'Relationship',
'empty' => 'There are no relationships',
);
/**
*
* @see TripalFieldFormatter::settingsForm()
*/
public function settingsForm($view_mode, $form, &$form_state) {
$display = $this->instance['display'][$view_mode];
$settings = $display['settings'];
$element = array();
$element['title'] = array(
'#type' => 'textfield',
'#title' => 'Table Header',
'#default_value' => array_key_exists('title', $settings) ? $settings['title'] : 'Relationship',
);
$element['empty'] = array(
'#type' => 'textfield',
'#title' => 'Empty text',
'#default_value' => array_key_exists('empty', $settings) ? $settings['empty'] : 'There are no relationships',
);
return $element;
}
/**
* @see TripalFieldFormatter::settingsSummary()
*/
public function settingsSummary($view_mode) {
$display = $this->instance['display'][$view_mode];
$settings = $display['settings'];
$summary = t('Title: @title
Empty: @empty', array('@title' => $settings['title'], '@empty' => $settings['empty']));
return $summary;
}
/**
*
* @see TripalFieldFormatter::view()
*/
public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
// Get the settings
$settings = $display['settings'];
$rows = array();
$headers = array($settings['title']);
foreach ($items as $delta => $item) {
if (empty($item['value'])) {
continue;
}
$subject_name = $item['value']['local:relationship_subject']['schema:name'];
$subject_type = $item['value']['local:relationship_subject']['rdfs:type'];
$object_name = $item['value']['local:relationship_object']['schema:name'];
$object_type = $item['value']['local:relationship_object']['rdfs:type'];
$phrase = $item['value']['SIO:000493'];
// Handle some special cases.
// For mRNA objects we don't want to show the CDS, exons, 5' UTR, etc.
// we want to show the parent gene and the protein.
if ($object_type == 'mRNA' and
(in_array($subject_type, array('CDS', 'exon', 'five_prime_UTR', 'three_prime_UTR')))) {
continue;
}
$phrase = preg_replace("/$subject_type/", "$subject_type", $phrase);
$phrase = preg_replace("/$object_type/", "$object_type", $phrase);
if (array_key_exists('entity', $item['value']['local:relationship_object'])) {
list($entity_type, $object_entity_id) = explode(':', $item['value']['local:relationship_object']['entity']);
if ($object_entity_id != $entity->id) {
$link = l($object_name, 'bio_data/' . $object_entity_id);
$phrase = preg_replace("/$object_name/", $link, $phrase);
}
}
if (array_key_exists('entity', $item['value']['local:relationship_subject'])) {
list($entity_type, $subject_entity_id) = explode(':', $item['value']['local:relationship_subject']['entity']);
if ($subject_entity_id != $entity->id) {
$link = l($subject_name, 'bio_data/' . $subject_entity_id);
$phrase = preg_replace("/$subject_name/", $link, $phrase);
}
}
$rows[][] = array(
'data' => $phrase,
'class' => array('tripal-entity-unattached field-items')
);
}
//$pager = $this->generate_pager(count($rows), $per_page);
// Get the total number of records from the pager query.
$total_records = chado_pager_get_count($this->getPagerElementID());
$pager = theme('pager', array(
'tags' => array(),
'element' => $this->getPagerElementID(),
'parameters' => array(),
'quantity' => ($total_records / 25) + 1,
));
$pager = $this->ajaxifyPager($pager, $entity);
$table = theme_table(array(
'header' => $headers,
'rows' => $rows, //$current_page ? $chunks[$current_page] : array(),
'attributes' => array(
'id' => 'sbo--relationship-table',
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => $settings['empty'],
));
// Once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
if (count($items) > 0) {
$element[0] = array(
'#type' => 'markup',
'#markup' => $table . $pager,
'#suffix' => '
' . $pager,
);
}
}
}