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

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 6d9071b7

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, $attributes = array()){
343	6d9071b7	Andreas Kohlbecker	_add_font_awesome_font();
344	38b27a36	Andreas Kohlbecker
345
346	b0aa9a8f	Andreas Kohlbecker	if($icon_name){
347			if(!isset($attributes['class'])){
348			$attributes['class'] = array();
349			}
350			$attributes['class'][] = 'fa';
351			$attributes['class'][] = $icon_name;
352
353			return '<i ' . drupal_attributes($attributes) . '></i>';
354	38b27a36	Andreas Kohlbecker	}
355
356	b0aa9a8f	Andreas Kohlbecker	return '';
357	38b27a36	Andreas Kohlbecker	}
358	94550ff9	Andreas Kohlbecker
359	6d9071b7	Andreas Kohlbecker	/**
360			* Adds the css containing the font awesome icons to the html header.
361			*/
362			function _add_font_awesome_font()
363			{
364			//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
365
366			$font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
367			//$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
368
369			drupal_add_html_head_link(
370			array(
371			'href' => $font_awesome_css_uri,
372			'rel' => 'stylesheet'
373			)
374			);
375			}
376
377	38b27a36	Andreas Kohlbecker
378	6d9071b7	Andreas Kohlbecker	/* ====================== hook implementations ====================== */
379	38b27a36	Andreas Kohlbecker	/**
380			* Implements hook_permission().
381			*
382			* Valid permissions for this module.
383			*
384			* @return array
385	8385a9f2	Andreas Kohlbecker	* An array of valid permissions for the cdm_dataportal module.
386	38b27a36	Andreas Kohlbecker	*/
387			function cdm_dataportal_permission() {
388			return array(
389			'administer cdm_dataportal' => array(
390	8385a9f2	Andreas Kohlbecker	'title' => t('Administer CDM DataPortal settings'),
391			'description' => t("Access the settings pages specific for the cdm_dataportal module"),
392	c6fe437b	Andreas Kohlbecker	),
393			'access cdm content' => array(
394			'title' => t('Access CDM content'),
395			'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
396			),
397	38b27a36	Andreas Kohlbecker	);
398			}
399	6657531f	Andreas Kohlbecker
400			/**
401	f19f47fa	Andreas Kohlbecker	* Implements hook_menu().
402			*/
403	6657531f	Andreas Kohlbecker	function cdm_dataportal_menu() {
404			$items = array();
405
406			// @see settings.php.
407			cdm_dataportal_menu_admin($items);
408			cdm_dataportal_menu_help($items);
409
410			$items['cdm_dataportal/names'] = array(
411			'page callback' => 'cdm_dataportal_view_names',
412	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
413	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
414			);
415
416			// Optional callback arguments: page.
417			$items['cdm_dataportal/taxon'] = array(
418			'page callback' => 'cdm_dataportal_taxon_page_view',
419	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
420	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
421			// Expected callback arguments: uuid.
422			);
423
424	30845bda	Andreas Kohlbecker	$items['cdm_dataportal/specimen'] = array(
425			'page callback' => 'cdm_dataportal_specimen_page_view',
426			'access arguments' => array('access cdm content'),
427			'type' => MENU_CALLBACK,
428			// Expected callback arguments: uuid.
429			);
430
431			$items['cdm_dataportal/named_area'] = array(
432			'page callback' => 'cdm_dataportal_named_area_page_view',
433			'access arguments' => array('access cdm content'),
434			'type' => MENU_CALLBACK,
435			// Expected callback arguments: uuid.
436			);
437	9d37c9d9	Patric Plitzner
438	6657531f	Andreas Kohlbecker	$items['cdm_dataportal/name'] = array(
439			'page callback' => 'cdm_dataportal_name_page_view',
440			/*
441			'page arguments' => array(
442			'taxon_name_uuid',
443			'taxon_to_hide_uuid',
444			'synonym_uuid' => NULL
445			),
446			*/
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'] = array(
453			'page callback' => 'cdm_dataportal_view_reference',
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/reference/list'] = array(
460			'page callback' => 'cdm_dataportal_view_reference_list',
461	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
462	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
463			// Expected callback arguments: uuid.
464			);
465
466			$items['cdm_dataportal/media'] = array(
467			'page callback' => 'cdm_dataportal_view_media',
468	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
469	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
470			// Expected callback arguments:
471			// uuid, mediarepresentation_uuid, part_uuid or part#.
472			);
473
474			$items['cdm_dataportal/polytomousKey'] = array(
475			'page callback' => 'cdm_dataportal_view_polytomousKey',
476	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
477	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
478			// Expected callback arguments: polytomousKey->uuid.
479			);
480
481			$items['cdm_dataportal/search'] = array(
482			'page callback' => 'cdm_dataportal_view_search_advanced',
483	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
484	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
485			);
486
487			$items['cdm_dataportal/search/advanced'] = array(
488	29077ee5	Andreas Kohlbecker	'title' => 'Advanced', // will be passed through t()
489	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_advanced',
490	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
491	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
492			);
493
494			$items['cdm_dataportal/search/taxon_by_description'] = array(
495	579c485d	Andreas Kohlbecker	'title' => 'By content category', // will be passed through t()
496	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
497	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
498	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
499			);
500
501			$items['cdm_dataportal/search/results/taxon'] = array(
502			'page callback' => 'cdm_dataportal_view_search_results_taxon',
503	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
504	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
505			);
506	a6ae799b	Andreas Kohlbecker	$items['cdm_dataportal/search/registration'] = array(
507			'page callback' => 'cdm_dataportal_view_search_registrations_results',
508			'access arguments' => array('access cdm content'),
509			'type' => MENU_CALLBACK,
510			);
511	e0d3e148	Andreas Kohlbecker	// Optional callback arguments: page.
512			$items['cdm_dataportal/registration'] = array(
513			'page callback' => 'cdm_dataportal_registration_page_view',
514			'access arguments' => array('access cdm content'),
515			'type' => MENU_CALLBACK,
516			// Expected callback arguments: uuid.
517			);
518	a6ae799b	Andreas Kohlbecker
519	6657531f	Andreas Kohlbecker	/*
520			$items['cdm/xml2json'] = array(
521			'page callback' => 'cdm_view_xml2json',
522	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
523	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
524			);
525			*/
526
527			// if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
528			// User configuration of cdm_dataportal.
529			$items['user/%/cdm_dataportal'] = array(
530			'title' => 'cdm_dataportal',
531	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
532	6657531f	Andreas Kohlbecker	'page callback' => 'drupal_get_form',
533			'page arguments' => array('cdm_dataportal_user_form'),
534			'type' => MENU_LOCAL_TASK,
535			'weight' => 10,
536			);
537			// }
538
539			// 'May not cache' in D5.
540			$items['cdm_dataportal/name/%'] = array(
541			// 'page callback' => 'cdm_dataportal_view_name',
542			'page callback' => 'cdm_dataportal_name_page_view',
543			'page arguments' => array(2, 3, 4),
544	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
545	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
546			);
547
548	6f1a217c	Andreas Kohlbecker	// --- Local tasks for Taxon.
549			// --- tabbed taxon page
550	6657531f	Andreas Kohlbecker	if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
551			$items['cdm_dataportal/taxon/%'] = array(
552	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
553	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
554	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
555	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
556			'weight' => 1,
557			'page arguments' => array(2, "description")
558	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
559	6657531f	Andreas Kohlbecker	);
560
561			$items['cdm_dataportal/taxon/%/all'] = array(
562	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
563	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
564	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
565	6657531f	Andreas Kohlbecker	'type' => MENU_CALLBACK,
566			'weight' => 2,
567			'page arguments' => array(2, "all")
568	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
569	6657531f	Andreas Kohlbecker	);
570
571			$items['cdm_dataportal/taxon/%/description'] = array(
572	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('General'),
573	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
574	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
575	6657531f	Andreas Kohlbecker	'type' => MENU_DEFAULT_LOCAL_TASK,
576			'weight' => 2,
577			'page arguments' => array(2, "description")
578	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
579	6657531f	Andreas Kohlbecker	);
580
581			$items['cdm_dataportal/taxon/%/synonymy'] = array(
582	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Synonymy'),
583	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
584	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
585	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
586			'weight' => 4,
587			'page arguments' => array(2, "synonymy", 4)
588	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid and ...
589	6657531f	Andreas Kohlbecker	);
590	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/images'] = array( // Images
591	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Images'),
592	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
593	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
594	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
595			'weight' => 5,
596			'page arguments' => array(2, "images")
597	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
598	6657531f	Andreas Kohlbecker	);
599
600	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
601	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Specimens'),
602	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
603	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
604	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
605			'weight' => 6,
606			'page arguments' => array(2, "specimens")
607	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
608	6657531f	Andreas Kohlbecker	);
609
610	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/keys'] = array( // Keys
611	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Keys'),
612	6657531f	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
613	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
614	6657531f	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
615			'weight' => 6,
616			'page arguments' => array(2, "keys")
617	7663cd0b	Andreas Kohlbecker	, // Expected callback arguments: taxon_uuid.
618			);
619
620	7cc085da	Andreas Kohlbecker	$items['cdm_dataportal/taxon/%/experts'] = array( // Experts
621	4feeabc7	Andreas Kohlbecker	'title' => cdm_taxonpage_tab_label('Experts'),
622	7663cd0b	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_taxon_page_view',
623	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
624	7663cd0b	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
625			'weight' => 6,
626			'page arguments' => array(2, "experts")
627			, // Expected callback arguments: taxon_uuid.
628	6657531f	Andreas Kohlbecker	);
629	93ae67cc	Patrick Plitzner
630	51cc509a	Patrick Plitzner	$items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
631	04a1d647	Patrick Plitzner	'page callback' => 'cdm_dataportal_taxon_autosuggest',
632	c6fe437b	Andreas Kohlbecker	'access arguments' => array('access cdm content'),
633	51cc509a	Patrick Plitzner	'page arguments' => array(3,4,5),
634	93ae67cc	Patrick Plitzner	'type' => MENU_CALLBACK
635			);
636	6657531f	Andreas Kohlbecker	}
637
638	6f1a217c	Andreas Kohlbecker	// --- refresh link for all cdmnode types
639			foreach (cdm_get_nodetypes() as $type=>$name) {
640			$items['cdm_dataportal/' . $name . '/%/refresh'] = array(
641	7cc085da	Andreas Kohlbecker	'title' => 'Refresh',
642	6f1a217c	Andreas Kohlbecker	'page callback' => 'cdm_dataportal_refresh_node',
643	3113db26	Andreas Kohlbecker	'access arguments' => array('administer cdm_dataportal'),
644	6f1a217c	Andreas Kohlbecker	'type' => MENU_LOCAL_TASK,
645			'weight' => 100,
646			'page arguments' => array($name, 2)
647			);
648			}
649
650	6657531f	Andreas Kohlbecker	return $items;
651			}
652
653			/**
654	b85ab055	Andreas Kohlbecker	* Implements hook_init().
655			*
656	6657531f	Andreas Kohlbecker	*/
657			function cdm_dataportal_init() {
658	8fc089e1	Saskia Gennrich	if (!path_is_admin(current_path())) {
659			//FIXME To add CSS or JS that should be present on all pages, modules
660			// should not implement this hook, but declare these files in their .info file.
661			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
662			// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
663			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
664	63f6d312	Saskia Gennrich	} else {
665			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
666	8fc089e1	Saskia Gennrich	}
667	2dd59bb5	Andreas Kohlbecker
668			if(variable_get('cdm_debug_mode', FALSE)){
669			$file = 'temporary://drupal_debug.txt';
670			file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
671			}
672	5611d467	Andreas Kohlbecker
673			$bibliography_settings = get_bibliography_settings();
674	57d513cb	Andreas Kohlbecker	$enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
675			FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
676	6657531f	Andreas Kohlbecker	}
677
678	6f1a217c	Andreas Kohlbecker	function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
679
680			$base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
681
682			if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
683			// force reloading of all and notify user about this special loading
684			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: ')
685			. l('Back to tabbed taxon page', $base_path));
686			$base_path .= '/all';
687			} else {
688			drupal_set_message(t('The level 2 cache has been cleared for this page'));
689			}
690
691			$parameters['cacheL2_refresh'] ='1';
692
693
694			drupal_goto($base_path, array('query' => $parameters));
695			}
696
697	102f8c26	Andreas Kohlbecker	/**
698			* Implements hook_requirements($phase)
699			*/
700			function cdm_dataportal_requirements($phase) {
701			$requirements = array();
702			if($phase == 'runtime'){
703
704			}
705			return $requirements;
706			}
707
708
709	6657531f	Andreas Kohlbecker	/**
710			* The function generate form for own user cdm dataportal configurations.
711			*/
712			function cdm_dataportal_user_form($form, &$form_state) {
713	36818236	Andreas Kohlbecker
714	6657531f	Andreas Kohlbecker	global $user;
715			$checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
716
717	8e1dc7ec	Andreas Kohlbecker	$form['taxon_page_tabs'] = array(
718			'#type' => 'fieldset',
719	36818236	Andreas Kohlbecker	'#tree' => true,
720	8e1dc7ec	Andreas Kohlbecker	'#title' => t('Taxon page tabs'),
721			);
722	36818236	Andreas Kohlbecker
723			$form['taxon_page_tabs']['user_defined'] = array(
724	6657531f	Andreas Kohlbecker	'#type' => 'checkbox',
725			'#title' => t('Activate user default configuration'),
726			'#default_value' => variable_get($checkbox_value, 0),
727			'#description' => t('Check this if you want configure your own default tab from the below menu.'),
728			);
729
730	36818236	Andreas Kohlbecker	$form['taxon_page_tabs']['default_tab'] = array(
731	6657531f	Andreas Kohlbecker	'#type' => 'select',
732			'#title' => t('Default tab to display'),
733			'#default_value' => get_default_taxon_tab(TRUE),
734			'#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
735			'#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
736			<strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
737	36818236	Andreas Kohlbecker	to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
738			);
739
740
741	f695daf4	Andreas Kohlbecker	if(false){
742			$form['developer_options'] = array(
743			'#type' => 'fieldset',
744			'#tree' => true,
745			'#title' => t('Developer options'),
746			);
747
748			$form['developer_options']['show_render_path'] = array(
749			'#type' => 'checkbox',
750			'#title' => t('Display the render path for each taxon name.'),
751			'#default_value' => variable_get($checkbox_value, 0),
752			'#description' => t('This option is very helpful if you are editing the !link for taxon names.',
753			array(
754			'!link' => l(
755			'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
756			)
757			),
758			);
759			}
760	6657531f	Andreas Kohlbecker
761			$form['submit'] = array(
762			'#type' => 'submit',
763			'#value' => t('Submit'),
764			);
765
766			return $form;
767			}
768
769			/**
770			* Form submission handler for user_form().
771			*
772			* Submits the user cdm dataportal configurations.
773			*/
774			function cdm_dataportal_user_form_submit($form, &$form_state) {
775			global $user;
776			$msg_type = 'status';
777			$username = $user->name;
778			$variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
779
780	36818236	Andreas Kohlbecker	// FIXME: this is completely wrong, see user_profile_form_submit()
781
782			// it is only possible to change own user settings
783			if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
784
785			// DEFAULT_TAXON_TAB
786	6657531f	Andreas Kohlbecker	$variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
787	36818236	Andreas Kohlbecker	variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
788			variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
789			if ($form_state['values']['taxon_page_tabs']['user_defined']) {
790	6657531f	Andreas Kohlbecker	drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
791			drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
792			'!tab' => $variable[variable_get($variable_to_use, 0)],
793			'!user' => $username,
794			))), $msg_type);
795			}
796			else {
797			drupal_set_message(check_plain(t('The user default tab wont be used for
798			the next taxon site, check the box if you want to use the user default configuration.')));
799			}
800	36818236	Andreas Kohlbecker
801	6657531f	Andreas Kohlbecker	}
802			else {
803	36818236	Andreas Kohlbecker	// Problem with the user id => variables wont be saved.
804	6657531f	Andreas Kohlbecker	$msg_type = 'warning';
805			drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
806			}
807			}
808
809			/**
810			* Implements hook_block_info().
811			*/
812			function cdm_dataportal_block_info() {
813
814			// $block[0]["info"] = t("CDM DataPortal DevLinks");
815			// $block[1]["info"] = t("CDM DataPortal Credits");
816	fc13aa30	Andreas Kohlbecker	$block["2"] = array(
817	beb914ef	Andreas Kohlbecker	"info" => t("CDM - Search Taxa"),
818	fc13aa30	Andreas Kohlbecker	"cache" => DRUPAL_NO_CACHE
819			);
820	6657531f	Andreas Kohlbecker	// $block[3]["info"] = t("CDM Filters");
821	beb914ef	Andreas Kohlbecker	$block["4"]["info"] = t("CDM - Dataportal Print");
822			$block["keys"]["info"] = t("CDM - Identification keys");
823	46a02272	Andreas Kohlbecker	$block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
824	f9a3d0f6	Andreas Kohlbecker	$block["classification_breadcrumbs"] = array(
825	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Classification breadcrumbs'),
826	f9a3d0f6	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
827			);
828	bc400a17	Andreas Kohlbecker	$block["taxonomic_children"] = array(
829	beb914ef	Andreas Kohlbecker	'info' => t('CDM - Taxonomic children'),
830	bc400a17	Andreas Kohlbecker	'cache' => DRUPAL_CACHE_PER_PAGE
831			);
832	beb914ef	Andreas Kohlbecker	$block["back_to_search_results"] = array(
833			'title' => '<none>',
834			'info' => t('CDM - Back to search Results'),
835			'cache' => DRUPAL_CACHE_PER_PAGE,
836			'visibility' => BLOCK_VISIBILITY_LISTED,
837			'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
838			);
839	a6ae799b	Andreas Kohlbecker	$block['registrations_search_filter'] = array(
840	810710a0	Andreas Kohlbecker	'title' => 'Search registrations',
841	a6ae799b	Andreas Kohlbecker	'info' => t('CDM - Registrations search filter'),
842			'cache' => DRUPAL_CACHE_PER_PAGE,
843	810710a0	Andreas Kohlbecker	'visibility' => BLOCK_VISIBILITY_NOTLISTED,
844	a6ae799b	Andreas Kohlbecker	'pages' => "cdm_dataportal/search/registration\ncdm_dataportal/search/registration/*", // multiple page paths separated by "\n"!!!
845			);
846	6657531f	Andreas Kohlbecker
847			return $block;
848			}
849
850			/**
851			* Implements hook_block_view().
852			*/
853			function cdm_dataportal_block_view($delta) {
854			// TODO Rename block deltas (e.g. '2') to readable strings.
855			switch ($delta) {
856			// case 'delta-1':
857			// $block['subject'] = t('Credits');
858			// $block['content'] = theme('cdm_credits');
859			// return $block;
860			case '2':
861			$block['subject'] = t('Search taxa');
862	191f88fd	Andreas Kohlbecker	$form = drupal_get_form('cdm_dataportal_search_taxon_form');
863			$block['content'] = drupal_render($form);
864	6657531f	Andreas Kohlbecker
865			if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
866			$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
867			}
868			return $block;
869			case '4':
870	c8234bdf	Andreas Kohlbecker	$block['subject'] = '';
871	6657531f	Andreas Kohlbecker	$block['content'] = theme('cdm_print_button');
872			return $block;
873			case "keys":
874			$block['subject'] = t('Identification Keys');
875			$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
876			return $block;
877			case "fundedByEDIT":
878			// t('Funded by EDIT');
879			$text = '<none>';
880			$block['subject'] = $text;
881	889c74b7	Andreas Kohlbecker	$img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
882			$block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
883	6657531f	Andreas Kohlbecker	'attributes' => array("target" => "EDIT"),
884			'absolute' => TRUE,
885			'html' => TRUE,
886			));
887			return $block;
888	f9a3d0f6	Andreas Kohlbecker	case 'classification_breadcrumbs':
889	0af3ce28	Andreas Kohlbecker	$taxon_uuid = get_current_taxon_uuid();
890	38da4e54	Andreas Kohlbecker	$block['subject'] = '<none>';
891			$block['content'] = compose_classification_breadcrumbs($taxon_uuid);
892			return $block;
893	bc400a17	Andreas Kohlbecker	case 'taxonomic_children':
894			$taxon_uuid = get_current_taxon_uuid();
895			$block['subject'] = '<none>';
896			$block['content'] = compose_taxonomic_children($taxon_uuid);
897			return $block;
898	beb914ef	Andreas Kohlbecker	case 'back_to_search_results':
899			$block['subject'] = '<none>';
900			if (isset($_SESSION['cdm']['search'])) {
901			$block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
902			}
903			return $block;
904	a6ae799b	Andreas Kohlbecker	case 'registrations_search_filter':
905			$block['subject'] = '<none>';
906			$block['content'] = $form = drupal_get_form('cdm_dataportal_search_registration_form'); // see cdm_dataportal_search_registration_form($form, &$form_state)
907			return $block;
908	beb914ef	Andreas Kohlbecker	default:
909			return null;
910	6657531f	Andreas Kohlbecker	}
911			}
912
913	0af3ce28	Andreas Kohlbecker	/**
914			* Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
915			*
916			* @return string
917			* the taxon uuid or NULL
918			*/
919			function get_current_taxon_uuid()
920			{
921			static $taxon_uuid;
922
923			if(!isset($taxon_uuid)){
924			if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
925			$taxon_uuid = $_REQUEST['currentTaxon'];
926			} else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
927			$taxon_uuid = arg(2);
928			} else {
929			$taxon_uuid = null;
930			}
931			}
932
933			return $taxon_uuid;
934			}
935
936			/**
937			* Returns the currently classification tree in use.
938			*
939			* @return string
940			* The uuid of the currently focused classification
941			*/
942			function get_current_classification_uuid() {
943			if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
944			return $_SESSION['cdm']['taxonomictree_uuid'];
945			}
946			else {
947			return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
948			}
949			}
950
951	6657531f	Andreas Kohlbecker	/*
952			function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
953			$_SESSION['cdm'] = NULL;
954			if(is_string($cdm_ws_uri_update)){
955			$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
956			}
957			}
958
959			function cdm_dataportal_session_validate(){
960			if(!isset($_SESSION['cdm']['ws_uri'])){
961			$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
962			} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
963			cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
964			}
965			}
966			*/
967
968			/**
969	d7588d36	Andreas Kohlbecker	* creates a selector form for taxonomic trees.
970			*
971	0af3ce28	Andreas Kohlbecker	* @return array
972			* a drupal form array
973	6657531f	Andreas Kohlbecker	*/
974			function cdm_taxonomictree_selector() {
975			_add_js_treeselector();
976
977	a8a8f23c	Andreas Kohlbecker	$form = drupal_get_form('cdm_taxonomictree_selector_form');
978	d7588d36	Andreas Kohlbecker	return $form;
979	6657531f	Andreas Kohlbecker	}
980
981			/**
982			* @todo Please document this function.
983			* @see http://drupal.org/node/1354
984	0af3ce28	Andreas Kohlbecker	*
985			* @deprecated use compose_classification_selector instead
986	6657531f	Andreas Kohlbecker	*/
987			function cdm_taxonomictree_selector_form($form, &$form_state) {
988
989			$url = url('cdm_api/setvalue/session', array('query' => NULL));
990			$form['#action'] = $url;
991
992			$form['var'] = array(
993			'#weight' => -3,
994			'#type' => 'hidden',
995			'#value' => '[cdm][taxonomictree_uuid]',
996			);
997
998			$destination_array = drupal_get_destination();
999			$destination = $destination_array['destination'];
1000
1001			$form['destination'] = array(
1002			'#weight' => -3,
1003			'#type' => 'hidden',
1004			'#value' => $destination,
1005			);
1006
1007	26fb3778	Andreas Kohlbecker	$options = cdm_get_taxontrees_as_options();
1008			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1009			if($taxontree_includes){
1010			$filtered_options = array();
1011			foreach($options as $uuid=>$label){
1012			if(!empty($taxontree_includes[$uuid])){
1013			$filtered_options[$uuid] = $label;
1014			}
1015			}
1016			$options = $filtered_options;
1017			}
1018
1019	6657531f	Andreas Kohlbecker	$form['val'] = array(
1020			'#type' => 'select',
1021			'#title' => t('Available classifications'),
1022	7663cd0b	Andreas Kohlbecker	'#default_value' => get_current_classification_uuid(),
1023	26fb3778	Andreas Kohlbecker	'#options' => $options,
1024	0af3ce28	Andreas Kohlbecker	'#attributes' => array('class' => array('highlite-first-child')),
1025	6657531f	Andreas Kohlbecker	);
1026
1027			return $form;
1028
1029			}
1030
1031	0af3ce28	Andreas Kohlbecker	/**
1032			*
1033			* @ingroup compose
1034			*/
1035			function compose_classification_selector() {
1036
1037			$destination_array = drupal_get_destination();
1038			$destination = $destination_array['destination'];
1039
1040			$options = cdm_get_taxontrees_as_options();
1041			$items = array();
1042			$taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1043
1044			$current_classification_uuid = get_current_classification_uuid();
1045
1046
1047			foreach($options as $uuid=>$label){
1048			if(!$taxontree_includes \|\| !empty($taxontree_includes[$uuid])){
1049
1050			$class_attributes = '';
1051			if($current_classification_uuid == $uuid){
1052			$class_attributes = array('focused');
1053			}
1054			$items[] = array(
1055			'data' => l($label,
1056			'cdm_api/setvalue/session',
1057			array(
1058			'query' => array(
1059			'destination' => $destination,
1060			'val' => $uuid,
1061			'var' => '[cdm][taxonomictree_uuid]'
1062			),
1063			)
1064			),
1065			'class' => $class_attributes
1066			);
1067			}
1068			}
1069
1070			$render_array = array(
1071			'#theme' => 'item_list',
1072			'#type' => 'ul',
1073			'#items' => $items
1074			);
1075
1076			return $render_array;
1077			}
1078
1079
1080	6657531f	Andreas Kohlbecker	/* UNREACHABLE since action of form directly links to view.
1081			function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1082
1083			$_SESSION['cdm']['search'] = $form_values;
1084			//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1085			return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1086			//$paramstr = compose_url_prameterstr($form_values);
1087			//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1088			}
1089			*/
1090			/* ====================== menu callback functions ====================== */
1091			/**
1092			* @todo Please document this function.
1093			* @see http://drupal.org/node/1354
1094			*/
1095			/*
1096			function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1097			static $comment_node_disabled = 0;
1098			static $comment_node_read_only = 1;
1099			static $comment_node_read_write = 2;
1100
1101			if ($form_id == 'node_type_form'
1102			&& isset($form['identity']['type'])
1103			&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1104			) {
1105			$form['workflow']['comment'] = array(
1106			'#type' => 'radios',
1107			'#title' => t('Default comment setting'),
1108			'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1109			'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1110			'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1111			);
1112			}
1113			}
1114			*/
1115
1116			/**
1117			* Displays a list of the known taxonomic names.
1118			*
1119			* When the list of taxonomic names is displayed, long lists are split up into
1120			* multiple pages.
1121			*
1122			* TODO: Parameters are still preliminary.
1123			*
1124			* @param string $beginsWith
1125			* @param string $page
1126			* Page number to diplay defaults to page 1.
1127			* @param bool $onlyAccepted
1128			*/
1129			function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1130
1131			$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1132
1133			/*
1134			// FIXME the filter for accepted names will be a form element, thus this
1135			// widget should be generated via form api preferably as block.
1136			$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1137			$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1138			$out .= theme('cdm_listof_taxa', $taxonPager);
1139			return $out;
1140			*/
1141			}
1142
1143			/**
1144			* @todo Please document this function.
1145			* @see http://drupal.org/node/1354
1146	c0223d83	Andreas Kohlbecker	* @throws Exception
1147	6657531f	Andreas Kohlbecker	*/
1148			function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1149	f26245c8	Andreas Kohlbecker
1150			cdm_check_valid_portal_page();
1151
1152	6cbefddc	Andreas Kohlbecker	return compose_cdm_reference_page($uuid);
1153	6657531f	Andreas Kohlbecker	}
1154
1155			/**
1156	b2ebf0d3	Andreas Kohlbecker	* Creates a view on a all references contained in the portal.
1157	b5dca1e2	Andreas Kohlbecker	*
1158			* This function is used at the path cdm_dataportal/reference/list
1159	6657531f	Andreas Kohlbecker	*/
1160			function cdm_dataportal_view_reference_list($pageNumber) {
1161			$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1162	b2ebf0d3	Andreas Kohlbecker	cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1163	6657531f	Andreas Kohlbecker	}
1164
1165			/**
1166			* @todo Please document this function.
1167			* @see http://drupal.org/node/1354
1168			*/
1169			function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1170	f26245c8	Andreas Kohlbecker
1171			cdm_check_valid_portal_page();
1172
1173	6657531f	Andreas Kohlbecker	$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1174			return theme('cdm_media_page', array(
1175			'media' => $media,
1176			'mediarepresentation_uuid' => $mediarepresentation_uuid,
1177			'partId' => $part,
1178			));
1179			}
1180
1181			/**
1182			* @todo Please document this function.
1183			* @see http://drupal.org/node/1354
1184			*/
1185			function _load_taxonBase(&$taxonBase) {
1186			if (isset($taxonBase->uuid)) {
1187			$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1188			$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1189			$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1190			}
1191			}
1192
1193	9438ad3a	Andreas Kohlbecker	/**
1194			* Loads the media associated to the given taxon from the cdm server.
1195			* The aggregation settings regarding taxon relathionships and
1196			* taxonnomic childen are taken into account.
1197			*
1198			* The media lists are cached in a static variable.
1199			*
1200			* @param Taxon $taxon
1201			* A CDM Taxon entitiy
1202			*
1203			* @return array
1204			* An array of CDM Media entities
1205			*
1206			*/
1207			function _load_media_for_taxon($taxon) {
1208
1209			static $media = NULL;
1210
1211			if(!isset($media)) {
1212			$media = array();
1213			}
1214			if (!isset($media[$taxon->uuid])) {
1215
1216	f19f47fa	Andreas Kohlbecker	// --- GET Images --- //
1217			$mediaQueryParameters = array(
1218			"type" => "ImageFile",
1219			);
1220
1221			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1222			$mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1223	a950f2f9	Andreas Kohlbecker	$mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1224
1225			$taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1226			$mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1227			$mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1228			$mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1229	9438ad3a	Andreas Kohlbecker
1230	f19f47fa	Andreas Kohlbecker	$ws_endpoint = NULL;
1231	9438ad3a	Andreas Kohlbecker	if ( variable_get('cdm_images_include_children', 0) == 0) {
1232			$ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1233			} else {
1234			$ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1235			}
1236	f19f47fa	Andreas Kohlbecker
1237			$media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1238			array(
1239			$taxon->uuid,
1240			),
1241	9438ad3a	Andreas Kohlbecker	queryString($mediaQueryParameters)
1242			);
1243			}
1244
1245			return $media[$taxon->uuid];
1246			}
1247
1248			/**
1249			*
1250			* @param Taxon $taxon
1251			* A CDM Taxon entitiy
1252			*
1253			* @return array
1254			* An array of CDM SpecimenOrObservation entities
1255			*
1256			function _load_occurences_for_taxon($taxon){
1257
1258			static $occurences = NULL;
1259	f19f47fa	Andreas Kohlbecker
1260			if(!isset($occurences)) {
1261			$occurences = array();
1262			}
1263	9438ad3a	Andreas Kohlbecker
1264			if (!isset($occurences[$taxon->uuid])){
1265
1266			$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1267			$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1268	f19f47fa	Andreas Kohlbecker	$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1269
1270			$by_associatedtaxon_query = http_build_query(array(
1271			'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1272			'relationships' => implode(',', $relationship_choice['direct']),
1273			'pageSize' => null // all hits in one page
1274			)
1275			);
1276
1277			$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1278			null,
1279			$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1280			);
1281
1282
1283			if(isset($pager->records[0])){
1284			$occurences[$taxon->uuid] = $pager->records;
1285			}
1286			}
1287	9438ad3a	Andreas Kohlbecker	return $occurences[$taxon->uuid];
1288			}
1289			*/
1290
1291	6657531f	Andreas Kohlbecker	/**
1292			* Gets a Drupal variable, string or array and returns it.
1293			*
1294			* Similar to the variable_get() function of Drupal, except that this function
1295			* is able to handle arrays correctly. This function is especially useful
1296	8c962983	Andreas Kohlbecker	* when dealing with collections of settings form elements (#tree = TRUE).
1297	6657531f	Andreas Kohlbecker	*
1298			* @param string $variableKey
1299			* The Unique key of the Drupal variable in the Drupal variables table.
1300			* @param string $defaultValueString
1301			* A string as for example derived from a CONSTANT.
1302			*
1303			* @return mixed
1304	8c962983	Andreas Kohlbecker	* usually an array, depending on the nature of the variable.
1305			*
1306			* TODO compare with get_array_variable_merged() duplicate functions?
1307	0f7c9d15	Andreas Kohlbecker	* @deprecated rather use get_array_variable_merged() since this function
1308			* used an array as second parameter
1309	6657531f	Andreas Kohlbecker	*/
1310			function mixed_variable_get($variableKey, $defaultValueString) {
1311			$systemDefaults = unserialize($defaultValueString);
1312			$storedSettings = variable_get($variableKey, array());
1313			if (is_array($storedSettings)) {
1314	8c962983	Andreas Kohlbecker	// TODO better use drupal_array_merge_deep() ?
1315	6657531f	Andreas Kohlbecker	$settings = array_merge($systemDefaults, $storedSettings);
1316			}
1317			else {
1318			$settings = $systemDefaults;
1319			}
1320			return $settings;
1321			}
1322
1323	b5519d3a	Andreas Kohlbecker	/**
1324	0f7c9d15	Andreas Kohlbecker	* Recursive function to convert an object into an array.
1325	b5519d3a	Andreas Kohlbecker	* also subordinate objects will be converted.
1326			*
1327			* @param object $object
1328	db725031	Andreas Kohlbecker	* the object to be converted
1329			* @return array
1330			* The array
1331	b5519d3a	Andreas Kohlbecker	*/
1332	db725031	Andreas Kohlbecker	function object_to_array($object) {
1333	b5519d3a	Andreas Kohlbecker	if(is_object($object) \|\| is_array($object)) {
1334			$array = (array)$object;
1335			foreach ($array as $key=>$value){
1336	db725031	Andreas Kohlbecker	$array[$key] = object_to_array($value);
1337	b5519d3a	Andreas Kohlbecker	}
1338			return $array;
1339			} else {
1340			return $object;
1341			}
1342			}
1343
1344	2fd6da0b	Andreas Kohlbecker	/**
1345			* Searches the $collection for the cdm entitiy given as $element.
1346			*
1347			* The elements are compared by their UUID.
1348			*
1349			* @param $element
1350			* the CDM entitiy to search for
1351			* @param $collection
1352			* the list of CDM entities to search in
1353			*
1354			* @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1355			*
1356			*/
1357			function contains_cdm_entitiy($element, $collection) {
1358			$result = FALSE;
1359			foreach ($collection as $a) {
1360			if ($a->uuid == $element->uuid) {
1361			$result = TRUE;
1362			}
1363			}
1364			return $result;
1365			}
1366
1367			/**
1368			* Fiters the array $entity_list of CDM entities by the list
1369			* of $excludes. Any element contained in the $excludes will be removed
1370			* from included int the retuned list.
1371			*
1372			* If the $entity_list is not an array the $excludes will be returned.
1373			*/
1374			function filter_cdm_entity_list($entity_list, $excludes) {
1375			if (is_array($entity_list)) {
1376			$result = $entity_list;
1377			if ($excludes) {
1378			foreach ($excludes as $exclude) {
1379			if (!contains_cdm_entitiy($exclude, $entity_list)) {
1380			$result[] = $exclude;
1381			}
1382			}
1383			}
1384			}
1385			else {
1386			$result = $excludes;
1387			}
1388			return $result;
1389			}
1390
1391	0a1151a4	Andreas Kohlbecker	/**
1392	6f5c7f2a	Andreas Kohlbecker	* Wraps the given $html string into a render array suitable for drupal_render()
1393	0a1151a4	Andreas Kohlbecker	*
1394	65345976	Andreas Kohlbecker	* @param $html
1395	0a1151a4	Andreas Kohlbecker	* the html string, see
1396			* http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1397	65345976	Andreas Kohlbecker	* @param $weight
1398	0a1151a4	Andreas Kohlbecker	* A positive or negative number (integer or decimal).
1399			* see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1400	65345976	Andreas Kohlbecker	* @param $prefix
1401			* Optional markup for the '#prefix' element of the render array
1402			* @param $suffix
1403			* Optional markup for the '#suffix' element of the render array
1404	0a1151a4	Andreas Kohlbecker	*
1405	65345976	Andreas Kohlbecker	* @return array
1406	0a1151a4	Andreas Kohlbecker	* A render array
1407			*
1408			*/
1409	65345976	Andreas Kohlbecker	function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1410	6f5c7f2a	Andreas Kohlbecker	$render_array = array(
1411			'#markup' => $html
1412	1ce9afb7	Patric Plitzner	);
1413	6f5c7f2a	Andreas Kohlbecker	if (is_numeric($weight)) {
1414			$render_array['#weight'] = $weight;
1415	65345976	Andreas Kohlbecker	}
1416			if($prefix){
1417			$render_array['#prefix'] = $prefix;
1418			}
1419			if($suffix) {
1420			$render_array['#suffix'] = $suffix;
1421			}
1422	6f5c7f2a	Andreas Kohlbecker	return $render_array;
1423	0a1151a4	Andreas Kohlbecker	}
1424
1425	6657531f	Andreas Kohlbecker	/**
1426			* Loads the subgraph of a given PolytomousKeyNode.
1427			*
1428			* Loads the subgraph of the given PolytomousKeyNode recursively from
1429			* the CDM REST service.
1430			*
1431			* @param mixed $polytomousKeyNode
1432			* PolytomousKeyNode passed by reference.
1433			*
1434			* @return void
1435			*/
1436			function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1437
1438			if (!$polytomousKeyNode) {
1439			return;
1440			}
1441			if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1442	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1443	6657531f	Andreas Kohlbecker	return;
1444			}
1445			if (!is_uuid($polytomousKeyNode->uuid)) {
1446	f19f47fa	Andreas Kohlbecker	drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1447	6657531f	Andreas Kohlbecker	return;
1448			}
1449
1450			$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1451
1452			if (!$polytomousKeyNode) {
1453			// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1454			return;
1455			}
1456
1457			// Load children.
1458			foreach ($polytomousKeyNode->children as &$childNode) {
1459			_load_polytomousKeySubGraph($childNode);
1460			}
1461
1462			// Load subkey.
1463			$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1464
1465			// Load taxon.
1466			$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1467			_load_taxonBase($polytomousKeyNode->taxon);
1468			return;
1469			}
1470
1471			/**
1472			* @todo Please document this function.
1473			* @see http://drupal.org/node/1354
1474			*/
1475			function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1476	f26245c8	Andreas Kohlbecker
1477			cdm_check_valid_portal_page();
1478
1479	6657531f	Andreas Kohlbecker	$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1480
1481			$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1482			if (is_array($sourcePager->records)) {
1483			$polytomousKey->sources = $sourcePager->records;
1484			// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1485			}
1486
1487			$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1488			if (is_array($annotationPager->records)) {
1489			$polytomousKey->annotations = $annotationPager->records;
1490			}
1491
1492			_load_polytomousKeySubGraph($polytomousKey->root);
1493			return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1494			}
1495
1496			/**
1497			* Creates a taxon page view or a chapter of it.
1498			*
1499			* The taxon page gives detailed information on a taxon, it shows:
1500			* - Taxon name.
1501			* - Full list of synonyms homotypic synonyms on top, followed by the
1502			* heterotypic and finally followed by misapplied names.
1503			* The list is ordered historically.
1504			* - All description associated with the taxon.
1505			*
1506			* @param string $uuid
1507			* @param string $chapter
1508			* Name of the part to display, valid values are:
1509			* 'description', 'images', 'synonymy', 'specimens', 'all'.
1510			*
1511	793dae0a	Andreas Kohlbecker	* @return string
1512	6657531f	Andreas Kohlbecker	*/
1513	0c5a23b6	Andreas Kohlbecker	function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1514	5ea8b301	Andreas Kohlbecker
1515	f26245c8	Andreas Kohlbecker	cdm_check_valid_taxon_page($chapter);
1516	2dd59bb5	Andreas Kohlbecker	cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1517	5ea8b301	Andreas Kohlbecker	// show a warning in case the javascript development mode is anabled
1518			if(variable_get('cdm_js_devel_mode', FALSE)) {
1519			drupal_set_message(t('The !url1 is enabled.
1520			WARNING: this is a performance penalty and must be turned off on production websites.', array(
1521			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1522			)),
1523			'warning'
1524			);
1525			}
1526
1527	6657531f	Andreas Kohlbecker	// Display the page for the taxon defined by $uuid.
1528			// set_last_taxon_page_tab(arg(3));
1529	0c5a23b6	Andreas Kohlbecker	$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1530	6657531f	Andreas Kohlbecker	if (!empty($taxonpage)) {
1531	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1532	6657531f	Andreas Kohlbecker	return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1533			}
1534			else {
1535	2dd59bb5	Andreas Kohlbecker	cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1536	6657531f	Andreas Kohlbecker	return '';
1537			}
1538			}
1539
1540			/**
1541	59f6da42	Andreas Kohlbecker	* This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1542			* which has two fields, one for the page title and one for the content. Later on in the
1543			* process chain the value contained in these fields will be passed to the cdm_node_show()
1544			* function as the function parameters $title and $content.
1545	6657531f	Andreas Kohlbecker	*
1546			* @param string $uuid
1547	59f6da42	Andreas Kohlbecker	* the uuid of the taxon to show
1548	6657531f	Andreas Kohlbecker	* @param string $chapter
1549			* Name of the part to display, valid values are:
1550			* 'description', 'images', 'synonymy', 'all'.
1551			*
1552	0c5a23b6	Andreas Kohlbecker	* @return object with the following fields:
1553	59f6da42	Andreas Kohlbecker	* - title : the title of the page
1554			* - content: the content of the page
1555			*
1556	6657531f	Andreas Kohlbecker	*/
1557	8cf9238f	Andreas Kohlbecker	function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1558	6657531f	Andreas Kohlbecker	// Taxon object.
1559			$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1560			if (empty($taxon)) {
1561			drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1562			return FALSE;
1563			}
1564			$taxonpage = new stdClass();
1565
1566			$taxonpage->title = theme('cdm_taxon_page_title', array(
1567	8cf9238f	Andreas Kohlbecker	'taxon' => $taxon
1568	6657531f	Andreas Kohlbecker	));
1569
1570			// Check if the taxon id contained in the currently selected tree.
1571	7663cd0b	Andreas Kohlbecker	$taxon_in_current_classification = taxon_in_current_classification($uuid);
1572	61b6ee11	Andreas Kohlbecker
1573	7663cd0b	Andreas Kohlbecker	if (!$taxon_in_current_classification) {
1574	61b6ee11	Andreas Kohlbecker	$classifications = get_classifications_for_taxon($taxon);
1575	e24d373b	Andreas Kohlbecker	RenderHints::pushToRenderStack('not_in_current_classification');
1576			$taxon_name_markup = render_taxon_or_name($taxon);
1577
1578	61b6ee11	Andreas Kohlbecker	if (count($classifications) == 0) {
1579	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.',
1580	fba00a4f	Andreas Kohlbecker	array(
1581	e24d373b	Andreas Kohlbecker	'!taxonname' => $taxon_name_markup,
1582	fba00a4f	Andreas Kohlbecker	)
1583			), 'warning');
1584	6657531f	Andreas Kohlbecker	}
1585			else {
1586			$trees = '';
1587	61b6ee11	Andreas Kohlbecker	foreach ($classifications as $classification) {
1588			if (isset($classification->titleCache)) {
1589			$trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1590	6657531f	Andreas Kohlbecker	}
1591			}
1592
1593	15b7c460	Andreas Kohlbecker	drupal_set_message(format_plural(count($trees),
1594	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',
1595			'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1596			array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1597	fba00a4f	Andreas Kohlbecker	) ,
1598			'warning');
1599	6657531f	Andreas Kohlbecker	}
1600	e24d373b	Andreas Kohlbecker	RenderHints::popFromRenderStack();
1601	6657531f	Andreas Kohlbecker	}
1602
1603			// Render the taxon page.
1604	9a607f17	Andreas Kohlbecker	$render_array = compose_cdm_taxon_page($taxon, $chapter);
1605			$taxonpage->content = drupal_render($render_array);
1606	6657531f	Andreas Kohlbecker
1607			return $taxonpage;
1608			}
1609
1610	9d37c9d9	Patric Plitzner	/**
1611			* Creates a specimen page view.
1612			* @param string $uuid the UUID of the specimen
1613			* @return array\|string
1614			*/
1615			function cdm_dataportal_specimen_page_view($uuid) {
1616
1617			//cdm_check_valid_taxon_page($chapter);
1618			//cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1619			// show a warning in case the javascript development mode is anabled
1620			if(variable_get('cdm_js_devel_mode', FALSE)) {
1621			drupal_set_message(t('The !url1 is enabled.
1622			WARNING: this is a performance penalty and must be turned off on production websites.', array(
1623			'!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1624			)),
1625			'warning'
1626			);
1627			}
1628
1629			// Display the page for the specimen defined by $uuid.
1630			$specimenpage = cdm_dataportal_specimen_view($uuid);
1631			if (!empty($specimenpage)) {
1632			return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1633			}
1634			else {
1635			return '';
1636			}
1637			}
1638
1639			/**
1640			*
1641			* Creates a specimen view.
1642			* @param string $uuid the UUID of the specimen
1643			* @return array\|string
1644			*/
1645			function cdm_dataportal_specimen_view($uuid) {
1646	907cc9b4	Patrick Plitzner	$specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1647	9d37c9d9	Patric Plitzner	if (empty($specimen)) {
1648			drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1649			return FALSE;
1650			}
1651			$specimenpage = new stdClass();
1652
1653			$specimenpage->title = theme('cdm_specimen_page_title', array(
1654			'specimen' => $specimen
1655			));
1656
1657	b810158e	Patric Plitzner	// Render the specimen page.
1658			$render_array = compose_cdm_specimen_page($uuid);
1659	9d37c9d9	Patric Plitzner	$specimenpage->content = drupal_render($render_array);
1660
1661			return $specimenpage;
1662			}
1663
1664	30845bda	Andreas Kohlbecker	/**
1665			*
1666			* Creates a named area view.
1667			* @param string $uuid the UUID of the specimen
1668			* * @return object
1669			* An object with two fields:
1670			* - title: the page title
1671			* - content: the page content
1672			*/
1673
1674			function cdm_dataportal_named_area_view($uuid) {
1675			$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1676			if (empty($named_area) \|\| $named_area->class !== 'NamedArea') {
1677			drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1678			return FALSE;
1679			}
1680			$named_area_page = new stdClass();
1681
1682			$named_area_page->title = $named_area->representation_L10n;
1683
1684			// Render the specimen page.
1685			$render_array = compose_cdm_named_area_page($uuid);
1686			$named_area_page->content = drupal_render($render_array);
1687
1688			return $named_area_page;
1689			}
1690
1691			function cdm_dataportal_named_area_page_view($uuid) {
1692
1693			cdm_check_valid_portal_page();
1694
1695			$named_area_page = cdm_dataportal_named_area_view($uuid);
1696			if (!empty($named_area_page)) {
1697			return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1698			}
1699			else {
1700			return '';
1701			}
1702
1703
1704			}
1705
1706	6657531f	Andreas Kohlbecker	/**
1707			* Returns a name page as a Drupal node ready to be renderized by Drupal.
1708			*
1709			* The node page shows the taxon name title and the list of taxon related
1710			* with such taxon. Name on the tree already in use.
1711			*
1712	51b04faf	Andreas Kohlbecker	* @param UUID $taxon_name_uuid
1713	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1714	51b04faf	Andreas Kohlbecker	* @param UUID $taxon_to_hide_uuid
1715			* A taxon which should not be displayed in the taxon list
1716			* @param UUID $highlite_synonym_uuid
1717			* Optinal parameter wich takes another taxon uuid, if given the
1718			* target taxon pages will show the syonymy tab where the taxon
1719			* refenrenced by the $highlite_synonym_uuid will be highlighted
1720			* in case it is found on this page.
1721	6657531f	Andreas Kohlbecker	*
1722			* @return mixed
1723			* The formatted name page as node.
1724			*/
1725			function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1726
1727	f26245c8	Andreas Kohlbecker	cdm_check_valid_portal_page();
1728
1729	6657531f	Andreas Kohlbecker	$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1730			if (!empty($taxonname_page)) {
1731			return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1732			}
1733			else {
1734			return '';
1735			}
1736			}
1737
1738			/**
1739	102f8c26	Andreas Kohlbecker	* View function for a TaxonName page.
1740	6657531f	Andreas Kohlbecker	*
1741	e3001c8d	Andreas Kohlbecker	* The name page lists all taxa for which the name specified by the
1742			* $taxon_name_uuid is being used. I case there is only one name the
1743			* page automatically redirects ti the according taxon page. Otherwise
1744			* the list of names is displayed.
1745	6657531f	Andreas Kohlbecker	*
1746	e3001c8d	Andreas Kohlbecker	* The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1747			* list of taxa. This is useful for example when referencing from a taxon
1748			* to the name page and the referring taxon should not be repeaded in the
1749			* name page.
1750	6657531f	Andreas Kohlbecker	*
1751	e3001c8d	Andreas Kohlbecker	*
1752			* @param UUID $taxon_name_uuid
1753	102f8c26	Andreas Kohlbecker	* The uuid of the CDM TaxonName to show a name page for
1754	e3001c8d	Andreas Kohlbecker	* @param UUID $taxon_to_hide_uuid
1755			* A taxon which should not be displayed in the taxon list
1756			* @param UUID $highlite_synonym_uuid
1757			* Optinal parameter wich takes another taxon uuid, if given the
1758			* target taxon pages will show the syonymy tab where the taxon
1759			* refenrenced by the $highlite_synonym_uuid will be highlighted
1760			* in case it is found on this page.
1761			*
1762			* @return object
1763			* An object with two fields:
1764			* - title: the page title
1765			* - content: the page content
1766	6657531f	Andreas Kohlbecker	*/
1767	e3001c8d	Andreas Kohlbecker	function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1768	6657531f	Andreas Kohlbecker	// Getting the full taxonname object from the server.
1769	d0d068e9	Andreas Kohlbecker	$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1770	6657531f	Andreas Kohlbecker	if (!$taxon_name) {
1771			drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1772			return FALSE;
1773			}
1774			// Searching for all the taxa connected with the taxon name on the tree
1775			// in use.
1776			$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1777			$request_params = array();
1778			$request_params['query'] = $name_cache;
1779	7663cd0b	Andreas Kohlbecker	$request_params['tree'] = get_current_classification_uuid();
1780	6657531f	Andreas Kohlbecker	$request_params['doTaxa'] = 1;
1781			$request_params['doSynonyms'] = 1;
1782			$request_params['doTaxaByCommonNames'] = 0;
1783			$request_params['matchMode'] = "EXACT";
1784			$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1785
1786	d0d068e9	Andreas Kohlbecker	// Removing the name where we came from.
1787	6657531f	Andreas Kohlbecker	foreach ($taxon_pager->records as $k => &$taxon) {
1788			if ($taxon->uuid == $taxon_to_hide_uuid) {
1789			unset($taxon_pager->records[$k]);
1790			}
1791			}
1792			// Show the taxa list or go to the singular taxon.
1793			if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1794	e3001c8d	Andreas Kohlbecker	$singleTaxon = array_pop($taxon_pager->records);
1795	6657531f	Andreas Kohlbecker	if ($singleTaxon->class != "Taxon") {
1796			// It is a Synonym -> look for the accepted.
1797	7635cc7d	Andreas Kohlbecker	$accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
1798	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
1799	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1800	6657531f	Andreas Kohlbecker	}
1801			else {
1802	7635cc7d	Andreas Kohlbecker	drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1803	6657531f	Andreas Kohlbecker	}
1804			}
1805			else {
1806			// It is an accepted taxon.
1807	e3001c8d	Andreas Kohlbecker	if (!empty($highlite_synonym_uuid)) {
1808			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1809	6657531f	Andreas Kohlbecker	}
1810			else {
1811			drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1812			}
1813			}
1814			}
1815			else {// More than one taxa case.
1816			$taxon_name_page = new stdClass();
1817	4f225a0f	Andreas Kohlbecker	$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1818	6657531f	Andreas Kohlbecker	if ($taxon_pager->records) {
1819	7272d19c	Andreas Kohlbecker	$taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1820	6657531f	Andreas Kohlbecker	}
1821			else {
1822	6b294c11	Andreas Kohlbecker	$taxon_name_page->content = 'This name is not assigned to a taxon.';
1823	6657531f	Andreas Kohlbecker	}
1824			return $taxon_name_page;
1825			}
1826			}
1827
1828	e0d3e148	Andreas Kohlbecker	/**
1829			* Returns a registration page as a Drupal node to be rendered by Drupal.
1830			*
1831			* @param string $registration_identifier_encoded
1832			* The persistent identifier of the registration urlencoded.
1833			* @return mixed
1834			* The formatted registration page as node.
1835			*/
1836			function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
1837
1838			cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
1839			$registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
1840			return cdm_node_show_simulate($registration_page);
1841			}
1842
1843			function cdm_dataportal_registration_view($registration_identifier_encoded) {
1844
1845			$registration_identifier = urldecode($registration_identifier_encoded);
1846
1847
1848
1849	6cbefddc	Andreas Kohlbecker	$render_array = array();
1850	e0d3e148	Andreas Kohlbecker	$registration_dto = cdm_ws_get("registrationDTO/identifier/" . $registration_identifier_encoded);
1851			if($registration_dto){
1852			drupal_set_title(t('Registration') . ' ' . $registration_identifier, PASS_THROUGH);
1853
1854	5e4cae59	Andreas Kohlbecker	$render_array = compose_registation_dto($registration_dto);
1855	e0d3e148	Andreas Kohlbecker
1856	db725031	Andreas Kohlbecker	if(is_object($registration_dto->orderdTypeDesignationWorkingSets)){
1857			$field_unit_uuids = array();
1858			foreach((array)$registration_dto->orderdTypeDesignationWorkingSets as $field_unit_ref => $obj){
1859			$tokens = explode("#", $field_unit_ref);
1860			$field_unit_uuids[] = $tokens[1];
1861			}
1862	67f32f09	Andreas Kohlbecker	$render_array['specimen_table'] = compose_specimen_table($field_unit_uuids);
1863	db725031	Andreas Kohlbecker	}
1864	e0d3e148	Andreas Kohlbecker
1865			} else {
1866			drupal_set_title(t('Registration not found'), PASS_THROUGH);
1867			$render_array['error'] = markup_to_render_array("A registration with the identifier " . $registration_identifier . " does not exist.");
1868			}
1869
1870			return $render_array ;
1871			}
1872
1873	6cbefddc	Andreas Kohlbecker	/**
1874	5e4cae59	Andreas Kohlbecker	* Composes information for a registation from a dtp object
1875			*
1876	6cbefddc	Andreas Kohlbecker	* @param $registration_dto
1877	5e4cae59	Andreas Kohlbecker	*
1878	6cbefddc	Andreas Kohlbecker	* @return array
1879	5e4cae59	Andreas Kohlbecker	* A drupal render array
1880			*
1881			* @ingroup compose
1882	6cbefddc	Andreas Kohlbecker	*/
1883			function compose_registation_dto($registration_dto, $with_citation = true, $with_identifier = false)
1884			{
1885			$render_array = array();
1886	84e766b2	Andreas Kohlbecker
1887	afe99f4d	Andreas Kohlbecker	$taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
1888			$registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
1889	6cbefddc	Andreas Kohlbecker	if($with_identifier){
1890			$registation_markup .= " " . l ($registration_dto->identifier, $registration_dto->identifier);
1891			}
1892			$render_array['summary'] = markup_to_render_array("<div>" . $registation_markup . "</div>");
1893	84e766b2	Andreas Kohlbecker
1894			if ($with_citation) {
1895			$render_array['citation'] = markup_to_render_array("<div class=\"" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
1896			. l($registration_dto->bibliographicCitationString, path_to_reference($registration_dto->citationUuid))
1897			. "</br> </div>");
1898			}
1899
1900	6cbefddc	Andreas Kohlbecker	return $render_array;
1901			}
1902	e0d3e148	Andreas Kohlbecker
1903
1904	6657531f	Andreas Kohlbecker	/**
1905	84b13813	Andreas Kohlbecker	* Creates a page with the advance search form.
1906			*
1907			* NOTE: The advance search form allows searching for taxa.
1908	6657531f	Andreas Kohlbecker	*/
1909			function cdm_dataportal_view_search_advanced() {
1910			drupal_set_title(t('Advanced search'), PASS_THROUGH);
1911			return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1912			}
1913
1914			/**
1915	84b13813	Andreas Kohlbecker	* Creates a page with the search form for searching by taxon descriptions.
1916	6657531f	Andreas Kohlbecker	*/
1917			function cdm_dataportal_view_search_taxon_by_description() {
1918	6441ddfb	Andreas Kohlbecker	drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1919	6657531f	Andreas Kohlbecker	return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1920			}
1921
1922			/**
1923			* Executes the search and generates the result list of taxa.
1924			*/
1925			function cdm_dataportal_view_search_results_taxon() {
1926
1927	24797d7f	Andreas Kohlbecker	$taxonPager = cdm_dataportal_search_taxon_execute();
1928	6657531f	Andreas Kohlbecker
1929	f19f47fa	Andreas Kohlbecker	$showThumbnails = do_showThumbnails();
1930
1931			$setSessionUri = url('cdm_api/setvalue/session', array(
1932			'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1933			));
1934
1935			drupal_add_js('jQuery(document).ready(function() {
1936
1937			// init
1938			if(' . $showThumbnails . ' == 1){
1939	1d69a96c	Andreas Kohlbecker	jQuery(\'.media_gallery\').show(20);
1940			} else {
1941			jQuery(\'.media_gallery\').hide(20);
1942			}
1943
1944			// add change handler
1945			jQuery(\'#showThumbnails input.showThumbnails\').change(
1946	f19f47fa	Andreas Kohlbecker	function(event){
1947	1d69a96c	Andreas Kohlbecker	var state = 0;
1948			if(jQuery(this).is(\':checked\')){
1949			jQuery(\'.media_gallery\').show(20);
1950			state = 1;
1951			} else {
1952			jQuery(\'.media_gallery\').hide(20);
1953			}
1954			// store state in session variable
1955			var uri = \'' . $setSessionUri . '\' + state;
1956			jQuery.get(uri);
1957			});
1958	78e178e2	Andreas Kohlbecker	});',
1959	f19f47fa	Andreas Kohlbecker	array('type' => "inline", 'scope' => JS_DEFAULT));
1960
1961	78e178e2	Andreas Kohlbecker	drupal_set_title(t('Search results'), PASS_THROUGH);
1962
1963	0a1dc066	Andreas Kohlbecker	return theme('cdm_search_taxa_results', array(
1964	6657531f	Andreas Kohlbecker	'pager' => $taxonPager,
1965			'path' => 'cdm_dataportal/search/results/taxon',
1966			));
1967			}
1968
1969	a6ae799b	Andreas Kohlbecker	/**
1970			* Executes the search for registrations and generates the result list..
1971			*/
1972			function cdm_dataportal_view_search_registrations_results() {
1973
1974			$block = block_load('cdm_dataportal', 'registrations_search_filter');
1975			$render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
1976
1977			$registration_pager = cdm_dataportal_search_registrations_execute();
1978
1979			drupal_set_title(t('Search registrations'), PASS_THROUGH);
1980
1981	24797d7f	Andreas Kohlbecker	$registrations_pager_array = compose_registrations_search_results($registration_pager);
1982	a6ae799b	Andreas Kohlbecker
1983			$render_array = array_merge($render_array, $registrations_pager_array);
1984
1985			return $render_array;
1986			}
1987
1988
1989	94550ff9	Andreas Kohlbecker	/**
1990			* Provides the standart image wich indicated a loading process
1991			*
1992			* @return string
1993			* The img html tag
1994			*/
1995			function loading_image_html() {
1996			return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1997			. '/images/loading_circle_grey_16.gif" style="display:none;">';
1998			}
1999
2000	78e178e2	Andreas Kohlbecker	/**
2001			* Returns the state of the the showThumbnails flag set in the
2002			* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
2003			*
2004	c5ed6357	Andreas Kohlbecker	* @return boolean
2005	78e178e2	Andreas Kohlbecker	* returns 1 if the flag is set
2006			*/
2007			function do_showThumbnails() {
2008			static $showThumbnails = null;
2009
2010			if($showThumbnails == null) {
2011	c5ed6357	Andreas Kohlbecker	$showThumbnails = 0;
2012			if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
2013			$showThumbnails = 0;
2014			$search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
2015			$showThumbnails = is_array($search_gallery_settings)
2016			&& isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
2017			&& (
2018			$search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
2019			$search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
2020			$search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
2021			)
2022			? 1 : 0;
2023	f19f47fa	Andreas Kohlbecker
2024	c5ed6357	Andreas Kohlbecker	drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
2025			}
2026	f19f47fa	Andreas Kohlbecker	$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
2027			if (!is_numeric($showThumbnails)) {
2028			$showThumbnails = 1;
2029			}
2030	78e178e2	Andreas Kohlbecker	}
2031
2032			return $showThumbnails;
2033			}
2034
2035	6657531f	Andreas Kohlbecker
2036	a6ae799b	Andreas Kohlbecker
2037	6657531f	Andreas Kohlbecker	/* ====================== other functions ====================== */
2038			/**
2039			* Creates a URL to the taxon page specified by the $uuid parameter.
2040			*
2041			* The URL will be prepended with a path element to a specific taxon page tab.
2042			*
2043			* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
2044			* be set globally in the administrative settings or individually in the user
2045			* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
2046			* the last portal will stay on this last tab.
2047			*
2048			* A third option is offerered by the $page_tab parameter which allows overwriting this
2049			* internal mechanism by a specific value.
2050			*
2051			* @param string $uuid
2052			* The UUID of the taxon.
2053			* @param string $page_tab
2054			* Overwriting the preset mechanism by defining specific value for the
2055			* taxon page tab.
2056			*
2057			* @return string
2058			* The created URL.
2059			*/
2060			function path_to_taxon($uuid, $page_tab = FALSE) {
2061
2062			$tab = get_default_taxon_tab();
2063			$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2064
2065			if (!$uuid) {
2066			return FALSE;
2067			}
2068
2069			if ($page_tab) {
2070			return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2071			}
2072			elseif (!$tab \|\| strtolower($tab) == 'general') {
2073			return 'cdm_dataportal/taxon/' . $uuid;
2074			}
2075			elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2076			return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2077			}
2078			else {
2079			return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2080			}
2081			}
2082
2083	9d37c9d9	Patric Plitzner	function path_to_specimen($uuid) {
2084
2085			if (!$uuid) {
2086			return FALSE;
2087			}
2088			else {
2089			return 'cdm_dataportal/specimen/' . $uuid;
2090			}
2091			}
2092
2093	30845bda	Andreas Kohlbecker	function path_to_named_area($uuid) {
2094
2095			if (!$uuid) {
2096			return FALSE;
2097			}
2098			else {
2099			return 'cdm_dataportal/named_area/' . $uuid;
2100			}
2101			}
2102
2103	6657531f	Andreas Kohlbecker	/**
2104	630c7044	Andreas Kohlbecker	* Creates a URL to show a synonmy in the according taxon page.
2105			*
2106			* The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2107			* The resulting URI will include query parameters to highlight the synonym, and to optionally display
2108			* the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2109			* include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2110			* in the page
2111			*
2112			* @param string $synonymUuid
2113			* The uuid of the synonym
2114			* @param string $acceptedUuid
2115			* The uuid of the according accepted taxon
2116			* @return string
2117			* The URL to show a synonmy in the according taxon page
2118	6657531f	Andreas Kohlbecker	*/
2119			function uri_to_synonym($synonymUuid, $acceptedUuid) {
2120			$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2121	d071bed7	Andreas Kohlbecker	return url($acceptedPath, array(
2122			'query' => array(
2123			// highlite the synony in the synonymy
2124			'highlite' => $synonymUuid,
2125			// the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2126			// see theme_taxon_page_title()
2127			'acceptedFor' => $synonymUuid
2128	630c7044	Andreas Kohlbecker	),
2129			'fragment' => $synonymUuid
2130	d071bed7	Andreas Kohlbecker	));
2131
2132	6657531f	Andreas Kohlbecker	}
2133
2134			/**
2135	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the key identified by the uuid.
2136	b8bfa4bd	Andreas Kohlbecker	*
2137			* @param string $keyType
2138			* the key typer corresponds to the specific class of the CDM
2139			* IdentificationKey. Possible values are
2140			* -PolytomousKey
2141			* -MultimediaKey
2142			* - ...
2143	e0d3e148	Andreas Kohlbecker	* @param string $keyUuid
2144	b8bfa4bd	Andreas Kohlbecker	* The UUID of the key
2145	6657531f	Andreas Kohlbecker	*/
2146			function path_to_key($keyType, $keyUuid) {
2147			if (!$keyUuid \|\| !$keyType) {
2148			return FALSE;
2149			}
2150			$keyType{0} = strtolower($keyType{0});
2151			return "cdm_dataportal/" . $keyType . "/$keyUuid";
2152			}
2153
2154			/**
2155	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the reference identified by the uuid.
2156			*
2157			* @param $uuid string String representation of the registration entity uuid.
2158			*
2159			* @return string
2160			* The drupal path
2161			*
2162	6657531f	Andreas Kohlbecker	*/
2163			function path_to_reference($uuid) {
2164			if (!$uuid) {
2165			return FALSE;
2166			}
2167			return 'cdm_dataportal/reference/' . $uuid;
2168			}
2169
2170	e0d3e148	Andreas Kohlbecker	/**
2171			* Composes the drupal path to the reference identified by the uuid.
2172			*
2173			* @param string $identifier
2174			* The persistent identifier of the registration entity (Registration.identifier).
2175			* @return string
2176			* The drupal path
2177			*/
2178			function path_to_registration($identifier) {
2179
2180			return 'cdm_dataportal/registration/' . urlencode($identifier);
2181			}
2182
2183	6657531f	Andreas Kohlbecker	/**
2184	51b04faf	Andreas Kohlbecker	* Creates the path to a cdm_dataportal taxon name page.
2185			*
2186	e0d3e148	Andreas Kohlbecker	* @param string $taxon_name_uuid
2187			* The uuid as string of the CDM TaxonName to show a name page for
2188			* @param string $taxon_to_hide_uuid
2189			* The uuid as string of a taxon which should not be displayed in the taxon list
2190			* @param string $highlite_synonym_uuid
2191			* Optional parameter which takes another taxon uuid, if given the
2192			* target taxon pages will show the synonymy tab where the taxon
2193			* referenced by the $highlite_synonym_uuid will be highlighted
2194	51b04faf	Andreas Kohlbecker	* in case it is found on this page.
2195			*
2196	e0d3e148	Andreas Kohlbecker	* @return string
2197			* URI path element as string
2198	6657531f	Andreas Kohlbecker	*/
2199	51b04faf	Andreas Kohlbecker	function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid = NULL) {
2200	6657531f	Andreas Kohlbecker	$res = FALSE;
2201			if ($name_uuid) {
2202			$res = 'cdm_dataportal/name/' . $name_uuid;
2203			}
2204	51b04faf	Andreas Kohlbecker	if($taxon_to_hide_uuid){
2205			$res .= '/' . $taxon_to_hide_uuid;
2206			if($synonym_uuid){
2207			$res .= '/' . $synonym_uuid;
2208			}
2209			}
2210	6657531f	Andreas Kohlbecker	return $res;
2211			}
2212
2213			/**
2214	e0d3e148	Andreas Kohlbecker	* Composes the drupal path to the media entity identified by the uuid.
2215			*
2216			* @param string $uuid
2217			* The persistent identifier of the entity entity
2218			* @return string
2219			* The drupal path
2220	6657531f	Andreas Kohlbecker	*/
2221			function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2222			if (!$uuid) {
2223			return FALSE;
2224			}
2225			$out = 'cdm_dataportal/media/' . $uuid;
2226			if ($representaion_uuid) {
2227			$out .= '/' . $representaion_uuid;
2228	a867b774	Andreas Kohlbecker	if (is_numeric($partId)) {
2229	6657531f	Andreas Kohlbecker	$out .= '/' . $partId;
2230			}
2231			}
2232			return $out;
2233			}
2234
2235			/**
2236			* Compares thisRank with thatRank.
2237			*
2238			* Returns a negative integer, zero, or a positive integer
2239			* as the of thisRank is higher than, equal to, or lower than thatRank.
2240			* e.g:
2241			* <ul>
2242			* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2243			* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2244			* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2245			* </ul>
2246			* <p>
2247			* This compare logic of the underlying webservice is the
2248			* <b>inverse logic</b> of the the one implemented in
2249			* java.lang.Comparable#compareTo(java.lang.Object)
2250			*
2251			* @param $thisRankUuid
2252			* @param $thatRankUuid
2253			*
2254			* @return int
2255			* A negative integer, zero, or a positive integer
2256			* as the thisRank is lower than, equal to, or higher than thatRank.
2257			*/
2258			function rank_compare($thisRankUuid, $thatRankUuid) {
2259			$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2260			return $result->Integer;
2261			}
2262
2263			/**
2264			* Composes an HTML element class attribute value composed of
2265	4b3be949	Andreas Kohlbecker	* the short-name of the cdm class and the uuid of the entity.
2266			* This class attribute should be used wherever an cdm-entity is rendered.
2267			*
2268			* In case of Taxon entities or TaxonNodeDTOs the secReference is also added
2269			* to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
2270			* Taxon uuid is added also as taxon_uuid:<uuid>
2271	6657531f	Andreas Kohlbecker	*
2272			* These according class selectors in css must be escaped, eg:
2273			* .cdm\:TextData
2274			*
2275	a6ae799b	Andreas Kohlbecker	* @param $cdm_entity
2276			* A CDM entity, TaxonNodeDTO or TypedEntityReference
2277	6657531f	Andreas Kohlbecker	*/
2278	a6ae799b	Andreas Kohlbecker	function html_class_attribute_ref($cdm_entity) {
2279	6657531f	Andreas Kohlbecker
2280	4b3be949	Andreas Kohlbecker	$attributes = '';
2281	a6ae799b	Andreas Kohlbecker	if (is_cdm_entity($cdm_entity)) {
2282			$attributes = "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
2283			} else if($cdm_entity->class == 'TypedEntityReference') {
2284			$attributes = "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
2285	4b3be949	Andreas Kohlbecker	}
2286	a6ae799b	Andreas Kohlbecker	if($cdm_entity->class == 'TaxonNodeDto'){
2287			$attributes .= " taxon_uuid:" . $cdm_entity->taxonUuid . " sec_uuid:" . $cdm_entity->secUuid;;
2288	4b3be949	Andreas Kohlbecker	}
2289	a6ae799b	Andreas Kohlbecker	if($cdm_entity->class == 'Taxon' && isset($cdm_entity->sec->uuid)){
2290			$attributes .= " sec_uuid:" . $cdm_entity->sec->uuid;
2291	6657531f	Andreas Kohlbecker	}
2292	4b3be949	Andreas Kohlbecker	return $attributes;
2293	6657531f	Andreas Kohlbecker	}
2294
2295
2296			/**
2297	a0e3ae5c	Andreas Kohlbecker	* Creates a short version of a taxonname.
2298	6657531f	Andreas Kohlbecker	*
2299	e90899ac	Andreas Kohlbecker	* The short name is created by using the taggedTitle field of
2300	a0e3ae5c	Andreas Kohlbecker	* TaxonNodeDTO instances.
2301	e90899ac	Andreas Kohlbecker	* If the taggedTitle if empty the fullname will be returned.
2302	6657531f	Andreas Kohlbecker	*
2303	a0e3ae5c	Andreas Kohlbecker	* @param object $taxonNodeDTO
2304			* A TaxonNodeDTO object
2305	6657531f	Andreas Kohlbecker	*
2306			* @return string
2307			*/
2308	a0e3ae5c	Andreas Kohlbecker	function cdm_dataportal_shortname_of($taxonNodeDTO) {
2309
2310	6657531f	Andreas Kohlbecker	$nameStr = '';
2311
2312	a0e3ae5c	Andreas Kohlbecker	normalize_tagged_text($taxonNodeDTO->taggedTitle);
2313	6657531f	Andreas Kohlbecker
2314			// Get all tagged text tokens of the scientific name.
2315	a0e3ae5c	Andreas Kohlbecker	foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2316	6657531f	Andreas Kohlbecker	if ($tagtxt->type == 'name' \|\| $tagtxt->type == 'rank') {
2317			$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2318			}
2319			}
2320			$nameStr = trim($nameStr);
2321
2322			if ($nameStr) {
2323
2324			// Do not return short names for these.
2325	a0e3ae5c	Andreas Kohlbecker	if ($taxonNodeDTO->unplaced \|\| $taxonNodeDTO->excluded) {
2326	6657531f	Andreas Kohlbecker	return $nameStr;
2327			}
2328
2329			/*
2330			1st capture group (^[a-zA-Z]): First letter of uninomial.
2331			Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2332			Third capture group (\s+[^(\x2E]+\s+.+$\|\s+[a-zA-Z]+$): letters of name,
2333			but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
2334			OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
2335			*/
2336			$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$\|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2337			if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2338			return $matches[1][0] . "." . $matches[3][0];
2339			}
2340			else {
2341			return $nameStr;
2342			}
2343			}
2344			else {
2345	a0e3ae5c	Andreas Kohlbecker	return $taxonNodeDTO->titleCache;
2346	6657531f	Andreas Kohlbecker	}
2347			}
2348
2349			/**
2350			* Check if a taxon is accepted by the current taxonomic tree.
2351			*
2352			* @param mixed $taxon
2353			* The Taxon obkect to check.
2354			*
2355			* @return bool
2356			* Returns TRUE if $taxon is accepted, FALSE otherwise.
2357			*/
2358			function _cdm_dataportal_acceptedByCurrentView($taxon) {
2359
2360	7663cd0b	Andreas Kohlbecker	$defaultTreeUuid = get_current_classification_uuid();
2361	6657531f	Andreas Kohlbecker
2362			if (isset($taxon->taxonNodes)) {
2363			$taxonNodes = $taxon->taxonNodes;
2364			}
2365			else {
2366			$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2367			}
2368
2369			if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2370			foreach ($taxonNodes as $node) {
2371	586fc780	Andreas Kohlbecker	if (isset($node->classification)){
2372			if(is_object($node->classification)) {
2373			if ($node->classification->uuid == $defaultTreeUuid) {
2374			return TRUE;
2375			}
2376	6657531f	Andreas Kohlbecker	}
2377	586fc780	Andreas Kohlbecker	else {
2378			if ($node->classification == $defaultTreeUuid) {
2379			return TRUE;
2380			}
2381	6657531f	Andreas Kohlbecker	}
2382			}
2383			}
2384			}
2385
2386			return FALSE;
2387			}
2388
2389			/**
2390	54cfa718	Andreas Kohlbecker	* Checks is the source has one of the given types.
2391			*
2392			* @param object $source
2393			* The original source entity
2394			* @param array $types
2395			* An array of elementd of the OriginalSourceType enumeration
2396			* If not set the default will be used which is:
2397			* - Lineage
2398			* - PrimaryMediaSource
2399			* - PrimaryTaxonomicSource
2400			* - Unknown
2401			* - Other
2402			* @return boolean
2403	6657531f	Andreas Kohlbecker	*/
2404	54cfa718	Andreas Kohlbecker	function _is_original_source_type($source, $types = null) {
2405			// this is the default
2406			// maybe this should also be put into the settings
2407			static $default = array(
2408			OriginalSourceType::Lineage,
2409			OriginalSourceType::PrimaryMediaSource,
2410			OriginalSourceType::PrimaryTaxonomicSource,
2411			OriginalSourceType::Unknown,
2412			OriginalSourceType::Other,
2413			);
2414
2415			if(!$types){
2416			$types = $default;
2417			}
2418			return isset($source->type) && in_array($source->type, $types);
2419			}
2420	6657531f	Andreas Kohlbecker
2421			/**
2422			* @todo Please document this function.
2423			* @see http://drupal.org/node/1354
2424			*/
2425			function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
2426			return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
2427			}
2428
2429
2430			/**
2431			* Collects all the media from a list of description elements.
2432			*
2433			* @param array $descriptionElements
2434			* The description elements from which to collect the media.
2435			*
2436			* @return array
2437			* The output with all the collected media.
2438			*/
2439			function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2440
2441			$outArrayOfMedia = array();
2442
2443			// Avoiding a warning box in Drupal for Flora Malesiana.
2444			if (isset($descriptionElements) && is_array($descriptionElements)) {
2445			foreach ($descriptionElements as $descriptionElement) {
2446			if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2447			foreach ($descriptionElement->media as $media) {
2448			if (is_object($media)) {
2449			$outArrayOfMedia[] = $media;
2450			}
2451			}
2452			}
2453			}
2454			}
2455			return $outArrayOfMedia;
2456			}
2457
2458			/**
2459			* @todo Please document this function.
2460			* @see http://drupal.org/node/1354
2461			*
2462	65345976	Andreas Kohlbecker	* @param array $cdm_entities
2463	6657531f	Andreas Kohlbecker	* An array of CdmBase instances or a single instance.
2464	28c5c87a	Andreas Kohlbecker	* @param string $footnote_list_key_suggestion
2465	6657531f	Andreas Kohlbecker	*
2466			* @return unknown
2467			*/
2468	65345976	Andreas Kohlbecker	function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2469	90597e37	Andreas Kohlbecker
2470			static $annotations_types_filter = null;
2471	6657531f	Andreas Kohlbecker	if(!$annotations_types_filter) {
2472	90597e37	Andreas Kohlbecker	$annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2473	6657531f	Andreas Kohlbecker	}
2474
2475			$footNoteKeys = array();
2476
2477			// Is argument cdmBase an array?
2478	65345976	Andreas Kohlbecker	if (!is_array($cdm_entities)) {
2479	6657531f	Andreas Kohlbecker	$cdmBase_array = array();
2480	65345976	Andreas Kohlbecker	$cdmBase_array[] = $cdm_entities;
2481	6657531f	Andreas Kohlbecker	}
2482			else {
2483	65345976	Andreas Kohlbecker	$cdmBase_array = $cdm_entities;
2484	6657531f	Andreas Kohlbecker	}
2485
2486			// Getting the key for the footnotemanager.
2487	28c5c87a	Andreas Kohlbecker	if (isset($footnote_list_key_suggestion)) {
2488			$footnote_list_key = $footnote_list_key_suggestion;
2489	6657531f	Andreas Kohlbecker	}
2490			else {
2491	28c5c87a	Andreas Kohlbecker	$footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2492	6657531f	Andreas Kohlbecker	}
2493
2494			// Adding the footnotes keys.
2495			foreach ($cdmBase_array as $cdmBase_element) {
2496			$annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2497			if (is_array($annotations)) {
2498			foreach ($annotations as $annotation) {
2499	28c5c87a	Andreas Kohlbecker	$footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2500	6657531f	Andreas Kohlbecker	}
2501			}
2502			}
2503
2504			return $footNoteKeys;
2505			}
2506
2507	d9763fd3	Andreas Kohlbecker
2508	6657531f	Andreas Kohlbecker	/**
2509	d9763fd3	Andreas Kohlbecker	* Creates a CDM Dynabox.
2510			*
2511	c1f5d897	Andreas Kohlbecker	* @param string $dynabox_id
2512	d9763fd3	Andreas Kohlbecker	* a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2513	6657531f	Andreas Kohlbecker	* @param string $label
2514			* The clickable text to show.
2515			* @param string $content_url
2516			* The cdm REST service request url wich will deliver the content to be shown
2517			* once the dynabox toggles open.
2518			* @param string $theme
2519	1ce9afb7	Patric Plitzner	* The theme to be used for rendering the cdm REST service response with is
2520	6657531f	Andreas Kohlbecker	* returned from the $content_url.
2521			* @param string $link_alt_text
2522			* The value for the alt attribute of the dynabox link.
2523			* @param array $enclosingtags
2524			* An array with two elements: $enclosingtags[0] will be used for the dynabox
2525			* element itself, $enclosingtags[1] is the tag to be used for the
2526	c1f5d897	Andreas Kohlbecker	* dynabox_content (optional)
2527	d9763fd3	Andreas Kohlbecker	* @param array $attributes
2528			* @param $content_element_selector
2529			* Optional jQuery selector which can be used to reference a dom element which should
2530			* be used as container for the content to be shown. The dynabox-<dynabox id>-content
2531			* element will be placed in this container.
2532			*
2533	c1f5d897	Andreas Kohlbecker	* @param string $open_callback
2534	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2535	c1f5d897	Andreas Kohlbecker	* the open state.
2536			* @param string $close_callback
2537	1ce9afb7	Patric Plitzner	* optional javascript call back function to be triggered after toggling the box to
2538	c1f5d897	Andreas Kohlbecker	* the closed state.
2539	d9763fd3	Andreas Kohlbecker	* @return string Returns HTML for a dynabox.
2540			* Returns HTML for a dynabox.
2541	6657531f	Andreas Kohlbecker	*/
2542	d9763fd3	Andreas Kohlbecker	function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2543			$enclosingtags = array('li', 'ul'), $attributes = array(),
2544			$content_element_selector = null,
2545			$open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2546	6657531f	Andreas Kohlbecker	$out = '';
2547	c1f5d897	Andreas Kohlbecker
2548			// check for plain class attribute string
2549			$dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2550
2551	9c9d11f7	Andreas Kohlbecker	if(!array_key_exists('class', $attributes)) {
2552			$attributes['class'] = array();
2553			}
2554	d9763fd3	Andreas Kohlbecker	$attributes['id'][] = 'dynabox-' . $dynabox_id;
2555	9c9d11f7	Andreas Kohlbecker	$dynabox_attributes = drupal_attributes($attributes);
2556
2557
2558	b386ae48	Andreas Kohlbecker	_add_js_domEvent(); // requires domEvent.js
2559	6657531f	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2560	c1f5d897	Andreas Kohlbecker	drupal_add_js("
2561	94bb8db6	Andreas Kohlbecker	jQuery(document).ready(
2562			function() {
2563			dynabox('". $dynabox_id ."',
2564			{
2565			open_callback: " . $open_callback .",
2566	d9763fd3	Andreas Kohlbecker	close_callback: " . $close_callback .
2567			($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2568	94bb8db6	Andreas Kohlbecker	}
2569			);
2570			}
2571			);",
2572			array(
2573			'type'=>'inline',
2574			'scope'=>'footer'
2575			)
2576			);
2577	6657531f	Andreas Kohlbecker
2578	9c9d11f7	Andreas Kohlbecker
2579	6657531f	Andreas Kohlbecker	$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2580	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox for ' . $content_url . ' -->';
2581	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>';
2582	d9763fd3	Andreas Kohlbecker	$out .= ' <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2583			$out .= ' <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2584			$out .= ' </' . $enclosingtags[1] . '>';
2585			$out .= ' </' . $enclosingtags[0] . '>';
2586	9c9d11f7	Andreas Kohlbecker	$out .= '<!-- dynabox end -->';
2587	6657531f	Andreas Kohlbecker	return $out;
2588			}
2589
2590			/**
2591			* Checks whether a feature has any description elements.
2592			*
2593			* @param mixed $featureNode
2594			* A feature node as produced by the function _mergeFeatureTreeDescriptions().
2595			*
2596			* @see _mergeFeatureTreeDescriptions()
2597			*
2598			* @return bool
2599			* Returns TRUE if the given $featureNode or any of its subordinate nodes
2600			* contains at least one non empty TextData or at least one DescriptionElement
2601			* of an other type. A TextData element holding a multilanguageText or a
2602			* source reference is considered to be not empty.
2603	159cd9bb	Andreas Kohlbecker	*
2604			* @TODO this function may have become obsolete by the new method of detecting empty blocks,
2605	1b756c5f	Andreas Kohlbecker	* see $block_content_is_not_empty in make_feature_block_list() and
2606	0ebb6efc	Andreas Kohlbecker	* $feature_block_has_content in compose_feature_block_items_generic
2607	6657531f	Andreas Kohlbecker	*/
2608	f19f47fa	Andreas Kohlbecker	function has_feature_node_description_elements($featureNode) {
2609	6657531f	Andreas Kohlbecker
2610			if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2611	092744e1	Andreas Kohlbecker	if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2612			foreach ($featureNode->descriptionElements as $descriptionElement) {
2613	159cd9bb	Andreas Kohlbecker	if ($descriptionElement->class != "TextData" \|\| isset($descriptionElement->multilanguageText_L10n->text)
2614			&& $descriptionElement->multilanguageText_L10n->text != ''
2615			\|\| isset($descriptionElement->sources[0])
2616			\|\| isset($descriptionElement->media[0]) ) {
2617	092744e1	Andreas Kohlbecker	return TRUE;
2618			}
2619	6657531f	Andreas Kohlbecker	}
2620			}
2621			}
2622	092744e1	Andreas Kohlbecker	else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2623	fae36a2a	Andreas Kohlbecker	foreach ($featureNode->childNodes as $child) {
2624	f19f47fa	Andreas Kohlbecker	if (has_feature_node_description_elements($child)) {
2625	6657531f	Andreas Kohlbecker	return TRUE;
2626			}
2627			}
2628			}
2629			return FALSE;
2630			}
2631	f26245c8	Andreas Kohlbecker
2632			/**
2633			* Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2634			*
2635			* @param $chapter
2636			* The taxon page chapter or part
2637			*/
2638			function cdm_check_valid_taxon_page($chapter){
2639			static $taxon_tabs = null;
2640
2641			cdm_check_valid_portal_page();
2642
2643			if($taxon_tabs == null){
2644			$taxon_tabs = array('all', 'description');
2645			foreach(get_taxon_tabs_list() as $tab){
2646			$taxon_tabs[] = strtolower($tab);
2647			}
2648			}
2649
2650			if(!in_array($chapter, $taxon_tabs)){
2651			// oops this is not a valid chapter name
2652	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2653	f26245c8	Andreas Kohlbecker	}
2654
2655			}
2656
2657			/**
2658	e0d3e148	Andreas Kohlbecker	* Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
2659			* The test applied by default it a check for the query parameter 'q' ending with a file suffix like '.'
2660	f26245c8	Andreas Kohlbecker	*
2661	e0d3e148	Andreas Kohlbecker	* @param $preg_pattern
2662			* Optional regular expression pattern to be used in preg_match().
2663	f26245c8	Andreas Kohlbecker	*/
2664	e0d3e148	Andreas Kohlbecker	function cdm_check_valid_portal_page($preg_pattern = null){
2665	595de9f0	Andreas Kohlbecker	$ends_with_file_suffix_pattern = '/\/[^\.\/][\.][^\.\/]$/';
2666	e0d3e148	Andreas Kohlbecker	if($preg_pattern === null){
2667			$preg_pattern = $ends_with_file_suffix_pattern;
2668			}
2669			if(preg_match($preg_pattern, $_GET['q'])){
2670	f26245c8	Andreas Kohlbecker	// oops this urls ends with a file_suffix and thus does not refer to a portal page
2671	b4a5c2be	Andreas Kohlbecker	http_response_code(404); // 404 = Not Found
2672	595de9f0	Andreas Kohlbecker	exit('HTTP 404');
2673	f26245c8	Andreas Kohlbecker	}
2674			}
2675	b2b9e057	Andreas Kohlbecker
2676			/**
2677			* Generates the diff of the texts and presents it in a HTML diff viewer.
2678			*
2679			* @param $text_a
2680			* @param $text_b
2681			* @return string
2682			*/
2683			function diff_viewer($text_a, $text_b) {
2684
2685			static $diff_viewer_count = 0;
2686
2687			$element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2688
2689			// http://code.stephenmorley.org/php/diff-implementation/
2690			module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2691			drupal_add_css(drupal_get_path('module',
2692			'cdm_dataportal') . '/css/diff.css');
2693	087bb473	Andreas Kohlbecker	_add_jquery_ui();
2694	b2b9e057	Andreas Kohlbecker	drupal_add_js(
2695			'jQuery(document).ready( function(){
2696			jQuery(\'#' . $element_id . '\').accordion({
2697			collapsible: true,
2698			active: false,
2699			fillSpace: true,
2700			}).children(\'div\').css({ \'height\': \'auto\' });
2701			jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2702			});'
2703			, array(
2704			'type' => 'inline',
2705			'scope' => 'footer'
2706			));
2707
2708			$diff = Diff::compare($text_a,
2709			$text_b);
2710			$diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2711			. Diff::toTable($diff, '', '')
2712			. '</div></div>';
2713			return $diff_viewer_markup;
2714			}
2715

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 6d9071b7