Register an already existing JBrowse instance to be managed by this module.

' . '
It is expected that the data directory for the existing JBrowse instance is @path where genus_species matches what you select for the organism. If this is not the location of your JBrowse, you should create a symbolic link between the current instance location and the expected one mentioned above.
'; $form['description_of_form']['#markup'] = t($msg, ['@path' => $path]); // Remove the file upload. unset($form['data']); // Change the submit button. $form['submit']['#value'] = 'Register Instance'; return $form; } /** * Validate the form. * * @param $form * @param $form_state */ function tripal_jbrowse_mgmt_register_form_validate($form, &$form_state) { $values = $form_state['values']; $organism = isset($values['organism']) ? $values['organism'] : NULL; // Check an instance does not already exist. $instances = tripal_jbrowse_mgmt_get_instances(['organism_id' => $organism]); if (!empty($instances)) { form_set_error( 'organism', 'A JBrowse instance for the selected organism already exists. You can edit the instance from the instances page.' ); } // Check that the organism does exist. $organism = db_select('chado.organism', 'CO') ->fields('CO') ->condition('organism_id', $organism) ->execute() ->fetchObject(); if (empty($organism)) { form_set_error('organism', 'Invalid organism selected ' . $organism); } // Check that the directory we assume contains the instance does exist. $title = tripal_jbrowse_mgmt_construct_organism_name($organism); $settings = tripal_jbrowse_mgmt_get_settings(); $path = $settings['data_dir']; $path .= '/' . tripal_jbrowse_mgmt_make_slug($title); $path .= '/data/trackList.json'; if (!file_exists($path)) { form_set_error('organism', "We expect there is already an existing instane at the following path: $path"); } } /** * @param $form * @param $form_state * * @throws \Exception */ function tripal_jbrowse_mgmt_register_form_submit($form, &$form_state) { global $user; $values = $form_state['values']; $organism_id = $values['organism']; $description = isset($values['description']) ? $values['description'] : ''; $organism = db_select('chado.organism', 'CO') ->fields('CO') ->condition('organism_id', $organism_id) ->execute() ->fetchObject(); $instance_id = tripal_jbrowse_mgmt_create_instance( [ 'organism_id' => $organism_id, 'title' => tripal_jbrowse_mgmt_construct_organism_name($organism), 'description' => $description, 'created_at' => time(), 'file' => '', ] ); if ($instance_id) { drupal_set_message('Instance registered successfully!'); $form_state['redirect'] = "admin/tripal/extension/tripal_jbrowse/management/instances/$instance_id"; } else { drupal_set_message('Failed to create instance!', 'error'); return; } // Now save the instance properties. tripal_jbrowse_mgmt_save_instance_properties( $instance_id, $form_state['values']['page'] ); }