Overrides TripalImporter::form

See also

TripalImporter::form()

File

tripal_chado/includes/TripalImporter/OBOImporter.inc, line 106

Class

OBOImporter

Code

public function form($form, &$form_state) {

  // get a list of db from chado for user to choose
  $sql = "SELECT * FROM {tripal_cv_obo} ORDER BY name";
  $results = db_query($sql);

  $obos = array();
  $obos[] = 'Select a Vocabulary';
  foreach ($results as $obo) {
    $obos[$obo->obo_id] = $obo->name;
  }

  $obo_id = '';
  if (array_key_exists('values', $form_state)) {
    $obo_id = array_key_exists('obo_id', $form_state['values']) ? $form_state['values']['obo_id'] : '';
  }


  $form['instructions']['info'] = array(
    '#type' => 'item',
    '#markup' => t('This page allows you to load vocabularies and ontologies
        that are in OBO format. Once loaded, the terms from these
        vocabularies can be used to create content.
        You may use the form below to either reload a vocabulary that is already
        loaded (as when new updates to that vocabulary are available) or load a new
        vocabulary.'),
  );

  $form['obo_existing'] = array(
    '#type' => 'fieldset',
    '#title' => t('Use a Saved Ontology OBO Reference'),
    '#prefix' => '<span id="obo-existing-fieldset">',
    '#suffix' => '</span>'
  );

  $form['obo_existing']['existing_instructions'] = array(
    '#type' => 'item',
    '#markup' => t('The vocabularies listed in the select box below have bene pre-populated
        upon installation of Tripal or have been previously loaded.  Select one to edit
        its settings or submit for loading.  You may reload any vocabulary that has
        already been loaded to retrieve any new updates.'),
  );

  $form['obo_existing']['obo_id'] = array(
    '#title' => t('Ontology OBO File Reference'),
    '#type' => 'select',
    '#options' => $obos,
    '#ajax' => array(
      'callback' => 'tripal_cv_obo_form_ajax_callback',
      'wrapper' => 'obo-existing-fieldset',
    ),
    '#description' => t('Select a vocabulary to import.')
  );

  // If the user has selected an OBO ID then get the form elements for
  // updating.
  if ($obo_id) {
    $uobo_name = '';
    $uobo_url = '';
    $uobo_file = '';

    $vocab = db_select('tripal_cv_obo', 't')
      ->fields('t', array('name', 'path'))
      ->condition('obo_id', $obo_id)
      ->execute()
      ->fetchObject();
    $uobo_name = $vocab->name;
    if (preg_match('/^http/', $vocab->path)) {
      $uobo_url = $vocab->path;
    }
    else {
      $uobo_file = trim($vocab->path);
      $matches = array();
      if (preg_match('/\{(.*?)\}/', $uobo_file, $matches)) {
        $modpath = drupal_get_path('module', $matches[1]);
        $uobo_file = preg_replace('/\{.*?\}/', $modpath, $uobo_file);
      }
    }
    // We don't want the previous value to remain. We want the new default to
    // show up, so remove the input values
    unset($form_state['input']['uobo_name']);
    unset($form_state['input']['uobo_url']);
    unset($form_state['input']['uobo_file']);

    $form['obo_existing']['uobo_name'] = array(
      '#type' => 'textfield',
      '#title' => t('Vocabulary Name'),
      '#description' => t('Please provide a name for this vocabulary.  After upload, this name will appear in the drop down
                             list above for use again later.'),
      '#default_value' => $uobo_name,
    );

    $form['obo_existing']['uobo_url'] = array(
      '#type' => 'textfield',
      '#title' => t('Remote URL'),
      '#description' => t('Please enter a URL for the online OBO file.  The file will be downloaded and parsed.
                             (e.g. http://www.obofoundry.org/ro/ro.obo)'),
      '#default_value' => $uobo_url,
    );

    $form['obo_existing']['uobo_file'] = array(
      '#type' => 'textfield',
      '#title' => t('Local File'),
      '#description' => t('Please enter the file system path for an OBO
          definition file. If entering a path relative to
          the Drupal installation you may use a relative path that excludes the
          Drupal installation directory (e.g. sites/default/files/xyz.obo). Note
          that Drupal relative paths have no preceeding slash.
          Otherwise, please provide the full path on the filesystem.  The path
          must be accessible to the web server on which this Drupal instance is running.'),
      '#default_value' => $uobo_file,
    );
    $form['obo_existing']['update_obo_details'] = array(
      '#type' => 'submit',
      '#value' => 'Update Ontology Details',
      '#name' => 'update_obo_details'
    );
  }

  $form['obo_new'] = array(
    '#type' => 'fieldset',
    '#title' => t('Add a New Ontology OBO Reference'),
    '#collapsible' => TRUE,
    '#collapsed' => TRUE,
  );

  $form['obo_new']['path_instructions'] = array(
    '#value' => t('Provide the name and path for the OBO file.  If the vocabulary OBO file
                     is stored local to the server provide a file name. If the vocabulry is stored remotely,
                     provide a URL.  Only provide a URL or a local file, not both.'),
  );

  $form['obo_new']['obo_name'] = array(
    '#type' => 'textfield',
    '#title' => t('New Vocabulary Name'),
    '#description' => t('Please provide a name for this vocabulary.  After upload, this name will appear in the drop down
                             list above for use again later. Additionally, if a default namespace is not provided in the OBO
                             header this name will be used as the default_namespace.'),
  );

  $form['obo_new']['obo_url'] = array(
    '#type' => 'textfield',
    '#title' => t('Remote URL'),
    '#description' => t('Please enter a URL for the online OBO file.  The file will be downloaded and parsed.
                             (e.g. http://www.obofoundry.org/ro/ro.obo)'),
  );

  $form['obo_new']['obo_file'] = array(
    '#type' => 'textfield',
    '#title' => t('Local File'),
    '#description' => t('Please enter the file system path for an OBO
          definition file. If entering a path relative to
          the Drupal installation you may use a relative path that excludes the
          Drupal installation directory (e.g. sites/default/files/xyz.obo). Note
          that Drupal relative paths have no preceeding slash.
          Otherwise, please provide the full path on the filesystem.  The path
          must be accessible to the web server on which this Drupal instance is running.'),
  );

  return $form;
}