$pub->pub_id, 'type_id' => array( 'name' => 'Citation', ), ); $citation_rec = tripal_core_generate_chado_var('pubprop', $values); $citation_rec = tripal_core_expand_chado_vars($citation_rec, 'field', 'pubprop.value'); // if we have the citation then use it, otherwise, just use the title if ($citation_rec->value) { $pub_info = $citation_rec->value; } else { $pub_info = $pub->title; } // if the publication has a node then link to it if ($pub->nid) { $pub_info = l($pub_info ,'node/' . $pub->nid, array('attributes' => array('target' => '_blank'))); } $rows[] = array(number_format($i) . ".", $pub->pyear, $pub_info); $i++; } $headers = array('', 'Year', 'Publication'); $table = theme('table', $headers, $rows); // join all to form the results $output .= "

Found " . number_format($total_items) . ". Page " . ($page + 1) . " of $total_pages. " . " Results
" . $table . '

' . $pager; } return $output; } /** * Purpose: Provides the form to search pubmed * * @ingroup tripal_pub */ function tripal_pub_search_form(&$form_state = NULL) { tripal_core_ahah_init_form(); // 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; // if the session has variables then use those. This should only happen when // the 'Test Criteria' button is clicked. $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 the form_state has variables then use those. This happens when an error occurs on the form or the // form is resbumitted using AJAX $num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $num_criteria; // change the number of criteria based on form_state post data. if (!$num_criteria) { $num_criteria = 0; } if($form_state['post']["add-$num_criteria"]) { $num_criteria++; } if($form_state['post']["remove-$num_criteria"]) { $num_criteria--; } $form['num_criteria']= array( '#type' => 'hidden', '#default_value' => $num_criteria, ); // get publication properties list $properties = array(); $properties[] = 'Any Field'; $sql = " SELECT 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' and NOT CVTS.is_obsolete = 1 ORDER BY CVTS.name ASC "; $prop_types = chado_query($sql); while ($prop = db_fetch_object($prop_types)) { $properties[$prop->cvterm_id] = $prop->name; } for($i = 0; $i <= $num_criteria; $i++) { $search_terms = ''; $scope = ''; $operation = ''; $mode = ''; // if we have criteria supplied from the database then use that, othrewise look from the form_state or the session if ($criteria) { $search_terms = $criteria['criteria'][$i]['search_terms']; $scope = $criteria['criteria'][$i]['scope']; $mode = $criteria['criteria'][$i]['mode']; $operation = $criteria['criteria'][$i]['operation']; } // first populate defaults using any values in the SESSION variable $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; // next populate defaults using any form values $search_terms = $form_state['values']["search_terms-$i"] ? $form_state['values']["search_terms-$i"] : $search_terms; $scope = $form_state['values']["scope-$i"] ? $form_state['values']["scope-$i"] : $scope; $mode = $form_state['values']["mode-$i"] ? $form_state['values']["mode-$i"] : $mode; $operation = $form_state['values']["operation-$i"] ? $form_state['values']["operation-$i"] : $operation; // default to searching the title and abstract if (!$scope) { $scope = 'abstract'; } $form['criteria'][$i]["search_terms-$i"] = array( '#type' => 'textfield', '#description' => t('Please provide a list of words for searching"'), '#default_value' => $search_terms, '#required' => TRUE, ); $form['criteria'][$i]["scope-$i"] = array( '#type' => 'select', '#description' => t('Please select the fields to search for this term.'), '#options' => $properties, '#default_value' => $scope, ); $form['criteria'][$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 > 0) { $form['criteria'][$i]["operation-$i"] = array( '#type' => 'select', '#options' => array( 'AND' => 'AND', 'OR' => 'OR', 'NOT' => 'NOT'), '#default_value' => $operation, ); } if ($i == $num_criteria) { if($i > 0) { $form['criteria'][$i]["remove-$i"] = array( '#type' => 'image_button', '#value' => t('Remove'), '#src' => drupal_get_path('theme', 'tripal') . '/images/minus.png', '#ahah' => array( 'path' => "find/publications/criteria/minus/$i", 'wrapper' => 'tripal-pub-search-form', 'event' => 'click', 'method' => 'replace', ), '#attributes' => array('onClick' => 'return false;'), ); } $form['criteria'][$i]["add-$i"] = array( '#type' => 'image_button', '#value' => t('Add'), '#src' => drupal_get_path('theme', 'tripal') . '/images/add.png', '#ahah' => array( 'path' => "find/publications/criteria/add/$i", 'wrapper' => 'tripal-pub-search-form', 'event' => 'click', 'method' => 'replace', ), '#attributes' => array('onClick' => 'return false;'), ); } } $form['criteria']["from_year"] = array( '#type' => 'textfield', '#default_value' => $from_year, '#required' => FALSE, '#title' => 'Years 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'), ); return $form; } /* * */ function theme_tripal_pub_search_form($form) { $rows = array(); foreach ($form['criteria'] as $i => $element) { if(is_numeric($i)) { $rows[] = array( array('data' => drupal_render($element["operation-$i"]), 'width' => '10%'), array('data' => drupal_render($element["scope-$i"]), 'width' => '10%'), drupal_render($element["mode-$i"]) . drupal_render($element["search_terms-$i"]), array('data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]), 'width' => '5%'), ); } } $headers = array('Operation','Scope', 'Search Terms', ''); $markup = "
". theme('table', $headers, $rows, array('id' => 'tripal-pub-search-table')) . "
". drupal_render($form['criteria']['from_year']) . drupal_render($form['criteria']['to_year']) . '
'; $form['criteria'] = array( '#type' => 'markup', '#value' => $markup, '#weight' => -10, ); return drupal_render($form); } /** * */ function tripal_pub_search_form_validate($form, &$form_state) { $from_year = $form_state['values']['from_year']; $to_year = $form_state['values']['to_year']; if($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/' , $to_year)) { form_set_error('to_year', 'Please provide a 4-digit year.'); } } /** * */ function tripal_pub_search_form_submit($form, &$form_state) { $num_criteria = $form_state['values']['num_criteria']; $from_year = $form_state['values']['from_year']; $to_year = $form_state['values']['to_year']; // set the session variables $_SESSION['tripal_pub_search_form']['num_criteria'] = $num_criteria; unset($_SESSION['tripal_pub_search_form']['criteria']); for ($i = 0; $i <= $num_criteria; $i++) { $search_terms = trim($form_state['values']["search_terms-$i"]); $scope = $form_state['values']["scope-$i"]; $mode = $form_state['values']["mode-$i"]; $operation = $form_state['values']["operation-$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; $_SESSION['tripal_pub_search_form']['perform_search'] = 1; } /* * AHAH callback */ function tripal_pub_search_page_update_criteria($action, $i) { $status = TRUE; // prepare and render the form $form = tripal_core_ahah_prepare_form(); $data = theme('tripal_pub_search_form', $form); // bind javascript events to the new objects that will be returned // so that AHAH enabled elements will work. $settings = tripal_core_ahah_bind_events(); // return the updated JSON drupal_json( array( 'status' => $status, 'data' => $data, 'settings' => $settings, ) ); } /* * */ function tripal_pub_get_search_results($search_array, $limit, $pager_id) { // 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 "; $where = "WHERE "; $order = "ORDER BY P.pyear DESC, P.title ASC"; $args = array(); $join = 0; $num_criteria = $search_array['num_criteria']; $from_year = $search_array['from_year']; $to_year = $search_array['to_year']; for ($i = 0; $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']; // 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'; } $action = "= lower('%s')"; if($mode == 'Contains') { $action = 'LIKE lower(\'%%%s%%\')'; } if($mode == 'Starts With') { $action = '= lower(\'%%%s\')'; } if($mode == 'Ends With') { $action = '= lower(\'%s%%\')'; } // get the scope type $values = array('cvterm_id' => $type_id); $cvterm = tripal_core_chado_select('cvterm', array('name'), $values); $type_name = $cvterm[0]->name; if ($type_name == 'Title') { $where .= " $op (lower(P.title) $action) "; $args[] = $value; } elseif ($type_name == 'Year') { $where .= " $op (lower(P.pyear) $action) "; $args[] = $value; } elseif ($type_name == 'Volume') { $where .= " $op (lower(P.volume) $action) "; $args[] = $value; } elseif ($type_name == 'Issue') { $where .= " $op (lower(P.issue) $action)"; $args[] = $value; } elseif ($type_name == 'Journal Name') { $join = 1; $where .= " $op (lower(P.series_name) $action OR (lower(PP.value) $action AND PP.type_id = %d)) "; $args[] = $value; $args[] = $value; $args[] = $type_id; } elseif ($type_id == 0) { //'Any Field' $join = 1; $where .= " $op (lower(PP.value) $action OR lower(P.title) $action OR lower(P.volumetitle) $action OR lower(P.publisher) $action OR lower(P.pubplace) $action OR lower(P.miniref) $action OR lower(P.series_name) $action) "; $args[] = $value; $args[] = $value; $args[] = $value; $args[] = $value; $args[] = $value; $args[] = $value; $args[] = $value; } else { $join = 1; $where .= " $op (lower(PP.value) $action AND PP.type_id = %d) "; $args[] = $value; $args[] = $type_id; } } if ($join) { $from .= " INNER JOIN {pubprop} PP ON PP.pub_id = P.pub_id "; } if($from_year and $to_year) { $where .= " AND (to_number(P.pyear,'9999') >= %d and to_number(P.pyear,'9999') <= %d) "; $args[] = $from_year; $args[] = $to_year; } $sql = "$select $from $where $order"; $count = "SELECT count(*) FROM ($select $from $where $order) as t1"; //dpm(array($mode, $sql, $args)); return chado_pager_query($sql, $limit, $pager_id, $count, $args); }