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

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 977bba78

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	2e31ea9e	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/name');
27	b7a20282	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
28			module_load_include('inc', 'cdm_dataportal', 'includes/references');
29	38b27a36	Andreas Kohlbecker	module_load_include('inc', 'cdm_dataportal', 'includes/pages');
30			module_load_include('inc', 'cdm_dataportal', 'includes/media');
31			module_load_include('inc', 'cdm_dataportal', 'includes/maps');
32			module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
33			module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
34			module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
35
36			module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
37			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
38			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
39			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
40			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
41			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
42			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
43			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
44			module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
45
46			module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
47			module_load_include('php', 'cdm_dataportal', 'classes/footnote');
48			module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
49			module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
50
51
52			/* ============================ java script functions ============================= */
53
54
55			/**
56			* loads external java script files asynchronously.
57			*
58			* @param unknown_type $script_url
59			*/
60			function drupal_add_js_async($script_url, $callback){
61
62			drupal_add_js("
63			jQuery(document).ready(function() {
64			jQuery.ajax({
65			url: '" . $script_url . "',
66			dataType: 'script',
67			cache: true, // otherwise will get fresh copy every page load
68			success: function() {
69			" . $callback . "
70			}
71			});
72			});"
73			, 'inline');
74	6657531f	Andreas Kohlbecker	}
75
76	38b27a36	Andreas Kohlbecker	/**
77			*/
78			function drupal_add_js_rowToggle($tableId){
79	6657531f	Andreas Kohlbecker
80	38b27a36	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
81			drupal_add_js('jQuery(document).ready(function(){
82			addRowToggle("' . $tableId . '");
83	6657531f	Andreas Kohlbecker	});
84	38b27a36	Andreas Kohlbecker	', array('type' => 'inline'));
85			}
86	d2fd2a4c	Andreas Kohlbecker
87	38b27a36	Andreas Kohlbecker	/**
88			* @param unknown_type $link_element_selector
89			* @param unknown_type $progress_element_selector
90			*/
91			function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
92
93			$callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
94
95			drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
96
97			// drupal_add_js("
98			// if (Drupal.jsEnabled) {
99			// $(document).ready(function() {
100			// $('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
101			// });
102			// }", 'inline');
103			}
104
105			/**
106			* @todo Please document this function.
107			* @see http://drupal.org/node/1354
108			*/
109			function _add_js_treeselector() {
110			// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
111			drupal_add_js("
112			jQuery(document).ready(function() {
113			jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
114			jQuery('#cdm-taxonomictree-selector-form').submit();
115			});
116
117			});
118			",
119			array(
120			'type' => 'inline',
121			'scope' => 'footer'
122			)
123			);
124	5ea8b301	Andreas Kohlbecker	}
125
126	6b605d3b	Andreas Kohlbecker	function _add_js_resizable_element($selector, $y_axis_only) {
127
128			_add_jquery_ui();
129			$options = "";
130			if($y_axis_only) {
131			$options = "resize: function(event, ui) {
132			ui.size.width = ui.originalSize.width;
133			},
134			handles: \"s\"";
135
136			}
137			drupal_add_js("
138			jQuery(document).ready(function() {
139			jQuery('" . $selector . "').resizable({". $options ."});
140			});
141			",
142			array(
143			'type' => 'inline',
144			'scope' => 'footer'
145			)
146			);
147			}
148
149	38b27a36	Andreas Kohlbecker	function _add_js_openlayers() {
150
151			$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
152			$proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
153
154			if(variable_get('cdm_js_devel_mode', FALSE)){
155			// develooper mode libs
156			// $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
157			$openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
158			$proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
159			}
160
161			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
162			array(
163			'type' => 'file',
164	4c21ffdb	Andreas Kohlbecker	'group' => JS_LIBRARY,
165			'weight' => 0,
166	38b27a36	Andreas Kohlbecker	'cache' => TRUE,
167			'preprocess' => FALSE
168			)
169			);
170
171			// see https://github.com/proj4js/proj4js
172			// http://openlayers.org/dev/examples/using-proj4js.html
173			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
174			array(
175			'type' => 'file',
176	4c21ffdb	Andreas Kohlbecker	'group' => JS_LIBRARY,
177			'weight' => -1, // before open layers
178	38b27a36	Andreas Kohlbecker	'cache' => TRUE,
179			)
180			);
181
182			// configure the theme
183			$openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
184			$openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
185			drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
186			'type' => 'inline',
187	4c21ffdb	Andreas Kohlbecker	'group' => JS_LIBRARY,
188			'weight' => 1, // after openlayers
189	38b27a36	Andreas Kohlbecker	'cache' => TRUE,
190			'preprocess' => FALSE
191			));
192
193			drupal_add_css($openlayers_theme_path . 'style.tidy.css',
194			array(
195			'type' => 'file',
196			'cache' => TRUE,
197			'preprocess' => FALSE
198			)
199			);
200	e3026d72	Andreas Kohlbecker
201	38b27a36	Andreas Kohlbecker	}
202	e3026d72	Andreas Kohlbecker
203	38b27a36	Andreas Kohlbecker	/**
204			* @todo Please document this function.
205			* @see http://drupal.org/node/1354
206			*/
207			function _add_js_thickbox() {
208			// ---- jQuery thickbox:
209			/*
210			* bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
211			* not triggered because of problems with compat-1.0.js' see INSTALL.txt
212			*/
213			// drupal_add_js(drupal_get_path('module',
214			// 'cdm_dataportal').'/js/jquery.imagetool.min.js');
215			//
216			// Add a setting for the path to cdm_dataportal module, used to find the path
217			// for the loading animation image in thickbox.
218			drupal_add_js(array(
219			'cdm_dataportal' => array(
220			'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
221	10f6aa4b	Andreas Kohlbecker	)
222	38b27a36	Andreas Kohlbecker	),
223			'setting'
224			);
225			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
226			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
227			}
228	94550ff9	Andreas Kohlbecker
229	38b27a36	Andreas Kohlbecker	/**
230			* @todo Please document this function.
231			* @see http://drupal.org/node/1354
232			*/
233			function _add_js_lightbox($galleryID) {
234			/*
235			* Important Notice: The jquery.lightbox-0.5.js has been modified in order to
236	fe19a89b	Andreas Kohlbecker	* allow using the "alt" attribute for captions instead of the "title"
237			* attribute
238			*/
239	38b27a36	Andreas Kohlbecker	$lightbox_base_path = drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
240			$lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
241			drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
242			drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
243			drupal_add_js('jQuery(document).ready(function() {
244			jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
245			fixedNavigation: true,
246			imageLoading: \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
247			imageBtnPrev: \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
248			imageBtnNext: \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
249			imageBtnClose: \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
250			imageBlank: \'' . $lightbox_image_path . 'lightbox-blank.gif\',
251			adjustToWindow: true
252			});
253	94550ff9	Andreas Kohlbecker	});
254	38b27a36	Andreas Kohlbecker	', array('type' => 'inline'));
255			}
256	94550ff9	Andreas Kohlbecker
257	38b27a36	Andreas Kohlbecker	/**
258			* @todo Please document this function.
259			* @see http://drupal.org/node/1354
260			*/
261			function _add_js_footnotes() {
262			_add_js_domEvent();
263			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
264			}
265	94550ff9	Andreas Kohlbecker
266	38b27a36	Andreas Kohlbecker	/**
267			* @todo Please document this function.
268			* @see http://drupal.org/node/1354
269			*/
270			function _add_js_ahah() {
271	b386ae48	Andreas Kohlbecker
272	38b27a36	Andreas Kohlbecker	_add_js_domEvent(); // requires domEvent.js
273			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
274			}
275	94550ff9	Andreas Kohlbecker
276	d0d23caa	Andreas Kohlbecker	/**
277			* @todo Please document this function.
278			* @see http://drupal.org/node/1354
279			*/
280			function _add_js_taxonomic_children($jquery_selector) {
281	b0adfd32	Andreas Kohlbecker
282			global $base_url;
283
284
285			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
286	faf4f771	Andreas Kohlbecker
287	d0d23caa	Andreas Kohlbecker	drupal_add_js('jQuery(document).ready(function() {
288	b0adfd32	Andreas Kohlbecker	jQuery(\'' . $jquery_selector . '\').taxonomic_children({
289	09edee9a	Andreas Kohlbecker	// hoverClass: "fa-rotate-90",
290			// activeClass: "fa-rotate-90",
291	b0adfd32	Andreas Kohlbecker	classificationUuid: "' . get_current_classification_uuid() . '",
292	0af3ce28	Andreas Kohlbecker	taxonUuid: "' . get_current_taxon_uuid() . '",
293	38da4e54	Andreas Kohlbecker	cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
294	b0adfd32	Andreas Kohlbecker	proxyBaseUri: "' . $base_url . '",
295
296			});
297	d0d23caa	Andreas Kohlbecker	});
298			', array('type' => 'inline'));
299			}
300
301	38b27a36	Andreas Kohlbecker	/**
302			* Adds the external javascript file for domEvent.js.
303			*
304			* @see drupal_add_js()
305			*/
306			function _add_js_domEvent() {
307			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
308			}
309	b386ae48	Andreas Kohlbecker
310	087bb473	Andreas Kohlbecker	function _add_jquery_ui()
311			{
312			drupal_add_css(drupal_get_path('module',
313			'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
314			drupal_add_js(drupal_get_path('module',
315			'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
316			array(
317			'type' => 'file',
318			'weight' => JS_LIBRARY,
319			'cache' => TRUE,
320			'preprocess' => FALSE
321			)
322			);
323			}
324
325	b18d70f6	Andreas Kohlbecker	function _add_js_ui_accordion(){
326			_add_jquery_ui();
327			drupal_add_js('jQuery(document).ready(function() {
328			jQuery( "#accordion" ).accordion();
329			});',
330			array('type' => 'inline')
331			);
332			}
333
334	38b27a36	Andreas Kohlbecker	/**
335			* Provides the markup for an font awesome icon.
336			*
337			* The icons is created in default size without any extra features.
338			*
339			* The available icons are listed here http://fontawesome.io/cheatsheet/
340	ef12d0c6	Andreas Kohlbecker	* fontawesome icons have much more features than implemented here in this function,
341			* for spinning icons, fixed width icons, rotation, etc please checkout the
342	38b27a36	Andreas Kohlbecker	* examples at http://fontawesome.io/examples/
343			*
344			* @parameter $icon_name
345			* The name of the icon which starts with 'fa-'
346			*
347			* @return String
348			* the markup for the icon in an <i> tag
349			*
350			*/
351	b0aa9a8f	Andreas Kohlbecker	function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
352	6d9071b7	Andreas Kohlbecker	_add_font_awesome_font();
353	38b27a36	Andreas Kohlbecker
354
355	b0aa9a8f	Andreas Kohlbecker	if($icon_name){
356			if(!isset($attributes['class'])){
357			$attributes['class'] = array();
358			}
359			$attributes['class'][] = 'fa';
360			$attributes['class'][] = $icon_name;
361
362			return '<i ' . drupal_attributes($attributes) . '></i>';
363	38b27a36	Andreas Kohlbecker	}
364
365	b0aa9a8f	Andreas Kohlbecker	return '';
366	38b27a36	Andreas Kohlbecker	}
367	94550ff9	Andreas Kohlbecker
368	6d9071b7	Andreas Kohlbecker	/**
369			* Adds the css containing the font awesome icons to the html header.
370			*/
371			function _add_font_awesome_font()
372			{
373			//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
374
375			$font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
376			//$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
377
378			drupal_add_html_head_link(
379			array(
380			'href' => $font_awesome_css_uri,
381			'rel' => 'stylesheet'
382			)
383			);
384			}
385
386	38b27a36	Andreas Kohlbecker
387	6d9071b7	Andreas Kohlbecker	/* ====================== hook implementations ====================== */
388	38b27a36	Andreas Kohlbecker	/**
389			* Implements hook_permission().
390			*
391			* Valid permissions for this module.
392			*
393			* @return array
394	8385a9f2	Andreas Kohlbecker	* An array of valid permissions for the cdm_dataportal module.
395	38b27a36	Andreas Kohlbecker	*/
396			function cdm_dataportal_permission() {
397			return array(
398			'administer cdm_dataportal' => array(
399	8385a9f2	Andreas Kohlbecker	'title' => t('Administer CDM DataPortal settings'),
400			'description' => t("Access the settings pages specific for the cdm_dataportal module"),
401	c6fe437b	Andreas Kohlbecker	),
402			'access cdm content' => array(
403			'title' => t('Access CDM content'),
404			'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
405			),
406	38b27a36	Andreas Kohlbecker	);
407			}
408	6657531f	Andreas Kohlbecker
409			/**
410	f19f47fa	Andreas Kohlbecker	* Implements hook_menu().
411			*/
412	6657531f	Andreas Kohlbecker	function cdm_dataportal_menu() {
413			$items = array();
414
415			// @see settings.php.
416			cdm_dataportal_menu_admin($items);
417			cdm_dataportal_menu_help($items);
418
419			$items['cdm_dataportal/names'] = array(
420			'page callback' => 'cdm_dataportal_view_names',
421	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
422	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
423			);
424
425			// Optional callback arguments: page.
426			$items['cdm_dataportal/taxon'] = array(
427			'page callback' => 'cdm_dataportal_taxon_page_view',
428	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
429	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
430			// Expected callback arguments: uuid.
431			);
432
433	30845bda	Andreas Kohlbecker	$items['cdm_dataportal/specimen'] = array(
434			'page callback' => 'cdm_dataportal_specimen_page_view',
435			'access arguments' => array('access cdm content'),
436			'type' => MENU_CALLBACK,
437			// Expected callback arguments: uuid.
438			);
439
440			$items['cdm_dataportal/named_area'] = array(
441			'page callback' => 'cdm_dataportal_named_area_page_view',
442			'access arguments' => array('access cdm content'),
443			'type' => MENU_CALLBACK,
444			// Expected callback arguments: uuid.
445			);
446	9d37c9d9	Patric Plitzner
447	6657531f	Andreas Kohlbecker	$items['cdm_dataportal/name'] = array(
448			'page callback' => 'cdm_dataportal_name_page_view',
449			/*
450			'page arguments' => array(
451			'taxon_name_uuid',
452			'taxon_to_hide_uuid',
453			'synonym_uuid' => NULL
454			),
455			*/
456	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
457	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
458			// Expected callback arguments: uuid.
459			);
460
461			$items['cdm_dataportal/reference'] = array(
462			'page callback' => 'cdm_dataportal_view_reference',
463	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
464	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
465			// Expected callback arguments: uuid.
466			);
467
468			$items['cdm_dataportal/reference/list'] = array(
469			'page callback' => 'cdm_dataportal_view_reference_list',
470	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
471	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
472			// Expected callback arguments: uuid.
473			);
474
475			$items['cdm_dataportal/media'] = array(
476			'page callback' => 'cdm_dataportal_view_media',
477	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
478	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
479			// Expected callback arguments:
480			// uuid, mediarepresentation_uuid, part_uuid or part#.
481			);
482
483			$items['cdm_dataportal/polytomousKey'] = array(
484			'page callback' => 'cdm_dataportal_view_polytomousKey',
485	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
486	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
487			// Expected callback arguments: polytomousKey->uuid.
488			);
489
490			$items['cdm_dataportal/search'] = array(
491			'page callback' => 'cdm_dataportal_view_search_advanced',
492	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
493	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
494			);
495
496			$items['cdm_dataportal/search/advanced'] = array(
497	29077ee5	Andreas Kohlbecker	'title' => 'Advanced', // will be passed through t()
498	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_advanced',
499	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
500	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
501			);
502
503			$items['cdm_dataportal/search/taxon_by_description'] = array(
504	579c485d	Andreas Kohlbecker	'title' => 'By content category', // will be passed through t()
505	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
506	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
507	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
508			);
509			$items['cdm_dataportal/search/results/taxon'] = array(
510			'page callback' => 'cdm_dataportal_view_search_results_taxon',
511	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
512	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
513			);
514	efbff4b3	Andreas Kohlbecker	/*
515			* MENU_CALLBACK at cdm_dataportal/registration-search is needed to make the
516			* tabs in the subordinate paths work, accessing this 'page' will cause the
517			* MENU_DEFAULT_LOCAL_TASK being displayed
518			*/
519			$items['cdm_dataportal/registration-search'] = array(
520			'title' => 'Search', // will be passed through t()
521	a6ae799b	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_registrations_results',
522	efbff4b3	Andreas Kohlbecker	'page arguments' => array("filter"),
523	a6ae799b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
524			'type' => MENU_CALLBACK,
525			);
526	efbff4b3	Andreas Kohlbecker	/*
527			* the MENU_DEFAULT_LOCAL_TASK creates a tab for the MENU_CALLBACK
528			* defined at a higher level of the path (cdm_dataportal/registration-search)
529			*/
530			$items['cdm_dataportal/registration-search/filter'] = array(
531			'title' => 'Search', // will be passed through t()
532			'page callback' => 'cdm_dataportal_view_search_registrations_results',
533			'page arguments' => array("filter"),
534			'access arguments' => array('access cdm content'),
535			'type' => MENU_DEFAULT_LOCAL_TASK,
536			);
537			/*
538			* the MENU_LOCAL_TASK creates another tab
539			*/
540			$items['cdm_dataportal/registration-search/taxongraph'] = array(
541			'title' => 'Taxonomic search', // will be passed through t()
542			'page callback' => 'cdm_dataportal_view_search_registrations_results',
543			'page arguments' => array("taxongraph"),
544			'access arguments' => array('access cdm content'),
545			'type' => MENU_LOCAL_TASK,
546			);
547
548	e0d3e148	Andreas Kohlbecker	// Optional callback arguments: page.
549			$items['cdm_dataportal/registration'] = array(
550			'page callback' => 'cdm_dataportal_registration_page_view',
551			'access arguments' => array('access cdm content'),
552			'type' => MENU_CALLBACK,
553			// Expected callback arguments: uuid.
554			);
555	a6ae799b	Andreas Kohlbecker
556	6657531f	Andreas Kohlbecker	/*
557			$items['cdm/xml2json'] = array(
558			'page callback' => 'cdm_view_xml2json',
559	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
560	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
561			);
562			*/
563
564			// 'May not cache' in D5.
565			$items['cdm_dataportal/name/%'] = array(
566			// 'page callback' => 'cdm_dataportal_view_name',
567			'page callback' => 'cdm_dataportal_name_page_view',
568			'page arguments' => array(2, 3, 4),
569	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
570	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
571			);
572
573	6f1a217c	Andreas Kohlbecker	// --- Local tasks for Taxon.
574			// --- tabbed taxon page
575	6657531f	Andreas Kohlbecker	if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
576			$items['cdm_dataportal/taxon/%'] = array(
577	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
578	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
579	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
580	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
581			'weight' => 1,
582			'page arguments' => array(2, "description")
583	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
584	6657531f	Andreas Kohlbecker	);
585
586			$items['cdm_dataportal/taxon/%/all'] = array(
587	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
588	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
589	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
590	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
591			'weight' => 2,
592			'page arguments' => array(2, "all")
593	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
594	6657531f	Andreas Kohlbecker	);
595
596			$items['cdm_dataportal/taxon/%/description'] = array(
597	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
598	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
599	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
600	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
601			'weight' => 2,
602			'page arguments' => array(2, "description")
603	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
604	6657531f	Andreas Kohlbecker	);
605
606			$items['cdm_dataportal/taxon/%/synonymy'] = array(
607	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Synonymy'),
608	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
609	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
610	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
611			'weight' => 4,
612			'page arguments' => array(2, "synonymy", 4)
613	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid and ...
614	6657531f	Andreas Kohlbecker	);
615	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/images'] = array( // Images
616	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Images'),
617	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
618	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
619	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
620			'weight' => 5,
621			'page arguments' => array(2, "images")
622	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
623	6657531f	Andreas Kohlbecker	);
624
625	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
626	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Specimens'),
627	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
628	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
629	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
630			'weight' => 6,
631			'page arguments' => array(2, "specimens")
632	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
633	6657531f	Andreas Kohlbecker	);
634
635	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/keys'] = array( // Keys
636	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Keys'),
637	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
638	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
639	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
640			'weight' => 6,
641			'page arguments' => array(2, "keys")
642	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
643			);
644
645	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/experts'] = array( // Experts
646	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Experts'),
647	7663cd0b	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
648	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
649	7663cd0b	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
650			'weight' => 6,
651			'page arguments' => array(2, "experts")
652			, // Expected callback arguments: taxon_uuid.
653	6657531f	Andreas Kohlbecker	);
654	93ae67cc	Patrick Plitzner
655	51cc509a	Patrick Plitzner	$items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
656	04a1d647	Patrick Plitzner	'page callback' => 'cdm_dataportal_taxon_autosuggest',
657	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
658	51cc509a	Patrick Plitzner	'page arguments' => array(3,4,5),
659	93ae67cc	Patrick Plitzner	'type' => MENU_CALLBACK
660			);
661	6657531f	Andreas Kohlbecker	}
662
663	6f1a217c	Andreas Kohlbecker	// --- refresh link for all cdmnode types
664			foreach (cdm_get_nodetypes() as $type=>$name) {
665			$items['cdm_dataportal/' . $name . '/%/refresh'] = array(
666	7cc085da	Andreas Kohlbecker	'title' => 'Refresh',
667	6f1a217c	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_refresh_node',
668	3113db26	Andreas Kohlbecker	'access arguments' => array('administer cdm_dataportal'),
669	6f1a217c	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
670			'weight' => 100,
671			'page arguments' => array($name, 2)
672			);
673			}
674
675	6657531f	Andreas Kohlbecker	return $items;
676			}
677
678			/**
679	b85ab055	Andreas Kohlbecker	* Implements hook_init().
680			*
681	6657531f	Andreas Kohlbecker	*/
682			function cdm_dataportal_init() {
683	8fc089e1	Saskia Gennrich	if (!path_is_admin(current_path())) {
684			//FIXME To add CSS or JS that should be present on all pages, modules
685			// should not implement this hook, but declare these files in their .info file.
686			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
687			// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
688			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
689	63f6d312	Saskia Gennrich	} else {
690			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
691	8fc089e1	Saskia Gennrich	}
692	2dd59bb5	Andreas Kohlbecker
693			if(variable_get('cdm_debug_mode', FALSE)){
694			$file = 'temporary://drupal_debug.txt';
695			file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
696			}
697	5611d467	Andreas Kohlbecker
698			$bibliography_settings = get_bibliography_settings();
699	57d513cb	Andreas Kohlbecker	$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
700			FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
701	6657531f	Andreas Kohlbecker	}
702
703	6f1a217c	Andreas Kohlbecker	function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
704
705			$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
706
707			if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
708			// force reloading of all and notify user about this special loading
709			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: ')
710			. l('Back to tabbed taxon page', $base_path));
711			$base_path .= '/all';
712			} else {
713			drupal_set_message(t('The level 2 cache has been cleared for this page'));
714			}
715
716			$parameters['cacheL2_refresh'] ='1';
717
718
719			drupal_goto($base_path, array('query' => $parameters));
720			}
721
722	102f8c26	Andreas Kohlbecker	/**
723			* Implements hook_requirements($phase)
724			*/
725			function cdm_dataportal_requirements($phase) {
726			$requirements = array();
727			if($phase == 'runtime'){
728
729			}
730			return $requirements;
731			}
732
733	6657531f	Andreas Kohlbecker	/**
734			* Implements hook_block_info().
735			*/
736			function cdm_dataportal_block_info() {
737
738			// $block[0]["info"] = t("CDM DataPortal DevLinks");
739			// $block[1]["info"] = t("CDM DataPortal Credits");
740	fc13aa30	Andreas Kohlbecker	$block["2"] = array(
741	beb914ef	Andreas Kohlbecker	"info" => t("CDM - Search Taxa"),
742	fc13aa30	Andreas Kohlbecker	"cache" => DRUPAL_NO_CACHE
743			);
744	6657531f	Andreas Kohlbecker	// $block[3]["info"] = t("CDM Filters");
745	beb914ef	Andreas Kohlbecker	$block["4"]["info"] = t("CDM - Dataportal Print");
746			$block["keys"]["info"] = t("CDM - Identification keys");
747	46a02272	Andreas Kohlbecker	$block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
748	f9a3d0f6	Andreas Kohlbecker	$block["classification_breadcrumbs"] = array(
749	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Classification breadcrumbs'),
750	f9a3d0f6	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
751			);
752	bc400a17	Andreas Kohlbecker	$block["taxonomic_children"] = array(
753	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Taxonomic children'),
754	bc400a17	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
755			);
756	beb914ef	Andreas Kohlbecker	$block["back_to_search_results"] = array(
757			'title' => '<none>',
758			'info' => t('CDM - Back to search Results'),
759			'cache' => DRUPAL_CACHE_PER_PAGE,
760			'visibility' => BLOCK_VISIBILITY_LISTED,
761			'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
762			);
763	a6ae799b	Andreas Kohlbecker	$block['registrations_search_filter'] = array(
764	b18d70f6	Andreas Kohlbecker	'title' => 'Filter registrations',
765	a6ae799b	Andreas Kohlbecker	'info' => t('CDM - Registrations search filter'),
766			'cache' => DRUPAL_CACHE_PER_PAGE,
767	810710a0	Andreas Kohlbecker	'visibility' => BLOCK_VISIBILITY_NOTLISTED,
768	b18d70f6	Andreas Kohlbecker	'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
769	a6ae799b	Andreas Kohlbecker	);
770	efbff4b3	Andreas Kohlbecker	$block['registrations_search_taxongraph'] = array(
771			'title' => 'Taxonomic registration search',
772			'info' => t('CDM - Registrations search by taxon graph'),
773			'cache' => DRUPAL_CACHE_PER_PAGE,
774			'visibility' => BLOCK_VISIBILITY_NOTLISTED,
775	b18d70f6	Andreas Kohlbecker	'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
776			);
777			$block['registrations_search'] = array(
778			'title' => 'Search',
779			'info' => t('CDM - Registrations search combining filter and taxon graph search' ),
780			'cache' => DRUPAL_CACHE_PER_PAGE,
781			'visibility' => BLOCK_VISIBILITY_NOTLISTED,
782			'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
783	efbff4b3	Andreas Kohlbecker	);
784			return $block;
785	6657531f	Andreas Kohlbecker	}
786
787			/**
788			* Implements hook_block_view().
789			*/
790			function cdm_dataportal_block_view($delta) {
791			// TODO Rename block deltas (e.g. '2') to readable strings.
792			switch ($delta) {
793			// case 'delta-1':
794			// $block['subject'] = t('Credits');
795			// $block['content'] = theme('cdm_credits');
796			// return $block;
797			case '2':
798			$block['subject'] = t('Search taxa');
799	191f88fd	Andreas Kohlbecker	$form = drupal_get_form('cdm_dataportal_search_taxon_form');
800			$block['content'] = drupal_render($form);
801	6657531f	Andreas Kohlbecker
802			if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
803			$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
804			}
805			return $block;
806			case '4':
807	c8234bdf	Andreas Kohlbecker	$block['subject'] = '';
808	6657531f	Andreas Kohlbecker	$block['content'] = theme('cdm_print_button');
809			return $block;
810			case "keys":
811			$block['subject'] = t('Identification Keys');
812			$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
813			return $block;
814			case "fundedByEDIT":
815			// t('Funded by EDIT');
816			$text = '<none>';
817			$block['subject'] = $text;
818	889c74b7	Andreas Kohlbecker	$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
819			$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
820	6657531f	Andreas Kohlbecker	'attributes' => array("target" => "EDIT"),
821			'absolute' => TRUE,
822			'html' => TRUE,
823			));
824			return $block;
825	f9a3d0f6	Andreas Kohlbecker	case 'classification_breadcrumbs':
826	0af3ce28	Andreas Kohlbecker	$taxon_uuid = get_current_taxon_uuid();
827	38da4e54	Andreas Kohlbecker	$block['subject'] = '<none>';
828			$block['content'] = compose_classification_breadcrumbs($taxon_uuid);
829			return $block;
830	bc400a17	Andreas Kohlbecker	case 'taxonomic_children':
831			$taxon_uuid = get_current_taxon_uuid();
832			$block['subject'] = '<none>';
833			$block['content'] = compose_taxonomic_children($taxon_uuid);
834			return $block;
835	beb914ef	Andreas Kohlbecker	case 'back_to_search_results':
836			$block['subject'] = '<none>';
837			if (isset($_SESSION['cdm']['search'])) {
838			$block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
839			}
840			return $block;
841	a6ae799b	Andreas Kohlbecker	case 'registrations_search_filter':
842			$block['subject'] = '<none>';
843	efbff4b3	Andreas Kohlbecker	$block['content'] = drupal_get_form('cdm_dataportal_search_registration_filter_form'); // see cdm_dataportal_search_registration_filter_form($form, &$form_state)
844			return $block;
845			case 'registrations_search_taxongraph':
846			$block['subject'] = '<none>';
847			$block['content'] = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form'); // see cdm_dataportal_search_registration_taxongraph_form($form, &$form_state)
848	a6ae799b	Andreas Kohlbecker	return $block;
849	b18d70f6	Andreas Kohlbecker	case 'registrations_search':
850			_add_js_ui_accordion();
851			_add_font_awesome_font();
852			$block['subject'] = '<none>';
853			$filter_form = drupal_get_form('cdm_dataportal_search_registration_filter_form');
854			$filter_form['#prefix'] = '<div>';
855			$filter_form['#suffix'] = '</div>';
856			$taxongraph_form = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form');
857			$taxongraph_form['#prefix'] = '<div>';
858			$taxongraph_form['#suffix'] = '</div>';
859			$block['content'] = array(
860			'accordion' => array(
861			'#markup' => '',
862			'#prefix' => '<div id="accordion">',
863			'#suffix' => '</div>',
864			'content' => array(
865			array('#markup' => '<h3>Filter</h3>'),
866			$filter_form,
867			array('#markup' => '<h3>Taxon graph</h3>'),
868			$taxongraph_form,
869			)
870			)
871			);
872			return $block;
873	beb914ef	Andreas Kohlbecker	default:
874			return null;
875	6657531f	Andreas Kohlbecker	}
876			}
877
878	0af3ce28	Andreas Kohlbecker	/**
879			* Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
880			*
881			* @return string
882			* the taxon uuid or NULL
883			*/
884			function get_current_taxon_uuid()
885			{
886			static $taxon_uuid;
887
888			if(!isset($taxon_uuid)){
889			if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
890			$taxon_uuid = $_REQUEST['currentTaxon'];
891			} else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
892			$taxon_uuid = arg(2);
893			} else {
894			$taxon_uuid = null;
895			}
896			}
897
898			return $taxon_uuid;
899			}
900
901			/**
902			* Returns the currently classification tree in use.
903			*
904			* @return string
905			* The uuid of the currently focused classification
906			*/
907			function get_current_classification_uuid() {
908			if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
909			return $_SESSION['cdm']['taxonomictree_uuid'];
910			}
911			else {
912			return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
913			}
914			}
915
916	6657531f	Andreas Kohlbecker	/*
917			function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
918			$_SESSION['cdm'] = NULL;
919			if(is_string($cdm_ws_uri_update)){
920			$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
921			}
922			}
923
924			function cdm_dataportal_session_validate(){
925			if(!isset($_SESSION['cdm']['ws_uri'])){
926			$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
927			} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
928			cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
929			}
930			}
931			*/
932
933			/**
934	d7588d36	Andreas Kohlbecker	* creates a selector form for taxonomic trees.
935			*
936	0af3ce28	Andreas Kohlbecker	* @return array
937			* a drupal form array
938	6657531f	Andreas Kohlbecker	*/
939			function cdm_taxonomictree_selector() {
940			_add_js_treeselector();
941
942	a8a8f23c	Andreas Kohlbecker	$form = drupal_get_form('cdm_taxonomictree_selector_form');
943	d7588d36	Andreas Kohlbecker	return $form;
944	6657531f	Andreas Kohlbecker	}
945
946			/**
947			* @todo Please document this function.
948			* @see http://drupal.org/node/1354
949	0af3ce28	Andreas Kohlbecker	*
950			* @deprecated use compose_classification_selector instead
951	6657531f	Andreas Kohlbecker	*/
952			function cdm_taxonomictree_selector_form($form, &$form_state) {
953
954			$url = url('cdm_api/setvalue/session', array('query' => NULL));
955			$form['#action'] = $url;
956
957			$form['var'] = array(
958			'#weight' => -3,
959			'#type' => 'hidden',
960			'#value' => '[cdm][taxonomictree_uuid]',
961			);
962
963			$destination_array = drupal_get_destination();
964			$destination = $destination_array['destination'];
965
966			$form['destination'] = array(
967			'#weight' => -3,
968			'#type' => 'hidden',
969			'#value' => $destination,
970			);
971
972	26fb3778	Andreas Kohlbecker	$options = cdm_get_taxontrees_as_options();
973			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
974			if($taxontree_includes){
975			$filtered_options = array();
976			foreach($options as $uuid=>$label){
977			if(!empty($taxontree_includes[$uuid])){
978			$filtered_options[$uuid] = $label;
979			}
980			}
981			$options = $filtered_options;
982			}
983
984	6657531f	Andreas Kohlbecker	$form['val'] = array(
985			'#type' => 'select',
986			'#title' => t('Available classifications'),
987	7663cd0b	Andreas Kohlbecker	'#default_value' => get_current_classification_uuid(),
988	26fb3778	Andreas Kohlbecker	'#options' => $options,
989	0af3ce28	Andreas Kohlbecker	'#attributes' => array('class' => array('highlite-first-child')),
990	6657531f	Andreas Kohlbecker	);
991
992			return $form;
993
994			}
995
996	0af3ce28	Andreas Kohlbecker	/**
997			*
998			* @ingroup compose
999			*/
1000			function compose_classification_selector() {
1001
1002			$destination_array = drupal_get_destination();
1003			$destination = $destination_array['destination'];
1004
1005			$options = cdm_get_taxontrees_as_options();
1006			$items = array();
1007			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1008
1009			$current_classification_uuid = get_current_classification_uuid();
1010
1011
1012			foreach($options as $uuid=>$label){
1013			if(!$taxontree_includes \|\| !empty($taxontree_includes[$uuid])){
1014
1015			$class_attributes = '';
1016			if($current_classification_uuid == $uuid){
1017			$class_attributes = array('focused');
1018			}
1019			$items[] = array(
1020			'data' => l($label,
1021			'cdm_api/setvalue/session',
1022			array(
1023			'query' => array(
1024			'destination' => $destination,
1025			'val' => $uuid,
1026			'var' => '[cdm][taxonomictree_uuid]'
1027			),
1028			)
1029			),
1030			'class' => $class_attributes
1031			);
1032			}
1033			}
1034
1035			$render_array = array(
1036			'#theme' => 'item_list',
1037			'#type' => 'ul',
1038			'#items' => $items
1039			);
1040
1041			return $render_array;
1042			}
1043
1044
1045	6657531f	Andreas Kohlbecker	/* UNREACHABLE since action of form directly links to view.
1046			function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1047
1048			$_SESSION['cdm']['search'] = $form_values;
1049			//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1050			return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1051			//$paramstr = compose_url_prameterstr($form_values);
1052			//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1053			}
1054			*/
1055			/* ====================== menu callback functions ====================== */
1056			/**
1057			* @todo Please document this function.
1058			* @see http://drupal.org/node/1354
1059			*/
1060			/*
1061			function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1062			static $comment_node_disabled = 0;
1063			static $comment_node_read_only = 1;
1064			static $comment_node_read_write = 2;
1065
1066			if ($form_id == 'node_type_form'
1067			&& isset($form['identity']['type'])
1068			&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1069			) {
1070			$form['workflow']['comment'] = array(
1071			'#type' => 'radios',
1072			'#title' => t('Default comment setting'),
1073			'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1074			'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1075			'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1076			);
1077			}
1078			}
1079			*/
1080
1081			/**
1082			* Displays a list of the known taxonomic names.
1083			*
1084			* When the list of taxonomic names is displayed, long lists are split up into
1085			* multiple pages.
1086			*
1087			* TODO: Parameters are still preliminary.
1088			*
1089			* @param string $beginsWith
1090			* @param string $page
1091			* Page number to diplay defaults to page 1.
1092			* @param bool $onlyAccepted
1093			*/
1094			function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1095
1096			$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1097
1098			/*
1099			// FIXME the filter for accepted names will be a form element, thus this
1100			// widget should be generated via form api preferably as block.
1101			$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1102			$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1103			$out .= theme('cdm_listof_taxa', $taxonPager);
1104			return $out;
1105			*/
1106			}
1107
1108			/**
1109			* @todo Please document this function.
1110			* @see http://drupal.org/node/1354
1111	c0223d83	Andreas Kohlbecker	* @throws Exception
1112	6657531f	Andreas Kohlbecker	*/
1113			function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1114	f26245c8	Andreas Kohlbecker
1115			cdm_check_valid_portal_page();
1116
1117	6cbefddc	Andreas Kohlbecker	return compose_cdm_reference_page($uuid);
1118	6657531f	Andreas Kohlbecker	}
1119
1120			/**
1121	b2ebf0d3	Andreas Kohlbecker	* Creates a view on a all references contained in the portal.
1122	b5dca1e2	Andreas Kohlbecker	*
1123			* This function is used at the path cdm_dataportal/reference/list
1124	6657531f	Andreas Kohlbecker	*/
1125			function cdm_dataportal_view_reference_list($pageNumber) {
1126			$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1127	b2ebf0d3	Andreas Kohlbecker	cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1128	6657531f	Andreas Kohlbecker	}
1129
1130			/**
1131			* @todo Please document this function.
1132			* @see http://drupal.org/node/1354
1133			*/
1134			function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1135	f26245c8	Andreas Kohlbecker
1136			cdm_check_valid_portal_page();
1137
1138	6657531f	Andreas Kohlbecker	$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1139			return theme('cdm_media_page', array(
1140			'media' => $media,
1141			'mediarepresentation_uuid' => $mediarepresentation_uuid,
1142			'partId' => $part,
1143			));
1144			}
1145
1146			/**
1147			* @todo Please document this function.
1148			* @see http://drupal.org/node/1354
1149			*/
1150			function _load_taxonBase(&$taxonBase) {
1151			if (isset($taxonBase->uuid)) {
1152			$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1153			$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1154			$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1155			}
1156			}
1157
1158	9438ad3a	Andreas Kohlbecker	/**
1159			* Loads the media associated to the given taxon from the cdm server.
1160			* The aggregation settings regarding taxon relathionships and
1161			* taxonnomic childen are taken into account.
1162			*
1163			* The media lists are cached in a static variable.
1164			*
1165			* @param Taxon $taxon
1166			* A CDM Taxon entitiy
1167			*
1168			* @return array
1169			* An array of CDM Media entities
1170			*
1171			*/
1172			function _load_media_for_taxon($taxon) {
1173
1174			static $media = NULL;
1175
1176			if(!isset($media)) {
1177			$media = array();
1178			}
1179			if (!isset($media[$taxon->uuid])) {
1180
1181	f19f47fa	Andreas Kohlbecker	// --- GET Images --- //
1182			$mediaQueryParameters = array(
1183			"type" => "ImageFile",
1184			);
1185
1186			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1187			$mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1188	a950f2f9	Andreas Kohlbecker	$mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1189
1190			$taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1191			$mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1192			$mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1193			$mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1194	9438ad3a	Andreas Kohlbecker
1195	f19f47fa	Andreas Kohlbecker	$ws_endpoint = NULL;
1196	9438ad3a	Andreas Kohlbecker	if ( variable_get('cdm_images_include_children', 0) == 0) {
1197			$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1198			} else {
1199			$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1200			}
1201	f19f47fa	Andreas Kohlbecker
1202			$media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1203			array(
1204			$taxon->uuid,
1205			),
1206	9438ad3a	Andreas Kohlbecker	queryString($mediaQueryParameters)
1207			);
1208			}
1209
1210			return $media[$taxon->uuid];
1211			}
1212
1213			/**
1214			*
1215			* @param Taxon $taxon
1216			* A CDM Taxon entitiy
1217			*
1218			* @return array
1219			* An array of CDM SpecimenOrObservation entities
1220			*
1221			function _load_occurences_for_taxon($taxon){
1222
1223			static $occurences = NULL;
1224	f19f47fa	Andreas Kohlbecker
1225			if(!isset($occurences)) {
1226			$occurences = array();
1227			}
1228	9438ad3a	Andreas Kohlbecker
1229			if (!isset($occurences[$taxon->uuid])){
1230
1231			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1232			$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1233	f19f47fa	Andreas Kohlbecker	$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1234
1235			$by_associatedtaxon_query = http_build_query(array(
1236			'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1237			'relationships' => implode(',', $relationship_choice['direct']),
1238			'pageSize' => null // all hits in one page
1239			)
1240			);
1241
1242			$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1243			null,
1244			$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1245			);
1246
1247
1248			if(isset($pager->records[0])){
1249			$occurences[$taxon->uuid] = $pager->records;
1250			}
1251			}
1252	9438ad3a	Andreas Kohlbecker	return $occurences[$taxon->uuid];
1253			}
1254			*/
1255
1256	6657531f	Andreas Kohlbecker	/**
1257			* Gets a Drupal variable, string or array and returns it.
1258			*
1259			* Similar to the variable_get() function of Drupal, except that this function
1260			* is able to handle arrays correctly. This function is especially useful
1261	8c962983	Andreas Kohlbecker	* when dealing with collections of settings form elements (#tree = TRUE).
1262	6657531f	Andreas Kohlbecker	*
1263			* @param string $variableKey
1264			* The Unique key of the Drupal variable in the Drupal variables table.
1265			* @param string $defaultValueString
1266			* A string as for example derived from a CONSTANT.
1267			*
1268			* @return mixed
1269	8c962983	Andreas Kohlbecker	* usually an array, depending on the nature of the variable.
1270			*
1271			* TODO compare with get_array_variable_merged() duplicate functions?
1272	0f7c9d15	Andreas Kohlbecker	* @deprecated rather use get_array_variable_merged() since this function
1273			* used an array as second parameter
1274	6657531f	Andreas Kohlbecker	*/
1275			function mixed_variable_get($variableKey, $defaultValueString) {
1276			$systemDefaults = unserialize($defaultValueString);
1277			$storedSettings = variable_get($variableKey, array());
1278			if (is_array($storedSettings)) {
1279	8c962983	Andreas Kohlbecker	// TODO better use drupal_array_merge_deep() ?
1280	6657531f	Andreas Kohlbecker	$settings = array_merge($systemDefaults, $storedSettings);
1281			}
1282			else {
1283			$settings = $systemDefaults;
1284			}
1285			return $settings;
1286			}
1287
1288	b5519d3a	Andreas Kohlbecker	/**
1289	0f7c9d15	Andreas Kohlbecker	* Recursive function to convert an object into an array.
1290	b5519d3a	Andreas Kohlbecker	* also subordinate objects will be converted.
1291			*
1292			* @param object $object
1293	db725031	Andreas Kohlbecker	* the object to be converted
1294			* @return array
1295			* The array
1296	b5519d3a	Andreas Kohlbecker	*/
1297	db725031	Andreas Kohlbecker	function object_to_array($object) {
1298	b5519d3a	Andreas Kohlbecker	if(is_object($object) \|\| is_array($object)) {
1299			$array = (array)$object;
1300			foreach ($array as $key=>$value){
1301	db725031	Andreas Kohlbecker	$array[$key] = object_to_array($value);
1302	b5519d3a	Andreas Kohlbecker	}
1303			return $array;
1304			} else {
1305			return $object;
1306			}
1307			}
1308
1309	2fd6da0b	Andreas Kohlbecker	/**
1310			* Searches the $collection for the cdm entitiy given as $element.
1311			*
1312			* The elements are compared by their UUID.
1313			*
1314			* @param $element
1315			* the CDM entitiy to search for
1316			* @param $collection
1317			* the list of CDM entities to search in
1318			*
1319			* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1320			*
1321			*/
1322			function contains_cdm_entitiy($element, $collection) {
1323			$result = FALSE;
1324			foreach ($collection as $a) {
1325			if ($a->uuid == $element->uuid) {
1326			$result = TRUE;
1327			}
1328			}
1329			return $result;
1330			}
1331
1332			/**
1333			* Fiters the array $entity_list of CDM entities by the list
1334			* of $excludes. Any element contained in the $excludes will be removed
1335			* from included int the retuned list.
1336			*
1337			* If the $entity_list is not an array the $excludes will be returned.
1338			*/
1339			function filter_cdm_entity_list($entity_list, $excludes) {
1340			if (is_array($entity_list)) {
1341			$result = $entity_list;
1342			if ($excludes) {
1343			foreach ($excludes as $exclude) {
1344			if (!contains_cdm_entitiy($exclude, $entity_list)) {
1345			$result[] = $exclude;
1346			}
1347			}
1348			}
1349			}
1350			else {
1351			$result = $excludes;
1352			}
1353			return $result;
1354			}
1355
1356	0a1151a4	Andreas Kohlbecker	/**
1357	6f5c7f2a	Andreas Kohlbecker	* Wraps the given $html string into a render array suitable for drupal_render()
1358	0a1151a4	Andreas Kohlbecker	*
1359	65345976	Andreas Kohlbecker	* @param $html
1360	0a1151a4	Andreas Kohlbecker	* the html string, see
1361			* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1362	65345976	Andreas Kohlbecker	* @param $weight
1363	0a1151a4	Andreas Kohlbecker	* A positive or negative number (integer or decimal).
1364			* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1365	65345976	Andreas Kohlbecker	* @param $prefix
1366			* Optional markup for the '#prefix' element of the render array
1367			* @param $suffix
1368			* Optional markup for the '#suffix' element of the render array
1369	0a1151a4	Andreas Kohlbecker	*
1370	65345976	Andreas Kohlbecker	* @return array
1371	0a1151a4	Andreas Kohlbecker	* A render array
1372			*
1373			*/
1374	65345976	Andreas Kohlbecker	function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1375	6f5c7f2a	Andreas Kohlbecker	$render_array = array(
1376			'#markup' => $html
1377	1ce9afb7	Patric Plitzner	);
1378	6f5c7f2a	Andreas Kohlbecker	if (is_numeric($weight)) {
1379			$render_array['#weight'] = $weight;
1380	65345976	Andreas Kohlbecker	}
1381			if($prefix){
1382			$render_array['#prefix'] = $prefix;
1383			}
1384			if($suffix) {
1385			$render_array['#suffix'] = $suffix;
1386			}
1387	6f5c7f2a	Andreas Kohlbecker	return $render_array;
1388	0a1151a4	Andreas Kohlbecker	}
1389
1390	6657531f	Andreas Kohlbecker	/**
1391			* Loads the subgraph of a given PolytomousKeyNode.
1392			*
1393			* Loads the subgraph of the given PolytomousKeyNode recursively from
1394			* the CDM REST service.
1395			*
1396			* @param mixed $polytomousKeyNode
1397			* PolytomousKeyNode passed by reference.
1398			*
1399			* @return void
1400			*/
1401			function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1402
1403			if (!$polytomousKeyNode) {
1404			return;
1405			}
1406			if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1407	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1408	6657531f	Andreas Kohlbecker	return;
1409			}
1410			if (!is_uuid($polytomousKeyNode->uuid)) {
1411	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1412	6657531f	Andreas Kohlbecker	return;
1413			}
1414
1415			$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1416
1417			if (!$polytomousKeyNode) {
1418			// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1419			return;
1420			}
1421
1422			// Load children.
1423			foreach ($polytomousKeyNode->children as &$childNode) {
1424			_load_polytomousKeySubGraph($childNode);
1425			}
1426
1427			// Load subkey.
1428			$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1429
1430			// Load taxon.
1431			$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1432			_load_taxonBase($polytomousKeyNode->taxon);
1433			return;
1434			}
1435
1436			/**
1437			* @todo Please document this function.
1438			* @see http://drupal.org/node/1354
1439			*/
1440			function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1441	f26245c8	Andreas Kohlbecker
1442			cdm_check_valid_portal_page();
1443
1444	6657531f	Andreas Kohlbecker	$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1445
1446			$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1447			if (is_array($sourcePager->records)) {
1448			$polytomousKey->sources = $sourcePager->records;
1449			// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1450			}
1451
1452			$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1453			if (is_array($annotationPager->records)) {
1454			$polytomousKey->annotations = $annotationPager->records;
1455			}
1456
1457			_load_polytomousKeySubGraph($polytomousKey->root);
1458			return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1459			}
1460
1461			/**
1462			* Creates a taxon page view or a chapter of it.
1463			*
1464			* The taxon page gives detailed information on a taxon, it shows:
1465			* - Taxon name.
1466			* - Full list of synonyms homotypic synonyms on top, followed by the
1467			* heterotypic and finally followed by misapplied names.
1468			* The list is ordered historically.
1469			* - All description associated with the taxon.
1470			*
1471			* @param string $uuid
1472			* @param string $chapter
1473			* Name of the part to display, valid values are:
1474			* 'description', 'images', 'synonymy', 'specimens', 'all'.
1475			*
1476	793dae0a	Andreas Kohlbecker	* @return string
1477	6657531f	Andreas Kohlbecker	*/
1478	0c5a23b6	Andreas Kohlbecker	function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1479	5ea8b301	Andreas Kohlbecker
1480	f26245c8	Andreas Kohlbecker	cdm_check_valid_taxon_page($chapter);
1481	2dd59bb5	Andreas Kohlbecker	cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1482	5ea8b301	Andreas Kohlbecker	// show a warning in case the javascript development mode is anabled
1483			if(variable_get('cdm_js_devel_mode', FALSE)) {
1484			drupal_set_message(t('The !url1 is enabled.
1485			WARNING: this is a performance penalty and must be turned off on production websites.', array(
1486			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1487			)),
1488			'warning'
1489			);
1490			}
1491
1492	6657531f	Andreas Kohlbecker	// Display the page for the taxon defined by $uuid.
1493			// set_last_taxon_page_tab(arg(3));
1494	0c5a23b6	Andreas Kohlbecker	$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1495	6657531f	Andreas Kohlbecker	if (!empty($taxonpage)) {
1496	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1497	6657531f	Andreas Kohlbecker	return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1498			}
1499			else {
1500	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1501	6657531f	Andreas Kohlbecker	return '';
1502			}
1503			}
1504
1505			/**
1506	59f6da42	Andreas Kohlbecker	* This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1507			* which has two fields, one for the page title and one for the content. Later on in the
1508			* process chain the value contained in these fields will be passed to the cdm_node_show()
1509			* function as the function parameters $title and $content.
1510	6657531f	Andreas Kohlbecker	*
1511			* @param string $uuid
1512	59f6da42	Andreas Kohlbecker	* the uuid of the taxon to show
1513	6657531f	Andreas Kohlbecker	* @param string $chapter
1514			* Name of the part to display, valid values are:
1515			* 'description', 'images', 'synonymy', 'all'.
1516			*
1517	0c5a23b6	Andreas Kohlbecker	* @return object with the following fields:
1518	59f6da42	Andreas Kohlbecker	* - title : the title of the page
1519			* - content: the content of the page
1520			*
1521	8a1b451e	Andreas Kohlbecker	* @throws Exception
1522			*
1523	6657531f	Andreas Kohlbecker	*/
1524	8cf9238f	Andreas Kohlbecker	function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1525	6657531f	Andreas Kohlbecker	// Taxon object.
1526			$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1527			if (empty($taxon)) {
1528			drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1529	8a1b451e	Andreas Kohlbecker	return null;
1530	6657531f	Andreas Kohlbecker	}
1531			$taxonpage = new stdClass();
1532
1533			$taxonpage->title = theme('cdm_taxon_page_title', array(
1534	8cf9238f	Andreas Kohlbecker	'taxon' => $taxon
1535	6657531f	Andreas Kohlbecker	));
1536
1537			// Check if the taxon id contained in the currently selected tree.
1538	7663cd0b	Andreas Kohlbecker	$taxon_in_current_classification = taxon_in_current_classification($uuid);
1539	61b6ee11	Andreas Kohlbecker
1540	7663cd0b	Andreas Kohlbecker	if (!$taxon_in_current_classification) {
1541	61b6ee11	Andreas Kohlbecker	$classifications = get_classifications_for_taxon($taxon);
1542	e24d373b	Andreas Kohlbecker	RenderHints::pushToRenderStack('not_in_current_classification');
1543			$taxon_name_markup = render_taxon_or_name($taxon);
1544
1545	61b6ee11	Andreas Kohlbecker	if (count($classifications) == 0) {
1546	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.',
1547	fba00a4f	Andreas Kohlbecker	array(
1548	e24d373b	Andreas Kohlbecker	'!taxonname' => $taxon_name_markup,
1549	fba00a4f	Andreas Kohlbecker	)
1550			), 'warning');
1551	6657531f	Andreas Kohlbecker	}
1552			else {
1553			$trees = '';
1554	61b6ee11	Andreas Kohlbecker	foreach ($classifications as $classification) {
1555			if (isset($classification->titleCache)) {
1556			$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1557	6657531f	Andreas Kohlbecker	}
1558			}
1559
1560	15b7c460	Andreas Kohlbecker	drupal_set_message(format_plural(count($trees),
1561	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',
1562			'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1563			array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1564	fba00a4f	Andreas Kohlbecker	) ,
1565			'warning');
1566	6657531f	Andreas Kohlbecker	}
1567	e24d373b	Andreas Kohlbecker	RenderHints::popFromRenderStack();
1568	6657531f	Andreas Kohlbecker	}
1569
1570			// Render the taxon page.
1571	9a607f17	Andreas Kohlbecker	$render_array = compose_cdm_taxon_page($taxon, $chapter);
1572			$taxonpage->content = drupal_render($render_array);
1573	6657531f	Andreas Kohlbecker
1574			return $taxonpage;
1575			}
1576
1577	9d37c9d9	Patric Plitzner	/**
1578			* Creates a specimen page view.
1579			* @param string $uuid the UUID of the specimen
1580			* @return array\|string
1581			*/
1582			function cdm_dataportal_specimen_page_view($uuid) {
1583
1584			//cdm_check_valid_taxon_page($chapter);
1585			//cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1586			// show a warning in case the javascript development mode is anabled
1587			if(variable_get('cdm_js_devel_mode', FALSE)) {
1588			drupal_set_message(t('The !url1 is enabled.
1589			WARNING: this is a performance penalty and must be turned off on production websites.', array(
1590			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1591			)),
1592			'warning'
1593			);
1594			}
1595
1596			// Display the page for the specimen defined by $uuid.
1597			$specimenpage = cdm_dataportal_specimen_view($uuid);
1598			if (!empty($specimenpage)) {
1599			return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1600			}
1601			else {
1602			return '';
1603			}
1604			}
1605
1606			/**
1607			*
1608			* Creates a specimen view.
1609			* @param string $uuid the UUID of the specimen
1610			* @return array\|string
1611			*/
1612			function cdm_dataportal_specimen_view($uuid) {
1613	a2acff0a	Katja Luther	//TODO: get the derivateDTO and don't call the webservice a second time in compose_cdm_specimen_page
1614	907cc9b4	Patrick Plitzner	$specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1615	9d37c9d9	Patric Plitzner	if (empty($specimen)) {
1616			drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1617			return FALSE;
1618			}
1619			$specimenpage = new stdClass();
1620
1621			$specimenpage->title = theme('cdm_specimen_page_title', array(
1622			'specimen' => $specimen
1623			));
1624
1625	b810158e	Patric Plitzner	// Render the specimen page.
1626	a2acff0a	Katja Luther	$render_array = compose_cdm_specimen_page($specimen);
1627	9d37c9d9	Patric Plitzner	$specimenpage->content = drupal_render($render_array);
1628
1629			return $specimenpage;
1630			}
1631
1632	30845bda	Andreas Kohlbecker	/**
1633			*
1634			* Creates a named area view.
1635			* @param string $uuid the UUID of the specimen
1636			* * @return object
1637			* An object with two fields:
1638			* - title: the page title
1639			* - content: the page content
1640			*/
1641
1642			function cdm_dataportal_named_area_view($uuid) {
1643			$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1644			if (empty($named_area) \|\| $named_area->class !== 'NamedArea') {
1645			drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1646			return FALSE;
1647			}
1648			$named_area_page = new stdClass();
1649
1650			$named_area_page->title = $named_area->representation_L10n;
1651
1652			// Render the specimen page.
1653			$render_array = compose_cdm_named_area_page($uuid);
1654			$named_area_page->content = drupal_render($render_array);
1655
1656			return $named_area_page;
1657			}
1658
1659			function cdm_dataportal_named_area_page_view($uuid) {
1660
1661			cdm_check_valid_portal_page();
1662
1663			$named_area_page = cdm_dataportal_named_area_view($uuid);
1664			if (!empty($named_area_page)) {
1665			return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1666			}
1667			else {
1668			return '';
1669			}
1670
1671
1672			}
1673
1674	6657531f	Andreas Kohlbecker	/**
1675			* Returns a name page as a Drupal node ready to be renderized by Drupal.
1676			*
1677			* The node page shows the taxon name title and the list of taxon related
1678			* with such taxon. Name on the tree already in use.
1679			*
1680	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_name_uuid
1681	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1682	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_to_hide_uuid
1683	51b04faf	Andreas Kohlbecker	* A taxon which should not be displayed in the taxon list
1684	d4ea0dd9	Andreas Kohlbecker	* @param string $highlite_synonym_uuid
1685	51b04faf	Andreas Kohlbecker	* Optinal parameter wich takes another taxon uuid, if given the
1686			* target taxon pages will show the syonymy tab where the taxon
1687			* refenrenced by the $highlite_synonym_uuid will be highlighted
1688			* in case it is found on this page.
1689	6657531f	Andreas Kohlbecker	*
1690			* @return mixed
1691			* The formatted name page as node.
1692			*/
1693			function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1694
1695	f26245c8	Andreas Kohlbecker	cdm_check_valid_portal_page();
1696
1697	6657531f	Andreas Kohlbecker	$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1698			if (!empty($taxonname_page)) {
1699			return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1700			}
1701			else {
1702			return '';
1703			}
1704			}
1705
1706			/**
1707	102f8c26	Andreas Kohlbecker	* View function for a TaxonName page.
1708	6657531f	Andreas Kohlbecker	*
1709	e3001c8d	Andreas Kohlbecker	* The name page lists all taxa for which the name specified by the
1710			* $taxon_name_uuid is being used. I case there is only one name the
1711			* page automatically redirects ti the according taxon page. Otherwise
1712			* the list of names is displayed.
1713	6657531f	Andreas Kohlbecker	*
1714	e3001c8d	Andreas Kohlbecker	* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1715			* list of taxa. This is useful for example when referencing from a taxon
1716			* to the name page and the referring taxon should not be repeaded in the
1717			* name page.
1718	6657531f	Andreas Kohlbecker	*
1719	e3001c8d	Andreas Kohlbecker	*
1720	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_name_uuid
1721	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1722	d4ea0dd9	Andreas Kohlbecker	* @param string $taxon_to_hide_uuid
1723	e3001c8d	Andreas Kohlbecker	* A taxon which should not be displayed in the taxon list
1724	d4ea0dd9	Andreas Kohlbecker	* @param string $highlite_synonym_uuid
1725	e3001c8d	Andreas Kohlbecker	* Optinal parameter wich takes another taxon uuid, if given the
1726			* target taxon pages will show the syonymy tab where the taxon
1727			* refenrenced by the $highlite_synonym_uuid will be highlighted
1728			* in case it is found on this page.
1729			*
1730			* @return object
1731			* An object with two fields:
1732			* - title: the page title
1733			* - content: the page content
1734	6657531f	Andreas Kohlbecker	*/
1735	e3001c8d	Andreas Kohlbecker	function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1736	6657531f	Andreas Kohlbecker	// Getting the full taxonname object from the server.
1737	d0d068e9	Andreas Kohlbecker	$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1738	6657531f	Andreas Kohlbecker	if (!$taxon_name) {
1739			drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1740			return FALSE;
1741			}
1742			// Searching for all the taxa connected with the taxon name on the tree
1743			// in use.
1744			$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1745			$request_params = array();
1746			$request_params['query'] = $name_cache;
1747	7663cd0b	Andreas Kohlbecker	$request_params['tree'] = get_current_classification_uuid();
1748	6657531f	Andreas Kohlbecker	$request_params['doTaxa'] = 1;
1749			$request_params['doSynonyms'] = 1;
1750			$request_params['doTaxaByCommonNames'] = 0;
1751			$request_params['matchMode'] = "EXACT";
1752			$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1753
1754	d0d068e9	Andreas Kohlbecker	// Removing the name where we came from.
1755	6657531f	Andreas Kohlbecker	foreach ($taxon_pager->records as $k => &$taxon) {
1756			if ($taxon->uuid == $taxon_to_hide_uuid) {
1757			unset($taxon_pager->records[$k]);
1758			}
1759			}
1760			// Show the taxa list or go to the singular taxon.
1761			if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1762	e3001c8d	Andreas Kohlbecker	$singleTaxon = array_pop($taxon_pager->records);
1763	6657531f	Andreas Kohlbecker	if ($singleTaxon->class != "Taxon") {
1764			// It is a Synonym -> look for the accepted.
1765	7635cc7d	Andreas Kohlbecker	$accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
1766	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
1767	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1768	6657531f	Andreas Kohlbecker	}
1769			else {
1770	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1771	6657531f	Andreas Kohlbecker	}
1772			}
1773			else {
1774			// It is an accepted taxon.
1775	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
1776			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1777	6657531f	Andreas Kohlbecker	}
1778			else {
1779			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1780			}
1781			}
1782			}
1783			else {// More than one taxa case.
1784			$taxon_name_page = new stdClass();
1785	4f225a0f	Andreas Kohlbecker	$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1786	6657531f	Andreas Kohlbecker	if ($taxon_pager->records) {
1787	7272d19c	Andreas Kohlbecker	$taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1788	6657531f	Andreas Kohlbecker	}
1789			else {
1790	6b294c11	Andreas Kohlbecker	$taxon_name_page->content = 'This name is not assigned to a taxon.';
1791	6657531f	Andreas Kohlbecker	}
1792			return $taxon_name_page;
1793			}
1794			}
1795
1796	e0d3e148	Andreas Kohlbecker	/**
1797			* Returns a registration page as a Drupal node to be rendered by Drupal.
1798			*
1799			* @param string $registration_identifier_encoded
1800			* The persistent identifier of the registration urlencoded.
1801			* @return mixed
1802			* The formatted registration page as node.
1803			*/
1804			function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
1805
1806			cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
1807			$registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
1808			return cdm_node_show_simulate($registration_page);
1809			}
1810
1811			function cdm_dataportal_registration_view($registration_identifier_encoded) {
1812
1813			$registration_identifier = urldecode($registration_identifier_encoded);
1814
1815	6cbefddc	Andreas Kohlbecker	$render_array = array();
1816	1e7459da	Andreas Kohlbecker	$registration_dto = cdm_ws_get(CDM_WS_REGISTRATION_DTO_BY_IDENTIFIER . $registration_identifier_encoded);
1817	e0d3e148	Andreas Kohlbecker	if($registration_dto){
1818	f8283d8a	Andreas Kohlbecker	drupal_set_title(t('Registration Id:') . ' ' . $registration_identifier, PASS_THROUGH);
1819	e0d3e148	Andreas Kohlbecker
1820	26b8a1bc	Andreas Kohlbecker	$render_array = compose_registration_dto_full($registration_dto, true);
1821	e0d3e148	Andreas Kohlbecker
1822			} else {
1823	1e7459da	Andreas Kohlbecker	$status_text = cdm_ws_get(CDM_WS_REGISTRATION_STATUS_BY_IDENTIFIER, array($registration_identifier));
1824	6c9d417d	Andreas Kohlbecker	if(isset($status_text->String)) {
1825	1e7459da	Andreas Kohlbecker	$status_text = strtolower($status_text->String);
1826			if($status_text == 'preparation' \|\| $status_text == 'curation'){
1827			$status_text = 'in ' . $status_text;
1828			}
1829			drupal_set_title(t('Registration ' . $status_text), PASS_THROUGH);
1830			//$status_message;
1831	5fdcad30	Andreas Kohlbecker	drupal_set_message("A registration with the identifier " . $registration_identifier . " is " . $status_text, "status");
1832	1e7459da	Andreas Kohlbecker	} else {
1833			drupal_set_title(t('Registration not found'), PASS_THROUGH);
1834	e42db5b0	Andreas Kohlbecker	drupal_set_message("A registration with the identifier " . $registration_identifier . " does not exist", "warning");
1835	1e7459da	Andreas Kohlbecker	}
1836	e0d3e148	Andreas Kohlbecker	}
1837
1838	5446f047	Andreas Kohlbecker	$render_array = array(
1839	5fdcad30	Andreas Kohlbecker	'#prefix' => '<div id="registration">',
1840	5446f047	Andreas Kohlbecker	'registration' => $render_array,
1841			'#suffix' => '</div>',
1842			);
1843
1844	e0d3e148	Andreas Kohlbecker	return $render_array ;
1845			}
1846
1847
1848	6657531f	Andreas Kohlbecker	/**
1849	84b13813	Andreas Kohlbecker	* Creates a page with the advance search form.
1850			*
1851			* NOTE: The advance search form allows searching for taxa.
1852	6657531f	Andreas Kohlbecker	*/
1853			function cdm_dataportal_view_search_advanced() {
1854			drupal_set_title(t('Advanced search'), PASS_THROUGH);
1855			return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1856			}
1857
1858			/**
1859	84b13813	Andreas Kohlbecker	* Creates a page with the search form for searching by taxon descriptions.
1860	6657531f	Andreas Kohlbecker	*/
1861			function cdm_dataportal_view_search_taxon_by_description() {
1862	6441ddfb	Andreas Kohlbecker	drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1863	6657531f	Andreas Kohlbecker	return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1864			}
1865
1866			/**
1867			* Executes the search and generates the result list of taxa.
1868			*/
1869			function cdm_dataportal_view_search_results_taxon() {
1870
1871	24797d7f	Andreas Kohlbecker	$taxonPager = cdm_dataportal_search_taxon_execute();
1872	6657531f	Andreas Kohlbecker
1873	f19f47fa	Andreas Kohlbecker	$showThumbnails = do_showThumbnails();
1874
1875			$setSessionUri = url('cdm_api/setvalue/session', array(
1876			'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1877			));
1878
1879			drupal_add_js('jQuery(document).ready(function() {
1880
1881			// init
1882			if(' . $showThumbnails . ' == 1){
1883	1d69a96c	Andreas Kohlbecker	jQuery(\'.media_gallery\').show(20);
1884			} else {
1885			jQuery(\'.media_gallery\').hide(20);
1886			}
1887
1888			// add change handler
1889			jQuery(\'#showThumbnails input.showThumbnails\').change(
1890	f19f47fa	Andreas Kohlbecker	function(event){
1891	1d69a96c	Andreas Kohlbecker	var state = 0;
1892			if(jQuery(this).is(\':checked\')){
1893			jQuery(\'.media_gallery\').show(20);
1894			state = 1;
1895			} else {
1896			jQuery(\'.media_gallery\').hide(20);
1897			}
1898			// store state in session variable
1899			var uri = \'' . $setSessionUri . '\' + state;
1900			jQuery.get(uri);
1901			});
1902	78e178e2	Andreas Kohlbecker	});',
1903	f19f47fa	Andreas Kohlbecker	array('type' => "inline", 'scope' => JS_DEFAULT));
1904
1905	78e178e2	Andreas Kohlbecker	drupal_set_title(t('Search results'), PASS_THROUGH);
1906
1907	0a1dc066	Andreas Kohlbecker	return theme('cdm_search_taxa_results', array(
1908	6657531f	Andreas Kohlbecker	'pager' => $taxonPager,
1909			'path' => 'cdm_dataportal/search/results/taxon',
1910			));
1911			}
1912
1913	a6ae799b	Andreas Kohlbecker	/**
1914			* Executes the search for registrations and generates the result list..
1915			*/
1916	efbff4b3	Andreas Kohlbecker	function cdm_dataportal_view_search_registrations_results($mode = 'filter') {
1917
1918			switch($mode ){
1919			case 'taxongraph':
1920			$block = block_load('cdm_dataportal', 'registrations_search_taxongraph');
1921			$registration_pager = cdm_dataportal_search_registrations_taxongraph_execute();
1922			break;
1923			case 'filter':
1924			default:
1925			$block = block_load('cdm_dataportal', 'registrations_search_filter');
1926			$registration_pager = cdm_dataportal_search_registrations_filter_execute();
1927			}
1928			$block->title = null;
1929	a6ae799b	Andreas Kohlbecker
1930			drupal_set_title(t('Search registrations'), PASS_THROUGH);
1931
1932	efbff4b3	Andreas Kohlbecker	$render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
1933	24797d7f	Andreas Kohlbecker	$registrations_pager_array = compose_registrations_search_results($registration_pager);
1934	a6ae799b	Andreas Kohlbecker	$render_array = array_merge($render_array, $registrations_pager_array);
1935
1936			return $render_array;
1937			}
1938
1939
1940	94550ff9	Andreas Kohlbecker	/**
1941			* Provides the standart image wich indicated a loading process
1942			*
1943			* @return string
1944			* The img html tag
1945			*/
1946			function loading_image_html() {
1947			return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1948			. '/images/loading_circle_grey_16.gif" style="display:none;">';
1949			}
1950
1951	78e178e2	Andreas Kohlbecker	/**
1952			* Returns the state of the the showThumbnails flag set in the
1953			* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
1954			*
1955	c5ed6357	Andreas Kohlbecker	* @return boolean
1956	78e178e2	Andreas Kohlbecker	* returns 1 if the flag is set
1957			*/
1958			function do_showThumbnails() {
1959			static $showThumbnails = null;
1960
1961			if($showThumbnails == null) {
1962	c5ed6357	Andreas Kohlbecker	$showThumbnails = 0;
1963			if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
1964			$showThumbnails = 0;
1965			$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
1966			$showThumbnails = is_array($search_gallery_settings)
1967			&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
1968			&& (
1969			$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
1970			$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
1971			$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
1972			)
1973			? 1 : 0;
1974	f19f47fa	Andreas Kohlbecker
1975	c5ed6357	Andreas Kohlbecker	drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
1976			}
1977	f19f47fa	Andreas Kohlbecker	$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
1978			if (!is_numeric($showThumbnails)) {
1979			$showThumbnails = 1;
1980			}
1981	78e178e2	Andreas Kohlbecker	}
1982
1983			return $showThumbnails;
1984			}
1985
1986	6657531f	Andreas Kohlbecker
1987	a6ae799b	Andreas Kohlbecker
1988	6657531f	Andreas Kohlbecker	/* ====================== other functions ====================== */
1989			/**
1990			* Creates a URL to the taxon page specified by the $uuid parameter.
1991			*
1992			* The URL will be prepended with a path element to a specific taxon page tab.
1993			*
1994			* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
1995			* be set globally in the administrative settings or individually in the user
1996			* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
1997			* the last portal will stay on this last tab.
1998			*
1999			* A third option is offerered by the $page_tab parameter which allows overwriting this
2000			* internal mechanism by a specific value.
2001			*
2002			* @param string $uuid
2003			* The UUID of the taxon.
2004			* @param string $page_tab
2005			* Overwriting the preset mechanism by defining specific value for the
2006			* taxon page tab.
2007			*
2008			* @return string
2009			* The created URL.
2010			*/
2011			function path_to_taxon($uuid, $page_tab = FALSE) {
2012
2013			$tab = get_default_taxon_tab();
2014			$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2015
2016			if (!$uuid) {
2017			return FALSE;
2018			}
2019
2020			if ($page_tab) {
2021			return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2022			}
2023			elseif (!$tab \|\| strtolower($tab) == 'general') {
2024			return 'cdm_dataportal/taxon/' . $uuid;
2025			}
2026			elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2027			return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2028			}
2029			else {
2030			return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2031			}
2032			}
2033
2034	9d37c9d9	Patric Plitzner	function path_to_specimen($uuid) {
2035
2036			if (!$uuid) {
2037			return FALSE;
2038			}
2039			else {
2040			return 'cdm_dataportal/specimen/' . $uuid;
2041			}
2042			}
2043
2044	30845bda	Andreas Kohlbecker	function path_to_named_area($uuid) {
2045
2046			if (!$uuid) {
2047			return FALSE;
2048			}
2049			else {
2050			return 'cdm_dataportal/named_area/' . $uuid;
2051			}
2052			}
2053
2054	6657531f	Andreas Kohlbecker	/**
2055	630c7044	Andreas Kohlbecker	* Creates a URL to show a synonmy in the according taxon page.
2056			*
2057			* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2058			* The resulting URI will include query parameters to highlight the synonym, and to optionally display
2059			* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2060			* include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2061			* in the page
2062			*
2063			* @param string $synonymUuid
2064			* The uuid of the synonym
2065			* @param string $acceptedUuid
2066			* The uuid of the according accepted taxon
2067			* @return string
2068			* The URL to show a synonmy in the according taxon page
2069	6657531f	Andreas Kohlbecker	*/
2070			function uri_to_synonym($synonymUuid, $acceptedUuid) {
2071			$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2072	d071bed7	Andreas Kohlbecker	return url($acceptedPath, array(
2073			'query' => array(
2074			// highlite the synony in the synonymy
2075			'highlite' => $synonymUuid,
2076			// the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2077			// see theme_taxon_page_title()
2078			'acceptedFor' => $synonymUuid
2079	630c7044	Andreas Kohlbecker	),
2080			'fragment' => $synonymUuid
2081	d071bed7	Andreas Kohlbecker	));
2082
2083	6657531f	Andreas Kohlbecker	}
2084
2085			/**
2086	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the key identified by the uuid.
2087	b8bfa4bd	Andreas Kohlbecker	*
2088			* @param string $keyType
2089			* the key typer corresponds to the specific class of the CDM
2090			* IdentificationKey. Possible values are
2091			* -PolytomousKey
2092			* -MultimediaKey
2093			* - ...
2094	e0d3e148	Andreas Kohlbecker	* @param string $keyUuid
2095	b8bfa4bd	Andreas Kohlbecker	* The UUID of the key
2096	6657531f	Andreas Kohlbecker	*/
2097			function path_to_key($keyType, $keyUuid) {
2098			if (!$keyUuid \|\| !$keyType) {
2099			return FALSE;
2100			}
2101			$keyType{0} = strtolower($keyType{0});
2102			return "cdm_dataportal/" . $keyType . "/$keyUuid";
2103			}
2104
2105			/**
2106	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the reference identified by the uuid.
2107			*
2108			* @param $uuid string String representation of the registration entity uuid.
2109			*
2110			* @return string
2111			* The drupal path
2112			*
2113	6657531f	Andreas Kohlbecker	*/
2114			function path_to_reference($uuid) {
2115			if (!$uuid) {
2116			return FALSE;
2117			}
2118			return 'cdm_dataportal/reference/' . $uuid;
2119			}
2120
2121	e0d3e148	Andreas Kohlbecker	/**
2122			* Composes the drupal path to the reference identified by the uuid.
2123			*
2124			* @param string $identifier
2125			* The persistent identifier of the registration entity (Registration.identifier).
2126			* @return string
2127			* The drupal path
2128			*/
2129			function path_to_registration($identifier) {
2130
2131	977bba78	Andreas Kohlbecker	if(variable_get(CDM_REGISTRATION_PRESISTENT_IDENTIFIER_AS_LINK)){
2132			return $identifier;
2133			} else {
2134			return 'cdm_dataportal/registration/' . urlencode($identifier);
2135			}
2136	e0d3e148	Andreas Kohlbecker	}
2137
2138	6657531f	Andreas Kohlbecker	/**
2139	51b04faf	Andreas Kohlbecker	* Creates the path to a cdm_dataportal taxon name page.
2140			*
2141	e0d3e148	Andreas Kohlbecker	* @param string $taxon_name_uuid
2142			* The uuid as string of the CDM TaxonName to show a name page for
2143			* @param string $taxon_to_hide_uuid
2144			* The uuid as string of a taxon which should not be displayed in the taxon list
2145	d4ea0dd9	Andreas Kohlbecker	* @param string $highlited_synonym_uuid
2146	e0d3e148	Andreas Kohlbecker	* Optional parameter which takes another taxon uuid, if given the
2147			* target taxon pages will show the synonymy tab where the taxon
2148			* referenced by the $highlite_synonym_uuid will be highlighted
2149	51b04faf	Andreas Kohlbecker	* in case it is found on this page.
2150			*
2151	e0d3e148	Andreas Kohlbecker	* @return string
2152			* URI path element as string
2153	6657531f	Andreas Kohlbecker	*/
2154	d4ea0dd9	Andreas Kohlbecker	function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $highlited_synonym_uuid = NULL) {
2155	6657531f	Andreas Kohlbecker	$res = FALSE;
2156			if ($name_uuid) {
2157			$res = 'cdm_dataportal/name/' . $name_uuid;
2158			}
2159	51b04faf	Andreas Kohlbecker	if($taxon_to_hide_uuid){
2160			$res .= '/' . $taxon_to_hide_uuid;
2161	d4ea0dd9	Andreas Kohlbecker	if($highlited_synonym_uuid){
2162			$res .= '/' . $highlited_synonym_uuid;
2163	51b04faf	Andreas Kohlbecker	}
2164			}
2165	6657531f	Andreas Kohlbecker	return $res;
2166			}
2167
2168			/**
2169	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the media entity identified by the uuid.
2170			*
2171			* @param string $uuid
2172			* The persistent identifier of the entity entity
2173			* @return string
2174			* The drupal path
2175	6657531f	Andreas Kohlbecker	*/
2176			function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2177			if (!$uuid) {
2178			return FALSE;
2179			}
2180			$out = 'cdm_dataportal/media/' . $uuid;
2181			if ($representaion_uuid) {
2182			$out .= '/' . $representaion_uuid;
2183	a867b774	Andreas Kohlbecker	if (is_numeric($partId)) {
2184	6657531f	Andreas Kohlbecker	$out .= '/' . $partId;
2185			}
2186			}
2187			return $out;
2188			}
2189
2190			/**
2191			* Compares thisRank with thatRank.
2192			*
2193			* Returns a negative integer, zero, or a positive integer
2194			* as the of thisRank is higher than, equal to, or lower than thatRank.
2195			* e.g:
2196			* <ul>
2197			* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2198			* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2199			* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2200			* </ul>
2201			* <p>
2202			* This compare logic of the underlying webservice is the
2203			* <b>inverse logic</b> of the the one implemented in
2204			* java.lang.Comparable#compareTo(java.lang.Object)
2205			*
2206			* @param $thisRankUuid
2207			* @param $thatRankUuid
2208			*
2209			* @return int
2210			* A negative integer, zero, or a positive integer
2211			* as the thisRank is lower than, equal to, or higher than thatRank.
2212			*/
2213			function rank_compare($thisRankUuid, $thatRankUuid) {
2214			$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2215			return $result->Integer;
2216			}
2217
2218			/**
2219			* Composes an HTML element class attribute value composed of
2220	4b3be949	Andreas Kohlbecker	* the short-name of the cdm class and the uuid of the entity.
2221			* This class attribute should be used wherever an cdm-entity is rendered.
2222			*
2223			* In case of Taxon entities or TaxonNodeDTOs the secReference is also added
2224			* to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
2225			* Taxon uuid is added also as taxon_uuid:<uuid>
2226	6657531f	Andreas Kohlbecker	*
2227			* These according class selectors in css must be escaped, eg:
2228			* .cdm\:TextData
2229			*
2230	a6ae799b	Andreas Kohlbecker	* @param $cdm_entity
2231			* A CDM entity, TaxonNodeDTO or TypedEntityReference
2232	6657531f	Andreas Kohlbecker	*/
2233	a6ae799b	Andreas Kohlbecker	function html_class_attribute_ref($cdm_entity) {
2234	6657531f	Andreas Kohlbecker
2235	4b3be949	Andreas Kohlbecker	$attributes = '';
2236	a6ae799b	Andreas Kohlbecker	if (is_cdm_entity($cdm_entity)) {
2237			$attributes = "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
2238			} else if($cdm_entity->class == 'TypedEntityReference') {
2239			$attributes = "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
2240	4b3be949	Andreas Kohlbecker	}
2241	a6ae799b	Andreas Kohlbecker	if($cdm_entity->class == 'TaxonNodeDto'){
2242			$attributes .= " taxon_uuid:" . $cdm_entity->taxonUuid . " sec_uuid:" . $cdm_entity->secUuid;;
2243	4b3be949	Andreas Kohlbecker	}
2244	a6ae799b	Andreas Kohlbecker	if($cdm_entity->class == 'Taxon' && isset($cdm_entity->sec->uuid)){
2245			$attributes .= " sec_uuid:" . $cdm_entity->sec->uuid;
2246	6657531f	Andreas Kohlbecker	}
2247	4b3be949	Andreas Kohlbecker	return $attributes;
2248	6657531f	Andreas Kohlbecker	}
2249
2250
2251			/**
2252	a0e3ae5c	Andreas Kohlbecker	* Creates a short version of a taxonname.
2253	6657531f	Andreas Kohlbecker	*
2254	e90899ac	Andreas Kohlbecker	* The short name is created by using the taggedTitle field of
2255	a0e3ae5c	Andreas Kohlbecker	* TaxonNodeDTO instances.
2256	e90899ac	Andreas Kohlbecker	* If the taggedTitle if empty the fullname will be returned.
2257	6657531f	Andreas Kohlbecker	*
2258	a0e3ae5c	Andreas Kohlbecker	* @param object $taxonNodeDTO
2259			* A TaxonNodeDTO object
2260	6657531f	Andreas Kohlbecker	*
2261			* @return string
2262			*/
2263	a0e3ae5c	Andreas Kohlbecker	function cdm_dataportal_shortname_of($taxonNodeDTO) {
2264
2265	6657531f	Andreas Kohlbecker	$nameStr = '';
2266
2267	a0e3ae5c	Andreas Kohlbecker	normalize_tagged_text($taxonNodeDTO->taggedTitle);
2268	6657531f	Andreas Kohlbecker
2269			// Get all tagged text tokens of the scientific name.
2270	a0e3ae5c	Andreas Kohlbecker	foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2271	6657531f	Andreas Kohlbecker	if ($tagtxt->type == 'name' \|\| $tagtxt->type == 'rank') {
2272			$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2273			}
2274			}
2275			$nameStr = trim($nameStr);
2276
2277			if ($nameStr) {
2278
2279			// Do not return short names for these.
2280	a0e3ae5c	Andreas Kohlbecker	if ($taxonNodeDTO->unplaced \|\| $taxonNodeDTO->excluded) {
2281	6657531f	Andreas Kohlbecker	return $nameStr;
2282			}
2283
2284			/*
2285			1st capture group (^[a-zA-Z]): First letter of uninomial.
2286			Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2287			Third capture group (\s+[^(\x2E]+\s+.+$\|\s+[a-zA-Z]+$): letters of name,
2288			but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
2289			OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
2290			*/
2291			$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$\|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2292			if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2293			return $matches[1][0] . "." . $matches[3][0];
2294			}
2295			else {
2296			return $nameStr;
2297			}
2298			}
2299			else {
2300	a0e3ae5c	Andreas Kohlbecker	return $taxonNodeDTO->titleCache;
2301	6657531f	Andreas Kohlbecker	}
2302			}
2303
2304			/**
2305			* Check if a taxon is accepted by the current taxonomic tree.
2306			*
2307			* @param mixed $taxon
2308			* The Taxon obkect to check.
2309			*
2310			* @return bool
2311			* Returns TRUE if $taxon is accepted, FALSE otherwise.
2312			*/
2313			function _cdm_dataportal_acceptedByCurrentView($taxon) {
2314
2315	7663cd0b	Andreas Kohlbecker	$defaultTreeUuid = get_current_classification_uuid();
2316	6657531f	Andreas Kohlbecker
2317			if (isset($taxon->taxonNodes)) {
2318			$taxonNodes = $taxon->taxonNodes;
2319			}
2320			else {
2321			$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2322			}
2323
2324			if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2325			foreach ($taxonNodes as $node) {
2326	586fc780	Andreas Kohlbecker	if (isset($node->classification)){
2327			if(is_object($node->classification)) {
2328			if ($node->classification->uuid == $defaultTreeUuid) {
2329			return TRUE;
2330			}
2331	6657531f	Andreas Kohlbecker	}
2332	586fc780	Andreas Kohlbecker	else {
2333			if ($node->classification == $defaultTreeUuid) {
2334			return TRUE;
2335			}
2336	6657531f	Andreas Kohlbecker	}
2337			}
2338			}
2339			}
2340
2341			return FALSE;
2342			}
2343
2344			/**
2345	54cfa718	Andreas Kohlbecker	* Checks is the source has one of the given types.
2346			*
2347			* @param object $source
2348			* The original source entity
2349			* @param array $types
2350			* An array of elementd of the OriginalSourceType enumeration
2351			* If not set the default will be used which is:
2352			* - Lineage
2353			* - PrimaryMediaSource
2354			* - PrimaryTaxonomicSource
2355			* - Unknown
2356			* - Other
2357			* @return boolean
2358	6657531f	Andreas Kohlbecker	*/
2359	54cfa718	Andreas Kohlbecker	function _is_original_source_type($source, $types = null) {
2360			// this is the default
2361			// maybe this should also be put into the settings
2362			static $default = array(
2363			OriginalSourceType::Lineage,
2364			OriginalSourceType::PrimaryMediaSource,
2365			OriginalSourceType::PrimaryTaxonomicSource,
2366			OriginalSourceType::Unknown,
2367			OriginalSourceType::Other,
2368			);
2369
2370			if(!$types){
2371			$types = $default;
2372			}
2373			return isset($source->type) && in_array($source->type, $types);
2374			}
2375	6657531f	Andreas Kohlbecker
2376			/**
2377			* Collects all the media from a list of description elements.
2378			*
2379			* @param array $descriptionElements
2380			* The description elements from which to collect the media.
2381			*
2382			* @return array
2383			* The output with all the collected media.
2384			*/
2385			function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2386
2387			$outArrayOfMedia = array();
2388
2389			// Avoiding a warning box in Drupal for Flora Malesiana.
2390			if (isset($descriptionElements) && is_array($descriptionElements)) {
2391			foreach ($descriptionElements as $descriptionElement) {
2392			if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2393			foreach ($descriptionElement->media as $media) {
2394			if (is_object($media)) {
2395			$outArrayOfMedia[] = $media;
2396			}
2397			}
2398			}
2399			}
2400			}
2401			return $outArrayOfMedia;
2402			}
2403
2404			/**
2405	7370f4f7	Andreas Kohlbecker	* Fetches the list of visible annotations for each of the cdm entities and returns the footnote keys for them.
2406			*
2407			* The footnotes are passed to the FootnoteManager in order to store the annotations and to create the footnote keys.
2408			*
2409			* @see cdm_fetch_visible_annotations()
2410	6657531f	Andreas Kohlbecker	*
2411	65345976	Andreas Kohlbecker	* @param array $cdm_entities
2412	6657531f	Andreas Kohlbecker	* An array of CdmBase instances or a single instance.
2413	28c5c87a	Andreas Kohlbecker	* @param string $footnote_list_key_suggestion
2414	6657531f	Andreas Kohlbecker	*
2415	7370f4f7	Andreas Kohlbecker	* @return array of footnote keys
2416	6657531f	Andreas Kohlbecker	*/
2417	65345976	Andreas Kohlbecker	function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2418	90597e37	Andreas Kohlbecker
2419	6657531f	Andreas Kohlbecker	$footNoteKeys = array();
2420
2421			// Is argument cdmBase an array?
2422	65345976	Andreas Kohlbecker	if (!is_array($cdm_entities)) {
2423	6657531f	Andreas Kohlbecker	$cdmBase_array = array();
2424	65345976	Andreas Kohlbecker	$cdmBase_array[] = $cdm_entities;
2425	6657531f	Andreas Kohlbecker	}
2426			else {
2427	65345976	Andreas Kohlbecker	$cdmBase_array = $cdm_entities;
2428	6657531f	Andreas Kohlbecker	}
2429
2430			// Getting the key for the footnotemanager.
2431	28c5c87a	Andreas Kohlbecker	if (isset($footnote_list_key_suggestion)) {
2432			$footnote_list_key = $footnote_list_key_suggestion;
2433	6657531f	Andreas Kohlbecker	}
2434			else {
2435	28c5c87a	Andreas Kohlbecker	$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2436	6657531f	Andreas Kohlbecker	}
2437
2438			// Adding the footnotes keys.
2439			foreach ($cdmBase_array as $cdmBase_element) {
2440	7370f4f7	Andreas Kohlbecker	$annotations = cdm_fetch_visible_annotations($cdmBase_element);
2441	6657531f	Andreas Kohlbecker	if (is_array($annotations)) {
2442			foreach ($annotations as $annotation) {
2443	28c5c87a	Andreas Kohlbecker	$footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2444	6657531f	Andreas Kohlbecker	}
2445			}
2446			}
2447
2448			return $footNoteKeys;
2449			}
2450
2451	d9763fd3	Andreas Kohlbecker
2452	6657531f	Andreas Kohlbecker	/**
2453	d9763fd3	Andreas Kohlbecker	* Creates a CDM Dynabox.
2454			*
2455	c1f5d897	Andreas Kohlbecker	* @param string $dynabox_id
2456	d9763fd3	Andreas Kohlbecker	* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2457	6657531f	Andreas Kohlbecker	* @param string $label
2458			* The clickable text to show.
2459			* @param string $content_url
2460			* The cdm REST service request url wich will deliver the content to be shown
2461			* once the dynabox toggles open.
2462			* @param string $theme
2463	1ce9afb7	Patric Plitzner	* The theme to be used for rendering the cdm REST service response with is
2464	6657531f	Andreas Kohlbecker	* returned from the $content_url.
2465			* @param string $link_alt_text
2466			* The value for the alt attribute of the dynabox link.
2467			* @param array $enclosingtags
2468			* An array with two elements: $enclosingtags[0] will be used for the dynabox
2469			* element itself, $enclosingtags[1] is the tag to be used for the
2470	c1f5d897	Andreas Kohlbecker	* dynabox_content (optional)
2471	d9763fd3	Andreas Kohlbecker	* @param array $attributes
2472			* @param $content_element_selector
2473			* Optional jQuery selector which can be used to reference a dom element which should
2474			* be used as container for the content to be shown. The dynabox-<dynabox id>-content
2475			* element will be placed in this container.
2476			*
2477	c1f5d897	Andreas Kohlbecker	* @param string $open_callback
2478	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2479	c1f5d897	Andreas Kohlbecker	* the open state.
2480			* @param string $close_callback
2481	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2482	c1f5d897	Andreas Kohlbecker	* the closed state.
2483	d9763fd3	Andreas Kohlbecker	* @return string Returns HTML for a dynabox.
2484			* Returns HTML for a dynabox.
2485	6657531f	Andreas Kohlbecker	*/
2486	d9763fd3	Andreas Kohlbecker	function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2487			$enclosingtags = array('li', 'ul'), $attributes = array(),
2488			$content_element_selector = null,
2489			$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2490	6657531f	Andreas Kohlbecker	$out = '';
2491	c1f5d897	Andreas Kohlbecker
2492			// check for plain class attribute string
2493			$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2494
2495	9c9d11f7	Andreas Kohlbecker	if(!array_key_exists('class', $attributes)) {
2496			$attributes['class'] = array();
2497			}
2498	d9763fd3	Andreas Kohlbecker	$attributes['id'][] = 'dynabox-' . $dynabox_id;
2499	9c9d11f7	Andreas Kohlbecker	$dynabox_attributes = drupal_attributes($attributes);
2500
2501
2502	b386ae48	Andreas Kohlbecker	_add_js_domEvent(); // requires domEvent.js
2503	6657531f	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2504	c1f5d897	Andreas Kohlbecker	drupal_add_js("
2505	94bb8db6	Andreas Kohlbecker	jQuery(document).ready(
2506			function() {
2507			dynabox('". $dynabox_id ."',
2508			{
2509			open_callback: " . $open_callback .",
2510	d9763fd3	Andreas Kohlbecker	close_callback: " . $close_callback .
2511			($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2512	94bb8db6	Andreas Kohlbecker	}
2513			);
2514			}
2515			);",
2516			array(
2517			'type'=>'inline',
2518			'scope'=>'footer'
2519			)
2520			);
2521	6657531f	Andreas Kohlbecker
2522	9c9d11f7	Andreas Kohlbecker
2523	6657531f	Andreas Kohlbecker	$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2524	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox for ' . $content_url . ' -->';
2525	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>';
2526	d9763fd3	Andreas Kohlbecker	$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2527			$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2528			$out .= ' </' . $enclosingtags[1] . '>';
2529			$out .= ' </' . $enclosingtags[0] . '>';
2530	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox end -->';
2531	6657531f	Andreas Kohlbecker	return $out;
2532			}
2533
2534			/**
2535			* Checks whether a feature has any description elements.
2536			*
2537			* @param mixed $featureNode
2538			* A feature node as produced by the function _mergeFeatureTreeDescriptions().
2539			*
2540			* @see _mergeFeatureTreeDescriptions()
2541			*
2542			* @return bool
2543			* Returns TRUE if the given $featureNode or any of its subordinate nodes
2544			* contains at least one non empty TextData or at least one DescriptionElement
2545			* of an other type. A TextData element holding a multilanguageText or a
2546			* source reference is considered to be not empty.
2547	159cd9bb	Andreas Kohlbecker	*
2548			* @TODO this function may have become obsolete by the new method of detecting empty blocks,
2549	1b756c5f	Andreas Kohlbecker	* see $block_content_is_not_empty in make_feature_block_list() and
2550	0ebb6efc	Andreas Kohlbecker	* $feature_block_has_content in compose_feature_block_items_generic
2551	6657531f	Andreas Kohlbecker	*/
2552	f19f47fa	Andreas Kohlbecker	function has_feature_node_description_elements($featureNode) {
2553	6657531f	Andreas Kohlbecker
2554			if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2555	092744e1	Andreas Kohlbecker	if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2556			foreach ($featureNode->descriptionElements as $descriptionElement) {
2557	159cd9bb	Andreas Kohlbecker	if ($descriptionElement->class != "TextData" \|\| isset($descriptionElement->multilanguageText_L10n->text)
2558			&& $descriptionElement->multilanguageText_L10n->text != ''
2559			\|\| isset($descriptionElement->sources[0])
2560			\|\| isset($descriptionElement->media[0]) ) {
2561	092744e1	Andreas Kohlbecker	return TRUE;
2562			}
2563	6657531f	Andreas Kohlbecker	}
2564			}
2565			}
2566	092744e1	Andreas Kohlbecker	else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2567	fae36a2a	Andreas Kohlbecker	foreach ($featureNode->childNodes as $child) {
2568	f19f47fa	Andreas Kohlbecker	if (has_feature_node_description_elements($child)) {
2569	6657531f	Andreas Kohlbecker	return TRUE;
2570			}
2571			}
2572			}
2573			return FALSE;
2574			}
2575	f26245c8	Andreas Kohlbecker
2576			/**
2577			* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2578			*
2579			* @param $chapter
2580			* The taxon page chapter or part
2581			*/
2582			function cdm_check_valid_taxon_page($chapter){
2583			static $taxon_tabs = null;
2584
2585			cdm_check_valid_portal_page();
2586
2587			if($taxon_tabs == null){
2588			$taxon_tabs = array('all', 'description');
2589			foreach(get_taxon_tabs_list() as $tab){
2590			$taxon_tabs[] = strtolower($tab);
2591			}
2592			}
2593
2594			if(!in_array($chapter, $taxon_tabs)){
2595			// oops this is not a valid chapter name
2596	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2597	f26245c8	Andreas Kohlbecker	}
2598
2599			}
2600
2601			/**
2602	e0d3e148	Andreas Kohlbecker	* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
2603			* The test applied by default it a check for the query parameter 'q' ending with a file suffix like '.'
2604	f26245c8	Andreas Kohlbecker	*
2605	e0d3e148	Andreas Kohlbecker	* @param $preg_pattern
2606			* Optional regular expression pattern to be used in preg_match().
2607	f26245c8	Andreas Kohlbecker	*/
2608	e0d3e148	Andreas Kohlbecker	function cdm_check_valid_portal_page($preg_pattern = null){
2609	595de9f0	Andreas Kohlbecker	$ends_with_file_suffix_pattern = '/\/[^\.\/][\.][^\.\/]$/';
2610	e0d3e148	Andreas Kohlbecker	if($preg_pattern === null){
2611			$preg_pattern = $ends_with_file_suffix_pattern;
2612			}
2613			if(preg_match($preg_pattern, $_GET['q'])){
2614	f26245c8	Andreas Kohlbecker	// oops this urls ends with a file_suffix and thus does not refer to a portal page
2615	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2616	595de9f0	Andreas Kohlbecker	exit('HTTP 404');
2617	f26245c8	Andreas Kohlbecker	}
2618			}
2619	b2b9e057	Andreas Kohlbecker
2620			/**
2621			* Generates the diff of the texts and presents it in a HTML diff viewer.
2622			*
2623			* @param $text_a
2624			* @param $text_b
2625			* @return string
2626			*/
2627			function diff_viewer($text_a, $text_b) {
2628
2629			static $diff_viewer_count = 0;
2630
2631			$element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2632
2633			// http://code.stephenmorley.org/php/diff-implementation/
2634			module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2635			drupal_add_css(drupal_get_path('module',
2636			'cdm_dataportal') . '/css/diff.css');
2637	087bb473	Andreas Kohlbecker	_add_jquery_ui();
2638	b2b9e057	Andreas Kohlbecker	drupal_add_js(
2639			'jQuery(document).ready( function(){
2640			jQuery(\'#' . $element_id . '\').accordion({
2641			collapsible: true,
2642			active: false,
2643			fillSpace: true,
2644			}).children(\'div\').css({ \'height\': \'auto\' });
2645			jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2646			});'
2647			, array(
2648			'type' => 'inline',
2649			'scope' => 'footer'
2650			));
2651
2652			$diff = Diff::compare($text_a,
2653			$text_b);
2654			$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2655			. Diff::toTable($diff, '', '')
2656			. '</div></div>';
2657			return $diff_viewer_markup;
2658			}
2659

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 977bba78