Validates an $options array for insert or update of a phylotree record.

If validation passes then any values that needed validation lookups (such as the dbxref, analysis, leaf_type, etc) will have their approriate primary_keys added to the $options array, and missing default values will also be added.

Parameters

$val_type: The type of validation. Can be either 'insert' or 'update'.

$options: An array of key/value pairs containing any of the valid keys for either the tripal_insert_phylotree() or tripal_update_phylotree() functions.

$errors: An empty array where validation error messages will be set. The keys of the array will be name of the field from the options array and the value is the error message.

$warnings: An empty array where validation warning messagges will be set. The warnings should not stop an insert or an update but should be provided to the user as information by a drupal_set_message() if appropriate. The keys of the array will be name of the field from the options array and the value is the error message.

Return value

If validation failes then FALSE is returned. Any options that do not pass validation checks will be added in the $errors array with the key being the option and the value being the error message. If validation is successful then TRUE is returned.

File

tripal_phylogeny/api/tripal_phylogeny.api.inc, line 34

Code

function tripal_validate_phylotree($val_type, &$options, &$errors, &$warnings) {

  if ($val_type != 'insert' and $val_type != 'update') {
    tripal_report_error('tripal_phylogeny', TRIPAL_ERROR, "The $val_type argument must be either 'update or 'insert'.");
  }

  // Set Defaults.
  if ($val_type == 'insert') {
    // Match by feature name.
    if (!array_key_exists('match', $options)) {
      $options['match'] = 'name';
    }
    // The regular expression is to match the entire node name.
    if (!array_key_exists('name_re', $options)) {
      $options['name_re'] = '^(.*)$';
    }
    // A dbxref is not required by Tripal but is required by the database
    // field in the phylotree table.  Therefore, if the dbxref is not provided
    // we can set this to be the null database and null dbxref which
    // is represented as 'null:local:null'
    if (!array_key_exists('dbxref', $options)) {
      $options['dbxref'] = "null:local:null";
    }
  }

  // Make sure required values are set.
  if ($val_type == 'insert') {
    if (!array_key_exists('name', $options)) {
      $errors['name'] = t('Please provide the name of the tree.');
      return FALSE;
    }
    if (!array_key_exists('description', $options)) {
      $errors['description'] = t('Please provide a description for this tree.');
      return FALSE;
    }
    if (!array_key_exists('analysis', $options) and !array_key_exists('analysis_id', $options)) {
      $errors['analysis'] = t('Please provide an analysis or analysis_id for this tree.');
      return FALSE;
    }
    if (!array_key_exists('tree_file', $options)) {
      $errors['tree_file'] = t('Please provide either the full path to the tree_file or a Drupal managed file ID number.');
      return FALSE;
    }
    if (!array_key_exists('format', $options) or !$options['format']) {
      $errors['format'] = t('Please provide a file format for the tree file.');
      return FALSE;
    }
    // Make sure the file format is correct
    if ($options['format'] != 'newick' and $options['format'] != 'taxonomy') {
      $errors['format'] = t('The file format is not supported. Currently only the "newick" file format is supported.');
      return FALSE;
    }
  }
  else {
    // Does the phylotree ID exist and is it valid
    if (!array_key_exists('phylotree_id', $options)) {
      $errors['phylotree_id'] = t('Please provide the ID for the tree.');
      return FALSE;
    }
    $exists = chado_select_record('phylotree', array('phylotree_id'), 
    array('phylotree_id' => $options['phylotree_id']), array('has_record' => 1));
    if (!$exists) {
      $errors['phylotree_id'] = t('The phylotree_id does not exist.');
      return FALSE;
    }

  }

  // Make sure the file exists if one is specified
  if (array_key_exists('tree_file', $options) and $options['tree_file']) {
    // If this is a numeric Drupal file then all is good, no need to check.
    if (!is_numeric($options['tree_file'])) {
      if (!file_exists($options['tree_file'])) {
        $errors['tree_file'] = t('The file provided does not exists.');
        return FALSE;
      }
    }
    // Make sure the file format is correct
    if (!array_key_exists('format', $options) or 
      ($options['format'] != 'newick' and $options['format'] != 'taxonomy')) {
      $errors['format'] = t('Please provide a supported file format. Currently only the "newick" file format is supported.');
      return FALSE;
    }

    // If no leaf type is provided then use the polypeptide term.
    if (!array_key_exists('leaf_type', $options) or !$options['leaf_type']) {
      $options['leaf_type'] = 'polypeptide';
    }
  }

  // Make sure the analysis exists.
  $analysis = NULL;
  if (array_key_exists('analysis_id', $options) and $options['analysis_id']) {
    $analysis = chado_select_record('analysis', array('analysis_id'), array('analysis_id' => $options['analysis_id']));
    if (!$analysis) {
      $errors['analysis_id'] = t('The analysis name provided does not exist.');
      return FALSE;
    }
    $options['analysis_id'] = $analysis[0]->analysis_id;
  }
  if (array_key_exists('analysis', $options) and $options['analysis']) {
    $analysis = chado_select_record('analysis', array('analysis_id'), array('name' => $options['analysis']));
    if (!$analysis) {
      $errors['analysis'] = t('The analysis ID provided does not exist.');
      return FALSE;
    }
    $options['analysis_id'] = $analysis[0]->analysis_id;
  }

  // Make sure the leaf type exists.
  $type = NULL;
  if (array_key_exists('leaf_type', $options) and $options['leaf_type']) {
    if ($options['leaf_type'] == 'taxonomy') {
      $values = array(
        'cv_id' => array(
          'name' => 'tripal_phylogeny'
        ),
        'name' => 'taxonomy'
      );
      $type = chado_select_record('cvterm', array('cvterm_id'), $values);
    }
    else {
      $values = array(
        'cv_id' => array(
          'name' => 'sequence'
        ),
        'name' => $options['leaf_type']
      );
      $type = chado_select_record('cvterm', array('cvterm_id'), $values);
      if (!$type) {
        $errors['leaf_type'] = t('The leaf_type provided is not a valid Sequence Ontology term: %term.');
        return FALSE;
      }
    }
    $options['type_id'] = $type[0]->cvterm_id;
  }

  // A Dbxref is required by the phylotree module, but if the
  // tree was generated in-house and the site admin doens't want to
  // assign a local dbxref then we will set it to the null db
  // and the local:null dbxref.
  if (array_key_exists('dbxref', $options)) {
    if (!$options['dbxref']) {
      $options['dbxref'] = 'null:local:null';
    }
    $matches = array();
    preg_match('/^(.*?):(.*)$/', $options['dbxref'], $matches);
    $db_name = $matches[1];
    $accession = $matches[2];
    $values = array(
      'accession' => $accession,
      'db_id' => array(
        'name' => $db_name
      ),
    );
    $dbxref = chado_generate_var('dbxref', $values);
    if (!$dbxref) {
      $errors['dbxref'] = t('The dbxref provided does not exist in the database: %dbxref.', array('%dbxref' => $dbxref));
      return FALSE;
    }
    $options['dbxref_id'] = $dbxref->dbxref_id;
  }

  // Make sure the tree name is unique
  if (array_key_exists('name', $options) and $options['name']) {
    $sql = "
      SELECT *
      FROM {phylotree} P
      WHERE
        P.name = :name
    ";
    $args = array(':name' => $options['name']);
    if ($val_type == 'update') {
      $sql .= " AND NOT P.phylotree_id = :phylotree_id";
      $args[':phylotree_id'] = $options['phylotree_id'];
    }
    $result = chado_query($sql, $args)->fetchObject();
    if ($result) {
      $errors['name'] = t("The tree name is in use by another tree. Please provide a different unique name for this tree.");
    }
  }

  return TRUE;
}