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							- <?php
 
- /**
 
-  * @file
 
-  * 
 
-  * Functions responsible for creating the publication search form that 
 
-  * allows a user of the site to search for publications that are currently 
 
-  * in Chado.
 
-  */
 
- /**
 
-  * The page that contains the publication search form and the results for the search
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_search_page() {
 
-   $limit = 25;
 
-   // generate the search form
 
-   $form = drupal_get_form('tripal_pub_search_form');
 
-   $output = drupal_render($form);
 
-   // retrieve any results
 
-   if (array_key_exists('tripal_pub_search_form', $_SESSION) and
 
-       $_SESSION['tripal_pub_search_form']['perform_search']) {
 
-     $num_criteria = $_SESSION['tripal_pub_search_form']['num_criteria'];
 
-     $from_year    = $_SESSION['tripal_pub_search_form']['from_year'];
 
-     $to_year      = $_SESSION['tripal_pub_search_form']['to_year'];
 
-     $search_array = array();
 
-     $search_array['num_criteria'] = $num_criteria;
 
-     $search_array['from_year']    = $from_year;
 
-     $search_array['to_year']      = $to_year;
 
-     for ($i = 0; $i <= $num_criteria; $i++) {
 
-       $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_search_form']['criteria'][$i]['search_terms'];
 
-       $search_array['criteria'][$i]['scope']        = $_SESSION['tripal_pub_search_form']['criteria'][$i]['scope'];
 
-       $search_array['criteria'][$i]['mode']         = $_SESSION['tripal_pub_search_form']['criteria'][$i]['mode'];
 
-       $search_array['criteria'][$i]['operation']    = $_SESSION['tripal_pub_search_form']['criteria'][$i]['operation'];
 
-     }
 
-     // get the list of publications from the remote database using the search criteria.
 
-     $pubs = tripal_pub_get_search_results($search_array, $limit);
 
-     $page = isset($_GET['page']) ? $_GET['page'] : '0';
 
-     $total_records = $_SESSION['chado_pager'][0]['total_records'];
 
-     $total_pages = (int) ($total_records / $limit) + 1;
 
-     // iterate through the results and construct the table displaying the publications
 
-     $rows = array();
 
-     $i = $page * $limit + 1;
 
-     foreach ($pubs as $pub) {
 
-       // get the citation for this publication
 
-       $values = array(
 
-         'pub_id' => $pub->pub_id,
 
-         'type_id' => array(
 
-           'name' => 'Citation',
 
-         ),
 
-       );
 
-       $citation_rec = chado_generate_var('pubprop', $values);
 
-       $citation_rec = chado_expand_var($citation_rec, 'field', 'pubprop.value');
 
-       // if we have the citation then use it, otherwise, just use the title
 
-       $title = htmlspecialchars($pub->title);
 
-       $result = $title;
 
-       if ($pub->nid) {
 
-         $result = l($title ,'node/' . $pub->nid, array('attributes' => array('target' => '_blank')));
 
-       }
 
-       if ($citation_rec->value) {
 
-         $citation = htmlspecialchars($citation_rec->value);
 
-         $result .= '<br>' . $citation;
 
-       }
 
-       $rows[] = array(
 
-       number_format($i) . ".",
 
-       $pub->pyear,
 
-       $result
 
-       );
 
-       $i++;
 
-     }
 
-     if (count($rows) == 0) {
 
-       $rows[] = array(
 
-         array(
 
-           'data' => 'No results found',
 
-           'colspan' => 3
 
-         )
 
-       );
 
-     }
 
-     $headers = array('', 'Year', 'Publication');
 
-     $table = array(
 
-       'header' => $headers,
 
-       'rows' => $rows,
 
-       'attributes' => array('id' => 'tripal-pub-search-results-table', 'border' => '0'),
 
-       'sticky' => TRUE,
 
-       'caption' => '',
 
-       'colgroups' => array(),
 
-       'empty' => '',
 
-     );
 
-     $results = theme_table($table);
 
-     // generate the pager
 
-     pager_default_initialize($total_records, $limit);
 
-     $pager = array(
 
-       'tags' => array(),
 
-       'element' => 0,
 
-       'parameters' => array(),
 
-       'quantity' => $limit,
 
-     );
 
-     $pager = theme_pager($pager);
 
-     // join all to form the results
 
-     $output .= "<br><p><b>Found " . number_format($total_records) .
 
-       ". Page " . ($page + 1) . " of $total_pages. " .
 
-       " Results</b></br>" . $results . $pager;
 
-   }
 
-   return $output;
 
- }
 
- /**
 
-  * Provides the form to search pubmed
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_search_form($form, &$form_state) {
 
-   // Default values can come in the following ways:
 
-   //
 
-   // 1) as elements of the $pub_importer object.  This occurs when editing an existing importer
 
-   // 2) in the $form_state['values'] array which occurs on a failed validation or
 
-   //    ajax callbacks from non submit form elements
 
-   // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit
 
-   //    form elements and the form is being rebuilt
 
-   //
 
-   // Set the default values. If the pub_import_id isn't already defined by the form values
 
-   // and one is provided then look it up in the database
 
-   $criteria = NULL;
 
-   $num_criteria = 2;
 
-   $from_year = '';
 
-   $to_year = '';
 
-   // if the session has variables then use those.  This should only happen when
 
-   // the 'Test Criteria' button is clicked.
 
-   if (array_key_exists('tripal_pub_search_form', $_SESSION)) {
 
-     $num_criteria = $_SESSION['tripal_pub_search_form']['num_criteria'] ? $_SESSION['tripal_pub_search_form']['num_criteria'] : $num_criteria;
 
-     $from_year    = $_SESSION['tripal_pub_search_form']['from_year']    ? $_SESSION['tripal_pub_search_form']['from_year']    : '';
 
-     $to_year      = $_SESSION['tripal_pub_search_form']['to_year']      ? $_SESSION['tripal_pub_search_form']['to_year']      : '';
 
-   }
 
-   if (array_key_exists('values', $form_state)) {
 
-     $num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $num_criteria;
 
-     $from_year    = $form_state['values']['from_year']    ? $form_state['values']['from_year']    : $from_year;
 
-     $to_year      = $form_state['values']['to_year']      ? $form_state['values']['to_year']      : $to_year;
 
-   }
 
-   if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
 
-     $num_criteria = $form_state['input']['num_criteria'] ? $form_state['input']['num_criteria'] : $num_criteria;
 
-     $from_year    = $form_state['input']['from_year']    ? $form_state['input']['from_year']    : $from_year;
 
-     $to_year      = $form_state['input']['to_year']      ? $form_state['input']['to_year']      : $to_year;
 
-   }
 
-   if (array_key_exists('triggering_element', $form_state) and
 
-   $form_state['triggering_element']['#name'] == 'add') {
 
-     $num_criteria++;
 
-   }
 
-   if (array_key_exists('triggering_element', $form_state) and
 
-   $form_state['triggering_element']['#name'] == 'remove') {
 
-     $num_criteria--;
 
-   }
 
-   $form['num_criteria']= array(
 
-     '#type'          => 'hidden',
 
-     '#default_value' => $num_criteria,
 
-   );
 
-   $form['admin-instructions'] = array(
 
-     '#markup'  =>  theme('tripal_admin_message', array('message' =>
 
-       t('Administrators, you can select the fields with which a user can use to search,
 
-          by checking the desired fields on the ' .
 
-          l('Publication Module Settings Page', 'admin/tripal/chado/tripal_pub/configuration'). ' in
 
-         the section titled "Search Options".  The selected fields will appear in the dropdowns below.'))),
 
-   );
 
-   $form['instructions'] = array(
 
-     '#markup'  =>  t('To search for publications enter keywords in the text boxes below.
 
-         You can limit your search by selecting the field in the dropdown box. Click the
 
-         add and remove buttons to add additional fields for searching. '),
 
-   );
 
-   // get publication properties list
 
-   $properties = array();
 
-   $properties[] = 'Any Field';
 
-   $sql = "
 
-     SELECT DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
 
-     FROM {cvtermpath} CVTP
 
-       INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
 
-       INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
 
-       INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
 
-     WHERE CV.name = 'tripal_pub' and
 
-       (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and
 
-       NOT CVTS.is_obsolete = 1
 
-     ORDER BY CVTS.name ASC
 
-   ";
 
-   $allowed_fields = variable_get('tripal_pub_allowed_search_fields', array());
 
-   $prop_types = chado_query($sql);
 
-   foreach ($prop_types as $prop) {
 
-     if(array_key_exists($prop->cvterm_id, $allowed_fields) and $allowed_fields[$prop->cvterm_id] > 0) {
 
-       $properties[$prop->cvterm_id] = $prop->name;
 
-     }
 
-   }
 
-   for($i = 1; $i <= $num_criteria; $i++) {
 
-     $search_terms = '';
 
-     $scope = '';
 
-     $operation = '';
 
-     $mode = '';
 
-     // first populate defaults using any values in the SESSION variable
 
-     if (array_key_exists('tripal_pub_search_form', $_SESSION)) {
 
-       $search_terms = $_SESSION['tripal_pub_search_form']['criteria'][$i]['search_terms'] ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['search_terms'] : $search_terms;
 
-       $scope        = $_SESSION['tripal_pub_search_form']['criteria'][$i]['scope']        ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['scope']        : $scope;
 
-       $mode         = $_SESSION['tripal_pub_search_form']['criteria'][$i]['mode']         ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['mode']         : $mode;
 
-       $operation    = $_SESSION['tripal_pub_search_form']['criteria'][$i]['operation']    ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['operation']    : $operation;
 
-     }
 
-     if (array_key_exists('values', $form_state)) {
 
-       $search_terms = array_key_exists("search_terms-$i", $form_state['values']) ? $form_state['values']["search_terms-$i"] : $search_terms;
 
-       $scope        = array_key_exists("scope-$i", $form_state['values'])        ? $form_state['values']["scope-$i"]        : $scope;
 
-       $mode         = array_key_exists("mode-$i", $form_state['values'])         ? $form_state['values']["mode-$i"]         : $mode;
 
-       $operation    = array_key_exists("operation-$i", $form_state['values'])    ? $form_state['values']["operation-$i"]    : $operation;
 
-     }
 
-     if (array_key_exists('input', $form_state)) {
 
-       $search_terms = array_key_exists("search_terms-$i", $form_state['input']) ? $form_state['input']["search_terms-$i"] : $search_terms;
 
-       $scope        = array_key_exists("scope-$i", $form_state['input'])        ? $form_state['input']["scope-$i"]        : $scope;
 
-       $mode         = array_key_exists("mode-$i", $form_state['input'])         ? $form_state['input']["mode-$i"]         : $mode;
 
-       $operation    = array_key_exists("operation-$i", $form_state['input'])    ? $form_state['input']["operation-$i"]    : $operation;
 
-     }
 
-     // default to searching the title and abstract
 
-     if (!$scope) {
 
-       $scope = 'abstract';
 
-     }
 
-     $form['criteria'][$i]["search_terms-$i"] = array(
 
-       '#type'          => 'textfield',
 
-       '#default_value' => $search_terms,
 
-       '#required'      => FALSE,
 
-     );
 
-     $form['criteria'][$i]["scope-$i"] = array(
 
-       '#type'          => 'select',
 
-       '#options'       => $properties,
 
-       '#default_value' => $scope,
 
-       '#attributes' => array('class' => array('tripal-pub-search-form-scope-select')),
 
-     );
 
-     /*
 
-      $form['criteria'][$i]["mode-$i"] = array(
 
-      '#type'          => 'select',
 
-      '#options'       => array(
 
-      'Contains'    => 'Contains',
 
-      'Starts With' => 'Starts With',
 
-      'Ends With'   => 'Ends With',
 
-      'Exactly'     => 'Exactly'),
 
-      '#default_value' => $mode,
 
-      );*/
 
-     if ($i > 1) {
 
-       $form['criteria'][$i]["operation-$i"] = array(
 
-         '#type'          => 'select',
 
-         '#options'       => array(
 
-           'AND' => 'AND',
 
-           'OR'  => 'OR',
 
-           'NOT' => 'NOT'),
 
-         '#default_value' => $operation,
 
-       );
 
-     }
 
-     if ($i == $num_criteria) {
 
-       if($i > 1) {
 
-         $form['criteria'][$i]["remove-$i"] = array(
 
-           '#type'  => 'button',
 
-           '#name'  => 'remove',
 
-           '#value' => t('Remove'),
 
-           '#ajax' => array(
 
-             'callback' => "tripal_pubs_search_form_ajax_update",
 
-             'wrapper'  => 'tripal-pub-search-form-criteria',
 
-             'effect'   => 'fade',
 
-             'method'   => 'replace',
 
-             'prevent'  => 'click'
 
-           ),
 
-           // When this button is clicked, the form will be validated and submitted.
 
-           // Therefore, we set custom submit and validate functions to override the
 
-           // default form submit.  In the validate function we set the form_state
 
-           // to rebuild the form so the submit function never actually gets called,
 
-           // but we need it or Drupal will run the default validate anyway.
 
-           // we also set #limit_validation_errors to empty so fields that
 
-           // are required that don't have values won't generate warnings.
 
-           '#submit'   => array('tripal_pub_search_form_ajax_button_submit'),
 
-           '#validate' => array('tripal_pub_search_form_ajax_button_validate'),
 
-           '#limit_validation_errors' => array(),
 
-         );
 
-       }
 
-       $form['criteria'][$i]["add-$i"] = array(
 
-         '#type'  => 'button',
 
-         '#name'  => 'add',
 
-         '#value' => t('Add'),
 
-         '#ajax' => array(
 
-           'callback' => "tripal_pubs_search_form_ajax_update",
 
-           'wrapper'  => 'tripal-pub-search-form-criteria',
 
-           'effect'   => 'fade',
 
-           'method'   => 'replace',
 
-           'prevent'  => 'click'
 
-         ),
 
-         // When this button is clicked, the form will be validated and submitted.
 
-         // Therefore, we set custom submit and validate functions to override the
 
-         // default form submit.  In the validate function we set the form_state
 
-         // to rebuild the form so the submit function never actually gets called,
 
-         // but we need it or Drupal will run the default validate anyway.
 
-         // we also set #limit_validation_errors to empty so fields that
 
-         // are required that don't have values won't generate warnings.
 
-         '#submit'   => array('tripal_pub_search_form_ajax_button_submit'),
 
-         '#validate' => array('tripal_pub_search_form_ajax_button_validate'),
 
-         '#limit_validation_errors' => array(),
 
-       );
 
-     }
 
-   }
 
-   $form['criteria']["date"] = array(
 
-       '#type'          => 'select',
 
-       '#options'       => array('Years' => 'Years'),
 
-       '#attributes'    => array('class' => array('tripal-pub-search-form-scope-select')),
 
-   );
 
-   $form['criteria']["from_year"] = array(
 
-     '#type'          => 'textfield',
 
-     '#default_value' => $from_year,
 
-     '#required'      => FALSE,
 
-     '#title'         => 'from',
 
-     '#size'          => 4,
 
-     '#maxlength'     => 4,
 
-   );
 
-   $form['criteria']["to_year"] = array(
 
-     '#type'          => 'textfield',
 
-     '#default_value' => $to_year,
 
-     '#required'      => FALSE,
 
-     '#title'         => 'to',
 
-     '#size'          => 4,
 
-     '#maxlength'     => 4,
 
-   );
 
-   $form['search'] = array(
 
-     '#type'         => 'submit',
 
-     '#value'        => t('Search'),
 
-   );
 
-   $form['reset'] = array(
 
-     '#type'         => 'submit',
 
-     '#value'        => t('Reset'),
 
-   );
 
-   $form['criteria']['#theme'] = 'tripal_pub_search_setup_form_elements';
 
-   return $form;
 
- }
 
- /**
 
-  * This function is used to rebuild the form if an ajax call is made vai a button.
 
-  * The button causes the form to be submitted. We don't want this so we override
 
-  * the validate and submit routines on the form button. Therefore, this function
 
-  * only needs to tell Drupal to rebuild the form
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_search_form_ajax_button_submit() {
 
-   $form_state['rebuild'] = TRUE;
 
- }
 
- /**
 
-  * This function is just a dummy to override the default form submit on ajax calls for buttons
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_search_form_ajax_button_validate() {
 
-   // do nothing
 
- }
 
- /**
 
-  * Validate the tripal_pub_search_form form
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_search_form_validate($form, &$form_state) {
 
-   $num_criteria = $form_state['values']['num_criteria'];
 
-   $from_year    = $form_state['values']['from_year'];
 
-   $to_year      = $form_state['values']['to_year'];
 
-   $op           = $form_state['values']['op'];
 
-   // no need to vlaidate on a reset
 
-   if ($op == 'Reset') {
 
-     return;
 
-   }
 
-   if($from_year and !$to_year) {
 
-     form_set_error('to_year', 'Please provide a 4-digit year.');
 
-   }
 
-   if(!$from_year and $to_year) {
 
-     form_set_error('from_year', 'Please provide a 4-digit year.');
 
-   }
 
-   if($from_year and !preg_match('/\d\d\d\d/' , $from_year)) {
 
-     form_set_error('from_year', 'Please provide a 4-digit year.');
 
-   }
 
-   if($to_year and !preg_match('/\d\d\d\d/' , $to_year)) {
 
-     form_set_error('to_year', 'Please provide a 4-digit year.');
 
-   }
 
- }
 
- /**
 
-  * Submit the tripal_pub_search_form form
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_search_form_submit($form, &$form_state) {
 
-   $num_criteria = $form_state['values']['num_criteria'];
 
-   $from_year    = $form_state['values']['from_year'];
 
-   $to_year      = $form_state['values']['to_year'];
 
-   $op           = $form_state['values']['op'];
 
-   // set the session variables
 
-   if($op == 'Search') {
 
-     $_SESSION['tripal_pub_search_form']['num_criteria'] = $num_criteria;
 
-     unset($_SESSION['tripal_pub_search_form']['criteria']);
 
-     for ($i = 0; $i <= $num_criteria; $i++) {
 
-       $search_terms = '';
 
-       $scope = '';
 
-       $mode = 'Contains';
 
-       $operation = '';
 
-       if (array_key_exists("search_terms-$i", $form_state['values'])) {
 
-         $search_terms =  trim($form_state['values']["search_terms-$i"]);
 
-       }
 
-       if (array_key_exists("scope-$i", $form_state['values'])) {
 
-         $scope =  $form_state['values']["scope-$i"];
 
-       }
 
-       if (array_key_exists("operation-$i", $form_state['values'])) {
 
-         $operation =  $form_state['values']["operation-$i"];
 
-       }
 
-       //$mode =  $form_state['values']["mode-$i"];
 
-       $_SESSION['tripal_pub_search_form']['criteria'][$i] = array(
 
-         'search_terms' => $search_terms,
 
-         'scope' => $scope,
 
-         'mode' => $mode,
 
-         'operation' => $operation
 
-       );
 
-     }
 
-     $_SESSION['tripal_pub_search_form']['from_year'] = $from_year;
 
-     $_SESSION['tripal_pub_search_form']['to_year'] = $to_year;
 
-     $_SESSION['tripal_pub_search_form']['perform_search'] = 1;
 
-   }
 
-   if($op == 'Reset') {
 
-     unset($_SESSION['tripal_pub_search_form']);
 
-   }
 
- }
 
- /**
 
-  * Builds the SQL statement need to search Chado for the publications
 
-  * that match the user supplied criteria
 
-  *
 
-  * @param $search_array
 
-  *   An array of search criteria provided by the user
 
-  * @param $limit
 
-  *   The numbe of records to retrieve
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pub_get_search_results($search_array, $limit) {
 
-   // build the SQL based on the criteria provided by the user
 
-   $select = "SELECT DISTINCT P.*, CP.nid ";
 
-   $from   = "FROM {pub} P
 
-                LEFT JOIN public.chado_pub CP on P.pub_id = CP.pub_id
 
-                INNER JOIN {cvterm} CVT on CVT.cvterm_id = P.type_id
 
-             ";
 
-   $where  = "WHERE (NOT P.title = 'null') "; // always exclude the dummy pub
 
-   $order  = "ORDER BY P.pyear DESC, P.title ASC";
 
-   $args = array();  // arguments for where clause
 
-   $join = 0;
 
-   $num_criteria = $search_array['num_criteria'];
 
-   $from_year    = $search_array['from_year'];
 
-   $to_year      = $search_array['to_year'];
 
-   for ($i = 1; $i <= $num_criteria; $i++) {
 
-     $value = $search_array['criteria'][$i]['search_terms'];
 
-     $type_id = $search_array['criteria'][$i]['scope'];
 
-     $mode = $search_array['criteria'][$i]['mode'];
 
-     $op = $search_array['criteria'][$i]['operation'];
 
-     // skip criteria with no values
 
-     if(!$value) {
 
-       continue;
 
-     }
 
-     // to prevent SQL injection make sure our operator is
 
-     // what we expect
 
-     if ($op and $op != "AND" and $op != "OR" and $op != 'NOT') {
 
-       $op = 'AND';
 
-     }
 
-     if ($op == 'NOT') {
 
-       $op = 'AND NOT';
 
-     }
 
-     if (!$op) {
 
-       $op = 'AND';
 
-     }
 
-     // get the scope type
 
-     $values = array('cvterm_id' => $type_id);
 
-     $cvterm = chado_select_record('cvterm', array('name'), $values);
 
-     $type_name = '';
 
-     if (count($cvterm) > 0) {
 
-       $type_name = $cvterm[0]->name;
 
-     }
 
-     if ($type_name == 'Title') {
 
-       $where .= " $op (lower(P.title) LIKE lower(:crit$i)) ";
 
-       $args[":crit$i"] = '%' . $value . '%';
 
-     }
 
-     elseif ($type_name == 'Year') {
 
-       $where .= " $op (lower(P.pyear) = lower(:crit$i)) ";
 
-       $args[":crit$i"] = '%' . $value . '%';
 
-     }
 
-     elseif ($type_name == 'Volume') {
 
-       $where .= " $op (lower(P.volume) = lower(:crit$i)) ";
 
-       $args[":crit$i"] = '%' . $value . '%';
 
-     }
 
-     elseif ($type_name == 'Issue') {
 
-       $where .= " $op (lower(P.issue) = lower(:crit$i)) ";
 
-       $args[":crit$i"] = '%' . $value . '%';
 
-     }
 
-     elseif ($type_name == 'Journal Name') {
 
-       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id AND PP$i.type_id = :crit$i ";
 
-       $where .= " $op ((lower(P.series_name) = lower(:crit$i) and CVT.name = 'Journal Article') OR
 
-                        (lower(PP$i.value) = lower(:crit$i))) ";
 
-       $args[":crit$i"] = $type_id;
 
-     }
 
-     elseif ($type_name == 'Conference Name') {
 
-       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id AND PP$i.type_id = :crit$i ";
 
-       $where .= " $op ((lower(P.series_name) = lower(:crit$i) and CVT.name = 'Conference Proceedings') OR
 
-                        (lower(PP$i.value) = lower(:crit$i))) ";
 
-       $args[":crit$i"] = $type_id;
 
-     }
 
-     elseif ($type_name == 'Publication Type') {
 
-       $where .= " $op (lower(CVT.name) = lower(:crit$i))";
 
-       $args[":crit$i"] = $value;
 
-     }
 
-     elseif ($type_id == 0) { //'Any Field'
 
-       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id ";
 
-       $where .= " $op (lower(PP$i.value)  LIKE lower(:crit$i) OR
 
-                        lower(P.title) LIKE lower(:crit$i) OR
 
-                        lower(P.volumetitle) LIKE lower(:crit$i) OR
 
-                        lower(P.publisher) LIKE lower(:crit$i) OR
 
-                        lower(P.uniquename) LIKE lower(:crit$i) OR
 
-                        lower(P.pubplace) LIKE lower(:crit$i) OR
 
-                        lower(P.miniref) LIKE lower(:crit$i) OR
 
-                        lower(P.series_name) LIKE lower(:crit$i)) ";
 
-       $args[":crit$i"] = '%' . $value . '%';
 
-     }
 
-     // for all other properties
 
-     else {
 
-       $from .= " LEFT JOIN {pubprop} PP$i ON PP$i.pub_id = P.pub_id AND PP$i.type_id = :type_id$i ";
 
-       $where .= " $op (lower(PP$i.value) LIKE lower(:crit$i)) ";
 
-       $args[":crit$i"] = '%' . $value . '%';
 
-       $args[":type_id$i"] = $type_id;
 
-     }
 
-   }
 
-   if($from_year and $to_year) {
 
-     $where .= " AND (P.pyear ~ '....' AND to_number(P.pyear,'9999') >= :from$i AND to_number(P.pyear,'9999') <= :to$i) ";
 
-     $args[":from$i"] = $from_year;
 
-     $args[":to$i"] = $to_year;
 
-   }
 
-   $sql = "$select $from $where $order";
 
-   $count = "SELECT count(*) FROM ($select $from $where $order) as t1";
 
-   return chado_pager_query($sql, $args, $limit, 0, $count);
 
- }
 
- /**
 
-  * Ajax callback to update the form
 
-  * 
 
-  * @param $form
 
-  *   The form array
 
-  * @param $form_state
 
-  *   The form state array
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function tripal_pubs_search_form_ajax_update($form, $form_state) {
 
-   return $form['criteria'];
 
- }
 
- /**
 
-  * Theme the tripal_pub_search_setup_form form
 
-  *
 
-  * @ingroup tripal_pub
 
-  */
 
- function theme_tripal_pub_search_setup_form_elements($variables) {
 
-   $form = $variables['form'];
 
-   $rows = array();
 
-   // put each criteria element in a single table row
 
-   foreach ($form as $i => $element) {
 
-     if(is_numeric($i)) {
 
-       $rows[] = array(
 
-         drupal_render($element["operation-$i"]),
 
-         drupal_render($element["scope-$i"]),
 
-         //drupal_render($element["mode-$i"]) .
 
-         drupal_render($element["search_terms-$i"]),
 
-         array(
 
-           'data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]),
 
-           'nowrap' => 'nowrap',
 
-         ),
 
-       );
 
-     }
 
-   }
 
-   // add in the from_year and to_year elements as the final row of the table
 
-   $rows[] = array(
 
-     ' ',
 
-     drupal_render($form['date']),
 
-     array(
 
-       'data' =>
 
-         "<div id=\"pub-search-form-dates-row\">
 
-            <div id=\"pub-search-form-dates\"> ".
 
-              drupal_render($form['from_year']) .
 
-              drupal_render($form['to_year']) . "
 
-            </div>
 
-          </div>
 
-         ",
 
-     ),
 
-     ''
 
-   );
 
-   $headers = array();
 
-   $table = array(
 
-     'header' => $headers,
 
-     'rows' => $rows,
 
-     'attributes' => array('id' => 'tripal-pub-search-form-table', 'border' => '0'),
 
-     'sticky' => TRUE,
 
-     'caption' => '',
 
-     'colgroups' => array(),
 
-     'empty' => '',
 
-   );
 
-   $results  = '<div id="tripal-pub-search-form-criteria">';
 
-   $results .= theme_table($table);
 
-   $results .= '</div>';
 
-   return $results;
 
- }
 
 
  |