Feature Settings page

File

legacy/tripal_feature/includes/tripal_feature.admin.inc, line 57

Administration of features

Code

function tripal_feature_admin() {

  // FEATURE PAGE TITLES
  // Using the Chado Node: Title & Path API
  $details = array(
    'module' => 'tripal_feature',
    'content_type' => 'chado_feature',
    // An array of options to use under "Page Titles"
    // the key should be the token and the value should be the human-readable option
    'options' => array(
      '[feature.name]' => 'Feature Name Only',
      '[feature.uniquename]' => 'Feature Unique Name Only',
      // there should always be one options matching the unique constraint.
      '[feature.name], [feature.uniquename] ([feature.type_id>cvterm.name]) [feature.organism_id>organism.genus] [feature.organism_id>organism.species]' => 'Unique Contraint: Includes the name, uniquename, type and scientific name'
    ),
    // the token indicating the unique constraint in the options array
    'unique_option' => '[feature.name], [feature.uniquename] ([feature.type_id>cvterm.name]) [feature.organism_id>organism.genus] [feature.organism_id>organism.species]'
  );
  // This call adds the configuration form to your current form
  // This sub-form handles it's own validation & submit
  chado_add_admin_form_set_title($form, $form_state, $details);

  // FEATURE NODE URL
  // Using the Chado Node: Title & Path API
  $details = array(
    'module' => 'tripal_feature',
    'content_type' => 'chado_feature',
    // An array of options to use under "Page URL"
    // the key should be the token and the value should be the human-readable option
    'options' => array(
      '/feature/[feature.feature_id]' => 'Feature ID',
      // there should always be one options matching the unique constraint.
      '/feature/[feature.organism_id>organism.genus]/[feature.organism_id>organism.species]/[feature.type_id>cvterm.name]/[feature.uniquename]' => 'Unique Contraint: Includes the name, uniquename, type and scientific name'
    )
  );
  // This call adds the configuration form to your current form
  // This sub-form handles it's own validation & submit
  chado_add_admin_form_set_url($form, $form_state, $details);

  // FEATURE BROWSER
  $form['browser'] = array(
    '#type' => 'fieldset',
    '#title' => t('Feature Browser'),
    '#collapsible' => TRUE,
    '#collapsed' => TRUE,
  );
  $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']['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' => TRUE,
  );
  $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);
}