Uses the value provided in the $id argument to find all features that match that ID by name, featurename or synonym. If it matches uniquenly to a single feature it will redirect to that feature page, otherwise, a list of matching features is shown.

File

tripal_chado/tripal_chado.module, line 1085

The Tripal Chado module.

Code

function tripal_feature_match_features_page($id) {

  // first check to see if the URL (e.g. /feature/$id) is already
  // assigned to a node. If so, then just go there.  Otherwise,
  // try to find the feature.
  $sql = "
    SELECT source
    FROM {url_alias}
    WHERE alias = :alias
  ";
  $match = db_query($sql, array(':alias' => "feature/$id"))->fetchObject();
  if ($match) {
    drupal_goto($match->source);
    return;
  }
  $sql = "
    SELECT
      F.name, F.uniquename, F.feature_id,
      O.genus, O.species, O.organism_id,
      CVT.cvterm_id, CVT.name as type_name,
      array_agg(S.name) as synonyms
    FROM {feature} F
      INNER JOIN {organism} O on F.organism_id = O.organism_id
      INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
      LEFT JOIN {feature_synonym} FS on FS.feature_id = F.feature_id
      LEFT JOIN {synonym} S on S.synonym_id = FS.synonym_id
    WHERE
      F.uniquename = :uname or
      F.name = :fname or
      S.name = :sname
    GROUP BY F.name, F.uniquename, F.feature_id, O.genus, O.species,
      O.organism_id, CVT.cvterm_id, CVT.name
  ";

  $args = array(':uname' => $id, ':fname' => $id, ':sname' => $id);
  $results = chado_query($sql, $args);

  $num_matches = $results->rowCount();

  // If there are no matches then just return a friendly message.
  if ($num_matches == 0) {
    drupal_set_message("No features matched the given name '$id'", 'warning');
    return "No matches found";
  }
  // if we have more than one match then generate the table, otherwise, redirect
  // to the matched feature
  elseif ($num_matches == 1) {
    $curr_match = $results->fetchObject();
    $entity_id = chado_get_record_entity_by_table('feature', $curr_match->feature_id);
    if ($entity_id) {
      drupal_goto("bio_data/" . $entity_id);
      return;
    }
    // If we are here it's because we couldn't find the entity. Check if a node
    // exists (Tv2 backwards compatibility).
    if (module_exists(tripal_feature)) {
      $nid = chado_get_nid_from_id('feature', $curr_match->feature_id);
      drupal_goto("node/" . $nid);
      return;
    }
    // If we are here it's because we couldn't find an entity_id or an nid
    drupal_set_message("No published features matched the given name '$id'", 'warning');
    return "No matches found";

  }
  elseif ($num_matches > 1) {
    // iterate through the matches and build the table for showing matches
    $header = array('Uniquename', 'Name', 'Type', 'Species', 'Synonyms');
    $rows = array();
    while ($match = $results->fetchObject()) {
      $curr_match = $match;
      $synonyms = $match->synonyms;
      $synonyms = preg_replace('/[\"\{\}]/', '', $synonyms);

      // Build the link to this page.
      $entity_id = chado_get_record_entity_by_table('feature', $curr_match->feature_id);
      $link = '';
      if ($entity_id) {
        $link = "bio_data/" . $entity_id;
      }
      // If we didn't find an entity ID we need to check nodes for
      // backwards compatibility with Tv2.
      if (!$entity_id and module_exists('tripal_feature')) {
        $nid = chado_get_nid_from_id('feature', $curr_match->feature_id);
        $link = "node/" . $nid;
      }
      if (!$link) {
        continue;
      }

      $rows[] = array(
        $match->uniquename,
        l($match->name, $link),
        $match->type_name,
        '<i>' . $match->genus . ' ' . $match->species . '</i>',
        $synonyms,
      );
      $num_matches++;
    }
    $table_attrs = array('class' => 'tripal-data-table');
    $output = "<p>The following features match the name '$id'.</p>";
    $output .= theme_table($header, $rows, $table_attrs, $caption);
    return $output;
  }


}