$item) {
if (!$item['value']) {
continue;
}
$subject_name = $item['value']['subject']['name'];
$subject_type = $item['value']['subject']['type'];
$object_name = $item['value']['object']['name'];
$object_type = $item['value']['object']['type'];
$phrase = $item['value']['phrase'];
// Handle some special cases.
// For mRNA objects we don't want to show the CDS, exons, 5' UTR, etc.
// we want to show the parent gene and the protein.
if ($object_type == 'mRNA' and ($subject_type != 'polypeptide')) {
continue;
}
if ($subject_type == 'mRNA' and ($object_type != 'gene')) {
continue;
}
$phrase = preg_replace("/$subject_type/", "$subject_type", $phrase);
$phrase = preg_replace("/$object_type/", "$object_type", $phrase);
if (array_key_exists('entity', $item['value']['object'])) {
list($entity_type, $object_entity_id) = explode(':', $item['value']['object']['entity']);
if ($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', $item['value']['subject'])) {
list($entity_type, $subject_entity_id) = explode(':', $item['value']['subject']['entity']);
if ($subject_entity_id != $entity->id) {
$link = l($subject_name, 'bio_data/' . $subject_entity_id);
$phrase = preg_replace("/$subject_name/", $link, $phrase);
}
}
$rows[] = array($phrase);
}
// the $table array contains the headers and rows array as well as other
// options for controlling the display of the table. Additional
// documentation can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$table = array(
'header' => $headers,
'rows' => $rows,
'attributes' => array(
'id' => 'chado-linker--relationship-table',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => 'There are no relationships',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
if (count($items) > 0) {
$element[0] = array(
'#type' => 'markup',
'#markup' => theme_table($table),
);
}
}
}