|
1
|
<?php
|
|
2
|
/**
|
|
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
|
|
|
24
|
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
|
module_load_include('inc', 'cdm_api', 'tagged_text');
|
|
31
|
|
|
32
|
/**
|
|
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
|
|
|
41
|
|
|
42
|
|
|
43
|
/**
|
|
44
|
* orderBy webservice query parameter value
|
|
45
|
*/
|
|
46
|
define('CDM_ORDER_BY_ID_ASC', 'BY_ID_ASC');
|
|
47
|
|
|
48
|
/**
|
|
49
|
* orderBy webservice query parameter value
|
|
50
|
*/
|
|
51
|
define('CDM_ORDER_BY_ID_DESC', 'BY_ID_DESC');
|
|
52
|
/**
|
|
53
|
* orderBy webservice query parameter value
|
|
54
|
*/
|
|
55
|
define('CDM_ORDER_BY_TITLE_CACHE_ASC', 'BY_TITLE_CACHE_ASC');
|
|
56
|
/**
|
|
57
|
* orderBy webservice query parameter value
|
|
58
|
*/
|
|
59
|
define('CDM_ORDER_BY_TITLE_CACHE_DESC', 'BY_TITLE_CACHE_DESC');
|
|
60
|
/**
|
|
61
|
* orderBy webservice query parameter value
|
|
62
|
*/
|
|
63
|
define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_ASC', 'BY_NOMENCLATURAL_ORDER_ASC');
|
|
64
|
/**
|
|
65
|
* orderBy webservice query parameter value
|
|
66
|
*/
|
|
67
|
define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_DESC', 'BY_NOMENCLATURAL_ORDER_DESC');
|
|
68
|
/**
|
|
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
|
|
|
78
|
/**
|
|
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
|
'access cdm content',
|
|
89
|
),
|
|
90
|
'type' => MENU_CALLBACK,
|
|
91
|
);
|
|
92
|
|
|
93
|
$items['cdm_api/setvalue/session'] = array(
|
|
94
|
'page callback' => 'setvalue_session',
|
|
95
|
'access arguments' => array(
|
|
96
|
'access cdm content',
|
|
97
|
),
|
|
98
|
'type' => MENU_CALLBACK,
|
|
99
|
);
|
|
100
|
|
|
101
|
return $items;
|
|
102
|
}
|
|
103
|
|
|
104
|
/**
|
|
105
|
* info hook implementation for the CDM web service debug block
|
|
106
|
*
|
|
107
|
* Implements hook_block_info().
|
|
108
|
*
|
|
109
|
* @see \cdm_api_block_view()
|
|
110
|
*/
|
|
111
|
function cdm_api_block_info() {
|
|
112
|
|
|
113
|
$block['cdm_ws_debug'] = array(
|
|
114
|
"info" => t("CDM web service debug"),
|
|
115
|
"cache" => DRUPAL_NO_CACHE
|
|
116
|
);
|
|
117
|
return $block;
|
|
118
|
}
|
|
119
|
|
|
120
|
/**
|
|
121
|
* block_view hook implementation for the CDM web service debug block
|
|
122
|
*
|
|
123
|
* Implements hook_block_view().
|
|
124
|
*
|
|
125
|
* @see cdm_api_block_info()
|
|
126
|
*/
|
|
127
|
function cdm_api_block_view($delta) {
|
|
128
|
switch ($delta) {
|
|
129
|
case 'cdm_ws_debug':
|
|
130
|
|
|
131
|
$cdm_ws_url = cdm_webservice_url();
|
|
132
|
|
|
133
|
$field_map = array(
|
|
134
|
'ws_uri' => t('URI') . ' <code>(' . $cdm_ws_url .'...)</code>',
|
|
135
|
'time' => t('Time'),
|
|
136
|
'fetch_seconds' => t('Fetching [s]'),
|
|
137
|
'parse_seconds' => t('Parsing [s]'),
|
|
138
|
'size_kb' => t('Size [kb]'),
|
|
139
|
'status' => t('Status'),
|
|
140
|
'data_links' => t('Links'),
|
|
141
|
);
|
|
142
|
|
|
143
|
|
|
144
|
if (!isset($_SESSION['cdm']['ws_debug'])) {
|
|
145
|
$_SESSION['cdm']['ws_debug'] = array();
|
|
146
|
}
|
|
147
|
|
|
148
|
$header = '<thead><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></thead>';
|
|
149
|
$footer = '<tfoot><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></tfoot>';
|
|
150
|
$rows = array();
|
|
151
|
|
|
152
|
foreach ($_SESSION['cdm']['ws_debug'] as $data){
|
|
153
|
|
|
154
|
$data = unserialize($data);
|
|
155
|
|
|
156
|
// stip of webservice base url
|
|
157
|
$data['ws_uri'] = str_replace($cdm_ws_url, '', $data['ws_uri']);
|
|
158
|
if($data['method'] == 'POST'){
|
|
159
|
$data['ws_uri'] = 'POST: ' . $data['ws_uri'] . '?' . $data['post_data'];
|
|
160
|
}
|
|
161
|
|
|
162
|
$cells = array();
|
|
163
|
foreach ($field_map as $field => $label){
|
|
164
|
$cells[] = '<td class="' . $field . '">' . $data[$field] . '</td>';
|
|
165
|
}
|
|
166
|
$rows[] = '<tr class="' . $data['status'] . '">' . join('' , $cells). '</tr>';
|
|
167
|
}
|
|
168
|
// clear session again
|
|
169
|
$_SESSION['cdm']['ws_debug'] = array();
|
|
170
|
|
|
171
|
_add_js_ws_debug();
|
|
172
|
|
|
173
|
$block['subject'] = ''; // no subject, title in content for having a defined element id
|
|
174
|
// otherwise it would depend on the theme
|
|
175
|
$block['content'] = array(
|
|
176
|
'#markup' => '<h4 id="cdm-ws-debug-button">' . t('CDM Debug') . '</h4>'
|
|
177
|
// cannot use theme_table() since table footer is not jet supported in D7
|
|
178
|
. '<div id="cdm-ws-debug-table-container"><table id="cdm-ws-debug-table">'
|
|
179
|
. $header
|
|
180
|
. '<tbody>' . join('', $rows) . '</tbody>'
|
|
181
|
. $footer
|
|
182
|
. '</table></div>',
|
|
183
|
'#attached' => array(
|
|
184
|
'css' => array(
|
|
185
|
drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_ws_debug.css'
|
|
186
|
)
|
|
187
|
)
|
|
188
|
);
|
|
189
|
return $block;
|
|
190
|
}
|
|
191
|
}
|
|
192
|
|
|
193
|
/**
|
|
194
|
* Implements hook_cron().
|
|
195
|
*
|
|
196
|
* Expire outdated cache entries.
|
|
197
|
*/
|
|
198
|
function cdm_api_cron() {
|
|
199
|
cache_clear_all(NULL, 'cache_cdm_ws');
|
|
200
|
}
|
|
201
|
|
|
202
|
/**
|
|
203
|
* Lists the classifications a taxon belongs to
|
|
204
|
*
|
|
205
|
* @param CDM type Taxon $taxon
|
|
206
|
* the taxon
|
|
207
|
*
|
|
208
|
* @return array
|
|
209
|
* aray of CDM instances of Type Classification
|
|
210
|
*/
|
|
211
|
function get_classifications_for_taxon($taxon) {
|
|
212
|
|
|
213
|
return cdm_ws_get(CDM_WS_TAXON_CLASSIFICATIONS, $taxon->uuid);
|
|
214
|
}
|
|
215
|
|
|
216
|
/**
|
|
217
|
* Returns the chosen FeatureTree to be used as FeatureTree for the taxon profile.
|
|
218
|
*
|
|
219
|
* The FeatureTree returned is the term tree one that has been set in the
|
|
220
|
* dataportal settings (layout->taxon:profile).
|
|
221
|
* When the chosen FeatureTree is not found in the database,
|
|
222
|
* the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
|
|
223
|
*
|
|
224
|
* @return object
|
|
225
|
* A cdm TermTree object.
|
|
226
|
*/
|
|
227
|
function get_profile_feature_tree() {
|
|
228
|
static $profile_featureTree;
|
|
229
|
|
|
230
|
if($profile_featureTree == NULL) {
|
|
231
|
$profile_featureTree = cdm_ws_get(
|
|
232
|
CDM_WS_TERMTREE,
|
|
233
|
variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
|
|
234
|
);
|
|
235
|
if (!$profile_featureTree) {
|
|
236
|
$profile_featureTree = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
|
|
237
|
}
|
|
238
|
}
|
|
239
|
|
|
240
|
return $profile_featureTree;
|
|
241
|
}
|
|
242
|
|
|
243
|
/**
|
|
244
|
* Returns the chosen TermTree to be used as FeatureTree for SpecimenDescriptions.
|
|
245
|
*
|
|
246
|
* The TermTree returned is the one that has been set in the
|
|
247
|
* dataportal settings (layout->taxon:specimen).
|
|
248
|
* When the chosen TermTree is not found in the database,
|
|
249
|
* the standard term tree (UUID_DEFAULT_TERMTREE) will be returned.
|
|
250
|
*
|
|
251
|
* @return object
|
|
252
|
* A cdm TermTree object.
|
|
253
|
*/
|
|
254
|
function cdm_get_occurrence_featureTree() {
|
|
255
|
static $occurrence_featureTree;
|
|
256
|
|
|
257
|
if($occurrence_featureTree == NULL) {
|
|
258
|
$occurrence_featureTree = cdm_ws_get(
|
|
259
|
CDM_WS_TERMTREE,
|
|
260
|
variable_get(CDM_OCCURRENCE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
|
|
261
|
);
|
|
262
|
if (!$occurrence_featureTree) {
|
|
263
|
$occurrence_featureTree = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
|
|
264
|
}
|
|
265
|
}
|
|
266
|
return $occurrence_featureTree;
|
|
267
|
}
|
|
268
|
|
|
269
|
/**
|
|
270
|
* Returns the FeatureTree for structured descriptions
|
|
271
|
*
|
|
272
|
* The FeatureTree returned is the one that has been set in the
|
|
273
|
* dataportal settings (layout->taxon:profile).
|
|
274
|
* When the chosen FeatureTree is not found in the database,
|
|
275
|
* the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
|
|
276
|
*
|
|
277
|
* @return mixed
|
|
278
|
* A cdm FeatureTree object.
|
|
279
|
*/
|
|
280
|
function get_structured_description_featureTree() {
|
|
281
|
static $structured_description_featureTree;
|
|
282
|
|
|
283
|
if($structured_description_featureTree == NULL) {
|
|
284
|
$structured_description_featureTree = cdm_ws_get(
|
|
285
|
CDM_WS_TERMTREE,
|
|
286
|
variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
|
|
287
|
);
|
|
288
|
if (!$structured_description_featureTree) {
|
|
289
|
$structured_description_featureTree = cdm_ws_get(
|
|
290
|
CDM_WS_TERMTREE,
|
|
291
|
UUID_DEFAULT_FEATURETREE
|
|
292
|
);
|
|
293
|
}
|
|
294
|
}
|
|
295
|
return $structured_description_featureTree;
|
|
296
|
}
|
|
297
|
|
|
298
|
|
|
299
|
/**
|
|
300
|
* @todo Please document this function.
|
|
301
|
* @see http://drupal.org/node/1354
|
|
302
|
*/
|
|
303
|
function set_last_taxon_page_tab($taxonPageTab) {
|
|
304
|
$_SESSION['cdm']['taxon_page_tab'] = $taxonPageTab;
|
|
305
|
}
|
|
306
|
|
|
307
|
/**
|
|
308
|
* @todo Please document this function.
|
|
309
|
* @see http://drupal.org/node/1354
|
|
310
|
*/
|
|
311
|
function get_last_taxon_page_tab() {
|
|
312
|
if (isset($_SESSION['cdm']['taxon_page_tab'])) {
|
|
313
|
return $_SESSION['cdm']['taxon_page_tab'];
|
|
314
|
}
|
|
315
|
else {
|
|
316
|
return FALSE;
|
|
317
|
}
|
|
318
|
}
|
|
319
|
|
|
320
|
/**
|
|
321
|
* NOTE: The cdm-library provides a very similar server side function. See
|
|
322
|
* eu.etaxonomy.cdm.model.media.MediaUtils.filterAndOrderMediaRepresentations()
|
|
323
|
*
|
|
324
|
* @param object $media
|
|
325
|
* @param array $mime_types
|
|
326
|
* an array of mimetypes in their order of preference. e.g:
|
|
327
|
* array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html')
|
|
328
|
* @param int $width
|
|
329
|
* The width of the optimal image. If null, the method will return the representation with the biggest expansion
|
|
330
|
* @param int $height
|
|
331
|
* The height of the optimal image. If null, the method will return the representation with the biggest expansion
|
|
332
|
* @param bool $mime_types_filter_excludes
|
|
333
|
* Toggles the mode of the $mime_types filter to exclude when set to TRUE
|
|
334
|
* @param bool $strict_size_limit
|
|
335
|
* Width an height parameters are treated as maximum values when this parameter is enabled.
|
|
336
|
* @return array
|
|
337
|
* An array with preferred media representations or else an empty array.
|
|
338
|
*/
|
|
339
|
function cdm_preferred_media_representations($media, array $mime_types, $width = NULL, $height = NULL, $mime_types_filter_excludes = FALSE, $strict_size_limit = FALSE) {
|
|
340
|
|
|
341
|
$matching_representations_by_rank = [];
|
|
342
|
if (!isset($media->representations[0])) {
|
|
343
|
return $matching_representations_by_rank;
|
|
344
|
}
|
|
345
|
|
|
346
|
foreach ($media->representations as &$representation) {
|
|
347
|
// If the mimetype is not known, try inferring it.
|
|
348
|
if (!$representation->mimeType) {
|
|
349
|
if (isset($representation->parts[0])) {
|
|
350
|
$representation->mimeType = infer_mime_type($representation->parts[0]->uri);
|
|
351
|
}
|
|
352
|
}
|
|
353
|
$mime_type_match = array_search($representation->mimeType, $mime_types) !== false;
|
|
354
|
$match_per_mime_type_filter = $mime_types_filter_excludes ? !$mime_type_match : $mime_type_match;
|
|
355
|
if ($match_per_mime_type_filter) {
|
|
356
|
$expansion_delta_sum = 0;
|
|
357
|
$valid_parts_cnt = 0;
|
|
358
|
// Look for part with the best matching size.
|
|
359
|
foreach ($representation->parts as $part) {
|
|
360
|
if (empty($part->uri)) {
|
|
361
|
// skip part if URI is missing
|
|
362
|
continue;
|
|
363
|
}
|
|
364
|
if($strict_size_limit){
|
|
365
|
if (isset($part->width) && isset($part->height) && $part->width <= $width && $part->height <= $height) {
|
|
366
|
$valid_parts_cnt++;
|
|
367
|
}
|
|
368
|
} else {
|
|
369
|
// calculate expansion delta
|
|
370
|
$valid_parts_cnt++;
|
|
371
|
$expansion_delta = PHP_INT_MAX; // biggest delta for unknown sizes
|
|
372
|
|
|
373
|
// determine the optimal size
|
|
374
|
if (isset($part->width) && isset($part->height)) {
|
|
375
|
$expansion = $part->width * $part->height;
|
|
376
|
if ($width != null && $height != null) {
|
|
377
|
$optimalExpansion = $height * $width;
|
|
378
|
} else {
|
|
379
|
$optimalExpansion = PHP_INT_MAX;
|
|
380
|
}
|
|
381
|
// determine the difference
|
|
382
|
$expansion_delta = $expansion > $optimalExpansion ? $expansion - $optimalExpansion : $optimalExpansion - $expansion;
|
|
383
|
}
|
|
384
|
// sum up the expansionDeltas of all parts contained in the representation
|
|
385
|
$expansion_delta_sum += $expansion_delta;
|
|
386
|
}// end parts
|
|
387
|
}
|
|
388
|
if($valid_parts_cnt > 0){
|
|
389
|
$expansion_delta_sum = $expansion_delta_sum / $valid_parts_cnt;
|
|
390
|
$matching_representations_by_rank[$expansion_delta_sum] = $representation;
|
|
391
|
}
|
|
392
|
}
|
|
393
|
}
|
|
394
|
|
|
395
|
// Sort the array so that the smallest key value is the first in the array
|
|
396
|
ksort($matching_representations_by_rank);
|
|
397
|
return $matching_representations_by_rank;
|
|
398
|
}
|
|
399
|
|
|
400
|
|
|
401
|
|
|
402
|
/**
|
|
403
|
* Infers the mime type of a file using the filename extension.
|
|
404
|
*
|
|
405
|
* The filename extension is used to infer the mime type.
|
|
406
|
*
|
|
407
|
* @param string $filepath
|
|
408
|
* The path to the respective file.
|
|
409
|
*
|
|
410
|
* @return string
|
|
411
|
* The mimetype for the file or FALSE if the according mime type could
|
|
412
|
* not be found.
|
|
413
|
*/
|
|
414
|
function infer_mime_type($filepath) {
|
|
415
|
static $mimemap = NULL;
|
|
416
|
if (!$mimemap) {
|
|
417
|
$mimemap = array(
|
|
418
|
'jpg' => 'image/jpeg',
|
|
419
|
'jpeg' => 'image/jpeg',
|
|
420
|
'png' => 'image/png',
|
|
421
|
'gif' => 'image/gif',
|
|
422
|
'giff' => 'image/gif',
|
|
423
|
'tif' => 'image/tif',
|
|
424
|
'tiff' => 'image/tif',
|
|
425
|
'pdf' => 'application/pdf',
|
|
426
|
'html' => 'text/html',
|
|
427
|
'htm' => 'text/html',
|
|
428
|
);
|
|
429
|
}
|
|
430
|
$extension = substr($filepath, strrpos($filepath, '.') + 1);
|
|
431
|
if (isset($mimemap[$extension])) {
|
|
432
|
return $mimemap[$extension];
|
|
433
|
}
|
|
434
|
else {
|
|
435
|
// FIXME remove this hack just return FALSE;
|
|
436
|
return 'text/html';
|
|
437
|
}
|
|
438
|
}
|
|
439
|
|
|
440
|
/**
|
|
441
|
* Formats a mysql datatime as string
|
|
442
|
*
|
|
443
|
* @param $datetime
|
|
444
|
* @param string $format
|
|
445
|
*
|
|
446
|
* @return
|
|
447
|
* the formatted string representation of the $datetime
|
|
448
|
*/
|
|
449
|
function format_datetime($datetime, $format = 'Y-m-d H:i:s O', $strip_zeros = true){
|
|
450
|
|
|
451
|
return date($format, strtotime($datetime));
|
|
452
|
}
|
|
453
|
|
|
454
|
/**
|
|
455
|
* Converts an ISO 8601 org.joda.time.Partial to a year.
|
|
456
|
*
|
|
457
|
* The function expects an ISO 8601 time representation of a
|
|
458
|
* org.joda.time.Partial of the form yyyy-MM-dd.
|
|
459
|
*
|
|
460
|
* @param string $partial
|
|
461
|
* ISO 8601 time representation of a org.joda.time.Partial.
|
|
462
|
*
|
|
463
|
* @return string
|
|
464
|
* Returns the year. In case the year is unknown (= ????), it returns NULL.
|
|
465
|
*/
|
|
466
|
function partialToYear($partial) {
|
|
467
|
if (is_string($partial)) {
|
|
468
|
$year = drupal_substr($partial, 0, 4);
|
|
469
|
if (preg_match("/[0-9][0-9][0-9][0-9]/", $year)) {
|
|
470
|
return $year;
|
|
471
|
}
|
|
472
|
}
|
|
473
|
return '';
|
|
474
|
}
|
|
475
|
|
|
476
|
/**
|
|
477
|
* Converts an ISO 8601 org.joda.time.Partial to a month.
|
|
478
|
*
|
|
479
|
* This function expects an ISO 8601 time representation of a
|
|
480
|
* org.joda.time.Partial of the form yyyy-MM-dd.
|
|
481
|
* In case the month is unknown (= ???) NULL is returned.
|
|
482
|
*
|
|
483
|
* @param string $partial
|
|
484
|
* ISO 8601 time representation of a org.joda.time.Partial.
|
|
485
|
*
|
|
486
|
* @return string
|
|
487
|
* A month.
|
|
488
|
*/
|
|
489
|
function partialToMonth($partial) {
|
|
490
|
if (is_string($partial)) {
|
|
491
|
$month = drupal_substr($partial, 5, 2);
|
|
492
|
if (preg_match("/[0-9][0-9]/", $month)) {
|
|
493
|
return $month;
|
|
494
|
}
|
|
495
|
}
|
|
496
|
return '';
|
|
497
|
}
|
|
498
|
|
|
499
|
/**
|
|
500
|
* Converts an ISO 8601 org.joda.time.Partial to a day.
|
|
501
|
*
|
|
502
|
* This function expects an ISO 8601 time representation of a
|
|
503
|
* org.joda.time.Partial of the form yyyy-MM-dd and returns the day as string.
|
|
504
|
* In case the day is unknown (= ???) NULL is returned.
|
|
505
|
*
|
|
506
|
* @param string $partial
|
|
507
|
* ISO 8601 time representation of a org.joda.time.Partial.
|
|
508
|
*
|
|
509
|
* @return string
|
|
510
|
* A day.
|
|
511
|
*/
|
|
512
|
function partialToDay($partial) {
|
|
513
|
if (is_string($partial)) {
|
|
514
|
$day = drupal_substr($partial, 8, 2);
|
|
515
|
if (preg_match("/[0-9][0-9]/", $day)) {
|
|
516
|
return $day;
|
|
517
|
}
|
|
518
|
}
|
|
519
|
return '';
|
|
520
|
}
|
|
521
|
|
|
522
|
/**
|
|
523
|
* Converts an ISO 8601 org.joda.time.Partial to YYYY-MM-DD.
|
|
524
|
*
|
|
525
|
* This function expects an ISO 8601 time representations of a
|
|
526
|
* org.joda.time.Partial of the form yyyy-MM-dd and returns
|
|
527
|
* four digit year, month and day with dashes:
|
|
528
|
* YYYY-MM-DD eg: "2012-06-30", "1956-00-00"
|
|
529
|
*
|
|
530
|
* The partial may contain question marks eg: "1973-??-??",
|
|
531
|
* these are turned in to '00' or are stripped depending of the $stripZeros
|
|
532
|
* parameter.
|
|
533
|
*
|
|
534
|
* @param string $partial
|
|
535
|
* org.joda.time.Partial.
|
|
536
|
* @param bool $stripZeros
|
|
537
|
* If set to TRUE the zero (00) month and days will be hidden:
|
|
538
|
* eg 1956-00-00 becomes 1956. The default is TRUE.
|
|
539
|
* @param string @format
|
|
540
|
* Can ve used to specify the format of the date string, currently the following format strings are supported
|
|
541
|
* - "YYYY": Year only
|
|
542
|
* - "YYYY-MM-DD": this is the default
|
|
543
|
*
|
|
544
|
* @return string
|
|
545
|
* YYYY-MM-DD formatted year, month, day.
|
|
546
|
*/
|
|
547
|
function partialToDate($partial, $stripZeros = TRUE, $format= "YYYY-MM-DD") {
|
|
548
|
|
|
549
|
$y = NULL; $m = NULL; $d = NULL;
|
|
550
|
|
|
551
|
if(strpos($format, 'YY') !== FALSE){
|
|
552
|
$y = partialToYear($partial);
|
|
553
|
}
|
|
554
|
if(strpos($format, 'MM') !== FALSE){
|
|
555
|
$m = partialToMonth($partial);
|
|
556
|
}
|
|
557
|
if(strpos($format, 'DD') !== FALSE){
|
|
558
|
$d = partialToDay($partial);
|
|
559
|
}
|
|
560
|
|
|
561
|
$y = $y ? $y : '0000';
|
|
562
|
$m = $m ? $m : '00';
|
|
563
|
$d = $d ? $d : '00';
|
|
564
|
|
|
565
|
$date = '';
|
|
566
|
|
|
567
|
if ($y == '0000' && $stripZeros && $m == '00' && $d == '00') {
|
|
568
|
return '';
|
|
569
|
}
|
|
570
|
else {
|
|
571
|
$date = $y;
|
|
572
|
}
|
|
573
|
|
|
574
|
if ($m == '00' && $stripZeros && $d == '00') {
|
|
575
|
return $date;
|
|
576
|
}
|
|
577
|
else {
|
|
578
|
$date .= "-" . $m;
|
|
579
|
}
|
|
580
|
|
|
581
|
if ($d == '00' && $stripZeros) {
|
|
582
|
return $date;
|
|
583
|
}
|
|
584
|
else {
|
|
585
|
$date .= "-" . $d;
|
|
586
|
}
|
|
587
|
return $date;
|
|
588
|
}
|
|
589
|
|
|
590
|
/**
|
|
591
|
* Converts a time period to a string.
|
|
592
|
*
|
|
593
|
* See also partialToDate($partial, $stripZeros).
|
|
594
|
*
|
|
595
|
* @param object $period
|
|
596
|
* An JodaTime org.joda.time.Period object.
|
|
597
|
* @param bool $stripZeros
|
|
598
|
* If set to True, the zero (00) month and days will be hidden:
|
|
599
|
* eg 1956-00-00 becomes 1956. The default is TRUE.
|
|
600
|
* @param string @format
|
|
601
|
* Can ve used to specify the format of the date string, currently the following format strings are supported
|
|
602
|
* - "YYYY": Year only
|
|
603
|
* - "YYYY-MM-DD": this is the default
|
|
604
|
*
|
|
605
|
* @return string
|
|
606
|
* Returns a date in the form of a string.
|
|
607
|
*/
|
|
608
|
function timePeriodToString($period, $stripZeros = TRUE, $format = "YYYY-MM-DD") {
|
|
609
|
$dateString = '';
|
|
610
|
if (is_string($period)){
|
|
611
|
$dateString = $period;
|
|
612
|
}else {
|
|
613
|
if ($period->freeText) {
|
|
614
|
$dateString = $period->freeText;
|
|
615
|
}elseif(isset_not_empty($period->timePeriod)){
|
|
616
|
$dateString = $period->timePeriod;
|
|
617
|
}else {
|
|
618
|
if ($period->start) {
|
|
619
|
$dateString = partialToDate($period->start, $stripZeros, $format);
|
|
620
|
}
|
|
621
|
if ($period->end) {
|
|
622
|
$end_str = partialToDate($period->end, $stripZeros, $format);
|
|
623
|
$dateString .= ($dateString && $end_str ? ' ' . t('to') . ' ' : '') . $end_str;
|
|
624
|
}
|
|
625
|
|
|
626
|
}
|
|
627
|
}
|
|
628
|
|
|
629
|
return $dateString;
|
|
630
|
}
|
|
631
|
|
|
632
|
/**
|
|
633
|
* returns the earliest date available in the $period in a normalized
|
|
634
|
* form suitable for sorting, e.g.:
|
|
635
|
*
|
|
636
|
* - 1956-00-00
|
|
637
|
* - 0000-00-00
|
|
638
|
* - 1957-03-00
|
|
639
|
*
|
|
640
|
* that is either the start date is returned if set otherwise the
|
|
641
|
* end date
|
|
642
|
*
|
|
643
|
* @param $period
|
|
644
|
* An JodaTime org.joda.time.Period object.
|
|
645
|
* @return string normalized form of the date
|
|
646
|
* suitable for sorting
|
|
647
|
*/
|
|
648
|
function timePeriodAsOrderKey($period) {
|
|
649
|
$dateString = '';
|
|
650
|
if ($period->start) {
|
|
651
|
$dateString = partialToDate($period->start, false);
|
|
652
|
}
|
|
653
|
if ($period->end) {
|
|
654
|
$dateString .= partialToDate($period->end, false);
|
|
655
|
}
|
|
656
|
return $dateString;
|
|
657
|
}
|
|
658
|
|
|
659
|
/**
|
|
660
|
* Composes a absolute CDM web service URI with parameters and querystring.
|
|
661
|
*
|
|
662
|
* @param string $uri_pattern
|
|
663
|
* String with place holders ($0, $1, ..) that should be replaced by the
|
|
664
|
* according element of the $pathParameters array.
|
|
665
|
* @param array $pathParameters
|
|
666
|
* An array of path elements, or a single element.
|
|
667
|
* @param string $query
|
|
668
|
* A query string to append to the URL.
|
|
669
|
*
|
|
670
|
* @return string
|
|
671
|
* A complete URL with parameters to a CDM webservice.
|
|
672
|
*/
|
|
673
|
function cdm_compose_ws_url($uri_pattern, $pathParameters = array(), $query = NULL) {
|
|
674
|
if (empty($pathParameters)) {
|
|
675
|
$pathParameters = array();
|
|
676
|
}
|
|
677
|
$path = cdm_compose_url($uri_pattern, $pathParameters, $query);
|
|
678
|
$url = cdm_webservice_url() . $path;
|
|
679
|
return $url;
|
|
680
|
}
|
|
681
|
|
|
682
|
/**
|
|
683
|
* Wrapper to access the 'cdm_webservice_url' and to ensure that
|
|
684
|
* the returned webservice url scheme conforms to the scheme of the
|
|
685
|
* page request.
|
|
686
|
*
|
|
687
|
* @param string $default optional parameter to set the default, by default an empty string is returned
|
|
688
|
*/
|
|
689
|
function cdm_webservice_url($default = ''){
|
|
690
|
static $conform_ws_url = null;
|
|
691
|
if($conform_ws_url === null) {
|
|
692
|
$ws_url = variable_get('cdm_webservice_url', $default);
|
|
693
|
if($ws_url && $_SERVER['REQUEST_SCHEME'] == 'https' && parse_url($ws_url, PHP_URL_SCHEME) === 'http'){
|
|
694
|
$conform_ws_url = preg_replace("/^http\:/", "https:", $ws_url);
|
|
695
|
drupal_set_message('The <stong>CDM web service URL</stong> scheme should be set to <strong>HTTPS</strong> the '
|
|
696
|
. l('CDM Data Portal settings', 'admin/config/cdm_dataportal/settings'), 'warning');
|
|
697
|
} else {
|
|
698
|
$conform_ws_url = $ws_url;
|
|
699
|
}
|
|
700
|
}
|
|
701
|
return $conform_ws_url;
|
|
702
|
}
|
|
703
|
|
|
704
|
/**
|
|
705
|
* Composes a relative Url with parameters and querystring.
|
|
706
|
*
|
|
707
|
* @param string $uri_pattern
|
|
708
|
* String with place holders ($0, $1, ..) that should be replaced by the
|
|
709
|
* according element of the $pathParameters array.
|
|
710
|
* @param array $pathParameters
|
|
711
|
* An array of path elements, or a single element.
|
|
712
|
* @param string $query
|
|
713
|
* A query string to append to the URL.
|
|
714
|
*
|
|
715
|
* @return string
|
|
716
|
* A relative URL with query parameters.
|
|
717
|
*/
|
|
718
|
function cdm_compose_url($uri_pattern, $pathParameters, $query = NULL) {
|
|
719
|
|
|
720
|
// (1)
|
|
721
|
// Substitute all place holders ($0, $1, ..) in the $uri_pattern by the
|
|
722
|
// according element of the $pathParameters array.
|
|
723
|
static $helperArray = [];
|
|
724
|
if (isset($pathParameters) && !is_array($pathParameters)) {
|
|
725
|
$helperArray[0] = $pathParameters;
|
|
726
|
$pathParameters = $helperArray;
|
|
727
|
}
|
|
728
|
|
|
729
|
$i = 0;
|
|
730
|
while (strpos($uri_pattern, "$" . $i) !== FALSE) {
|
|
731
|
if (count($pathParameters) <= $i) {
|
|
732
|
drupal_set_message('cdm_compose_url(): missing pathParameter ' . $i .' for ' . $uri_pattern, 'error');
|
|
733
|
break;
|
|
734
|
}
|
|
735
|
$uri_pattern = str_replace("$" . $i, rawurlencode($pathParameters[$i]), $uri_pattern);
|
|
736
|
++$i;
|
|
737
|
}
|
|
738
|
|
|
739
|
// (2)
|
|
740
|
// Append all remaining element of the $pathParameters array as path
|
|
741
|
// elements.
|
|
742
|
if (count($pathParameters) > $i) {
|
|
743
|
// Strip trailing slashes.
|
|
744
|
if (strrchr($uri_pattern, '/') == strlen($uri_pattern)) {
|
|
745
|
$uri_pattern = substr($uri_pattern, 0, strlen($uri_pattern) - 1);
|
|
746
|
}
|
|
747
|
while (count($pathParameters) > $i) {
|
|
748
|
$uri_pattern .= '/' . rawurlencode($pathParameters[$i]);
|
|
749
|
++$i;
|
|
750
|
}
|
|
751
|
}
|
|
752
|
|
|
753
|
// (3)
|
|
754
|
// Append the query string supplied by $query.
|
|
755
|
$uri_pattern = append_query_parameters($uri_pattern, $query);
|
|
756
|
|
|
757
|
$path = $uri_pattern;
|
|
758
|
return $path;
|
|
759
|
}
|
|
760
|
|
|
761
|
/**
|
|
762
|
* @param string $uri
|
|
763
|
*
|
|
764
|
* @param $query_string
|
|
765
|
*
|
|
766
|
* @return string
|
|
767
|
*/
|
|
768
|
function append_query_parameters($uri, $query_string) {
|
|
769
|
|
|
770
|
if (isset($query_string)) {
|
|
771
|
$uri .= (strpos($uri, '?') !== FALSE ? '&' : '?') . $query_string;
|
|
772
|
}
|
|
773
|
|
|
774
|
return $uri;
|
|
775
|
}
|
|
776
|
|
|
777
|
/**
|
|
778
|
* @todo wouldn't it more elegant and secure to only pass a uuid and additional function parameters
|
|
779
|
* together with a theme name to such a proxy function?
|
|
780
|
* Well this would not be covering all use cases but maybe all which involve AHAH.
|
|
781
|
* Maybe we want to have two different proxy functions, one with theming and one without?
|
|
782
|
*
|
|
783
|
* @param string $uri
|
|
784
|
* A URI to a CDM Rest service from which to retrieve an object
|
|
785
|
* @param string|null $hook
|
|
786
|
* (optional) The hook name to which the retrieved object should be passed.
|
|
787
|
* Hooks can either be a theme_hook() or compose_hook() implementation
|
|
788
|
* 'theme' hook functions return a string whereas 'compose' hooks are returning render arrays
|
|
789
|
* suitable for drupal_render()
|
|
790
|
*
|
|
791
|
* @todo Please document this function.
|
|
792
|
* @see http://drupal.org/node/1354
|
|
793
|
*/
|
|
794
|
function proxy_content($uri, $hook = NULL) {
|
|
795
|
|
|
796
|
$args = func_get_args();
|
|
797
|
$do_gzip = function_exists('gzencode');
|
|
798
|
$uriEncoded = array_shift($args);
|
|
799
|
$uri = urldecode($uriEncoded);
|
|
800
|
$hook = array_shift($args);
|
|
801
|
$request_method = strtoupper($_SERVER["REQUEST_METHOD"]);
|
|
802
|
|
|
803
|
$post_data = null;
|
|
804
|
|
|
805
|
if ($request_method == "POST" || $request_method == "PUT") {
|
|
806
|
// read response body via inputstream module
|
|
807
|
$post_data = file_get_contents("php://input");
|
|
808
|
}
|
|
809
|
|
|
810
|
// Find and deserialize arrays.
|
|
811
|
foreach ($args as &$arg) {
|
|
812
|
// FIXME use regex to find serialized arrays.
|
|
813
|
// or should we accept json instead of php serializations?
|
|
814
|
if (strpos($arg, "a:") === 0) {
|
|
815
|
$arg = unserialize($arg);
|
|
816
|
}
|
|
817
|
}
|
|
818
|
|
|
819
|
// In all these cases perform a simple get request.
|
|
820
|
// TODO reconsider caching logic in this function.
|
|
821
|
|
|
822
|
if (empty($hook)) {
|
|
823
|
// simply return the webservice response
|
|
824
|
// Print out JSON, the cache cannot be used since it contains objects.
|
|
825
|
$http_response = cdm_http_request($uri, $request_method, $post_data);
|
|
826
|
if (isset($http_response->headers)) {
|
|
827
|
foreach ($http_response->headers as $hname => $hvalue) {
|
|
828
|
drupal_add_http_header($hname, $hvalue);
|
|
829
|
}
|
|
830
|
}
|
|
831
|
if (isset($http_response->data)) {
|
|
832
|
print $http_response->data;
|
|
833
|
flush();
|
|
834
|
}
|
|
835
|
exit(); // leave drupal here
|
|
836
|
} else {
|
|
837
|
// $hook has been supplied
|
|
838
|
// handle $hook either as compose or theme hook
|
|
839
|
// pass through theme or compose hook
|
|
840
|
// compose hooks can be called without data, therefore
|
|
841
|
// passing the $uri in this case is not always a requirement
|
|
842
|
|
|
843
|
if($uri && $uri != 'NULL') {
|
|
844
|
// do a security check since the $uri will be passed
|
|
845
|
// as absolute URI to cdm_ws_get()
|
|
846
|
if (!_is_cdm_ws_uri($uri)) {
|
|
847
|
drupal_set_message(
|
|
848
|
'Invalid call of proxy_content() with callback parameter \'' . $hook . '\' and URI:' . $uri,
|
|
849
|
'error'
|
|
850
|
);
|
|
851
|
return '';
|
|
852
|
}
|
|
853
|
|
|
854
|
$obj = cdm_ws_get($uri, NULL, $post_data, $request_method, TRUE);
|
|
855
|
} else {
|
|
856
|
$obj = NULL;
|
|
857
|
}
|
|
858
|
|
|
859
|
$response_data = NULL;
|
|
860
|
|
|
861
|
if (function_exists('compose_' . $hook)){
|
|
862
|
// call compose hook
|
|
863
|
|
|
864
|
$elements = call_user_func('compose_' . $hook, $obj);
|
|
865
|
// pass the render array to drupal_render()
|
|
866
|
$response_data = drupal_render($elements);
|
|
867
|
} else {
|
|
868
|
// call theme hook
|
|
869
|
|
|
870
|
// TODO use theme registry to get the registered hook info and
|
|
871
|
// use these defaults
|
|
872
|
switch($hook) {
|
|
873
|
case 'cdm_taxontree':
|
|
874
|
$variables = array(
|
|
875
|
'tree' => $obj,
|
|
876
|
'filterIncludes' => isset($args[0]) ? $args[0] : NULL,
|
|
877
|
'show_filter_switch' => isset($args[1]) ? $args[1] : FALSE,
|
|
878
|
'tree_node_callback' => isset($args[2]) ? $args[2] : FALSE,
|
|
879
|
'element_name'=> isset($args[3]) ? $args[3] : FALSE,
|
|
880
|
);
|
|
881
|
$response_data = theme($hook, $variables);
|
|
882
|
break;
|
|
883
|
|
|
884
|
case 'cdm_list_of_taxa':
|
|
885
|
$variables = array(
|
|
886
|
'records' => $obj,
|
|
887
|
'freetextSearchResults' => isset($args[0]) ? $args[0] : array(),
|
|
888
|
'show_classification' => isset($args[1]) ? $args[1] : FALSE);
|
|
889
|
$response_data = theme($hook, $variables);
|
|
890
|
break;
|
|
891
|
|
|
892
|
default:
|
|
893
|
drupal_set_message(t(
|
|
894
|
'Theme !theme is not yet supported by the function !function.', array(
|
|
895
|
'!theme' => $hook,
|
|
896
|
'!function' => __FUNCTION__,
|
|
897
|
)), 'error');
|
|
898
|
break;
|
|
899
|
} // END of theme hook switch
|
|
900
|
} // END of tread as theme hook
|
|
901
|
|
|
902
|
|
|
903
|
if($do_gzip){
|
|
904
|
$response_data = gzencode($response_data, 2, FORCE_GZIP);
|
|
905
|
drupal_add_http_header('Content-Encoding', 'gzip');
|
|
906
|
}
|
|
907
|
drupal_add_http_header('Content-Type', 'text/html; charset=utf-8');
|
|
908
|
drupal_add_http_header('Content-Length', strlen($response_data));
|
|
909
|
|
|
910
|
print $response_data;
|
|
911
|
} // END of handle $hook either as compose ot theme hook
|
|
912
|
|
|
913
|
}
|
|
914
|
|
|
915
|
/**
|
|
916
|
* @todo Please document this function.
|
|
917
|
* @see http://drupal.org/node/1354
|
|
918
|
*/
|
|
919
|
function setvalue_session() {
|
|
920
|
if ($_REQUEST['var'] && strlen($_REQUEST['var']) > 4) {
|
|
921
|
$var_keys = substr($_REQUEST['var'], 1, strlen($_REQUEST['var']) - 2);
|
|
922
|
$var_keys = explode('][', $var_keys);
|
|
923
|
}
|
|
924
|
else {
|
|
925
|
return;
|
|
926
|
}
|
|
927
|
$val = isset($_REQUEST['val']) ? $_REQUEST['val'] : NULL;
|
|
928
|
|
|
929
|
// Prevent from malicous tags.
|
|
930
|
$val = strip_tags($val);
|
|
931
|
|
|
932
|
$session_var = &$_SESSION;
|
|
933
|
//$i = 0;
|
|
934
|
foreach ($var_keys as $key) {
|
|
935
|
// $hasMoreKeys = ++$i < count($session);
|
|
936
|
if (!isset($session_var[$key]) || !is_array($session_var[$key])) {
|
|
937
|
$session_var[$key] = array();
|
|
938
|
}
|
|
939
|
$session_var = &$session_var[$key];
|
|
940
|
}
|
|
941
|
$session_var = $val;
|
|
942
|
if (isset($_REQUEST['destination'])) {
|
|
943
|
drupal_goto($_REQUEST['destination']);
|
|
944
|
}
|
|
945
|
}
|
|
946
|
|
|
947
|
/**
|
|
948
|
* @todo Please document this function.
|
|
949
|
* @see http://drupal.org/node/1354
|
|
950
|
*/
|
|
951
|
function uri_uriByProxy($uri, $theme = FALSE) {
|
|
952
|
// usage: url('cdm_api/proxy/'.urlencode($content_url)."/$theme");)
|
|
953
|
return url('cdm_api/proxy/' . urlencode($uri) . (isset($theme) ? "/$theme" : ''));
|
|
954
|
}
|
|
955
|
|
|
956
|
/**
|
|
957
|
* Composes the the absolute REST service URI to the annotations pager
|
|
958
|
* for the given CDM entity.
|
|
959
|
*
|
|
960
|
* NOTE: Not all CDM Base types are yet supported.
|
|
961
|
*
|
|
962
|
* @param $cdm_entity
|
|
963
|
* The CDM entity to construct the annotations pager uri for
|
|
964
|
*/
|
|
965
|
function cdm_compose_annotations_uri($cdm_entity) {
|
|
966
|
$cdm_entity_type = "";
|
|
967
|
if (isset_not_empty($cdm_entity->class)){
|
|
968
|
$cdm_entity_type = $cdm_entity->class;
|
|
969
|
}elseif(isset_not_empty($cdm_entity->clazz)){
|
|
970
|
$cdm_entity_type = $cdm_entity->clazz;
|
|
971
|
}
|
|
972
|
|
|
973
|
|
|
974
|
|
|
975
|
if($cdm_entity_type == 'DerivedUnitFacade'){
|
|
976
|
// TODO with the below code we may miss annotations.
|
|
977
|
// Better implement a derivedUnitFacade/{uuid}/annotations service and use that instead
|
|
978
|
if(isset($cdm_entity->fieldUnitEntityReference)){
|
|
979
|
$cdm_entity_type = $cdm_entity->fieldUnitEntityReference->type;
|
|
980
|
$cdm_entity_uuid = $cdm_entity->fieldUnitEntityReference->uuid;
|
|
981
|
} elseif(isset($cdm_entity->baseUnitEntityReference)){
|
|
982
|
$cdm_entity_type = $cdm_entity->baseUnitEntityReference->type;
|
|
983
|
$cdm_entity_uuid = $cdm_entity->baseUnitEntityReference->uuid;
|
|
984
|
}
|
|
985
|
} elseif ($cdm_entity_type == 'TypedEntityReference'){
|
|
986
|
$cdm_entity_type = $cdm_entity->type;
|
|
987
|
$cdm_entity_uuid = $cdm_entity->uuid;
|
|
988
|
} else {
|
|
989
|
if (isset($cdm_entity->uuid)) {
|
|
990
|
$cdm_entity_uuid = $cdm_entity->uuid;
|
|
991
|
}
|
|
992
|
}
|
|
993
|
|
|
994
|
if(!isset($cdm_entity_uuid) || !isset($cdm_entity_type) || !$cdm_entity_type ){
|
|
995
|
// silently give up
|
|
996
|
return;
|
|
997
|
}
|
|
998
|
|
|
999
|
$ws_base_uri = cdm_ws_base_uri($cdm_entity_type);
|
|
1000
|
|
|
1001
|
if($ws_base_uri === null){
|
|
1002
|
trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdm_entity_type), E_USER_ERROR);
|
|
1003
|
}
|
|
1004
|
return cdm_compose_ws_url($ws_base_uri, array(
|
|
1005
|
$cdm_entity_uuid,
|
|
1006
|
'annotations',
|
|
1007
|
));
|
|
1008
|
}
|
|
1009
|
|
|
1010
|
/**
|
|
1011
|
* Provides the base URI of the cdm REST service responsible for the passed simple name
|
|
1012
|
* of a CDM java class. For example 'TaxonName' is the simple name of 'eu.etaxonomy.cdm.model.name.TaxonName'
|
|
1013
|
*
|
|
1014
|
* @param $cdm_type_simple
|
|
1015
|
* simple name of a CDM java class
|
|
1016
|
* @return null|string
|
|
1017
|
*/
|
|
1018
|
function cdm_ws_base_uri($cdm_type_simple)
|
|
1019
|
{
|
|
1020
|
switch ($cdm_type_simple) {
|
|
1021
|
case 'TaxonNode':
|
|
1022
|
case 'TaxonNodeDto':
|
|
1023
|
$ws_base_uri = CDM_WS_TAXONNODE;
|
|
1024
|
break;
|
|
1025
|
|
|
1026
|
case 'TaxonBase':
|
|
1027
|
case 'Taxon':
|
|
1028
|
case 'Synonym':
|
|
1029
|
$ws_base_uri = CDM_WS_TAXON;
|
|
1030
|
break;
|
|
1031
|
|
|
1032
|
case 'TaxonName':
|
|
1033
|
$ws_base_uri = CDM_WS_NAME;
|
|
1034
|
break;
|
|
1035
|
|
|
1036
|
case 'Media':
|
|
1037
|
$ws_base_uri = CDM_WS_MEDIA;
|
|
1038
|
break;
|
|
1039
|
|
|
1040
|
case 'Reference':
|
|
1041
|
$ws_base_uri = CDM_WS_REFERENCE;
|
|
1042
|
break;
|
|
1043
|
|
|
1044
|
case 'Registration':
|
|
1045
|
$ws_base_uri = CDM_WS_REGISTRATION;
|
|
1046
|
break;
|
|
1047
|
|
|
1048
|
case 'FieldUnit':
|
|
1049
|
case 'DerivedUnit':
|
|
1050
|
case 'DnaSample':
|
|
1051
|
case 'MediaSpecimen':
|
|
1052
|
case 'DerivedUnitDTO':
|
|
1053
|
case 'FieldUnitDTO':
|
|
1054
|
case 'DNASampleDTO':
|
|
1055
|
$ws_base_uri = CDM_WS_OCCURRENCE;
|
|
1056
|
break;
|
|
1057
|
|
|
1058
|
case 'Amplification':
|
|
1059
|
case 'DerivationEvent':
|
|
1060
|
case 'DeterminationEvent':
|
|
1061
|
case 'GatheringEvent':
|
|
1062
|
case 'MaterialOrMethodEvent':
|
|
1063
|
case 'SingleRead':
|
|
1064
|
$ws_base_uri = CDM_WS_EVENTBASE;
|
|
1065
|
break;
|
|
1066
|
|
|
1067
|
case 'Distribution':
|
|
1068
|
case 'TextData':
|
|
1069
|
case 'TaxonInteraction':
|
|
1070
|
case 'QuantitativeData':
|
|
1071
|
case 'IndividualsAssociation':
|
|
1072
|
case 'CommonTaxonName':
|
|
1073
|
case 'CategoricalData':
|
|
1074
|
case 'FactDto':
|
|
1075
|
case 'CommonNameDto':
|
|
1076
|
case 'IndividualsAssociationDto':
|
|
1077
|
$ws_base_uri = CDM_WS_DESCRIPTIONELEMENT;
|
|
1078
|
break;
|
|
1079
|
|
|
1080
|
case 'Person':
|
|
1081
|
case 'Team':
|
|
1082
|
case 'AgentBase':
|
|
1083
|
$ws_base_uri = CDM_WS_AGENT;
|
|
1084
|
break;
|
|
1085
|
|
|
1086
|
case 'PolytomousKey':
|
|
1087
|
case 'MediaKey':
|
|
1088
|
case 'MultiAccessKey':
|
|
1089
|
$ws_base_uri = $cdm_type_simple;
|
|
1090
|
$ws_base_uri[0] = strtolower($ws_base_uri[0]);
|
|
1091
|
break;
|
|
1092
|
|
|
1093
|
case 'TextualTypeDesignation':
|
|
1094
|
case 'SpecimenTypeDesignation':
|
|
1095
|
case 'NameTypeDesignation':
|
|
1096
|
case 'TypeDesignationDTO':
|
|
1097
|
$ws_base_uri = CDM_WS_TYPEDESIGNATION;
|
|
1098
|
break;
|
|
1099
|
default:
|
|
1100
|
$ws_base_uri = null;
|
|
1101
|
drupal_set_message(
|
|
1102
|
t('cdm_ws_base_uri() - cdm type name "@cdm_type_simple" unsupported',
|
|
1103
|
array('@cdm_type_simple' => $cdm_type_simple )),
|
|
1104
|
'error');
|
|
1105
|
}
|
|
1106
|
return $ws_base_uri;
|
|
1107
|
}
|
|
1108
|
|
|
1109
|
function cdm_type_has_tagged_text($cdm_type_name){
|
|
1110
|
return array_search($cdm_type_name, ['TaxonName', 'Taxon', 'Synonym']) !== false;
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
/**
|
|
1114
|
* Enter description here...
|
|
1115
|
*
|
|
1116
|
* @param string $resource_uri
|
|
1117
|
* @param int $page_size
|
|
1118
|
* The maximum number of entities returned per page.
|
|
1119
|
* The default page size as configured in the cdm server
|
|
1120
|
* will be used if set to NULL
|
|
1121
|
* to return all entities in a single page).
|
|
1122
|
* @param int $page_index
|
|
1123
|
* The number of the page to be returned, the first page has the
|
|
1124
|
* page_index = 0
|
|
1125
|
* @param array $query
|
|
1126
|
* A array holding the HTTP request query parameters for the request
|
|
1127
|
* @param string $method
|
|
1128
|
* The HTTP method to use, valid values are "GET" or "POST"
|
|
1129
|
* @param bool $absolute_uri
|
|
1130
|
* TRUE when the URL should be treated as absolute URL.
|
|
1131
|
*
|
|
1132
|
* @return object
|
|
1133
|
* A CDM Pager object
|
|
1134
|
*
|
|
1135
|
*/
|
|
1136
|
function cdm_ws_page($resource_uri, $page_size, $page_index, array $query = array(), $method = 'GET', $absolute_uri = FALSE) {
|
|
1137
|
|
|
1138
|
$query['pageIndex'] = $page_index;
|
|
1139
|
$query['pageSize'] = $page_size;
|
|
1140
|
|
|
1141
|
$pager = cdm_ws_get($resource_uri, NULL, queryString($query), $method, $absolute_uri);
|
|
1142
|
if(is_array($pager)){
|
|
1143
|
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);
|
|
1144
|
$records = $pager;
|
|
1145
|
$pager = new stdClass();
|
|
1146
|
$pager->records = $records;
|
|
1147
|
$pager->count = count($records);
|
|
1148
|
$pager->pageSize = $pager->count;
|
|
1149
|
$pager->nextIndex = null;
|
|
1150
|
}
|
|
1151
|
return $pager;
|
|
1152
|
}
|
|
1153
|
|
|
1154
|
|
|
1155
|
/**
|
|
1156
|
* Sends a http GET request to the generic page method which allows for filtering entities by Restrictions.
|
|
1157
|
*
|
|
1158
|
* @param $cdm_entity_type
|
|
1159
|
* @param $class_restriction
|
|
1160
|
* Optional param to narrow down polymorph types to a specific type.
|
|
1161
|
* @param array $restrictions
|
|
1162
|
* An array of Restriction objects
|
|
1163
|
* @param array $init_strategy
|
|
1164
|
* The init strategy to initialize the entity beans while being loaded from the
|
|
1165
|
* persistent storage by the cdm
|
|
1166
|
* @param int $page_size
|
|
1167
|
* The maximum number of entities returned per page.
|
|
1168
|
* The default page size as configured in the cdm server
|
|
1169
|
* will be used if set to NULL
|
|
1170
|
* to return all entities in a single page).
|
|
1171
|
* @param int $page_index
|
|
1172
|
* The number of the page to be returned, the first page has the
|
|
1173
|
* pageNumber = 0
|
|
1174
|
*
|
|
1175
|
* @return object
|
|
1176
|
* A CDM Pager object
|
|
1177
|
*/
|
|
1178
|
function cdm_ws_page_by_restriction($cdm_entity_type, $class_restriction, array $restrictions, array $init_strategy, $page_size, $page_index) {
|
|
1179
|
|
|
1180
|
$restrictions_json = array(); // json_encode($restrictions);
|
|
1181
|
foreach ($restrictions as $restr){
|
|
1182
|
$restrictions_json[] = json_encode($restr);
|
|
1183
|
}
|
|
1184
|
$filter_parameters = [
|
|
1185
|
'restriction' => $restrictions_json,
|
|
1186
|
'initStrategy' => $init_strategy
|
|
1187
|
];
|
|
1188
|
if($class_restriction){
|
|
1189
|
$filter_parameters['class'] = $class_restriction;
|
|
1190
|
}
|
|
1191
|
|
|
1192
|
return cdm_ws_page(
|
|
1193
|
'portal/' . cdm_ws_base_uri($cdm_entity_type),
|
|
1194
|
$page_size,
|
|
1195
|
$page_index,
|
|
1196
|
$filter_parameters,
|
|
1197
|
"GET"
|
|
1198
|
);
|
|
1199
|
}
|
|
1200
|
|
|
1201
|
/**
|
|
1202
|
* Fetches all entities returned by the the generic page method for the Restrictions applied as filter.
|
|
1203
|
*
|
|
1204
|
* @param $cdm_entity_type
|
|
1205
|
* @param $class_restriction
|
|
1206
|
* Optional param to narrow down polymorph types to a specific type.
|
|
1207
|
* @param array $restrictions
|
|
1208
|
* An array of Restriction objects
|
|
1209
|
* @param array $init_strategy
|
|
1210
|
* The init strategy to initialize the entity beans while being loaded from the
|
|
1211
|
* persistent storage by the cdm
|
|
1212
|
*
|
|
1213
|
* @return array
|
|
1214
|
* A array of CDM entities
|
|
1215
|
*/
|
|
1216
|
function cdm_ws_fetch_all_by_restriction($cdm_entity_type, $class_restriction, array $restrictions, array $init_strategy){
|
|
1217
|
$page_index = 0;
|
|
1218
|
// using a bigger page size to avoid to many multiple requests
|
|
1219
|
$page_size = 500;
|
|
1220
|
$entities = array();
|
|
1221
|
|
|
1222
|
while ($page_index !== FALSE && $page_index < 1){
|
|
1223
|
$pager = cdm_ws_page_by_restriction($cdm_entity_type, $class_restriction, $restrictions, $init_strategy, $page_size, $page_index);
|
|
1224
|
if(isset($pager->records) && is_array($pager->records)) {
|
|
1225
|
$entities = array_merge($entities, $pager->records);
|
|
1226
|
if(!empty($pager->nextIndex)){
|
|
1227
|
$page_index = $pager->nextIndex;
|
|
1228
|
} else {
|
|
1229
|
$page_index = FALSE;
|
|
1230
|
}
|
|
1231
|
} else {
|
|
1232
|
$page_index = FALSE;
|
|
1233
|
}
|
|
1234
|
}
|
|
1235
|
return $entities;
|
|
1236
|
}
|
|
1237
|
|
|
1238
|
|
|
1239
|
/**
|
|
1240
|
* Fetches all entities from the given REST endpoint using the pager mechanism.
|
|
1241
|
*
|
|
1242
|
* @param string $resourceURI
|
|
1243
|
* @param array $query
|
|
1244
|
* A array holding the HTTP request query parameters for the request
|
|
1245
|
* @param string $method
|
|
1246
|
* The HTTP method to use, valid values are "GET" or "POST";
|
|
1247
|
* @param bool $absoluteURI
|
|
1248
|
* TRUE when the URL should be treated as absolute URL.
|
|
1249
|
*
|
|
1250
|
* @return array
|
|
1251
|
* A list of CDM entitites
|
|
1252
|
*
|
|
1253
|
*/
|
|
1254
|
function cdm_ws_fetch_all($resourceURI, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
|
|
1255
|
$page_index = 0;
|
|
1256
|
// using a bigger page size to avoid too many multiple requests
|
|
1257
|
$page_size = 500;
|
|
1258
|
$entities = [];
|
|
1259
|
|
|
1260
|
while (true){
|
|
1261
|
$pager = cdm_ws_page($resourceURI, $page_size, $page_index, $query, $method, $absoluteURI);
|
|
1262
|
if(isset($pager->records) && is_array($pager->records)) {
|
|
1263
|
$entities = array_merge($entities, $pager->records);
|
|
1264
|
if(is_numeric($pager->nextIndex) && $page_index < $pager->nextIndex){
|
|
1265
|
$page_index = $pager->nextIndex;
|
|
1266
|
} else {
|
|
1267
|
break;
|
|
1268
|
}
|
|
1269
|
} else {
|
|
1270
|
break;
|
|
1271
|
}
|
|
1272
|
}
|
|
1273
|
return $entities;
|
|
1274
|
}
|
|
1275
|
|
|
1276
|
/*
|
|
1277
|
function cdm_ws_taxonomy_compose_resourcePath($path = NULL){
|
|
1278
|
$viewrank = _cdm_taxonomy_compose_viewrank();
|
|
1279
|
return CDM_WS_PORTAL_TAXONOMY . '/' . ($viewrank ? $viewrank : '' ) . ($path
|
|
1280
|
? '/' . $path : '') ;
|
|
1281
|
}
|
|
1282
|
*/
|
|
1283
|
|
|
1284
|
/**
|
|
1285
|
* @todo Enter description here...
|
|
1286
|
*
|
|
1287
|
* @param string $taxon_uuid
|
|
1288
|
* The UUID of a cdm taxon instance
|
|
1289
|
* @param string $ignore_rank_limit
|
|
1290
|
* Whether to ignore the variable 'taxontree_ranklimit' set by admin in the settings
|
|
1291
|
*
|
|
1292
|
* @return string
|
|
1293
|
* A cdm REST service URL path to a Classification
|
|
1294
|
*/
|
|
1295
|
function cdm_compose_taxonomy_root_level_path($taxon_uuid = FALSE, $ignore_rank_limit = FALSE) {
|
|
1296
|
|
|
1297
|
$view_uuid = get_current_classification_uuid();
|
|
1298
|
$rank_uuid = NULL;
|
|
1299
|
if (!$ignore_rank_limit) {
|
|
1300
|
$rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
|
|
1301
|
}
|
|
1302
|
|
|
1303
|
if (!empty($taxon_uuid)) {
|
|
1304
|
return cdm_compose_ws_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
|
|
1305
|
$view_uuid,
|
|
1306
|
$taxon_uuid,
|
|
1307
|
));
|
|
1308
|
}
|
|
1309
|
else {
|
|
1310
|
if (is_uuid($rank_uuid)) {
|
|
1311
|
return cdm_compose_ws_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_AT_RANK, array(
|
|
1312
|
$view_uuid,
|
|
1313
|
$rank_uuid,
|
|
1314
|
));
|
|
1315
|
}
|
|
1316
|
else {
|
|
1317
|
return cdm_compose_ws_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES, array(
|
|
1318
|
$view_uuid,
|
|
1319
|
));
|
|
1320
|
}
|
|
1321
|
}
|
|
1322
|
}
|
|
1323
|
|
|
1324
|
/**
|
|
1325
|
* Retrieves from the cdm web service with the first level of childnodes of a classification.
|
|
1326
|
*
|
|
1327
|
* The level is either the real root level ot it is a lover level if a rank limit has been set.
|
|
1328
|
* (@see cdm_compose_taxonomy_root_level_path() for more on the rank limit).
|
|
1329
|
*
|
|
1330
|
* Operates in two modes depending on whether the parameter
|
|
1331
|
* $taxon_uuid is set or NULL.
|
|
1332
|
*
|
|
1333
|
* A) $taxon_uuid = NULL:
|
|
1334
|
* 1. retrieve the Classification for the uuid set in the $_SESSION['cdm']['taxonomictree_uuid']
|
|
1335
|
* 2. otherwise return the default classification as defined by the admin via the settings
|
|
1336
|
*
|
|
1337
|
* b) $taxon_uuid is set:
|
|
1338
|
* return the classification to whcih the taxon belongs to.
|
|
1339
|
*
|
|
1340
|
* @param UUID $taxon_uuid
|
|
1341
|
* The UUID of a cdm taxon instance
|
|
1342
|
*/
|
|
1343
|
function cdm_ws_taxonomy_root_level($taxon_uuid = NULL) {
|
|
1344
|
|
|
1345
|
$response = NULL;
|
|
1346
|
|
|
1347
|
// 1st try
|
|
1348
|
$response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid), NULL, NULL, 'GET', TRUE);
|
|
1349
|
|
|
1350
|
if ($response == NULL) {
|
|
1351
|
// 2dn try by ignoring the rank limit
|
|
1352
|
$response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid, TRUE), NULL, NULL, 'GET', TRUE);
|
|
1353
|
}
|
|
1354
|
|
|
1355
|
if ($response == NULL) {
|
|
1356
|
// 3rd try, last fallback:
|
|
1357
|
// return the default classification
|
|
1358
|
if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
|
|
1359
|
// Delete the session value and try again with the default.
|
|
1360
|
unset($_SESSION['cdm']['taxonomictree_uuid']);
|
|
1361
|
drupal_set_message("Could not find a valid classification, falling back to the default classification.", 'warning');
|
|
1362
|
return cdm_ws_taxonomy_root_level($taxon_uuid);
|
|
1363
|
}
|
|
1364
|
else {
|
|
1365
|
// Check if taxonomictree_uuid is valid.
|
|
1366
|
// expecting an array of taxonNodes,
|
|
1367
|
// empty classifications are ok so no warning in this case!
|
|
1368
|
$test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
|
|
1369
|
if (!is_array($test)) {
|
|
1370
|
// The default set by the admin seems to be invalid or is not even set.
|
|
1371
|
drupal_set_message(_no_classfication_uuid_message(), 'warning');
|
|
1372
|
} else if (count($test) == 0) {
|
|
1373
|
// The default set by the admin seems to be invalid or is not even set.
|
|
1374
|
drupal_set_message("The chosen classification is empty.", 'status');
|
|
1375
|
}
|
|
1376
|
}
|
|
1377
|
}
|
|
1378
|
|
|
1379
|
return $response;
|
|
1380
|
}
|
|
1381
|
|
|
1382
|
/**
|
|
1383
|
* Determines the tree path of the taxon given as uuid to the root of the classification tree.
|
|
1384
|
*
|
|
1385
|
* The root either is the absolute root of the tree or a rank specific root if the TAXONTREE_RANKLIMIT
|
|
1386
|
* variable is set.
|
|
1387
|
*
|
|
1388
|
* @param string $taxon_uuid
|
|
1389
|
*
|
|
1390
|
* @return array
|
|
1391
|
* An array of CDM TaxonNodeDTO objects
|
|
1392
|
*/
|
|
1393
|
function cdm_ws_taxonomy_pathFromRoot($taxon_uuid) {
|
|
1394
|
$view_uuid = get_current_classification_uuid();
|
|
1395
|
$rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
|
|
1396
|
|
|
1397
|
$response = NULL;
|
|
1398
|
if (is_uuid($rank_uuid)) {
|
|
1399
|
$response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM_TO_RANK, array(
|
|
1400
|
$view_uuid,
|
|
1401
|
$taxon_uuid,
|
|
1402
|
$rank_uuid,
|
|
1403
|
));
|
|
1404
|
}
|
|
1405
|
else {
|
|
1406
|
$response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM, array(
|
|
1407
|
$view_uuid,
|
|
1408
|
$taxon_uuid,
|
|
1409
|
));
|
|
1410
|
}
|
|
1411
|
|
|
1412
|
if ($response == NULL) {
|
|
1413
|
// Error handing.
|
|
1414
|
// if (is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
|
|
1415
|
// // Delete the session value and try again with the default.
|
|
1416
|
// unset($_SESSION['cdm']['taxonomictree_uuid']);
|
|
1417
|
// return cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
|
|
1418
|
// }
|
|
1419
|
// else {
|
|
1420
|
// Check if taxonomictree_uuid is valid.
|
|
1421
|
$test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
|
|
1422
|
if ($test == NULL) {
|
|
1423
|
// The default set by the admin seems to be invalid or is not even set.
|
|
1424
|
drupal_set_message(_no_classfication_uuid_message(), 'warning');
|
|
1425
|
}
|
|
1426
|
// }
|
|
1427
|
}
|
|
1428
|
|
|
1429
|
return $response;
|
|
1430
|
}
|
|
1431
|
|
|
1432
|
|
|
1433
|
// =============================Terms and Vocabularies ========================================= //
|
|
1434
|
|
|
1435
|
/**
|
|
1436
|
* Returns the localized representation for the given term.
|
|
1437
|
*
|
|
1438
|
* @param Object $definedTermBase
|
|
1439
|
* of cdm type DefinedTermBase
|
|
1440
|
* @return string
|
|
1441
|
* the localized representation_L10n of the term,
|
|
1442
|
* otherwise the titleCache as fall back,
|
|
1443
|
* otherwise the default_representation which defaults to an empty string
|
|
1444
|
*/
|
|
1445
|
function cdm_term_representation($definedTermBase, $default_representation = '') {
|
|
1446
|
if ( isset($definedTermBase->representation_L10n) ) {
|
|
1447
|
return $definedTermBase->representation_L10n;
|
|
1448
|
} elseif ( isset($definedTermBase->titleCache)) {
|
|
1449
|
return $definedTermBase->titleCache;
|
|
1450
|
} elseif (isset($definedTermBase->label)){
|
|
1451
|
return $definedTermBase->label;
|
|
1452
|
}
|
|
1453
|
|
|
1454
|
if (is_string($definedTermBase)){
|
|
1455
|
return $definedTermBase;
|
|
1456
|
}
|
|
1457
|
return $default_representation;
|
|
1458
|
}
|
|
1459
|
|
|
1460
|
/**
|
|
1461
|
* Returns the abbreviated localized representation for the given term.
|
|
1462
|
*
|
|
1463
|
* @param Object $definedTermBase
|
|
1464
|
* of cdm type DefinedTermBase
|
|
1465
|
* @return string
|
|
1466
|
* the localized representation_L10n_abbreviatedLabel of the term,
|
|
1467
|
* if this representation is not available the function delegates the
|
|
1468
|
* call to cdm_term_representation()
|
|
1469
|
*/
|
|
1470
|
function cdm_term_representation_abbreviated($definedTermBase, $default_representation = '') {
|
|
1471
|
if ( isset($definedTermBase->representation_L10n_abbreviatedLabel) ) {
|
|
1472
|
return $definedTermBase->representation_L10n_abbreviatedLabel;
|
|
1473
|
} else {
|
|
1474
|
cdm_term_representation($definedTermBase, $default_representation);
|
|
1475
|
}
|
|
1476
|
}
|
|
1477
|
|
|
1478
|
/**
|
|
1479
|
* Transforms the list of the given term base instances to a alphabetical ordered options array.
|
|
1480
|
*
|
|
1481
|
* The options array is suitable for drupal form API elements that allow multiple choices.
|
|
1482
|
* @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
|
|
1483
|
*
|
|
1484
|
* @param array $terms
|
|
1485
|
* a list of CDM DefinedTermBase instances
|
|
1486
|
*
|
|
1487
|
* @param $term_label_callback
|
|
1488
|
* A callback function to override the term representations
|
|
1489
|
*
|
|
1490
|
* @param bool $empty_option
|
|
1491
|
* An additional element do be placed at the beginning og the list. This element will be the default option.
|
|
1492
|
*
|
|
1493
|
* @return array
|
|
1494
|
* the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
|
|
1495
|
|
|
1496
|
*/
|
|
1497
|
function cdm_terms_as_options($terms, $term_label_callback = NULL, $empty_option = FALSE){
|
|
1498
|
$options = array();
|
|
1499
|
if(isset($terms) && is_array($terms)) {
|
|
1500
|
foreach ($terms as $term) {
|
|
1501
|
if ($term_label_callback && function_exists($term_label_callback)) {
|
|
1502
|
$options[$term->uuid] = call_user_func($term_label_callback, $term);
|
|
1503
|
} else {
|
|
1504
|
//TODO use cdm_term_representation() here?
|
|
1505
|
$options[$term->uuid] = t('@term', array('@term' => $term->representation_L10n));
|
|
1506
|
}
|
|
1507
|
}
|
|
1508
|
}
|
|
1509
|
|
|
1510
|
if($empty_option !== FALSE){
|
|
1511
|
array_unshift ($options, "");
|
|
1512
|
}
|
|
1513
|
|
|
1514
|
return $options;
|
|
1515
|
}
|
|
1516
|
|
|
1517
|
/**
|
|
1518
|
* Creates and array of options for drupal select form elements.
|
|
1519
|
*
|
|
1520
|
* @param $vocabulary_uuid
|
|
1521
|
* The UUID of the CDM Term Vocabulary
|
|
1522
|
* @param $term_label_callback
|
|
1523
|
* An optional call back function which can be used to modify the term label
|
|
1524
|
* @param bool $empty_option
|
|
1525
|
* An additional element do be placed at the beginning og the list. This element will be the default option.
|
|
1526
|
* @param array $include_filter
|
|
1527
|
* An associative array consisting of a field name an regular expression. All term matching
|
|
1528
|
* these filter are included. The value of the field is converted to a String by var_export()
|
|
1529
|
* so a boolean 'true' can be matched by '/true/'
|
|
1530
|
* @param string $order_by
|
|
1531
|
* One of the order by constants defined in this file
|
|
1532
|
* @return array
|
|
1533
|
* the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
|
|
1534
|
*/
|
|
1535
|
function cdm_vocabulary_as_option($vocabulary_uuid, $term_label_callback = NULL, $empty_option = FALSE,
|
|
1536
|
array $include_filter = null, $order_by = CDM_ORDER_BY_ORDER_INDEX_ASC) {
|
|
1537
|
|
|
1538
|
static $vocabularyOptions = array();
|
|
1539
|
|
|
1540
|
if (!isset($vocabularyOptions[$vocabulary_uuid])) {
|
|
1541
|
$terms = cdm_ws_fetch_all('termVocabulary/' . $vocabulary_uuid . '/terms',
|
|
1542
|
array(
|
|
1543
|
'orderBy' => $order_by
|
|
1544
|
)
|
|
1545
|
);
|
|
1546
|
|
|
1547
|
// apply the include filter
|
|
1548
|
if($include_filter != null){
|
|
1549
|
$included_terms = array();
|
|
1550
|
|
|
1551
|
foreach ($terms as $term){
|
|
1552
|
$include = true;
|
|
1553
|
foreach ($include_filter as $field=>$regex){
|
|
1554
|
$include = preg_match($regex, var_export($term->$field, true)) === 1;
|
|
1555
|
if(!$include){
|
|
1556
|
break;
|
|
1557
|
}
|
|
1558
|
}
|
|
1559
|
if($include){
|
|
1560
|
$included_terms[] = $term;
|
|
1561
|
}
|
|
1562
|
}
|
|
1563
|
|
|
1564
|
$terms = $included_terms;
|
|
1565
|
}
|
|
1566
|
|
|
1567
|
// make options list
|
|
1568
|
$vocabularyOptions[$vocabulary_uuid] = cdm_terms_as_options($terms, $term_label_callback, $empty_option);
|
|
1569
|
}
|
|
1570
|
|
|
1571
|
$options = $vocabularyOptions[$vocabulary_uuid];
|
|
1572
|
|
|
1573
|
return $options;
|
|
1574
|
}
|
|
1575
|
|
|
1576
|
/**
|
|
1577
|
* Creates and array of defaults for drupal select form elements.
|
|
1578
|
*
|
|
1579
|
* @param $vocabulary_uuid
|
|
1580
|
* The UUID of the CDM Term Vocabulary
|
|
1581
|
* @param $term_label_callback
|
|
1582
|
* An optional call back function which can be used to modify the term label
|
|
1583
|
* @param bool $empty_option
|
|
1584
|
* An additional element do be placed at the beginning og the list. This element will be the default option.
|
|
1585
|
* @param array $include_filter
|
|
1586
|
* An associative array consisting of a field name an regular expression. All term matching
|
|
1587
|
* these filter are included. The value of the field is converted to a String by var_export()
|
|
1588
|
* so a boolean 'true' can be matched by '/true/'
|
|
1589
|
* @param string $order_by
|
|
1590
|
* One of the order by constants defined in this file
|
|
1591
|
* @return array
|
|
1592
|
* the terms in an array (key: uuid => value: uuid) as defaults for a form element that allows multiple choices.
|
|
1593
|
*/
|
|
1594
|
function cdm_vocabulary_as_defaults($vocabulary_uuid, array $include_filter = null) {
|
|
1595
|
|
|
1596
|
$options = cdm_vocabulary_as_option($vocabulary_uuid, null, null, $include_filter);
|
|
1597
|
$defaults = array();
|
|
1598
|
foreach ($options as $uuid => $value){
|
|
1599
|
$defaults[$uuid] = $uuid;
|
|
1600
|
}
|
|
1601
|
|
|
1602
|
return $defaults;
|
|
1603
|
}
|
|
1604
|
|
|
1605
|
/**
|
|
1606
|
* @param $term_type string one of
|
|
1607
|
* - Unknown
|
|
1608
|
* - Language
|
|
1609
|
* - NamedArea
|
|
1610
|
* - Rank
|
|
1611
|
* - Feature
|
|
1612
|
* - AnnotationType
|
|
1613
|
* - MarkerType
|
|
1614
|
* - ExtensionType
|
|
1615
|
* - DerivationEventType
|
|
1616
|
* - PresenceAbsenceTerm
|
|
1617
|
* - NomenclaturalStatusType
|
|
1618
|
* - NameRelationshipType
|
|
1619
|
* - HybridRelationshipType
|
|
1620
|
* - SynonymRelationshipType
|
|
1621
|
* - TaxonRelationshipType
|
|
1622
|
* - NameTypeDesignationStatus
|
|
1623
|
* - SpecimenTypeDesignationStatus
|
|
1624
|
* - InstitutionType
|
|
1625
|
* - NamedAreaType
|
|
1626
|
* - NamedAreaLevel
|
|
1627
|
* - RightsType
|
|
1628
|
* - MeasurementUnit
|
|
1629
|
* - StatisticalMeasure
|
|
1630
|
* - MaterialOrMethod
|
|
1631
|
* - Material
|
|
1632
|
* - Method
|
|
1633
|
* - Modifier
|
|
1634
|
* - Scope
|
|
1635
|
* - Stage
|
|
1636
|
* - KindOfUnit
|
|
1637
|
* - Sex
|
|
1638
|
* - ReferenceSystem
|
|
1639
|
* - State
|
|
1640
|
* - NaturalLanguageTerm
|
|
1641
|
* - TextFormat
|
|
1642
|
* - DeterminationModifier
|
|
1643
|
* - DnaMarker
|
|
1644
|
*
|
|
1645
|
* @param $order_by
|
|
1646
|
* Optionally sort option (default: CDM_ORDER_BY_TITLE_CACHE_ASC)
|
|
1647
|
* possible values:
|
|
1648
|
* - CDM_ORDER_BY_ID_ASC
|
|
1649
|
* - CDM_ORDER_BY_ID_DESC
|
|
1650
|
* - CDM_ORDER_BY_TITLE_CACHE_ASC
|
|
1651
|
* - CDM_ORDER_BY_TITLE_CACHE_DESC
|
|
1652
|
* - CDM_ORDER_BY_ORDER_INDEX_ASC (can only be used with OrderedTerms!!)
|
|
1653
|
* - CDM_ORDER_BY_ORDER_INDEX_DESC (can only be used with OrderedTerms!!)
|
|
1654
|
* @param bool $empty_option
|
|
1655
|
* An additional element do be placed at the beginning og the list. This element will be the default option.
|
|
1656
|
* @return array
|
|
1657
|
* the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
|
|
1658
|
*/
|
|
1659
|
function cdm_terms_by_type_as_option($term_type, $order_by = CDM_ORDER_BY_TITLE_CACHE_ASC, $term_label_callback = NULL, $empty_option = FALSE){
|
|
1660
|
$terms = cdm_ws_fetch_all(
|
|
1661
|
CDM_WS_TERM,
|
|
1662
|
array(
|
|
1663
|
'class' => $term_type,
|
|
1664
|
'orderBy' => $order_by
|
|
1665
|
)
|
|
1666
|
);
|
|
1667
|
return cdm_terms_as_options($terms, $term_label_callback, $empty_option);
|
|
1668
|
}
|
|
1669
|
|
|
1670
|
/**
|
|
1671
|
* @param array $none_option
|
|
1672
|
* Will add a filter option to search for NULL values
|
|
1673
|
* @param $with_empty_option
|
|
1674
|
* Will add an empty option to the beginning. Choosing this option will disable the filtering.
|
|
1675
|
* @return array
|
|
1676
|
* An array of options with uuids as key and the localized term representation as value
|
|
1677
|
*/
|
|
1678
|
function cdm_type_designation_status_filter_terms_as_options($none_option_label, $with_empty_option = false){
|
|
1679
|
$filter_terms = cdm_ws_get(CDM_WS_TYPE_DESIGNATION_STATUS_FILTER_TERMS);
|
|
1680
|
|
|
1681
|
$options = [];
|
|
1682
|
|
|
1683
|
if(isset($filter_terms) && is_array($filter_terms)) {
|
|
1684
|
foreach ($filter_terms as $filter_term) {
|
|
1685
|
$options[join(',', $filter_term->uuids)] = $filter_term->label;
|
|
1686
|
}
|
|
1687
|
}
|
|
1688
|
|
|
1689
|
if(is_string($none_option_label)){
|
|
1690
|
$options = array_merge(array('NULL' => $none_option_label), $options);
|
|
1691
|
}
|
|
1692
|
|
|
1693
|
if($with_empty_option !== FALSE){
|
|
1694
|
array_unshift ($options, "");
|
|
1695
|
}
|
|
1696
|
|
|
1697
|
return $options;
|
|
1698
|
}
|
|
1699
|
|
|
1700
|
|
|
1701
|
|
|
1702
|
/**
|
|
1703
|
* Callback function which provides the localized representation of a cdm term.
|
|
1704
|
*
|
|
1705
|
* The representation is build by concatenating the abbreviated label with the label
|
|
1706
|
* and thus is especially useful for relationship terms
|
|
1707
|
* The localized representation provided by the cdm can be overwritten by
|
|
1708
|
* providing a drupal translation.
|
|
1709
|
*
|
|
1710
|
*/
|
|
1711
|
function _cdm_relationship_type_term_label_callback($term) {
|
|
1712
|
if (isset($term->representation_L10n_abbreviatedLabel)) {
|
|
1713
|
return $term->representation_L10n_abbreviatedLabel . ' : '
|
|
1714
|
. t('@term', array('@term' => $term->representation_L10n));
|
|
1715
|
}
|
|
1716
|
else {
|
|
1717
|
return t('@term', array('@term' => $term->representation_L10n));
|
|
1718
|
}
|
|
1719
|
}
|
|
1720
|
|
|
1721
|
/**
|
|
1722
|
* Callback function which provides the localized inverse representation of a cdm term.
|
|
1723
|
*
|
|
1724
|
* The representation is build by concatenating the abbreviated label with the label
|
|
1725
|
* and thus is especially useful for relationship terms
|
|
1726
|
* The localized representation provided by the cdm can be overwritten by
|
|
1727
|
* providing a drupal translation.
|
|
1728
|
*
|
|
1729
|
*/
|
|
1730
|
function _cdm_relationship_type_term_inverse_label_callback($term) {
|
|
1731
|
if (isset($term->inverseRepresentation_L10n_abbreviatedLabel)) {
|
|
1732
|
return $term->inverseRepresentation_L10n_abbreviatedLabel . ' : '
|
|
1733
|
. t('@term', array('@term' => $term->inverseRepresentation_L10n));
|
|
1734
|
}
|
|
1735
|
else {
|
|
1736
|
return t('@term', array('@term' => $term->inverseRepresentation_L10n));
|
|
1737
|
}
|
|
1738
|
}
|
|
1739
|
|
|
1740
|
/**
|
|
1741
|
* Returns the localized abbreviated label of the relationship term.
|
|
1742
|
*
|
|
1743
|
* In case the abbreviated label is not set the normal representation is returned.
|
|
1744
|
*
|
|
1745
|
* @param $term
|
|
1746
|
* @param bool $is_inverse_relation
|
|
1747
|
* @return string
|
|
1748
|
* The abbreviated label
|
|
1749
|
*/
|
|
1750
|
function cdm_relationship_type_term_abbreviated_label($term, $is_inverse_relation = false){
|
|
1751
|
|
|
1752
|
if($is_inverse_relation) {
|
|
1753
|
if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
|
|
1754
|
$abbr_label = $term->inverseResentation_L10n_abbreviatedLabel;
|
|
1755
|
} else {
|
|
1756
|
$abbr_label = $term->inverseRepresentation_L10n;
|
|
1757
|
}
|
|
1758
|
} else {
|
|
1759
|
if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
|
|
1760
|
$abbr_label = $term->representation_L10n_abbreviatedLabel;
|
|
1761
|
} else {
|
|
1762
|
$abbr_label = $term->representation_L10n;
|
|
1763
|
}
|
|
1764
|
}
|
|
1765
|
return $abbr_label;
|
|
1766
|
}
|
|
1767
|
|
|
1768
|
/**
|
|
1769
|
* Returns the symbol of the relationship term.
|
|
1770
|
*
|
|
1771
|
* In case the symbol is not set the function falls back to use the abbreviated label or
|
|
1772
|
* the normal representation..
|
|
1773
|
*
|
|
1774
|
* @param $term
|
|
1775
|
* @param bool $is_inverse_relation
|
|
1776
|
* @return string
|
|
1777
|
* The abbreviated label
|
|
1778
|
*/
|
|
1779
|
function cdm_relationship_type_term_symbol($term, $is_inverse_relation = false){
|
|
1780
|
|
|
1781
|
if($is_inverse_relation) {
|
|
1782
|
if (isset($term->inverseSymbol) && $term->inverseSymbol) {
|
|
1783
|
$symbol = $term->inverseSymbol;
|
|
1784
|
} else if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
|
|
1785
|
$symbol = $term->inverseResentation_L10n_abbreviatedLabel;
|
|
1786
|
} else {
|
|
1787
|
$symbol = $term->inverseRepresentation_L10n;
|
|
1788
|
}
|
|
1789
|
} else {
|
|
1790
|
if (isset($term->symbol) && $term->symbol) {
|
|
1791
|
$symbol = $term->symbol;
|
|
1792
|
} else if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
|
|
1793
|
$symbol = $term->representation_L10n_abbreviatedLabel;
|
|
1794
|
} else {
|
|
1795
|
$symbol = $term->representation_L10n;
|
|
1796
|
}
|
|
1797
|
}
|
|
1798
|
return $symbol;
|
|
1799
|
}
|
|
1800
|
|
|
1801
|
// ========================================================================================== //
|
|
1802
|
/**
|
|
1803
|
* @todo Improve documentation of this function.
|
|
1804
|
*
|
|
1805
|
* eu.etaxonomy.cdm.model.description.
|
|
1806
|
* CategoricalData
|
|
1807
|
* CommonTaxonName
|
|
1808
|
* Distribution
|
|
1809
|
* IndividualsAssociation
|
|
1810
|
* QuantitativeData
|
|
1811
|
* TaxonInteraction
|
|
1812
|
* TextData
|
|
1813
|
*/
|
|
1814
|
function cdm_descriptionElementTypes_as_option($prependEmptyElement = FALSE) {
|
|
1815
|
static $types = array(
|
|
1816
|
"CategoricalData",
|
|
1817
|
"CommonTaxonName",
|
|
1818
|
"Distribution",
|
|
1819
|
"IndividualsAssociation",
|
|
1820
|
"QuantitativeData",
|
|
1821
|
"TaxonInteraction",
|
|
1822
|
"TextData",
|
|
1823
|
);
|
|
1824
|
|
|
1825
|
static $options = NULL;
|
|
1826
|
if ($options == NULL) {
|
|
1827
|
$options = array();
|
|
1828
|
if ($prependEmptyElement) {
|
|
1829
|
$options[' '] = '';
|
|
1830
|
}
|
|
1831
|
foreach ($types as $type) {
|
|
1832
|
// No internatianalization here since these are purely technical terms.
|
|
1833
|
$options["eu.etaxonomy.cdm.model.description." . $type] = $type;
|
|
1834
|
}
|
|
1835
|
}
|
|
1836
|
return $options;
|
|
1837
|
}
|
|
1838
|
|
|
1839
|
|
|
1840
|
/**
|
|
1841
|
* Fetches all TaxonDescription descriptions elements which are associated to the
|
|
1842
|
* Taxon specified by the $taxon_uuid and merges the elements into the given
|
|
1843
|
* feature tree.
|
|
1844
|
* @param $feature_tree
|
|
1845
|
* The CDM FeatureTree to be used as template
|
|
1846
|
* @param $taxon_uuid
|
|
1847
|
* The UUID of the taxon
|
|
1848
|
* @param $excludes
|
|
1849
|
* UUIDs of features to be excluded
|
|
1850
|
* @return object
|
|
1851
|
* The CDM FeatureTree which was given as parameter merged tree whereas the
|
|
1852
|
* CDM FeatureNodes are extended by an additional field 'descriptionElements'
|
|
1853
|
* witch will hold the according $descriptionElements.
|
|
1854
|
*/
|
|
1855
|
function cdm_ws_descriptions_by_featuretree($feature_tree, $taxon_uuid, $exclude_uuids = array()) {
|
|
1856
|
|
|
1857
|
if (!$feature_tree) {
|
|
1858
|
drupal_set_message(check_plain(t("No 'FeatureTree' has been set so far.
|
|
1859
|
In order to see the species profiles of your taxa, please select a
|
|
1860
|
'FeatureTree' in the !settings"), array('!settings' => l(t('CDM Dataportal Settings'), 'admin/config/cdm_dataportal/layout'))), 'warning');
|
|
1861
|
return FALSE;
|
|
1862
|
}
|
|
1863
|
|
|
1864
|
$description_elements = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
|
|
1865
|
array(
|
|
1866
|
'taxon' => $taxon_uuid,
|
|
1867
|
'features' => cdm_featureTree_elements_toString($feature_tree->root, ',', 'uuid', $exclude_uuids)
|
|
1868
|
),
|
|
1869
|
'POST'
|
|
1870
|
);
|
|
1871
|
|
|
1872
|
// Combine all descriptions into one feature tree.
|
|
1873
|
$merged_nodes = _mergeFeatureTreeDescriptions($feature_tree->root->childNodes, $description_elements);
|
|
1874
|
$feature_tree->root->childNodes = $merged_nodes;
|
|
1875
|
|
|
1876
|
return $feature_tree;
|
|
1877
|
}
|
|
1878
|
|
|
1879
|
/**
|
|
1880
|
* Returns a filtered a list of annotations for the cdm entity given as parameter $cdm_entity.
|
|
1881
|
* If the annotations are not yet already loded with the cdm entity the cdm REST service will
|
|
1882
|
* be requested for the annotations.
|
|
1883
|
*
|
|
1884
|
* @param string $cdm_entity_or_dto
|
|
1885
|
* An annotatable cdm entity, or corresponding DTO, DTOs containig AnnotationDTOs
|
|
1886
|
* in an array field named 'annotations' is supported by this method.
|
|
1887
|
* @param array $include_types
|
|
1888
|
* If an array of annotation type uuids is supplied by this parameter the
|
|
1889
|
* list of annotations is resticted to those which belong to this type.
|
|
1890
|
*
|
|
1891
|
* @return array
|
|
1892
|
* An array of Annotation objects or an empty array.
|
|
1893
|
*/
|
|
1894
|
function cdm_ws_fetch_annotations(&$cdm_entity_or_dto, $include_types = FALSE) {
|
|
1895
|
|
|
1896
|
if(!isset($cdm_entity_or_dto->annotations)){
|
|
1897
|
$annotation_url = cdm_compose_annotations_uri($cdm_entity_or_dto);
|
|
1898
|
if ($annotation_url){
|
|
1899
|
$cdm_entity_or_dto->annotations = cdm_ws_fetch_all($annotation_url, array(), 'GET', TRUE);
|
|
1900
|
}
|
|
1901
|
|
|
1902
|
}
|
|
1903
|
|
|
1904
|
$annotations_or_dtos = array();
|
|
1905
|
if (!isset($cdm_entity_or_dto->annotations)){
|
|
1906
|
return $annotations_or_dtos;
|
|
1907
|
}
|
|
1908
|
|
|
1909
|
if (is_array($cdm_entity_or_dto->annotations)){
|
|
1910
|
$annotation_or_dtos = $cdm_entity_or_dto->annotations;
|
|
1911
|
}else{
|
|
1912
|
$annotation_or_dtos = $cdm_entity_or_dto->annotations->items;
|
|
1913
|
}
|
|
1914
|
foreach ($annotation_or_dtos as $annotation_or_dto) {
|
|
1915
|
if ($include_types) {
|
|
1916
|
$is_dto = is_cdm_dto($annotation_or_dto);
|
|
1917
|
if (($is_dto ? annotation_dto_has_type($annotation_or_dto, $include_types) : annotation_has_type($annotation_or_dto, $include_types))) {
|
|
1918
|
$annotations_or_dtos[] = $annotation_or_dto;
|
|
1919
|
}
|
|
1920
|
}
|
|
1921
|
else {
|
|
1922
|
$annotations_or_dtos[] = $annotation_or_dto;
|
|
1923
|
}
|
|
1924
|
}
|
|
1925
|
return $annotations_or_dtos;
|
|
1926
|
}
|
|
1927
|
|
|
1928
|
/**
|
|
1929
|
* @param $annotation
|
|
1930
|
* @param array $include_types
|
|
1931
|
*
|
|
1932
|
* @return bool
|
|
1933
|
*/
|
|
1934
|
function annotation_has_type($annotation, array $include_types) {
|
|
1935
|
return (isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $include_types, TRUE))
|
|
1936
|
|| (!isset($annotation->annotationType) && in_array('NULL_VALUE', $include_types, TRUE));
|
|
1937
|
}
|
|
1938
|
|
|
1939
|
/**
|
|
1940
|
* @param $annotation_dto
|
|
1941
|
* @param array $include_types
|
|
1942
|
*
|
|
1943
|
* @return bool
|
|
1944
|
*/
|
|
1945
|
function annotation_dto_has_type($annotation_dto, array $include_types) {
|
|
1946
|
return (isset($annotation_dto->annotationTypeUuid) && in_array($annotation_dto->annotationTypeUuid, $include_types, TRUE))
|
|
1947
|
|| ($annotation_dto->annotationTypeUuid === NULL && in_array('NULL_VALUE', $include_types, TRUE));
|
|
1948
|
}
|
|
1949
|
|
|
1950
|
/**
|
|
1951
|
* Tests if the passed object is a DTO exposed by the cdm webservices.
|
|
1952
|
* All these DTOs contain a field `class` with the Java class simple name
|
|
1953
|
* as value. As all DTO classes are suffixed with "DTO" this method can test
|
|
1954
|
* for this class name suffix.
|
|
1955
|
*
|
|
1956
|
* @param $cdm_dto
|
|
1957
|
* The potential cdm dto to test
|
|
1958
|
*
|
|
1959
|
* @return bool
|
|
1960
|
* True in case the $cdm_dto is a DTO
|
|
1961
|
*/
|
|
1962
|
function is_cdm_dto(&$cdm_dto) {
|
|
1963
|
return isset_not_empty($cdm_dto->type) && isset_not_empty($cdm_dto->class) && (str_endsWith($cdm_dto->class , 'DTO') || str_endsWith($cdm_dto->class , 'Dto') );
|
|
1964
|
}
|
|
1965
|
|
|
1966
|
/**
|
|
1967
|
* Provides the list of visible annotations for the $cdm_entity.
|
|
1968
|
*
|
|
1969
|
* @param $cdm_entity_or_dto
|
|
1970
|
* The annotatable CDM entity or corresponding DTO, DTOs containig AnnotationDTOs
|
|
1971
|
* in an array field named 'annotations' is supported by this method
|
|
1972
|
*
|
|
1973
|
* @return array of the annotations entities or DTOs which are visible according
|
|
1974
|
* to the settings as stored in ANNOTATION_TYPES_VISIBLE
|
|
1975
|
*/
|
|
1976
|
function cdm_fetch_visible_annotations($cdm_entity_or_dto){
|
|
1977
|
|
|
1978
|
static $annotations_types_filter = null;
|
|
1979
|
if(!$annotations_types_filter) {
|
|
1980
|
$annotations_types_filter = unserialize(EXTENSION_TYPES_VISIBLE_DEFAULT);
|
|
1981
|
}
|
|
1982
|
return cdm_ws_fetch_annotations($cdm_entity_or_dto, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
|
|
1983
|
}
|
|
1984
|
|
|
1985
|
function cdm_load_tagged_full_title($taxon_name){
|
|
1986
|
if(isset($taxon_name) && !isset($taxon_name->taggedFullTitle)){
|
|
1987
|
$tagged_full_title = cdm_ws_get(CDM_WS_NAME, array($taxon_name->uuid, 'taggedFullTitle'));
|
|
1988
|
if(is_array($tagged_full_title)){
|
|
1989
|
$taxon_name->taggedFullTitle = $tagged_full_title;
|
|
1990
|
|
|
1991
|
}
|
|
1992
|
}
|
|
1993
|
}
|
|
1994
|
|
|
1995
|
/**
|
|
1996
|
* Extends the $cdm_entity object by the field if it is not already existing.
|
|
1997
|
*
|
|
1998
|
* This function can only be used for fields with 1 to many relations.
|
|
1999
|
*
|
|
2000
|
* @param $cdm_base_type
|
|
2001
|
* @param $field_name
|
|
2002
|
* @param $cdm_entity
|
|
2003
|
*/
|
|
2004
|
function cdm_lazyload_array_field($cdm_base_type, $field_name, &$cdm_entity)
|
|
2005
|
{
|
|
2006
|
if (!isset($cdm_entity->$field_name)) {
|
|
2007
|
$items = cdm_ws_fetch_all('portal/' . $cdm_base_type . '/' . $cdm_entity->uuid . '/' . $field_name);
|
|
2008
|
$cdm_entity->$field_name = $items;
|
|
2009
|
}
|
|
2010
|
}
|
|
2011
|
|
|
2012
|
|
|
2013
|
/**
|
|
2014
|
* Get a NomenclaturalReference string.
|
|
2015
|
*
|
|
2016
|
* Returns the NomenclaturalReference string with correctly placed
|
|
2017
|
* microreference (= reference detail) e.g.
|
|
2018
|
* in Phytotaxa 43: 1-48. 2012.
|
|
2019
|
*
|
|
2020
|
* @param string $referenceUuid
|
|
2021
|
* UUID of the reference.
|
|
2022
|
* @param string $microreference
|
|
2023
|
* Reference detail.
|
|
2024
|
*
|
|
2025
|
* @return string
|
|
2026
|
* a NomenclaturalReference.
|
|
2027
|
*/
|
|
2028
|
function cdm_ws_getNomenclaturalReference($referenceUuid, $microreference) {
|
|
2029
|
|
|
2030
|
// TODO the below statement avoids error boxes due to #4644 remove it once this ticket is solved
|
|
2031
|
if(is_array($microreference) || is_object($microreference)) {
|
|
2032
|
return '';
|
|
2033
|
}
|
|
2034
|
|
|
2035
|
$obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
|
|
2036
|
$referenceUuid,
|
|
2037
|
), "microReference=" . urlencode($microreference));
|
|
2038
|
|
|
2039
|
if ($obj) {
|
|
2040
|
return $obj->String;
|
|
2041
|
}
|
|
2042
|
else {
|
|
2043
|
return NULL;
|
|
2044
|
}
|
|
2045
|
}
|
|
2046
|
|
|
2047
|
/**
|
|
2048
|
* finds and returns the FeatureNode denoted by the given $feature_uuid
|
|
2049
|
*
|
|
2050
|
* @param $feature_tree_nodes
|
|
2051
|
* The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
|
|
2052
|
* @param $feature_uuid
|
|
2053
|
* The UUID of the Feature
|
|
2054
|
* @return object
|
|
2055
|
* the FeatureNode or null
|
|
2056
|
*/
|
|
2057
|
function &cdm_feature_tree_find_node($feature_tree_nodes, $feature_uuid){
|
|
2058
|
|
|
2059
|
// 1. scan this level
|
|
2060
|
foreach ($feature_tree_nodes as $node){
|
|
2061
|
if($node->term->uuid == $feature_uuid){
|
|
2062
|
return $node;
|
|
2063
|
}
|
|
2064
|
}
|
|
2065
|
|
|
2066
|
// 2. descend into childen
|
|
2067
|
foreach ($feature_tree_nodes as $node){
|
|
2068
|
if(is_array($node->childNodes)){
|
|
2069
|
$node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
|
|
2070
|
if($node) {
|
|
2071
|
return $node;
|
|
2072
|
}
|
|
2073
|
}
|
|
2074
|
}
|
|
2075
|
$null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
|
|
2076
|
return $null_var;
|
|
2077
|
}
|
|
2078
|
|
|
2079
|
/**
|
|
2080
|
* finds and returns the FeatureNode denoted by the given $feature_uuid
|
|
2081
|
*
|
|
2082
|
* TODO: This needs to be adapted to the new DTO implementation
|
|
2083
|
*
|
|
2084
|
* @param $feature_tree_nodes
|
|
2085
|
* The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
|
|
2086
|
* @param $feature_uuid
|
|
2087
|
* The UUID of the Feature
|
|
2088
|
* @return object
|
|
2089
|
* the FeatureNode or null
|
|
2090
|
*/
|
|
2091
|
function &cdm_feature_tree_new_find_node($feature_tree_nodes, $feature_uuid){
|
|
2092
|
|
|
2093
|
// 1. scan this level
|
|
2094
|
foreach ($feature_tree_nodes as $node){
|
|
2095
|
if($node->uuid == $feature_uuid){
|
|
2096
|
return $node;
|
|
2097
|
}
|
|
2098
|
}
|
|
2099
|
|
|
2100
|
// 2. descend into childen do we need this in the new implementation???
|
|
2101
|
foreach ($feature_tree_nodes as $node){
|
|
2102
|
if(is_array($node->childNodes)){
|
|
2103
|
$node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
|
|
2104
|
if($node) {
|
|
2105
|
return $node;
|
|
2106
|
}
|
|
2107
|
}
|
|
2108
|
}
|
|
2109
|
$null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
|
|
2110
|
return $null_var;
|
|
2111
|
}
|
|
2112
|
|
|
2113
|
/**
|
|
2114
|
* finds and returns the FeatureNodes for distributions
|
|
2115
|
*
|
|
2116
|
* @param $feature_tree_nodes
|
|
2117
|
* The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
|
|
2118
|
* @return object
|
|
2119
|
* the FeatureNode or null
|
|
2120
|
*/
|
|
2121
|
function &cdm_feature_tree_new_find_distributionNode($feature_tree_nodes){
|
|
2122
|
|
|
2123
|
// 1. scan this level
|
|
2124
|
$nodes = array();
|
|
2125
|
foreach ($feature_tree_nodes as $node){
|
|
2126
|
if(isset_not_empty($node->facts) && isset_not_empty($node->facts->items) && $node->facts->items[0]->clazz == 'DistributionInfoDto'){
|
|
2127
|
$nodes[] = $node;
|
|
2128
|
}
|
|
2129
|
}
|
|
2130
|
|
|
2131
|
// 2. descend into childen do we need this in the new implementation???
|
|
2132
|
foreach ($feature_tree_nodes as $node){
|
|
2133
|
if(isset($node->childNodes) && is_array($node->childNodes)){
|
|
2134
|
$node = cdm_feature_tree_new_find_distributionNode($node->childNodes);
|
|
2135
|
if($node) {
|
|
2136
|
$nodes[] = $node;
|
|
2137
|
}
|
|
2138
|
}
|
|
2139
|
}
|
|
2140
|
|
|
2141
|
return $nodes;
|
|
2142
|
}
|
|
2143
|
|
|
2144
|
|
|
2145
|
|
|
2146
|
/**
|
|
2147
|
* Merges the given featureNodes structure with the descriptionElements.
|
|
2148
|
*
|
|
2149
|
* This method is used in preparation for rendering the descriptionElements.
|
|
2150
|
* The descriptionElements which belong to a specific feature node are appended
|
|
2151
|
* to a feature node by creating a new field:
|
|
2152
|
* - descriptionElements: the CDM DescriptionElements which belong to this feature
|
|
2153
|
* The descriptionElements will be cleared in advance in order to allow reusing the
|
|
2154
|
* same feature tree without the risk of mixing sets of description elements.
|
|
2155
|
*
|
|
2156
|
* which originally is not existing in the cdm.
|
|
2157
|
*
|
|
2158
|
*
|
|
2159
|
*
|
|
2160
|
* @param array $featureNodes
|
|
2161
|
* An array of cdm FeatureNodes which may be hierarchical since feature nodes
|
|
2162
|
* may have children.
|
|
2163
|
* @param array $descriptionElements
|
|
2164
|
* A flat array of cdm DescriptionElements
|
|
2165
|
* @return array
|
|
2166
|
* The $featureNodes structure enriched with the according $descriptionElements
|
|
2167
|
*/
|
|
2168
|
function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
|
|
2169
|
|
|
2170
|
foreach ($featureNodes as &$feature_node) {
|
|
2171
|
// since the $featureNodes array is reused for each description
|
|
2172
|
// it is necessary to clear the custom node fields in advance
|
|
2173
|
if(isset($feature_node->descriptionElements)){
|
|
2174
|
unset($feature_node->descriptionElements);
|
|
2175
|
}
|
|
2176
|
|
|
2177
|
// Append corresponding elements to an additional node field:
|
|
2178
|
// $node->descriptionElements.
|
|
2179
|
foreach ($descriptionElements as $element) {
|
|
2180
|
if ($element->feature->uuid == $feature_node->term->uuid) {
|
|
2181
|
if (!isset($feature_node->descriptionElements)) {
|
|
2182
|
$feature_node->descriptionElements = array();
|
|
2183
|
}
|
|
2184
|
$feature_node->descriptionElements[] = $element;
|
|
2185
|
}
|
|
2186
|
}
|
|
2187
|
|
|
2188
|
// Recurse into node children.
|
|
2189
|
if (isset($feature_node->childNodes[0])) {
|
|
2190
|
$mergedChildNodes = _mergeFeatureTreeDescriptions($feature_node->childNodes, $descriptionElements);
|
|
2191
|
$feature_node->childNodes = $mergedChildNodes;
|
|
2192
|
}
|
|
2193
|
|
|
2194
|
if(!isset($feature_node->descriptionElements) && !isset($feature_node->childNodes[0])){
|
|
2195
|
unset($feature_node);
|
|
2196
|
}
|
|
2197
|
|
|
2198
|
}
|
|
2199
|
|
|
2200
|
return $featureNodes;
|
|
2201
|
}
|
|
2202
|
|
|
2203
|
/**
|
|
2204
|
* Sends a GET or POST request to a CDM RESTService and returns a de-serialized object.
|
|
2205
|
*
|
|
2206
|
* The response from the HTTP GET request is returned as object.
|
|
2207
|
* The response objects coming from the webservice configured in the
|
|
2208
|
* 'cdm_webservice_url' variable are being cached in a level 1 (L1) and / or
|
|
2209
|
* in a level 2 (L2) cache.
|
|
2210
|
*
|
|
2211
|
* Since the L1 cache is implemented as static variable of the cdm_ws_get()
|
|
2212
|
* function, this cache persists only per each single page execution.
|
|
2213
|
* Any object coming from the webservice is stored into it by default.
|
|
2214
|
* In contrast to this default caching mechanism the L2 cache only is used if
|
|
2215
|
* the 'cdm_webservice_cache' variable is set to TRUE,
|
|
2216
|
* which can be set using the modules administrative settings section.
|
|
2217
|
* Objects stored in this L2 cache are serialized and stored
|
|
2218
|
* using the drupal cache in the '{prefix}cache_cdm_ws' cache table. So the
|
|
2219
|
* objects that are stored in the database will persist as
|
|
2220
|
* long as the drupal cache is not being cleared and are available across
|
|
2221
|
* multiple script executions.
|
|
2222
|
*
|
|
2223
|
* @param string $uri
|
|
2224
|
* URL to the webservice.
|
|
2225
|
* @param array $pathParameters
|
|
2226
|
* An array of path parameters.
|
|
2227
|
* @param string $query_string
|
|
2228
|
* A query_string string to be appended to the URL.
|
|
2229
|
* @param string $method
|
|
2230
|
* The HTTP method to use, valid values are "GET" or "POST";
|
|
2231
|
* @param bool $absoluteURI
|
|
2232
|
* TRUE when the URL should be treated as absolute URL.
|
|
2233
|
*
|
|
2234
|
* @return object| array
|
|
2235
|
* The de-serialized webservice response object.
|
|
2236
|
*/
|
|
2237
|
function cdm_ws_get($uri, $pathParameters = array(), $query_string = NULL, $method = "GET", $absoluteURI = FALSE) {
|
|
2238
|
|
|
2239
|
static $cacheL1 = array();
|
|
2240
|
|
|
2241
|
$data = NULL;
|
|
2242
|
// store query_string string in $data and clear the query_string, $data will be set as HTTP request body
|
|
2243
|
if($method == 'POST'){
|
|
2244
|
$data = $query_string;
|
|
2245
|
$query_string = NULL;
|
|
2246
|
}
|
|
2247
|
|
|
2248
|
// Transform the given uri path or pattern into a proper webservice uri.
|
|
2249
|
if (!$absoluteURI) {
|
|
2250
|
$uri = cdm_compose_ws_url($uri, $pathParameters, $query_string);
|
|
2251
|
} else {
|
|
2252
|
if($query_string){
|
|
2253
|
$uri = append_query_parameters($uri, $query_string);
|
|
2254
|
}
|
|
2255
|
}
|
|
2256
|
cdm_ws_apply_classification_subtree_filter($uri);
|
|
2257
|
|
|
2258
|
// read request parameter 'cacheL2_refresh'
|
|
2259
|
// which allows refreshing the level 2 cache
|
|
2260
|
$do_cacheL2_refresh = isset($_REQUEST['cacheL2_refresh']) && $_REQUEST['cacheL2_refresh'] == 1;
|
|
2261
|
|
|
2262
|
$is_cdm_ws_uri = _is_cdm_ws_uri($uri);
|
|
2263
|
$use_cacheL2 = variable_get('cdm_webservice_cache', 1);
|
|
2264
|
|
|
2265
|
if($method == 'GET'){
|
|
2266
|
$cache_key = $uri;
|
|
2267
|
} else {
|
|
2268
|
// sha1 creates longer hashes and thus will cause fewer collisions than md5.
|
|
2269
|
// crc32 is faster but creates much shorter hashes
|
|
2270
|
$cache_key = $uri . '[' . $method . ':' . sha1($data) .']';
|
|
2271
|
}
|
|
2272
|
|
|
2273
|
if (array_key_exists($cache_key, $cacheL1)) {
|
|
2274
|
$cacheL1_obj = $cacheL1[$uri];
|
|
2275
|
}
|
|
2276
|
|
|
2277
|
$set_cacheL1 = FALSE;
|
|
2278
|
if ($is_cdm_ws_uri && !isset($cacheL1_obj)) {
|
|
2279
|
$set_cacheL1 = TRUE;
|
|
2280
|
}
|
|
2281
|
|
|
2282
|
// Only cache cdm webservice URIs.
|
|
2283
|
$set_cacheL2 = $use_cacheL2 && $is_cdm_ws_uri && $set_cacheL1;
|
|
2284
|
$cacheL2_entry = FALSE;
|
|
2285
|
|
|
2286
|
if ($use_cacheL2 && !$do_cacheL2_refresh) {
|
|
2287
|
// Try to get object from cacheL2.
|
|
2288
|
$cacheL2_entry = cache_get($cache_key, 'cache_cdm_ws');
|
|
2289
|
}
|
|
2290
|
|
|
2291
|
if (isset($cacheL1_obj)) {
|
|
2292
|
//
|
|
2293
|
// The object has been found in the L1 cache.
|
|
2294
|
//
|
|
2295
|
$obj = $cacheL1_obj;
|
|
2296
|
if (cdm_debug_block_visible()) {
|
|
2297
|
cdm_ws_debug_add($uri, $method, $data, 0, 0, NULL, 'cacheL1');
|
|
2298
|
}
|
|
2299
|
}
|
|
2300
|
elseif ($cacheL2_entry) {
|
|
2301
|
//
|
|
2302
|
// The object has been found in the L2 cache.
|
|
2303
|
//
|
|
2304
|
$duration_parse_start = microtime(TRUE);
|
|
2305
|
$obj = unserialize($cacheL2_entry->data);
|
|
2306
|
$duration_parse = microtime(TRUE) - $duration_parse_start;
|
|
2307
|
|
|
2308
|
if (cdm_debug_block_visible()) {
|
|
2309
|
cdm_ws_debug_add($uri, $method, $data, 0, $duration_parse, NULL, 'cacheL2');
|
|
2310
|
}
|
|
2311
|
}
|
|
2312
|
else {
|
|
2313
|
//
|
|
2314
|
// Get the object from the webservice and cache it.
|
|
2315
|
//
|
|
2316
|
$duration_fetch_start = microtime(TRUE);
|
|
2317
|
// Request data from webservice JSON or XML.
|
|
2318
|
$response = cdm_http_request($uri, $method, $data);
|
|
2319
|
$response_body = NULL;
|
|
2320
|
if (isset($response->data)) {
|
|
2321
|
$response_body = $response->data;
|
|
2322
|
}
|
|
2323
|
$duration_fetch = microtime(TRUE) - $duration_fetch_start;
|
|
2324
|
$duration_parse_start = microtime(TRUE);
|
|
2325
|
|
|
2326
|
// Parse data and create object.
|
|
2327
|
$obj = cdm_load_obj($response_body);
|
|
2328
|
|
|
2329
|
if(isset($obj->servlet) && isset($obj->status) && is_numeric($obj->status)){
|
|
2330
|
// this is json error message returned by jetty #8914
|
|
2331
|
// wee need to replace it by null to avoid breaking existing assumptions in the code here
|
|
2332
|
// this is also related to #2711
|
|
2333
|
$obj = null;
|
|
2334
|
}
|
|
2335
|
|
|
2336
|
$duration_parse = microtime(TRUE) - $duration_parse_start;
|
|
2337
|
|
|
2338
|
if (cdm_debug_block_visible()) {
|
|
2339
|
if ($obj || $response_body == "[]") {
|
|
2340
|
$status = 'valid';
|
|
2341
|
}
|
|
2342
|
else {
|
|
2343
|
$status = 'invalid';
|
|
2344
|
}
|
|
2345
|
cdm_ws_debug_add($uri, $method, $data, $duration_fetch, $duration_parse, strlen($response_body), $status);
|
|
2346
|
}
|
|
2347
|
if ($set_cacheL2) {
|
|
2348
|
// Store the object in cache L2.
|
|
2349
|
// Comment @WA perhaps better if Drupal serializedatas here? Then the
|
|
2350
|
// flag serialized is set properly in the cache table.
|
|
2351
|
cache_set($cache_key, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
|
|
2352
|
}
|
|
2353
|
}
|
|
2354
|
if ($obj) {
|
|
2355
|
// Store the object in cache L1.
|
|
2356
|
if ($set_cacheL1) {
|
|
2357
|
$cacheL1[$cache_key] = $obj;
|
|
2358
|
}
|
|
2359
|
}
|
|
2360
|
return $obj;
|
|
2361
|
}
|
|
2362
|
|
|
2363
|
function cdm_ws_apply_classification_subtree_filter(&$uri){
|
|
2364
|
|
|
2365
|
$classification_subtree_filter_patterns = &drupal_static('classification_subtree_filter_patterns', array(
|
|
2366
|
"#/classification/[0-9a-f\-]{36}/childNodes#",
|
|
2367
|
/* covered by above pattern:
|
|
2368
|
"#/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
|
|
2369
|
'#/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
|
|
2370
|
*/
|
|
2371
|
"#/portal/classification/[0-9a-f\-]{36}/childNodes#",
|
|
2372
|
/* covered by above pattern:
|
|
2373
|
"#/portal/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
|
|
2374
|
'#/portal/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
|
|
2375
|
*/
|
|
2376
|
'#/portal/classification/[0-9a-f\-]{36}/pathFrom/[0-9a-f\-]{36}#',
|
|
2377
|
"#/portal/taxon/search#",
|
|
2378
|
"#/portal/taxon/find#",
|
|
2379
|
/* covered by above pattern:
|
|
2380
|
"#/portal/taxon/findByDescriptionElementFullText#",
|
|
2381
|
"#/portal/taxon/findByFullText#",
|
|
2382
|
"#/portal/taxon/findByEverythingFullText#",
|
|
2383
|
"#/portal/taxon/findByIdentifier#",
|
|
2384
|
"#/portal/taxon/findByMarker#",
|
|
2385
|
"#/portal/taxon/findByMarker#",
|
|
2386
|
"#/portal/taxon/findByMarker#",
|
|
2387
|
*/
|
|
2388
|
"#/portal/taxon/[0-9a-f\-]{36}#"
|
|
2389
|
/* covered by above pattern:
|
|
2390
|
"#/portal/taxon/[0-9a-f\-]{36}/taxonNodes#",
|
|
2391
|
*/
|
|
2392
|
));
|
|
2393
|
|
|
2394
|
$sub_tree_filter_uuid_value = variable_get(CDM_SUB_TREE_FILTER_UUID, FALSE);
|
|
2395
|
if(is_uuid($sub_tree_filter_uuid_value)){
|
|
2396
|
foreach($classification_subtree_filter_patterns as $preg_pattern){
|
|
2397
|
if(preg_match($preg_pattern, $uri)){
|
|
2398
|
// no need to take care for uri fragments with ws uris!
|
|
2399
|
if(strpos( $uri, '?')){
|
|
2400
|
$uri .= '&subtree=' . $sub_tree_filter_uuid_value;
|
|
2401
|
} else {
|
|
2402
|
$uri .= '?subtree='. $sub_tree_filter_uuid_value;
|
|
2403
|
}
|
|
2404
|
break;
|
|
2405
|
}
|
|
2406
|
}
|
|
2407
|
}
|
|
2408
|
|
|
2409
|
}
|
|
2410
|
/**
|
|
2411
|
* Processes and stores the given information in $_SESSION['cdm']['ws_debug'] as table row.
|
|
2412
|
*
|
|
2413
|
* The cdm_ws_debug block will display the debug information.
|
|
2414
|
*
|
|
2415
|
* @param $uri
|
|
2416
|
* The CDM REST URI to which the request has been send
|
|
2417
|
* @param string $method
|
|
2418
|
* The HTTP request method, either 'GET' or 'POST'
|
|
2419
|
* @param string $post_data
|
|
2420
|
* The datastring send with a post request
|
|
2421
|
* @param $duration_fetch
|
|
2422
|
* The time in seconds it took to fetch the data from the web service
|
|
2423
|
* @param $duration_parse
|
|
2424
|
* Time in seconds which was needed to parse the json response
|
|
2425
|
* @param $datasize
|
|
2426
|
* Size of the data received from the server
|
|
2427
|
* @param $status
|
|
2428
|
* A status string, possible values are: 'valid', 'invalid', 'cacheL1', 'cacheL2'
|
|
2429
|
* @return bool
|
|
2430
|
* TRUE if adding the debug information was successful
|
|
2431
|
*/
|
|
2432
|
function cdm_ws_debug_add($uri, $method, $post_data, $duration_fetch, $duration_parse, $datasize, $status) {
|
|
2433
|
|
|
2434
|
static $initial_time = NULL;
|
|
2435
|
if(!$initial_time) {
|
|
2436
|
$initial_time = microtime(TRUE);
|
|
2437
|
}
|
|
2438
|
$time = microtime(TRUE) - $initial_time;
|
|
2439
|
|
|
2440
|
// Decompose uri into path and query element.
|
|
2441
|
$uri_parts = explode("?", $uri);
|
|
2442
|
$query = array();
|
|
2443
|
if (count($uri_parts) == 2) {
|
|
2444
|
$path = $uri_parts[0];
|
|
2445
|
}
|
|
2446
|
else {
|
|
2447
|
$path = $uri;
|
|
2448
|
}
|
|
2449
|
|
|
2450
|
if(strpos($uri, '?') > 0){
|
|
2451
|
$json_uri = str_replace('?', '.json?', $uri);
|
|
2452
|
$xml_uri = str_replace('?', '.xml?', $uri);
|
|
2453
|
} else {
|
|
2454
|
$json_uri = $uri . '.json';
|
|
2455
|
$xml_uri = $json_uri . '.xml';
|
|
2456
|
}
|
|
2457
|
|
|
2458
|
// data links to make data accessible as json and xml
|
|
2459
|
$data_links = '';
|
|
2460
|
if (_is_cdm_ws_uri($path)) {
|
|
2461
|
|
|
2462
|
// see ./js/http-method-link.js
|
|
2463
|
|
|
2464
|
if($method == 'GET'){
|
|
2465
|
$data_links .= '<a href="' . $xml_uri . '" target="data">xml</a>-';
|
|
2466
|
$data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">proxied</a>';
|
|
2467
|
$data_links .= '<br/>';
|
|
2468
|
$data_links .= '<a href="' . $json_uri . '" target="data">json</a>-';
|
|
2469
|
$data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">proxied</a>';
|
|
2470
|
} else {
|
|
2471
|
$js_link_activation = 'class="http-' . $method . '-link" data-cdm-http-post="' . $post_data . '" type="application/x-www-form-urlencoded"';
|
|
2472
|
$data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">xml-proxied</a>';
|
|
2473
|
$data_links .= '<br/>';
|
|
2474
|
$data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">json-proxied</a>';
|
|
2475
|
}
|
|
2476
|
}
|
|
2477
|
else {
|
|
2478
|
$data_links .= '<a href="' . $uri . '" target="data">open</a>';
|
|
2479
|
}
|
|
2480
|
|
|
2481
|
//
|
|
2482
|
$data = array(
|
|
2483
|
'ws_uri' => $uri,
|
|
2484
|
'method' => $method,
|
|
2485
|
'post_data' => $post_data,
|
|
2486
|
'time' => sprintf('%3.3f', $time),
|
|
2487
|
'fetch_seconds' => sprintf('%3.3f', $duration_fetch),
|
|
2488
|
'parse_seconds' => sprintf('%3.3f', $duration_parse),
|
|
2489
|
'size_kb' => sprintf('%3.1f', ($datasize / 1024)) ,
|
|
2490
|
'status' => $status,
|
|
2491
|
'data_links' => $data_links
|
|
2492
|
);
|
|
2493
|
if (!isset($_SESSION['cdm']['ws_debug'])) {
|
|
2494
|
$_SESSION['cdm']['ws_debug'] = array();
|
|
2495
|
}
|
|
2496
|
$_SESSION['cdm']['ws_debug'][] = serialize($data);
|
|
2497
|
|
|
2498
|
// Mark this page as being uncacheable.
|
|
2499
|
// taken over from drupal_get_messages() but it is unsure if we really need this here
|
|
2500
|
drupal_page_is_cacheable(FALSE);
|
|
2501
|
|
|
2502
|
// Messages not set when DB connection fails.
|
|
2503
|
return isset($_SESSION['cdm']['ws_debug']) ? $_SESSION['cdm']['ws_debug'] : NULL;
|
|
2504
|
}
|
|
2505
|
|
|
2506
|
/**
|
|
2507
|
* helper function to dtermine if the cdm_debug_block should be displayed or not
|
|
2508
|
* the visibility depends on whether
|
|
2509
|
* - the block is enabled
|
|
2510
|
* - the visibility restrictions in the block settings are satisfied
|
|
2511
|
*/
|
|
2512
|
function cdm_debug_block_visible() {
|
|
2513
|
static $is_visible = null;
|
|
2514
|
|
|
2515
|
if($is_visible === null){
|
|
2516
|
$block = block_load('cdm_api', 'cdm_ws_debug');
|
|
2517
|
$is_visible = isset($block->status) && $block->status == 1;
|
|
2518
|
if($is_visible){
|
|
2519
|
$blocks = array($block);
|
|
2520
|
// Checks the page, user role, and user-specific visibilty settings.
|
|
2521
|
block_block_list_alter($blocks);
|
|
2522
|
$is_visible = count($blocks) > 0;
|
|
2523
|
}
|
|
2524
|
}
|
|
2525
|
return $is_visible;
|
|
2526
|
}
|
|
2527
|
|
|
2528
|
/**
|
|
2529
|
* @todo Please document this function.
|
|
2530
|
* @see http://drupal.org/node/1354
|
|
2531
|
*/
|
|
2532
|
function cdm_load_obj($response_body) {
|
|
2533
|
$obj = json_decode($response_body);
|
|
2534
|
|
|
2535
|
if (!(is_object($obj) || is_array($obj))) {
|
|
2536
|
ob_start();
|
|
2537
|
$obj_dump = ob_get_contents();
|
|
2538
|
ob_clean();
|
|
2539
|
return FALSE;
|
|
2540
|
}
|
|
2541
|
|
|
2542
|
return $obj;
|
|
2543
|
}
|
|
2544
|
|
|
2545
|
/**
|
|
2546
|
* Do a http request to a CDM RESTful web service.
|
|
2547
|
*
|
|
2548
|
* @param string $uri
|
|
2549
|
* The webservice url.
|
|
2550
|
* @param string $method
|
|
2551
|
* The HTTP method to use, valid values are "GET" or "POST"; defaults to
|
|
2552
|
* "GET" even if NULL, FALSE or any invalid value is supplied.
|
|
2553
|
* @param $data: A string containing the request body, formatted as
|
|
2554
|
* 'param=value¶m=value&...'. Defaults to NULL.
|
|
2555
|
*
|
|
2556
|
* @return object
|
|
2557
|
* The object as returned by drupal_http_request():
|
|
2558
|
* An object that can have one or more of the following components:
|
|
2559
|
* - request: A string containing the request body that was sent.
|
|
2560
|
* - code: An integer containing the response status code, or the error code
|
|
2561
|
* if an error occurred.
|
|
2562
|
* - protocol: The response protocol (e.g. HTTP/1.1 or HTTP/1.0).
|
|
2563
|
* - status_message: The status message from the response, if a response was
|
|
2564
|
* received.
|
|
2565
|
* - redirect_code: If redirected, an integer containing the initial response
|
|
2566
|
* status code.
|
|
2567
|
* - redirect_url: If redirected, a string containing the URL of the redirect
|
|
2568
|
* target.
|
|
2569
|
* - error: If an error occurred, the error message. Otherwise not set.
|
|
2570
|
* - headers: An array containing the response headers as name/value pairs.
|
|
2571
|
* HTTP header names are case-insensitive (RFC 2616, section 4.2), so for
|
|
2572
|
* easy access the array keys are returned in lower case.
|
|
2573
|
* - data: A string containing the response body that was received.
|
|
2574
|
*/
|
|
2575
|
function cdm_http_request($uri, $method = "GET", $data = NULL) {
|
|
2576
|
static $acceptLanguage = NULL;
|
|
2577
|
$header = array();
|
|
2578
|
|
|
2579
|
if(!$acceptLanguage && module_exists('i18n')){
|
|
2580
|
$acceptLanguage = i18n_language_content()->language;
|
|
2581
|
}
|
|
2582
|
|
|
2583
|
if (!$acceptLanguage) {
|
|
2584
|
if (function_exists('apache_request_headers')) {
|
|
2585
|
$headers = apache_request_headers();
|
|
2586
|
if (isset($headers['Accept-Language'])) {
|
|
2587
|
$acceptLanguage = $headers['Accept-Language'];
|
|
2588
|
}
|
|
2589
|
}
|
|
2590
|
}
|
|
2591
|
|
|
2592
|
if ($method != "GET" && $method != "POST") {
|
|
2593
|
drupal_set_message('cdm_api.module#cdm_http_request() : unsupported HTTP request method ', 'error');
|
|
2594
|
}
|
|
2595
|
|
|
2596
|
if (_is_cdm_ws_uri($uri)) {
|
|
2597
|
$header['Accept'] = 'application/json';
|
|
2598
|
$header['Accept-Language'] = $acceptLanguage;
|
|
2599
|
$header['Accept-Charset'] = 'UTF-8';
|
|
2600
|
}
|
|
2601
|
|
|
2602
|
if($method == "POST") {
|
|
2603
|
// content type is application/x-www-form-urlencoded, so the request body uses the same format as the query string
|
|
2604
|
$header['Content-Type'] = 'application/x-www-form-urlencoded';
|
|
2605
|
}
|
|
2606
|
|
|
2607
|
$context_resource = null;
|
|
2608
|
if(!variable_get('cdm_webservice_url_ssl_verify', 1)){
|
|
2609
|
$context_resource = stream_context_create(array('ssl' => array('verify_peer' => FALSE, 'verify_peer_name' => FALSE)));
|
|
2610
|
}
|
|
2611
|
cdm_dd($uri);
|
|
2612
|
return drupal_http_request($uri, array(
|
|
2613
|
'headers' => $header,
|
|
2614
|
'method' => $method,
|
|
2615
|
'data' => $data,
|
|
2616
|
'timeout' => CDM_HTTP_REQUEST_TIMEOUT,
|
|
2617
|
'context' => $context_resource
|
|
2618
|
)
|
|
2619
|
);
|
|
2620
|
}
|
|
2621
|
|
|
2622
|
/**
|
|
2623
|
* Concatenates recursively the fields of all features contained in the given
|
|
2624
|
* CDM FeatureTree root node.
|
|
2625
|
*
|
|
2626
|
* @param $rootNode
|
|
2627
|
* A CDM FeatureTree node
|
|
2628
|
* @param
|
|
2629
|
* The character to be used as glue for concatenation, default is ', '
|
|
2630
|
* @param $field_name
|
|
2631
|
* The field name of the CDM Features
|
|
2632
|
* @param $excludes
|
|
2633
|
* Allows defining a set of values to be excluded. This refers to the values
|
|
2634
|
* in the field denoted by the $field_name parameter
|
|
2635
|
*
|
|
2636
|
*/
|
|
2637
|
function cdm_featureTree_elements_toString($root_node, $separator = ', ', $field_name = 'representation_L10n', $excludes = array()) {
|
|
2638
|
$out = '';
|
|
2639
|
|
|
2640
|
$pre_child_separator = $separator;
|
|
2641
|
$post_child_separator = '';
|
|
2642
|
|
|
2643
|
foreach ($root_node->childNodes as $feature_node) {
|
|
2644
|
$out .= ($out ? $separator : '');
|
|
2645
|
if(!in_array($feature_node->term->$field_name, $excludes)) {
|
|
2646
|
$out .= $feature_node->term->$field_name;
|
|
2647
|
if (is_array($feature_node->childNodes) && count($feature_node->childNodes) > 0) {
|
|
2648
|
$childlabels = cdm_featureTree_elements_toString($feature_node, $separator, $field_name);
|
|
2649
|
if (strlen($childlabels)) {
|
|
2650
|
$out .= $pre_child_separator . $childlabels . $post_child_separator;
|
|
2651
|
}
|
|
2652
|
}
|
|
2653
|
}
|
|
2654
|
}
|
|
2655
|
return $out;
|
|
2656
|
}
|
|
2657
|
|
|
2658
|
/**
|
|
2659
|
* Create a one-dimensional form options array.
|
|
2660
|
*
|
|
2661
|
* Creates an array of all features in the feature tree of feature nodes,
|
|
2662
|
* the node labels are indented by $node_char and $childIndent depending on the
|
|
2663
|
* hierachy level.
|
|
2664
|
*
|
|
2665
|
* @param - $rootNode
|
|
2666
|
* @param - $node_char
|
|
2667
|
* @param - $childIndentStr
|
|
2668
|
* @param - $childIndent
|
|
2669
|
* ONLY USED INTERNALLY!
|
|
2670
|
*
|
|
2671
|
* @return array
|
|
2672
|
* A one dimensional Drupal form options array.
|
|
2673
|
*/
|
|
2674
|
function _featureTree_nodes_as_feature_options($rootNode, $node_char = "├─ ", $childIndentStr = ' ', $childIndent = '') {
|
|
2675
|
$options = array();
|
|
2676
|
foreach ($rootNode->childNodes as $featureNode) {
|
|
2677
|
$indent_prefix = '';
|
|
2678
|
if ($childIndent) {
|
|
2679
|
$indent_prefix = $childIndent . $node_char . " ";
|
|
2680
|
}
|
|
2681
|
$options[$featureNode->term->uuid] = $indent_prefix . $featureNode->term->representation_L10n;
|
|
2682
|
if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
|
|
2683
|
// Foreach ($featureNode->childNodes as $childNode){
|
|
2684
|
$childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
|
|
2685
|
$options = array_merge_recursive($options, $childList);
|
|
2686
|
// }
|
|
2687
|
}
|
|
2688
|
}
|
|
2689
|
return $options;
|
|
2690
|
}
|
|
2691
|
|
|
2692
|
/**
|
|
2693
|
* Returns an array with all available FeatureTrees and the representations of the selected
|
|
2694
|
* FeatureTree as a detail view.
|
|
2695
|
*
|
|
2696
|
* @param boolean $add_default_feature_free
|
|
2697
|
* @param boolean $show_weight
|
|
2698
|
* Show the weight which will be applied to the according feature block
|
|
2699
|
* @return array
|
|
2700
|
* associative array with following keys:
|
|
2701
|
* -options: Returns an array with all available Feature Trees
|
|
2702
|
* -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
|
|
2703
|
*
|
|
2704
|
*/
|
|
2705
|
function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE, $show_weight = FALSE) {
|
|
2706
|
|
|
2707
|
$options = array();
|
|
2708
|
$tree_representations = array();
|
|
2709
|
$feature_trees = array();
|
|
2710
|
|
|
2711
|
// Set tree that contains all features.
|
|
2712
|
if ($add_default_feature_free) {
|
|
2713
|
$options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
|
|
2714
|
$feature_trees[] = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
|
|
2715
|
}
|
|
2716
|
|
|
2717
|
// Get feature trees from database.
|
|
2718
|
$persisted_trees = cdm_ws_fetch_all(CDM_WS_TERMTREES, array("termType" => "Feature"));
|
|
2719
|
if (is_array($persisted_trees)) {
|
|
2720
|
$feature_trees = array_merge($feature_trees, $persisted_trees);
|
|
2721
|
}
|
|
2722
|
|
|
2723
|
foreach ($feature_trees as $featureTree) {
|
|
2724
|
|
|
2725
|
if(!is_object($featureTree)){
|
|
2726
|
continue;
|
|
2727
|
}
|
|
2728
|
// Do not add the DEFAULT_FEATURETREE again,
|
|
2729
|
if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
|
|
2730
|
$options[$featureTree->uuid] = $featureTree->representation_L10n;
|
|
2731
|
}
|
|
2732
|
|
|
2733
|
// Render the hierarchic tree structure
|
|
2734
|
if (is_array( $featureTree->root->childNodes) && count( $featureTree->root->childNodes) > 0) {
|
|
2735
|
|
|
2736
|
// Render the hierarchic tree structure.
|
|
2737
|
$treeDetails = '<div class="featuretree_structure">'
|
|
2738
|
. render_feature_tree_hierarchy($featureTree->uuid, $show_weight)
|
|
2739
|
. '</div>';
|
|
2740
|
|
|
2741
|
$form = array();
|
|
2742
|
$form['featureTree-' . $featureTree->uuid] = array(
|
|
2743
|
'#type' => 'fieldset',
|
|
2744
|
'#title' => 'Show details',
|
|
2745
|
'#attributes' => array('class' => array('collapsible collapsed')),
|
|
2746
|
// '#collapsible' => TRUE,
|
|
2747
|
// '#collapsed' => TRUE,
|
|
2748
|
);
|
|
2749
|
$form['featureTree-' . $featureTree->uuid]['details'] = array(
|
|
2750
|
'#markup' => $treeDetails,
|
|
2751
|
);
|
|
2752
|
|
|
2753
|
$tree_representations[$featureTree->uuid] = drupal_render($form);
|
|
2754
|
}
|
|
2755
|
|
|
2756
|
} // END loop over feature trees
|
|
2757
|
|
|
2758
|
// return $options;
|
|
2759
|
return array('options' => $options, 'treeRepresentations' => $tree_representations);
|
|
2760
|
}
|
|
2761
|
/*
|
|
2762
|
**
|
|
2763
|
* Returns an array with all available FeatureTrees and the representations of the selected
|
|
2764
|
* FeatureTree as a detail view.
|
|
2765
|
*
|
|
2766
|
* @param boolean $add_default_feature_free
|
|
2767
|
* @param boolean $show_weight
|
|
2768
|
* Show the weight which will be applied to the according feature block
|
|
2769
|
* @return array
|
|
2770
|
* associative array with following keys:
|
|
2771
|
* -options: Returns an array with all available Feature Trees
|
|
2772
|
* -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
|
|
2773
|
*
|
|
2774
|
*/
|
|
2775
|
function cdm_get_statusTrees_as_options($add_default_feature_free = TRUE) {
|
|
2776
|
|
|
2777
|
$options = array();
|
|
2778
|
$tree_representations = array();
|
|
2779
|
$status_trees = array();
|
|
2780
|
|
|
2781
|
// Set tree that contains all features.
|
|
2782
|
//if ($add_default_feature_free) {
|
|
2783
|
// $options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
|
|
2784
|
// $feature_trees[] = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
|
|
2785
|
//}
|
|
2786
|
|
|
2787
|
// Get feature trees from database.
|
|
2788
|
$persisted_trees = cdm_ws_fetch_all(CDM_WS_TERMTREES, array("termType" => "PresenceAbsenceTerm"));
|
|
2789
|
if (is_array($persisted_trees)) {
|
|
2790
|
$status_trees = array_merge($status_trees, $persisted_trees);
|
|
2791
|
}
|
|
2792
|
|
|
2793
|
|
|
2794
|
foreach ($status_trees as $status_tree) {
|
|
2795
|
|
|
2796
|
if(!is_object($status_tree)){
|
|
2797
|
continue;
|
|
2798
|
}
|
|
2799
|
//if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
|
|
2800
|
$options[$status_tree->uuid] = $status_tree->representation_L10n;
|
|
2801
|
//}
|
|
2802
|
// Render the hierarchic tree structure
|
|
2803
|
if (is_array( $status_tree->root->childNodes) && count( $status_tree->root->childNodes) > 0) {
|
|
2804
|
|
|
2805
|
// Render the hierarchic tree structure.
|
|
2806
|
$treeDetails = '<div class="featuretree_structure">'
|
|
2807
|
. render_feature_tree_hierarchy($status_tree->uuid, false)
|
|
2808
|
. '</div>';
|
|
2809
|
|
|
2810
|
$form = array();
|
|
2811
|
$form['statusTree-' . $status_tree->uuid] = array(
|
|
2812
|
'#type' => 'fieldset',
|
|
2813
|
'#title' => 'Show details',
|
|
2814
|
'#attributes' => array('class' => array('collapsible collapsed')),
|
|
2815
|
// '#collapsible' => TRUE,
|
|
2816
|
// '#collapsed' => TRUE,
|
|
2817
|
);
|
|
2818
|
$form['statusTree-' . $status_tree->uuid]['details'] = array(
|
|
2819
|
'#markup' => $treeDetails,
|
|
2820
|
);
|
|
2821
|
|
|
2822
|
$tree_representations[$status_tree->uuid] = drupal_render($form);
|
|
2823
|
}
|
|
2824
|
|
|
2825
|
} // END loop over feature trees
|
|
2826
|
|
|
2827
|
// return $options;
|
|
2828
|
return array('options' => $options, 'treeRepresentations' => $tree_representations);
|
|
2829
|
}
|
|
2830
|
|
|
2831
|
/*
|
|
2832
|
**
|
|
2833
|
* Returns an array with all available FeatureTrees and the representations of the selected
|
|
2834
|
* FeatureTree as a detail view.
|
|
2835
|
*
|
|
2836
|
* @param boolean $add_default_feature_free
|
|
2837
|
* @param boolean $show_weight
|
|
2838
|
* Show the weight which will be applied to the according feature block
|
|
2839
|
* @return array
|
|
2840
|
* associative array with following keys:
|
|
2841
|
* -options: Returns an array with all available Feature Trees
|
|
2842
|
* -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
|
|
2843
|
*
|
|
2844
|
*/
|
|
2845
|
function cdm_get_areaTrees_as_options($add_default_feature_free = TRUE) {
|
|
2846
|
|
|
2847
|
$options = array();
|
|
2848
|
$tree_representations = array();
|
|
2849
|
$area_trees = array();
|
|
2850
|
|
|
2851
|
// Set tree that contains all features.
|
|
2852
|
//if ($add_default_feature_free) {
|
|
2853
|
// $options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
|
|
2854
|
// $feature_trees[] = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
|
|
2855
|
//}
|
|
2856
|
|
|
2857
|
// Get feature trees from database.
|
|
2858
|
$persisted_trees = cdm_ws_fetch_all(CDM_WS_TERMTREES, array("termType" => "NamedArea"));
|
|
2859
|
if (is_array($persisted_trees)) {
|
|
2860
|
$area_trees = array_merge($area_trees, $persisted_trees);
|
|
2861
|
}
|
|
2862
|
|
|
2863
|
|
|
2864
|
foreach ($area_trees as $areaTree) {
|
|
2865
|
|
|
2866
|
if(!is_object($areaTree)){
|
|
2867
|
continue;
|
|
2868
|
}
|
|
2869
|
//if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
|
|
2870
|
$options[$areaTree->uuid] = $areaTree->representation_L10n;
|
|
2871
|
//}
|
|
2872
|
// Render the hierarchic tree structure
|
|
2873
|
if (is_array( $areaTree->root->childNodes) && count( $areaTree->root->childNodes) > 0) {
|
|
2874
|
|
|
2875
|
// Render the hierarchic tree structure.
|
|
2876
|
$treeDetails = '<div class="featuretree_structure">'
|
|
2877
|
. render_feature_tree_hierarchy($areaTree->uuid, false)
|
|
2878
|
. '</div>';
|
|
2879
|
|
|
2880
|
$form = array();
|
|
2881
|
$form['areaTree-' . $areaTree->uuid] = array(
|
|
2882
|
'#type' => 'fieldset',
|
|
2883
|
'#title' => 'Show details',
|
|
2884
|
'#attributes' => array('class' => array('collapsible collapsed')),
|
|
2885
|
// '#collapsible' => TRUE,
|
|
2886
|
// '#collapsed' => TRUE,
|
|
2887
|
);
|
|
2888
|
$form['areaTree-' . $areaTree->uuid]['details'] = array(
|
|
2889
|
'#markup' => $treeDetails,
|
|
2890
|
);
|
|
2891
|
|
|
2892
|
$tree_representations[$areaTree->uuid] = drupal_render($form);
|
|
2893
|
}
|
|
2894
|
|
|
2895
|
} // END loop over feature trees
|
|
2896
|
|
|
2897
|
// return $options;
|
|
2898
|
return array('options' => $options, 'treeRepresentations' => $tree_representations);
|
|
2899
|
}
|
|
2900
|
|
|
2901
|
/**
|
|
2902
|
* Provides the list of available classifications in form of an options array.
|
|
2903
|
*
|
|
2904
|
* The options array is suitable for drupal form API elements that allow multiple choices.
|
|
2905
|
* @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
|
|
2906
|
*
|
|
2907
|
* The classifications are ordered alphabetically whereas the classification
|
|
2908
|
* chosen as default will always appear on top of the array, followed by a
|
|
2909
|
* blank line below.
|
|
2910
|
*
|
|
2911
|
* @param bool $add_none_option
|
|
2912
|
* is true an additional 'none' option will be added if and only if there are
|
|
2913
|
* more than one options. Defaults to FALSE
|
|
2914
|
*
|
|
2915
|
* @param $include_uuids
|
|
2916
|
* The taxon tree uuids to be included, other taxon trees will be filtered out.
|
|
2917
|
* You may want to use here:
|
|
2918
|
* variable_get(CDM_TAXONTREE_INCLUDES, [])
|
|
2919
|
*
|
|
2920
|
*
|
|
2921
|
* @return array
|
|
2922
|
* classifications in an array as options for a form element that allows multiple choices.
|
|
2923
|
*/
|
|
2924
|
function cdm_get_taxontrees_as_options($add_none_option = FALSE, $include_uuids = []) {
|
|
2925
|
|
|
2926
|
$taxonTrees = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
|
|
2927
|
|
|
2928
|
$default_classification_uuid = variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
|
|
2929
|
$default_classification_label = '';
|
|
2930
|
|
|
2931
|
// add all classifications
|
|
2932
|
$taxonomic_tree_options = array();
|
|
2933
|
if ($add_none_option) {
|
|
2934
|
$taxonomic_tree_options['NONE'] = ' '; // one Space character at beginning to force on top;
|
|
2935
|
}
|
|
2936
|
if ($taxonTrees) {
|
|
2937
|
foreach ($taxonTrees as $tree) {
|
|
2938
|
if(is_array($include_uuids) && count($include_uuids) > 0 && array_search($tree->uuid, $include_uuids) === FALSE){
|
|
2939
|
continue;
|
|
2940
|
}
|
|
2941
|
if (!$default_classification_uuid || $default_classification_uuid != $tree->uuid) {
|
|
2942
|
$taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
|
|
2943
|
} else {
|
|
2944
|
$taxonomic_tree_options[$tree->uuid] = ' '; // two Space characters to force on top but below 'none' option , will be replaced below by titleCache
|
|
2945
|
$default_classification_label = $tree->titleCache;
|
|
2946
|
}
|
|
2947
|
}
|
|
2948
|
}
|
|
2949
|
// oder alphabetically the space
|
|
2950
|
asort($taxonomic_tree_options);
|
|
2951
|
|
|
2952
|
// now set the labels for none
|
|
2953
|
if ($add_none_option && count($taxonomic_tree_options) > 2) {
|
|
2954
|
$taxonomic_tree_options['NONE'] =t('--- ALL ---');
|
|
2955
|
} else {
|
|
2956
|
unset($taxonomic_tree_options['NONE']);
|
|
2957
|
}
|
|
2958
|
|
|
2959
|
// for default_classification
|
|
2960
|
if (is_uuid($default_classification_uuid)) {
|
|
2961
|
$taxonomic_tree_options[$default_classification_uuid] =
|
|
2962
|
$default_classification_label ? $default_classification_label : '--- INVALID CHOICE ---'
|
|
2963
|
. (count($taxonTrees) > 1 ? ' [' . t('DEFAULT CLASSIFICATION') . ']': '');
|
|
2964
|
}
|
|
2965
|
|
|
2966
|
return $taxonomic_tree_options;
|
|
2967
|
}
|
|
2968
|
|
|
2969
|
/**
|
|
2970
|
* @todo Please document this function.
|
|
2971
|
* @see http://drupal.org/node/1354
|
|
2972
|
*/
|
|
2973
|
function cdm_api_secref_cache_prefetch(&$secUuids) {
|
|
2974
|
// Comment @WA: global variables should start with a single underscore
|
|
2975
|
// followed by the module and another underscore.
|
|
2976
|
global $_cdm_api_secref_cache;
|
|
2977
|
if (!is_array($_cdm_api_secref_cache)) {
|
|
2978
|
$_cdm_api_secref_cache = array();
|
|
2979
|
}
|
|
2980
|
$uniqueUuids = array_unique($secUuids);
|
|
2981
|
$i = 0;
|
|
2982
|
$param = '';
|
|
2983
|
while ($i++ < count($uniqueUuids)) {
|
|
2984
|
$param .= $secUuids[$i] . ',';
|
|
2985
|
if (strlen($param) + 37 > 2000) {
|
|
2986
|
_cdm_api_secref_cache_add($param);
|
|
2987
|
$param = '';
|
|
2988
|
}
|
|
2989
|
}
|
|
2990
|
if ($param) {
|
|
2991
|
_cdm_api_secref_cache_add($param);
|
|
2992
|
}
|
|
2993
|
}
|
|
2994
|
|
|
2995
|
/**
|
|
2996
|
* @todo Please document this function.
|
|
2997
|
* @see http://drupal.org/node/1354
|
|
2998
|
*/
|
|
2999
|
function cdm_api_secref_cache_get($secUuid) {
|
|
3000
|
global $_cdm_api_secref_cache;
|
|
3001
|
if (!is_array($_cdm_api_secref_cache)) {
|
|
3002
|
$_cdm_api_secref_cache = array();
|
|
3003
|
}
|
|
3004
|
if (!array_key_exists($secUuid, $_cdm_api_secref_cache)) {
|
|
3005
|
_cdm_api_secref_cache_add($secUuid);
|
|
3006
|
}
|
|
3007
|
return $_cdm_api_secref_cache[$secUuid];
|
|
3008
|
}
|
|
3009
|
|
|
3010
|
/**
|
|
3011
|
* @todo Please document this function.
|
|
3012
|
* @see http://drupal.org/node/1354
|
|
3013
|
*/
|
|
3014
|
function cdm_api_secref_cache_clear() {
|
|
3015
|
global $_cdm_api_secref_cache;
|
|
3016
|
$_cdm_api_secref_cache = array();
|
|
3017
|
}
|
|
3018
|
|
|
3019
|
|
|
3020
|
/**
|
|
3021
|
* @todo Please document this function.
|
|
3022
|
* @see http://drupal.org/node/1354
|
|
3023
|
*/
|
|
3024
|
function _cdm_api_secref_cache_add($secUuidsStr) {
|
|
3025
|
global $_cdm_api_secref_cache;
|
|
3026
|
$ref = cdm_ws_get(CDM_WS_REFERENCE, $secUuidsStr);
|
|
3027
|
// Batch fetching not jet reimplemented thus:
|
|
3028
|
/*
|
|
3029
|
$assocRefSTOs = array(); if($refSTOs) { foreach($refSTOs as $ref){
|
|
3030
|
$assocRefSTOs[$ref->uuid] = $ref; } $_cdm_api_secref_cache =
|
|
3031
|
array_merge($_cdm_api_secref_cache, $assocRefSTOs); }
|
|
3032
|
*/
|
|
3033
|
$_cdm_api_secref_cache[$ref->uuid] = $ref;
|
|
3034
|
}
|
|
3035
|
|
|
3036
|
/**
|
|
3037
|
* Checks if the given uri starts with a cdm webservice url.
|
|
3038
|
*
|
|
3039
|
* Checks if the uri starts with the cdm webservice url stored in the
|
|
3040
|
* Drupal variable 'cdm_webservice_url'.
|
|
3041
|
* The 'cdm_webservice_url' can be set in the admins section of the portal.
|
|
3042
|
*
|
|
3043
|
* @param string $uri
|
|
3044
|
* The URI to test.
|
|
3045
|
*
|
|
3046
|
* @return bool
|
|
3047
|
* True if the uri starts with a cdm webservice url.
|
|
3048
|
*/
|
|
3049
|
function _is_cdm_ws_uri($uri) {
|
|
3050
|
return str_beginsWith($uri, cdm_webservice_url('#EMPTY#'));
|
|
3051
|
}
|
|
3052
|
|
|
3053
|
/**
|
|
3054
|
* @todo Please document this function.
|
|
3055
|
* @see http://drupal.org/node/1354
|
|
3056
|
*/
|
|
3057
|
function queryString($elements) {
|
|
3058
|
$query = '';
|
|
3059
|
foreach ($elements as $key => $value) {
|
|
3060
|
if (is_array($value) && !empty($value)) {
|
|
3061
|
foreach ($value as $v) {
|
|
3062
|
$query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($v);
|
|
3063
|
}
|
|
3064
|
}
|
|
3065
|
else {
|
|
3066
|
//if (is_numeric($value) || !empty($value)){
|
|
3067
|
$query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($value);
|
|
3068
|
//}
|
|
3069
|
|
|
3070
|
}
|
|
3071
|
}
|
|
3072
|
return $query;
|
|
3073
|
}
|
|
3074
|
|
|
3075
|
/**
|
|
3076
|
* Compares the given CDM Term instances by the representationL10n.
|
|
3077
|
*
|
|
3078
|
* Can also be used with TermDTOs. To be used in usort()
|
|
3079
|
*
|
|
3080
|
* @see http://php.net/manual/en/function.usort.php
|
|
3081
|
*
|
|
3082
|
* @param $term1
|
|
3083
|
* The first CDM Term instance
|
|
3084
|
* @param $term2
|
|
3085
|
* The second CDM Term instance
|
|
3086
|
* @return int
|
|
3087
|
* The result of the comparison
|
|
3088
|
*/
|
|
3089
|
function compare_terms_by_representationL10n($term1, $term2) {
|
|
3090
|
|
|
3091
|
if (!isset($term1->representation_L10n)) {
|
|
3092
|
$term1->representationL10n = '';
|
|
3093
|
}
|
|
3094
|
if (!isset($term2->representation_L10n)) {
|
|
3095
|
$term2->representationL10n = '';
|
|
3096
|
}
|
|
3097
|
|
|
3098
|
return strcmp($term1->representation_L10n, $term2->representation_L10n);
|
|
3099
|
}
|
|
3100
|
|
|
3101
|
function compare_terms_by_order_index($term1, $term2) {
|
|
3102
|
|
|
3103
|
|
|
3104
|
if (!isset($term1->orderIndex)) {
|
|
3105
|
$a = 0;
|
|
3106
|
} else {
|
|
3107
|
$a = $term1->orderIndex;
|
|
3108
|
}
|
|
3109
|
if (!isset($term2->orderIndex)) {
|
|
3110
|
$b = 0;
|
|
3111
|
} else {
|
|
3112
|
$b = $term2->orderIndex;
|
|
3113
|
}
|
|
3114
|
|
|
3115
|
if ($a == $b) {
|
|
3116
|
return 0;
|
|
3117
|
}
|
|
3118
|
return ($a < $b) ? -1 : 1;
|
|
3119
|
|
|
3120
|
}
|
|
3121
|
|
|
3122
|
|
|
3123
|
/**
|
|
3124
|
* Make a 'deep copy' of an array.
|
|
3125
|
*
|
|
3126
|
* Make a complete deep copy of an array replacing
|
|
3127
|
* references with deep copies until a certain depth is reached
|
|
3128
|
* ($maxdepth) whereupon references are copied as-is...
|
|
3129
|
*
|
|
3130
|
* @see http://us3.php.net/manual/en/ref.array.php
|
|
3131
|
*
|
|
3132
|
* @param array $array
|
|
3133
|
* @param array $copy passed by reference
|
|
3134
|
* @param int $maxdepth
|
|
3135
|
* @param int $depth
|
|
3136
|
*/
|
|
3137
|
function array_deep_copy(&$array, &$copy, $maxdepth = 50, $depth = 0) {
|
|
3138
|
if ($depth > $maxdepth) {
|
|
3139
|
$copy = $array;
|
|
3140
|
return;
|
|
3141
|
}
|
|
3142
|
if (!is_array($copy)) {
|
|
3143
|
$copy = array();
|
|
3144
|
}
|
|
3145
|
foreach ($array as $k => &$v) {
|
|
3146
|
if (is_array($v)) {
|
|
3147
|
array_deep_copy($v, $copy[$k], $maxdepth, ++$depth);
|
|
3148
|
}
|
|
3149
|
else {
|
|
3150
|
$copy[$k] = $v;
|
|
3151
|
}
|
|
3152
|
}
|
|
3153
|
}
|
|
3154
|
|
|
3155
|
/**
|
|
3156
|
* Concatenated the uuids of the passed cdm entity with `,` as glue.
|
|
3157
|
* The returned string is suitable for cdm webservices consuming UUIDList as
|
|
3158
|
* parameter
|
|
3159
|
*
|
|
3160
|
* @param array $cdm_entities
|
|
3161
|
*
|
|
3162
|
* @return string
|
|
3163
|
*/
|
|
3164
|
function cdm_uuid_list_parameter_value(array $cdm_entities){
|
|
3165
|
$uuids = [];
|
|
3166
|
foreach ($cdm_entities as $entity){
|
|
3167
|
if(isset($entity) && is_uuid($entity->uuid) ){
|
|
3168
|
$uuids[] = $entity->uuid;
|
|
3169
|
}
|
|
3170
|
}
|
|
3171
|
return join(',', $uuids);
|
|
3172
|
}
|
|
3173
|
|
|
3174
|
/**
|
|
3175
|
* Adds java script to create and enable a toggler for the cdm webservice debug block content.
|
|
3176
|
*
|
|
3177
|
*/
|
|
3178
|
function _add_js_ws_debug() {
|
|
3179
|
|
|
3180
|
$data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.min.js';
|
|
3181
|
$colorbox_js = '/js/colorbox/jquery.colorbox-min.js';
|
|
3182
|
if (variable_get('cdm_js_devel_mode', FALSE)) {
|
|
3183
|
// use the developer versions of js libs
|
|
3184
|
$data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.js';
|
|
3185
|
$colorbox_js = '/js/colorbox/jquery.colorbox.js';
|
|
3186
|
}
|
|
3187
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $data_tables_js,
|
|
3188
|
array(
|
|
3189
|
'type' => 'file',
|
|
3190
|
'weight' => JS_LIBRARY,
|
|
3191
|
'cache' => TRUE)
|
|
3192
|
);
|
|
3193
|
|
|
3194
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $colorbox_js,
|
|
3195
|
array(
|
|
3196
|
'type' => 'file',
|
|
3197
|
'weight' => JS_LIBRARY,
|
|
3198
|
'cache' => TRUE)
|
|
3199
|
);
|
|
3200
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/colorbox/colorbox.css');
|
|
3201
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/DataTables-1.9.4/media/css/cdm_debug_table.css');
|
|
3202
|
|
|
3203
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ws_debug_block.js',
|
|
3204
|
array(
|
|
3205
|
'type' => 'file',
|
|
3206
|
'weight' => JS_LIBRARY,
|
|
3207
|
'cache' => TRUE)
|
|
3208
|
);
|
|
3209
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/http-method-link.js',
|
|
3210
|
array(
|
|
3211
|
'type' => 'file',
|
|
3212
|
'weight' => JS_LIBRARY,
|
|
3213
|
'cache' => TRUE)
|
|
3214
|
);
|
|
3215
|
|
|
3216
|
}
|
|
3217
|
|
|
3218
|
/**
|
|
3219
|
* @todo Please document this function.
|
|
3220
|
* @see http://drupal.org/node/1354
|
|
3221
|
*/
|
|
3222
|
function _no_classfication_uuid_message() {
|
|
3223
|
if (!cdm_ws_get(CDM_WS_PORTAL_TAXONOMY)) {
|
|
3224
|
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.');
|
|
3225
|
}
|
|
3226
|
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.');
|
|
3227
|
}
|
|
3228
|
|
|
3229
|
/**
|
|
3230
|
* Implementation of hook flush_caches
|
|
3231
|
*
|
|
3232
|
* Add custom cache tables to the list of cache tables that
|
|
3233
|
* will be cleared by the Clear button on the Performance page or whenever
|
|
3234
|
* drupal_flush_all_caches is invoked.
|
|
3235
|
*
|
|
3236
|
* @author W.Addink <waddink@eti.uva.nl>
|
|
3237
|
*
|
|
3238
|
* @return array
|
|
3239
|
* An array with custom cache tables to include.
|
|
3240
|
*/
|
|
3241
|
function cdm_api_flush_caches() {
|
|
3242
|
return array('cache_cdm_ws');
|
|
3243
|
}
|
|
3244
|
|
|
3245
|
/**
|
|
3246
|
* Logs if the drupal variable 'cdm_debug_mode' ist set true to drupal_debug.txt in the site's temp directory.
|
|
3247
|
*
|
|
3248
|
* @param $data
|
|
3249
|
* The variable to log to the drupal_debug.txt log file.
|
|
3250
|
* @param $label
|
|
3251
|
* (optional) If set, a label to output before $data in the log file.
|
|
3252
|
*
|
|
3253
|
* @return
|
|
3254
|
* No return value if successful, FALSE if the log file could not be written
|
|
3255
|
* to.
|
|
3256
|
*
|
|
3257
|
* @see cdm_dataportal_init() where the log file is reset on each requests
|
|
3258
|
* @see dd()
|
|
3259
|
* @see http://drupal.org/node/314112
|
|
3260
|
*
|
|
3261
|
*/
|
|
3262
|
function cdm_dd($data, $label = NULL) {
|
|
3263
|
if(module_exists('devel') && variable_get('cdm_debug_mode', FALSE) && file_stream_wrapper_get_class('temporary') ){
|
|
3264
|
return dd($data, $label);
|
|
3265
|
}
|
|
3266
|
}
|
|
3267
|
|