tripal/tripal_feature/indexFeatures.php

<?php
/**
 * @file
 * @todo Add file header description
 */


// This script can be run as a stand-alone script to sync all the features from chado to drupal
//
// To index a single feature
// -i feature_id
// -n node_id
//
// To index all features
// -i 0

$arguments = getopt("i:n:");

if (isset($arguments['i'])) {
  $drupal_base_url = parse_url('http://www.example.com');
  $_SERVER['HTTP_HOST'] = $drupal_base_url['host'];
  $_SERVER['REQUEST_URI'] = $_SERVER['SCRIPT_NAME'] = $_SERVER['PHP_SELF'];
  $_SERVER['REMOTE_ADDR'] = NULL;
  $_SERVER['REQUEST_METHOD'] = NULL;

  require_once 'includes/bootstrap.inc';
  drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);

  $feature_id = $arguments['i'];
  $nid        = $arguments['n'];

  # print "\n";
  # print "feature id is $feature_id\n";
  # print "nid is $nid\n";
  # print "\n";

  if ($feature_id > 0) {
    # print "indexing feature $feature_id\n";
   // We register a shutdown function to ensure that the nodes
   // that are indexed will have proper entries in the search_totals
   // table.  Without these entries, the searching doesn't work
   // properly. This function may run for quite a while since
   // it must calculate the sum of the scores of all entries in
   // the search_index table.  In the case of common words like
   // 'contig', this will take quite a while
    register_shutdown_function('search_update_totals');
    tripal_feature_index_feature($feature_id, $nid);
  }
  else{
    print "indexing all features...\n";
    tripal_features_reindex(0);
  }

}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_features_reindex($max_sync, $job_id = NULL) {
  $i = 0;

  // We register a shutdown function to ensure that the nodes
  // that are indexed will have proper entries in the search_totals
  // table.  Without these entries, the searching doesn't work
  // properly. This function may run for quite a while since
  // it must calculate the sum of the scores of all entries in
  // the search_index table.  In the case of common words like
  // 'contig', this will take quite a while
  register_shutdown_function('search_update_totals');

  // use this SQL statement to get the features that we're going to index. This
  // SQL statement is derived from the hook_search function in the Drupal API.
  // Essentially, this is the SQL statement that finds all nodes that need
  // reindexing, but adjusted to include the chado_feature
  $sql = "SELECT N.nid, N.title, CF.feature_id ".
        "FROM {node} N ".
        "  INNER JOIN chado_feature CF ON CF.nid = N.nid ";
  $results = db_query($sql);

  // load into ids array
  $count = 0;
  $chado_features = array();
  while ($chado_feature = db_fetch_object($results)) {
    $chado_features[$count] = $chado_feature;
    $count++;
  }

  // Iterate through features that need to be indexed
  $interval = intval($count * 0.01);
  if ($interval >= 0) {
    $interval = 1;
  }
  foreach ($chado_features as $chado_feature) {

    // update the job status every 1% features
    if ($job_id and $i % $interval == 0) {
      $prog = intval(($i/$count)*100);
      tripal_job_set_progress($job_id, $prog);
      print "$prog%\n";
    }

    // sync only the max requested
    if ($max_sync and $i == $max_sync) {
      return '';
    }
    $i++;

  /**
    * tripal_feature_index_feature ($chado_feature->feature_id,$chado_feature->nid);
    * parsing all the features can cause memory overruns
    * we are not sure why PHP does not clean up the memory as it goes
    * to avoid this problem we will call this script through an
    * independent system call
    */

    $cmd = "php " . drupal_get_path('module', 'tripal_feature') . "/indexFeatures.php ";
    $cmd .= "-i $chado_feature->feature_id -n $chado_feature->nid ";

    # print "\t$cmd\n";
    # print "\tfeature id is $chado_feature->feature_id\n";
    # print "\tnid is $chado_feature->nid\n";
    # print "\n";

    system($cmd);
    }

  return '';
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_index_feature($feature_id, $nid) {
  #print "\tfeature $feature_id nid $nid\n";
  // return if we haven't been provided with a feature_id
  if (!$feature_id) {
    return 0;
  }

  // if we only have a feature_id then let's find a corresponding
  // node.  If we can't find a node then return.
  if (!$nid) {
    $nsql = "SELECT N.nid,N.title FROM {chado_feature} CF ".
            "  INNER JOIN {node} N ON N.nid = CF.nid ".
            "WHERE CF.feature_id = %d";
    $node = db_fetch_object(db_query($nsql, $feature_id));
    if (!$node) {
      return 0;
    }
    $node = node_load($node->nid);
  }
  else {
    $node = node_load($nid);
  }

  // node load the noad, the comments and the taxonomy and
  // index
  $node->build_mode = NODE_BUILD_SEARCH_INDEX;
  $node = node_build_content($node, FALSE, FALSE);
  $node->body = drupal_render($node->content);
  node_invoke_nodeapi($node, 'view', FALSE, FALSE);
  //   $node->body .= module_invoke('comment', 'nodeapi', $node, 'update index');
  //   $node->body .= module_invoke('taxonomy','nodeapi', $node, 'update index');
  //   print "$node->title: $node->body\n";
  search_index($node->nid, 'node', $node->body);

  # $mem = memory_get_usage(TRUE);
  # $mb = $mem/1048576;
  # print "$mb mb\n";

  return 1;
}