tripal/tripal_feature/includes/tripal_feature.admin.inc

<?php
/**
 * @file
 * Administration of features
 */

/**
 * Launchpad for feature administration.
 *
 * @ingroup tripal_feature
 */
function tripal_feature_admin_feature_view() {
  $output = '';

  // set the breadcrumb
  $breadcrumb = array();
  $breadcrumb[] = l('Home', '<front>');
  $breadcrumb[] = l('Administration', 'admin');
  $breadcrumb[] = l('Tripal', 'admin/tripal');
  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
  $breadcrumb[] = l('Features', 'admin/tripal/chado/tripal_feature');
  drupal_set_breadcrumb($breadcrumb);

  // Add the view
  $view = views_embed_view('tripal_feature_admin_features','default');
  if (isset($view)) {
    $output .= $view;
  }
  else {
    $output .= '<p>The Feature module uses primarily views to provide an '
      . 'administrative interface. Currently one or more views needed for this '
      . 'administrative interface are disabled. <strong>Click each of the following links to '
      . 'enable the pertinent views</strong>:</p>';
    $output .= '<ul>';
      $output .= '<li>'.l('Features View', 'admin/tripal/chado/tripal_feature/views/features/enable').'</li>';
    $output .= '</ul>';
  }

  return $output;
}

/**
 * Feature Settings page
 *
 * @ingroup tripal_feature
 */
function tripal_feature_admin() {

  // FEATURE PAGE TITLES
  $form['title'] = array(
    '#type' => 'fieldset',
    '#title' => t('Feature Page Titles'),
    '#collapsible' => TRUE,
    '#collapsed' => FALSE,
  );
  $form['title']['desc'] = array(
    '#markup' => t(
      'Each synced feature must have a unique page title, however, features
       may have the same name if they are of different types or from
       different organisms.  Therefore, we must be sure that the
       page titles can uniquely identify the feature being viewed.  Select
       an option below that will uniquely identify all features on your site.'),
  );
  $options = array(
    'feature_unique_name'  => 'Feature unique name',
    'feature_name'         => 'Feature name',
    'unique_constraint'    => 'Feature Name, uniquename, type and species',
  );
  $form['title']['chado_feature_title'] = array(
    '#title'         => t('Feature Page Titles'),
    '#type'          => 'radios',
    '#description'   => t('Choose a title type  from the list above that is
      guaranteed to be unique for all features.  If in doubt it is safest to
      choose the last option as that guarantees uniqueness. Click the
      \'Save Configuration\' button at the bottom to save your selection.'),
    '#required'      => FALSE,
    '#options'       => $options,
    '#default_value' => variable_get('chado_feature_title', 'unique_constraint'),
  );
    
  // FEATURE URL PATHS
  $form['url'] = array(
    '#type' => 'fieldset',
    '#title' => t('Feature URL Path'),
    '#collapsible' => TRUE,
    '#collapsed' => FALSE,
  );
  
  $options = array(
    'SID[id]'      => '[id]:' . t('The Chado feature_id'),
    'feature'      => 'feature:' . t('Chado table name'),
    '[genus]'      => '[genus]:' . t('Genus to which the feature belongs'),
    '[species]'    => '[species]:' . t('Species to which the feature belongs'),
    '[type]'       => '[type]:' . t('The type of feature'),
    '[uniquename]' => '[uniquename]:' . t('The feature unique name'),
    '[name]'       => '[name]:' . t('The feature name'),
    'reset'        => t('Reset'),
  );
  
  $form['url']['chado_feature_url_string'] = array(
    '#title' => 'URL Syntax',
    '#type' => 'textfield',
    '#description' => t('You may rearrange elements in this text box to
    customize the URLs.  The available tags include: [id],
    [uniquename]. [name], [species], [genus], [type]. You can separate or
    include any text between the tags. Click the "Set Feature URLs" button to
    reset the URLs for all feature pages.  Click the "Save Configuration" button to
    simply save this setup. <b>Important</b>: be sure that whatever you choose will always be unique even considering
    future data that may be added.  If you include the Chado table name, genus, species, type
    and uniquename you are guaranteed to have a unique URL. For example feature/[genus]/[species]/[type]/[uniquename]'),
    '#size' => 150,
    '#default_value' => variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]'),
  );
  
  $form['url']['chado_feature_url'] = array(
    '#title'         => t('URL components'),
    '#type'          => 'checkboxes',
    '#required'      => FALSE,
    '#options'       => $options,
    '#description'   => t('Click the item above to make it appear in the URL Syntax box'),
    '#attributes'    => array(
      'onclick' => '
      box = $(\'#edit-chado-feature-url-string\');
      if (this.value == \'reset\') {
        box.val(\'\');
      }
      else {
        box.val(box.val() + "/" + this.value);
      }
      this.checked = false;
    ',
    ),
  );
  
  $form['url']['button'] = array(
    '#type' => 'submit',
    '#value' => t('Set Feature URLs'),
  );
    
    
    
  // FEATURE BROWSER
  $form['browser'] = array(
     '#type' => 'fieldset',
     '#title' => t('Feature Browser'),
     '#collapsible' => TRUE,
     '#collapsed' => FALSE,
  );
  $allowedoptions1  = array(
    'show_feature_browser' => "Show the feature browser on the organism page. The browser loads when page loads. This may be slow for large sites.",
    'hide_feature_browser' => "Hide the feature browser on the organism page. Disables the feature browser completely.",
  );
//      $allowedoptions ['allow_feature_browser'] = "Allow loading of the feature browsing through AJAX. For large sites the initial page load will be quick with the feature browser loading afterwards.";

  $form['browser']['browser_desc'] = array(
     '#markup' => t('A feature browser can be added to an organism page to allow users to quickly ' .
        'access a feature.  This will most likely not be the ideal mechanism for accessing feature ' .
        'information, especially for large sites, but it will alow users exploring the site (such ' .
        'as students) to better understand the data types available on the site.'),

  );
  $form['browser']['feature_types'] = array(
     '#title'       => t('Feature Types'),
     '#type'        => 'textarea',
     '#description' => t("Enter the Sequence Ontology (SO) terms for the feature types that " .
                         "will be shown in the feature browser."),
     '#default_value' => variable_get('chado_browser_feature_types', 'gene mRNA'),
  );


  $form['browser']['browse_features'] = array(
     '#title' => 'Feature Browser on Organism Page',
     '#type' => 'radios',
     '#options' => $allowedoptions1,
     '#default_value' => variable_get('tripal_feature_browse_setting', 'show_feature_browser'),
  );

  $form['browser']['browse_features_library'] = array(
    '#title' => 'Feature Browser on Library Page',
    '#type' => 'radios',
    '#options' => array(
      'show_feature_browser' => "Show the feature browse on the library page. The browser loads when page loads. This may be slow for large sites.",
      'hide_feature_browser' => "Hide the feature browser on the library page. Disables the feature browser completely.",
    ),
    '#default_value' => variable_get('tripal_library_feature_browse_setting', 'show_feature_browser'),
  );

  $form['browser']['browse_features_analysis'] = array(
    '#title' => 'Feature Browser on Analysis Page',
    '#type' => 'radios',
    '#options' => array(
      'show_feature_browser' => "Show the feature browse on the analysis page. The browser loads when page loads. This may be slow for large sites.",
      'hide_feature_browser' => "Hide the feature browser on the analysis page. Disables the feature browser completely.",
    ),
   '#default_value' => variable_get('tripal_analysis_feature_browse_setting', 'show_feature_browser'),
  );

  $form['browser']['set_browse_button'] = array(
     '#type' => 'submit',
     '#value' => t('Set Browser'),
     '#weight' => 2,
  );

  // FEATURE SUMMARY REPORT
  $form['summary'] = array(
     '#type' => 'fieldset',
     '#title' => t('Feature Summary Report'),
     '#collapsible' => TRUE,
     '#collapsed' => FALSE,
  );
  $allowedoptions2 ['show_feature_summary'] = "Show the feature summary on the organism page. The summary loads when page loads.";
  $allowedoptions2 ['hide_feature_summary'] = "Hide the feature summary on the organism page. Disables the feature summary.";

  $form['summary']['feature_summary'] = array(
     '#title' => 'Feature Summary on Organism Page',
     '#description' => 'A feature summary can be added to an organism page to allow users to see the ' .
        'type and quantity of features available for the organism.',
     '#type' => 'radios',
     '#options' => $allowedoptions2,
     '#default_value' => variable_get('tripal_feature_summary_setting', 'show_feature_summary'),
  );
  $form['summary']['feature_mapping'] = array(
     '#title' => 'Map feature types',
     '#description' => t('You may specify which Sequence Ontology (SO) terms to show in the ' .
        'feature summary report by listing them in the following text area.   Enter one per line. ' .
        'If left blank, all SO terms for all features will be shown in the report. Only those terms ' .
        'listed below will be shown in the report. Terms will appear in the report in the same order listed. To rename a ' .
        'SO term to be more human readable form, use an \'=\' sign after the SO term (e.g. \'polypeptide = Protein\')'),
     '#type' => 'textarea',
     '#rows' => 15,
     '#default_value' => variable_get('tripal_feature_summary_report_mapping', ''),
  );
  $form['summary']['set_summary_button'] = array(
     '#type' => 'submit',
     '#value' => t('Set Summary'),
     '#weight' => 2,
  );
  
  return system_settings_form($form);
}

/**
 * Validate the feature settings forms
 *
 * @ingroup tripal_feature
 */
function tripal_feature_admin_validate($form, &$form_state) {
  global $user;  // we need access to the user info
  $job_args = array();

  variable_set('chado_browser_feature_types', $form_state['values']['feature_types']);

  switch ($form_state['values']['op']) {

    case t('Set Browser') :
      variable_set('tripal_feature_browse_setting', $form_state['values']['browse_features']);
      variable_set('tripal_library_feature_browse_setting', $form_state['values']['browse_features_library']);
      variable_set('tripal_analysis_feature_browse_setting', $form_state['values']['browse_features_analysis']);
      break;

    case t('Set Summary') :
      variable_set('tripal_feature_summary_setting', $form_state['values']['feature_summary']);
      variable_set('tripal_feature_summary_report_mapping', $form_state['values']['feature_mapping']);
      break;

    case t('Set Feature URLs') :
      variable_set('chado_feature_url', $form_state['values']['feature_url']);
      tripal_add_job('Set Feature URLs', 'tripal_feature',
        'tripal_feature_set_urls', $job_args, $user->uid);
      break;
  }

}