tripal_blast/blast_ui.module

<?php

/**
 * @file
 * Contains all functions for the blast module
 */

require_once 'includes/blast_ui.blastn.inc';
require_once 'includes/blast_ui.blastp.inc';
require_once 'includes/blast_ui.node.inc';
require_once 'theme/blast_ui.theme.inc';

/**
 *
 * Implements hook_theme()
 *
 */

function blast_ui_theme() {
  $items = array();

  $path = drupal_get_path('module', 'blast_ui');

  $items['show_blast_report'] = array(
    'template' => 'blast_report',
    'path' => "$path/theme",
  );

  $items['blast_report_alignment_row'] = array(
    'template' => 'blast_report_alignment_row',
    'variables' => array('hsps' => NULL),
    'path' => "$path/theme",
  );

  return $items;
}

/**
 *
 * Implements hook_menu()
 *
 */
function blast_ui_menu() {

  $items['blast'] = array(
    'title' => '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' => '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)) {
    // 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;

    if (file_exists($full_path_filename)) {
    //  $result = t('<br /><h3>BLAST Results: <a href="@url" target="_blank">HTML</a></h3>', array('@url' => url('sites/default/files/' . $args)));
    //  $result .= check_markup(file_get_contents($full_path_filename), 'full_html');
    //  $result = str_replace('<script src="blastResult.js"></script>','',$result);

	$result = theme('show_blast_report');
    }
    else {
      tripal_report_error(
        'blast_ui',
        TRIPAL_ERROR,
        'Unable to open blast results file (%file)',
        array('%file' => $full_path_filename)
      );
      $result = '<p>An error was encountered while trying to process your blast results</p>';
    }
  }
  else {
    $result = '<p>An error was encountered while trying to process your blast results</p>';
  }

  return $result;
}