modules/cdm_dataportal/cdm_dataportal.search.php

   1 <?php
   2 /**
   3  * @file
   4  * Search related functions.
   5  */
   6
   7 const SESSION_KEY_SEARCH_REGISTRATION_FILTER = "SESSION_KEY_SEARCH_REGISTRATION_FILTER";
   8 const SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER = 'SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER';
   9 const SESSION_KEY_SEARCH_AGENT_FILTER = 'SEARCH_AGENT_FILTER';
  10
  11 /**
  12  * Returns a Drupal path to a search form for a CDM webservice.
  13  *
  14  * For a given CDM webservice end-point, the drupal page path to the
  15  * according search form is returned.
  16  * cdm webservice end points are defined in constant variables like:
  17  * <code>CDM_WS_PORTAL_TAXON_FIND</code> and
  18  * <code>CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT</code>
  19  *
  20  * @param string $ws_endpoint
  21  *   The cdm webservice endpoint for which to find the search form path.
  22  *
  23  * @return string
  24  *   The Drupal path found.
  25  */
  26 function cdm_dataportal_search_form_path_for_ws($ws_endpoint) {
  27   static $form_ws_map = array(
  28     CDM_WS_PORTAL_TAXON_FIND => "cdm_dataportal/search",
  29     CDM_WS_PORTAL_TAXON_SEARCH => "cdm_dataportal/search",
  30     CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT => "cdm_dataportal/search/taxon_by_description",
  31   );
  32   return $form_ws_map[$ws_endpoint];
  33 }
  34
  35 /**
  36  * Prepares a form array for a general purpose search form.
  37  *
  38  * The form is used for general purpose search functionality in the
  39  * dataportal. The form returned is populated with all necessary fields
  40  * for internal processing and has the textfield element $form['query']
  41  * which holds the query term.
  42  *
  43  * @param string $action_path
  44  *   The Drupal path to be put into the action url to which the form will
  45  *   be submitted.
  46  * @param string $search_webservice
  47  *   The cdm-remote webservice to be used, valid values are defined by
  48  *   the constants: FIXME.
  49  * @param string $query_field_default_value
  50  *   A default text for the query field
  51  * @param string $query_field_description
  52  *   The description text for the query field
  53  *
  54  * @return array
  55  *   The prepared form array.
  56  */
  57 function cdm_dataportal_search_form_prepare($action_path, $search_webservice, $query_field_default_value, $query_field_description) {
  58
  59
  60   $form['#method'] = 'get';
  61   $form['#action'] = url($action_path, array(
  62     'absolute' => TRUE,
  63   ));
  64
  65   $form['ws'] = array(
  66     '#type' => 'hidden',
  67     '#value' => $search_webservice,
  68     '#name' => 'ws',
  69   );
  70
  71   $form['query'] = array(
  72     '#weight' => 0,
  73     '#type' => 'textfield',
  74     '#size' => 68,
  75     // This causes the description to display also when hovering over
  76     // the textfield.
  77     // This is wanted behaviour for the simple seach but could
  78     // be disabled for the advances search.
  79     '#attributes' => array(
  80       'title' => $query_field_description,
  81     ),
  82     '#description' => $query_field_description,
  83     '#value' => $query_field_default_value,
  84     // '#description' => $query_field_description,
  85   );
  86   if(variable_get(SIMPLE_SEARCH_AUTO_SUGGEST)){
  87       $form['query']['#autocomplete_path'] = 'cdm_dataportal/taxon/autosuggest////';
  88   }
  89
  90     $form['search'] = array(
  91     '#weight' => 3,
  92     '#tree' => TRUE,
  93     // '#type' => $advanced_form ? 'fieldset': 'hidden',
  94     '#title' => t('Options'),
  95   );
  96
  97   // Clean URL get forms breaks if we don't give it a 'q'.
  98   if (!(bool) variable_get('clean_url', '0')) {
  99     $form['search']['q'] = array(
 100       '#type' => 'hidden',
 101       '#value' => $action_path,
 102       '#name' => 'q',
 103     );
 104   }
 105
 106   $form['submit'] = array(
 107     '#weight' => 5,
 108     '#type' => 'submit',
 109     '#name' => '',
 110     '#value' => t('Search'),
 111   );
 112
 113   return $form;
 114 }
 115
 116 function cdm_dataportal_taxon_autosuggest($classificationUuid = NULL, $areaUuid = NULL, $status = NULL, $string) {
 117   $matches = array();
 118
 119   $queryParams = array();
 120   $queryParams['query'] = $string.'*';
 121   if((is_null($classificationUuid) || $classificationUuid=='') && isset($_SESSION['cdm']['taxonomictree_uuid'])){
 122     $classificationUuid = $_SESSION['cdm']['taxonomictree_uuid'];// if no classification uuid is set use the current one
 123   }
 124   if($classificationUuid){
 125     $queryParams['classificationUuid'] = $classificationUuid;
 126   }
 127   if($areaUuid){
 128     $queryParams['area'] = $areaUuid;
 129   }
 130   if($status){
 131     $queryParams['status'] = $status ;
 132   }
 133   $queryParams['pageIndex'] = '0';
 134   $queryParams['pageSize'] = '10';
 135   $queryParams['doTaxa'] = true;
 136   $queryParams['doSynonyms'] = true;
 137   $queryParams['doMisappliedNames'] = true;
 138   $queryParams['doTaxaByCommonNames'] = true;
 139
 140   $search_results = cdm_ws_get(CDM_WS_TAXON_SEARCH, NULL, queryString($queryParams));
 141   foreach($search_results->records as $record){
 142       $titleCache = $record->entity->titleCache;
 143       preg_match('/(.*) sec.*/', $titleCache, $trimmedTitle); //remove sec reference
 144       $trimmedTitle = trim($trimmedTitle[1]);
 145       $matches[$trimmedTitle] = check_plain($trimmedTitle);
 146   }
 147   drupal_json_output($matches);
 148 }
 149
 150
 151   /**
 152  * Creates a search form for searching on taxa.
 153  *
 154  * If advanced $advanced_form id TRUE the form will offer additional choices
 155  *
 156  * @param array $form
 157  *   A drupal form array
 158  * @param array $form_state
 159  *   The drupal form state passed as reference
 160  * @param bool $advanced_form
 161  *   default is FALSE
 162  * @param bool $classification_select
 163  *   set TRUE to offer a classification selector in the form - default is FALSE
 164  *   if only available in the advanced mode
 165  *
 166  * @return array
 167  *   the form array
 168  */
 169 function cdm_dataportal_search_taxon_form($form, &$form_state, $advanced_form = FALSE, $classification_select = TRUE)
 170 {
 171
 172     if ($form_state['build_info']['form_id'] == 'cdm_dataportal_search_blast_form') {
 173         $form = cdm_dataportal_search_blast_form($form, $form_state);
 174     } else {
 175
 176
 177         $query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
 178
 179         if ($advanced_form || variable_get(SIMPLE_SEARCH_USE_LUCENE_BACKEND, FALSE)) {
 180             $search_service_endpoint = CDM_WS_PORTAL_TAXON_SEARCH;
 181         } else {
 182             $search_service_endpoint = CDM_WS_PORTAL_TAXON_FIND;
 183         }
 184
 185         $form = cdm_dataportal_search_form_prepare(
 186             'cdm_dataportal/search/results/taxon',
 187             $search_service_endpoint,
 188             $query_field_default_value,
 189             t('Enter the name or part of a name you wish to search for.
 190           The asterisk  character * can be used as wildcard, but must not be used as first character.')
 191         );
 192     }
 193   if (!$advanced_form) {
 194     $form['query']['#size'] = 20;
 195   }
 196
 197   $form['search']['pageSize'] = array(
 198     '#weight' => -1,
 199     '#type' => 'hidden',
 200     '#value' => variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT),
 201   );
 202
 203   $form['search']['pageIndex'] = array(
 204     '#weight' => -1,
 205     '#type' => 'hidden',
 206     '#value' => 0,
 207   );
 208
 209   $search_taxa_mode_settings = get_array_variable_merged(
 210     CDM_SEARCH_TAXA_MODE,
 211     CDM_SEARCH_TAXA_MODE_DEFAULT
 212   );
 213   $preset_do_taxa = $search_taxa_mode_settings['doTaxa'] !== 0;
 214   $preset_do_synonyms = $search_taxa_mode_settings['doSynonyms'] !== 0;
 215   $preset_do_taxa_by_common_names = $search_taxa_mode_settings['doTaxaByCommonNames'] !== 0;
 216   $preset_do_misapplied_names = $search_taxa_mode_settings['doMisappliedNames'] !== 0;
 217
 218   if ($advanced_form) {
 219
 220     // --- ADVANCED SEARCH FORM ---
 221     //
 222
 223     // Get presets from settings.
 224     $preset_classification_uuid = get_current_classification_uuid();
 225
 226     // Overwrite presets by user choice stored in session.
 227     if (isset($_SESSION['cdm']['search'])) {
 228       $preset_do_taxa = (isset($_SESSION['cdm']['search']['doTaxa']) ? 1 : 0);
 229       $preset_do_synonyms = (isset($_SESSION['cdm']['search']['doSynonyms']) ? 1 : 0);
 230       $preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);
 231       $preset_do_taxa_by_common_names = (isset($_SESSION['cdm']['search']['doTaxaByCommonNames']) ? 1 : 0);
 232       if (isset($_SESSION['cdm']['search']['tree'])) {
 233         $preset_classification_uuid = $_SESSION['cdm']['search']['tree'];
 234       }
 235     }
 236
 237     if ($classification_select === TRUE) {
 238       $form['search']['tree'] = array(
 239         '#title' => t('Classification'),
 240         '#weight' => 1,
 241         '#type' => 'select',
 242         '#default_value' => $preset_classification_uuid,
 243         '#options' => cdm_get_taxontrees_as_options(
 244           TRUE,
 245           variable_get(CDM_TAXONTREE_INCLUDES, []) ),
 246         '#description' => t('A filter to limit the search to a specific classification. Choosing <em>--- ALL ---</em> will disable this filter.'),
 247       );
 248     }
 249
 250     // General search parameters.
 251     $form['search']['doTaxa'] = array(
 252       '#weight' => 2,
 253       '#type' => 'checkbox',
 254       '#title' => t('Include') . ' ' . t('accepted taxa'),
 255       '#value' => $preset_do_taxa,
 256     );
 257     $form['search']['doSynonyms'] = array(
 258       '#weight' => 3,
 259       '#type' => 'checkbox',
 260       '#title' => t('Include') . ' ' . t('synonyms'),
 261       '#value' => $preset_do_synonyms,
 262     );
 263     $form['search']['doMisappliedNames'] = array(
 264       '#weight' => 4,
 265       '#type' => 'checkbox',
 266       '#title' => t('Include') . ' ' . t('misapplied names'),
 267       '#value' => $preset_do_misapplied_names,
 268     );
 269     $form['search']['doTaxaByCommonNames'] = array(
 270       '#weight' => 5,
 271       '#type' => 'checkbox',
 272       '#title' => t('Include') . ' ' . t('common names'),
 273       '#value' => $preset_do_taxa_by_common_names,
 274     );
 275
 276     $area_term_dtos = cdm_ws_fetch_all(
 277       CDM_WS_DESCRIPTION_NAMEDAREAS_IN_USE,
 278       array('includeAllParents' => 'true')
 279     );
 280
 281     // create map: term_uuid => term
 282     $term_map = array();
 283     foreach ($area_term_dtos as $term_dto) {
 284       $term_map[$term_dto->uuid] = $term_dto;
 285     }
 286
 287     $term_tree = array();
 288     // mixed_vocabularies will contain the uuid vocabularies which
 289     // also contain terms of foreign vocabularies due to the term
 290     // hierarchy
 291     $mixed_vocabularies = array();
 292
 293     // Build hierarchy of the terms regardless of the vocabulary.
 294     foreach ($term_map as $term_dto) {
 295       if (!empty($term_dto->partOfUuid)) {
 296         // Children.
 297         $parent =& $term_map[$term_dto->partOfUuid];
 298         if ($parent) {
 299           if (!isset($parent->children)) {
 300             $parent->children = array();
 301           }
 302           $parent->children[$term_dto->uuid] = $term_dto;
 303           if ($parent->vocabularyUuid != $term_dto->vocabularyUuid) {
 304             $mixed_vocabularies[$parent->vocabularyUuid] = $parent->vocabularyUuid;
 305           }
 306         }
 307       }
 308       else {
 309         // group root nodes by vocabulary
 310         if (!isset($term_tree[$term_dto->vocabularyUuid])) {
 311           $term_tree[$term_dto->vocabularyUuid] = array();
 312         }
 313         $term_tree[$term_dto->vocabularyUuid][$term_dto->uuid] = $term_dto;
 314       }
 315     }
 316
 317     $show_area_filter = ! variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '');
 318
 319     if($show_area_filter){
 320       drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/search_area_filter.js');
 321
 322       drupal_add_js('jQuery(document).ready(function() {
 323         jQuery(\'#edit-search-areas\').search_area_filter(\'#edit-search-areas-areas-filter\');
 324       });
 325       ', array('type' => 'inline'));
 326
 327       $form['search']['areas'] = array(
 328         '#type' => 'fieldset',
 329         '#title' => t('Filter by distribution areas'),
 330         '#description' => t('The search will return taxa having distribution
 331         information for at least one of the selected areas.') . ' '
 332           .(count($term_tree) > 1 ? t('The areas are grouped
 333         by the vocabularies to which the highest level areas belong.') : ''),
 334       );
 335       $form['search']['areas']['areas_filter'] = array(
 336         '#type' => 'textfield',
 337         '#description' => t('Type to filter the areas listed below.'),
 338       );
 339       $vocab_cnt = 0;
 340       $areas_defaults = array();
 341       if (isset($_SESSION['cdm']['search']['area'])) {
 342         $areas_defaults = explode(',', $_SESSION['cdm']['search']['area']);
 343       }
 344       _add_js_resizable_element('.resizable-box', true);
 345       foreach ($term_tree as $vocab_uuid => $term_dto_tree) {
 346         $vocabulary = cdm_ws_get(CDM_WS_TERMVOCABULARY, array($vocab_uuid));
 347         $areas_options = term_tree_as_options($term_dto_tree);
 348         $form['search']['areas']['area'][$vocab_cnt++] = array(
 349           '#prefix' => '<strong>' . $vocabulary->representation_L10n
 350             . (isset($mixed_vocabularies[$vocab_uuid]) ? ' <span title="Contains terms of at least one other area vocabulary.">(' . t('mixed') . ')</span>': '')
 351             . '</strong><div class="resizable-container"><div class="resizable-box">',
 352           '#type' => 'checkboxes',
 353           '#default_value' => $areas_defaults,
 354           '#options' => $areas_options,
 355           '#suffix' => '</div></div>'
 356         );
 357       }
 358     }
 359
 360   }
 361   else {
 362     // --- SIMPLE SEARCH FORM ---
 363     //
 364
 365     // Overwrite presets by user choice stored in session.
 366     if (isset($_SESSION['cdm']['search'])) {
 367       $preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);
 368     }
 369
 370     $form['search']['doTaxa'] = array(
 371       '#weight' => -2,
 372       '#type' => 'hidden',
 373       '#value' => $preset_do_taxa,
 374     );
 375     $form['search']['doSynonyms'] = array(
 376       '#weight' => -3,
 377       '#type' => 'hidden',
 378       '#value' => $preset_do_synonyms,
 379     );
 380     $form['search']['doMisappliedNames'] = array(
 381       '#weight' => -4,
 382       '#type' => 'checkbox',
 383       '#title' => t('Misapplied names'),
 384       '#value' => $preset_do_misapplied_names,
 385     );
 386     $form['search']['doTaxaByCommonNames'] = array(
 387       '#weight' => -5,
 388       '#type' => 'hidden',
 389       '#value' => $preset_do_taxa_by_common_names,
 390     );
 391   }
 392
 393   return $form;
 394 }
 395
 396 /**
 397  * Creates a search form for searching on taxa.
 398  *
 399  * If advanced $advanced_form id TRUE the form will offer additional choices
 400  *
 401  * @param array $form
 402  *   A drupal form array
 403  * @param array $form_state
 404  *   The drupal form state passed as reference
 405  * @param bool $advanced_form
 406  *   default is FALSE
 407  * @param bool $classification_select
 408  *   set TRUE to offer a classification selector in the form - default is FALSE
 409  *   if only available in the advanced mode
 410  *
 411  * @return array
 412  *   the form array
 413  */
 414 function cdm_dataportal_search_blast_form($form, &$form_state) {
 415
 416     $query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
 417
 418     $search_service_endpoint = CDM_SEARCH_BLAST_SERVICE_URI;
 419
 420
 421     $form = cdm_dataportal_search_blast_form_prepare(
 422         'cdm_dataportal/search/results/specimen',
 423         $search_service_endpoint,
 424         $query_field_default_value,
 425         t('Enter the sequence or part of a sequence you wish to search for.')
 426     );
 427
 428
 429
 430     $form['search']['pageSize'] = array(
 431         '#weight' => -1,
 432         '#type' => 'hidden',
 433         '#value' => variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT),
 434     );
 435
 436     $form['search']['pageIndex'] = array(
 437         '#weight' => -1,
 438         '#type' => 'hidden',
 439         '#value' => 0,
 440     );
 441
 442
 443
 444
 445
 446     return $form;
 447 }
 448
 449 /**
 450  * Prepares a form array for a general purpose search form.
 451  *
 452  * The form is used for general purpose search functionality in the
 453  * dataportal. The form returned is populated with all necessary fields
 454  * for internal processing and has the textfield element $form['query']
 455  * which holds the query term.
 456  *
 457  * @param string $action_path
 458  *   The Drupal path to be put into the action url to which the form will
 459  *   be submitted.
 460  * @param string $search_webservice
 461  *   The cdm-remote webservice to be used, valid values are defined by
 462  *   the constants: FIXME.
 463  * @param string $query_field_default_value
 464  *   A default text for the query field
 465  * @param string $query_field_description
 466  *   The description text for the query field
 467  * @param string $process
 468  *   The value for #process, if NULL (default), 'cdm_dataportal_search_process'
 469  *   is used.
 470  *
 471  * @return array
 472  *   The prepared form array.
 473  */
 474 function cdm_dataportal_search_blast_form_prepare($action_path, $search_webservice, $query_field_default_value, $query_field_description, $process = NULL) {
 475
 476     if ($process == NULL) {
 477         $process = 'cdm_dataportal_search_process';
 478     }
 479
 480     $form['#method'] = 'get';
 481     //
 482     //  $form['#process'] = array(
 483     //  $process => array(),
 484     //  );
 485     //
 486     $form['#action'] = url($action_path, array(
 487         'absolute' => TRUE,
 488     ));
 489
 490     $form['ws'] = array(
 491         '#type' => 'hidden',
 492         '#value' => $search_webservice,
 493         '#name' => 'ws',
 494     );
 495
 496     $form['query'] = array(
 497         '#weight' => 0,
 498         '#type' => 'textarea',
 499         '#size' => 68,
 500         // This causes the description to display also when hovering over
 501         // the textfield.
 502         // This is wanted behaviour for the simple seach but could
 503         // be disabled for the advances search.
 504         '#attributes' => array(
 505             'title' => $query_field_description,
 506         ),
 507         '#description' => $query_field_description,
 508        // '#value' => $query_field_default_value,
 509         // '#description' => $query_field_description,
 510     );
 511
 512
 513     $form['search'] = array(
 514         '#weight' => 3,
 515         '#tree' => TRUE,
 516         // '#type' => $advanced_form ? 'fieldset': 'hidden',
 517         '#title' => t('Options'),
 518     );
 519
 520     // Clean URL get forms breaks if we don't give it a 'q'.
 521     if (!(bool) variable_get('clean_url', '0')) {
 522         $form['search']['q'] = array(
 523             '#type' => 'hidden',
 524             '#value' => $action_path,
 525             '#name' => 'q',
 526         );
 527     }
 528
 529     $form['search']['word_size'] = array(
 530         '#weight' => 1,
 531         '#type' => 'textfield',
 532         '#title' => t('Word size'),
 533         '#default_value' => 7,
 534         '#description' => t('Length of initial exact match'),
 535     );
 536
 537     $form['search']['reward'] = array(
 538         '#weight' => 2,
 539         '#type' => 'textfield',
 540         '#title' => t('Reward'),
 541         '#default_value' => 1,
 542         '#description' => t('Reward for Matching'),
 543     );
 544
 545     $form['search']['penalty'] = array(
 546         '#weight' => 3,
 547         '#type' => 'textfield',
 548         '#title' => t('Penalty'),
 549         '#default_value' => -2,
 550         '#description' => t('Penalty for mismatching'),
 551     );
 552
 553     $form['search']['gap_open'] = array(
 554         '#weight' => 4,
 555         '#type' => 'textfield',
 556         '#title' => t('Gap open'),
 557         '#default_value' => 5,
 558         '#description' => t('Cost to open a gap'),
 559     );
 560
 561     $form['search']['gap_extend'] = array(
 562         '#weight' => 5,
 563         '#type' => 'textfield',
 564         '#title' => t('Gap extend'),
 565         '#default_value' => -2,
 566         '#description' => t('Cost for extend a gap'),
 567     );
 568
 569     $form['submit'] = array(
 570         '#weight' => 5,
 571         '#type' => 'submit',
 572         '#name' => '',
 573         '#value' => t('Search'),
 574     );
 575
 576     return $form;
 577 }
 578 /**
 579  * Wrapper function for cdm_dataportal_search_taxon_form().
 580  *
 581  * This function makes ot possible possible to just pass the
 582  * correct $form_id 'cdm_dataportal_search_taxon_form_advanced' to
 583  * drupal_get_form like:
 584  * drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
 585  *
 586  * @param array $form
 587  *   A drupal form array
 588  * @param array $form_state
 589  *   The drupal form state passed as reference
 590  *
 591  * @return array
 592  *   The form array
 593  */
 594 function cdm_dataportal_search_taxon_form_advanced($form, &$form_state) {
 595   return cdm_dataportal_search_taxon_form($form, $form_state, TRUE);
 596 }
 597
 598 /**
 599  * Form for searching taxa by the findByDescriptionElementFullText rest service.
 600  */
 601 function cdm_dataportal_search_taxon_by_description_form() {
 602   $query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
 603
 604   $form = cdm_dataportal_search_form_prepare(
 605     'cdm_dataportal/search/results/taxon',
 606     CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT,
 607     $query_field_default_value,
 608     t("Enter the text you wish to search for. The asterisk character * can be
 609         used as wildcard, but must not be used as first character. Terms can be combined with 'AND'. To search for a
 610         full phrase enclose the terms in parentheses. For more syntactical
 611         options please refer to the !link.",
 612       array(
 613         '!link' => l(
 614           t('Apache Lucene - Query Parser Syntax'),
 615           'http://lucene.apache.org/core/old_versioned_docs/versions/2_9_1/queryparsersyntax.html', array(
 616             'attributes' => array(
 617               'absolute' => TRUE,
 618               'html' => TRUE),
 619           )
 620         ),
 621       )
 622     )
 623   );
 624
 625   $form['search']['tree'] = array(
 626     '#weight' => -1,
 627     '#type' => 'hidden',
 628     '#value' => get_current_classification_uuid(),
 629   );
 630
 631   $form['search']['hl'] = array(
 632     '#weight' => -1,
 633     '#type' => 'hidden',
 634     '#value' => 1,
 635   );
 636
 637   // Only available to admins:
 638   if (!isset($_SESSION['cdm']['search']['clazz'])) {
 639     $_SESSION['cdm']['search']['clazz'] = '';
 640   }
 641   if (module_exists("user") && user_access('administer')) {
 642     $form['search']['clazz'] = array(
 643       '#type' => 'select',
 644       '#title' => t('Limit to description item type'),
 645       '#default_value' => $_SESSION['cdm']['search']['clazz'],
 646       '#options' => cdm_descriptionElementTypes_as_option(TRUE),
 647     );
 648   }
 649
 650   $profile_feature_tree = get_profile_feature_tree();
 651   $feature_options = _featureTree_nodes_as_feature_options($profile_feature_tree->root);
 652   if (isset($_SESSION['cdm']['search']['features'])) {
 653     $form['search']['features'] = array(
 654       '#type' => 'checkboxes',
 655       '#title' => t('Limit to selected features'),
 656       '#default_value' => $_SESSION['cdm']['search']['features'],
 657       '#options' => $feature_options,
 658     );
 659   }
 660   else {
 661     $form['search']['features'] = array(
 662       '#type' => 'checkboxes',
 663       '#title' => t('Limit to selected features'),
 664       '#options' => $feature_options,
 665     );
 666   }
 667   return $form;
 668 }
 669
 670 /**
 671  * Processes the query parameters of the search form.
 672  *
 673  * Reads the query parameters from $_REQUEST and modifies and adds additional
 674  * query parameters if necessary.
 675  *
 676  *  - Filters $_REQUEST by a list of valid request parameters
 677  *  - modifies geographic_range parameters
 678  *  - adds taxon tree uuid if it is missing and if it should not be
 679  *    ignored (parameter value = 'IGNORE')
 680  *  - and more
 681  *
 682  * @param $search_endpoint string
 683  *    The web service endpoint which will be used for executing the search.
 684  *    Usually one of CDM_WS_PORTAL_TAXON_SEARCH, CDM_WS_PORTAL_TAXON_FIND,
 685  *    CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT.
 686  * @return array
 687  *   the processed request parameters submitted by the search form and
 688  *   also stores them in $_SESSION['cdm']['search']
 689  */
 690 function cdm_dataportal_search_request($search_endpoint)
 691 {
 692
 693   $form_params = array();
 694
 695   if (isset($_REQUEST['search']) && is_array($_REQUEST['search'])) {
 696     array_deep_copy($_REQUEST['search'], $form_params);
 697   }
 698
 699   if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
 700     $form_params = array_merge($form_params, $_REQUEST['pager']);
 701   }
 702
 703   $form_params['query'] = trim($_REQUEST['query']);
 704
 705
 706   // --- handle geographic range
 707   // Split of geographic range.
 708   unset($form_params['areas']);
 709
 710   $area_filter_preset = null;
 711   if (variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '')) {
 712     $area_filter_preset = explode(',', variable_get(CDM_SEARCH_AREA_FILTER_PRESET, ''));
 713   }
 714
 715   $area_uuids = array();
 716   if($area_filter_preset){
 717     $area_uuids = $area_filter_preset;
 718   }
 719   elseif (isset($_REQUEST['search']['areas']['area']) && is_array($_REQUEST['search']['areas']['area'])) {
 720     foreach ($_REQUEST['search']['areas']['area'] as $areas) {
 721       $area_uuids = array_merge($area_uuids, $areas);
 722     }
 723     // The area filter is limited to areas with non absent distribution status
 724     $presence_terms_options = cdm_vocabulary_as_option(UUID_PRESENCE_ABSENCE_TERM, null, FALSE, array('absenceTerm' => '/false/'));
 725     $presence_term_uuids = array_keys($presence_terms_options);
 726     $form_params['status'] = $presence_term_uuids;
 727   }
 728   if(count($area_uuids) > 0){
 729     $form_params['area'] = implode(',', $area_uuids);
 730   }
 731
 732   // Simple search will not submit a 'tree' query parameter,
 733   // so we add it here from what is stored in the session unless
 734   // SIMPLE_SEARCH_IGNORE_CLASSIFICATION is checked in the settings.
 735   if (!isset($form_params['tree']) && !variable_get(SIMPLE_SEARCH_IGNORE_CLASSIFICATION, 0)) {
 736     $form_params['tree'] = get_current_classification_uuid();
 737   }
 738   // Store in session.
 739   $_SESSION['cdm']['search'] = $form_params;
 740
 741   // ----------- further processing that must not be store in the session --------- //
 742
 743   if($search_endpoint == CDM_WS_PORTAL_TAXON_SEARCH){
 744     // HACK to allow using dot characters
 745     $form_params['query'] = str_replace('.', '*', $form_params['query']);
 746     // lucene based taxon search always as phrase search if the query string contains a whitespace --> enclose it in "
 747     if(preg_match("/\s+/", $form_params['query'])){
 748       if(!str_beginsWith($form_params['query'], '"')){
 749         $form_params['query'] = '"' . $form_params['query'];
 750       }
 751       if(!str_endsWith($form_params['query'], '"')){
 752         $form_params['query'] = $form_params['query'] . '"' ;
 753       }
 754     }
 755   }
 756
 757   // If the 'NONE' classification has been chosen (advanced search)
 758   // delete the tree information to avoid unknown uuid exceptions in the
 759   // cdm service.
 760   if (isset($form_params['tree'])
 761     && ($form_params['tree'] == 'NONE' || !is_uuid($form_params['tree']))
 762   ) {
 763     // $form_params['ignore_classification'] =  TRUE;
 764     unset($form_params['tree']);
 765   }
 766
 767
 768   // else {
 769   //   $form_params['ignore_classification'] =  NULL;
 770   // }
 771
 772
 773   return $form_params;
 774 }
 775
 776 /**
 777  * Processes the query parameters of the blast search form.
 778  *
 779  * Reads the query parameters from $_REQUEST and modifies and adds additional
 780  * query parameters if necessary.
 781  *
 782  *  - Filters $_REQUEST by a list of valid request parameters
 783  *
 784  *
 785  * @param $search_endpoint string
 786  *    The web service endpoint which will be used for executing the search.
 787  *
 788  * @return array
 789  *   the processed request parameters submitted by the search form and
 790  *   also stores them in $_SESSION['cdm']['search']
 791  */
 792 function cdm_dataportal_blast_search_request($search_endpoint)
 793 {
 794     $form_params = array();
 795
 796     if (isset($_REQUEST['search']) && is_array($_REQUEST['search'])) {
 797         array_deep_copy($_REQUEST['search'], $form_params['data']);
 798     }
 799     $form_params['data'] = formatWSParams($_REQUEST['search']);
 800     $form_params['query']= trim($_REQUEST['query']).$form_params['data'];
 801     // Store in session.
 802     $_SESSION['cdm']['search'] = $form_params;
 803     return $form_params;
 804 }
 805
 806 /**
 807  * Provides the classification to which the last search has been limited to..
 808  *
 809  * This function should only be used after the cdm_dataportal_search_taxon_execute()
 810  * handler has been run, otherwise it will return the information from the last
 811  * search executed. The information is retrieved from
 812  * the $_SESSION variable:  $_SESSION['cdm']['search']['tree']
 813  *
 814  * @return object
 815  *   the CDM classification instance which has been used a filter for the
 816  *   last processed search
 817  *   or NULL, it it was on all classifications
 818  */
 819 function cdm_dataportal_searched_in_classification() {
 820
 821   $classification = &drupal_static(__FUNCTION__);
 822
 823   if (!isset($classification)) {
 824     if (isset($_SESSION['cdm']['search']['tree'])) {
 825       $classification = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY, ($_SESSION['cdm']['search']['tree']));
 826     }
 827     else {
 828       $classification = FALSE;
 829     }
 830   }
 831
 832   return $classification !== FALSE ? $classification : NULL;
 833 }
 834
 835 /**
 836  * Removed the drupal internal form parameters 'form_id', 'form_token', 'form_build_id' from the request array.
 837  *
 838  * @param $request array
 839  *   Pass $_REQUEST as paramter
 840  * @return array
 841  *  The $request array without drupal internal form parameters
 842  */
 843 function remove_drupal_form_params($request) {
 844
 845   static $exclude_keys = array('form_id', 'form_token', 'form_build_id');
 846   $request_sanitized = array();
 847   foreach ($request as $key => $value) {
 848     if(!array_search($key, $exclude_keys)){
 849       $request_sanitized[$key] = $value;
 850     }
 851   }
 852
 853   return $request_sanitized;
 854 }
 855
 856 /**
 857  * Sends a search request to the cdm server.
 858  *
 859  * The parameters to build the query are taken obtained by calling
 860  * cdm_dataportal_search_request() which reads the query parameters
 861  * from $_REQUEST and add additional query parameters if nessecary.
 862  *
 863  * @see cdm_dataportal_search_request()
 864  */
 865 function cdm_dataportal_search_taxon_execute() {
 866
 867   // Store as last search in session.
 868   $_SESSION['cdm']['last_search'] = $_SERVER['REQUEST_URI'];
 869
 870   // Validate the search webservice parameter:
 871   if (!isset($_REQUEST['ws'])) {
 872     drupal_set_message(
 873       t("Invalid search, webservice parameter 'ws' is missing"), 'warning'
 874     );
 875     return NULL;
 876   }
 877   if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {
 878     // Endpoint is unknown.
 879     drupal_set_message(
 880       t("Invalid search webservice parameter 'ws' given"), 'warning'
 881     );
 882     return NULL;
 883   }
 884
 885   // Read the query parameters from $_REQUEST and add additional query
 886   // parameters if necessary.
 887   $request_params = cdm_dataportal_search_request($_REQUEST['ws']);
 888
 889   $taxon_pager = cdm_ws_get($_REQUEST['ws'], NULL, queryString($request_params));
 890
 891   return $taxon_pager;
 892 }
 893
 894 /**
 895  * Sends a search request to the cdm server.
 896  *
 897  * The parameters to build the query are taken obtained by calling
 898  * cdm_dataportal_search_request() which reads the query parameters
 899  * from $_REQUEST and add additional query parameters if nessecary.
 900  *
 901  * @see cdm_dataportal_search_request()
 902  */
 903 function cdm_dataportal_search_blast_execute() {
 904
 905     // Store as last search in session.
 906     $_SESSION['cdm']['last_blast_search'] = $_SERVER['REQUEST_URI'];
 907
 908     // Validate the search webservice parameter:
 909     if (!isset($_REQUEST['ws'])) {
 910         drupal_set_message(
 911             t("Invalid search, webservice parameter 'ws' is missing"), 'warning'
 912         );
 913         return NULL;
 914     }
 915 //    if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {
 916 //        // Endpoint is unknown.
 917 //        drupal_set_message(
 918 //            t("Invalid search webservice parameter 'ws' given"), 'warning'
 919 //        );
 920 //        return NULL;
 921 //    }
 922
 923     // Read the query parameters from $_REQUEST and add additional query
 924     // parameters if necessary.
 925     $request_params = cdm_dataportal_blast_search_request($_REQUEST['ws']);
 926    // $url = drupal_http_build_query($_REQUEST['ws'], $request_params);
 927     $request_params['timeout'] = 200;
 928     $taxon_pager = drupal_http_request($_REQUEST['ws'].'?sequence='.$request_params['query'], $request_params);
 929
 930     return $taxon_pager;
 931 }
 932
 933
 934
 935 /**
 936  * Sends a request for a registrations filter search to the cdm server.
 937  */
 938 function cdm_dataportal_search_registrations_filter_execute()
 939 {
 940
 941   static $query_param_map = array(
 942     'identifier' => 'identifierFilterPattern',
 943     'taxon_name'=> 'taxonNameFilterPattern',
 944     'reference_citation' => 'referenceFilterPattern',
 945     'type_designation_status_uuids' => 'typeDesignationStatusUuids',
 946   );
 947
 948   $session_key = SESSION_KEY_SEARCH_REGISTRATION_FILTER;
 949   $request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
 950
 951   // cleanup
 952   if(isset($request_params['typeDesignationStatusUuids'])){
 953     if(!$request_params['typeDesignationStatusUuids']
 954       || $request_params['typeDesignationStatusUuids'] == "0"
 955       || (isset($request_params['typeDesignationStatusUuids'][0]) && !$request_params['typeDesignationStatusUuids'][0])){
 956       unset($request_params['typeDesignationStatusUuids']);
 957     }
 958   }
 959   if(isset($request_params['taxonNameFilterPattern'])){
 960     // trim and remove empty taxon name query strings
 961     $request_params['taxonNameFilterPattern'] = trim($request_params['taxonNameFilterPattern']);
 962     if(!$request_params['taxonNameFilterPattern']){
 963       unset($request_params['taxonNameFilterPattern']);
 964     }
 965   }
 966   // reference_citation
 967   if(isset($request_params['referenceFilterPattern'])){
 968     // trim and remove empty taxon name query strings
 969     $request_params['referenceFilterPattern'] = trim($request_params['referenceFilterPattern']);
 970     if(!$request_params['referenceFilterPattern']){
 971       unset($request_params['referenceFilterPattern']);
 972     }
 973   }
 974
 975   $registration_pager = cdm_ws_get('registrationDTO/find', NULL, queryString($request_params));
 976
 977   return $registration_pager;
 978 }
 979
 980 /**
 981  * Sends a request for a registrations taxongraph search to the cdm server.
 982  */
 983 function cdm_dataportal_search_registrations_taxongraph_execute()
 984 {
 985
 986   static $query_param_map = array(
 987     'taxon_name'=> 'taxonNameFilter'
 988   );
 989
 990   $session_key = SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER;
 991   $request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
 992
 993   // cleanup
 994   if(isset($request_params['taxonNameFilter'])){
 995     // trim and remove empty taxon name query strings
 996     $request_params['taxonNameFilter'] = trim($request_params['taxonNameFilter']);
 997     if(!$request_params['taxonNameFilter']){
 998       unset($request_params['taxonNameFilter']);
 999     }
1000   }
1001
1002   $registration_pager = cdm_ws_get('registrationDTO/findInTaxonGraph', NULL, queryString($request_params));
1003
1004   return $registration_pager;
1005 }
1006
1007 /**
1008  * @param $session_key
1009  *   The key to be used for storing the search params in $_SESSION['cdm'][]
1010  * @param $query_param_map
1011  *    An array which maps the filter_key to the web service query parameter.
1012  *    The filter key may be used as form element name or as drupal url
1013  *    query parameter.
1014  * @return array
1015  */
1016 function cdm_dataportal_search_request_params($session_key, $query_param_map)
1017 {
1018   // Read the query parameters from $_REQUEST and add additional query
1019   // parameters if necessary.
1020   $request_params = array();
1021
1022   $request = remove_drupal_form_params($_REQUEST);
1023
1024   if (count($request) > 0) {
1025     $_SESSION['cdm'][$session_key] = $request;
1026     foreach ($query_param_map as $filter_key => $query_param) {
1027       if (isset($request[$filter_key])) {
1028         $request_params[$query_param] = $request[$filter_key];
1029       }
1030     }
1031     if (isset($request['pager']['pageIndex'])) {
1032       $request_params['pageIndex'] = $request['pager']['pageIndex'];
1033     }
1034   }
1035
1036   if (count($request_params) == 0 && isset($_SESSION['cdm'][$session_key])) {
1037     foreach ($query_param_map as $filter_key => $query_param) {
1038       if (isset($_SESSION['cdm'][$session_key][$filter_key])) {
1039         $request_params[$query_param] = $_SESSION['cdm'][$session_key][$filter_key];
1040       }
1041     }
1042     if (isset($_SESSION['cdm'][$session_key]['pager']['pageIndex'])) {
1043       $request_params['pageIndex'] = $_SESSION['cdm'][$session_key]['pager']['pageIndex'];
1044     }
1045   }
1046   return $request_params;
1047 }
1048
1049 /**
1050  * Transforms the termDTO tree into options array.
1051  *
1052  *   TermDto:
1053  *      - partOfUuid:
1054  *      - representation_L10n:
1055  *      - representation_L10n_abbreviatedLabel:
1056  *      - uuid:
1057  *      - vocabularyUuid:
1058  *      - children: array of TermDto
1059  *
1060  * The options array is suitable for drupal form API elements that
1061  * allow multiple choices.
1062  * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
1063  *
1064  * @param array $term_dto_tree
1065  *   a hierarchic array of CDM TermDto instances, with additional
1066  * 'children' field:
1067  * @param array $options
1068  *   Internally used for recursive calls
1069  * @param string $prefix
1070  *   Internally used for recursive calls
1071  *
1072  * @return array
1073  *   the terms in an array as options for a form element that allows
1074  *   multiple choices.
1075  */
1076 function term_tree_as_options($term_dto_tree, &$options = array(), $prefix = '') {
1077
1078   uasort($term_dto_tree, 'compare_terms_by_order_index');
1079   foreach ($term_dto_tree as $uuid => $dto) {
1080     $label = $prefix . '<span class="child-label">'
1081       .  $dto->representation_L10n
1082       . '</span><span class="child-label-abbreviated"> (' . $dto->representation_L10n_abbreviatedLabel . ')</span>';
1083     $options[$uuid] = $label;
1084     if (isset($dto->children) && is_array($dto->children)) {
1085       term_tree_as_options(
1086         $dto->children,
1087         $options, $prefix
1088           . '<span data-cdm-parent="' . $uuid . '" class="parent"></span>'
1089       );
1090     }
1091   }
1092
1093   return $options;
1094 }
1095
1096
1097 function cdm_dataportal_search_registration_filter_form($form, &$form_state) {
1098
1099   static $filter_presets_empty = array(
1100     'identifier'=> null,
1101     'taxon_name'=> null,
1102     'reference_citation'=> null,
1103     'type_designation_status_uuids' => null
1104   );
1105
1106   _add_font_awesome_font();
1107
1108   if(isset($_REQUEST['q']) && ($_REQUEST['q'] == 'cdm_dataportal/registration-search/filter' || $_REQUEST['q'] == 'cdm_dataportal/registration-search')){
1109     // read the $request_params only if it was send from this form
1110     $request_params = remove_drupal_form_params($_REQUEST);
1111   } else {
1112     $request_params = array();
1113   }
1114   $filter_presets = (isset($_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER]) ? $_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER] : array());
1115   $filter_presets = array_merge($filter_presets_empty, $filter_presets, $request_params);
1116   $form['#action'] =  url('/cdm_dataportal/registration-search/filter');
1117   $form['#method'] = 'get';
1118   $form['#attributes'] = array('class' => array('search-filter'));
1119   $form['identifier'] = array(
1120     '#type' => 'textfield',
1121     '#title' => t('Identifier'),
1122     '#default_value' => $filter_presets['identifier'],
1123     '#size' => 20,
1124     '#maxlength' => 128
1125   );
1126   $form['taxon_name'] = array(
1127     '#type' => 'textfield',
1128     '#title' => t('Scientific name'),
1129     '#default_value' => $filter_presets['taxon_name'],
1130     '#size' => 20,
1131     '#maxlength' => 128
1132   );
1133   $form['reference_citation'] = array(
1134     '#type' => 'textfield',
1135     '#title' => t('Publication'),
1136     '#default_value' => $filter_presets['reference_citation'],
1137     '#size' => 20,
1138     '#maxlength' => 128
1139   );
1140   $form['type_designation_status_uuids'] = array(
1141     '#type' => 'select',
1142     '#title' => t('Type designation status'),
1143     '#multiple' => true,
1144     '#options' => cdm_type_designation_status_filter_terms_as_options('- none -'),
1145     '#default_value' => $filter_presets['type_designation_status_uuids'],
1146     "#description" => '<i>' . t('Ctrl + Click to unselect') . '</i>'
1147   );
1148
1149   $form['submit'] = array(
1150     '#markup' => '<button type="submit" title="Search" class="form-submit">' . font_awesome_icon_markup('fa-search') . '</button>'
1151 //    '#prefix' => "<div class=\"form-item\"><label>&nbsp</label>",
1152 //    '#suffix' => "</div>"
1153
1154   );
1155   return $form;
1156 }
1157
1158
1159 function cdm_dataportal_search_registration_taxongraph_form($form, &$form_state) {
1160
1161   static $filter_presets_empty = array(
1162     'taxon_name'=> null
1163   );
1164
1165   _add_font_awesome_font();
1166
1167   if(isset($_REQUEST['q']) && $_REQUEST['q']  == 'cdm_dataportal/registration-search/taxongraph'){
1168     // read the $request_params only if it was send from this form
1169     $request_params = remove_drupal_form_params($_REQUEST);
1170   } else {
1171     $request_params = array();
1172   }
1173   $filter_presets = (isset($_SESSION['cdm'][SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER]) ? $_SESSION['cdm'][SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER] : array());
1174   $filter_presets = array_merge($filter_presets_empty, $filter_presets, $request_params);
1175
1176   $form['#action'] =  url('/cdm_dataportal/registration-search/taxongraph');
1177   $form['#method'] = 'get';
1178   $form['#attributes'] = array('class' => array('search-filter'));
1179   $form['taxon_name'] = array(
1180     '#type' => 'textfield',
1181     '#title' => t('Scientific name'),
1182     '#default_value' => $filter_presets['taxon_name'],
1183     '#size' => 20,
1184     '#maxlength' => 128
1185   );
1186
1187   $form['submit'] = array(
1188     '#markup' => '<button type="submit" title="Search" class="form-submit">' . font_awesome_icon_markup('fa-search') . '</button>'
1189 //    '#prefix' => "<div class=\"form-item\"><label>&nbsp</label>",
1190 //    '#suffix' => "</div>"
1191
1192   );
1193   return $form;
1194 }
1195
1196 /**
1197  * Compose the result set of a registration search from a pager object
1198  *
1199  * @param $cdm_item_pager
1200  *    The pager containing registration objects
1201  *
1202  * @return
1203  *   A drupal render array.
1204  *
1205  * @ingroup compose
1206  *
1207  * TODO compose function into search.inc ?
1208  */
1209 function compose_search_results($cdm_item_pager, ItemComposeHandler $item_compose_handler){
1210
1211   $render_array = array();
1212   $render_array['pre'] = markup_to_render_array("<div class=\"cdm-item-list\">");
1213
1214   if($cdm_item_pager != null && count($cdm_item_pager->records) > 0){
1215     $items_render_array = array();
1216     foreach($cdm_item_pager->records as $registration_dto) {
1217
1218       $items_render_array[]  = array(
1219         '#prefix' => "<div class=\"item\"><div class=\"" . $item_compose_handler->getClassAttributes($registration_dto) . "\">",
1220          'item_data' => $item_compose_handler->composeItem($registration_dto),
1221         '#suffix' => "</div></div>"
1222         );
1223       ;
1224     }
1225
1226     $render_array['items'] = $items_render_array;
1227     $render_array['pager'] =  markup_to_render_array(theme('cdm_pager', array(
1228           'pager' => $cdm_item_pager,
1229           'path' => $_REQUEST['q'], // stay on same page
1230           'parameters' => $_REQUEST,
1231         )));
1232
1233   } else {
1234     if($cdm_item_pager != null && $cdm_item_pager->count > 0 && count($cdm_item_pager->records) == 0){
1235       $render_array['items'] = markup_to_render_array("<div id=\"no_results\">Result page out of range.</div>");
1236     } else {
1237       $render_array['items'] = markup_to_render_array("<div id=\"no_results\">No results found.</div>");
1238     }
1239   }
1240   $render_array['post'] = markup_to_render_array("</div>");
1241
1242   return $render_array;
1243
1244 }
1245
1246
1247 /**
1248  * Sends a search request for agents to the cdm server.
1249  */
1250 function cdm_dataportal_search_agent_execute()
1251 {
1252
1253   static $query_param_map = array(
1254     'markerType' => 'markerType',
1255     'cdmType' => 'class'
1256   );
1257
1258   $session_key = SESSION_KEY_SEARCH_AGENT_FILTER;
1259   $request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
1260
1261   // cleanup
1262   if(isset($request_params['taxonNameFilter'])){
1263     // trim and remove empty taxon name query strings
1264     $request_params['taxonNameFilter'] = trim($request_params['taxonNameFilter']);
1265     if(!$request_params['taxonNameFilter']){
1266       unset($request_params['taxonNameFilter']);
1267     }
1268   }
1269   $restrictions = [];
1270   if( isset($request_params['markerType'])){
1271     $restrictions = array(new Restriction("markers.markerType.uuid","EXACT", array($request_params['markerType']), 'AND'));
1272   }
1273   $init_strategy = array(
1274     "$",
1275     "titleCache",
1276     "extensions.$",
1277     "identifiers.type"
1278   );
1279
1280   $type_restriction = null;
1281   if(isset($request_params['class']) && ($request_params['class'] == 'Team' || $request_params['class'] == 'Person')){
1282     $type_restriction = $request_params['class'];
1283   }
1284   $page_index = 0;
1285   if(isset($_REQUEST['pager']['pageIndex'])){
1286     $page_index = $_REQUEST['pager']['pageIndex'];
1287   }
1288   $pager = cdm_ws_page_by_restriction('AgentBase', $type_restriction, $restrictions, $init_strategy, 50, $page_index);
1289
1290   return $pager;
1291 }
1292