icsearch/dbsf_ssaha2.inc

Go to the documentation of this file.

<?php
// $Id: dbsf_ssaha2.inc,v 1.1 2010-01-02 17:06:45 alexie Exp $


/*
 * For server usage we will implement
 *  ssaha2Build (build hashtable of subject database)
 *  Hashtables will be saved in module's directory
 *  CMD:   ssaha2Build [OPTIONS] -save hash_name subject_file
 * ssaha2Build -kmer 10 -skip 10  -save ButterflyBase.fsa /db/blastdb/butterflybase/ButterflyBase.fsa
 *  Kmer is also very important and it should be set to 13 or 14 if the
 *  database is more than 1 GB.
 *
 *  CMD:   ssaha2 [OPTIONS] -save hash_name query_file
 * ssaha2 [-454/-solexa/-abi] -save ButterflyBase.fsa
 *
 * The following functions are needed in this include file for SSAHA2 to operate
 *  dbsf_admin_ssaha_page
 *  dbsf_ssaha_page
 *  dbsf_add_software_ssaha2
 *
 * The following can be done conditionally via the main module
 *  administration-> where the executable is
 *
 * The following must be done conditionally via the main .install file
 *  add ssaha2 as a software in ontology
 *  add options as CV
 *
 **/
function dbsf_ssaha2_menu() {
  $items = array();
  $items['admin/dbsf/ssaha2'] = array(
    'file' => 'dbsf_ssaha2.inc',
    'title' => 'SSAHA2 Server administration',
    'page callback' => 'dbsf_admin_ssaha2_page',
    'access arguments' => array('Administrate SSAHA2 Server'),
    'description' => 'Configure SSAHA2 specific settings',
    'type' => MENU_NORMAL_ITEM,
  );
  $items['dbsf/ssaha2'] = array(
    'file' => 'dbsf_ssaha2.inc',
    'title' => 'dbsf SSAHA2 Server',
    'page callback' => 'dbsf_ssaha2_page',
    'access arguments' => array('Access SSAHA2 Server'),
    'type' => MENU_CALLBACK,
  );
  $items['dbsf/ssaha2_result'] = array(
    'title' => 'dbsf SSAHA2 Results',
    'page callback' => 'dbsf_ssaha2_result_page',
    'page arguments' => array(2),
    'access arguments' => array('Access SSAHA2 Server'),
    'type' => MENU_CALLBACK,
  );
  return $items;
}

function dbsf_add_software_ssaha2() {
  db_query("INSERT INTO {ic_software} (uniquename,description) VALUES ('ssaha2Build','Format reference sequences as a SSAHA2 database. Needed for creating your own SSAHA2 databases.')");

  $dbxref_id     = icbasic_get_add_dbxref_withnames('Sanger', 'SSAHA2');
  $cvterm_id     = icbasic_get_add_cv_withnames('resource_type', 'software option');
  $link_sql      = 'INSERT INTO {ic_software_resource} (software_id,resource_id) VALUES (' . "(SELECT software_id from {ic_software} where uniquename='%s')" . ",(SELECT resource_id from {ic_resource} where uniquename='%s')" . ')';
  $options_array = array(
    'ssaha_seeds' => 'Number of kmer matches required to flag a hit',
    'ssaha_score' => 'Minimum score for match to be reported',
    'ssaha_identity' => 'Minimum identity for match to be reported',
    'ssaha_cmatch' => 'Minimum match length for cross_match matching',
    'ssaha_ckmer' => 'Word size for cross_match matching',
    'ssaha_cut' => 'Number of repeats allowed before this kmer is ignored',
    'ssaha_depth' => 'Number of hits to consider for alignment',
    'ssaha_best' => 'Only report best alignment',
    'ssaha_query_type' => 'Optimize options for a specific query sequencing technology',
  );
  foreach ($options_array as $option => $description) {
    dbsf_add_software_option($option, $dbxref_id, $cvterm_id, $description);

    switch ($option) {
      case 'ssaha_seeds':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '5', '1', '2', '8', '10', '12', '14', '18', '22', '30',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'ssaha_score':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '30', '5', '12', '15', '18', '20', '25', '30', '50', '100', '200', '500', '1000', '1500', '2000',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'ssaha_identity':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '50', '20', '30', '40', '45', '55', '60', '65', '70', '75', '80', '85', '90', '95', '98',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'ssaha_cmatch':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '14', '5', '9', '16', '18', '20', '22', '24', '28', '32', '40', '50', '100',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'ssaha_ckmer':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '10', '4', '5', '6', '8', '11', '12', '14', '18', '20', '30',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'ssaha_cut':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '10000', '3000', '5000', '8000', '15000', '20000', '40000', '80000', '100000', '500000',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'ssaha_depth':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '50',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('textfield'));
        break;

      case 'ssaha_best':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '0',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('checkbox'));
        break;

      case 'ssaha_query_type':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            'Custom', 'Sanger ABI', '454', 'Illumina-Solexa',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;
    }
    db_query($link_sql, 'ssaha2', $option);
  }
}

function dbsf_software_ssaha2_core_settings_form($form_state) {
  $software = 'ssaha2';
  $form     = array();
  $res      = db_fetch_array(db_query("SELECT active from {ic_software} where uniquename='%s'", $software));
  if ($res['active'] == 'f') {
    return $form;
  }
  $select_software_path = 'SELECT value FROM {ic_softwareprop} where software_id=' . "(SELECT software_id from {ic_software} where uniquename='%s')" . ' AND rank=0 AND type_id=' . "(SELECT cvterm_id from {ic_cvterm} as cvterm JOIN {ic_cv} as cv on cv.cv_id=cvterm.cv_id where cv.name='software path' AND cvterm.name='%s')";
  $core_exec = db_fetch_array(db_query($select_software_path, $software, 'executable'));
  $format_exec = db_fetch_array(db_query($select_software_path, 'ssaha2Build', 'executable'));


  $form['settings'] = array(
    '#type' => 'fieldset',
    '#title' => $software . t(' core settings'),
    '#description' => t('Please set some important settings for ') . $software,
    'submit' => array(
      '#type' => 'submit',
      '#value' => "Save core $software settings",
      '#weight' => 5,
    ),
    'core_executable' => array(
      '#type' => 'textfield',
      '#title' => t('Core executable path'),
      '#description' => t("Please provide the <b>full path</b> to the <b>$software</b> executable on the server, e.g. /usr/bin/$software ."),
      '#required' => TRUE,
      '#default_value' => $core_exec['value'],
    ),
    'format_executable' => array(
      '#type' => 'textfield',
      '#title' => t('Executable path for database formating'),
      '#description' => t('Please provide the <b>full path</b> to the <b>ssaha2Build</b> executable on the server, e.g. /usr/bin/ssaha2Build .'),
      '#required' => TRUE,
      '#default_value' => $format_exec['value'],
    ),
  );
  return $form;
}

function dbsf_software_ssaha2_core_settings_form_validate($form, &$form_state) {
  $software    = 'ssaha2';
  $core_exec   = escapeshellcmd(trim($form_state['values']['core_executable']));
  $format_exec = escapeshellcmd(trim($form_state['values']['format_executable']));

  if (!empty($core_exec)) {
    if (!file_exists($core_exec)) {
      form_set_error('core_executable', "Cannot find executable $core_exec on the server.");
    }
    $form_state['values']['core_executable'] = $core_exec;
  }

  if (!empty($format_exec)) {
    if (!file_exists($format_exec)) {
      form_set_error('format_executable', "Cannot find executable $format_exec on the server.");
    }
    $form_state['values']['format_executable'] = $format_exec;
  }
}

function dbsf_software_ssaha2_core_settings_form_submit($form, &$form_state) {
  $software = 'ssaha2';
  $store_software_path = 'INSERT INTO {ic_softwareprop} (software_id,type_id,rank,value) VALUES (' . "(SELECT software_id from {ic_software} where uniquename='%s')" . ",(SELECT cvterm_id from {ic_cvterm} as cvterm JOIN {ic_cv} as cv on cv.cv_id=cvterm.cv_id where cv.name='software path' AND cvterm.name='%s')" . ",0,'%s')";
  $delete_software_path = 'DELETE FROM {ic_softwareprop} where software_id=' . "(SELECT software_id from {ic_software} where uniquename='%s')" . ' AND rank=0 AND type_id=' . "(SELECT cvterm_id from {ic_cvterm} as cvterm JOIN {ic_cv} as cv on cv.cv_id=cvterm.cv_id where cv.name='software path' AND cvterm.name='%s')";
  $select_software_path = 'SELECT value FROM {ic_softwareprop} where software_id=' . "(SELECT software_id from {ic_software} where uniquename='%s')" . ' AND rank=0 AND type_id=' . "(SELECT cvterm_id from {ic_cvterm} as cvterm JOIN {ic_cv} as cv on cv.cv_id=cvterm.cv_id where cv.name='software path' AND cvterm.name='%s')";

  $core_exec = db_fetch_array(db_query($select_software_path, $software, 'executable'));
  $format_exec = db_fetch_array(db_query($select_software_path, 'ssaha2Build', 'executable'));

  $user_core_exec = $form_state['values']['core_executable'];
  $user_format_exec = $form_state['values']['format_executable'];

  if (!empty($user_core_exec) && $user_core_exec != $core_exec['value']) {
    db_query($delete_software_path, $software, 'executable');
    db_query($store_software_path, $software, 'executable', $user_core_exec);
    drupal_set_message("$user_core_exec is now the $software executable.", 'warning');
  }
  if (!empty($user_format_exec) && $user_format_exec != $format_exec['value']) {
    db_query($delete_software_path, 'ssaha2Build', 'executable');
    db_query($store_software_path, 'ssaha2Build', 'executable', $user_format_exec);
    drupal_set_message("$user_format_exec is now the ssaha2Build executable.", 'warning');
  }
}

function dbsf_admin_ssaha2_page($software = 'ssaha2') {
  $software = 'ssaha2';
  $check_active = dbsf_check_software_active($software);
  if (empty($check_active)) {
    drupal_set_message("I'm sorry, but $software does not seem to have been activated yet.<br>".
      l('See the software settings page', 'admin/dbsf/software'), 'error'
    );
    return FALSE;
  }
  $database_link_form = drupal_get_form('dbsf_admin_link_dataset_software_form', $software);
  if (strlen($database_link_form) < 600) {
    $database_link_form = "You have no datasets defined to link them to $software. Please see ". l('the dataset administration page', 'admin/dbsf/software', array('fragment' => 'available-datasets'));
  }
  $table = dbsf_admin_database_table($software);

  $page_tabs = array(
    'settings' => array(
      '#type' => 'tabset',
      'variables' => array(
        '#type' => 'tabpage',
        '#title' => 'Link datasets to '. strtoupper($software),
        '#content' => $database_link_form . $table,
        '#weight' => 0,
      ),
    ),
  );
  $return_text = tabs_render($page_tabs);
  return $return_text;
}

function dbsf_check_ssaha2($software) {
  $check_active = dbsf_check_software_active($software);
  if (empty($check_active)) {
    return 'active';
  }
  $check = 0;
  $software_prop = dbsf_get_softwareprop(NULL, TRUE);
  if (!empty($software_prop)) {
    foreach ($software_prop as $name => $data) {
      if (in_array($name, array('ssaha2', 'ssaha2Build'))) {
        foreach ($data as $term_name => $v) {
          if ($term_name == 'executable' || $term_name == 'data') {
            $check++;
          }
        }
      }
    }
  }
  if ($check < 2) {
    return 'variables';
  }
  $sql = 'SELECT count(distinct rcv.cvterm_id) from {ic_resource_cvterm} rcv ' . ' JOIN {ic_software_resource} sr ON sr.resource_id=rcv.resource_id ' . " WHERE sr.software_id=(SELECT software_id from {ic_software} where uniquename='%s') " . " AND rcv.cvterm_id IN (SELECT cvterm_id FROM {ic_cvterm} where cv_id=(SELECT cv_id from {ic_cv} where name='dataset_type'))";
  $count = db_fetch_array(db_query($sql, $software));
  if ($count['count'] < 1) {
    return 'datasets';
  }
  return TRUE;
}

function dbsf_ssaha2_page() {
  $setup = dbsf_check_ssaha2('ssaha2');
  if ($setup === TRUE) {
    return drupal_get_form('dbsf_ssaha2_form');
  }
  else {
    $return_text = "<p>I'm sorry but your SSAHA2 software has not been setup properly.</p><ul>";
    switch ($setup) {
      case 'datasets':
        $return_text .= '<li>Not enough datasets have been defined. Please define at least one dataset at the '. l('dataset registration page', 'admin/dbsf/dataset', array('fragment' => 'available-datasets')) .' and then register them with SSAHA2 at the '. l('SSAHA2 settings page', 'admin/dbsf/ssaha2');
        break;

      case 'active':
        $return_text .= '<li>SSAHA2 has not been activated. Please activate it at the '. l('software settings page', 'admin/dbsf/software');
        break;

      case 'variables':
        $return_text .= '<li>SSAHA2 variable paths have not been defined. Please define them at at the '. l('SSAHA2 settings page', 'admin/dbsf/software', array('fragment' => 'ssaha2'));
        break;
    }
    drupal_set_message($return_text .'</ul>', 'error');
    return ' ';
  }
}

function dbsf_ssaha2_form($form_state) {
  $form             = array();
  $software         = 'ssaha2';
  $software_options = _dbsf_generate_options($software);

  $dbs = dbsf_get_user_datasets($software);
  //returns in the form of ['dbtype']['group_name']['id']]=['name'];
  $nucleotide_dbs = (array)$dbs['nucleotide'];
  $option_form = array();
  if (empty($nucleotide_dbs)) {
    global $user;
    $roles_str = implode(', ', $user->roles);
    drupal_set_message("I'm sorry, but the system administrator has not authorized your role ($roles_str) to have access to at least 1 dataset with $software. Please let them know.", 'error');
    return FALSE;
  }
  if (!empty($software_options)) {
    foreach ($software_options as $name => $data) {
      $option_form[$name] = array(
        '#type' => $data['type'],
        '#title' => $name,
        '#description' => $data['description'],
      );
      if ($data['type'] !== 'textfield') {
        $option_form[$name]['#options'] = $data['options'];
      }
    }
  }
  $form['program'] = array(
    '#type' => 'fieldset',
    '#title' => strtoupper($software),
    'query_sequence' => array(
      '#type' => 'textarea',
      '#title' => t('Enter query sequence in simple text, FASTA or FASTQ format'),
    ),
    'query_file_'. $software => array(
      '#type' => 'file',
      '#title' => t('or upload query sequence in FASTA or FASTQ format'),
      '#description' => t('Please give a text file, not a MS-Word or other document'),
      // Needed because of drupal bug
      '#tree' => FALSE,
    ),
    'subject_db' => array(
      '#type' => 'select',
      '#title' => t('Dataset(s)'),
      '#description' => t('Please select one dataset.'),
      '#size' => 1,
      '#options' => $nucleotide_dbs,
    ),
    'subject_file_'. $software => array(
      '#type' => 'file',
      '#title' => t('or upload your own database as a FASTA'),
      '#description' => t('Please give a FASTA text file, not a MS-Word or other document'),
      // Needed because of drupal bug
      '#tree' => FALSE,
    ),
    'advanced parameters' => array(
      '#type' => 'fieldset',
      '#title' => 'Advance Search Parameters',
      '#collapsible' => TRUE,
      '#collapsed' => TRUE,
      $option_form,
    ),
  );

  $form['buttons'] = array(
    '#weight' => 10,
    'db_submit' => array(
      '#type' => 'submit',
      '#value' => t('Run '. $software),
      '#disabled' => TRUE,
    ),
    'clear' => array(
      '#attributes' => array('title' => t('Clear the form')),
      '#type' => 'submit',
      '#value' => 'Reset data',
      '#validate' => array('dbsf_form_clear'),
      '#weight' => 2,
    ),
  );
  $form['#attributes']['enctype'] = "multipart/form-data";
  return $form;
}

function dbsf_ssaha2_form_validate($form, &$form_state) {
  $data = $form_state['values'];
  if (!empty($data['query_sequence'])) {
    if (!empty($_FILES['files']['tmp_name']['query_file_' . 'ssaha2'])) {
      form_set_error("query_sequence", "It seems you both typed a query sequence and uploaded one.");
      return FALSE;
    }
    if (empty($data['subject_db']) && empty($_FILES['files']['tmp_name']['subject_file_' . 'ssaha2'])) {
      form_set_error("query_sequence", "It seems you provided a query sequence but no subject database (or file).");
      return FALSE;
    }
    // First Query (i.e. check for query first; query must exist if subject exists)
    $result = icbasic_validate_seq_dna($data['query_sequence']);
    if ($result === FALSE || is_numeric($result)) {
      form_set_error("query_sequence", "Sorry your sequence does not seem to be a valid DNA sequence ($result errors).");
      return FALSE;
    }
    else {
      $form_state['query_sequence'] = $result;
    }
  }
  elseif (!empty($_FILES['files']['tmp_name']['query_file_' . 'ssaha2'])) {
    //report an error if no database has been selected. and query is uploaded
    if (empty($data['subject_db']) && empty($_FILES['files']['tmp_name']['subject_file_' . 'ssaha2'])) {
      form_set_error("query_sequence", "It seems you provided a query but no database database (or file).");
      return FALSE;
    }
  }
  // now check for subject and make sure that if a query is selected, then subject is too.
  if (!empty($data['subject_db'])) {
    if (empty($data['query_sequence']) && empty($_FILES['files']['tmp_name']['query_file_' . 'ssaha2'])) {
      form_set_error("subject_db", "It seems you provided a subject database but no query sequence (or file).");
      return FALSE;
    }
    //  No need to check if it is nucleootide or protein as it is a pre-formated db
  }
  elseif (!empty($_FILES['files']['tmp_name']['subject_file_' . 'ssaha2'])) {
    //report an error if no query has been selected.
    if (empty($data['query_sequence']) && empty($_FILES['files']['tmp_name']['query_file_' . 'ssaha2'])) {
      form_set_error("subject_db", "It seems you provided a subject database but no query sequence (or file).");
      return FALSE;
    }
  }
}

function dbsf_ssaha2_form_submit($form, &$form_state) {
  dpm($form_state);
  // 10 Mb
  $validators_file = array('file_validate_size' => array(10000));
  $tmpdir = file_directory_temp();
  // all files, same timestamp
  $timestamp = time();
  $sessionid = session_id();
  $dirpath   = file_create_path() .'/dbsf';
  $data      = $form_state['values'];
  // BATCH API
  $operations = array();
  // for future use
  $save_array = array();
  $subject_dbs = '';
  // the form_uid will allow users to have multiple windows open.
  $form_uid = icbasic_create_uid($sessionid, $timestamp, 'ssaha2');
  $batch_file_data = array();

  $file_type = 'nucleotide';
  $verify    = array();
  $uid       = icbasic_create_uid($sessionid, $timestamp, 'ssaha2');
  // XML output
  //TODO   $par=' -m 7 ';
  // process user data
  // first, the query. check if file or text
  if (isset($_FILES['files']) && !empty($_FILES['files']['tmp_name']['query_file_' . 'ssaha2'])) {
    $file = file_save_upload('query_file_' . 'ssaha2', $validators_file, $tmpdir, FILE_EXISTS_RENAME);
    if (empty($file)) {
      form_set_error('query_file_' . 'ssaha2', "Sorry your file for 'ssaha2' was not saved. Maybe it is too large (>1 Mb)? Otherwise, ". l('contact', 'contact') ." the administrator  (quote $uid).");
    }
    else {
      $verify['runq']++;
      file_set_status($file, FILE_STATUS_TEMPORARY);
      $batch_file_data['infile'][$uid] = $file->filepath;
      $batch_file_data['outfile'][$uid] = $dirpath .'/'. $uid .'.query';
      $batch_file_data['filetype'][$uid] = $file_type;
      $batch_file_data['format'][$uid] = FALSE;
    }
  }
  elseif (!empty($data['query_sequence'])) {
    $verify['runq']++;
    // textfield
    $batch_file_data['infile'][$uid] = $data['query_sequence'];
    $batch_file_data['outfile'][$uid] = $dirpath .'/'. $uid .'.query';
    $batch_file_data['filetype'][$uid] = $file_type;
    $batch_file_data['format'][$uid] = FALSE;
  }
  // now subject which will decide the database
  $file_type = 'nucleotide';
  // if subject has been provided by user, either format it and add it to -d or reject it.
  if (isset($_FILES['files']) && !empty($_FILES['files']['tmp_name']['subject_file_' . 'ssaha2'])) {
    $file = file_save_upload('subject_file_' . 'ssaha2', $validators_file, $tmpdir, FILE_EXISTS_RENAME);
    if (empty($file)) {
      form_set_error('subject_file_' . 'ssaha2', "Sorry your file for 'ssaha2' was not saved. Maybe it is too large (>10 Mb)? Otherwise, ". l('contact', 'contact') ." the administrator  (quote $uid).");
    }
    else {
      $verify['rundb']++;
      file_set_status($file, FILE_STATUS_TEMPORARY);
      $batch_file_data['infile'][$uid] = $file->filepath;
      $batch_file_data['outfile'][$uid] = $dirpath .'/'. $uid .'.subject';
      $batch_file_data['filetype'][$uid] = $file_type;
      $batch_file_data['format'][$uid] = TRUE;
    }
  }
  if (!empty($data['subject_db'])) {
    // get database from select box
    //select box ->  grab path first then store into par
    foreach ($data['subject_db'] as $db => $value) {
      $verify['rundb']++;
      $subject_dbs[] = dbsf_get_dataset_path($db);
    }
  }
  //if it is going to run (both query and subject are ok)
  if (!empty($verify['runq']) && $verify['runq'] == 1 && !empty($verify['rundb'])) {
    //TODO      $par.=dbsf_blastall_software_pars($data['advanced parameters'][0],'ssaha2');
    $save_array[$form_uid][$uid]['par'] = $par;
    $save_array[$form_uid][$uid]['sub'] = $subject_dbs;
    $save_array[$form_uid][$uid]['algorithm'] = 'ssaha2';
  }

  // ended each algorithm
  $operations[] = array('dbsf_batch_upload_fasta', array($batch_file_data));
  $operations[] = array('dbsf_batch_save_data', array($save_array));
  $batch        = array(
    'title' => t('Preparing data needed for SSAHA2...'),
    'operations' => $operations,
    'init_message' => t('Starting SSAHA2 submission...'),
    'progress_message' => t('@remaining operations remaining...'),
    'error_message' => t('Your SSAHA2 submission encountered an error.'),
    'finished' => 'dbsf_ssaha2_batch_finished',
  );
  batch_set($batch);
  $form_state['redirect'] = array('dbsf/ssaha2_result', "submission_uid=$form_uid");
  return "dbsf/ssaha2_result?submission_uid=$form_uid";
}

function dbsf_ssaha2_result_page($submission_uid = NULL) {
  if (empty($submission_uid)) {
    $submission_uid = $_GET['submission_uid'];
    if (empty($submission_uid)) {
      return 'No submission data provided';
    }
  }
  $basepath = file_create_path();
  $dirpath  = $basepath .'/dbsf/';
  $data     = array();
  // one algorithm type for each submission.
  // we get this from a file.
  $infile = $dirpath . $submission_uid .'.submission';
  if (file_exists($infile)) {
    if ($inhandle = fopen($infile, 'rb')) {
      while (!feof($inhandle)) {
        $line = trim(fgets($inhandle));
        if (!empty($line)&& preg_match('/^algorithm;id=/', $line)) {
          $line_data          = explode('=', $line);
          $alg_data           = explode(';', $line_data[1]);
          $data[$alg_data[0]] = $alg_data[1];
        }
      }
    }
  }
  else {
    dpm("Did not find $infile");
    return 'Submission ID not found. Maybe it has expired or is invalid?';
  }
  if (empty($data)) {
    dpm("$infile has no data");
    return 'Not a valid submission ID or ID has expired.';
  }
  $content = '';
  foreach ($data as $algorithm => $uid) {
    $ssaha2file = $dirpath . $uid .'.output';
    $graph      = $ssaha2file .'.graph.png';
    $content    = t('Your report is not ready yet. Please wait or ') . l('try again', 'dbsf/ssaha2_result/'. $submission_uid
    ) . t(' in a few moments or bookmark this page.');
    if (file_exists($graph)) {
      $content = '<p>'. l(
        theme_image($graph, 'SSAHA2 results of all queries', 'SSAHA2 results graphical overview', array('width' => '100%'), FALSE)
        , $ssaha2file .'.html', array('html' => TRUE, 'alias' => TRUE, 'attributes' => array('target' => '_blank'))
      ) .'</p>'. drupal_get_form('dbsf_ssaha2_result_form', $uid, $ssaha2file);
    }
    else {
      drupal_set_html_head('<meta http-equiv="refresh" content="15;url=http://'. $_SERVER['SERVER_NAME'] . $basename .'/dbsf/ssaha2_result/'. $submission_uid .'" />');
    }
  }
  return $content;
}

//TODO:::

---