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6657531f
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Andreas Kohlbecker
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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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38b27a36
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Andreas Kohlbecker
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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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2e31ea9e
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Andreas Kohlbecker
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module_load_include('inc', 'cdm_dataportal', 'includes/name');
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b7a20282
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Andreas Kohlbecker
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module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
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module_load_include('inc', 'cdm_dataportal', 'includes/references');
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38b27a36
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Andreas Kohlbecker
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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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" . $callback . "
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}
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});
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});"
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, 'inline');
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6657531f
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Andreas Kohlbecker
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}
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38b27a36
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Andreas Kohlbecker
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/**
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*/
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function drupal_add_js_rowToggle($tableId){
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6657531f
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Andreas Kohlbecker
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38b27a36
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Andreas Kohlbecker
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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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6657531f
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Andreas Kohlbecker
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});
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38b27a36
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Andreas Kohlbecker
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', array('type' => 'inline'));
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}
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d2fd2a4c
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Andreas Kohlbecker
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38b27a36
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Andreas Kohlbecker
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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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5ea8b301
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Andreas Kohlbecker
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}
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38b27a36
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Andreas Kohlbecker
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function _add_js_openlayers() {
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$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
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$proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
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if(variable_get('cdm_js_devel_mode', FALSE)){
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// develooper mode libs
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// $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
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$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
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$proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
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}
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
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array(
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'type' => 'file',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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'preprocess' => FALSE
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)
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);
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// see https://github.com/proj4js/proj4js
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// http://openlayers.org/dev/examples/using-proj4js.html
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
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array(
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'type' => 'file',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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)
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);
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// configure the theme
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$openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
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$openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
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drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
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'type' => 'inline',
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'weight' => JS_LIBRARY,
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'cache' => TRUE,
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'preprocess' => FALSE
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));
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drupal_add_css($openlayers_theme_path . 'style.tidy.css',
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array(
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'type' => 'file',
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'cache' => TRUE,
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'preprocess' => FALSE
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)
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);
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e3026d72
|
Andreas Kohlbecker
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| 175 |
38b27a36
|
Andreas Kohlbecker
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}
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| 176 |
e3026d72
|
Andreas Kohlbecker
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38b27a36
|
Andreas Kohlbecker
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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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10f6aa4b
|
Andreas Kohlbecker
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)
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38b27a36
|
Andreas Kohlbecker
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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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| 202 |
94550ff9
|
Andreas Kohlbecker
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| 203 |
38b27a36
|
Andreas Kohlbecker
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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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94550ff9
|
Andreas Kohlbecker
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});
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38b27a36
|
Andreas Kohlbecker
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', array('type' => 'inline'));
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}
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| 230 |
94550ff9
|
Andreas Kohlbecker
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| 231 |
38b27a36
|
Andreas Kohlbecker
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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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| 239 |
94550ff9
|
Andreas Kohlbecker
|
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| 240 |
38b27a36
|
Andreas Kohlbecker
|
/**
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| 241 |
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function _add_js_cluetip() {
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// TODO replace by
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// @see http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.min.js');
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.dimensions.js');
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.hoverIntent.js');
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if(variable_get('cdm_js_devel_mode', FALSE)){
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| 252 |
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.js');
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| 253 |
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}
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| 254 |
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drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.css');
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| 255 |
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drupal_add_js("jQuery(document).ready(function(){
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| 256 |
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jQuery('.cluetip').css({color: '#0062C2'}).cluetip({
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splitTitle: '|',
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showTitle: true,
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activation: 'hover',
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sicky: true,
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arrows: true,
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dropShadow: false,
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cluetipClass: 'rounded'
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});
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| 265 |
d0d23caa
|
Andreas Kohlbecker
|
});",
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array(
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'type' => 'inline',
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'scope' => 'footer'
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| 269 |
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)
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| 270 |
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);
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| 271 |
5ea8b301
|
Andreas Kohlbecker
|
}
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| 272 |
94550ff9
|
Andreas Kohlbecker
|
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| 273 |
38b27a36
|
Andreas Kohlbecker
|
/**
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| 274 |
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* @todo Please document this function.
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| 275 |
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* @see http://drupal.org/node/1354
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| 276 |
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*/
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| 277 |
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function _add_js_ahah() {
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| 278 |
b386ae48
|
Andreas Kohlbecker
|
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| 279 |
38b27a36
|
Andreas Kohlbecker
|
_add_js_domEvent(); // requires domEvent.js
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| 280 |
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
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| 281 |
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}
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| 282 |
94550ff9
|
Andreas Kohlbecker
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| 283 |
d0d23caa
|
Andreas Kohlbecker
|
/**
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| 284 |
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* @todo Please document this function.
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| 285 |
|
|
* @see http://drupal.org/node/1354
|
| 286 |
|
|
*/
|
| 287 |
|
|
function _add_js_taxonomic_children($jquery_selector) {
|
| 288 |
b0adfd32
|
Andreas Kohlbecker
|
|
| 289 |
|
|
global $base_url;
|
| 290 |
|
|
|
| 291 |
|
|
|
| 292 |
|
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
|
| 293 |
faf4f771
|
Andreas Kohlbecker
|
|
| 294 |
d0d23caa
|
Andreas Kohlbecker
|
drupal_add_js('jQuery(document).ready(function() {
|
| 295 |
b0adfd32
|
Andreas Kohlbecker
|
jQuery(\'' . $jquery_selector . '\').taxonomic_children({
|
| 296 |
|
|
hoverClass: "fa-rotate-90",
|
| 297 |
|
|
activeClass: "fa-rotate-90",
|
| 298 |
|
|
classificationUuid: "' . get_current_classification_uuid() . '",
|
| 299 |
0af3ce28
|
Andreas Kohlbecker
|
taxonUuid: "' . get_current_taxon_uuid() . '",
|
| 300 |
38da4e54
|
Andreas Kohlbecker
|
cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
|
| 301 |
b0adfd32
|
Andreas Kohlbecker
|
proxyBaseUri: "' . $base_url . '",
|
| 302 |
|
|
|
| 303 |
|
|
});
|
| 304 |
d0d23caa
|
Andreas Kohlbecker
|
});
|
| 305 |
|
|
', array('type' => 'inline'));
|
| 306 |
|
|
}
|
| 307 |
|
|
|
| 308 |
38b27a36
|
Andreas Kohlbecker
|
/**
|
| 309 |
|
|
* Adds the external javascript file for domEvent.js.
|
| 310 |
|
|
*
|
| 311 |
|
|
* @see drupal_add_js()
|
| 312 |
|
|
*/
|
| 313 |
|
|
function _add_js_domEvent() {
|
| 314 |
|
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
|
| 315 |
|
|
}
|
| 316 |
b386ae48
|
Andreas Kohlbecker
|
|
| 317 |
087bb473
|
Andreas Kohlbecker
|
function _add_jquery_ui()
|
| 318 |
|
|
{
|
| 319 |
|
|
drupal_add_css(drupal_get_path('module',
|
| 320 |
|
|
'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
|
| 321 |
|
|
drupal_add_js(drupal_get_path('module',
|
| 322 |
|
|
'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
|
| 323 |
|
|
array(
|
| 324 |
|
|
'type' => 'file',
|
| 325 |
|
|
'weight' => JS_LIBRARY,
|
| 326 |
|
|
'cache' => TRUE,
|
| 327 |
|
|
'preprocess' => FALSE
|
| 328 |
|
|
)
|
| 329 |
|
|
);
|
| 330 |
|
|
}
|
| 331 |
|
|
|
| 332 |
38b27a36
|
Andreas Kohlbecker
|
/**
|
| 333 |
|
|
* Provides the markup for an font awesome icon.
|
| 334 |
|
|
*
|
| 335 |
|
|
* The icons is created in default size without any extra features.
|
| 336 |
|
|
*
|
| 337 |
|
|
* The available icons are listed here http://fontawesome.io/cheatsheet/
|
| 338 |
ef12d0c6
|
Andreas Kohlbecker
|
* fontawesome icons have much more features than implemented here in this function,
|
| 339 |
|
|
* for spinning icons, fixed width icons, rotation, etc please checkout the
|
| 340 |
38b27a36
|
Andreas Kohlbecker
|
* examples at http://fontawesome.io/examples/
|
| 341 |
|
|
*
|
| 342 |
|
|
* @parameter $icon_name
|
| 343 |
|
|
* The name of the icon which starts with 'fa-'
|
| 344 |
|
|
*
|
| 345 |
|
|
* @return String
|
| 346 |
|
|
* the markup for the icon in an <i> tag
|
| 347 |
|
|
*
|
| 348 |
|
|
*/
|
| 349 |
b0aa9a8f
|
Andreas Kohlbecker
|
function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
|
| 350 |
38b27a36
|
Andreas Kohlbecker
|
|
| 351 |
|
|
|
| 352 |
|
|
//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
|
| 353 |
|
|
|
| 354 |
793dae0a
|
Andreas Kohlbecker
|
$font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal').'/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
|
| 355 |
74f9f871
|
Andreas Kohlbecker
|
//$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
|
| 356 |
38b27a36
|
Andreas Kohlbecker
|
|
| 357 |
|
|
drupal_add_html_head_link(
|
| 358 |
|
|
array(
|
| 359 |
|
|
'href' => $font_awesome_css_uri,
|
| 360 |
|
|
'rel' => 'stylesheet'
|
| 361 |
|
|
)
|
| 362 |
|
|
);
|
| 363 |
|
|
|
| 364 |
b0aa9a8f
|
Andreas Kohlbecker
|
if($icon_name){
|
| 365 |
|
|
if(!isset($attributes['class'])){
|
| 366 |
|
|
$attributes['class'] = array();
|
| 367 |
|
|
}
|
| 368 |
|
|
$attributes['class'][] = 'fa';
|
| 369 |
|
|
$attributes['class'][] = $icon_name;
|
| 370 |
|
|
|
| 371 |
|
|
return '<i ' . drupal_attributes($attributes) . '></i>';
|
| 372 |
38b27a36
|
Andreas Kohlbecker
|
}
|
| 373 |
|
|
|
| 374 |
b0aa9a8f
|
Andreas Kohlbecker
|
return '';
|
| 375 |
38b27a36
|
Andreas Kohlbecker
|
}
|
| 376 |
94550ff9
|
Andreas Kohlbecker
|
|
| 377 |
38b27a36
|
Andreas Kohlbecker
|
|
| 378 |
|
|
/* ====================== hook implementations ====================== */
|
| 379 |
|
|
/**
|
| 380 |
|
|
* Implements hook_permission().
|
| 381 |
|
|
*
|
| 382 |
|
|
* Valid permissions for this module.
|
| 383 |
|
|
*
|
| 384 |
|
|
* @return array
|
| 385 |
|
|
* An array of valid permissions for the portfolio module.
|
| 386 |
|
|
*/
|
| 387 |
|
|
function cdm_dataportal_permission() {
|
| 388 |
|
|
return array(
|
| 389 |
|
|
'administer cdm_dataportal' => array(
|
| 390 |
|
|
'title' => t('administer cdm_dataportal'),
|
| 391 |
|
|
'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
|
| 392 |
|
|
),
|
| 393 |
|
|
'cdm_dataportal view notes' => array(
|
| 394 |
|
|
'title' => t('cdm_dataportal view notes'),
|
| 395 |
|
|
'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
|
| 396 |
|
|
),
|
| 397 |
|
|
// TODO Which other permissions are required?
|
| 398 |
|
|
// -> check the WP6 requirements document.
|
| 399 |
|
|
);
|
| 400 |
|
|
}
|
| 401 |
6657531f
|
Andreas Kohlbecker
|
|
| 402 |
|
|
/**
|
| 403 |
f19f47fa
|
Andreas Kohlbecker
|
* Implements hook_menu().
|
| 404 |
|
|
*/
|
| 405 |
6657531f
|
Andreas Kohlbecker
|
function cdm_dataportal_menu() {
|
| 406 |
|
|
$items = array();
|
| 407 |
|
|
|
| 408 |
|
|
// @see settings.php.
|
| 409 |
|
|
cdm_dataportal_menu_admin($items);
|
| 410 |
|
|
cdm_dataportal_menu_help($items);
|
| 411 |
|
|
|
| 412 |
|
|
$items['cdm_dataportal/names'] = array(
|
| 413 |
|
|
'page callback' => 'cdm_dataportal_view_names',
|
| 414 |
|
|
'access arguments' => array('access content'),
|
| 415 |
|
|
'type' => MENU_CALLBACK,
|
| 416 |
|
|
);
|
| 417 |
|
|
|
| 418 |
|
|
// Optional callback arguments: page.
|
| 419 |
|
|
$items['cdm_dataportal/taxon'] = array(
|
| 420 |
|
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 421 |
|
|
'access arguments' => array('access content'),
|
| 422 |
|
|
'type' => MENU_CALLBACK,
|
| 423 |
|
|
// Expected callback arguments: uuid.
|
| 424 |
|
|
);
|
| 425 |
|
|
|
| 426 |
9d37c9d9
|
Patric Plitzner
|
// Optional callback arguments: page.
|
| 427 |
d6d4cc03
|
Patric Plitzner
|
//FIXME point to view/page method in this module
|
| 428 |
9d37c9d9
|
Patric Plitzner
|
$items['cdm_dataportal/specimen'] = array(
|
| 429 |
b810158e
|
Patric Plitzner
|
'page callback' => 'cdm_dataportal_specimen_page_view',
|
| 430 |
9d37c9d9
|
Patric Plitzner
|
'access arguments' => array('access content'),
|
| 431 |
|
|
'type' => MENU_CALLBACK,
|
| 432 |
|
|
// Expected callback arguments: uuid.
|
| 433 |
|
|
);
|
| 434 |
|
|
|
| 435 |
6657531f
|
Andreas Kohlbecker
|
$items['cdm_dataportal/name'] = array(
|
| 436 |
|
|
'page callback' => 'cdm_dataportal_name_page_view',
|
| 437 |
|
|
/*
|
| 438 |
|
|
'page arguments' => array(
|
| 439 |
|
|
'taxon_name_uuid',
|
| 440 |
|
|
'taxon_to_hide_uuid',
|
| 441 |
|
|
'synonym_uuid' => NULL
|
| 442 |
|
|
),
|
| 443 |
|
|
*/
|
| 444 |
|
|
'access arguments' => array('access content'),
|
| 445 |
|
|
'type' => MENU_CALLBACK,
|
| 446 |
|
|
// Expected callback arguments: uuid.
|
| 447 |
|
|
);
|
| 448 |
|
|
|
| 449 |
|
|
$items['cdm_dataportal/reference'] = array(
|
| 450 |
|
|
'page callback' => 'cdm_dataportal_view_reference',
|
| 451 |
|
|
'access arguments' => array('access content'),
|
| 452 |
|
|
'type' => MENU_CALLBACK,
|
| 453 |
|
|
// Expected callback arguments: uuid.
|
| 454 |
|
|
);
|
| 455 |
|
|
|
| 456 |
|
|
$items['cdm_dataportal/reference/list'] = array(
|
| 457 |
|
|
'page callback' => 'cdm_dataportal_view_reference_list',
|
| 458 |
|
|
'access arguments' => array('access content'),
|
| 459 |
|
|
'type' => MENU_CALLBACK,
|
| 460 |
|
|
// Expected callback arguments: uuid.
|
| 461 |
|
|
);
|
| 462 |
|
|
|
| 463 |
|
|
$items['cdm_dataportal/media'] = array(
|
| 464 |
|
|
'page callback' => 'cdm_dataportal_view_media',
|
| 465 |
|
|
'access arguments' => array('access content'),
|
| 466 |
|
|
'type' => MENU_CALLBACK,
|
| 467 |
|
|
// Expected callback arguments:
|
| 468 |
|
|
// uuid, mediarepresentation_uuid, part_uuid or part#.
|
| 469 |
|
|
);
|
| 470 |
|
|
|
| 471 |
|
|
$items['cdm_dataportal/polytomousKey'] = array(
|
| 472 |
|
|
'page callback' => 'cdm_dataportal_view_polytomousKey',
|
| 473 |
|
|
'access arguments' => array('access content'),
|
| 474 |
|
|
'type' => MENU_CALLBACK,
|
| 475 |
|
|
// Expected callback arguments: polytomousKey->uuid.
|
| 476 |
|
|
);
|
| 477 |
|
|
|
| 478 |
|
|
$items['cdm_dataportal/search'] = array(
|
| 479 |
|
|
'page callback' => 'cdm_dataportal_view_search_advanced',
|
| 480 |
|
|
'access arguments' => array('access content'),
|
| 481 |
|
|
'type' => MENU_CALLBACK,
|
| 482 |
|
|
);
|
| 483 |
|
|
|
| 484 |
|
|
$items['cdm_dataportal/search/advanced'] = array(
|
| 485 |
29077ee5
|
Andreas Kohlbecker
|
'title' => 'Advanced', // will be passed through t()
|
| 486 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_view_search_advanced',
|
| 487 |
|
|
'access arguments' => array('access content'),
|
| 488 |
|
|
'type' => MENU_DEFAULT_LOCAL_TASK,
|
| 489 |
|
|
);
|
| 490 |
|
|
|
| 491 |
|
|
$items['cdm_dataportal/search/taxon_by_description'] = array(
|
| 492 |
579c485d
|
Andreas Kohlbecker
|
'title' => 'By content category', // will be passed through t()
|
| 493 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
|
| 494 |
|
|
'access arguments' => array('access content'),
|
| 495 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 496 |
|
|
);
|
| 497 |
|
|
|
| 498 |
|
|
$items['cdm_dataportal/search/results/taxon'] = array(
|
| 499 |
|
|
'page callback' => 'cdm_dataportal_view_search_results_taxon',
|
| 500 |
|
|
'access arguments' => array('access content'),
|
| 501 |
|
|
'type' => MENU_CALLBACK,
|
| 502 |
|
|
);
|
| 503 |
|
|
/*
|
| 504 |
|
|
$items['cdm/xml2json'] = array(
|
| 505 |
|
|
'page callback' => 'cdm_view_xml2json',
|
| 506 |
|
|
'access arguments' => array('access content'),
|
| 507 |
|
|
'type' => MENU_CALLBACK,
|
| 508 |
|
|
);
|
| 509 |
|
|
*/
|
| 510 |
|
|
|
| 511 |
|
|
// if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
|
| 512 |
|
|
// User configuration of cdm_dataportal.
|
| 513 |
|
|
$items['user/%/cdm_dataportal'] = array(
|
| 514 |
|
|
'title' => 'cdm_dataportal',
|
| 515 |
|
|
'access arguments' => array('access content'),
|
| 516 |
|
|
'page callback' => 'drupal_get_form',
|
| 517 |
|
|
'page arguments' => array('cdm_dataportal_user_form'),
|
| 518 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 519 |
|
|
'weight' => 10,
|
| 520 |
|
|
);
|
| 521 |
|
|
// }
|
| 522 |
|
|
|
| 523 |
|
|
// 'May not cache' in D5.
|
| 524 |
|
|
$items['cdm_dataportal/name/%'] = array(
|
| 525 |
|
|
// 'page callback' => 'cdm_dataportal_view_name',
|
| 526 |
|
|
'page callback' => 'cdm_dataportal_name_page_view',
|
| 527 |
|
|
'page arguments' => array(2, 3, 4),
|
| 528 |
|
|
'access arguments' => array('access content'),
|
| 529 |
|
|
'type' => MENU_CALLBACK,
|
| 530 |
|
|
);
|
| 531 |
|
|
|
| 532 |
6f1a217c
|
Andreas Kohlbecker
|
// --- Local tasks for Taxon.
|
| 533 |
|
|
// --- tabbed taxon page
|
| 534 |
6657531f
|
Andreas Kohlbecker
|
if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
|
| 535 |
|
|
$items['cdm_dataportal/taxon/%'] = array(
|
| 536 |
7cc085da
|
Andreas Kohlbecker
|
'title' => '@tabname',
|
| 537 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'General'))),
|
| 538 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 539 |
|
|
'access arguments' => array('access content'),
|
| 540 |
|
|
'type' => MENU_CALLBACK,
|
| 541 |
|
|
'weight' => 1,
|
| 542 |
|
|
'page arguments' => array(2, "description")
|
| 543 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 544 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 545 |
|
|
|
| 546 |
|
|
$items['cdm_dataportal/taxon/%/all'] = array(
|
| 547 |
7cc085da
|
Andreas Kohlbecker
|
'title' => '@tabname',
|
| 548 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'General'))),
|
| 549 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 550 |
|
|
'access arguments' => array('access content'),
|
| 551 |
|
|
'type' => MENU_CALLBACK,
|
| 552 |
|
|
'weight' => 2,
|
| 553 |
|
|
'page arguments' => array(2, "all")
|
| 554 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 555 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 556 |
|
|
|
| 557 |
|
|
$items['cdm_dataportal/taxon/%/description'] = array(
|
| 558 |
7cc085da
|
Andreas Kohlbecker
|
'title' => '@tabname',
|
| 559 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'General'))),
|
| 560 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 561 |
|
|
'access arguments' => array('access content'),
|
| 562 |
|
|
'type' => MENU_DEFAULT_LOCAL_TASK,
|
| 563 |
|
|
'weight' => 2,
|
| 564 |
|
|
'page arguments' => array(2, "description")
|
| 565 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 566 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 567 |
|
|
|
| 568 |
|
|
$items['cdm_dataportal/taxon/%/synonymy'] = array(
|
| 569 |
7cc085da
|
Andreas Kohlbecker
|
'title' => '@tabname',
|
| 570 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy'))),
|
| 571 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 572 |
|
|
'access arguments' => array('access content'),
|
| 573 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 574 |
|
|
'weight' => 4,
|
| 575 |
|
|
'page arguments' => array(2, "synonymy", 4)
|
| 576 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid and ...
|
| 577 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 578 |
7cc085da
|
Andreas Kohlbecker
|
$items['cdm_dataportal/taxon/%/images'] = array( // Images
|
| 579 |
|
|
'title' => '@tabname',
|
| 580 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Images'))),
|
| 581 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 582 |
|
|
'access arguments' => array('access content'),
|
| 583 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 584 |
|
|
'weight' => 5,
|
| 585 |
|
|
'page arguments' => array(2, "images")
|
| 586 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 587 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 588 |
|
|
|
| 589 |
7cc085da
|
Andreas Kohlbecker
|
$items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
|
| 590 |
|
|
'title' => '@tabname',
|
| 591 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens'))),
|
| 592 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 593 |
|
|
'access arguments' => array('access content'),
|
| 594 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 595 |
|
|
'weight' => 6,
|
| 596 |
|
|
'page arguments' => array(2, "specimens")
|
| 597 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 598 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 599 |
|
|
|
| 600 |
7cc085da
|
Andreas Kohlbecker
|
$items['cdm_dataportal/taxon/%/keys'] = array( // Keys
|
| 601 |
|
|
'title' => '@tabname',
|
| 602 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys'))),
|
| 603 |
6657531f
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 604 |
|
|
'access arguments' => array('access content'),
|
| 605 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 606 |
|
|
'weight' => 6,
|
| 607 |
|
|
'page arguments' => array(2, "keys")
|
| 608 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 609 |
|
|
);
|
| 610 |
|
|
|
| 611 |
7cc085da
|
Andreas Kohlbecker
|
$items['cdm_dataportal/taxon/%/experts'] = array( // Experts
|
| 612 |
|
|
'title' => '@tabname',
|
| 613 |
|
|
'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Experts'))),
|
| 614 |
|
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
| 615 |
|
|
'access arguments' => array('access content'),
|
| 616 |
|
|
'type' => MENU_LOCAL_TASK,
|
| 617 |
|
|
'weight' => 6,
|
| 618 |
|
|
'page arguments' => array(2, "experts")
|
| 619 |
7663cd0b
|
Andreas Kohlbecker
|
, // Expected callback arguments: taxon_uuid.
|
| 620 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 621 |
93ae67cc
|
Patrick Plitzner
|
|
| 622 |
04a1d647
|
Patrick Plitzner
|
$items['cdm_dataportal/taxon/autosuggest'] = array(
|
| 623 |
|
|
'page callback' => 'cdm_dataportal_taxon_autosuggest',
|
| 624 |
|
|
'access arguments' => array('access taxon autosuggest'),
|
| 625 |
93ae67cc
|
Patrick Plitzner
|
'type' => MENU_CALLBACK
|
| 626 |
|
|
);
|
| 627 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 628 |
|
|
|
| 629 |
6f1a217c
|
Andreas Kohlbecker
|
// --- refresh link for all cdmnode types
|
| 630 |
|
|
foreach (cdm_get_nodetypes() as $type=>$name) {
|
| 631 |
|
|
$items['cdm_dataportal/' . $name . '/%/refresh'] = array(
|
| 632 |
7cc085da
|
Andreas Kohlbecker
|
'title' => 'Refresh',
|
| 633 |
6f1a217c
|
Andreas Kohlbecker
|
'page callback' => 'cdm_dataportal_refresh_node',
|
| 634 |
3113db26
|
Andreas Kohlbecker
|
'access arguments' => array('administer cdm_dataportal'),
|
| 635 |
6f1a217c
|
Andreas Kohlbecker
|
'type' => MENU_LOCAL_TASK,
|
| 636 |
|
|
'weight' => 100,
|
| 637 |
|
|
'page arguments' => array($name, 2)
|
| 638 |
|
|
);
|
| 639 |
|
|
}
|
| 640 |
|
|
|
| 641 |
6657531f
|
Andreas Kohlbecker
|
return $items;
|
| 642 |
|
|
}
|
| 643 |
|
|
|
| 644 |
|
|
/**
|
| 645 |
b85ab055
|
Andreas Kohlbecker
|
* Implements hook_init().
|
| 646 |
|
|
*
|
| 647 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 648 |
|
|
function cdm_dataportal_init() {
|
| 649 |
5ea8b301
|
Andreas Kohlbecker
|
//FIXME To add CSS or JS that should be present on all pages, modules
|
| 650 |
|
|
// should not implement this hook, but declare these files in their .info file.
|
| 651 |
6657531f
|
Andreas Kohlbecker
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
|
| 652 |
|
|
// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
|
| 653 |
|
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
|
| 654 |
2dd59bb5
|
Andreas Kohlbecker
|
|
| 655 |
|
|
if(variable_get('cdm_debug_mode', FALSE)){
|
| 656 |
|
|
$file = 'temporary://drupal_debug.txt';
|
| 657 |
|
|
file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
|
| 658 |
|
|
}
|
| 659 |
5611d467
|
Andreas Kohlbecker
|
|
| 660 |
|
|
$bibliography_settings = get_bibliography_settings();
|
| 661 |
57d513cb
|
Andreas Kohlbecker
|
$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
|
| 662 |
|
|
FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
|
| 663 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 664 |
|
|
|
| 665 |
6f1a217c
|
Andreas Kohlbecker
|
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
|
| 666 |
|
|
|
| 667 |
|
|
$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
|
| 668 |
|
|
|
| 669 |
|
|
if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
|
| 670 |
|
|
// force reloading of all and notify user about this special loading
|
| 671 |
|
|
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: ')
|
| 672 |
|
|
. l('Back to tabbed taxon page', $base_path));
|
| 673 |
|
|
$base_path .= '/all';
|
| 674 |
|
|
} else {
|
| 675 |
|
|
drupal_set_message(t('The level 2 cache has been cleared for this page'));
|
| 676 |
|
|
}
|
| 677 |
|
|
|
| 678 |
|
|
$parameters['cacheL2_refresh'] ='1';
|
| 679 |
|
|
|
| 680 |
|
|
|
| 681 |
|
|
drupal_goto($base_path, array('query' => $parameters));
|
| 682 |
|
|
}
|
| 683 |
|
|
|
| 684 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 685 |
|
|
* The function generate form for own user cdm dataportal configurations.
|
| 686 |
|
|
*/
|
| 687 |
|
|
function cdm_dataportal_user_form($form, &$form_state) {
|
| 688 |
36818236
|
Andreas Kohlbecker
|
|
| 689 |
6657531f
|
Andreas Kohlbecker
|
global $user;
|
| 690 |
|
|
$checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
|
| 691 |
|
|
|
| 692 |
8e1dc7ec
|
Andreas Kohlbecker
|
$form['taxon_page_tabs'] = array(
|
| 693 |
|
|
'#type' => 'fieldset',
|
| 694 |
36818236
|
Andreas Kohlbecker
|
'#tree' => true,
|
| 695 |
8e1dc7ec
|
Andreas Kohlbecker
|
'#title' => t('Taxon page tabs'),
|
| 696 |
|
|
);
|
| 697 |
36818236
|
Andreas Kohlbecker
|
|
| 698 |
|
|
$form['taxon_page_tabs']['user_defined'] = array(
|
| 699 |
6657531f
|
Andreas Kohlbecker
|
'#type' => 'checkbox',
|
| 700 |
|
|
'#title' => t('Activate user default configuration'),
|
| 701 |
|
|
'#default_value' => variable_get($checkbox_value, 0),
|
| 702 |
|
|
'#description' => t('Check this if you want configure your own default tab from the below menu.'),
|
| 703 |
|
|
);
|
| 704 |
|
|
|
| 705 |
36818236
|
Andreas Kohlbecker
|
$form['taxon_page_tabs']['default_tab'] = array(
|
| 706 |
6657531f
|
Andreas Kohlbecker
|
'#type' => 'select',
|
| 707 |
|
|
'#title' => t('Default tab to display'),
|
| 708 |
|
|
'#default_value' => get_default_taxon_tab(TRUE),
|
| 709 |
|
|
'#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
|
| 710 |
|
|
'#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
|
| 711 |
|
|
<strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
|
| 712 |
36818236
|
Andreas Kohlbecker
|
to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
|
| 713 |
|
|
);
|
| 714 |
|
|
|
| 715 |
|
|
|
| 716 |
f695daf4
|
Andreas Kohlbecker
|
if(false){
|
| 717 |
|
|
$form['developer_options'] = array(
|
| 718 |
|
|
'#type' => 'fieldset',
|
| 719 |
|
|
'#tree' => true,
|
| 720 |
|
|
'#title' => t('Developer options'),
|
| 721 |
|
|
);
|
| 722 |
|
|
|
| 723 |
|
|
$form['developer_options']['show_render_path'] = array(
|
| 724 |
|
|
'#type' => 'checkbox',
|
| 725 |
|
|
'#title' => t('Display the render path for each taxon name.'),
|
| 726 |
|
|
'#default_value' => variable_get($checkbox_value, 0),
|
| 727 |
|
|
'#description' => t('This option is very helpful if you are editing the !link for taxon names.',
|
| 728 |
|
|
array(
|
| 729 |
|
|
'!link' => l(
|
| 730 |
|
|
'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
|
| 731 |
|
|
)
|
| 732 |
|
|
),
|
| 733 |
|
|
);
|
| 734 |
|
|
}
|
| 735 |
6657531f
|
Andreas Kohlbecker
|
|
| 736 |
|
|
$form['submit'] = array(
|
| 737 |
|
|
'#type' => 'submit',
|
| 738 |
|
|
'#value' => t('Submit'),
|
| 739 |
|
|
);
|
| 740 |
|
|
|
| 741 |
|
|
return $form;
|
| 742 |
|
|
}
|
| 743 |
|
|
|
| 744 |
|
|
/**
|
| 745 |
|
|
* Form submission handler for user_form().
|
| 746 |
|
|
*
|
| 747 |
|
|
* Submits the user cdm dataportal configurations.
|
| 748 |
|
|
*/
|
| 749 |
|
|
function cdm_dataportal_user_form_submit($form, &$form_state) {
|
| 750 |
|
|
global $user;
|
| 751 |
|
|
$msg_type = 'status';
|
| 752 |
|
|
$username = $user->name;
|
| 753 |
|
|
$variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
|
| 754 |
|
|
|
| 755 |
36818236
|
Andreas Kohlbecker
|
// FIXME: this is completely wrong, see user_profile_form_submit()
|
| 756 |
|
|
|
| 757 |
|
|
// it is only possible to change own user settings
|
| 758 |
|
|
if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
|
| 759 |
|
|
|
| 760 |
|
|
// DEFAULT_TAXON_TAB
|
| 761 |
6657531f
|
Andreas Kohlbecker
|
$variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
|
| 762 |
36818236
|
Andreas Kohlbecker
|
variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
|
| 763 |
|
|
variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
|
| 764 |
|
|
if ($form_state['values']['taxon_page_tabs']['user_defined']) {
|
| 765 |
6657531f
|
Andreas Kohlbecker
|
drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
|
| 766 |
|
|
drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
|
| 767 |
|
|
'!tab' => $variable[variable_get($variable_to_use, 0)],
|
| 768 |
|
|
'!user' => $username,
|
| 769 |
|
|
))), $msg_type);
|
| 770 |
|
|
}
|
| 771 |
|
|
else {
|
| 772 |
|
|
drupal_set_message(check_plain(t('The user default tab wont be used for
|
| 773 |
|
|
the next taxon site, check the box if you want to use the user default configuration.')));
|
| 774 |
|
|
}
|
| 775 |
36818236
|
Andreas Kohlbecker
|
|
| 776 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 777 |
|
|
else {
|
| 778 |
36818236
|
Andreas Kohlbecker
|
// Problem with the user id => variables wont be saved.
|
| 779 |
6657531f
|
Andreas Kohlbecker
|
$msg_type = 'warning';
|
| 780 |
|
|
drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
|
| 781 |
|
|
}
|
| 782 |
|
|
}
|
| 783 |
|
|
|
| 784 |
|
|
/**
|
| 785 |
|
|
* Implements hook_block_info().
|
| 786 |
|
|
*/
|
| 787 |
|
|
function cdm_dataportal_block_info() {
|
| 788 |
|
|
|
| 789 |
|
|
// $block[0]["info"] = t("CDM DataPortal DevLinks");
|
| 790 |
|
|
// $block[1]["info"] = t("CDM DataPortal Credits");
|
| 791 |
fc13aa30
|
Andreas Kohlbecker
|
$block["2"] = array(
|
| 792 |
|
|
"info" => t("CDM Search Taxa"),
|
| 793 |
|
|
"cache" => DRUPAL_NO_CACHE
|
| 794 |
|
|
);
|
| 795 |
6657531f
|
Andreas Kohlbecker
|
// $block[3]["info"] = t("CDM Filters");
|
| 796 |
|
|
$block["4"]["info"] = t("CDM Dataportal Print");
|
| 797 |
|
|
$block["keys"]["info"] = t("CDM identification keys");
|
| 798 |
|
|
$block["fundedByEDIT"]["info"] = t('Funded by EDIT');
|
| 799 |
f9a3d0f6
|
Andreas Kohlbecker
|
$block["classification_breadcrumbs"] = array(
|
| 800 |
|
|
'info' => t('Classification breadcrumbs'),
|
| 801 |
|
|
'cache' => DRUPAL_CACHE_PER_PAGE
|
| 802 |
|
|
);
|
| 803 |
bc400a17
|
Andreas Kohlbecker
|
$block["taxonomic_children"] = array(
|
| 804 |
|
|
'info' => t('Taxonomic children'),
|
| 805 |
|
|
'cache' => DRUPAL_CACHE_PER_PAGE
|
| 806 |
|
|
);
|
| 807 |
6657531f
|
Andreas Kohlbecker
|
|
| 808 |
|
|
return $block;
|
| 809 |
|
|
}
|
| 810 |
|
|
|
| 811 |
|
|
/**
|
| 812 |
|
|
* Implements hook_block_view().
|
| 813 |
|
|
*/
|
| 814 |
|
|
function cdm_dataportal_block_view($delta) {
|
| 815 |
|
|
// TODO Rename block deltas (e.g. '2') to readable strings.
|
| 816 |
|
|
switch ($delta) {
|
| 817 |
|
|
// case 'delta-1':
|
| 818 |
|
|
// $block['subject'] = t('Credits');
|
| 819 |
|
|
// $block['content'] = theme('cdm_credits');
|
| 820 |
|
|
// return $block;
|
| 821 |
|
|
case '2':
|
| 822 |
|
|
$block['subject'] = t('Search taxa');
|
| 823 |
191f88fd
|
Andreas Kohlbecker
|
$form = drupal_get_form('cdm_dataportal_search_taxon_form');
|
| 824 |
|
|
$block['content'] = drupal_render($form);
|
| 825 |
6657531f
|
Andreas Kohlbecker
|
|
| 826 |
|
|
if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
|
| 827 |
|
|
$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
|
| 828 |
|
|
}
|
| 829 |
|
|
return $block;
|
| 830 |
|
|
case '4':
|
| 831 |
c8234bdf
|
Andreas Kohlbecker
|
$block['subject'] = '';
|
| 832 |
6657531f
|
Andreas Kohlbecker
|
$block['content'] = theme('cdm_print_button');
|
| 833 |
|
|
return $block;
|
| 834 |
|
|
case "keys":
|
| 835 |
|
|
$block['subject'] = t('Identification Keys');
|
| 836 |
|
|
$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
|
| 837 |
|
|
return $block;
|
| 838 |
|
|
case "fundedByEDIT":
|
| 839 |
|
|
// t('Funded by EDIT');
|
| 840 |
|
|
$text = '<none>';
|
| 841 |
|
|
$block['subject'] = $text;
|
| 842 |
889c74b7
|
Andreas Kohlbecker
|
$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
|
| 843 |
|
|
$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
|
| 844 |
6657531f
|
Andreas Kohlbecker
|
'attributes' => array("target" => "EDIT"),
|
| 845 |
|
|
'absolute' => TRUE,
|
| 846 |
|
|
'html' => TRUE,
|
| 847 |
|
|
));
|
| 848 |
|
|
return $block;
|
| 849 |
f9a3d0f6
|
Andreas Kohlbecker
|
case 'classification_breadcrumbs':
|
| 850 |
0af3ce28
|
Andreas Kohlbecker
|
$taxon_uuid = get_current_taxon_uuid();
|
| 851 |
38da4e54
|
Andreas Kohlbecker
|
$block['subject'] = '<none>';
|
| 852 |
|
|
$block['content'] = compose_classification_breadcrumbs($taxon_uuid);
|
| 853 |
|
|
return $block;
|
| 854 |
bc400a17
|
Andreas Kohlbecker
|
case 'taxonomic_children':
|
| 855 |
|
|
$taxon_uuid = get_current_taxon_uuid();
|
| 856 |
|
|
$block['subject'] = '<none>';
|
| 857 |
|
|
$block['content'] = compose_taxonomic_children($taxon_uuid);
|
| 858 |
|
|
return $block;
|
| 859 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 860 |
|
|
}
|
| 861 |
|
|
|
| 862 |
0af3ce28
|
Andreas Kohlbecker
|
/**
|
| 863 |
|
|
* Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
|
| 864 |
|
|
*
|
| 865 |
|
|
* @return string
|
| 866 |
|
|
* the taxon uuid or NULL
|
| 867 |
|
|
*/
|
| 868 |
|
|
function get_current_taxon_uuid()
|
| 869 |
|
|
{
|
| 870 |
|
|
static $taxon_uuid;
|
| 871 |
|
|
|
| 872 |
|
|
if(!isset($taxon_uuid)){
|
| 873 |
|
|
if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
|
| 874 |
|
|
$taxon_uuid = $_REQUEST['currentTaxon'];
|
| 875 |
|
|
} else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
|
| 876 |
|
|
$taxon_uuid = arg(2);
|
| 877 |
|
|
} else {
|
| 878 |
|
|
$taxon_uuid = null;
|
| 879 |
|
|
}
|
| 880 |
|
|
}
|
| 881 |
|
|
|
| 882 |
|
|
return $taxon_uuid;
|
| 883 |
|
|
}
|
| 884 |
|
|
|
| 885 |
|
|
/**
|
| 886 |
|
|
* Returns the currently classification tree in use.
|
| 887 |
|
|
*
|
| 888 |
|
|
* @return string
|
| 889 |
|
|
* The uuid of the currently focused classification
|
| 890 |
|
|
*/
|
| 891 |
|
|
function get_current_classification_uuid() {
|
| 892 |
|
|
if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
|
| 893 |
|
|
return $_SESSION['cdm']['taxonomictree_uuid'];
|
| 894 |
|
|
}
|
| 895 |
|
|
else {
|
| 896 |
|
|
return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
|
| 897 |
|
|
}
|
| 898 |
|
|
}
|
| 899 |
|
|
|
| 900 |
6657531f
|
Andreas Kohlbecker
|
/*
|
| 901 |
|
|
function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
|
| 902 |
|
|
$_SESSION['cdm'] = NULL;
|
| 903 |
|
|
if(is_string($cdm_ws_uri_update)){
|
| 904 |
|
|
$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
|
| 905 |
|
|
}
|
| 906 |
|
|
}
|
| 907 |
|
|
|
| 908 |
|
|
function cdm_dataportal_session_validate(){
|
| 909 |
|
|
if(!isset($_SESSION['cdm']['ws_uri'])){
|
| 910 |
|
|
$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
|
| 911 |
|
|
} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
|
| 912 |
|
|
cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
|
| 913 |
|
|
}
|
| 914 |
|
|
}
|
| 915 |
|
|
*/
|
| 916 |
|
|
|
| 917 |
|
|
/**
|
| 918 |
d7588d36
|
Andreas Kohlbecker
|
* creates a selector form for taxonomic trees.
|
| 919 |
|
|
*
|
| 920 |
0af3ce28
|
Andreas Kohlbecker
|
* @return array
|
| 921 |
|
|
* a drupal form array
|
| 922 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 923 |
|
|
function cdm_taxonomictree_selector() {
|
| 924 |
|
|
_add_js_treeselector();
|
| 925 |
|
|
|
| 926 |
a8a8f23c
|
Andreas Kohlbecker
|
$form = drupal_get_form('cdm_taxonomictree_selector_form');
|
| 927 |
d7588d36
|
Andreas Kohlbecker
|
return $form;
|
| 928 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 929 |
|
|
|
| 930 |
|
|
/**
|
| 931 |
|
|
* @todo Please document this function.
|
| 932 |
|
|
* @see http://drupal.org/node/1354
|
| 933 |
0af3ce28
|
Andreas Kohlbecker
|
*
|
| 934 |
|
|
* @deprecated use compose_classification_selector instead
|
| 935 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 936 |
|
|
function cdm_taxonomictree_selector_form($form, &$form_state) {
|
| 937 |
|
|
|
| 938 |
|
|
$url = url('cdm_api/setvalue/session', array('query' => NULL));
|
| 939 |
|
|
$form['#action'] = $url;
|
| 940 |
|
|
|
| 941 |
|
|
$form['var'] = array(
|
| 942 |
|
|
'#weight' => -3,
|
| 943 |
|
|
'#type' => 'hidden',
|
| 944 |
|
|
'#value' => '[cdm][taxonomictree_uuid]',
|
| 945 |
|
|
);
|
| 946 |
|
|
|
| 947 |
|
|
$destination_array = drupal_get_destination();
|
| 948 |
|
|
$destination = $destination_array['destination'];
|
| 949 |
|
|
|
| 950 |
|
|
$form['destination'] = array(
|
| 951 |
|
|
'#weight' => -3,
|
| 952 |
|
|
'#type' => 'hidden',
|
| 953 |
|
|
'#value' => $destination,
|
| 954 |
|
|
);
|
| 955 |
|
|
|
| 956 |
26fb3778
|
Andreas Kohlbecker
|
$options = cdm_get_taxontrees_as_options();
|
| 957 |
|
|
$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
|
| 958 |
|
|
if($taxontree_includes){
|
| 959 |
|
|
$filtered_options = array();
|
| 960 |
|
|
foreach($options as $uuid=>$label){
|
| 961 |
|
|
if(!empty($taxontree_includes[$uuid])){
|
| 962 |
|
|
$filtered_options[$uuid] = $label;
|
| 963 |
|
|
}
|
| 964 |
|
|
}
|
| 965 |
|
|
$options = $filtered_options;
|
| 966 |
|
|
}
|
| 967 |
|
|
|
| 968 |
6657531f
|
Andreas Kohlbecker
|
$form['val'] = array(
|
| 969 |
|
|
'#type' => 'select',
|
| 970 |
|
|
'#title' => t('Available classifications'),
|
| 971 |
7663cd0b
|
Andreas Kohlbecker
|
'#default_value' => get_current_classification_uuid(),
|
| 972 |
26fb3778
|
Andreas Kohlbecker
|
'#options' => $options,
|
| 973 |
0af3ce28
|
Andreas Kohlbecker
|
'#attributes' => array('class' => array('highlite-first-child')),
|
| 974 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 975 |
|
|
|
| 976 |
|
|
return $form;
|
| 977 |
|
|
|
| 978 |
|
|
}
|
| 979 |
|
|
|
| 980 |
0af3ce28
|
Andreas Kohlbecker
|
/**
|
| 981 |
|
|
*
|
| 982 |
|
|
* @ingroup compose
|
| 983 |
|
|
*/
|
| 984 |
|
|
function compose_classification_selector() {
|
| 985 |
|
|
|
| 986 |
|
|
$destination_array = drupal_get_destination();
|
| 987 |
|
|
$destination = $destination_array['destination'];
|
| 988 |
|
|
|
| 989 |
|
|
$options = cdm_get_taxontrees_as_options();
|
| 990 |
|
|
$items = array();
|
| 991 |
|
|
$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
|
| 992 |
|
|
|
| 993 |
|
|
$current_classification_uuid = get_current_classification_uuid();
|
| 994 |
|
|
|
| 995 |
|
|
|
| 996 |
|
|
foreach($options as $uuid=>$label){
|
| 997 |
|
|
if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
|
| 998 |
|
|
|
| 999 |
|
|
$class_attributes = '';
|
| 1000 |
|
|
if($current_classification_uuid == $uuid){
|
| 1001 |
|
|
$class_attributes = array('focused');
|
| 1002 |
|
|
}
|
| 1003 |
|
|
$items[] = array(
|
| 1004 |
|
|
'data' => l($label,
|
| 1005 |
|
|
'cdm_api/setvalue/session',
|
| 1006 |
|
|
array(
|
| 1007 |
|
|
'query' => array(
|
| 1008 |
|
|
'destination' => $destination,
|
| 1009 |
|
|
'val' => $uuid,
|
| 1010 |
|
|
'var' => '[cdm][taxonomictree_uuid]'
|
| 1011 |
|
|
),
|
| 1012 |
|
|
)
|
| 1013 |
|
|
),
|
| 1014 |
|
|
'class' => $class_attributes
|
| 1015 |
|
|
);
|
| 1016 |
|
|
}
|
| 1017 |
|
|
}
|
| 1018 |
|
|
|
| 1019 |
|
|
$render_array = array(
|
| 1020 |
|
|
'#theme' => 'item_list',
|
| 1021 |
|
|
'#type' => 'ul',
|
| 1022 |
|
|
'#items' => $items
|
| 1023 |
|
|
);
|
| 1024 |
|
|
|
| 1025 |
|
|
return $render_array;
|
| 1026 |
|
|
}
|
| 1027 |
|
|
|
| 1028 |
|
|
|
| 1029 |
6657531f
|
Andreas Kohlbecker
|
/* UNREACHABLE since action of form directly links to view.
|
| 1030 |
|
|
function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
|
| 1031 |
|
|
|
| 1032 |
|
|
$_SESSION['cdm']['search'] = $form_values;
|
| 1033 |
|
|
//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
|
| 1034 |
|
|
return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
|
| 1035 |
|
|
//$paramstr = compose_url_prameterstr($form_values);
|
| 1036 |
|
|
//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
|
| 1037 |
|
|
}
|
| 1038 |
|
|
*/
|
| 1039 |
|
|
/* ====================== menu callback functions ====================== */
|
| 1040 |
|
|
/**
|
| 1041 |
|
|
* @todo Please document this function.
|
| 1042 |
|
|
* @see http://drupal.org/node/1354
|
| 1043 |
|
|
*/
|
| 1044 |
|
|
/*
|
| 1045 |
|
|
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
|
| 1046 |
|
|
static $comment_node_disabled = 0;
|
| 1047 |
|
|
static $comment_node_read_only = 1;
|
| 1048 |
|
|
static $comment_node_read_write = 2;
|
| 1049 |
|
|
|
| 1050 |
|
|
if ($form_id == 'node_type_form'
|
| 1051 |
|
|
&& isset($form['identity']['type'])
|
| 1052 |
|
|
&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
|
| 1053 |
|
|
) {
|
| 1054 |
|
|
$form['workflow']['comment'] = array(
|
| 1055 |
|
|
'#type' => 'radios',
|
| 1056 |
|
|
'#title' => t('Default comment setting'),
|
| 1057 |
|
|
'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
|
| 1058 |
|
|
'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
|
| 1059 |
|
|
'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
|
| 1060 |
|
|
);
|
| 1061 |
|
|
}
|
| 1062 |
|
|
}
|
| 1063 |
|
|
*/
|
| 1064 |
|
|
|
| 1065 |
|
|
/**
|
| 1066 |
|
|
* Displays a list of the known taxonomic names.
|
| 1067 |
|
|
*
|
| 1068 |
|
|
* When the list of taxonomic names is displayed, long lists are split up into
|
| 1069 |
|
|
* multiple pages.
|
| 1070 |
|
|
*
|
| 1071 |
|
|
* TODO: Parameters are still preliminary.
|
| 1072 |
|
|
*
|
| 1073 |
|
|
* @param string $beginsWith
|
| 1074 |
|
|
* @param string $page
|
| 1075 |
|
|
* Page number to diplay defaults to page 1.
|
| 1076 |
|
|
* @param bool $onlyAccepted
|
| 1077 |
|
|
*/
|
| 1078 |
|
|
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
|
| 1079 |
|
|
|
| 1080 |
|
|
$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
|
| 1081 |
|
|
|
| 1082 |
|
|
/*
|
| 1083 |
|
|
// FIXME the filter for accepted names will be a form element, thus this
|
| 1084 |
|
|
// widget should be generated via form api preferably as block.
|
| 1085 |
|
|
$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
|
| 1086 |
|
|
$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
|
| 1087 |
|
|
$out .= theme('cdm_listof_taxa', $taxonPager);
|
| 1088 |
|
|
return $out;
|
| 1089 |
|
|
*/
|
| 1090 |
|
|
}
|
| 1091 |
|
|
|
| 1092 |
|
|
/**
|
| 1093 |
|
|
* @todo Please document this function.
|
| 1094 |
|
|
* @see http://drupal.org/node/1354
|
| 1095 |
|
|
*/
|
| 1096 |
|
|
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
|
| 1097 |
f26245c8
|
Andreas Kohlbecker
|
|
| 1098 |
|
|
cdm_check_valid_portal_page();
|
| 1099 |
|
|
|
| 1100 |
6657531f
|
Andreas Kohlbecker
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
| 1101 |
|
|
return theme('cdm_reference_page', array('reference' => $reference));
|
| 1102 |
|
|
}
|
| 1103 |
|
|
|
| 1104 |
|
|
/**
|
| 1105 |
b2ebf0d3
|
Andreas Kohlbecker
|
* Creates a view on a all references contained in the portal.
|
| 1106 |
b5dca1e2
|
Andreas Kohlbecker
|
*
|
| 1107 |
|
|
* This function is used at the path cdm_dataportal/reference/list
|
| 1108 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1109 |
|
|
function cdm_dataportal_view_reference_list($pageNumber) {
|
| 1110 |
|
|
$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
|
| 1111 |
b2ebf0d3
|
Andreas Kohlbecker
|
cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
|
| 1112 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1113 |
|
|
|
| 1114 |
|
|
/**
|
| 1115 |
|
|
* @todo Please document this function.
|
| 1116 |
|
|
* @see http://drupal.org/node/1354
|
| 1117 |
|
|
*/
|
| 1118 |
|
|
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
|
| 1119 |
f26245c8
|
Andreas Kohlbecker
|
|
| 1120 |
|
|
cdm_check_valid_portal_page();
|
| 1121 |
|
|
|
| 1122 |
6657531f
|
Andreas Kohlbecker
|
$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
|
| 1123 |
|
|
return theme('cdm_media_page', array(
|
| 1124 |
|
|
'media' => $media,
|
| 1125 |
|
|
'mediarepresentation_uuid' => $mediarepresentation_uuid,
|
| 1126 |
|
|
'partId' => $part,
|
| 1127 |
|
|
));
|
| 1128 |
|
|
}
|
| 1129 |
|
|
|
| 1130 |
|
|
/**
|
| 1131 |
|
|
* @todo Please document this function.
|
| 1132 |
|
|
* @see http://drupal.org/node/1354
|
| 1133 |
|
|
*/
|
| 1134 |
|
|
function _load_taxonBase(&$taxonBase) {
|
| 1135 |
|
|
if (isset($taxonBase->uuid)) {
|
| 1136 |
|
|
$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
|
| 1137 |
|
|
$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
|
| 1138 |
|
|
$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
|
| 1139 |
|
|
}
|
| 1140 |
|
|
}
|
| 1141 |
|
|
|
| 1142 |
9438ad3a
|
Andreas Kohlbecker
|
/**
|
| 1143 |
|
|
* Loads the media associated to the given taxon from the cdm server.
|
| 1144 |
|
|
* The aggregation settings regarding taxon relathionships and
|
| 1145 |
|
|
* taxonnomic childen are taken into account.
|
| 1146 |
|
|
*
|
| 1147 |
|
|
* The media lists are cached in a static variable.
|
| 1148 |
|
|
*
|
| 1149 |
|
|
* @param Taxon $taxon
|
| 1150 |
|
|
* A CDM Taxon entitiy
|
| 1151 |
|
|
*
|
| 1152 |
|
|
* @return array
|
| 1153 |
|
|
* An array of CDM Media entities
|
| 1154 |
|
|
*
|
| 1155 |
|
|
*/
|
| 1156 |
|
|
function _load_media_for_taxon($taxon) {
|
| 1157 |
|
|
|
| 1158 |
|
|
static $media = NULL;
|
| 1159 |
|
|
|
| 1160 |
|
|
if(!isset($media)) {
|
| 1161 |
|
|
$media = array();
|
| 1162 |
|
|
}
|
| 1163 |
|
|
if (!isset($media[$taxon->uuid])) {
|
| 1164 |
|
|
|
| 1165 |
f19f47fa
|
Andreas Kohlbecker
|
// --- GET Images --- //
|
| 1166 |
|
|
$mediaQueryParameters = array(
|
| 1167 |
|
|
"type" => "ImageFile",
|
| 1168 |
|
|
);
|
| 1169 |
|
|
|
| 1170 |
|
|
$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
|
| 1171 |
|
|
$mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
|
| 1172 |
a950f2f9
|
Andreas Kohlbecker
|
$mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
|
| 1173 |
|
|
|
| 1174 |
|
|
$taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
|
| 1175 |
|
|
$mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
|
| 1176 |
|
|
$mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
|
| 1177 |
|
|
$mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
|
| 1178 |
9438ad3a
|
Andreas Kohlbecker
|
|
| 1179 |
f19f47fa
|
Andreas Kohlbecker
|
$ws_endpoint = NULL;
|
| 1180 |
9438ad3a
|
Andreas Kohlbecker
|
if ( variable_get('cdm_images_include_children', 0) == 0) {
|
| 1181 |
|
|
$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
|
| 1182 |
|
|
} else {
|
| 1183 |
|
|
$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
|
| 1184 |
|
|
}
|
| 1185 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 1186 |
|
|
$media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
|
| 1187 |
|
|
array(
|
| 1188 |
|
|
$taxon->uuid,
|
| 1189 |
|
|
),
|
| 1190 |
9438ad3a
|
Andreas Kohlbecker
|
queryString($mediaQueryParameters)
|
| 1191 |
|
|
);
|
| 1192 |
|
|
}
|
| 1193 |
|
|
|
| 1194 |
|
|
return $media[$taxon->uuid];
|
| 1195 |
|
|
}
|
| 1196 |
|
|
|
| 1197 |
|
|
/**
|
| 1198 |
|
|
*
|
| 1199 |
|
|
* @param Taxon $taxon
|
| 1200 |
|
|
* A CDM Taxon entitiy
|
| 1201 |
|
|
*
|
| 1202 |
|
|
* @return array
|
| 1203 |
|
|
* An array of CDM SpecimenOrObservation entities
|
| 1204 |
|
|
*
|
| 1205 |
|
|
function _load_occurences_for_taxon($taxon){
|
| 1206 |
|
|
|
| 1207 |
|
|
static $occurences = NULL;
|
| 1208 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 1209 |
|
|
if(!isset($occurences)) {
|
| 1210 |
|
|
$occurences = array();
|
| 1211 |
|
|
}
|
| 1212 |
9438ad3a
|
Andreas Kohlbecker
|
|
| 1213 |
|
|
if (!isset($occurences[$taxon->uuid])){
|
| 1214 |
|
|
|
| 1215 |
|
|
$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
|
| 1216 |
|
|
$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
|
| 1217 |
f19f47fa
|
Andreas Kohlbecker
|
$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
|
| 1218 |
|
|
|
| 1219 |
|
|
$by_associatedtaxon_query = http_build_query(array(
|
| 1220 |
|
|
'relationshipsInvers' => implode(',', $relationship_choice['invers']),
|
| 1221 |
|
|
'relationships' => implode(',', $relationship_choice['direct']),
|
| 1222 |
|
|
'pageSize' => null // all hits in one page
|
| 1223 |
|
|
)
|
| 1224 |
|
|
);
|
| 1225 |
|
|
|
| 1226 |
|
|
$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
|
| 1227 |
|
|
null,
|
| 1228 |
|
|
$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
|
| 1229 |
|
|
);
|
| 1230 |
|
|
|
| 1231 |
|
|
|
| 1232 |
|
|
if(isset($pager->records[0])){
|
| 1233 |
|
|
$occurences[$taxon->uuid] = $pager->records;
|
| 1234 |
|
|
}
|
| 1235 |
|
|
}
|
| 1236 |
9438ad3a
|
Andreas Kohlbecker
|
return $occurences[$taxon->uuid];
|
| 1237 |
|
|
}
|
| 1238 |
|
|
*/
|
| 1239 |
|
|
|
| 1240 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 1241 |
|
|
* Gets a Drupal variable, string or array and returns it.
|
| 1242 |
|
|
*
|
| 1243 |
|
|
* Similar to the variable_get() function of Drupal, except that this function
|
| 1244 |
|
|
* is able to handle arrays correctly. This function is especially useful
|
| 1245 |
8c962983
|
Andreas Kohlbecker
|
* when dealing with collections of settings form elements (#tree = TRUE).
|
| 1246 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 1247 |
|
|
* @param string $variableKey
|
| 1248 |
|
|
* The Unique key of the Drupal variable in the Drupal variables table.
|
| 1249 |
|
|
* @param string $defaultValueString
|
| 1250 |
|
|
* A string as for example derived from a CONSTANT.
|
| 1251 |
|
|
*
|
| 1252 |
|
|
* @return mixed
|
| 1253 |
8c962983
|
Andreas Kohlbecker
|
* usually an array, depending on the nature of the variable.
|
| 1254 |
|
|
*
|
| 1255 |
|
|
* TODO compare with get_array_variable_merged() duplicate functions?
|
| 1256 |
0f7c9d15
|
Andreas Kohlbecker
|
* @deprecated rather use get_array_variable_merged() since this function
|
| 1257 |
|
|
* used an array as second parameter
|
| 1258 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1259 |
|
|
function mixed_variable_get($variableKey, $defaultValueString) {
|
| 1260 |
|
|
$systemDefaults = unserialize($defaultValueString);
|
| 1261 |
|
|
$storedSettings = variable_get($variableKey, array());
|
| 1262 |
|
|
if (is_array($storedSettings)) {
|
| 1263 |
8c962983
|
Andreas Kohlbecker
|
// TODO better use drupal_array_merge_deep() ?
|
| 1264 |
6657531f
|
Andreas Kohlbecker
|
$settings = array_merge($systemDefaults, $storedSettings);
|
| 1265 |
|
|
}
|
| 1266 |
|
|
else {
|
| 1267 |
|
|
$settings = $systemDefaults;
|
| 1268 |
|
|
}
|
| 1269 |
|
|
return $settings;
|
| 1270 |
|
|
}
|
| 1271 |
|
|
|
| 1272 |
b5519d3a
|
Andreas Kohlbecker
|
/**
|
| 1273 |
0f7c9d15
|
Andreas Kohlbecker
|
* Recursive function to convert an object into an array.
|
| 1274 |
b5519d3a
|
Andreas Kohlbecker
|
* also subordinate objects will be converted.
|
| 1275 |
|
|
*
|
| 1276 |
|
|
* @param object $object
|
| 1277 |
|
|
* @return the array
|
| 1278 |
|
|
*/
|
| 1279 |
|
|
function convert_to_array($object) {
|
| 1280 |
|
|
if(is_object($object) || is_array($object)) {
|
| 1281 |
|
|
$array = (array)$object;
|
| 1282 |
|
|
foreach ($array as $key=>$value){
|
| 1283 |
|
|
$array[$key] = convert_to_array($value);
|
| 1284 |
|
|
}
|
| 1285 |
|
|
return $array;
|
| 1286 |
|
|
} else {
|
| 1287 |
|
|
return $object;
|
| 1288 |
|
|
}
|
| 1289 |
|
|
}
|
| 1290 |
|
|
|
| 1291 |
2fd6da0b
|
Andreas Kohlbecker
|
/**
|
| 1292 |
|
|
* Searches the $collection for the cdm entitiy given as $element.
|
| 1293 |
|
|
*
|
| 1294 |
|
|
* The elements are compared by their UUID.
|
| 1295 |
|
|
*
|
| 1296 |
|
|
* @param $element
|
| 1297 |
|
|
* the CDM entitiy to search for
|
| 1298 |
|
|
* @param $collection
|
| 1299 |
|
|
* the list of CDM entities to search in
|
| 1300 |
|
|
*
|
| 1301 |
|
|
* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
|
| 1302 |
|
|
*
|
| 1303 |
|
|
*/
|
| 1304 |
|
|
function contains_cdm_entitiy($element, $collection) {
|
| 1305 |
|
|
$result = FALSE;
|
| 1306 |
|
|
foreach ($collection as $a) {
|
| 1307 |
|
|
if ($a->uuid == $element->uuid) {
|
| 1308 |
|
|
$result = TRUE;
|
| 1309 |
|
|
}
|
| 1310 |
|
|
}
|
| 1311 |
|
|
return $result;
|
| 1312 |
|
|
}
|
| 1313 |
|
|
|
| 1314 |
|
|
/**
|
| 1315 |
|
|
* Fiters the array $entity_list of CDM entities by the list
|
| 1316 |
|
|
* of $excludes. Any element contained in the $excludes will be removed
|
| 1317 |
|
|
* from included int the retuned list.
|
| 1318 |
|
|
*
|
| 1319 |
|
|
* If the $entity_list is not an array the $excludes will be returned.
|
| 1320 |
|
|
*/
|
| 1321 |
|
|
function filter_cdm_entity_list($entity_list, $excludes) {
|
| 1322 |
|
|
if (is_array($entity_list)) {
|
| 1323 |
|
|
$result = $entity_list;
|
| 1324 |
|
|
if ($excludes) {
|
| 1325 |
|
|
foreach ($excludes as $exclude) {
|
| 1326 |
|
|
if (!contains_cdm_entitiy($exclude, $entity_list)) {
|
| 1327 |
|
|
$result[] = $exclude;
|
| 1328 |
|
|
}
|
| 1329 |
|
|
}
|
| 1330 |
|
|
}
|
| 1331 |
|
|
}
|
| 1332 |
|
|
else {
|
| 1333 |
|
|
$result = $excludes;
|
| 1334 |
|
|
}
|
| 1335 |
|
|
return $result;
|
| 1336 |
|
|
}
|
| 1337 |
|
|
|
| 1338 |
0a1151a4
|
Andreas Kohlbecker
|
/**
|
| 1339 |
6f5c7f2a
|
Andreas Kohlbecker
|
* Wraps the given $html string into a render array suitable for drupal_render()
|
| 1340 |
0a1151a4
|
Andreas Kohlbecker
|
*
|
| 1341 |
65345976
|
Andreas Kohlbecker
|
* @param $html
|
| 1342 |
0a1151a4
|
Andreas Kohlbecker
|
* the html string, see
|
| 1343 |
|
|
* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
|
| 1344 |
65345976
|
Andreas Kohlbecker
|
* @param $weight
|
| 1345 |
0a1151a4
|
Andreas Kohlbecker
|
* A positive or negative number (integer or decimal).
|
| 1346 |
|
|
* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
|
| 1347 |
65345976
|
Andreas Kohlbecker
|
* @param $prefix
|
| 1348 |
|
|
* Optional markup for the '#prefix' element of the render array
|
| 1349 |
|
|
* @param $suffix
|
| 1350 |
|
|
* Optional markup for the '#suffix' element of the render array
|
| 1351 |
0a1151a4
|
Andreas Kohlbecker
|
*
|
| 1352 |
65345976
|
Andreas Kohlbecker
|
* @return array
|
| 1353 |
0a1151a4
|
Andreas Kohlbecker
|
* A render array
|
| 1354 |
|
|
*
|
| 1355 |
|
|
*/
|
| 1356 |
65345976
|
Andreas Kohlbecker
|
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
|
| 1357 |
6f5c7f2a
|
Andreas Kohlbecker
|
$render_array = array(
|
| 1358 |
|
|
'#markup' => $html
|
| 1359 |
1ce9afb7
|
Patric Plitzner
|
);
|
| 1360 |
6f5c7f2a
|
Andreas Kohlbecker
|
if (is_numeric($weight)) {
|
| 1361 |
|
|
$render_array['#weight'] = $weight;
|
| 1362 |
65345976
|
Andreas Kohlbecker
|
}
|
| 1363 |
|
|
if($prefix){
|
| 1364 |
|
|
$render_array['#prefix'] = $prefix;
|
| 1365 |
|
|
}
|
| 1366 |
|
|
if($suffix) {
|
| 1367 |
|
|
$render_array['#suffix'] = $suffix;
|
| 1368 |
|
|
}
|
| 1369 |
6f5c7f2a
|
Andreas Kohlbecker
|
return $render_array;
|
| 1370 |
0a1151a4
|
Andreas Kohlbecker
|
}
|
| 1371 |
|
|
|
| 1372 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 1373 |
|
|
* Loads the subgraph of a given PolytomousKeyNode.
|
| 1374 |
|
|
*
|
| 1375 |
|
|
* Loads the subgraph of the given PolytomousKeyNode recursively from
|
| 1376 |
|
|
* the CDM REST service.
|
| 1377 |
|
|
*
|
| 1378 |
|
|
* @param mixed $polytomousKeyNode
|
| 1379 |
|
|
* PolytomousKeyNode passed by reference.
|
| 1380 |
|
|
*
|
| 1381 |
|
|
* @return void
|
| 1382 |
|
|
*/
|
| 1383 |
|
|
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
|
| 1384 |
|
|
|
| 1385 |
|
|
if (!$polytomousKeyNode) {
|
| 1386 |
|
|
return;
|
| 1387 |
|
|
}
|
| 1388 |
|
|
if ($polytomousKeyNode->class != "PolytomousKeyNode") {
|
| 1389 |
f19f47fa
|
Andreas Kohlbecker
|
drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
|
| 1390 |
6657531f
|
Andreas Kohlbecker
|
return;
|
| 1391 |
|
|
}
|
| 1392 |
|
|
if (!is_uuid($polytomousKeyNode->uuid)) {
|
| 1393 |
f19f47fa
|
Andreas Kohlbecker
|
drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
|
| 1394 |
6657531f
|
Andreas Kohlbecker
|
return;
|
| 1395 |
|
|
}
|
| 1396 |
|
|
|
| 1397 |
|
|
$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
|
| 1398 |
|
|
|
| 1399 |
|
|
if (!$polytomousKeyNode) {
|
| 1400 |
|
|
// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
|
| 1401 |
|
|
return;
|
| 1402 |
|
|
}
|
| 1403 |
|
|
|
| 1404 |
|
|
// Load children.
|
| 1405 |
|
|
foreach ($polytomousKeyNode->children as &$childNode) {
|
| 1406 |
|
|
_load_polytomousKeySubGraph($childNode);
|
| 1407 |
|
|
}
|
| 1408 |
|
|
|
| 1409 |
|
|
// Load subkey.
|
| 1410 |
|
|
$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
|
| 1411 |
|
|
|
| 1412 |
|
|
// Load taxon.
|
| 1413 |
|
|
$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
|
| 1414 |
|
|
_load_taxonBase($polytomousKeyNode->taxon);
|
| 1415 |
|
|
return;
|
| 1416 |
|
|
}
|
| 1417 |
|
|
|
| 1418 |
|
|
/**
|
| 1419 |
|
|
* @todo Please document this function.
|
| 1420 |
|
|
* @see http://drupal.org/node/1354
|
| 1421 |
|
|
*/
|
| 1422 |
|
|
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
|
| 1423 |
f26245c8
|
Andreas Kohlbecker
|
|
| 1424 |
|
|
cdm_check_valid_portal_page();
|
| 1425 |
|
|
|
| 1426 |
6657531f
|
Andreas Kohlbecker
|
$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
|
| 1427 |
|
|
|
| 1428 |
|
|
$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
|
| 1429 |
|
|
if (is_array($sourcePager->records)) {
|
| 1430 |
|
|
$polytomousKey->sources = $sourcePager->records;
|
| 1431 |
|
|
// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
|
| 1432 |
|
|
}
|
| 1433 |
|
|
|
| 1434 |
|
|
$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
|
| 1435 |
|
|
if (is_array($annotationPager->records)) {
|
| 1436 |
|
|
$polytomousKey->annotations = $annotationPager->records;
|
| 1437 |
|
|
}
|
| 1438 |
|
|
|
| 1439 |
|
|
_load_polytomousKeySubGraph($polytomousKey->root);
|
| 1440 |
|
|
return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
|
| 1441 |
|
|
}
|
| 1442 |
|
|
|
| 1443 |
|
|
/**
|
| 1444 |
|
|
* Creates a taxon page view or a chapter of it.
|
| 1445 |
|
|
*
|
| 1446 |
|
|
* The taxon page gives detailed information on a taxon, it shows:
|
| 1447 |
|
|
* - Taxon name.
|
| 1448 |
|
|
* - Full list of synonyms homotypic synonyms on top, followed by the
|
| 1449 |
|
|
* heterotypic and finally followed by misapplied names.
|
| 1450 |
|
|
* The list is ordered historically.
|
| 1451 |
|
|
* - All description associated with the taxon.
|
| 1452 |
|
|
*
|
| 1453 |
|
|
* @param string $uuid
|
| 1454 |
|
|
* @param string $chapter
|
| 1455 |
|
|
* Name of the part to display, valid values are:
|
| 1456 |
|
|
* 'description', 'images', 'synonymy', 'specimens', 'all'.
|
| 1457 |
|
|
*
|
| 1458 |
793dae0a
|
Andreas Kohlbecker
|
* @return string
|
| 1459 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1460 |
|
|
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
|
| 1461 |
5ea8b301
|
Andreas Kohlbecker
|
|
| 1462 |
f26245c8
|
Andreas Kohlbecker
|
cdm_check_valid_taxon_page($chapter);
|
| 1463 |
2dd59bb5
|
Andreas Kohlbecker
|
cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
|
| 1464 |
5ea8b301
|
Andreas Kohlbecker
|
// show a warning in case the javascript development mode is anabled
|
| 1465 |
|
|
if(variable_get('cdm_js_devel_mode', FALSE)) {
|
| 1466 |
|
|
drupal_set_message(t('The !url1 is enabled.
|
| 1467 |
|
|
WARNING: this is a performance penalty and must be turned off on production websites.', array(
|
| 1468 |
|
|
'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
|
| 1469 |
793dae0a
|
Andreas Kohlbecker
|
)),
|
| 1470 |
|
|
'warning'
|
| 1471 |
|
|
);
|
| 1472 |
5ea8b301
|
Andreas Kohlbecker
|
}
|
| 1473 |
|
|
|
| 1474 |
6657531f
|
Andreas Kohlbecker
|
// Display the page for the taxon defined by $uuid.
|
| 1475 |
|
|
// set_last_taxon_page_tab(arg(3));
|
| 1476 |
|
|
$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
|
| 1477 |
|
|
if (!empty($taxonpage)) {
|
| 1478 |
2dd59bb5
|
Andreas Kohlbecker
|
cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
|
| 1479 |
6657531f
|
Andreas Kohlbecker
|
return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
|
| 1480 |
|
|
}
|
| 1481 |
|
|
else {
|
| 1482 |
2dd59bb5
|
Andreas Kohlbecker
|
cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
|
| 1483 |
6657531f
|
Andreas Kohlbecker
|
return '';
|
| 1484 |
|
|
}
|
| 1485 |
|
|
}
|
| 1486 |
|
|
|
| 1487 |
|
|
/**
|
| 1488 |
59f6da42
|
Andreas Kohlbecker
|
* This function will genreate the taxon page part ($chapter) and returns a taxonpage object
|
| 1489 |
|
|
* which has two fields, one for the page title and one for the content. Later on in the
|
| 1490 |
|
|
* process chain the value contained in these fields will be passed to the cdm_node_show()
|
| 1491 |
|
|
* function as the function parameters $title and $content.
|
| 1492 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 1493 |
|
|
* @param string $uuid
|
| 1494 |
59f6da42
|
Andreas Kohlbecker
|
* the uuid of the taxon to show
|
| 1495 |
6657531f
|
Andreas Kohlbecker
|
* @param string $chapter
|
| 1496 |
|
|
* Name of the part to display, valid values are:
|
| 1497 |
|
|
* 'description', 'images', 'synonymy', 'all'.
|
| 1498 |
|
|
*
|
| 1499 |
59f6da42
|
Andreas Kohlbecker
|
* @return taxonpage object with the following fields:
|
| 1500 |
|
|
* - title : the title of the page
|
| 1501 |
|
|
* - content: the content of the page
|
| 1502 |
|
|
*
|
| 1503 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1504 |
8cf9238f
|
Andreas Kohlbecker
|
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
|
| 1505 |
6657531f
|
Andreas Kohlbecker
|
// Taxon object.
|
| 1506 |
|
|
$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
|
| 1507 |
|
|
if (empty($taxon)) {
|
| 1508 |
|
|
drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
|
| 1509 |
|
|
return FALSE;
|
| 1510 |
|
|
}
|
| 1511 |
|
|
$taxonpage = new stdClass();
|
| 1512 |
|
|
|
| 1513 |
|
|
$taxonpage->title = theme('cdm_taxon_page_title', array(
|
| 1514 |
8cf9238f
|
Andreas Kohlbecker
|
'taxon' => $taxon
|
| 1515 |
6657531f
|
Andreas Kohlbecker
|
));
|
| 1516 |
|
|
|
| 1517 |
|
|
// Check if the taxon id contained in the currently selected tree.
|
| 1518 |
7663cd0b
|
Andreas Kohlbecker
|
$taxon_in_current_classification = taxon_in_current_classification($uuid);
|
| 1519 |
61b6ee11
|
Andreas Kohlbecker
|
|
| 1520 |
7663cd0b
|
Andreas Kohlbecker
|
if (!$taxon_in_current_classification) {
|
| 1521 |
61b6ee11
|
Andreas Kohlbecker
|
$classifications = get_classifications_for_taxon($taxon);
|
| 1522 |
e24d373b
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('not_in_current_classification');
|
| 1523 |
|
|
$taxon_name_markup = render_taxon_or_name($taxon);
|
| 1524 |
|
|
|
| 1525 |
61b6ee11
|
Andreas Kohlbecker
|
if (count($classifications) == 0) {
|
| 1526 |
e24d373b
|
Andreas Kohlbecker
|
drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
|
| 1527 |
fba00a4f
|
Andreas Kohlbecker
|
array(
|
| 1528 |
e24d373b
|
Andreas Kohlbecker
|
'!taxonname' => $taxon_name_markup,
|
| 1529 |
fba00a4f
|
Andreas Kohlbecker
|
)
|
| 1530 |
|
|
), 'warning');
|
| 1531 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1532 |
|
|
else {
|
| 1533 |
|
|
$trees = '';
|
| 1534 |
61b6ee11
|
Andreas Kohlbecker
|
foreach ($classifications as $classification) {
|
| 1535 |
|
|
if (isset($classification->titleCache)) {
|
| 1536 |
|
|
$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
|
| 1537 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1538 |
|
|
}
|
| 1539 |
|
|
|
| 1540 |
15b7c460
|
Andreas Kohlbecker
|
drupal_set_message(format_plural(count($trees),
|
| 1541 |
e24d373b
|
Andreas Kohlbecker
|
'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
|
| 1542 |
|
|
'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
|
| 1543 |
|
|
array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
|
| 1544 |
fba00a4f
|
Andreas Kohlbecker
|
) ,
|
| 1545 |
|
|
'warning');
|
| 1546 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1547 |
e24d373b
|
Andreas Kohlbecker
|
RenderHints::popFromRenderStack();
|
| 1548 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1549 |
|
|
|
| 1550 |
|
|
// Render the taxon page.
|
| 1551 |
9a607f17
|
Andreas Kohlbecker
|
$render_array = compose_cdm_taxon_page($taxon, $chapter);
|
| 1552 |
|
|
$taxonpage->content = drupal_render($render_array);
|
| 1553 |
6657531f
|
Andreas Kohlbecker
|
|
| 1554 |
|
|
return $taxonpage;
|
| 1555 |
|
|
}
|
| 1556 |
|
|
|
| 1557 |
9d37c9d9
|
Patric Plitzner
|
/**
|
| 1558 |
|
|
* Creates a specimen page view.
|
| 1559 |
|
|
* @param string $uuid the UUID of the specimen
|
| 1560 |
|
|
* @return array|string
|
| 1561 |
|
|
*/
|
| 1562 |
|
|
function cdm_dataportal_specimen_page_view($uuid) {
|
| 1563 |
|
|
|
| 1564 |
|
|
//cdm_check_valid_taxon_page($chapter);
|
| 1565 |
|
|
//cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
|
| 1566 |
|
|
// show a warning in case the javascript development mode is anabled
|
| 1567 |
|
|
if(variable_get('cdm_js_devel_mode', FALSE)) {
|
| 1568 |
|
|
drupal_set_message(t('The !url1 is enabled.
|
| 1569 |
|
|
WARNING: this is a performance penalty and must be turned off on production websites.', array(
|
| 1570 |
|
|
'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
|
| 1571 |
|
|
)),
|
| 1572 |
|
|
'warning'
|
| 1573 |
|
|
);
|
| 1574 |
|
|
}
|
| 1575 |
|
|
|
| 1576 |
|
|
// Display the page for the specimen defined by $uuid.
|
| 1577 |
|
|
$specimenpage = cdm_dataportal_specimen_view($uuid);
|
| 1578 |
|
|
if (!empty($specimenpage)) {
|
| 1579 |
|
|
return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
|
| 1580 |
|
|
}
|
| 1581 |
|
|
else {
|
| 1582 |
|
|
return '';
|
| 1583 |
|
|
}
|
| 1584 |
|
|
}
|
| 1585 |
|
|
|
| 1586 |
|
|
/**
|
| 1587 |
|
|
*
|
| 1588 |
|
|
* Creates a specimen view.
|
| 1589 |
|
|
* @param string $uuid the UUID of the specimen
|
| 1590 |
|
|
* @return array|string
|
| 1591 |
|
|
*/
|
| 1592 |
|
|
function cdm_dataportal_specimen_view($uuid) {
|
| 1593 |
|
|
$specimen = cdm_ws_get(CDM_WS_OCCURRENCE, $uuid);
|
| 1594 |
|
|
if (empty($specimen)) {
|
| 1595 |
|
|
drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
|
| 1596 |
|
|
return FALSE;
|
| 1597 |
|
|
}
|
| 1598 |
|
|
$specimenpage = new stdClass();
|
| 1599 |
|
|
|
| 1600 |
|
|
$specimenpage->title = theme('cdm_specimen_page_title', array(
|
| 1601 |
|
|
'specimen' => $specimen
|
| 1602 |
|
|
));
|
| 1603 |
|
|
|
| 1604 |
b810158e
|
Patric Plitzner
|
// Render the specimen page.
|
| 1605 |
|
|
$render_array = compose_cdm_specimen_page($uuid);
|
| 1606 |
9d37c9d9
|
Patric Plitzner
|
$specimenpage->content = drupal_render($render_array);
|
| 1607 |
|
|
|
| 1608 |
|
|
return $specimenpage;
|
| 1609 |
|
|
}
|
| 1610 |
|
|
|
| 1611 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 1612 |
|
|
* Returns a name page as a Drupal node ready to be renderized by Drupal.
|
| 1613 |
|
|
*
|
| 1614 |
|
|
* The node page shows the taxon name title and the list of taxon related
|
| 1615 |
|
|
* with such taxon. Name on the tree already in use.
|
| 1616 |
|
|
*
|
| 1617 |
51b04faf
|
Andreas Kohlbecker
|
* @param UUID $taxon_name_uuid
|
| 1618 |
|
|
* The uuid of the CDM TaxonNameBase to show a name page for
|
| 1619 |
|
|
* @param UUID $taxon_to_hide_uuid
|
| 1620 |
|
|
* A taxon which should not be displayed in the taxon list
|
| 1621 |
|
|
* @param UUID $highlite_synonym_uuid
|
| 1622 |
|
|
* Optinal parameter wich takes another taxon uuid, if given the
|
| 1623 |
|
|
* target taxon pages will show the syonymy tab where the taxon
|
| 1624 |
|
|
* refenrenced by the $highlite_synonym_uuid will be highlighted
|
| 1625 |
|
|
* in case it is found on this page.
|
| 1626 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 1627 |
|
|
* @return mixed
|
| 1628 |
|
|
* The formatted name page as node.
|
| 1629 |
|
|
*/
|
| 1630 |
|
|
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
|
| 1631 |
|
|
|
| 1632 |
f26245c8
|
Andreas Kohlbecker
|
cdm_check_valid_portal_page();
|
| 1633 |
|
|
|
| 1634 |
6657531f
|
Andreas Kohlbecker
|
$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
|
| 1635 |
|
|
if (!empty($taxonname_page)) {
|
| 1636 |
|
|
return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
|
| 1637 |
|
|
}
|
| 1638 |
|
|
else {
|
| 1639 |
|
|
return '';
|
| 1640 |
|
|
}
|
| 1641 |
|
|
}
|
| 1642 |
|
|
|
| 1643 |
|
|
/**
|
| 1644 |
e3001c8d
|
Andreas Kohlbecker
|
* View function for a TaxonNameBase page.
|
| 1645 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 1646 |
e3001c8d
|
Andreas Kohlbecker
|
* The name page lists all taxa for which the name specified by the
|
| 1647 |
|
|
* $taxon_name_uuid is being used. I case there is only one name the
|
| 1648 |
|
|
* page automatically redirects ti the according taxon page. Otherwise
|
| 1649 |
|
|
* the list of names is displayed.
|
| 1650 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 1651 |
e3001c8d
|
Andreas Kohlbecker
|
* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
|
| 1652 |
|
|
* list of taxa. This is useful for example when referencing from a taxon
|
| 1653 |
|
|
* to the name page and the referring taxon should not be repeaded in the
|
| 1654 |
|
|
* name page.
|
| 1655 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 1656 |
e3001c8d
|
Andreas Kohlbecker
|
*
|
| 1657 |
|
|
* @param UUID $taxon_name_uuid
|
| 1658 |
|
|
* The uuid of the CDM TaxonNameBase to show a name page for
|
| 1659 |
|
|
* @param UUID $taxon_to_hide_uuid
|
| 1660 |
|
|
* A taxon which should not be displayed in the taxon list
|
| 1661 |
|
|
* @param UUID $highlite_synonym_uuid
|
| 1662 |
|
|
* Optinal parameter wich takes another taxon uuid, if given the
|
| 1663 |
|
|
* target taxon pages will show the syonymy tab where the taxon
|
| 1664 |
|
|
* refenrenced by the $highlite_synonym_uuid will be highlighted
|
| 1665 |
|
|
* in case it is found on this page.
|
| 1666 |
|
|
*
|
| 1667 |
|
|
* @return object
|
| 1668 |
|
|
* An object with two fields:
|
| 1669 |
|
|
* - title: the page title
|
| 1670 |
|
|
* - content: the page content
|
| 1671 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1672 |
e3001c8d
|
Andreas Kohlbecker
|
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
|
| 1673 |
6657531f
|
Andreas Kohlbecker
|
// Getting the full taxonname object from the server.
|
| 1674 |
d0d068e9
|
Andreas Kohlbecker
|
$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
|
| 1675 |
6657531f
|
Andreas Kohlbecker
|
if (!$taxon_name) {
|
| 1676 |
|
|
drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
|
| 1677 |
|
|
return FALSE;
|
| 1678 |
|
|
}
|
| 1679 |
|
|
// Searching for all the taxa connected with the taxon name on the tree
|
| 1680 |
|
|
// in use.
|
| 1681 |
|
|
$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
|
| 1682 |
|
|
$request_params = array();
|
| 1683 |
|
|
$request_params['query'] = $name_cache;
|
| 1684 |
7663cd0b
|
Andreas Kohlbecker
|
$request_params['tree'] = get_current_classification_uuid();
|
| 1685 |
6657531f
|
Andreas Kohlbecker
|
$request_params['doTaxa'] = 1;
|
| 1686 |
|
|
$request_params['doSynonyms'] = 1;
|
| 1687 |
|
|
$request_params['doTaxaByCommonNames'] = 0;
|
| 1688 |
|
|
$request_params['matchMode'] = "EXACT";
|
| 1689 |
|
|
$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
|
| 1690 |
|
|
|
| 1691 |
d0d068e9
|
Andreas Kohlbecker
|
// Removing the name where we came from.
|
| 1692 |
6657531f
|
Andreas Kohlbecker
|
foreach ($taxon_pager->records as $k => &$taxon) {
|
| 1693 |
|
|
if ($taxon->uuid == $taxon_to_hide_uuid) {
|
| 1694 |
|
|
unset($taxon_pager->records[$k]);
|
| 1695 |
|
|
}
|
| 1696 |
|
|
}
|
| 1697 |
|
|
// Show the taxa list or go to the singular taxon.
|
| 1698 |
|
|
if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
|
| 1699 |
e3001c8d
|
Andreas Kohlbecker
|
$singleTaxon = array_pop($taxon_pager->records);
|
| 1700 |
6657531f
|
Andreas Kohlbecker
|
if ($singleTaxon->class != "Taxon") {
|
| 1701 |
|
|
// It is a Synonym -> look for the accepted.
|
| 1702 |
7663cd0b
|
Andreas Kohlbecker
|
$accepted_taxa = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_current_classification_uuid()));
|
| 1703 |
e3001c8d
|
Andreas Kohlbecker
|
if (!empty($highlite_synonym_uuid)) {
|
| 1704 |
f0bf24e7
|
Andreas Kohlbecker
|
drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
|
| 1705 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1706 |
|
|
else {
|
| 1707 |
f0bf24e7
|
Andreas Kohlbecker
|
drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
|
| 1708 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1709 |
|
|
}
|
| 1710 |
|
|
else {
|
| 1711 |
|
|
// It is an accepted taxon.
|
| 1712 |
e3001c8d
|
Andreas Kohlbecker
|
if (!empty($highlite_synonym_uuid)) {
|
| 1713 |
|
|
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
|
| 1714 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1715 |
|
|
else {
|
| 1716 |
|
|
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
|
| 1717 |
|
|
}
|
| 1718 |
|
|
}
|
| 1719 |
|
|
}
|
| 1720 |
|
|
else {// More than one taxa case.
|
| 1721 |
|
|
$taxon_name_page = new stdClass();
|
| 1722 |
4f225a0f
|
Andreas Kohlbecker
|
$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
|
| 1723 |
6657531f
|
Andreas Kohlbecker
|
if ($taxon_pager->records) {
|
| 1724 |
7272d19c
|
Andreas Kohlbecker
|
$taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
|
| 1725 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1726 |
|
|
else {
|
| 1727 |
|
|
$taxon_name_page->content = 'This name has no taxa';
|
| 1728 |
|
|
}
|
| 1729 |
|
|
return $taxon_name_page;
|
| 1730 |
|
|
}
|
| 1731 |
|
|
}
|
| 1732 |
|
|
|
| 1733 |
|
|
/**
|
| 1734 |
84b13813
|
Andreas Kohlbecker
|
* Creates a page with the advance search form.
|
| 1735 |
|
|
*
|
| 1736 |
|
|
* NOTE: The advance search form allows searching for taxa.
|
| 1737 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1738 |
|
|
function cdm_dataportal_view_search_advanced() {
|
| 1739 |
|
|
drupal_set_title(t('Advanced search'), PASS_THROUGH);
|
| 1740 |
|
|
return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
|
| 1741 |
|
|
}
|
| 1742 |
|
|
|
| 1743 |
|
|
/**
|
| 1744 |
84b13813
|
Andreas Kohlbecker
|
* Creates a page with the search form for searching by taxon descriptions.
|
| 1745 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1746 |
|
|
function cdm_dataportal_view_search_taxon_by_description() {
|
| 1747 |
6441ddfb
|
Andreas Kohlbecker
|
drupal_set_title(t('Search by factual data'), PASS_THROUGH);
|
| 1748 |
6657531f
|
Andreas Kohlbecker
|
return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
|
| 1749 |
|
|
}
|
| 1750 |
|
|
|
| 1751 |
|
|
/**
|
| 1752 |
|
|
* Executes the search and generates the result list of taxa.
|
| 1753 |
|
|
*/
|
| 1754 |
|
|
function cdm_dataportal_view_search_results_taxon() {
|
| 1755 |
|
|
|
| 1756 |
|
|
$taxonPager = cdm_dataportal_search_execute();
|
| 1757 |
|
|
|
| 1758 |
f19f47fa
|
Andreas Kohlbecker
|
$showThumbnails = do_showThumbnails();
|
| 1759 |
|
|
|
| 1760 |
|
|
$setSessionUri = url('cdm_api/setvalue/session', array(
|
| 1761 |
|
|
'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
|
| 1762 |
|
|
));
|
| 1763 |
|
|
|
| 1764 |
|
|
drupal_add_js('jQuery(document).ready(function() {
|
| 1765 |
|
|
|
| 1766 |
|
|
// init
|
| 1767 |
|
|
if(' . $showThumbnails . ' == 1){
|
| 1768 |
1d69a96c
|
Andreas Kohlbecker
|
jQuery(\'.media_gallery\').show(20);
|
| 1769 |
|
|
} else {
|
| 1770 |
|
|
jQuery(\'.media_gallery\').hide(20);
|
| 1771 |
|
|
}
|
| 1772 |
|
|
|
| 1773 |
|
|
// add change handler
|
| 1774 |
|
|
jQuery(\'#showThumbnails input.showThumbnails\').change(
|
| 1775 |
f19f47fa
|
Andreas Kohlbecker
|
function(event){
|
| 1776 |
1d69a96c
|
Andreas Kohlbecker
|
var state = 0;
|
| 1777 |
|
|
if(jQuery(this).is(\':checked\')){
|
| 1778 |
|
|
jQuery(\'.media_gallery\').show(20);
|
| 1779 |
|
|
state = 1;
|
| 1780 |
|
|
} else {
|
| 1781 |
|
|
jQuery(\'.media_gallery\').hide(20);
|
| 1782 |
|
|
}
|
| 1783 |
|
|
// store state in session variable
|
| 1784 |
|
|
var uri = \'' . $setSessionUri . '\' + state;
|
| 1785 |
|
|
jQuery.get(uri);
|
| 1786 |
|
|
});
|
| 1787 |
78e178e2
|
Andreas Kohlbecker
|
});',
|
| 1788 |
f19f47fa
|
Andreas Kohlbecker
|
array('type' => "inline", 'scope' => JS_DEFAULT));
|
| 1789 |
|
|
|
| 1790 |
78e178e2
|
Andreas Kohlbecker
|
drupal_set_title(t('Search results'), PASS_THROUGH);
|
| 1791 |
|
|
|
| 1792 |
6657531f
|
Andreas Kohlbecker
|
return theme('cdm_search_results', array(
|
| 1793 |
|
|
'pager' => $taxonPager,
|
| 1794 |
|
|
'path' => 'cdm_dataportal/search/results/taxon',
|
| 1795 |
|
|
));
|
| 1796 |
|
|
}
|
| 1797 |
|
|
|
| 1798 |
94550ff9
|
Andreas Kohlbecker
|
/**
|
| 1799 |
|
|
* Provides the standart image wich indicated a loading process
|
| 1800 |
|
|
*
|
| 1801 |
|
|
* @return string
|
| 1802 |
|
|
* The img html tag
|
| 1803 |
|
|
*/
|
| 1804 |
|
|
function loading_image_html() {
|
| 1805 |
|
|
return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
|
| 1806 |
|
|
. '/images/loading_circle_grey_16.gif" style="display:none;">';
|
| 1807 |
|
|
}
|
| 1808 |
|
|
|
| 1809 |
78e178e2
|
Andreas Kohlbecker
|
/**
|
| 1810 |
|
|
* Returns the state of the the showThumbnails flag set in the
|
| 1811 |
|
|
* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
|
| 1812 |
|
|
*
|
| 1813 |
c5ed6357
|
Andreas Kohlbecker
|
* @return boolean
|
| 1814 |
78e178e2
|
Andreas Kohlbecker
|
* returns 1 if the flag is set
|
| 1815 |
|
|
*/
|
| 1816 |
|
|
function do_showThumbnails() {
|
| 1817 |
|
|
static $showThumbnails = null;
|
| 1818 |
|
|
|
| 1819 |
|
|
if($showThumbnails == null) {
|
| 1820 |
c5ed6357
|
Andreas Kohlbecker
|
$showThumbnails = 0;
|
| 1821 |
|
|
if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
|
| 1822 |
|
|
$showThumbnails = 0;
|
| 1823 |
|
|
$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
|
| 1824 |
|
|
$showThumbnails = is_array($search_gallery_settings)
|
| 1825 |
|
|
&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
|
| 1826 |
|
|
&& (
|
| 1827 |
|
|
$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
|
| 1828 |
|
|
$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
|
| 1829 |
|
|
$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
|
| 1830 |
|
|
)
|
| 1831 |
|
|
? 1 : 0;
|
| 1832 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 1833 |
c5ed6357
|
Andreas Kohlbecker
|
drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
|
| 1834 |
|
|
}
|
| 1835 |
f19f47fa
|
Andreas Kohlbecker
|
$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
|
| 1836 |
|
|
if (!is_numeric($showThumbnails)) {
|
| 1837 |
|
|
$showThumbnails = 1;
|
| 1838 |
|
|
}
|
| 1839 |
78e178e2
|
Andreas Kohlbecker
|
}
|
| 1840 |
|
|
|
| 1841 |
|
|
return $showThumbnails;
|
| 1842 |
|
|
}
|
| 1843 |
|
|
|
| 1844 |
6657531f
|
Andreas Kohlbecker
|
|
| 1845 |
|
|
/* ====================== other functions ====================== */
|
| 1846 |
|
|
/**
|
| 1847 |
|
|
* Creates a URL to the taxon page specified by the $uuid parameter.
|
| 1848 |
|
|
*
|
| 1849 |
|
|
* The URL will be prepended with a path element to a specific taxon page tab.
|
| 1850 |
|
|
*
|
| 1851 |
|
|
* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
|
| 1852 |
|
|
* be set globally in the administrative settings or individually in the user
|
| 1853 |
|
|
* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
|
| 1854 |
|
|
* the last portal will stay on this last tab.
|
| 1855 |
|
|
*
|
| 1856 |
|
|
* A third option is offerered by the $page_tab parameter which allows overwriting this
|
| 1857 |
|
|
* internal mechanism by a specific value.
|
| 1858 |
|
|
*
|
| 1859 |
|
|
* @param string $uuid
|
| 1860 |
|
|
* The UUID of the taxon.
|
| 1861 |
|
|
* @param string $page_tab
|
| 1862 |
|
|
* Overwriting the preset mechanism by defining specific value for the
|
| 1863 |
|
|
* taxon page tab.
|
| 1864 |
|
|
*
|
| 1865 |
|
|
* @return string
|
| 1866 |
|
|
* The created URL.
|
| 1867 |
|
|
*/
|
| 1868 |
|
|
function path_to_taxon($uuid, $page_tab = FALSE) {
|
| 1869 |
|
|
|
| 1870 |
|
|
$tab = get_default_taxon_tab();
|
| 1871 |
|
|
$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
|
| 1872 |
|
|
|
| 1873 |
|
|
if (!$uuid) {
|
| 1874 |
|
|
return FALSE;
|
| 1875 |
|
|
}
|
| 1876 |
|
|
|
| 1877 |
|
|
if ($page_tab) {
|
| 1878 |
|
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
|
| 1879 |
|
|
}
|
| 1880 |
|
|
elseif (!$tab || strtolower($tab) == 'general') {
|
| 1881 |
|
|
return 'cdm_dataportal/taxon/' . $uuid;
|
| 1882 |
|
|
}
|
| 1883 |
|
|
elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
|
| 1884 |
|
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
|
| 1885 |
|
|
}
|
| 1886 |
|
|
else {
|
| 1887 |
|
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
|
| 1888 |
|
|
}
|
| 1889 |
|
|
}
|
| 1890 |
|
|
|
| 1891 |
9d37c9d9
|
Patric Plitzner
|
function path_to_specimen($uuid) {
|
| 1892 |
|
|
|
| 1893 |
|
|
if (!$uuid) {
|
| 1894 |
|
|
return FALSE;
|
| 1895 |
|
|
}
|
| 1896 |
|
|
else {
|
| 1897 |
|
|
return 'cdm_dataportal/specimen/' . $uuid;
|
| 1898 |
|
|
}
|
| 1899 |
|
|
}
|
| 1900 |
|
|
|
| 1901 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 1902 |
630c7044
|
Andreas Kohlbecker
|
* Creates a URL to show a synonmy in the according taxon page.
|
| 1903 |
|
|
*
|
| 1904 |
|
|
* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
|
| 1905 |
|
|
* The resulting URI will include query parameters to highlight the synonym, and to optionally display
|
| 1906 |
|
|
* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
|
| 1907 |
|
|
* include the sysnonym uuid as fragment in order to let the browser scroll to the according location
|
| 1908 |
|
|
* in the page
|
| 1909 |
|
|
*
|
| 1910 |
|
|
* @param string $synonymUuid
|
| 1911 |
|
|
* The uuid of the synonym
|
| 1912 |
|
|
* @param string $acceptedUuid
|
| 1913 |
|
|
* The uuid of the according accepted taxon
|
| 1914 |
|
|
* @return string
|
| 1915 |
|
|
* The URL to show a synonmy in the according taxon page
|
| 1916 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1917 |
|
|
function uri_to_synonym($synonymUuid, $acceptedUuid) {
|
| 1918 |
|
|
$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
|
| 1919 |
d071bed7
|
Andreas Kohlbecker
|
return url($acceptedPath, array(
|
| 1920 |
|
|
'query' => array(
|
| 1921 |
|
|
// highlite the synony in the synonymy
|
| 1922 |
|
|
'highlite' => $synonymUuid,
|
| 1923 |
|
|
// the taxon page is refered from a synonym and the synonym can optionally be named in the page title
|
| 1924 |
|
|
// see theme_taxon_page_title()
|
| 1925 |
|
|
'acceptedFor' => $synonymUuid
|
| 1926 |
630c7044
|
Andreas Kohlbecker
|
),
|
| 1927 |
|
|
'fragment' => $synonymUuid
|
| 1928 |
d071bed7
|
Andreas Kohlbecker
|
));
|
| 1929 |
|
|
|
| 1930 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1931 |
|
|
|
| 1932 |
|
|
/**
|
| 1933 |
b8bfa4bd
|
Andreas Kohlbecker
|
* Compses the drupal path to the key identified by the uuid.
|
| 1934 |
|
|
*
|
| 1935 |
|
|
* @param string $keyType
|
| 1936 |
|
|
* the key typer corresponds to the specific class of the CDM
|
| 1937 |
|
|
* IdentificationKey. Possible values are
|
| 1938 |
|
|
* -PolytomousKey
|
| 1939 |
|
|
* -MultimediaKey
|
| 1940 |
|
|
* - ...
|
| 1941 |
|
|
* @param UUID $keyUuid
|
| 1942 |
|
|
* The UUID of the key
|
| 1943 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1944 |
|
|
function path_to_key($keyType, $keyUuid) {
|
| 1945 |
|
|
if (!$keyUuid || !$keyType) {
|
| 1946 |
|
|
return FALSE;
|
| 1947 |
|
|
}
|
| 1948 |
|
|
$keyType{0} = strtolower($keyType{0});
|
| 1949 |
|
|
return "cdm_dataportal/" . $keyType . "/$keyUuid";
|
| 1950 |
|
|
}
|
| 1951 |
|
|
|
| 1952 |
|
|
/**
|
| 1953 |
|
|
* @todo Please document this function.
|
| 1954 |
|
|
* @see http://drupal.org/node/1354
|
| 1955 |
|
|
*/
|
| 1956 |
|
|
function path_to_reference($uuid) {
|
| 1957 |
|
|
if (!$uuid) {
|
| 1958 |
|
|
return FALSE;
|
| 1959 |
|
|
}
|
| 1960 |
|
|
return 'cdm_dataportal/reference/' . $uuid;
|
| 1961 |
|
|
}
|
| 1962 |
|
|
|
| 1963 |
|
|
/**
|
| 1964 |
51b04faf
|
Andreas Kohlbecker
|
* Creates the path to a cdm_dataportal taxon name page.
|
| 1965 |
|
|
*
|
| 1966 |
|
|
* @param UUID $taxon_name_uuid
|
| 1967 |
|
|
* The uuid of the CDM TaxonNameBase to show a name page for
|
| 1968 |
|
|
* @param UUID $taxon_to_hide_uuid
|
| 1969 |
|
|
* A taxon which should not be displayed in the taxon list
|
| 1970 |
|
|
* @param UUID $highlite_synonym_uuid
|
| 1971 |
|
|
* Optinal parameter wich takes another taxon uuid, if given the
|
| 1972 |
|
|
* target taxon pages will show the syonymy tab where the taxon
|
| 1973 |
|
|
* refenrenced by the $highlite_synonym_uuid will be highlighted
|
| 1974 |
|
|
* in case it is found on this page.
|
| 1975 |
|
|
*
|
| 1976 |
|
|
* @return a URI path element as string
|
| 1977 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 1978 |
51b04faf
|
Andreas Kohlbecker
|
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid = NULL) {
|
| 1979 |
6657531f
|
Andreas Kohlbecker
|
$res = FALSE;
|
| 1980 |
|
|
if ($name_uuid) {
|
| 1981 |
|
|
$res = 'cdm_dataportal/name/' . $name_uuid;
|
| 1982 |
|
|
}
|
| 1983 |
51b04faf
|
Andreas Kohlbecker
|
if($taxon_to_hide_uuid){
|
| 1984 |
|
|
$res .= '/' . $taxon_to_hide_uuid;
|
| 1985 |
|
|
if($synonym_uuid){
|
| 1986 |
|
|
$res .= '/' . $synonym_uuid;
|
| 1987 |
|
|
}
|
| 1988 |
|
|
}
|
| 1989 |
6657531f
|
Andreas Kohlbecker
|
return $res;
|
| 1990 |
|
|
}
|
| 1991 |
|
|
|
| 1992 |
|
|
/**
|
| 1993 |
|
|
* @todo Please document this function.
|
| 1994 |
|
|
* @see http://drupal.org/node/1354
|
| 1995 |
|
|
*/
|
| 1996 |
|
|
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
|
| 1997 |
|
|
if (!$uuid) {
|
| 1998 |
|
|
return FALSE;
|
| 1999 |
|
|
}
|
| 2000 |
|
|
$out = 'cdm_dataportal/media/' . $uuid;
|
| 2001 |
|
|
if ($representaion_uuid) {
|
| 2002 |
|
|
$out .= '/' . $representaion_uuid;
|
| 2003 |
|
|
if ($partId !== FALSE) {
|
| 2004 |
|
|
$out .= '/' . $partId;
|
| 2005 |
|
|
}
|
| 2006 |
|
|
}
|
| 2007 |
|
|
return $out;
|
| 2008 |
|
|
}
|
| 2009 |
|
|
|
| 2010 |
|
|
/**
|
| 2011 |
|
|
* Compares thisRank with thatRank.
|
| 2012 |
|
|
*
|
| 2013 |
|
|
* Returns a negative integer, zero, or a positive integer
|
| 2014 |
|
|
* as the of thisRank is higher than, equal to, or lower than thatRank.
|
| 2015 |
|
|
* e.g:
|
| 2016 |
|
|
* <ul>
|
| 2017 |
|
|
* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
|
| 2018 |
|
|
* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
|
| 2019 |
|
|
* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
|
| 2020 |
|
|
* </ul>
|
| 2021 |
|
|
* <p>
|
| 2022 |
|
|
* This compare logic of the underlying webservice is the
|
| 2023 |
|
|
* <b>inverse logic</b> of the the one implemented in
|
| 2024 |
|
|
* java.lang.Comparable#compareTo(java.lang.Object)
|
| 2025 |
|
|
*
|
| 2026 |
|
|
* @param $thisRankUuid
|
| 2027 |
|
|
* @param $thatRankUuid
|
| 2028 |
|
|
*
|
| 2029 |
|
|
* @return int
|
| 2030 |
|
|
* A negative integer, zero, or a positive integer
|
| 2031 |
|
|
* as the thisRank is lower than, equal to, or higher than thatRank.
|
| 2032 |
|
|
*/
|
| 2033 |
|
|
function rank_compare($thisRankUuid, $thatRankUuid) {
|
| 2034 |
|
|
$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
|
| 2035 |
|
|
return $result->Integer;
|
| 2036 |
|
|
}
|
| 2037 |
|
|
|
| 2038 |
|
|
/**
|
| 2039 |
|
|
* Composes an HTML element class attribute value composed of
|
| 2040 |
|
|
* the shortname of the cdm class and the uuid of the entity.
|
| 2041 |
|
|
* This class attribute should be used whereever an cdm-entity is rendered.
|
| 2042 |
|
|
*
|
| 2043 |
|
|
* These according class selectors in css must be escaped, eg:
|
| 2044 |
|
|
* .cdm\:TextData
|
| 2045 |
|
|
*
|
| 2046 |
|
|
* @param $cdmEntity
|
| 2047 |
|
|
*/
|
| 2048 |
f19f47fa
|
Andreas Kohlbecker
|
function html_class_attribute_ref($cdmEntity) {
|
| 2049 |
6657531f
|
Andreas Kohlbecker
|
|
| 2050 |
|
|
if (is_cdm_entity($cdmEntity)) {
|
| 2051 |
|
|
return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
|
| 2052 |
|
|
}
|
| 2053 |
|
|
}
|
| 2054 |
|
|
|
| 2055 |
|
|
|
| 2056 |
|
|
/**
|
| 2057 |
|
|
* Creates a short taxonname.
|
| 2058 |
|
|
*
|
| 2059 |
e90899ac
|
Andreas Kohlbecker
|
* The short name is created by using the taggedTitle field of
|
| 2060 |
6657531f
|
Andreas Kohlbecker
|
* NameSTO or NameTO instances.
|
| 2061 |
e90899ac
|
Andreas Kohlbecker
|
* If the taggedTitle if empty the fullname will be returned.
|
| 2062 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 2063 |
|
|
* @param unknown_type $name
|
| 2064 |
|
|
* Name or TreeNode.
|
| 2065 |
|
|
*
|
| 2066 |
|
|
* @return string
|
| 2067 |
|
|
*/
|
| 2068 |
|
|
function cdm_dataportal_shortname_of($name) {
|
| 2069 |
|
|
$nameStr = '';
|
| 2070 |
|
|
|
| 2071 |
e90899ac
|
Andreas Kohlbecker
|
normalize_tagged_text($name->taggedTitle);
|
| 2072 |
6657531f
|
Andreas Kohlbecker
|
|
| 2073 |
|
|
// Get all tagged text tokens of the scientific name.
|
| 2074 |
|
|
foreach ($name->taggedTitle as $tagtxt) {
|
| 2075 |
|
|
if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
|
| 2076 |
|
|
$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
|
| 2077 |
|
|
}
|
| 2078 |
|
|
}
|
| 2079 |
|
|
$nameStr = trim($nameStr);
|
| 2080 |
|
|
|
| 2081 |
|
|
if ($nameStr) {
|
| 2082 |
|
|
|
| 2083 |
|
|
// Do not return short names for these.
|
| 2084 |
|
|
if ($name->unplaced || $name->excluded) {
|
| 2085 |
|
|
return $nameStr;
|
| 2086 |
|
|
}
|
| 2087 |
|
|
|
| 2088 |
|
|
/*
|
| 2089 |
|
|
1st capture group (^[a-zA-Z]): First letter of uninomial.
|
| 2090 |
|
|
Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
|
| 2091 |
|
|
Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
|
| 2092 |
|
|
but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
|
| 2093 |
|
|
OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
|
| 2094 |
|
|
*/
|
| 2095 |
|
|
$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
|
| 2096 |
|
|
if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
|
| 2097 |
|
|
return $matches[1][0] . "." . $matches[3][0];
|
| 2098 |
|
|
}
|
| 2099 |
|
|
else {
|
| 2100 |
|
|
return $nameStr;
|
| 2101 |
|
|
}
|
| 2102 |
|
|
}
|
| 2103 |
|
|
else {
|
| 2104 |
|
|
return $name->titleCache;
|
| 2105 |
|
|
}
|
| 2106 |
|
|
}
|
| 2107 |
|
|
|
| 2108 |
|
|
/**
|
| 2109 |
|
|
* Check if a taxon is accepted by the current taxonomic tree.
|
| 2110 |
|
|
*
|
| 2111 |
|
|
* @param mixed $taxon
|
| 2112 |
|
|
* The Taxon obkect to check.
|
| 2113 |
|
|
*
|
| 2114 |
|
|
* @return bool
|
| 2115 |
|
|
* Returns TRUE if $taxon is accepted, FALSE otherwise.
|
| 2116 |
|
|
*/
|
| 2117 |
|
|
function _cdm_dataportal_acceptedByCurrentView($taxon) {
|
| 2118 |
|
|
|
| 2119 |
7663cd0b
|
Andreas Kohlbecker
|
$defaultTreeUuid = get_current_classification_uuid();
|
| 2120 |
6657531f
|
Andreas Kohlbecker
|
|
| 2121 |
|
|
if (isset($taxon->taxonNodes)) {
|
| 2122 |
|
|
$taxonNodes = $taxon->taxonNodes;
|
| 2123 |
|
|
}
|
| 2124 |
|
|
else {
|
| 2125 |
|
|
$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
|
| 2126 |
|
|
}
|
| 2127 |
|
|
|
| 2128 |
|
|
if ($taxon->class == "Taxon" && isset($taxonNodes)) {
|
| 2129 |
|
|
foreach ($taxonNodes as $node) {
|
| 2130 |
586fc780
|
Andreas Kohlbecker
|
if (isset($node->classification)){
|
| 2131 |
|
|
if(is_object($node->classification)) {
|
| 2132 |
|
|
if ($node->classification->uuid == $defaultTreeUuid) {
|
| 2133 |
|
|
return TRUE;
|
| 2134 |
|
|
}
|
| 2135 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2136 |
586fc780
|
Andreas Kohlbecker
|
else {
|
| 2137 |
|
|
if ($node->classification == $defaultTreeUuid) {
|
| 2138 |
|
|
return TRUE;
|
| 2139 |
|
|
}
|
| 2140 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2141 |
|
|
}
|
| 2142 |
|
|
}
|
| 2143 |
|
|
}
|
| 2144 |
|
|
|
| 2145 |
|
|
return FALSE;
|
| 2146 |
|
|
}
|
| 2147 |
|
|
|
| 2148 |
|
|
/**
|
| 2149 |
54cfa718
|
Andreas Kohlbecker
|
* Checks is the source has one of the given types.
|
| 2150 |
|
|
*
|
| 2151 |
|
|
* @param object $source
|
| 2152 |
|
|
* The original source entity
|
| 2153 |
|
|
* @param array $types
|
| 2154 |
|
|
* An array of elementd of the OriginalSourceType enumeration
|
| 2155 |
|
|
* If not set the default will be used which is:
|
| 2156 |
|
|
* - Lineage
|
| 2157 |
|
|
* - PrimaryMediaSource
|
| 2158 |
|
|
* - PrimaryTaxonomicSource
|
| 2159 |
|
|
* - Unknown
|
| 2160 |
|
|
* - Other
|
| 2161 |
|
|
* @return boolean
|
| 2162 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 2163 |
54cfa718
|
Andreas Kohlbecker
|
function _is_original_source_type($source, $types = null) {
|
| 2164 |
|
|
// this is the default
|
| 2165 |
|
|
// maybe this should also be put into the settings
|
| 2166 |
|
|
static $default = array(
|
| 2167 |
|
|
OriginalSourceType::Lineage,
|
| 2168 |
|
|
OriginalSourceType::PrimaryMediaSource,
|
| 2169 |
|
|
OriginalSourceType::PrimaryTaxonomicSource,
|
| 2170 |
|
|
OriginalSourceType::Unknown,
|
| 2171 |
|
|
OriginalSourceType::Other,
|
| 2172 |
|
|
);
|
| 2173 |
|
|
|
| 2174 |
|
|
if(!$types){
|
| 2175 |
|
|
$types = $default;
|
| 2176 |
|
|
}
|
| 2177 |
|
|
return isset($source->type) && in_array($source->type, $types);
|
| 2178 |
|
|
}
|
| 2179 |
6657531f
|
Andreas Kohlbecker
|
|
| 2180 |
|
|
/**
|
| 2181 |
|
|
* @todo Please document this function.
|
| 2182 |
|
|
* @see http://drupal.org/node/1354
|
| 2183 |
|
|
*/
|
| 2184 |
|
|
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
|
| 2185 |
|
|
return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
|
| 2186 |
|
|
}
|
| 2187 |
|
|
|
| 2188 |
|
|
|
| 2189 |
|
|
/**
|
| 2190 |
|
|
* Collects all the media from a list of description elements.
|
| 2191 |
|
|
*
|
| 2192 |
|
|
* @param array $descriptionElements
|
| 2193 |
|
|
* The description elements from which to collect the media.
|
| 2194 |
|
|
*
|
| 2195 |
|
|
* @return array
|
| 2196 |
|
|
* The output with all the collected media.
|
| 2197 |
|
|
*/
|
| 2198 |
|
|
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
|
| 2199 |
|
|
|
| 2200 |
|
|
$outArrayOfMedia = array();
|
| 2201 |
|
|
|
| 2202 |
|
|
// Avoiding a warning box in Drupal for Flora Malesiana.
|
| 2203 |
|
|
if (isset($descriptionElements) && is_array($descriptionElements)) {
|
| 2204 |
|
|
foreach ($descriptionElements as $descriptionElement) {
|
| 2205 |
|
|
if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
|
| 2206 |
|
|
foreach ($descriptionElement->media as $media) {
|
| 2207 |
|
|
if (is_object($media)) {
|
| 2208 |
|
|
$outArrayOfMedia[] = $media;
|
| 2209 |
|
|
}
|
| 2210 |
|
|
}
|
| 2211 |
|
|
}
|
| 2212 |
|
|
}
|
| 2213 |
|
|
}
|
| 2214 |
|
|
return $outArrayOfMedia;
|
| 2215 |
|
|
}
|
| 2216 |
|
|
|
| 2217 |
|
|
/**
|
| 2218 |
|
|
* @todo Please document this function.
|
| 2219 |
|
|
* @see http://drupal.org/node/1354
|
| 2220 |
|
|
*
|
| 2221 |
65345976
|
Andreas Kohlbecker
|
* @param array $cdm_entities
|
| 2222 |
6657531f
|
Andreas Kohlbecker
|
* An array of CdmBase instances or a single instance.
|
| 2223 |
28c5c87a
|
Andreas Kohlbecker
|
* @param string $footnote_list_key_suggestion
|
| 2224 |
6657531f
|
Andreas Kohlbecker
|
*
|
| 2225 |
|
|
* @return unknown
|
| 2226 |
|
|
*/
|
| 2227 |
65345976
|
Andreas Kohlbecker
|
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
|
| 2228 |
90597e37
|
Andreas Kohlbecker
|
|
| 2229 |
|
|
static $annotations_types_filter = null;
|
| 2230 |
6657531f
|
Andreas Kohlbecker
|
if(!$annotations_types_filter) {
|
| 2231 |
90597e37
|
Andreas Kohlbecker
|
$annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
|
| 2232 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2233 |
|
|
|
| 2234 |
|
|
$footNoteKeys = array();
|
| 2235 |
|
|
|
| 2236 |
|
|
// Is argument cdmBase an array?
|
| 2237 |
65345976
|
Andreas Kohlbecker
|
if (!is_array($cdm_entities)) {
|
| 2238 |
6657531f
|
Andreas Kohlbecker
|
$cdmBase_array = array();
|
| 2239 |
65345976
|
Andreas Kohlbecker
|
$cdmBase_array[] = $cdm_entities;
|
| 2240 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2241 |
|
|
else {
|
| 2242 |
65345976
|
Andreas Kohlbecker
|
$cdmBase_array = $cdm_entities;
|
| 2243 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2244 |
|
|
|
| 2245 |
|
|
// Getting the key for the footnotemanager.
|
| 2246 |
28c5c87a
|
Andreas Kohlbecker
|
if (isset($footnote_list_key_suggestion)) {
|
| 2247 |
|
|
$footnote_list_key = $footnote_list_key_suggestion;
|
| 2248 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2249 |
|
|
else {
|
| 2250 |
28c5c87a
|
Andreas Kohlbecker
|
$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
|
| 2251 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2252 |
|
|
|
| 2253 |
|
|
// Adding the footnotes keys.
|
| 2254 |
|
|
foreach ($cdmBase_array as $cdmBase_element) {
|
| 2255 |
|
|
$annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
|
| 2256 |
|
|
if (is_array($annotations)) {
|
| 2257 |
|
|
foreach ($annotations as $annotation) {
|
| 2258 |
28c5c87a
|
Andreas Kohlbecker
|
$footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
|
| 2259 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2260 |
|
|
}
|
| 2261 |
|
|
}
|
| 2262 |
|
|
|
| 2263 |
|
|
return $footNoteKeys;
|
| 2264 |
|
|
}
|
| 2265 |
|
|
|
| 2266 |
d9763fd3
|
Andreas Kohlbecker
|
|
| 2267 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 2268 |
d9763fd3
|
Andreas Kohlbecker
|
* Creates a CDM Dynabox.
|
| 2269 |
|
|
*
|
| 2270 |
c1f5d897
|
Andreas Kohlbecker
|
* @param string $dynabox_id
|
| 2271 |
d9763fd3
|
Andreas Kohlbecker
|
* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
|
| 2272 |
6657531f
|
Andreas Kohlbecker
|
* @param string $label
|
| 2273 |
|
|
* The clickable text to show.
|
| 2274 |
|
|
* @param string $content_url
|
| 2275 |
|
|
* The cdm REST service request url wich will deliver the content to be shown
|
| 2276 |
|
|
* once the dynabox toggles open.
|
| 2277 |
|
|
* @param string $theme
|
| 2278 |
1ce9afb7
|
Patric Plitzner
|
* The theme to be used for rendering the cdm REST service response with is
|
| 2279 |
6657531f
|
Andreas Kohlbecker
|
* returned from the $content_url.
|
| 2280 |
|
|
* @param string $link_alt_text
|
| 2281 |
|
|
* The value for the alt attribute of the dynabox link.
|
| 2282 |
|
|
* @param array $enclosingtags
|
| 2283 |
|
|
* An array with two elements: $enclosingtags[0] will be used for the dynabox
|
| 2284 |
|
|
* element itself, $enclosingtags[1] is the tag to be used for the
|
| 2285 |
c1f5d897
|
Andreas Kohlbecker
|
* dynabox_content (optional)
|
| 2286 |
d9763fd3
|
Andreas Kohlbecker
|
* @param array $attributes
|
| 2287 |
|
|
* @param $content_element_selector
|
| 2288 |
|
|
* Optional jQuery selector which can be used to reference a dom element which should
|
| 2289 |
|
|
* be used as container for the content to be shown. The dynabox-<dynabox id>-content
|
| 2290 |
|
|
* element will be placed in this container.
|
| 2291 |
|
|
*
|
| 2292 |
c1f5d897
|
Andreas Kohlbecker
|
* @param string $open_callback
|
| 2293 |
1ce9afb7
|
Patric Plitzner
|
* optional javascript call back function to be triggered after toggling the box to
|
| 2294 |
c1f5d897
|
Andreas Kohlbecker
|
* the open state.
|
| 2295 |
|
|
* @param string $close_callback
|
| 2296 |
1ce9afb7
|
Patric Plitzner
|
* optional javascript call back function to be triggered after toggling the box to
|
| 2297 |
c1f5d897
|
Andreas Kohlbecker
|
* the closed state.
|
| 2298 |
d9763fd3
|
Andreas Kohlbecker
|
* @return string Returns HTML for a dynabox.
|
| 2299 |
|
|
* Returns HTML for a dynabox.
|
| 2300 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 2301 |
d9763fd3
|
Andreas Kohlbecker
|
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
|
| 2302 |
|
|
$enclosingtags = array('li', 'ul'), $attributes = array(),
|
| 2303 |
|
|
$content_element_selector = null,
|
| 2304 |
|
|
$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
|
| 2305 |
6657531f
|
Andreas Kohlbecker
|
$out = '';
|
| 2306 |
c1f5d897
|
Andreas Kohlbecker
|
|
| 2307 |
|
|
// check for plain class attribute string
|
| 2308 |
|
|
$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
|
| 2309 |
|
|
|
| 2310 |
9c9d11f7
|
Andreas Kohlbecker
|
if(!array_key_exists('class', $attributes)) {
|
| 2311 |
|
|
$attributes['class'] = array();
|
| 2312 |
|
|
}
|
| 2313 |
d9763fd3
|
Andreas Kohlbecker
|
$attributes['id'][] = 'dynabox-' . $dynabox_id;
|
| 2314 |
9c9d11f7
|
Andreas Kohlbecker
|
$dynabox_attributes = drupal_attributes($attributes);
|
| 2315 |
|
|
|
| 2316 |
|
|
|
| 2317 |
b386ae48
|
Andreas Kohlbecker
|
_add_js_domEvent(); // requires domEvent.js
|
| 2318 |
6657531f
|
Andreas Kohlbecker
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
|
| 2319 |
c1f5d897
|
Andreas Kohlbecker
|
drupal_add_js("
|
| 2320 |
94bb8db6
|
Andreas Kohlbecker
|
jQuery(document).ready(
|
| 2321 |
|
|
function() {
|
| 2322 |
|
|
dynabox('". $dynabox_id ."',
|
| 2323 |
|
|
{
|
| 2324 |
|
|
open_callback: " . $open_callback .",
|
| 2325 |
d9763fd3
|
Andreas Kohlbecker
|
close_callback: " . $close_callback .
|
| 2326 |
|
|
($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
|
| 2327 |
94bb8db6
|
Andreas Kohlbecker
|
}
|
| 2328 |
|
|
);
|
| 2329 |
|
|
}
|
| 2330 |
|
|
);",
|
| 2331 |
|
|
array(
|
| 2332 |
|
|
'type'=>'inline',
|
| 2333 |
|
|
'scope'=>'footer'
|
| 2334 |
|
|
)
|
| 2335 |
|
|
);
|
| 2336 |
6657531f
|
Andreas Kohlbecker
|
|
| 2337 |
9c9d11f7
|
Andreas Kohlbecker
|
|
| 2338 |
6657531f
|
Andreas Kohlbecker
|
$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
|
| 2339 |
9c9d11f7
|
Andreas Kohlbecker
|
$out .= '<!-- dynabox for ' . $content_url . ' -->';
|
| 2340 |
7cc085da
|
Andreas Kohlbecker
|
$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>';
|
| 2341 |
d9763fd3
|
Andreas Kohlbecker
|
$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
|
| 2342 |
|
|
$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
|
| 2343 |
|
|
$out .= ' </' . $enclosingtags[1] . '>';
|
| 2344 |
|
|
$out .= ' </' . $enclosingtags[0] . '>';
|
| 2345 |
9c9d11f7
|
Andreas Kohlbecker
|
$out .= '<!-- dynabox end -->';
|
| 2346 |
6657531f
|
Andreas Kohlbecker
|
return $out;
|
| 2347 |
|
|
}
|
| 2348 |
|
|
|
| 2349 |
|
|
/**
|
| 2350 |
|
|
* Checks whether a feature has any description elements.
|
| 2351 |
|
|
*
|
| 2352 |
|
|
* @param mixed $featureNode
|
| 2353 |
|
|
* A feature node as produced by the function _mergeFeatureTreeDescriptions().
|
| 2354 |
|
|
*
|
| 2355 |
|
|
* @see _mergeFeatureTreeDescriptions()
|
| 2356 |
|
|
*
|
| 2357 |
|
|
* @return bool
|
| 2358 |
|
|
* Returns TRUE if the given $featureNode or any of its subordinate nodes
|
| 2359 |
|
|
* contains at least one non empty TextData or at least one DescriptionElement
|
| 2360 |
|
|
* of an other type. A TextData element holding a multilanguageText or a
|
| 2361 |
|
|
* source reference is considered to be not empty.
|
| 2362 |
159cd9bb
|
Andreas Kohlbecker
|
*
|
| 2363 |
|
|
* @TODO this function may have become obsolete by the new method of detecting empty blocks,
|
| 2364 |
aa26f9f0
|
Andreas Kohlbecker
|
* see $block_content_is_not_empty in compose_feature_blocks() and
|
| 2365 |
0ebb6efc
|
Andreas Kohlbecker
|
* $feature_block_has_content in compose_feature_block_items_generic
|
| 2366 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 2367 |
f19f47fa
|
Andreas Kohlbecker
|
function has_feature_node_description_elements($featureNode) {
|
| 2368 |
6657531f
|
Andreas Kohlbecker
|
|
| 2369 |
|
|
if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
|
| 2370 |
092744e1
|
Andreas Kohlbecker
|
if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
|
| 2371 |
|
|
foreach ($featureNode->descriptionElements as $descriptionElement) {
|
| 2372 |
159cd9bb
|
Andreas Kohlbecker
|
if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
|
| 2373 |
|
|
&& $descriptionElement->multilanguageText_L10n->text != ''
|
| 2374 |
|
|
|| isset($descriptionElement->sources[0])
|
| 2375 |
|
|
|| isset($descriptionElement->media[0]) ) {
|
| 2376 |
092744e1
|
Andreas Kohlbecker
|
return TRUE;
|
| 2377 |
|
|
}
|
| 2378 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 2379 |
|
|
}
|
| 2380 |
|
|
}
|
| 2381 |
092744e1
|
Andreas Kohlbecker
|
else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
|
| 2382 |
fae36a2a
|
Andreas Kohlbecker
|
foreach ($featureNode->childNodes as $child) {
|
| 2383 |
f19f47fa
|
Andreas Kohlbecker
|
if (has_feature_node_description_elements($child)) {
|
| 2384 |
6657531f
|
Andreas Kohlbecker
|
return TRUE;
|
| 2385 |
|
|
}
|
| 2386 |
|
|
}
|
| 2387 |
|
|
}
|
| 2388 |
|
|
return FALSE;
|
| 2389 |
|
|
}
|
| 2390 |
f26245c8
|
Andreas Kohlbecker
|
|
| 2391 |
|
|
/**
|
| 2392 |
|
|
* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
|
| 2393 |
|
|
*
|
| 2394 |
|
|
* @param $chapter
|
| 2395 |
|
|
* The taxon page chapter or part
|
| 2396 |
|
|
*/
|
| 2397 |
|
|
function cdm_check_valid_taxon_page($chapter){
|
| 2398 |
|
|
static $taxon_tabs = null;
|
| 2399 |
|
|
|
| 2400 |
|
|
cdm_check_valid_portal_page();
|
| 2401 |
|
|
|
| 2402 |
|
|
if($taxon_tabs == null){
|
| 2403 |
|
|
$taxon_tabs = array('all', 'description');
|
| 2404 |
|
|
foreach(get_taxon_tabs_list() as $tab){
|
| 2405 |
|
|
$taxon_tabs[] = strtolower($tab);
|
| 2406 |
|
|
}
|
| 2407 |
|
|
}
|
| 2408 |
|
|
|
| 2409 |
|
|
if(!in_array($chapter, $taxon_tabs)){
|
| 2410 |
|
|
// oops this is not a valid chapter name
|
| 2411 |
b4a5c2be
|
Andreas Kohlbecker
|
http_response_code(404); // 404 = Not Found
|
| 2412 |
f26245c8
|
Andreas Kohlbecker
|
}
|
| 2413 |
|
|
|
| 2414 |
|
|
}
|
| 2415 |
|
|
|
| 2416 |
|
|
/**
|
| 2417 |
|
|
* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise
|
| 2418 |
|
|
*
|
| 2419 |
|
|
* @param $chapter
|
| 2420 |
|
|
* The taxon page chapter or part
|
| 2421 |
|
|
*/
|
| 2422 |
|
|
function cdm_check_valid_portal_page(){
|
| 2423 |
595de9f0
|
Andreas Kohlbecker
|
$ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
|
| 2424 |
f26245c8
|
Andreas Kohlbecker
|
if(preg_match($ends_with_file_suffix_pattern, $_GET['q'])){
|
| 2425 |
|
|
// oops this urls ends with a file_suffix and thus does not refer to a portal page
|
| 2426 |
b4a5c2be
|
Andreas Kohlbecker
|
http_response_code(404); // 404 = Not Found
|
| 2427 |
595de9f0
|
Andreas Kohlbecker
|
exit('HTTP 404');
|
| 2428 |
f26245c8
|
Andreas Kohlbecker
|
}
|
| 2429 |
|
|
}
|
| 2430 |
b2b9e057
|
Andreas Kohlbecker
|
|
| 2431 |
|
|
/**
|
| 2432 |
|
|
* Generates the diff of the texts and presents it in a HTML diff viewer.
|
| 2433 |
|
|
*
|
| 2434 |
|
|
* @param $text_a
|
| 2435 |
|
|
* @param $text_b
|
| 2436 |
|
|
* @return string
|
| 2437 |
|
|
*/
|
| 2438 |
|
|
function diff_viewer($text_a, $text_b) {
|
| 2439 |
|
|
|
| 2440 |
|
|
static $diff_viewer_count = 0;
|
| 2441 |
|
|
|
| 2442 |
|
|
$element_id = 'part_definitions_diff_' . $diff_viewer_count++;
|
| 2443 |
|
|
|
| 2444 |
|
|
// http://code.stephenmorley.org/php/diff-implementation/
|
| 2445 |
|
|
module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
|
| 2446 |
|
|
drupal_add_css(drupal_get_path('module',
|
| 2447 |
|
|
'cdm_dataportal') . '/css/diff.css');
|
| 2448 |
087bb473
|
Andreas Kohlbecker
|
_add_jquery_ui();
|
| 2449 |
b2b9e057
|
Andreas Kohlbecker
|
drupal_add_js(
|
| 2450 |
|
|
'jQuery(document).ready( function(){
|
| 2451 |
|
|
jQuery(\'#' . $element_id . '\').accordion({
|
| 2452 |
|
|
collapsible: true,
|
| 2453 |
|
|
active: false,
|
| 2454 |
|
|
fillSpace: true,
|
| 2455 |
|
|
}).children(\'div\').css({ \'height\': \'auto\' });
|
| 2456 |
|
|
jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
|
| 2457 |
|
|
});'
|
| 2458 |
|
|
, array(
|
| 2459 |
|
|
'type' => 'inline',
|
| 2460 |
|
|
'scope' => 'footer'
|
| 2461 |
|
|
));
|
| 2462 |
|
|
|
| 2463 |
|
|
$diff = Diff::compare($text_a,
|
| 2464 |
|
|
$text_b);
|
| 2465 |
|
|
$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
|
| 2466 |
|
|
. Diff::toTable($diff, '', '')
|
| 2467 |
|
|
. '</div></div>';
|
| 2468 |
|
|
return $diff_viewer_markup;
|
| 2469 |
|
|
}
|
| 2470 |
|
|
|