/modules/cdm_dataportal/cdm_dataportal.module - Annotate - EDIT - EDIT Project Management

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 6679207a

1	6657531f	Andreas Kohlbecker	<?php
2			/**
3			* @file
4			* Module to provide a CDM Dataportal.
5			*
6			* @copyright
7			* (C) 2007-2012 EDIT
8			* European Distributed Institute of Taxonomy
9			* http://www.e-taxonomy.eu
10			*
11			* The contents of this module are subject to the Mozilla
12			* Public License Version 1.1.
13			* @see http://www.mozilla.org/MPL/MPL-1.1.html
14			*
15			* @author
16			* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
17			* - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
18			*/
19
20	38b27a36	Andreas Kohlbecker	module_load_include('php', 'cdm_dataportal', 'node_types');
21			module_load_include('php', 'cdm_dataportal', 'settings');
22			module_load_include('php', 'cdm_dataportal', 'help');
23			module_load_include('php', 'cdm_dataportal', 'cdm_dataportal.search');
24
25			module_load_include('inc', 'cdm_dataportal', 'includes/common');
26	dd0767b6	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/footnotes');
27	e2617c7e	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/agent');
28	2e31ea9e	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/name');
29	b7a20282	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
30	bd56cbc1	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/taxon-node');
31	b7a20282	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/references');
32	38b27a36	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/pages');
33			module_load_include('inc', 'cdm_dataportal', 'includes/media');
34			module_load_include('inc', 'cdm_dataportal', 'includes/maps');
35			module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
36			module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
37			module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
38
39			module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
40			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
41			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
42			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
43			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
44			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
45			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
46			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
47			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
48
49			module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
50			module_load_include('php', 'cdm_dataportal', 'classes/footnote');
51			module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
52			module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
53
54
55			/* ============================ java script functions ============================= */
56
57
58			/**
59			* loads external java script files asynchronously.
60			*
61			* @param unknown_type $script_url
62			*/
63			function drupal_add_js_async($script_url, $callback){
64
65			drupal_add_js("
66			jQuery(document).ready(function() {
67			jQuery.ajax({
68			url: '" . $script_url . "',
69			dataType: 'script',
70			cache: true, // otherwise will get fresh copy every page load
71			success: function() {
72			" . $callback . "
73			}
74			});
75			});"
76			, 'inline');
77	6657531f	Andreas Kohlbecker	}
78
79	38b27a36	Andreas Kohlbecker	/**
80			*/
81			function drupal_add_js_rowToggle($tableId){
82	6657531f	Andreas Kohlbecker
83	38b27a36	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
84			drupal_add_js('jQuery(document).ready(function(){
85			addRowToggle("' . $tableId . '");
86	6657531f	Andreas Kohlbecker	});
87	38b27a36	Andreas Kohlbecker	', array('type' => 'inline'));
88			}
89	d2fd2a4c	Andreas Kohlbecker
90	38b27a36	Andreas Kohlbecker	/**
91			* @param unknown_type $link_element_selector
92			* @param unknown_type $progress_element_selector
93			*/
94			function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
95
96			$callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
97
98			drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
99
100			// drupal_add_js("
101			// if (Drupal.jsEnabled) {
102			// $(document).ready(function() {
103			// $('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
104			// });
105			// }", 'inline');
106			}
107
108			/**
109			* @todo Please document this function.
110			* @see http://drupal.org/node/1354
111			*/
112			function _add_js_treeselector() {
113			// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
114			drupal_add_js("
115			jQuery(document).ready(function() {
116			jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
117			jQuery('#cdm-taxonomictree-selector-form').submit();
118			});
119
120			});
121			",
122			array(
123			'type' => 'inline',
124			'scope' => 'footer'
125			)
126			);
127	5ea8b301	Andreas Kohlbecker	}
128
129	6b605d3b	Andreas Kohlbecker	function _add_js_resizable_element($selector, $y_axis_only) {
130
131			_add_jquery_ui();
132			$options = "";
133			if($y_axis_only) {
134			$options = "resize: function(event, ui) {
135			ui.size.width = ui.originalSize.width;
136			},
137			handles: \"s\"";
138
139			}
140			drupal_add_js("
141			jQuery(document).ready(function() {
142			jQuery('" . $selector . "').resizable({". $options ."});
143			});
144			",
145			array(
146			'type' => 'inline',
147			'scope' => 'footer'
148			)
149			);
150			}
151
152	38b27a36	Andreas Kohlbecker	function _add_js_openlayers() {
153
154			$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
155			$proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
156
157			if(variable_get('cdm_js_devel_mode', FALSE)){
158			// develooper mode libs
159			// $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
160			$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
161			$proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
162			}
163
164			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
165			array(
166			'type' => 'file',
167	4c21ffdb	Andreas Kohlbecker	'group' => JS_LIBRARY,
168			'weight' => 0,
169	38b27a36	Andreas Kohlbecker	'cache' => TRUE,
170			'preprocess' => FALSE
171			)
172			);
173	2020828c	Andreas Kohlbecker
174	c1fc969a	Andreas Kohlbecker
175	38b27a36	Andreas Kohlbecker	// see https://github.com/proj4js/proj4js
176			// http://openlayers.org/dev/examples/using-proj4js.html
177			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
178			array(
179			'type' => 'file',
180	4c21ffdb	Andreas Kohlbecker	'group' => JS_LIBRARY,
181			'weight' => -1, // before open layers
182	38b27a36	Andreas Kohlbecker	'cache' => TRUE,
183			)
184			);
185
186			// configure the theme
187			$openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
188			$openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
189			drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
190			'type' => 'inline',
191	4c21ffdb	Andreas Kohlbecker	'group' => JS_LIBRARY,
192			'weight' => 1, // after openlayers
193	38b27a36	Andreas Kohlbecker	'cache' => TRUE,
194			'preprocess' => FALSE
195			));
196
197			drupal_add_css($openlayers_theme_path . 'style.tidy.css',
198			array(
199			'type' => 'file',
200			'cache' => TRUE,
201			'preprocess' => FALSE
202			)
203			);
204	e3026d72	Andreas Kohlbecker
205	38b27a36	Andreas Kohlbecker	}
206	e3026d72	Andreas Kohlbecker
207	38b27a36	Andreas Kohlbecker	/**
208			* @todo Please document this function.
209			* @see http://drupal.org/node/1354
210			*/
211			function _add_js_thickbox() {
212			// ---- jQuery thickbox:
213			/*
214			* bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
215			* not triggered because of problems with compat-1.0.js' see INSTALL.txt
216			*/
217			// drupal_add_js(drupal_get_path('module',
218			// 'cdm_dataportal').'/js/jquery.imagetool.min.js');
219			//
220			// Add a setting for the path to cdm_dataportal module, used to find the path
221			// for the loading animation image in thickbox.
222			drupal_add_js(array(
223			'cdm_dataportal' => array(
224			'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
225	10f6aa4b	Andreas Kohlbecker	)
226	38b27a36	Andreas Kohlbecker	),
227			'setting'
228			);
229			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
230			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
231			}
232	94550ff9	Andreas Kohlbecker
233	38b27a36	Andreas Kohlbecker	/**
234			* @todo Please document this function.
235			* @see http://drupal.org/node/1354
236			*/
237			function _add_js_lightbox($galleryID) {
238			/*
239			* Important Notice: The jquery.lightbox-0.5.js has been modified in order to
240	fe19a89b	Andreas Kohlbecker	* allow using the "alt" attribute for captions instead of the "title"
241			* attribute
242			*/
243	38b27a36	Andreas Kohlbecker	$lightbox_base_path = drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
244			$lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
245			drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
246			drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
247			drupal_add_js('jQuery(document).ready(function() {
248			jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
249			fixedNavigation: true,
250			imageLoading: \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
251			imageBtnPrev: \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
252			imageBtnNext: \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
253			imageBtnClose: \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
254			imageBlank: \'' . $lightbox_image_path . 'lightbox-blank.gif\',
255			adjustToWindow: true
256			});
257	94550ff9	Andreas Kohlbecker	});
258	38b27a36	Andreas Kohlbecker	', array('type' => 'inline'));
259			}
260	94550ff9	Andreas Kohlbecker
261	38b27a36	Andreas Kohlbecker	/**
262			* @todo Please document this function.
263			* @see http://drupal.org/node/1354
264			*/
265			function _add_js_footnotes() {
266			_add_js_domEvent();
267			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
268			}
269	94550ff9	Andreas Kohlbecker
270	38b27a36	Andreas Kohlbecker	/**
271			* @todo Please document this function.
272			* @see http://drupal.org/node/1354
273			*/
274			function _add_js_ahah() {
275	b386ae48	Andreas Kohlbecker
276	38b27a36	Andreas Kohlbecker	_add_js_domEvent(); // requires domEvent.js
277			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
278			}
279	94550ff9	Andreas Kohlbecker
280	d0d23caa	Andreas Kohlbecker	/**
281			* @todo Please document this function.
282			* @see http://drupal.org/node/1354
283			*/
284			function _add_js_taxonomic_children($jquery_selector) {
285	b0adfd32	Andreas Kohlbecker
286			global $base_url;
287
288
289			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
290	faf4f771	Andreas Kohlbecker
291	d0d23caa	Andreas Kohlbecker	drupal_add_js('jQuery(document).ready(function() {
292	b0adfd32	Andreas Kohlbecker	jQuery(\'' . $jquery_selector . '\').taxonomic_children({
293	09edee9a	Andreas Kohlbecker	// hoverClass: "fa-rotate-90",
294			// activeClass: "fa-rotate-90",
295	b0adfd32	Andreas Kohlbecker	classificationUuid: "' . get_current_classification_uuid() . '",
296	0af3ce28	Andreas Kohlbecker	taxonUuid: "' . get_current_taxon_uuid() . '",
297	38da4e54	Andreas Kohlbecker	cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
298	b0adfd32	Andreas Kohlbecker	proxyBaseUri: "' . $base_url . '",
299
300			});
301	d0d23caa	Andreas Kohlbecker	});
302			', array('type' => 'inline'));
303			}
304
305	38b27a36	Andreas Kohlbecker	/**
306			* Adds the external javascript file for domEvent.js.
307			*
308			* @see drupal_add_js()
309			*/
310			function _add_js_domEvent() {
311			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
312			}
313	b386ae48	Andreas Kohlbecker
314	087bb473	Andreas Kohlbecker	function _add_jquery_ui()
315			{
316			drupal_add_css(drupal_get_path('module',
317			'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
318			drupal_add_js(drupal_get_path('module',
319			'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
320			array(
321			'type' => 'file',
322			'weight' => JS_LIBRARY,
323			'cache' => TRUE,
324			'preprocess' => FALSE
325			)
326			);
327			}
328
329	b18d70f6	Andreas Kohlbecker	function _add_js_ui_accordion(){
330			_add_jquery_ui();
331			drupal_add_js('jQuery(document).ready(function() {
332			jQuery( "#accordion" ).accordion();
333			});',
334			array('type' => 'inline')
335			);
336			}
337
338	c05d1cfb	Andreas Kohlbecker
339			function _add_js_utis_client($jquery_selector){
340
341			drupal_add_js(drupal_get_path('module',
342			'cdm_dataportal') . '/js/utis-client/utis-client.js',
343			array(
344			'type' => 'file',
345			'weight' => JS_LIBRARY,
346			'cache' => TRUE,
347			'preprocess' => FALSE
348			)
349			);
350
351			drupal_add_js('jQuery(document).ready(function() {
352			jQuery( "' . $jquery_selector . '" ).utis_client(
353			{
354	e27e3ff2	Andreas Kohlbecker	spinnerIcon: \'' . font_awesome_icon_markup('fa-sync', array('class' => array('fa-3x', 'fa-spin'), 'style' => array('opacity: 0.3;'))) . '\',
355			externalLinkIcon: \'' . font_awesome_icon_markup('fa-external-link-alt') . '\'
356	c05d1cfb	Andreas Kohlbecker	});
357			});',
358			array('type' => 'inline')
359			);
360			}
361
362	4a462641	Andreas Kohlbecker	function _add_js_universalviewer($jquery_selector, $manifest_uri){
363	a1f7edc0	Andreas Kohlbecker
364			$universalviewer_path = drupal_get_path('module', 'cdm_dataportal') . '/js/universalviewer';
365
366			drupal_add_css($universalviewer_path . '/uv/uv.css');
367	a6f91032	Andreas Kohlbecker	drupal_add_css($universalviewer_path . '/uv-fix.css');
368	a1f7edc0	Andreas Kohlbecker
369			// offline.js is all of these dependencies concatenated (jQuery, CoreJS, and JSViews)
370			drupal_add_js($universalviewer_path . '/uv/lib/offline.js',
371			array(
372			'type' => 'file',
373			'group' => JS_LIBRARY,
374			'cache' => TRUE,
375			'preprocess' => FALSE
376			)
377			);
378			drupal_add_js($universalviewer_path . '/uv/helpers.js',
379			array(
380			'type' => 'file',
381			'group' => JS_LIBRARY,
382			'cache' => TRUE,
383			'preprocess' => FALSE
384			)
385			);
386	b45a8503	Andreas Kohlbecker	// from UV 3.x documentation:
387			// "root:
388			// The path to the uv directory. Use a relative path e.g. root: '../../uv'
389			// Don't start your path with a / otherwise requirejs will not append .js to
390			// dependencies and they won't load."
391			//
392			// universalviewerPath will be used to build the root config variable.
393	6c1a6712	Andreas Kohlbecker	$iCleanUrlRequest = strpos($_SERVER['REQUEST_URI'], 'q=cdm_dataportal/') === false;
394			if($iCleanUrlRequest){
395			$folders_up = preg_replace('/[^\/]+/', '..', $_GET['q']);
396			$folders_up = preg_replace('/\.\.$/', '', $folders_up);
397			} else {
398			$folders_up = '';
399			}
400			$basePath = base_path();
401	b45a8503	Andreas Kohlbecker	$config_file = 'uv-config.json';
402	a1f7edc0	Andreas Kohlbecker	drupal_add_js('
403			console.log(\'jQuery inline: \' + jQuery.fn.jquery);
404			jQuery(window).on(\'uvLoaded\', function() {
405			jQuery( "' . $jquery_selector . '" ).jqUniversalviewer(
406			{
407	b45a8503	Andreas Kohlbecker	root: \'' . $folders_up . $universalviewer_path . '/uv\',
408	6c1a6712	Andreas Kohlbecker	configUri: \'' . $basePath . $universalviewer_path . '/'. $config_file . '\',
409	4a462641	Andreas Kohlbecker	manifestUri: \'' . $manifest_uri . '\'
410	a1f7edc0	Andreas Kohlbecker	}
411			);
412			});',
413			array(
414			'type' => 'inline',
415			'scope' => 'footer',
416			'group' => JS_DEFAULT,
417			'weight' => 0,
418			)
419			);
420			drupal_add_js($universalviewer_path . '/jq-universalviewer.js',
421			array(
422			'type' => 'file',
423			'scope' => 'footer',
424			'group' => JS_DEFAULT,
425			'weight' => 10,
426			'cache' => TRUE,
427			'preprocess' => FALSE
428			)
429			);
430			// ui.js must be last
431			drupal_add_js($universalviewer_path . '/uv/uv.js',
432			array(
433			'type' => 'file',
434			'scope' => 'footer',
435			'group' => 300, // IMPORTANT!
436			'cache' => TRUE,
437			'preprocess' => FALSE
438			)
439			);
440			}
441
442	38b27a36	Andreas Kohlbecker	/**
443			* Provides the markup for an font awesome icon.
444			*
445			* The icons is created in default size without any extra features.
446			*
447			* The available icons are listed here http://fontawesome.io/cheatsheet/
448	ef12d0c6	Andreas Kohlbecker	* fontawesome icons have much more features than implemented here in this function,
449			* for spinning icons, fixed width icons, rotation, etc please checkout the
450	38b27a36	Andreas Kohlbecker	* examples at http://fontawesome.io/examples/
451			*
452			* @parameter $icon_name
453			* The name of the icon which starts with 'fa-'
454			*
455			* @return String
456			* the markup for the icon in an <i> tag
457			*
458			*/
459	b0aa9a8f	Andreas Kohlbecker	function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
460	6d9071b7	Andreas Kohlbecker	_add_font_awesome_font();
461	38b27a36	Andreas Kohlbecker
462
463	b0aa9a8f	Andreas Kohlbecker	if($icon_name){
464			if(!isset($attributes['class'])){
465			$attributes['class'] = array();
466			}
467			$attributes['class'][] = 'fa';
468			$attributes['class'][] = $icon_name;
469
470			return '<i ' . drupal_attributes($attributes) . '></i>';
471	38b27a36	Andreas Kohlbecker	}
472
473	b0aa9a8f	Andreas Kohlbecker	return '';
474	38b27a36	Andreas Kohlbecker	}
475	94550ff9	Andreas Kohlbecker
476	2ffe4d59	Andreas Kohlbecker	/**
477			* @param string $glyph_name
478			* The name of the gloyph (e.g. 'icon-interal-link-alt-solid') for the foll list please
479			* refer to modules/cdm_dataportal/fonts/custom-icon-font
480			* @param array $attributes
481			* @return string
482			*/
483			function custom_icon_font_markup($glyph_name = NULL, $attributes = array()){
484			_add_font_custom_icon_font();
485
486
487			if($glyph_name){
488			if(!isset($attributes['class'])){
489			$attributes['class'] = array();
490			}
491			$attributes['class'][] = $glyph_name;
492
493			return '<i ' . drupal_attributes($attributes) . '></i>';
494			}
495
496			return '';
497			}
498
499	6d9071b7	Andreas Kohlbecker	/**
500			* Adds the css containing the font awesome icons to the html header.
501			*/
502			function _add_font_awesome_font()
503			{
504	2393d9c5	Andreas Kohlbecker	// $fa_font_version = 'font-awesome-4.6.3/css/font-awesome.min.css';
505			$fa_font_version = 'fontawesome-free-5.9.0-web/css/all.css';
506			$font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/' . $fa_font_version;
507	6d9071b7	Andreas Kohlbecker
508			drupal_add_html_head_link(
509			array(
510			'href' => $font_awesome_css_uri,
511			'rel' => 'stylesheet'
512			)
513			);
514			}
515
516	2ffe4d59	Andreas Kohlbecker	/**
517			* Adds the css containing the font awesome icons to the html header.
518			*/
519			function _add_font_custom_icon_font()
520			{
521
522			$custom_icon_font_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/custom-icon-font/style.css';
523
524			drupal_add_html_head_link(
525			array(
526			'href' => $custom_icon_font_css_uri,
527			'rel' => 'stylesheet'
528			)
529			);
530			}
531	38b27a36	Andreas Kohlbecker
532	6d9071b7	Andreas Kohlbecker	/* ====================== hook implementations ====================== */
533	38b27a36	Andreas Kohlbecker	/**
534			* Implements hook_permission().
535			*
536			* Valid permissions for this module.
537			*
538			* @return array
539	8385a9f2	Andreas Kohlbecker	* An array of valid permissions for the cdm_dataportal module.
540	38b27a36	Andreas Kohlbecker	*/
541			function cdm_dataportal_permission() {
542			return array(
543			'administer cdm_dataportal' => array(
544	8385a9f2	Andreas Kohlbecker	'title' => t('Administer CDM DataPortal settings'),
545			'description' => t("Access the settings pages specific for the cdm_dataportal module"),
546	c6fe437b	Andreas Kohlbecker	),
547			'access cdm content' => array(
548			'title' => t('Access CDM content'),
549			'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
550			),
551	38b27a36	Andreas Kohlbecker	);
552			}
553	6657531f	Andreas Kohlbecker
554			/**
555	f19f47fa	Andreas Kohlbecker	* Implements hook_menu().
556			*/
557	6657531f	Andreas Kohlbecker	function cdm_dataportal_menu() {
558			$items = array();
559
560			// @see settings.php.
561			cdm_dataportal_menu_admin($items);
562			cdm_dataportal_menu_help($items);
563
564			$items['cdm_dataportal/names'] = array(
565			'page callback' => 'cdm_dataportal_view_names',
566	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
567	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
568			);
569
570			// Optional callback arguments: page.
571			$items['cdm_dataportal/taxon'] = array(
572			'page callback' => 'cdm_dataportal_taxon_page_view',
573	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
574	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
575			// Expected callback arguments: uuid.
576			);
577
578	a1ce57ce	Katja Luther	$items['cdm_dataportal/occurrence'] = array(
579	6eaec849	Katja Luther	'page callback' => 'cdm_dataportal_specimen_page_view',
580			'access arguments' => array('access cdm content'),
581			'type' => MENU_CALLBACK,
582			// Expected callback arguments: uuid.
583			);
584	30845bda	Andreas Kohlbecker
585	e170a53e	Patrick Plitzner	$items['cdm_dataportal/description'] = array(
586			'page callback' => 'cdm_dataportal_description_page_view',
587			'access arguments' => array('access cdm content'),
588			'type' => MENU_CALLBACK,
589			// Expected callback arguments: uuid.
590			);
591
592	4c812e71	Katja Luther	$items['cdm_dataportal/specimen/accession_number'] = array(
593	6eaec849	Katja Luther	'page callback' => 'cdm_dataportal_specimen_by_accession_number_page_view',
594			'access arguments' => array('access cdm content'),
595			'type' => MENU_CALLBACK,
596			// Expected callback arguments: accession number.
597			);
598	30845bda	Andreas Kohlbecker	$items['cdm_dataportal/named_area'] = array(
599			'page callback' => 'cdm_dataportal_named_area_page_view',
600			'access arguments' => array('access cdm content'),
601			'type' => MENU_CALLBACK,
602			// Expected callback arguments: uuid.
603			);
604	9d37c9d9	Patric Plitzner
605	6657531f	Andreas Kohlbecker	$items['cdm_dataportal/name'] = array(
606			'page callback' => 'cdm_dataportal_name_page_view',
607			/*
608			'page arguments' => array(
609			'taxon_name_uuid',
610			'taxon_to_hide_uuid',
611			'synonym_uuid' => NULL
612			),
613			*/
614	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
615	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
616			// Expected callback arguments: uuid.
617			);
618
619			$items['cdm_dataportal/reference'] = array(
620			'page callback' => 'cdm_dataportal_view_reference',
621	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
622	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
623			// Expected callback arguments: uuid.
624			);
625
626			$items['cdm_dataportal/reference/list'] = array(
627			'page callback' => 'cdm_dataportal_view_reference_list',
628	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
629	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
630			// Expected callback arguments: uuid.
631			);
632
633			$items['cdm_dataportal/media'] = array(
634			'page callback' => 'cdm_dataportal_view_media',
635	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
636	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
637			// Expected callback arguments:
638			// uuid, mediarepresentation_uuid, part_uuid or part#.
639			);
640
641			$items['cdm_dataportal/polytomousKey'] = array(
642			'page callback' => 'cdm_dataportal_view_polytomousKey',
643	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
644	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
645			// Expected callback arguments: polytomousKey->uuid.
646			);
647
648			$items['cdm_dataportal/search'] = array(
649			'page callback' => 'cdm_dataportal_view_search_advanced',
650	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
651	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
652			);
653
654	7e219fcc	Andreas Kohlbecker	// Optional callback arguments: page.
655			$items['cdm_dataportal/registration'] = array(
656			'page callback' => 'cdm_dataportal_registration_page_view',
657			'access arguments' => array('access cdm content'),
658			'type' => MENU_CALLBACK,
659			// Expected callback arguments: uuid.
660			);
661
662			// ------------ SEARCH -----------
663	6657531f	Andreas Kohlbecker	$items['cdm_dataportal/search/advanced'] = array(
664	29077ee5	Andreas Kohlbecker	'title' => 'Advanced', // will be passed through t()
665	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_advanced',
666	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
667	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
668			);
669	4c812e71	Katja Luther	$items['cdm_dataportal/search/blast'] = array(
670			'title' => 'Blast', // will be passed through t()
671			'page callback' => 'cdm_dataportal_view_search_blast',
672			'access arguments' => array('access cdm content'),
673			'type' => MENU_LOCAL_TASK,
674			);
675
676	6657531f	Andreas Kohlbecker	$items['cdm_dataportal/search/taxon_by_description'] = array(
677	579c485d	Andreas Kohlbecker	'title' => 'By content category', // will be passed through t()
678	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
679	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
680	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
681			);
682			$items['cdm_dataportal/search/results/taxon'] = array(
683			'page callback' => 'cdm_dataportal_view_search_results_taxon',
684	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
685	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
686			);
687	a1ce57ce	Katja Luther
688	2f30124c	Andreas Kohlbecker	$items['cdm_dataportal/search/results/specimen'] = array(
689			'page callback' => 'cdm_dataportal_view_search_results_specimen',
690			'access arguments' => array('access cdm content'),
691			'type' => MENU_CALLBACK,
692			);
693
694	efbff4b3	Andreas Kohlbecker	/*
695			* MENU_CALLBACK at cdm_dataportal/registration-search is needed to make the
696			* tabs in the subordinate paths work, accessing this 'page' will cause the
697			* MENU_DEFAULT_LOCAL_TASK being displayed
698			*/
699			$items['cdm_dataportal/registration-search'] = array(
700			'title' => 'Search', // will be passed through t()
701	a6ae799b	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_registrations_results',
702	efbff4b3	Andreas Kohlbecker	'page arguments' => array("filter"),
703	a6ae799b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
704			'type' => MENU_CALLBACK,
705			);
706	efbff4b3	Andreas Kohlbecker	/*
707			* the MENU_DEFAULT_LOCAL_TASK creates a tab for the MENU_CALLBACK
708			* defined at a higher level of the path (cdm_dataportal/registration-search)
709			*/
710			$items['cdm_dataportal/registration-search/filter'] = array(
711			'title' => 'Search', // will be passed through t()
712			'page callback' => 'cdm_dataportal_view_search_registrations_results',
713			'page arguments' => array("filter"),
714			'access arguments' => array('access cdm content'),
715			'type' => MENU_DEFAULT_LOCAL_TASK,
716			);
717			/*
718			* the MENU_LOCAL_TASK creates another tab
719			*/
720			$items['cdm_dataportal/registration-search/taxongraph'] = array(
721	5087fadc	Andreas Kohlbecker	'title' => 'Taxon graph search', // will be passed through t()
722	efbff4b3	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_registrations_results',
723			'page arguments' => array("taxongraph"),
724			'access arguments' => array('access cdm content'),
725			'type' => MENU_LOCAL_TASK,
726			);
727
728	e2617c7e	Andreas Kohlbecker	// Optional callback arguments: page.
729			$items['cdm_dataportal/search/agent'] = array(
730			'page callback' => 'cdm_dataportal_view_search_agent',
731			'access arguments' => array('access cdm content'),
732			'type' => MENU_CALLBACK,
733			// Expected callback arguments: uuid.
734			);
735
736	7e219fcc	Andreas Kohlbecker	// ------------ menu items with variable path elements -----------
737	6657531f	Andreas Kohlbecker
738			// 'May not cache' in D5.
739			$items['cdm_dataportal/name/%'] = array(
740			// 'page callback' => 'cdm_dataportal_view_name',
741			'page callback' => 'cdm_dataportal_name_page_view',
742	2f65af04	Andreas Kohlbecker	'page arguments' => array(2, 3, 4, 5),
743	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
744	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
745			);
746
747	6f1a217c	Andreas Kohlbecker	// --- Local tasks for Taxon.
748			// --- tabbed taxon page
749	6657531f	Andreas Kohlbecker	if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
750			$items['cdm_dataportal/taxon/%'] = array(
751	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
752	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
753	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
754	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
755			'weight' => 1,
756			'page arguments' => array(2, "description")
757	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
758	6657531f	Andreas Kohlbecker	);
759
760			$items['cdm_dataportal/taxon/%/all'] = array(
761	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
762	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
763	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
764	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
765			'weight' => 2,
766			'page arguments' => array(2, "all")
767	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
768	6657531f	Andreas Kohlbecker	);
769
770			$items['cdm_dataportal/taxon/%/description'] = array(
771	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
772	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
773	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
774	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
775			'weight' => 2,
776			'page arguments' => array(2, "description")
777	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
778	6657531f	Andreas Kohlbecker	);
779
780			$items['cdm_dataportal/taxon/%/synonymy'] = array(
781	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Synonymy'),
782	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
783	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
784	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
785			'weight' => 4,
786			'page arguments' => array(2, "synonymy", 4)
787	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid and ...
788	6657531f	Andreas Kohlbecker	);
789	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/images'] = array( // Images
790	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Images'),
791	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
792	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
793	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
794			'weight' => 5,
795			'page arguments' => array(2, "images")
796	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
797	6657531f	Andreas Kohlbecker	);
798
799	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
800	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Specimens'),
801	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
802	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
803	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
804			'weight' => 6,
805			'page arguments' => array(2, "specimens")
806	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
807	6657531f	Andreas Kohlbecker	);
808
809	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/keys'] = array( // Keys
810	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Keys'),
811	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
812	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
813	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
814			'weight' => 6,
815			'page arguments' => array(2, "keys")
816	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
817			);
818
819	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/experts'] = array( // Experts
820	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Experts'),
821	7663cd0b	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
822	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
823	7663cd0b	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
824			'weight' => 6,
825			'page arguments' => array(2, "experts")
826			, // Expected callback arguments: taxon_uuid.
827	6657531f	Andreas Kohlbecker	);
828	93ae67cc	Patrick Plitzner
829	51cc509a	Patrick Plitzner	$items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
830	04a1d647	Patrick Plitzner	'page callback' => 'cdm_dataportal_taxon_autosuggest',
831	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
832	51cc509a	Patrick Plitzner	'page arguments' => array(3,4,5),
833	93ae67cc	Patrick Plitzner	'type' => MENU_CALLBACK
834			);
835	6657531f	Andreas Kohlbecker	}
836
837	6f1a217c	Andreas Kohlbecker	// --- refresh link for all cdmnode types
838			foreach (cdm_get_nodetypes() as $type=>$name) {
839			$items['cdm_dataportal/' . $name . '/%/refresh'] = array(
840	7cc085da	Andreas Kohlbecker	'title' => 'Refresh',
841	6f1a217c	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_refresh_node',
842	3113db26	Andreas Kohlbecker	'access arguments' => array('administer cdm_dataportal'),
843	6f1a217c	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
844			'weight' => 100,
845			'page arguments' => array($name, 2)
846			);
847			}
848
849	6657531f	Andreas Kohlbecker	return $items;
850			}
851
852			/**
853	b85ab055	Andreas Kohlbecker	* Implements hook_init().
854			*
855	6657531f	Andreas Kohlbecker	*/
856			function cdm_dataportal_init() {
857	8fc089e1	Saskia Gennrich	if (!path_is_admin(current_path())) {
858			//FIXME To add CSS or JS that should be present on all pages, modules
859			// should not implement this hook, but declare these files in their .info file.
860			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
861			// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
862			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
863	63f6d312	Saskia Gennrich	} else {
864			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
865	8fc089e1	Saskia Gennrich	}
866	2dd59bb5	Andreas Kohlbecker
867			if(variable_get('cdm_debug_mode', FALSE)){
868			$file = 'temporary://drupal_debug.txt';
869			file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
870			}
871	5611d467	Andreas Kohlbecker
872			$bibliography_settings = get_bibliography_settings();
873	57d513cb	Andreas Kohlbecker	$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
874			FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
875	6657531f	Andreas Kohlbecker	}
876
877	6f1a217c	Andreas Kohlbecker	function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
878
879			$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
880
881			if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
882			// force reloading of all and notify user about this special loading
883			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: ')
884			. l('Back to tabbed taxon page', $base_path));
885			$base_path .= '/all';
886			} else {
887			drupal_set_message(t('The level 2 cache has been cleared for this page'));
888			}
889
890			$parameters['cacheL2_refresh'] ='1';
891
892
893			drupal_goto($base_path, array('query' => $parameters));
894			}
895
896	102f8c26	Andreas Kohlbecker	/**
897			* Implements hook_requirements($phase)
898			*/
899			function cdm_dataportal_requirements($phase) {
900			$requirements = array();
901			if($phase == 'runtime'){
902
903			}
904			return $requirements;
905			}
906
907	6657531f	Andreas Kohlbecker	/**
908			* Implements hook_block_info().
909			*/
910			function cdm_dataportal_block_info() {
911
912			// $block[0]["info"] = t("CDM DataPortal DevLinks");
913			// $block[1]["info"] = t("CDM DataPortal Credits");
914	fc13aa30	Andreas Kohlbecker	$block["2"] = array(
915	beb914ef	Andreas Kohlbecker	"info" => t("CDM - Search Taxa"),
916	fc13aa30	Andreas Kohlbecker	"cache" => DRUPAL_NO_CACHE
917			);
918	6657531f	Andreas Kohlbecker	// $block[3]["info"] = t("CDM Filters");
919	beb914ef	Andreas Kohlbecker	$block["4"]["info"] = t("CDM - Dataportal Print");
920			$block["keys"]["info"] = t("CDM - Identification keys");
921	46a02272	Andreas Kohlbecker	$block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
922	f9a3d0f6	Andreas Kohlbecker	$block["classification_breadcrumbs"] = array(
923	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Classification breadcrumbs'),
924	f9a3d0f6	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
925			);
926	bc400a17	Andreas Kohlbecker	$block["taxonomic_children"] = array(
927	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Taxonomic children'),
928	bc400a17	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
929			);
930	beb914ef	Andreas Kohlbecker	$block["back_to_search_results"] = array(
931			'title' => '<none>',
932			'info' => t('CDM - Back to search Results'),
933			'cache' => DRUPAL_CACHE_PER_PAGE,
934			'visibility' => BLOCK_VISIBILITY_LISTED,
935			'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
936			);
937	a6ae799b	Andreas Kohlbecker	$block['registrations_search_filter'] = array(
938	b18d70f6	Andreas Kohlbecker	'title' => 'Filter registrations',
939	a6ae799b	Andreas Kohlbecker	'info' => t('CDM - Registrations search filter'),
940			'cache' => DRUPAL_CACHE_PER_PAGE,
941	810710a0	Andreas Kohlbecker	'visibility' => BLOCK_VISIBILITY_NOTLISTED,
942	b18d70f6	Andreas Kohlbecker	'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
943	a6ae799b	Andreas Kohlbecker	);
944	efbff4b3	Andreas Kohlbecker	$block['registrations_search_taxongraph'] = array(
945			'title' => 'Taxonomic registration search',
946			'info' => t('CDM - Registrations search by taxon graph'),
947			'cache' => DRUPAL_CACHE_PER_PAGE,
948			'visibility' => BLOCK_VISIBILITY_NOTLISTED,
949	b18d70f6	Andreas Kohlbecker	'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
950			);
951			$block['registrations_search'] = array(
952			'title' => 'Search',
953			'info' => t('CDM - Registrations search combining filter and taxon graph search' ),
954			'cache' => DRUPAL_CACHE_PER_PAGE,
955			'visibility' => BLOCK_VISIBILITY_NOTLISTED,
956			'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
957	efbff4b3	Andreas Kohlbecker	);
958	c05d1cfb	Andreas Kohlbecker	$block['utis_search'] = array(
959			'title' => 'UTIS Search',
960			'info' => t('Query the Unified Taxonomic Information Service (UTIS)' ),
961			'cache' => DRUPAL_CACHE_PER_PAGE,
962			'visibility' => BLOCK_VISIBILITY_NOTLISTED
963			);
964	efbff4b3	Andreas Kohlbecker	return $block;
965	6657531f	Andreas Kohlbecker	}
966
967			/**
968			* Implements hook_block_view().
969			*/
970			function cdm_dataportal_block_view($delta) {
971			// TODO Rename block deltas (e.g. '2') to readable strings.
972			switch ($delta) {
973			// case 'delta-1':
974			// $block['subject'] = t('Credits');
975			// $block['content'] = theme('cdm_credits');
976			// return $block;
977			case '2':
978			$block['subject'] = t('Search taxa');
979	191f88fd	Andreas Kohlbecker	$form = drupal_get_form('cdm_dataportal_search_taxon_form');
980			$block['content'] = drupal_render($form);
981	6657531f	Andreas Kohlbecker
982			if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
983			$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
984	6eaec849	Katja Luther	}
985	2f30124c	Andreas Kohlbecker	if (variable_get(CDM_SEARCH_BLAST_ENABLED)){
986	6eaec849	Katja Luther	$block['content'] .= '<div>' . l(t('Blast Search'), 'cdm_dataportal/search/blast') . '</div>';
987	6657531f	Andreas Kohlbecker	}
988			return $block;
989			case '4':
990	c8234bdf	Andreas Kohlbecker	$block['subject'] = '';
991	6657531f	Andreas Kohlbecker	$block['content'] = theme('cdm_print_button');
992			return $block;
993			case "keys":
994			$block['subject'] = t('Identification Keys');
995			$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
996			return $block;
997			case "fundedByEDIT":
998			// t('Funded by EDIT');
999			$text = '<none>';
1000			$block['subject'] = $text;
1001	889c74b7	Andreas Kohlbecker	$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
1002			$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
1003	6657531f	Andreas Kohlbecker	'attributes' => array("target" => "EDIT"),
1004			'absolute' => TRUE,
1005			'html' => TRUE,
1006			));
1007			return $block;
1008	f9a3d0f6	Andreas Kohlbecker	case 'classification_breadcrumbs':
1009	0af3ce28	Andreas Kohlbecker	$taxon_uuid = get_current_taxon_uuid();
1010	38da4e54	Andreas Kohlbecker	$block['subject'] = '<none>';
1011			$block['content'] = compose_classification_breadcrumbs($taxon_uuid);
1012			return $block;
1013	bc400a17	Andreas Kohlbecker	case 'taxonomic_children':
1014			$taxon_uuid = get_current_taxon_uuid();
1015			$block['subject'] = '<none>';
1016			$block['content'] = compose_taxonomic_children($taxon_uuid);
1017			return $block;
1018	beb914ef	Andreas Kohlbecker	case 'back_to_search_results':
1019			$block['subject'] = '<none>';
1020			if (isset($_SESSION['cdm']['search'])) {
1021			$block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
1022			}
1023			return $block;
1024	a6ae799b	Andreas Kohlbecker	case 'registrations_search_filter':
1025			$block['subject'] = '<none>';
1026	efbff4b3	Andreas Kohlbecker	$block['content'] = drupal_get_form('cdm_dataportal_search_registration_filter_form'); // see cdm_dataportal_search_registration_filter_form($form, &$form_state)
1027			return $block;
1028			case 'registrations_search_taxongraph':
1029			$block['subject'] = '<none>';
1030			$block['content'] = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form'); // see cdm_dataportal_search_registration_taxongraph_form($form, &$form_state)
1031	a6ae799b	Andreas Kohlbecker	return $block;
1032	b18d70f6	Andreas Kohlbecker	case 'registrations_search':
1033			_add_js_ui_accordion();
1034			_add_font_awesome_font();
1035			$block['subject'] = '<none>';
1036			$filter_form = drupal_get_form('cdm_dataportal_search_registration_filter_form');
1037			$filter_form['#prefix'] = '<div>';
1038			$filter_form['#suffix'] = '</div>';
1039			$taxongraph_form = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form');
1040			$taxongraph_form['#prefix'] = '<div>';
1041			$taxongraph_form['#suffix'] = '</div>';
1042			$block['content'] = array(
1043			'accordion' => array(
1044			'#markup' => '',
1045			'#prefix' => '<div id="accordion">',
1046			'#suffix' => '</div>',
1047			'content' => array(
1048			array('#markup' => '<h3>Filter</h3>'),
1049			$filter_form,
1050			array('#markup' => '<h3>Taxon graph</h3>'),
1051			$taxongraph_form,
1052			)
1053			)
1054			);
1055			return $block;
1056	c05d1cfb	Andreas Kohlbecker	case 'utis_search':
1057			_add_js_utis_client('.utis_client');
1058			$block['subject'] = '<none>';
1059	579bc6e3	Andreas Kohlbecker	$block['content'] = '<div class="utis_client"></div>';
1060	c05d1cfb	Andreas Kohlbecker	return $block;
1061	beb914ef	Andreas Kohlbecker	default:
1062			return null;
1063	6657531f	Andreas Kohlbecker	}
1064			}
1065
1066	e27e3ff2	Andreas Kohlbecker
1067	0af3ce28	Andreas Kohlbecker	/**
1068			* Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
1069			*
1070			* @return string
1071			* the taxon uuid or NULL
1072			*/
1073			function get_current_taxon_uuid()
1074			{
1075			static $taxon_uuid;
1076
1077			if(!isset($taxon_uuid)){
1078			if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
1079			$taxon_uuid = $_REQUEST['currentTaxon'];
1080			} else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
1081			$taxon_uuid = arg(2);
1082			} else {
1083			$taxon_uuid = null;
1084			}
1085			}
1086
1087			return $taxon_uuid;
1088			}
1089
1090			/**
1091			* Returns the currently classification tree in use.
1092			*
1093			* @return string
1094			* The uuid of the currently focused classification
1095			*/
1096			function get_current_classification_uuid() {
1097			if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
1098			return $_SESSION['cdm']['taxonomictree_uuid'];
1099			}
1100			else {
1101			return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
1102			}
1103			}
1104
1105	6657531f	Andreas Kohlbecker	/*
1106			function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
1107			$_SESSION['cdm'] = NULL;
1108			if(is_string($cdm_ws_uri_update)){
1109			$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
1110			}
1111			}
1112
1113			function cdm_dataportal_session_validate(){
1114			if(!isset($_SESSION['cdm']['ws_uri'])){
1115			$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
1116			} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
1117			cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
1118			}
1119			}
1120			*/
1121
1122			/**
1123	d7588d36	Andreas Kohlbecker	* creates a selector form for taxonomic trees.
1124			*
1125	0af3ce28	Andreas Kohlbecker	* @return array
1126			* a drupal form array
1127	6657531f	Andreas Kohlbecker	*/
1128			function cdm_taxonomictree_selector() {
1129			_add_js_treeselector();
1130
1131	a8a8f23c	Andreas Kohlbecker	$form = drupal_get_form('cdm_taxonomictree_selector_form');
1132	d7588d36	Andreas Kohlbecker	return $form;
1133	6657531f	Andreas Kohlbecker	}
1134
1135			/**
1136			* @todo Please document this function.
1137			* @see http://drupal.org/node/1354
1138	0af3ce28	Andreas Kohlbecker	*
1139			* @deprecated use compose_classification_selector instead
1140	6657531f	Andreas Kohlbecker	*/
1141			function cdm_taxonomictree_selector_form($form, &$form_state) {
1142
1143			$url = url('cdm_api/setvalue/session', array('query' => NULL));
1144			$form['#action'] = $url;
1145
1146			$form['var'] = array(
1147			'#weight' => -3,
1148			'#type' => 'hidden',
1149			'#value' => '[cdm][taxonomictree_uuid]',
1150			);
1151
1152			$destination_array = drupal_get_destination();
1153			$destination = $destination_array['destination'];
1154
1155			$form['destination'] = array(
1156			'#weight' => -3,
1157			'#type' => 'hidden',
1158			'#value' => $destination,
1159			);
1160
1161	26fb3778	Andreas Kohlbecker	$options = cdm_get_taxontrees_as_options();
1162			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1163			if($taxontree_includes){
1164			$filtered_options = array();
1165			foreach($options as $uuid=>$label){
1166			if(!empty($taxontree_includes[$uuid])){
1167			$filtered_options[$uuid] = $label;
1168			}
1169			}
1170			$options = $filtered_options;
1171			}
1172
1173	6657531f	Andreas Kohlbecker	$form['val'] = array(
1174			'#type' => 'select',
1175			'#title' => t('Available classifications'),
1176	7663cd0b	Andreas Kohlbecker	'#default_value' => get_current_classification_uuid(),
1177	26fb3778	Andreas Kohlbecker	'#options' => $options,
1178	0af3ce28	Andreas Kohlbecker	'#attributes' => array('class' => array('highlite-first-child')),
1179	6657531f	Andreas Kohlbecker	);
1180
1181			return $form;
1182
1183			}
1184
1185	0af3ce28	Andreas Kohlbecker	/**
1186			*
1187			* @ingroup compose
1188			*/
1189			function compose_classification_selector() {
1190
1191			$destination_array = drupal_get_destination();
1192			$destination = $destination_array['destination'];
1193
1194			$options = cdm_get_taxontrees_as_options();
1195			$items = array();
1196			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1197
1198			$current_classification_uuid = get_current_classification_uuid();
1199
1200
1201			foreach($options as $uuid=>$label){
1202			if(!$taxontree_includes \|\| !empty($taxontree_includes[$uuid])){
1203
1204			$class_attributes = '';
1205			if($current_classification_uuid == $uuid){
1206			$class_attributes = array('focused');
1207			}
1208			$items[] = array(
1209			'data' => l($label,
1210			'cdm_api/setvalue/session',
1211			array(
1212			'query' => array(
1213			'destination' => $destination,
1214			'val' => $uuid,
1215			'var' => '[cdm][taxonomictree_uuid]'
1216			),
1217			)
1218			),
1219			'class' => $class_attributes
1220			);
1221			}
1222			}
1223
1224			$render_array = array(
1225			'#theme' => 'item_list',
1226			'#type' => 'ul',
1227			'#items' => $items
1228			);
1229
1230			return $render_array;
1231			}
1232
1233
1234	6657531f	Andreas Kohlbecker	/* UNREACHABLE since action of form directly links to view.
1235			function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1236
1237			$_SESSION['cdm']['search'] = $form_values;
1238			//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1239			return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1240			//$paramstr = compose_url_prameterstr($form_values);
1241			//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1242			}
1243			*/
1244			/* ====================== menu callback functions ====================== */
1245			/**
1246			* @todo Please document this function.
1247			* @see http://drupal.org/node/1354
1248			*/
1249			/*
1250			function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1251			static $comment_node_disabled = 0;
1252			static $comment_node_read_only = 1;
1253			static $comment_node_read_write = 2;
1254
1255			if ($form_id == 'node_type_form'
1256			&& isset($form['identity']['type'])
1257			&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1258			) {
1259			$form['workflow']['comment'] = array(
1260			'#type' => 'radios',
1261			'#title' => t('Default comment setting'),
1262			'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1263			'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1264			'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1265			);
1266			}
1267			}
1268			*/
1269
1270			/**
1271			* Displays a list of the known taxonomic names.
1272			*
1273			* When the list of taxonomic names is displayed, long lists are split up into
1274			* multiple pages.
1275			*
1276			* TODO: Parameters are still preliminary.
1277			*
1278			* @param string $beginsWith
1279			* @param string $page
1280			* Page number to diplay defaults to page 1.
1281			* @param bool $onlyAccepted
1282			*/
1283			function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1284
1285			$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1286
1287			/*
1288			// FIXME the filter for accepted names will be a form element, thus this
1289			// widget should be generated via form api preferably as block.
1290			$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1291			$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1292			$out .= theme('cdm_listof_taxa', $taxonPager);
1293			return $out;
1294			*/
1295			}
1296
1297			/**
1298			* @todo Please document this function.
1299			* @see http://drupal.org/node/1354
1300	c0223d83	Andreas Kohlbecker	* @throws Exception
1301	6657531f	Andreas Kohlbecker	*/
1302			function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1303	f26245c8	Andreas Kohlbecker
1304			cdm_check_valid_portal_page();
1305
1306	6cbefddc	Andreas Kohlbecker	return compose_cdm_reference_page($uuid);
1307	6657531f	Andreas Kohlbecker	}
1308
1309			/**
1310	b2ebf0d3	Andreas Kohlbecker	* Creates a view on a all references contained in the portal.
1311	b5dca1e2	Andreas Kohlbecker	*
1312			* This function is used at the path cdm_dataportal/reference/list
1313	6657531f	Andreas Kohlbecker	*/
1314			function cdm_dataportal_view_reference_list($pageNumber) {
1315	44458b04	Andreas Kohlbecker	$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT), $pageNumber);
1316	b2ebf0d3	Andreas Kohlbecker	cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1317	6657531f	Andreas Kohlbecker	}
1318
1319			/**
1320			* @todo Please document this function.
1321			* @see http://drupal.org/node/1354
1322			*/
1323			function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1324	f26245c8	Andreas Kohlbecker
1325			cdm_check_valid_portal_page();
1326
1327	6657531f	Andreas Kohlbecker	$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1328	4d9660ef	Andreas Kohlbecker	if (!$media) {
1329			drupal_set_title(t('Media does not exist'), PASS_THROUGH);
1330	de017852	Andreas Kohlbecker	return "";
1331	4d9660ef	Andreas Kohlbecker	}
1332	6657531f	Andreas Kohlbecker	return theme('cdm_media_page', array(
1333			'media' => $media,
1334			'mediarepresentation_uuid' => $mediarepresentation_uuid,
1335			'partId' => $part,
1336			));
1337			}
1338
1339			/**
1340			* @todo Please document this function.
1341			* @see http://drupal.org/node/1354
1342			*/
1343			function _load_taxonBase(&$taxonBase) {
1344			if (isset($taxonBase->uuid)) {
1345	6679207a	Andreas Kohlbecker	$taxonBase->name = cdm_ws_get(CDM_WS_PORTAL_TAXON, array($taxonBase->uuid, "name"));
1346			$taxonBase->name->nomenclaturalSource = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalSource"));
1347	6657531f	Andreas Kohlbecker	}
1348			}
1349
1350	9438ad3a	Andreas Kohlbecker	/**
1351			* Loads the media associated to the given taxon from the cdm server.
1352			* The aggregation settings regarding taxon relathionships and
1353			* taxonnomic childen are taken into account.
1354			*
1355			* The media lists are cached in a static variable.
1356			*
1357			* @param Taxon $taxon
1358	4a462641	Andreas Kohlbecker	* A CDM Taxon entity
1359	9438ad3a	Andreas Kohlbecker	*
1360			* @return array
1361			* An array of CDM Media entities
1362			*
1363			*/
1364	4a462641	Andreas Kohlbecker	function _load_media_for_taxon($taxon) {
1365	9438ad3a	Andreas Kohlbecker
1366			static $media = NULL;
1367
1368			if(!isset($media)) {
1369			$media = array();
1370			}
1371			if (!isset($media[$taxon->uuid])) {
1372
1373	a950f2f9	Andreas Kohlbecker
1374	4a462641	Andreas Kohlbecker	$mediaQueryParameters = taxon_media_query_parameters();
1375	9438ad3a	Andreas Kohlbecker
1376	f19f47fa	Andreas Kohlbecker	$ws_endpoint = NULL;
1377	4a462641	Andreas Kohlbecker	if ( $mediaQueryParameters['includeTaxonomicChildren']) {
1378	9438ad3a	Andreas Kohlbecker	$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1379	4a462641	Andreas Kohlbecker	} else {
1380			$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1381	9438ad3a	Andreas Kohlbecker	}
1382	4a462641	Andreas Kohlbecker	// this parameter is not yet used by the CDM_WS_PORTAL_TAXON_*MEDIA
1383			// services
1384			unset($mediaQueryParameters['includeTaxonomicChildren']);
1385	f19f47fa	Andreas Kohlbecker
1386			$media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1387			array(
1388			$taxon->uuid,
1389			),
1390	9438ad3a	Andreas Kohlbecker	queryString($mediaQueryParameters)
1391			);
1392			}
1393
1394			return $media[$taxon->uuid];
1395			}
1396
1397			/**
1398			*
1399			* @param Taxon $taxon
1400			* A CDM Taxon entitiy
1401			*
1402			* @return array
1403			* An array of CDM SpecimenOrObservation entities
1404			*
1405			function _load_occurences_for_taxon($taxon){
1406
1407			static $occurences = NULL;
1408	f19f47fa	Andreas Kohlbecker
1409			if(!isset($occurences)) {
1410			$occurences = array();
1411			}
1412	9438ad3a	Andreas Kohlbecker
1413			if (!isset($occurences[$taxon->uuid])){
1414
1415			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1416			$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1417	f19f47fa	Andreas Kohlbecker	$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1418
1419			$by_associatedtaxon_query = http_build_query(array(
1420			'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1421			'relationships' => implode(',', $relationship_choice['direct']),
1422			'pageSize' => null // all hits in one page
1423			)
1424			);
1425
1426			$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1427			null,
1428			$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1429			);
1430
1431
1432			if(isset($pager->records[0])){
1433			$occurences[$taxon->uuid] = $pager->records;
1434			}
1435			}
1436	9438ad3a	Andreas Kohlbecker	return $occurences[$taxon->uuid];
1437			}
1438			*/
1439
1440	6657531f	Andreas Kohlbecker	/**
1441			* Gets a Drupal variable, string or array and returns it.
1442			*
1443			* Similar to the variable_get() function of Drupal, except that this function
1444			* is able to handle arrays correctly. This function is especially useful
1445	8c962983	Andreas Kohlbecker	* when dealing with collections of settings form elements (#tree = TRUE).
1446	6657531f	Andreas Kohlbecker	*
1447			* @param string $variableKey
1448			* The Unique key of the Drupal variable in the Drupal variables table.
1449			* @param string $defaultValueString
1450			* A string as for example derived from a CONSTANT.
1451			*
1452			* @return mixed
1453	8c962983	Andreas Kohlbecker	* usually an array, depending on the nature of the variable.
1454			*
1455			* TODO compare with get_array_variable_merged() duplicate functions?
1456	0f7c9d15	Andreas Kohlbecker	* @deprecated rather use get_array_variable_merged() since this function
1457			* used an array as second parameter
1458	6657531f	Andreas Kohlbecker	*/
1459			function mixed_variable_get($variableKey, $defaultValueString) {
1460			$systemDefaults = unserialize($defaultValueString);
1461			$storedSettings = variable_get($variableKey, array());
1462			if (is_array($storedSettings)) {
1463	8c962983	Andreas Kohlbecker	// TODO better use drupal_array_merge_deep() ?
1464	6657531f	Andreas Kohlbecker	$settings = array_merge($systemDefaults, $storedSettings);
1465			}
1466			else {
1467			$settings = $systemDefaults;
1468			}
1469			return $settings;
1470			}
1471
1472	b5519d3a	Andreas Kohlbecker	/**
1473	0f7c9d15	Andreas Kohlbecker	* Recursive function to convert an object into an array.
1474	b5519d3a	Andreas Kohlbecker	* also subordinate objects will be converted.
1475			*
1476			* @param object $object
1477	db725031	Andreas Kohlbecker	* the object to be converted
1478			* @return array
1479			* The array
1480	b5519d3a	Andreas Kohlbecker	*/
1481	db725031	Andreas Kohlbecker	function object_to_array($object) {
1482	b5519d3a	Andreas Kohlbecker	if(is_object($object) \|\| is_array($object)) {
1483			$array = (array)$object;
1484			foreach ($array as $key=>$value){
1485	db725031	Andreas Kohlbecker	$array[$key] = object_to_array($value);
1486	b5519d3a	Andreas Kohlbecker	}
1487			return $array;
1488			} else {
1489			return $object;
1490			}
1491			}
1492
1493	2fd6da0b	Andreas Kohlbecker	/**
1494			* Searches the $collection for the cdm entitiy given as $element.
1495			*
1496			* The elements are compared by their UUID.
1497			*
1498			* @param $element
1499			* the CDM entitiy to search for
1500			* @param $collection
1501			* the list of CDM entities to search in
1502			*
1503			* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1504			*
1505			*/
1506			function contains_cdm_entitiy($element, $collection) {
1507			$result = FALSE;
1508			foreach ($collection as $a) {
1509			if ($a->uuid == $element->uuid) {
1510			$result = TRUE;
1511			}
1512			}
1513			return $result;
1514			}
1515
1516			/**
1517	14076b88	Andreas Kohlbecker	* Filters the array $entity_list of CDM entities by the list
1518	2fd6da0b	Andreas Kohlbecker	* of $excludes. Any element contained in the $excludes will be removed
1519	14076b88	Andreas Kohlbecker	* from included int the returned list.
1520	2fd6da0b	Andreas Kohlbecker	*
1521			* If the $entity_list is not an array the $excludes will be returned.
1522			*/
1523			function filter_cdm_entity_list($entity_list, $excludes) {
1524			if (is_array($entity_list)) {
1525			$result = $entity_list;
1526			if ($excludes) {
1527			foreach ($excludes as $exclude) {
1528			if (!contains_cdm_entitiy($exclude, $entity_list)) {
1529			$result[] = $exclude;
1530			}
1531			}
1532			}
1533			}
1534			else {
1535			$result = $excludes;
1536			}
1537			return $result;
1538			}
1539
1540	0a1151a4	Andreas Kohlbecker	/**
1541	6f5c7f2a	Andreas Kohlbecker	* Wraps the given $html string into a render array suitable for drupal_render()
1542	0a1151a4	Andreas Kohlbecker	*
1543	65345976	Andreas Kohlbecker	* @param $html
1544	0a1151a4	Andreas Kohlbecker	* the html string, see
1545			* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1546	65345976	Andreas Kohlbecker	* @param $weight
1547	0a1151a4	Andreas Kohlbecker	* A positive or negative number (integer or decimal).
1548			* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1549	65345976	Andreas Kohlbecker	* @param $prefix
1550			* Optional markup for the '#prefix' element of the render array
1551			* @param $suffix
1552			* Optional markup for the '#suffix' element of the render array
1553	0a1151a4	Andreas Kohlbecker	*
1554	65345976	Andreas Kohlbecker	* @return array
1555	0a1151a4	Andreas Kohlbecker	* A render array
1556			*
1557			*/
1558	65345976	Andreas Kohlbecker	function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1559	6f5c7f2a	Andreas Kohlbecker	$render_array = array(
1560			'#markup' => $html
1561	1ce9afb7	Patric Plitzner	);
1562	6f5c7f2a	Andreas Kohlbecker	if (is_numeric($weight)) {
1563			$render_array['#weight'] = $weight;
1564	65345976	Andreas Kohlbecker	}
1565			if($prefix){
1566			$render_array['#prefix'] = $prefix;
1567			}
1568			if($suffix) {
1569			$render_array['#suffix'] = $suffix;
1570			}
1571	6f5c7f2a	Andreas Kohlbecker	return $render_array;
1572	0a1151a4	Andreas Kohlbecker	}
1573
1574	6657531f	Andreas Kohlbecker	/**
1575			* Loads the subgraph of a given PolytomousKeyNode.
1576			*
1577			* Loads the subgraph of the given PolytomousKeyNode recursively from
1578			* the CDM REST service.
1579			*
1580			* @param mixed $polytomousKeyNode
1581			* PolytomousKeyNode passed by reference.
1582			*
1583			* @return void
1584			*/
1585			function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1586
1587			if (!$polytomousKeyNode) {
1588			return;
1589			}
1590			if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1591	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1592	6657531f	Andreas Kohlbecker	return;
1593			}
1594			if (!is_uuid($polytomousKeyNode->uuid)) {
1595	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1596	6657531f	Andreas Kohlbecker	return;
1597			}
1598
1599			$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1600
1601			if (!$polytomousKeyNode) {
1602			// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1603			return;
1604			}
1605
1606			// Load children.
1607			foreach ($polytomousKeyNode->children as &$childNode) {
1608			_load_polytomousKeySubGraph($childNode);
1609			}
1610
1611			// Load subkey.
1612			$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1613
1614			// Load taxon.
1615			$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1616			_load_taxonBase($polytomousKeyNode->taxon);
1617			return;
1618			}
1619
1620			/**
1621			* @todo Please document this function.
1622			* @see http://drupal.org/node/1354
1623			*/
1624			function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1625	f26245c8	Andreas Kohlbecker
1626			cdm_check_valid_portal_page();
1627
1628	6657531f	Andreas Kohlbecker	$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1629	4d9660ef	Andreas Kohlbecker	if (!$polytomousKey) {
1630			drupal_set_title(t('Polytomous key does not exist'), PASS_THROUGH);
1631	de017852	Andreas Kohlbecker	return "";
1632	4d9660ef	Andreas Kohlbecker	}
1633	6657531f	Andreas Kohlbecker
1634			$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1635			if (is_array($sourcePager->records)) {
1636			$polytomousKey->sources = $sourcePager->records;
1637			// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1638			}
1639
1640			$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1641			if (is_array($annotationPager->records)) {
1642			$polytomousKey->annotations = $annotationPager->records;
1643			}
1644
1645			_load_polytomousKeySubGraph($polytomousKey->root);
1646			return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1647			}
1648
1649			/**
1650			* Creates a taxon page view or a chapter of it.
1651			*
1652			* The taxon page gives detailed information on a taxon, it shows:
1653			* - Taxon name.
1654			* - Full list of synonyms homotypic synonyms on top, followed by the
1655			* heterotypic and finally followed by misapplied names.
1656			* The list is ordered historically.
1657			* - All description associated with the taxon.
1658			*
1659			* @param string $uuid
1660			* @param string $chapter
1661			* Name of the part to display, valid values are:
1662			* 'description', 'images', 'synonymy', 'specimens', 'all'.
1663			*
1664	793dae0a	Andreas Kohlbecker	* @return string
1665	6657531f	Andreas Kohlbecker	*/
1666	0c5a23b6	Andreas Kohlbecker	function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1667	5ea8b301	Andreas Kohlbecker
1668	f26245c8	Andreas Kohlbecker	cdm_check_valid_taxon_page($chapter);
1669	2dd59bb5	Andreas Kohlbecker	cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1670	b654a866	Andreas Kohlbecker
1671	5ea8b301	Andreas Kohlbecker
1672	6657531f	Andreas Kohlbecker	// Display the page for the taxon defined by $uuid.
1673			// set_last_taxon_page_tab(arg(3));
1674	0c5a23b6	Andreas Kohlbecker	$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1675	6657531f	Andreas Kohlbecker	if (!empty($taxonpage)) {
1676	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1677	6657531f	Andreas Kohlbecker	return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1678			}
1679			else {
1680	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1681	6657531f	Andreas Kohlbecker	return '';
1682			}
1683			}
1684
1685			/**
1686	43d01429	Andreas Kohlbecker	* This function will generate the taxon page part ($chapter) and returns a taxonpage object
1687	59f6da42	Andreas Kohlbecker	* which has two fields, one for the page title and one for the content. Later on in the
1688			* process chain the value contained in these fields will be passed to the cdm_node_show()
1689			* function as the function parameters $title and $content.
1690	6657531f	Andreas Kohlbecker	*
1691			* @param string $uuid
1692	59f6da42	Andreas Kohlbecker	* the uuid of the taxon to show
1693	6657531f	Andreas Kohlbecker	* @param string $chapter
1694			* Name of the part to display, valid values are:
1695			* 'description', 'images', 'synonymy', 'all'.
1696			*
1697	0c5a23b6	Andreas Kohlbecker	* @return object with the following fields:
1698	59f6da42	Andreas Kohlbecker	* - title : the title of the page
1699			* - content: the content of the page
1700			*
1701	8a1b451e	Andreas Kohlbecker	* @throws Exception
1702			*
1703	6657531f	Andreas Kohlbecker	*/
1704	8cf9238f	Andreas Kohlbecker	function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1705	6657531f	Andreas Kohlbecker	// Taxon object.
1706			$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1707			if (empty($taxon)) {
1708			drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1709	8a1b451e	Andreas Kohlbecker	return null;
1710	6657531f	Andreas Kohlbecker	}
1711			$taxonpage = new stdClass();
1712
1713			$taxonpage->title = theme('cdm_taxon_page_title', array(
1714	8cf9238f	Andreas Kohlbecker	'taxon' => $taxon
1715	6657531f	Andreas Kohlbecker	));
1716
1717			// Check if the taxon id contained in the currently selected tree.
1718	7663cd0b	Andreas Kohlbecker	$taxon_in_current_classification = taxon_in_current_classification($uuid);
1719	61b6ee11	Andreas Kohlbecker
1720	7663cd0b	Andreas Kohlbecker	if (!$taxon_in_current_classification) {
1721	61b6ee11	Andreas Kohlbecker	$classifications = get_classifications_for_taxon($taxon);
1722	e24d373b	Andreas Kohlbecker	RenderHints::pushToRenderStack('not_in_current_classification');
1723	8202a2c0	Andreas Kohlbecker	RenderHints::setFootnoteListKey('not_in_current_classification');
1724			FootnoteManager::blockFootnotesFor('not_in_current_classification');
1725	e24d373b	Andreas Kohlbecker	$taxon_name_markup = render_taxon_or_name($taxon);
1726	8202a2c0	Andreas Kohlbecker	FootnoteManager::unblockFootnotesFor('not_in_current_classification');
1727			RenderHints::clearFootnoteListKey();
1728	e24d373b	Andreas Kohlbecker
1729	61b6ee11	Andreas Kohlbecker	if (count($classifications) == 0) {
1730	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.',
1731	fba00a4f	Andreas Kohlbecker	array(
1732	e24d373b	Andreas Kohlbecker	'!taxonname' => $taxon_name_markup,
1733	fba00a4f	Andreas Kohlbecker	)
1734			), 'warning');
1735	6657531f	Andreas Kohlbecker	}
1736			else {
1737			$trees = '';
1738	61b6ee11	Andreas Kohlbecker	foreach ($classifications as $classification) {
1739			if (isset($classification->titleCache)) {
1740			$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1741	6657531f	Andreas Kohlbecker	}
1742			}
1743
1744	15b7c460	Andreas Kohlbecker	drupal_set_message(format_plural(count($trees),
1745	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',
1746			'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1747			array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1748	fba00a4f	Andreas Kohlbecker	) ,
1749			'warning');
1750	6657531f	Andreas Kohlbecker	}
1751	e24d373b	Andreas Kohlbecker	RenderHints::popFromRenderStack();
1752	6657531f	Andreas Kohlbecker	}
1753
1754			// Render the taxon page.
1755	9a607f17	Andreas Kohlbecker	$render_array = compose_cdm_taxon_page($taxon, $chapter);
1756			$taxonpage->content = drupal_render($render_array);
1757	6657531f	Andreas Kohlbecker
1758			return $taxonpage;
1759			}
1760	961319fe	Andreas Kohlbecker
1761
1762	6eaec849	Katja Luther	function cdm_dataportal_specimen_by_accession_number_page_view($accession_number)
1763			{
1764	961319fe	Andreas Kohlbecker	cdm_check_valid_portal_page();
1765	6eaec849	Katja Luther
1766	961319fe	Andreas Kohlbecker	$specimenpage = specimen_by_accession_number_view($accession_number);
1767
1768			if (!empty($specimenpage)) {
1769			return cdm_node_show_simulate($specimenpage->content);
1770			}
1771			else {
1772			return '';
1773			}
1774	4c812e71	Katja Luther
1775	6657531f	Andreas Kohlbecker
1776	6eaec849	Katja Luther	}
1777	961319fe	Andreas Kohlbecker
1778	9d37c9d9	Patric Plitzner	/**
1779			* Creates a specimen page view.
1780			* @param string $uuid the UUID of the specimen
1781			* @return array\|string
1782			*/
1783	961319fe	Andreas Kohlbecker	function cdm_dataportal_specimen_page_view($uuid) {
1784	9d37c9d9	Patric Plitzner
1785	b654a866	Andreas Kohlbecker	cdm_check_valid_portal_page();
1786	961319fe	Andreas Kohlbecker	$specimenpage = cdm_dataportal_specimen_view($uuid);
1787			if (!empty($specimenpage)) {
1788			return cdm_node_show_simulate($specimenpage->content);
1789			}
1790			else {
1791			return '';
1792			}
1793			}
1794	4c812e71	Katja Luther
1795
1796	961319fe	Andreas Kohlbecker	/**
1797			* Creates a specimen page view.
1798			* @param string $uuid the UUID of the specimen
1799			* @return object
1800			* The page object with the following fields:
1801			* - 'title': the page title
1802			* - 'content' : the page content rendered as markup
1803			*/
1804	ff51c1cd	Katja Luther	function specimen_by_accession_number_view($accession_number = null) {
1805	961319fe	Andreas Kohlbecker
1806			$field_unit_dto = cdm_ws_get(CDM_WS_OCCURRENCE_ACCESSION_NUMBER, null, 'accessionNumber=' . $accession_number);
1807
1808			// Display the page for the specimen defined by $uuid.
1809			if (isset($field_unit_dto)){
1810			$dto_array = array($field_unit_dto);
1811			$specimen_array = specimen_render_array_items($dto_array);
1812			$specimen_table = array(
1813			'#theme' => 'table',
1814			'#weight' => 2,
1815			// prefix attributes and rows with '#' to let it pass toF the theme function,
1816			// otherwise it is handled as child render array
1817			'#attributes' => array('class' => 'specimens'),
1818			'#rows' => array(),
1819			'#prefix' => '<div id="specimens">',
1820			'#suffix' => '</div>',
1821			);
1822			foreach($specimen_array as $value){
1823			$renderArray = array(
1824			'#theme' => 'item_list',
1825			'#items' => array($value),
1826			'#type' => 'ul');
1827			$output = drupal_render($renderArray);
1828			$specimen_table['#rows'][] = array(
1829			// An array of table rows. Every row is an array of cells, or an associative array
1830			'data' => array($output),
1831			'class' => array(
1832			'descriptionElement',
1833			'descriptionElement_IndividualsAssociation'
1834			),
1835			);
1836	4c812e71	Katja Luther
1837
1838	961319fe	Andreas Kohlbecker	}
1839			$specimenpage = new stdClass();
1840	4c812e71	Katja Luther
1841	961319fe	Andreas Kohlbecker	$specimenpage->title = theme('theme_cdm_specimen_dto_page_title', array(
1842			'specimen' => $field_unit_dto
1843			));
1844	4c812e71	Katja Luther
1845	ff51c1cd	Katja Luther	$render_array['markup'] = $specimen_table;
1846			$specimenpage->content = drupal_render($render_array);
1847	961319fe	Andreas Kohlbecker	}
1848	4c812e71	Katja Luther
1849	961319fe	Andreas Kohlbecker	return $specimenpage;
1850	9d37c9d9	Patric Plitzner	}
1851
1852	961319fe	Andreas Kohlbecker
1853	9d37c9d9	Patric Plitzner	/**
1854			*
1855			* Creates a specimen view.
1856			* @param string $uuid the UUID of the specimen
1857	961319fe	Andreas Kohlbecker	* @return object
1858			* Page object with the fields
1859			* - title
1860			* - content
1861	9d37c9d9	Patric Plitzner	*/
1862			function cdm_dataportal_specimen_view($uuid) {
1863	a2acff0a	Katja Luther	//TODO: get the derivateDTO and don't call the webservice a second time in compose_cdm_specimen_page
1864	907cc9b4	Patrick Plitzner	$specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1865	9d37c9d9	Patric Plitzner	if (empty($specimen)) {
1866			drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1867			return FALSE;
1868			}
1869			$specimenpage = new stdClass();
1870
1871	961319fe	Andreas Kohlbecker	$specimenpage->title = specimen_page_title($specimen);
1872	9d37c9d9	Patric Plitzner
1873	b810158e	Patric Plitzner	// Render the specimen page.
1874	a2acff0a	Katja Luther	$render_array = compose_cdm_specimen_page($specimen);
1875	9d37c9d9	Patric Plitzner	$specimenpage->content = drupal_render($render_array);
1876
1877			return $specimenpage;
1878			}
1879
1880	e170a53e	Patrick Plitzner	/**
1881			*
1882			* Creates a description view.
1883	ea0ae3c7	Patrick Plitzner	*
1884	e170a53e	Patrick Plitzner	* @param string $uuid the UUID of the description
1885	ea0ae3c7	Patrick Plitzner	* @param null $descriptive_dataset_uuid the uuid of the data set which defines
1886			* the display of the description detail page
1887			*
1888			* @return object Page object with the fields
1889			* Page object with the fields
1890			* - title
1891			* - content
1892	e170a53e	Patrick Plitzner	*/
1893	ea0ae3c7	Patrick Plitzner	function cdm_dataportal_description_view($uuid, $descriptive_dataset_uuid = NULL) {
1894	e170a53e	Patrick Plitzner	$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $uuid);
1895	de017852	Andreas Kohlbecker	$description_page = new stdClass();
1896	e170a53e	Patrick Plitzner	if (empty($description)) {
1897	de017852	Andreas Kohlbecker	$description_page->title = t('Description does not exist');
1898			drupal_set_title($description_page->title, PASS_THROUGH); // not necessary if correctly implemented as drupal node
1899			$description_page->content = "";
1900	e170a53e	Patrick Plitzner
1901	de017852	Andreas Kohlbecker	} else {
1902			$description_page->title = $description->titleCache;
1903			drupal_set_title($description_page->title); // not necessary if correctly implemented as drupal node
1904	e170a53e	Patrick Plitzner
1905	de017852	Andreas Kohlbecker	// Render the description page.
1906	fec3fd41	Andreas Kohlbecker	$render_array = compose_description_table($description->uuid, $descriptive_dataset_uuid);
1907	20bfe15b	Andreas Kohlbecker	if($render_array['title']){
1908			$page_title = strip_tags($render_array['title']['#markup']);
1909			drupal_set_title($page_title);
1910			unset($render_array['title']);
1911			}
1912	de017852	Andreas Kohlbecker	$description_page->content = drupal_render($render_array);
1913			}
1914	e170a53e	Patrick Plitzner
1915	de017852	Andreas Kohlbecker	return $description_page;
1916	e170a53e	Patrick Plitzner	}
1917
1918	ea0ae3c7	Patrick Plitzner	function cdm_dataportal_description_page_view($uuid, $descriptive_dataset_uuid = NULL) {
1919	e170a53e	Patrick Plitzner
1920			cdm_check_valid_portal_page();
1921	ea0ae3c7	Patrick Plitzner	$descriptionpage = cdm_dataportal_description_view($uuid, $descriptive_dataset_uuid);
1922	e170a53e	Patrick Plitzner	if (!empty($descriptionpage)) {
1923			return cdm_node_show_simulate($descriptionpage->content);
1924			}
1925			else {
1926	de017852	Andreas Kohlbecker	return NULL;
1927	e170a53e	Patrick Plitzner	}
1928			}
1929
1930	30845bda	Andreas Kohlbecker	/**
1931			*
1932			* Creates a named area view.
1933			* @param string $uuid the UUID of the specimen
1934			* * @return object
1935			* An object with two fields:
1936			* - title: the page title
1937			* - content: the page content
1938			*/
1939
1940			function cdm_dataportal_named_area_view($uuid) {
1941			$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1942			if (empty($named_area) \|\| $named_area->class !== 'NamedArea') {
1943			drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1944	4d9660ef	Andreas Kohlbecker	return null;
1945	30845bda	Andreas Kohlbecker	}
1946			$named_area_page = new stdClass();
1947
1948			$named_area_page->title = $named_area->representation_L10n;
1949
1950			// Render the specimen page.
1951			$render_array = compose_cdm_named_area_page($uuid);
1952			$named_area_page->content = drupal_render($render_array);
1953
1954			return $named_area_page;
1955			}
1956
1957			function cdm_dataportal_named_area_page_view($uuid) {
1958
1959			cdm_check_valid_portal_page();
1960
1961			$named_area_page = cdm_dataportal_named_area_view($uuid);
1962			if (!empty($named_area_page)) {
1963			return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1964			}
1965			else {
1966			return '';
1967			}
1968
1969
1970			}
1971
1972	6657531f	Andreas Kohlbecker	/**
1973			* Returns a name page as a Drupal node ready to be renderized by Drupal.
1974			*
1975			* The node page shows the taxon name title and the list of taxon related
1976			* with such taxon. Name on the tree already in use.
1977			*
1978	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_name_uuid
1979	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1980	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_to_hide_uuid
1981	51b04faf	Andreas Kohlbecker	* A taxon which should not be displayed in the taxon list
1982	2f65af04	Andreas Kohlbecker	* @param $redirect_to_taxon
1983			* Automatically redirect to the related taxon if there is only one
1984			* accepted taxon for this name.
1985	d4ea0dd9	Andreas Kohlbecker	* @param string $highlite_synonym_uuid
1986	51b04faf	Andreas Kohlbecker	* Optinal parameter wich takes another taxon uuid, if given the
1987			* target taxon pages will show the syonymy tab where the taxon
1988			* refenrenced by the $highlite_synonym_uuid will be highlighted
1989			* in case it is found on this page.
1990	6657531f	Andreas Kohlbecker	*
1991			* @return mixed
1992			* The formatted name page as node.
1993			*/
1994	b648739e	Andreas Kohlbecker	function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL, $redirect_to_taxon = false) {
1995	6657531f	Andreas Kohlbecker
1996	f26245c8	Andreas Kohlbecker	cdm_check_valid_portal_page();
1997
1998	b648739e	Andreas Kohlbecker	$taxonname_page = cdm_dataportal_name_view(
1999			is_uuid($taxon_name_uuid) ? $taxon_name_uuid : null,
2000			is_uuid($taxon_to_hide_uuid) ? $taxon_to_hide_uuid : null,
2001			$redirect_to_taxon == 'redirect_to_taxon',
2002			is_uuid($synonym_uuid) ? $synonym_uuid : null);
2003	6657531f	Andreas Kohlbecker	if (!empty($taxonname_page)) {
2004			return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
2005			}
2006			else {
2007			return '';
2008			}
2009			}
2010
2011			/**
2012	102f8c26	Andreas Kohlbecker	* View function for a TaxonName page.
2013	6657531f	Andreas Kohlbecker	*
2014	e3001c8d	Andreas Kohlbecker	* The name page lists all taxa for which the name specified by the
2015			* $taxon_name_uuid is being used. I case there is only one name the
2016			* page automatically redirects ti the according taxon page. Otherwise
2017			* the list of names is displayed.
2018	6657531f	Andreas Kohlbecker	*
2019	e3001c8d	Andreas Kohlbecker	* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
2020			* list of taxa. This is useful for example when referencing from a taxon
2021			* to the name page and the referring taxon should not be repeaded in the
2022			* name page.
2023	6657531f	Andreas Kohlbecker	*
2024	e3001c8d	Andreas Kohlbecker	*
2025	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_name_uuid
2026	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
2027	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_to_hide_uuid
2028	e3001c8d	Andreas Kohlbecker	* A taxon which should not be displayed in the taxon list
2029	2f65af04	Andreas Kohlbecker	* @param $redirect_to_taxon
2030			* Automatically redirect to the related taxon if there is only one
2031			* accepted taxon for this name.
2032	d4ea0dd9	Andreas Kohlbecker	* @param string $highlite_synonym_uuid
2033	2f65af04	Andreas Kohlbecker	* Optional parameter which takes another taxon uuid, if given the
2034			* target taxon pages will show the synonymy tab where the taxon
2035			* referenced by the $highlite_synonym_uuid will be highlighted
2036	e3001c8d	Andreas Kohlbecker	* in case it is found on this page.
2037			*
2038	2f65af04	Andreas Kohlbecker	* @return object\|boolean
2039	e3001c8d	Andreas Kohlbecker	* An object with two fields:
2040			* - title: the page title
2041			* - content: the page content
2042	2f65af04	Andreas Kohlbecker	* or FALSE
2043			*
2044	6657531f	Andreas Kohlbecker	*/
2045	2f65af04	Andreas Kohlbecker	function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $redirect_to_taxon, $highlite_synonym_uuid = NULL) {
2046	6657531f	Andreas Kohlbecker	// Getting the full taxonname object from the server.
2047	d0d068e9	Andreas Kohlbecker	$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
2048	6657531f	Andreas Kohlbecker	if (!$taxon_name) {
2049			drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
2050			return FALSE;
2051			}
2052	a7560a18	Andreas Kohlbecker	cdm_load_tagged_full_title($taxon_name);
2053	6657531f	Andreas Kohlbecker	// Searching for all the taxa connected with the taxon name on the tree
2054			// in use.
2055	fb308159	Andreas Kohlbecker	$name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
2056			$restrictions = array(new Restriction("name.titleCache","EXACT", array($name->titleCache), 'AND'));
2057			$init_strategy = array(
2058			"name.titleCache",
2059			"name.nomenclaturalReference.authorship",
2060			"name.nomenclaturalReference.inReference.authorship",
2061			"name.nomenclaturalReference.inReference.inReference.authorship",
2062			"name.nomenclaturalReference.inReference.inReference.inReference.authorship"
2063			);
2064	e2617c7e	Andreas Kohlbecker	$taxa = cdm_ws_fetch_all_by_restriction("Taxon", NULL, $restrictions, $init_strategy);
2065	6657531f	Andreas Kohlbecker
2066	d0d068e9	Andreas Kohlbecker	// Removing the name where we came from.
2067	fb308159	Andreas Kohlbecker	foreach ($taxa as $k => &$taxon) {
2068	6657531f	Andreas Kohlbecker	if ($taxon->uuid == $taxon_to_hide_uuid) {
2069	fb308159	Andreas Kohlbecker	unset($taxa[$k]);
2070	6657531f	Andreas Kohlbecker	}
2071			}
2072			// Show the taxa list or go to the singular taxon.
2073	fb308159	Andreas Kohlbecker	if (sizeof($taxa) == 1 && $redirect_to_taxon) {
2074	2f65af04	Andreas Kohlbecker	// redirect to the taxon if there is only one.
2075	fb308159	Andreas Kohlbecker	$singleTaxon = array_pop($taxa);
2076	6657531f	Andreas Kohlbecker	if ($singleTaxon->class != "Taxon") {
2077			// It is a Synonym -> look for the accepted.
2078	7635cc7d	Andreas Kohlbecker	$accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
2079	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
2080	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
2081	6657531f	Andreas Kohlbecker	}
2082			else {
2083	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
2084	6657531f	Andreas Kohlbecker	}
2085			}
2086			else {
2087			// It is an accepted taxon.
2088	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
2089			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
2090	6657531f	Andreas Kohlbecker	}
2091			else {
2092			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
2093			}
2094			}
2095			}
2096	2f65af04	Andreas Kohlbecker	else {
2097			// display the name page content
2098	6657531f	Andreas Kohlbecker	$taxon_name_page = new stdClass();
2099	4f225a0f	Andreas Kohlbecker	$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
2100	2f65af04	Andreas Kohlbecker	$content = array();
2101
2102	a7560a18	Andreas Kohlbecker	RenderHints::pushToRenderStack('name_page');
2103	222784c5	Andreas Kohlbecker	RenderHints::setFootnoteListKey('name_page');
2104	c040bba0	Andreas Kohlbecker	$content['taxon_name'] = markup_to_render_array(render_taxon_or_name($taxon_name), null, '<div class="name-page-name">', '</div>');
2105	d64f1d61	Andreas Kohlbecker
2106	a7560a18	Andreas Kohlbecker
2107	2f65af04	Andreas Kohlbecker	// name relationships
2108	d64f1d61	Andreas Kohlbecker	$name_relations = cdm_ws_fetch_all(str_replace("$0", $taxon_name->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
2109			if(count($name_relations) > 0){
2110			$content['name_relationships'] = compose_name_relationships_list($name_relations, $taxon_name->uuid, null);
2111			}
2112	14076b88	Andreas Kohlbecker
2113	a9a04561	Andreas Kohlbecker	// type designations
2114	a44d210c	Andreas Kohlbecker	$type_designations_render_array = compose_type_designations($taxon_name->uuid);
2115	ae177dac	Andreas Kohlbecker	$content = array_merge($content, $type_designations_render_array);
2116	efff6ee1	Andreas Kohlbecker	// registrations
2117			$registrationDTOs= cdm_ws_fetch_all(CDM_WS_REGISTRATION_DTO, array('nameUuid' => $taxon_name_uuid));
2118			if(isset($registrationDTOs) && count($registrationDTOs ) > 0 ){
2119			$content['registrations'][] = markup_to_render_array('<h2>' . t("Registrations") . '</h2>') ;
2120			foreach ($registrationDTOs as $regDTO){
2121			$content['registrations'][] = compose_registration_dto_compact($regDTO);
2122			}
2123			}
2124
2125
2126	2f65af04	Andreas Kohlbecker	// related taxa
2127	c05ac190	Andreas Kohlbecker	$show_taxa_section = variable_get(CDM_NAME_PAGE_SECTION_TAXA, CDM_NAME_PAGE_SECTION_TAXA_DEFAULT);
2128			if($show_taxa_section){
2129			if ($taxa) {
2130			$content['related_taxa_header'] = markup_to_render_array("<h2>Taxa for this name</h2>");
2131			$content['related_taxa'] = compose_list_of_taxa($taxa);
2132			}
2133			else {
2134			$content['related_taxa'] = markup_to_render_array('This name is not assigned to a taxon.', null, '<div class="no-taxon-message">', '</div>');
2135			}
2136	6657531f	Andreas Kohlbecker	}
2137	a7560a18	Andreas Kohlbecker
2138	d0d0a092	Andreas Kohlbecker	$content['footnotes'] = markup_to_render_array(render_footnotes());
2139	deb2fc24	Andreas Kohlbecker
2140	2f65af04	Andreas Kohlbecker	$taxon_name_page->content = $content;
2141	a7560a18	Andreas Kohlbecker	RenderHints::popFromRenderStack();
2142	222784c5	Andreas Kohlbecker	RenderHints::clearFootnoteListKey();
2143	6657531f	Andreas Kohlbecker	return $taxon_name_page;
2144			}
2145			}
2146
2147	a9a04561	Andreas Kohlbecker
2148	e0d3e148	Andreas Kohlbecker	/**
2149			* Returns a registration page as a Drupal node to be rendered by Drupal.
2150			*
2151	aea2f0ea	Andreas Kohlbecker	* @param string $registration_identifie
2152	e0d3e148	Andreas Kohlbecker	* The persistent identifier of the registration urlencoded.
2153			* @return mixed
2154			* The formatted registration page as node.
2155			*/
2156	aea2f0ea	Andreas Kohlbecker	function cdm_dataportal_registration_page_view() {
2157	e0d3e148	Andreas Kohlbecker
2158	aea2f0ea	Andreas Kohlbecker	cdm_check_valid_portal_page("/\/cdm_dataportal\/registration/");
2159			$registration_identifier = $_REQUEST['identifier'];
2160			$registration_page = cdm_dataportal_registration_view($registration_identifier);
2161	e0d3e148	Andreas Kohlbecker	return cdm_node_show_simulate($registration_page);
2162			}
2163
2164	961319fe	Andreas Kohlbecker	/**
2165	aea2f0ea	Andreas Kohlbecker	* @param $registration_identifier
2166	961319fe	Andreas Kohlbecker	* @return array
2167			* The drupal render array for the registration view.
2168			*/
2169	aea2f0ea	Andreas Kohlbecker	function cdm_dataportal_registration_view($registration_identifier) {
2170	e0d3e148	Andreas Kohlbecker
2171	a7560a18	Andreas Kohlbecker	RenderHints::pushToRenderStack('registration_page');
2172	222784c5	Andreas Kohlbecker	RenderHints::setFootnoteListKey('registration_page');
2173	a7560a18	Andreas Kohlbecker
2174	6cbefddc	Andreas Kohlbecker	$render_array = array();
2175	bd15166b	Andreas Kohlbecker	$registration_dto = cdm_ws_get(CDM_WS_REGISTRATION_DTO, null, 'identifier=' . $registration_identifier);
2176	e0d3e148	Andreas Kohlbecker	if($registration_dto){
2177
2178	a7560a18	Andreas Kohlbecker	drupal_set_title(t('Registration Id:') . ' ' . $registration_identifier, PASS_THROUGH);
2179	26b8a1bc	Andreas Kohlbecker	$render_array = compose_registration_dto_full($registration_dto, true);
2180	e0d3e148	Andreas Kohlbecker
2181			} else {
2182	bd15166b	Andreas Kohlbecker	$status_text = cdm_ws_get(CDM_WS_REGISTRATION_STATUS, null, 'identifier=' . $registration_identifier);
2183	6c9d417d	Andreas Kohlbecker	if(isset($status_text->String)) {
2184	1e7459da	Andreas Kohlbecker	$status_text = strtolower($status_text->String);
2185			if($status_text == 'preparation' \|\| $status_text == 'curation'){
2186			$status_text = 'in ' . $status_text;
2187			}
2188			drupal_set_title(t('Registration ' . $status_text), PASS_THROUGH);
2189			//$status_message;
2190	5fdcad30	Andreas Kohlbecker	drupal_set_message("A registration with the identifier " . $registration_identifier . " is " . $status_text, "status");
2191	1e7459da	Andreas Kohlbecker	} else {
2192			drupal_set_title(t('Registration not found'), PASS_THROUGH);
2193	e42db5b0	Andreas Kohlbecker	drupal_set_message("A registration with the identifier " . $registration_identifier . " does not exist", "warning");
2194	1e7459da	Andreas Kohlbecker	}
2195	e0d3e148	Andreas Kohlbecker	}
2196
2197	5446f047	Andreas Kohlbecker	$render_array = array(
2198	5fdcad30	Andreas Kohlbecker	'#prefix' => '<div id="registration">',
2199	5446f047	Andreas Kohlbecker	'registration' => $render_array,
2200			'#suffix' => '</div>',
2201			);
2202
2203	a7560a18	Andreas Kohlbecker	RenderHints::popFromRenderStack();
2204	222784c5	Andreas Kohlbecker	RenderHints::clearFootnoteListKey();
2205	a7560a18	Andreas Kohlbecker
2206	e0d3e148	Andreas Kohlbecker	return $render_array ;
2207			}
2208
2209
2210	6657531f	Andreas Kohlbecker	/**
2211	84b13813	Andreas Kohlbecker	* Creates a page with the advance search form.
2212			*
2213			* NOTE: The advance search form allows searching for taxa.
2214	6657531f	Andreas Kohlbecker	*/
2215	2f30124c	Andreas Kohlbecker	function cdm_dataportal_view_search_advanced() {
2216	6657531f	Andreas Kohlbecker	drupal_set_title(t('Advanced search'), PASS_THROUGH);
2217			return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
2218			}
2219
2220	a1ce57ce	Katja Luther	/**
2221			* Creates a page with the blast search form.
2222			*
2223			* NOTE: The advance search form allows searching for specimen in blast DB.
2224			*/
2225			function cdm_dataportal_view_search_blast() {
2226			drupal_set_title(t('Blast search'), PASS_THROUGH);
2227			return drupal_get_form('cdm_dataportal_search_blast_form');
2228			}
2229
2230	6657531f	Andreas Kohlbecker	/**
2231	84b13813	Andreas Kohlbecker	* Creates a page with the search form for searching by taxon descriptions.
2232	6657531f	Andreas Kohlbecker	*/
2233			function cdm_dataportal_view_search_taxon_by_description() {
2234	6441ddfb	Andreas Kohlbecker	drupal_set_title(t('Search by factual data'), PASS_THROUGH);
2235	6657531f	Andreas Kohlbecker	return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
2236			}
2237
2238			/**
2239			* Executes the search and generates the result list of taxa.
2240			*/
2241			function cdm_dataportal_view_search_results_taxon() {
2242
2243	24797d7f	Andreas Kohlbecker	$taxonPager = cdm_dataportal_search_taxon_execute();
2244	6657531f	Andreas Kohlbecker
2245	f19f47fa	Andreas Kohlbecker	$showThumbnails = do_showThumbnails();
2246
2247			$setSessionUri = url('cdm_api/setvalue/session', array(
2248			'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
2249			));
2250
2251			drupal_add_js('jQuery(document).ready(function() {
2252
2253			// init
2254			if(' . $showThumbnails . ' == 1){
2255	1d69a96c	Andreas Kohlbecker	jQuery(\'.media_gallery\').show(20);
2256			} else {
2257			jQuery(\'.media_gallery\').hide(20);
2258			}
2259
2260			// add change handler
2261			jQuery(\'#showThumbnails input.showThumbnails\').change(
2262	f19f47fa	Andreas Kohlbecker	function(event){
2263	1d69a96c	Andreas Kohlbecker	var state = 0;
2264			if(jQuery(this).is(\':checked\')){
2265			jQuery(\'.media_gallery\').show(20);
2266			state = 1;
2267			} else {
2268			jQuery(\'.media_gallery\').hide(20);
2269			}
2270			// store state in session variable
2271			var uri = \'' . $setSessionUri . '\' + state;
2272			jQuery.get(uri);
2273			});
2274	78e178e2	Andreas Kohlbecker	});',
2275	f19f47fa	Andreas Kohlbecker	array('type' => "inline", 'scope' => JS_DEFAULT));
2276
2277	78e178e2	Andreas Kohlbecker	drupal_set_title(t('Search results'), PASS_THROUGH);
2278
2279	0a1dc066	Andreas Kohlbecker	return theme('cdm_search_taxa_results', array(
2280	6657531f	Andreas Kohlbecker	'pager' => $taxonPager,
2281			'path' => 'cdm_dataportal/search/results/taxon',
2282			));
2283			}
2284
2285	a1ce57ce	Katja Luther	/**
2286			* Executes the blast search and generates the result list of specimen.
2287			*/
2288			function cdm_dataportal_view_search_results_specimen() {
2289
2290			$specimenPager = cdm_dataportal_search_blast_execute();
2291
2292			return theme('cdm_search_specimen_results', array(
2293			'pager' => $specimenPager,
2294			'path' => 'cdm_dataportal/search/results/specimen',
2295			));
2296			}
2297
2298
2299	a6ae799b	Andreas Kohlbecker	/**
2300			* Executes the search for registrations and generates the result list..
2301			*/
2302	efbff4b3	Andreas Kohlbecker	function cdm_dataportal_view_search_registrations_results($mode = 'filter') {
2303
2304			switch($mode ){
2305			case 'taxongraph':
2306			$block = block_load('cdm_dataportal', 'registrations_search_taxongraph');
2307			$registration_pager = cdm_dataportal_search_registrations_taxongraph_execute();
2308			break;
2309			case 'filter':
2310			default:
2311			$block = block_load('cdm_dataportal', 'registrations_search_filter');
2312			$registration_pager = cdm_dataportal_search_registrations_filter_execute();
2313			}
2314			$block->title = null;
2315	a6ae799b	Andreas Kohlbecker
2316			drupal_set_title(t('Search registrations'), PASS_THROUGH);
2317
2318	efbff4b3	Andreas Kohlbecker	$render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
2319	e2617c7e	Andreas Kohlbecker	$registrations_pager_array = compose_search_results($registration_pager, new RegistrationDTOComposeHandler());
2320	a6ae799b	Andreas Kohlbecker	$render_array = array_merge($render_array, $registrations_pager_array);
2321
2322			return $render_array;
2323			}
2324
2325	e2617c7e	Andreas Kohlbecker	/**
2326			* Executes the search for registrations and generates the result list..
2327			*/
2328			function cdm_dataportal_view_search_agent() {
2329
2330			$render_array = [];
2331			$title = isset($_REQUEST['class']) && $_REQUEST['class'] ? $_REQUEST['class'] : 'Persons & Teams';
2332			drupal_set_title(t($title), PASS_THROUGH);
2333			// TODO $block = block_load('cdm_dataportal', 'search_agent_filter');
2334			// $block->title = null;
2335			// $render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
2336			$pager = cdm_dataportal_search_agent_execute();
2337			$pager_render_array = compose_search_results($pager, new AgentComposeHandler());
2338			$render_array = array_merge($render_array, $pager_render_array);
2339			return $render_array;
2340			}
2341
2342	a6ae799b	Andreas Kohlbecker
2343	94550ff9	Andreas Kohlbecker	/**
2344	bb5a542c	Andreas Kohlbecker	* Provides the standard image which indicated a loading process
2345	94550ff9	Andreas Kohlbecker	*
2346			* @return string
2347			* The img html tag
2348			*/
2349			function loading_image_html() {
2350			return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
2351			. '/images/loading_circle_grey_16.gif" style="display:none;">';
2352			}
2353
2354	78e178e2	Andreas Kohlbecker	/**
2355			* Returns the state of the the showThumbnails flag set in the
2356			* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
2357			*
2358	c5ed6357	Andreas Kohlbecker	* @return boolean
2359	78e178e2	Andreas Kohlbecker	* returns 1 if the flag is set
2360			*/
2361			function do_showThumbnails() {
2362			static $showThumbnails = null;
2363
2364			if($showThumbnails == null) {
2365	c5ed6357	Andreas Kohlbecker	$showThumbnails = 0;
2366			if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
2367			$showThumbnails = 0;
2368			$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
2369			$showThumbnails = is_array($search_gallery_settings)
2370			&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
2371			&& (
2372			$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
2373			$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
2374			$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
2375			)
2376			? 1 : 0;
2377	f19f47fa	Andreas Kohlbecker
2378	c5ed6357	Andreas Kohlbecker	drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
2379			}
2380	f19f47fa	Andreas Kohlbecker	$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
2381			if (!is_numeric($showThumbnails)) {
2382			$showThumbnails = 1;
2383			}
2384	78e178e2	Andreas Kohlbecker	}
2385
2386			return $showThumbnails;
2387			}
2388
2389	6657531f	Andreas Kohlbecker
2390	a6ae799b	Andreas Kohlbecker
2391	6657531f	Andreas Kohlbecker	/* ====================== other functions ====================== */
2392			/**
2393			* Creates a URL to the taxon page specified by the $uuid parameter.
2394			*
2395			* The URL will be prepended with a path element to a specific taxon page tab.
2396			*
2397			* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
2398			* be set globally in the administrative settings or individually in the user
2399			* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
2400			* the last portal will stay on this last tab.
2401			*
2402			* A third option is offerered by the $page_tab parameter which allows overwriting this
2403			* internal mechanism by a specific value.
2404			*
2405			* @param string $uuid
2406			* The UUID of the taxon.
2407			* @param string $page_tab
2408			* Overwriting the preset mechanism by defining specific value for the
2409			* taxon page tab.
2410			* @return string
2411			* The created URL.
2412			*/
2413			function path_to_taxon($uuid, $page_tab = FALSE) {
2414
2415			$tab = get_default_taxon_tab();
2416			$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2417
2418			if (!$uuid) {
2419			return FALSE;
2420			}
2421
2422			if ($page_tab) {
2423	fec3fd41	Andreas Kohlbecker	$url = 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2424	6657531f	Andreas Kohlbecker	}
2425			elseif (!$tab \|\| strtolower($tab) == 'general') {
2426	fec3fd41	Andreas Kohlbecker	$url = 'cdm_dataportal/taxon/' . $uuid;
2427	6657531f	Andreas Kohlbecker	}
2428			elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2429	fec3fd41	Andreas Kohlbecker	$url = 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2430	6657531f	Andreas Kohlbecker	}
2431			else {
2432	fec3fd41	Andreas Kohlbecker	$url = 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2433	6657531f	Andreas Kohlbecker	}
2434	fec3fd41	Andreas Kohlbecker	return $url;
2435	6657531f	Andreas Kohlbecker	}
2436
2437	ea0ae3c7	Patrick Plitzner	function path_to_description($uuid, $descriptive_dataset_uuid = NULL) {
2438	e170a53e	Patrick Plitzner
2439			if (!$uuid) {
2440			return FALSE;
2441			}
2442			else {
2443	9705e44e	Patrick Plitzner	return 'cdm_dataportal/description/' . $uuid
2444			. (is_uuid($descriptive_dataset_uuid) ? '/' . $descriptive_dataset_uuid : '');
2445	e170a53e	Patrick Plitzner	}
2446			}
2447
2448	9d37c9d9	Patric Plitzner	function path_to_specimen($uuid) {
2449
2450			if (!$uuid) {
2451			return FALSE;
2452			}
2453			else {
2454	a1ce57ce	Katja Luther	return 'cdm_dataportal/occurrence/' . $uuid;
2455	9d37c9d9	Patric Plitzner	}
2456			}
2457
2458	6eaec849	Katja Luther	function path_to_specimen_by_accession_number($accession_number) {
2459
2460			if (!$accession_number) {
2461			return FALSE;
2462			}
2463			else {
2464			return 'cdm_dataportal/specimen/accession_number/' . $accession_number;
2465			}
2466			}
2467
2468	30845bda	Andreas Kohlbecker	function path_to_named_area($uuid) {
2469
2470			if (!$uuid) {
2471			return FALSE;
2472			}
2473			else {
2474			return 'cdm_dataportal/named_area/' . $uuid;
2475			}
2476			}
2477
2478	6657531f	Andreas Kohlbecker	/**
2479	630c7044	Andreas Kohlbecker	* Creates a URL to show a synonmy in the according taxon page.
2480			*
2481			* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2482			* The resulting URI will include query parameters to highlight the synonym, and to optionally display
2483			* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2484			* include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2485			* in the page
2486			*
2487			* @param string $synonymUuid
2488			* The uuid of the synonym
2489			* @param string $acceptedUuid
2490			* The uuid of the according accepted taxon
2491			* @return string
2492			* The URL to show a synonmy in the according taxon page
2493	6657531f	Andreas Kohlbecker	*/
2494			function uri_to_synonym($synonymUuid, $acceptedUuid) {
2495			$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2496	d071bed7	Andreas Kohlbecker	return url($acceptedPath, array(
2497			'query' => array(
2498			// highlite the synony in the synonymy
2499			'highlite' => $synonymUuid,
2500			// the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2501			// see theme_taxon_page_title()
2502			'acceptedFor' => $synonymUuid
2503	630c7044	Andreas Kohlbecker	),
2504			'fragment' => $synonymUuid
2505	d071bed7	Andreas Kohlbecker	));
2506
2507	6657531f	Andreas Kohlbecker	}
2508
2509			/**
2510	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the key identified by the uuid.
2511	b8bfa4bd	Andreas Kohlbecker	*
2512			* @param string $keyType
2513			* the key typer corresponds to the specific class of the CDM
2514			* IdentificationKey. Possible values are
2515			* -PolytomousKey
2516			* -MultimediaKey
2517			* - ...
2518	e0d3e148	Andreas Kohlbecker	* @param string $keyUuid
2519	b8bfa4bd	Andreas Kohlbecker	* The UUID of the key
2520	6657531f	Andreas Kohlbecker	*/
2521			function path_to_key($keyType, $keyUuid) {
2522			if (!$keyUuid \|\| !$keyType) {
2523			return FALSE;
2524			}
2525			$keyType{0} = strtolower($keyType{0});
2526			return "cdm_dataportal/" . $keyType . "/$keyUuid";
2527			}
2528
2529			/**
2530	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the reference identified by the uuid.
2531			*
2532			* @param $uuid string String representation of the registration entity uuid.
2533			*
2534			* @return string
2535			* The drupal path
2536			*
2537	6657531f	Andreas Kohlbecker	*/
2538			function path_to_reference($uuid) {
2539			if (!$uuid) {
2540			return FALSE;
2541			}
2542			return 'cdm_dataportal/reference/' . $uuid;
2543			}
2544
2545	e0d3e148	Andreas Kohlbecker	/**
2546			* Composes the drupal path to the reference identified by the uuid.
2547			*
2548			* @param string $identifier
2549			* The persistent identifier of the registration entity (Registration.identifier).
2550			* @return string
2551			* The drupal path
2552			*/
2553			function path_to_registration($identifier) {
2554
2555	977bba78	Andreas Kohlbecker	if(variable_get(CDM_REGISTRATION_PRESISTENT_IDENTIFIER_AS_LINK)){
2556			return $identifier;
2557			} else {
2558			return 'cdm_dataportal/registration/' . urlencode($identifier);
2559			}
2560	e0d3e148	Andreas Kohlbecker	}
2561
2562	6657531f	Andreas Kohlbecker	/**
2563	51b04faf	Andreas Kohlbecker	* Creates the path to a cdm_dataportal taxon name page.
2564			*
2565	e0d3e148	Andreas Kohlbecker	* @param string $taxon_name_uuid
2566			* The uuid as string of the CDM TaxonName to show a name page for
2567			* @param string $taxon_to_hide_uuid
2568			* The uuid as string of a taxon which should not be displayed in the taxon list
2569	d4ea0dd9	Andreas Kohlbecker	* @param string $highlited_synonym_uuid
2570	e0d3e148	Andreas Kohlbecker	* Optional parameter which takes another taxon uuid, if given the
2571			* target taxon pages will show the synonymy tab where the taxon
2572			* referenced by the $highlite_synonym_uuid will be highlighted
2573	51b04faf	Andreas Kohlbecker	* in case it is found on this page.
2574	2f65af04	Andreas Kohlbecker	* @param $redirect_to_taxon
2575			* If true, the name page will redirect to the related taxon if there is a single one
2576			* for this name only.
2577	51b04faf	Andreas Kohlbecker	*
2578	e0d3e148	Andreas Kohlbecker	* @return string
2579			* URI path element as string
2580	6657531f	Andreas Kohlbecker	*/
2581	2f65af04	Andreas Kohlbecker	function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $highlited_synonym_uuid = NULL, $redirect_to_taxon = false) {
2582	6657531f	Andreas Kohlbecker	$res = FALSE;
2583			if ($name_uuid) {
2584	2f65af04	Andreas Kohlbecker	$res = 'cdm_dataportal/name/' . $name_uuid .
2585			'/' . (is_uuid($taxon_to_hide_uuid) ? $taxon_to_hide_uuid : "null") .
2586			'/' . (is_uuid($highlited_synonym_uuid) ? $highlited_synonym_uuid : "null") .
2587	14832ae9	Andreas Kohlbecker	'/' . ($redirect_to_taxon \|\| variable_get(CDM_NAME_PAGE_AUTOREDIRECT, 0) ? "redirect_to_taxon" : "");
2588	51b04faf	Andreas Kohlbecker	}
2589	2f65af04	Andreas Kohlbecker
2590	6657531f	Andreas Kohlbecker	return $res;
2591			}
2592
2593			/**
2594	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the media entity identified by the uuid.
2595			*
2596			* @param string $uuid
2597			* The persistent identifier of the entity entity
2598			* @return string
2599			* The drupal path
2600	6657531f	Andreas Kohlbecker	*/
2601			function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2602			if (!$uuid) {
2603			return FALSE;
2604			}
2605			$out = 'cdm_dataportal/media/' . $uuid;
2606			if ($representaion_uuid) {
2607			$out .= '/' . $representaion_uuid;
2608	a867b774	Andreas Kohlbecker	if (is_numeric($partId)) {
2609	6657531f	Andreas Kohlbecker	$out .= '/' . $partId;
2610			}
2611			}
2612			return $out;
2613			}
2614
2615			/**
2616			* Compares thisRank with thatRank.
2617			*
2618			* Returns a negative integer, zero, or a positive integer
2619			* as the of thisRank is higher than, equal to, or lower than thatRank.
2620			* e.g:
2621			* <ul>
2622			* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2623			* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2624			* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2625			* </ul>
2626			* <p>
2627			* This compare logic of the underlying webservice is the
2628			* <b>inverse logic</b> of the the one implemented in
2629			* java.lang.Comparable#compareTo(java.lang.Object)
2630			*
2631			* @param $thisRankUuid
2632			* @param $thatRankUuid
2633			*
2634			* @return int
2635			* A negative integer, zero, or a positive integer
2636			* as the thisRank is lower than, equal to, or higher than thatRank.
2637			*/
2638			function rank_compare($thisRankUuid, $thatRankUuid) {
2639			$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2640			return $result->Integer;
2641			}
2642
2643			/**
2644	a0e3ae5c	Andreas Kohlbecker	* Creates a short version of a taxonname.
2645	6657531f	Andreas Kohlbecker	*
2646	e90899ac	Andreas Kohlbecker	* The short name is created by using the taggedTitle field of
2647	a0e3ae5c	Andreas Kohlbecker	* TaxonNodeDTO instances.
2648	e90899ac	Andreas Kohlbecker	* If the taggedTitle if empty the fullname will be returned.
2649	6657531f	Andreas Kohlbecker	*
2650	a0e3ae5c	Andreas Kohlbecker	* @param object $taxonNodeDTO
2651			* A TaxonNodeDTO object
2652	6657531f	Andreas Kohlbecker	*
2653			* @return string
2654			*/
2655	a0e3ae5c	Andreas Kohlbecker	function cdm_dataportal_shortname_of($taxonNodeDTO) {
2656
2657	6657531f	Andreas Kohlbecker	$nameStr = '';
2658
2659	a0e3ae5c	Andreas Kohlbecker	normalize_tagged_text($taxonNodeDTO->taggedTitle);
2660	6657531f	Andreas Kohlbecker
2661			// Get all tagged text tokens of the scientific name.
2662	a0e3ae5c	Andreas Kohlbecker	foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2663	6657531f	Andreas Kohlbecker	if ($tagtxt->type == 'name' \|\| $tagtxt->type == 'rank') {
2664			$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2665			}
2666			}
2667			$nameStr = trim($nameStr);
2668
2669			if ($nameStr) {
2670	54164245	Andreas Kohlbecker	if(isset($taxonNodeDTO->status->symbol)){
2671			$nameStr = $taxonNodeDTO->status->symbol . ' ' . $nameStr;
2672	9282ac6e	Andreas Kohlbecker	}
2673	6657531f	Andreas Kohlbecker	// Do not return short names for these.
2674	a0e3ae5c	Andreas Kohlbecker	if ($taxonNodeDTO->unplaced \|\| $taxonNodeDTO->excluded) {
2675	6657531f	Andreas Kohlbecker	return $nameStr;
2676			}
2677
2678			/*
2679			1st capture group (^[a-zA-Z]): First letter of uninomial.
2680			Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2681			Third capture group (\s+[^(\x2E]+\s+.+$\|\s+[a-zA-Z]+$): letters of name,
2682			but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
2683			OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
2684			*/
2685			$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$\|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2686			if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2687			return $matches[1][0] . "." . $matches[3][0];
2688			}
2689			else {
2690			return $nameStr;
2691			}
2692			}
2693			else {
2694	a0e3ae5c	Andreas Kohlbecker	return $taxonNodeDTO->titleCache;
2695	6657531f	Andreas Kohlbecker	}
2696			}
2697
2698			/**
2699			* Check if a taxon is accepted by the current taxonomic tree.
2700			*
2701			* @param mixed $taxon
2702			* The Taxon obkect to check.
2703			*
2704			* @return bool
2705			* Returns TRUE if $taxon is accepted, FALSE otherwise.
2706			*/
2707			function _cdm_dataportal_acceptedByCurrentView($taxon) {
2708
2709	3049fdcd	Andreas Kohlbecker	$default_classification_uuid = get_current_classification_uuid();
2710	6657531f	Andreas Kohlbecker
2711			if (isset($taxon->taxonNodes)) {
2712	3049fdcd	Andreas Kohlbecker	$taxon_nodes = $taxon->taxonNodes;
2713	6657531f	Andreas Kohlbecker	}
2714			else {
2715	3049fdcd	Andreas Kohlbecker	$taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2716	6657531f	Andreas Kohlbecker	}
2717
2718	3049fdcd	Andreas Kohlbecker	if ($taxon->class == "Taxon" && isset($taxon_nodes)) {
2719			foreach ($taxon_nodes as $node) {
2720			if($node->class == 'TaxonNodeDto' && isset($node->classificationUUID)){
2721			// case of TaxonNodeDto
2722			return $node->classificationUUID == $default_classification_uuid;
2723			} else if($node->class == 'TaxonNode' && isset($node->classification->uuid)) {
2724			return $node->classification->uuid == $default_classification_uuid;
2725	6657531f	Andreas Kohlbecker	}
2726			}
2727			}
2728			return FALSE;
2729			}
2730
2731			/**
2732	54cfa718	Andreas Kohlbecker	* Checks is the source has one of the given types.
2733			*
2734			* @param object $source
2735			* The original source entity
2736			* @param array $types
2737	b08a856c	Andreas Kohlbecker	* An array of element of the OriginalSourceType enumeration
2738	54cfa718	Andreas Kohlbecker	* If not set the default will be used which is:
2739			* - Lineage
2740			* - PrimaryMediaSource
2741			* - PrimaryTaxonomicSource
2742			* - Unknown
2743			* - Other
2744			* @return boolean
2745	6657531f	Andreas Kohlbecker	*/
2746	54cfa718	Andreas Kohlbecker	function _is_original_source_type($source, $types = null) {
2747			// this is the default
2748			// maybe this should also be put into the settings
2749			static $default = array(
2750			OriginalSourceType::Lineage,
2751			OriginalSourceType::PrimaryMediaSource,
2752			OriginalSourceType::PrimaryTaxonomicSource,
2753			OriginalSourceType::Unknown,
2754			OriginalSourceType::Other,
2755	fe3a5674	Andreas Kohlbecker	OriginalSourceType::Aggregation
2756	54cfa718	Andreas Kohlbecker	);
2757
2758			if(!$types){
2759			$types = $default;
2760			}
2761			return isset($source->type) && in_array($source->type, $types);
2762			}
2763	6657531f	Andreas Kohlbecker
2764			/**
2765			* Collects all the media from a list of description elements.
2766			*
2767			* @param array $descriptionElements
2768			* The description elements from which to collect the media.
2769			*
2770			* @return array
2771			* The output with all the collected media.
2772			*/
2773			function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2774
2775			$outArrayOfMedia = array();
2776
2777			// Avoiding a warning box in Drupal for Flora Malesiana.
2778			if (isset($descriptionElements) && is_array($descriptionElements)) {
2779			foreach ($descriptionElements as $descriptionElement) {
2780			if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2781			foreach ($descriptionElement->media as $media) {
2782			if (is_object($media)) {
2783			$outArrayOfMedia[] = $media;
2784			}
2785			}
2786			}
2787			}
2788			}
2789			return $outArrayOfMedia;
2790			}
2791
2792	178d1ae6	Andreas Kohlbecker
2793
2794	d9763fd3	Andreas Kohlbecker
2795	6657531f	Andreas Kohlbecker	/**
2796	d9763fd3	Andreas Kohlbecker	* Creates a CDM Dynabox.
2797			*
2798	c1f5d897	Andreas Kohlbecker	* @param string $dynabox_id
2799	d9763fd3	Andreas Kohlbecker	* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2800	6657531f	Andreas Kohlbecker	* @param string $label
2801			* The clickable text to show.
2802			* @param string $content_url
2803			* The cdm REST service request url wich will deliver the content to be shown
2804			* once the dynabox toggles open.
2805			* @param string $theme
2806	1ce9afb7	Patric Plitzner	* The theme to be used for rendering the cdm REST service response with is
2807	6657531f	Andreas Kohlbecker	* returned from the $content_url.
2808			* @param string $link_alt_text
2809			* The value for the alt attribute of the dynabox link.
2810			* @param array $enclosingtags
2811			* An array with two elements: $enclosingtags[0] will be used for the dynabox
2812			* element itself, $enclosingtags[1] is the tag to be used for the
2813	c1f5d897	Andreas Kohlbecker	* dynabox_content (optional)
2814	d9763fd3	Andreas Kohlbecker	* @param array $attributes
2815			* @param $content_element_selector
2816			* Optional jQuery selector which can be used to reference a dom element which should
2817			* be used as container for the content to be shown. The dynabox-<dynabox id>-content
2818			* element will be placed in this container.
2819			*
2820	c1f5d897	Andreas Kohlbecker	* @param string $open_callback
2821	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2822	c1f5d897	Andreas Kohlbecker	* the open state.
2823			* @param string $close_callback
2824	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2825	c1f5d897	Andreas Kohlbecker	* the closed state.
2826	d9763fd3	Andreas Kohlbecker	* @return string Returns HTML for a dynabox.
2827			* Returns HTML for a dynabox.
2828	6657531f	Andreas Kohlbecker	*/
2829	d9763fd3	Andreas Kohlbecker	function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2830			$enclosingtags = array('li', 'ul'), $attributes = array(),
2831			$content_element_selector = null,
2832			$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2833	6657531f	Andreas Kohlbecker	$out = '';
2834	c1f5d897	Andreas Kohlbecker
2835			// check for plain class attribute string
2836			$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2837
2838	9c9d11f7	Andreas Kohlbecker	if(!array_key_exists('class', $attributes)) {
2839	bcc70074	Andreas Kohlbecker	$attributes['class'] = ["dynabox"];
2840			} else {
2841			$attributes['class'] = array_merge($attributes['class'], ["dynabox"]);
2842	9c9d11f7	Andreas Kohlbecker	}
2843	d9763fd3	Andreas Kohlbecker	$attributes['id'][] = 'dynabox-' . $dynabox_id;
2844	9c9d11f7	Andreas Kohlbecker	$dynabox_attributes = drupal_attributes($attributes);
2845
2846
2847	b386ae48	Andreas Kohlbecker	_add_js_domEvent(); // requires domEvent.js
2848	6657531f	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2849	c1f5d897	Andreas Kohlbecker	drupal_add_js("
2850	94bb8db6	Andreas Kohlbecker	jQuery(document).ready(
2851			function() {
2852			dynabox('". $dynabox_id ."',
2853			{
2854			open_callback: " . $open_callback .",
2855	d9763fd3	Andreas Kohlbecker	close_callback: " . $close_callback .
2856			($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2857	94bb8db6	Andreas Kohlbecker	}
2858			);
2859			}
2860			);",
2861			array(
2862			'type'=>'inline',
2863			'scope'=>'footer'
2864			)
2865			);
2866	6657531f	Andreas Kohlbecker
2867	9c9d11f7	Andreas Kohlbecker
2868	6657531f	Andreas Kohlbecker	$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2869	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox for ' . $content_url . ' -->';
2870	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>';
2871	d9763fd3	Andreas Kohlbecker	$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2872			$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2873			$out .= ' </' . $enclosingtags[1] . '>';
2874			$out .= ' </' . $enclosingtags[0] . '>';
2875	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox end -->';
2876	6657531f	Andreas Kohlbecker	return $out;
2877			}
2878
2879			/**
2880			* Checks whether a feature has any description elements.
2881			*
2882			* @param mixed $featureNode
2883			* A feature node as produced by the function _mergeFeatureTreeDescriptions().
2884			*
2885			* @see _mergeFeatureTreeDescriptions()
2886			*
2887			* @return bool
2888			* Returns TRUE if the given $featureNode or any of its subordinate nodes
2889			* contains at least one non empty TextData or at least one DescriptionElement
2890			* of an other type. A TextData element holding a multilanguageText or a
2891			* source reference is considered to be not empty.
2892	159cd9bb	Andreas Kohlbecker	*
2893			* @TODO this function may have become obsolete by the new method of detecting empty blocks,
2894	1b756c5f	Andreas Kohlbecker	* see $block_content_is_not_empty in make_feature_block_list() and
2895	0ebb6efc	Andreas Kohlbecker	* $feature_block_has_content in compose_feature_block_items_generic
2896	6657531f	Andreas Kohlbecker	*/
2897	f19f47fa	Andreas Kohlbecker	function has_feature_node_description_elements($featureNode) {
2898	6657531f	Andreas Kohlbecker
2899			if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2900	092744e1	Andreas Kohlbecker	if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2901			foreach ($featureNode->descriptionElements as $descriptionElement) {
2902	159cd9bb	Andreas Kohlbecker	if ($descriptionElement->class != "TextData" \|\| isset($descriptionElement->multilanguageText_L10n->text)
2903			&& $descriptionElement->multilanguageText_L10n->text != ''
2904			\|\| isset($descriptionElement->sources[0])
2905			\|\| isset($descriptionElement->media[0]) ) {
2906	092744e1	Andreas Kohlbecker	return TRUE;
2907			}
2908	6657531f	Andreas Kohlbecker	}
2909			}
2910			}
2911	092744e1	Andreas Kohlbecker	else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2912	fae36a2a	Andreas Kohlbecker	foreach ($featureNode->childNodes as $child) {
2913	f19f47fa	Andreas Kohlbecker	if (has_feature_node_description_elements($child)) {
2914	6657531f	Andreas Kohlbecker	return TRUE;
2915			}
2916			}
2917			}
2918			return FALSE;
2919			}
2920	f26245c8	Andreas Kohlbecker
2921			/**
2922			* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2923			*
2924			* @param $chapter
2925			* The taxon page chapter or part
2926			*/
2927			function cdm_check_valid_taxon_page($chapter){
2928			static $taxon_tabs = null;
2929
2930			cdm_check_valid_portal_page();
2931
2932			if($taxon_tabs == null){
2933			$taxon_tabs = array('all', 'description');
2934			foreach(get_taxon_tabs_list() as $tab){
2935			$taxon_tabs[] = strtolower($tab);
2936			}
2937			}
2938
2939			if(!in_array($chapter, $taxon_tabs)){
2940			// oops this is not a valid chapter name
2941	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2942	f26245c8	Andreas Kohlbecker	}
2943
2944			}
2945
2946	b654a866	Andreas Kohlbecker	function check_js_devel_mode_disabled() {
2947			if(variable_get('cdm_js_devel_mode', FALSE)) {
2948			drupal_set_message(t('The !url1 is enabled.
2949			WARNING: this is a performance penalty and must be turned off on production websites.', array(
2950			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
2951			)),
2952			'warning'
2953			);
2954			}
2955			}
2956
2957	f26245c8	Andreas Kohlbecker	/**
2958	e0d3e148	Andreas Kohlbecker	* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
2959			* The test applied by default it a check for the query parameter 'q' ending with a file suffix like '.'
2960	f26245c8	Andreas Kohlbecker	*
2961	e0d3e148	Andreas Kohlbecker	* @param $preg_pattern
2962			* Optional regular expression pattern to be used in preg_match().
2963	f26245c8	Andreas Kohlbecker	*/
2964	e0d3e148	Andreas Kohlbecker	function cdm_check_valid_portal_page($preg_pattern = null){
2965	595de9f0	Andreas Kohlbecker	$ends_with_file_suffix_pattern = '/\/[^\.\/][\.][^\.\/]$/';
2966	e0d3e148	Andreas Kohlbecker	if($preg_pattern === null){
2967			$preg_pattern = $ends_with_file_suffix_pattern;
2968			}
2969			if(preg_match($preg_pattern, $_GET['q'])){
2970	f26245c8	Andreas Kohlbecker	// oops this urls ends with a file_suffix and thus does not refer to a portal page
2971	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2972	595de9f0	Andreas Kohlbecker	exit('HTTP 404');
2973	f26245c8	Andreas Kohlbecker	}
2974	b654a866	Andreas Kohlbecker	check_js_devel_mode_disabled();
2975	f26245c8	Andreas Kohlbecker	}
2976	b2b9e057	Andreas Kohlbecker
2977			/**
2978			* Generates the diff of the texts and presents it in a HTML diff viewer.
2979			*
2980			* @param $text_a
2981			* @param $text_b
2982			* @return string
2983			*/
2984			function diff_viewer($text_a, $text_b) {
2985
2986			static $diff_viewer_count = 0;
2987
2988			$element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2989
2990			// http://code.stephenmorley.org/php/diff-implementation/
2991			module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2992			drupal_add_css(drupal_get_path('module',
2993			'cdm_dataportal') . '/css/diff.css');
2994	087bb473	Andreas Kohlbecker	_add_jquery_ui();
2995	b2b9e057	Andreas Kohlbecker	drupal_add_js(
2996			'jQuery(document).ready( function(){
2997			jQuery(\'#' . $element_id . '\').accordion({
2998			collapsible: true,
2999			active: false,
3000			fillSpace: true,
3001			}).children(\'div\').css({ \'height\': \'auto\' });
3002			jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
3003			});'
3004			, array(
3005			'type' => 'inline',
3006			'scope' => 'footer'
3007			));
3008
3009			$diff = Diff::compare($text_a,
3010			$text_b);
3011			$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
3012			. Diff::toTable($diff, '', '')
3013			. '</div></div>';
3014			return $diff_viewer_markup;
3015			}
3016

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 6679207a