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cdm-dataportal / modules / cdm_dataportal / cdm_api / cdm_api.module @ cf4b9055

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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
    $year = substr($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
    $month = substr($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
    $day = substr($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 > 0 ? ' ' . 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 $empty_option
1242
 *   An additional element do be placed at the beginning og the list. This element will be the default option.
1243
 *
1244
 * @return array
1245
 *   the terms in an array as options for a form element that allows multiple choices.
1246
 */
1247
function cdm_terms_as_options($terms, $term_label_callback = NULL, $empty_option = FALSE){
1248
  $options = array();
1249
  if(isset($terms) && is_array($terms)) {
1250
    foreach ($terms as $term) {
1251
      if ($term_label_callback && function_exists($term_label_callback)) {
1252
        $options[$term->uuid] = call_user_func($term_label_callback, $term);
1253
      } else {
1254
        //TODO use cdm_term_representation() here?
1255
        $options[$term->uuid] = t('@term', array('@term' => $term->representation_L10n));
1256
      }
1257
    }
1258
  }
1259

    
1260
  if($empty_option !== FALSE){
1261
    array_unshift ($options, "");
1262
  }
1263

    
1264
  return $options;
1265
}
1266

    
1267
/**
1268
 * Creates and array of options for drupal select form elements.
1269
 *
1270
 * @param $vocabulary_uuid
1271
 *   The UUID of the CDM Term Vocabulary
1272
 * @param $term_label_callback
1273
 *   An optional call back function which can be used to modify the term label
1274
 * @param bool $empty_option
1275
 *   An additional element do be placed at the beginning og the list. This element will be the default option.
1276
 * @param array $include_filter
1277
 *   An associative array consisting of a field name an regular expression. All term matching
1278
 *   these filter are included. The value of the field is converted to a String by var_export()
1279
 *   so a boolean 'true' can be matched by '/true/'
1280
 * @param string $order_by
1281
 *   One of the order by constants defined in this file
1282
 * @return mixed
1283
 */
1284
function cdm_vocabulary_as_option($vocabulary_uuid, $term_label_callback = NULL, $empty_option = FALSE,
1285
                                  array $include_filter = null, $order_by = CDM_ORDER_BY_ORDER_INDEX_ASC) {
1286

    
1287
  static $vocabularyOptions = array();
1288

    
1289
  if (!isset($vocabularyOptions[$vocabulary_uuid])) {
1290
    $terms = cdm_ws_fetch_all('termVocabulary/' . $vocabulary_uuid . '/terms',
1291
      array(
1292
        'orderBy' => $order_by
1293
      )
1294
    );
1295

    
1296
    // apply the include filter
1297
    if($include_filter != null){
1298
      $included_terms = array();
1299

    
1300
      foreach ($terms as $term){
1301
        $include = true;
1302
        foreach ($include_filter as $field=>$regex){
1303
          $include =  preg_match($regex, var_export($term->$field, true)) === 1;
1304
          if(!$include){
1305
            break;
1306
          }
1307
        }
1308
        if($include){
1309
          $included_terms[] = $term;
1310
        }
1311
      }
1312

    
1313
      $terms = $included_terms;
1314
    }
1315

    
1316
    // make options list
1317
    $vocabularyOptions[$vocabulary_uuid] = cdm_terms_as_options($terms, $term_label_callback, $empty_option);
1318
  }
1319

    
1320
  $options = $vocabularyOptions[$vocabulary_uuid];
1321

    
1322
  return $options;
1323
}
1324

    
1325
/**
1326
 * @param $term_type string one of
1327
 *  - Unknown
1328
 *  - Language
1329
 *  - NamedArea
1330
 *  - Rank
1331
 *  - Feature
1332
 *  - AnnotationType
1333
 *  - MarkerType
1334
 *  - ExtensionType
1335
 *  - DerivationEventType
1336
 *  - PresenceAbsenceTerm
1337
 *  - NomenclaturalStatusType
1338
 *  - NameRelationshipType
1339
 *  - HybridRelationshipType
1340
 *  - SynonymRelationshipType
1341
 *  - TaxonRelationshipType
1342
 *  - NameTypeDesignationStatus
1343
 *  - SpecimenTypeDesignationStatus
1344
 *  - InstitutionType
1345
 *  - NamedAreaType
1346
 *  - NamedAreaLevel
1347
 *  - RightsType
1348
 *  - MeasurementUnit
1349
 *  - StatisticalMeasure
1350
 *  - MaterialOrMethod
1351
 *  - Material
1352
 *  - Method
1353
 *  - Modifier
1354
 *  - Scope
1355
 *  - Stage
1356
 *  - KindOfUnit
1357
 *  - Sex
1358
 *  - ReferenceSystem
1359
 *  - State
1360
 *  - NaturalLanguageTerm
1361
 *  - TextFormat
1362
 *  - DeterminationModifier
1363
 *  - DnaMarker
1364
 *
1365
 * @param  $order_by
1366
 *  Optionally sort option (default: CDM_ORDER_BY_TITLE_CACHE_ASC)
1367
 *  possible values:
1368
 *    - CDM_ORDER_BY_ID_ASC
1369
 *    - CDM_ORDER_BY_ID_DESC
1370
 *    - CDM_ORDER_BY_TITLE_CACHE_ASC
1371
 *    - CDM_ORDER_BY_TITLE_CACHE_DESC
1372
 *    - CDM_ORDER_BY_ORDER_INDEX_ASC (can only be used with OrderedTerms!!)
1373
 *    - CDM_ORDER_BY_ORDER_INDEX_DESC (can only be used with OrderedTerms!!)
1374
 * @param bool $empty_option
1375
 *   An additional element do be placed at the beginning og the list. This element will be the default option.
1376
 * @return array
1377
 *    the terms in an array as options for a form element that allows multiple choices.
1378
 */
1379
function cdm_terms_by_type_as_option($term_type, $order_by = CDM_ORDER_BY_TITLE_CACHE_ASC, $term_label_callback = NULL, $empty_option = FALSE){
1380
  $terms = cdm_ws_fetch_all(
1381
    CDM_WS_TERM,
1382
    array(
1383
      'class' => $term_type,
1384
      'orderBy' => $order_by
1385
    )
1386
  );
1387
  return cdm_terms_as_options($terms, $term_label_callback, $empty_option);
1388
}
1389

    
1390

    
1391
/**
1392
 * @todo Please document this function.
1393
 * @see http://drupal.org/node/1354
1394
 */
1395
function _cdm_relationship_type_term_label_callback($term) {
1396
  if (isset($term->representation_L10n_abbreviatedLabel)) {
1397
    return $term->representation_L10n_abbreviatedLabel . ' : '
1398
    . t('@term', array('@term' => $term->representation_L10n));
1399
  }
1400
else {
1401
    return t('@term', array('@term' => $term->representation_L10n));
1402
  }
1403
}
1404

    
1405
// ========================================================================================== //
1406
/**
1407
 * @todo Improve documentation of this function.
1408
 *
1409
 * eu.etaxonomy.cdm.model.description.
1410
 * CategoricalData
1411
 * CommonTaxonName
1412
 * Distribution
1413
 * IndividualsAssociation
1414
 * QuantitativeData
1415
 * TaxonInteraction
1416
 * TextData
1417
 */
1418
function cdm_descriptionElementTypes_as_option($prependEmptyElement = FALSE) {
1419
  static $types = array(
1420
    "CategoricalData",
1421
    "CommonTaxonName",
1422
    "Distribution",
1423
    "IndividualsAssociation",
1424
    "QuantitativeData",
1425
    "TaxonInteraction",
1426
    "TextData",
1427
  );
1428

    
1429
  static $options = NULL;
1430
  if ($options == NULL) {
1431
    $options = array();
1432
    if ($prependEmptyElement) {
1433
      $options[' '] = '';
1434
    }
1435
    foreach ($types as $type) {
1436
      // No internatianalization here since these are purely technical terms.
1437
      $options["eu.etaxonomy.cdm.model.description." . $type] = $type;
1438
    }
1439
  }
1440
  return $options;
1441
}
1442

    
1443

    
1444
/**
1445
 * Fetches all TaxonDescription descriptions elements which are associated to the
1446
 * Taxon specified by the $taxon_uuid and merges the elements into the given
1447
 * feature tree.
1448
 * @param $feature_tree
1449
 *     The CDM FeatureTree to be used as template
1450
 * @param $taxon_uuid
1451
 *     The UUID of the taxon
1452
 * @param $excludes
1453
 *     UUIDs of features to be excluded
1454
 * @return$feature_tree
1455
 *     The CDM FeatureTree which was given as parameter merged tree whereas the
1456
 *     CDM FeatureNodes are extended by an additional field 'descriptionElements'
1457
 *     witch will hold the according $descriptionElements.
1458
 */
1459
function cdm_ws_descriptions_by_featuretree($feature_tree, $taxon_uuid, $exclude_uuids = array()) {
1460

    
1461
  if (!$feature_tree) {
1462
    drupal_set_message(check_plain(t("No 'FeatureTree' has been set so far.
1463
      In order to see the species profiles of your taxa, please select a
1464
      'FeatureTree' in the !settings"), array('!settings' => l(t('CDM Dataportal Settings'), 'admin/config/cdm_dataportal/layout'))), 'warning');
1465
    return FALSE;
1466
  }
1467

    
1468
  $description_elements = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
1469
      array(
1470
      'taxon' => $taxon_uuid,
1471
      'features' => cdm_featureTree_elements_toString($feature_tree->root, ',', 'uuid', $exclude_uuids)
1472
      ),
1473
      'POST'
1474
  );
1475

    
1476
  // Combine all descriptions into one feature tree.
1477
  $merged_nodes = _mergeFeatureTreeDescriptions($feature_tree->root->childNodes, $description_elements);
1478
  $feature_tree->root->childNodes = $merged_nodes;
1479

    
1480
  return $feature_tree;
1481
}
1482

    
1483
/**
1484
 * Returns a filtered a list of annotations for the cdm entity given as parameter $cdmBase.
1485
 * If the annotations are not yet already loded with the cdm entity the cdm REST service will
1486
 * be requested for the annotations.
1487
 *
1488
 * @param string $cdmBase
1489
 *   An annotatable cdm entity.
1490
 * @param array $includeTypes
1491
 *   If an array of annotation type uuids is supplied by this parameter the
1492
 *   list of annotations is resticted to those which belong to this type.
1493
 *
1494
 * @return array
1495
 *   An array of Annotation objects or an empty array.
1496
 */
1497
function cdm_ws_getAnnotationsFor(&$cdmBase, $includeTypes = FALSE) {
1498

    
1499
  if(!isset($cdmBase->annotations)){
1500
    $annotationUrl = cdm_compose_annotations_uri($cdmBase);
1501
    $cdmBase->annotations = cdm_ws_fetch_all($annotationUrl, array(), 'GET', TRUE);
1502
  }
1503

    
1504
  $annotations = array();
1505
  foreach ($cdmBase->annotations as $annotation) {
1506
    if ($includeTypes) {
1507
      if (
1508
        ( isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $includeTypes, TRUE) )
1509
        || ($annotation->annotationType === NULL && in_array('NULL_VALUE', $includeTypes, TRUE))
1510
      ) {
1511
        $annotations[] = $annotation;
1512
      }
1513
    }
1514
    else {
1515
      $annotations[] = $annotation;
1516
    }
1517
  }
1518
  return $annotations;
1519

    
1520
}
1521

    
1522
/**
1523
 * Provides the list of visible annotations for the $cdmBase.
1524
 *
1525
 * @param $cdmBase
1526
 *     The annotatable CDM entity
1527
 *
1528
 * @return array of the annotations which are visible according to the settings as stored in ANNOTATION_TYPES_VISIBLE
1529
 */
1530
function cdm_fetch_visible_annotations($cdmBase){
1531

    
1532
  static $annotations_types_filter = null;
1533
  if(!$annotations_types_filter) {
1534
    $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
1535
  }
1536
  return cdm_ws_getAnnotationsFor($cdmBase, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
1537
}
1538

    
1539
/**
1540
 * Loads the annotations from the REST service an adds them as field to the given $annotatable_entity.
1541
 *
1542
 * NOTE: The annotations are not filtered by the ANNOTATION_TYPES_VISIBLE settings since this method is meant to act
1543
 * like the annotations have been fetched in the ORM-framework in the service.
1544
 *
1545
 * @param object $annotatable_entity
1546
 *   The CDM AnnotatableEntity to load annotations for
1547
 */
1548
function cdm_load_annotations(&$annotatable_entity) {
1549
  if (isset($annotatable_entity) && !isset($annotatable_entity->annotations)) {
1550
    $annotations = cdm_ws_getAnnotationsFor($annotatable_entity);
1551
    if (is_array($annotations)) {
1552
      $annotatable_entity->annotations = $annotations;
1553
    }
1554
  }
1555
}
1556

    
1557
/**
1558
 * Extends the $cdm_entity object by the field if it is not already existing.
1559
 *
1560
 * This function can only be used for fields with 1 to many relations.
1561
  *
1562
 * @param $cdm_base_type
1563
 * @param $field_name
1564
 * @param $cdm_entity
1565
 */
1566
function cdm_lazyload_array_field($cdm_base_type, $field_name, &$cdm_entity)
1567
{
1568
  if (!isset($cdm_entity->$field_name)) {
1569
    $items = cdm_ws_fetch_all('portal/' . $cdm_base_type . '/' . $cdm_entity->uuid . '/' . $field_name);
1570
    $cdm_entity->$field_name = $items;
1571
  }
1572
}
1573

    
1574

    
1575
/**
1576
 * Get a NomenclaturalReference string.
1577
 *
1578
 * Returns the NomenclaturalReference string with correctly placed
1579
 * microreference (= reference detail) e.g.
1580
 * in Phytotaxa 43: 1-48. 2012.
1581
 *
1582
 * @param string $referenceUuid
1583
 *   UUID of the reference.
1584
 * @param string $microreference
1585
 *   Reference detail.
1586
 *
1587
 * @return string
1588
 *   a NomenclaturalReference.
1589
 */
1590
function cdm_ws_getNomenclaturalReference($referenceUuid, $microreference) {
1591

    
1592
  // TODO the below statement avoids error boxes due to #4644 remove it once this ticket is solved
1593
  if(is_array($microreference) || is_object($microreference)) {
1594
    return '';
1595
  }
1596

    
1597
  $obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
1598
    $referenceUuid,
1599
  ), "microReference=" . urlencode($microreference));
1600

    
1601
  if ($obj) {
1602
    return $obj->String;
1603
  }
1604
  else {
1605
    return NULL;
1606
  }
1607
}
1608

    
1609
/**
1610
 * finds and returns the FeatureNode denoted by the given $feature_uuid
1611
 *
1612
 * @param $feature_tree_nodes
1613
 *    The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
1614
 * @param $feature_uuid
1615
 *    The UUID of the Feature
1616
 * @return returns the FeatureNode or null
1617
 */
1618
function &cdm_feature_tree_find_node($feature_tree_nodes, $feature_uuid){
1619

    
1620
  // 1. scan this level
1621
  foreach ($feature_tree_nodes as $node){
1622
    if($node->feature->uuid == $feature_uuid){
1623
      return $node;
1624
    }
1625
  }
1626

    
1627
  // 2. descend into childen
1628
  foreach ($feature_tree_nodes as $node){
1629
    if(is_array($node->childNodes)){
1630
      $node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
1631
      if($node) {
1632
        return $node;
1633
      }
1634
    }
1635
  }
1636
  $null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
1637
  return $null_var;
1638
}
1639

    
1640
/**
1641
 * Merges the given featureNodes structure with the descriptionElements.
1642
 *
1643
 * This method is used in preparation for rendering the descriptionElements.
1644
 * The descriptionElements which belong to a specific feature node are appended
1645
 * to a the feature node by creating a new field:
1646
 *  - descriptionElements: the CDM DescriptionElements which belong to this feature
1647
 * The descriptionElements will be cleared in advance in order to allow reusing the
1648
 * same feature tree without the risk of mixing sets of description elements.
1649
 *
1650
 * which originally is not existing in the cdm.
1651
 *
1652
 *
1653
 *
1654
 * @param array $featureNodes
1655
 *    An array of cdm FeatureNodes which may be hierarchical since feature nodes
1656
 *    may have children.
1657
 * @param array $descriptionElements
1658
 *    An flat array of cdm DescriptionElements
1659
 * @return array
1660
 *    The $featureNodes structure enriched with the according $descriptionElements
1661
 */
1662
function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
1663

    
1664
  foreach ($featureNodes as &$node) {
1665
    // since the $featureNodes array is reused for each description
1666
    // it is necessary to clear the custom node fields in advance
1667
    if(isset($node->descriptionElements)){
1668
      unset($node->descriptionElements);
1669
    }
1670

    
1671
    // Append corresponding elements to an additional node field:
1672
    // $node->descriptionElements.
1673
    foreach ($descriptionElements as $element) {
1674
      if ($element->feature->uuid == $node->feature->uuid) {
1675
        if (!isset($node->descriptionElements)) {
1676
          $node->descriptionElements = array();
1677
        }
1678
        $node->descriptionElements[] = $element;
1679
      }
1680
    }
1681

    
1682
    // Recurse into node children.
1683
    if (isset($node->childNodes[0])) {
1684
      $mergedChildNodes = _mergeFeatureTreeDescriptions($node->childNodes, $descriptionElements);
1685
      $node->childNodes = $mergedChildNodes;
1686
    }
1687

    
1688
    if(!isset($node->descriptionElements) && !isset($node->childNodes[0])){
1689
      unset($node);
1690
    }
1691

    
1692
  }
1693

    
1694
  return $featureNodes;
1695
}
1696

    
1697
/**
1698
 * Sends a GET or POST request to a CDM RESTService and returns a de-serialized object.
1699
 *
1700
 * The response from the HTTP GET request is returned as object.
1701
 * The response objects coming from the webservice configured in the
1702
 * 'cdm_webservice_url' variable are being cached in a level 1 (L1) and / or
1703
 *  in a level 2 (L2) cache.
1704
 *
1705
 * Since the L1 cache is implemented as static variable of the cdm_ws_get()
1706
 * function, this cache persists only per each single page execution.
1707
 * Any object coming from the webservice is stored into it by default.
1708
 * In contrast to this default caching mechanism the L2 cache only is used if
1709
 * the 'cdm_webservice_cache' variable is set to TRUE,
1710
 * which can be set using the modules administrative settings section.
1711
 * Objects stored in this L2 cache are serialized and stored
1712
 * using the drupal cache in the '{prefix}cache_cdm_ws' cache table. So the
1713
 * objects that are stored in the database will persist as
1714
 * long as the drupal cache is not being cleared and are available across
1715
 * multiple script executions.
1716
 *
1717
 * @param string $uri
1718
 *   URL to the webservice.
1719
 * @param array $pathParameters
1720
 *   An array of path parameters.
1721
 * @param string $query
1722
 *   A query string to be appended to the URL.
1723
 * @param string $method
1724
 *   The HTTP method to use, valid values are "GET" or "POST";
1725
 * @param bool $absoluteURI
1726
 *   TRUE when the URL should be treated as absolute URL.
1727
 *
1728
 * @return object| array
1729
 *   The de-serialized webservice response object.
1730
 */
1731
function cdm_ws_get($uri, $pathParameters = array(), $query = NULL, $method = "GET", $absoluteURI = FALSE) {
1732

    
1733
  static $cacheL1 = array();
1734

    
1735
  $data = NULL;
1736
  // store query string in $data and clear the query, $data will be set as HTTP request body
1737
  if($method == 'POST'){
1738
    $data = $query;
1739
    $query = NULL;
1740
  }
1741

    
1742
  // Transform the given uri path or pattern into a proper webservice uri.
1743
  if (!$absoluteURI) {
1744
    $uri = cdm_compose_url($uri, $pathParameters, $query);
1745
  }
1746
  cdm_ws_apply_classification_subtree_filter($uri);
1747

    
1748
  // read request parameter 'cacheL2_refresh'
1749
  // which allows refreshing the level 2 cache
1750
  $do_cacheL2_refresh = isset($_REQUEST['cacheL2_refresh']) && $_REQUEST['cacheL2_refresh'] == 1;
1751

    
1752
  $is_cdm_ws_uri = _is_cdm_ws_uri($uri);
1753
  $use_cacheL2 = variable_get('cdm_webservice_cache', 1);
1754

    
1755
  if($method == 'GET'){
1756
    $cache_key = $uri;
1757
  } else {
1758
    // sha1 creates longer hashes and thus will cause fewer collisions than md5.
1759
    // crc32 is faster but creates much shorter hashes
1760
    $cache_key = $uri . '[' . $method . ':' . sha1($data) .']';
1761
  }
1762

    
1763
  if (array_key_exists($cache_key, $cacheL1)) {
1764
    $cacheL1_obj = $cacheL1[$uri];
1765
  }
1766

    
1767
  $set_cacheL1 = FALSE;
1768
  if ($is_cdm_ws_uri && !isset($cacheL1_obj)) {
1769
    $set_cacheL1 = TRUE;
1770
  }
1771

    
1772
  // Only cache cdm webservice URIs.
1773
  $set_cacheL2 = $use_cacheL2 && $is_cdm_ws_uri && $set_cacheL1;
1774
  $cacheL2_entry = FALSE;
1775

    
1776
  if ($use_cacheL2 && !$do_cacheL2_refresh) {
1777
    // Try to get object from cacheL2.
1778
    $cacheL2_entry = cache_get($cache_key, 'cache_cdm_ws');
1779
  }
1780

    
1781
  if (isset($cacheL1_obj)) {
1782
    //
1783
    // The object has been found in the L1 cache.
1784
    //
1785
    $obj = $cacheL1_obj;
1786
    if (cdm_debug_block_visible()) {
1787
      cdm_ws_debug_add($uri, $method, $data, 0, 0, NULL, 'cacheL1');
1788
    }
1789
  }
1790
  elseif ($cacheL2_entry) {
1791
    //
1792
    // The object has been found in the L2 cache.
1793
    //
1794
    $duration_parse_start = microtime(TRUE);
1795
    $obj = unserialize($cacheL2_entry->data);
1796
    $duration_parse = microtime(TRUE) - $duration_parse_start;
1797

    
1798
    if (cdm_debug_block_visible()) {
1799
      cdm_ws_debug_add($uri, $method, $data, 0, $duration_parse, NULL, 'cacheL2');
1800
    }
1801
  }
1802
  else {
1803
    //
1804
    // Get the object from the webservice and cache it.
1805
    //
1806
    $duration_fetch_start = microtime(TRUE);
1807
    // Request data from webservice JSON or XML.
1808
    $response = cdm_http_request($uri, $method, $data);
1809
    $response_body = NULL;
1810
    if (isset($response->data)) {
1811
      $response_body = $response->data;
1812
    }
1813
    $duration_fetch = microtime(TRUE) - $duration_fetch_start;
1814
    $duration_parse_start = microtime(TRUE);
1815

    
1816
    // Parse data and create object.
1817
    $obj = cdm_load_obj($response_body);
1818

    
1819
    $duration_parse = microtime(TRUE) - $duration_parse_start;
1820

    
1821
    if (cdm_debug_block_visible()) {
1822
      if ($obj || $response_body == "[]") {
1823
        $status = 'valid';
1824
      }
1825
      else {
1826
        $status = 'invalid';
1827
      }
1828
      cdm_ws_debug_add($uri, $method, $data, $duration_fetch, $duration_parse, strlen($response_body), $status);
1829
    }
1830
    if ($set_cacheL2) {
1831
      // Store the object in cache L2.
1832
      // Comment @WA perhaps better if Drupal serializedatas here? Then the
1833
      // flag serialized is set properly in the cache table.
1834
      cache_set($cache_key, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
1835
    }
1836
  }
1837
  if ($obj) {
1838
    // Store the object in cache L1.
1839
    if ($set_cacheL1) {
1840
      $cacheL1[$cache_key] = $obj;
1841
    }
1842
  }
1843
  return $obj;
1844
}
1845

    
1846
function cdm_ws_apply_classification_subtree_filter(&$uri){
1847

    
1848
  $classification_subtree_filter_patterns = &drupal_static('classification_subtree_filter_patterns', array(
1849
    "#/classification/[0-9a-f\-]{36}/childNodes#",
1850
    /* covered by above pattern:
1851
    "#/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
1852
    '#/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
1853
    */
1854
    "#/portal/classification/[0-9a-f\-]{36}/childNodes#",
1855
    /* covered by above pattern:
1856
    "#/portal/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
1857
    '#/portal/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
1858
    */
1859
    '#/portal/classification/[0-9a-f\-]{36}/pathFrom/[0-9a-f\-]{36}#',
1860
    "#/portal/taxon/search#",
1861
    "#/portal/taxon/find#",
1862
    /* covered by above pattern:
1863
    "#/portal/taxon/findByDescriptionElementFullText#",
1864
    "#/portal/taxon/findByFullText#",
1865
    "#/portal/taxon/findByEverythingFullText#",
1866
    "#/portal/taxon/findByIdentifier#",
1867
    "#/portal/taxon/findByMarker#",
1868
    "#/portal/taxon/findByMarker#",
1869
    "#/portal/taxon/findByMarker#",
1870
    */
1871
    "#/portal/taxon/[0-9a-f\-]{36}#"
1872
    /* covered by above pattern:
1873
    "#/portal/taxon/[0-9a-f\-]{36}/taxonNodes#",
1874
    */
1875
  ));
1876

    
1877
  $sub_tree_filter_uuid_value = variable_get(CDM_SUB_TREE_FILTER_UUID, FALSE);
1878
  if(is_uuid($sub_tree_filter_uuid_value)){
1879
    foreach($classification_subtree_filter_patterns as $preg_pattern){
1880
      if(preg_match($preg_pattern, $uri)){
1881
        // no need to take care for uri fragments with ws uris!
1882
        if(strpos( $uri, '?')){
1883
          $uri .= '&subtree=' . $sub_tree_filter_uuid_value;
1884
        } else {
1885
          $uri .= '?subtree='. $sub_tree_filter_uuid_value;
1886
        }
1887
        break;
1888
      }
1889
    }
1890
  }
1891

    
1892
}
1893
/**
1894
 * Processes and stores the given information in $_SESSION['cdm']['ws_debug'] as table row.
1895
 *
1896
 * The cdm_ws_debug block will display the debug information.
1897
 *
1898
 * @param $uri
1899
 *    The CDM REST URI to which the request has been send
1900
 * @param string $method
1901
 *    The HTTP request method, either 'GET' or 'POST'
1902
 * @param string $post_data
1903
 *    The datastring send with a post request
1904
 * @param $duration_fetch
1905
 *    The time in seconds it took to fetch the data from the web service
1906
 * @param $duration_parse
1907
 *    Time in seconds which was needed to parse the json response
1908
 * @param $datasize
1909
 *    Size of the data received from the server
1910
 * @param $status
1911
 *    A status string, possible values are: 'valid', 'invalid', 'cacheL1', 'cacheL2'
1912
 * @return bool
1913
 *    TRUE if adding the debug information was successful
1914
 */
1915
function cdm_ws_debug_add($uri, $method, $post_data, $duration_fetch, $duration_parse, $datasize, $status) {
1916

    
1917
  static $initial_time = NULL;
1918
  if(!$initial_time) {
1919
    $initial_time = microtime(TRUE);
1920
  }
1921
  $time = microtime(TRUE) - $initial_time;
1922

    
1923
  // Decompose uri into path and query element.
1924
  $uri_parts = explode("?", $uri);
1925
  $query = array();
1926
  if (count($uri_parts) == 2) {
1927
    $path = $uri_parts[0];
1928
  }
1929
  else {
1930
    $path = $uri;
1931
  }
1932

    
1933
  if(strpos($uri, '?') > 0){
1934
    $json_uri = str_replace('?', '.json?', $uri);
1935
    $xml_uri = str_replace('?', '.xml?', $uri);
1936
  } else {
1937
    $json_uri = $uri . '.json';
1938
    $xml_uri = $json_uri . '.xml';
1939
  }
1940

    
1941
  // data links to make data accecsible as json and xml
1942
  $data_links = '';
1943
  if (_is_cdm_ws_uri($path)) {
1944

    
1945
    // see ./js/http-method-link.js
1946

    
1947
    if($method == 'GET'){
1948
      $data_links .= '<a href="' . $xml_uri . '" target="data">xml</a>-';
1949
      $data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">proxied</a>';
1950
      $data_links .= '<br/>';
1951
      $data_links .= '<a href="' . $json_uri . '" target="data">json</a>-';
1952
      $data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">proxied</a>';
1953
    } else {
1954
      $js_link_activation = 'class="http-' . $method . '-link" data-cdm-http-post="' . $post_data . '" type="application/x-www-form-urlencoded"';
1955
      $data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">xml-proxied</a>';
1956
      $data_links .= '<br/>';
1957
      $data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">json-proxied</a>';
1958
    }
1959
  }
1960
  else {
1961
    $data_links .= '<a href="' . $uri . '" target="data">open</a>';
1962
  }
1963

    
1964
  //
1965
  $data = array(
1966
      'ws_uri' => $uri,
1967
      'method' => $method,
1968
      'post_data' => $post_data,
1969
      'time' => sprintf('%3.3f', $time),
1970
      'fetch_seconds' => sprintf('%3.3f', $duration_fetch),
1971
      'parse_seconds' => sprintf('%3.3f', $duration_parse),
1972
      'size_kb' => sprintf('%3.1f', ($datasize / 1024)) ,
1973
      'status' => $status,
1974
      'data_links' => $data_links
1975
  );
1976
  if (!isset($_SESSION['cdm']['ws_debug'])) {
1977
    $_SESSION['cdm']['ws_debug'] = array();
1978
  }
1979
  $_SESSION['cdm']['ws_debug'][] = serialize($data);
1980

    
1981
  // Mark this page as being uncacheable.
1982
  // taken over from drupal_get_messages() but it is unsure if we really need this here
1983
  drupal_page_is_cacheable(FALSE);
1984

    
1985
  // Messages not set when DB connection fails.
1986
  return isset($_SESSION['cdm']['ws_debug']) ? $_SESSION['cdm']['ws_debug'] : NULL;
1987
}
1988

    
1989
/**
1990
 * helper function to dtermine if the cdm_debug_block should be displayed or not
1991
 * the visibility depends on whether
1992
 *  - the block is enabled
1993
 *  - the visibility restrictions in the block settings are satisfied
1994
 */
1995
function cdm_debug_block_visible() {
1996
  static $is_visible = null;
1997

    
1998
  if($is_visible === null){
1999
      $block = block_load('cdm_api', 'cdm_ws_debug');
2000
      $is_visible = isset($block->status) && $block->status == 1;
2001
      if($is_visible){
2002
        $blocks = array($block);
2003
        // Checks the page, user role, and user-specific visibilty settings.
2004
        block_block_list_alter($blocks);
2005
        $is_visible = count($blocks) > 0;
2006
      }
2007
  }
2008
  return $is_visible;
2009
}
2010

    
2011
/**
2012
 * @todo Please document this function.
2013
 * @see http://drupal.org/node/1354
2014
 */
2015
function cdm_load_obj($response_body) {
2016
  $obj = json_decode($response_body);
2017

    
2018
  if (!(is_object($obj) || is_array($obj))) {
2019
    ob_start();
2020
    $obj_dump = ob_get_contents();
2021
    ob_clean();
2022
    return FALSE;
2023
  }
2024

    
2025
  return $obj;
2026
}
2027

    
2028
/**
2029
 * Do a http request to a CDM RESTful web service.
2030
 *
2031
 * @param string $uri
2032
 *   The webservice url.
2033
 * @param string $method
2034
 *   The HTTP method to use, valid values are "GET" or "POST"; defaults to
2035
 *   "GET" even if NULL, FALSE or any invalid value is supplied.
2036
 * @param $data: A string containing the request body, formatted as
2037
 *     'param=value&param=value&...'. Defaults to NULL.
2038
 *
2039
 * @return object
2040
 *   The object as returned by drupal_http_request():
2041
 *   An object that can have one or more of the following components:
2042
 *   - request: A string containing the request body that was sent.
2043
 *   - code: An integer containing the response status code, or the error code
2044
 *     if an error occurred.
2045
 *   - protocol: The response protocol (e.g. HTTP/1.1 or HTTP/1.0).
2046
 *   - status_message: The status message from the response, if a response was
2047
 *     received.
2048
 *   - redirect_code: If redirected, an integer containing the initial response
2049
 *     status code.
2050
 *   - redirect_url: If redirected, a string containing the URL of the redirect
2051
 *     target.
2052
 *   - error: If an error occurred, the error message. Otherwise not set.
2053
 *   - headers: An array containing the response headers as name/value pairs.
2054
 *     HTTP header names are case-insensitive (RFC 2616, section 4.2), so for
2055
 *     easy access the array keys are returned in lower case.
2056
 *   - data: A string containing the response body that was received.
2057
 */
2058
function cdm_http_request($uri, $method = "GET", $data = NULL) {
2059
  static $acceptLanguage = NULL;
2060
  $header = array();
2061
  
2062
  if(!$acceptLanguage && module_exists('i18n')){
2063
    $acceptLanguage = i18n_language_content()->language;
2064
  }
2065

    
2066
  if (!$acceptLanguage) {
2067
    if (function_exists('apache_request_headers')) {
2068
      $headers = apache_request_headers();
2069
      if (isset($headers['Accept-Language'])) {
2070
        $acceptLanguage = $headers['Accept-Language'];
2071
      }
2072
    }
2073
  }
2074

    
2075
  if ($method != "GET" && $method != "POST") {
2076
    drupal_set_message('cdm_api.module#cdm_http_request() : unsupported HTTP request method ', 'error');
2077
  }
2078

    
2079
  if (_is_cdm_ws_uri($uri)) {
2080
    $header['Accept'] = 'application/json';
2081
    $header['Accept-Language'] = $acceptLanguage;
2082
    $header['Accept-Charset'] = 'UTF-8';
2083
  }
2084

    
2085
  if($method == "POST") {
2086
    // content type is application/x-www-form-urlencoded, so the request body uses the same format as the query string
2087
    $header['Content-Type'] = 'application/x-www-form-urlencoded';
2088
  }
2089

    
2090

    
2091
  cdm_dd($uri);
2092
  return drupal_http_request($uri, array(
2093
      'headers' => $header,
2094
      'method' => $method,
2095
      'data' => $data,
2096
      'timeout' => CDM_HTTP_REQUEST_TIMEOUT
2097
      )
2098
   );
2099
}
2100

    
2101
/**
2102
 * Concatenates recursively the fields of all features contained in the given
2103
 * CDM FeatureTree root node.
2104
 *
2105
 * @param $rootNode
2106
 *     A CDM FeatureTree node
2107
 * @param
2108
 *     The character to be used as glue for concatenation, default is ', '
2109
 * @param $field_name
2110
 *     The field name of the CDM Features
2111
 * @param $excludes
2112
 *     Allows defining a set of values to be excluded. This refers to the values
2113
 *     in the field denoted by the $field_name parameter
2114
 *
2115
 */
2116
function cdm_featureTree_elements_toString($root_node, $separator = ', ', $field_name = 'representation_L10n', $excludes = array()) {
2117
  $out = '';
2118

    
2119
  $pre_child_separator = $separator;
2120
  $post_child_separator = '';
2121

    
2122
  foreach ($root_node->childNodes as $feature_node) {
2123
    $out .= ($out ? $separator : '');
2124
    if(!in_array($feature_node->feature->$field_name, $excludes)) {
2125
      $out .= $feature_node->feature->$field_name;
2126
      if (is_array($feature_node->childNodes) && count($feature_node->childNodes) > 0) {
2127
        $childlabels = cdm_featureTree_elements_toString($feature_node, $separator, $field_name);
2128
        if (strlen($childlabels)) {
2129
            $out .=  $pre_child_separator . $childlabels . $post_child_separator;
2130
        }
2131
      }
2132
    }
2133
  }
2134
  return $out;
2135
}
2136

    
2137
/**
2138
 * Create a one-dimensional form options array.
2139
 *
2140
 * Creates an array of all features in the feature tree of feature nodes,
2141
 * the node labels are indented by $node_char and $childIndent depending on the
2142
 * hierachy level.
2143
 *
2144
 * @param - $rootNode
2145
 * @param - $node_char
2146
 * @param - $childIndentStr
2147
 * @param - $childIndent
2148
 *   ONLY USED INTERNALLY!
2149
 *
2150
 * @return array
2151
 *   A one dimensional Drupal form options array.
2152
 */
2153
function _featureTree_nodes_as_feature_options($rootNode, $node_char = "&#9500;&#9472; ", $childIndentStr = '&nbsp;', $childIndent = '') {
2154
  $options = array();
2155
  foreach ($rootNode->childNodes as $featureNode) {
2156
    $indent_prefix = '';
2157
    if ($childIndent) {
2158
      $indent_prefix = $childIndent . $node_char . " ";
2159
    }
2160
    $options[$featureNode->feature->uuid] = $indent_prefix . $featureNode->feature->representation_L10n;
2161
    if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2162
      // Foreach ($featureNode->childNodes as $childNode){
2163
      $childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
2164
      $options = array_merge_recursive($options, $childList);
2165
      // }
2166
    }
2167
  }
2168
  return $options;
2169
}
2170

    
2171
/**
2172
 * Returns an array with all available FeatureTrees and the representations of the selected
2173
 * FeatureTree as a detail view.
2174
 *
2175
 * @param boolean $add_default_feature_free
2176
 * @return array
2177
 *  associative array with following keys:
2178
 *  -options: Returns an array with all available Feature Trees
2179
 *  -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
2180
 *
2181
 */
2182
function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE) {
2183

    
2184
  $options = array();
2185
  $tree_representations = array();
2186
  $feature_trees = array();
2187

    
2188
  // Set tree that contains all features.
2189
  if ($add_default_feature_free) {
2190
    $options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
2191
    $feature_trees[] = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
2192
  }
2193

    
2194
  // Get feature trees from database.
2195
  $persited_trees = cdm_ws_fetch_all(CDM_WS_FEATURETREES);
2196
  if (is_array($persited_trees)) {
2197
    $feature_trees = array_merge($feature_trees, $persited_trees);
2198
  }
2199

    
2200
  foreach ($feature_trees as $featureTree) {
2201

    
2202
    if(!is_object($featureTree)){
2203
      continue;
2204
    }
2205
    // Do not add the DEFAULT_FEATURETREE again,
2206
    if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
2207
      $options[$featureTree->uuid] = $featureTree->titleCache;
2208
    }
2209

    
2210
    // Render the hierarchic tree structure
2211
    if (is_array( $featureTree->root->childNodes) && count( $featureTree->root->childNodes) > 0) {
2212

    
2213
      // Render the hierarchic tree structure.
2214
      $treeDetails = '<div class="featuretree_structure">'
2215
        . theme('FeatureTree_hierarchy', array('FeatureTreeUuid' =>  $featureTree->uuid))
2216
        . '</div>';
2217

    
2218
      $form = array();
2219
      $form['featureTree-' .  $featureTree->uuid] = array(
2220
        '#type' => 'fieldset',
2221
        '#title' => 'Show details',
2222
        '#attributes' => array('class' => array('collapsible collapsed')),
2223
        // '#collapsible' => TRUE,
2224
        // '#collapsed' => TRUE,
2225
      );
2226
      $form['featureTree-' .  $featureTree->uuid]['details'] = array(
2227
        '#markup' => $treeDetails,
2228
      );
2229

    
2230
      $tree_representations[$featureTree->uuid] = drupal_render($form);
2231
    }
2232

    
2233
  } // END loop over feature trees
2234

    
2235
  // return $options;
2236
  return array('options' => $options, 'treeRepresentations' => $tree_representations);
2237
}
2238

    
2239
/**
2240
 * Provides the list of available classifications in form of an options array.
2241
 *
2242
 * The options array is suitable for drupal form API elements that allow multiple choices.
2243
 * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
2244
 *
2245
 * The classifications are ordered alphabetically whereas the classification
2246
 * chosen as default will always appear on top of the array, followed by a
2247
 * blank line below.
2248
 *
2249
 * @param bool $add_none_option
2250
 *   is true an addtional 'none' option will be added, optional parameter, defaults to FALSE
2251
 *
2252
 * @return array
2253
 *   classifications in an array as options for a form element that allows multiple choices.
2254
 */
2255
function cdm_get_taxontrees_as_options($add_none_option = FALSE) {
2256

    
2257
  $taxonTrees = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
2258

    
2259
  $default_classification_uuid = variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
2260
  $default_classification_label = '';
2261

    
2262
  // add all classifications
2263
  $taxonomic_tree_options = array();
2264
  if ($add_none_option) {
2265
    $taxonomic_tree_options['NONE'] = ' '; // one Space character at beginning to force on top;
2266
  }
2267
  if ($taxonTrees) {
2268
    foreach ($taxonTrees as $tree) {
2269
      if (!$default_classification_uuid || $default_classification_uuid != $tree->uuid) {
2270
        $taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
2271
      } else {
2272
        $taxonomic_tree_options[$tree->uuid] = '  '; // two Space characters to force on top but below 'none' option , will be replaced below by titleCache
2273
        $default_classification_label = $tree->titleCache;
2274
      }
2275
    }
2276
  }
2277
  // oder alphabetically the space
2278
  asort($taxonomic_tree_options);
2279

    
2280
  // now set the labels
2281
  //   for none
2282
  if ($add_none_option) {
2283
    $taxonomic_tree_options['NONE'] =t('--- ALL ---');
2284
  }
2285

    
2286
  //   for default_classification
2287
  if (is_uuid($default_classification_uuid)) {
2288
    $taxonomic_tree_options[$default_classification_uuid] =
2289
      $default_classification_label ? $default_classification_label : '--- INVALID CHOICE ---'
2290
      . (count($taxonTrees) > 1 ? ' [' . t('DEFAULT CLASSIFICATION') . ']': '');
2291
  }
2292

    
2293
  return $taxonomic_tree_options;
2294
}
2295

    
2296
/**
2297
 * @todo Please document this function.
2298
 * @see http://drupal.org/node/1354
2299
 */
2300
function cdm_api_secref_cache_prefetch(&$secUuids) {
2301
  // Comment @WA: global variables should start with a single underscore
2302
  // followed by the module and another underscore.
2303
  global $_cdm_api_secref_cache;
2304
  if (!is_array($_cdm_api_secref_cache)) {
2305
    $_cdm_api_secref_cache = array();
2306
  }
2307
  $uniqueUuids = array_unique($secUuids);
2308
  $i = 0;
2309
  $param = '';
2310
  while ($i++ < count($uniqueUuids)) {
2311
    $param .= $secUuids[$i] . ',';
2312
    if (strlen($param) + 37 > 2000) {
2313
      _cdm_api_secref_cache_add($param);
2314
      $param = '';
2315
    }
2316
  }
2317
  if ($param) {
2318
    _cdm_api_secref_cache_add($param);
2319
  }
2320
}
2321

    
2322
/**
2323
 * @todo Please document this function.
2324
 * @see http://drupal.org/node/1354
2325
 */
2326
function cdm_api_secref_cache_get($secUuid) {
2327
  global $_cdm_api_secref_cache;
2328
  if (!is_array($_cdm_api_secref_cache)) {
2329
    $_cdm_api_secref_cache = array();
2330
  }
2331
  if (!array_key_exists($secUuid, $_cdm_api_secref_cache)) {
2332
    _cdm_api_secref_cache_add($secUuid);
2333
  }
2334
  return $_cdm_api_secref_cache[$secUuid];
2335
}
2336

    
2337
/**
2338
 * @todo Please document this function.
2339
 * @see http://drupal.org/node/1354
2340
 */
2341
function cdm_api_secref_cache_clear() {
2342
  global $_cdm_api_secref_cache;
2343
  $_cdm_api_secref_cache = array();
2344
}
2345

    
2346

    
2347
/**
2348
 * Validates if the given string is a uuid.
2349
 *
2350
 * @param string $str
2351
 *   The string to validate.
2352
 *
2353
 * return bool
2354
 *   TRUE if the string is a UUID.
2355
 */
2356
function is_uuid($str) {
2357
  return is_string($str) && strlen($str) == 36 && strpos($str, '-');
2358
}
2359

    
2360
/**
2361
 * Checks if the given $object is a valid cdm entity.
2362
 *
2363
 * An object is considered a cdm entity if it has a string field $object->class
2364
 * with at least 3 characters and if it has a valid uuid in $object->uuid.
2365
 * The function is null save.
2366
 *
2367
 * @author a.kohlbecker <a.kohlbecker@bgbm.org>
2368
 *
2369
 * @param mixed $object
2370
 *   The object to validate
2371
 *
2372
 * @return bool
2373
 *   True if the object is a cdm entity.
2374
 */
2375
function is_cdm_entity($object) {
2376
  return
2377
    isset($object->class) && is_string($object->class) && strlen($object->class) > 2 && $object->class != 'TypedEntityReference'
2378
    && is_string($object->uuid) && is_uuid($object->uuid);
2379
}
2380

    
2381
/**
2382
 * @todo Please document this function.
2383
 * @see http://drupal.org/node/1354
2384
 */
2385
function _cdm_api_secref_cache_add($secUuidsStr) {
2386
  global $_cdm_api_secref_cache;
2387
  $ref = cdm_ws_get(CDM_WS_REFERENCE, $secUuidsStr);
2388
  // Batch fetching not jet reimplemented thus:
2389
  /*
2390
  $assocRefSTOs = array(); if($refSTOs) { foreach($refSTOs as $ref){
2391
  $assocRefSTOs[$ref->uuid] = $ref; } $_cdm_api_secref_cache =
2392
  array_merge($_cdm_api_secref_cache, $assocRefSTOs); }
2393
  */
2394
  $_cdm_api_secref_cache[$ref->uuid] = $ref;
2395
}
2396

    
2397
/**
2398
 * Checks if the given uri starts with a cdm webservice url.
2399
 *
2400
 * Checks if the uri starts with the cdm webservice url stored in the
2401
 * Drupal variable 'cdm_webservice_url'.
2402
 * The 'cdm_webservice_url' can be set in the admins section of the portal.
2403
 *
2404
 * @param string $uri
2405
 *   The URI to test.
2406
 *
2407
 * @return bool
2408
 *   True if the uri starts with a cdm webservice url.
2409
 */
2410
function _is_cdm_ws_uri($uri) {
2411
  return str_beginsWith($uri, variable_get('cdm_webservice_url', '#EMPTY#'));
2412
}
2413

    
2414
/**
2415
 * @todo Please document this function.
2416
 * @see http://drupal.org/node/1354
2417
 */
2418
function queryString($elements) {
2419
  $query = '';
2420
  foreach ($elements as $key => $value) {
2421
    if (is_array($value)) {
2422
      foreach ($value as $v) {
2423
        $query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($v);
2424
      }
2425
    }
2426
    else {
2427
      $query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($value);
2428
    }
2429
  }
2430
  return $query;
2431
}
2432

    
2433
/**
2434
 * Implementation of the magic method __clone to allow deep cloning of objects
2435
 * and arrays.
2436
 */
2437
function __clone() {
2438
  foreach ($this as $name => $value) {
2439
    if (gettype($value) == 'object' || gettype($value) == 'array') {
2440
      $this->$name = clone($this->$name);
2441
    }
2442
  }
2443
}
2444

    
2445
/**
2446
 * Compares the given CDM Term instances by the  representationL10n.
2447
 *
2448
 * Can also be used with TermDTOs. To be used in usort()
2449
 *
2450
 * @see http://php.net/manual/en/function.usort.php
2451
 *
2452
 * @param $term1
2453
 *   The first CDM Term instance
2454
 * @param $term2
2455
 *   The second CDM Term instance
2456
 * @return int
2457
 *   The result of the comparison
2458
 */
2459
function compare_terms_by_representationL10n($term1, $term2) {
2460

    
2461
  if (!isset($term1->representation_L10n)) {
2462
    $term1->representationL10n = '';
2463
  }
2464
  if (!isset($term2->representation_L10n)) {
2465
    $term2->representationL10n = '';
2466
  }
2467

    
2468
  return strcmp($term1->representation_L10n, $term2->representation_L10n);
2469
}
2470

    
2471
function compare_terms_by_order_index($term1, $term2) {
2472

    
2473

    
2474
  if (!isset($term1->orderIndex)) {
2475
    $a = 0;
2476
  } else {
2477
    $a = $term1->orderIndex;
2478
  }
2479
  if (!isset($term2->orderIndex)) {
2480
    $b = 0;
2481
  } else {
2482
    $b = $term2->orderIndex;
2483
  }
2484

    
2485
  if ($a == $b) {
2486
    return 0;
2487
  }
2488
  return ($a < $b) ? -1 : 1;
2489

    
2490
}
2491

    
2492

    
2493
/**
2494
 * Make a 'deep copy' of an array.
2495
 *
2496
 * Make a complete deep copy of an array replacing
2497
 * references with deep copies until a certain depth is reached
2498
 * ($maxdepth) whereupon references are copied as-is...
2499
 *
2500
 * @see http://us3.php.net/manual/en/ref.array.php
2501
 *
2502
 * @param array $array
2503
 * @param array $copy passed by reference
2504
 * @param int $maxdepth
2505
 * @param int $depth
2506
 */
2507
function array_deep_copy(&$array, &$copy, $maxdepth = 50, $depth = 0) {
2508
  if ($depth > $maxdepth) {
2509
    $copy = $array;
2510
    return;
2511
  }
2512
  if (!is_array($copy)) {
2513
    $copy = array();
2514
  }
2515
  foreach ($array as $k => &$v) {
2516
    if (is_array($v)) {
2517
      array_deep_copy($v, $copy[$k], $maxdepth, ++$depth);
2518
    }
2519
    else {
2520
      $copy[$k] = $v;
2521
    }
2522
  }
2523
}
2524

    
2525
/**
2526
 * Adds java script to create and enable a toggler for the cdm webservice debug block content.
2527
 *
2528
 */
2529
function _add_js_ws_debug() {
2530

    
2531
  $data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.min.js';
2532
  $colorbox_js = '/js/colorbox/jquery.colorbox-min.js';
2533
  if (variable_get('cdm_js_devel_mode', FALSE)) {
2534
    // use the developer versions of js libs
2535
    $data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.js';
2536
    $colorbox_js = '/js/colorbox/jquery.colorbox.js';
2537
  }
2538
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $data_tables_js,
2539
    array(
2540
      'type' => 'file',
2541
      'weight' => JS_LIBRARY,
2542
      'cache' => TRUE)
2543
    );
2544

    
2545
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $colorbox_js,
2546
    array(
2547
      'type' => 'file',
2548
      'weight' => JS_LIBRARY,
2549
      'cache' => TRUE)
2550
    );
2551
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/colorbox/colorbox.css');
2552
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/DataTables-1.9.4/media/css/cdm_debug_table.css');
2553

    
2554
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ws_debug_block.js',
2555
    array(
2556
      'type' => 'file',
2557
      'weight' => JS_LIBRARY,
2558
      'cache' => TRUE)
2559
    );
2560
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/http-method-link.js',
2561
    array(
2562
    'type' => 'file',
2563
    'weight' => JS_LIBRARY,
2564
    'cache' => TRUE)
2565
    );
2566

    
2567
}
2568

    
2569
/**
2570
 * @todo Please document this function.
2571
 * @see http://drupal.org/node/1354
2572
 */
2573
function _no_classfication_uuid_message() {
2574
  if (!cdm_ws_get(CDM_WS_PORTAL_TAXONOMY)) {
2575
    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.');
2576
  }
2577
  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.');
2578
}
2579

    
2580
/**
2581
 * Implementation of hook flush_caches
2582
 *
2583
 * Add custom cache tables to the list of cache tables that
2584
 * will be cleared by the Clear button on the Performance page or whenever
2585
 * drupal_flush_all_caches is invoked.
2586
 *
2587
 * @author W.Addink <waddink@eti.uva.nl>
2588
 *
2589
 * @return array
2590
 *   An array with custom cache tables to include.
2591
 */
2592
function cdm_api_flush_caches() {
2593
  return array('cache_cdm_ws');
2594
}
2595

    
2596
/**
2597
 * Logs if the drupal variable 'cdm_debug_mode' ist set true to drupal_debug.txt in the site's temp directory.
2598
 *
2599
 * @param $data
2600
 *   The variable to log to the drupal_debug.txt log file.
2601
 * @param $label
2602
 *   (optional) If set, a label to output before $data in the log file.
2603
 *
2604
 * @return
2605
 *   No return value if successful, FALSE if the log file could not be written
2606
 *   to.
2607
 *
2608
 * @see cdm_dataportal_init() where the log file is reset on each requests
2609
 * @see dd()
2610
 * @see http://drupal.org/node/314112
2611
 *
2612
 */
2613
function cdm_dd($data, $label = NULL) {
2614
  if(module_exists('devel') && variable_get('cdm_debug_mode', FALSE) && file_stream_wrapper_get_class('temporary') ){
2615
    return dd($data, $label);
2616
  }
2617
}
2618

    
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