icsearch/dbsf.module

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<?php
// $Id: dbsf.module,v 1.1 2010-01-02 17:06:44 alexie Exp $


function dbsf_init() {
  drupal_add_css(drupal_get_path('module', 'dbsf') .'/icbasic.css', 'module');
}

function dbsf_perm() {
  $perms = array('Access dbsf', 'Access BLAST Server', 'Allow sequence retrieval', 'Administrate BLAST Server', 'Administrate dbsf');
  if (file_exists(drupal_get_path('module', 'dbsf') .'/dbsf_ssaha2.inc')) {
    $perms[] = 'Access SSAHA2 Server';
    $perms[] = 'Administrate SSAHA2 Server';
  }
  return $perms;
}

function dbsf_theme() {
  $themes = array(
    'dbsf_blast_result_form' => array(
      'arguments' => array('form'),
      'function' => 'dbsf_theme_blast_result_form',
    ),
  );
  return ($themes);
}

function dbsf_menu() {
  $items = array();
  $items['dbsf/blast_result'] = array(
    'title' => 'dbsf BLAST Results',
    'page callback' => 'dbsf_blast_result_page',
    'page arguments' => array(2),
    'access arguments' => array('Access BLAST Server'),
    'type' => MENU_CALLBACK,
  );
  $items['dbsf/get_sequences'] = array(
    'title' => 'dbsf Retrieve sequences',
    'page callback' => 'dbsf_get_sequence',
    'page arguments' => array(2),
    'access arguments' => array('Allow sequence retrieval'),
    'type' => MENU_CALLBACK,
  );
  $items['dbsf/software'] = array(
    'title' => 'Select dbsf software to use',
    'page callback' => 'dbsf_software_select_page',
    'access arguments' => array('Access dbsf'),
    'type' => MENU_CALLBACK,
  );
  $items['dbsf/blast'] = array(
    'title' => 'dbsf BLAST Server',
    'page callback' => 'dbsf_blast_page',
    'page arguments' => array(2),
    'access arguments' => array('Access BLAST Server'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/settings/dbsf'] = array(
    'title' => 'Drupal Bioinformatic Server framework settings',
    'page callback' => 'dbsf_admin_page',
    'access arguments' => array('Administrate dbsf'),
    'description' => 'Configure the dbsf module',
    // needed in order to appear at /admin/settings
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/dbsf/software'] = array(
    'title' => 'Administrate Software for the dbsf',
    'page callback' => 'dbsf_admin_software_page',
    'access arguments' => array('Administrate dbsf'),
    'description' => 'Configure which software are made available via the dbsf',
    'type' => MENU_CALLBACK,
  );
  $items['admin/dbsf/dataset'] = array(
    'title' => 'Administrate datasets/db for the dbsf',
    'page callback' => 'dbsf_admin_dataset_page',
    'access arguments' => array('Administrate dbsf'),
    'description' => 'Configure which datasets/databases are loaded for dbsf',
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/dbsf/blast'] = array(
    'title' => 'BLAST Server administration',
    'page callback' => 'dbsf_admin_blast_page',
    'access arguments' => array('Administrate BLAST Server'),
    'description' => 'Configure BLASTALL specific settings',
    'type' => MENU_NORMAL_ITEM,
  );

  if (file_exists(drupal_get_path('module', 'dbsf') .'/dbsf_ssaha2.inc')) {
    require_once (drupal_get_path('module', 'dbsf') .'/dbsf_ssaha2.inc');
    $new_items = dbsf_ssaha2_menu();
    $items = array_merge($items, $new_items);
  }
  return $items;
}

function dbsf_software_select_page() {
  $software_avail = array();
  $software_res = db_query('SELECT uniquename,description from {ic_software} where active is true');
  while ($row = db_fetch_array($software_res)) {
    $software_avail[$row['uniquename']] = $row['description'];
  }
  if (empty($software_avail)) {
    drupal_set_message('Sorry, but the administrator has not activated any software', 'error');
    return ' ';
  }
  $links = '';
  if (!empty($software_avail['blastall'])) {
    $links .= "<dt>NCBI's ". l('BLASTALL', 'dbsf/blast') .'</dt><dd>'. $software_avail['blastall'] .'</dd>';
  }
  // this should be somehow taken from plugin inc files.
  if (!empty($software_avail['ssaha2'])) {
    $links .= "<dt>Sanger's ". l('SSAHA2', 'dbsf/ssaha2') .'</dt><dd>'. $software_avail['ssaha2'] .'</dd>';
  }
  if (empty($links)) {
    drupal_set_message($sorry, 'error');
    return ' ';
  }
  return '<dl>'. $links .'</dl>';
}

function dbsf_admin_page() {
  $return_text = '<dl><dt>'. l('Setup the software available', 'admin/dbsf/software', array('attributes' => array('target' => '_blank'))) .'</dt><dd>Specify which software to activate for your search server</dd>';
  $return_text .= '<dt>'. l('Setup available reference datasets/databases', 'admin/dbsf/dataset', array('attributes' => array('target' => '_blank'))) .'</dt><dd>Load databases and datasets, specify which software and which users will have access to them.';
  $return_text .= '<dt>'. l('Setup the BLAST server', 'admin/dbsf/blast', array('attributes' => array('target' => '_blank'))) ."</dt><dd>Specify the necessary variables and databases to use with NCBI's BLAST</dd></dl>";
  if (file_exists(drupal_get_path('module', 'dbsf') .'/dbsf_ssaha2.inc')) {
    $return_text .= '<dt>'. l('Setup the SSAHA2 server', 'admin/dbsf/ssaha2', array('attributes' => array('target' => '_blank'))) ."</dt><dd>Specify the necessary variables and databases to use with Sangers's SSAHA2</dd></dl>";
  }
  return $return_text;
}

function dbsf_check_software_active($software) {
  if (empty($software)) {
    return FALSE;
  }
  $active_sql = "SELECT active from {ic_software} where ";
  if (is_numeric($software)) {
    $active_sql .= " software_id=$software";
  }
  else {
    $active_sql .= " uniquename='$software'";
  }
  $res = db_fetch_array(db_query($active_sql));
  if ($res['active'] == 'f') {
    return FALSE;
  }
  else {
    return TRUE;
  }
}

function dbsf_admin_dataset_page() {
  $add_dataset_variables = drupal_get_form('dbsf_admin_dataset_variables_form');
  $add_dataset_data = drupal_get_form('dbsf_admin_newdataset_form');
  $dataset_perm = drupal_get_form('dbsf_admin_dataset_perms_form');
  $link_dataset = drupal_get_form('dbsf_admin_link_dataset_software_form');
  $db_table = dbsf_admin_database_table();
  $file_table = dbsf_admin_database_files_table();

  if (strlen($link_dataset) < 600) {
    $link_dataset = '';
  }
  if (strlen($add_dataset_data) < 600) {
    $add_dataset_data = '';
    drupal_set_message('You will need to define at least one group and one directory in </b>Dataset variables</b> before registering new datasets.', 'error');
  }
  if (strlen($dataset_perm) < 600) {
    $dataset_perm = '';
  }
  $dataset_perm .= $db_table;
  $link_dataset .= $db_table;
  $add_dataset_data .= $file_table;

  $page_tabs = array(
    'dataset' => array(
      '#type' => 'tabset',
      'variables' => array(
        '#type' => 'tabpage',
        '#title' => 'Dataset variables',
        '#content' => $add_dataset_variables,
        '#weight' => 4,
      ),
      'add' => array(
        '#type' => 'tabpage',
        '#title' => 'Available datasets',
        '#content' => $add_dataset_data,
        '#weight' => 2,
      ),
      'perm' => array(
        '#type' => 'tabpage',
        '#title' => 'User permissions',
        '#content' => $dataset_perm,
        '#weight' => 3,
      ),
      'link' => array(
        '#type' => 'tabpage',
        '#title' => 'Link dataset w/ software',
        '#content' => $link_dataset,
        '#weight' => 4,
      ),
    ),
  );
  $return_text = tabs_render($page_tabs);
  return $return_text;
}

function dbsf_admin_software_page() {
  $software_data = drupal_get_form('dbsf_software_form');
  $blast_data = drupal_get_form('dbsf_software_blast_core_settings_form');
  if (strlen($blast_data) < 600) {
    $blast_data = '';
  }
  $page_tabs = array(
    'software' => array(
      '#type' => 'tabset',
      'available' => array(
        '#type' => 'tabpage',
        '#title' => 'Available software',
        '#content' => $software_data,
        '#weight' => 0,
      ),
      'blast' => array(
        '#type' => 'tabpage',
        '#title' => 'BLASTALL',
        '#content' => $blast_data,
        '#weight' => 4,
      ),
    ),
  );

  // plugins
  $plugin_path = drupal_get_path('module', 'dbsf') .'/';
  $plugins = array();
  if (file_exists($plugin_path .'dbsf_ssaha2.inc')) {
    $plugins['ssaha2']['file'] = $plugin_path .'dbsf_ssaha2.inc';
  }
  foreach ($plugins as $plugin_name => $plugin_data) {
    require_once ($plugin_data['file']);
    $data = '';
    if (function_exists('dbsf_software_'. $plugin_name .'_core_settings_form')) {
      $data = drupal_get_form('dbsf_software_'. $plugin_name .'_core_settings_form');
      if (strlen($data) < 600) {
        $data = '';
      }
      if (!empty($data)) {
        $page_tabs['software'][$plugin_name] = array(
          '#type' => 'tabpage',
          '#title' => strtoupper($plugin_name),
          '#content' => $data,
          '#weight' => 5,
        );
      }
    }
  }

  $return_text = tabs_render($page_tabs);
  return $return_text;
}

function dbsf_software_form($form_state) {
  $software_array  = array();
  $software_select = 'SELECT uniquename,description,active from {ic_software}';
  $res             = db_query($software_select);
  while ($row = db_fetch_array($res)) {
    $software_array[$row['uniquename']]['description'] = $row['description'];
    $software_array[$row['uniquename']]['active'] = $row['active'];
  }

  $form = array();
  $form['software'] = array(
    '#type' => 'fieldset',
    '#title' => t('Availabe software'),
    '#description' => t('Please specify which software will be active.'),
    '#tree' => TRUE,
    '#weight' => 1,
  );
  foreach ($software_array as $software => $value) {
    if ($value['active'] == 'f') {
      $value['active'] = FALSE;
    }
    else {
      $value['active'] = TRUE;
    }
    $form['software'][$software] = array(
      '#type' => 'checkbox',
      '#title' => t($software),
      '#description' => t($value['description']),
      '#default_value' => $value['active'],
    );
  }
  $form['buttons'] = array(
    '#type' => 'submit',
    '#value' => t('Update'),
    '#weight' => 2,
  );
  return $form;
}

function dbsf_software_form_submit($form, &$form_state) {
  //alter 1: for each option, activate into the _software table.
  //alter 2: If a software is present in _software table but not present in database, inactivate it
  $options        = $form_state['values']['software'];
  $sql_activate   = "UPDATE {ic_software} set active=TRUE where uniquename='%s'";
  $sql_deactivate = "UPDATE {ic_software} set active=FALSE where uniquename='%s'";
  foreach ($options as $name => $active) {
    if ($active === 1) {
      db_query($sql_activate, $name);
      drupal_set_message("Software $name is active.", 'warning');
    }
    else {
      db_query($sql_deactivate, $name);
      drupal_set_message("Software $name is not active.", 'warning');
    }
  }
}

function dbsf_admin_dataset_variables_form($form_state) {
  $form = array();
  $form['directories'] = array(
    '#type' => 'fieldset',
    '#title' => "Dataset/DB paths",
    'directory_name' => array(
      '#type' => 'textfield',
      '#description' => 'Here you can register a directory on the server that contains one or more databases for BLAST or other software.',
      '#size' => 50,
      '#title' => "Full path to directory containing your datasets",
    ),
    'directory_submit' => array(
      '#type' => 'submit',
      '#value' => t('Register directory'),
    ),
  );

  $form['groups'] = array(
    '#type' => 'fieldset',
    '#title' => "File Groups",
    'group_name' => array(
      '#type' => 'textfield',
      '#description' => 'In order to help users when viewing a large number of datasets, you can create groups for them.',
      '#size' => 20,
      '#title' => "Group name",
    ),
    'group_submit' => array(
      '#type' => 'submit',
      '#value' => t('Create group'),
    ),
  );
  return $form;
}

function dbsf_admin_dataset_variables_form_validate($form, &$form_state) {
  switch ($form_state['clicked_button']['#value']) {
    case 'Register directory':
      $directory_name = check_plain(trim($form_state['values']['directory_name']));
      if (empty($directory_name)) {
        form_set_error('directory_name', 'If you want to register a new directory, you must provide a name!');
      }
      if (!file_exists($directory_name)) {
        form_set_error('directory_name', "Cannot find directory $directory_name.");
      }
      elseif (substr($directory_name, -1) !== '/') {
        $directory_name .= '/';
        $form_state['values']['directory_name'] = $directory_name;
      }
      break;

    case 'Create group':
      $group_name = check_plain(trim($form_state['values']['group_name']));
      if (empty($group_name)) {
        form_set_error('group_name', 'If you want to create a new group, you must provide a name!');
      }
      else {
        $form_state['values']['group_name'] = $group_name;
      }
      break;
  }
}

function dbsf_admin_dataset_variables_form_submit($form, &$form_state) {
  switch ($form_state['clicked_button']['#value']) {
    case 'Register directory':
      $directory_name = $form_state['values']['directory_name'];
      if (empty($directory_name)) {
        return FALSE;
      }
      $res = icbasic_get_add_resource('directory', array('uniquename' => $directory_name, 'dbxref_name' => 'local resource'), 'ADD');
      if (!empty($res)) {
        drupal_set_message("Directory $directory_name saved.", 'warning');
      }
      break;

    case 'Create group':
      $group_name = $form_state['values']['group_name'];
      if (empty($group_name)) {
        return FALSE;
      }
      icbasic_get_add_resource('dataset_group', array('uniquename' => $group_name, 'dbxref_name' => 'local resource'), 'ADD');
      if (!empty($res)) {
        drupal_set_message("Group $group_name saved.", 'warning');
      }
      break;
  }
}

function dbsf_admin_newdataset_form($form_state) {
  $form = array();
  // TODO: consider setting dbtypes to checkboxes and dropping 'both'
  $directory_array = icbasic_get_add_resource('directory');
  $group_array     = icbasic_get_add_resource('dataset_group');
  $dbtypes_array   = icbasic_get_add_cv_withnames('dataset_type', NULL, 'BOTH');
  if (empty($directory_array)) {
    //drupal_set_message('Warning: before you can add databases, you will need to register at least one directory in the Register System Variables page.','error');
    return $form;
  }
  if (empty($group_array)) {
    //drupal_set_message('Warning: before you can add databases, you will need to register at least one group in the Register System Variables page.','error');
    return $form;
  }

  $form['data'] = array(
    '#type' => 'fieldset',
    '#title' => 'Database settings',
    '#description' => 'You can register new datasets to the system by providing the filename and the directory on the server. In order to remove datasets, just provide the <b>friendly name</b> you gave before and click <b>remove DB</b>.',
    'friendly_name' => array(
      '#type' => 'textfield',
      '#size' => 50,
      '#title' => 'Friendly name',
      '#description' => 'This will be shown to users instead of the filename',
      '#weight' => 2,
      '#required' => TRUE,
    ),
    'filename' => array(
      '#weight' => 1,
      '#type' => 'textfield',
      '#size' => 100,
      '#title' => t('Filename'),
      '#description' => t('Please provide the basename of the database (e.g. as you would pass it to the -d option of BLASTALL).' . ' <b>Avoid any suffix created by a particular software (e.g. for BLAST, .pal/.nal can be created)</b>.'
      ),
    ),
    'db_type' => array(
      '#weight' => 2,
      '#type' => 'radios',
      '#title' => 'Molecule type',
      '#description' => 'Select what molecule types are supported by this basename. You can select <i>both</i> if, for example, a nucleotide and protein BLAST database share the same basename.',
      '#options' => $dbtypes_array,
    ),
    'directory_id' => array(
      '#weight' => 2,
      '#type' => 'select',
      '#size' => 1,
      '#title' => 'Directory',
      '#options' => $directory_array,
    ),
    'group_id' => array(
      '#weight' => 3,
      '#type' => 'select',
      '#size' => 1,
      '#title' => 'Group',
      '#options' => $group_array,
    ),
  );

  $form['db_add'] = array(
    '#type' => 'submit',
    '#value' => t('Add DB'),
    '#weight' => 1,
  );
  $form['db_remove'] = array(
    '#type' => 'submit',
    '#value' => 'Remove DB',
    '#weight' => 2,
  );
  return $form;
}

function dbsf_admin_newdataset_form_validate($form, &$form_state) {
  // security checks
  $db_type = check_plain($form_state['values']['db_type']);
  $form_state['values']['db_type'] = $db_type;
  $filename = check_plain(trim($form_state['values']['filename']));
  $form_state['values']['filename'] = $filename;
  $fullname = check_plain(trim($form_state['values']['friendly_name']));
  $form_state['values']['friendly_name'] = $fullname;
  $directory_id = check_plain($form_state['values']['directory_id']);
  $form_state['values']['directory_id'] = $directory_id;
  $group_id = check_plain($form_state['values']['group_id']);
  $form_state['values']['group_id'] = $group_id;
  $blast_id = check_plain($form_state['values']['dataset']);
  $form_state['values']['dataset'] = $blast_id;
  //one cmd to rule them all
  $sql_select = 'SELECT uniquename from {ic_resource} WHERE resource_id=%d';
  //$dbtypes_array=icbasic_get_add_cv_withnames('dataset_type');
  switch ($form_state['clicked_button']['#value']) {
    case 'Add DB':
      if (!empty($filename)) {
        if (empty($fullname)) {
          form_set_error('friendly_name', 'Please give a friendly name for your database.');
        }
        $res = icbasic_get_add_resource('dataset', array('uniquename' => $fullname));
        if (!empty($res)) {
          form_set_error('friendly_name', "Name $fullname has been registered already.");
        }
        if (empty($group_id)) {
          form_set_error('group_id', 'You must specify a group.');
        }
        if (empty($directory_id)) {
          form_set_error('directory_id', 'You must specify a directory.');
        }
        if (empty($db_type)) {
          form_set_error('db_type', 'You must specify a type of molecule.');
        }
        // check for file existence
        $dbdata = db_fetch_array(db_query($sql_select, $directory_id));
        $filename = $dbdata['uniquename'] . $filename;
        if ((file_exists($filename .'.nin') || file_exists($filename .'.nal'))
          && (file_exists($filename .'.pin') || file_exists($filename .'.pal'))
        ) {
          if ($db_type !== 'both') {
            form_set_error('filename', 'You asked for '. $db_type .' as molecule type but I found it formatted as ' . 'both.');
          }
        }
        elseif (file_exists($filename .'.nin') || file_exists($filename .'.nal')) {
          if ($db_type !== 'nucleotide') {
            form_set_error('filename', 'You asked for '. $dbtypes_array[$db_type] .' as molecule type but I found it formatted as ' . 'nucleotide.');
          }
        }
        elseif (file_exists($filename .'.pin') || file_exists($filename .'.pal')) {
          if ($db_type !== 'protein') {
            form_set_error('filename', 'You asked for '. $dbtypes_array[$db_type] .' as molecule type but I found it formatted as ' . 'protein.');
          }
        }
        elseif (file_exists($filename)) {
          dpm($db_type);
          drupal_set_message("I found $filename in your system but it does not seem to be a BLAST database formatted with formatdb. Perhaps you gave the formatdb suffix as well? Do ignore this warning if it is not meant to be used with BLAST.", 'warning');
        }
        else {
          form_set_error('filename', "Sorry, cannot find file $filename in your system.");
        }
      }
      else {
        form_set_error('filename', "Filename cannot be empty when you're trying to add a database.");
      }
      break;

    case 'Remove DB':
      $res = icbasic_get_add_resource('dataset', array('uniquename' => $fullname));
      if (empty($res)) {
        form_set_error('name', "Database $fullname does not exist.");
      }
      break;
  }
}

function dbsf_admin_newdataset_form_submit($form, &$form_state) {
  // security checks already performed during validate
  $filename     = $form_state['values']['filename'];
  $fullname     = $form_state['values']['friendly_name'];
  $directory_id = $form_state['values']['directory_id'];
  $group_id     = $form_state['values']['group_id'];
  $db_type      = $form_state['values']['db_type'];
  //$dbtypes_array=icbasic_get_add_cv_withnames('dataset_type');

  switch ($form_state['clicked_button']['#value']) {
    case 'Add DB':
      if (empty($filename)) {
        return;
      }
      // add database name as the core resource
      $dataset_data = icbasic_get_add_resource('dataset', array('uniquename' => $fullname, 'dbxref_name' => 'BLAST database'), 'REPLACE', TRUE);
      // add database filename, link it (use resource_ids as a security check
      $filename_data = icbasic_get_add_resource('filename', array('uniquename' => $filename, 'dbxref_name' => 'BLAST database'), 'REPLACE', TRUE);
      icbasic_link_unlink_resources($dataset_data[$fullname], 'uses', $filename_data[$filename]);
      // directory and group already exist as resources, link them.
      icbasic_link_unlink_resources($dataset_data[$fullname], 'uses', $group_id);
      icbasic_link_unlink_resources($dataset_data[$fullname], 'uses', $directory_id);

      // set dbtype into resource_cvterm
      if ($db_type == 'both') {
        icbasic_populate_cvterms('ic_resource', $fullname, 'dataset_type', array('nucleotide', 'protein'));
      }
      else {
        icbasic_populate_cvterms('ic_resource', $fullname, 'dataset_type', array($db_type));
      }
      // link role
      $role_link = dbsf_link_unlink_resource_role($fullname, 'authenticated user');
      drupal_set_message("Dataset $filename saved.", 'warning');
      break;

    case 'Remove DB':
      icbasic_link_unlink_resources($dataset_data[$fullname], 'uses', NULL, 'DELETE');
      $dataset_data = icbasic_get_add_resource('dataset',
        array('uniquename' => $fullname, 'dbxref_name' => 'BLAST database'),
        'DELETE'
      );
      drupal_set_message("BLASTDB $fullname removed.", 'warning');
      break;
  }
}

function dbsf_admin_link_dataset_software_form($form_state, $software = NULL) {
  $form = array();
  $software_array = array();
  if (empty($software)) {
    $software_array = dbsf_get_software(array('active' => TRUE), 'BOTH');
    if (empty($software_array)) {
      drupal_set_message('Sorry, but you have not activated any software', 'error');
      return $form;
    }
  }
  $dataset_array = icbasic_get_add_resource('dataset', NULL, FALSE, 'BOTH');
  if (empty($dataset_array)) {
    return $form;
  }
  $form['dataset_link'] = array(
    '#type' => 'fieldset',
    '#title' => "Link datasets with software",
    '#description' => 'Here you can link datasets you have submitted earlier with activated software',
    'dataset' => array(
      '#options' => $dataset_array,
      '#size' => 5,
      '#title' => 'Dataset',
      '#description' => 'Which dataset/database to link.',
      '#required' => TRUE,
    ),
    'submit' => array(
      '#type' => 'submit',
      '#value' => t('Toggle link'),
      '#weight' => 10,
    ),
  );

  if (empty($software)) {
    $form['dataset_link']['dataset']['#type'] = 'select';
    $form['dataset_link']['dataset']['#multiple'] = TRUE;
    $form['dataset_link']['software'] = array(
      '#type' => 'select',
      '#size' => 1,
      '#title' => 'Software',
      '#description' => 'These are the activated software',
      '#options' => $software_array,
    );
  }
  else {
    $form['dataset_link']['dataset']['#type'] = 'checkboxes';
    $form['dataset_link']['software'] = array(
      '#type' => 'value',
      '#value' => $software,
    );
  }

  return $form;
}

function dbsf_admin_link_dataset_software_form_validate($form, &$form_state) {
  $dataset_array = $form_state['values']['dataset'];
  $software = check_plain($form_state['values']['software']);
  if (empty($dataset_array) || empty($software)) {
    form_set_error();
  }
  //TODO code this into DB
  $suffix_array = array(
    'blastall' => array('suffix' => array('pin', 'nin', 'pal', 'nal'), 'switch' => 'ANY'),
    'ssaha2' => array('suffix' => array('head', 'body', 'base', 'name', 'size'), 'switch' => 'ALL'),
  );
  if (empty($suffix_array[$software])) {
    form_set_error('software', "Software $software does not allow dataset linking.");
    return FALSE;
  }
  foreach ($dataset_array as $key => $dataset) {
    $dataset = check_plain($dataset);
    $dataset_array[$key] = $dataset;
    if (empty($dataset)) {
      continue;
    }
    $format_check = 0;
    $fullpath     = dbsf_get_dataset_path($dataset);
    $basename     = basename($fullpath);
    $dirname      = dirname($fullpath);
    $f            = file_scan_directory($dirname, $basename .'\..+$', array('.', '..', 'CVS'), 0, FALSE, 'basename');
    foreach ($f as $fname => $obj) {
      $suffix = str_replace($basename .'.', '', $fname);
      if (in_array($suffix, $suffix_array[$software]['suffix'])) {
        $format_check++;
      }
    }
    switch ($suffix_array[$software]['switch']) {
      case 'ANY':
        if ($format_check < 1) {
          form_set_error('dataset', "It doesn't seem that $dataset is properly formatted for $software.");
        }
        break;

      case 'ALL':
        if ($format_check < count($suffix_array[$software]['suffix'])) {
          form_set_error('dataset', "It doesn't seem that $dataset is properly formatted for $software.");
        }
        break;
    }
  }
  $form_state['values']['software'] = $software;
  $form_state['values']['dataset'] = $dataset_array;
}

function dbsf_admin_link_dataset_software_form_submit($form, &$form_state) {
  $dataset_array = $form_state['values']['dataset'];
  $software = $form_state['values']['software'];
  if (empty($dataset_array) || empty($software)) {
    return FALSE;
  }
  foreach ($dataset_array as $dataset) {
    if (empty($dataset)) {
      continue;
    }
    $result = dbsf_link_unlink_software_resource($software, $dataset, 'TOGGLE');
    switch ($result) {
      case FALSE:
        drupal_set_message("Failed to change link of $dataset with $software", 'error');
        break;

      case 'GRANTED':
        drupal_set_message("Dataset $dataset linked with $software.", 'warning');
        break;

      case 'REVOKED':
        drupal_set_message("Dataset $dataset unlinked from $software.", 'warning');
        break;
    }
  }
}

function dbsf_admin_dataset_perms_form($form_state) {
  $form = array();
  //keys are resource_ids and values are the user-friendly names
  $dataset_array = icbasic_get_add_resource('dataset');
  $role_array = dbsf_get_role();
  if (empty($dataset_array)) {
    return $form;
  }
  if (empty($role_array)) {
    drupal_set_message('This is very weird, it seems I cannot get the roles from your Drupal installation. Please file a bug report.');
    return $form;
  }
  $form['access'] = array(
    '#type' => 'fieldset',
    '#title' => "Data access settings",
    '#description' => 'If you wish, you can protect datasets (e.g. databases for BLAST or other software) by asking that they are accessible only to users belonging to specific user roles.' . ' By default, all new datasets are accessible only to logged in users (authenticated). If you wish for  all users to be able to see the database, add permissions for the anonymous' . ' group too; alternatively, you may remove permissions from the authenticated group and add them to a new private one you created via Drupal.',
    'role' => array(
      '#type' => 'select',
      '#size' => 1,
      '#title' => 'Role',
      '#description' => 'These roles are defined by '. l("Drupal's role management", 'admin/user/roles'),
      '#options' => $role_array,
    ),
    'dataset' => array(
      '#type' => 'select',
      '#size' => 10,
      '#multiple' => TRUE,
      '#title' => 'Dataset',
      '#description' => 'Which dataset(s) to protect.',
      '#options' => $dataset_array,
    ),
    'access_submit' => array(
      '#type' => 'submit',
      '#value' => t('Toggle permission setting'),
    ),
  );
  return $form;
}

function dbsf_admin_dataset_perms_form_submit($form, &$form_state) {
  $role_id = $form_state['values']['role'];
  $dataset_id_array = $form_state['values']['dataset'];
  if (empty($dataset_id_array) || empty($role_id)) {
    return FALSE;
  }
  foreach ($dataset_id_array as $dataset_id) {
    $result = dbsf_link_unlink_resource_role($dataset_id, $role_id, 'TOGGLE');
    switch ($result) {
      case FALSE:
        drupal_set_message('Failed to change dataset permissions', 'error');
        break;

      case 'GRANTED':
        drupal_set_message("Permission granted.", 'warning');
        break;

      case 'REVOKED':
        drupal_set_message("Permission revoked.", 'warning');
        break;
    }
  }
}

function dbsf_form_clear($form, &$form_state) {
  unset($form_state['values']);
  unset($form_state['storage']);
  $form_state['rebuild'] = TRUE;
}

function dbsf_admin_database_table($software = NULL) {
  $software_avail_array = dbsf_get_software(array('active' => TRUE), TRUE);
  if (!empty($software) && empty($software_avail_array[$software])) {
    drupal_set_message("It seems that $software is not active yet. Will show no databases for it.", 'error');
    return FALSE;
  }
  elseif (empty($software_avail_array)) {
    drupal_set_message("It seems that no software is not active yet. Will show no databases.", 'error');
    return FALSE;
  }
  $table_caption = 'Databases currently registered';
  $table_header  = array('Linked with', 'Role permitted', 'File', 'Name shown to users', 'Grouping', 'Database type');
  $table_rows    = array();
  // get all datasets
  if (empty($software)) {
    $dataset_software = dbsf_get_software_resources(array('rcvterm.name' => 'dataset'), 'RESOURCE');
    $dataset_array = icbasic_get_add_resource('dataset');
    if (!empty($dataset_array)) {
      foreach ($dataset_array as $dataset_id => $dataset_name) {
        $linked_with = '';
        if (!empty($dataset_software) && !empty($dataset_software[$dataset_name])) {
          foreach ($dataset_software[$dataset_name] as $software_name => $d) {
            $linked_with .= $software_name .' ';
          }
        }
        $linked_with = trim($linked_with);
        if (empty($linked_with)) {
          $linked_with = 'none';
        }
        $to_add    = array();
        $role_str  = 'none';
        $role_data = dbsf_get_resource_roles($dataset_id);
        if (!empty($role_data)) {
          $role_str = implode(', ', $role_data);
        }
        $dataset_extra   = icbasic_get_resource_cvterm_and_prop($dataset_id);
        $dbtype          = implode(', ', $dataset_extra['cvterm']['dataset_type']);
        $linked_res_data = icbasic_get_linked_resources($dataset_id, NULL, TRUE);
        foreach ($linked_res_data as $object_name => $object_data) {
          $object_type = $object_data['type_name'];
          $to_add[$object_type] = $object_name;
        }
        $table_rows[] = array($linked_with, $role_str, $to_add['directory'] . $to_add['filename'], $dataset_name, $to_add['dataset_group'], $dbtype);
      }
    }
  }
  else {
    $table_caption .= " to $software";
    $table_header = array('Role permitted', 'File', 'Name shown to users', 'Grouping', 'Database type');
    foreach ($software_avail_array as $software_name => $software_id) {
      if (!empty($software) && $software_name !== $software) {
        continue;
      }
      $software_data = dbsf_get_software_resources(
        array('sr.software_id' => $software_id, 'rcvterm.name' => 'dataset'),
        FALSE
      );
      if (empty($software_data[$software_id])) {
        continue;
      }
      foreach ($software_data[$software_id] as $dataset_id => $dataset_data) {
        $to_add       = array();
        $dataset_name = $dataset_data['uniquename'];
        $role_data    = dbsf_get_resource_roles($dataset_id);
        if (!empty($role_data)) {
          $role_str = implode(', ', $role_data);
        }
        $dataset_extra   = icbasic_get_resource_cvterm_and_prop($dataset_id);
        $dbtype          = implode(', ', $dataset_extra['cvterm']['dataset_type']);
        $linked_res_data = icbasic_get_linked_resources($dataset_id, NULL, TRUE);
        foreach ($linked_res_data as $object_name => $object_data) {
          $object_type = $object_data['type_name'];
          $to_add[$object_type] = $object_name;
        }
        $table_rows[] = array($role_str, $to_add['directory'] . $to_add['filename'], $dataset_name, $to_add['dataset_group'], $dbtype);
      }
    }
  }
  $table = theme_table($table_header, $table_rows, array('width' => '750px'), $table_caption);
  return $table;
}

function dbsf_admin_database_files_table() {
  $software_avail_array = dbsf_get_software(array('active' => TRUE), TRUE);
  if (empty($software_avail_array)) {
    drupal_set_message("It seems that no software is not active yet. Will show no databases.", 'error');
    return FALSE;
  }
  $directory_array = icbasic_get_add_resource('directory');
  if (empty($directory_array)) {
    drupal_set_message("It seems that no directory paths have been registered yet. Will show no databases.", 'error');
    return FALSE;
  }
  //TODO code this into DB
  $suffix_array = array(
    'blastall' => array('suffix' => array('pin', 'nin', 'pal', 'nal'), 'switch' => 'ANY'),
    'ssaha2' => array('suffix' => array('head', 'body', 'base', 'name', 'size'), 'switch' => 'ALL'),
  );

  $table_caption = 'Files in your registered directories which could act as databases';
  $table_header  = array('Directory', 'Filename', 'Formatted for', 'Suffixes found');
  $table_rows    = array();

  // get all datasets
  foreach ($directory_array as $id => $name) {
    $name = rtrim($name, '/');
    foreach ($suffix_array as $software_name => $data) {
      //TODO:$switch=$data['switch'];
      $files_array = array();
      foreach ($data['suffix'] as $suffix) {
        $f = file_scan_directory($name, '.+\.'. $suffix .'$', array('.', '..', 'CVS'), 0, FALSE, 'name');
        foreach ($f as $fname => $obj) {
          $files_array[$fname][] = $suffix;
        }
      }
      foreach ($files_array as $basename => $f_data) {
        $suffix_str = implode(', ', $f_data);
        $table_rows[] = array($name, $basename, $software_name, $suffix_str);
      }
    }
  }
  $table = theme_table($table_header, $table_rows, array('width' => '750px'), $table_caption);
  return $table;
}

function dbsf_get_role($limit = NULL) {
  $role_array = array();
  $sql_select = "SELECT rid,name from {role}";
  if (!empty($limit)) {
    if (is_array($limit)) {
      $sql_select .= " WHERE $limit[0]=$limit[1]";
    }
    else {
      $sql_select .= " WHERE $limit";
    }
  }
  $db_results = db_query($sql_select);
  while ($dbdata = db_fetch_array($db_results)) {
    $role_array[$dbdata['rid']] = $dbdata['name'];
  }
  if (!empty($role_array)) {
    return $role_array;
  }
  else {
    return FALSE;
  }
}

function _dbsf_generate_options($software_name) {
  if (empty($software_name)) {
    return FALSE;
  }
  $return_array = array();
  $resources = dbsf_get_software_resources(array('s.uniquename' => $software_name, 'rcvterm.name' => 'software option'), TRUE);

  if (empty($resources[$software_name])) {
    drupal_set_message("Sorry, cannot find any options for $software_name stored in the database", 'error');
    return FALSE;
  }
  foreach ($resources[$software_name] as $id => $base_data) {
    $name = $base_data['uniquename'];
    $extra_data = icbasic_get_resource_cvterm_and_prop($id);
    if (empty($extra_data['cvterm']['input type'])) {
      continue;
      //not an option
    }
    //dpm($extra_data);
    //Format option array as it will be expected for form API
    if ($name == 'query genetic code' || $name == 'DB genetic code') {
      $return_array[$name]['options'] = $extra_data['prop']['software option'];
    }
    elseif (!empty($extra_data['prop']['software option'])) {
      foreach ($extra_data['prop']['software option'] as $value) {
        $return_array[$name]['options'][$value] = $value;
      }
    }
    $return_array[$name]['type'] = implode('', $extra_data['cvterm']['input type']);
    $return_array[$name]['description'] = $base_data['description'];
  }
  //  dpm($return_array);
  return $return_array;
}

function dbsf_batch_upload_fasta($batch_file_data, &$context) {
  //dpm(array($infilelist,$outfilelist,$filetype,$formatlist,$uid));
  $infilelist  = $batch_file_data['infile'];
  $outfilelist = $batch_file_data['outfile'];
  $filetype    = $batch_file_data['filetype'];
  $formatlist  = $batch_file_data['format'];
  if (empty($infilelist) || empty($outfilelist) ||
    empty($filetype) || empty($formatlist)
  ) {
    dvm('Failed');
    return FALSE;
  }
  $max = count($infilelist);
  $progress = 0;
  foreach ($infilelist as $uid => $infile) {
    if (empty($infile)) {
      $progress++;
      continue;
    }
    icbasic_write_fastafile($infile, $outfilelist[$uid], TRUE);
    if ($formatlist[$uid] === TRUE) {
      // I/O friendship?
      sleep(1);
      dbsf_formatdb_fastafile($outfilelist[$uid], $filetype[$uid]);
      $context['results'][$uid]['subject'][] = basename($outfilelist[$uid]);
    }
    $progress++;
  }
  $context['finished'] = $progress / $max;
}

function dbsf_batch_save_data($data = NULL, &$context) {
  $context['results']['data'] = $data;
}

function dbsf_parameter_daemon($uid, $dir, $par, $software = 'blastall', $other_data = NULL) {
  if (empty($uid) || empty($dir) || empty($par)) {
    return FALSE;
  }
  // need to print uid, software, par and condor. No spaces.

  $data = "uid:$uid\nsoftware:$software\n";
  if (!empty($other_data)) {
    if (is_array($other_data)) {
      foreach ($other_data as $key => $value) {
        if (is_array($value)) {
          foreach ($value as $element) {
            if (!empty($element)) {
              $data .= $key .':'. $element ."\n";
            }
          }
        }
        else {
          if (!empty($value)) {
            $data .= $key .':'. $value ."\n";
          }
        }
      }
    }
    else {
      $data .= $other_data ."\n";
    }
  }
  $data .= "par:$par -i $uid.query -o $uid.output\n";
  $outfile = $dir .'/'. $uid .'.wait';
  if (!$outhandle = fopen($outfile, 'wt')) {
    drupal_set_message(t("Could not create $outfile."), 'error');
    return FALSE;
  }
  fwrite($outhandle, $data);
  fclose($outhandle);
  return TRUE;
}

function dbsf_formatdb_fastafile($infile, $file_type = 'protein') {
  if (empty($infile) || !file_exists($infile)) {
    return FALSE;
  }
  $is_protein = 'T';
  if ($file_type == 'protein') {
    $is_protein = 'T';
  }
  else {
    $is_protein = 'F';
  }
  $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')";
  $res = db_fetch_array(db_query($select_software_path, 'formatdb', 'executable'));
  $formatdb_exec = $res['value'];
  if (empty($formatdb_exec)) {
    drupal_set_message(t('The administrator has not activated the formatdb program yet.'), 'error');
    return FALSE;
  }
  // run formatdb as a child
  $args = " -p $is_protein -o T -i $infile -l /dev/stdout";
  $result = exec($formatdb_exec . $args);
  return $result;
}

function dbsf_get_user_datasets($software_name) {
  if (empty($software_name)) {
    return FALSE;
  }
  // activate $user
  global $user;
  // get name from $user object
  $rid = $user->name;
  // an array of all the roles a user has.
  $user_roles = $user->roles;
  $return_array = array();
  // role IDs
  //$roles_str=icbasic_array2csv($roles_array,NULL,',',TRUE);
  //dbtype,group,resource_id=name

  $dataset_array = dbsf_get_software_resources(array('s.uniquename' => $software_name, 'rcvterm.name' => 'dataset'), TRUE);
  if (empty($dataset_array) || empty($dataset_array[$software_name])) {
    return FALSE;
  }
  $dataset_array = $dataset_array[$software_name];

  foreach ($dataset_array as $name => $db_data) {
    $id             = $db_data['id'];
    $dbroles        = dbsf_get_resource_roles($id);
    $security_check = array_intersect($user_roles, $dbroles);
    if (!empty($dbroles) && empty($security_check)) {
      continue;
    }
    $dbgroup = '';
    $data = icbasic_get_resource_cvterm_and_prop($id);
    if (empty($data['cvterm']['dataset_type'])) {
      continue;
    }
    $linked_data = icbasic_get_linked_resources($id, 'uses', FALSE, "rocvterm.name='dataset_group'");
    if (!empty($linked_data)) {
      foreach ($linked_data as $lid => $d) {
        $dbgroup = $d['uniquename'];
      }
    }
    $dbtype_array = $data['cvterm']['dataset_type'];
    foreach ($dbtype_array as $dbtype) {
      $return_array[$dbtype][$dbgroup][$id] = $name;
    }
  }
  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function dbsf_get_sequence($uid = NULL, $database = NULL) {
  if (empty($uid) && empty($database)) {
    return 'No method to acquire the database was provided';
  }

  $seqs_to_get_array = $_POST['features'];
  if (empty($seqs_to_get_array)) {
    return 'No sequences were requested for retrieval';
  }
  $seqs_to_get = '';
  foreach ($seqs_to_get_array as $seq) {
    $seqs_to_get .= escapeshellarg($seq) .' ';
  }
  $seqs_to_get = trim($seqs_to_get);
  // currently only FASTA
  $operation = isset($_POST['op']) ? $_POST['op'] : 'FASTA';

  $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')";
  $res = db_fetch_array(db_query($select_software_path, 'fastacmd', 'executable'));
  $fastacmd_exec = $res['value'];
  if (empty($fastacmd_exec)) {
    drupal_set_message('Failed to find an executable for fastacmd', 'error');
    return ' ';
  }

  $database_array = array();
  //first get database using $uid.
  if (!empty($uid)) {
    // get databases with which to search for ID.
    $dirpath = file_create_path() .'/dbsf/';
    $infile = $dirpath . $uid .'.wait';
    if (!file_exists($infile)) {
      return 'Seems the UID you provided is invalid or expired';
    }
    if ($inhandle = fopen($infile, 'rb')) {
      while (!feof($inhandle)) {
        $line = trim(fgets($inhandle));
        if (!empty($line) && preg_match('/^database:/', $line)) {
          $line_data = explode(':', $line);
          //set as key so that we avoid duplicates
          $database_array[trim(escapeshellarg($line_data[1]))] = 1;
        }
      }
    }
    else {
      dpm("Could not read $infile");
    }
  }
  elseif (!empty($database)) {
    if (is_array($database)) {
      foreach ($database as $db) {
        $database_array[$db] = 1;
      }
    }
    else {
      $database_array[$database] = 1;
    }
  }
  //$database_str=trim($database_str);

  // run fastacmd
  $exec_output = array();
  $html_output = '';
  $fasta_data  = '';
  //dpm($database_array);

  foreach ($database_array as $database_str => $dummy) {
    $args = " -d '$database_str' -s '$seqs_to_get'";
    //dvm("$fastacmd_exec.$args");
    $result = exec($fastacmd_exec . $args, $exec_output);
  }

  if (empty($exec_output)) {
    dpm($fastacmd_exec . $args);
    return 'Sorry, cannot find your sequence entries in any database. If you want, you can '. l('contact', 'contact') .' the administrator.';
  }
  foreach ($exec_output as $line) {
    if (strpos($line, '>') !== FALSE) {
      $line = str_replace(' No definition line found', '', $line);
      $fasta_data .= $line ."\n";
      $html_output .= '</p><p>'. $line .'<br>';
    }
    else {
      $fasta_data .= $line ."\n";
      $html_output .= $line .'<br>';
    }
  }
  $return_text = '';
  $outfile = $infile . time() .'.get';
  // OS compatibility
  ini_set('auto_detect_line_endings', TRUE);
  if (!$outhandle = fopen($outfile, 'wt')) {
    drupal_set_message(t("Could not create output FASTA file $outfile."), 'error');
  }
  else {
    fwrite($outhandle, $fasta_data);
    fclose($outhandle);
    $return_text .= '<p>You can download a '. l('FASTA file', $outfile) .' or copy-paste it from below.</p>';
  }

  $return_text .= '<pre>'. $html_output .'</pre>';
  return $return_text;
}

function dbsf_cron() {
  //not sure if this is to be @ .module or .install (probably .module)
  $dirpath = file_create_path() .'/dbsf';
  file_scan_directory($dirpath, '.+\.query$', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.subject.*', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.wait$', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.done$', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.parameter$', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.output.*', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.submission$', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
  file_scan_directory($dirpath, '.+\.get$', array('.', '..', 'CVS'), 'dbsf_delete_temp', FALSE);
}

function dbsf_delete_temp($file = NULL) {
  if (empty($file)) {
    return FALSE;
  }

  $timestamp = time();
  //check date if older than 1 week i.e. 7*24*60*60 secs=604800
  $age = filemtime($file);
  if (!empty($age) && !empty($timestamp)) {
    $diff = $timestamp - $age;
    if ($diff > 604800) {
      file_delete($file);
    }
  }
}

function dbsf_link_unlink_resource_role($resource, $role, $switch = FALSE) {
  if (empty($resource) || empty($role)) {
    return FALSE;
  }
  $role       = check_plain($role);
  $resource   = check_plain($resource);
  $sql_check  = '';
  $sql_insert = '';
  $sql_delete = '';
  if (is_numeric($role)) {
    $sql_check  = "SELECT resource_role_id from {ic_resource_role} where role_id=%d AND resource_id=";
    $sql_insert = "INSERT INTO {ic_resource_role} (role_id,resource_id) VALUES (%d,";
    $sql_delete = "DELETE FROM {ic_resource_role} where role_id=%d AND resource_id=";
  }
  else {
    $sql_check  = 'SELECT resource_role_id from {ic_resource_role} where role_id=' . "(SELECT rid from {role} where name='%s') AND resource_id=";
    $sql_insert = 'INSERT INTO {ic_resource_role} (role_id,resource_id) VALUES (' . "(SELECT rid from {role} where name='%s'),";
    $sql_delete = 'DELETE FROM {ic_resource_role} where role_id=' . "(SELECT rid from {role} where name='%s') AND resource_id=";
  }
  if (is_numeric($resource)) {
    $sql_check .= "%d";
    $sql_insert .= "%d)";
    $sql_delete .= "%d";
  }
  else {
    $sql_check .= "(SELECT resource_id from {ic_resource} where uniquename='%s')";
    $sql_insert .= "(SELECT resource_id from {ic_resource} where uniquename='%s'))";
    $sql_delete .= "(SELECT resource_id from {ic_resource} where uniquename='%s')";
  }

  $res = db_fetch_array(db_query($sql_check));
  switch ($switch) {
    case FALSE:
      if (empty($res)) {
        db_query($sql_insert, array($role, $resource));
        return 'GRANTED';
      }
      else {
        return 'GRANTED';
      }
      break;

    case 'TOGGLE':
      if (empty($res)) {
        db_query($sql_insert, array($role, $resource));
        return 'GRANTED';
      }
      else {
        db_query($sql_delete, array($role, $resource));
        $res = db_fetch_array(db_query($sql_check, array($role, $resource)));
        if (empty($res)) {
          return 'REVOKED';
        }
        else {
          dvm("Failed to delete previous link for role $role and resource $resource.");
          return FALSE;
        }
      }
      break;

    case TRUE:
      if (empty($res)) {
        return 'REVOKED';
      }
      else {
        db_query($sql_delete, array($role, $resource));
        $res = db_fetch_array(db_query($sql_check, array($role, $resource)));
        if (empty($res)) {
          return 'REVOKED';
        }
        else {
          dvm("Failed to delete previous link for role $role and resource $resource.");
          return FALSE;
        }
      }
      break;
  }
}

function dbsf_link_unlink_software_resource($software, $resource, $switch = FALSE) {
  if (empty($resource) || empty($software)) {
    return FALSE;
  }
  $software   = check_plain($software);
  $resource   = check_plain($resource);
  $sql_check  = '';
  $sql_insert = '';
  $sql_delete = '';
  if (is_numeric($software)) {
    $sql_check  = "SELECT software_resource_id from {ic_software_resource} where software_id=%d AND resource_id=";
    $sql_insert = "INSERT INTO {ic_software_resource} (software_id,resource_id) VALUES (%d,";
    $sql_delete = "DELETE FROM {ic_software_resource} where software_id=%d AND resource_id=";
  }
  else {
    $sql_check  = 'SELECT software_resource_id from {ic_software_resource} where software_id=' . "(SELECT software_id from {ic_software} where uniquename='%s') AND resource_id=";
    $sql_insert = 'INSERT INTO {ic_software_resource} (software_id,resource_id) VALUES (' . "(SELECT software_id from {ic_software} where uniquename='%s'),";
    $sql_delete = 'DELETE FROM {ic_software_resource} where software_id=' . "(SELECT software_id from {ic_software} where uniquename='%s') AND resource_id=";
  }
  if (is_numeric($resource)) {
    $sql_check .= '%d';
    $sql_insert .= '%d' . ')';
    $sql_delete .= '%d';
  }
  else {
    $sql_check .= " (SELECT resource_id from {ic_resource} where uniquename='%s')";
    $sql_insert .= "(SELECT resource_id from {ic_resource} where uniquename='%s')" . ')';
    $sql_delete .= "(SELECT resource_id from {ic_resource} where uniquename='%s')";
  }


  $res = db_fetch_array(db_query($sql_check));
  switch ($switch) {
    case FALSE:
      if (empty($res)) {
        db_query($sql_insert, array($software, $resource));
        return 'GRANTED';
      }
      else {
        return 'GRANTED';
      }
      break;

    case 'TOGGLE':
      if (empty($res)) {
        db_query($sql_insert, array($software, $resource));
        return 'GRANTED';
      }
      else {
        db_query($sql_delete);
        $res = db_fetch_array(db_query($sql_check, array($software, $resource)));
        if (empty($res)) {
          return 'REVOKED';
        }
      }
      break;

    case TRUE:
      if (empty($res)) {
        return 'REVOKED';
      }
      else {
        db_query($sql_delete);
        $res = db_fetch_array(db_query($sql_check, array($software, $resource)));
        if (empty($res)) {
          return 'REVOKED';
        }
        else {
          dvm("Failed to delete previous link for software $software and resource $resource.");
          return FALSE;
        }
      }
      break;
  }
}

function dbsf_get_softwareprop($limit = NULL, $name_as_key = FALSE) {
  $return_array = array();
  $sql_select = 'SELECT s.uniquename as software_name,s.software_id as software_id,' . ' cvterm.name as type_name,sp.value,sp.rank ' . ' from {ic_softwareprop} as sp ' . ' JOIN {ic_software} as s ON s.software_id=sp.software_id ' . ' JOIN {ic_cvterm as cvterm on sp.type_id=cvterm.cvterm_id ' . ' WHERE TRUE';

  if (!empty($limit)) {
    if (is_array($limit)) {
      foreach ($limit as $column => $data) {
        $sql_select .= " AND $column='$data'";
      }
    }
    else {
      $sql_select .= " AND $limit";
    }
  }
  $res = db_query($sql_select);
  while ($row = db_fetch_array($res)) {
    if (!empty($name_as_key)) {
      $return_array[$row['software_name']][$row['type_name']][$row['rank']] = $row['value'];
    }
    else {
      $return_array[$row['software_id']][$row['type_name']][$row['rank']] = $row['value'];
    }
  }
  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function dbsf_get_software_resources($limit = NULL, $name_as_key = FALSE) {

  $return_array = array();
  $sql_select = 'SELECT sr.software_id as software_id,sr.resource_id as resource_id' . ',s.uniquename as software_name,r.uniquename as resource_name ' . ',rcvterm.name as rtype_name,r.description from {ic_software_resource} as sr ' . ' JOIN {ic_resource} as r on r.resource_id=sr.resource_id ' . ' JOIN {ic_software} as s on sr.software_id=s.software_id ' . ' JOIN {ic_cvterm as rcvterm on r.type_id=rcvterm.cvterm_id ' . ' WHERE TRUE';
  if (!empty($limit)) {
    if (is_array($limit)) {
      foreach ($limit as $column => $data) {
        $sql_select .= " AND $column='$data'";
      }
    }
    else {
      $sql_select .= " AND $limit";
    }
  }

  $res = db_query($sql_select);
  while ($row = db_fetch_array($res)) {
    if (!empty($name_as_key) && $name_as_key === 'RESOURCE') {
      $return_array[$row['resource_name']][$row['software_name']] = array(
        'type_name' => $row['rtype_name'],
        'uniquename' => $row['software_name'],
        'id' => $row['software_id'],
        'description' => $row['description'],
      );
    }
    elseif (!empty($name_as_key)) {
      $return_array[$row['software_name']][$row['resource_name']] = array(
        'type_name' => $row['rtype_name'],
        'uniquename' => $row['resource_name'],
        'id' => $row['resource_id'],
        'description' => $row['description'],
      );
    }
    else {
      $return_array[$row['software_id']][$row['resource_id']] = array(
        'type_name' => $row['rtype_name'],
        'uniquename' => $row['resource_name'],
        'id' => $row['resource_id'],
        'description' => $row['description'],
      );
    }
  }
  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function dbsf_get_software($limit = NULL, $name_as_key = NULL) {
  $return_array = array();
  $sql_select = "SELECT software_id,uniquename from {ic_software} WHERE TRUE ";
  if (!empty($limit)) {
    if (is_array($limit)) {
      foreach ($limit as $column => $data) {
        if ($column === 'active' && empty($data)) {
          $sql_select .= ' AND active is FALSE';
        }
        elseif ($column === 'active') {
          $sql_select .= ' AND active is TRUE';
        }
        else {
          $sql_select .= " AND $column='$data'";
        }
      }
    }
    else {
      $sql_select .= " AND $limit";
    }
  }

  $res = db_query($sql_select);
  while ($row = db_fetch_array($res)) {
    if (!empty($name_as_key) && $name_as_key === 'BOTH') {
      $return_array[$row['uniquename']] = $row['uniquename'];
    }
    elseif (!empty($name_as_key)) {
      $return_array[$row['uniquename']] = $row['software_id'];
    }
    else {
      $return_array[$row['software_id']] = $row['uniquename'];
    }
  }
  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function dbsf_get_resource_roles($resource, $name_as_key = NULL) {
  $return_array = array();
  if (empty($resource)) {
    return FALSE;
  }
  $resource = check_plain($resource);
  $sql_select = 'SELECT rr.role_id,r.name as role_name ' . 'from {ic_resource_role} as rr ' . ' JOIN {role} as r ON r.rid=rr.role_id ';

  if (is_numeric($resource)) {
    $sql_select .= 'WHERE rr.resource_id=' . '%d';
  }
  else {
    $sql_select .= "WHERE rr.resource_id=(SELECT resource_id from {ic_resource} where uniquename='%s')";
  }
  $res = db_query($sql_select, $resource);
  while ($row = db_fetch_array($res)) {
    if (!empty($name_as_key)) {
      $return_array[$row['role_name']] = $row['role_id'];
    }
    else {
      $return_array[$row['role_id']] = $row['role_name'];
    }
  }

  if (!empty($return_array)) {
    return $return_array;
  }
  else {
    return FALSE;
  }
}

function dbsf_get_dataset_path($dataset) {
  if (empty($dataset)) {
    return FALSE;
  }
  $dataset = check_plain($dataset);

  $linked_data = icbasic_get_linked_resources($dataset, 'uses');
  $dir         = '';
  $basename    = '';
  foreach ($linked_data as $d) {
    switch ($d['type_name']) {
      case 'filename':
        $basename = $d['uniquename'];
        break;

      case 'directory':
        $dir = $d['uniquename'];
        break;
    }
  }
  return $dir . $basename;
}

function dbsf_software_blast_core_settings_form($form_state) {
  $form = array();
  $active = dbsf_check_software_active('blastall');
  if ($active === FALSE) {
    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, 'blastall', 'executable'));
  $data          = db_fetch_array(db_query($select_software_path, 'blastall', 'data'));
  $format_exec   = db_fetch_array(db_query($select_software_path, 'formatdb', 'executable'));
  $fastacmd_exec = db_fetch_array(db_query($select_software_path, 'fastacmd', 'executable'));

  $form['settings'] = array(
    '#type' => 'fieldset',
    '#title' => t('BLAST core settings'),
    '#description' => t('Please set some important settings for the blastall program.'),
    'submit' => array(
      '#type' => 'submit',
      '#value' => 'Save core BLAST settings',
      '#weight' => 5,
    ),
    'blast_executable' => array(
      '#type' => 'textfield',
      '#title' => t('BLASTALL executable path'),
      '#description' => t('Please provide the <b>full path</b> to the <b>blastall</b> executable on the server, e.g. /usr/bin/blastall .'),
      '#required' => TRUE,
      '#default_value' => $core_exec['value'],
    ),
    'formatdb_executable' => array(
      '#type' => 'textfield',
      '#title' => t('FORMATDB executable path'),
      '#description' => t('Please provide the <b>full path</b> to the <b>formatdb</b> executable on the server, e.g. /usr/bin/formatdb .'),
      '#required' => TRUE,
      '#default_value' => $format_exec['value'],
    ),
    'fastacmd_executable' => array(
      '#type' => 'textfield',
      '#title' => t('FASTACMD executable path'),
      '#description' => t('Please provide the <b>full path</b> to the <b>fastacmd</b> executable on the server, e.g. /usr/bin/fastacmd .'),
      '#required' => TRUE,
      '#default_value' => $fastacmd_exec['value'],
    ),
    'blast_data' => array(
      '#type' => 'textfield',
      '#title' => t('Data directory'),
      '#description' => t('Please provide the <b>full path</b> to the <b>blastall data</b> directory on the server, e.g. /usr/share/ncbi/data/ . ' . 'This is the directory where the BLOSUM62 etc matrixes reside; if you do not know how to find it, try the command "locate BLOSUM62"'
      ),
      '#required' => TRUE,
      '#default_value' => $data['value'],
    ),
  );
  return $form;
}

function dbsf_software_blast_core_settings_form_validate($form, &$form_state) {
  $data          = escapeshellcmd(trim($form_state['values']['blast_data']));
  $core_exec     = escapeshellcmd(trim($form_state['values']['blast_executable']));
  $format_exec   = escapeshellcmd(trim($form_state['values']['formatdb_executable']));
  $fastacmd_exec = escapeshellcmd(trim($form_state['values']['fastacmd_executable']));

  if (!empty($data) && substr($data, -1) !== '/') {
    $data .= '/';
  }
  if (!empty($core_exec)) {
    if (!file_exists($core_exec)) {
      form_set_error('blast_executable', "Cannot find executable $core_exec on the server.");
    }
    $form_state['values']['blast_executable'] = $core_exec;
  }
  if (!empty($data)) {
    if (!file_exists($data .'/BLOSUM62')) {
      form_set_error('blast_data', 'Cannot find matrix '. $data .'/BLOSUM62 on the server.');
    }
    //store trimmed values
    $form_state['values']['blast_data'] = $data;
  }
  if (!empty($format_exec)) {
    if (!file_exists($format_exec)) {
      form_set_error('formatdb_executable', "Cannot find executable $format_exec on the server.");
    }
    $form_state['values']['formatdb_executable'] = $format_exec;
  }
  if (!empty($fastacmd_exec)) {
    if (!file_exists($fastacmd_exec)) {
      form_set_error('fastacmd_executable', "Cannot find executable $fastacmd_exec on the server.");
    }
    $form_state['values']['fastacmd_executable'] = $fastacmd_exec;
  }
}

function dbsf_software_blast_core_settings_form_submit($form, &$form_state) {
  $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, 'blastall', 'executable'));
  $format_exec   = db_fetch_array(db_query($select_software_path, 'formatdb', 'executable'));
  $fastacmd_exec = db_fetch_array(db_query($select_software_path, 'fastacmd', 'executable'));
  $data          = db_fetch_array(db_query($select_software_path, 'blastall', 'data'));

  $user_bexec         = $form_state['values']['blast_executable'];
  $user_fexec         = $form_state['values']['formatdb_executable'];
  $user_fastacmd_exec = $form_state['values']['fastacmd_executable'];

  $user_data = $form_state['values']['blast_data'];
  if (!empty($user_bexec) && $user_bexec != $core_exec['value']) {
    db_query($delete_software_path, 'blastall', 'executable');
    db_query($store_software_path, 'blastall', 'executable', $user_bexec);
    drupal_set_message("$user_bexec is now the blastall executable.", 'warning');
  }
  if (!empty($user_fexec) && $user_fexec != $format_exec['value']) {
    db_query($delete_software_path, 'formatdb', 'executable');
    db_query($store_software_path, 'formatdb', 'executable', $user_fexec);
    drupal_set_message("$user_fexec is now the formatdb executable.", 'warning');
  }
  if (!empty($user_fastacmd_exec) && $user_fastacmd_exec != $fastacmd_exec['value']) {
    db_query($delete_software_path, 'fastacmd', 'executable');
    db_query($store_software_path, 'fastacmd', 'executable', $user_fastacmd_exec);
    drupal_set_message("$user_fexec is now the fastacmd executable.", 'warning');
  }
  if (!empty($user_data) && $user_data != $data['value']) {
    db_query($delete_software_path, 'blastall', 'data');
    db_query($store_software_path, 'blastall', 'data', $user_data);
    drupal_set_message("$user_data is now the blastall data directory.", 'warning');
  }
}

function dbsf_admin_blast_page() {
  $software = 'blastall';
  $check_active = dbsf_check_software_active($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/dataset');
  }
  $table = dbsf_admin_database_table($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_blast($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 => $data) {
      if (!empty($data) && in_array($name, array('blastall', 'formatdb', 'fastacmd'))) {
        foreach ($data as $term_name => $v) {
          if ($term_name == 'executable' || $term_name == 'data') {
            $check++;
          }
        }
      }
    }
  }
  if ($check < 4) {
    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='blastall') " . " 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));
  if ($count['count'] < 2) {
    return 'datasets';
  }

  return TRUE;
}

function dbsf_blast_page($sample_data = FALSE) {
  $setup = dbsf_check_blast('blastall');
  if ($setup === TRUE) {
    $return = '';
    if (empty($sample_data)) {
      $return = '<h3>Demonstration</h3><p> Click to '. l('load some sample data', 'dbsf/blast/demo');
      $return .= ' or you can download sample '. l('protein FASTA', drupal_get_path('module', 'dbsf') .'/test_prot.fsa') .' and '. l('nucleotide FASTA', drupal_get_path('module', 'dbsf') .'/test_nuc.fsa') .' files from the Arabidopsis thaliana database (TAIR), suitable for uploading as queries or databases.</p><br>';
      $return .= drupal_get_form('dbsf_blast_form');
    }
    else {
      $return = drupal_get_form('dbsf_blast_form', $sample_data);
    }
    return $return;
  }
  else {
    $return_text = "<p>I'm sorry but your blastall software has not been setup properly.</p><ul>";
    switch ($setup) {
      case 'datasets':
        $return_text .= '<li>Not enough datasets have been defined. Please define at least one protein and one nucleotide dataset at the '. l('dataset registration page', 'admin/dbsf/dataset', array('fragment' => 'available-datasets')) .' and then register them with BLAST at the '. l('BLAST database settings page', 'admin/dbsf/blast');
        break;

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

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

function dbsf_blast_form($form_state, $sample_data = FALSE) {
  $software_options = _dbsf_generate_options('blastall');
  $form             = array();
  $dbs              = dbsf_get_user_datasets('blastall');
  //returns in the form of ['dbtype']['group_name']['id']]=['name'];
  $nucleotide_dbs  = $dbs['nucleotide'];
  $protein_dbs     = $dbs['protein'];
  $sample_seq_nuc  = '';
  $sample_seq_prot = '';
  $sample_db_prot  = '';
  $sample_db_nuc   = '';

  if ($sample_data) {
    $sample_data = TRUE;
    foreach ($nucleotide_dbs as $group) {
      foreach ($group as $n => $n2) {
        if ($n2 == 'Arabidopsis thaliana genes') {
          $sample_db_nuc = $n;
          $sample_seq_nuc = '>antiporter' . "\n". wordwrap('GTCATGGAATCCTTCATTCCCGAGTTTCAGGAGCTCCGCTGTTTCCGGACCAAAGTCATCACTGAAGCTGAACAGGTTTTTAAGAAACTGTGCAAGTACGAATCAGGAGCTTGTTGTTGATGGAGAAACCGGAAATGGGTCGATTTCGGAGCTCCAAGGAGATGCAGCAAATGGTTCGATTTCGCCGGTGGAAGTGGAAGCAGAAGTAGAAGAAGTGAAGGTAGATGATTTGGCGACTCAGAGCATTTGGGGACAGATGAAAGAGATCGTCATGTTTACCGGACCTGCCGCGGGATTGTGGCTATGTGGGCCGTTGATGAGTCTCATTGATACGGCGGTGATTGGTCAAGGAAGCTCACTCGAACTCGCTGCTTTAGGTCCTGCTACCGTCATCTGTGATTATTTGTGTTATACGTTCATGTTCCTCTCAGTTGCGACTTCAAATCTTGTTGCTACCTCTCTTGCTCGGCAGGATAAAGATGAAGTACAACATCAGATATCGATCTTGCTTTTCATTGGGTTGGCTTGTGGAGTCACGATGATGGTGTTGACAAGACTGTTTGGTTCCTGGGCACTAACTGCTTTTACAGGGGTAAAGAATGCCGACATTGTTCCAGCAGCTAATAAATATGTTCAGATTCGTGGTTTAGCATGGCCAGCTGTTCTCATTGGATGGGTTGCTCAAAGTGCAAGTCTTGGTATGAAAGACTCATGGGGACCTCTTAAGGCTTTGGCGGTTGCTAGTGCAATAAACGGTGTTGGTGATGTGGTCTTATGCACCTTTCTAGGATATGGTATAGCAGGTGCAGCTTGGGCAACTATGGTGTCACAAGTTGTTGCTGCTTATATGATGATGGACGCATTGAACAAGAAAGGATACAGCGCATTCTCATTCTGTGTTCCTTCTCCAAGTGAACTTTTGACGATTTTTGGACTCGCTGCCCCTGTCTTTATAACTATGATGTCAAAGGTTTTGTTCTATACGCTCCTTGTGTACTTTGCTACATCAATGGGTACAAATATCATAGCTGCTCATCAGGTTATGCTTCAGATATATACCATGAGTACGGTTTGGGGGGAGCCTCTCTCTCAAACTGCACAGTCCTTTATGCCTGAGCTTTTATTCGGAATCAATCGTAATTTGCCTAAAGCTAGGGTGCTTCTGAAGTCACTAGTTATCATCGGAGCTACGCTAGGAATAGTAGTCGGAACCATTGGCACAGCAGTTCCATGGCTGTTCCCTGGCATCTTCACACGTGACAAGGTTGTCACATCCGAGATGCACAAGGTCATAATACCGTATTTTCTTGCTTTATCCATCACTCCAAGTACTCACAGTCTTGAAGGCACCTTACTGGCTGGAAGAGATCTTAGATATATCAGCTTGTCAAT', 80, "\n", TRUE);
          break(2);
        }
      }
    }
    foreach ($protein_dbs as $group) {
      foreach ($group as $p => $p2) {
        if ($p2 == 'Arabidopsis thaliana proteins') {
          $sample_db_prot = $p;
          $sample_seq_prot = wordwrap('DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRVMAYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCNAKHARVLQDEKLSFDLTWCGSTLRAPHSCHLQYMANMDSIASLVMAVVVNEEDGEGDAPDATTQPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEVELDNQMVEKNIXRTQTLLCDMLMRDAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIASWLCEYHMDLTGLSTDSLHDAGFPRALSLGDSVCGMAAVRISSKDMIFWFRSHTAGEVRWGGAKHDPDDRDDARRMHPTSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDSETTDVNTKVIYSKPNDLKIDGIQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHFLTLVEDSSVEIVKRMLENALEGTEEQNVQFEIKTHLSRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIIQ', 80, "\n", TRUE);
          break(2);
        }
      }
    }
  }


  $option_form = array();
  if (empty($nucleotide_dbs) || empty($protein_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 protein and 1 nucleotide database. Please let them know.", 'error');
    return FALSE;
  }

  foreach ($software_options as $name => $data) {
    $option_form[$name] = array(
      '#type' => $data['type'],
      '#title' => $name,
      '#description' => !empty($data['description']) ? $data['description'] : '',
    );

    if ($data['type'] !== 'textfield' && !empty($data['options'])) {
      //dpm($data['options']);
      $option_form[$name]['#options'] = $data['options'];
    }
  }

  $form['program'] = array(
    '#type' => 'fieldset',
    '#title' => 'Available algorithms',
    '#tree' => TRUE,
    'blastn' => array(
      '#type' => 'fieldset',
      '#title' => 'blastn',
      '#collapsible' => TRUE,
      '#collapsed' => $sample_data ? FALSE : TRUE,
      'query_sequence' => array(
        '#type' => 'textarea',
        '#title' => t('Enter query sequence in simple text or FASTA format'),
        '#default_value' => $sample_seq_nuc ? $sample_seq_nuc : '',
      ),
      'query_file_blastn' => array(
        '#type' => 'file',
        '#title' => t('or upload query sequence in FASTA 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('multiples allowed (use option/control keys; likewise to deselect).'),
        '#size' => 5,
        '#multiple' => '1',
        '#options' => $nucleotide_dbs,
        '#default_value' => $sample_db_nuc ? $sample_db_nuc : '',
      ),
      'subject_file_blastn' => array(
        '#type' => 'file',
        '#title' => t('or upload your own database'),
        '#description' => t('Please give a 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,
      ),
    ),
    'blastp' => array(
      '#type' => 'fieldset',
      '#title' => 'blastp',
      '#collapsible' => TRUE,
      '#collapsed' => $sample_data ? FALSE : TRUE,
      '#options' => $result,
      'query_sequence' => array(
        '#type' => 'textarea',
        '#title' => t('Enter query sequence in simple text or FASTA format'),
        '#default_value' => $sample_seq_prot ? $sample_seq_prot : '',
      ),
      'query_file_blastp' => array(
        '#type' => 'file',
        '#title' => t('or upload query sequence in FASTA 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('multiples allowed (use option/control keys; likewise to deselect).'),
        '#size' => 5,
        '#multiple' => '1',
        '#options' => $protein_dbs,
        '#default_value' => $sample_db_prot ? $sample_db_prot : '',
      ),
      'subject_file_blastp' => array(
        '#type' => 'file',
        '#title' => t('or upload your own database'),
        // Needed because of drupal bug
        '#tree' => FALSE,
        '#description' => t('Please give a text file, not a MS-Word or other document'),
      ),
      'advanced parameters' => array(
        '#type' => 'fieldset',
        '#title' => 'Advance Search Parameters',
        '#collapsible' => TRUE,
        '#collapsed' => TRUE,
        $option_form,
      ),
    ),
    'blastx' => array(
      '#type' => 'fieldset',
      '#title' => 'blastx',
      '#collapsible' => TRUE,
      '#collapsed' => $sample_data ? FALSE : TRUE,
      'query_sequence' => array(
        '#type' => 'textarea',
        '#title' => t('Enter query sequence in simple text or FASTA format'),
        '#default_value' => $sample_seq_nuc ? $sample_seq_nuc : '',
      ),
      'query_file_blastx' => array(
        '#type' => 'file',
        '#title' => t('or upload query sequence in FASTA 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('multiples allowed (use option/control keys; likewise to deselect).'),
        '#size' => 5,
        '#multiple' => '1',
        '#options' => $protein_dbs,
        '#default_value' => $sample_db_prot ? $sample_db_prot : '',
      ),
      'subject_file_blastx' => array(
        '#type' => 'file',
        '#title' => t('or upload your own database'),
        '#description' => t('Please give a 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,
      ),
    ),
    'tblastn' => array(
      '#type' => 'fieldset',
      '#title' => 'tblastn',
      '#collapsible' => TRUE,
      '#collapsed' => TRUE,
      'query_sequence' => array(
        '#type' => 'textarea',
        '#title' => t('Enter query sequence in simple text or FASTA format'),
      ),
      'query_file_tblastn' => array(
        '#type' => 'file',
        '#title' => t('or upload query sequence in FASTA 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('multiples allowed (use option/control keys; likewise to deselect).'),
        '#size' => 5,
        '#multiple' => '1',
        '#options' => $nucleotide_dbs,
      ),
      'subject_file_tblastn' => array(
        '#type' => 'file',
        '#title' => t('or upload your own database'),
        '#description' => t('Please give a 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,
      ),
    ),
    'tblastx' => array(
      '#type' => 'fieldset',
      '#title' => 'tblastx',
      '#collapsible' => TRUE,
      '#collapsed' => TRUE,
      'query_sequence' => array(
        '#type' => 'textarea',
        '#title' => t('Enter query sequence in simple text or in FASTA format'),
      ),
      'query_file_tblastx' => array(
        '#type' => 'file',
        '#title' => t('or upload query sequence in FASTA 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('multiples allowed (use option/control keys; likewise to deselect).'),
        '#size' => 5,
        '#multiple' => '1',
        '#options' => $protein_dbs,
      ),
      'subject_file_tblastx' => array(
        '#type' => 'file',
        '#title' => t('or upload your own database'),
        '#description' => t('Please give a 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 search'),
    ),
    '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_blast_form_validate($form, &$form_state) {
  $algorithm_data = $form_state['values']['program'];
  // nuc queries: blastn,blastx,tblastx
  // protein queries:blastp,tblastn
  foreach ($algorithm_data as $algorithm => $data) {
    if (!empty($data['query_sequence'])) {
      if (!empty($_FILES['files']['tmp_name']['query_file_'. $algorithm])) {
        form_set_error("program][$algorithm][query_sequence", "$algorithm: It seems you both typed a query sequence and uploaded one.");
        return FALSE;
      }
      if (empty($data['subject_db']) && empty($_FILES['files']['tmp_name']['subject_file_'. $algorithm])) {
        form_set_error("program][$algorithm][query_sequence", "$algorithm: It seems you provided a query sequence but no subject database (or file).");
        return FALSE;
      }
      // First Query (i.e. check for query first; query must exist if subject exists)
      if ($algorithm == 'blastn' || $algorithm == 'blastx' || $algorithm == 'tblastx') {
        $result = icbasic_validate_seq_dna($data['query_sequence']);
        if ($result === FALSE || is_numeric($result)) {
          form_set_error("program][$algorithm][query_sequence", "$algorithm: Sorry your sequence does not seem to be a valid DNA sequence ($result errors).");
          return FALSE;
        }
        else {
          $form_state['values']['program'][$algorithm]['query_sequence'] = $result;
        }
      }
      elseif ($algorithm == 'blastp' || $algorithm == 'tblastn') {
        $result = icbasic_validate_seq_protein($data['query_sequence']);
        if ($result === FALSE || is_numeric($result)) {
          form_set_error("program][$algorithm][query_sequence", "$algorithm: Sorry your sequence does not seem to be a valid protein sequence ($result errors).");
          return FALSE;
        }
        else {
          $form_state['values']['program'][$algorithm]['query_sequence'] = $result;
        }
      }
    }
    elseif (!empty($_FILES['files']['tmp_name']['query_file_'. $algorithm])) {
      //report an error if no database has been selected. and query is uploaded
      if (empty($data['subject_db']) && empty($_FILES['files']['tmp_name']['subject_file_'. $algorithm])) {
        form_set_error("program][$algorithm][query_sequence", "$algorithm: It seems you provided a query but no database database (or file).");
        return FALSE;
      }
    }
    // now check for subject and make sure that if a query is selected, then subject is too.
    // nuc subjects:blastn,tblastx,tblastn
    // protein subjects:blastx,blastp,
    if (!empty($data['subject_db'])) {
      if (empty($data['query_sequence']) && empty($_FILES['files']['tmp_name']['query_file_'. $algorithm])) {
        //dpm(array($data,$_FILES['files']['tmp_name']));
        form_set_error("program][$algorithm][subject_db", "$algorithm: It seems you provided a subject database but no query sequence (or file).");
        return FALSE;
      }
      //  No need to check if it is nucleootide or protein as it is a pre-formated db
    }
    elseif (!empty($_FILES['files']['tmp_name']['subject_file_'. $algorithm])) {
      //report an error if no query has been selected.
      if (empty($data['query_sequence']) && empty($_FILES['files']['tmp_name']['query_file_'. $algorithm])) {
        form_set_error("program][$algorithm][subject_db", "$algorithm: It seems you provided a subject database but no query sequence (or file).");
        return FALSE;
      }
    }
  }
}

function dbsf_blast_form_submit($form, &$form_state) {
  //dpm($form_state);
  // 1000 Kb
  $validators_file = array('file_validate_size' => array(1000));
  $tmpdir = file_directory_temp();
  // all files, same timestamp
  $timestamp      = time();
  $sessionid      = session_id();
  $dirpath        = file_create_path() .'/dbsf';
  $algorithm_data = $form_state['values']['program'];
  // 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, 'blastall');
  $batch_file_data = array();

  //populate this with the various data needed for the operations so that they are performed for all algorithms together
  foreach ($algorithm_data as $algorithm => $data) {
    $file_type = 'nucleotide';
    if ($algorithm == 'blastn' || $algorithm == 'blastx' || $algorithm == 'tblastx') {
      $file_type = 'nucleotide';
    }
    elseif ($algorithm == 'blastp' || $algorithm == 'tblastn') {
      $file_type = 'protein';
    }
    $verify = array();
    $uid = icbasic_create_uid($sessionid, $timestamp, $algorithm);
    // XML output
    $par = ' -m 7 ';
    // process user data
    // first, the query. check if file or text
    if (isset($_FILES['files']) && !empty($_FILES['files']['tmp_name']['query_file_'. $algorithm])) {
      $file = file_save_upload('query_file_'. $algorithm, $validators_file, $tmpdir, FILE_EXISTS_RENAME);
      if (empty($file)) {
        form_set_error('query_file_'. $algorithm, "Sorry your file for $algorithm 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 build the -d variable

    $file_type = 'nucleotide';
    if ($algorithm == 'blastn' || $algorithm == 'tblastn' || $algorithm == 'tblastx') {
      $file_type = 'nucleotide';
    }
    elseif ($algorithm == 'blastp' || $algorithm == 'blastx') {
      $file_type = 'protein';
    }
    // if subject has been provided by user, either format it and add it to -d or reject it.
    if (isset($_FILES['files']) && !empty($_FILES['files']['tmp_name']['subject_file_'. $algorithm])) {
      $file = file_save_upload('subject_file_'. $algorithm, $validators_file, $tmpdir, FILE_EXISTS_RENAME);
      if (empty($file)) {
        form_set_error('subject_file_'. $algorithm, "Sorry your file for $algorithm was not saved. Maybe it is too large (>1 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'])) {
      $par .= dbsf_blastall_software_pars($data['advanced parameters'][0], $algorithm);
      $save_array[$form_uid][$uid]['par'] = $par;
      $save_array[$form_uid][$uid]['sub'] = $subject_dbs;
      $save_array[$form_uid][$uid]['algorithm'] = $algorithm;
    }
  }
  // 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 BLAST jobs...'),
    'operations' => $operations,
    'init_message' => t('Starting BLAST submission...'),
    'progress_message' => t('@remaining operations remaining...'),
    'error_message' => t('Your BLAST submission encountered an error.'),
    'finished' => 'dbsf_blast_batch_finished',
  );
  batch_set($batch);
  // foreach output, create an XML table and results.
  // output has been processed if $uid.output.graph.png exists
  // (also show the graph and any other links)
  // do result processing and give error or redirect
  $form_state['redirect'] = array('dbsf/blast_result', "submission_uid=$form_uid");
  return "dbsf/blast_result?submission_uid=$form_uid";
}

function dbsf_blastall_software_pars($data, $algorithm) {
  if (empty($data) || empty($algorithm)) {
    return FALSE;
  }
  $par = ' -p '. check_plain($algorithm);
  foreach ($data as $name => $option) {
    if (empty($option)) {
      continue;
    }
    switch ($name) {
      case 'Scoring matrix':
        $par .= ' -M '. check_plain($option);
        break;

      case 'Filtering':
        if (!empty($option['Low complexity regions'])) {
          $par .= " -F T";
        }
        if (!empty($option['Lower-case letters'])) {
          $par .= " -U T";
        }
        break;

      case 'E-value cutoff':
        $par .= ' -e '. check_plain($option);
        break;

      case 'Advanced BLAST options':
        if (!empty($option['ungapped']) && $algorithm != 'tblastx') {
          $par .= " -g F";
        }
        if (!empty($option['megablast']) && $algorithm == 'blastn') {
          $par .= " -n T";
        }
        break;

      case 'query genetic code':
        $par .= ' -Q '. check_plain($option);
        break;

      case 'DB genetic code':
        $par .= ' -D '. check_plain($option);
        break;

      case 'Frame shift penalty':
        $par .= ' -w '. check_plain($option);
        break;

      case 'Number of results':
        $par .= ' -b '. check_plain($option) .' -v '. check_plain($option);
        break;
    }
  }
  return $par;
}

function dbsf_blast_batch_finished($success, $results, $operations) {
  // store uids to report in case of error.
  $uid_array      = array();
  $submission_uid = '';
  $data           = array();
  $to_store       = "submission_uid:$submission_uid\nsoftware:blastall\n";
  $dirpath        = file_create_path() .'/dbsf';
  $message        = '';
  //one form uid
  foreach ($results['data'] as $form_uid => $batch_data) {
    //for use later
    $submission_uid = $form_uid;
    $data = $batch_data;
    foreach ($batch_data as $uid => $values) {
      $to_store .= 'algorithm;id='. $values['algorithm'] .";$uid\n";
      $uid_array[] = $uid;
    }
  }

  if ($success) {
    // store what the users is performing in this submission, so that the results
    // can be accurately retrieved.
    $outfile = $dirpath .'/'. $submission_uid .'.submission';
    if (!$outhandle = fopen($outfile, 'wt')) {
      drupal_set_message(t("Could not create $outfile."), 'error');
      return FALSE;
    }
    fwrite($outhandle, $to_store);
    fclose($outhandle);
    foreach ($data as $uid => $values) {
      $subject_dbs     = array_merge((array)$values['sub'], (array)$results[$uid]['subject']);
      $subject_dbs_str = trim(implode(' ', $subject_dbs));
      $par             = $values['par'] ." -d '". $subject_dbs_str ."'";
      dbsf_parameter_daemon($uid, $dirpath, $par, 'blastall', array('database' => $subject_dbs));
    }
    $message = t('Your request has been submitted to the queue for processing...');
  }
  else {
    $error_operation = reset($operations);
    $uids            = implode(' ', $uid_array);
    $message         = t('An error occurred while processing your request. Please '. l('contact', 'contact') ." the administrator reporting: $uids.");
    dpm($error_operation);
    return FALSE;
  }
  drupal_set_message($message, 'warning');
}

function dbsf_blast_result_xml($blastfile = NULL) {
  $result_array = array();
  if (file_exists($blastfile)) {
    $xml_in    = simplexml_load_file($blastfile, 'SimpleXMLElement');
    $algorithm = (string)$xml_in->BlastOutput_program;
    $xml       = $xml_in->BlastOutput_iterations;
    //is either an object (one query) or an array. so convert to array.
    $array_iterations = get_object_vars($xml);
    $array_iterations = $array_iterations['Iteration'];
    if (is_object($array_iterations)) {
      $array_iterations = array(0 => $array_iterations);
    }
    $query_rank;
    foreach ($array_iterations as $iteration_obj) {
      $query_rank++;
      $query_id           = '';
      $name_of_hit        = '';
      $accession_of_hit   = '';
      $average_bit_score  = '';
      $top_bit_score      = '';
      $average_evalue     = '';
      $lowest_evalue      = '';
      $average_identity   = '';
      $average_similarity = '';
      // we need array-ize to get query_id
      $iteration_data_array = get_object_vars($iteration_obj);

      $query_id = $iteration_data_array['Iteration_query-ID'] .' '. $iteration_data_array['Iteration_query-def'];
      $query_id = preg_replace('/\s*lcl\|\d+_\d+\s*/', '', $query_id);
      $query_id = str_replace('No definition line found', '', $query_id);
      if (empty($query_id)) {
        $query_id = "User query $query_rank";
      }
      if (!empty($iteration_data_array['Iteration_message'])) {
        drupal_set_message($algorithm .': '. $iteration_data_array['Iteration_message'] ." for $query_id", 'warning');
      }
      $hit_iteration_hits = $iteration_data_array['Iteration_hits'];
      if (empty($hit_iteration_hits)) {
        continue;
      }

      $hits_array = get_object_vars($hit_iteration_hits);
      //dvm($hits_array);
      $hits_array = $hits_array['Hit'];
      if (is_object($hits_array)) {
        $hits_array = array(0 => $hits_array);
      }
      //dvm($hits_array);

      foreach ($hits_array as $rank0 => $hit_object) {

        // cast objects as strings to avoid extra lines of code
        $name_of_hit        = (string)$hit_object->Hit_id;
        $accession_of_hit   = (string)$hit_object->Hit_accession;
        $description_of_hit = (string)$hit_object->Hit_def;
        if ($description_of_hit == 'No definition line found') {
          $description_of_hit = '';
        }
        $hsps_array = get_object_vars($hit_object->Hit_hsps);
        // cannot get Hit_hsps->Hsp directly, because if HSP is an array, then get_object_vars only returns first element of array
        // so get Hit_hsps only. Then retrieve second element of resulting array (first is the XML key)
        $hsps_array = $hsps_array['Hsp'];
        // result is sometimes an array (multiple HSPs) and sometimes an object (one HSP)
        // So check
        if (is_object($hsps_array)) {
          // then one HSP and we got first HSP object directly. Convert to an array with one key.
          $hsps_array = array(0 => $hsps_array);
        }
        //$hsps_array is now an array of objects, each object is an hsp, key is hsp_rank.
        $total_bit_score  = 0;
        $total_evalue     = 0;
        $hsp_number       = 0;
        $total_identity   = 0;
        $total_similarity = 0;
        foreach ($hsps_array as $hsp_rank => $hsp_obj) {
          $hsp_data = get_object_vars($hsp_obj);
          //dpm($hsp_data);
          $bit_score  = $hsp_data['Hsp_bit-score'];
          $aln_length = $hsp_data['Hsp_align-len'];
          $evalue     = $hsp_data['Hsp_evalue'];
          if (!empty($aln_length)) {
            $identity = $hsp_data['Hsp_identity'] / $aln_length;
            $similarity = $hsp_data['Hsp_positive'] / $aln_length;
          }
          $total_bit_score += $bit_score;
          $total_evalue += $evalue;
          $total_identity += $identity;
          $total_similarity += $similarity;
          $hsp_number++;
          if (empty($lowest_evalue) || $evalue < $lowest_evalue) {
            $lowest_evalue = $evalue;
          }
          if (empty($top_bit_score) || $bit_score > $top_bit_score) {
            $top_bit_score = $bit_score;
          }
        }
        $lowest_evalue = sprintf('%.2e', $lowest_evalue);
        $average_bit_score = $hsp_number ? sprintf('%.2f', $total_bit_score / $hsp_number) : 'NA';
        $average_evalue = $hsp_number ? sprintf('%.2e', $total_evalue / $hsp_number) : 'NA';
        $top_bit_score = sprintf('%.2f', $top_bit_score);
        $average_identity = $hsp_number ? sprintf('%.2f %%', $total_identity * 100 / $hsp_number) : 'NA';
        $average_similarity = $hsp_number ? sprintf('%.2f %%', $total_similarity * 100 / $hsp_number) : 'NA';
        $result_array[$query_id][$rank0 + 1] = array(
          'name_of_hit' => $name_of_hit,
          'accession_of_hit' => $accession_of_hit,
          'average_bit_score' => $average_bit_score,
          'top_bit_score' => $top_bit_score,
          'average_evalue' => $average_evalue,
          'lowest_evalue' => $lowest_evalue,
          'average_identity' => $average_identity,
          'average_similarity' => $average_similarity,
        );
      }
    }
    return ($result_array);
  }
  else {
    drupal_set_message("Failed to parse $blastfile.", 'error');
    return FALSE;
  }
}

function dbsf_blast_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.';
  }

  $page_tabs = array(
    'blast_results' => array(
      '#type' => 'tabset',
    ),
  );
  $return_html = '';
  foreach ($data as $algorithm => $uid) {
    $blastfile = $dirpath . $uid .'.output';
    $graph     = $blastfile .'.graph.png';
    $content   = t('Your report is not ready yet. Please wait or ') . l('try again', 'dbsf/blast_result/'. $submission_uid
    ) . t(' in a few moments or bookmark this page.');
    if (file_exists($graph)) {
      $results = drupal_get_form('dbsf_blast_result_form', $uid, $blastfile);
      if (strlen($results) < 600) {
        $results = "No hits found for any of your queries using $algorithm. Perhaps you can try a different algorithm or database?";
      }
      $content = '<p>'. l(
        theme_image($graph, 'BLAST results of all queries', 'BLAST results graphical overview', array('width' => '100%'), FALSE)
        , $blastfile .'.html', array('html' => TRUE, 'alias' => TRUE, 'attributes' => array('target' => '_blank'))
      ) .'</p>'. $results;
    }
    else {
      drupal_set_html_head('<meta http-equiv="refresh" content="15;url=http://'. $_SERVER['SERVER_NAME'] . $basename .'/dbsf/blast_result/'. $submission_uid .'" />');
    }
    $page_tabs['blast_results'][$algorithm] = array(
      '#type' => 'tabpage',
      '#title' => 'Results for '. $algorithm,
      '#content' => $content,
    );
  }
  $return_text = '<br><p>If you want, you can bookmark this page: your results will be stored on the server at least until '. date("F j, Y, g:i a", time() + 604800) .'. Let us '. l('know', 'contact') .' if you would like to keep them for longer.</p>';
  $return_text .= tabs_render($page_tabs);
  return $return_text;
}

function dbsf_blast_result_form($form_state, $uid, $blastfile) {
  $form = array();
  if (empty($blastfile)) {
    return $form;
  }
  $array_from_xml = array();
  $array_from_xml = dbsf_blast_result_xml($blastfile);
  //$xml=dbsf_blast_result_xml($blastfile);dpm($xml);
  // all data
  $table_row = array();
  // for checkboxes to get hit
  $row_check_data = array();
  if (empty($array_from_xml) || is_array($array_from_xml) === FALSE) {
    //drupal_set_message(t('No significant hits for any of your queries of UID '.$uid.'.'),'warning');
    return $form;
  }
  $query_rank = 0;
  foreach ($array_from_xml as $query_id => $hit_array) {
    $query_rank++;
    foreach ($hit_array as $hit_rank => $data) {
      $hit_id    = $data['accession_of_hit'] ? $data['accession_of_hit'] : $data['name_of_hit'];
      $bit_score = $data['average_bit_score'] .' ('. $data['top_bit_score'] .')';
      $evalue    = $data['average_evalue'] .' ('. $data['lowest_evalue'] .')';
      $identity  = $data['average_identity'] .' ('. $data['average_similarity'] .')';
      $links     = ''. l(
        theme_image(drupal_get_path('module', 'dbsf') .'/images/xml.png', 'Report as XML', 'Report as XML (recommended for parsing with other software)'), $blastfile,
        array(
          'html' => TRUE,
          'alias' => TRUE,
          'attributes' => array('target' => '_blank'),
        )
      ) . l(
        theme_image(drupal_get_path('module', 'dbsf') .'/images/html.png', 'Report as HTML', 'Report as HTML'), "$blastfile.Query$query_rank.html",
        array(
          'html' => TRUE,
          'alias' => TRUE,
          'attributes' => array('target' => '_blank'),
        )
      ) . l(
        theme_image(drupal_get_path('module', 'dbsf') .'/images/txt.png', 'Report as text', 'Report as text'), "$blastfile.Query$query_rank.txt",
        array(
          'html' => TRUE,
          'alias' => TRUE,
          'attributes' => array('target' => '_blank'),
        )
      );
      $table_row[] = array($query_id, $hit_id, $bit_score, $evalue, $identity, $links);
      // checkboxes will retrieve hit_id but will be anchored on query_id
      // key to be passed for checkboxes and value to show to user.
      $row_check_data[$hit_id] = $query_id;
    }
  }
  $table_header     = array('Query ID', 'Hit ID', 'Average bit score (top)', 'Average e-value (lowest)', 'Average identity (av. similarity)', 'Links');
  $table_attributes = array('class' => 'padded-table sortable');
  $table_caption    = 'Overview of significant results';
  $table_array      = array(
    //  '#links' => array('previous'=>$previous_link,'next'=>$next_link,'bookmark'=>$bookmark),
    'header' => $table_header,
    'caption' => $table_caption,
    'attributes' => $table_attributes,
    'data' => $table_row,
  );

  $form['#blastfile'] = array('#value' => $blastfile);
  $form['data']       = array('#value' => $table_array);
  $form['features']   = array(
    '#type' => 'checkboxes',
    '#options' => $row_check_data,
  );
  $form['buttons'] = array(
    '#type' => 'fieldset',
    '#title' => t('Download hits of selected results as'),
    '#description' => t('If the reference database has been indexed then you can download the hits. Warning, the server will refuse to serve you with very large hits (such as a whole chromosome of a genome).'),
    '#collapsible' => FALSE,
    '#weight' => 20,
    'FASTA' => array(
      '#type' => 'submit',
      '#value' => t('FASTA'),
      '#weight' => 15,
    ),
    /*'GFF' => array(
        '#type' => 'submit',
        '#value' => t('GFF'),
        '#weight' => 16
  )*/
  );
  $form['#action'] = url("dbsf/get_sequences/$uid");
  return $form;
}

function dbsf_theme_blast_result_form($form) {
  $table_array = $form['data']['#value'];
  // Sortable sorttable actually does not work in our table because it has been converted to a form. this should be fixed by someone with javascript knowledge.
  drupal_add_js(drupal_get_path('module', 'icexplore') .'/sorttable.js');
  // our output
  $output = '';
  // prepare table data for checkboxes
  $row_checked = array();
  $checkall = theme('table_select_header_cell');
  $table_array['header'][0] = array(
    'data' => $table_array['header'][0], 'class' => $checkall['class'] .' sortable',
  );
  // replace first field with checkboxes
  if (empty($table_array['data'])) {
    // no rows!
    return FALSE;
  }
  foreach ($table_array['data'] as $value) {
    $feature_toreplace = $value[1];
    $render            = drupal_render($form['features'][$feature_toreplace]);
    $row_checked[]     = array(
      'data' => array_merge((array)$render, array_slice($value, 1)),
    );
  }
  $output .= '<p>';
  if (!empty($table_array['#links']['previous'])) {
    $output .= $table_array['#links']['previous'];
  }
  if (!empty($table_array['#links']['next'])) {
    $output .= $table_array['#links']['next'];
  }
  if (!empty($table_array['#links']['bookmark'])) {
    $output .= $table_array['#links']['bookmark'];
  }
  $output .= '</p>';
  $themed_table = theme_table($table_array['header'], $row_checked, $table_array['attributes'], $table_array['caption']);
  $output .= $themed_table;

  $output .= drupal_render($form['buttons']);
  return ($output);
}

---