Using the chado_expand_var function to retrieve a set of relationships can be very slow, especialy if there are many relationships This function is intended to help speed up the retrieval of relationships by only retrieving the base information for the relationship and returning an array with

Parameters

$feature: The feature object

Return value

An array with two objects

Related topics

File

tripal_feature/theme/tripal_feature.theme.inc, line 781

Code

function tripal_feature_get_feature_relationships($feature) {
  // expand the feature object to include the feature relationships.
  $options = array(
    'return_array' => 1,
    'order_by' => array('rank' => 'ASC'),
    // we don't want to fully recurse we only need information about the
    // relationship type and the object and subject features (including feature type
    // and organism)
    'include_fk' => array(
      'type_id' => 1,
      'object_id' => array(
        'type_id' => 1,
        'organism_id' => 1
      ),
      'subject_id' => array(
        'type_id' => 1,
        'organism_id' => 1
      ),
    ),
  );
  $feature = chado_expand_var($feature, 'table', 'feature_relationship', $options);

  // get the subject relationships
  $srelationships = $feature->feature_relationship->subject_id;
  $orelationships = $feature->feature_relationship->object_id;


  // get alignment as child. The $feature->featureloc element
  // is already populated from the alignment preprocess function
  $options = array(
    'include_fk' => array(
      'srcfeature_id' => 1,
      'feature_id' => 1,
    ),
  );
  $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
  $cfeaturelocs = $feature->featureloc->feature_id;
  if (!$cfeaturelocs) {
    $cfeaturelocs = array();
  }
  elseif (!is_array($cfeaturelocs)) {
    $cfeaturelocs = array($cfeaturelocs);
  }

  // prepare the SQL statement to get the featureloc for the
  // feature in the relationships.
  $flrels_sql = "
    SELECT
      FL.featureloc_id, F.name as srcfeature_name, FL.srcfeature_id,
      FL.feature_id, FL.fmin, FL.fmax, FL.strand, FL.phase
    FROM {featureloc} FL
      INNER JOIN {feature} F ON F.feature_id = FL.srcfeature_id
    WHERE FL.feature_id = :feature_id and FL.srcfeature_id = :srcfeature_id
  ";

  // combine both object and subject relationshisp into a single array
  $relationships = array();
  $relationships['object'] = array();
  $relationships['subject'] = array();

  // iterate through the object relationships
  if ($orelationships) {
    foreach ($orelationships as $relationship) {
      $rel = new stdClass();
      // get locations where the child feature and this feature overlap with the
      // same landmark feature.
      $rel->child_featurelocs = array();
      foreach ($cfeaturelocs as $featureloc) {
        $res = chado_query($flrels_sql, array(':feature_id' => $relationship->subject_id->feature_id, ':srcfeature_id' => $featureloc->srcfeature_id->feature_id));
        while ($loc = $res->fetchObject()) {
          // add in the node id of the src feature if it exists and save this location
          if (property_exists($featureloc->srcfeature_id, 'nid')) {
            $loc->nid = $featureloc->srcfeature_id->nid;
          }
          $rel->child_featurelocs[] = $loc;
        }
      }
      $rel->record = $relationship;

      // get the relationship and child types
      $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
      $child_type = $relationship->subject_id->type_id->name;

      // get the node id of the subject
      $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
      $n = db_query($sql, array(':feature_id' => $relationship->subject_id->feature_id))->fetchObject();
      if ($n) {
        $rel->record->nid = $n->nid;
      }

      if (!array_key_exists($rel_type, $relationships['object'])) {
        $relationships['object'][$rel_type] = array();
      }
      if (!array_key_exists($child_type, $relationships['object'][$rel_type])) {
        $relationships['object'][$rel_type][$child_type] = array();
      }
      $relationships['object'][$rel_type][$child_type][] = $rel;
    }
  }

  // now add in the subject relationships
  if ($srelationships) {
    foreach ($srelationships as $relationship) {
      $rel = new stdClass();
      // get locations where this feature overlaps with the parent
      $rel->parent_featurelocs = array();
      foreach ($cfeaturelocs as $featureloc) {
        $res = chado_query($flrels_sql, array(':feature_id' => $relationship->object_id->feature_id, ':srcfeature_id' => $featureloc->srcfeature_id->feature_id));
        while ($loc = $res->fetchObject()) {
          // add in the node id of the src feature if it exists and save this location
          if (property_exists($featureloc->srcfeature_id, 'nid')) {
            $loc->nid = $featureloc->srcfeature_id->nid;
          }
          $rel->parent_featurelocs[] = $loc;
        }
      }
      $rel->record = $relationship;
      $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
      $parent_type = $relationship->object_id->type_id->name;

      // get the node id of the subject
      $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
      $n = db_query($sql, array(':feature_id' => $relationship->object_id->feature_id))->fetchObject();
      if ($n) {
        $rel->record->nid = $n->nid;
      }

      if (!array_key_exists($rel_type, $relationships['subject'])) {
        $relationships['subject'][$rel_type] = array();
      }
      if (!array_key_exists($parent_type, $relationships['subject'][$rel_type])) {
        $relationships['subject'][$rel_type][$parent_type] = array();
      }
      $relationships['subject'][$rel_type][$parent_type][] = $rel;
    }
  }
  return $relationships;
}