Load any aliases for a feature

Parameters

$feature:

$aliases:

Related topics

File

tripal_feature/includes/tripal_feature.gff_loader.inc, line 1547

Provides gff3 loading functionality. Creates features based on their specification in a GFF3 file.

Code

function tripal_feature_load_gff3_alias($feature, $aliases) {

  // make sure we have a 'synonym_type' vocabulary
  $select = array('name' => 'synonym_type');
  $results = chado_select_record('cv', array('*'), $select);

  if (count($results) == 0) {
    // insert the 'synonym_type' vocabulary
    $values = array(
      'name' => 'synonym_type',
      'definition' => 'vocabulary for synonym types',
    );
    $success = chado_insert_record('cv', $values);
    if (!$success) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Failed to add the synonyms type vocabulary", array());
      return 0;
    }
    // now that we've added the cv we need to get the record
    $results = chado_select_record('cv', array('*'), $select);
    if (count($results) > 0) {
      $syncv = $results[0];
    }
  }
  else {
    $syncv = $results[0];
  }

  // get the 'exact' cvterm, which is the type of synonym we're adding
  $select = array(
    'name' => 'exact',
    'cv_id' => array(
      'name' => 'synonym_type'
    ),
  );
  $result = chado_select_record('cvterm', array('*'), $select);
  if (count($result) == 0) {
    $term = array(
      'name' => 'exact',
      'id' => "local:exact",
      'definition' => '',
      'is_obsolete' => 0,
      'cv_name' => $syncv->name,
      'is_relationship' => FALSE
    );
    $syntype = tripal_insert_cvterm($term, array('update_existing' => TRUE));
    if (!$syntype) {
      tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot add synonym type: internal:$type", array());
      return 0;
    }
  }
  else {
    $syntype = $result[0];
  }

  // iterate through all of the aliases and add each one
  foreach ($aliases as $alias) {

    // check to see if the alias already exists in the synonym table
    // if not, then add it
    $select = array(
      'name' => $alias,
      'type_id' => $syntype->cvterm_id,
    );
    $result = chado_select_record('synonym', array('*'), $select);
    if (count($result) == 0) {
      $values = array(
        'name' => $alias,
        'type_id' => $syntype->cvterm_id,
        'synonym_sgml' => '',
      );
      $success = chado_insert_record('synonym', $values);
      if (!$success) {
        tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot add alias $alias to synonym table", array());
        return 0;
      }
      $result = chado_select_record('synonym', array('*'), $select);
      $synonym = $result[0];
    }
    else {
      $synonym = $result[0];
    }

    // check to see if we have a NULL publication in the pub table.  If not,
    // then add one.
    $select = array('uniquename' => 'null');
    $result = chado_select_record('pub', array('*'), $select);
    if (count($result) == 0) {
      $pub_sql = "
        INSERT INTO {pub} (uniquename,type_id)
        VALUES (:uname,
          (SELECT cvterm_id
           FROM {cvterm} CVT
             INNER JOIN {dbxref} DBX ON DBX.dbxref_id = CVT.dbxref_id
             INNER JOIN {db} DB      ON DB.db_id      = DBX.db_id
           WHERE CVT.name = :type_id))
      ";
      $status = chado_query($psql);
      if (!$status) {
        tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot prepare statement 'ins_pub_uniquename_typeid", array());
        return 0;
      }

      // insert the null pub
      $result = chado_query($pub_sql, array(':uname' => 'null', ':type_id' => 'null'))->fetchObject();
      if (!$result) {
        tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot add null publication needed for setup of alias", array());
        return 0;
      }
      $result = chado_select_record('pub', array('*'), $select);
      $pub = $result[0];
    }
    else {
      $pub = $result[0];
    }

    // check to see if the synonym exists in the feature_synonym table
    // if not, then add it.
    $values = array(
      'synonym_id' => $synonym->synonym_id,
      'feature_id' => $feature->feature_id,
      'pub_id' => $pub->pub_id,
    );
    $columns = array('feature_synonym_id');
    $result = chado_select_record('feature_synonym', $columns, $values);
    if (count($result) == 0) {
      $values = array(
        'synonym_id' => $synonym->synonym_id,
        'feature_id' => $feature->feature_id,
        'pub_id' => $pub->pub_id,
      );
      $success = chado_insert_record('feature_synonym', $values);

      if (!$success) {
        tripal_report_error("tripal_feature", TRIPAL_WARNING, "Cannot add alias $alias to feature synonym table", array());
        return 0;
      }
    }
  }
  return 1;
}