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

| Branch: | Tag: | Revision:

cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ c0223d83

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	38b27a36	Andreas Kohlbecker	/**
326			* Provides the markup for an font awesome icon.
327			*
328			* The icons is created in default size without any extra features.
329			*
330			* The available icons are listed here http://fontawesome.io/cheatsheet/
331	ef12d0c6	Andreas Kohlbecker	* fontawesome icons have much more features than implemented here in this function,
332			* for spinning icons, fixed width icons, rotation, etc please checkout the
333	38b27a36	Andreas Kohlbecker	* examples at http://fontawesome.io/examples/
334			*
335			* @parameter $icon_name
336			* The name of the icon which starts with 'fa-'
337			*
338			* @return String
339			* the markup for the icon in an <i> tag
340			*
341			*/
342	b0aa9a8f	Andreas Kohlbecker	function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
343	38b27a36	Andreas Kohlbecker
344
345			//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
346
347	793dae0a	Andreas Kohlbecker	$font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal').'/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
348	74f9f871	Andreas Kohlbecker	//$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
349	38b27a36	Andreas Kohlbecker
350			drupal_add_html_head_link(
351			array(
352			'href' => $font_awesome_css_uri,
353			'rel' => 'stylesheet'
354			)
355			);
356
357	b0aa9a8f	Andreas Kohlbecker	if($icon_name){
358			if(!isset($attributes['class'])){
359			$attributes['class'] = array();
360			}
361			$attributes['class'][] = 'fa';
362			$attributes['class'][] = $icon_name;
363
364			return '<i ' . drupal_attributes($attributes) . '></i>';
365	38b27a36	Andreas Kohlbecker	}
366
367	b0aa9a8f	Andreas Kohlbecker	return '';
368	38b27a36	Andreas Kohlbecker	}
369	94550ff9	Andreas Kohlbecker
370	38b27a36	Andreas Kohlbecker
371			/* ====================== hook implementations ====================== */
372			/**
373			* Implements hook_permission().
374			*
375			* Valid permissions for this module.
376			*
377			* @return array
378	8385a9f2	Andreas Kohlbecker	* An array of valid permissions for the cdm_dataportal module.
379	38b27a36	Andreas Kohlbecker	*/
380			function cdm_dataportal_permission() {
381			return array(
382			'administer cdm_dataportal' => array(
383	8385a9f2	Andreas Kohlbecker	'title' => t('Administer CDM DataPortal settings'),
384			'description' => t("Access the settings pages specific for the cdm_dataportal module"),
385	c6fe437b	Andreas Kohlbecker	),
386			'access cdm content' => array(
387			'title' => t('Access CDM content'),
388			'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
389			),
390	38b27a36	Andreas Kohlbecker	);
391			}
392	6657531f	Andreas Kohlbecker
393			/**
394	f19f47fa	Andreas Kohlbecker	* Implements hook_menu().
395			*/
396	6657531f	Andreas Kohlbecker	function cdm_dataportal_menu() {
397			$items = array();
398
399			// @see settings.php.
400			cdm_dataportal_menu_admin($items);
401			cdm_dataportal_menu_help($items);
402
403			$items['cdm_dataportal/names'] = array(
404			'page callback' => 'cdm_dataportal_view_names',
405	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
406	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
407			);
408
409			// Optional callback arguments: page.
410			$items['cdm_dataportal/taxon'] = array(
411			'page callback' => 'cdm_dataportal_taxon_page_view',
412	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
413	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
414			// Expected callback arguments: uuid.
415			);
416
417	30845bda	Andreas Kohlbecker	$items['cdm_dataportal/specimen'] = array(
418			'page callback' => 'cdm_dataportal_specimen_page_view',
419			'access arguments' => array('access cdm content'),
420			'type' => MENU_CALLBACK,
421			// Expected callback arguments: uuid.
422			);
423
424			$items['cdm_dataportal/named_area'] = array(
425			'page callback' => 'cdm_dataportal_named_area_page_view',
426			'access arguments' => array('access cdm content'),
427			'type' => MENU_CALLBACK,
428			// Expected callback arguments: uuid.
429			);
430	9d37c9d9	Patric Plitzner
431	6657531f	Andreas Kohlbecker	$items['cdm_dataportal/name'] = array(
432			'page callback' => 'cdm_dataportal_name_page_view',
433			/*
434			'page arguments' => array(
435			'taxon_name_uuid',
436			'taxon_to_hide_uuid',
437			'synonym_uuid' => NULL
438			),
439			*/
440	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
441	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
442			// Expected callback arguments: uuid.
443			);
444
445			$items['cdm_dataportal/reference'] = array(
446			'page callback' => 'cdm_dataportal_view_reference',
447	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
448	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
449			// Expected callback arguments: uuid.
450			);
451
452			$items['cdm_dataportal/reference/list'] = array(
453			'page callback' => 'cdm_dataportal_view_reference_list',
454	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
455	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
456			// Expected callback arguments: uuid.
457			);
458
459			$items['cdm_dataportal/media'] = array(
460			'page callback' => 'cdm_dataportal_view_media',
461	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
462	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
463			// Expected callback arguments:
464			// uuid, mediarepresentation_uuid, part_uuid or part#.
465			);
466
467			$items['cdm_dataportal/polytomousKey'] = array(
468			'page callback' => 'cdm_dataportal_view_polytomousKey',
469	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
470	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
471			// Expected callback arguments: polytomousKey->uuid.
472			);
473
474			$items['cdm_dataportal/search'] = array(
475			'page callback' => 'cdm_dataportal_view_search_advanced',
476	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
477	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
478			);
479
480			$items['cdm_dataportal/search/advanced'] = array(
481	29077ee5	Andreas Kohlbecker	'title' => 'Advanced', // will be passed through t()
482	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_advanced',
483	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
484	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
485			);
486
487			$items['cdm_dataportal/search/taxon_by_description'] = array(
488	579c485d	Andreas Kohlbecker	'title' => 'By content category', // will be passed through t()
489	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
490	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
491	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
492			);
493
494			$items['cdm_dataportal/search/results/taxon'] = array(
495			'page callback' => 'cdm_dataportal_view_search_results_taxon',
496	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
497	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
498			);
499	a6ae799b	Andreas Kohlbecker	$items['cdm_dataportal/search/registration'] = array(
500			'page callback' => 'cdm_dataportal_view_search_registrations_results',
501			'access arguments' => array('access cdm content'),
502			'type' => MENU_CALLBACK,
503			);
504	e0d3e148	Andreas Kohlbecker	// Optional callback arguments: page.
505			$items['cdm_dataportal/registration'] = array(
506			'page callback' => 'cdm_dataportal_registration_page_view',
507			'access arguments' => array('access cdm content'),
508			'type' => MENU_CALLBACK,
509			// Expected callback arguments: uuid.
510			);
511	a6ae799b	Andreas Kohlbecker
512	6657531f	Andreas Kohlbecker	/*
513			$items['cdm/xml2json'] = array(
514			'page callback' => 'cdm_view_xml2json',
515	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
516	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
517			);
518			*/
519
520			// if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
521			// User configuration of cdm_dataportal.
522			$items['user/%/cdm_dataportal'] = array(
523			'title' => 'cdm_dataportal',
524	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
525	6657531f	Andreas Kohlbecker	'page callback' => 'drupal_get_form',
526			'page arguments' => array('cdm_dataportal_user_form'),
527			'type' => MENU_LOCAL_TASK,
528			'weight' => 10,
529			);
530			// }
531
532			// 'May not cache' in D5.
533			$items['cdm_dataportal/name/%'] = array(
534			// 'page callback' => 'cdm_dataportal_view_name',
535			'page callback' => 'cdm_dataportal_name_page_view',
536			'page arguments' => array(2, 3, 4),
537	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
538	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
539			);
540
541	6f1a217c	Andreas Kohlbecker	// --- Local tasks for Taxon.
542			// --- tabbed taxon page
543	6657531f	Andreas Kohlbecker	if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
544			$items['cdm_dataportal/taxon/%'] = array(
545	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
546	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
547	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
548	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
549			'weight' => 1,
550			'page arguments' => array(2, "description")
551	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
552	6657531f	Andreas Kohlbecker	);
553
554			$items['cdm_dataportal/taxon/%/all'] = array(
555	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
556	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
557	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
558	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
559			'weight' => 2,
560			'page arguments' => array(2, "all")
561	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
562	6657531f	Andreas Kohlbecker	);
563
564			$items['cdm_dataportal/taxon/%/description'] = array(
565	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
566	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
567	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
568	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
569			'weight' => 2,
570			'page arguments' => array(2, "description")
571	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
572	6657531f	Andreas Kohlbecker	);
573
574			$items['cdm_dataportal/taxon/%/synonymy'] = array(
575	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Synonymy'),
576	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
577	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
578	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
579			'weight' => 4,
580			'page arguments' => array(2, "synonymy", 4)
581	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid and ...
582	6657531f	Andreas Kohlbecker	);
583	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/images'] = array( // Images
584	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Images'),
585	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
586	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
587	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
588			'weight' => 5,
589			'page arguments' => array(2, "images")
590	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
591	6657531f	Andreas Kohlbecker	);
592
593	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
594	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Specimens'),
595	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
596	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
597	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
598			'weight' => 6,
599			'page arguments' => array(2, "specimens")
600	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
601	6657531f	Andreas Kohlbecker	);
602
603	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/keys'] = array( // Keys
604	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Keys'),
605	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
606	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
607	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
608			'weight' => 6,
609			'page arguments' => array(2, "keys")
610	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
611			);
612
613	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/experts'] = array( // Experts
614	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Experts'),
615	7663cd0b	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
616	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
617	7663cd0b	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
618			'weight' => 6,
619			'page arguments' => array(2, "experts")
620			, // Expected callback arguments: taxon_uuid.
621	6657531f	Andreas Kohlbecker	);
622	93ae67cc	Patrick Plitzner
623	51cc509a	Patrick Plitzner	$items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
624	04a1d647	Patrick Plitzner	'page callback' => 'cdm_dataportal_taxon_autosuggest',
625	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
626	51cc509a	Patrick Plitzner	'page arguments' => array(3,4,5),
627	93ae67cc	Patrick Plitzner	'type' => MENU_CALLBACK
628			);
629	6657531f	Andreas Kohlbecker	}
630
631	6f1a217c	Andreas Kohlbecker	// --- refresh link for all cdmnode types
632			foreach (cdm_get_nodetypes() as $type=>$name) {
633			$items['cdm_dataportal/' . $name . '/%/refresh'] = array(
634	7cc085da	Andreas Kohlbecker	'title' => 'Refresh',
635	6f1a217c	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_refresh_node',
636	3113db26	Andreas Kohlbecker	'access arguments' => array('administer cdm_dataportal'),
637	6f1a217c	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
638			'weight' => 100,
639			'page arguments' => array($name, 2)
640			);
641			}
642
643	6657531f	Andreas Kohlbecker	return $items;
644			}
645
646			/**
647	b85ab055	Andreas Kohlbecker	* Implements hook_init().
648			*
649	6657531f	Andreas Kohlbecker	*/
650			function cdm_dataportal_init() {
651	8fc089e1	Saskia Gennrich	if (!path_is_admin(current_path())) {
652			//FIXME To add CSS or JS that should be present on all pages, modules
653			// should not implement this hook, but declare these files in their .info file.
654			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
655			// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
656			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
657	63f6d312	Saskia Gennrich	} else {
658			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
659	8fc089e1	Saskia Gennrich	}
660	2dd59bb5	Andreas Kohlbecker
661			if(variable_get('cdm_debug_mode', FALSE)){
662			$file = 'temporary://drupal_debug.txt';
663			file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
664			}
665	5611d467	Andreas Kohlbecker
666			$bibliography_settings = get_bibliography_settings();
667	57d513cb	Andreas Kohlbecker	$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
668			FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
669	6657531f	Andreas Kohlbecker	}
670
671	6f1a217c	Andreas Kohlbecker	function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
672
673			$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
674
675			if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
676			// force reloading of all and notify user about this special loading
677			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: ')
678			. l('Back to tabbed taxon page', $base_path));
679			$base_path .= '/all';
680			} else {
681			drupal_set_message(t('The level 2 cache has been cleared for this page'));
682			}
683
684			$parameters['cacheL2_refresh'] ='1';
685
686
687			drupal_goto($base_path, array('query' => $parameters));
688			}
689
690	102f8c26	Andreas Kohlbecker	/**
691			* Implements hook_requirements($phase)
692			*/
693			function cdm_dataportal_requirements($phase) {
694			$requirements = array();
695			if($phase == 'runtime'){
696
697			}
698			return $requirements;
699			}
700
701
702	6657531f	Andreas Kohlbecker	/**
703			* The function generate form for own user cdm dataportal configurations.
704			*/
705			function cdm_dataportal_user_form($form, &$form_state) {
706	36818236	Andreas Kohlbecker
707	6657531f	Andreas Kohlbecker	global $user;
708			$checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
709
710	8e1dc7ec	Andreas Kohlbecker	$form['taxon_page_tabs'] = array(
711			'#type' => 'fieldset',
712	36818236	Andreas Kohlbecker	'#tree' => true,
713	8e1dc7ec	Andreas Kohlbecker	'#title' => t('Taxon page tabs'),
714			);
715	36818236	Andreas Kohlbecker
716			$form['taxon_page_tabs']['user_defined'] = array(
717	6657531f	Andreas Kohlbecker	'#type' => 'checkbox',
718			'#title' => t('Activate user default configuration'),
719			'#default_value' => variable_get($checkbox_value, 0),
720			'#description' => t('Check this if you want configure your own default tab from the below menu.'),
721			);
722
723	36818236	Andreas Kohlbecker	$form['taxon_page_tabs']['default_tab'] = array(
724	6657531f	Andreas Kohlbecker	'#type' => 'select',
725			'#title' => t('Default tab to display'),
726			'#default_value' => get_default_taxon_tab(TRUE),
727			'#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
728			'#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
729			<strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
730	36818236	Andreas Kohlbecker	to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
731			);
732
733
734	f695daf4	Andreas Kohlbecker	if(false){
735			$form['developer_options'] = array(
736			'#type' => 'fieldset',
737			'#tree' => true,
738			'#title' => t('Developer options'),
739			);
740
741			$form['developer_options']['show_render_path'] = array(
742			'#type' => 'checkbox',
743			'#title' => t('Display the render path for each taxon name.'),
744			'#default_value' => variable_get($checkbox_value, 0),
745			'#description' => t('This option is very helpful if you are editing the !link for taxon names.',
746			array(
747			'!link' => l(
748			'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
749			)
750			),
751			);
752			}
753	6657531f	Andreas Kohlbecker
754			$form['submit'] = array(
755			'#type' => 'submit',
756			'#value' => t('Submit'),
757			);
758
759			return $form;
760			}
761
762			/**
763			* Form submission handler for user_form().
764			*
765			* Submits the user cdm dataportal configurations.
766			*/
767			function cdm_dataportal_user_form_submit($form, &$form_state) {
768			global $user;
769			$msg_type = 'status';
770			$username = $user->name;
771			$variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
772
773	36818236	Andreas Kohlbecker	// FIXME: this is completely wrong, see user_profile_form_submit()
774
775			// it is only possible to change own user settings
776			if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
777
778			// DEFAULT_TAXON_TAB
779	6657531f	Andreas Kohlbecker	$variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
780	36818236	Andreas Kohlbecker	variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
781			variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
782			if ($form_state['values']['taxon_page_tabs']['user_defined']) {
783	6657531f	Andreas Kohlbecker	drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
784			drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
785			'!tab' => $variable[variable_get($variable_to_use, 0)],
786			'!user' => $username,
787			))), $msg_type);
788			}
789			else {
790			drupal_set_message(check_plain(t('The user default tab wont be used for
791			the next taxon site, check the box if you want to use the user default configuration.')));
792			}
793	36818236	Andreas Kohlbecker
794	6657531f	Andreas Kohlbecker	}
795			else {
796	36818236	Andreas Kohlbecker	// Problem with the user id => variables wont be saved.
797	6657531f	Andreas Kohlbecker	$msg_type = 'warning';
798			drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
799			}
800			}
801
802			/**
803			* Implements hook_block_info().
804			*/
805			function cdm_dataportal_block_info() {
806
807			// $block[0]["info"] = t("CDM DataPortal DevLinks");
808			// $block[1]["info"] = t("CDM DataPortal Credits");
809	fc13aa30	Andreas Kohlbecker	$block["2"] = array(
810	beb914ef	Andreas Kohlbecker	"info" => t("CDM - Search Taxa"),
811	fc13aa30	Andreas Kohlbecker	"cache" => DRUPAL_NO_CACHE
812			);
813	6657531f	Andreas Kohlbecker	// $block[3]["info"] = t("CDM Filters");
814	beb914ef	Andreas Kohlbecker	$block["4"]["info"] = t("CDM - Dataportal Print");
815			$block["keys"]["info"] = t("CDM - Identification keys");
816	46a02272	Andreas Kohlbecker	$block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
817	f9a3d0f6	Andreas Kohlbecker	$block["classification_breadcrumbs"] = array(
818	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Classification breadcrumbs'),
819	f9a3d0f6	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
820			);
821	bc400a17	Andreas Kohlbecker	$block["taxonomic_children"] = array(
822	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Taxonomic children'),
823	bc400a17	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
824			);
825	beb914ef	Andreas Kohlbecker	$block["back_to_search_results"] = array(
826			'title' => '<none>',
827			'info' => t('CDM - Back to search Results'),
828			'cache' => DRUPAL_CACHE_PER_PAGE,
829			'visibility' => BLOCK_VISIBILITY_LISTED,
830			'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
831			);
832	a6ae799b	Andreas Kohlbecker	$block['registrations_search_filter'] = array(
833	810710a0	Andreas Kohlbecker	'title' => 'Search registrations',
834	a6ae799b	Andreas Kohlbecker	'info' => t('CDM - Registrations search filter'),
835			'cache' => DRUPAL_CACHE_PER_PAGE,
836	810710a0	Andreas Kohlbecker	'visibility' => BLOCK_VISIBILITY_NOTLISTED,
837	a6ae799b	Andreas Kohlbecker	'pages' => "cdm_dataportal/search/registration\ncdm_dataportal/search/registration/*", // multiple page paths separated by "\n"!!!
838			);
839	6657531f	Andreas Kohlbecker
840			return $block;
841			}
842
843			/**
844			* Implements hook_block_view().
845			*/
846			function cdm_dataportal_block_view($delta) {
847			// TODO Rename block deltas (e.g. '2') to readable strings.
848			switch ($delta) {
849			// case 'delta-1':
850			// $block['subject'] = t('Credits');
851			// $block['content'] = theme('cdm_credits');
852			// return $block;
853			case '2':
854			$block['subject'] = t('Search taxa');
855	191f88fd	Andreas Kohlbecker	$form = drupal_get_form('cdm_dataportal_search_taxon_form');
856			$block['content'] = drupal_render($form);
857	6657531f	Andreas Kohlbecker
858			if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
859			$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
860			}
861			return $block;
862			case '4':
863	c8234bdf	Andreas Kohlbecker	$block['subject'] = '';
864	6657531f	Andreas Kohlbecker	$block['content'] = theme('cdm_print_button');
865			return $block;
866			case "keys":
867			$block['subject'] = t('Identification Keys');
868			$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
869			return $block;
870			case "fundedByEDIT":
871			// t('Funded by EDIT');
872			$text = '<none>';
873			$block['subject'] = $text;
874	889c74b7	Andreas Kohlbecker	$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
875			$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
876	6657531f	Andreas Kohlbecker	'attributes' => array("target" => "EDIT"),
877			'absolute' => TRUE,
878			'html' => TRUE,
879			));
880			return $block;
881	f9a3d0f6	Andreas Kohlbecker	case 'classification_breadcrumbs':
882	0af3ce28	Andreas Kohlbecker	$taxon_uuid = get_current_taxon_uuid();
883	38da4e54	Andreas Kohlbecker	$block['subject'] = '<none>';
884			$block['content'] = compose_classification_breadcrumbs($taxon_uuid);
885			return $block;
886	bc400a17	Andreas Kohlbecker	case 'taxonomic_children':
887			$taxon_uuid = get_current_taxon_uuid();
888			$block['subject'] = '<none>';
889			$block['content'] = compose_taxonomic_children($taxon_uuid);
890			return $block;
891	beb914ef	Andreas Kohlbecker	case 'back_to_search_results':
892			$block['subject'] = '<none>';
893			if (isset($_SESSION['cdm']['search'])) {
894			$block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
895			}
896			return $block;
897	a6ae799b	Andreas Kohlbecker	case 'registrations_search_filter':
898			$block['subject'] = '<none>';
899			$block['content'] = $form = drupal_get_form('cdm_dataportal_search_registration_form'); // see cdm_dataportal_search_registration_form($form, &$form_state)
900			return $block;
901	beb914ef	Andreas Kohlbecker	default:
902			return null;
903	6657531f	Andreas Kohlbecker	}
904			}
905
906	0af3ce28	Andreas Kohlbecker	/**
907			* Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
908			*
909			* @return string
910			* the taxon uuid or NULL
911			*/
912			function get_current_taxon_uuid()
913			{
914			static $taxon_uuid;
915
916			if(!isset($taxon_uuid)){
917			if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
918			$taxon_uuid = $_REQUEST['currentTaxon'];
919			} else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
920			$taxon_uuid = arg(2);
921			} else {
922			$taxon_uuid = null;
923			}
924			}
925
926			return $taxon_uuid;
927			}
928
929			/**
930			* Returns the currently classification tree in use.
931			*
932			* @return string
933			* The uuid of the currently focused classification
934			*/
935			function get_current_classification_uuid() {
936			if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
937			return $_SESSION['cdm']['taxonomictree_uuid'];
938			}
939			else {
940			return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
941			}
942			}
943
944	6657531f	Andreas Kohlbecker	/*
945			function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
946			$_SESSION['cdm'] = NULL;
947			if(is_string($cdm_ws_uri_update)){
948			$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
949			}
950			}
951
952			function cdm_dataportal_session_validate(){
953			if(!isset($_SESSION['cdm']['ws_uri'])){
954			$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
955			} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
956			cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
957			}
958			}
959			*/
960
961			/**
962	d7588d36	Andreas Kohlbecker	* creates a selector form for taxonomic trees.
963			*
964	0af3ce28	Andreas Kohlbecker	* @return array
965			* a drupal form array
966	6657531f	Andreas Kohlbecker	*/
967			function cdm_taxonomictree_selector() {
968			_add_js_treeselector();
969
970	a8a8f23c	Andreas Kohlbecker	$form = drupal_get_form('cdm_taxonomictree_selector_form');
971	d7588d36	Andreas Kohlbecker	return $form;
972	6657531f	Andreas Kohlbecker	}
973
974			/**
975			* @todo Please document this function.
976			* @see http://drupal.org/node/1354
977	0af3ce28	Andreas Kohlbecker	*
978			* @deprecated use compose_classification_selector instead
979	6657531f	Andreas Kohlbecker	*/
980			function cdm_taxonomictree_selector_form($form, &$form_state) {
981
982			$url = url('cdm_api/setvalue/session', array('query' => NULL));
983			$form['#action'] = $url;
984
985			$form['var'] = array(
986			'#weight' => -3,
987			'#type' => 'hidden',
988			'#value' => '[cdm][taxonomictree_uuid]',
989			);
990
991			$destination_array = drupal_get_destination();
992			$destination = $destination_array['destination'];
993
994			$form['destination'] = array(
995			'#weight' => -3,
996			'#type' => 'hidden',
997			'#value' => $destination,
998			);
999
1000	26fb3778	Andreas Kohlbecker	$options = cdm_get_taxontrees_as_options();
1001			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1002			if($taxontree_includes){
1003			$filtered_options = array();
1004			foreach($options as $uuid=>$label){
1005			if(!empty($taxontree_includes[$uuid])){
1006			$filtered_options[$uuid] = $label;
1007			}
1008			}
1009			$options = $filtered_options;
1010			}
1011
1012	6657531f	Andreas Kohlbecker	$form['val'] = array(
1013			'#type' => 'select',
1014			'#title' => t('Available classifications'),
1015	7663cd0b	Andreas Kohlbecker	'#default_value' => get_current_classification_uuid(),
1016	26fb3778	Andreas Kohlbecker	'#options' => $options,
1017	0af3ce28	Andreas Kohlbecker	'#attributes' => array('class' => array('highlite-first-child')),
1018	6657531f	Andreas Kohlbecker	);
1019
1020			return $form;
1021
1022			}
1023
1024	0af3ce28	Andreas Kohlbecker	/**
1025			*
1026			* @ingroup compose
1027			*/
1028			function compose_classification_selector() {
1029
1030			$destination_array = drupal_get_destination();
1031			$destination = $destination_array['destination'];
1032
1033			$options = cdm_get_taxontrees_as_options();
1034			$items = array();
1035			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1036
1037			$current_classification_uuid = get_current_classification_uuid();
1038
1039
1040			foreach($options as $uuid=>$label){
1041			if(!$taxontree_includes \|\| !empty($taxontree_includes[$uuid])){
1042
1043			$class_attributes = '';
1044			if($current_classification_uuid == $uuid){
1045			$class_attributes = array('focused');
1046			}
1047			$items[] = array(
1048			'data' => l($label,
1049			'cdm_api/setvalue/session',
1050			array(
1051			'query' => array(
1052			'destination' => $destination,
1053			'val' => $uuid,
1054			'var' => '[cdm][taxonomictree_uuid]'
1055			),
1056			)
1057			),
1058			'class' => $class_attributes
1059			);
1060			}
1061			}
1062
1063			$render_array = array(
1064			'#theme' => 'item_list',
1065			'#type' => 'ul',
1066			'#items' => $items
1067			);
1068
1069			return $render_array;
1070			}
1071
1072
1073	6657531f	Andreas Kohlbecker	/* UNREACHABLE since action of form directly links to view.
1074			function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1075
1076			$_SESSION['cdm']['search'] = $form_values;
1077			//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1078			return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1079			//$paramstr = compose_url_prameterstr($form_values);
1080			//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1081			}
1082			*/
1083			/* ====================== menu callback functions ====================== */
1084			/**
1085			* @todo Please document this function.
1086			* @see http://drupal.org/node/1354
1087			*/
1088			/*
1089			function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1090			static $comment_node_disabled = 0;
1091			static $comment_node_read_only = 1;
1092			static $comment_node_read_write = 2;
1093
1094			if ($form_id == 'node_type_form'
1095			&& isset($form['identity']['type'])
1096			&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1097			) {
1098			$form['workflow']['comment'] = array(
1099			'#type' => 'radios',
1100			'#title' => t('Default comment setting'),
1101			'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1102			'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1103			'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1104			);
1105			}
1106			}
1107			*/
1108
1109			/**
1110			* Displays a list of the known taxonomic names.
1111			*
1112			* When the list of taxonomic names is displayed, long lists are split up into
1113			* multiple pages.
1114			*
1115			* TODO: Parameters are still preliminary.
1116			*
1117			* @param string $beginsWith
1118			* @param string $page
1119			* Page number to diplay defaults to page 1.
1120			* @param bool $onlyAccepted
1121			*/
1122			function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1123
1124			$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1125
1126			/*
1127			// FIXME the filter for accepted names will be a form element, thus this
1128			// widget should be generated via form api preferably as block.
1129			$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1130			$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1131			$out .= theme('cdm_listof_taxa', $taxonPager);
1132			return $out;
1133			*/
1134			}
1135
1136			/**
1137			* @todo Please document this function.
1138			* @see http://drupal.org/node/1354
1139	c0223d83	Andreas Kohlbecker	* @throws Exception
1140	6657531f	Andreas Kohlbecker	*/
1141			function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1142	f26245c8	Andreas Kohlbecker
1143			cdm_check_valid_portal_page();
1144
1145	6cbefddc	Andreas Kohlbecker	return compose_cdm_reference_page($uuid);
1146	6657531f	Andreas Kohlbecker	}
1147
1148			/**
1149	b2ebf0d3	Andreas Kohlbecker	* Creates a view on a all references contained in the portal.
1150	b5dca1e2	Andreas Kohlbecker	*
1151			* This function is used at the path cdm_dataportal/reference/list
1152	6657531f	Andreas Kohlbecker	*/
1153			function cdm_dataportal_view_reference_list($pageNumber) {
1154			$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1155	b2ebf0d3	Andreas Kohlbecker	cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1156	6657531f	Andreas Kohlbecker	}
1157
1158			/**
1159			* @todo Please document this function.
1160			* @see http://drupal.org/node/1354
1161			*/
1162			function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1163	f26245c8	Andreas Kohlbecker
1164			cdm_check_valid_portal_page();
1165
1166	6657531f	Andreas Kohlbecker	$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1167			return theme('cdm_media_page', array(
1168			'media' => $media,
1169			'mediarepresentation_uuid' => $mediarepresentation_uuid,
1170			'partId' => $part,
1171			));
1172			}
1173
1174			/**
1175			* @todo Please document this function.
1176			* @see http://drupal.org/node/1354
1177			*/
1178			function _load_taxonBase(&$taxonBase) {
1179			if (isset($taxonBase->uuid)) {
1180			$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1181			$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1182			$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1183			}
1184			}
1185
1186	9438ad3a	Andreas Kohlbecker	/**
1187			* Loads the media associated to the given taxon from the cdm server.
1188			* The aggregation settings regarding taxon relathionships and
1189			* taxonnomic childen are taken into account.
1190			*
1191			* The media lists are cached in a static variable.
1192			*
1193			* @param Taxon $taxon
1194			* A CDM Taxon entitiy
1195			*
1196			* @return array
1197			* An array of CDM Media entities
1198			*
1199			*/
1200			function _load_media_for_taxon($taxon) {
1201
1202			static $media = NULL;
1203
1204			if(!isset($media)) {
1205			$media = array();
1206			}
1207			if (!isset($media[$taxon->uuid])) {
1208
1209	f19f47fa	Andreas Kohlbecker	// --- GET Images --- //
1210			$mediaQueryParameters = array(
1211			"type" => "ImageFile",
1212			);
1213
1214			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1215			$mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1216	a950f2f9	Andreas Kohlbecker	$mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1217
1218			$taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1219			$mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1220			$mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1221			$mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1222	9438ad3a	Andreas Kohlbecker
1223	f19f47fa	Andreas Kohlbecker	$ws_endpoint = NULL;
1224	9438ad3a	Andreas Kohlbecker	if ( variable_get('cdm_images_include_children', 0) == 0) {
1225			$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1226			} else {
1227			$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1228			}
1229	f19f47fa	Andreas Kohlbecker
1230			$media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1231			array(
1232			$taxon->uuid,
1233			),
1234	9438ad3a	Andreas Kohlbecker	queryString($mediaQueryParameters)
1235			);
1236			}
1237
1238			return $media[$taxon->uuid];
1239			}
1240
1241			/**
1242			*
1243			* @param Taxon $taxon
1244			* A CDM Taxon entitiy
1245			*
1246			* @return array
1247			* An array of CDM SpecimenOrObservation entities
1248			*
1249			function _load_occurences_for_taxon($taxon){
1250
1251			static $occurences = NULL;
1252	f19f47fa	Andreas Kohlbecker
1253			if(!isset($occurences)) {
1254			$occurences = array();
1255			}
1256	9438ad3a	Andreas Kohlbecker
1257			if (!isset($occurences[$taxon->uuid])){
1258
1259			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1260			$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1261	f19f47fa	Andreas Kohlbecker	$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1262
1263			$by_associatedtaxon_query = http_build_query(array(
1264			'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1265			'relationships' => implode(',', $relationship_choice['direct']),
1266			'pageSize' => null // all hits in one page
1267			)
1268			);
1269
1270			$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1271			null,
1272			$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1273			);
1274
1275
1276			if(isset($pager->records[0])){
1277			$occurences[$taxon->uuid] = $pager->records;
1278			}
1279			}
1280	9438ad3a	Andreas Kohlbecker	return $occurences[$taxon->uuid];
1281			}
1282			*/
1283
1284	6657531f	Andreas Kohlbecker	/**
1285			* Gets a Drupal variable, string or array and returns it.
1286			*
1287			* Similar to the variable_get() function of Drupal, except that this function
1288			* is able to handle arrays correctly. This function is especially useful
1289	8c962983	Andreas Kohlbecker	* when dealing with collections of settings form elements (#tree = TRUE).
1290	6657531f	Andreas Kohlbecker	*
1291			* @param string $variableKey
1292			* The Unique key of the Drupal variable in the Drupal variables table.
1293			* @param string $defaultValueString
1294			* A string as for example derived from a CONSTANT.
1295			*
1296			* @return mixed
1297	8c962983	Andreas Kohlbecker	* usually an array, depending on the nature of the variable.
1298			*
1299			* TODO compare with get_array_variable_merged() duplicate functions?
1300	0f7c9d15	Andreas Kohlbecker	* @deprecated rather use get_array_variable_merged() since this function
1301			* used an array as second parameter
1302	6657531f	Andreas Kohlbecker	*/
1303			function mixed_variable_get($variableKey, $defaultValueString) {
1304			$systemDefaults = unserialize($defaultValueString);
1305			$storedSettings = variable_get($variableKey, array());
1306			if (is_array($storedSettings)) {
1307	8c962983	Andreas Kohlbecker	// TODO better use drupal_array_merge_deep() ?
1308	6657531f	Andreas Kohlbecker	$settings = array_merge($systemDefaults, $storedSettings);
1309			}
1310			else {
1311			$settings = $systemDefaults;
1312			}
1313			return $settings;
1314			}
1315
1316	b5519d3a	Andreas Kohlbecker	/**
1317	0f7c9d15	Andreas Kohlbecker	* Recursive function to convert an object into an array.
1318	b5519d3a	Andreas Kohlbecker	* also subordinate objects will be converted.
1319			*
1320			* @param object $object
1321	db725031	Andreas Kohlbecker	* the object to be converted
1322			* @return array
1323			* The array
1324	b5519d3a	Andreas Kohlbecker	*/
1325	db725031	Andreas Kohlbecker	function object_to_array($object) {
1326	b5519d3a	Andreas Kohlbecker	if(is_object($object) \|\| is_array($object)) {
1327			$array = (array)$object;
1328			foreach ($array as $key=>$value){
1329	db725031	Andreas Kohlbecker	$array[$key] = object_to_array($value);
1330	b5519d3a	Andreas Kohlbecker	}
1331			return $array;
1332			} else {
1333			return $object;
1334			}
1335			}
1336
1337	2fd6da0b	Andreas Kohlbecker	/**
1338			* Searches the $collection for the cdm entitiy given as $element.
1339			*
1340			* The elements are compared by their UUID.
1341			*
1342			* @param $element
1343			* the CDM entitiy to search for
1344			* @param $collection
1345			* the list of CDM entities to search in
1346			*
1347			* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1348			*
1349			*/
1350			function contains_cdm_entitiy($element, $collection) {
1351			$result = FALSE;
1352			foreach ($collection as $a) {
1353			if ($a->uuid == $element->uuid) {
1354			$result = TRUE;
1355			}
1356			}
1357			return $result;
1358			}
1359
1360			/**
1361			* Fiters the array $entity_list of CDM entities by the list
1362			* of $excludes. Any element contained in the $excludes will be removed
1363			* from included int the retuned list.
1364			*
1365			* If the $entity_list is not an array the $excludes will be returned.
1366			*/
1367			function filter_cdm_entity_list($entity_list, $excludes) {
1368			if (is_array($entity_list)) {
1369			$result = $entity_list;
1370			if ($excludes) {
1371			foreach ($excludes as $exclude) {
1372			if (!contains_cdm_entitiy($exclude, $entity_list)) {
1373			$result[] = $exclude;
1374			}
1375			}
1376			}
1377			}
1378			else {
1379			$result = $excludes;
1380			}
1381			return $result;
1382			}
1383
1384	0a1151a4	Andreas Kohlbecker	/**
1385	6f5c7f2a	Andreas Kohlbecker	* Wraps the given $html string into a render array suitable for drupal_render()
1386	0a1151a4	Andreas Kohlbecker	*
1387	65345976	Andreas Kohlbecker	* @param $html
1388	0a1151a4	Andreas Kohlbecker	* the html string, see
1389			* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1390	65345976	Andreas Kohlbecker	* @param $weight
1391	0a1151a4	Andreas Kohlbecker	* A positive or negative number (integer or decimal).
1392			* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1393	65345976	Andreas Kohlbecker	* @param $prefix
1394			* Optional markup for the '#prefix' element of the render array
1395			* @param $suffix
1396			* Optional markup for the '#suffix' element of the render array
1397	0a1151a4	Andreas Kohlbecker	*
1398	65345976	Andreas Kohlbecker	* @return array
1399	0a1151a4	Andreas Kohlbecker	* A render array
1400			*
1401			*/
1402	65345976	Andreas Kohlbecker	function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1403	6f5c7f2a	Andreas Kohlbecker	$render_array = array(
1404			'#markup' => $html
1405	1ce9afb7	Patric Plitzner	);
1406	6f5c7f2a	Andreas Kohlbecker	if (is_numeric($weight)) {
1407			$render_array['#weight'] = $weight;
1408	65345976	Andreas Kohlbecker	}
1409			if($prefix){
1410			$render_array['#prefix'] = $prefix;
1411			}
1412			if($suffix) {
1413			$render_array['#suffix'] = $suffix;
1414			}
1415	6f5c7f2a	Andreas Kohlbecker	return $render_array;
1416	0a1151a4	Andreas Kohlbecker	}
1417
1418	6657531f	Andreas Kohlbecker	/**
1419			* Loads the subgraph of a given PolytomousKeyNode.
1420			*
1421			* Loads the subgraph of the given PolytomousKeyNode recursively from
1422			* the CDM REST service.
1423			*
1424			* @param mixed $polytomousKeyNode
1425			* PolytomousKeyNode passed by reference.
1426			*
1427			* @return void
1428			*/
1429			function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1430
1431			if (!$polytomousKeyNode) {
1432			return;
1433			}
1434			if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1435	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1436	6657531f	Andreas Kohlbecker	return;
1437			}
1438			if (!is_uuid($polytomousKeyNode->uuid)) {
1439	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1440	6657531f	Andreas Kohlbecker	return;
1441			}
1442
1443			$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1444
1445			if (!$polytomousKeyNode) {
1446			// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1447			return;
1448			}
1449
1450			// Load children.
1451			foreach ($polytomousKeyNode->children as &$childNode) {
1452			_load_polytomousKeySubGraph($childNode);
1453			}
1454
1455			// Load subkey.
1456			$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1457
1458			// Load taxon.
1459			$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1460			_load_taxonBase($polytomousKeyNode->taxon);
1461			return;
1462			}
1463
1464			/**
1465			* @todo Please document this function.
1466			* @see http://drupal.org/node/1354
1467			*/
1468			function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1469	f26245c8	Andreas Kohlbecker
1470			cdm_check_valid_portal_page();
1471
1472	6657531f	Andreas Kohlbecker	$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1473
1474			$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1475			if (is_array($sourcePager->records)) {
1476			$polytomousKey->sources = $sourcePager->records;
1477			// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1478			}
1479
1480			$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1481			if (is_array($annotationPager->records)) {
1482			$polytomousKey->annotations = $annotationPager->records;
1483			}
1484
1485			_load_polytomousKeySubGraph($polytomousKey->root);
1486			return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1487			}
1488
1489			/**
1490			* Creates a taxon page view or a chapter of it.
1491			*
1492			* The taxon page gives detailed information on a taxon, it shows:
1493			* - Taxon name.
1494			* - Full list of synonyms homotypic synonyms on top, followed by the
1495			* heterotypic and finally followed by misapplied names.
1496			* The list is ordered historically.
1497			* - All description associated with the taxon.
1498			*
1499			* @param string $uuid
1500			* @param string $chapter
1501			* Name of the part to display, valid values are:
1502			* 'description', 'images', 'synonymy', 'specimens', 'all'.
1503			*
1504	793dae0a	Andreas Kohlbecker	* @return string
1505	6657531f	Andreas Kohlbecker	*/
1506	0c5a23b6	Andreas Kohlbecker	function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1507	5ea8b301	Andreas Kohlbecker
1508	f26245c8	Andreas Kohlbecker	cdm_check_valid_taxon_page($chapter);
1509	2dd59bb5	Andreas Kohlbecker	cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1510	5ea8b301	Andreas Kohlbecker	// show a warning in case the javascript development mode is anabled
1511			if(variable_get('cdm_js_devel_mode', FALSE)) {
1512			drupal_set_message(t('The !url1 is enabled.
1513			WARNING: this is a performance penalty and must be turned off on production websites.', array(
1514			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1515			)),
1516			'warning'
1517			);
1518			}
1519
1520	6657531f	Andreas Kohlbecker	// Display the page for the taxon defined by $uuid.
1521			// set_last_taxon_page_tab(arg(3));
1522	0c5a23b6	Andreas Kohlbecker	$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1523	6657531f	Andreas Kohlbecker	if (!empty($taxonpage)) {
1524	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1525	6657531f	Andreas Kohlbecker	return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1526			}
1527			else {
1528	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1529	6657531f	Andreas Kohlbecker	return '';
1530			}
1531			}
1532
1533			/**
1534	59f6da42	Andreas Kohlbecker	* This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1535			* which has two fields, one for the page title and one for the content. Later on in the
1536			* process chain the value contained in these fields will be passed to the cdm_node_show()
1537			* function as the function parameters $title and $content.
1538	6657531f	Andreas Kohlbecker	*
1539			* @param string $uuid
1540	59f6da42	Andreas Kohlbecker	* the uuid of the taxon to show
1541	6657531f	Andreas Kohlbecker	* @param string $chapter
1542			* Name of the part to display, valid values are:
1543			* 'description', 'images', 'synonymy', 'all'.
1544			*
1545	0c5a23b6	Andreas Kohlbecker	* @return object with the following fields:
1546	59f6da42	Andreas Kohlbecker	* - title : the title of the page
1547			* - content: the content of the page
1548			*
1549	6657531f	Andreas Kohlbecker	*/
1550	8cf9238f	Andreas Kohlbecker	function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1551	6657531f	Andreas Kohlbecker	// Taxon object.
1552			$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1553			if (empty($taxon)) {
1554			drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1555			return FALSE;
1556			}
1557			$taxonpage = new stdClass();
1558
1559			$taxonpage->title = theme('cdm_taxon_page_title', array(
1560	8cf9238f	Andreas Kohlbecker	'taxon' => $taxon
1561	6657531f	Andreas Kohlbecker	));
1562
1563			// Check if the taxon id contained in the currently selected tree.
1564	7663cd0b	Andreas Kohlbecker	$taxon_in_current_classification = taxon_in_current_classification($uuid);
1565	61b6ee11	Andreas Kohlbecker
1566	7663cd0b	Andreas Kohlbecker	if (!$taxon_in_current_classification) {
1567	61b6ee11	Andreas Kohlbecker	$classifications = get_classifications_for_taxon($taxon);
1568	e24d373b	Andreas Kohlbecker	RenderHints::pushToRenderStack('not_in_current_classification');
1569			$taxon_name_markup = render_taxon_or_name($taxon);
1570
1571	61b6ee11	Andreas Kohlbecker	if (count($classifications) == 0) {
1572	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.',
1573	fba00a4f	Andreas Kohlbecker	array(
1574	e24d373b	Andreas Kohlbecker	'!taxonname' => $taxon_name_markup,
1575	fba00a4f	Andreas Kohlbecker	)
1576			), 'warning');
1577	6657531f	Andreas Kohlbecker	}
1578			else {
1579			$trees = '';
1580	61b6ee11	Andreas Kohlbecker	foreach ($classifications as $classification) {
1581			if (isset($classification->titleCache)) {
1582			$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1583	6657531f	Andreas Kohlbecker	}
1584			}
1585
1586	15b7c460	Andreas Kohlbecker	drupal_set_message(format_plural(count($trees),
1587	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',
1588			'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1589			array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1590	fba00a4f	Andreas Kohlbecker	) ,
1591			'warning');
1592	6657531f	Andreas Kohlbecker	}
1593	e24d373b	Andreas Kohlbecker	RenderHints::popFromRenderStack();
1594	6657531f	Andreas Kohlbecker	}
1595
1596			// Render the taxon page.
1597	9a607f17	Andreas Kohlbecker	$render_array = compose_cdm_taxon_page($taxon, $chapter);
1598			$taxonpage->content = drupal_render($render_array);
1599	6657531f	Andreas Kohlbecker
1600			return $taxonpage;
1601			}
1602
1603	9d37c9d9	Patric Plitzner	/**
1604			* Creates a specimen page view.
1605			* @param string $uuid the UUID of the specimen
1606			* @return array\|string
1607			*/
1608			function cdm_dataportal_specimen_page_view($uuid) {
1609
1610			//cdm_check_valid_taxon_page($chapter);
1611			//cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1612			// show a warning in case the javascript development mode is anabled
1613			if(variable_get('cdm_js_devel_mode', FALSE)) {
1614			drupal_set_message(t('The !url1 is enabled.
1615			WARNING: this is a performance penalty and must be turned off on production websites.', array(
1616			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1617			)),
1618			'warning'
1619			);
1620			}
1621
1622			// Display the page for the specimen defined by $uuid.
1623			$specimenpage = cdm_dataportal_specimen_view($uuid);
1624			if (!empty($specimenpage)) {
1625			return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1626			}
1627			else {
1628			return '';
1629			}
1630			}
1631
1632			/**
1633			*
1634			* Creates a specimen view.
1635			* @param string $uuid the UUID of the specimen
1636			* @return array\|string
1637			*/
1638			function cdm_dataportal_specimen_view($uuid) {
1639	907cc9b4	Patrick Plitzner	$specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1640	9d37c9d9	Patric Plitzner	if (empty($specimen)) {
1641			drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1642			return FALSE;
1643			}
1644			$specimenpage = new stdClass();
1645
1646			$specimenpage->title = theme('cdm_specimen_page_title', array(
1647			'specimen' => $specimen
1648			));
1649
1650	b810158e	Patric Plitzner	// Render the specimen page.
1651			$render_array = compose_cdm_specimen_page($uuid);
1652	9d37c9d9	Patric Plitzner	$specimenpage->content = drupal_render($render_array);
1653
1654			return $specimenpage;
1655			}
1656
1657	30845bda	Andreas Kohlbecker	/**
1658			*
1659			* Creates a named area view.
1660			* @param string $uuid the UUID of the specimen
1661			* * @return object
1662			* An object with two fields:
1663			* - title: the page title
1664			* - content: the page content
1665			*/
1666
1667			function cdm_dataportal_named_area_view($uuid) {
1668			$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1669			if (empty($named_area) \|\| $named_area->class !== 'NamedArea') {
1670			drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1671			return FALSE;
1672			}
1673			$named_area_page = new stdClass();
1674
1675			$named_area_page->title = $named_area->representation_L10n;
1676
1677			// Render the specimen page.
1678			$render_array = compose_cdm_named_area_page($uuid);
1679			$named_area_page->content = drupal_render($render_array);
1680
1681			return $named_area_page;
1682			}
1683
1684			function cdm_dataportal_named_area_page_view($uuid) {
1685
1686			cdm_check_valid_portal_page();
1687
1688			$named_area_page = cdm_dataportal_named_area_view($uuid);
1689			if (!empty($named_area_page)) {
1690			return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1691			}
1692			else {
1693			return '';
1694			}
1695
1696
1697			}
1698
1699	6657531f	Andreas Kohlbecker	/**
1700			* Returns a name page as a Drupal node ready to be renderized by Drupal.
1701			*
1702			* The node page shows the taxon name title and the list of taxon related
1703			* with such taxon. Name on the tree already in use.
1704			*
1705	51b04faf	Andreas Kohlbecker	* @param UUID $taxon_name_uuid
1706	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1707	51b04faf	Andreas Kohlbecker	* @param UUID $taxon_to_hide_uuid
1708			* A taxon which should not be displayed in the taxon list
1709			* @param UUID $highlite_synonym_uuid
1710			* Optinal parameter wich takes another taxon uuid, if given the
1711			* target taxon pages will show the syonymy tab where the taxon
1712			* refenrenced by the $highlite_synonym_uuid will be highlighted
1713			* in case it is found on this page.
1714	6657531f	Andreas Kohlbecker	*
1715			* @return mixed
1716			* The formatted name page as node.
1717			*/
1718			function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1719
1720	f26245c8	Andreas Kohlbecker	cdm_check_valid_portal_page();
1721
1722	6657531f	Andreas Kohlbecker	$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1723			if (!empty($taxonname_page)) {
1724			return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1725			}
1726			else {
1727			return '';
1728			}
1729			}
1730
1731			/**
1732	102f8c26	Andreas Kohlbecker	* View function for a TaxonName page.
1733	6657531f	Andreas Kohlbecker	*
1734	e3001c8d	Andreas Kohlbecker	* The name page lists all taxa for which the name specified by the
1735			* $taxon_name_uuid is being used. I case there is only one name the
1736			* page automatically redirects ti the according taxon page. Otherwise
1737			* the list of names is displayed.
1738	6657531f	Andreas Kohlbecker	*
1739	e3001c8d	Andreas Kohlbecker	* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1740			* list of taxa. This is useful for example when referencing from a taxon
1741			* to the name page and the referring taxon should not be repeaded in the
1742			* name page.
1743	6657531f	Andreas Kohlbecker	*
1744	e3001c8d	Andreas Kohlbecker	*
1745			* @param UUID $taxon_name_uuid
1746	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1747	e3001c8d	Andreas Kohlbecker	* @param UUID $taxon_to_hide_uuid
1748			* A taxon which should not be displayed in the taxon list
1749			* @param UUID $highlite_synonym_uuid
1750			* Optinal parameter wich takes another taxon uuid, if given the
1751			* target taxon pages will show the syonymy tab where the taxon
1752			* refenrenced by the $highlite_synonym_uuid will be highlighted
1753			* in case it is found on this page.
1754			*
1755			* @return object
1756			* An object with two fields:
1757			* - title: the page title
1758			* - content: the page content
1759	6657531f	Andreas Kohlbecker	*/
1760	e3001c8d	Andreas Kohlbecker	function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1761	6657531f	Andreas Kohlbecker	// Getting the full taxonname object from the server.
1762	d0d068e9	Andreas Kohlbecker	$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1763	6657531f	Andreas Kohlbecker	if (!$taxon_name) {
1764			drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1765			return FALSE;
1766			}
1767			// Searching for all the taxa connected with the taxon name on the tree
1768			// in use.
1769			$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1770			$request_params = array();
1771			$request_params['query'] = $name_cache;
1772	7663cd0b	Andreas Kohlbecker	$request_params['tree'] = get_current_classification_uuid();
1773	6657531f	Andreas Kohlbecker	$request_params['doTaxa'] = 1;
1774			$request_params['doSynonyms'] = 1;
1775			$request_params['doTaxaByCommonNames'] = 0;
1776			$request_params['matchMode'] = "EXACT";
1777			$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1778
1779	d0d068e9	Andreas Kohlbecker	// Removing the name where we came from.
1780	6657531f	Andreas Kohlbecker	foreach ($taxon_pager->records as $k => &$taxon) {
1781			if ($taxon->uuid == $taxon_to_hide_uuid) {
1782			unset($taxon_pager->records[$k]);
1783			}
1784			}
1785			// Show the taxa list or go to the singular taxon.
1786			if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1787	e3001c8d	Andreas Kohlbecker	$singleTaxon = array_pop($taxon_pager->records);
1788	6657531f	Andreas Kohlbecker	if ($singleTaxon->class != "Taxon") {
1789			// It is a Synonym -> look for the accepted.
1790	7635cc7d	Andreas Kohlbecker	$accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
1791	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
1792	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1793	6657531f	Andreas Kohlbecker	}
1794			else {
1795	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1796	6657531f	Andreas Kohlbecker	}
1797			}
1798			else {
1799			// It is an accepted taxon.
1800	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
1801			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1802	6657531f	Andreas Kohlbecker	}
1803			else {
1804			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1805			}
1806			}
1807			}
1808			else {// More than one taxa case.
1809			$taxon_name_page = new stdClass();
1810	4f225a0f	Andreas Kohlbecker	$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1811	6657531f	Andreas Kohlbecker	if ($taxon_pager->records) {
1812	7272d19c	Andreas Kohlbecker	$taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1813	6657531f	Andreas Kohlbecker	}
1814			else {
1815	6b294c11	Andreas Kohlbecker	$taxon_name_page->content = 'This name is not assigned to a taxon.';
1816	6657531f	Andreas Kohlbecker	}
1817			return $taxon_name_page;
1818			}
1819			}
1820
1821	e0d3e148	Andreas Kohlbecker	/**
1822			* Returns a registration page as a Drupal node to be rendered by Drupal.
1823			*
1824			* @param string $registration_identifier_encoded
1825			* The persistent identifier of the registration urlencoded.
1826			* @return mixed
1827			* The formatted registration page as node.
1828			*/
1829			function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
1830
1831			cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
1832			$registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
1833			return cdm_node_show_simulate($registration_page);
1834			}
1835
1836			function cdm_dataportal_registration_view($registration_identifier_encoded) {
1837
1838			$registration_identifier = urldecode($registration_identifier_encoded);
1839
1840
1841
1842	6cbefddc	Andreas Kohlbecker	$render_array = array();
1843	e0d3e148	Andreas Kohlbecker	$registration_dto = cdm_ws_get("registrationDTO/identifier/" . $registration_identifier_encoded);
1844			if($registration_dto){
1845			drupal_set_title(t('Registration') . ' ' . $registration_identifier, PASS_THROUGH);
1846
1847	5e4cae59	Andreas Kohlbecker	$render_array = compose_registation_dto($registration_dto);
1848	e0d3e148	Andreas Kohlbecker
1849	db725031	Andreas Kohlbecker	if(is_object($registration_dto->orderdTypeDesignationWorkingSets)){
1850			$field_unit_uuids = array();
1851			foreach((array)$registration_dto->orderdTypeDesignationWorkingSets as $field_unit_ref => $obj){
1852			$tokens = explode("#", $field_unit_ref);
1853			$field_unit_uuids[] = $tokens[1];
1854			}
1855	67f32f09	Andreas Kohlbecker	$render_array['specimen_table'] = compose_specimen_table($field_unit_uuids);
1856	db725031	Andreas Kohlbecker	}
1857	e0d3e148	Andreas Kohlbecker
1858			} else {
1859			drupal_set_title(t('Registration not found'), PASS_THROUGH);
1860			$render_array['error'] = markup_to_render_array("A registration with the identifier " . $registration_identifier . " does not exist.");
1861			}
1862
1863			return $render_array ;
1864			}
1865
1866	6cbefddc	Andreas Kohlbecker	/**
1867	5e4cae59	Andreas Kohlbecker	* Composes information for a registation from a dtp object
1868			*
1869	6cbefddc	Andreas Kohlbecker	* @param $registration_dto
1870	5e4cae59	Andreas Kohlbecker	*
1871	6cbefddc	Andreas Kohlbecker	* @return array
1872	5e4cae59	Andreas Kohlbecker	* A drupal render array
1873			*
1874			* @ingroup compose
1875	6cbefddc	Andreas Kohlbecker	*/
1876			function compose_registation_dto($registration_dto, $with_citation = true, $with_identifier = false)
1877			{
1878			$render_array = array();
1879	84e766b2	Andreas Kohlbecker
1880	6cbefddc	Andreas Kohlbecker	$registation_markup = cdm_tagged_text_to_markup($registration_dto->summaryTaggedText);
1881			if($with_identifier){
1882			$registation_markup .= " " . l ($registration_dto->identifier, $registration_dto->identifier);
1883			}
1884			$render_array['summary'] = markup_to_render_array("<div>" . $registation_markup . "</div>");
1885	84e766b2	Andreas Kohlbecker
1886			if ($with_citation) {
1887			$render_array['citation'] = markup_to_render_array("<div class=\"" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
1888			. l($registration_dto->bibliographicCitationString, path_to_reference($registration_dto->citationUuid))
1889			. "</br> </div>");
1890			}
1891
1892	6cbefddc	Andreas Kohlbecker	return $render_array;
1893			}
1894	e0d3e148	Andreas Kohlbecker
1895
1896	6657531f	Andreas Kohlbecker	/**
1897	84b13813	Andreas Kohlbecker	* Creates a page with the advance search form.
1898			*
1899			* NOTE: The advance search form allows searching for taxa.
1900	6657531f	Andreas Kohlbecker	*/
1901			function cdm_dataportal_view_search_advanced() {
1902			drupal_set_title(t('Advanced search'), PASS_THROUGH);
1903			return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1904			}
1905
1906			/**
1907	84b13813	Andreas Kohlbecker	* Creates a page with the search form for searching by taxon descriptions.
1908	6657531f	Andreas Kohlbecker	*/
1909			function cdm_dataportal_view_search_taxon_by_description() {
1910	6441ddfb	Andreas Kohlbecker	drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1911	6657531f	Andreas Kohlbecker	return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1912			}
1913
1914			/**
1915			* Executes the search and generates the result list of taxa.
1916			*/
1917			function cdm_dataportal_view_search_results_taxon() {
1918
1919	24797d7f	Andreas Kohlbecker	$taxonPager = cdm_dataportal_search_taxon_execute();
1920	6657531f	Andreas Kohlbecker
1921	f19f47fa	Andreas Kohlbecker	$showThumbnails = do_showThumbnails();
1922
1923			$setSessionUri = url('cdm_api/setvalue/session', array(
1924			'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1925			));
1926
1927			drupal_add_js('jQuery(document).ready(function() {
1928
1929			// init
1930			if(' . $showThumbnails . ' == 1){
1931	1d69a96c	Andreas Kohlbecker	jQuery(\'.media_gallery\').show(20);
1932			} else {
1933			jQuery(\'.media_gallery\').hide(20);
1934			}
1935
1936			// add change handler
1937			jQuery(\'#showThumbnails input.showThumbnails\').change(
1938	f19f47fa	Andreas Kohlbecker	function(event){
1939	1d69a96c	Andreas Kohlbecker	var state = 0;
1940			if(jQuery(this).is(\':checked\')){
1941			jQuery(\'.media_gallery\').show(20);
1942			state = 1;
1943			} else {
1944			jQuery(\'.media_gallery\').hide(20);
1945			}
1946			// store state in session variable
1947			var uri = \'' . $setSessionUri . '\' + state;
1948			jQuery.get(uri);
1949			});
1950	78e178e2	Andreas Kohlbecker	});',
1951	f19f47fa	Andreas Kohlbecker	array('type' => "inline", 'scope' => JS_DEFAULT));
1952
1953	78e178e2	Andreas Kohlbecker	drupal_set_title(t('Search results'), PASS_THROUGH);
1954
1955	0a1dc066	Andreas Kohlbecker	return theme('cdm_search_taxa_results', array(
1956	6657531f	Andreas Kohlbecker	'pager' => $taxonPager,
1957			'path' => 'cdm_dataportal/search/results/taxon',
1958			));
1959			}
1960
1961	a6ae799b	Andreas Kohlbecker	/**
1962			* Executes the search for registrations and generates the result list..
1963			*/
1964			function cdm_dataportal_view_search_registrations_results() {
1965
1966			$block = block_load('cdm_dataportal', 'registrations_search_filter');
1967			$render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
1968
1969			$registration_pager = cdm_dataportal_search_registrations_execute();
1970
1971			drupal_set_title(t('Search registrations'), PASS_THROUGH);
1972
1973	24797d7f	Andreas Kohlbecker	$registrations_pager_array = compose_registrations_search_results($registration_pager);
1974	a6ae799b	Andreas Kohlbecker
1975			$render_array = array_merge($render_array, $registrations_pager_array);
1976
1977			return $render_array;
1978			}
1979
1980
1981	94550ff9	Andreas Kohlbecker	/**
1982			* Provides the standart image wich indicated a loading process
1983			*
1984			* @return string
1985			* The img html tag
1986			*/
1987			function loading_image_html() {
1988			return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1989			. '/images/loading_circle_grey_16.gif" style="display:none;">';
1990			}
1991
1992	78e178e2	Andreas Kohlbecker	/**
1993			* Returns the state of the the showThumbnails flag set in the
1994			* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
1995			*
1996	c5ed6357	Andreas Kohlbecker	* @return boolean
1997	78e178e2	Andreas Kohlbecker	* returns 1 if the flag is set
1998			*/
1999			function do_showThumbnails() {
2000			static $showThumbnails = null;
2001
2002			if($showThumbnails == null) {
2003	c5ed6357	Andreas Kohlbecker	$showThumbnails = 0;
2004			if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
2005			$showThumbnails = 0;
2006			$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
2007			$showThumbnails = is_array($search_gallery_settings)
2008			&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
2009			&& (
2010			$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
2011			$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
2012			$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
2013			)
2014			? 1 : 0;
2015	f19f47fa	Andreas Kohlbecker
2016	c5ed6357	Andreas Kohlbecker	drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
2017			}
2018	f19f47fa	Andreas Kohlbecker	$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
2019			if (!is_numeric($showThumbnails)) {
2020			$showThumbnails = 1;
2021			}
2022	78e178e2	Andreas Kohlbecker	}
2023
2024			return $showThumbnails;
2025			}
2026
2027	6657531f	Andreas Kohlbecker
2028	a6ae799b	Andreas Kohlbecker
2029	6657531f	Andreas Kohlbecker	/* ====================== other functions ====================== */
2030			/**
2031			* Creates a URL to the taxon page specified by the $uuid parameter.
2032			*
2033			* The URL will be prepended with a path element to a specific taxon page tab.
2034			*
2035			* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
2036			* be set globally in the administrative settings or individually in the user
2037			* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
2038			* the last portal will stay on this last tab.
2039			*
2040			* A third option is offerered by the $page_tab parameter which allows overwriting this
2041			* internal mechanism by a specific value.
2042			*
2043			* @param string $uuid
2044			* The UUID of the taxon.
2045			* @param string $page_tab
2046			* Overwriting the preset mechanism by defining specific value for the
2047			* taxon page tab.
2048			*
2049			* @return string
2050			* The created URL.
2051			*/
2052			function path_to_taxon($uuid, $page_tab = FALSE) {
2053
2054			$tab = get_default_taxon_tab();
2055			$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2056
2057			if (!$uuid) {
2058			return FALSE;
2059			}
2060
2061			if ($page_tab) {
2062			return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2063			}
2064			elseif (!$tab \|\| strtolower($tab) == 'general') {
2065			return 'cdm_dataportal/taxon/' . $uuid;
2066			}
2067			elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2068			return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2069			}
2070			else {
2071			return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2072			}
2073			}
2074
2075	9d37c9d9	Patric Plitzner	function path_to_specimen($uuid) {
2076
2077			if (!$uuid) {
2078			return FALSE;
2079			}
2080			else {
2081			return 'cdm_dataportal/specimen/' . $uuid;
2082			}
2083			}
2084
2085	30845bda	Andreas Kohlbecker	function path_to_named_area($uuid) {
2086
2087			if (!$uuid) {
2088			return FALSE;
2089			}
2090			else {
2091			return 'cdm_dataportal/named_area/' . $uuid;
2092			}
2093			}
2094
2095	6657531f	Andreas Kohlbecker	/**
2096	630c7044	Andreas Kohlbecker	* Creates a URL to show a synonmy in the according taxon page.
2097			*
2098			* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2099			* The resulting URI will include query parameters to highlight the synonym, and to optionally display
2100			* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2101			* include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2102			* in the page
2103			*
2104			* @param string $synonymUuid
2105			* The uuid of the synonym
2106			* @param string $acceptedUuid
2107			* The uuid of the according accepted taxon
2108			* @return string
2109			* The URL to show a synonmy in the according taxon page
2110	6657531f	Andreas Kohlbecker	*/
2111			function uri_to_synonym($synonymUuid, $acceptedUuid) {
2112			$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2113	d071bed7	Andreas Kohlbecker	return url($acceptedPath, array(
2114			'query' => array(
2115			// highlite the synony in the synonymy
2116			'highlite' => $synonymUuid,
2117			// the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2118			// see theme_taxon_page_title()
2119			'acceptedFor' => $synonymUuid
2120	630c7044	Andreas Kohlbecker	),
2121			'fragment' => $synonymUuid
2122	d071bed7	Andreas Kohlbecker	));
2123
2124	6657531f	Andreas Kohlbecker	}
2125
2126			/**
2127	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the key identified by the uuid.
2128	b8bfa4bd	Andreas Kohlbecker	*
2129			* @param string $keyType
2130			* the key typer corresponds to the specific class of the CDM
2131			* IdentificationKey. Possible values are
2132			* -PolytomousKey
2133			* -MultimediaKey
2134			* - ...
2135	e0d3e148	Andreas Kohlbecker	* @param string $keyUuid
2136	b8bfa4bd	Andreas Kohlbecker	* The UUID of the key
2137	6657531f	Andreas Kohlbecker	*/
2138			function path_to_key($keyType, $keyUuid) {
2139			if (!$keyUuid \|\| !$keyType) {
2140			return FALSE;
2141			}
2142			$keyType{0} = strtolower($keyType{0});
2143			return "cdm_dataportal/" . $keyType . "/$keyUuid";
2144			}
2145
2146			/**
2147	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the reference identified by the uuid.
2148			*
2149			* @param $uuid string String representation of the registration entity uuid.
2150			*
2151			* @return string
2152			* The drupal path
2153			*
2154	6657531f	Andreas Kohlbecker	*/
2155			function path_to_reference($uuid) {
2156			if (!$uuid) {
2157			return FALSE;
2158			}
2159			return 'cdm_dataportal/reference/' . $uuid;
2160			}
2161
2162	e0d3e148	Andreas Kohlbecker	/**
2163			* Composes the drupal path to the reference identified by the uuid.
2164			*
2165			* @param string $identifier
2166			* The persistent identifier of the registration entity (Registration.identifier).
2167			* @return string
2168			* The drupal path
2169			*/
2170			function path_to_registration($identifier) {
2171
2172			return 'cdm_dataportal/registration/' . urlencode($identifier);
2173			}
2174
2175	6657531f	Andreas Kohlbecker	/**
2176	51b04faf	Andreas Kohlbecker	* Creates the path to a cdm_dataportal taxon name page.
2177			*
2178	e0d3e148	Andreas Kohlbecker	* @param string $taxon_name_uuid
2179			* The uuid as string of the CDM TaxonName to show a name page for
2180			* @param string $taxon_to_hide_uuid
2181			* The uuid as string of a taxon which should not be displayed in the taxon list
2182			* @param string $highlite_synonym_uuid
2183			* Optional parameter which takes another taxon uuid, if given the
2184			* target taxon pages will show the synonymy tab where the taxon
2185			* referenced by the $highlite_synonym_uuid will be highlighted
2186	51b04faf	Andreas Kohlbecker	* in case it is found on this page.
2187			*
2188	e0d3e148	Andreas Kohlbecker	* @return string
2189			* URI path element as string
2190	6657531f	Andreas Kohlbecker	*/
2191	51b04faf	Andreas Kohlbecker	function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid = NULL) {
2192	6657531f	Andreas Kohlbecker	$res = FALSE;
2193			if ($name_uuid) {
2194			$res = 'cdm_dataportal/name/' . $name_uuid;
2195			}
2196	51b04faf	Andreas Kohlbecker	if($taxon_to_hide_uuid){
2197			$res .= '/' . $taxon_to_hide_uuid;
2198			if($synonym_uuid){
2199			$res .= '/' . $synonym_uuid;
2200			}
2201			}
2202	6657531f	Andreas Kohlbecker	return $res;
2203			}
2204
2205			/**
2206	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the media entity identified by the uuid.
2207			*
2208			* @param string $uuid
2209			* The persistent identifier of the entity entity
2210			* @return string
2211			* The drupal path
2212	6657531f	Andreas Kohlbecker	*/
2213			function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2214			if (!$uuid) {
2215			return FALSE;
2216			}
2217			$out = 'cdm_dataportal/media/' . $uuid;
2218			if ($representaion_uuid) {
2219			$out .= '/' . $representaion_uuid;
2220	a867b774	Andreas Kohlbecker	if (is_numeric($partId)) {
2221	6657531f	Andreas Kohlbecker	$out .= '/' . $partId;
2222			}
2223			}
2224			return $out;
2225			}
2226
2227			/**
2228			* Compares thisRank with thatRank.
2229			*
2230			* Returns a negative integer, zero, or a positive integer
2231			* as the of thisRank is higher than, equal to, or lower than thatRank.
2232			* e.g:
2233			* <ul>
2234			* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2235			* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2236			* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2237			* </ul>
2238			* <p>
2239			* This compare logic of the underlying webservice is the
2240			* <b>inverse logic</b> of the the one implemented in
2241			* java.lang.Comparable#compareTo(java.lang.Object)
2242			*
2243			* @param $thisRankUuid
2244			* @param $thatRankUuid
2245			*
2246			* @return int
2247			* A negative integer, zero, or a positive integer
2248			* as the thisRank is lower than, equal to, or higher than thatRank.
2249			*/
2250			function rank_compare($thisRankUuid, $thatRankUuid) {
2251			$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2252			return $result->Integer;
2253			}
2254
2255			/**
2256			* Composes an HTML element class attribute value composed of
2257	4b3be949	Andreas Kohlbecker	* the short-name of the cdm class and the uuid of the entity.
2258			* This class attribute should be used wherever an cdm-entity is rendered.
2259			*
2260			* In case of Taxon entities or TaxonNodeDTOs the secReference is also added
2261			* to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
2262			* Taxon uuid is added also as taxon_uuid:<uuid>
2263	6657531f	Andreas Kohlbecker	*
2264			* These according class selectors in css must be escaped, eg:
2265			* .cdm\:TextData
2266			*
2267	a6ae799b	Andreas Kohlbecker	* @param $cdm_entity
2268			* A CDM entity, TaxonNodeDTO or TypedEntityReference
2269	6657531f	Andreas Kohlbecker	*/
2270	a6ae799b	Andreas Kohlbecker	function html_class_attribute_ref($cdm_entity) {
2271	6657531f	Andreas Kohlbecker
2272	4b3be949	Andreas Kohlbecker	$attributes = '';
2273	a6ae799b	Andreas Kohlbecker	if (is_cdm_entity($cdm_entity)) {
2274			$attributes = "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
2275			} else if($cdm_entity->class == 'TypedEntityReference') {
2276			$attributes = "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
2277	4b3be949	Andreas Kohlbecker	}
2278	a6ae799b	Andreas Kohlbecker	if($cdm_entity->class == 'TaxonNodeDto'){
2279			$attributes .= " taxon_uuid:" . $cdm_entity->taxonUuid . " sec_uuid:" . $cdm_entity->secUuid;;
2280	4b3be949	Andreas Kohlbecker	}
2281	a6ae799b	Andreas Kohlbecker	if($cdm_entity->class == 'Taxon' && isset($cdm_entity->sec->uuid)){
2282			$attributes .= " sec_uuid:" . $cdm_entity->sec->uuid;
2283	6657531f	Andreas Kohlbecker	}
2284	4b3be949	Andreas Kohlbecker	return $attributes;
2285	6657531f	Andreas Kohlbecker	}
2286
2287
2288			/**
2289	a0e3ae5c	Andreas Kohlbecker	* Creates a short version of a taxonname.
2290	6657531f	Andreas Kohlbecker	*
2291	e90899ac	Andreas Kohlbecker	* The short name is created by using the taggedTitle field of
2292	a0e3ae5c	Andreas Kohlbecker	* TaxonNodeDTO instances.
2293	e90899ac	Andreas Kohlbecker	* If the taggedTitle if empty the fullname will be returned.
2294	6657531f	Andreas Kohlbecker	*
2295	a0e3ae5c	Andreas Kohlbecker	* @param object $taxonNodeDTO
2296			* A TaxonNodeDTO object
2297	6657531f	Andreas Kohlbecker	*
2298			* @return string
2299			*/
2300	a0e3ae5c	Andreas Kohlbecker	function cdm_dataportal_shortname_of($taxonNodeDTO) {
2301
2302	6657531f	Andreas Kohlbecker	$nameStr = '';
2303
2304	a0e3ae5c	Andreas Kohlbecker	normalize_tagged_text($taxonNodeDTO->taggedTitle);
2305	6657531f	Andreas Kohlbecker
2306			// Get all tagged text tokens of the scientific name.
2307	a0e3ae5c	Andreas Kohlbecker	foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2308	6657531f	Andreas Kohlbecker	if ($tagtxt->type == 'name' \|\| $tagtxt->type == 'rank') {
2309			$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2310			}
2311			}
2312			$nameStr = trim($nameStr);
2313
2314			if ($nameStr) {
2315
2316			// Do not return short names for these.
2317	a0e3ae5c	Andreas Kohlbecker	if ($taxonNodeDTO->unplaced \|\| $taxonNodeDTO->excluded) {
2318	6657531f	Andreas Kohlbecker	return $nameStr;
2319			}
2320
2321			/*
2322			1st capture group (^[a-zA-Z]): First letter of uninomial.
2323			Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2324			Third capture group (\s+[^(\x2E]+\s+.+$\|\s+[a-zA-Z]+$): letters of name,
2325			but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
2326			OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
2327			*/
2328			$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$\|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2329			if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2330			return $matches[1][0] . "." . $matches[3][0];
2331			}
2332			else {
2333			return $nameStr;
2334			}
2335			}
2336			else {
2337	a0e3ae5c	Andreas Kohlbecker	return $taxonNodeDTO->titleCache;
2338	6657531f	Andreas Kohlbecker	}
2339			}
2340
2341			/**
2342			* Check if a taxon is accepted by the current taxonomic tree.
2343			*
2344			* @param mixed $taxon
2345			* The Taxon obkect to check.
2346			*
2347			* @return bool
2348			* Returns TRUE if $taxon is accepted, FALSE otherwise.
2349			*/
2350			function _cdm_dataportal_acceptedByCurrentView($taxon) {
2351
2352	7663cd0b	Andreas Kohlbecker	$defaultTreeUuid = get_current_classification_uuid();
2353	6657531f	Andreas Kohlbecker
2354			if (isset($taxon->taxonNodes)) {
2355			$taxonNodes = $taxon->taxonNodes;
2356			}
2357			else {
2358			$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2359			}
2360
2361			if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2362			foreach ($taxonNodes as $node) {
2363	586fc780	Andreas Kohlbecker	if (isset($node->classification)){
2364			if(is_object($node->classification)) {
2365			if ($node->classification->uuid == $defaultTreeUuid) {
2366			return TRUE;
2367			}
2368	6657531f	Andreas Kohlbecker	}
2369	586fc780	Andreas Kohlbecker	else {
2370			if ($node->classification == $defaultTreeUuid) {
2371			return TRUE;
2372			}
2373	6657531f	Andreas Kohlbecker	}
2374			}
2375			}
2376			}
2377
2378			return FALSE;
2379			}
2380
2381			/**
2382	54cfa718	Andreas Kohlbecker	* Checks is the source has one of the given types.
2383			*
2384			* @param object $source
2385			* The original source entity
2386			* @param array $types
2387			* An array of elementd of the OriginalSourceType enumeration
2388			* If not set the default will be used which is:
2389			* - Lineage
2390			* - PrimaryMediaSource
2391			* - PrimaryTaxonomicSource
2392			* - Unknown
2393			* - Other
2394			* @return boolean
2395	6657531f	Andreas Kohlbecker	*/
2396	54cfa718	Andreas Kohlbecker	function _is_original_source_type($source, $types = null) {
2397			// this is the default
2398			// maybe this should also be put into the settings
2399			static $default = array(
2400			OriginalSourceType::Lineage,
2401			OriginalSourceType::PrimaryMediaSource,
2402			OriginalSourceType::PrimaryTaxonomicSource,
2403			OriginalSourceType::Unknown,
2404			OriginalSourceType::Other,
2405			);
2406
2407			if(!$types){
2408			$types = $default;
2409			}
2410			return isset($source->type) && in_array($source->type, $types);
2411			}
2412	6657531f	Andreas Kohlbecker
2413			/**
2414			* @todo Please document this function.
2415			* @see http://drupal.org/node/1354
2416			*/
2417			function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
2418			return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
2419			}
2420
2421
2422			/**
2423			* Collects all the media from a list of description elements.
2424			*
2425			* @param array $descriptionElements
2426			* The description elements from which to collect the media.
2427			*
2428			* @return array
2429			* The output with all the collected media.
2430			*/
2431			function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2432
2433			$outArrayOfMedia = array();
2434
2435			// Avoiding a warning box in Drupal for Flora Malesiana.
2436			if (isset($descriptionElements) && is_array($descriptionElements)) {
2437			foreach ($descriptionElements as $descriptionElement) {
2438			if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2439			foreach ($descriptionElement->media as $media) {
2440			if (is_object($media)) {
2441			$outArrayOfMedia[] = $media;
2442			}
2443			}
2444			}
2445			}
2446			}
2447			return $outArrayOfMedia;
2448			}
2449
2450			/**
2451			* @todo Please document this function.
2452			* @see http://drupal.org/node/1354
2453			*
2454	65345976	Andreas Kohlbecker	* @param array $cdm_entities
2455	6657531f	Andreas Kohlbecker	* An array of CdmBase instances or a single instance.
2456	28c5c87a	Andreas Kohlbecker	* @param string $footnote_list_key_suggestion
2457	6657531f	Andreas Kohlbecker	*
2458			* @return unknown
2459			*/
2460	65345976	Andreas Kohlbecker	function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2461	90597e37	Andreas Kohlbecker
2462			static $annotations_types_filter = null;
2463	6657531f	Andreas Kohlbecker	if(!$annotations_types_filter) {
2464	90597e37	Andreas Kohlbecker	$annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2465	6657531f	Andreas Kohlbecker	}
2466
2467			$footNoteKeys = array();
2468
2469			// Is argument cdmBase an array?
2470	65345976	Andreas Kohlbecker	if (!is_array($cdm_entities)) {
2471	6657531f	Andreas Kohlbecker	$cdmBase_array = array();
2472	65345976	Andreas Kohlbecker	$cdmBase_array[] = $cdm_entities;
2473	6657531f	Andreas Kohlbecker	}
2474			else {
2475	65345976	Andreas Kohlbecker	$cdmBase_array = $cdm_entities;
2476	6657531f	Andreas Kohlbecker	}
2477
2478			// Getting the key for the footnotemanager.
2479	28c5c87a	Andreas Kohlbecker	if (isset($footnote_list_key_suggestion)) {
2480			$footnote_list_key = $footnote_list_key_suggestion;
2481	6657531f	Andreas Kohlbecker	}
2482			else {
2483	28c5c87a	Andreas Kohlbecker	$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2484	6657531f	Andreas Kohlbecker	}
2485
2486			// Adding the footnotes keys.
2487			foreach ($cdmBase_array as $cdmBase_element) {
2488			$annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2489			if (is_array($annotations)) {
2490			foreach ($annotations as $annotation) {
2491	28c5c87a	Andreas Kohlbecker	$footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2492	6657531f	Andreas Kohlbecker	}
2493			}
2494			}
2495
2496			return $footNoteKeys;
2497			}
2498
2499	d9763fd3	Andreas Kohlbecker
2500	6657531f	Andreas Kohlbecker	/**
2501	d9763fd3	Andreas Kohlbecker	* Creates a CDM Dynabox.
2502			*
2503	c1f5d897	Andreas Kohlbecker	* @param string $dynabox_id
2504	d9763fd3	Andreas Kohlbecker	* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2505	6657531f	Andreas Kohlbecker	* @param string $label
2506			* The clickable text to show.
2507			* @param string $content_url
2508			* The cdm REST service request url wich will deliver the content to be shown
2509			* once the dynabox toggles open.
2510			* @param string $theme
2511	1ce9afb7	Patric Plitzner	* The theme to be used for rendering the cdm REST service response with is
2512	6657531f	Andreas Kohlbecker	* returned from the $content_url.
2513			* @param string $link_alt_text
2514			* The value for the alt attribute of the dynabox link.
2515			* @param array $enclosingtags
2516			* An array with two elements: $enclosingtags[0] will be used for the dynabox
2517			* element itself, $enclosingtags[1] is the tag to be used for the
2518	c1f5d897	Andreas Kohlbecker	* dynabox_content (optional)
2519	d9763fd3	Andreas Kohlbecker	* @param array $attributes
2520			* @param $content_element_selector
2521			* Optional jQuery selector which can be used to reference a dom element which should
2522			* be used as container for the content to be shown. The dynabox-<dynabox id>-content
2523			* element will be placed in this container.
2524			*
2525	c1f5d897	Andreas Kohlbecker	* @param string $open_callback
2526	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2527	c1f5d897	Andreas Kohlbecker	* the open state.
2528			* @param string $close_callback
2529	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2530	c1f5d897	Andreas Kohlbecker	* the closed state.
2531	d9763fd3	Andreas Kohlbecker	* @return string Returns HTML for a dynabox.
2532			* Returns HTML for a dynabox.
2533	6657531f	Andreas Kohlbecker	*/
2534	d9763fd3	Andreas Kohlbecker	function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2535			$enclosingtags = array('li', 'ul'), $attributes = array(),
2536			$content_element_selector = null,
2537			$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2538	6657531f	Andreas Kohlbecker	$out = '';
2539	c1f5d897	Andreas Kohlbecker
2540			// check for plain class attribute string
2541			$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2542
2543	9c9d11f7	Andreas Kohlbecker	if(!array_key_exists('class', $attributes)) {
2544			$attributes['class'] = array();
2545			}
2546	d9763fd3	Andreas Kohlbecker	$attributes['id'][] = 'dynabox-' . $dynabox_id;
2547	9c9d11f7	Andreas Kohlbecker	$dynabox_attributes = drupal_attributes($attributes);
2548
2549
2550	b386ae48	Andreas Kohlbecker	_add_js_domEvent(); // requires domEvent.js
2551	6657531f	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2552	c1f5d897	Andreas Kohlbecker	drupal_add_js("
2553	94bb8db6	Andreas Kohlbecker	jQuery(document).ready(
2554			function() {
2555			dynabox('". $dynabox_id ."',
2556			{
2557			open_callback: " . $open_callback .",
2558	d9763fd3	Andreas Kohlbecker	close_callback: " . $close_callback .
2559			($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2560	94bb8db6	Andreas Kohlbecker	}
2561			);
2562			}
2563			);",
2564			array(
2565			'type'=>'inline',
2566			'scope'=>'footer'
2567			)
2568			);
2569	6657531f	Andreas Kohlbecker
2570	9c9d11f7	Andreas Kohlbecker
2571	6657531f	Andreas Kohlbecker	$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2572	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox for ' . $content_url . ' -->';
2573	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>';
2574	d9763fd3	Andreas Kohlbecker	$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2575			$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2576			$out .= ' </' . $enclosingtags[1] . '>';
2577			$out .= ' </' . $enclosingtags[0] . '>';
2578	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox end -->';
2579	6657531f	Andreas Kohlbecker	return $out;
2580			}
2581
2582			/**
2583			* Checks whether a feature has any description elements.
2584			*
2585			* @param mixed $featureNode
2586			* A feature node as produced by the function _mergeFeatureTreeDescriptions().
2587			*
2588			* @see _mergeFeatureTreeDescriptions()
2589			*
2590			* @return bool
2591			* Returns TRUE if the given $featureNode or any of its subordinate nodes
2592			* contains at least one non empty TextData or at least one DescriptionElement
2593			* of an other type. A TextData element holding a multilanguageText or a
2594			* source reference is considered to be not empty.
2595	159cd9bb	Andreas Kohlbecker	*
2596			* @TODO this function may have become obsolete by the new method of detecting empty blocks,
2597	1b756c5f	Andreas Kohlbecker	* see $block_content_is_not_empty in make_feature_block_list() and
2598	0ebb6efc	Andreas Kohlbecker	* $feature_block_has_content in compose_feature_block_items_generic
2599	6657531f	Andreas Kohlbecker	*/
2600	f19f47fa	Andreas Kohlbecker	function has_feature_node_description_elements($featureNode) {
2601	6657531f	Andreas Kohlbecker
2602			if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2603	092744e1	Andreas Kohlbecker	if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2604			foreach ($featureNode->descriptionElements as $descriptionElement) {
2605	159cd9bb	Andreas Kohlbecker	if ($descriptionElement->class != "TextData" \|\| isset($descriptionElement->multilanguageText_L10n->text)
2606			&& $descriptionElement->multilanguageText_L10n->text != ''
2607			\|\| isset($descriptionElement->sources[0])
2608			\|\| isset($descriptionElement->media[0]) ) {
2609	092744e1	Andreas Kohlbecker	return TRUE;
2610			}
2611	6657531f	Andreas Kohlbecker	}
2612			}
2613			}
2614	092744e1	Andreas Kohlbecker	else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2615	fae36a2a	Andreas Kohlbecker	foreach ($featureNode->childNodes as $child) {
2616	f19f47fa	Andreas Kohlbecker	if (has_feature_node_description_elements($child)) {
2617	6657531f	Andreas Kohlbecker	return TRUE;
2618			}
2619			}
2620			}
2621			return FALSE;
2622			}
2623	f26245c8	Andreas Kohlbecker
2624			/**
2625			* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2626			*
2627			* @param $chapter
2628			* The taxon page chapter or part
2629			*/
2630			function cdm_check_valid_taxon_page($chapter){
2631			static $taxon_tabs = null;
2632
2633			cdm_check_valid_portal_page();
2634
2635			if($taxon_tabs == null){
2636			$taxon_tabs = array('all', 'description');
2637			foreach(get_taxon_tabs_list() as $tab){
2638			$taxon_tabs[] = strtolower($tab);
2639			}
2640			}
2641
2642			if(!in_array($chapter, $taxon_tabs)){
2643			// oops this is not a valid chapter name
2644	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2645	f26245c8	Andreas Kohlbecker	}
2646
2647			}
2648
2649			/**
2650	e0d3e148	Andreas Kohlbecker	* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
2651			* The test applied by default it a check for the query parameter 'q' ending with a file suffix like '.'
2652	f26245c8	Andreas Kohlbecker	*
2653	e0d3e148	Andreas Kohlbecker	* @param $preg_pattern
2654			* Optional regular expression pattern to be used in preg_match().
2655	f26245c8	Andreas Kohlbecker	*/
2656	e0d3e148	Andreas Kohlbecker	function cdm_check_valid_portal_page($preg_pattern = null){
2657	595de9f0	Andreas Kohlbecker	$ends_with_file_suffix_pattern = '/\/[^\.\/][\.][^\.\/]$/';
2658	e0d3e148	Andreas Kohlbecker	if($preg_pattern === null){
2659			$preg_pattern = $ends_with_file_suffix_pattern;
2660			}
2661			if(preg_match($preg_pattern, $_GET['q'])){
2662	f26245c8	Andreas Kohlbecker	// oops this urls ends with a file_suffix and thus does not refer to a portal page
2663	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2664	595de9f0	Andreas Kohlbecker	exit('HTTP 404');
2665	f26245c8	Andreas Kohlbecker	}
2666			}
2667	b2b9e057	Andreas Kohlbecker
2668			/**
2669			* Generates the diff of the texts and presents it in a HTML diff viewer.
2670			*
2671			* @param $text_a
2672			* @param $text_b
2673			* @return string
2674			*/
2675			function diff_viewer($text_a, $text_b) {
2676
2677			static $diff_viewer_count = 0;
2678
2679			$element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2680
2681			// http://code.stephenmorley.org/php/diff-implementation/
2682			module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2683			drupal_add_css(drupal_get_path('module',
2684			'cdm_dataportal') . '/css/diff.css');
2685	087bb473	Andreas Kohlbecker	_add_jquery_ui();
2686	b2b9e057	Andreas Kohlbecker	drupal_add_js(
2687			'jQuery(document).ready( function(){
2688			jQuery(\'#' . $element_id . '\').accordion({
2689			collapsible: true,
2690			active: false,
2691			fillSpace: true,
2692			}).children(\'div\').css({ \'height\': \'auto\' });
2693			jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2694			});'
2695			, array(
2696			'type' => 'inline',
2697			'scope' => 'footer'
2698			));
2699
2700			$diff = Diff::compare($text_a,
2701			$text_b);
2702			$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2703			. Diff::toTable($diff, '', '')
2704			. '</div></div>';
2705			return $diff_viewer_markup;
2706			}
2707

Project

General

Profile

EDIT

cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ c0223d83