tripal_chado.pub_search.inc

Functions responsible for creating the publication search form that allows a user of the site to search for publications that are currently in Chado.

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tripal_chado/includes/tripal_chado.pub_search.inc
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  1. <?php

  2. /**

  3.  * @file

  4.  *

  5.  * Functions responsible for creating the publication search form that

  6.  * allows a user of the site to search for publications that are currently

  7.  * in Chado.

  8.  */

  9. 

  10. function tripal_chado_pub_search_admin_form($form, &$form_state) {

  11.   // -----------------------------------------

  12.   // add in the fields for selecting which fields are used when search for pubs

  13.   $form['searching'] = array(

  14.     '#type' => 'fieldset',

  15.     '#title' => t('Searching Options'),

  16.     '#description' => t("The list of checkboxes below indicate which fields a user

  17.       can search with when using the publication search tool.  Check the fields that you want

  18.       to allow users to search with.  Click the 'Save configuration' button below to save changes."),

  19.   );

  20. 

  21.   // get publication properties list

  22.   $properties = array();

  23.   $properties[] = 'Any Field';

  24.   $sql = "

  25.     SELECT DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition

  26.     FROM {cvtermpath} CVTP

  27.       INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id

  28.       INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id

  29.       INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id

  30.     WHERE CV.name = 'tripal_pub' and

  31.       (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and

  32.       NOT CVTS.is_obsolete = 1

  33.     ORDER BY CVTS.name ASC

  34.   ";

  35.   $prop_types = chado_query($sql);

  36.   while ($prop = $prop_types->fetchObject()) {

  37.     $properties[$prop->cvterm_id] = $prop->name;

  38.   }

  39.   $form['allowed_search_fields'] = array(

  40.     '#type'    => 'checkboxes',

  41.     '#options' => $properties,

  42.     '#default_value' => variable_get('tripal_pub_allowed_search_fields', array()),

  43.   );

  44. 

  45.   $form['button'] = array(

  46.     '#type' => 'submit',

  47.     '#value' => 'Save configuration',

  48.     '#name' => 'sumbit',

  49.   );

  50.   return $form;

  51. }

  52. /**

  53.  *

  54.  */

  55. function tripal_chado_pub_search_admin_form_submit($form, &$form_state) {

  56.   // set the allowed search fields

  57.   $allowed_fields = $form_state['values']['allowed_search_fields'];

  58.   foreach ($allowed_fields as $cvterm_id => $selected) {

  59.     if (!$selected) {

  60.       unset($allowed_fields[$cvterm_id]);

  61.     }

  62.   }

  63.   variable_set('tripal_pub_allowed_search_fields', $allowed_fields);

  64.   drupal_set_message('Changes saved.');

  65. }

  66. /**

  67.  * The page that contains the publication search form and the results for the search

  68.  *

  69.  * @ingroup tripal_pub

  70.  */

  71. function tripal_chado_pub_search_page() {

  72. 

  73.   // This line may not be required, but on some sites the $_SESSION

  74.   // variable wasn't being set for anonymous users. This line solves that

  75.   // problem

  76.   drupal_session_start();

  77. 

  78.   $limit = 25;

  79. 

  80.   // generate the search form

  81.   $form = drupal_get_form('tripal_chado_pub_search_form');

  82.   $output = drupal_render($form);

  83. 

  84.   // retrieve any results

  85.   if (array_key_exists('tripal_chado_pub_search_form', $_SESSION) and

  86.       $_SESSION['tripal_chado_pub_search_form']['perform_search']) {

  87.         $num_criteria = $_SESSION['tripal_chado_pub_search_form']['num_criteria'];

  88.         $from_year    = $_SESSION['tripal_chado_pub_search_form']['from_year'];

  89.         $to_year      = $_SESSION['tripal_chado_pub_search_form']['to_year'];

  90. 

  91.         $search_array = array();

  92.         $search_array['num_criteria'] = $num_criteria;

  93.         $search_array['from_year']    = $from_year;

  94.         $search_array['to_year']      = $to_year;

  95.         for ($i = 0; $i <= $num_criteria; $i++) {

  96.           $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['search_terms'];

  97.           $search_array['criteria'][$i]['scope']        = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['scope'];

  98.           $search_array['criteria'][$i]['mode']         = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['mode'];

  99.           $search_array['criteria'][$i]['operation']    = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['operation'];

  100.         }

  101. 

  102.         // get the list of publications from the remote database using the search criteria.

  103.         $page = isset($_GET['page']) ? $_GET['page'] : '0';

  104.         $offset = $page * $limit;

  105.         $total_records = 0;

  106.         $pubs = tripal_search_publications($search_array, $offset, $limit, $total_records);

  107.         pager_default_initialize($total_records, $limit, 0);

  108. 

  109.         // iterate through the results and construct the table displaying the publications

  110.         $rows = array();

  111.         $i = $page * $limit + 1;

  112.         foreach ($pubs as $pub) {

  113.           // get the citation for this publication

  114.           $values = array(

  115.             'pub_id' => $pub->pub_id,

  116.             'type_id' => array(

  117.               'name' => 'Citation',

  118.             ),

  119.           );

  120.           $citation_rec = chado_generate_var('pubprop', $values);

  121.           $citation_rec = chado_expand_var($citation_rec, 'field', 'pubprop.value');

  122. 

  123.           // if we have the citation then use it, otherwise, just use the title

  124.           $title = htmlspecialchars($pub->title);

  125.           $result = $title;

  126.           $link = NULL;

  127. 

  128.           // tripal v2 link (node)

  129.           if (module_exists('tripal_pub')) {

  130.             $nid = chado_get_nid_from_id ('pub', $pub->pub_id);

  131.             if ($nid) {

  132.               $link = "/node/$nid";

  133.             }

  134.           }

  135.           // try tripal v3 link (entity), if it exists, update the link to entity

  136.           $entity_id = chado_get_record_entity_by_table('pub', $pub->pub_id);

  137.           if ($entity_id) {

  138.             $link = "/bio_data/$entity_id";

  139.           }

  140. 

  141.           if ($link) {

  142.             $result = l($title , $link, array('attributes' => array('target' => '_blank')));

  143.           }

  144.           if ($citation_rec->value) {

  145.             $citation = htmlspecialchars($citation_rec->value);

  146.             $result .= '<br>' . $citation;

  147.           }

  148.           $rows[] = array(

  149.             number_format($i) . ".",

  150.             $pub->pyear,

  151.             $result

  152.           );

  153.           $i++;

  154.         }

  155. 

  156.         $headers = array('', 'Year', 'Reference');

  157.         $table = array(

  158.           'header' => $headers,

  159.           'rows' => $rows,

  160.           'attributes' => array(

  161.             'id' => 'tripal-pub-search-results-table',

  162.             'border' => '0',

  163.             'class' => array('tripal-data-table')

  164.           ),

  165.           'sticky' => TRUE,

  166.           'caption' => '',

  167.           'colgroups' => array(),

  168.           'empty' => 'No publications found',

  169.         );

  170.         $results = theme_table($table);

  171. 

  172.         // generate the pager

  173.         $pager = array(

  174.           'tags' => array(),

  175.           'element' => 0,

  176.           'parameters' => array(),

  177.           'quantity' => $limit,

  178.         );

  179.         $pager = theme_pager($pager);

  180. 

  181.         // join all to form the results

  182.         $output .= "<p><b>Found " . number_format($total_records) .

  183.         " Results</b></br>" . $results . $pager;

  184.       }

  185.       return $output;

  186. }

  187. 

  188. /**

  189.  * Provides the form to search pubmed

  190.  *

  191.  * @ingroup tripal_pub

  192.  */

  193. function tripal_chado_pub_search_form($form, &$form_state) {

  194.   // Default values can come in the following ways:

  195.   //

  196.   // 1) as elements of the $pub_importer object.  This occurs when editing an existing importer

  197.   // 2) in the $form_state['values'] array which occurs on a failed validation or

  198.   //    ajax callbacks from non submit form elements

  199.   // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit

  200.   //    form elements and the form is being rebuilt

  201.   //

  202. 

  203.   // Set the default values. If the pub_import_id isn't already defined by the form values

  204.   // and one is provided then look it up in the database

  205.   $criteria = NULL;

  206.   $num_criteria = 2;

  207.   $from_year = '';

  208.   $to_year = '';

  209. 

  210.   // if the session has variables then use those.  This should only happen when

  211.   // the 'Test Criteria' button is clicked.

  212.   if (array_key_exists('storage', $form_state)) {

  213.     $num_criteria = $form_state['storage']['num_criteria'];

  214.   }

  215.   if (array_key_exists('tripal_chado_pub_search_form', $_SESSION)) {

  216.     $num_criteria = $_SESSION['tripal_chado_pub_search_form']['num_criteria'] ? $_SESSION['tripal_chado_pub_search_form']['num_criteria'] : $num_criteria;

  217.     $from_year    = $_SESSION['tripal_chado_pub_search_form']['from_year']    ? $_SESSION['tripal_chado_pub_search_form']['from_year']    : '';

  218.     $to_year      = $_SESSION['tripal_chado_pub_search_form']['to_year']      ? $_SESSION['tripal_chado_pub_search_form']['to_year']      : '';

  219.   }

  220.   if (array_key_exists('values', $form_state)) {

  221.     $from_year    = $form_state['values']['from_year']    ? $form_state['values']['from_year']    : $from_year;

  222.     $to_year      = $form_state['values']['to_year']      ? $form_state['values']['to_year']      : $to_year;

  223.   }

  224.   if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {

  225.     $from_year    = $form_state['input']['from_year']    ? $form_state['input']['from_year']    : $from_year;

  226.     $to_year      = $form_state['input']['to_year']      ? $form_state['input']['to_year']      : $to_year;

  227.   }

  228. 

  229.   if (array_key_exists('triggering_element', $form_state) and

  230.       $form_state['triggering_element']['#name'] == 'add') {

  231.         $num_criteria++;

  232.   }

  233.   if (array_key_exists('triggering_element', $form_state) and

  234.       $form_state['triggering_element']['#name'] == 'remove') {

  235.         $num_criteria--;

  236.   }

  237. 

  238.   $form_state['storage']['num_criteria'] = $num_criteria;

  239. 

  240.   $form['admin-instructions'] = array(

  241.     '#markup'  =>  tripal_set_message(

  242.         t('Administrators, you can select the fields with which a user can use to search, by checking the desired fields on the ' .

  243.         l('Publication Search Settings Page', 'admin/tripal/storage/chado/pub-search-config', array('attributes' => array('target' => '_blank'))) . '

  244.       in the section titled "Search Options".  The selected fields will appear in the dropdowns below.'),

  245.       TRIPAL_INFO,

  246.       array('return_html' => 1)),

  247.   );

  248.   $form['instructions'] = array(

  249.     '#markup'  =>  t('To search for publications enter keywords in the text boxes below.

  250.     You can limit your search by selecting the field in the dropdown box. Click the

  251.     add and remove buttons to add additional fields for searching. '),

  252.   );

  253. 

  254.   // get publication properties list

  255.   $properties = array();

  256.   $properties[] = 'Any Field';

  257.   $sql = "

  258.     SELECT DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition

  259.     FROM {cvtermpath} CVTP

  260.       INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id

  261.       INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id

  262.       INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id

  263.     WHERE CV.name = 'tripal_pub' and

  264.       (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and

  265.       NOT CVTS.is_obsolete = 1

  266.     ORDER BY CVTS.name ASC

  267.   ";

  268.   $allowed_fields = variable_get('tripal_pub_allowed_search_fields', array());

  269.   $prop_types = chado_query($sql);

  270.   foreach ($prop_types as $prop) {

  271.     if(array_key_exists($prop->cvterm_id, $allowed_fields) and $allowed_fields[$prop->cvterm_id] > 0) {

  272.       $properties[$prop->cvterm_id] = $prop->name;

  273.     }

  274.   }

  275. 

  276.   for($i = 1; $i <= $num_criteria; $i++) {

  277.     $search_terms = '';

  278.     $scope = '';

  279.     $operation = '';

  280.     $mode = '';

  281. 

  282.     // first populate defaults using any values in the SESSION variable

  283.     if (array_key_exists('tripal_chado_pub_search_form', $_SESSION)) {

  284.       $search_terms = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['search_terms'] ? $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['search_terms'] : $search_terms;

  285.       $scope        = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['scope']        ? $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['scope']        : $scope;

  286.       $mode         = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['mode']         ? $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['mode']         : $mode;

  287.       $operation    = $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['operation']    ? $_SESSION['tripal_chado_pub_search_form']['criteria'][$i]['operation']    : $operation;

  288.     }

  289.     if (array_key_exists('values', $form_state)) {

  290.       $search_terms = array_key_exists("search_terms-$i", $form_state['values']) ? $form_state['values']["search_terms-$i"] : $search_terms;

  291.       $scope        = array_key_exists("scope-$i", $form_state['values'])        ? $form_state['values']["scope-$i"]        : $scope;

  292.       $mode         = array_key_exists("mode-$i", $form_state['values'])         ? $form_state['values']["mode-$i"]         : $mode;

  293.       $operation    = array_key_exists("operation-$i", $form_state['values'])    ? $form_state['values']["operation-$i"]    : $operation;

  294.     }

  295.     if (array_key_exists('input', $form_state)) {

  296.       $search_terms = array_key_exists("search_terms-$i", $form_state['input']) ? $form_state['input']["search_terms-$i"] : $search_terms;

  297.       $scope        = array_key_exists("scope-$i", $form_state['input'])        ? $form_state['input']["scope-$i"]        : $scope;

  298.       $mode         = array_key_exists("mode-$i", $form_state['input'])         ? $form_state['input']["mode-$i"]         : $mode;

  299.       $operation    = array_key_exists("operation-$i", $form_state['input'])    ? $form_state['input']["operation-$i"]    : $operation;

  300.     }

  301. 

  302.     // default to searching the title and abstract

  303.     if (!$scope) {

  304.       $scope = 'abstract';

  305.     }

  306. 

  307.     $form['criteria'][$i]["search_terms-$i"] = array(

  308.       '#type'          => 'textfield',

  309.       '#default_value' => $search_terms,

  310.       '#required'      => FALSE,

  311.     );

  312.     $form['criteria'][$i]["scope-$i"] = array(

  313.       '#type'          => 'select',

  314.       '#options'       => $properties,

  315.       '#default_value' => $scope,

  316.       '#attributes' => array('class' => array('tripal-pub-search-form-scope-select')),

  317.     );

  318.     /*

  319.      $form['criteria'][$i]["mode-$i"] = array(

  320.      '#type'          => 'select',

  321.      '#options'       => array(

  322.      'Contains'    => 'Contains',

  323.      'Starts With' => 'Starts With',

  324.      'Ends With'   => 'Ends With',

  325.      'Exactly'     => 'Exactly'),

  326.      '#default_value' => $mode,

  327.      );*/

  328. 

  329.     if ($i > 1) {

  330.       $form['criteria'][$i]["operation-$i"] = array(

  331.         '#type'          => 'select',

  332.         '#options'       => array(

  333.           'AND' => 'AND',

  334.           'OR'  => 'OR',

  335.           'NOT' => 'NOT'),

  336.         '#default_value' => $operation,

  337.       );

  338.     }

  339.     if ($i == $num_criteria) {

  340.       if($i > 1) {

  341.         $form['criteria'][$i]["remove-$i"] = array(

  342.           '#type'  => 'button',

  343.           '#name'  => 'remove',

  344.           '#value' => t('Remove'),

  345.           '#ajax' => array(

  346.             'callback' => "tripal_pubs_search_form_ajax_update",

  347.             'wrapper'  => 'tripal-pub-search-form-criteria',

  348.             'effect'   => 'fade',

  349.             'method'   => 'replace',

  350.             'prevent'  => 'click'

  351.           ),

  352.           // When this button is clicked, the form will be validated and submitted.

  353.           // Therefore, we set custom submit and validate functions to override the

  354.           // default form submit.  In the validate function we set the form_state

  355.           // to rebuild the form so the submit function never actually gets called,

  356.           // but we need it or Drupal will run the default validate anyway.

  357.           // we also set #limit_validation_errors to empty so fields that

  358.           // are required that don't have values won't generate warnings.

  359.           '#submit'   => array('tripal_chado_pub_search_form_ajax_button_submit'),

  360.           '#validate' => array('tripal_chado_pub_search_form_ajax_button_validate'),

  361.           '#limit_validation_errors' => array(),

  362.         );

  363.       }

  364.       $form['criteria'][$i]["add-$i"] = array(

  365.         '#type'  => 'button',

  366.         '#name'  => 'add',

  367.         '#value' => t('Add'),

  368.         '#ajax' => array(

  369.           'callback' => "tripal_pubs_search_form_ajax_update",

  370.           'wrapper'  => 'tripal-pub-search-form-criteria',

  371.           'effect'   => 'fade',

  372.           'method'   => 'replace',

  373.           'prevent'  => 'click'

  374.         ),

  375.         // When this button is clicked, the form will be validated and submitted.

  376.         // Therefore, we set custom submit and validate functions to override the

  377.         // default form submit.  In the validate function we set the form_state

  378.         // to rebuild the form so the submit function never actually gets called,

  379.         // but we need it or Drupal will run the default validate anyway.

  380.         // we also set #limit_validation_errors to empty so fields that

  381.         // are required that don't have values won't generate warnings.

  382.         '#submit'   => array('tripal_chado_pub_search_form_ajax_button_submit'),

  383.         '#validate' => array('tripal_chado_pub_search_form_ajax_button_validate'),

  384.         '#limit_validation_errors' => array(),

  385.       );

  386.     }

  387.   }

  388.   $form['criteria']["date"] = array(

  389.     '#type'          => 'select',

  390.     '#options'       => array('Years' => 'Years'),

  391.     '#attributes'    => array('class' => array('tripal-pub-search-form-scope-select')),

  392.   );

  393.   $form['criteria']["from_year"] = array(

  394.     '#type'          => 'textfield',

  395.     '#default_value' => $from_year,

  396.     '#required'      => FALSE,

  397.     '#title'         => 'from',

  398.     '#size'          => 4,

  399.     '#maxlength'     => 4,

  400.   );

  401.   $form['criteria']["to_year"] = array(

  402.     '#type'          => 'textfield',

  403.     '#default_value' => $to_year,

  404.     '#required'      => FALSE,

  405.     '#title'         => 'to',

  406.     '#size'          => 4,

  407.     '#maxlength'     => 4,

  408.   );

  409. 

  410.   $form['search'] = array(

  411.     '#type'         => 'submit',

  412.     '#value'        => t('Search'),

  413.   );

  414.   $form['reset'] = array(

  415.     '#type'         => 'submit',

  416.     '#value'        => t('Reset'),

  417.   );

  418. 

  419.   $form['criteria']['#theme'] = 'tripal_chado_pub_search_setup_form_elements';

  420. 

  421.   return $form;

  422. }

  423. 

  424. /**

  425.  * This function is used to rebuild the form if an ajax call is made vai a button.

  426.  * The button causes the form to be submitted. We don't want this so we override

  427.  * the validate and submit routines on the form button. Therefore, this function

  428.  * only needs to tell Drupal to rebuild the form

  429.  *

  430.  * @ingroup tripal_pub

  431.  */

  432. function tripal_chado_pub_search_form_ajax_button_submit() {

  433.   $form_state['rebuild'] = TRUE;

  434. }

  435. 

  436. /**

  437.  * This function is just a dummy to override the default form submit on ajax calls for buttons

  438.  *

  439.  * @ingroup tripal_pub

  440.  */

  441. function tripal_chado_pub_search_form_ajax_button_validate() {

  442.   // do nothing

  443. }

  444. 

  445. /**

  446.  * Validate the tripal_chado_pub_search_form form

  447.  *

  448.  * @ingroup tripal_pub

  449.  */

  450. function tripal_chado_pub_search_form_validate($form, &$form_state) {

  451.   $num_criteria = $form_state['storage']['num_criteria'];

  452.   $from_year    = $form_state['values']['from_year'];

  453.   $to_year      = $form_state['values']['to_year'];

  454.   $op           = $form_state['values']['op'];

  455. 

  456.   // no need to vlaidate on a reset

  457.   if ($op == 'Reset') {

  458.     return;

  459.   }

  460. 

  461.   if($from_year and !$to_year) {

  462.     form_set_error('to_year', 'Please provide a 4-digit year.');

  463.   }

  464.   if(!$from_year and $to_year) {

  465.     form_set_error('from_year', 'Please provide a 4-digit year.');

  466.   }

  467.   if($from_year and !preg_match('/\d\d\d\d/' , $from_year)) {

  468.     form_set_error('from_year', 'Please provide a 4-digit year.');

  469.   }

  470.   if($to_year and !preg_match('/\d\d\d\d/' , $to_year)) {

  471.     form_set_error('to_year', 'Please provide a 4-digit year.');

  472.   }

  473. }

  474. 

  475. /**

  476.  * Submit the tripal_chado_pub_search_form form

  477.  *

  478.  * @ingroup tripal_pub

  479.  */

  480. function tripal_chado_pub_search_form_submit($form, &$form_state) {

  481.   $num_criteria = $form_state['storage']['num_criteria'];

  482.   $from_year    = $form_state['values']['from_year'];

  483.   $to_year      = $form_state['values']['to_year'];

  484.   $op           = $form_state['values']['op'];

  485. 

  486.   // set the session variables

  487.   if($op == 'Search') {

  488.     $_SESSION['tripal_chado_pub_search_form']['num_criteria'] = $num_criteria;

  489.     unset($_SESSION['tripal_chado_pub_search_form']['criteria']);

  490.     for ($i = 0; $i <= $num_criteria; $i++) {

  491.       $search_terms = '';

  492.       $scope = '';

  493.       $mode = 'Contains';

  494.       $operation = '';

  495.       if (array_key_exists("search_terms-$i", $form_state['values'])) {

  496.         $search_terms =  trim($form_state['values']["search_terms-$i"]);

  497.       }

  498.       if (array_key_exists("scope-$i", $form_state['values'])) {

  499.         $scope =  $form_state['values']["scope-$i"];

  500.       }

  501.       if (array_key_exists("operation-$i", $form_state['values'])) {

  502.         $operation =  $form_state['values']["operation-$i"];

  503.       }

  504.       //$mode =  $form_state['values']["mode-$i"];

  505. 

  506.       $_SESSION['tripal_chado_pub_search_form']['criteria'][$i] = array(

  507.         'search_terms' => $search_terms,

  508.         'scope' => $scope,

  509.         'mode' => $mode,

  510.         'operation' => $operation

  511.       );

  512. 

  513.     }

  514.     $_SESSION['tripal_chado_pub_search_form']['from_year'] = $from_year;

  515.     $_SESSION['tripal_chado_pub_search_form']['to_year'] = $to_year;

  516.     $_SESSION['tripal_chado_pub_search_form']['perform_search'] = 1;

  517.   }

  518.   if($op == 'Reset') {

  519.     unset($_SESSION['tripal_chado_pub_search_form']);

  520.   }

  521. }

  522. 

  523. 

  524. /**

  525.  * Ajax callback to update the form

  526.  *

  527.  * @param $form

  528.  *   The form array

  529.  * @param $form_state

  530.  *   The form state array

  531.  *

  532.  * @ingroup tripal_pub

  533.  */

  534. function tripal_pubs_search_form_ajax_update($form, $form_state) {

  535.   return $form['criteria'];

  536. }

  537. 

  538. /**

  539.  * Theme the tripal_chado_pub_search_setup_form form

  540.  *

  541.  * @ingroup tripal_pub

  542.  */

  543. function theme_tripal_chado_pub_search_setup_form_elements($variables) {

  544.   $form = $variables['form'];

  545. 

  546.   $rows = array();

  547.   // put each criteria element in a single table row

  548.   foreach ($form as $i => $element) {

  549.     if(is_numeric($i)) {

  550.       $rows[] = array(

  551.         drupal_render($element["operation-$i"]),

  552.         drupal_render($element["scope-$i"]),

  553.         //drupal_render($element["mode-$i"]) .

  554.         drupal_render($element["search_terms-$i"]),

  555.         array(

  556.           'data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]),

  557.           'nowrap' => 'nowrap',

  558.         ),

  559.       );

  560.     }

  561.   }

  562. 

  563.   // add in the from_year and to_year elements as the final row of the table

  564.   $rows[] = array(

  565.     '&nbsp;',

  566.     drupal_render($form['date']),

  567.     array(

  568.       'data' =>

  569.       "<div id=\"pub-search-form-dates-row\">

  570.          <div id=\"pub-search-form-dates\"> ".

  571.            drupal_render($form['from_year']) .

  572.            drupal_render($form['to_year']) . "

  573.          </div>

  574.        </div>

  575.       ",

  576.     ),

  577.     ''

  578.   );

  579. 

  580.   $headers = array();

  581.   $table = array(

  582.     'header' => $headers,

  583.     'rows' => $rows,

  584.     'attributes' => array(

  585.       'id' => 'tripal-pub-search-form-table',

  586.       'border' => '0',

  587.       'class' => 'tripal-data-table'

  588.     ),

  589.     'sticky' => TRUE,

  590.     'caption' => '',

  591.     'colgroups' => array(),

  592.     'empty' => '',

  593.   );

  594.   $results  = '<div id="tripal-pub-search-form-criteria">';

  595.   $results .= theme_table($table);

  596.   $results .= '</div>';

  597.   return $results;

  598. }

  599. 

  600. 

  601. /**

  602.  * Builds the SQL statement need to search Chado for the publications

  603.  * that match the user supplied criteria.  Tpyically, this function is

  604.  * called by the search form generated by the tripal_chado_pub_search_form()

  605.  * function but this function is included in the API for calling by anyone.

  606.  *

  607.  * @param $search_array

  608.  *   An array of search criteria provided by the user. The search array is

  609.  *   an associative array with the following keys:

  610.  *     'num_criteria': an integer indicating the number of search criteria

  611.  *        supplied

  612.  *     'from_year':    filters records by a start year

  613.  *     'to_year':      filters records by an end year

  614.  *     'criteria':     an array of criteria. Each criteria is an associative

  615.  *                     array with the following keys:

  616.  *                     'search_terms':   The text used for searching

  617.  *                     'scope':          The cvterm_id of the property used for

  618.  *                        filtering

  619.  *                     'mode':           The operation (e.g. AND, OR or NOT)

  620.  * @param $offset

  621.  *   The offset for paging records.  The first record returned will be

  622.  *   at the offset indicated here, and the next $limit number of records

  623.  *   will be returned.

  624.  *

  625.  * @param $limit

  626.  *   The number of records to retrieve

  627.  *

  628.  * @param total_records

  629.  *   A value passed by reference. This value will get set to the total

  630.  *   number of matching records

  631.  *

  632.  * @return

  633.  *   a PDO database object of the query results.

  634.  *

  635.  * @ingroup tripal_pub

  636.  */

  637. function tripal_search_publications($search_array, $offset, $limit, &$total_records) {

  638. 

  639.   // Build the SQL based on the criteria provided by the user

  640.   $select = "SELECT DISTINCT P.* ";

  641.   $from   = "FROM {pub} P INNER JOIN {cvterm} CVT on CVT.cvterm_id = P.type_id ";

  642.   $where  = "WHERE (NOT P.title = 'null') ";

  643.   $order  = "ORDER BY P.pyear DESC, P.title ASC";

  644.   $args = array();

  645.   $join = 0;

  646. 

  647.   $num_criteria = $search_array['num_criteria'];

  648.   $from_year    = $search_array['from_year'];

  649.   $to_year      = $search_array['to_year'];

  650. 

  651.   for ($i = 1; $i <= $num_criteria; $i++) {

  652.     $value = $search_array['criteria'][$i]['search_terms'];

  653.     $type_id = $search_array['criteria'][$i]['scope'];

  654.     $mode = $search_array['criteria'][$i]['mode'];

  655.     $op = $search_array['criteria'][$i]['operation'];

  656. 

  657.     // skip criteria with no values

  658.     if(!$value) {

  659.       continue;

  660.     }

  661. 

  662.     // to prevent SQL injection make sure our operator is

  663.     // what we expect

  664.     if ($op and $op != "AND" and $op != "OR" and $op != 'NOT') {

  665.       $op = 'AND';

  666.     }

  667.     if ($op == 'NOT') {

  668.       $op = 'AND NOT';

  669.     }

  670.     if (!$op) {

  671.       $op = 'AND';

  672.     }

  673. 

  674.     // get the scope type

  675.     $values = array('cvterm_id' => $type_id);

  676.     $cvterm = chado_select_record('cvterm', array('name'), $values);

  677.     $type_name = '';

  678.     if (count($cvterm) > 0) {

  679.       $type_name = $cvterm[0]->name;

  680.     }

  681.     if ($type_name == 'Title') {

  682.       $where .= " $op (lower(P.title) LIKE lower(:crit$i)) ";

  683.       $args[":crit$i"] = '%' . $value . '%';

  684.     }

  685.     elseif ($type_name == 'Year') {

  686.       $where .= " $op (lower(P.pyear) = lower(:crit$i)) ";

  687.       $args[":crit$i"] = '%' . $value . '%';

  688.     }

  689.     elseif ($type_name == 'Volume') {

  690.       $where .= " $op (lower(P.volume) = lower(:crit$i)) ";

  691.       $args[":crit$i"] = '%' . $value . '%';

  692.     }

  693.     elseif ($type_name == 'Issue') {

  694.       $where .= " $op (lower(P.issue) = lower(:crit$i)) ";

  695.       $args[":crit$i"] = '%' . $value . '%';

  696.     }

  697.     elseif ($type_name == 'Journal Name') {

  698.       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id AND PP$i.type_id = :crit$i ";

  699.       $where .= " $op ((lower(P.series_name) = lower(:crit$i) and CVT.name = 'Journal Article') OR

  700.       (lower(PP$i.value) = lower(:crit$i))) ";

  701.       $args[":crit$i"] = $type_id;

  702.     }

  703.     elseif ($type_name == 'Conference Name') {

  704.       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id AND PP$i.type_id = :crit$i ";

  705.       $where .= " $op ((lower(P.series_name) = lower(:crit$i) and CVT.name = 'Conference Proceedings') OR

  706.       (lower(PP$i.value) = lower(:crit$i))) ";

  707.       $args[":crit$i"] = $type_id;

  708.     }

  709.     elseif ($type_name == 'Publication Type') {

  710.       $where .= " $op (lower(CVT.name) = lower(:crit$i))";

  711.       $args[":crit$i"] = $value;

  712.     }

  713.     elseif ($type_id == 0) { //'Any Field'

  714.       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id ";

  715.       $where .= " $op (lower(PP$i.value)  LIKE lower(:crit$i) OR

  716.       lower(P.title) LIKE lower(:crit$i) OR

  717.       lower(P.volumetitle) LIKE lower(:crit$i) OR

  718.       lower(P.publisher) LIKE lower(:crit$i) OR

  719.       lower(P.uniquename) LIKE lower(:crit$i) OR

  720.       lower(P.pubplace) LIKE lower(:crit$i) OR

  721.       lower(P.miniref) LIKE lower(:crit$i) OR

  722.       lower(P.series_name) LIKE lower(:crit$i)) ";

  723.       $args[":crit$i"] = '%' . $value . '%';

  724.     }

  725.     // for all other properties

  726.     else {

  727.       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id AND PP$i.type_id = :type_id$i ";

  728.       $where .= " $op (lower(PP$i.value) LIKE lower(:crit$i)) ";

  729.       $args[":crit$i"] = '%' . $value . '%';

  730.       $args[":type_id$i"] = $type_id;

  731.     }

  732.   }

  733.   if($from_year and $to_year) {

  734.     $where .= " AND (P.pyear ~ '....' AND to_number(P.pyear,'9999') >= :from$i AND to_number(P.pyear,'9999') <= :to$i) ";

  735.     $args[":from$i"] = $from_year;

  736.     $args[":to$i"] = $to_year;

  737.   }

  738.   $sql = "$select $from $where $order  LIMIT " . (int) $limit . ' OFFSET ' . (int) $offset;

  739.   $count = "SELECT count(*) FROM ($select $from $where $order) as t1";

  740. 

  741.   // first get the total number of matches

  742.   $total_records = chado_query($count, $args)->fetchField();

  743.   $results = chado_query($sql, $args);

  744. 

  745.   return $results;

  746. }