tripal_blast/blast_ui.module

<?php

/**
 * @file
 * The main file for the blast UI module.
 */

// Type-specific BLAST functionality
require_once 'includes/blast_ui.blastn.inc';
require_once 'includes/blast_ui.blastp.inc';

// BLAST DB Node functionality
require_once 'includes/blast_ui.node.inc';

// Functions specific to themeing (ie: preprocess)
require_once 'theme/blast_ui.theme.inc';

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

  // Parent menu-item for BLAST submission
  $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,
  );

  // 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 = '<p>An error was encountered while trying to process your blast results</p>';
    }
  }
  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 = '<p>An error was encountered while trying to process your blast results</p>';
  }

  return $result;
}