 862 |
} else {
|
| 863 |
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
|
| 864 |
} |
| 865 |
|
| 866 |
if(variable_get('cdm_debug_mode', FALSE)){
|
| 867 |
$file = 'temporary://drupal_debug.txt'; |
| 868 |
file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file |
| 869 |
} |
| 870 |
|
| 871 |
$bibliography_settings = get_bibliography_settings(); |
| 872 |
$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span'; |
| 873 |
FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
|
| 874 |
} |
| 875 |
|
| 876 |
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
|
| 877 |
|
| 878 |
$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid; |
| 879 |
|
| 880 |
if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
|
| 881 |
// force reloading of all and notify user about this special loading |
| 882 |
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: ')
|
| 883 |
. l('Back to tabbed taxon page', $base_path));
|
| 884 |
$base_path .= '/all'; |
| 885 |
} else {
|
| 886 |
drupal_set_message(t('The level 2 cache has been cleared for this page'));
|
| 887 |
} |
| 888 |
|
| 889 |
$parameters['cacheL2_refresh'] ='1'; |
| 890 |
|
| 891 |
|
| 892 |
drupal_goto($base_path, array('query' => $parameters));
|
| 893 |
} |
| 894 |
|
| 895 |
/** |
| 896 |
* Implements hook_requirements($phase) |
| 897 |
*/ |
| 898 |
function cdm_dataportal_requirements($phase) {
|
| 899 |
$requirements = array(); |
| 900 |
if($phase == 'runtime'){
|
| 901 |
|
| 902 |
} |
| 903 |
return $requirements; |
| 904 |
} |
| 905 |
|
| 906 |
/** |
| 907 |
* Implements hook_block_info(). |
| 908 |
*/ |
| 909 |
function cdm_dataportal_block_info() {
|
| 910 |
|
| 911 |
// $block[0]["info"] = t("CDM DataPortal DevLinks");
|
| 912 |
// $block[1]["info"] = t("CDM DataPortal Credits");
|
| 913 |
$block["2"] = array( |
| 914 |
"info" => t("CDM - Search Taxa"),
|
| 915 |
"cache" => DRUPAL_NO_CACHE |
| 916 |
); |
| 917 |
// $block[3]["info"] = t("CDM Filters");
|
| 918 |
$block["4"]["info"] = t("CDM - Dataportal Print");
|
| 919 |
$block["keys"]["info"] = t("CDM - Identification keys");
|
| 920 |
$block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
|
| 921 |
$block["classification_breadcrumbs"] = array( |
| 922 |
'info' => t('CDM - Classification breadcrumbs'),
|
| 923 |
'cache' => DRUPAL_CACHE_PER_PAGE |
| 924 |
); |
| 925 |
$block["taxonomic_children"] = array( |
| 926 |
'info' => t('CDM - Taxonomic children'),
|
| 927 |
'cache' => DRUPAL_CACHE_PER_PAGE |
| 928 |
); |
| 929 |
$block["back_to_search_results"] = array( |
| 930 |
'title' => '<none>', |
| 931 |
'info' => t('CDM - Back to search Results'),
|
| 932 |
'cache' => DRUPAL_CACHE_PER_PAGE, |
| 933 |
'visibility' => BLOCK_VISIBILITY_LISTED, |
| 934 |
'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!! |
| 935 |
); |
| 936 |
$block['registrations_search_filter'] = array( |
| 937 |
'title' => 'Filter registrations', |
| 938 |
'info' => t('CDM - Registrations search filter'),
|
| 939 |
'cache' => DRUPAL_CACHE_PER_PAGE, |
| 940 |
'visibility' => BLOCK_VISIBILITY_NOTLISTED, |
| 941 |
'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!! |
| 942 |
); |
| 943 |
$block['registrations_search_taxongraph'] = array( |
| 944 |
'title' => 'Taxonomic registration search', |
| 945 |
'info' => t('CDM - Registrations search by taxon graph'),
|
| 946 |
'cache' => DRUPAL_CACHE_PER_PAGE, |
| 947 |
'visibility' => BLOCK_VISIBILITY_NOTLISTED, |
| 948 |
'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!! |
| 949 |
); |
| 950 |
$block['registrations_search'] = array( |
| 951 |
'title' => 'Search', |
| 952 |
'info' => t('CDM - Registrations search combining filter and taxon graph search' ),
|
| 953 |
'cache' => DRUPAL_CACHE_PER_PAGE, |
| 954 |
'visibility' => BLOCK_VISIBILITY_NOTLISTED, |
| 955 |
'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!! |
| 956 |
); |
| 957 |
$block['utis_search'] = array( |
| 958 |
'title' => 'UTIS Search', |
| 959 |
'info' => t('Query the Unified Taxonomic Information Service (UTIS)' ),
|
| 960 |
'cache' => DRUPAL_CACHE_PER_PAGE, |
| 961 |
'visibility' => BLOCK_VISIBILITY_NOTLISTED |
| 962 |
); |
| 963 |
return $block; |
| 964 |
} |
| 965 |
|
| 966 |
/** |
| 967 |
* Implements hook_block_view(). |
| 968 |
*/ |
| 969 |
function cdm_dataportal_block_view($delta) {
|
| 970 |
// TODO Rename block deltas (e.g. '2') to readable strings. |
| 971 |
switch ($delta) {
|
| 972 |
// case 'delta-1': |
| 973 |
// $block['subject'] = t('Credits');
|
| 974 |
// $block['content'] = theme('cdm_credits');
|
| 975 |
// return $block; |
| 976 |
case '2': |
| 977 |
$block['subject'] = t('Search taxa');
|
| 978 |
$form = drupal_get_form('cdm_dataportal_search_taxon_form');
|
| 979 |
$block['content'] = drupal_render($form); |
| 980 |
|
| 981 |
if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
|
| 982 |
$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
|
| 983 |
} |
| 984 |
if (variable_get(CDM_SEARCH_BLAST_ENABLED)){
|
| 985 |
$block['content'] .= '<div>' . l(t('Blast Search'), 'cdm_dataportal/search/blast') . '</div>';
|
| 986 |
} |
| 987 |
return $block; |
| 988 |
case '4': |
| 989 |
$block['subject'] = ''; |
| 990 |
$block['content'] = theme('cdm_print_button');
|
| 991 |
return $block; |
| 992 |
case "keys": |
| 993 |
$block['subject'] = t('Identification Keys');
|
| 994 |
$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
|
| 995 |
return $block; |
| 996 |
case "fundedByEDIT": |
| 997 |
// t('Funded by EDIT');
|
| 998 |
$text = '<none>'; |
| 999 |
$block['subject'] = $text; |
| 1000 |
$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
|
| 1001 |
$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array( |
| 1002 |
'attributes' => array("target" => "EDIT"),
|
| 1003 |
'absolute' => TRUE, |
| 1004 |
'html' => TRUE, |
| 1005 |
)); |
| 1006 |
return $block; |
| 1007 |
case 'classification_breadcrumbs': |
| 1008 |
$taxon_uuid = get_current_taxon_uuid(); |
| 1009 |
$block['subject'] = '<none>'; |
| 1010 |
$block['content'] = compose_classification_breadcrumbs($taxon_uuid); |
| 1011 |
return $block; |
| 1012 |
case 'taxonomic_children': |
| 1013 |
$taxon_uuid = get_current_taxon_uuid(); |
| 1014 |
$block['subject'] = '<none>'; |
| 1015 |
$block['content'] = compose_taxonomic_children($taxon_uuid); |
| 1016 |
return $block; |
| 1017 |
case 'back_to_search_results': |
| 1018 |
$block['subject'] = '<none>'; |
| 1019 |
if (isset($_SESSION['cdm']['search'])) {
|
| 1020 |
$block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
|
| 1021 |
} |
| 1022 |
return $block; |
| 1023 |
case 'registrations_search_filter': |
| 1024 |
$block['subject'] = '<none>'; |
| 1025 |
$block['content'] = drupal_get_form('cdm_dataportal_search_registration_filter_form'); // see cdm_dataportal_search_registration_filter_form($form, &$form_state)
|
| 1026 |
return $block; |
| 1027 |
case 'registrations_search_taxongraph': |
| 1028 |
$block['subject'] = '<none>'; |
| 1029 |
$block['content'] = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form'); // see cdm_dataportal_search_registration_taxongraph_form($form, &$form_state)
|
| 1030 |
return $block; |
| 1031 |
case 'registrations_search': |
| 1032 |
_add_js_ui_accordion(); |
| 1033 |
_add_font_awesome_font(); |
| 1034 |
$block['subject'] = '<none>'; |
| 1035 |
$filter_form = drupal_get_form('cdm_dataportal_search_registration_filter_form');
|
| 1036 |
$filter_form['#prefix'] = '<div>'; |
| 1037 |
$filter_form['#suffix'] = '</div>'; |
| 1038 |
$taxongraph_form = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form');
|
| 1039 |
$taxongraph_form['#prefix'] = '<div>'; |
| 1040 |
$taxongraph_form['#suffix'] = '</div>'; |
| 1041 |
$block['content'] = array( |
| 1042 |
'accordion' => array( |
| 1043 |
'#markup' => '', |
| 1044 |
'#prefix' => '<div id="accordion">', |
| 1045 |
'#suffix' => '</div>', |
| 1046 |
'content' => array( |
| 1047 |
array('#markup' => '<h3>Filter</h3>'),
|
| 1048 |
$filter_form, |
| 1049 |
array('#markup' => '<h3>Taxon graph</h3>'),
|
| 1050 |
$taxongraph_form, |
| 1051 |
) |
| 1052 |
) |
| 1053 |
); |
| 1054 |
return $block; |
| 1055 |
case 'utis_search': |
| 1056 |
_add_js_utis_client('.utis_client');
|
| 1057 |
$block['subject'] = '<none>'; |
| 1058 |
$block['content'] = '<div class="utis_client"></div>'; |
| 1059 |
return $block; |
| 1060 |
default: |
| 1061 |
return null; |
| 1062 |
} |
| 1063 |
} |
| 1064 |
|
| 1065 |
|
| 1066 |
/** |
| 1067 |
* Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
|
| 1068 |
* |
| 1069 |
* @return string |
| 1070 |
* the taxon uuid or NULL |
| 1071 |
*/ |
| 1072 |
function get_current_taxon_uuid() |
| 1073 |
{
|
| 1074 |
static $taxon_uuid; |
| 1075 |
|
| 1076 |
if(!isset($taxon_uuid)){
|
| 1077 |
if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
|
| 1078 |
$taxon_uuid = $_REQUEST['currentTaxon']; |
| 1079 |
} else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
|
| 1080 |
$taxon_uuid = arg(2); |
| 1081 |
} else {
|
| 1082 |
$taxon_uuid = null; |
| 1083 |
} |
| 1084 |
} |
| 1085 |
|
| 1086 |
return $taxon_uuid; |
| 1087 |
} |
| 1088 |
|
| 1089 |
/** |
| 1090 |
* Returns the currently classification tree in use. |
| 1091 |
* |
| 1092 |
* @return string |
| 1093 |
* The uuid of the currently focused classification |
| 1094 |
*/ |
| 1095 |
function get_current_classification_uuid() {
|
| 1096 |
if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
|
| 1097 |
return $_SESSION['cdm']['taxonomictree_uuid']; |
| 1098 |
} |
| 1099 |
else {
|
| 1100 |
return variable_get(CDM_TAXONOMICTREE_UUID, FALSE); |
| 1101 |
} |
| 1102 |
} |
| 1103 |
|
| 1104 |
/* |
| 1105 |
function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
|
| 1106 |
$_SESSION['cdm'] = NULL; |
| 1107 |
if(is_string($cdm_ws_uri_update)){
|
| 1108 |
$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
|
| 1109 |
} |
| 1110 |
} |
| 1111 |
|
| 1112 |
function cdm_dataportal_session_validate(){
|
| 1113 |
if(!isset($_SESSION['cdm']['ws_uri'])){
|
| 1114 |
$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
|
| 1115 |
} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
|
| 1116 |
cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
|
| 1117 |
} |
| 1118 |
} |
| 1119 |
*/ |
| 1120 |
|
| 1121 |
/** |
| 1122 |
* creates a selector form for taxonomic trees. |
| 1123 |
* |
| 1124 |
* @return array |
| 1125 |
* a drupal form array |
| 1126 |
*/ |
| 1127 |
function cdm_taxonomictree_selector() {
|
| 1128 |
_add_js_treeselector(); |
| 1129 |
|
| 1130 |
$form = drupal_get_form('cdm_taxonomictree_selector_form');
|
| 1131 |
return $form; |
| 1132 |
} |
| 1133 |
|
| 1134 |
/** |
| 1135 |
* @todo Please document this function. |
| 1136 |
* @see http://drupal.org/node/1354 |
| 1137 |
* |
| 1138 |
* @deprecated use compose_classification_selector instead |
| 1139 |
*/ |
| 1140 |
function cdm_taxonomictree_selector_form($form, &$form_state) {
|
| 1141 |
|
| 1142 |
$url = url('cdm_api/setvalue/session', array('query' => NULL));
|
| 1143 |
$form['#action'] = $url; |
| 1144 |
|
| 1145 |
$form['var'] = array( |
| 1146 |
'#weight' => -3, |
| 1147 |
'#type' => 'hidden', |
| 1148 |
'#value' => '[cdm][taxonomictree_uuid]', |
| 1149 |
); |
| 1150 |
|
| 1151 |
$destination_array = drupal_get_destination(); |
| 1152 |
$destination = $destination_array['destination']; |
| 1153 |
|
| 1154 |
$form['destination'] = array( |
| 1155 |
'#weight' => -3, |
| 1156 |
'#type' => 'hidden', |
| 1157 |
'#value' => $destination, |
| 1158 |
); |
| 1159 |
|
| 1160 |
$options = cdm_get_taxontrees_as_options(); |
| 1161 |
$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null); |
| 1162 |
if($taxontree_includes){
|
| 1163 |
$filtered_options = array(); |
| 1164 |
foreach($options as $uuid=>$label){
|
| 1165 |
if(!empty($taxontree_includes[$uuid])){
|
| 1166 |
$filtered_options[$uuid] = $label; |
| 1167 |
} |
| 1168 |
} |
| 1169 |
$options = $filtered_options; |
| 1170 |
} |
| 1171 |
|
| 1172 |
$form['val'] = array( |
| 1173 |
'#type' => 'select', |
| 1174 |
'#title' => t('Available classifications'),
|
| 1175 |
'#default_value' => get_current_classification_uuid(), |
| 1176 |
'#options' => $options, |
| 1177 |
'#attributes' => array('class' => array('highlite-first-child')),
|
| 1178 |
); |
| 1179 |
|
| 1180 |
return $form; |
| 1181 |
|
| 1182 |
} |
| 1183 |
|
| 1184 |
/** |
| 1185 |
* |
| 1186 |
* @ingroup compose |
| 1187 |
*/ |
| 1188 |
function compose_classification_selector() {
|
| 1189 |
|
| 1190 |
$destination_array = drupal_get_destination(); |
| 1191 |
$destination = $destination_array['destination']; |
| 1192 |
|
| 1193 |
$options = cdm_get_taxontrees_as_options(); |
| 1194 |
$items = array(); |
| 1195 |
$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null); |
| 1196 |
|
| 1197 |
$current_classification_uuid = get_current_classification_uuid(); |
| 1198 |
|
| 1199 |
|
| 1200 |
foreach($options as $uuid=>$label){
|
| 1201 |
if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
|
| 1202 |
|
| 1203 |
$class_attributes = ''; |
| 1204 |
if($current_classification_uuid == $uuid){
|
| 1205 |
$class_attributes = array('focused');
|
| 1206 |
} |
| 1207 |
$items[] = array( |
| 1208 |
'data' => l($label, |
| 1209 |
'cdm_api/setvalue/session', |
| 1210 |
array( |
| 1211 |
'query' => array( |
| 1212 |
'destination' => $destination, |
| 1213 |
'val' => $uuid, |
| 1214 |
'var' => '[cdm][taxonomictree_uuid]' |
| 1215 |
), |
| 1216 |
) |
| 1217 |
), |
| 1218 |
'class' => $class_attributes |
| 1219 |
); |
| 1220 |
} |
| 1221 |
} |
| 1222 |
|
| 1223 |
$render_array = array( |
| 1224 |
'#theme' => 'item_list', |
| 1225 |
'#type' => 'ul', |
| 1226 |
'#items' => $items |
| 1227 |
); |
| 1228 |
|
| 1229 |
return $render_array; |
| 1230 |
} |
| 1231 |
|
| 1232 |
|
| 1233 |
/* UNREACHABLE since action of form directly links to view. |
| 1234 |
function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
|
| 1235 |
|
| 1236 |
$_SESSION['cdm']['search'] = $form_values; |
| 1237 |
//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language']; |
| 1238 |
return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0'); |
| 1239 |
//$paramstr = compose_url_prameterstr($form_values); |
| 1240 |
//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
|
| 1241 |
} |
| 1242 |
*/ |
| 1243 |
/* ====================== menu callback functions ====================== */ |
| 1244 |
/** |
| 1245 |
* @todo Please document this function. |
| 1246 |
* @see http://drupal.org/node/1354 |
| 1247 |
*/ |
| 1248 |
/* |
| 1249 |
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
|
| 1250 |
static $comment_node_disabled = 0; |
| 1251 |
static $comment_node_read_only = 1; |
| 1252 |
static $comment_node_read_write = 2; |
| 1253 |
|
| 1254 |
if ($form_id == 'node_type_form' |
| 1255 |
&& isset($form['identity']['type']) |
| 1256 |
&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes()) |
| 1257 |
) {
|
| 1258 |
$form['workflow']['comment'] = array( |
| 1259 |
'#type' => 'radios', |
| 1260 |
'#title' => t('Default comment setting'),
|
| 1261 |
'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
|
| 1262 |
'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
|
| 1263 |
'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
|
| 1264 |
); |
| 1265 |
} |
| 1266 |
} |
| 1267 |
*/ |
| 1268 |
|
| 1269 |
/** |
| 1270 |
* Displays a list of the known taxonomic names. |
| 1271 |
* |
| 1272 |
* When the list of taxonomic names is displayed, long lists are split up into |
| 1273 |
* multiple pages. |
| 1274 |
* |
| 1275 |
* TODO: Parameters are still preliminary. |
| 1276 |
* |
| 1277 |
* @param string $beginsWith |
| 1278 |
* @param string $page |
| 1279 |
* Page number to diplay defaults to page 1. |
| 1280 |
* @param bool $onlyAccepted |
| 1281 |
*/ |
| 1282 |
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
|
| 1283 |
|
| 1284 |
$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
|
| 1285 |
|
| 1286 |
/* |
| 1287 |
// FIXME the filter for accepted names will be a form element, thus this |
| 1288 |
// widget should be generated via form api preferably as block. |
| 1289 |
$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
|
| 1290 |
$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
|
| 1291 |
$out .= theme('cdm_listof_taxa', $taxonPager);
|
| 1292 |
return $out; |
| 1293 |
*/ |
| 1294 |
} |
| 1295 |
|
| 1296 |
/** |
| 1297 |
* @todo Please document this function. |
| 1298 |
* @see http://drupal.org/node/1354 |
| 1299 |
* @throws Exception |
| 1300 |
*/ |
| 1301 |
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
|
| 1302 |
|
| 1303 |
cdm_check_valid_portal_page(); |
| 1304 |
|
| 1305 |
return compose_cdm_reference_page($uuid); |
| 1306 |
} |
| 1307 |
|
| 1308 |
/** |
| 1309 |
* Creates a view on a all references contained in the portal. |
| 1310 |
* |
| 1311 |
* This function is used at the path cdm_dataportal/reference/list |
| 1312 |
*/ |
| 1313 |
function cdm_dataportal_view_reference_list($pageNumber) {
|
| 1314 |
$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
|
| 1315 |
cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/'); |
| 1316 |
} |
| 1317 |
|
| 1318 |
/** |
| 1319 |
* @todo Please document this function. |
| 1320 |
* @see http://drupal.org/node/1354 |
| 1321 |
*/ |
| 1322 |
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
|
| 1323 |
|
| 1324 |
cdm_check_valid_portal_page(); |
| 1325 |
|
| 1326 |
$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid); |
| 1327 |
if (!$media) {
|
| 1328 |
drupal_set_title(t('Media does not exist'), PASS_THROUGH);
|
| 1329 |
return ""; |
| 1330 |
} |
| 1331 |
return theme('cdm_media_page', array(
|
| 1332 |
'media' => $media, |
| 1333 |
'mediarepresentation_uuid' => $mediarepresentation_uuid, |
| 1334 |
'partId' => $part, |
| 1335 |
)); |
| 1336 |
} |
| 1337 |
|
| 1338 |
/** |
| 1339 |
* @todo Please document this function. |
| 1340 |
* @see http://drupal.org/node/1354 |
| 1341 |
*/ |
| 1342 |
function _load_taxonBase(&$taxonBase) {
|
| 1343 |
if (isset($taxonBase->uuid)) {
|
| 1344 |
$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name")); |
| 1345 |
$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName")); |
| 1346 |
$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference")); |
| 1347 |
} |
| 1348 |
} |
| 1349 |
|
| 1350 |
/** |
| 1351 |
* Loads the media associated to the given taxon from the cdm server. |
| 1352 |
* The aggregation settings regarding taxon relathionships and |
| 1353 |
* taxonnomic childen are taken into account. |
| 1354 |
* |
| 1355 |
* The media lists are cached in a static variable. |
| 1356 |
* |
| 1357 |
* @param Taxon $taxon |
| 1358 |
* A CDM Taxon entity |
| 1359 |
* |
| 1360 |
* @return array |
| 1361 |
* An array of CDM Media entities |
| 1362 |
* |
| 1363 |
*/ |
| 1364 |
function _load_media_for_taxon($taxon) {
|
| 1365 |
|
| 1366 |
static $media = NULL; |
| 1367 |
|
| 1368 |
if(!isset($media)) {
|
| 1369 |
$media = array(); |
| 1370 |
} |
| 1371 |
if (!isset($media[$taxon->uuid])) {
|
| 1372 |
|
| 1373 |
|
| 1374 |
$mediaQueryParameters = taxon_media_query_parameters(); |
| 1375 |
|
| 1376 |
$ws_endpoint = NULL; |
| 1377 |
if ( $mediaQueryParameters['includeTaxonomicChildren']) {
|
| 1378 |
$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA; |
| 1379 |
} else {
|
| 1380 |
$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA; |
| 1381 |
} |
| 1382 |
// this parameter is not yet used by the CDM_WS_PORTAL_TAXON_*MEDIA |
| 1383 |
// services |
| 1384 |
unset($mediaQueryParameters['includeTaxonomicChildren']); |
| 1385 |
|
| 1386 |
$media[$taxon->uuid] = cdm_ws_get($ws_endpoint, |
| 1387 |
array( |
| 1388 |
$taxon->uuid, |
| 1389 |
), |
| 1390 |
queryString($mediaQueryParameters) |
| 1391 |
); |
| 1392 |
} |
| 1393 |
|
| 1394 |
return $media[$taxon->uuid]; |
| 1395 |
} |
| 1396 |
|
| 1397 |
/** |
| 1398 |
* |
| 1399 |
* @param Taxon $taxon |
| 1400 |
* A CDM Taxon entitiy |
| 1401 |
* |
| 1402 |
* @return array |
| 1403 |
* An array of CDM SpecimenOrObservation entities |
| 1404 |
* |
| 1405 |
function _load_occurences_for_taxon($taxon){
|
| 1406 |
|
| 1407 |
static $occurences = NULL; |
| 1408 |
|
| 1409 |
if(!isset($occurences)) {
|
| 1410 |
$occurences = array(); |
| 1411 |
} |
| 1412 |
|
| 1413 |
if (!isset($occurences[$taxon->uuid])){
|
| 1414 |
|
| 1415 |
$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT)); |
| 1416 |
$relationship_choice['direct'] = get_selection($relationship_choice['direct']); |
| 1417 |
$relationship_choice['invers'] = get_selection($relationship_choice['invers']); |
| 1418 |
|
| 1419 |
$by_associatedtaxon_query = http_build_query(array( |
| 1420 |
'relationshipsInvers' => implode(',', $relationship_choice['invers']),
|
| 1421 |
'relationships' => implode(',', $relationship_choice['direct']),
|
| 1422 |
'pageSize' => null // all hits in one page |
| 1423 |
) |
| 1424 |
); |
| 1425 |
|
| 1426 |
$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON, |
| 1427 |
null, |
| 1428 |
$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid |
| 1429 |
); |
| 1430 |
|
| 1431 |
|
| 1432 |
if(isset($pager->records[0])){
|
| 1433 |
$occurences[$taxon->uuid] = $pager->records; |
| 1434 |
} |
| 1435 |
} |
| 1436 |
return $occurences[$taxon->uuid]; |
| 1437 |
} |
| 1438 |
*/ |
| 1439 |
|
| 1440 |
/** |
| 1441 |
* Gets a Drupal variable, string or array and returns it. |
| 1442 |
* |
| 1443 |
* Similar to the variable_get() function of Drupal, except that this function |
| 1444 |
* is able to handle arrays correctly. This function is especially useful |
| 1445 |
* when dealing with collections of settings form elements (#tree = TRUE). |
| 1446 |
* |
| 1447 |
* @param string $variableKey |
| 1448 |
* The Unique key of the Drupal variable in the Drupal variables table. |
| 1449 |
* @param string $defaultValueString |
| 1450 |
* A string as for example derived from a CONSTANT. |
| 1451 |
* |
| 1452 |
* @return mixed |
| 1453 |
* usually an array, depending on the nature of the variable. |
| 1454 |
* |
| 1455 |
* TODO compare with get_array_variable_merged() duplicate functions? |
| 1456 |
* @deprecated rather use get_array_variable_merged() since this function |
| 1457 |
* used an array as second parameter |
| 1458 |
*/ |
| 1459 |
function mixed_variable_get($variableKey, $defaultValueString) {
|
| 1460 |
$systemDefaults = unserialize($defaultValueString); |
| 1461 |
$storedSettings = variable_get($variableKey, array()); |
| 1462 |
if (is_array($storedSettings)) {
|
| 1463 |
// TODO better use drupal_array_merge_deep() ? |
| 1464 |
$settings = array_merge($systemDefaults, $storedSettings); |
| 1465 |
} |
| 1466 |
else {
|
| 1467 |
$settings = $systemDefaults; |
| 1468 |
} |
| 1469 |
return $settings; |
| 1470 |
} |
| 1471 |
|
| 1472 |
/** |
| 1473 |
* Recursive function to convert an object into an array. |
| 1474 |
* also subordinate objects will be converted. |
| 1475 |
* |
| 1476 |
* @param object $object |
| 1477 |
* the object to be converted |
| 1478 |
* @return array |
| 1479 |
* The array |
| 1480 |
*/ |
| 1481 |
function object_to_array($object) {
|
| 1482 |
if(is_object($object) || is_array($object)) {
|
| 1483 |
$array = (array)$object; |
| 1484 |
foreach ($array as $key=>$value){
|
| 1485 |
$array[$key] = object_to_array($value); |
| 1486 |
} |
| 1487 |
return $array; |
| 1488 |
} else {
|
| 1489 |
return $object; |
| 1490 |
} |
| 1491 |
} |
| 1492 |
|
| 1493 |
/** |
| 1494 |
* Searches the $collection for the cdm entitiy given as $element. |
| 1495 |
* |
| 1496 |
* The elements are compared by their UUID. |
| 1497 |
* |
| 1498 |
* @param $element |
| 1499 |
* the CDM entitiy to search for |
| 1500 |
* @param $collection |
| 1501 |
* the list of CDM entities to search in |
| 1502 |
* |
| 1503 |
* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE |
| 1504 |
* |
| 1505 |
*/ |
| 1506 |
function contains_cdm_entitiy($element, $collection) {
|
| 1507 |
$result = FALSE; |
| 1508 |
foreach ($collection as $a) {
|
| 1509 |
if ($a->uuid == $element->uuid) {
|
| 1510 |
$result = TRUE; |
| 1511 |
} |
| 1512 |
} |
| 1513 |
return $result; |
| 1514 |
} |
| 1515 |
|
| 1516 |
/** |
| 1517 |
* Filters the array $entity_list of CDM entities by the list |
| 1518 |
* of $excludes. Any element contained in the $excludes will be removed |
| 1519 |
* from included int the returned list. |
| 1520 |
* |
| 1521 |
* If the $entity_list is not an array the $excludes will be returned. |
| 1522 |
*/ |
| 1523 |
function filter_cdm_entity_list($entity_list, $excludes) {
|
| 1524 |
if (is_array($entity_list)) {
|
| 1525 |
$result = $entity_list; |
| 1526 |
if ($excludes) {
|
| 1527 |
foreach ($excludes as $exclude) {
|
| 1528 |
if (!contains_cdm_entitiy($exclude, $entity_list)) {
|
| 1529 |
$result[] = $exclude; |
| 1530 |
} |
| 1531 |
} |
| 1532 |
} |
| 1533 |
} |
| 1534 |
else {
|
| 1535 |
$result = $excludes; |
| 1536 |
} |
| 1537 |
return $result; |
| 1538 |
} |
| 1539 |
|
| 1540 |
/** |
| 1541 |
* Wraps the given $html string into a render array suitable for drupal_render() |
| 1542 |
* |
| 1543 |
* @param $html |
| 1544 |
* the html string, see |
| 1545 |
* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup |
| 1546 |
* @param $weight |
| 1547 |
* A positive or negative number (integer or decimal). |
| 1548 |
* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval |
| 1549 |
* @param $prefix |
| 1550 |
* Optional markup for the '#prefix' element of the render array |
| 1551 |
* @param $suffix |
| 1552 |
* Optional markup for the '#suffix' element of the render array |
| 1553 |
* |
| 1554 |
* @return array |
| 1555 |
* A render array |
| 1556 |
* |
| 1557 |
*/ |
| 1558 |
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
|
| 1559 |
$render_array = array( |
| 1560 |
'#markup' => $html |
| 1561 |
); |
| 1562 |
if (is_numeric($weight)) {
|
| 1563 |
$render_array['#weight'] = $weight; |
| 1564 |
} |
| 1565 |
if($prefix){
|
| 1566 |
$render_array['#prefix'] = $prefix; |
| 1567 |
} |
| 1568 |
if($suffix) {
|
| 1569 |
$render_array['#suffix'] = $suffix; |
| 1570 |
} |
| 1571 |
return $render_array; |
| 1572 |
} |
| 1573 |
|
| 1574 |
/** |
| 1575 |
* Loads the subgraph of a given PolytomousKeyNode. |
| 1576 |
* |
| 1577 |
* Loads the subgraph of the given PolytomousKeyNode recursively from |
| 1578 |
* the CDM REST service. |
| 1579 |
* |
| 1580 |
* @param mixed $polytomousKeyNode |
| 1581 |
* PolytomousKeyNode passed by reference. |
| 1582 |
* |
| 1583 |
* @return void |
| 1584 |
*/ |
| 1585 |
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
|
| 1586 |
|
| 1587 |
if (!$polytomousKeyNode) {
|
| 1588 |
return; |
| 1589 |
} |
| 1590 |
if ($polytomousKeyNode->class != "PolytomousKeyNode") {
|
| 1591 |
drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
|
| 1592 |
return; |
| 1593 |
} |
| 1594 |
if (!is_uuid($polytomousKeyNode->uuid)) {
|
| 1595 |
drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
|
| 1596 |
return; |
| 1597 |
} |
| 1598 |
|
| 1599 |
$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid); |
| 1600 |
|
| 1601 |
if (!$polytomousKeyNode) {
|
| 1602 |
// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
|
| 1603 |
return; |
| 1604 |
} |
| 1605 |
|
| 1606 |
// Load children. |
| 1607 |
foreach ($polytomousKeyNode->children as &$childNode) {
|
| 1608 |
_load_polytomousKeySubGraph($childNode); |
| 1609 |
} |
| 1610 |
|
| 1611 |
// Load subkey. |
| 1612 |
$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey")); |
| 1613 |
|
| 1614 |
// Load taxon. |
| 1615 |
$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon")); |
| 1616 |
_load_taxonBase($polytomousKeyNode->taxon); |
| 1617 |
return; |
| 1618 |
} |
| 1619 |
|
| 1620 |
/** |
| 1621 |
* @todo Please document this function. |
| 1622 |
* @see http://drupal.org/node/1354 |
| 1623 |
*/ |
| 1624 |
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
|
| 1625 |
|
| 1626 |
cdm_check_valid_portal_page(); |
| 1627 |
|
| 1628 |
$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid); |
| 1629 |
if (!$polytomousKey) {
|
| 1630 |
drupal_set_title(t('Polytomous key does not exist'), PASS_THROUGH);
|
| 1631 |
return ""; |
| 1632 |
} |
| 1633 |
|
| 1634 |
$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources')); |
| 1635 |
if (is_array($sourcePager->records)) {
|
| 1636 |
$polytomousKey->sources = $sourcePager->records; |
| 1637 |
// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources')); |
| 1638 |
} |
| 1639 |
|
| 1640 |
$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations')); |
| 1641 |
if (is_array($annotationPager->records)) {
|
| 1642 |
$polytomousKey->annotations = $annotationPager->records; |
| 1643 |
} |
| 1644 |
|
| 1645 |
_load_polytomousKeySubGraph($polytomousKey->root); |
| 1646 |
return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
|
| 1647 |
} |
| 1648 |
|
| 1649 |
/** |
| 1650 |
* Creates a taxon page view or a chapter of it. |
| 1651 |
* |
| 1652 |
* The taxon page gives detailed information on a taxon, it shows: |
| 1653 |
* - Taxon name. |
| 1654 |
* - Full list of synonyms homotypic synonyms on top, followed by the |
| 1655 |
* heterotypic and finally followed by misapplied names. |
| 1656 |
* The list is ordered historically. |
| 1657 |
* - All description associated with the taxon. |
| 1658 |
* |
| 1659 |
* @param string $uuid |
| 1660 |
* @param string $chapter |
| 1661 |
* Name of the part to display, valid values are: |
| 1662 |
* 'description', 'images', 'synonymy', 'specimens', 'all'. |
| 1663 |
* |
| 1664 |
* @return string |
| 1665 |
*/ |
| 1666 |
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
|
| 1667 |
|
| 1668 |
cdm_check_valid_taxon_page($chapter); |
| 1669 |
cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
|
| 1670 |
|
| 1671 |
|
| 1672 |
// Display the page for the taxon defined by $uuid. |
| 1673 |
// set_last_taxon_page_tab(arg(3)); |
| 1674 |
$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter); |
| 1675 |
if (!empty($taxonpage)) {
|
| 1676 |
cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
|
| 1677 |
return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content); |
| 1678 |
} |
| 1679 |
else {
|
| 1680 |
cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
|
| 1681 |
return ''; |
| 1682 |
} |
| 1683 |
} |
| 1684 |
|
| 1685 |
/** |
| 1686 |
* This function will generate the taxon page part ($chapter) and returns a taxonpage object |
| 1687 |
* which has two fields, one for the page title and one for the content. Later on in the |
| 1688 |
* process chain the value contained in these fields will be passed to the cdm_node_show() |
| 1689 |
* function as the function parameters $title and $content. |
| 1690 |
* |
| 1691 |
* @param string $uuid |
| 1692 |
* the uuid of the taxon to show |
| 1693 |
* @param string $chapter |
| 1694 |
* Name of the part to display, valid values are: |
| 1695 |
* 'description', 'images', 'synonymy', 'all'. |
| 1696 |
* |
| 1697 |
* @return object with the following fields: |
| 1698 |
* - title : the title of the page |
| 1699 |
* - content: the content of the page |
| 1700 |
* |
| 1701 |
* @throws Exception |
| 1702 |
* |
| 1703 |
*/ |
| 1704 |
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
|
| 1705 |
// Taxon object. |
| 1706 |
$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid); |
| 1707 |
if (empty($taxon)) {
|
| 1708 |
drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
|
| 1709 |
return null; |
| 1710 |
} |
| 1711 |
$taxonpage = new stdClass(); |
| 1712 |
|
| 1713 |
$taxonpage->title = theme('cdm_taxon_page_title', array(
|
| 1714 |
'taxon' => $taxon |
| 1715 |
)); |
| 1716 |
|
| 1717 |
// Check if the taxon id contained in the currently selected tree. |
| 1718 |
$taxon_in_current_classification = taxon_in_current_classification($uuid); |
| 1719 |
|
| 1720 |
if (!$taxon_in_current_classification) {
|
| 1721 |
$classifications = get_classifications_for_taxon($taxon); |
| 1722 |
RenderHints::pushToRenderStack('not_in_current_classification');
|
| 1723 |
$taxon_name_markup = render_taxon_or_name($taxon); |
| 1724 |
|
| 1725 |
if (count($classifications) == 0) {
|
| 1726 |
drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
|
| 1727 |
array( |
| 1728 |
'!taxonname' => $taxon_name_markup, |
| 1729 |
) |
| 1730 |
), 'warning'); |
| 1731 |
} |
| 1732 |
else {
|
| 1733 |
$trees = ''; |
| 1734 |
foreach ($classifications as $classification) {
|
| 1735 |
if (isset($classification->titleCache)) {
|
| 1736 |
$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>'; |
| 1737 |
} |
| 1738 |
} |
| 1739 |
|
| 1740 |
drupal_set_message(format_plural(count($trees), |
| 1741 |
'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees', |
| 1742 |
'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees', |
| 1743 |
array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
|
| 1744 |
) , |
| 1745 |
'warning'); |
| 1746 |
} |
| 1747 |
RenderHints::popFromRenderStack(); |
| 1748 |
} |
| 1749 |
|
| 1750 |
// Render the taxon page. |
| 1751 |
$render_array = compose_cdm_taxon_page($taxon, $chapter); |
| 1752 |
$taxonpage->content = drupal_render($render_array); |
| 1753 |
|
| 1754 |
return $taxonpage; |
| 1755 |
} |
| 1756 |
|
| 1757 |
|
| 1758 |
function cdm_dataportal_specimen_by_accession_number_page_view($accession_number) |
| 1759 |
{
|
| 1760 |
cdm_check_valid_portal_page(); |
| 1761 |
|
| 1762 |
$specimenpage = specimen_by_accession_number_view($accession_number); |
| 1763 |
|
| 1764 |
if (!empty($specimenpage)) {
|
| 1765 |
return cdm_node_show_simulate($specimenpage->content); |
| 1766 |
} |
| 1767 |
else {
|
| 1768 |
return ''; |
| 1769 |
} |
| 1770 |
|
| 1771 |
|
| 1772 |
} |
| 1773 |
|
| 1774 |
/** |
| 1775 |
* Creates a specimen page view. |
| 1776 |
* @param string $uuid the UUID of the specimen |
| 1777 |
* @return array|string |
| 1778 |
*/ |
| 1779 |
function cdm_dataportal_specimen_page_view($uuid) {
|
| 1780 |
|
| 1781 |
cdm_check_valid_portal_page(); |
| 1782 |
$specimenpage = cdm_dataportal_specimen_view($uuid); |
| 1783 |
if (!empty($specimenpage)) {
|
| 1784 |
return cdm_node_show_simulate($specimenpage->content); |
| 1785 |
} |
| 1786 |
else {
|
| 1787 |
return ''; |
| 1788 |
} |
| 1789 |
} |
| 1790 |
|
| 1791 |
|
| 1792 |
/** |
| 1793 |
* Creates a specimen page view. |
| 1794 |
* @param string $uuid the UUID of the specimen |
| 1795 |
* @return object |
| 1796 |
* The page object with the following fields: |
| 1797 |
* - 'title': the page title |
| 1798 |
* - 'content' : the page content rendered as markup |
| 1799 |
*/ |
| 1800 |
function specimen_by_accession_number_view($accession_number = null) {
|
| 1801 |
|
| 1802 |
$field_unit_dto = cdm_ws_get(CDM_WS_OCCURRENCE_ACCESSION_NUMBER, null, 'accessionNumber=' . $accession_number); |
| 1803 |
|
| 1804 |
// Display the page for the specimen defined by $uuid. |
| 1805 |
if (isset($field_unit_dto)){
|
| 1806 |
$dto_array = array($field_unit_dto); |
| 1807 |
$specimen_array = specimen_render_array_items($dto_array); |
| 1808 |
$specimen_table = array( |
| 1809 |
'#theme' => 'table', |
| 1810 |
'#weight' => 2, |
| 1811 |
// prefix attributes and rows with '#' to let it pass toF the theme function, |
| 1812 |
// otherwise it is handled as child render array |
| 1813 |
'#attributes' => array('class' => 'specimens'),
|
| 1814 |
'#rows' => array(), |
| 1815 |
'#prefix' => '<div id="specimens">', |
| 1816 |
'#suffix' => '</div>', |
| 1817 |
); |
| 1818 |
foreach($specimen_array as $value){
|
| 1819 |
$renderArray = array( |
| 1820 |
'#theme' => 'item_list', |
| 1821 |
'#items' => array($value), |
| 1822 |
'#type' => 'ul'); |
| 1823 |
$output = drupal_render($renderArray); |
| 1824 |
$specimen_table['#rows'][] = array( |
| 1825 |
// An array of table rows. Every row is an array of cells, or an associative array |
| 1826 |
'data' => array($output), |
| 1827 |
'class' => array( |
| 1828 |
'descriptionElement', |
| 1829 |
'descriptionElement_IndividualsAssociation' |
| 1830 |
), |
| 1831 |
); |
| 1832 |
|
| 1833 |
|
| 1834 |
} |
| 1835 |
$specimenpage = new stdClass(); |
| 1836 |
|
| 1837 |
$specimenpage->title = theme('theme_cdm_specimen_dto_page_title', array(
|
| 1838 |
'specimen' => $field_unit_dto |
| 1839 |
)); |
| 1840 |
|
| 1841 |
$render_array['markup'] = $specimen_table; |
| 1842 |
$specimenpage->content = drupal_render($render_array); |
| 1843 |
} |
| 1844 |
|
| 1845 |
return $specimenpage; |
| 1846 |
} |
| 1847 |
|
| 1848 |
|
| 1849 |
/** |
| 1850 |
* |
| 1851 |
* Creates a specimen view. |
| 1852 |
* @param string $uuid the UUID of the specimen |
| 1853 |
* @return object |
| 1854 |
* Page object with the fields |
| 1855 |
* - title |
| 1856 |
* - content |
| 1857 |
*/ |
| 1858 |
function cdm_dataportal_specimen_view($uuid) {
|
| 1859 |
//TODO: get the derivateDTO and don't call the webservice a second time in compose_cdm_specimen_page |
| 1860 |
$specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid); |
| 1861 |
if (empty($specimen)) {
|
| 1862 |
drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
|
| 1863 |
return FALSE; |
| 1864 |
} |
| 1865 |
$specimenpage = new stdClass(); |
| 1866 |
|
| 1867 |
$specimenpage->title = specimen_page_title($specimen); |
| 1868 |
|
| 1869 |
// Render the specimen page. |
| 1870 |
$render_array = compose_cdm_specimen_page($specimen); |
| 1871 |
$specimenpage->content = drupal_render($render_array); |
| 1872 |
|
| 1873 |
return $specimenpage; |
| 1874 |
} |
| 1875 |
|
| 1876 |
/** |
| 1877 |
* |
| 1878 |
* Creates a description view. |
| 1879 |
* |
| 1880 |
* @param string $uuid the UUID of the description |
| 1881 |
* @param null $descriptive_dataset_uuid the uuid of the data set which defines |
| 1882 |
* the display of the description detail page |
| 1883 |
* |
| 1884 |
* @return object Page object with the fields |
| 1885 |
* Page object with the fields |
| 1886 |
* - title |
| 1887 |
* - content |
| 1888 |
*/ |
| 1889 |
function cdm_dataportal_description_view($uuid, $descriptive_dataset_uuid = NULL) {
|
| 1890 |
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $uuid); |
| 1891 |
$description_page = new stdClass(); |
| 1892 |
if (empty($description)) {
|
| 1893 |
$description_page->title = t('Description does not exist');
|
| 1894 |
drupal_set_title($description_page->title, PASS_THROUGH); // not necessary if correctly implemented as drupal node |
| 1895 |
$description_page->content = ""; |
| 1896 |
|
| 1897 |
} else {
|
| 1898 |
$description_page->title = $description->titleCache; |
| 1899 |
drupal_set_title($description_page->title); // not necessary if correctly implemented as drupal node |
| 1900 |
|
| 1901 |
// Render the description page. |
| 1902 |
$render_array = compose_description_table($description->uuid, $descriptive_dataset_uuid); |
| 1903 |
if($render_array['title']){
|
| 1904 |
$page_title = strip_tags($render_array['title']['#markup']); |
| 1905 |
drupal_set_title($page_title); |
| 1906 |
unset($render_array['title']); |
| 1907 |
} |
| 1908 |
$description_page->content = drupal_render($render_array); |
| 1909 |
} |
| 1910 |
|
| 1911 |
return $description_page; |
| 1912 |
} |
| 1913 |
|
| 1914 |
function cdm_dataportal_description_page_view($uuid, $descriptive_dataset_uuid = NULL) {
|
| 1915 |
|
| 1916 |
cdm_check_valid_portal_page(); |
| 1917 |
$descriptionpage = cdm_dataportal_description_view($uuid, $descriptive_dataset_uuid); |
| 1918 |
if (!empty($descriptionpage)) {
|
| 1919 |
return cdm_node_show_simulate($descriptionpage->content); |
| 1920 |
} |
| 1921 |
else {
|
| 1922 |
return NULL; |
| 1923 |
} |
| 1924 |
} |
| 1925 |
|
| 1926 |
/** |
| 1927 |
* |
| 1928 |
* Creates a named area view. |
| 1929 |
* @param string $uuid the UUID of the specimen |
| 1930 |
* * @return object |
| 1931 |
* An object with two fields: |
| 1932 |
* - title: the page title |
| 1933 |
* - content: the page content |
| 1934 |
*/ |
| 1935 |
|
| 1936 |
function cdm_dataportal_named_area_view($uuid) {
|
| 1937 |
$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid); |
| 1938 |
if (empty($named_area) || $named_area->class !== 'NamedArea') {
|
| 1939 |
drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
|
| 1940 |
return null; |
| 1941 |
} |
| 1942 |
$named_area_page = new stdClass(); |
| 1943 |
|
| 1944 |
$named_area_page->title = $named_area->representation_L10n; |
| 1945 |
|
| 1946 |
// Render the specimen page. |
| 1947 |
$render_array = compose_cdm_named_area_page($uuid); |
| 1948 |
$named_area_page->content = drupal_render($render_array); |
| 1949 |
|
| 1950 |
return $named_area_page; |
| 1951 |
} |
| 1952 |
|
| 1953 |
function cdm_dataportal_named_area_page_view($uuid) {
|
| 1954 |
|
| 1955 |
cdm_check_valid_portal_page(); |
| 1956 |
|
| 1957 |
$named_area_page = cdm_dataportal_named_area_view($uuid); |
| 1958 |
if (!empty($named_area_page)) {
|
| 1959 |
return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content); |
| 1960 |
} |
| 1961 |
else {
|
| 1962 |
return ''; |
| 1963 |
} |
| 1964 |
|
| 1965 |
|
| 1966 |
} |
| 1967 |
|
| 1968 |
/** |
| 1969 |
* Returns a name page as a Drupal node ready to be renderized by Drupal. |
| 1970 |
* |
| 1971 |
* The node page shows the taxon name title and the list of taxon related |
| 1972 |
* with such taxon. Name on the tree already in use. |
| 1973 |
* |
| 1974 |
* @param string $taxon_name_uuid |
| 1975 |
* The uuid of the CDM TaxonName to show a name page for |
| 1976 |
* @param string $taxon_to_hide_uuid |
| 1977 |
* A taxon which should not be displayed in the taxon list |
| 1978 |
* @param $redirect_to_taxon |
| 1979 |
* Automatically redirect to the related taxon if there is only one |
| 1980 |
* accepted taxon for this name. |
| 1981 |
* @param string $highlite_synonym_uuid |
| 1982 |
* Optinal parameter wich takes another taxon uuid, if given the |
| 1983 |
* target taxon pages will show the syonymy tab where the taxon |
| 1984 |
* refenrenced by the $highlite_synonym_uuid will be highlighted |
| 1985 |
* in case it is found on this page. |
| 1986 |
* |
| 1987 |
* @return mixed |
| 1988 |
* The formatted name page as node. |
| 1989 |
*/ |
| 1990 |
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL, $redirect_to_taxon = false) {
|
| 1991 |
|
| 1992 |
cdm_check_valid_portal_page(); |
| 1993 |
|
| 1994 |
$taxonname_page = cdm_dataportal_name_view( |
| 1995 |
is_uuid($taxon_name_uuid) ? $taxon_name_uuid : null, |
| 1996 |
is_uuid($taxon_to_hide_uuid) ? $taxon_to_hide_uuid : null, |
| 1997 |
$redirect_to_taxon == 'redirect_to_taxon', |
| 1998 |
is_uuid($synonym_uuid) ? $synonym_uuid : null); |
| 1999 |
if (!empty($taxonname_page)) {
|
| 2000 |
return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content); |
| 2001 |
} |
| 2002 |
else {
|
| 2003 |
return ''; |
| 2004 |
} |
| 2005 |
} |
| 2006 |
|
| 2007 |
/** |
| 2008 |
* View function for a TaxonName page. |
| 2009 |
* |
| 2010 |
* The name page lists all taxa for which the name specified by the |
| 2011 |
* $taxon_name_uuid is being used. I case there is only one name the |
| 2012 |
* page automatically redirects ti the according taxon page. Otherwise |
| 2013 |
* the list of names is displayed. |
| 2014 |
* |
| 2015 |
* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the |
| 2016 |
* list of taxa. This is useful for example when referencing from a taxon |
| 2017 |
* to the name page and the referring taxon should not be repeaded in the |
| 2018 |
* name page. |
| 2019 |
* |
| 2020 |
* |
| 2021 |
* @param string $taxon_name_uuid |
| 2022 |
* The uuid of the CDM TaxonName to show a name page for |
| 2023 |
* @param string $taxon_to_hide_uuid |
| 2024 |
* A taxon which should not be displayed in the taxon list |
| 2025 |
* @param $redirect_to_taxon |
| 2026 |
* Automatically redirect to the related taxon if there is only one |
| 2027 |
* accepted taxon for this name. |
| 2028 |
* @param string $highlite_synonym_uuid |
| 2029 |
* Optional parameter which takes another taxon uuid, if given the |
| 2030 |
* target taxon pages will show the synonymy tab where the taxon |
| 2031 |
* referenced by the $highlite_synonym_uuid will be highlighted |
| 2032 |
* in case it is found on this page. |
| 2033 |
* |
| 2034 |
* @return object|boolean |
| 2035 |
* An object with two fields: |
| 2036 |
* - title: the page title |
| 2037 |
* - content: the page content |
| 2038 |
* or FALSE |
| 2039 |
* |
| 2040 |
*/ |
| 2041 |
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $redirect_to_taxon, $highlite_synonym_uuid = NULL) {
|
| 2042 |
// Getting the full taxonname object from the server. |
| 2043 |
$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid)); |
| 2044 |
if (!$taxon_name) {
|
| 2045 |
drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
|
| 2046 |
return FALSE; |
| 2047 |
} |
| 2048 |
cdm_load_tagged_full_title($taxon_name); |
| 2049 |
// Searching for all the taxa connected with the taxon name on the tree |
| 2050 |
// in use. |
| 2051 |
$name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid)); |
| 2052 |
$restrictions = array(new Restriction("name.titleCache","EXACT", array($name->titleCache), 'AND'));
|
| 2053 |
$init_strategy = array( |
| 2054 |
"name.titleCache", |
| 2055 |
"name.nomenclaturalReference.authorship", |
| 2056 |
"name.nomenclaturalReference.inReference.authorship", |
| 2057 |
"name.nomenclaturalReference.inReference.inReference.authorship", |
| 2058 |
"name.nomenclaturalReference.inReference.inReference.inReference.authorship" |
| 2059 |
); |
| 2060 |
$taxa = cdm_ws_fetch_all_by_restriction("Taxon", NULL, $restrictions, $init_strategy);
|
| 2061 |
|
| 2062 |
// Removing the name where we came from. |
| 2063 |
foreach ($taxa as $k => &$taxon) {
|
| 2064 |
if ($taxon->uuid == $taxon_to_hide_uuid) {
|
| 2065 |
unset($taxa[$k]); |
| 2066 |
} |
| 2067 |
} |
| 2068 |
// Show the taxa list or go to the singular taxon. |
| 2069 |
if (sizeof($taxa) == 1 && $redirect_to_taxon) {
|
| 2070 |
// redirect to the taxon if there is only one. |
| 2071 |
$singleTaxon = array_pop($taxa); |
| 2072 |
if ($singleTaxon->class != "Taxon") {
|
| 2073 |
// It is a Synonym -> look for the accepted. |
| 2074 |
$accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid()); |
| 2075 |
if (!empty($highlite_synonym_uuid)) {
|
| 2076 |
drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
|
| 2077 |
} |
| 2078 |
else {
|
| 2079 |
drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
|
| 2080 |
} |
| 2081 |
} |
| 2082 |
else {
|
| 2083 |
// It is an accepted taxon. |
| 2084 |
if (!empty($highlite_synonym_uuid)) {
|
| 2085 |
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
|
| 2086 |
} |
| 2087 |
else {
|
| 2088 |
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
|
| 2089 |
} |
| 2090 |
} |
| 2091 |
} |
| 2092 |
else {
|
| 2093 |
// display the name page content |
| 2094 |
$taxon_name_page = new stdClass(); |
| 2095 |
$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
|
| 2096 |
$content = array(); |
| 2097 |
|
| 2098 |
RenderHints::pushToRenderStack('name_page');
|
| 2099 |
RenderHints::setFootnoteListKey('name_page');
|
| 2100 |
$content['taxon_name'] = markup_to_render_array(render_taxon_or_name($taxon_name), null, '<div class="name-page-name">', '</div>'); |
| 2101 |
|
| 2102 |
|
| 2103 |
// name relationships |
| 2104 |
$name_relations = cdm_ws_fetch_all(str_replace("$0", $taxon_name->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
|
| 2105 |
if(count($name_relations) > 0){
|
| 2106 |
$content['name_relationships'] = compose_name_relationships_list($name_relations, $taxon_name->uuid, null); |
| 2107 |
} |
| 2108 |
|
| 2109 |
// type designations |
| 2110 |
$type_designations_render_array = compose_type_designations($taxon_name->uuid); |
| 2111 |
$content = array_merge($content, $type_designations_render_array); |
| 2112 |
// registrations |
| 2113 |
$registrationDTOs= cdm_ws_fetch_all(CDM_WS_REGISTRATION_DTO, array('nameUuid' => $taxon_name_uuid));
|
| 2114 |
if(isset($registrationDTOs) && count($registrationDTOs ) > 0 ){
|
| 2115 |
$content['registrations'][] = markup_to_render_array('<h2>' . t("Registrations") . '</h2>') ;
|
| 2116 |
foreach ($registrationDTOs as $regDTO){
|
| 2117 |
$content['registrations'][] = compose_registration_dto_compact($regDTO); |
| 2118 |
} |
| 2119 |
} |
| 2120 |
|
| 2121 |
|
| 2122 |
// related taxa |
| 2123 |
$show_taxa_section = variable_get(CDM_NAME_PAGE_SECTION_TAXA, CDM_NAME_PAGE_SECTION_TAXA_DEFAULT); |
| 2124 |
if($show_taxa_section){
|
| 2125 |
if ($taxa) {
|
| 2126 |
$content['related_taxa_header'] = markup_to_render_array("<h2>Taxa for this name</h2>");
|
| 2127 |
$content['related_taxa'] = compose_list_of_taxa($taxa); |
| 2128 |
} |
| 2129 |
else {
|
| 2130 |
$content['related_taxa'] = markup_to_render_array('This name is not assigned to a taxon.', null, '<div class="no-taxon-message">', '</div>');
|
| 2131 |
} |
| 2132 |
} |
| 2133 |
|
| 2134 |
$content['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
|
| 2135 |
|
| 2136 |
$taxon_name_page->content = $content; |
| 2137 |
RenderHints::popFromRenderStack(); |
| 2138 |
RenderHints::clearFootnoteListKey(); |
| 2139 |
return $taxon_name_page; |
| 2140 |
} |
| 2141 |
} |
| 2142 |
|
| 2143 |
|
| 2144 |
/** |
| 2145 |
* Returns a registration page as a Drupal node to be rendered by Drupal. |
| 2146 |
* |
| 2147 |
* @param string $registration_identifier_encoded |
| 2148 |
* The persistent identifier of the registration urlencoded. |
| 2149 |
* @return mixed |
| 2150 |
* The formatted registration page as node. |
| 2151 |
*/ |
| 2152 |
function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
|
| 2153 |
|
| 2154 |
cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
|
| 2155 |
$registration_page = cdm_dataportal_registration_view($registration_identifier_encoded); |
| 2156 |
return cdm_node_show_simulate($registration_page); |
| 2157 |
} |
| 2158 |
|
| 2159 |
/** |
| 2160 |
* @param $registration_identifier_encoded |
| 2161 |
* @return array |
| 2162 |
* The drupal render array for the registration view. |
| 2163 |
*/ |
| 2164 |
function cdm_dataportal_registration_view($registration_identifier_encoded) {
|
| 2165 |
|
| 2166 |
$registration_identifier = urldecode($registration_identifier_encoded); |
| 2167 |
|
| 2168 |
RenderHints::pushToRenderStack('registration_page');
|
| 2169 |
RenderHints::setFootnoteListKey('registration_page');
|
| 2170 |
|
| 2171 |
$render_array = array(); |
| 2172 |
$registration_dto = cdm_ws_get(CDM_WS_REGISTRATION_DTO_BY_IDENTIFIER . $registration_identifier_encoded); |
| 2173 |
if($registration_dto){
|
| 2174 |
|
| 2175 |
drupal_set_title(t('Registration Id:') . ' ' . $registration_identifier, PASS_THROUGH);
|
| 2176 |
$render_array = compose_registration_dto_full($registration_dto, true); |
| 2177 |
|
| 2178 |
} else {
|
| 2179 |
$status_text = cdm_ws_get(CDM_WS_REGISTRATION_STATUS_BY_IDENTIFIER, array($registration_identifier)); |
| 2180 |
if(isset($status_text->String)) {
|
| 2181 |
$status_text = strtolower($status_text->String); |
| 2182 |
if($status_text == 'preparation' || $status_text == 'curation'){
|
| 2183 |
$status_text = 'in ' . $status_text; |
| 2184 |
} |
| 2185 |
drupal_set_title(t('Registration ' . $status_text), PASS_THROUGH);
|
| 2186 |
//$status_message; |
| 2187 |
drupal_set_message("A registration with the identifier " . $registration_identifier . " is " . $status_text, "status");
|
| 2188 |
} else {
|
| 2189 |
drupal_set_title(t('Registration not found'), PASS_THROUGH);
|
| 2190 |
drupal_set_message("A registration with the identifier " . $registration_identifier . " does not exist", "warning");
|
| 2191 |
} |
| 2192 |
} |
| 2193 |
|
| 2194 |
$render_array = array( |
| 2195 |
'#prefix' => '<div id="registration">', |
| 2196 |
'registration' => $render_array, |
| 2197 |
'#suffix' => '</div>', |
| 2198 |
); |
| 2199 |
|
| 2200 |
RenderHints::popFromRenderStack(); |
| 2201 |
RenderHints::clearFootnoteListKey(); |
| 2202 |
|
| 2203 |
return $render_array ; |
| 2204 |
} |
| 2205 |
|
| 2206 |
|
| 2207 |
/** |
| 2208 |
* Creates a page with the advance search form. |
| 2209 |
* |
| 2210 |
* NOTE: The advance search form allows searching for taxa. |
| 2211 |
*/ |
| 2212 |
function cdm_dataportal_view_search_advanced() {
|
| 2213 |
drupal_set_title(t('Advanced search'), PASS_THROUGH);
|
| 2214 |
return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
|
| 2215 |
} |
| 2216 |
|
| 2217 |
/** |
| 2218 |
* Creates a page with the blast search form. |
| 2219 |
* |
| 2220 |
* NOTE: The advance search form allows searching for specimen in blast DB. |
| 2221 |
*/ |
| 2222 |
function cdm_dataportal_view_search_blast() {
|
| 2223 |
drupal_set_title(t('Blast search'), PASS_THROUGH);
|
| 2224 |
return drupal_get_form('cdm_dataportal_search_blast_form');
|
| 2225 |
} |
| 2226 |
|
| 2227 |
/** |
| 2228 |
* Creates a page with the search form for searching by taxon descriptions. |
| 2229 |
*/ |
| 2230 |
function cdm_dataportal_view_search_taxon_by_description() {
|
| 2231 |
drupal_set_title(t('Search by factual data'), PASS_THROUGH);
|
| 2232 |
return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
|
| 2233 |
} |
| 2234 |
|
| 2235 |
/** |
| 2236 |
* Executes the search and generates the result list of taxa. |
| 2237 |
*/ |
| 2238 |
function cdm_dataportal_view_search_results_taxon() {
|
| 2239 |
|
| 2240 |
$taxonPager = cdm_dataportal_search_taxon_execute(); |
| 2241 |
|
| 2242 |
$showThumbnails = do_showThumbnails(); |
| 2243 |
|
| 2244 |
$setSessionUri = url('cdm_api/setvalue/session', array(
|
| 2245 |
'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
|
| 2246 |
)); |
| 2247 |
|
| 2248 |
drupal_add_js('jQuery(document).ready(function() {
|
| 2249 |
|
| 2250 |
// init |
| 2251 |
if(' . $showThumbnails . ' == 1){
|
| 2252 |
jQuery(\'.media_gallery\').show(20); |
| 2253 |
} else {
|
| 2254 |
jQuery(\'.media_gallery\').hide(20); |
| 2255 |
} |
| 2256 |
|
| 2257 |
// add change handler |
| 2258 |
jQuery(\'#showThumbnails input.showThumbnails\').change( |
| 2259 |
function(event){
|
| 2260 |
var state = 0; |
| 2261 |
if(jQuery(this).is(\':checked\')){
|
| 2262 |
jQuery(\'.media_gallery\').show(20); |
| 2263 |
state = 1; |
| 2264 |
} else {
|
| 2265 |
jQuery(\'.media_gallery\').hide(20); |
| 2266 |
} |
| 2267 |
// store state in session variable |
| 2268 |
var uri = \'' . $setSessionUri . '\' + state; |
| 2269 |
jQuery.get(uri); |
| 2270 |
}); |
| 2271 |
});', |
| 2272 |
array('type' => "inline", 'scope' => JS_DEFAULT));
|
| 2273 |
|
| 2274 |
drupal_set_title(t('Search results'), PASS_THROUGH);
|
| 2275 |
|
| 2276 |
return theme('cdm_search_taxa_results', array(
|
| 2277 |
'pager' => $taxonPager, |
| 2278 |
'path' => 'cdm_dataportal/search/results/taxon', |
| 2279 |
)); |
| 2280 |
} |
| 2281 |
|
| 2282 |
/** |
| 2283 |
* Executes the blast search and generates the result list of specimen. |
| 2284 |
*/ |
| 2285 |
function cdm_dataportal_view_search_results_specimen() {
|
| 2286 |
|
| 2287 |
$specimenPager = cdm_dataportal_search_blast_execute(); |
| 2288 |
|
| 2289 |
return theme('cdm_search_specimen_results', array(
|
| 2290 |
'pager' => $specimenPager, |
| 2291 |
'path' => 'cdm_dataportal/search/results/specimen', |
| 2292 |
)); |
| 2293 |
} |
| 2294 |
|
| 2295 |
|
| 2296 |
/** |
| 2297 |
* Executes the search for registrations and generates the result list.. |
| 2298 |
*/ |
| 2299 |
function cdm_dataportal_view_search_registrations_results($mode = 'filter') {
|
| 2300 |
|
| 2301 |
switch($mode ){
|
| 2302 |
case 'taxongraph': |
| 2303 |
$block = block_load('cdm_dataportal', 'registrations_search_taxongraph');
|
| 2304 |
$registration_pager = cdm_dataportal_search_registrations_taxongraph_execute(); |
| 2305 |
break; |
| 2306 |
case 'filter': |
| 2307 |
default: |
| 2308 |
$block = block_load('cdm_dataportal', 'registrations_search_filter');
|
| 2309 |
$registration_pager = cdm_dataportal_search_registrations_filter_execute(); |
| 2310 |
} |
| 2311 |
$block->title = null; |
| 2312 |
|
| 2313 |
drupal_set_title(t('Search registrations'), PASS_THROUGH);
|
| 2314 |
|
| 2315 |
$render_array = _block_get_renderable_array(_block_render_blocks(array($block))); |
| 2316 |
$registrations_pager_array = compose_search_results($registration_pager, new RegistrationDTOComposeHandler()); |
| 2317 |
$render_array = array_merge($render_array, $registrations_pager_array); |
| 2318 |
|
| 2319 |
return $render_array; |
| 2320 |
} |
| 2321 |
|
| 2322 |
/** |
| 2323 |
* Executes the search for registrations and generates the result list.. |
| 2324 |
*/ |
| 2325 |
function cdm_dataportal_view_search_agent() {
|
| 2326 |
|
| 2327 |
$render_array = []; |
| 2328 |
$title = isset($_REQUEST['class']) && $_REQUEST['class'] ? $_REQUEST['class'] : 'Persons & Teams'; |
| 2329 |
drupal_set_title(t($title), PASS_THROUGH); |
| 2330 |
// TODO $block = block_load('cdm_dataportal', 'search_agent_filter');
|
| 2331 |
// $block->title = null; |
| 2332 |
// $render_array = _block_get_renderable_array(_block_render_blocks(array($block))); |
| 2333 |
$pager = cdm_dataportal_search_agent_execute(); |
| 2334 |
$pager_render_array = compose_search_results($pager, new AgentComposeHandler()); |
| 2335 |
$render_array = array_merge($render_array, $pager_render_array); |
| 2336 |
return $render_array; |
| 2337 |
} |
| 2338 |
|
| 2339 |
|
| 2340 |
/** |
| 2341 |
* Provides the standard image which indicated a loading process |
| 2342 |
* |
| 2343 |
* @return string |
| 2344 |
* The img html tag |
| 2345 |
*/ |
| 2346 |
function loading_image_html() {
|
| 2347 |
return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
|
| 2348 |
. '/images/loading_circle_grey_16.gif" style="display:none;">'; |
| 2349 |
} |
| 2350 |
|
| 2351 |
/** |
| 2352 |
* Returns the state of the the showThumbnails flag set in the |
| 2353 |
* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']). |
| 2354 |
* |
| 2355 |
* @return boolean |
| 2356 |
* returns 1 if the flag is set |
| 2357 |
*/ |
| 2358 |
function do_showThumbnails() {
|
| 2359 |
static $showThumbnails = null; |
| 2360 |
|
| 2361 |
if($showThumbnails == null) {
|
| 2362 |
$showThumbnails = 0; |
| 2363 |
if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
|
| 2364 |
$showThumbnails = 0; |
| 2365 |
$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null); |
| 2366 |
$showThumbnails = is_array($search_gallery_settings) |
| 2367 |
&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails']) |
| 2368 |
&& ( |
| 2369 |
$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] + |
| 2370 |
$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] + |
| 2371 |
$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0 |
| 2372 |
) |
| 2373 |
? 1 : 0; |
| 2374 |
|
| 2375 |
drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
|
| 2376 |
} |
| 2377 |
$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails']; |
| 2378 |
if (!is_numeric($showThumbnails)) {
|
| 2379 |
$showThumbnails = 1; |
| 2380 |
} |
| 2381 |
} |
| 2382 |
|
| 2383 |
return $showThumbnails; |
| 2384 |
} |
| 2385 |
|
| 2386 |
|
| 2387 |
|
| 2388 |
/* ====================== other functions ====================== */ |
| 2389 |
/** |
| 2390 |
* Creates a URL to the taxon page specified by the $uuid parameter. |
| 2391 |
* |
| 2392 |
* The URL will be prepended with a path element to a specific taxon page tab. |
| 2393 |
* |
| 2394 |
* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can |
| 2395 |
* be set globally in the administrative settings or individually in the user |
| 2396 |
* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB |
| 2397 |
* the last portal will stay on this last tab. |
| 2398 |
* |
| 2399 |
* A third option is offerered by the $page_tab parameter which allows overwriting this |
| 2400 |
* internal mechanism by a specific value. |
| 2401 |
* |
| 2402 |
* @param string $uuid |
| 2403 |
* The UUID of the taxon. |
| 2404 |
* @param string $page_tab |
| 2405 |
* Overwriting the preset mechanism by defining specific value for the |
| 2406 |
* taxon page tab. |
| 2407 |
* @return string |
| 2408 |
* The created URL. |
| 2409 |
*/ |
| 2410 |
function path_to_taxon($uuid, $page_tab = FALSE) {
|
| 2411 |
|
| 2412 |
$tab = get_default_taxon_tab(); |
| 2413 |
$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB); |
| 2414 |
|
| 2415 |
if (!$uuid) {
|
| 2416 |
return FALSE; |
| 2417 |
} |
| 2418 |
|
| 2419 |
if ($page_tab) {
|
| 2420 |
$url = 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab; |
| 2421 |
} |
| 2422 |
elseif (!$tab || strtolower($tab) == 'general') {
|
| 2423 |
$url = 'cdm_dataportal/taxon/' . $uuid; |
| 2424 |
} |
| 2425 |
elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
|
| 2426 |
$url = 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab(); |
| 2427 |
} |
| 2428 |
else {
|
| 2429 |
$url = 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab); |
| 2430 |
} |
| 2431 |
return $url; |
| 2432 |
} |
| 2433 |
|
| 2434 |
function path_to_description($uuid, $descriptive_dataset_uuid = NULL) {
|
| 2435 |
|
| 2436 |
if (!$uuid) {
|
| 2437 |
return FALSE; |
| 2438 |
} |
| 2439 |
else {
|
| 2440 |
return 'cdm_dataportal/description/' . $uuid |
| 2441 |
. (is_uuid($descriptive_dataset_uuid) ? '/' . $descriptive_dataset_uuid : ''); |
| 2442 |
} |
| 2443 |
} |
| 2444 |
|
| 2445 |
function path_to_specimen($uuid) {
|
| 2446 |
|
| 2447 |
if (!$uuid) {
|
| 2448 |
return FALSE; |
| 2449 |
} |
| 2450 |
else {
|
| 2451 |
return 'cdm_dataportal/occurrence/' . $uuid; |
| 2452 |
} |
| 2453 |
} |
| 2454 |
|
| 2455 |
function path_to_specimen_by_accession_number($accession_number) {
|
| 2456 |
|
| 2457 |
if (!$accession_number) {
|
| 2458 |
return FALSE; |
| 2459 |
} |
| 2460 |
else {
|
| 2461 |
return 'cdm_dataportal/specimen/accession_number/' . $accession_number; |
| 2462 |
} |
| 2463 |
} |
| 2464 |
|
| 2465 |
function path_to_named_area($uuid) {
|
| 2466 |
|
| 2467 |
if (!$uuid) {
|
| 2468 |
return FALSE; |
| 2469 |
} |
| 2470 |
else {
|
| 2471 |
return 'cdm_dataportal/named_area/' . $uuid; |
| 2472 |
} |
| 2473 |
} |
| 2474 |
|
| 2475 |
/** |
| 2476 |
* Creates a URL to show a synonmy in the according taxon page. |
| 2477 |
* |
| 2478 |
* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid. |
| 2479 |
* The resulting URI will include query parameters to highlight the synonym, and to optionally display |
| 2480 |
* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also |
| 2481 |
* include the sysnonym uuid as fragment in order to let the browser scroll to the according location |
| 2482 |
* in the page |
| 2483 |
* |
| 2484 |
* @param string $synonymUuid |
| 2485 |
* The uuid of the synonym |
| 2486 |
* @param string $acceptedUuid |
| 2487 |
* The uuid of the according accepted taxon |
| 2488 |
* @return string |
| 2489 |
* The URL to show a synonmy in the according taxon page |
| 2490 |
*/ |
| 2491 |
function uri_to_synonym($synonymUuid, $acceptedUuid) {
|
| 2492 |
$acceptedPath = path_to_taxon($acceptedUuid, "synonymy"); |
| 2493 |
return url($acceptedPath, array( |
| 2494 |
'query' => array( |
| 2495 |
// highlite the synony in the synonymy |
| 2496 |
'highlite' => $synonymUuid, |
| 2497 |
// the taxon page is refered from a synonym and the synonym can optionally be named in the page title |
| 2498 |
// see theme_taxon_page_title() |
| 2499 |
'acceptedFor' => $synonymUuid |
| 2500 |
), |
| 2501 |
'fragment' => $synonymUuid |
| 2502 |
)); |
| 2503 |
|
| 2504 |
} |
| 2505 |
|
| 2506 |
/** |
| 2507 |
* Composes the drupal path to the key identified by the uuid. |
| 2508 |
* |
| 2509 |
* @param string $keyType |
| 2510 |
* the key typer corresponds to the specific class of the CDM |
| 2511 |
* IdentificationKey. Possible values are |
| 2512 |
* -PolytomousKey |
| 2513 |
* -MultimediaKey |
| 2514 |
* - ... |
| 2515 |
* @param string $keyUuid |
| 2516 |
* The UUID of the key |
| 2517 |
*/ |
| 2518 |
function path_to_key($keyType, $keyUuid) {
|
| 2519 |
if (!$keyUuid || !$keyType) {
|
| 2520 |
return FALSE; |
| 2521 |
} |
| 2522 |
$keyType{0} = strtolower($keyType{0});
|
| 2523 |
return "cdm_dataportal/" . $keyType . "/$keyUuid"; |
| 2524 |
} |
| 2525 |
|
| 2526 |
/** |
| 2527 |
* Composes the drupal path to the reference identified by the uuid. |
| 2528 |
* |
| 2529 |
* @param $uuid string String representation of the registration entity uuid. |
| 2530 |
* |
| 2531 |
* @return string |
| 2532 |
* The drupal path |
| 2533 |
* |
| 2534 |
*/ |
| 2535 |
function path_to_reference($uuid) {
|
| 2536 |
if (!$uuid) {
|
| 2537 |
return FALSE; |
| 2538 |
} |
| 2539 |
return 'cdm_dataportal/reference/' . $uuid; |
| 2540 |
} |
| 2541 |
|
| 2542 |
/** |
| 2543 |
* Composes the drupal path to the reference identified by the uuid. |
| 2544 |
* |
| 2545 |
* @param string $identifier |
| 2546 |
* The persistent identifier of the registration entity (Registration.identifier). |
| 2547 |
* @return string |
| 2548 |
* The drupal path |
| 2549 |
*/ |
| 2550 |
function path_to_registration($identifier) {
|
| 2551 |
|
| 2552 |
if(variable_get(CDM_REGISTRATION_PRESISTENT_IDENTIFIER_AS_LINK)){
|
| 2553 |
return $identifier; |
| 2554 |
} else {
|
| 2555 |
return 'cdm_dataportal/registration/' . urlencode($identifier); |
| 2556 |
} |
| 2557 |
} |
| 2558 |
|
| 2559 |
/** |
| 2560 |
* Creates the path to a cdm_dataportal taxon name page. |
| 2561 |
* |
| 2562 |
* @param string $taxon_name_uuid |
| 2563 |
* The uuid as string of the CDM TaxonName to show a name page for |
| 2564 |
* @param string $taxon_to_hide_uuid |
| 2565 |
* The uuid as string of a taxon which should not be displayed in the taxon list |
| 2566 |
* @param string $highlited_synonym_uuid |
| 2567 |
* Optional parameter which takes another taxon uuid, if given the |
| 2568 |
* target taxon pages will show the synonymy tab where the taxon |
| 2569 |
* referenced by the $highlite_synonym_uuid will be highlighted |
| 2570 |
* in case it is found on this page. |
| 2571 |
* @param $redirect_to_taxon |
| 2572 |
* If true, the name page will redirect to the related taxon if there is a single one |
| 2573 |
* for this name only. |
| 2574 |
* |
| 2575 |
* @return string |
| 2576 |
* URI path element as string |
| 2577 |
*/ |
| 2578 |
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $highlited_synonym_uuid = NULL, $redirect_to_taxon = false) {
|
| 2579 |
$res = FALSE; |
| 2580 |
if ($name_uuid) {
|
| 2581 |
$res = 'cdm_dataportal/name/' . $name_uuid . |
| 2582 |
'/' . (is_uuid($taxon_to_hide_uuid) ? $taxon_to_hide_uuid : "null") . |
| 2583 |
'/' . (is_uuid($highlited_synonym_uuid) ? $highlited_synonym_uuid : "null") . |
| 2584 |
'/' . ($redirect_to_taxon || variable_get(CDM_NAME_PAGE_AUTOREDIRECT, 0) ? "redirect_to_taxon" : ""); |
| 2585 |
} |
| 2586 |
|
| 2587 |
return $res; |
| 2588 |
} |
| 2589 |
|
| 2590 |
/** |
| 2591 |
* Composes the drupal path to the media entity identified by the uuid. |
| 2592 |
* |
| 2593 |
* @param string $uuid |
| 2594 |
* The persistent identifier of the entity entity |
| 2595 |
* @return string |
| 2596 |
* The drupal path |
| 2597 |
*/ |
| 2598 |
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
|
| 2599 |
if (!$uuid) {
|
| 2600 |
return FALSE; |
| 2601 |
} |
| 2602 |
$out = 'cdm_dataportal/media/' . $uuid; |
| 2603 |
if ($representaion_uuid) {
|
| 2604 |
$out .= '/' . $representaion_uuid; |
| 2605 |
if (is_numeric($partId)) {
|
| 2606 |
$out .= '/' . $partId; |
| 2607 |
} |
| 2608 |
} |
| 2609 |
return $out; |
| 2610 |
} |
| 2611 |
|
| 2612 |
/** |
| 2613 |
* Compares thisRank with thatRank. |
| 2614 |
* |
| 2615 |
* Returns a negative integer, zero, or a positive integer |
| 2616 |
* as the of thisRank is higher than, equal to, or lower than thatRank. |
| 2617 |
* e.g: |
| 2618 |
* <ul> |
| 2619 |
* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
|
| 2620 |
* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
|
| 2621 |
* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
|
| 2622 |
* </ul> |
| 2623 |
* <p> |
| 2624 |
* This compare logic of the underlying webservice is the |
| 2625 |
* <b>inverse logic</b> of the the one implemented in |
| 2626 |
* java.lang.Comparable#compareTo(java.lang.Object) |
| 2627 |
* |
| 2628 |
* @param $thisRankUuid |
| 2629 |
* @param $thatRankUuid |
| 2630 |
* |
| 2631 |
* @return int |
| 2632 |
* A negative integer, zero, or a positive integer |
| 2633 |
* as the thisRank is lower than, equal to, or higher than thatRank. |
| 2634 |
*/ |
| 2635 |
function rank_compare($thisRankUuid, $thatRankUuid) {
|
| 2636 |
$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid)); |
| 2637 |
return $result->Integer; |
| 2638 |
} |
| 2639 |
|
| 2640 |
/** |
| 2641 |
* Creates a short version of a taxonname. |
| 2642 |
* |
| 2643 |
* The short name is created by using the taggedTitle field of |
| 2644 |
* TaxonNodeDTO instances. |
| 2645 |
* If the taggedTitle if empty the fullname will be returned. |
| 2646 |
* |
| 2647 |
* @param object $taxonNodeDTO |
| 2648 |
* A TaxonNodeDTO object |
| 2649 |
* |
| 2650 |
* @return string |
| 2651 |
*/ |
| 2652 |
function cdm_dataportal_shortname_of($taxonNodeDTO) {
|
| 2653 |
|
| 2654 |
$nameStr = ''; |
| 2655 |
|
| 2656 |
normalize_tagged_text($taxonNodeDTO->taggedTitle); |
| 2657 |
|
| 2658 |
// Get all tagged text tokens of the scientific name. |
| 2659 |
foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
|
| 2660 |
if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
|
| 2661 |
$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text; |
| 2662 |
} |
| 2663 |
} |
| 2664 |
$nameStr = trim($nameStr); |
| 2665 |
|
| 2666 |
if ($nameStr) {
|
| 2667 |
if(isset($taxonNodeDTO->nodeStatus->symbol)){
|
| 2668 |
$nameStr = $taxonNodeDTO->nodeStatus->symbol . ' ' . $nameStr; |
| 2669 |
} |
| 2670 |
// Do not return short names for these. |
| 2671 |
if ($taxonNodeDTO->unplaced || $taxonNodeDTO->excluded) {
|
| 2672 |
return $nameStr; |
| 2673 |
} |
| 2674 |
|
| 2675 |
/* |
| 2676 |
1st capture group (^[a-zA-Z]): First letter of uninomial. |
| 2677 |
Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
|
| 2678 |
Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name, |
| 2679 |
but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
|
| 2680 |
OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
|
| 2681 |
*/ |
| 2682 |
$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
|
| 2683 |
if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
|
| 2684 |
return $matches[1][0] . "." . $matches[3][0]; |
| 2685 |
} |
| 2686 |
else {
|
| 2687 |
return $nameStr; |
| 2688 |
} |
| 2689 |
} |
| 2690 |
else {
|
| 2691 |
return $taxonNodeDTO->titleCache; |
| 2692 |
} |
| 2693 |
} |
| 2694 |
|
| 2695 |
/** |
| 2696 |
* Check if a taxon is accepted by the current taxonomic tree. |
| 2697 |
* |
| 2698 |
* @param mixed $taxon |
| 2699 |
* The Taxon obkect to check. |
| 2700 |
* |
| 2701 |
* @return bool |
| 2702 |
* Returns TRUE if $taxon is accepted, FALSE otherwise. |
| 2703 |
*/ |
| 2704 |
function _cdm_dataportal_acceptedByCurrentView($taxon) {
|
| 2705 |
|
| 2706 |
$defaultTreeUuid = get_current_classification_uuid(); |
| 2707 |
|
| 2708 |
if (isset($taxon->taxonNodes)) {
|
| 2709 |
$taxonNodes = $taxon->taxonNodes; |
| 2710 |
} |
| 2711 |
else {
|
| 2712 |
$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid); |
| 2713 |
} |
| 2714 |
|
| 2715 |
if ($taxon->class == "Taxon" && isset($taxonNodes)) {
|
| 2716 |
foreach ($taxonNodes as $node) {
|
| 2717 |
if (isset($node->classificationUUID)){
|
| 2718 |
if ($node->classificationUUID == $defaultTreeUuid) {
|
| 2719 |
return TRUE; |
| 2720 |
} |
| 2721 |
} |
| 2722 |
else {
|
| 2723 |
if ($node->classification == $defaultTreeUuid) {
|
| 2724 |
return TRUE; |
| 2725 |
} |
| 2726 |
} |
| 2727 |
} |
| 2728 |
} |
| 2729 |
|
| 2730 |
return FALSE; |
| 2731 |
} |
| 2732 |
|
| 2733 |
/** |
| 2734 |
* Checks is the source has one of the given types. |
| 2735 |
* |
| 2736 |
* @param object $source |
| 2737 |
* The original source entity |
| 2738 |
* @param array $types |
| 2739 |
* An array of element of the OriginalSourceType enumeration |
| 2740 |
* If not set the default will be used which is: |
| 2741 |
* - Lineage |
| 2742 |
* - PrimaryMediaSource |
| 2743 |
* - PrimaryTaxonomicSource |
| 2744 |
* - Unknown |
| 2745 |
* - Other |
| 2746 |
* @return boolean |
| 2747 |
*/ |
| 2748 |
function _is_original_source_type($source, $types = null) {
|
| 2749 |
// this is the default |
| 2750 |
// maybe this should also be put into the settings |
| 2751 |
static $default = array( |
| 2752 |
OriginalSourceType::Lineage, |
| 2753 |
OriginalSourceType::PrimaryMediaSource, |
| 2754 |
OriginalSourceType::PrimaryTaxonomicSource, |
| 2755 |
OriginalSourceType::Unknown, |
| 2756 |
OriginalSourceType::Other, |
| 2757 |
OriginalSourceType::Aggregation |
| 2758 |
); |
| 2759 |
|
| 2760 |
if(!$types){
|
| 2761 |
$types = $default; |
| 2762 |
} |
| 2763 |
return isset($source->type) && in_array($source->type, $types); |
| 2764 |
} |
| 2765 |
|
| 2766 |
/** |
| 2767 |
* Collects all the media from a list of description elements. |
| 2768 |
* |
| 2769 |
* @param array $descriptionElements |
| 2770 |
* The description elements from which to collect the media. |
| 2771 |
* |
| 2772 |
* @return array |
| 2773 |
* The output with all the collected media. |
| 2774 |
*/ |
| 2775 |
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
|
| 2776 |
|
| 2777 |
$outArrayOfMedia = array(); |
| 2778 |
|
| 2779 |
// Avoiding a warning box in Drupal for Flora Malesiana. |
| 2780 |
if (isset($descriptionElements) && is_array($descriptionElements)) {
|
| 2781 |
foreach ($descriptionElements as $descriptionElement) {
|
| 2782 |
if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
|
| 2783 |
foreach ($descriptionElement->media as $media) {
|
| 2784 |
if (is_object($media)) {
|
| 2785 |
$outArrayOfMedia[] = $media; |
| 2786 |
} |
| 2787 |
} |
| 2788 |
} |
| 2789 |
} |
| 2790 |
} |
| 2791 |
return $outArrayOfMedia; |
| 2792 |
} |
| 2793 |
|
| 2794 |
/** |
| 2795 |
* Fetches the list of visible annotations for each of the cdm entities and returns the footnote keys for them. |
| 2796 |
* |
| 2797 |
* The footnotes are passed to the FootnoteManager in order to store the annotations and to create the footnote keys. |
| 2798 |
* |
| 2799 |
* @see cdm_fetch_visible_annotations() |
| 2800 |
* |
| 2801 |
* @param array $cdm_entities |
| 2802 |
* An array of CdmBase instances or a single instance. |
| 2803 |
* @param $footnote_list_key_suggestion string |
| 2804 |
* optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined be set to |
| 2805 |
* RenderHints::getFootnoteListKey().'-annotations' otherwise the supplied key will be used. |
| 2806 |
* |
| 2807 |
* @return array of footnote keys |
| 2808 |
*/ |
| 2809 |
function cdm_annotations_as_footnotekeys(array $cdm_entities, $footnote_list_key_suggestion = NULL) {
|
| 2810 |
|
| 2811 |
$foot_note_keys = array(); |
| 2812 |
|
| 2813 |
// Is argument cdmBase an array? |
| 2814 |
if (!is_array($cdm_entities)) {
|
| 2815 |
$enties = array(); |
| 2816 |
$enties[] = $cdm_entities; |
| 2817 |
} |
| 2818 |
else {
|
| 2819 |
$enties = $cdm_entities; |
| 2820 |
} |
| 2821 |
|
| 2822 |
// Getting the key for the footnotemanager. |
| 2823 |
if (isset($footnote_list_key_suggestion)) {
|
| 2824 |
$footnote_list_key = $footnote_list_key_suggestion; |
| 2825 |
} |
| 2826 |
else {
|
| 2827 |
$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations'; |
| 2828 |
} |
| 2829 |
|
| 2830 |
// Adding the footnotes keys. |
| 2831 |
foreach ($enties as $cdm_entity) {
|
| 2832 |
$annotations = cdm_fetch_visible_annotations($cdm_entity); |
| 2833 |
if (is_array($annotations)) {
|
| 2834 |
foreach ($annotations as $annotation) {
|
| 2835 |
$foot_note_keys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text); |
| 2836 |
} |
| 2837 |
} |
| 2838 |
} |
| 2839 |
|
| 2840 |
return $foot_note_keys; |
| 2841 |
} |
| 2842 |
|
| 2843 |
/** |
| 2844 |
* Fetches the list of visible annotations for each of the cdm entities and returns the footnote keys for them. |
| 2845 |
* |
| 2846 |
* The footnotes are passed to the FootnoteManager in order to store the annotations and to create the footnote keys. |
| 2847 |
* |
| 2848 |
* @see cdm_fetch_visible_annotations() |
| 2849 |
* |
| 2850 |
* @param array $cdm_entities |
| 2851 |
* An array of CdmBase instances or a single instance. |
| 2852 |
* @param $footnote_list_key_suggestion string |
| 2853 |
* optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined be set to |
| 2854 |
* RenderHints::getFootnoteListKey().'-annotations' otherwise the supplied key will be used. |
| 2855 |
* |
| 2856 |
* @return array of footnote keys |
| 2857 |
*/ |
| 2858 |
function cdm_entity_annotations_as_footnotekeys($cdm_entity, $footnote_list_key_suggestion = NULL) {
|
| 2859 |
|
| 2860 |
$foot_note_keys = array(); |
| 2861 |
|
| 2862 |
// Getting the key for the footnotemanager. |
| 2863 |
if (isset($footnote_list_key_suggestion)) {
|
| 2864 |
$footnote_list_key = $footnote_list_key_suggestion; |
| 2865 |
} else {
|
| 2866 |
$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations'; |
| 2867 |
} |
| 2868 |
|
| 2869 |
// Adding the footnotes keys. |
| 2870 |
$annotations = cdm_fetch_visible_annotations($cdm_entity); |
| 2871 |
if (is_array($annotations)) {
|
| 2872 |
foreach ($annotations as $annotation) {
|
| 2873 |
$foot_note_keys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text); |
| 2874 |
} |
| 2875 |
} |
| 2876 |
|
| 2877 |
return $foot_note_keys; |
| 2878 |
} |
| 2879 |
|
| 2880 |
|
| 2881 |
/** |
| 2882 |
* Creates a CDM Dynabox. |
| 2883 |
* |
| 2884 |
* @param string $dynabox_id |
| 2885 |
* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice. |
| 2886 |
* @param string $label |
| 2887 |
* The clickable text to show. |
| 2888 |
* @param string $content_url |
| 2889 |
* The cdm REST service request url wich will deliver the content to be shown |
| 2890 |
* once the dynabox toggles open. |
| 2891 |
* @param string $theme |
| 2892 |
* The theme to be used for rendering the cdm REST service response with is |
| 2893 |
* returned from the $content_url. |
| 2894 |
* @param string $link_alt_text |
| 2895 |
* The value for the alt attribute of the dynabox link. |
| 2896 |
* @param array $enclosingtags |
| 2897 |
* An array with two elements: $enclosingtags[0] will be used for the dynabox |
| 2898 |
* element itself, $enclosingtags[1] is the tag to be used for the |
| 2899 |
* dynabox_content (optional) |
| 2900 |
* @param array $attributes |
| 2901 |
* @param $content_element_selector |
| 2902 |
* Optional jQuery selector which can be used to reference a dom element which should |
| 2903 |
* be used as container for the content to be shown. The dynabox-<dynabox id>-content |
| 2904 |
* element will be placed in this container. |
| 2905 |
* |
| 2906 |
* @param string $open_callback |
| 2907 |
* optional javascript call back function to be triggered after toggling the box to |
| 2908 |
* the open state. |
| 2909 |
* @param string $close_callback |
| 2910 |
* optional javascript call back function to be triggered after toggling the box to |
| 2911 |
* the closed state. |
| 2912 |
* @return string Returns HTML for a dynabox. |
| 2913 |
* Returns HTML for a dynabox. |
| 2914 |
*/ |
| 2915 |
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text, |
| 2916 |
$enclosingtags = array('li', 'ul'), $attributes = array(),
|
| 2917 |
$content_element_selector = null, |
| 2918 |
$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
|
| 2919 |
$out = ''; |
| 2920 |
|
| 2921 |
// check for plain class attribute string |
| 2922 |
$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
|
| 2923 |
|
| 2924 |
if(!array_key_exists('class', $attributes)) {
|
| 2925 |
$attributes['class'] = array(); |
| 2926 |
} |
| 2927 |
$attributes['id'][] = 'dynabox-' . $dynabox_id; |
| 2928 |
$dynabox_attributes = drupal_attributes($attributes); |
| 2929 |
|
| 2930 |
|
| 2931 |
_add_js_domEvent(); // requires domEvent.js |
| 2932 |
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
|
| 2933 |
drupal_add_js("
|
| 2934 |
jQuery(document).ready( |
| 2935 |
function() {
|
| 2936 |
dynabox('". $dynabox_id ."',
|
| 2937 |
{
|
| 2938 |
open_callback: " . $open_callback .", |
| 2939 |
close_callback: " . $close_callback . |
| 2940 |
($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . " |
| 2941 |
} |
| 2942 |
); |
| 2943 |
} |
| 2944 |
);", |
| 2945 |
array( |
| 2946 |
'type'=>'inline', |
| 2947 |
'scope'=>'footer' |
| 2948 |
) |
| 2949 |
); |
| 2950 |
|
| 2951 |
|
| 2952 |
$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
|
| 2953 |
$out .= '<!-- dynabox for ' . $content_url . ' -->'; |
| 2954 |
$out .= '<' . $enclosingtags[0] . ' ' . $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t('@link-alt-text', array('@link-alt-text' => $link_alt_text)) . '">' . $label . '</a>';
|
| 2955 |
$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">'; |
| 2956 |
$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>'; |
| 2957 |
$out .= ' </' . $enclosingtags[1] . '>'; |
| 2958 |
$out .= ' </' . $enclosingtags[0] . '>'; |
| 2959 |
$out .= '<!-- dynabox end -->'; |
| 2960 |
return $out; |
| 2961 |
} |
| 2962 |
|
| 2963 |
/** |
| 2964 |
* Checks whether a feature has any description elements. |
| 2965 |
* |
| 2966 |
* @param mixed $featureNode |
| 2967 |
* A feature node as produced by the function _mergeFeatureTreeDescriptions(). |
| 2968 |
* |
| 2969 |
* @see _mergeFeatureTreeDescriptions() |
| 2970 |
* |
| 2971 |
* @return bool |
| 2972 |
* Returns TRUE if the given $featureNode or any of its subordinate nodes |
| 2973 |
* contains at least one non empty TextData or at least one DescriptionElement |
| 2974 |
* of an other type. A TextData element holding a multilanguageText or a |
| 2975 |
* source reference is considered to be not empty. |
| 2976 |
* |
| 2977 |
* @TODO this function may have become obsolete by the new method of detecting empty blocks, |
| 2978 |
* see $block_content_is_not_empty in make_feature_block_list() and |
| 2979 |
* $feature_block_has_content in compose_feature_block_items_generic |
| 2980 |
*/ |
| 2981 |
function has_feature_node_description_elements($featureNode) {
|
| 2982 |
|
| 2983 |
if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
|
| 2984 |
if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
|
| 2985 |
foreach ($featureNode->descriptionElements as $descriptionElement) {
|
| 2986 |
if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text) |
| 2987 |
&& $descriptionElement->multilanguageText_L10n->text != '' |
| 2988 |
|| isset($descriptionElement->sources[0]) |
| 2989 |
|| isset($descriptionElement->media[0]) ) {
|
| 2990 |
return TRUE; |
| 2991 |
} |
| 2992 |
} |
| 2993 |
} |
| 2994 |
} |
| 2995 |
else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
|
| 2996 |
foreach ($featureNode->childNodes as $child) {
|
| 2997 |
if (has_feature_node_description_elements($child)) {
|
| 2998 |
return TRUE; |
| 2999 |
} |
| 3000 |
} |
| 3001 |
} |
| 3002 |
return FALSE; |
| 3003 |
} |
| 3004 |
|
| 3005 |
/** |
| 3006 |
* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise |
| 3007 |
* |
| 3008 |
* @param $chapter |
| 3009 |
* The taxon page chapter or part |
| 3010 |
*/ |
| 3011 |
function cdm_check_valid_taxon_page($chapter){
|
| 3012 |
static $taxon_tabs = null; |
| 3013 |
|
| 3014 |
cdm_check_valid_portal_page(); |
| 3015 |
|
| 3016 |
if($taxon_tabs == null){
|
| 3017 |
$taxon_tabs = array('all', 'description');
|
| 3018 |
foreach(get_taxon_tabs_list() as $tab){
|
| 3019 |
$taxon_tabs[] = strtolower($tab); |
| 3020 |
} |
| 3021 |
} |
| 3022 |
|
| 3023 |
if(!in_array($chapter, $taxon_tabs)){
|
| 3024 |
// oops this is not a valid chapter name |
| 3025 |
http_response_code(404); // 404 = Not Found |
| 3026 |
} |
| 3027 |
|
| 3028 |
} |
| 3029 |
|
| 3030 |
function check_js_devel_mode_disabled() {
|
| 3031 |
if(variable_get('cdm_js_devel_mode', FALSE)) {
|
| 3032 |
drupal_set_message(t('The !url1 is enabled.
|
| 3033 |
WARNING: this is a performance penalty and must be turned off on production websites.', array( |
| 3034 |
'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
|
| 3035 |
)), |
| 3036 |
'warning' |
| 3037 |
); |
| 3038 |
} |
| 3039 |
} |
| 3040 |
|
| 3041 |
/** |
| 3042 |
* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise. |
| 3043 |
* The test applied by default it a check for the query parameter 'q' ending with a file suffix like '*.*' |
| 3044 |
* |
| 3045 |
* @param $preg_pattern |
| 3046 |
* Optional regular expression pattern to be used in preg_match(). |
| 3047 |
*/ |
| 3048 |
function cdm_check_valid_portal_page($preg_pattern = null){
|
| 3049 |
$ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/'; |
| 3050 |
if($preg_pattern === null){
|
| 3051 |
$preg_pattern = $ends_with_file_suffix_pattern; |
| 3052 |
} |
| 3053 |
if(preg_match($preg_pattern, $_GET['q'])){
|
| 3054 |
// oops this urls ends with a file_suffix and thus does not refer to a portal page |
| 3055 |
http_response_code(404); // 404 = Not Found |
| 3056 |
exit('HTTP 404');
|
| 3057 |
} |
| 3058 |
check_js_devel_mode_disabled(); |
| 3059 |
} |
| 3060 |
|
| 3061 |
/** |
| 3062 |
* Generates the diff of the texts and presents it in a HTML diff viewer. |
| 3063 |
* |
| 3064 |
* @param $text_a |
| 3065 |
* @param $text_b |
| 3066 |
* @return string |
| 3067 |
*/ |
| 3068 |
function diff_viewer($text_a, $text_b) {
|
| 3069 |
|
| 3070 |
static $diff_viewer_count = 0; |
| 3071 |
|
| 3072 |
$element_id = 'part_definitions_diff_' . $diff_viewer_count++; |
| 3073 |
|
| 3074 |
// http://code.stephenmorley.org/php/diff-implementation/ |
| 3075 |
module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
|
| 3076 |
drupal_add_css(drupal_get_path('module',
|
| 3077 |
'cdm_dataportal') . '/css/diff.css'); |
| 3078 |
_add_jquery_ui(); |
| 3079 |
drupal_add_js( |
| 3080 |
'jQuery(document).ready( function(){
|
| 3081 |
jQuery(\'#' . $element_id . '\').accordion({
|
| 3082 |
collapsible: true, |
| 3083 |
active: false, |
| 3084 |
fillSpace: true, |
| 3085 |
}).children(\'div\').css({ \'height\': \'auto\' });
|
| 3086 |
jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\'); |
| 3087 |
});' |
| 3088 |
, array( |
| 3089 |
'type' => 'inline', |
| 3090 |
'scope' => 'footer' |
| 3091 |
)); |
| 3092 |
|
| 3093 |
$diff = Diff::compare($text_a, |
| 3094 |
$text_b); |
| 3095 |
$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>' |
| 3096 |
. Diff::toTable($diff, '', '') |
| 3097 |
. '</div></div>'; |
| 3098 |
return $diff_viewer_markup; |
| 3099 |
} |
| 3100 |
|
| 3101 |
|
