');
$breadcrumb[] = l('Administration', 'admin');
$breadcrumb[] = l('Tripal', 'admin/tripal');
$breadcrumb[] = l('Chado', 'admin/tripal/legacy');
$breadcrumb[] = l('Features', 'admin/tripal/legacy/tripal_feature');
drupal_set_breadcrumb($breadcrumb);
// Add the view
$view = views_embed_view('tripal_feature_admin_features', 'default');
if (isset($view)) {
$output .= $view;
}
else {
$output .= 'The Feature module uses primarily views to provide an '
. 'administrative interface. Currently one or more views needed for this '
. 'administrative interface are disabled. Click each of the following links to '
. 'enable the pertinent views:
';
$output .= '';
$output .= '- ' . l('Features View', 'admin/tripal/legacy/tripal_feature/views/features/enable') . '
';
$output .= '
';
}
// Add a summary chart.
//-----------------------------------
$output .= theme('tripal_feature_bar_chart_type_organism_summary');
drupal_add_js('
Drupal.behaviors.tripalFeature_moveAdminSummaryChart = {
attach: function (context, settings) {
jQuery("#tripal-feature-admin-summary").insertBefore( jQuery(".view-filters") );
}};
', 'inline');
return $output;
}
/**
* Feature Settings page
*
* @ingroup tripal_legacy_feature
*/
function tripal_feature_admin() {
// FEATURE PAGE TITLES
// Using the Chado Node: Title & Path API
$details = [
'module' => 'tripal_feature',
'content_type' => 'chado_feature',
// An array of options to use under "Page Titles"
// the key should be the token and the value should be the human-readable option
'options' => [
'[feature.name]' => 'Feature Name Only',
'[feature.uniquename]' => 'Feature Unique Name Only',
// there should always be one options matching the unique constraint.
'[feature.name], [feature.uniquename] ([feature.type_id>cvterm.name]) [feature.organism_id>organism.genus] [feature.organism_id>organism.species]' => 'Unique Contraint: Includes the name, uniquename, type and scientific name',
],
// the token indicating the unique constraint in the options array
'unique_option' => '[feature.name], [feature.uniquename] ([feature.type_id>cvterm.name]) [feature.organism_id>organism.genus] [feature.organism_id>organism.species]',
];
// This call adds the configuration form to your current form
// This sub-form handles it's own validation & submit
chado_add_admin_form_set_title($form, $form_state, $details);
// FEATURE NODE URL
// Using the Chado Node: Title & Path API
$details = [
'module' => 'tripal_feature',
'content_type' => 'chado_feature',
// An array of options to use under "Page URL"
// the key should be the token and the value should be the human-readable option
'options' => [
'/feature/[feature.feature_id]' => 'Feature ID',
// there should always be one options matching the unique constraint.
'/feature/[feature.organism_id>organism.genus]/[feature.organism_id>organism.species]/[feature.type_id>cvterm.name]/[feature.uniquename]' => 'Unique Contraint: Includes the name, uniquename, type and scientific name',
],
];
// This call adds the configuration form to your current form
// This sub-form handles it's own validation & submit
chado_add_admin_form_set_url($form, $form_state, $details);
// FEATURE BROWSER
$form['browser'] = [
'#type' => 'fieldset',
'#title' => t('Feature Browser'),
'#collapsible' => TRUE,
'#collapsed' => TRUE,
];
$form['browser']['browser_desc'] = [
'#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'] = [
'#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'] = [
'#type' => 'submit',
'#value' => t('Set Browser'),
'#weight' => 2,
];
// FEATURE SUMMARY REPORT
$form['summary'] = [
'#type' => 'fieldset',
'#title' => t('Feature Summary Report'),
'#collapsible' => TRUE,
'#collapsed' => TRUE,
];
$form['summary']['feature_mapping'] = [
'#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', ''),
];
$form['summary']['set_summary_button'] = [
'#type' => 'submit',
'#value' => t('Set Summary'),
'#weight' => 2,
];
return system_settings_form($form);
}
/**
* Validate the feature settings forms
*
* @ingroup tripal_legacy_feature
*/
function tripal_feature_admin_validate($form, &$form_state) {
global $user; // we need access to the user info
$job_args = [];
variable_set('chado_browser_feature_types', $form_state['values']['feature_types']);
switch ($form_state['values']['op']) {
case t('Set Summary') :
variable_set('tripal_feature_summary_report_mapping', $form_state['values']['feature_mapping']);
break;
}
}
/**
* USort function for the admin summary chart.
* Not meant to be called directly.
*/
function tripal_feature_admin_summary_sort($a, $b) {
if ($a['total_features'] == $b['total_features']) {
return 0;
}
return $b['total_features'] - $a['total_features'];
}