blast_ui.node.inc

<?php

/**
 * @file
 * Contains all functions for creating the blastdb node type
 */


/**
 * Implements hook_node_info().
 */
function blast_ui_node_info() {
  return array(
    'blastdb' => array(
      'name' => t('Blast Database'),
      'base' => 'blastdb',
      'description' => t('Registers a BLAST Database for use with the BLAST UI.'),
    ),
  );
}

/**
 * Implements hook_node_access().
 */
function blastdb_node_access($node, $op, $account) {
  $node_type = $node;
  if (is_object($node)) {
    $node_type = $node->type;
  }

  if($node_type == 'blastdb') {
    if ($op == 'create') {
      if (!user_access('create Blast Database', $account)) {
        return NODE_ACCESS_DENY;
      }
      return NODE_ACCESS_ALLOW;
    }
    if ($op == 'update') {
      if (!user_access('edit Blast Database', $account)) {
        return NODE_ACCESS_DENY;
      }
    }
    if ($op == 'delete') {
      if (!user_access('delete Blast Database', $account)) {
        return NODE_ACCESS_DENY;
      }
    }
    if ($op == 'view') {
      if (!user_access('access Blast Database', $account)) {
        return NODE_ACCESS_DENY;
      }
    }

    return NODE_ACCESS_IGNORE;
  }
}

/**
 * Form constructor for the blastdb node
 *
 * @see blastdb_insert()
 * @see blastdb_update()
 * @see blastdb_delete()
 * @see blastdb_load()
 */
function blastdb_form($node, &$form_state) {
  $form = array();

  $form['#validate'] = array('blastdb_form_validate');

  $form['#attached']['css'] = array(
    drupal_get_path('module', 'blast_ui') . '/theme/css/form.css',
  );

  $form['core'] = array(
    '#type' => 'fieldset',
    '#title' => 'General'
  );

  $form['core']['db_name']= array(
    '#type' => 'textfield',
    '#title' => t('Human-readable Name for Blast database'),
    '#required' => TRUE,
    '#default_value' => isset($node->db_name) ? $node->db_name : '',
  );

  $form['core']['db_path']= array(
    '#type' => 'textfield',
    '#title' => t('File Prefix including Full Path'),
    '#description' => t('The full path to your blast database including the file name but not the file type suffix. For example, /var/www/website/sites/default/files/myblastdb'),
    '#required' => TRUE,
    '#default_value' => isset($node->db_path) ? $node->db_path : '',
  );

  $form['core']['db_dbtype'] = array(
    '#type' => 'radios',
    '#title' => t('Type of the blast database'),
    '#options' => array(
      'nucleotide' => t('Nucleotide'),
      'protein' => t('Protein'),
    ),
    '#required' => TRUE,
    '#default_value' => isset($node->db_dbtype) ? $node->db_dbtype : 'n',
  );

  $form['dbxref'] = array(
    '#type' => 'fieldset',
    '#title' => 'Link-outs',
    '#description' => 'These settings will be used to <em>transform the hit name into a
      link to additional information</em>.',
  );

  $types = module_invoke_all('blast_linkout_info');
  $options = array();
  foreach ($types as $machine_name => $details) {
    $options[$machine_name] = (isset($details['name'])) ? $details['name'] : $machine_name;
  }
  $linkout_type = (isset($node->linkout->type)) ? $node->linkout->type : 'none';
  $linkout_type = (isset($form_state['values'])) ? $form_state['values']['dbxref_linkout_type'] : $linkout_type;
  $form['dbxref']['dbxref_linkout_type'] = array(
    '#type' => 'radios',
    '#title' => 'Link-out Type',
    '#description' => 'This determines how the URL to be linked to is formed. <strong>Make
      sure the database chosen supports this type of link</strong> (ie: the database
      should point to a GBrowse instance if you choose GBrowse here).',
    '#options' => $options,
    '#default_value' => $linkout_type,
    '#ajax' => array(
      'callback' => 'ajax_blast_ui_node_linkout_custom_callback',
      'wrapper' => 'link-outs',
    )
  );

  $form['dbxref']['details'] = array(
    '#prefix' => '<div id="link-outs">',
    '#suffix' => '</div>',
  );

  // Add information about each format to the description.
  if ($linkout_type) {
    $form['dbxref']['details']['dbxref_linkout_description'] = array(
      '#type' => 'item',
      '#markup' => '<p class="blastdb-extra-info">'
        .'<strong>'.$types[$linkout_type]['name'].'</strong>: '
        .$types[$linkout_type]['help']
        .'</p>',
      '#prefix' => '<div id="link-outs">',
      '#suffix' => '</div>',
    );
  }

  if ($types[$linkout_type]['require_regex']) {
    $regex = array(
      'default' => array(
        'title' => 'Generic',
        'help' => 'A single word followed by a free-text definition. '
        . 'The first word contains only alphanumeric characters and optionally '
        . 'underscores and will be used as the ID of the sequence.'
      ),
      'genbank' => array(
        'title' => 'NCBI GenBank',
        'help' => 'Follows the same format as the first option '
        . 'except that the first "word" is of the following form: '
        . 'gb|accession|locus. The accession will be used as the ID of the sequence.'
      ),
      'embl' => array(
        'title' => 'EMBL Data Library',
        'help' => 'Follows the same format as the first option '
        . 'except that the first "word" is of the following form: '
        . 'emb|accession|locus. The accession will be used as the ID of the sequence.'
      ),
      'swissprot' => array(
        'title' => 'SWISS-PROT',
        'help' => 'Follows the same format as the first option '
        . 'except that the first "word" is of the following form: '
        . 'sp|accession|entry name. The accession will be used as the ID of the sequence.'
      ),
      'custom' => array(
        'title' => 'Custom Format',
        'help' => 'Allows you to use a regular expression (define one below) to '
        . 'extract a specifc portion of the FASTA header to be used as the ID.'
      ),
    );
    $regex_type = (isset($node->linkout->regex_type)) ? $node->linkout->regex_type : 'default';
    $regex_type = (isset($form_state['values'])) ? $form_state['values']['dbxref_id_type'] : $regex_type;
    $form['dbxref']['details']['dbxref_id_type'] = array(
      '#type' => 'radios',
      '#title' => 'FASTA header format',
      '#description' => 'Choose the format that matches the format of the FASTA '
        . 'headers in this BLAST database or choose custom to define your own '
        . 'using regular expressions. This ID will be used to create the URL for the link-out.',
      '#options' => array(
        'default' => '<span title="' . $regex['default']['help'] . '">' . $regex['default']['title'] . '</span>',
        'genbank' => '<span title="' . $regex['genbank']['help'] . '">' . $regex['genbank']['title'] . '</span>',
        'embl' => '<span title="' . $regex['embl']['help'] . '">' . $regex['embl']['title'] . '</span>',
        'swissprot' => '<span title="' . $regex['swissprot']['help'] . '">' . $regex['swissprot']['title'] . '</span>',
        'custom' => '<span title="' . $regex['custom']['help'] . '">' . $regex['custom']['title'] . '</span>',
      ),
      '#default_value' => $regex_type,
      '#required' => TRUE,
      '#ajax' => array(
        'callback' => 'ajax_blast_ui_node_linkout_custom_callback',
        'wrapper' => 'link-outs',
      )
    );
    // Add information about each format to the description.
    if ($regex_type) {
      $form['dbxref']['details']['dbxref_id_type']['#description'] .= '
        <p class="blastdb-extra-info"><strong>'.$regex[$regex_type]['title'].'</strong>: '.$regex[$regex_type]['help'].'</p>';
    }

    if ($regex_type == 'custom') {
      $form['dbxref']['details']['regex'] = array(
        '#type' => 'textfield',
        '#title' => 'Regular Expression',
        '#description' => t('A PHP Regular expression with curved brackets '
          . 'surrounding the ID that should be used in the URL to provide a link-'
          . 'out to additional information. See <a href="@url" target="_blank">PHP.net Regular '
          . 'Expression Documentation</a> for more information. <strong>Be sure '
          . 'to include the opening and closing slashes</strong>. This is only '
          . 'available if custom was choosen for the FASTA header format above.',
          array('@url' => 'http://php.net/manual/en/reference.pcre.pattern.syntax.php')),
        '#required' => TRUE,
        '#default_value' => (isset($node->linkout->regex)) ? $node->linkout->regex : ''
      );
    }
  }

  if ($types[$linkout_type]['require_db']) {
    $db_options = tripal_get_db_select_options();
    $db_options[0] = '';
    asort($db_options);
    $form['dbxref']['details']['db_id'] = array(
      '#type' => 'select',
      '#title' => 'External Database',
      '#description' => 'The external database you would like to link-out to. '
        . 'Note that this list includes all Tripal Databases and if the database '
        . 'you would like to link-out to is not included you can add it through '
        . l('Administration > Tripal > Data Loaders > Chado Databases','admin/tripal/loaders/chado_db/add', array('attributes' => array('target' => '_blank')))
        . '.',
      '#options' => $db_options,
      '#required' => TRUE,
      '#default_value' => (isset($node->linkout->db_id->db_id)) ? $node->linkout->db_id->db_id : 0
    );
  }

  // CViTjs settings, if enabled
  if (variable_get('blast_ui_cvitjs_enabled', false)) {
    $form['cvitjs'] = array(
      '#type' => 'fieldset',
      '#title' => 'Whole Genome Visualization',
      '#description' => 'Settings for the display of BLAST hits on an entire genome assembly using CViTjs.',
      '#prefix' => '<div id="cvitjs-settings">',
      '#suffix' => '</div>',
    );

    $form['cvitjs']['cvitjs_enabled'] = array(
      '#type' => 'checkbox',
      '#title' => t('Show BLAST hits on the genome in the results page.'),
      '#description' => t('Uses CViTjs to display BLAST hits on the entire genome'),
      '#default_value' => (isset($node->cvitjs_enabled)) ? $node->cvitjs_enabled : false,
    );
    $cvitjs_msg_class = 'blastdb-extra-info';
    $cvitjs_msg = 'Target Genome Configuration should be under <strong>[data.'.$node->db_name.']</strong> in the main cvit.conf.';

    $conf_section = blast_ui_get_cvit_conf_text('data.'.$node->db_name);
    if (!$conf_section) {
      $cvitjs_msg_class .= ' messages warning';
      $cvitjs_msg .= '<br /><br />There is no section for this genome target defined in the CViTjs
        configuration file. <strong>No genome visualization will be shown until you define a
        configuration section, "[data.'.$form_state['values']['db_name'].']", at '
        .l('Admin > Tripal > Extensions > Tripal BLAST > BLAST UI', 'admin/tripal/extension/tripal_blast')
        .'</strong>.';
    }
    else {
      $cvitjs_msg .= '<br /><br /><strong>Current Configuration:</strong><pre>'.$conf_section.'</pre>';
    }

    $form['cvitjs']['cvitjs_enabled']['#description'] .= '<div class="'.$cvitjs_msg_class.'">'.$cvitjs_msg.'</p>';

  }

  return $form;
}

function blastdb_form_validate($form, $form_state) {

  // Check the database path does not include the file format suffix.
  $suffix = ['.ndb', '.nhr', '.nin', '.not', '.nsq', '.ntf', '.nto',
    '.pdb', '.phr', '.pin', '.pot', '.psq', '.ptf', '.pto'];
  foreach ($suffix as $ending) {
    if (strpos($form_state['values']['db_path'], $ending) !== false) {
      form_set_error('db_path', "You blast database path should not include the file type suffix. Specifically, remove '$ending'.");
    }
  }
  if (isset($form_state['values']['regex']) AND !empty($form_state['values']['regex'])) {
    // Check that any supplied regex includes //.
    if (!preg_match('/\/.*\//', $form_state['values']['regex'])) {
      form_set_error('regex', 'Regular Expressions require opening and closing slashes to delinate them. For example, <em>/^(\s+) .*/</em>');
    }
    // Check that the supplied regex is valid.
    elseif (@preg_match($form_state['values']['regex'], NULL) === FALSE) {
      form_set_error('regex', 'Regular Expression not valid. See '
        . '<a href="http://php.net/manual/en/reference.pcre.pattern.syntax.php" target="_blank">PHP.net Regular '
        . 'Expression Documentation</a> for more information.');
    }
  }

  // Check that the supplied db actually contains a URL prefix.
  if (isset($form_state['values']['db_id'])) {
    $db = tripal_get_db(array('db_id' => $form_state['values']['db_id']));
    if (empty($db)) {
      form_set_error('db_id', 'The database chosen no longer exists.');
    }
    if (empty($db->urlprefix)) {
      form_set_error('db_id', 'The database choosen does not have a URL prefix '
        . 'listed which means a link-out could not be created for BLAST hits. '
        . 'Please edit the database '
        . l('here', 'admin/tripal/chado/tripal_db/edit/' . $db->db_id,
            array('attributes' => array('target' => '_blank')))
        . ' to include a URL prefix before continuing'
      );
    }
  }

  // Check that there is a cvitjs section for the current
  if (isset($form_state['values']['cvitjs_enabled']) AND $form_state['values']['cvitjs_enabled']) {
    $conf_section = blast_ui_get_cvit_conf_text('data.'.$form_state['values']['db_name']);
    if (!$conf_section) {
      drupal_set_message('There is no section for this genome target defined in the CViTjs
        configuration file. <strong>No genome visualization will be shown until you define a
        configuration section, "[data.'.$form_state['values']['db_name'].']", at '
        .l('Admin > Tripal > Extensions > Tripal BLAST > BLAST UI', 'admin/tripal/extension/tripal_blast')
        .'</strong>.',
      'warning');
    }
  }
}

/**
 * Implements hook_insert().
 */
function blastdb_insert($node) {

  // Handle Link-out Rules.
  $regex = '';
  if (isset($node->dbxref_id_type)) {
    if ($node->dbxref_id_type == 'custom') {
      $regex = $node->regex;
    }
    else {
      $regex = $node->dbxref_id_type;
    }
  }

  $db_id = 0;
  if (isset($node->db_id)) {
    $db_id = $node->db_id;
  }

  if (!$node->dbxref_linkout_type) {
    $node->dbxref_linkout_type = 'none';
  }

  if (!isset($node->cvitjs_enabled)) {
    $node->cvitjs_enabled = 0;
  }

  // Actually insert the record.
  db_insert('blastdb')->fields(array(
    'nid'                 => $node->nid,
    'name'                => $node->db_name,
    'path'                => trim($node->db_path),
    'dbtype'              => $node->db_dbtype,
    'dbxref_id_regex'     => $regex,
    'dbxref_db_id'        => $db_id,
    'dbxref_linkout_type' => $node->dbxref_linkout_type,
    'cvitjs_enabled'      => $node->cvitjs_enabled,
  ))->execute();
}

/**
 * Implements hook_node_insert().
 * This function acts on ALL NODES
 */
function blast_ui_node_insert($node) {
  if ($node->type == 'blastdb') {
    $node->title = $node->db_name;
  }
}

/**
 * Implements hook_update().
 */
function blastdb_update($node) {

  // Handle Link-out Rules.
  $regex = '';
  if (isset($node->dbxref_id_type)) {
    if ($node->dbxref_id_type == 'custom') {
      $regex = $node->regex;
    }
    else {
      $regex = $node->dbxref_id_type;
    }
  }

  $db_id = 0;
  if (isset($node->db_id)) {
    $db_id = $node->db_id;
  }

  if (!$node->cvitjs_enabled) {
    $node->cvitjs_enabled = 0;
  }

  if (!$node->dbxref_linkout_type) {
    $node->dbxref_linkout_type = 'none';
  }

  // Update the record.
  db_update('blastdb')->fields(array(
    'name'                => $node->db_name,
    'path'                => $node->db_path,
    'dbtype'              => $node->db_dbtype,
    'dbxref_id_regex'     => $regex,
    'dbxref_db_id'        => $db_id,
    'dbxref_linkout_type' => $node->dbxref_linkout_type,
    'cvitjs_enabled'      => $node->cvitjs_enabled,
  ))->condition('nid', $node->nid)->execute();
}

/**
 * Implements hook_node_update().
 * This  function acts on ALL NODES
 */
function blast_ui_node_update($node) {
  if ($node->type == 'blastdb')  {
    $node->title = $node->db_name;
  }
}

/**
 * Implements hook_delete().
 */
function blastdb_delete($node) {
  db_delete('blastdb')->condition('nid',$node->nid)->execute();
}

/**
 * Implements hook_load().
 */
function blastdb_load($nodes) {

  $sql = "
    SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id,
           dbxref_linkout_type, cvitjs_enabled
    FROM {blastdb}
    WHERE nid IN (:nids)";
  $result = db_query($sql, array(':nids' => array_keys($nodes)));

  foreach ($result as $record) {

    // Add basic blast node information.
    $nodes[$record->nid]->db_name = $record->name;
    $nodes[$record->nid]->db_path = $record->path;
    $nodes[$record->nid]->title = $record->name;
    $nodes[$record->nid]->db_dbtype = $record->dbtype;

    // CViTjs status
    $nodes[$record->nid]->cvitjs_enabled  = $record->cvitjs_enabled;

    // Determine the type of link-out chosen.
    $types = module_invoke_all('blast_linkout_info');
    $type = NULL;
    if (isset($types[ $record->dbxref_linkout_type ])) {
      $type = $types[ $record->dbxref_linkout_type ];
    }
    else {
      tripal_report_error(
        'blast_ui',
        TRIPAL_ERROR,
        'Unable to find details on the type of link-out choosen (%type). Have you defined hook_blast_linkout_info()? Make sure to clear the cache once you do so.',
        array('%type' => $record->dbxref_linkout_type)
      );
    }

    // Now determine if this node meets the requirements for the linkout
    // chosen before adding linkout information.
    $add_linkout = TRUE;
    if (!$type OR $record->dbxref_linkout_type == 'none') {
      $add_linkout = FALSE;
    }
    else {
      if ($type['require_regex'] AND !$record->dbxref_id_regex) {
        $add_linkout = FALSE;
      }
      if ($type['require_db'] AND !$record->dbxref_db_id) {
        $add_linkout = FALSE;
      }
    }

    // Add information related to link-outs to the node.
    if ($add_linkout) {
      $nodes[$record->nid]->linkout = new stdClass();

      // If the link-out type requires a regex then provide one.
      if ($type['require_regex']) {
        if (preg_match('/\/.*\//', $record->dbxref_id_regex)) {
          $nodes[$record->nid]->linkout->regex_type = 'custom';
          $nodes[$record->nid]->linkout->regex = $record->dbxref_id_regex;
        }
        else {
          $nodes[$record->nid]->linkout->regex_type = $record->dbxref_id_regex;
          $nodes[$record->nid]->linkout->regex = get_blastdb_linkout_regex($nodes[$record->nid]);
        }
      }
      else {
          $nodes[$record->nid]->linkout->regex_type = 'none';
          $nodes[$record->nid]->linkout->regex = NULL;
      }

      // If the link-out type requires a db then provide one.
      if (isset($type['require_db'])) {
        $nodes[$record->nid]->linkout->db_id = tripal_get_db(array('db_id' => $record->dbxref_db_id));
      }
      else {
        $nodes[$record->nid]->linkout->db_id = NULL;
      }

      $nodes[$record->nid]->linkout->none = FALSE;

      // Support complex link-outs.
      $nodes[$record->nid]->linkout->type = $record->dbxref_linkout_type;
      $nodes[$record->nid]->linkout->url_function = $type['process function'];

    }
    // If there is no linkout then provide some defaults.
    else {
      $nodes[$record->nid]->linkout = new stdClass();
      $nodes[$record->nid]->linkout->regex = '';
      $nodes[$record->nid]->linkout->db_id = 0;
      $nodes[$record->nid]->linkout->none = TRUE;
    }
  }
}

/**
 * AJAX Callback: Update Node Link-out Regex Textfield.
 *
 * On BlastDB node form the Link-out (dbxref) options allow for settings of a
 * custom regex which should only be enabled when "Custom" is selected. This
 * callback refreshes the regex textfield so it can change (ie: become enabled)
 * when someone selects custom.
 */
function ajax_blast_ui_node_linkout_custom_callback($form, $form_state) {
  return $form['dbxref']['details'];
}