fix issue realted to creating symlink, also make it selected as default

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt.api.inc

@@ -731,6 +731,8 @@ function tripal_jbrowse_mgmt_get_instance_properties($id) {
    $local_directory = isset($values['dir_path']) ? $values['dir_path'] : NULL;
    $symbolic_link = $values['symbolic_link'];
 
+   dpm($path, '$path in validation');
+
    if (empty($file) && empty($index) && empty($local_directory)) {
      form_set_error('Please provide a local directory path or upload files.');
    }
@@ -746,19 +748,19 @@ function tripal_jbrowse_mgmt_get_instance_properties($id) {
        else {
          // Retrieve an array of data file and index
          // to ensure there is only one of each.
-         $file_file = [];
-         $file_index = [];
+
          foreach (scandir($local_directory) as $f) {
            $fparts = pathinfo($f);
 
            if (in_array($fparts['extension'], ['gz', 'bam', 'cram'])) {
-             $file_file[] = $f;
+             $file_file[] = $local_directory . '/' . $f;
            }
            if (in_array($fparts['extension'], ['csi','tbi','idx','bai','crai'])) {
-             $file_index[] = $f;
+             $file_index[] = $local_directory . '/' . $f;
            }
          }
          // CHECK: Only a single data file and index.
+
          if (count($file_file) != 1 || count($file_index) != 1) {
            form_set_error('file_path',
              'Please provide a directory with exactly one data file and one index file.');

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

@@ -105,6 +105,7 @@ function tripal_jbrowse_mgmt_add_track_form($form, &$form_state, $instance_id) {
   $form['data']['symbolic_link'] = [
     '#type' => 'checkbox',
     '#title' => t('Symbolic Link'),
+    '#default_value' => true,
     '#description' => t('Create a symbolic link rather than make a copy of the file. This only applies when a path on the server is supplied.<br>Please have Symbolic Link selected if the same file is used for new track.'),
   ];