File

tripal_pub/includes/importers/PMID.inc, line 41

Tripal Pub PubMed Interface

Code

function tripal_pub_remote_search_PMID($search_array, $num_to_retrieve, $pager_id) {

  // convert the terms list provicded by the caller into a string with words
  // separated by a '+' symbol.
  $num_criteria = $search_array['num_criteria'];
  $days = $search_array['days'];

  $search_str = '';

  for ($i = 1; $i <= $num_criteria; $i++) {
    $search_terms = trim($search_array['criteria'][$i]['search_terms']);
    $scope = $search_array['criteria'][$i]['scope'];
    $is_phrase = $search_array['criteria'][$i]['is_phrase'];
    $op = $search_array['criteria'][$i]['operation'];

    if ($op) {
      $search_str .= "$op ";
    }

    // if this is phrase make sure the search terms are surrounded by quotes
    if ($is_phrase) {
      $search_str .= "(\"$search_terms\" |SCOPE|) ";
    }
    // if this is not a phase then we want to separate each 'OR or 'AND' into a unique criteria
    else {
      $search_str .= "(";
      if (preg_match('/and/i', $search_terms)) {
        $elements = preg_split('/\s+and+\s/i', $search_terms);
        foreach ($elements as $element) {
          $search_str .= "($element |SCOPE|) AND ";
        }
        $search_str = substr($search_str, 0, -5); // remove trailing 'AND '              
      }
      elseif (preg_match('/or/i', $search_terms)) {
        $elements = preg_split('/\s+or+\s/i', $search_terms);
        foreach ($elements as $element) {
          $search_str .= "($element |SCOPE|) OR ";
        }
        $search_str = substr($search_str, 0, -4); // remove trailing 'OR '        
      }
      else {
        $search_str .= "($search_terms |SCOPE|) ";
      }
      $search_str .= ') ';
    }

    if ($scope == 'title') {
      $search_str = preg_replace('/\|SCOPE\|/', '[Title]', $search_str);
    }
    elseif ($scope == 'author') {
      $search_str = preg_replace('/\|SCOPE\|/', '[Author]', $search_str);
    }
    elseif ($scope == 'abstract') {
      $search_str = preg_replace('/\|SCOPE\|/', '[Title/Abstract]', $search_str);
    }
    elseif ($scope == 'journal') {
      $search_str = preg_replace('/\|SCOPE\|/', '[Journal]', $search_str);
    }
    elseif ($scope == 'id') {
      $search_str = preg_replace('/PMID:([^\s]*)/', '$1', $search_str);
      $search_str = preg_replace('/\|SCOPE\|/', '[Uid]', $search_str);
    }
    else {
      $search_str = preg_replace('/\|SCOPE\|/', '', $search_str);
    }
  }
  if ($days) {
    // get the date of the day suggested
    $past_timestamp = time() - ($days * 86400);
    $past_date = getdate($past_timestamp);
    $search_str .= " AND (\"" . sprintf("%04d/%02d/%02d", $past_date['year'], $past_date['mon'], $past_date['mday']) . "\"[Date - Create] : \"3000\"[Date - Create]))";
  }

  $search_array['limit'] = $num_to_retrieve;
  $search_array['search_string'] = $search_str;

  //dpm($search_str);
  unset($_SESSION['tripal_pub_PMID_query']);
  // we want to get the list of pubs using the search terms but using a Drupal style pager
  $pubs = tripal_pager_callback('tripal_pub_PMID_range', $num_to_retrieve, $pager_id, 
  'tripal_pub_PMID_count', $search_array);

  return $pubs;
}