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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
 * Implements hook_block_info().
106
 */
107
function cdm_api_block_info() {
108

    
109
  $block['cdm_ws_debug'] = array(
110
      "info" => t("CDM web service debug"),
111
      "cache" => DRUPAL_NO_CACHE
112
  );
113
  return $block;
114
}
115

    
116
/**
117
 * Implements hook_block_view().
118
 */
119
function cdm_api_block_view($delta) {
120
  switch ($delta) {
121
    case 'cdm_ws_debug':
122

    
123
    $cdm_ws_url = variable_get('cdm_webservice_url', '');
124

    
125
    $field_map = array(
126
        'ws_uri' => t('URI') . ' <code>(' . $cdm_ws_url .'...)</code>',
127
        'time' => t('Time'),
128
        'fetch_seconds' => t('Fetching [s]'),
129
        'parse_seconds' => t('Parsing [s]'),
130
        'size_kb' => t('Size [kb]'),
131
        'status' => t('Status'),
132
        'data_links' =>  t('Links'),
133
    );
134

    
135

    
136
    if (!isset($_SESSION['cdm']['ws_debug'])) {
137
      $_SESSION['cdm']['ws_debug'] = array();
138
    }
139

    
140
    $header = '<thead><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></thead>';
141
    $footer = '<tfoot><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></tfoot>';
142
    $rows = array();
143

    
144
    foreach ($_SESSION['cdm']['ws_debug'] as $data){
145

    
146
      $data = unserialize($data);
147

    
148
      // stip of webservice base url
149
      $data['ws_uri'] = str_replace($cdm_ws_url, '', $data['ws_uri']);
150
      if($data['method'] == 'POST'){
151
        $data['ws_uri'] = 'POST: ' . $data['ws_uri'] . '?' . $data['post_data'];
152
      }
153

    
154
      $cells = array();
155
      foreach ($field_map as $field => $label){
156
        $cells[] = '<td class="' . $field . '">' .  $data[$field] . '</td>';
157
      }
158
      $rows[] = '<tr class="' . $data['status']  . '">' . join('' , $cells). '</tr>';
159
    }
160
    // clear session again
161
    $_SESSION['cdm']['ws_debug'] = array();
162

    
163
    _add_js_ws_debug();
164

    
165
    $block['subject'] = ''; // no subject, title in content for having a defined element id
166
    // otherwise it would depend on the theme
167
    $block['content'] = array(
168
      '#markup' => '<h4 id="cdm-ws-debug-button">' . t('CDM Debug') . '</h4>'
169
        // cannot use theme_table() since table footer is not jet supported in D7
170
        . '<div id="cdm-ws-debug-table-container"><table id="cdm-ws-debug-table">'
171
        . $header
172
        . '<tbody>' . join('', $rows) . '</tbody>'
173
        . $footer
174
        . '</table></div>',
175
      '#attached' => array(
176
        'css' => array(
177
          drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_ws_debug.css'
178
        )
179
      )
180
    );
181
    return $block;
182
  }
183
}
184

    
185
/**
186
 * Implements hook_cron().
187
 *
188
 * Expire outdated cache entries.
189
 */
190
function cdm_api_cron() {
191
  cache_clear_all(NULL, 'cache_cdm_ws');
192
}
193

    
194
/**
195
 * Lists the classifications a taxon belongs to
196
 *
197
 * @param CDM type Taxon $taxon
198
 *   the taxon
199
 *
200
 * @return array
201
 *   aray of CDM instances of Type Classification
202
 */
203
function get_classifications_for_taxon($taxon) {
204

    
205
  return cdm_ws_get(CDM_WS_TAXON_CLASSIFICATIONS, $taxon->uuid);;
206
}
207

    
208
/**
209
 * Returns the chosen FeatureTree for the taxon profile.
210
 *
211
 * The FeatureTree profile returned is the one that has been set in the
212
 * dataportal settings (layout->taxon:profile).
213
 * When the chosen FeatureTree is not found in the database,
214
 * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
215
 *
216
 * @return mixed
217
 *   A cdm FeatureTree object.
218
 */
219
function get_profile_feature_tree() {
220
  static $profile_featureTree;
221

    
222
  if($profile_featureTree == NULL) {
223
    $profile_featureTree = cdm_ws_get(
224
      CDM_WS_FEATURETREE,
225
      variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
226
    );
227
    if (!$profile_featureTree) {
228
      $profile_featureTree = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
229
    }
230
  }
231

    
232
  return $profile_featureTree;
233
}
234

    
235
/**
236
 * Returns the chosen FeatureTree for SpecimenDescriptions.
237
 *
238
 * The FeatureTree returned is the one that has been set in the
239
 * dataportal settings (layout->taxon:specimen).
240
 * When the chosen FeatureTree is not found in the database,
241
 * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
242
 *
243
 * @return mixed
244
 *   A cdm FeatureTree object.
245
 */
246
function cdm_get_occurrence_featureTree() {
247
  static $occurrence_featureTree;
248

    
249
  if($occurrence_featureTree == NULL) {
250
    $occurrence_featureTree = cdm_ws_get(
251
      CDM_WS_FEATURETREE,
252
      variable_get(CDM_OCCURRENCE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
253
    );
254
    if (!$occurrence_featureTree) {
255
      $occurrence_featureTree = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
256
    }
257
  }
258
  return $occurrence_featureTree;
259
}
260

    
261
/**
262
 * Returns the FeatureTree for structured descriptions
263
 *
264
 * The FeatureTree returned is the one that has been set in the
265
 * dataportal settings (layout->taxon:profile).
266
 * When the chosen FeatureTree is not found in the database,
267
 * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
268
 *
269
 * @return mixed
270
 *   A cdm FeatureTree object.
271
 */
272
function get_structured_description_featureTree() {
273
  static $structured_description_featureTree;
274

    
275
  if($structured_description_featureTree == NULL) {
276
    $structured_description_featureTree = cdm_ws_get(
277
        CDM_WS_FEATURETREE,
278
        variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
279
    );
280
    if (!$structured_description_featureTree) {
281
      $structured_description_featureTree = cdm_ws_get(
282
          CDM_WS_FEATURETREE,
283
          UUID_DEFAULT_FEATURETREE
284
      );
285
    }
286
  }
287
  return $structured_description_featureTree;
288
}
289

    
290

    
291
/**
292
 * @todo Please document this function.
293
 * @see http://drupal.org/node/1354
294
 */
295
function set_last_taxon_page_tab($taxonPageTab) {
296
  $_SESSION['cdm']['taxon_page_tab'] = $taxonPageTab;
297
}
298

    
299
/**
300
 * @todo Please document this function.
301
 * @see http://drupal.org/node/1354
302
 */
303
function get_last_taxon_page_tab() {
304
  if (isset($_SESSION['cdm']['taxon_page_tab'])) {
305
    return $_SESSION['cdm']['taxon_page_tab'];
306
  }
307
  else {
308
    return FALSE;
309
  }
310
}
311

    
312
/**
313
 *
314
 * @param object $media
315
 * @param array $mimeTypes
316
 *    an array of mimetypes in their order of preference. e.g:
317
 *    array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html')
318
 * @param int $width
319
 *    The width of the optimal image. If null, the method will return the representation with the biggest expansion
320
 * @param int $height
321
 *    The height of the optimal image. If null, the method will return the representation with the biggest expansion
322
 *
323
 * @return array
324
 *   An array with preferred media representations or else an empty array.
325
 */
326
function cdm_preferred_media_representations($media, array $mimeTypes, $width = NULL, $height = NULL) {
327
  $prefRepr = array();
328
  if (!isset($media->representations[0])) {
329
    return $prefRepr;
330
  }
331

    
332
  while (count($mimeTypes) > 0) {
333
    // getRepresentationByMimeType
334
    $mimeType = array_shift($mimeTypes);
335

    
336
    foreach ($media->representations as &$representation) {
337
      // If the mimetype is not known, try inferring it.
338
      if (!$representation->mimeType) {
339
        if (isset($representation->parts[0])) {
340
          $representation->mimeType = infer_mime_type($representation->parts[0]->uri);
341
        }
342
      }
343

    
344
      if ($representation->mimeType == $mimeType) {
345
        // Preferred mimetype found -> erase all remaining mimetypes
346
        // to end loop.
347
        $mimeTypes = array();
348
        $expansionDeltaSum = 0;
349
        $valid_parts_cnt = 0;
350
        // Look for part with the best matching size.
351
        foreach ($representation->parts as $part) {
352
          if (empty($part->uri)) {
353
            // skip part if URI is missing
354
            continue;
355
          }
356
          $valid_parts_cnt++;
357
          $expansionDelta = PHP_INT_MAX; // biggest delta for unknown sizes
358

    
359
          // determine the optimal size
360
          if (isset($part->width) && isset($part->height)) {
361
            $expansion = $part->width * $part->height;
362
            if ($width != null && $height != null) {
363
              $optimalExpansion = $height * $width;
364
            } else {
365
              $optimalExpansion = PHP_INT_MAX;
366
            }
367
            // determine the difference
368
            $expansionDelta = $expansion > $optimalExpansion ? $expansion - $optimalExpansion : $optimalExpansion - $expansion;
369
          }
370
          // sum up the expansionDeltas of all parts contained in the representation
371
          $expansionDeltaSum += $expansionDelta;
372
        }
373
        if($valid_parts_cnt > 0){
374
          $expansionDeltaSum = $expansionDeltaSum / $valid_parts_cnt;
375
          $prefRepr[$expansionDeltaSum] = $representation;
376
        }
377
      }
378
    }
379
  }
380
  // Sort the array so that the smallest key value is the first in the array
381
  ksort($prefRepr);
382
  return $prefRepr;
383
}
384

    
385
/**
386
 * Infers the mime type of a file using the filename extension.
387
 *
388
 * The filename extension is used to infer the mime type.
389
 *
390
 * @param string $filepath
391
 *   The path to the respective file.
392
 *
393
 * @return string
394
 *   The mimetype for the file or FALSE if the according mime type could
395
 *   not be found.
396
 */
397
function infer_mime_type($filepath) {
398
  static $mimemap = NULL;
399
  if (!$mimemap) {
400
    $mimemap = array(
401
      'jpg' => 'image/jpeg',
402
      'jpeg' => 'image/jpeg',
403
      'png' => 'image/png',
404
      'gif' => 'image/gif',
405
      'giff' => 'image/gif',
406
      'tif' => 'image/tif',
407
      'tiff' => 'image/tif',
408
      'pdf' => 'application/pdf',
409
      'html' => 'text/html',
410
      'htm' => 'text/html',
411
    );
412
  }
413
  $extension = substr($filepath, strrpos($filepath, '.') + 1);
414
  if (isset($mimemap[$extension])) {
415
    return $mimemap[$extension];
416
  }
417
  else {
418
    // FIXME remove this hack just return FALSE;
419
    return 'text/html';
420
  }
421
}
422

    
423
/**
424
 * Formats a mysql datatime as string
425
 *
426
 * @param $datetime
427
 * @param string $format
428
 *
429
 * @return
430
 *  the formatted string representation of the $datetime
431
 */
432
function format_datetime($datetime, $format = 'Y-m-d H:i:s'){
433
  return date($format, strtotime($datetime));
434
}
435

    
436
/**
437
 * Converts an ISO 8601 org.joda.time.Partial to a year.
438
 *
439
 * The function expects an ISO 8601 time representation of a
440
 * org.joda.time.Partial of the form yyyy-MM-dd.
441
 *
442
 * @param string $partial
443
 *   ISO 8601 time representation of a org.joda.time.Partial.
444
 *
445
 * @return string
446
 *   Returns the year. In case the year is unknown (= ????), it returns NULL.
447
 */
448
function partialToYear($partial) {
449
  if (is_string($partial)) {
450
    $year = drupal_substr($partial, 0, 4);
451
    if (preg_match("/[0-9][0-9][0-9][0-9]/", $year)) {
452
      return $year;
453
    }
454
  }
455
  return '';
456
}
457

    
458
/**
459
 * Converts an ISO 8601 org.joda.time.Partial to a month.
460
 *
461
 * This function expects an ISO 8601 time representation of a
462
 * org.joda.time.Partial of the form yyyy-MM-dd.
463
 * In case the month is unknown (= ???) NULL is returned.
464
 *
465
 * @param string $partial
466
 *   ISO 8601 time representation of a org.joda.time.Partial.
467
 *
468
 * @return string
469
 *   A month.
470
 */
471
function partialToMonth($partial) {
472
  if (is_string($partial)) {
473
    $month = drupal_substr($partial, 5, 2);
474
    if (preg_match("/[0-9][0-9]/", $month)) {
475
      return $month;
476
    }
477
  }
478
  return '';
479
}
480

    
481
/**
482
 * Converts an ISO 8601 org.joda.time.Partial to a day.
483
 *
484
 * This function expects an ISO 8601 time representation of a
485
 * org.joda.time.Partial of the form yyyy-MM-dd and returns the day as string.
486
 * In case the day is unknown (= ???) NULL is returned.
487
 *
488
 * @param string $partial
489
 *   ISO 8601 time representation of a org.joda.time.Partial.
490
 *
491
 * @return string
492
 *   A day.
493
 */
494
function partialToDay($partial) {
495
  if (is_string($partial)) {
496
    $day = drupal_substr($partial, 8, 2);
497
    if (preg_match("/[0-9][0-9]/", $day)) {
498
      return $day;
499
    }
500
  }
501
  return '';
502
}
503

    
504
/**
505
 * Converts an ISO 8601 org.joda.time.Partial to YYYY-MM-DD.
506
 *
507
 * This function expects an ISO 8601 time representations of a
508
 * org.joda.time.Partial of the form yyyy-MM-dd and returns
509
 * four digit year, month and day with dashes:
510
 * YYYY-MM-DD eg: "2012-06-30", "1956-00-00"
511
 *
512
 * The partial may contain question marks eg: "1973-??-??",
513
 * these are turned in to '00' or are stripped depending of the $stripZeros
514
 * parameter.
515
 *
516
 * @param string $partial
517
 *   org.joda.time.Partial.
518
 * @param bool $stripZeros
519
 *   If set to TRUE the zero (00) month and days will be hidden:
520
 *   eg 1956-00-00 becomes 1956. The default is TRUE.
521
 * @param string @format
522
 * 	 Can ve used to specify the format of the date string, currently the following format strings are supported
523
 *    - "YYYY": Year only
524
 *    - "YYYY-MM-DD": this is the default
525
 *
526
 * @return string
527
 *   YYYY-MM-DD formatted year, month, day.
528
 */
529
function partialToDate($partial, $stripZeros = TRUE, $format= "YYYY-MM-DD") {
530

    
531
  $y = NULL; $m = NULL; $d = NULL;
532

    
533
  if(strpos($format, 'YY') !== FALSE){
534
    $y = partialToYear($partial);
535
  }
536
  if(strpos($format, 'MM') !== FALSE){
537
    $m = partialToMonth($partial);
538
  }
539
  if(strpos($format, 'DD') !== FALSE){
540
    $d = partialToDay($partial);
541
  }
542

    
543
  $y = $y ? $y : '00';
544
  $m = $m ? $m : '00';
545
  $d = $d ? $d : '00';
546

    
547
  $date = '';
548

    
549
  if ($y == '00' && $stripZeros) {
550
    return '';
551
  }
552
  else {
553
    $date = $y;
554
  }
555

    
556
  if ($m == '00' && $stripZeros) {
557
    return $date;
558
  }
559
  else {
560
    $date .= "-" . $m;
561
  }
562

    
563
  if ($d == '00' && $stripZeros) {
564
    return $date;
565
  }
566
  else {
567
    $date .= "-" . $d;
568
  }
569
  return $date;
570
}
571

    
572
/**
573
 * Converts a time period to a string.
574
 *
575
 * See also partialToDate($partial, $stripZeros).
576
 *
577
 * @param object $period
578
 *   An JodaTime org.joda.time.Period object.
579
 * @param bool $stripZeros
580
 *   If set to True, the zero (00) month and days will be hidden:
581
 *   eg 1956-00-00 becomes 1956. The default is TRUE.
582
 * @param string @format
583
 * 	 Can ve used to specify the format of the date string, currently the following format strings are supported
584
 *    - "YYYY": Year only
585
 *    - "YYYY-MM-DD": this is the default
586
 *
587
 * @return string
588
 *   Returns a date in the form of a string.
589
 */
590
function timePeriodToString($period, $stripZeros = TRUE, $format = "YYYY-MM-DD") {
591
  $dateString = '';
592
  if($period->freeText){
593
    $dateString = $period->freeText;
594
  } else {
595
    if ($period->start) {
596
      $dateString = partialToDate($period->start, $stripZeros, $format);
597
    }
598
    if ($period->end) {
599
      $end_str = partialToDate($period->end, $stripZeros, $format);
600
      $dateString .= ($dateString && $end_str ? ' ' . t('to') . ' ' : '') . $end_str;
601
    }
602
  }
603
  return $dateString;
604
}
605

    
606
/**
607
 * returns the earliest date available in the $period in a normalized
608
 * form suitable for sorting, e.g.:
609
 *
610
 *  - 1956-00-00
611
 *  - 0000-00-00
612
 *  - 1957-03-00
613
 *
614
 * that is either the start date is returned if set otherwise the
615
 * end date
616
 *
617
 * @param  $period
618
 *    An JodaTime org.joda.time.Period object.
619
 * @return string normalized form of the date
620
 *   suitable for sorting
621
 */
622
function timePeriodAsOrderKey($period) {
623
  $dateString = '';
624
  if ($period->start) {
625
    $dateString = partialToDate($period->start, false);
626
  }
627
  if ($period->end) {
628
    $dateString .= partialToDate($period->end, false);
629
  }
630
  return $dateString;
631
}
632

    
633
/**
634
 * Composes a absolute CDM web service URI with parameters and querystring.
635
 *
636
 * @param string $uri_pattern
637
 *   String with place holders ($0, $1, ..) that should be replaced by the
638
 *   according element of the $pathParameters array.
639
 * @param array $pathParameters
640
 *   An array of path elements, or a single element.
641
 * @param string $query
642
 *   A query string to append to the URL.
643
 *
644
 * @return string
645
 *   A complete URL with parameters to a CDM webservice.
646
 */
647
function cdm_compose_url($uri_pattern, $pathParameters = array(), $query = NULL) {
648
  if (empty($pathParameters)) {
649
    $pathParameters = array();
650
  }
651

    
652
  // (1)
653
  // Substitute all place holders ($0, $1, ..) in the $uri_pattern by the
654
  // according element of the $pathParameters array.
655
  static $helperArray = array();
656
  if (isset($pathParameters) && !is_array($pathParameters)) {
657
    $helperArray[0] = $pathParameters;
658
    $pathParameters = $helperArray;
659
  }
660

    
661
  $i = 0;
662
  while (strpos($uri_pattern, "$" . $i) !== FALSE) {
663
    if (count($pathParameters) <= $i) {
664
        drupal_set_message(
665
          t('cdm_compose_url(): missing pathParameter @index for !uri_pattern',
666
            array('@index' => $i, '!uri-pattern' => $uri_pattern )),
667
          'error');
668
      break;
669
    }
670
    $uri_pattern = str_replace("$" . $i, rawurlencode($pathParameters[$i]), $uri_pattern);
671
    ++$i;
672
  }
673

    
674
  // (2)
675
  // Append all remaining element of the $pathParameters array as path
676
  // elements.
677
  if (count($pathParameters) > $i) {
678
    // Strip trailing slashes.
679
    if (strrchr($uri_pattern, '/') == strlen($uri_pattern)) {
680
      $uri_pattern = substr($uri_pattern, 0, strlen($uri_pattern) - 1);
681
    }
682
    while (count($pathParameters) > $i) {
683
      $uri_pattern .= '/' . rawurlencode($pathParameters[$i]);
684
      ++$i;
685
    }
686
  }
687

    
688
  // (3)
689
  // Append the query string supplied by $query.
690
  if (isset($query)) {
691
    $uri_pattern .= (strpos($uri_pattern, '?') !== FALSE ? '&' : '?') . $query;
692
  }
693

    
694
  $path = $uri_pattern;
695

    
696
  $uri = variable_get('cdm_webservice_url', '') . $path;
697
  return $uri;
698
}
699

    
700
/**
701
 * @todo wouldn't it more elegant and secure to only pass a uuid and additional function parameters
702
 *     together with a theme name to such a proxy function?
703
 *     Well this would not be covering all use cases but maybe all which involve AHAH.
704
 *     Maybe we want to have two different proxy functions, one with theming and one without?
705
 *
706
 * @param string $uri
707
 *     A URI to a CDM Rest service from which to retrieve an object
708
 * @param string|null $hook
709
 *     (optional) The hook name to which the retrieved object should be passed.
710
 *     Hooks can either be a theme_hook() or compose_hook() implementation
711
 *     'theme' hook functions return a string whereas 'compose' hooks are returning render arrays
712
 *     suitable for drupal_render()
713
 *
714
 * @todo Please document this function.
715
 * @see http://drupal.org/node/1354
716
 */
717
function proxy_content($uri, $hook = NULL) {
718

    
719
  $args = func_get_args();
720
  $do_gzip = function_exists('gzencode');
721
  $uriEncoded = array_shift($args);
722
  $uri = urldecode($uriEncoded);
723
  $hook = array_shift($args);
724
  $request_method = strtoupper($_SERVER["REQUEST_METHOD"]);
725

    
726
  $post_data = null;
727

    
728
  if ($request_method == "POST" || $request_method == "PUT") {
729
    // read response body via inputstream module
730
    $post_data = file_get_contents("php://input");
731
  }
732

    
733
  // Find and deserialize arrays.
734
  foreach ($args as &$arg) {
735
    // FIXME use regex to find serialized arrays.
736
    //       or should we accept json instead of php serializations?
737
    if (strpos($arg, "a:") === 0) {
738
      $arg = unserialize($arg);
739
    }
740
  }
741

    
742
  // In all these cases perform a simple get request.
743
  // TODO reconsider caching logic in this function.
744

    
745
  if (empty($hook)) {
746
    // simply return the webservice response
747
    // Print out JSON, the cache cannot be used since it contains objects.
748
    $http_response = cdm_http_request($uri, $request_method, $post_data);
749
    if (isset($http_response->headers)) {
750
      foreach ($http_response->headers as $hname => $hvalue) {
751
        drupal_add_http_header($hname, $hvalue);
752
      }
753
    }
754
    if (isset($http_response->data)) {
755
      print $http_response->data;
756
      flush();
757
    }
758
    exit(); // leave drupal here
759
  } else {
760
    // $hook has been supplied
761
    // handle $hook either as compose or theme hook
762
    // pass through theme or compose hook
763
    // compose hooks can be called without data, therefore
764
    // passing the $uri in this case is not always a requirement
765

    
766
    if($uri && $uri != 'NULL') {
767
    // do a security check since the $uri will be passed
768
    // as absolute URI to cdm_ws_get()
769
      if (!_is_cdm_ws_uri($uri)) {
770
        drupal_set_message(
771
          'Invalid call of proxy_content() with callback parameter \'' . $hook . '\' and URI:' . $uri,
772
          'error'
773
        );
774
        return '';
775
      }
776

    
777
      $obj = cdm_ws_get($uri, NULL, $post_data, $request_method, TRUE);
778
    } else {
779
      $obj = NULL;
780
    }
781

    
782
    $reponse_data = NULL;
783

    
784
    if (function_exists('compose_' . $hook)){
785
      // call compose hook
786

    
787
      $elements =  call_user_func('compose_' . $hook, $obj);
788
      // pass the render array to drupal_render()
789
      $reponse_data = drupal_render($elements);
790
    } else {
791
      // call theme hook
792

    
793
      // TODO use theme registry to get the registered hook info and
794
      //    use these defaults
795
      switch($hook) {
796
        case 'cdm_taxontree':
797
          $variables = array(
798
            'tree' => $obj,
799
            'filterIncludes' => isset($args[0]) ? $args[0] : NULL,
800
            'show_filter_switch' => isset($args[1]) ? $args[1] : FALSE,
801
            'tree_node_callback' => isset($args[2]) ? $args[2] : FALSE,
802
            'element_name'=> isset($args[3]) ? $args[3] : FALSE,
803
            );
804
          $reponse_data = theme($hook, $variables);
805
          break;
806

    
807
        case 'cdm_list_of_taxa':
808
            $variables = array(
809
              'records' => $obj,
810
              'freetextSearchResults' => isset($args[0]) ? $args[0] : array(),
811
              'show_classification' => isset($args[1]) ? $args[1] : FALSE);
812
            $reponse_data = theme($hook, $variables);
813
            break;
814

    
815
        case 'cdm_media_caption':
816
          $variables = $arg;
817
          $variables['media'] = $obj;
818

    
819
          $reponse_data = theme($hook, $variables);
820
          break;
821

    
822
        default:
823
          drupal_set_message(t(
824
          'Theme !theme is not yet supported by the function !function.', array(
825
          '!theme' => $hook,
826
          '!function' => __FUNCTION__,
827
          )), 'error');
828
          break;
829
      } // END of theme hook switch
830
    } // END of tread as theme hook
831

    
832

    
833
    if($do_gzip){
834
      $reponse_data = gzencode($reponse_data, 2, FORCE_GZIP);
835
      drupal_add_http_header('Content-Encoding', 'gzip');
836
    }
837
    drupal_add_http_header('Content-Type', 'text/html; charset=utf-8');
838
    drupal_add_http_header('Content-Length', strlen($reponse_data));
839

    
840
    print $reponse_data;
841
  } // END of handle $hook either as compose ot theme hook
842

    
843
}
844

    
845
/**
846
 * @todo Please document this function.
847
 * @see http://drupal.org/node/1354
848
 */
849
function setvalue_session() {
850
  if ($_REQUEST['var'] && strlen($_REQUEST['var']) > 4) {
851
    $var_keys = substr($_REQUEST['var'], 1, strlen($_REQUEST['var']) - 2);
852
    $var_keys = explode('][', $var_keys);
853
  }
854
  else {
855
    return;
856
  }
857
  $val = isset($_REQUEST['val']) ? $_REQUEST['val'] : NULL;
858

    
859
  // Prevent from malicous tags.
860
  $val = strip_tags($val);
861

    
862
  $session_var = &$_SESSION;
863
  //$i = 0;
864
  foreach ($var_keys as $key) {
865
    // $hasMoreKeys = ++$i < count($session);
866
    if (!isset($session_var[$key]) || !is_array($session_var[$key])) {
867
      $session_var[$key] = array();
868
    }
869
    $session_var = &$session_var[$key];
870
  }
871
  $session_var = $val;
872
  if (isset($_REQUEST['destination'])) {
873
    drupal_goto($_REQUEST['destination']);
874
  }
875
}
876

    
877
/**
878
 * @todo Please document this function.
879
 * @see http://drupal.org/node/1354
880
 */
881
function uri_uriByProxy($uri, $theme = FALSE) {
882
  // usage: url('cdm_api/proxy/'.urlencode($content_url)."/$theme");)
883
  return url('cdm_api/proxy/' . urlencode($uri) . (isset($theme) ? "/$theme" : ''));
884
}
885

    
886
/**
887
 * Composes the the absolute REST service URI to the annotations pager
888
 * for the given CDM entity.
889
 *
890
 * NOTE: Not all CDM Base types are yet supported.
891
 *
892
 * @param $cdmBase
893
 *   The CDM entity to construct the annotations pager uri for
894
 */
895
function cdm_compose_annotations_uri($cdmBase) {
896

    
897
  if (!$cdmBase->uuid) {
898
    return;
899
  }
900

    
901
  $ws_base_uri = cdm_ws_base_uri($cdmBase->class);
902

    
903
  if($ws_base_uri === null){
904
      trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdmBase->class), E_USER_ERROR);
905
  }
906
  return cdm_compose_url($ws_base_uri, array(
907
    $cdmBase->uuid,
908
    'annotations',
909
  ));
910
}
911

    
912
/**
913
 * Provides the base URI of the cdm REST service responsible for the passed simple name
914
 * of a CDM java class. For example 'TaxonName' is the simple name of 'eu.etaxonomy.cdm.model.name.TaxonName'
915
 *
916
 * @param $cdm_type_simple
917
 *    simple name of a CDM java class
918
 * @return null|string
919
 */
920
function cdm_ws_base_uri($cdm_type_simple)
921
{
922
  $ws_base_uri = NULL;
923
  switch ($cdm_type_simple) {
924
    case 'TaxonBase':
925
    case 'Taxon':
926
    case 'Synonym':
927
      $ws_base_uri = CDM_WS_TAXON;
928
      break;
929

    
930
    case 'TaxonName':
931
      $ws_base_uri = CDM_WS_NAME;
932
      break;
933

    
934
    case 'Media':
935
      $ws_base_uri = CDM_WS_MEDIA;
936
      break;
937

    
938
    case 'Reference':
939
      $ws_base_uri = CDM_WS_REFERENCE;
940
      break;
941

    
942
    case 'Distribution':
943
    case 'TextData':
944
    case 'TaxonInteraction':
945
    case 'QuantitativeData':
946
    case 'IndividualsAssociation':
947
    case 'CommonTaxonName':
948
    case 'CategoricalData':
949
      $ws_base_uri = CDM_WS_DESCRIPTIONELEMENT;
950
      break;
951

    
952
    case 'PolytomousKey':
953
    case 'MediaKey':
954
    case 'MultiAccessKey':
955
      $ws_base_uri = $cdm_type_simple;
956
      $ws_base_uri{0} = strtolower($ws_base_uri{0});
957
      break;
958

    
959
    default:
960
      $ws_base_uri = null;
961
  }
962
  return $ws_base_uri;
963
}
964

    
965
/**
966
 * Enter description here...
967
 *
968
 * @param string $resourceURI
969
 * @param int $pageSize
970
 *   The maximum number of entities returned per page.
971
 *   The default page size as configured in the cdm server
972
 *   will be used if set to NULL
973
 *   to return all entities in a single page).
974
 * @param int $pageNumber
975
 *   The number of the page to be returned, the first page has the
976
 *   pageNumber = 0
977
 * @param array $query
978
 *   A array holding the HTTP request query parameters for the request
979
 * @param string $method
980
 *   The HTTP method to use, valid values are "GET" or "POST"
981
 * @param bool $absoluteURI
982
 *   TRUE when the URL should be treated as absolute URL.
983
 *
984
 * @return the a CDM Pager object
985
 *
986
 */
987
function cdm_ws_page($resourceURI, $pageSize, $pageNumber, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
988

    
989
  $query['pageNumber'] = $pageNumber;
990
  $query['pageSize'] = $pageSize;
991

    
992
  return cdm_ws_get($resourceURI, NULL, queryString($query), $method, $absoluteURI);
993
}
994

    
995
/**
996
 * Fetches all entities from the given REST endpoint using the pager mechanism.
997
 *
998
 * @param string $resourceURI
999
 * @param array $query
1000
 *   A array holding the HTTP request query parameters for the request
1001
 * @param string $method
1002
 *   The HTTP method to use, valid values are "GET" or "POST";
1003
 * @param bool $absoluteURI
1004
 *   TRUE when the URL should be treated as absolute URL.
1005
 *
1006
 * @return array
1007
 *     A list of CDM entitites
1008
 *
1009
 */
1010
function cdm_ws_fetch_all($resourceURI, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
1011
  $page_index = 0;
1012
  // using a bigger page size to avoid to many multiple requests
1013
  $page_size = 500;
1014
  $entities = array();
1015

    
1016
  while ($page_index !== FALSE){
1017
    $pager =  cdm_ws_page($resourceURI, $page_size, $page_index, $query,  $method, $absoluteURI);
1018
    if(isset($pager->records) && is_array($pager->records)) {
1019
      $entities = array_merge($entities, $pager->records);
1020
      if(!empty($pager->nextIndex)){
1021
        $page_index = $pager->nextIndex;
1022
      } else {
1023
        $page_index = FALSE;
1024
      }
1025
    } else {
1026
      $page_index = FALSE;
1027
    }
1028
  }
1029
  return $entities;
1030
}
1031

    
1032
/*
1033
function cdm_ws_taxonomy_compose_resourcePath($path = NULL){
1034
  $viewrank = _cdm_taxonomy_compose_viewrank();
1035
  return CDM_WS_PORTAL_TAXONOMY . '/' . ($viewrank ? $viewrank : '' ) . ($path
1036
  ? '/' . $path : '') ;
1037
}
1038
*/
1039

    
1040
/**
1041
 * @todo Enter description here...
1042
 *
1043
 * @param string $taxon_uuid
1044
 *  The UUID of a cdm taxon instance
1045
 * @param string $ignore_rank_limit
1046
 *   Whether to ignore the variable 'taxontree_ranklimit' set by admin in the settings
1047
 *
1048
 * @return string
1049
 *   A cdm REST service URL path to a Classification
1050
 */
1051
function cdm_compose_taxonomy_root_level_path($taxon_uuid = FALSE, $ignore_rank_limit = FALSE) {
1052

    
1053
  $view_uuid = get_current_classification_uuid();
1054
  $rank_uuid = NULL;
1055
  if (!$ignore_rank_limit) {
1056
    $rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1057
  }
1058

    
1059
  if (!empty($taxon_uuid)) {
1060
    return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
1061
      $view_uuid,
1062
      $taxon_uuid,
1063
    ));
1064
  }
1065
  else {
1066
    if (is_uuid($rank_uuid)) {
1067
      return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_AT_RANK, array(
1068
        $view_uuid,
1069
        $rank_uuid,
1070
      ));
1071
    }
1072
    else {
1073
      return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES, array(
1074
        $view_uuid,
1075
      ));
1076
    }
1077
  }
1078
}
1079

    
1080
/**
1081
 * Retrieves from the cdm web service with the first level of childnodes of a classification.
1082
 *
1083
 * The level is either the real root level ot it is a lover level if a rank limit has been set.
1084
 * (@see  cdm_compose_taxonomy_root_level_path() for more on the rank limit).
1085
 *
1086
 * Operates in two modes depending on whether the parameter
1087
 * $taxon_uuid is set or NULL.
1088
 *
1089
 * A) $taxon_uuid = NULL:
1090
 *  1. retrieve the Classification for the uuid set in the $_SESSION['cdm']['taxonomictree_uuid']
1091
 *  2. otherwise return the default classification as defined by the admin via the settings
1092
 *
1093
 * b) $taxon_uuid is set:
1094
 *   return the classification to whcih the taxon belongs to.
1095
 *
1096
 * @param UUID $taxon_uuid
1097
 *   The UUID of a cdm taxon instance
1098
 */
1099
function cdm_ws_taxonomy_root_level($taxon_uuid = NULL) {
1100

    
1101
    $response = NULL;
1102

    
1103
    // 1st try
1104
    $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid), NULL, NULL, 'GET', TRUE);
1105

    
1106
    if ($response == NULL) {
1107
      // 2dn try by ignoring the rank limit
1108
      $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid, TRUE), NULL, NULL, 'GET', TRUE);
1109
    }
1110

    
1111
    if ($response == NULL) {
1112
      // 3rd try, last fallback:
1113
      //    return the default classification
1114
      if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
1115
        // Delete the session value and try again with the default.
1116
        unset($_SESSION['cdm']['taxonomictree_uuid']);
1117
        drupal_set_message("Could not find a valid classification, falling back to the default classification.", 'warning');
1118
        return cdm_ws_taxonomy_root_level($taxon_uuid);
1119
      }
1120
      else {
1121
        // Check if taxonomictree_uuid is valid.
1122
        // expecting an array of taxonNodes,
1123
        // empty classifications are ok so no warning in this case!
1124
        $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
1125
        if (!is_array($test)) {
1126
          // The default set by the admin seems to be invalid or is not even set.
1127
          drupal_set_message(_no_classfication_uuid_message(), 'warning');
1128
        }
1129
        if (count($test) == 0) {
1130
          // The default set by the admin seems to be invalid or is not even set.
1131
          drupal_set_message("The chosen classification is empty.", 'status');
1132
        }
1133
      }
1134
    }
1135

    
1136
  return $response;
1137
}
1138

    
1139
/**
1140
 * Determines the tree path of the taxon given as uuid to the root of the classification tree.
1141
 * 
1142
 * The root either is the absolute root of the tree or a rank specific root if the TAXONTREE_RANKLIMIT
1143
 * variable is set.
1144
 *
1145
 * @param string $taxon_uuid
1146
 *
1147
 * @return array
1148
 *   An array of CDM TaxonNodeDTO objects
1149
 */
1150
function cdm_ws_taxonomy_pathFromRoot($taxon_uuid) {
1151
  $view_uuid = get_current_classification_uuid();
1152
  $rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1153

    
1154
  $response = NULL;
1155
  if (is_uuid($rank_uuid)) {
1156
    $response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM_TO_RANK, array(
1157
      $view_uuid,
1158
      $taxon_uuid,
1159
      $rank_uuid,
1160
    ));
1161
  }
1162
  else {
1163
    $response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM, array(
1164
      $view_uuid,
1165
      $taxon_uuid,
1166
    ));
1167
  }
1168

    
1169
  if ($response == NULL) {
1170
    // Error handing.
1171
//    if (is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
1172
//      // Delete the session value and try again with the default.
1173
//      unset($_SESSION['cdm']['taxonomictree_uuid']);
1174
//      return cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
1175
//    }
1176
//    else {
1177
      // Check if taxonomictree_uuid is valid.
1178
      $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
1179
      if ($test == NULL) {
1180
        // The default set by the admin seems to be invalid or is not even set.
1181
        drupal_set_message(_no_classfication_uuid_message(), 'warning');
1182
      }
1183
//    }
1184
  }
1185

    
1186
  return $response;
1187
}
1188

    
1189

    
1190
// =============================Terms and Vocabularies ========================================= //
1191

    
1192
/**
1193
 * Returns the localized representation for the given term.
1194
 *
1195
 * @param Object $definedTermBase
1196
 * 	  of cdm type DefinedTermBase
1197
 * @return string
1198
 * 	  the localized representation_L10n of the term,
1199
 *    otherwise the titleCache as fall back,
1200
 *    otherwise the default_representation which defaults to an empty string
1201
 */
1202
function cdm_term_representation($definedTermBase, $default_representation = '') {
1203
  if ( isset($definedTermBase->representation_L10n) ) {
1204
    return $definedTermBase->representation_L10n;
1205
  } elseif ( isset($definedTermBase->titleCache)) {
1206
    return $definedTermBase->titleCache;
1207
  }
1208
  return $default_representation;
1209
}
1210

    
1211
/**
1212
 * Returns the abbreviated localized representation for the given term.
1213
 *
1214
 * @param Object $definedTermBase
1215
 * 	  of cdm type DefinedTermBase
1216
 * @return string
1217
 * 	  the localized representation_L10n_abbreviatedLabel of the term,
1218
 *    if this representation is not available the function delegates the
1219
 *    call to cdm_term_representation()
1220
 */
1221
function cdm_term_representation_abbreviated($definedTermBase, $default_representation = '') {
1222
  if ( isset($definedTermBase->representation_L10n_abbreviatedLabel) ) {
1223
    return $definedTermBase->representation_L10n_abbreviatedLabel;
1224
  } else {
1225
    cdm_term_representation($definedTermBase, $default_representation);
1226
  }
1227
}
1228

    
1229
/**
1230
 * Transforms the list of the given term base instances to a alphabetical ordered options array.
1231
 *
1232
 * The options array is suitable for drupal form API elements that allow multiple choices.
1233
 * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
1234
 *
1235
 * @param array $terms
1236
 *   a list of CDM DefinedTermBase instances
1237
 *
1238
 * @param $term_label_callback
1239
 *   A callback function to override the term representations
1240
 *
1241
 * @param bool $empty_option
1242
 *   An additional element do be placed at the beginning og the list. This element will be the default option.
1243
 *
1244
 * @return array
1245
 *   the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
1246

    
1247
 */
1248
function cdm_terms_as_options($terms, $term_label_callback = NULL, $empty_option = FALSE){
1249
  $options = array();
1250
  if(isset($terms) && is_array($terms)) {
1251
    foreach ($terms as $term) {
1252
      if ($term_label_callback && function_exists($term_label_callback)) {
1253
        $options[$term->uuid] = call_user_func($term_label_callback, $term);
1254
      } else {
1255
        //TODO use cdm_term_representation() here?
1256
        $options[$term->uuid] = t('@term', array('@term' => $term->representation_L10n));
1257
      }
1258
    }
1259
  }
1260

    
1261
  if($empty_option !== FALSE){
1262
    array_unshift ($options, "");
1263
  }
1264

    
1265
  return $options;
1266
}
1267

    
1268
/**
1269
 * Creates and array of options for drupal select form elements.
1270
 *
1271
 * @param $vocabulary_uuid
1272
 *   The UUID of the CDM Term Vocabulary
1273
 * @param $term_label_callback
1274
 *   An optional call back function which can be used to modify the term label
1275
 * @param bool $empty_option
1276
 *   An additional element do be placed at the beginning og the list. This element will be the default option.
1277
 * @param array $include_filter
1278
 *   An associative array consisting of a field name an regular expression. All term matching
1279
 *   these filter are included. The value of the field is converted to a String by var_export()
1280
 *   so a boolean 'true' can be matched by '/true/'
1281
 * @param string $order_by
1282
 *   One of the order by constants defined in this file
1283
 * @return array
1284
 *   the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
1285
 */
1286
function cdm_vocabulary_as_option($vocabulary_uuid, $term_label_callback = NULL, $empty_option = FALSE,
1287
                                  array $include_filter = null, $order_by = CDM_ORDER_BY_ORDER_INDEX_ASC) {
1288

    
1289
  static $vocabularyOptions = array();
1290

    
1291
  if (!isset($vocabularyOptions[$vocabulary_uuid])) {
1292
    $terms = cdm_ws_fetch_all('termVocabulary/' . $vocabulary_uuid . '/terms',
1293
      array(
1294
        'orderBy' => $order_by
1295
      )
1296
    );
1297

    
1298
    // apply the include filter
1299
    if($include_filter != null){
1300
      $included_terms = array();
1301

    
1302
      foreach ($terms as $term){
1303
        $include = true;
1304
        foreach ($include_filter as $field=>$regex){
1305
          $include =  preg_match($regex, var_export($term->$field, true)) === 1;
1306
          if(!$include){
1307
            break;
1308
          }
1309
        }
1310
        if($include){
1311
          $included_terms[] = $term;
1312
        }
1313
      }
1314

    
1315
      $terms = $included_terms;
1316
    }
1317

    
1318
    // make options list
1319
    $vocabularyOptions[$vocabulary_uuid] = cdm_terms_as_options($terms, $term_label_callback, $empty_option);
1320
  }
1321

    
1322
  $options = $vocabularyOptions[$vocabulary_uuid];
1323

    
1324
  return $options;
1325
}
1326

    
1327
/**
1328
 * @param $term_type string one of
1329
 *  - Unknown
1330
 *  - Language
1331
 *  - NamedArea
1332
 *  - Rank
1333
 *  - Feature
1334
 *  - AnnotationType
1335
 *  - MarkerType
1336
 *  - ExtensionType
1337
 *  - DerivationEventType
1338
 *  - PresenceAbsenceTerm
1339
 *  - NomenclaturalStatusType
1340
 *  - NameRelationshipType
1341
 *  - HybridRelationshipType
1342
 *  - SynonymRelationshipType
1343
 *  - TaxonRelationshipType
1344
 *  - NameTypeDesignationStatus
1345
 *  - SpecimenTypeDesignationStatus
1346
 *  - InstitutionType
1347
 *  - NamedAreaType
1348
 *  - NamedAreaLevel
1349
 *  - RightsType
1350
 *  - MeasurementUnit
1351
 *  - StatisticalMeasure
1352
 *  - MaterialOrMethod
1353
 *  - Material
1354
 *  - Method
1355
 *  - Modifier
1356
 *  - Scope
1357
 *  - Stage
1358
 *  - KindOfUnit
1359
 *  - Sex
1360
 *  - ReferenceSystem
1361
 *  - State
1362
 *  - NaturalLanguageTerm
1363
 *  - TextFormat
1364
 *  - DeterminationModifier
1365
 *  - DnaMarker
1366
 *
1367
 * @param  $order_by
1368
 *  Optionally sort option (default: CDM_ORDER_BY_TITLE_CACHE_ASC)
1369
 *  possible values:
1370
 *    - CDM_ORDER_BY_ID_ASC
1371
 *    - CDM_ORDER_BY_ID_DESC
1372
 *    - CDM_ORDER_BY_TITLE_CACHE_ASC
1373
 *    - CDM_ORDER_BY_TITLE_CACHE_DESC
1374
 *    - CDM_ORDER_BY_ORDER_INDEX_ASC (can only be used with OrderedTerms!!)
1375
 *    - CDM_ORDER_BY_ORDER_INDEX_DESC (can only be used with OrderedTerms!!)
1376
 * @param bool $empty_option
1377
 *   An additional element do be placed at the beginning og the list. This element will be the default option.
1378
 * @return array
1379
 *    the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
1380
 */
1381
function cdm_terms_by_type_as_option($term_type, $order_by = CDM_ORDER_BY_TITLE_CACHE_ASC, $term_label_callback = NULL, $empty_option = FALSE){
1382
  $terms = cdm_ws_fetch_all(
1383
    CDM_WS_TERM,
1384
    array(
1385
      'class' => $term_type,
1386
      'orderBy' => $order_by
1387
    )
1388
  );
1389
  return cdm_terms_as_options($terms, $term_label_callback, $empty_option);
1390
}
1391

    
1392
/**
1393
 * @param array $none_option
1394
 *    Will add a filter option to search for NULL values
1395
 * @param $with_empty_option
1396
 *    Will add an empty option to the beginning. Choosing this option will disable the filtering.
1397
 * @return array
1398
 *   An array of options with uuids as key and the localized term representation as value
1399
 */
1400
function cdm_type_designation_status_filter_terms_as_options($none_option_label, $with_empty_option = false){
1401
  $filter_terms = cdm_ws_get(CDM_WS_TYPE_DESIGNATION_STATUS_FILTER_TERMS);
1402

    
1403
  if(isset($filter_terms) && is_array($filter_terms)) {
1404
    foreach ($filter_terms as $filter_term) {
1405
      $options[join(',', $filter_term->uuids)] = $filter_term->label;
1406
    }
1407
  }
1408

    
1409
  if(is_string($none_option_label)){
1410
    $options = array_merge(array('NULL' => $none_option_label), $options);
1411
  }
1412

    
1413
  if($with_empty_option !== FALSE){
1414
    array_unshift ($options, "");
1415
  }
1416

    
1417

    
1418
  return $options;
1419
}
1420

    
1421

    
1422

    
1423
/**
1424
 * Callback function which provides the localized representation of a cdm term.
1425
 *
1426
 * The representation is build by concatenating the abbreviated label with the label
1427
 * and thus is especially useful for relationship terms
1428
 * The localized representation provided by the cdm can be overwritten by
1429
 * providing a drupal translation.
1430
 *
1431
 */
1432
function _cdm_relationship_type_term_label_callback($term) {
1433
  if (isset($term->representation_L10n_abbreviatedLabel)) {
1434
    return $term->representation_L10n_abbreviatedLabel . ' : '
1435
    . t('@term', array('@term' => $term->representation_L10n));
1436
  }
1437
else {
1438
    return t('@term', array('@term' => $term->representation_L10n));
1439
  }
1440
}
1441

    
1442
/**
1443
 * Callback function which provides the localized inverse representation of a cdm term.
1444
 *
1445
 * The representation is build by concatenating the abbreviated label with the label
1446
 * and thus is especially useful for relationship terms
1447
 * The localized representation provided by the cdm can be overwritten by
1448
 * providing a drupal translation.
1449
 *
1450
 */
1451
function _cdm_relationship_type_term_inverse_label_callback($term) {
1452
  if (isset($term->inverseRepresentation_L10n_abbreviatedLabel)) {
1453
    return $term->inverseRepresentation_L10n_abbreviatedLabel . ' : '
1454
      . t('@term', array('@term' => $term->inverseRepresentation_L10n));
1455
  }
1456
  else {
1457
    return t('@term', array('@term' => $term->inverseRepresentation_L10n));
1458
  }
1459
}
1460

    
1461
/**
1462
 * Returns the localized abbreviated label of the relationship term.
1463
 *
1464
 * In case the abbreviated label is not set the normal representation is returned.
1465
 *
1466
 * @param $term
1467
 * @param bool $is_inverse_relation
1468
 * @return string
1469
 *   The abbreviated label
1470
 */
1471
function cdm_relationship_type_term_abbreviated_label($term, $is_inverse_relation = false){
1472

    
1473
  if($is_inverse_relation) {
1474
    if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
1475
      $abbr_label = $term->inverseResentation_L10n_abbreviatedLabel;
1476
    } else {
1477
      $abbr_label = $term->inverseRepresentation_L10n;
1478
    }
1479
  } else {
1480
    if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
1481
      $abbr_label = $term->representation_L10n_abbreviatedLabel;
1482
    } else {
1483
      $abbr_label = $term->representation_L10n;
1484
    }
1485
  }
1486
  return $abbr_label;
1487
}
1488

    
1489
/**
1490
 * Returns the symbol of the relationship term.
1491
 *
1492
 * In case the symbol is not set the function falls back to use the abbreviated label or
1493
 * the normal representation..
1494
 *
1495
 * @param $term
1496
 * @param bool $is_inverse_relation
1497
 * @return string
1498
 *   The abbreviated label
1499
 */
1500
function cdm_relationship_type_term_symbol($term, $is_inverse_relation = false){
1501

    
1502
  if($is_inverse_relation) {
1503
    if (isset($term->inverseSymbol) && $term->inverseSymbol) {
1504
      $symbol = $term->inverseSymbol;
1505
    } else if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
1506
      $symbol = $term->inverseResentation_L10n_abbreviatedLabel;
1507
    } else {
1508
      $symbol = $term->inverseRepresentation_L10n;
1509
    }
1510
  } else {
1511
    if (isset($term->symbol) && $term->symbol) {
1512
      $symbol = $term->symbol;
1513
    } else if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
1514
      $symbol = $term->representation_L10n_abbreviatedLabel;
1515
    } else {
1516
      $symbol = $term->representation_L10n;
1517
    }
1518
  }
1519
  return $symbol;
1520
}
1521

    
1522
// ========================================================================================== //
1523
/**
1524
 * @todo Improve documentation of this function.
1525
 *
1526
 * eu.etaxonomy.cdm.model.description.
1527
 * CategoricalData
1528
 * CommonTaxonName
1529
 * Distribution
1530
 * IndividualsAssociation
1531
 * QuantitativeData
1532
 * TaxonInteraction
1533
 * TextData
1534
 */
1535
function cdm_descriptionElementTypes_as_option($prependEmptyElement = FALSE) {
1536
  static $types = array(
1537
    "CategoricalData",
1538
    "CommonTaxonName",
1539
    "Distribution",
1540
    "IndividualsAssociation",
1541
    "QuantitativeData",
1542
    "TaxonInteraction",
1543
    "TextData",
1544
  );
1545

    
1546
  static $options = NULL;
1547
  if ($options == NULL) {
1548
    $options = array();
1549
    if ($prependEmptyElement) {
1550
      $options[' '] = '';
1551
    }
1552
    foreach ($types as $type) {
1553
      // No internatianalization here since these are purely technical terms.
1554
      $options["eu.etaxonomy.cdm.model.description." . $type] = $type;
1555
    }
1556
  }
1557
  return $options;
1558
}
1559

    
1560

    
1561
/**
1562
 * Fetches all TaxonDescription descriptions elements which are associated to the
1563
 * Taxon specified by the $taxon_uuid and merges the elements into the given
1564
 * feature tree.
1565
 * @param $feature_tree
1566
 *     The CDM FeatureTree to be used as template
1567
 * @param $taxon_uuid
1568
 *     The UUID of the taxon
1569
 * @param $excludes
1570
 *     UUIDs of features to be excluded
1571
 * @return$feature_tree
1572
 *     The CDM FeatureTree which was given as parameter merged tree whereas the
1573
 *     CDM FeatureNodes are extended by an additional field 'descriptionElements'
1574
 *     witch will hold the according $descriptionElements.
1575
 */
1576
function cdm_ws_descriptions_by_featuretree($feature_tree, $taxon_uuid, $exclude_uuids = array()) {
1577

    
1578
  if (!$feature_tree) {
1579
    drupal_set_message(check_plain(t("No 'FeatureTree' has been set so far.
1580
      In order to see the species profiles of your taxa, please select a
1581
      'FeatureTree' in the !settings"), array('!settings' => l(t('CDM Dataportal Settings'), 'admin/config/cdm_dataportal/layout'))), 'warning');
1582
    return FALSE;
1583
  }
1584

    
1585
  $description_elements = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
1586
      array(
1587
      'taxon' => $taxon_uuid,
1588
      'features' => cdm_featureTree_elements_toString($feature_tree->root, ',', 'uuid', $exclude_uuids)
1589
      ),
1590
      'POST'
1591
  );
1592

    
1593
  // Combine all descriptions into one feature tree.
1594
  $merged_nodes = _mergeFeatureTreeDescriptions($feature_tree->root->childNodes, $description_elements);
1595
  $feature_tree->root->childNodes = $merged_nodes;
1596

    
1597
  return $feature_tree;
1598
}
1599

    
1600
/**
1601
 * Returns a filtered a list of annotations for the cdm entity given as parameter $cdmBase.
1602
 * If the annotations are not yet already loded with the cdm entity the cdm REST service will
1603
 * be requested for the annotations.
1604
 *
1605
 * @param string $cdmBase
1606
 *   An annotatable cdm entity.
1607
 * @param array $includeTypes
1608
 *   If an array of annotation type uuids is supplied by this parameter the
1609
 *   list of annotations is resticted to those which belong to this type.
1610
 *
1611
 * @return array
1612
 *   An array of Annotation objects or an empty array.
1613
 */
1614
function cdm_ws_getAnnotationsFor(&$cdmBase, $includeTypes = FALSE) {
1615

    
1616
  if(!isset($cdmBase->annotations)){
1617
    $annotationUrl = cdm_compose_annotations_uri($cdmBase);
1618
    $cdmBase->annotations = cdm_ws_fetch_all($annotationUrl, array(), 'GET', TRUE);
1619
  }
1620

    
1621
  $annotations = array();
1622
  foreach ($cdmBase->annotations as $annotation) {
1623
    if ($includeTypes) {
1624
      if (
1625
        ( isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $includeTypes, TRUE) )
1626
        || ($annotation->annotationType === NULL && in_array('NULL_VALUE', $includeTypes, TRUE))
1627
      ) {
1628
        $annotations[] = $annotation;
1629
      }
1630
    }
1631
    else {
1632
      $annotations[] = $annotation;
1633
    }
1634
  }
1635
  return $annotations;
1636

    
1637
}
1638

    
1639
/**
1640
 * Provides the list of visible annotations for the $cdmBase.
1641
 *
1642
 * @param $cdmBase
1643
 *     The annotatable CDM entity
1644
 *
1645
 * @return array of the annotations which are visible according to the settings as stored in ANNOTATION_TYPES_VISIBLE
1646
 */
1647
function cdm_fetch_visible_annotations($cdmBase){
1648

    
1649
  static $annotations_types_filter = null;
1650
  if(!$annotations_types_filter) {
1651
    $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
1652
  }
1653
  return cdm_ws_getAnnotationsFor($cdmBase, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
1654
}
1655

    
1656
/**
1657
 * Loads the annotations from the REST service an adds them as field to the given $annotatable_entity.
1658
 *
1659
 * NOTE: The annotations are not filtered by the ANNOTATION_TYPES_VISIBLE settings since this method is meant to act
1660
 * like the annotations have been fetched in the ORM-framework in the service.
1661
 *
1662
 * @param object $annotatable_entity
1663
 *   The CDM AnnotatableEntity to load annotations for
1664
 */
1665
function cdm_load_annotations(&$annotatable_entity) {
1666
  if (isset($annotatable_entity) && !isset($annotatable_entity->annotations)) {
1667
    $annotations = cdm_ws_getAnnotationsFor($annotatable_entity);
1668
    if (is_array($annotations)) {
1669
      $annotatable_entity->annotations = $annotations;
1670
    }
1671
  }
1672
}
1673

    
1674
/**
1675
 * Extends the $cdm_entity object by the field if it is not already existing.
1676
 *
1677
 * This function can only be used for fields with 1 to many relations.
1678
  *
1679
 * @param $cdm_base_type
1680
 * @param $field_name
1681
 * @param $cdm_entity
1682
 */
1683
function cdm_lazyload_array_field($cdm_base_type, $field_name, &$cdm_entity)
1684
{
1685
  if (!isset($cdm_entity->$field_name)) {
1686
    $items = cdm_ws_fetch_all('portal/' . $cdm_base_type . '/' . $cdm_entity->uuid . '/' . $field_name);
1687
    $cdm_entity->$field_name = $items;
1688
  }
1689
}
1690

    
1691

    
1692
/**
1693
 * Get a NomenclaturalReference string.
1694
 *
1695
 * Returns the NomenclaturalReference string with correctly placed
1696
 * microreference (= reference detail) e.g.
1697
 * in Phytotaxa 43: 1-48. 2012.
1698
 *
1699
 * @param string $referenceUuid
1700
 *   UUID of the reference.
1701
 * @param string $microreference
1702
 *   Reference detail.
1703
 *
1704
 * @return string
1705
 *   a NomenclaturalReference.
1706
 */
1707
function cdm_ws_getNomenclaturalReference($referenceUuid, $microreference) {
1708

    
1709
  // TODO the below statement avoids error boxes due to #4644 remove it once this ticket is solved
1710
  if(is_array($microreference) || is_object($microreference)) {
1711
    return '';
1712
  }
1713

    
1714
  $obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
1715
    $referenceUuid,
1716
  ), "microReference=" . urlencode($microreference));
1717

    
1718
  if ($obj) {
1719
    return $obj->String;
1720
  }
1721
  else {
1722
    return NULL;
1723
  }
1724
}
1725

    
1726
/**
1727
 * finds and returns the FeatureNode denoted by the given $feature_uuid
1728
 *
1729
 * @param $feature_tree_nodes
1730
 *    The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
1731
 * @param $feature_uuid
1732
 *    The UUID of the Feature
1733
 * @return returns the FeatureNode or null
1734
 */
1735
function &cdm_feature_tree_find_node($feature_tree_nodes, $feature_uuid){
1736

    
1737
  // 1. scan this level
1738
  foreach ($feature_tree_nodes as $node){
1739
    if($node->term->uuid == $feature_uuid){
1740
      return $node;
1741
    }
1742
  }
1743

    
1744
  // 2. descend into childen
1745
  foreach ($feature_tree_nodes as $node){
1746
    if(is_array($node->childNodes)){
1747
      $node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
1748
      if($node) {
1749
        return $node;
1750
      }
1751
    }
1752
  }
1753
  $null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
1754
  return $null_var;
1755
}
1756

    
1757
/**
1758
 * Merges the given featureNodes structure with the descriptionElements.
1759
 *
1760
 * This method is used in preparation for rendering the descriptionElements.
1761
 * The descriptionElements which belong to a specific feature node are appended
1762
 * to a the feature node by creating a new field:
1763
 *  - descriptionElements: the CDM DescriptionElements which belong to this feature
1764
 * The descriptionElements will be cleared in advance in order to allow reusing the
1765
 * same feature tree without the risk of mixing sets of description elements.
1766
 *
1767
 * which originally is not existing in the cdm.
1768
 *
1769
 *
1770
 *
1771
 * @param array $featureNodes
1772
 *    An array of cdm FeatureNodes which may be hierarchical since feature nodes
1773
 *    may have children.
1774
 * @param array $descriptionElements
1775
 *    An flat array of cdm DescriptionElements
1776
 * @return array
1777
 *    The $featureNodes structure enriched with the according $descriptionElements
1778
 */
1779
function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
1780

    
1781
  foreach ($featureNodes as &$feature_node) {
1782
    // since the $featureNodes array is reused for each description
1783
    // it is necessary to clear the custom node fields in advance
1784
    if(isset($feature_node->descriptionElements)){
1785
      unset($feature_node->descriptionElements);
1786
    }
1787

    
1788
    // Append corresponding elements to an additional node field:
1789
    // $node->descriptionElements.
1790
    foreach ($descriptionElements as $element) {
1791
      if ($element->feature->uuid == $feature_node->term->uuid) {
1792
        if (!isset($feature_node->descriptionElements)) {
1793
          $feature_node->descriptionElements = array();
1794
        }
1795
        $feature_node->descriptionElements[] = $element;
1796
      }
1797
    }
1798

    
1799
    // Recurse into node children.
1800
    if (isset($feature_node->childNodes[0])) {
1801
      $mergedChildNodes = _mergeFeatureTreeDescriptions($feature_node->childNodes, $descriptionElements);
1802
      $feature_node->childNodes = $mergedChildNodes;
1803
    }
1804

    
1805
    if(!isset($feature_node->descriptionElements) && !isset($feature_node->childNodes[0])){
1806
      unset($feature_node);
1807
    }
1808

    
1809
  }
1810

    
1811
  return $featureNodes;
1812
}
1813

    
1814
/**
1815
 * Sends a GET or POST request to a CDM RESTService and returns a de-serialized object.
1816
 *
1817
 * The response from the HTTP GET request is returned as object.
1818
 * The response objects coming from the webservice configured in the
1819
 * 'cdm_webservice_url' variable are being cached in a level 1 (L1) and / or
1820
 *  in a level 2 (L2) cache.
1821
 *
1822
 * Since the L1 cache is implemented as static variable of the cdm_ws_get()
1823
 * function, this cache persists only per each single page execution.
1824
 * Any object coming from the webservice is stored into it by default.
1825
 * In contrast to this default caching mechanism the L2 cache only is used if
1826
 * the 'cdm_webservice_cache' variable is set to TRUE,
1827
 * which can be set using the modules administrative settings section.
1828
 * Objects stored in this L2 cache are serialized and stored
1829
 * using the drupal cache in the '{prefix}cache_cdm_ws' cache table. So the
1830
 * objects that are stored in the database will persist as
1831
 * long as the drupal cache is not being cleared and are available across
1832
 * multiple script executions.
1833
 *
1834
 * @param string $uri
1835
 *   URL to the webservice.
1836
 * @param array $pathParameters
1837
 *   An array of path parameters.
1838
 * @param string $query
1839
 *   A query string to be appended to the URL.
1840
 * @param string $method
1841
 *   The HTTP method to use, valid values are "GET" or "POST";
1842
 * @param bool $absoluteURI
1843
 *   TRUE when the URL should be treated as absolute URL.
1844
 *
1845
 * @return object| array
1846
 *   The de-serialized webservice response object.
1847
 */
1848
function cdm_ws_get($uri, $pathParameters = array(), $query = NULL, $method = "GET", $absoluteURI = FALSE) {
1849

    
1850
  static $cacheL1 = array();
1851

    
1852
  $data = NULL;
1853
  // store query string in $data and clear the query, $data will be set as HTTP request body
1854
  if($method == 'POST'){
1855
    $data = $query;
1856
    $query = NULL;
1857
  }
1858

    
1859
  // Transform the given uri path or pattern into a proper webservice uri.
1860
  if (!$absoluteURI) {
1861
    $uri = cdm_compose_url($uri, $pathParameters, $query);
1862
  }
1863
  cdm_ws_apply_classification_subtree_filter($uri);
1864

    
1865
  // read request parameter 'cacheL2_refresh'
1866
  // which allows refreshing the level 2 cache
1867
  $do_cacheL2_refresh = isset($_REQUEST['cacheL2_refresh']) && $_REQUEST['cacheL2_refresh'] == 1;
1868

    
1869
  $is_cdm_ws_uri = _is_cdm_ws_uri($uri);
1870
  $use_cacheL2 = variable_get('cdm_webservice_cache', 1);
1871

    
1872
  if($method == 'GET'){
1873
    $cache_key = $uri;
1874
  } else {
1875
    // sha1 creates longer hashes and thus will cause fewer collisions than md5.
1876
    // crc32 is faster but creates much shorter hashes
1877
    $cache_key = $uri . '[' . $method . ':' . sha1($data) .']';
1878
  }
1879

    
1880
  if (array_key_exists($cache_key, $cacheL1)) {
1881
    $cacheL1_obj = $cacheL1[$uri];
1882
  }
1883

    
1884
  $set_cacheL1 = FALSE;
1885
  if ($is_cdm_ws_uri && !isset($cacheL1_obj)) {
1886
    $set_cacheL1 = TRUE;
1887
  }
1888

    
1889
  // Only cache cdm webservice URIs.
1890
  $set_cacheL2 = $use_cacheL2 && $is_cdm_ws_uri && $set_cacheL1;
1891
  $cacheL2_entry = FALSE;
1892

    
1893
  if ($use_cacheL2 && !$do_cacheL2_refresh) {
1894
    // Try to get object from cacheL2.
1895
    $cacheL2_entry = cache_get($cache_key, 'cache_cdm_ws');
1896
  }
1897

    
1898
  if (isset($cacheL1_obj)) {
1899
    //
1900
    // The object has been found in the L1 cache.
1901
    //
1902
    $obj = $cacheL1_obj;
1903
    if (cdm_debug_block_visible()) {
1904
      cdm_ws_debug_add($uri, $method, $data, 0, 0, NULL, 'cacheL1');
1905
    }
1906
  }
1907
  elseif ($cacheL2_entry) {
1908
    //
1909
    // The object has been found in the L2 cache.
1910
    //
1911
    $duration_parse_start = microtime(TRUE);
1912
    $obj = unserialize($cacheL2_entry->data);
1913
    $duration_parse = microtime(TRUE) - $duration_parse_start;
1914

    
1915
    if (cdm_debug_block_visible()) {
1916
      cdm_ws_debug_add($uri, $method, $data, 0, $duration_parse, NULL, 'cacheL2');
1917
    }
1918
  }
1919
  else {
1920
    //
1921
    // Get the object from the webservice and cache it.
1922
    //
1923
    $duration_fetch_start = microtime(TRUE);
1924
    // Request data from webservice JSON or XML.
1925
    $response = cdm_http_request($uri, $method, $data);
1926
    $response_body = NULL;
1927
    if (isset($response->data)) {
1928
      $response_body = $response->data;
1929
    }
1930
    $duration_fetch = microtime(TRUE) - $duration_fetch_start;
1931
    $duration_parse_start = microtime(TRUE);
1932

    
1933
    // Parse data and create object.
1934
    $obj = cdm_load_obj($response_body);
1935

    
1936
    $duration_parse = microtime(TRUE) - $duration_parse_start;
1937

    
1938
    if (cdm_debug_block_visible()) {
1939
      if ($obj || $response_body == "[]") {
1940
        $status = 'valid';
1941
      }
1942
      else {
1943
        $status = 'invalid';
1944
      }
1945
      cdm_ws_debug_add($uri, $method, $data, $duration_fetch, $duration_parse, strlen($response_body), $status);
1946
    }
1947
    if ($set_cacheL2) {
1948
      // Store the object in cache L2.
1949
      // Comment @WA perhaps better if Drupal serializedatas here? Then the
1950
      // flag serialized is set properly in the cache table.
1951
      cache_set($cache_key, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
1952
    }
1953
  }
1954
  if ($obj) {
1955
    // Store the object in cache L1.
1956
    if ($set_cacheL1) {
1957
      $cacheL1[$cache_key] = $obj;
1958
    }
1959
  }
1960
  return $obj;
1961
}
1962

    
1963
function cdm_ws_apply_classification_subtree_filter(&$uri){
1964

    
1965
  $classification_subtree_filter_patterns = &drupal_static('classification_subtree_filter_patterns', array(
1966
    "#/classification/[0-9a-f\-]{36}/childNodes#",
1967
    /* covered by above pattern:
1968
    "#/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
1969
    '#/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
1970
    */
1971
    "#/portal/classification/[0-9a-f\-]{36}/childNodes#",
1972
    /* covered by above pattern:
1973
    "#/portal/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
1974
    '#/portal/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
1975
    */
1976
    '#/portal/classification/[0-9a-f\-]{36}/pathFrom/[0-9a-f\-]{36}#',
1977
    "#/portal/taxon/search#",
1978
    "#/portal/taxon/find#",
1979
    /* covered by above pattern:
1980
    "#/portal/taxon/findByDescriptionElementFullText#",
1981
    "#/portal/taxon/findByFullText#",
1982
    "#/portal/taxon/findByEverythingFullText#",
1983
    "#/portal/taxon/findByIdentifier#",
1984
    "#/portal/taxon/findByMarker#",
1985
    "#/portal/taxon/findByMarker#",
1986
    "#/portal/taxon/findByMarker#",
1987
    */
1988
    "#/portal/taxon/[0-9a-f\-]{36}#"
1989
    /* covered by above pattern:
1990
    "#/portal/taxon/[0-9a-f\-]{36}/taxonNodes#",
1991
    */
1992
  ));
1993

    
1994
  $sub_tree_filter_uuid_value = variable_get(CDM_SUB_TREE_FILTER_UUID, FALSE);
1995
  if(is_uuid($sub_tree_filter_uuid_value)){
1996
    foreach($classification_subtree_filter_patterns as $preg_pattern){
1997
      if(preg_match($preg_pattern, $uri)){
1998
        // no need to take care for uri fragments with ws uris!
1999
        if(strpos( $uri, '?')){
2000
          $uri .= '&subtree=' . $sub_tree_filter_uuid_value;
2001
        } else {
2002
          $uri .= '?subtree='. $sub_tree_filter_uuid_value;
2003
        }
2004
        break;
2005
      }
2006
    }
2007
  }
2008

    
2009
}
2010
/**
2011
 * Processes and stores the given information in $_SESSION['cdm']['ws_debug'] as table row.
2012
 *
2013
 * The cdm_ws_debug block will display the debug information.
2014
 *
2015
 * @param $uri
2016
 *    The CDM REST URI to which the request has been send
2017
 * @param string $method
2018
 *    The HTTP request method, either 'GET' or 'POST'
2019
 * @param string $post_data
2020
 *    The datastring send with a post request
2021
 * @param $duration_fetch
2022
 *    The time in seconds it took to fetch the data from the web service
2023
 * @param $duration_parse
2024
 *    Time in seconds which was needed to parse the json response
2025
 * @param $datasize
2026
 *    Size of the data received from the server
2027
 * @param $status
2028
 *    A status string, possible values are: 'valid', 'invalid', 'cacheL1', 'cacheL2'
2029
 * @return bool
2030
 *    TRUE if adding the debug information was successful
2031
 */
2032
function cdm_ws_debug_add($uri, $method, $post_data, $duration_fetch, $duration_parse, $datasize, $status) {
2033

    
2034
  static $initial_time = NULL;
2035
  if(!$initial_time) {
2036
    $initial_time = microtime(TRUE);
2037
  }
2038
  $time = microtime(TRUE) - $initial_time;
2039

    
2040
  // Decompose uri into path and query element.
2041
  $uri_parts = explode("?", $uri);
2042
  $query = array();
2043
  if (count($uri_parts) == 2) {
2044
    $path = $uri_parts[0];
2045
  }
2046
  else {
2047
    $path = $uri;
2048
  }
2049

    
2050
  if(strpos($uri, '?') > 0){
2051
    $json_uri = str_replace('?', '.json?', $uri);
2052
    $xml_uri = str_replace('?', '.xml?', $uri);
2053
  } else {
2054
    $json_uri = $uri . '.json';
2055
    $xml_uri = $json_uri . '.xml';
2056
  }
2057

    
2058
  // data links to make data accecsible as json and xml
2059
  $data_links = '';
2060
  if (_is_cdm_ws_uri($path)) {
2061

    
2062
    // see ./js/http-method-link.js
2063

    
2064
    if($method == 'GET'){
2065
      $data_links .= '<a href="' . $xml_uri . '" target="data">xml</a>-';
2066
      $data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">proxied</a>';
2067
      $data_links .= '<br/>';
2068
      $data_links .= '<a href="' . $json_uri . '" target="data">json</a>-';
2069
      $data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">proxied</a>';
2070
    } else {
2071
      $js_link_activation = 'class="http-' . $method . '-link" data-cdm-http-post="' . $post_data . '" type="application/x-www-form-urlencoded"';
2072
      $data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">xml-proxied</a>';
2073
      $data_links .= '<br/>';
2074
      $data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">json-proxied</a>';
2075
    }
2076
  }
2077
  else {
2078
    $data_links .= '<a href="' . $uri . '" target="data">open</a>';
2079
  }
2080

    
2081
  //
2082
  $data = array(
2083
      'ws_uri' => $uri,
2084
      'method' => $method,
2085
      'post_data' => $post_data,
2086
      'time' => sprintf('%3.3f', $time),
2087
      'fetch_seconds' => sprintf('%3.3f', $duration_fetch),
2088
      'parse_seconds' => sprintf('%3.3f', $duration_parse),
2089
      'size_kb' => sprintf('%3.1f', ($datasize / 1024)) ,
2090
      'status' => $status,
2091
      'data_links' => $data_links
2092
  );
2093
  if (!isset($_SESSION['cdm']['ws_debug'])) {
2094
    $_SESSION['cdm']['ws_debug'] = array();
2095
  }
2096
  $_SESSION['cdm']['ws_debug'][] = serialize($data);
2097

    
2098
  // Mark this page as being uncacheable.
2099
  // taken over from drupal_get_messages() but it is unsure if we really need this here
2100
  drupal_page_is_cacheable(FALSE);
2101

    
2102
  // Messages not set when DB connection fails.
2103
  return isset($_SESSION['cdm']['ws_debug']) ? $_SESSION['cdm']['ws_debug'] : NULL;
2104
}
2105

    
2106
/**
2107
 * helper function to dtermine if the cdm_debug_block should be displayed or not
2108
 * the visibility depends on whether
2109
 *  - the block is enabled
2110
 *  - the visibility restrictions in the block settings are satisfied
2111
 */
2112
function cdm_debug_block_visible() {
2113
  static $is_visible = null;
2114

    
2115
  if($is_visible === null){
2116
      $block = block_load('cdm_api', 'cdm_ws_debug');
2117
      $is_visible = isset($block->status) && $block->status == 1;
2118
      if($is_visible){
2119
        $blocks = array($block);
2120
        // Checks the page, user role, and user-specific visibilty settings.
2121
        block_block_list_alter($blocks);
2122
        $is_visible = count($blocks) > 0;
2123
      }
2124
  }
2125
  return $is_visible;
2126
}
2127

    
2128
/**
2129
 * @todo Please document this function.
2130
 * @see http://drupal.org/node/1354
2131
 */
2132
function cdm_load_obj($response_body) {
2133
  $obj = json_decode($response_body);
2134

    
2135
  if (!(is_object($obj) || is_array($obj))) {
2136
    ob_start();
2137
    $obj_dump = ob_get_contents();
2138
    ob_clean();
2139
    return FALSE;
2140
  }
2141

    
2142
  return $obj;
2143
}
2144

    
2145
/**
2146
 * Do a http request to a CDM RESTful web service.
2147
 *
2148
 * @param string $uri
2149
 *   The webservice url.
2150
 * @param string $method
2151
 *   The HTTP method to use, valid values are "GET" or "POST"; defaults to
2152
 *   "GET" even if NULL, FALSE or any invalid value is supplied.
2153
 * @param $data: A string containing the request body, formatted as
2154
 *     'param=value&param=value&...'. Defaults to NULL.
2155
 *
2156
 * @return object
2157
 *   The object as returned by drupal_http_request():
2158
 *   An object that can have one or more of the following components:
2159
 *   - request: A string containing the request body that was sent.
2160
 *   - code: An integer containing the response status code, or the error code
2161
 *     if an error occurred.
2162
 *   - protocol: The response protocol (e.g. HTTP/1.1 or HTTP/1.0).
2163
 *   - status_message: The status message from the response, if a response was
2164
 *     received.
2165
 *   - redirect_code: If redirected, an integer containing the initial response
2166
 *     status code.
2167
 *   - redirect_url: If redirected, a string containing the URL of the redirect
2168
 *     target.
2169
 *   - error: If an error occurred, the error message. Otherwise not set.
2170
 *   - headers: An array containing the response headers as name/value pairs.
2171
 *     HTTP header names are case-insensitive (RFC 2616, section 4.2), so for
2172
 *     easy access the array keys are returned in lower case.
2173
 *   - data: A string containing the response body that was received.
2174
 */
2175
function cdm_http_request($uri, $method = "GET", $data = NULL) {
2176
  static $acceptLanguage = NULL;
2177
  $header = array();
2178
  
2179
  if(!$acceptLanguage && module_exists('i18n')){
2180
    $acceptLanguage = i18n_language_content()->language;
2181
  }
2182

    
2183
  if (!$acceptLanguage) {
2184
    if (function_exists('apache_request_headers')) {
2185
      $headers = apache_request_headers();
2186
      if (isset($headers['Accept-Language'])) {
2187
        $acceptLanguage = $headers['Accept-Language'];
2188
      }
2189
    }
2190
  }
2191

    
2192
  if ($method != "GET" && $method != "POST") {
2193
    drupal_set_message('cdm_api.module#cdm_http_request() : unsupported HTTP request method ', 'error');
2194
  }
2195

    
2196
  if (_is_cdm_ws_uri($uri)) {
2197
    $header['Accept'] = 'application/json';
2198
    $header['Accept-Language'] = $acceptLanguage;
2199
    $header['Accept-Charset'] = 'UTF-8';
2200
  }
2201

    
2202
  if($method == "POST") {
2203
    // content type is application/x-www-form-urlencoded, so the request body uses the same format as the query string
2204
    $header['Content-Type'] = 'application/x-www-form-urlencoded';
2205
  }
2206

    
2207

    
2208
  cdm_dd($uri);
2209
  return drupal_http_request($uri, array(
2210
      'headers' => $header,
2211
      'method' => $method,
2212
      'data' => $data,
2213
      'timeout' => CDM_HTTP_REQUEST_TIMEOUT
2214
      )
2215
   );
2216
}
2217

    
2218
/**
2219
 * Concatenates recursively the fields of all features contained in the given
2220
 * CDM FeatureTree root node.
2221
 *
2222
 * @param $rootNode
2223
 *     A CDM FeatureTree node
2224
 * @param
2225
 *     The character to be used as glue for concatenation, default is ', '
2226
 * @param $field_name
2227
 *     The field name of the CDM Features
2228
 * @param $excludes
2229
 *     Allows defining a set of values to be excluded. This refers to the values
2230
 *     in the field denoted by the $field_name parameter
2231
 *
2232
 */
2233
function cdm_featureTree_elements_toString($root_node, $separator = ', ', $field_name = 'representation_L10n', $excludes = array()) {
2234
  $out = '';
2235

    
2236
  $pre_child_separator = $separator;
2237
  $post_child_separator = '';
2238

    
2239
  foreach ($root_node->childNodes as $feature_node) {
2240
    $out .= ($out ? $separator : '');
2241
    if(!in_array($feature_node->term->$field_name, $excludes)) {
2242
      $out .= $feature_node->term->$field_name;
2243
      if (is_array($feature_node->childNodes) && count($feature_node->childNodes) > 0) {
2244
        $childlabels = cdm_featureTree_elements_toString($feature_node, $separator, $field_name);
2245
        if (strlen($childlabels)) {
2246
            $out .=  $pre_child_separator . $childlabels . $post_child_separator;
2247
        }
2248
      }
2249
    }
2250
  }
2251
  return $out;
2252
}
2253

    
2254
/**
2255
 * Create a one-dimensional form options array.
2256
 *
2257
 * Creates an array of all features in the feature tree of feature nodes,
2258
 * the node labels are indented by $node_char and $childIndent depending on the
2259
 * hierachy level.
2260
 *
2261
 * @param - $rootNode
2262
 * @param - $node_char
2263
 * @param - $childIndentStr
2264
 * @param - $childIndent
2265
 *   ONLY USED INTERNALLY!
2266
 *
2267
 * @return array
2268
 *   A one dimensional Drupal form options array.
2269
 */
2270
function _featureTree_nodes_as_feature_options($rootNode, $node_char = "&#9500;&#9472; ", $childIndentStr = '&nbsp;', $childIndent = '') {
2271
  $options = array();
2272
  foreach ($rootNode->childNodes as $featureNode) {
2273
    $indent_prefix = '';
2274
    if ($childIndent) {
2275
      $indent_prefix = $childIndent . $node_char . " ";
2276
    }
2277
    $options[$featureNode->term->uuid] = $indent_prefix . $featureNode->term->representation_L10n;
2278
    if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2279
      // Foreach ($featureNode->childNodes as $childNode){
2280
      $childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
2281
      $options = array_merge_recursive($options, $childList);
2282
      // }
2283
    }
2284
  }
2285
  return $options;
2286
}
2287

    
2288
/**
2289
 * Returns an array with all available FeatureTrees and the representations of the selected
2290
 * FeatureTree as a detail view.
2291
 *
2292
 * @param boolean $add_default_feature_free
2293
 * @return array
2294
 *  associative array with following keys:
2295
 *  -options: Returns an array with all available Feature Trees
2296
 *  -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
2297
 *
2298
 */
2299
function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE) {
2300

    
2301
  $options = array();
2302
  $tree_representations = array();
2303
  $feature_trees = array();
2304

    
2305
  // Set tree that contains all features.
2306
  if ($add_default_feature_free) {
2307
    $options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
2308
    $feature_trees[] = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
2309
  }
2310

    
2311
  // Get feature trees from database.
2312
  $persited_trees = cdm_ws_fetch_all(CDM_WS_FEATURETREES);
2313
  if (is_array($persited_trees)) {
2314
    $feature_trees = array_merge($feature_trees, $persited_trees);
2315
  }
2316

    
2317
  foreach ($feature_trees as $featureTree) {
2318

    
2319
    if(!is_object($featureTree)){
2320
      continue;
2321
    }
2322
    // Do not add the DEFAULT_FEATURETREE again,
2323
    if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
2324
      $options[$featureTree->uuid] = $featureTree->titleCache;
2325
    }
2326

    
2327
    // Render the hierarchic tree structure
2328
    if (is_array( $featureTree->root->childNodes) && count( $featureTree->root->childNodes) > 0) {
2329

    
2330
      // Render the hierarchic tree structure.
2331
      $treeDetails = '<div class="featuretree_structure">'
2332
        . theme('FeatureTree_hierarchy', array('FeatureTreeUuid' =>  $featureTree->uuid))
2333
        . '</div>';
2334

    
2335
      $form = array();
2336
      $form['featureTree-' .  $featureTree->uuid] = array(
2337
        '#type' => 'fieldset',
2338
        '#title' => 'Show details',
2339
        '#attributes' => array('class' => array('collapsible collapsed')),
2340
        // '#collapsible' => TRUE,
2341
        // '#collapsed' => TRUE,
2342
      );
2343
      $form['featureTree-' .  $featureTree->uuid]['details'] = array(
2344
        '#markup' => $treeDetails,
2345
      );
2346

    
2347
      $tree_representations[$featureTree->uuid] = drupal_render($form);
2348
    }
2349

    
2350
  } // END loop over feature trees
2351

    
2352
  // return $options;
2353
  return array('options' => $options, 'treeRepresentations' => $tree_representations);
2354
}
2355

    
2356
/**
2357
 * Provides the list of available classifications in form of an options array.
2358
 *
2359
 * The options array is suitable for drupal form API elements that allow multiple choices.
2360
 * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
2361
 *
2362
 * The classifications are ordered alphabetically whereas the classification
2363
 * chosen as default will always appear on top of the array, followed by a
2364
 * blank line below.
2365
 *
2366
 * @param bool $add_none_option
2367
 *   is true an addtional 'none' option will be added, optional parameter, defaults to FALSE
2368
 *
2369
 * @return array
2370
 *   classifications in an array as options for a form element that allows multiple choices.
2371
 */
2372
function cdm_get_taxontrees_as_options($add_none_option = FALSE) {
2373

    
2374
  $taxonTrees = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
2375

    
2376
  $default_classification_uuid = variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
2377
  $default_classification_label = '';
2378

    
2379
  // add all classifications
2380
  $taxonomic_tree_options = array();
2381
  if ($add_none_option) {
2382
    $taxonomic_tree_options['NONE'] = ' '; // one Space character at beginning to force on top;
2383
  }
2384
  if ($taxonTrees) {
2385
    foreach ($taxonTrees as $tree) {
2386
      if (!$default_classification_uuid || $default_classification_uuid != $tree->uuid) {
2387
        $taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
2388
      } else {
2389
        $taxonomic_tree_options[$tree->uuid] = '  '; // two Space characters to force on top but below 'none' option , will be replaced below by titleCache
2390
        $default_classification_label = $tree->titleCache;
2391
      }
2392
    }
2393
  }
2394
  // oder alphabetically the space
2395
  asort($taxonomic_tree_options);
2396

    
2397
  // now set the labels
2398
  //   for none
2399
  if ($add_none_option) {
2400
    $taxonomic_tree_options['NONE'] =t('--- ALL ---');
2401
  }
2402

    
2403
  //   for default_classification
2404
  if (is_uuid($default_classification_uuid)) {
2405
    $taxonomic_tree_options[$default_classification_uuid] =
2406
      $default_classification_label ? $default_classification_label : '--- INVALID CHOICE ---'
2407
      . (count($taxonTrees) > 1 ? ' [' . t('DEFAULT CLASSIFICATION') . ']': '');
2408
  }
2409

    
2410
  return $taxonomic_tree_options;
2411
}
2412

    
2413
/**
2414
 * @todo Please document this function.
2415
 * @see http://drupal.org/node/1354
2416
 */
2417
function cdm_api_secref_cache_prefetch(&$secUuids) {
2418
  // Comment @WA: global variables should start with a single underscore
2419
  // followed by the module and another underscore.
2420
  global $_cdm_api_secref_cache;
2421
  if (!is_array($_cdm_api_secref_cache)) {
2422
    $_cdm_api_secref_cache = array();
2423
  }
2424
  $uniqueUuids = array_unique($secUuids);
2425
  $i = 0;
2426
  $param = '';
2427
  while ($i++ < count($uniqueUuids)) {
2428
    $param .= $secUuids[$i] . ',';
2429
    if (strlen($param) + 37 > 2000) {
2430
      _cdm_api_secref_cache_add($param);
2431
      $param = '';
2432
    }
2433
  }
2434
  if ($param) {
2435
    _cdm_api_secref_cache_add($param);
2436
  }
2437
}
2438

    
2439
/**
2440
 * @todo Please document this function.
2441
 * @see http://drupal.org/node/1354
2442
 */
2443
function cdm_api_secref_cache_get($secUuid) {
2444
  global $_cdm_api_secref_cache;
2445
  if (!is_array($_cdm_api_secref_cache)) {
2446
    $_cdm_api_secref_cache = array();
2447
  }
2448
  if (!array_key_exists($secUuid, $_cdm_api_secref_cache)) {
2449
    _cdm_api_secref_cache_add($secUuid);
2450
  }
2451
  return $_cdm_api_secref_cache[$secUuid];
2452
}
2453

    
2454
/**
2455
 * @todo Please document this function.
2456
 * @see http://drupal.org/node/1354
2457
 */
2458
function cdm_api_secref_cache_clear() {
2459
  global $_cdm_api_secref_cache;
2460
  $_cdm_api_secref_cache = array();
2461
}
2462

    
2463

    
2464
/**
2465
 * Validates if the given string is a uuid.
2466
 *
2467
 * @param string $str
2468
 *   The string to validate.
2469
 *
2470
 * return bool
2471
 *   TRUE if the string is a UUID.
2472
 */
2473
function is_uuid($str) {
2474
  return is_string($str) && strlen($str) == 36 && strpos($str, '-');
2475
}
2476

    
2477
/**
2478
 * Checks if the given $object is a valid cdm entity.
2479
 *
2480
 * An object is considered a cdm entity if it has a string field $object->class
2481
 * with at least 3 characters and if it has a valid uuid in $object->uuid.
2482
 * The function is null save.
2483
 *
2484
 * @author a.kohlbecker <a.kohlbecker@bgbm.org>
2485
 *
2486
 * @param mixed $object
2487
 *   The object to validate
2488
 *
2489
 * @return bool
2490
 *   True if the object is a cdm entity.
2491
 */
2492
function is_cdm_entity($object) {
2493
  return
2494
    isset($object->class) && is_string($object->class) && strlen($object->class) > 2 && $object->class != 'TypedEntityReference'
2495
    && is_string($object->uuid) && is_uuid($object->uuid);
2496
}
2497

    
2498
/**
2499
 * @todo Please document this function.
2500
 * @see http://drupal.org/node/1354
2501
 */
2502
function _cdm_api_secref_cache_add($secUuidsStr) {
2503
  global $_cdm_api_secref_cache;
2504
  $ref = cdm_ws_get(CDM_WS_REFERENCE, $secUuidsStr);
2505
  // Batch fetching not jet reimplemented thus:
2506
  /*
2507
  $assocRefSTOs = array(); if($refSTOs) { foreach($refSTOs as $ref){
2508
  $assocRefSTOs[$ref->uuid] = $ref; } $_cdm_api_secref_cache =
2509
  array_merge($_cdm_api_secref_cache, $assocRefSTOs); }
2510
  */
2511
  $_cdm_api_secref_cache[$ref->uuid] = $ref;
2512
}
2513

    
2514
/**
2515
 * Checks if the given uri starts with a cdm webservice url.
2516
 *
2517
 * Checks if the uri starts with the cdm webservice url stored in the
2518
 * Drupal variable 'cdm_webservice_url'.
2519
 * The 'cdm_webservice_url' can be set in the admins section of the portal.
2520
 *
2521
 * @param string $uri
2522
 *   The URI to test.
2523
 *
2524
 * @return bool
2525
 *   True if the uri starts with a cdm webservice url.
2526
 */
2527
function _is_cdm_ws_uri($uri) {
2528
  return str_beginsWith($uri, variable_get('cdm_webservice_url', '#EMPTY#'));
2529
}
2530

    
2531
/**
2532
 * @todo Please document this function.
2533
 * @see http://drupal.org/node/1354
2534
 */
2535
function queryString($elements) {
2536
  $query = '';
2537
  foreach ($elements as $key => $value) {
2538
    if (is_array($value)) {
2539
      foreach ($value as $v) {
2540
        $query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($v);
2541
      }
2542
    }
2543
    else {
2544
      $query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($value);
2545
    }
2546
  }
2547
  return $query;
2548
}
2549

    
2550
/**
2551
 * Implementation of the magic method __clone to allow deep cloning of objects
2552
 * and arrays.
2553
 */
2554
function __clone() {
2555
  foreach ($this as $name => $value) {
2556
    if (gettype($value) == 'object' || gettype($value) == 'array') {
2557
      $this->$name = clone($this->$name);
2558
    }
2559
  }
2560
}
2561

    
2562
/**
2563
 * Compares the given CDM Term instances by the  representationL10n.
2564
 *
2565
 * Can also be used with TermDTOs. To be used in usort()
2566
 *
2567
 * @see http://php.net/manual/en/function.usort.php
2568
 *
2569
 * @param $term1
2570
 *   The first CDM Term instance
2571
 * @param $term2
2572
 *   The second CDM Term instance
2573
 * @return int
2574
 *   The result of the comparison
2575
 */
2576
function compare_terms_by_representationL10n($term1, $term2) {
2577

    
2578
  if (!isset($term1->representation_L10n)) {
2579
    $term1->representationL10n = '';
2580
  }
2581
  if (!isset($term2->representation_L10n)) {
2582
    $term2->representationL10n = '';
2583
  }
2584

    
2585
  return strcmp($term1->representation_L10n, $term2->representation_L10n);
2586
}
2587

    
2588
function compare_terms_by_order_index($term1, $term2) {
2589

    
2590

    
2591
  if (!isset($term1->orderIndex)) {
2592
    $a = 0;
2593
  } else {
2594
    $a = $term1->orderIndex;
2595
  }
2596
  if (!isset($term2->orderIndex)) {
2597
    $b = 0;
2598
  } else {
2599
    $b = $term2->orderIndex;
2600
  }
2601

    
2602
  if ($a == $b) {
2603
    return 0;
2604
  }
2605
  return ($a < $b) ? -1 : 1;
2606

    
2607
}
2608

    
2609

    
2610
/**
2611
 * Make a 'deep copy' of an array.
2612
 *
2613
 * Make a complete deep copy of an array replacing
2614
 * references with deep copies until a certain depth is reached
2615
 * ($maxdepth) whereupon references are copied as-is...
2616
 *
2617
 * @see http://us3.php.net/manual/en/ref.array.php
2618
 *
2619
 * @param array $array
2620
 * @param array $copy passed by reference
2621
 * @param int $maxdepth
2622
 * @param int $depth
2623
 */
2624
function array_deep_copy(&$array, &$copy, $maxdepth = 50, $depth = 0) {
2625
  if ($depth > $maxdepth) {
2626
    $copy = $array;
2627
    return;
2628
  }
2629
  if (!is_array($copy)) {
2630
    $copy = array();
2631
  }
2632
  foreach ($array as $k => &$v) {
2633
    if (is_array($v)) {
2634
      array_deep_copy($v, $copy[$k], $maxdepth, ++$depth);
2635
    }
2636
    else {
2637
      $copy[$k] = $v;
2638
    }
2639
  }
2640
}
2641

    
2642
/**
2643
 * Adds java script to create and enable a toggler for the cdm webservice debug block content.
2644
 *
2645
 */
2646
function _add_js_ws_debug() {
2647

    
2648
  $data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.min.js';
2649
  $colorbox_js = '/js/colorbox/jquery.colorbox-min.js';
2650
  if (variable_get('cdm_js_devel_mode', FALSE)) {
2651
    // use the developer versions of js libs
2652
    $data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.js';
2653
    $colorbox_js = '/js/colorbox/jquery.colorbox.js';
2654
  }
2655
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $data_tables_js,
2656
    array(
2657
      'type' => 'file',
2658
      'weight' => JS_LIBRARY,
2659
      'cache' => TRUE)
2660
    );
2661

    
2662
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $colorbox_js,
2663
    array(
2664
      'type' => 'file',
2665
      'weight' => JS_LIBRARY,
2666
      'cache' => TRUE)
2667
    );
2668
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/colorbox/colorbox.css');
2669
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/DataTables-1.9.4/media/css/cdm_debug_table.css');
2670

    
2671
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ws_debug_block.js',
2672
    array(
2673
      'type' => 'file',
2674
      'weight' => JS_LIBRARY,
2675
      'cache' => TRUE)
2676
    );
2677
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/http-method-link.js',
2678
    array(
2679
    'type' => 'file',
2680
    'weight' => JS_LIBRARY,
2681
    'cache' => TRUE)
2682
    );
2683

    
2684
}
2685

    
2686
/**
2687
 * @todo Please document this function.
2688
 * @see http://drupal.org/node/1354
2689
 */
2690
function _no_classfication_uuid_message() {
2691
  if (!cdm_ws_get(CDM_WS_PORTAL_TAXONOMY)) {
2692
    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.');
2693
  }
2694
  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.');
2695
}
2696

    
2697
/**
2698
 * Implementation of hook flush_caches
2699
 *
2700
 * Add custom cache tables to the list of cache tables that
2701
 * will be cleared by the Clear button on the Performance page or whenever
2702
 * drupal_flush_all_caches is invoked.
2703
 *
2704
 * @author W.Addink <waddink@eti.uva.nl>
2705
 *
2706
 * @return array
2707
 *   An array with custom cache tables to include.
2708
 */
2709
function cdm_api_flush_caches() {
2710
  return array('cache_cdm_ws');
2711
}
2712

    
2713
/**
2714
 * Logs if the drupal variable 'cdm_debug_mode' ist set true to drupal_debug.txt in the site's temp directory.
2715
 *
2716
 * @param $data
2717
 *   The variable to log to the drupal_debug.txt log file.
2718
 * @param $label
2719
 *   (optional) If set, a label to output before $data in the log file.
2720
 *
2721
 * @return
2722
 *   No return value if successful, FALSE if the log file could not be written
2723
 *   to.
2724
 *
2725
 * @see cdm_dataportal_init() where the log file is reset on each requests
2726
 * @see dd()
2727
 * @see http://drupal.org/node/314112
2728
 *
2729
 */
2730
function cdm_dd($data, $label = NULL) {
2731
  if(module_exists('devel') && variable_get('cdm_debug_mode', FALSE) && file_stream_wrapper_get_class('temporary') ){
2732
    return dd($data, $label);
2733
  }
2734
}
2735

    
(5-5/12)