'BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_nucleotide_form'),
'access arguments' => array('access content'),
'type' => MENU_NORMAL_ITEM,
'expanded' => TRUE,
);
// Nucleotide BLAST submission form
$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
);
// Protein BLAST submission form
$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
);
// BLAST Results page
$items['blast/report/%'] = array(
'title' => 'BLAST result:',
'page callback' => 'show_blast_output',
'page arguments' => array(2),
'access arguments' => array('access content'),
'type' => MENU_CALLBACK,
);
return $items;
}
/**
* Implements hook_theme().
*/
function blast_ui_theme() {
$items = array();
$path = drupal_get_path('module', 'blast_ui');
// Displays the BLAST results for each job
$items['show_blast_report'] = array(
'template' => 'blast_report',
'path' => "$path/theme",
);
// Themes the alignments in a BLAST result display
$items['blast_report_alignment_row'] = array(
'template' => 'blast_report_alignment_row',
'variables' => array('hsps' => NULL),
'path' => "$path/theme",
);
return $items;
}
/**
* Facilitate presenting the result of the blast search
*
* @param $args
* A string containing name of the blast output file.
*
* @return $result
* Return HTML output of the BLAST results to be displayed to the user
*
*/
function show_blast_output($args = 'all') {
// Double-check that there are no directory slashes in the path since this could be used
// present a security risk (ie: if the path contained ../../../etc/someconfig.file this
// we don't want to process or display anything.
if (preg_match('/^[^\/]*$/',$args)) {
// Since the blast results are in the files directory
// we can use public:// to get around hard-coding the full path
$full_path_filename = 'public://'.$args;
// check that the XML file exists before trying to display results
if (file_exists($full_path_filename)) {
// Use the show_blast_output.tpl.php to generate the HTML
$result = theme('show_blast_report');
}
else {
// If the file doesn't exist then throw a tripal error
// as well as displaying an error to the user
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 {
// If there are directory slashes in the path then just display an error to the user
// rather than risk the security of the server
$result = 'An error was encountered while trying to process your blast results
';
}
return $result;
}