Submit the GFF3 loading job

Related topics

File

tripal_feature/includes/tripal_feature.gff_loader.inc, line 329

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

Code

function tripal_feature_gff3_load_form_submit($form, &$form_state) {
  global $user;

  $gff_file = trim($form_state['values']['gff_file']);
  $organism_id = $form_state['values']['organism_id'];
  $add_only = $form_state['values']['add_only'];
  $update = $form_state['values']['update'];
  $refresh = 0; //$form_state['values']['refresh'];
  $remove = 0; //$form_state['values']['remove'];
  $analysis_id = $form_state['values']['analysis_id'];
  $use_transaction = $form_state['values']['use_transaction'];
  $target_organism_id = $form_state['values']['target_organism_id'];
  $target_type = trim($form_state['values']['target_type']);
  $create_target = $form_state['values']['create_target'];
  $line_number = trim($form_state['values']['line_number']);
  $landmark_type = trim($form_state['values']['landmark_type']);
  $alt_id_attr = trim($form_state['values']['alt_id_attr']);
  $create_organism = $form_state['values']['create_organism'];
  $re_mrna = trim($form_state['values']['re_mrna']);
  $re_protein = trim($form_state['values']['re_protein']);


  $args = array($gff_file, $organism_id, $analysis_id, $add_only,
    $update, $refresh, $remove, $use_transaction, $target_organism_id,
    $target_type, $create_target, $line_number, $landmark_type, $alt_id_attr,
    $create_organism, $re_mrna, $re_protein);

  $type = '';
  if ($add_only) {
    $type = 'import only new features';
  }
  if ($update) {
    $type = 'import all and update';
  }
  if ($refresh) {
    $type = 'import all and replace';
  }
  if ($remove) {
    $type = 'delete features';
  }
  $fname = preg_replace("/.*\/(.*)/", "$1", $gff_file);
  tripal_add_job("$type GFF3 file: $fname", 'tripal_feature', 
  'tripal_feature_load_gff3', $args, $user->uid);

  return '';
}