'BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_nucleotide_form'),
'access arguments' => array('access content'),
'type' => MENU_NORMAL_ITEM,
'expanded' => TRUE,
);
$items['blast/report/%'] = array(
'title' => 'Nucleotide BLAST result:',
'page callback' => 'show_blast_output',
'page arguments' => array(2),
'access arguments' => array('access content'),
'type' => MENU_CALLBACK,
);
$items['blast/blastn'] = array(
'title' => 'Nucleotide BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_nucleotide_form'),
'access arguments' => array('access content'),
'type' => MENU_NORMAL_ITEM
);
// $items['blast/blastp'] = array(
// 'title' => 'Protein BLAST',
// 'page callback' => 'drupal_get_form',
// 'page arguments' => array('blast_protein_form'),
// 'access arguments' => array('access content'),
// 'type' => MENU_NORMAL_ITEM
// );
return $items;
}
/**
* Facilitate presenting the result of the blast search
*
* @param $args
* A string containing name of the blast output file.
*
* @return $result
* Return a string containing the blast search output. A link is also provided to let users download the output file.
*
*/
function show_blast_output($args = 'all') {
if (preg_match('/^[^\/]*/',$args)) {
$full_path_filename = '/var/www/kp-amir/sites/default/files/' . $args;
if (file_exists($full_path_filename)) {
$result = t('Download your BLAST result', array('@url' => url('sites/default/files/' . $args)));
$result .= check_markup(file_get_contents($full_path_filename), 'full_html');
$result = str_replace('','',$result);
}
else {
tripal_report_error(
'blast_ui',
TRIPAL_ERROR,
'Unable to open blast results file (%file)',
array('%file' => $full_path_filename)
);
$result = 'An error was encountered while trying to process your blast results
';
}
}
else {
$result = 'An error was encountered while trying to process your blast results
';
}
return $result;
}