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cdm-dataportal/modules/cdm_dataportal/cdm_api/cdm_api.module @ 991ae630

1	6657531f	Andreas Kohlbecker	<?php
2	54cfa718	Andreas Kohlbecker	/**
3			* @file
4			* Required or useful functions for using CDM Data Store Webservices.
5			*
6			* Naming conventions:
7			* ----------------------
8			* - All webservice access methods are prefixed with cdm_ws.
9			*
10			* @copyright
11			* (C) 2007-2012 EDIT
12			* European Distributed Institute of Taxonomy
13			* http://www.e-taxonomy.eu
14			*
15			* The contents of this module are subject to the Mozilla
16			* Public License Version 1.1.
17			* @see http://www.mozilla.org/MPL/MPL-1.1.html
18			*
19			* @author
20			* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
21			* - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
22			*/
23	6657531f	Andreas Kohlbecker
24	54cfa718	Andreas Kohlbecker	module_load_include('php', 'cdm_api', 'xml2json');
25			module_load_include('php', 'cdm_api', 'commons');
26			module_load_include('php', 'cdm_api', 'uuids');
27			module_load_include('php', 'cdm_api', 'enums');
28			module_load_include('php', 'cdm_api', 'webservice_uris');
29			module_load_include('php', 'cdm_api', 'cdm_node');
30	2978b0c8	Andreas Kohlbecker	module_load_include('inc', 'cdm_api', 'tagged_text');
31	6657531f	Andreas Kohlbecker
32	54cfa718	Andreas Kohlbecker	/**
33			* Timeout used to override the default of 30 seconds
34			* in @see drupal_http_request()
35			*
36			* @var CDM_HTTP_REQUEST_TIMEOUT: A float representing the maximum number of seconds the function
37			* call may take
38			*/
39			define('CDM_HTTP_REQUEST_TIMEOUT', 90.0);
40	1042dbc0	Andreas Kohlbecker
41	7ca5ef1e	Andreas Kohlbecker
42
43			/**
44			* orderBy webservice query parameter value
45			*/
46	f8234b76	Andreas Kohlbecker	define('CDM_ORDER_BY_ID_ASC', 'BY_ID_ASC');
47	7ca5ef1e	Andreas Kohlbecker
48			/**
49			* orderBy webservice query parameter value
50			*/
51	f8234b76	Andreas Kohlbecker	define('CDM_ORDER_BY_ID_DESC', 'BY_ID_DESC');
52	7ca5ef1e	Andreas Kohlbecker	/**
53			* orderBy webservice query parameter value
54			*/
55	f8234b76	Andreas Kohlbecker	define('CDM_ORDER_BY_TITLE_CACHE_ASC', 'BY_TITLE_CACHE_ASC');
56	7ca5ef1e	Andreas Kohlbecker	/**
57			* orderBy webservice query parameter value
58			*/
59	f8234b76	Andreas Kohlbecker	define('CDM_ORDER_BY_TITLE_CACHE_DESC', 'BY_TITLE_CACHE_DESC');
60	7ca5ef1e	Andreas Kohlbecker	/**
61			* orderBy webservice query parameter value
62			*/
63	a33be830	Andreas Kohlbecker	define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_ASC', 'BY_NOMENCLATURAL_ORDER_ASC');
64	7ca5ef1e	Andreas Kohlbecker	/**
65			* orderBy webservice query parameter value
66			*/
67	a33be830	Andreas Kohlbecker	define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_DESC', 'BY_NOMENCLATURAL_ORDER_DESC');
68	7ca5ef1e	Andreas Kohlbecker	/**
69			* orderBy webservice query parameter value
70			*/
71			define('CDM_ORDER_BY_ORDER_INDEX_ASC', 'BY_ORDER_INDEX_ASC');
72			/**
73			* orderBy webservice query parameter value
74			*/
75			define('CDM_ORDER_BY_ORDER_INDEX_DESC', 'BY_ORDER_INDEX_DESC');
76
77	fa782b11	Andreas Kohlbecker
78	6657531f	Andreas Kohlbecker	/**
79			* Implements hook_menu().
80			*/
81			function cdm_api_menu() {
82			$items = array();
83
84			// usage: url('cdm_api/proxy/'.urlencode($content_url)."/$theme");
85			$items['cdm_api/proxy'] = array(
86			'page callback' => 'proxy_content',
87			'access arguments' => array(
88	c6fe437b	Andreas Kohlbecker	'access cdm content',
89	6657531f	Andreas Kohlbecker	),
90			'type' => MENU_CALLBACK,
91			);
92
93			$items['cdm_api/setvalue/session'] = array(
94			'page callback' => 'setvalue_session',
95			'access arguments' => array(
96	c6fe437b	Andreas Kohlbecker	'access cdm content',
97	6657531f	Andreas Kohlbecker	),
98			'type' => MENU_CALLBACK,
99			);
100
101			return $items;
102			}
103
104	e2464cf8	Andreas Kohlbecker	/**
105			* Implements hook_block_info().
106			*/
107			function cdm_api_block_info() {
108
109			$block['cdm_ws_debug'] = array(
110			"info" => t("CDM web service debug"),
111			"cache" => DRUPAL_NO_CACHE
112			);
113			return $block;
114			}
115
116			/**
117			* Implements hook_block_view().
118			*/
119			function cdm_api_block_view($delta) {
120			switch ($delta) {
121			case 'cdm_ws_debug':
122
123	6b5815cd	Andreas Kohlbecker	$cdm_ws_url = variable_get('cdm_webservice_url', '');
124
125	e2464cf8	Andreas Kohlbecker	$field_map = array(
126	6b5815cd	Andreas Kohlbecker	'ws_uri' => t('URI') . ' <code>(' . $cdm_ws_url .'...)</code>',
127	e2464cf8	Andreas Kohlbecker	'time' => t('Time'),
128			'fetch_seconds' => t('Fetching [s]'),
129			'parse_seconds' => t('Parsing [s]'),
130			'size_kb' => t('Size [kb]'),
131			'status' => t('Status'),
132			'data_links' => t('Links'),
133			);
134
135
136			if (!isset($_SESSION['cdm']['ws_debug'])) {
137			$_SESSION['cdm']['ws_debug'] = array();
138			}
139
140			$header = '<thead><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></thead>';
141			$footer = '<tfoot><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></tfoot>';
142			$rows = array();
143
144			foreach ($_SESSION['cdm']['ws_debug'] as $data){
145	6b5815cd	Andreas Kohlbecker
146	e2464cf8	Andreas Kohlbecker	$data = unserialize($data);
147	6b5815cd	Andreas Kohlbecker
148			// stip of webservice base url
149			$data['ws_uri'] = str_replace($cdm_ws_url, '', $data['ws_uri']);
150	2ebf0428	Andreas Kohlbecker	if($data['method'] == 'POST'){
151			$data['ws_uri'] = 'POST: ' . $data['ws_uri'] . '?' . $data['post_data'];
152			}
153	6b5815cd	Andreas Kohlbecker
154			$cells = array();
155	e2464cf8	Andreas Kohlbecker	foreach ($field_map as $field => $label){
156			$cells[] = '<td class="' . $field . '">' . $data[$field] . '</td>';
157			}
158			$rows[] = '<tr class="' . $data['status'] . '">' . join('' , $cells). '</tr>';
159			}
160			// clear session again
161			$_SESSION['cdm']['ws_debug'] = array();
162
163			_add_js_ws_debug();
164
165	86b65fa0	Andreas Kohlbecker	$block['subject'] = ''; // no subject, title in content for having a defined element id
166			// otherwise it would depend on the theme
167	63f6d312	Saskia Gennrich	$block['content'] = array(
168			'#markup' => '<h4 id="cdm-ws-debug-button">' . t('CDM Debug') . '</h4>'
169			// cannot use theme_table() since table footer is not jet supported in D7
170	86b65fa0	Andreas Kohlbecker	. '<div id="cdm-ws-debug-table-container"><table id="cdm-ws-debug-table">'
171	e2464cf8	Andreas Kohlbecker	. $header
172			. '<tbody>' . join('', $rows) . '</tbody>'
173			. $footer
174	63f6d312	Saskia Gennrich	. '</table></div>',
175			'#attached' => array(
176			'css' => array(
177			drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_ws_debug.css'
178			)
179			)
180			);
181	e2464cf8	Andreas Kohlbecker	return $block;
182			}
183			}
184
185	6657531f	Andreas Kohlbecker	/**
186			* Implements hook_cron().
187			*
188			* Expire outdated cache entries.
189			*/
190			function cdm_api_cron() {
191			cache_clear_all(NULL, 'cache_cdm_ws');
192			}
193
194	61b6ee11	Andreas Kohlbecker	/**
195			* Lists the classifications a taxon belongs to
196			*
197			* @param CDM type Taxon $taxon
198			* the taxon
199			*
200			* @return array
201			* aray of CDM instances of Type Classification
202			*/
203			function get_classifications_for_taxon($taxon) {
204
205	9dddc68a	Andreas Kohlbecker	return cdm_ws_get(CDM_WS_TAXON_CLASSIFICATIONS, $taxon->uuid);
206	61b6ee11	Andreas Kohlbecker	}
207
208	6657531f	Andreas Kohlbecker	/**
209	9dddc68a	Andreas Kohlbecker	* Returns the chosen FeatureTree to be used as FeatureTree for the taxon profile.
210	6657531f	Andreas Kohlbecker	*
211	9dddc68a	Andreas Kohlbecker	* The FeatureTree returned is the term tree one that has been set in the
212	6657531f	Andreas Kohlbecker	* dataportal settings (layout->taxon:profile).
213			* When the chosen FeatureTree is not found in the database,
214			* the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
215			*
216	9dddc68a	Andreas Kohlbecker	* @return object
217			* A cdm TermTree object.
218	6657531f	Andreas Kohlbecker	*/
219	642b323b	Andreas Kohlbecker	function get_profile_feature_tree() {
220	bfb2b81a	Andreas Kohlbecker	static $profile_featureTree;
221
222			if($profile_featureTree == NULL) {
223	6657531f	Andreas Kohlbecker	$profile_featureTree = cdm_ws_get(
224	9dddc68a	Andreas Kohlbecker	CDM_WS_TERMTREE,
225	bfb2b81a	Andreas Kohlbecker	variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
226	6657531f	Andreas Kohlbecker	);
227	bfb2b81a	Andreas Kohlbecker	if (!$profile_featureTree) {
228	9dddc68a	Andreas Kohlbecker	$profile_featureTree = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
229	bfb2b81a	Andreas Kohlbecker	}
230	6657531f	Andreas Kohlbecker	}
231	092744e1	Andreas Kohlbecker
232	6657531f	Andreas Kohlbecker	return $profile_featureTree;
233			}
234
235	f19f47fa	Andreas Kohlbecker	/**
236	9dddc68a	Andreas Kohlbecker	* Returns the chosen TermTree to be used as FeatureTree for SpecimenDescriptions.
237	f19f47fa	Andreas Kohlbecker	*
238	9dddc68a	Andreas Kohlbecker	* The TermTree returned is the one that has been set in the
239	f19f47fa	Andreas Kohlbecker	* dataportal settings (layout->taxon:specimen).
240	9dddc68a	Andreas Kohlbecker	* When the chosen TermTree is not found in the database,
241			* the standard term tree (UUID_DEFAULT_TERMTREE) will be returned.
242	f19f47fa	Andreas Kohlbecker	*
243	9dddc68a	Andreas Kohlbecker	* @return object
244			* A cdm TermTree object.
245	bfb2b81a	Andreas Kohlbecker	*/
246	f19f47fa	Andreas Kohlbecker	function cdm_get_occurrence_featureTree() {
247	bfb2b81a	Andreas Kohlbecker	static $occurrence_featureTree;
248
249			if($occurrence_featureTree == NULL) {
250			$occurrence_featureTree = cdm_ws_get(
251	9dddc68a	Andreas Kohlbecker	CDM_WS_TERMTREE,
252	bfb2b81a	Andreas Kohlbecker	variable_get(CDM_OCCURRENCE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
253			);
254			if (!$occurrence_featureTree) {
255	9dddc68a	Andreas Kohlbecker	$occurrence_featureTree = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
256	bfb2b81a	Andreas Kohlbecker	}
257			}
258	f19f47fa	Andreas Kohlbecker	return $occurrence_featureTree;
259	bfb2b81a	Andreas Kohlbecker	}
260
261	f19f47fa	Andreas Kohlbecker	/**
262			* Returns the FeatureTree for structured descriptions
263			*
264			* The FeatureTree returned is the one that has been set in the
265			* dataportal settings (layout->taxon:profile).
266			* When the chosen FeatureTree is not found in the database,
267			* the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
268			*
269			* @return mixed
270			* A cdm FeatureTree object.
271			*/
272			function get_structured_description_featureTree() {
273			static $structured_description_featureTree;
274
275	bfb2b81a	Andreas Kohlbecker	if($structured_description_featureTree == NULL) {
276	f19f47fa	Andreas Kohlbecker	$structured_description_featureTree = cdm_ws_get(
277	9dddc68a	Andreas Kohlbecker	CDM_WS_TERMTREE,
278	f19f47fa	Andreas Kohlbecker	variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
279			);
280			if (!$structured_description_featureTree) {
281			$structured_description_featureTree = cdm_ws_get(
282	9dddc68a	Andreas Kohlbecker	CDM_WS_TERMTREE,
283	f19f47fa	Andreas Kohlbecker	UUID_DEFAULT_FEATURETREE
284			);
285	bfb2b81a	Andreas Kohlbecker	}
286	f19f47fa	Andreas Kohlbecker	}
287			return $structured_description_featureTree;
288	bfb2b81a	Andreas Kohlbecker	}
289
290	6657531f	Andreas Kohlbecker
291			/**
292			* @todo Please document this function.
293			* @see http://drupal.org/node/1354
294			*/
295			function set_last_taxon_page_tab($taxonPageTab) {
296			$_SESSION['cdm']['taxon_page_tab'] = $taxonPageTab;
297			}
298
299			/**
300			* @todo Please document this function.
301			* @see http://drupal.org/node/1354
302			*/
303			function get_last_taxon_page_tab() {
304			if (isset($_SESSION['cdm']['taxon_page_tab'])) {
305			return $_SESSION['cdm']['taxon_page_tab'];
306			}
307			else {
308			return FALSE;
309			}
310			}
311
312			/**
313	4a462641	Andreas Kohlbecker	* NOTE: The cdm-library provides a very similar server side function. See
314			* eu.etaxonomy.cdm.model.media.MediaUtils.filterAndOrderMediaRepresentations()
315	6657531f	Andreas Kohlbecker	*
316			* @param object $media
317			* @param array $mimeTypes
318	4fa6f9ba	Andreas Kohlbecker	* an array of mimetypes in their order of preference. e.g:
319			* array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html')
320	6657531f	Andreas Kohlbecker	* @param int $width
321	673929dd	Andreas Kohlbecker	* The width of the optimal image. If null, the method will return the representation with the biggest expansion
322	6657531f	Andreas Kohlbecker	* @param int $height
323	673929dd	Andreas Kohlbecker	* The height of the optimal image. If null, the method will return the representation with the biggest expansion
324	6657531f	Andreas Kohlbecker	*
325			* @return array
326			* An array with preferred media representations or else an empty array.
327			*/
328	5dc25a7d	Andreas Kohlbecker	function cdm_preferred_media_representations($media, array $mimeTypes, $width = NULL, $height = NULL) {
329	6657531f	Andreas Kohlbecker	$prefRepr = array();
330			if (!isset($media->representations[0])) {
331			return $prefRepr;
332			}
333
334			while (count($mimeTypes) > 0) {
335			// getRepresentationByMimeType
336			$mimeType = array_shift($mimeTypes);
337
338			foreach ($media->representations as &$representation) {
339			// If the mimetype is not known, try inferring it.
340			if (!$representation->mimeType) {
341			if (isset($representation->parts[0])) {
342			$representation->mimeType = infer_mime_type($representation->parts[0]->uri);
343			}
344			}
345
346			if ($representation->mimeType == $mimeType) {
347			// Preferred mimetype found -> erase all remaining mimetypes
348			// to end loop.
349			$mimeTypes = array();
350	673929dd	Andreas Kohlbecker	$expansionDeltaSum = 0;
351	275b2642	Andreas Kohlbecker	$valid_parts_cnt = 0;
352	6657531f	Andreas Kohlbecker	// Look for part with the best matching size.
353			foreach ($representation->parts as $part) {
354	4fa6f9ba	Andreas Kohlbecker	if (empty($part->uri)) {
355	275b2642	Andreas Kohlbecker	// skip part if URI is missing
356			continue;
357			}
358			$valid_parts_cnt++;
359	f6408572	Andreas Kohlbecker	$expansionDelta = PHP_INT_MAX; // biggest delta for unknown sizes
360	4fa6f9ba	Andreas Kohlbecker
361			// determine the optimal size
362	6657531f	Andreas Kohlbecker	if (isset($part->width) && isset($part->height)) {
363	673929dd	Andreas Kohlbecker	$expansion = $part->width * $part->height;
364	4fa6f9ba	Andreas Kohlbecker	if ($width != null && $height != null) {
365	673929dd	Andreas Kohlbecker	$optimalExpansion = $height * $width;
366	4fa6f9ba	Andreas Kohlbecker	} else {
367	673929dd	Andreas Kohlbecker	$optimalExpansion = PHP_INT_MAX;
368	4fa6f9ba	Andreas Kohlbecker	}
369			// determine the difference
370	673929dd	Andreas Kohlbecker	$expansionDelta = $expansion > $optimalExpansion ? $expansion - $optimalExpansion : $optimalExpansion - $expansion;
371	6657531f	Andreas Kohlbecker	}
372	673929dd	Andreas Kohlbecker	// sum up the expansionDeltas of all parts contained in the representation
373			$expansionDeltaSum += $expansionDelta;
374	6657531f	Andreas Kohlbecker	}
375	275b2642	Andreas Kohlbecker	if($valid_parts_cnt > 0){
376	673929dd	Andreas Kohlbecker	$expansionDeltaSum = $expansionDeltaSum / $valid_parts_cnt;
377			$prefRepr[$expansionDeltaSum] = $representation;
378	275b2642	Andreas Kohlbecker	}
379	6657531f	Andreas Kohlbecker	}
380			}
381			}
382	4fa6f9ba	Andreas Kohlbecker	// Sort the array so that the smallest key value is the first in the array
383			ksort($prefRepr);
384	6657531f	Andreas Kohlbecker	return $prefRepr;
385			}
386
387			/**
388			* Infers the mime type of a file using the filename extension.
389			*
390			* The filename extension is used to infer the mime type.
391			*
392			* @param string $filepath
393			* The path to the respective file.
394			*
395			* @return string
396			* The mimetype for the file or FALSE if the according mime type could
397			* not be found.
398			*/
399			function infer_mime_type($filepath) {
400			static $mimemap = NULL;
401			if (!$mimemap) {
402			$mimemap = array(
403			'jpg' => 'image/jpeg',
404			'jpeg' => 'image/jpeg',
405			'png' => 'image/png',
406			'gif' => 'image/gif',
407			'giff' => 'image/gif',
408			'tif' => 'image/tif',
409			'tiff' => 'image/tif',
410			'pdf' => 'application/pdf',
411			'html' => 'text/html',
412			'htm' => 'text/html',
413			);
414			}
415			$extension = substr($filepath, strrpos($filepath, '.') + 1);
416			if (isset($mimemap[$extension])) {
417			return $mimemap[$extension];
418			}
419			else {
420			// FIXME remove this hack just return FALSE;
421			return 'text/html';
422			}
423			}
424
425	250f2a96	Andreas Kohlbecker	/**
426			* Formats a mysql datatime as string
427			*
428			* @param $datetime
429			* @param string $format
430			*
431			* @return
432			* the formatted string representation of the $datetime
433			*/
434	ef6a4ce9	Andreas Kohlbecker	function format_datetime($datetime, $format = 'Y-m-d H:i:s', $strip_zeros = true){
435	250f2a96	Andreas Kohlbecker	return date($format, strtotime($datetime));
436			}
437
438	6657531f	Andreas Kohlbecker	/**
439			* Converts an ISO 8601 org.joda.time.Partial to a year.
440			*
441			* The function expects an ISO 8601 time representation of a
442			* org.joda.time.Partial of the form yyyy-MM-dd.
443			*
444			* @param string $partial
445			* ISO 8601 time representation of a org.joda.time.Partial.
446			*
447			* @return string
448			* Returns the year. In case the year is unknown (= ????), it returns NULL.
449			*/
450			function partialToYear($partial) {
451			if (is_string($partial)) {
452	d0e8e73c	Andreas Kohlbecker	$year = drupal_substr($partial, 0, 4);
453	6657531f	Andreas Kohlbecker	if (preg_match("/[0-9][0-9][0-9][0-9]/", $year)) {
454			return $year;
455			}
456			}
457	c7f92453	Andreas Kohlbecker	return '';
458	6657531f	Andreas Kohlbecker	}
459
460			/**
461			* Converts an ISO 8601 org.joda.time.Partial to a month.
462			*
463			* This function expects an ISO 8601 time representation of a
464			* org.joda.time.Partial of the form yyyy-MM-dd.
465			* In case the month is unknown (= ???) NULL is returned.
466			*
467			* @param string $partial
468			* ISO 8601 time representation of a org.joda.time.Partial.
469			*
470			* @return string
471			* A month.
472			*/
473			function partialToMonth($partial) {
474			if (is_string($partial)) {
475	d0e8e73c	Andreas Kohlbecker	$month = drupal_substr($partial, 5, 2);
476	6657531f	Andreas Kohlbecker	if (preg_match("/[0-9][0-9]/", $month)) {
477			return $month;
478			}
479			}
480	c7f92453	Andreas Kohlbecker	return '';
481	6657531f	Andreas Kohlbecker	}
482
483			/**
484			* Converts an ISO 8601 org.joda.time.Partial to a day.
485			*
486			* This function expects an ISO 8601 time representation of a
487			* org.joda.time.Partial of the form yyyy-MM-dd and returns the day as string.
488			* In case the day is unknown (= ???) NULL is returned.
489			*
490			* @param string $partial
491			* ISO 8601 time representation of a org.joda.time.Partial.
492			*
493			* @return string
494			* A day.
495			*/
496			function partialToDay($partial) {
497			if (is_string($partial)) {
498	d0e8e73c	Andreas Kohlbecker	$day = drupal_substr($partial, 8, 2);
499	6657531f	Andreas Kohlbecker	if (preg_match("/[0-9][0-9]/", $day)) {
500			return $day;
501			}
502			}
503	c7f92453	Andreas Kohlbecker	return '';
504	6657531f	Andreas Kohlbecker	}
505
506			/**
507			* Converts an ISO 8601 org.joda.time.Partial to YYYY-MM-DD.
508			*
509			* This function expects an ISO 8601 time representations of a
510			* org.joda.time.Partial of the form yyyy-MM-dd and returns
511			* four digit year, month and day with dashes:
512			* YYYY-MM-DD eg: "2012-06-30", "1956-00-00"
513			*
514			* The partial may contain question marks eg: "1973-??-??",
515			* these are turned in to '00' or are stripped depending of the $stripZeros
516			* parameter.
517			*
518			* @param string $partial
519			* org.joda.time.Partial.
520			* @param bool $stripZeros
521			* If set to TRUE the zero (00) month and days will be hidden:
522			* eg 1956-00-00 becomes 1956. The default is TRUE.
523	fe2edf33	Andreas Kohlbecker	* @param string @format
524			* Can ve used to specify the format of the date string, currently the following format strings are supported
525			* - "YYYY": Year only
526			* - "YYYY-MM-DD": this is the default
527	6657531f	Andreas Kohlbecker	*
528			* @return string
529			* YYYY-MM-DD formatted year, month, day.
530			*/
531	fe2edf33	Andreas Kohlbecker	function partialToDate($partial, $stripZeros = TRUE, $format= "YYYY-MM-DD") {
532
533			$y = NULL; $m = NULL; $d = NULL;
534
535	8dfe695c	Andreas Kohlbecker	if(strpos($format, 'YY') !== FALSE){
536	fe2edf33	Andreas Kohlbecker	$y = partialToYear($partial);
537			}
538	8dfe695c	Andreas Kohlbecker	if(strpos($format, 'MM') !== FALSE){
539	fe2edf33	Andreas Kohlbecker	$m = partialToMonth($partial);
540			}
541	8dfe695c	Andreas Kohlbecker	if(strpos($format, 'DD') !== FALSE){
542	fe2edf33	Andreas Kohlbecker	$d = partialToDay($partial);
543			}
544	6657531f	Andreas Kohlbecker
545	ef6a4ce9	Andreas Kohlbecker	$y = $y ? $y : '0000';
546	6657531f	Andreas Kohlbecker	$m = $m ? $m : '00';
547			$d = $d ? $d : '00';
548
549			$date = '';
550
551	ef6a4ce9	Andreas Kohlbecker	if ($y == '0000' && $stripZeros && $m == '00' && $d == '00') {
552	c7f92453	Andreas Kohlbecker	return '';
553	6657531f	Andreas Kohlbecker	}
554			else {
555			$date = $y;
556			}
557
558	ef6a4ce9	Andreas Kohlbecker	if ($m == '00' && $stripZeros && $d == '00') {
559	6657531f	Andreas Kohlbecker	return $date;
560			}
561			else {
562			$date .= "-" . $m;
563			}
564
565			if ($d == '00' && $stripZeros) {
566			return $date;
567			}
568			else {
569			$date .= "-" . $d;
570			}
571			return $date;
572			}
573
574			/**
575			* Converts a time period to a string.
576			*
577			* See also partialToDate($partial, $stripZeros).
578			*
579			* @param object $period
580			* An JodaTime org.joda.time.Period object.
581			* @param bool $stripZeros
582			* If set to True, the zero (00) month and days will be hidden:
583			* eg 1956-00-00 becomes 1956. The default is TRUE.
584	fe2edf33	Andreas Kohlbecker	* @param string @format
585			* Can ve used to specify the format of the date string, currently the following format strings are supported
586			* - "YYYY": Year only
587			* - "YYYY-MM-DD": this is the default
588	6657531f	Andreas Kohlbecker	*
589			* @return string
590			* Returns a date in the form of a string.
591			*/
592	fe2edf33	Andreas Kohlbecker	function timePeriodToString($period, $stripZeros = TRUE, $format = "YYYY-MM-DD") {
593	6657531f	Andreas Kohlbecker	$dateString = '';
594	0a288588	Andreas Kohlbecker	if($period->freeText){
595			$dateString = $period->freeText;
596			} else {
597			if ($period->start) {
598			$dateString = partialToDate($period->start, $stripZeros, $format);
599			}
600			if ($period->end) {
601	c0223d83	Andreas Kohlbecker	$end_str = partialToDate($period->end, $stripZeros, $format);
602	d0e8e73c	Andreas Kohlbecker	$dateString .= ($dateString && $end_str ? ' ' . t('to') . ' ' : '') . $end_str;
603	0a288588	Andreas Kohlbecker	}
604	6657531f	Andreas Kohlbecker	}
605			return $dateString;
606			}
607	fe2edf33	Andreas Kohlbecker
608	c2486c6b	Andreas Kohlbecker	/**
609			* returns the earliest date available in the $period in a normalized
610			* form suitable for sorting, e.g.:
611			*
612			* - 1956-00-00
613			* - 0000-00-00
614			* - 1957-03-00
615			*
616			* that is either the start date is returned if set otherwise the
617			* end date
618			*
619			* @param $period
620			* An JodaTime org.joda.time.Period object.
621			* @return string normalized form of the date
622			* suitable for sorting
623			*/
624			function timePeriodAsOrderKey($period) {
625			$dateString = '';
626			if ($period->start) {
627			$dateString = partialToDate($period->start, false);
628			}
629			if ($period->end) {
630			$dateString .= partialToDate($period->end, false);
631			}
632			return $dateString;
633			}
634	6657531f	Andreas Kohlbecker
635			/**
636	42f2e1e0	Andreas Kohlbecker	* Composes a absolute CDM web service URI with parameters and querystring.
637	6657531f	Andreas Kohlbecker	*
638			* @param string $uri_pattern
639			* String with place holders ($0, $1, ..) that should be replaced by the
640			* according element of the $pathParameters array.
641			* @param array $pathParameters
642			* An array of path elements, or a single element.
643			* @param string $query
644			* A query string to append to the URL.
645			*
646			* @return string
647			* A complete URL with parameters to a CDM webservice.
648			*/
649			function cdm_compose_url($uri_pattern, $pathParameters = array(), $query = NULL) {
650			if (empty($pathParameters)) {
651			$pathParameters = array();
652			}
653
654			// (1)
655			// Substitute all place holders ($0, $1, ..) in the $uri_pattern by the
656			// according element of the $pathParameters array.
657			static $helperArray = array();
658			if (isset($pathParameters) && !is_array($pathParameters)) {
659			$helperArray[0] = $pathParameters;
660			$pathParameters = $helperArray;
661			}
662
663			$i = 0;
664			while (strpos($uri_pattern, "$" . $i) !== FALSE) {
665			if (count($pathParameters) <= $i) {
666	7cc085da	Andreas Kohlbecker	drupal_set_message(
667			t('cdm_compose_url(): missing pathParameter @index for !uri_pattern',
668	5213125b	Andreas Kohlbecker	array('@index' => $i, '!uri_pattern' => $uri_pattern )),
669	7cc085da	Andreas Kohlbecker	'error');
670	6657531f	Andreas Kohlbecker	break;
671			}
672			$uri_pattern = str_replace("$" . $i, rawurlencode($pathParameters[$i]), $uri_pattern);
673			++$i;
674			}
675
676			// (2)
677			// Append all remaining element of the $pathParameters array as path
678			// elements.
679			if (count($pathParameters) > $i) {
680			// Strip trailing slashes.
681			if (strrchr($uri_pattern, '/') == strlen($uri_pattern)) {
682			$uri_pattern = substr($uri_pattern, 0, strlen($uri_pattern) - 1);
683			}
684			while (count($pathParameters) > $i) {
685			$uri_pattern .= '/' . rawurlencode($pathParameters[$i]);
686			++$i;
687			}
688			}
689
690			// (3)
691			// Append the query string supplied by $query.
692			if (isset($query)) {
693			$uri_pattern .= (strpos($uri_pattern, '?') !== FALSE ? '&' : '?') . $query;
694			}
695
696			$path = $uri_pattern;
697
698			$uri = variable_get('cdm_webservice_url', '') . $path;
699			return $uri;
700			}
701
702			/**
703	5ba85170	Andreas Kohlbecker	* @todo wouldn't it more elegant and secure to only pass a uuid and additional function parameters
704			* together with a theme name to such a proxy function?
705			* Well this would not be covering all use cases but maybe all which involve AHAH.
706			* Maybe we want to have two different proxy functions, one with theming and one without?
707	088448e1	Andreas Kohlbecker	*
708			* @param string $uri
709			* A URI to a CDM Rest service from which to retrieve an object
710	f1f05758	Andreas Kohlbecker	* @param string\|null $hook
711			* (optional) The hook name to which the retrieved object should be passed.
712			* Hooks can either be a theme_hook() or compose_hook() implementation
713			* 'theme' hook functions return a string whereas 'compose' hooks are returning render arrays
714	088448e1	Andreas Kohlbecker	* suitable for drupal_render()
715			*
716	6657531f	Andreas Kohlbecker	* @todo Please document this function.
717			* @see http://drupal.org/node/1354
718			*/
719	f1f05758	Andreas Kohlbecker	function proxy_content($uri, $hook = NULL) {
720	2ebf0428	Andreas Kohlbecker
721	6657531f	Andreas Kohlbecker	$args = func_get_args();
722	104dde69	Andreas Kohlbecker	$do_gzip = function_exists('gzencode');
723	6657531f	Andreas Kohlbecker	$uriEncoded = array_shift($args);
724			$uri = urldecode($uriEncoded);
725	f1f05758	Andreas Kohlbecker	$hook = array_shift($args);
726	2ebf0428	Andreas Kohlbecker	$request_method = strtoupper($_SERVER["REQUEST_METHOD"]);
727
728	68ab2885	Andreas Kohlbecker	$post_data = null;
729
730	2ebf0428	Andreas Kohlbecker	if ($request_method == "POST" \|\| $request_method == "PUT") {
731			// read response body via inputstream module
732			$post_data = file_get_contents("php://input");
733			}
734	6657531f	Andreas Kohlbecker
735			// Find and deserialize arrays.
736			foreach ($args as &$arg) {
737			// FIXME use regex to find serialized arrays.
738	2ebf0428	Andreas Kohlbecker	// or should we accept json instead of php serializations?
739	6657531f	Andreas Kohlbecker	if (strpos($arg, "a:") === 0) {
740			$arg = unserialize($arg);
741			}
742			}
743
744	2ebf0428	Andreas Kohlbecker	// In all these cases perform a simple get request.
745			// TODO reconsider caching logic in this function.
746	6657531f	Andreas Kohlbecker
747	2ebf0428	Andreas Kohlbecker	if (empty($hook)) {
748			// simply return the webservice response
749			// Print out JSON, the cache cannot be used since it contains objects.
750			$http_response = cdm_http_request($uri, $request_method, $post_data);
751			if (isset($http_response->headers)) {
752			foreach ($http_response->headers as $hname => $hvalue) {
753			drupal_add_http_header($hname, $hvalue);
754	088448e1	Andreas Kohlbecker	}
755	2ebf0428	Andreas Kohlbecker	}
756			if (isset($http_response->data)) {
757			print $http_response->data;
758			flush();
759			}
760			exit(); // leave drupal here
761			} else {
762			// $hook has been supplied
763	34a67c62	Andreas Kohlbecker	// handle $hook either as compose or theme hook
764			// pass through theme or compose hook
765	0af3ce28	Andreas Kohlbecker	// compose hooks can be called without data, therefore
766			// passing the $uri in this case is not always a requirement
767	2ebf0428	Andreas Kohlbecker
768	0af3ce28	Andreas Kohlbecker	if($uri && $uri != 'NULL') {
769	2ebf0428	Andreas Kohlbecker	// do a security check since the $uri will be passed
770			// as absolute URI to cdm_ws_get()
771	0af3ce28	Andreas Kohlbecker	if (!_is_cdm_ws_uri($uri)) {
772			drupal_set_message(
773			'Invalid call of proxy_content() with callback parameter \'' . $hook . '\' and URI:' . $uri,
774			'error'
775			);
776			return '';
777			}
778	088448e1	Andreas Kohlbecker
779	0af3ce28	Andreas Kohlbecker	$obj = cdm_ws_get($uri, NULL, $post_data, $request_method, TRUE);
780			} else {
781			$obj = NULL;
782			}
783	2fe78f3c	Andreas Kohlbecker
784	2ebf0428	Andreas Kohlbecker	$reponse_data = NULL;
785	5b3d713e	Andreas Kohlbecker
786	2ebf0428	Andreas Kohlbecker	if (function_exists('compose_' . $hook)){
787			// call compose hook
788
789			$elements = call_user_func('compose_' . $hook, $obj);
790			// pass the render array to drupal_render()
791			$reponse_data = drupal_render($elements);
792			} else {
793			// call theme hook
794
795			// TODO use theme registry to get the registered hook info and
796			// use these defaults
797			switch($hook) {
798			case 'cdm_taxontree':
799			$variables = array(
800	9c9d11f7	Andreas Kohlbecker	'tree' => $obj,
801			'filterIncludes' => isset($args[0]) ? $args[0] : NULL,
802			'show_filter_switch' => isset($args[1]) ? $args[1] : FALSE,
803			'tree_node_callback' => isset($args[2]) ? $args[2] : FALSE,
804			'element_name'=> isset($args[3]) ? $args[3] : FALSE,
805			);
806	2ebf0428	Andreas Kohlbecker	$reponse_data = theme($hook, $variables);
807			break;
808
809	9c9d11f7	Andreas Kohlbecker	case 'cdm_list_of_taxa':
810			$variables = array(
811			'records' => $obj,
812			'freetextSearchResults' => isset($args[0]) ? $args[0] : array(),
813			'show_classification' => isset($args[1]) ? $args[1] : FALSE);
814			$reponse_data = theme($hook, $variables);
815			break;
816
817	2ebf0428	Andreas Kohlbecker	case 'cdm_media_caption':
818	cf4b9055	Andreas Kohlbecker	$variables = $arg;
819			$variables['media'] = $obj;
820
821	2ebf0428	Andreas Kohlbecker	$reponse_data = theme($hook, $variables);
822			break;
823
824			default:
825			drupal_set_message(t(
826	9c9d11f7	Andreas Kohlbecker	'Theme !theme is not yet supported by the function !function.', array(
827	2ebf0428	Andreas Kohlbecker	'!theme' => $hook,
828			'!function' => __FUNCTION__,
829			)), 'error');
830			break;
831			} // END of theme hook switch
832			} // END of tread as theme hook
833
834
835			if($do_gzip){
836			$reponse_data = gzencode($reponse_data, 2, FORCE_GZIP);
837			drupal_add_http_header('Content-Encoding', 'gzip');
838			}
839			drupal_add_http_header('Content-Type', 'text/html; charset=utf-8');
840			drupal_add_http_header('Content-Length', strlen($reponse_data));
841
842			print $reponse_data;
843			} // END of handle $hook either as compose ot theme hook
844	5b3d713e	Andreas Kohlbecker
845	6657531f	Andreas Kohlbecker	}
846
847			/**
848			* @todo Please document this function.
849			* @see http://drupal.org/node/1354
850			*/
851			function setvalue_session() {
852			if ($_REQUEST['var'] && strlen($_REQUEST['var']) > 4) {
853	0af3ce28	Andreas Kohlbecker	$var_keys = substr($_REQUEST['var'], 1, strlen($_REQUEST['var']) - 2);
854			$var_keys = explode('][', $var_keys);
855	6657531f	Andreas Kohlbecker	}
856			else {
857			return;
858			}
859	1d69a96c	Andreas Kohlbecker	$val = isset($_REQUEST['val']) ? $_REQUEST['val'] : NULL;
860	6657531f	Andreas Kohlbecker
861			// Prevent from malicous tags.
862			$val = strip_tags($val);
863
864	0af3ce28	Andreas Kohlbecker	$session_var = &$_SESSION;
865			//$i = 0;
866			foreach ($var_keys as $key) {
867			// $hasMoreKeys = ++$i < count($session);
868			if (!isset($session_var[$key]) \|\| !is_array($session_var[$key])) {
869			$session_var[$key] = array();
870	6657531f	Andreas Kohlbecker	}
871	0af3ce28	Andreas Kohlbecker	$session_var = &$session_var[$key];
872	6657531f	Andreas Kohlbecker	}
873	0af3ce28	Andreas Kohlbecker	$session_var = $val;
874	6657531f	Andreas Kohlbecker	if (isset($_REQUEST['destination'])) {
875			drupal_goto($_REQUEST['destination']);
876			}
877			}
878
879			/**
880			* @todo Please document this function.
881			* @see http://drupal.org/node/1354
882			*/
883			function uri_uriByProxy($uri, $theme = FALSE) {
884			// usage: url('cdm_api/proxy/'.urlencode($content_url)."/$theme");)
885			return url('cdm_api/proxy/' . urlencode($uri) . (isset($theme) ? "/$theme" : ''));
886			}
887
888			/**
889	42f2e1e0	Andreas Kohlbecker	* Composes the the absolute REST service URI to the annotations pager
890			* for the given CDM entity.
891			*
892			* NOTE: Not all CDM Base types are yet supported.
893			*
894	0e617798	Andreas Kohlbecker	* @param $cdm_entity
895	42f2e1e0	Andreas Kohlbecker	* The CDM entity to construct the annotations pager uri for
896	6657531f	Andreas Kohlbecker	*/
897	0e617798	Andreas Kohlbecker	function cdm_compose_annotations_uri($cdm_entity) {
898
899			$cdm_entity_type = $cdm_entity->class;
900
901			if($cdm_entity_type == 'DerivedUnitFacade'){
902			// TODO we may want to implement a derivedUnitFacade/{uuid}/annotations service and use that instead
903			$cdm_entity_type = $cdm_entity->fieldUnitEntityReference->type;
904			$cdm_entity_uuid = $cdm_entity->fieldUnitEntityReference->uuid;
905	991ae630	Andreas Kohlbecker	} elseif ($cdm_entity_type == 'TypedEntityReference'){
906			$cdm_entity_type = $cdm_entity->type;
907			$cdm_entity_uuid = $cdm_entity->uuid;
908	0e617798	Andreas Kohlbecker	} else {
909			if (isset($cdm_entity->uuid)) {
910			$cdm_entity_uuid = $cdm_entity->uuid;
911			}
912			}
913	afe99f4d	Andreas Kohlbecker
914	0e617798	Andreas Kohlbecker	if(!$cdm_entity_uuid){
915			// silently give up
916	6657531f	Andreas Kohlbecker	return;
917			}
918
919	0e617798	Andreas Kohlbecker	$ws_base_uri = cdm_ws_base_uri($cdm_entity_type);
920	afe99f4d	Andreas Kohlbecker
921			if($ws_base_uri === null){
922	0e617798	Andreas Kohlbecker	trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdm_entity_type), E_USER_ERROR);
923	afe99f4d	Andreas Kohlbecker	}
924			return cdm_compose_url($ws_base_uri, array(
925	0e617798	Andreas Kohlbecker	$cdm_entity_uuid,
926	afe99f4d	Andreas Kohlbecker	'annotations',
927			));
928			}
929
930			/**
931			* Provides the base URI of the cdm REST service responsible for the passed simple name
932			* of a CDM java class. For example 'TaxonName' is the simple name of 'eu.etaxonomy.cdm.model.name.TaxonName'
933			*
934			* @param $cdm_type_simple
935			* simple name of a CDM java class
936			* @return null\|string
937			*/
938			function cdm_ws_base_uri($cdm_type_simple)
939			{
940	6657531f	Andreas Kohlbecker	$ws_base_uri = NULL;
941	afe99f4d	Andreas Kohlbecker	switch ($cdm_type_simple) {
942	178d1ae6	Andreas Kohlbecker
943			case 'TaxonNode':
944	64cfdac1	Andreas Kohlbecker	case 'TaxonNodeDto':
945	178d1ae6	Andreas Kohlbecker	$ws_base_uri = CDM_WS_TAXONNODE;
946	6657531f	Andreas Kohlbecker	case 'TaxonBase':
947			case 'Taxon':
948			case 'Synonym':
949			$ws_base_uri = CDM_WS_TAXON;
950			break;
951
952	b20f6a5f	Andreas Kohlbecker	case 'TaxonName':
953	6657531f	Andreas Kohlbecker	$ws_base_uri = CDM_WS_NAME;
954			break;
955
956			case 'Media':
957			$ws_base_uri = CDM_WS_MEDIA;
958			break;
959
960			case 'Reference':
961			$ws_base_uri = CDM_WS_REFERENCE;
962			break;
963
964	5213125b	Andreas Kohlbecker	case 'Registration':
965			$ws_base_uri = CDM_WS_REFERENCE;
966			break;
967
968			case 'FieldUnit':
969			case 'DerivedUnit':
970			case 'DnaSample':
971			case 'MediaSpecimen':
972			$ws_base_uri = CDM_WS_OCCURRENCE;
973			break;
974
975			case 'Amplification':
976			case 'DerivationEvent':
977			case 'DeterminationEvent':
978			case 'GatheringEvent':
979			case 'MaterialOrMethodEvent':
980			case 'SingleRead':
981			$ws_base_uri = CDM_WS_EVENTBASE;
982			break;
983
984	6657531f	Andreas Kohlbecker	case 'Distribution':
985			case 'TextData':
986			case 'TaxonInteraction':
987			case 'QuantitativeData':
988			case 'IndividualsAssociation':
989			case 'CommonTaxonName':
990			case 'CategoricalData':
991			$ws_base_uri = CDM_WS_DESCRIPTIONELEMENT;
992			break;
993
994	e2617c7e	Andreas Kohlbecker	case 'Person':
995			case 'Team':
996			case 'AgentBase':
997			$ws_base_uri = CDM_WS_AGENT;
998			break;
999
1000	6657531f	Andreas Kohlbecker	case 'PolytomousKey':
1001			case 'MediaKey':
1002			case 'MultiAccessKey':
1003	afe99f4d	Andreas Kohlbecker	$ws_base_uri = $cdm_type_simple;
1004	6657531f	Andreas Kohlbecker	$ws_base_uri{0} = strtolower($ws_base_uri{0});
1005			break;
1006
1007	2d95e99f	Andreas Kohlbecker	case 'TextualTypeDesignation':
1008			case 'SpecimenTypeDesignation':
1009			case 'NameTypeDesignation':
1010			$ws_base_uri = CDM_WS_TYPEDESIGNATION;
1011			break;
1012	6657531f	Andreas Kohlbecker	default:
1013	afe99f4d	Andreas Kohlbecker	$ws_base_uri = null;
1014	5213125b	Andreas Kohlbecker	drupal_set_message(
1015			t('cdm_ws_base_uri() - cdm type name "@cdm_type_simple" unsupported',
1016			array('@cdm_type_simple' => $cdm_type_simple )),
1017			'error');
1018	6657531f	Andreas Kohlbecker	}
1019	afe99f4d	Andreas Kohlbecker	return $ws_base_uri;
1020	6657531f	Andreas Kohlbecker	}
1021
1022			/**
1023			* Enter description here...
1024			*
1025	a6c4c53c	Andreas Kohlbecker	* @param string $resource_uri
1026			* @param int $page_size
1027	b5dca1e2	Andreas Kohlbecker	* The maximum number of entities returned per page.
1028			* The default page size as configured in the cdm server
1029			* will be used if set to NULL
1030	6657531f	Andreas Kohlbecker	* to return all entities in a single page).
1031	a6c4c53c	Andreas Kohlbecker	* @param int $page_index
1032	6657531f	Andreas Kohlbecker	* The number of the page to be returned, the first page has the
1033	a6c4c53c	Andreas Kohlbecker	* page_index = 0
1034	2ebf0428	Andreas Kohlbecker	* @param array $query
1035			* A array holding the HTTP request query parameters for the request
1036			* @param string $method
1037			* The HTTP method to use, valid values are "GET" or "POST"
1038	a6c4c53c	Andreas Kohlbecker	* @param bool $absolute_uri
1039	42f2e1e0	Andreas Kohlbecker	* TRUE when the URL should be treated as absolute URL.
1040	2ebf0428	Andreas Kohlbecker	*
1041	fb308159	Andreas Kohlbecker	* @return object
1042			* A CDM Pager object
1043	6657531f	Andreas Kohlbecker	*
1044			*/
1045	a6c4c53c	Andreas Kohlbecker	function cdm_ws_page($resource_uri, $page_size, $page_index, array $query = array(), $method = 'GET', $absolute_uri = FALSE) {
1046
1047			$query['page_index'] = $page_index;
1048			$query['page_size'] = $page_size;
1049
1050			$pager = cdm_ws_get($resource_uri, NULL, queryString($query), $method, $absolute_uri);
1051			if(is_array($pager)){
1052	3a81b245	Andreas Kohlbecker	trigger_error("Expecting web service to return pager objects but received an array:<br/>" . $resource_uri . '?' . queryString($query) . '<br/>Wrapping response in pager to recover from error.', E_USER_WARNING);
1053	a6c4c53c	Andreas Kohlbecker	$records = $pager;
1054			$pager = new stdClass();
1055			$pager->records = $records;
1056			$pager->count = count($records);
1057			$pager->pageSize = $pager->count;
1058			$pager->nextIndex = null;
1059			}
1060			return $pager;
1061	6657531f	Andreas Kohlbecker	}
1062
1063	fb308159	Andreas Kohlbecker
1064			/**
1065			* Sends a http GET request to the generic page method which allows for filtering entities by Restrictions.
1066			*
1067			* @param $cdm_entity_type
1068	e2617c7e	Andreas Kohlbecker	* @param $class_restriction
1069			* Optional param to narrow down polymorph types to a specific type.
1070	fb308159	Andreas Kohlbecker	* @param array $restrictions
1071			* An array of Restriction objects
1072			* @param array $init_strategy
1073			* The init strategy to initialize the entity beans while being loaded from the
1074			* persistent storage by the cdm
1075			* @param int $page_size
1076			* The maximum number of entities returned per page.
1077			* The default page size as configured in the cdm server
1078			* will be used if set to NULL
1079			* to return all entities in a single page).
1080			* @param int $page_index
1081			* The number of the page to be returned, the first page has the
1082			* pageNumber = 0
1083			*
1084			* @return object
1085			* A CDM Pager object
1086			*/
1087	e2617c7e	Andreas Kohlbecker	function cdm_ws_page_by_restriction($cdm_entity_type, $class_restriction, array $restrictions, array $init_strategy, $page_size, $page_index) {
1088	fb308159	Andreas Kohlbecker
1089			$restrictions_json = array(); // json_encode($restrictions);
1090			foreach ($restrictions as $restr){
1091			$restrictions_json[] = json_encode($restr);
1092			}
1093	e2617c7e	Andreas Kohlbecker	$filter_parameters = [
1094			'restriction' => $restrictions_json,
1095			'initStrategy' => $init_strategy
1096			];
1097			if($class_restriction){
1098			$filter_parameters['class'] = $class_restriction;
1099			}
1100
1101	fb308159	Andreas Kohlbecker	return cdm_ws_page(
1102			'portal/' . cdm_ws_base_uri($cdm_entity_type),
1103			$page_size,
1104			$page_index,
1105	e2617c7e	Andreas Kohlbecker	$filter_parameters,
1106			"GET"
1107	fb308159	Andreas Kohlbecker	);
1108			}
1109
1110	b5dca1e2	Andreas Kohlbecker	/**
1111	fb308159	Andreas Kohlbecker	* Fetches all entities returned by the the generic page method for the Restrictions applied as filter.
1112			*
1113			* @param $cdm_entity_type
1114	e2617c7e	Andreas Kohlbecker	* @param $class_restriction
1115			* Optional param to narrow down polymorph types to a specific type.
1116	fb308159	Andreas Kohlbecker	* @param array $restrictions
1117			* An array of Restriction objects
1118			* @param array $init_strategy
1119			* The init strategy to initialize the entity beans while being loaded from the
1120			* persistent storage by the cdm
1121			*
1122			* @return array
1123			* A array of CDM entities
1124			*/
1125	e2617c7e	Andreas Kohlbecker	function cdm_ws_fetch_all_by_restriction($cdm_entity_type, $class_restriction, array $restrictions, array $init_strategy){
1126	fb308159	Andreas Kohlbecker	$page_index = 0;
1127			// using a bigger page size to avoid to many multiple requests
1128			$page_size = 500;
1129			$entities = array();
1130
1131			while ($page_index !== FALSE && $page_index < 1){
1132	e2617c7e	Andreas Kohlbecker	$pager = cdm_ws_page_by_restriction($cdm_entity_type, $class_restriction, $restrictions, $init_strategy, $page_size, $page_index);
1133	fb308159	Andreas Kohlbecker	if(isset($pager->records) && is_array($pager->records)) {
1134			$entities = array_merge($entities, $pager->records);
1135			if(!empty($pager->nextIndex)){
1136			$page_index = $pager->nextIndex;
1137			} else {
1138			$page_index = FALSE;
1139			}
1140			} else {
1141			$page_index = FALSE;
1142			}
1143			}
1144			return $entities;
1145			}
1146
1147
1148			/**
1149	b5dca1e2	Andreas Kohlbecker	* Fetches all entities from the given REST endpoint using the pager mechanism.
1150			*
1151			* @param string $resourceURI
1152	2ebf0428	Andreas Kohlbecker	* @param array $query
1153			* A array holding the HTTP request query parameters for the request
1154			* @param string $method
1155			* The HTTP method to use, valid values are "GET" or "POST";
1156	42f2e1e0	Andreas Kohlbecker	* @param bool $absoluteURI
1157			* TRUE when the URL should be treated as absolute URL.
1158	b5dca1e2	Andreas Kohlbecker	*
1159			* @return array
1160			* A list of CDM entitites
1161			*
1162			*/
1163	2ebf0428	Andreas Kohlbecker	function cdm_ws_fetch_all($resourceURI, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
1164	b5dca1e2	Andreas Kohlbecker	$page_index = 0;
1165	0b6d2193	Andreas Kohlbecker	// using a bigger page size to avoid too many multiple requests
1166	f9da0eb9	Andreas Kohlbecker	$page_size = 500;
1167	0b6d2193	Andreas Kohlbecker	$entities = [];
1168	b5dca1e2	Andreas Kohlbecker
1169			while ($page_index !== FALSE){
1170	2ebf0428	Andreas Kohlbecker	$pager = cdm_ws_page($resourceURI, $page_size, $page_index, $query, $method, $absoluteURI);
1171	b5dca1e2	Andreas Kohlbecker	if(isset($pager->records) && is_array($pager->records)) {
1172	dc66315d	Andreas Kohlbecker	$entities = array_merge($entities, $pager->records);
1173	b5dca1e2	Andreas Kohlbecker	if(!empty($pager->nextIndex)){
1174			$page_index = $pager->nextIndex;
1175			} else {
1176			$page_index = FALSE;
1177			}
1178			} else {
1179			$page_index = FALSE;
1180			}
1181			}
1182			return $entities;
1183			}
1184
1185	6657531f	Andreas Kohlbecker	/*
1186			function cdm_ws_taxonomy_compose_resourcePath($path = NULL){
1187			$viewrank = _cdm_taxonomy_compose_viewrank();
1188			return CDM_WS_PORTAL_TAXONOMY . '/' . ($viewrank ? $viewrank : '' ) . ($path
1189			? '/' . $path : '') ;
1190			}
1191			*/
1192
1193			/**
1194			* @todo Enter description here...
1195			*
1196	50172c55	Andreas Kohlbecker	* @param string $taxon_uuid
1197			* The UUID of a cdm taxon instance
1198			* @param string $ignore_rank_limit
1199			* Whether to ignore the variable 'taxontree_ranklimit' set by admin in the settings
1200	6657531f	Andreas Kohlbecker	*
1201	aaa81689	Andreas Kohlbecker	* @return string
1202			* A cdm REST service URL path to a Classification
1203	6657531f	Andreas Kohlbecker	*/
1204	50172c55	Andreas Kohlbecker	function cdm_compose_taxonomy_root_level_path($taxon_uuid = FALSE, $ignore_rank_limit = FALSE) {
1205
1206	7663cd0b	Andreas Kohlbecker	$view_uuid = get_current_classification_uuid();
1207	50172c55	Andreas Kohlbecker	$rank_uuid = NULL;
1208			if (!$ignore_rank_limit) {
1209	aaa81689	Andreas Kohlbecker	$rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1210	50172c55	Andreas Kohlbecker	}
1211	6657531f	Andreas Kohlbecker
1212	50172c55	Andreas Kohlbecker	if (!empty($taxon_uuid)) {
1213	6657531f	Andreas Kohlbecker	return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
1214	50172c55	Andreas Kohlbecker	$view_uuid,
1215			$taxon_uuid,
1216	6657531f	Andreas Kohlbecker	));
1217			}
1218			else {
1219	aaa81689	Andreas Kohlbecker	if (is_uuid($rank_uuid)) {
1220	6657531f	Andreas Kohlbecker	return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_AT_RANK, array(
1221	50172c55	Andreas Kohlbecker	$view_uuid,
1222			$rank_uuid,
1223	6657531f	Andreas Kohlbecker	));
1224			}
1225			else {
1226	50172c55	Andreas Kohlbecker	return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES, array(
1227			$view_uuid,
1228	6657531f	Andreas Kohlbecker	));
1229			}
1230			}
1231			}
1232
1233			/**
1234	50172c55	Andreas Kohlbecker	* Retrieves from the cdm web service with the first level of childnodes of a classification.
1235			*
1236			* The level is either the real root level ot it is a lover level if a rank limit has been set.
1237			* (@see cdm_compose_taxonomy_root_level_path() for more on the rank limit).
1238			*
1239			* Operates in two modes depending on whether the parameter
1240			* $taxon_uuid is set or NULL.
1241			*
1242			* A) $taxon_uuid = NULL:
1243			* 1. retrieve the Classification for the uuid set in the $_SESSION['cdm']['taxonomictree_uuid']
1244			* 2. otherwise return the default classification as defined by the admin via the settings
1245			*
1246			* b) $taxon_uuid is set:
1247			* return the classification to whcih the taxon belongs to.
1248			*
1249			* @param UUID $taxon_uuid
1250			* The UUID of a cdm taxon instance
1251	6657531f	Andreas Kohlbecker	*/
1252	50172c55	Andreas Kohlbecker	function cdm_ws_taxonomy_root_level($taxon_uuid = NULL) {
1253	6657531f	Andreas Kohlbecker
1254	50172c55	Andreas Kohlbecker	$response = NULL;
1255	6657531f	Andreas Kohlbecker
1256	50172c55	Andreas Kohlbecker	// 1st try
1257	2ebf0428	Andreas Kohlbecker	$response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid), NULL, NULL, 'GET', TRUE);
1258	50172c55	Andreas Kohlbecker
1259			if ($response == NULL) {
1260			// 2dn try by ignoring the rank limit
1261	2ebf0428	Andreas Kohlbecker	$response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid, TRUE), NULL, NULL, 'GET', TRUE);
1262	6657531f	Andreas Kohlbecker	}
1263	50172c55	Andreas Kohlbecker
1264			if ($response == NULL) {
1265			// 3rd try, last fallback:
1266			// return the default classification
1267			if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
1268			// Delete the session value and try again with the default.
1269			unset($_SESSION['cdm']['taxonomictree_uuid']);
1270	795fcdb3	Andreas Kohlbecker	drupal_set_message("Could not find a valid classification, falling back to the default classification.", 'warning');
1271	50172c55	Andreas Kohlbecker	return cdm_ws_taxonomy_root_level($taxon_uuid);
1272			}
1273			else {
1274			// Check if taxonomictree_uuid is valid.
1275	a50c8468	Andreas Kohlbecker	// expecting an array of taxonNodes,
1276			// empty classifications are ok so no warning in this case!
1277	2ebf0428	Andreas Kohlbecker	$test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
1278	a50c8468	Andreas Kohlbecker	if (!is_array($test)) {
1279	50172c55	Andreas Kohlbecker	// The default set by the admin seems to be invalid or is not even set.
1280			drupal_set_message(_no_classfication_uuid_message(), 'warning');
1281			}
1282	a50c8468	Andreas Kohlbecker	if (count($test) == 0) {
1283			// The default set by the admin seems to be invalid or is not even set.
1284			drupal_set_message("The chosen classification is empty.", 'status');
1285			}
1286	6657531f	Andreas Kohlbecker	}
1287			}
1288
1289			return $response;
1290			}
1291
1292			/**
1293	aaa81689	Andreas Kohlbecker	* Determines the tree path of the taxon given as uuid to the root of the classification tree.
1294			*
1295			* The root either is the absolute root of the tree or a rank specific root if the TAXONTREE_RANKLIMIT
1296			* variable is set.
1297	6657531f	Andreas Kohlbecker	*
1298	50172c55	Andreas Kohlbecker	* @param string $taxon_uuid
1299	6657531f	Andreas Kohlbecker	*
1300	eb9fdcf7	Andreas Kohlbecker	* @return array
1301	aaa81689	Andreas Kohlbecker	* An array of CDM TaxonNodeDTO objects
1302	6657531f	Andreas Kohlbecker	*/
1303	50172c55	Andreas Kohlbecker	function cdm_ws_taxonomy_pathFromRoot($taxon_uuid) {
1304	7663cd0b	Andreas Kohlbecker	$view_uuid = get_current_classification_uuid();
1305	aaa81689	Andreas Kohlbecker	$rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1306	6657531f	Andreas Kohlbecker
1307			$response = NULL;
1308	aaa81689	Andreas Kohlbecker	if (is_uuid($rank_uuid)) {
1309	6657531f	Andreas Kohlbecker	$response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM_TO_RANK, array(
1310	50172c55	Andreas Kohlbecker	$view_uuid,
1311			$taxon_uuid,
1312			$rank_uuid,
1313	6657531f	Andreas Kohlbecker	));
1314			}
1315			else {
1316			$response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM, array(
1317	50172c55	Andreas Kohlbecker	$view_uuid,
1318			$taxon_uuid,
1319	6657531f	Andreas Kohlbecker	));
1320			}
1321
1322			if ($response == NULL) {
1323			// Error handing.
1324	0af3ce28	Andreas Kohlbecker	// if (is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
1325			// // Delete the session value and try again with the default.
1326			// unset($_SESSION['cdm']['taxonomictree_uuid']);
1327			// return cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
1328			// }
1329			// else {
1330	6657531f	Andreas Kohlbecker	// Check if taxonomictree_uuid is valid.
1331	2ebf0428	Andreas Kohlbecker	$test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
1332	6657531f	Andreas Kohlbecker	if ($test == NULL) {
1333			// The default set by the admin seems to be invalid or is not even set.
1334			drupal_set_message(_no_classfication_uuid_message(), 'warning');
1335			}
1336	0af3ce28	Andreas Kohlbecker	// }
1337	6657531f	Andreas Kohlbecker	}
1338
1339			return $response;
1340			}
1341
1342	d8e85b2d	Andreas Kohlbecker
1343			// =============================Terms and Vocabularies ========================================= //
1344	6657531f	Andreas Kohlbecker
1345			/**
1346	0686f307	Andreas Kohlbecker	* Returns the localized representation for the given term.
1347	6657531f	Andreas Kohlbecker	*
1348			* @param Object $definedTermBase
1349			* of cdm type DefinedTermBase
1350			* @return string
1351			* the localized representation_L10n of the term,
1352			* otherwise the titleCache as fall back,
1353	28c5c87a	Andreas Kohlbecker	* otherwise the default_representation which defaults to an empty string
1354	6657531f	Andreas Kohlbecker	*/
1355	28c5c87a	Andreas Kohlbecker	function cdm_term_representation($definedTermBase, $default_representation = '') {
1356	6657531f	Andreas Kohlbecker	if ( isset($definedTermBase->representation_L10n) ) {
1357			return $definedTermBase->representation_L10n;
1358			} elseif ( isset($definedTermBase->titleCache)) {
1359			return $definedTermBase->titleCache;
1360			}
1361	28c5c87a	Andreas Kohlbecker	return $default_representation;
1362	6657531f	Andreas Kohlbecker	}
1363
1364	0686f307	Andreas Kohlbecker	/**
1365			* Returns the abbreviated localized representation for the given term.
1366			*
1367			* @param Object $definedTermBase
1368			* of cdm type DefinedTermBase
1369			* @return string
1370			* the localized representation_L10n_abbreviatedLabel of the term,
1371			* if this representation is not available the function delegates the
1372			* call to cdm_term_representation()
1373			*/
1374			function cdm_term_representation_abbreviated($definedTermBase, $default_representation = '') {
1375			if ( isset($definedTermBase->representation_L10n_abbreviatedLabel) ) {
1376			return $definedTermBase->representation_L10n_abbreviatedLabel;
1377			} else {
1378			cdm_term_representation($definedTermBase, $default_representation);
1379			}
1380			}
1381
1382	d8e85b2d	Andreas Kohlbecker	/**
1383			* Transforms the list of the given term base instances to a alphabetical ordered options array.
1384			*
1385			* The options array is suitable for drupal form API elements that allow multiple choices.
1386			* @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
1387			*
1388			* @param array $terms
1389			* a list of CDM DefinedTermBase instances
1390			*
1391			* @param $term_label_callback
1392			* A callback function to override the term representations
1393			*
1394	a6ae799b	Andreas Kohlbecker	* @param bool $empty_option
1395			* An additional element do be placed at the beginning og the list. This element will be the default option.
1396			*
1397	d8e85b2d	Andreas Kohlbecker	* @return array
1398	ef686dd8	Andreas Kohlbecker	* the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
1399
1400	d8e85b2d	Andreas Kohlbecker	*/
1401	a6ae799b	Andreas Kohlbecker	function cdm_terms_as_options($terms, $term_label_callback = NULL, $empty_option = FALSE){
1402	d8e85b2d	Andreas Kohlbecker	$options = array();
1403	7ca5ef1e	Andreas Kohlbecker	if(isset($terms) && is_array($terms)) {
1404			foreach ($terms as $term) {
1405	d8e85b2d	Andreas Kohlbecker	if ($term_label_callback && function_exists($term_label_callback)) {
1406			$options[$term->uuid] = call_user_func($term_label_callback, $term);
1407			} else {
1408			//TODO use cdm_term_representation() here?
1409	7cc085da	Andreas Kohlbecker	$options[$term->uuid] = t('@term', array('@term' => $term->representation_L10n));
1410	d8e85b2d	Andreas Kohlbecker	}
1411			}
1412			}
1413
1414	a6ae799b	Andreas Kohlbecker	if($empty_option !== FALSE){
1415			array_unshift ($options, "");
1416			}
1417
1418	d8e85b2d	Andreas Kohlbecker	return $options;
1419			}
1420
1421			/**
1422	7ca5ef1e	Andreas Kohlbecker	* Creates and array of options for drupal select form elements.
1423			*
1424			* @param $vocabulary_uuid
1425			* The UUID of the CDM Term Vocabulary
1426			* @param $term_label_callback
1427			* An optional call back function which can be used to modify the term label
1428	a6ae799b	Andreas Kohlbecker	* @param bool $empty_option
1429	7ca5ef1e	Andreas Kohlbecker	* An additional element do be placed at the beginning og the list. This element will be the default option.
1430	efa372e9	Andreas Kohlbecker	* @param array $include_filter
1431			* An associative array consisting of a field name an regular expression. All term matching
1432			* these filter are included. The value of the field is converted to a String by var_export()
1433			* so a boolean 'true' can be matched by '/true/'
1434			* @param string $order_by
1435	7ca5ef1e	Andreas Kohlbecker	* One of the order by constants defined in this file
1436	ef686dd8	Andreas Kohlbecker	* @return array
1437			* the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
1438	d8e85b2d	Andreas Kohlbecker	*/
1439	a6ae799b	Andreas Kohlbecker	function cdm_vocabulary_as_option($vocabulary_uuid, $term_label_callback = NULL, $empty_option = FALSE,
1440	efa372e9	Andreas Kohlbecker	array $include_filter = null, $order_by = CDM_ORDER_BY_ORDER_INDEX_ASC) {
1441
1442	d8e85b2d	Andreas Kohlbecker	static $vocabularyOptions = array();
1443
1444	7ca5ef1e	Andreas Kohlbecker	if (!isset($vocabularyOptions[$vocabulary_uuid])) {
1445			$terms = cdm_ws_fetch_all('termVocabulary/' . $vocabulary_uuid . '/terms',
1446			array(
1447			'orderBy' => $order_by
1448			)
1449			);
1450	efa372e9	Andreas Kohlbecker
1451			// apply the include filter
1452			if($include_filter != null){
1453			$included_terms = array();
1454
1455			foreach ($terms as $term){
1456			$include = true;
1457			foreach ($include_filter as $field=>$regex){
1458			$include = preg_match($regex, var_export($term->$field, true)) === 1;
1459			if(!$include){
1460			break;
1461			}
1462			}
1463			if($include){
1464			$included_terms[] = $term;
1465			}
1466			}
1467
1468			$terms = $included_terms;
1469			}
1470
1471			// make options list
1472	a6ae799b	Andreas Kohlbecker	$vocabularyOptions[$vocabulary_uuid] = cdm_terms_as_options($terms, $term_label_callback, $empty_option);
1473	d8e85b2d	Andreas Kohlbecker	}
1474	f5bc56a0	Andreas Kohlbecker
1475	7ca5ef1e	Andreas Kohlbecker	$options = $vocabularyOptions[$vocabulary_uuid];
1476	a6ae799b	Andreas Kohlbecker
1477	f5bc56a0	Andreas Kohlbecker	return $options;
1478	d8e85b2d	Andreas Kohlbecker	}
1479
1480	85669a85	Andreas Kohlbecker	/**
1481			* Creates and array of defaults for drupal select form elements.
1482			*
1483			* @param $vocabulary_uuid
1484			* The UUID of the CDM Term Vocabulary
1485			* @param $term_label_callback
1486			* An optional call back function which can be used to modify the term label
1487			* @param bool $empty_option
1488			* An additional element do be placed at the beginning og the list. This element will be the default option.
1489			* @param array $include_filter
1490			* An associative array consisting of a field name an regular expression. All term matching
1491			* these filter are included. The value of the field is converted to a String by var_export()
1492			* so a boolean 'true' can be matched by '/true/'
1493			* @param string $order_by
1494			* One of the order by constants defined in this file
1495			* @return array
1496			* the terms in an array (key: uuid => value: uuid) as defaults for a form element that allows multiple choices.
1497			*/
1498			function cdm_vocabulary_as_defaults($vocabulary_uuid, array $include_filter = null) {
1499
1500			$options = cdm_vocabulary_as_option($vocabulary_uuid, null, null, $include_filter);
1501			$defaults = array();
1502			foreach ($options as $uuid => $value){
1503			$defaults[$uuid] = $uuid;
1504			}
1505
1506			return $defaults;
1507			}
1508
1509	d8e85b2d	Andreas Kohlbecker	/**
1510	a6ae799b	Andreas Kohlbecker	* @param $term_type string one of
1511	d8e85b2d	Andreas Kohlbecker	* - Unknown
1512			* - Language
1513			* - NamedArea
1514			* - Rank
1515			* - Feature
1516			* - AnnotationType
1517			* - MarkerType
1518			* - ExtensionType
1519			* - DerivationEventType
1520			* - PresenceAbsenceTerm
1521			* - NomenclaturalStatusType
1522			* - NameRelationshipType
1523			* - HybridRelationshipType
1524			* - SynonymRelationshipType
1525			* - TaxonRelationshipType
1526			* - NameTypeDesignationStatus
1527			* - SpecimenTypeDesignationStatus
1528			* - InstitutionType
1529			* - NamedAreaType
1530			* - NamedAreaLevel
1531			* - RightsType
1532			* - MeasurementUnit
1533			* - StatisticalMeasure
1534			* - MaterialOrMethod
1535			* - Material
1536			* - Method
1537			* - Modifier
1538			* - Scope
1539			* - Stage
1540			* - KindOfUnit
1541			* - Sex
1542			* - ReferenceSystem
1543			* - State
1544			* - NaturalLanguageTerm
1545			* - TextFormat
1546			* - DeterminationModifier
1547			* - DnaMarker
1548	7ca5ef1e	Andreas Kohlbecker	*
1549			* @param $order_by
1550			* Optionally sort option (default: CDM_ORDER_BY_TITLE_CACHE_ASC)
1551			* possible values:
1552			* - CDM_ORDER_BY_ID_ASC
1553			* - CDM_ORDER_BY_ID_DESC
1554			* - CDM_ORDER_BY_TITLE_CACHE_ASC
1555			* - CDM_ORDER_BY_TITLE_CACHE_DESC
1556			* - CDM_ORDER_BY_ORDER_INDEX_ASC (can only be used with OrderedTerms!!)
1557			* - CDM_ORDER_BY_ORDER_INDEX_DESC (can only be used with OrderedTerms!!)
1558	a6ae799b	Andreas Kohlbecker	* @param bool $empty_option
1559			* An additional element do be placed at the beginning og the list. This element will be the default option.
1560	2d3d6556	Andreas Kohlbecker	* @return array
1561	ef686dd8	Andreas Kohlbecker	* the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
1562	d8e85b2d	Andreas Kohlbecker	*/
1563	a6ae799b	Andreas Kohlbecker	function cdm_terms_by_type_as_option($term_type, $order_by = CDM_ORDER_BY_TITLE_CACHE_ASC, $term_label_callback = NULL, $empty_option = FALSE){
1564	7ca5ef1e	Andreas Kohlbecker	$terms = cdm_ws_fetch_all(
1565			CDM_WS_TERM,
1566			array(
1567			'class' => $term_type,
1568			'orderBy' => $order_by
1569			)
1570			);
1571	a6ae799b	Andreas Kohlbecker	return cdm_terms_as_options($terms, $term_label_callback, $empty_option);
1572	d8e85b2d	Andreas Kohlbecker	}
1573
1574	dc58a71b	Andreas Kohlbecker	/**
1575			* @param array $none_option
1576			* Will add a filter option to search for NULL values
1577			* @param $with_empty_option
1578			* Will add an empty option to the beginning. Choosing this option will disable the filtering.
1579			* @return array
1580			* An array of options with uuids as key and the localized term representation as value
1581			*/
1582			function cdm_type_designation_status_filter_terms_as_options($none_option_label, $with_empty_option = false){
1583			$filter_terms = cdm_ws_get(CDM_WS_TYPE_DESIGNATION_STATUS_FILTER_TERMS);
1584
1585			if(isset($filter_terms) && is_array($filter_terms)) {
1586			foreach ($filter_terms as $filter_term) {
1587			$options[join(',', $filter_term->uuids)] = $filter_term->label;
1588			}
1589			}
1590
1591			if(is_string($none_option_label)){
1592			$options = array_merge(array('NULL' => $none_option_label), $options);
1593			}
1594
1595			if($with_empty_option !== FALSE){
1596			array_unshift ($options, "");
1597			}
1598
1599
1600			return $options;
1601			}
1602
1603
1604	d8e85b2d	Andreas Kohlbecker
1605			/**
1606	cd4f8f20	Andreas Kohlbecker	* Callback function which provides the localized representation of a cdm term.
1607			*
1608			* The representation is build by concatenating the abbreviated label with the label
1609			* and thus is especially useful for relationship terms
1610			* The localized representation provided by the cdm can be overwritten by
1611			* providing a drupal translation.
1612			*
1613	d8e85b2d	Andreas Kohlbecker	*/
1614			function _cdm_relationship_type_term_label_callback($term) {
1615			if (isset($term->representation_L10n_abbreviatedLabel)) {
1616	7cc085da	Andreas Kohlbecker	return $term->representation_L10n_abbreviatedLabel . ' : '
1617			. t('@term', array('@term' => $term->representation_L10n));
1618	d8e85b2d	Andreas Kohlbecker	}
1619			else {
1620	7cc085da	Andreas Kohlbecker	return t('@term', array('@term' => $term->representation_L10n));
1621	d8e85b2d	Andreas Kohlbecker	}
1622			}
1623
1624	cd4f8f20	Andreas Kohlbecker	/**
1625			* Callback function which provides the localized inverse representation of a cdm term.
1626			*
1627			* The representation is build by concatenating the abbreviated label with the label
1628			* and thus is especially useful for relationship terms
1629			* The localized representation provided by the cdm can be overwritten by
1630			* providing a drupal translation.
1631			*
1632			*/
1633			function _cdm_relationship_type_term_inverse_label_callback($term) {
1634			if (isset($term->inverseRepresentation_L10n_abbreviatedLabel)) {
1635			return $term->inverseRepresentation_L10n_abbreviatedLabel . ' : '
1636			. t('@term', array('@term' => $term->inverseRepresentation_L10n));
1637			}
1638			else {
1639			return t('@term', array('@term' => $term->inverseRepresentation_L10n));
1640			}
1641			}
1642
1643	ef686dd8	Andreas Kohlbecker	/**
1644			* Returns the localized abbreviated label of the relationship term.
1645			*
1646			* In case the abbreviated label is not set the normal representation is returned.
1647			*
1648			* @param $term
1649			* @param bool $is_inverse_relation
1650			* @return string
1651			* The abbreviated label
1652			*/
1653			function cdm_relationship_type_term_abbreviated_label($term, $is_inverse_relation = false){
1654
1655			if($is_inverse_relation) {
1656			if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
1657			$abbr_label = $term->inverseResentation_L10n_abbreviatedLabel;
1658			} else {
1659			$abbr_label = $term->inverseRepresentation_L10n;
1660			}
1661			} else {
1662			if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
1663			$abbr_label = $term->representation_L10n_abbreviatedLabel;
1664			} else {
1665			$abbr_label = $term->representation_L10n;
1666			}
1667			}
1668			return $abbr_label;
1669			}
1670
1671			/**
1672			* Returns the symbol of the relationship term.
1673			*
1674			* In case the symbol is not set the function falls back to use the abbreviated label or
1675			* the normal representation..
1676			*
1677			* @param $term
1678			* @param bool $is_inverse_relation
1679			* @return string
1680			* The abbreviated label
1681			*/
1682			function cdm_relationship_type_term_symbol($term, $is_inverse_relation = false){
1683
1684			if($is_inverse_relation) {
1685			if (isset($term->inverseSymbol) && $term->inverseSymbol) {
1686			$symbol = $term->inverseSymbol;
1687			} else if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
1688			$symbol = $term->inverseResentation_L10n_abbreviatedLabel;
1689			} else {
1690			$symbol = $term->inverseRepresentation_L10n;
1691			}
1692			} else {
1693			if (isset($term->symbol) && $term->symbol) {
1694			$symbol = $term->symbol;
1695			} else if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
1696			$symbol = $term->representation_L10n_abbreviatedLabel;
1697			} else {
1698			$symbol = $term->representation_L10n;
1699			}
1700			}
1701			return $symbol;
1702			}
1703
1704	d8e85b2d	Andreas Kohlbecker	// ========================================================================================== //
1705	6657531f	Andreas Kohlbecker	/**
1706			* @todo Improve documentation of this function.
1707			*
1708			* eu.etaxonomy.cdm.model.description.
1709			* CategoricalData
1710			* CommonTaxonName
1711			* Distribution
1712			* IndividualsAssociation
1713			* QuantitativeData
1714			* TaxonInteraction
1715			* TextData
1716			*/
1717			function cdm_descriptionElementTypes_as_option($prependEmptyElement = FALSE) {
1718			static $types = array(
1719			"CategoricalData",
1720			"CommonTaxonName",
1721			"Distribution",
1722			"IndividualsAssociation",
1723			"QuantitativeData",
1724			"TaxonInteraction",
1725			"TextData",
1726			);
1727
1728			static $options = NULL;
1729			if ($options == NULL) {
1730			$options = array();
1731			if ($prependEmptyElement) {
1732			$options[' '] = '';
1733			}
1734			foreach ($types as $type) {
1735			// No internatianalization here since these are purely technical terms.
1736			$options["eu.etaxonomy.cdm.model.description." . $type] = $type;
1737			}
1738			}
1739			return $options;
1740			}
1741
1742
1743			/**
1744	8cbbc22a	Andreas Kohlbecker	* Fetches all TaxonDescription descriptions elements which are associated to the
1745			* Taxon specified by the $taxon_uuid and merges the elements into the given
1746	37252893	Andreas Kohlbecker	* feature tree.
1747			* @param $feature_tree
1748			* The CDM FeatureTree to be used as template
1749			* @param $taxon_uuid
1750			* The UUID of the taxon
1751	092744e1	Andreas Kohlbecker	* @param $excludes
1752			* UUIDs of features to be excluded
1753	6527c2f5	Andreas Kohlbecker	* @return object
1754	8cbbc22a	Andreas Kohlbecker	* The CDM FeatureTree which was given as parameter merged tree whereas the
1755			* CDM FeatureNodes are extended by an additional field 'descriptionElements'
1756			* witch will hold the according $descriptionElements.
1757	6657531f	Andreas Kohlbecker	*/
1758	092744e1	Andreas Kohlbecker	function cdm_ws_descriptions_by_featuretree($feature_tree, $taxon_uuid, $exclude_uuids = array()) {
1759	37252893	Andreas Kohlbecker
1760			if (!$feature_tree) {
1761	6657531f	Andreas Kohlbecker	drupal_set_message(check_plain(t("No 'FeatureTree' has been set so far.
1762			In order to see the species profiles of your taxa, please select a
1763			'FeatureTree' in the !settings"), array('!settings' => l(t('CDM Dataportal Settings'), 'admin/config/cdm_dataportal/layout'))), 'warning');
1764			return FALSE;
1765			}
1766
1767	092744e1	Andreas Kohlbecker	$description_elements = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
1768	37252893	Andreas Kohlbecker	array(
1769			'taxon' => $taxon_uuid,
1770	092744e1	Andreas Kohlbecker	'features' => cdm_featureTree_elements_toString($feature_tree->root, ',', 'uuid', $exclude_uuids)
1771	2ebf0428	Andreas Kohlbecker	),
1772			'POST'
1773	37252893	Andreas Kohlbecker	);
1774	6657531f	Andreas Kohlbecker
1775	7508605c	Andreas Kohlbecker	// Combine all descriptions into one feature tree.
1776	092744e1	Andreas Kohlbecker	$merged_nodes = _mergeFeatureTreeDescriptions($feature_tree->root->childNodes, $description_elements);
1777	fae36a2a	Andreas Kohlbecker	$feature_tree->root->childNodes = $merged_nodes;
1778	6657531f	Andreas Kohlbecker
1779	37252893	Andreas Kohlbecker	return $feature_tree;
1780	6657531f	Andreas Kohlbecker	}
1781
1782			/**
1783	a6c4c53c	Andreas Kohlbecker	* Returns a filtered a list of annotations for the cdm entity given as parameter $cdm_entity.
1784	4a15731a	Andreas Kohlbecker	* If the annotations are not yet already loded with the cdm entity the cdm REST service will
1785			* be requested for the annotations.
1786	6657531f	Andreas Kohlbecker	*
1787	a6c4c53c	Andreas Kohlbecker	* @param string $cdm_entity
1788	6657531f	Andreas Kohlbecker	* An annotatable cdm entity.
1789	a6c4c53c	Andreas Kohlbecker	* @param array $include_types
1790	6657531f	Andreas Kohlbecker	* If an array of annotation type uuids is supplied by this parameter the
1791			* list of annotations is resticted to those which belong to this type.
1792			*
1793			* @return array
1794			* An array of Annotation objects or an empty array.
1795			*/
1796	0e617798	Andreas Kohlbecker	function cdm_ws_fetch_annotations(&$cdm_entity, $include_types = FALSE) {
1797	4a15731a	Andreas Kohlbecker
1798	a6c4c53c	Andreas Kohlbecker	if(!isset($cdm_entity->annotations)){
1799			$annotation_url = cdm_compose_annotations_uri($cdm_entity);
1800			$cdm_entity->annotations = cdm_ws_fetch_all($annotation_url, array(), 'GET', TRUE);
1801	6657531f	Andreas Kohlbecker	}
1802	4a15731a	Andreas Kohlbecker
1803	b5dca1e2	Andreas Kohlbecker	$annotations = array();
1804	a6c4c53c	Andreas Kohlbecker	foreach ($cdm_entity->annotations as $annotation) {
1805			if ($include_types) {
1806	d8e85b2d	Andreas Kohlbecker	if (
1807	a6c4c53c	Andreas Kohlbecker	( isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $include_types, TRUE) )
1808			\|\| ($annotation->annotationType === NULL && in_array('NULL_VALUE', $include_types, TRUE))
1809	d8e85b2d	Andreas Kohlbecker	) {
1810	4a15731a	Andreas Kohlbecker	$annotations[] = $annotation;
1811			}
1812			}
1813			else {
1814			$annotations[] = $annotation;
1815			}
1816			}
1817			return $annotations;
1818
1819	6657531f	Andreas Kohlbecker	}
1820
1821	7370f4f7	Andreas Kohlbecker	/**
1822	a6c4c53c	Andreas Kohlbecker	* Provides the list of visible annotations for the $cdm_entity.
1823	7370f4f7	Andreas Kohlbecker	*
1824	a6c4c53c	Andreas Kohlbecker	* @param $cdm_entity
1825	7370f4f7	Andreas Kohlbecker	* The annotatable CDM entity
1826			*
1827			* @return array of the annotations which are visible according to the settings as stored in ANNOTATION_TYPES_VISIBLE
1828			*/
1829	a6c4c53c	Andreas Kohlbecker	function cdm_fetch_visible_annotations($cdm_entity){
1830	7370f4f7	Andreas Kohlbecker
1831			static $annotations_types_filter = null;
1832			if(!$annotations_types_filter) {
1833	e2617c7e	Andreas Kohlbecker	$annotations_types_filter = unserialize(EXTENSION_TYPES_VISIBLE_DEFAULT);
1834	7370f4f7	Andreas Kohlbecker	}
1835	0e617798	Andreas Kohlbecker	return cdm_ws_fetch_annotations($cdm_entity, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
1836	7370f4f7	Andreas Kohlbecker	}
1837
1838	eeb98da8	Andreas Kohlbecker	/**
1839			* Loads the annotations from the REST service an adds them as field to the given $annotatable_entity.
1840			*
1841	7370f4f7	Andreas Kohlbecker	* NOTE: The annotations are not filtered by the ANNOTATION_TYPES_VISIBLE settings since this method is meant to act
1842			* like the annotations have been fetched in the ORM-framework in the service.
1843			*
1844	eeb98da8	Andreas Kohlbecker	* @param object $annotatable_entity
1845			* The CDM AnnotatableEntity to load annotations for
1846			*/
1847			function cdm_load_annotations(&$annotatable_entity) {
1848			if (isset($annotatable_entity) && !isset($annotatable_entity->annotations)) {
1849	0e617798	Andreas Kohlbecker	$annotations = cdm_ws_fetch_annotations($annotatable_entity);
1850	eeb98da8	Andreas Kohlbecker	if (is_array($annotations)) {
1851			$annotatable_entity->annotations = $annotations;
1852			}
1853			}
1854			}
1855
1856	de7bcbcc	Andreas Kohlbecker	function cdm_load_tagged_full_title($taxon_name){
1857			if(isset($taxon_name) && !isset($taxon_name->taggedFullTitle)){
1858			$tagged_full_title = cdm_ws_get(CDM_WS_NAME, array($taxon_name->uuid, 'taggedFullTitle'));
1859			if(is_array($tagged_full_title)){
1860			$taxon_name->taggedFullTitle = $tagged_full_title;
1861
1862			}
1863			}
1864			}
1865
1866	0c2b9b9d	Andreas Kohlbecker	/**
1867			* Extends the $cdm_entity object by the field if it is not already existing.
1868			*
1869			* This function can only be used for fields with 1 to many relations.
1870			*
1871			* @param $cdm_base_type
1872			* @param $field_name
1873			* @param $cdm_entity
1874			*/
1875			function cdm_lazyload_array_field($cdm_base_type, $field_name, &$cdm_entity)
1876			{
1877			if (!isset($cdm_entity->$field_name)) {
1878			$items = cdm_ws_fetch_all('portal/' . $cdm_base_type . '/' . $cdm_entity->uuid . '/' . $field_name);
1879			$cdm_entity->$field_name = $items;
1880			}
1881			}
1882
1883
1884	6657531f	Andreas Kohlbecker	/**
1885			* Get a NomenclaturalReference string.
1886			*
1887			* Returns the NomenclaturalReference string with correctly placed
1888			* microreference (= reference detail) e.g.
1889			* in Phytotaxa 43: 1-48. 2012.
1890			*
1891			* @param string $referenceUuid
1892			* UUID of the reference.
1893			* @param string $microreference
1894			* Reference detail.
1895			*
1896			* @return string
1897			* a NomenclaturalReference.
1898			*/
1899			function cdm_ws_getNomenclaturalReference($referenceUuid, $microreference) {
1900	ecb8526d	Andreas Kohlbecker
1901			// TODO the below statement avoids error boxes due to #4644 remove it once this ticket is solved
1902			if(is_array($microreference) \|\| is_object($microreference)) {
1903			return '';
1904			}
1905
1906	6657531f	Andreas Kohlbecker	$obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
1907			$referenceUuid,
1908			), "microReference=" . urlencode($microreference));
1909
1910			if ($obj) {
1911			return $obj->String;
1912			}
1913			else {
1914			return NULL;
1915			}
1916			}
1917
1918	092744e1	Andreas Kohlbecker	/**
1919			* finds and returns the FeatureNode denoted by the given $feature_uuid
1920			*
1921			* @param $feature_tree_nodes
1922			* The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
1923			* @param $feature_uuid
1924			* The UUID of the Feature
1925	9dddc68a	Andreas Kohlbecker	* @return object
1926			* the FeatureNode or null
1927	092744e1	Andreas Kohlbecker	*/
1928			function &cdm_feature_tree_find_node($feature_tree_nodes, $feature_uuid){
1929
1930			// 1. scan this level
1931			foreach ($feature_tree_nodes as $node){
1932	b011743c	Andreas Kohlbecker	if($node->term->uuid == $feature_uuid){
1933	092744e1	Andreas Kohlbecker	return $node;
1934			}
1935			}
1936
1937			// 2. descend into childen
1938			foreach ($feature_tree_nodes as $node){
1939			if(is_array($node->childNodes)){
1940	4b4ae204	Andreas Kohlbecker	$node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
1941	092744e1	Andreas Kohlbecker	if($node) {
1942			return $node;
1943			}
1944			}
1945			}
1946	4b4ae204	Andreas Kohlbecker	$null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
1947			return $null_var;
1948	092744e1	Andreas Kohlbecker	}
1949
1950	6657531f	Andreas Kohlbecker	/**
1951	bfb2b81a	Andreas Kohlbecker	* Merges the given featureNodes structure with the descriptionElements.
1952			*
1953			* This method is used in preparation for rendering the descriptionElements.
1954	28c5c87a	Andreas Kohlbecker	* The descriptionElements which belong to a specific feature node are appended
1955	fae36a2a	Andreas Kohlbecker	* to a the feature node by creating a new field:
1956	328005fd	Andreas Kohlbecker	* - descriptionElements: the CDM DescriptionElements which belong to this feature
1957			* The descriptionElements will be cleared in advance in order to allow reusing the
1958	28c5c87a	Andreas Kohlbecker	* same feature tree without the risk of mixing sets of description elements.
1959	328005fd	Andreas Kohlbecker	*
1960	bfb2b81a	Andreas Kohlbecker	* which originally is not existing in the cdm.
1961			*
1962	328005fd	Andreas Kohlbecker	*
1963			*
1964	bfb2b81a	Andreas Kohlbecker	* @param array $featureNodes
1965	28c5c87a	Andreas Kohlbecker	* An array of cdm FeatureNodes which may be hierarchical since feature nodes
1966	bfb2b81a	Andreas Kohlbecker	* may have children.
1967			* @param array $descriptionElements
1968			* An flat array of cdm DescriptionElements
1969			* @return array
1970	28c5c87a	Andreas Kohlbecker	* The $featureNodes structure enriched with the according $descriptionElements
1971	6657531f	Andreas Kohlbecker	*/
1972			function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
1973	a67e7364	Andreas Kohlbecker
1974	c5a114a8	Andreas Kohlbecker	foreach ($featureNodes as &$feature_node) {
1975	a67e7364	Andreas Kohlbecker	// since the $featureNodes array is reused for each description
1976	28c5c87a	Andreas Kohlbecker	// it is necessary to clear the custom node fields in advance
1977	c5a114a8	Andreas Kohlbecker	if(isset($feature_node->descriptionElements)){
1978			unset($feature_node->descriptionElements);
1979	a67e7364	Andreas Kohlbecker	}
1980
1981	6657531f	Andreas Kohlbecker	// Append corresponding elements to an additional node field:
1982			// $node->descriptionElements.
1983			foreach ($descriptionElements as $element) {
1984	c5a114a8	Andreas Kohlbecker	if ($element->feature->uuid == $feature_node->term->uuid) {
1985			if (!isset($feature_node->descriptionElements)) {
1986			$feature_node->descriptionElements = array();
1987	6657531f	Andreas Kohlbecker	}
1988	c5a114a8	Andreas Kohlbecker	$feature_node->descriptionElements[] = $element;
1989	6657531f	Andreas Kohlbecker	}
1990			}
1991
1992			// Recurse into node children.
1993	c5a114a8	Andreas Kohlbecker	if (isset($feature_node->childNodes[0])) {
1994			$mergedChildNodes = _mergeFeatureTreeDescriptions($feature_node->childNodes, $descriptionElements);
1995			$feature_node->childNodes = $mergedChildNodes;
1996	6657531f	Andreas Kohlbecker	}
1997	a67e7364	Andreas Kohlbecker
1998	c5a114a8	Andreas Kohlbecker	if(!isset($feature_node->descriptionElements) && !isset($feature_node->childNodes[0])){
1999			unset($feature_node);
2000	328005fd	Andreas Kohlbecker	}
2001
2002	6657531f	Andreas Kohlbecker	}
2003	a67e7364	Andreas Kohlbecker
2004	6657531f	Andreas Kohlbecker	return $featureNodes;
2005			}
2006
2007			/**
2008	84fdac2a	Andreas Kohlbecker	* Sends a GET or POST request to a CDM RESTService and returns a de-serialized object.
2009	6657531f	Andreas Kohlbecker	*
2010			* The response from the HTTP GET request is returned as object.
2011			* The response objects coming from the webservice configured in the
2012	84fdac2a	Andreas Kohlbecker	* 'cdm_webservice_url' variable are being cached in a level 1 (L1) and / or
2013	6657531f	Andreas Kohlbecker	* in a level 2 (L2) cache.
2014			*
2015			* Since the L1 cache is implemented as static variable of the cdm_ws_get()
2016			* function, this cache persists only per each single page execution.
2017			* Any object coming from the webservice is stored into it by default.
2018			* In contrast to this default caching mechanism the L2 cache only is used if
2019			* the 'cdm_webservice_cache' variable is set to TRUE,
2020			* which can be set using the modules administrative settings section.
2021			* Objects stored in this L2 cache are serialized and stored
2022			* using the drupal cache in the '{prefix}cache_cdm_ws' cache table. So the
2023			* objects that are stored in the database will persist as
2024	84fdac2a	Andreas Kohlbecker	* long as the drupal cache is not being cleared and are available across
2025	6657531f	Andreas Kohlbecker	* multiple script executions.
2026			*
2027			* @param string $uri
2028			* URL to the webservice.
2029			* @param array $pathParameters
2030			* An array of path parameters.
2031			* @param string $query
2032			* A query string to be appended to the URL.
2033			* @param string $method
2034			* The HTTP method to use, valid values are "GET" or "POST";
2035			* @param bool $absoluteURI
2036			* TRUE when the URL should be treated as absolute URL.
2037			*
2038	4d3c2389	Andreas Kohlbecker	* @return object\| array
2039	84fdac2a	Andreas Kohlbecker	* The de-serialized webservice response object.
2040	6657531f	Andreas Kohlbecker	*/
2041			function cdm_ws_get($uri, $pathParameters = array(), $query = NULL, $method = "GET", $absoluteURI = FALSE) {
2042	d071bed7	Andreas Kohlbecker
2043	6657531f	Andreas Kohlbecker	static $cacheL1 = array();
2044
2045	2ebf0428	Andreas Kohlbecker	$data = NULL;
2046			// store query string in $data and clear the query, $data will be set as HTTP request body
2047			if($method == 'POST'){
2048			$data = $query;
2049			$query = NULL;
2050			}
2051
2052	088448e1	Andreas Kohlbecker	// Transform the given uri path or pattern into a proper webservice uri.
2053	6657531f	Andreas Kohlbecker	if (!$absoluteURI) {
2054			$uri = cdm_compose_url($uri, $pathParameters, $query);
2055			}
2056	80d21b78	Andreas Kohlbecker	cdm_ws_apply_classification_subtree_filter($uri);
2057	6657531f	Andreas Kohlbecker
2058	72032ea6	Andreas Kohlbecker	// read request parameter 'cacheL2_refresh'
2059	84fdac2a	Andreas Kohlbecker	// which allows refreshing the level 2 cache
2060	72032ea6	Andreas Kohlbecker	$do_cacheL2_refresh = isset($_REQUEST['cacheL2_refresh']) && $_REQUEST['cacheL2_refresh'] == 1;
2061
2062	6657531f	Andreas Kohlbecker	$is_cdm_ws_uri = _is_cdm_ws_uri($uri);
2063			$use_cacheL2 = variable_get('cdm_webservice_cache', 1);
2064
2065	2ebf0428	Andreas Kohlbecker	if($method == 'GET'){
2066			$cache_key = $uri;
2067			} else {
2068			// sha1 creates longer hashes and thus will cause fewer collisions than md5.
2069			// crc32 is faster but creates much shorter hashes
2070			$cache_key = $uri . '[' . $method . ':' . sha1($data) .']';
2071			}
2072
2073			if (array_key_exists($cache_key, $cacheL1)) {
2074	6657531f	Andreas Kohlbecker	$cacheL1_obj = $cacheL1[$uri];
2075			}
2076
2077			$set_cacheL1 = FALSE;
2078			if ($is_cdm_ws_uri && !isset($cacheL1_obj)) {
2079			$set_cacheL1 = TRUE;
2080			}
2081
2082			// Only cache cdm webservice URIs.
2083			$set_cacheL2 = $use_cacheL2 && $is_cdm_ws_uri && $set_cacheL1;
2084			$cacheL2_entry = FALSE;
2085
2086	72032ea6	Andreas Kohlbecker	if ($use_cacheL2 && !$do_cacheL2_refresh) {
2087	6657531f	Andreas Kohlbecker	// Try to get object from cacheL2.
2088	2ebf0428	Andreas Kohlbecker	$cacheL2_entry = cache_get($cache_key, 'cache_cdm_ws');
2089	6657531f	Andreas Kohlbecker	}
2090
2091			if (isset($cacheL1_obj)) {
2092			//
2093			// The object has been found in the L1 cache.
2094			//
2095			$obj = $cacheL1_obj;
2096	a4f964ee	Andreas Kohlbecker	if (cdm_debug_block_visible()) {
2097	2ebf0428	Andreas Kohlbecker	cdm_ws_debug_add($uri, $method, $data, 0, 0, NULL, 'cacheL1');
2098	6657531f	Andreas Kohlbecker	}
2099			}
2100			elseif ($cacheL2_entry) {
2101			//
2102			// The object has been found in the L2 cache.
2103			//
2104	e2464cf8	Andreas Kohlbecker	$duration_parse_start = microtime(TRUE);
2105	6657531f	Andreas Kohlbecker	$obj = unserialize($cacheL2_entry->data);
2106	e2464cf8	Andreas Kohlbecker	$duration_parse = microtime(TRUE) - $duration_parse_start;
2107	6657531f	Andreas Kohlbecker
2108	a4f964ee	Andreas Kohlbecker	if (cdm_debug_block_visible()) {
2109	2ebf0428	Andreas Kohlbecker	cdm_ws_debug_add($uri, $method, $data, 0, $duration_parse, NULL, 'cacheL2');
2110	6657531f	Andreas Kohlbecker	}
2111			}
2112			else {
2113			//
2114			// Get the object from the webservice and cache it.
2115			//
2116	e2464cf8	Andreas Kohlbecker	$duration_fetch_start = microtime(TRUE);
2117	6657531f	Andreas Kohlbecker	// Request data from webservice JSON or XML.
2118	2ebf0428	Andreas Kohlbecker	$response = cdm_http_request($uri, $method, $data);
2119			$response_body = NULL;
2120	2fe78f3c	Andreas Kohlbecker	if (isset($response->data)) {
2121	2ebf0428	Andreas Kohlbecker	$response_body = $response->data;
2122	2fe78f3c	Andreas Kohlbecker	}
2123	e2464cf8	Andreas Kohlbecker	$duration_fetch = microtime(TRUE) - $duration_fetch_start;
2124			$duration_parse_start = microtime(TRUE);
2125	6657531f	Andreas Kohlbecker
2126			// Parse data and create object.
2127	2ebf0428	Andreas Kohlbecker	$obj = cdm_load_obj($response_body);
2128	6657531f	Andreas Kohlbecker
2129	4e5b23ae	Andreas Kohlbecker	if(isset($obj->servlet) && isset($obj->status) && is_numeric($obj->status)){
2130			// this is json error message returned by jetty #8914
2131			// wee need to replace it by null to avoid breaking existing assumptions in the code here
2132			// this is also related to #2711
2133			$obj = null;
2134			}
2135
2136	e2464cf8	Andreas Kohlbecker	$duration_parse = microtime(TRUE) - $duration_parse_start;
2137	a4f964ee	Andreas Kohlbecker
2138			if (cdm_debug_block_visible()) {
2139	2ebf0428	Andreas Kohlbecker	if ($obj \|\| $response_body == "[]") {
2140	e2464cf8	Andreas Kohlbecker	$status = 'valid';
2141	6657531f	Andreas Kohlbecker	}
2142			else {
2143	e2464cf8	Andreas Kohlbecker	$status = 'invalid';
2144	6657531f	Andreas Kohlbecker	}
2145	2ebf0428	Andreas Kohlbecker	cdm_ws_debug_add($uri, $method, $data, $duration_fetch, $duration_parse, strlen($response_body), $status);
2146	6657531f	Andreas Kohlbecker	}
2147			if ($set_cacheL2) {
2148			// Store the object in cache L2.
2149	2ebf0428	Andreas Kohlbecker	// Comment @WA perhaps better if Drupal serializedatas here? Then the
2150	6657531f	Andreas Kohlbecker	// flag serialized is set properly in the cache table.
2151	2ebf0428	Andreas Kohlbecker	cache_set($cache_key, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
2152	6657531f	Andreas Kohlbecker	}
2153			}
2154			if ($obj) {
2155			// Store the object in cache L1.
2156			if ($set_cacheL1) {
2157	2ebf0428	Andreas Kohlbecker	$cacheL1[$cache_key] = $obj;
2158	6657531f	Andreas Kohlbecker	}
2159			}
2160			return $obj;
2161			}
2162
2163	80d21b78	Andreas Kohlbecker	function cdm_ws_apply_classification_subtree_filter(&$uri){
2164
2165			$classification_subtree_filter_patterns = &drupal_static('classification_subtree_filter_patterns', array(
2166			"#/classification/[0-9a-f\-]{36}/childNodes#",
2167	6e2a9ba9	Andreas Kohlbecker	/* covered by above pattern:
2168			"#/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
2169			'#/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
2170			*/
2171	80d21b78	Andreas Kohlbecker	"#/portal/classification/[0-9a-f\-]{36}/childNodes#",
2172	6e2a9ba9	Andreas Kohlbecker	/* covered by above pattern:
2173	80d21b78	Andreas Kohlbecker	"#/portal/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
2174	6e2a9ba9	Andreas Kohlbecker	'#/portal/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
2175			*/
2176	d961cf30	Andreas Kohlbecker	'#/portal/classification/[0-9a-f\-]{36}/pathFrom/[0-9a-f\-]{36}#',
2177	80d21b78	Andreas Kohlbecker	"#/portal/taxon/search#",
2178			"#/portal/taxon/find#",
2179	6e2a9ba9	Andreas Kohlbecker	/* covered by above pattern:
2180	80d21b78	Andreas Kohlbecker	"#/portal/taxon/findByDescriptionElementFullText#",
2181			"#/portal/taxon/findByFullText#",
2182			"#/portal/taxon/findByEverythingFullText#",
2183			"#/portal/taxon/findByIdentifier#",
2184	6e2a9ba9	Andreas Kohlbecker	"#/portal/taxon/findByMarker#",
2185			"#/portal/taxon/findByMarker#",
2186			"#/portal/taxon/findByMarker#",
2187			*/
2188			"#/portal/taxon/[0-9a-f\-]{36}#"
2189			/* covered by above pattern:
2190			"#/portal/taxon/[0-9a-f\-]{36}/taxonNodes#",
2191			*/
2192	80d21b78	Andreas Kohlbecker	));
2193
2194			$sub_tree_filter_uuid_value = variable_get(CDM_SUB_TREE_FILTER_UUID, FALSE);
2195			if(is_uuid($sub_tree_filter_uuid_value)){
2196			foreach($classification_subtree_filter_patterns as $preg_pattern){
2197			if(preg_match($preg_pattern, $uri)){
2198			// no need to take care for uri fragments with ws uris!
2199			if(strpos( $uri, '?')){
2200			$uri .= '&subtree=' . $sub_tree_filter_uuid_value;
2201			} else {
2202			$uri .= '?subtree='. $sub_tree_filter_uuid_value;
2203			}
2204			break;
2205			}
2206			}
2207			}
2208
2209			}
2210	6657531f	Andreas Kohlbecker	/**
2211	e2464cf8	Andreas Kohlbecker	* Processes and stores the given information in $_SESSION['cdm']['ws_debug'] as table row.
2212			*
2213			* The cdm_ws_debug block will display the debug information.
2214			*
2215			* @param $uri
2216			* The CDM REST URI to which the request has been send
2217	2ebf0428	Andreas Kohlbecker	* @param string $method
2218			* The HTTP request method, either 'GET' or 'POST'
2219			* @param string $post_data
2220			* The datastring send with a post request
2221	e2464cf8	Andreas Kohlbecker	* @param $duration_fetch
2222			* The time in seconds it took to fetch the data from the web service
2223			* @param $duration_parse
2224			* Time in seconds which was needed to parse the json response
2225			* @param $datasize
2226			* Size of the data received from the server
2227			* @param $status
2228			* A status string, possible values are: 'valid', 'invalid', 'cacheL1', 'cacheL2'
2229			* @return bool
2230			* TRUE if adding the debug information was successful
2231	6657531f	Andreas Kohlbecker	*/
2232	2ebf0428	Andreas Kohlbecker	function cdm_ws_debug_add($uri, $method, $post_data, $duration_fetch, $duration_parse, $datasize, $status) {
2233	6657531f	Andreas Kohlbecker
2234	e2464cf8	Andreas Kohlbecker	static $initial_time = NULL;
2235			if(!$initial_time) {
2236			$initial_time = microtime(TRUE);
2237			}
2238			$time = microtime(TRUE) - $initial_time;
2239	6657531f	Andreas Kohlbecker
2240			// Decompose uri into path and query element.
2241			$uri_parts = explode("?", $uri);
2242	98038f4c	w.addink	$query = array();
2243	6657531f	Andreas Kohlbecker	if (count($uri_parts) == 2) {
2244			$path = $uri_parts[0];
2245			}
2246			else {
2247			$path = $uri;
2248			}
2249
2250	c1bcfc1b	Andreas Kohlbecker	if(strpos($uri, '?') > 0){
2251			$json_uri = str_replace('?', '.json?', $uri);
2252			$xml_uri = str_replace('?', '.xml?', $uri);
2253			} else {
2254			$json_uri = $uri . '.json';
2255			$xml_uri = $json_uri . '.xml';
2256			}
2257
2258	e2464cf8	Andreas Kohlbecker	// data links to make data accecsible as json and xml
2259			$data_links = '';
2260	6657531f	Andreas Kohlbecker	if (_is_cdm_ws_uri($path)) {
2261	2ebf0428	Andreas Kohlbecker
2262			// see ./js/http-method-link.js
2263
2264			if($method == 'GET'){
2265			$data_links .= '<a href="' . $xml_uri . '" target="data">xml</a>-';
2266			$data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">proxied</a>';
2267			$data_links .= '<br/>';
2268			$data_links .= '<a href="' . $json_uri . '" target="data">json</a>-';
2269			$data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">proxied</a>';
2270			} else {
2271			$js_link_activation = 'class="http-' . $method . '-link" data-cdm-http-post="' . $post_data . '" type="application/x-www-form-urlencoded"';
2272			$data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">xml-proxied</a>';
2273			$data_links .= '<br/>';
2274			$data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">json-proxied</a>';
2275			}
2276	6657531f	Andreas Kohlbecker	}
2277			else {
2278	c1bcfc1b	Andreas Kohlbecker	$data_links .= '<a href="' . $uri . '" target="data">open</a>';
2279	e2464cf8	Andreas Kohlbecker	}
2280
2281			//
2282			$data = array(
2283			'ws_uri' => $uri,
2284	2ebf0428	Andreas Kohlbecker	'method' => $method,
2285			'post_data' => $post_data,
2286	e2464cf8	Andreas Kohlbecker	'time' => sprintf('%3.3f', $time),
2287			'fetch_seconds' => sprintf('%3.3f', $duration_fetch),
2288			'parse_seconds' => sprintf('%3.3f', $duration_parse),
2289			'size_kb' => sprintf('%3.1f', ($datasize / 1024)) ,
2290			'status' => $status,
2291			'data_links' => $data_links
2292			);
2293			if (!isset($_SESSION['cdm']['ws_debug'])) {
2294			$_SESSION['cdm']['ws_debug'] = array();
2295	6657531f	Andreas Kohlbecker	}
2296	e2464cf8	Andreas Kohlbecker	$_SESSION['cdm']['ws_debug'][] = serialize($data);
2297
2298			// Mark this page as being uncacheable.
2299			// taken over from drupal_get_messages() but it is unsure if we really need this here
2300			drupal_page_is_cacheable(FALSE);
2301
2302			// Messages not set when DB connection fails.
2303			return isset($_SESSION['cdm']['ws_debug']) ? $_SESSION['cdm']['ws_debug'] : NULL;
2304	6657531f	Andreas Kohlbecker	}
2305
2306	a4f964ee	Andreas Kohlbecker	/**
2307			* helper function to dtermine if the cdm_debug_block should be displayed or not
2308			* the visibility depends on whether
2309			* - the block is enabled
2310			* - the visibility restrictions in the block settings are satisfied
2311			*/
2312			function cdm_debug_block_visible() {
2313			static $is_visible = null;
2314
2315			if($is_visible === null){
2316			$block = block_load('cdm_api', 'cdm_ws_debug');
2317	af932304	Andreas Kohlbecker	$is_visible = isset($block->status) && $block->status == 1;
2318	a4f964ee	Andreas Kohlbecker	if($is_visible){
2319			$blocks = array($block);
2320			// Checks the page, user role, and user-specific visibilty settings.
2321			block_block_list_alter($blocks);
2322			$is_visible = count($blocks) > 0;
2323			}
2324			}
2325			return $is_visible;
2326			}
2327
2328	6657531f	Andreas Kohlbecker	/**
2329			* @todo Please document this function.
2330			* @see http://drupal.org/node/1354
2331			*/
2332	2ebf0428	Andreas Kohlbecker	function cdm_load_obj($response_body) {
2333			$obj = json_decode($response_body);
2334	6657531f	Andreas Kohlbecker
2335			if (!(is_object($obj) \|\| is_array($obj))) {
2336			ob_start();
2337			$obj_dump = ob_get_contents();
2338			ob_clean();
2339			return FALSE;
2340			}
2341
2342			return $obj;
2343			}
2344
2345			/**
2346	2fe78f3c	Andreas Kohlbecker	* Do a http request to a CDM RESTful web service.
2347	6657531f	Andreas Kohlbecker	*
2348			* @param string $uri
2349			* The webservice url.
2350			* @param string $method
2351			* The HTTP method to use, valid values are "GET" or "POST"; defaults to
2352			* "GET" even if NULL, FALSE or any invalid value is supplied.
2353	2ebf0428	Andreas Kohlbecker	* @param $data: A string containing the request body, formatted as
2354			* 'param=value&param=value&...'. Defaults to NULL.
2355	6657531f	Andreas Kohlbecker	*
2356	2fe78f3c	Andreas Kohlbecker	* @return object
2357			* The object as returned by drupal_http_request():
2358			* An object that can have one or more of the following components:
2359			* - request: A string containing the request body that was sent.
2360			* - code: An integer containing the response status code, or the error code
2361			* if an error occurred.
2362			* - protocol: The response protocol (e.g. HTTP/1.1 or HTTP/1.0).
2363			* - status_message: The status message from the response, if a response was
2364			* received.
2365			* - redirect_code: If redirected, an integer containing the initial response
2366			* status code.
2367			* - redirect_url: If redirected, a string containing the URL of the redirect
2368			* target.
2369			* - error: If an error occurred, the error message. Otherwise not set.
2370			* - headers: An array containing the response headers as name/value pairs.
2371			* HTTP header names are case-insensitive (RFC 2616, section 4.2), so for
2372			* easy access the array keys are returned in lower case.
2373			* - data: A string containing the response body that was received.
2374	6657531f	Andreas Kohlbecker	*/
2375	2ebf0428	Andreas Kohlbecker	function cdm_http_request($uri, $method = "GET", $data = NULL) {
2376	6657531f	Andreas Kohlbecker	static $acceptLanguage = NULL;
2377	0b606c0d	Andreas Kohlbecker	$header = array();
2378	af0cde1a	Andreas Kohlbecker
2379			if(!$acceptLanguage && module_exists('i18n')){
2380			$acceptLanguage = i18n_language_content()->language;
2381			}
2382	6657531f	Andreas Kohlbecker
2383			if (!$acceptLanguage) {
2384			if (function_exists('apache_request_headers')) {
2385			$headers = apache_request_headers();
2386			if (isset($headers['Accept-Language'])) {
2387			$acceptLanguage = $headers['Accept-Language'];
2388			}
2389			}
2390			}
2391
2392			if ($method != "GET" && $method != "POST") {
2393	2ebf0428	Andreas Kohlbecker	drupal_set_message('cdm_api.module#cdm_http_request() : unsupported HTTP request method ', 'error');
2394	6657531f	Andreas Kohlbecker	}
2395
2396	0b606c0d	Andreas Kohlbecker	if (_is_cdm_ws_uri($uri)) {
2397	3db2866c	Andreas Kohlbecker	$header['Accept'] = 'application/json';
2398	6657531f	Andreas Kohlbecker	$header['Accept-Language'] = $acceptLanguage;
2399			$header['Accept-Charset'] = 'UTF-8';
2400			}
2401
2402	2ebf0428	Andreas Kohlbecker	if($method == "POST") {
2403			// content type is application/x-www-form-urlencoded, so the request body uses the same format as the query string
2404			$header['Content-Type'] = 'application/x-www-form-urlencoded';
2405			}
2406
2407	2dd59bb5	Andreas Kohlbecker
2408			cdm_dd($uri);
2409	2fe78f3c	Andreas Kohlbecker	return drupal_http_request($uri, array(
2410			'headers' => $header,
2411			'method' => $method,
2412	2ebf0428	Andreas Kohlbecker	'data' => $data,
2413	2fe78f3c	Andreas Kohlbecker	'timeout' => CDM_HTTP_REQUEST_TIMEOUT
2414			)
2415			);
2416	6657531f	Andreas Kohlbecker	}
2417
2418			/**
2419	37252893	Andreas Kohlbecker	* Concatenates recursively the fields of all features contained in the given
2420			* CDM FeatureTree root node.
2421			*
2422			* @param $rootNode
2423			* A CDM FeatureTree node
2424			* @param
2425			* The character to be used as glue for concatenation, default is ', '
2426			* @param $field_name
2427			* The field name of the CDM Features
2428	092744e1	Andreas Kohlbecker	* @param $excludes
2429			* Allows defining a set of values to be excluded. This refers to the values
2430			* in the field denoted by the $field_name parameter
2431			*
2432	6657531f	Andreas Kohlbecker	*/
2433	092744e1	Andreas Kohlbecker	function cdm_featureTree_elements_toString($root_node, $separator = ', ', $field_name = 'representation_L10n', $excludes = array()) {
2434	6657531f	Andreas Kohlbecker	$out = '';
2435
2436	37252893	Andreas Kohlbecker	$pre_child_separator = $separator;
2437			$post_child_separator = '';
2438
2439	fae36a2a	Andreas Kohlbecker	foreach ($root_node->childNodes as $feature_node) {
2440	6657531f	Andreas Kohlbecker	$out .= ($out ? $separator : '');
2441	b011743c	Andreas Kohlbecker	if(!in_array($feature_node->term->$field_name, $excludes)) {
2442			$out .= $feature_node->term->$field_name;
2443	092744e1	Andreas Kohlbecker	if (is_array($feature_node->childNodes) && count($feature_node->childNodes) > 0) {
2444			$childlabels = cdm_featureTree_elements_toString($feature_node, $separator, $field_name);
2445			if (strlen($childlabels)) {
2446			$out .= $pre_child_separator . $childlabels . $post_child_separator;
2447			}
2448	6657531f	Andreas Kohlbecker	}
2449			}
2450			}
2451			return $out;
2452			}
2453
2454			/**
2455			* Create a one-dimensional form options array.
2456			*
2457			* Creates an array of all features in the feature tree of feature nodes,
2458			* the node labels are indented by $node_char and $childIndent depending on the
2459			* hierachy level.
2460			*
2461			* @param - $rootNode
2462			* @param - $node_char
2463			* @param - $childIndentStr
2464			* @param - $childIndent
2465			* ONLY USED INTERNALLY!
2466			*
2467			* @return array
2468			* A one dimensional Drupal form options array.
2469			*/
2470			function _featureTree_nodes_as_feature_options($rootNode, $node_char = "├─ ", $childIndentStr = ' ', $childIndent = '') {
2471			$options = array();
2472	fae36a2a	Andreas Kohlbecker	foreach ($rootNode->childNodes as $featureNode) {
2473	6657531f	Andreas Kohlbecker	$indent_prefix = '';
2474			if ($childIndent) {
2475			$indent_prefix = $childIndent . $node_char . " ";
2476			}
2477	b011743c	Andreas Kohlbecker	$options[$featureNode->term->uuid] = $indent_prefix . $featureNode->term->representation_L10n;
2478	fae36a2a	Andreas Kohlbecker	if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2479			// Foreach ($featureNode->childNodes as $childNode){
2480	6657531f	Andreas Kohlbecker	$childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
2481			$options = array_merge_recursive($options, $childList);
2482			// }
2483			}
2484			}
2485			return $options;
2486			}
2487
2488			/**
2489	72294996	Andreas Kohlbecker	* Returns an array with all available FeatureTrees and the representations of the selected
2490			* FeatureTree as a detail view.
2491			*
2492	cdafd99f	Alexander Oppermann	* @param boolean $add_default_feature_free
2493	c3a41ddb	Andreas Kohlbecker	* @param boolean $show_weight
2494			* Show the weight which will be applied to the according feature block
2495	72294996	Andreas Kohlbecker	* @return array
2496	cdafd99f	Alexander Oppermann	* associative array with following keys:
2497			* -options: Returns an array with all available Feature Trees
2498			* -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
2499	72294996	Andreas Kohlbecker	*
2500	6657531f	Andreas Kohlbecker	*/
2501	c3a41ddb	Andreas Kohlbecker	function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE, $show_weight = FALSE) {
2502	3f485c6d	Andreas Kohlbecker
2503			$options = array();
2504			$tree_representations = array();
2505	6657531f	Andreas Kohlbecker	$feature_trees = array();
2506
2507			// Set tree that contains all features.
2508	6188d24e	Andreas Kohlbecker	if ($add_default_feature_free) {
2509	3f485c6d	Andreas Kohlbecker	$options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
2510	9dddc68a	Andreas Kohlbecker	$feature_trees[] = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
2511	3f485c6d	Andreas Kohlbecker	}
2512
2513			// Get feature trees from database.
2514	9725f08e	Andreas Kohlbecker	$persited_trees = cdm_ws_fetch_all(CDM_WS_TERMTREES, array("termType" => "Feature"));
2515	3f485c6d	Andreas Kohlbecker	if (is_array($persited_trees)) {
2516			$feature_trees = array_merge($feature_trees, $persited_trees);
2517	6657531f	Andreas Kohlbecker	}
2518
2519	3f485c6d	Andreas Kohlbecker	foreach ($feature_trees as $featureTree) {
2520	6657531f	Andreas Kohlbecker
2521	8c962983	Andreas Kohlbecker	if(!is_object($featureTree)){
2522			continue;
2523			}
2524	3f485c6d	Andreas Kohlbecker	// Do not add the DEFAULT_FEATURETREE again,
2525			if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
2526	1717116c	Andreas Kohlbecker	$options[$featureTree->uuid] = $featureTree->titleCache;
2527	3f485c6d	Andreas Kohlbecker	}
2528
2529			// Render the hierarchic tree structure
2530	fae36a2a	Andreas Kohlbecker	if (is_array( $featureTree->root->childNodes) && count( $featureTree->root->childNodes) > 0) {
2531	3f485c6d	Andreas Kohlbecker
2532			// Render the hierarchic tree structure.
2533			$treeDetails = '<div class="featuretree_structure">'
2534	c3a41ddb	Andreas Kohlbecker	. render_feature_tree_hierarchy($featureTree->uuid, $show_weight)
2535	3f485c6d	Andreas Kohlbecker	. '</div>';
2536
2537			$form = array();
2538			$form['featureTree-' . $featureTree->uuid] = array(
2539			'#type' => 'fieldset',
2540			'#title' => 'Show details',
2541			'#attributes' => array('class' => array('collapsible collapsed')),
2542			// '#collapsible' => TRUE,
2543			// '#collapsed' => TRUE,
2544			);
2545			$form['featureTree-' . $featureTree->uuid]['details'] = array(
2546			'#markup' => $treeDetails,
2547			);
2548
2549			$tree_representations[$featureTree->uuid] = drupal_render($form);
2550	6657531f	Andreas Kohlbecker	}
2551	8734e506	Alexander Oppermann
2552	3f485c6d	Andreas Kohlbecker	} // END loop over feature trees
2553	6657531f	Andreas Kohlbecker
2554	3f485c6d	Andreas Kohlbecker	// return $options;
2555			return array('options' => $options, 'treeRepresentations' => $tree_representations);
2556	6657531f	Andreas Kohlbecker	}
2557
2558			/**
2559	0af3ce28	Andreas Kohlbecker	* Provides the list of available classifications in form of an options array.
2560	de8b5b32	Andreas Kohlbecker	*
2561			* The options array is suitable for drupal form API elements that allow multiple choices.
2562			* @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
2563			*
2564			* The classifications are ordered alphabetically whereas the classification
2565			* chosen as default will always appear on top of the array, followed by a
2566			* blank line below.
2567			*
2568	61b6ee11	Andreas Kohlbecker	* @param bool $add_none_option
2569	1717116c	Andreas Kohlbecker	* is true an addtional 'none' option will be added, optional parameter, defaults to FALSE
2570	61b6ee11	Andreas Kohlbecker	*
2571	de8b5b32	Andreas Kohlbecker	* @return array
2572			* classifications in an array as options for a form element that allows multiple choices.
2573	6657531f	Andreas Kohlbecker	*/
2574	61b6ee11	Andreas Kohlbecker	function cdm_get_taxontrees_as_options($add_none_option = FALSE) {
2575
2576	a488aeb6	Andreas Kohlbecker	$taxonTrees = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
2577	de8b5b32	Andreas Kohlbecker
2578			$default_classification_uuid = variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
2579			$default_classification_label = '';
2580
2581			// add all classifications
2582	6188d24e	Andreas Kohlbecker	$taxonomic_tree_options = array();
2583	61b6ee11	Andreas Kohlbecker	if ($add_none_option) {
2584			$taxonomic_tree_options['NONE'] = ' '; // one Space character at beginning to force on top;
2585			}
2586	6657531f	Andreas Kohlbecker	if ($taxonTrees) {
2587			foreach ($taxonTrees as $tree) {
2588	de8b5b32	Andreas Kohlbecker	if (!$default_classification_uuid \|\| $default_classification_uuid != $tree->uuid) {
2589			$taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
2590			} else {
2591	61b6ee11	Andreas Kohlbecker	$taxonomic_tree_options[$tree->uuid] = ' '; // two Space characters to force on top but below 'none' option , will be replaced below by titleCache
2592	de8b5b32	Andreas Kohlbecker	$default_classification_label = $tree->titleCache;
2593			}
2594	6657531f	Andreas Kohlbecker	}
2595			}
2596	61b6ee11	Andreas Kohlbecker	// oder alphabetically the space
2597	de8b5b32	Andreas Kohlbecker	asort($taxonomic_tree_options);
2598
2599	61b6ee11	Andreas Kohlbecker	// now set the labels
2600			// for none
2601	f19f47fa	Andreas Kohlbecker	if ($add_none_option) {
2602	8ae3cfe3	Andreas Kohlbecker	$taxonomic_tree_options['NONE'] =t('--- ALL ---');
2603	61b6ee11	Andreas Kohlbecker	}
2604
2605			// for default_classification
2606	805795b6	Andreas Kohlbecker	if (is_uuid($default_classification_uuid)) {
2607	d88a1df7	Andreas Kohlbecker	$taxonomic_tree_options[$default_classification_uuid] =
2608			$default_classification_label ? $default_classification_label : '--- INVALID CHOICE ---'
2609	6b1e5ae3	Andreas Kohlbecker	. (count($taxonTrees) > 1 ? ' [' . t('DEFAULT CLASSIFICATION') . ']': '');
2610	de8b5b32	Andreas Kohlbecker	}
2611
2612	6188d24e	Andreas Kohlbecker	return $taxonomic_tree_options;
2613	6657531f	Andreas Kohlbecker	}
2614
2615			/**
2616			* @todo Please document this function.
2617			* @see http://drupal.org/node/1354
2618			*/
2619			function cdm_api_secref_cache_prefetch(&$secUuids) {
2620			// Comment @WA: global variables should start with a single underscore
2621			// followed by the module and another underscore.
2622			global $_cdm_api_secref_cache;
2623			if (!is_array($_cdm_api_secref_cache)) {
2624			$_cdm_api_secref_cache = array();
2625			}
2626			$uniqueUuids = array_unique($secUuids);
2627			$i = 0;
2628			$param = '';
2629			while ($i++ < count($uniqueUuids)) {
2630			$param .= $secUuids[$i] . ',';
2631			if (strlen($param) + 37 > 2000) {
2632			_cdm_api_secref_cache_add($param);
2633			$param = '';
2634			}
2635			}
2636			if ($param) {
2637			_cdm_api_secref_cache_add($param);
2638			}
2639			}
2640
2641			/**
2642			* @todo Please document this function.
2643			* @see http://drupal.org/node/1354
2644			*/
2645			function cdm_api_secref_cache_get($secUuid) {
2646			global $_cdm_api_secref_cache;
2647			if (!is_array($_cdm_api_secref_cache)) {
2648			$_cdm_api_secref_cache = array();
2649			}
2650			if (!array_key_exists($secUuid, $_cdm_api_secref_cache)) {
2651			_cdm_api_secref_cache_add($secUuid);
2652			}
2653			return $_cdm_api_secref_cache[$secUuid];
2654			}
2655
2656			/**
2657			* @todo Please document this function.
2658			* @see http://drupal.org/node/1354
2659			*/
2660			function cdm_api_secref_cache_clear() {
2661			global $_cdm_api_secref_cache;
2662			$_cdm_api_secref_cache = array();
2663			}
2664
2665	f26245c8	Andreas Kohlbecker
2666	6657531f	Andreas Kohlbecker	/**
2667			* @todo Please document this function.
2668			* @see http://drupal.org/node/1354
2669			*/
2670			function _cdm_api_secref_cache_add($secUuidsStr) {
2671			global $_cdm_api_secref_cache;
2672			$ref = cdm_ws_get(CDM_WS_REFERENCE, $secUuidsStr);
2673			// Batch fetching not jet reimplemented thus:
2674			/*
2675			$assocRefSTOs = array(); if($refSTOs) { foreach($refSTOs as $ref){
2676			$assocRefSTOs[$ref->uuid] = $ref; } $_cdm_api_secref_cache =
2677			array_merge($_cdm_api_secref_cache, $assocRefSTOs); }
2678			*/
2679			$_cdm_api_secref_cache[$ref->uuid] = $ref;
2680			}
2681
2682			/**
2683			* Checks if the given uri starts with a cdm webservice url.
2684			*
2685			* Checks if the uri starts with the cdm webservice url stored in the
2686			* Drupal variable 'cdm_webservice_url'.
2687			* The 'cdm_webservice_url' can be set in the admins section of the portal.
2688			*
2689			* @param string $uri
2690			* The URI to test.
2691			*
2692			* @return bool
2693			* True if the uri starts with a cdm webservice url.
2694			*/
2695			function _is_cdm_ws_uri($uri) {
2696			return str_beginsWith($uri, variable_get('cdm_webservice_url', '#EMPTY#'));
2697			}
2698
2699			/**
2700			* @todo Please document this function.
2701			* @see http://drupal.org/node/1354
2702			*/
2703			function queryString($elements) {
2704			$query = '';
2705			foreach ($elements as $key => $value) {
2706			if (is_array($value)) {
2707			foreach ($value as $v) {
2708			$query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($v);
2709			}
2710			}
2711			else {
2712			$query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($value);
2713			}
2714			}
2715			return $query;
2716			}
2717
2718	a783afbc	Andreas Kohlbecker	/**
2719			* Compares the given CDM Term instances by the representationL10n.
2720			*
2721			* Can also be used with TermDTOs. To be used in usort()
2722			*
2723			* @see http://php.net/manual/en/function.usort.php
2724			*
2725			* @param $term1
2726			* The first CDM Term instance
2727			* @param $term2
2728			* The second CDM Term instance
2729			* @return int
2730			* The result of the comparison
2731			*/
2732			function compare_terms_by_representationL10n($term1, $term2) {
2733
2734			if (!isset($term1->representation_L10n)) {
2735			$term1->representationL10n = '';
2736			}
2737			if (!isset($term2->representation_L10n)) {
2738			$term2->representationL10n = '';
2739			}
2740
2741			return strcmp($term1->representation_L10n, $term2->representation_L10n);
2742			}
2743
2744	c079337e	Andreas Kohlbecker	function compare_terms_by_order_index($term1, $term2) {
2745
2746
2747			if (!isset($term1->orderIndex)) {
2748			$a = 0;
2749			} else {
2750			$a = $term1->orderIndex;
2751			}
2752			if (!isset($term2->orderIndex)) {
2753			$b = 0;
2754			} else {
2755			$b = $term2->orderIndex;
2756			}
2757
2758			if ($a == $b) {
2759			return 0;
2760			}
2761			return ($a < $b) ? -1 : 1;
2762
2763			}
2764
2765	a783afbc	Andreas Kohlbecker
2766	6657531f	Andreas Kohlbecker	/**
2767			* Make a 'deep copy' of an array.
2768			*
2769			* Make a complete deep copy of an array replacing
2770			* references with deep copies until a certain depth is reached
2771			* ($maxdepth) whereupon references are copied as-is...
2772			*
2773			* @see http://us3.php.net/manual/en/ref.array.php
2774			*
2775			* @param array $array
2776	cc3c9807	Andreas Kohlbecker	* @param array $copy passed by reference
2777	6657531f	Andreas Kohlbecker	* @param int $maxdepth
2778			* @param int $depth
2779			*/
2780			function array_deep_copy(&$array, &$copy, $maxdepth = 50, $depth = 0) {
2781			if ($depth > $maxdepth) {
2782			$copy = $array;
2783			return;
2784			}
2785			if (!is_array($copy)) {
2786			$copy = array();
2787			}
2788			foreach ($array as $k => &$v) {
2789			if (is_array($v)) {
2790			array_deep_copy($v, $copy[$k], $maxdepth, ++$depth);
2791			}
2792			else {
2793			$copy[$k] = $v;
2794			}
2795			}
2796			}
2797
2798	7844642a	Andreas Kohlbecker	/**
2799			* Concatenated the uuids of the passed cdm entity with `,` as glue.
2800			* The returned string is suitable for cdm webservices consuming UUIDList as
2801			* parameter
2802			*
2803			* @param array $cdm_entities
2804			*
2805			* @return string
2806			*/
2807			function cdm_uuid_list_parameter_value(array $cdm_entities){
2808			$uuids = [];
2809			foreach ($cdm_entities as $entity){
2810			if(isset($entity) && is_uuid($entity->uuid) ){
2811			$uuids[] = $entity->uuid;
2812			}
2813			}
2814			return join(',', $uuids);
2815			}
2816
2817	6657531f	Andreas Kohlbecker	/**
2818	e2464cf8	Andreas Kohlbecker	* Adds java script to create and enable a toggler for the cdm webservice debug block content.
2819	6657531f	Andreas Kohlbecker	*
2820			*/
2821	e2464cf8	Andreas Kohlbecker	function _add_js_ws_debug() {
2822
2823	5ea8b301	Andreas Kohlbecker	$data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.min.js';
2824			$colorbox_js = '/js/colorbox/jquery.colorbox-min.js';
2825			if (variable_get('cdm_js_devel_mode', FALSE)) {
2826			// use the developer versions of js libs
2827			$data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.js';
2828			$colorbox_js = '/js/colorbox/jquery.colorbox.js';
2829			}
2830			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $data_tables_js,
2831	e2464cf8	Andreas Kohlbecker	array(
2832			'type' => 'file',
2833			'weight' => JS_LIBRARY,
2834			'cache' => TRUE)
2835			);
2836
2837	5ea8b301	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $colorbox_js,
2838	e2464cf8	Andreas Kohlbecker	array(
2839			'type' => 'file',
2840			'weight' => JS_LIBRARY,
2841			'cache' => TRUE)
2842			);
2843			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/colorbox/colorbox.css');
2844			drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/DataTables-1.9.4/media/css/cdm_debug_table.css');
2845
2846			drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ws_debug_block.js',
2847			array(
2848			'type' => 'file',
2849			'weight' => JS_LIBRARY,
2850			'cache' => TRUE)
2851			);
2852	2ebf0428	Andreas Kohlbecker	drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/http-method-link.js',
2853			array(
2854			'type' => 'file',
2855			'weight' => JS_LIBRARY,
2856			'cache' => TRUE)
2857			);
2858	6657531f	Andreas Kohlbecker
2859			}
2860
2861			/**
2862			* @todo Please document this function.
2863			* @see http://drupal.org/node/1354
2864			*/
2865			function _no_classfication_uuid_message() {
2866			if (!cdm_ws_get(CDM_WS_PORTAL_TAXONOMY)) {
2867			return t('This DataPortal is not configured properly or the CDM-Server may be absent.') . ' Please check the ' . l(t('CDM web service URL'), 'admin/config/cdm_dataportal/settings/general') . t(', or contact the maintainer of this DataPortal.');
2868			}
2869			return t('This DataPortal is not configured properly.') . l(t('Please choose a valid classification'), 'admin/config/cdm_dataportal/settings/general') . t(', or contact the maintainer of this DataPortal.');
2870			}
2871
2872			/**
2873			* Implementation of hook flush_caches
2874			*
2875			* Add custom cache tables to the list of cache tables that
2876			* will be cleared by the Clear button on the Performance page or whenever
2877			* drupal_flush_all_caches is invoked.
2878			*
2879			* @author W.Addink <waddink@eti.uva.nl>
2880			*
2881			* @return array
2882			* An array with custom cache tables to include.
2883			*/
2884			function cdm_api_flush_caches() {
2885			return array('cache_cdm_ws');
2886			}
2887	f26245c8	Andreas Kohlbecker
2888	2dd59bb5	Andreas Kohlbecker	/**
2889			* Logs if the drupal variable 'cdm_debug_mode' ist set true to drupal_debug.txt in the site's temp directory.
2890			*
2891			* @param $data
2892			* The variable to log to the drupal_debug.txt log file.
2893			* @param $label
2894			* (optional) If set, a label to output before $data in the log file.
2895			*
2896			* @return
2897			* No return value if successful, FALSE if the log file could not be written
2898			* to.
2899			*
2900			* @see cdm_dataportal_init() where the log file is reset on each requests
2901			* @see dd()
2902			* @see http://drupal.org/node/314112
2903			*
2904			*/
2905			function cdm_dd($data, $label = NULL) {
2906	43251923	Andreas Kohlbecker	if(module_exists('devel') && variable_get('cdm_debug_mode', FALSE) && file_stream_wrapper_get_class('temporary') ){
2907	2dd59bb5	Andreas Kohlbecker	return dd($data, $label);
2908			}
2909			}

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