Moved the synchronize functions from the main module to syncFeatures.php. Moved the search indexing functions to indexFeatures.php. This allows each sync or index job to be submitted as a separate system call, thus circumventing a problem with php not releasing memory. Also, syncing and indexing all features may now be done through a command line call instead of only through the web interface.

tripal_feature/indexFeatures.php

@@ -0,0 +1,158 @@
+<?php
+
+//
+// Copyright 2009 Clemson University
+//
+// 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 $feature_id\n";
+      tripal_feature_index_feature($feature_id, $nid); 
+   }
+   else{ 
+      print "indexing all features...\n";
+      tripal_features_reindex(0);
+   }
+
+}
+
+/************************************************************************
+ *
+ */
+function tripal_features_reindex ($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);
+   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 '';
+}
+
+/************************************************************************
+ *
+ */
+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;
+}
+
+?>

tripal_feature/syncFeatures.php

@@ -0,0 +1,275 @@
+<?php
+
+//
+// Copyright 2009 Clemson University
+//
+# This script can be run as a stand-alone script to sync all the features from chado to drupal
+// Parameter f specifies the feature_id to sync
+// -f 0 will sync all features 
+
+$arguments = getopt("f:");
+
+if(isset($arguments['f'])){
+   $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 = $arguments['f'];
+
+   if($feature_id > 0 ){ 
+      print "syncing feature $feature_id\n";
+      tripal_feature_sync_feature($feature_id); 
+   }
+   else{ 
+      print "syncing all features...\n";
+      tripal_feature_sync_features();
+   }   
+}
+   
+
+/************************************************************************
+ *
+ */
+function tripal_feature_sync_features ($max_sync = 0, $job_id = NULL){
+   //print "Syncing features (max of $max_sync)\n";
+   $i = 0;
+
+   // get the list of available sequence ontology terms for which
+   // we will build drupal pages from features in chado.  If a feature
+   // is not one of the specified typse we won't build a node for it.
+   $allowed_types = variable_get('chado_feature_types','EST contig');
+   $allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
+   $so_terms = split(' ',$allowed_types);
+   $where_cvt = "";
+   foreach ($so_terms as $term){
+      $where_cvt .= "CVT.name = '$term' OR ";
+   }
+   $where_cvt = substr($where_cvt,0,strlen($where_cvt)-3);  # strip trailing 'OR'
+
+   // get the list of organisms that are synced and only include features from
+   // those organisms
+   $orgs = organism_get_synced();
+   $where_org = "";
+   foreach($orgs as $org){
+      $where_org .= "F.organism_id = $org->organism_id OR ";
+   }
+   $where_org = substr($where_org,0,strlen($where_org)-3);  # strip trailing 'OR'
+
+   // use this SQL statement to get the features that we're going to upload
+   $sql = "SELECT feature_id ".
+          "FROM {FEATURE} F ".
+          "   INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
+          "WHERE ($where_cvt) AND ($where_org) ".
+          "ORDER BY feature_id";
+   // get the list of features
+   $previous_db = db_set_active('chado');  // use chado database
+   $results = db_query($sql);
+
+   db_set_active($previous_db);  // now use drupal database
+
+   // load into ids array
+   $count = 0;
+   $ids = array();
+   while($id = db_fetch_object($results)){
+      $ids[$count] = $id->feature_id;
+      $count++;
+   }
+
+   // make sure our vocabularies are set before proceeding
+   tripal_feature_set_vocabulary();
+
+   // pre-create the SQL statement that will be used to check
+   // if a feature has already been synced.  We skip features
+   // that have been synced
+   $sql = "SELECT * FROM {chado_feature} WHERE feature_id = %d";
+
+   // Iterate through features that need to be synced
+   $interval = intval($count * 0.01);
+   foreach($ids as $feature_id){
+      // update the job status every 1% features
+      if($job_id and $i % $interval == 0){
+         tripal_job_set_progress($job_id,intval(($i/$count)*100));
+      }
+      // if we have a maximum number to sync then stop when we get there
+      // if not then just continue on
+      if($max_sync and $i == $max_sync){
+         return '';
+      }
+      if(!db_fetch_object(db_query($sql,$feature_id))){
+        
+         # 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') . "/syncFeatures.php -f $feature_id ";
+         system($cmd);
+
+      }
+      $i++;
+   }
+
+   return '';
+}
+
+function tripal_feature_sync_feature ($feature_id){
+   print "\tfeature $feature_id\n";
+
+   $mem = memory_get_usage(TRUE);
+   $mb = $mem/1048576;
+   print "$mb mb\n";
+
+   global $user;
+   $create_node = 1;   // set to 0 if the node exists and we just sync and not create
+
+   // get the accession prefix
+   $aprefix = variable_get('chado_feature_accession_prefix','ID');
+
+   // if we don't have a feature_id then return
+   if(!$feature_id){
+      drupal_set_message(t("Please provide a feature_id to sync"));
+      return '';
+   }
+
+   // get information about this feature
+   $fsql = "SELECT F.feature_id, F.name, F.uniquename,O.genus, ".
+           "    O.species,CVT.name as cvname,F.residues,F.organism_id ".
+           "FROM {FEATURE} F ".
+           "  INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
+           "  INNER JOIN Organism O ON F.organism_id = O.organism_ID ".
+           "WHERE F.feature_id = %d";
+   $previous_db = db_set_active('chado');  // use chado database
+   $feature = db_fetch_object(db_query($fsql,$feature_id));
+   db_set_active($previous_db);  // now use drupal database
+
+   // check to make sure that we don't have any nodes with this feature name as a title
+   // but without a corresponding entry in the chado_feature table if so then we want to
+   // clean up that node.  (If a node is found we don't know if it belongs to our feature or
+   // not since features can have the same name/title.)
+   $tsql =  "SELECT * FROM {node} N ".
+            "WHERE title = '%s'";
+   $cnsql = "SELECT * FROM {chado_feature} ".
+            "WHERE nid = %d";
+   $nodes = db_query($tsql,$feature->name);
+   // cycle through all nodes that may have this title
+   while($node = db_fetch_object($nodes)){
+      $feature_nid = db_fetch_object(db_query($cnsql,$node->nid));
+      if(!$feature_nid){
+         drupal_set_message(t("$feature_id: A node is present but the chado_feature entry is missing... correcting"));
+         node_delete($node->nid);
+      }
+   }
+
+   // check if this feature already exists in the chado_feature table.
+   // if we have a chado feature, we want to check to see if we have a node
+   $cfsql = "SELECT * FROM {chado_feature} ".
+            "WHERE feature_id = %d";
+   $nsql =  "SELECT * FROM {node} ".
+            "WHERE nid = %d";
+   $chado_feature = db_fetch_object(db_query($cfsql,$feature->feature_id));
+   if($chado_feature){
+      drupal_set_message(t("$feature_id: A chado_feature entry exists"));
+      $node = db_fetch_object(db_query($nsql,$chado_feature->nid));
+      if(!$node){
+         // if we have a chado_feature but not a node then we have a problem and
+         // need to cleanup
+         drupal_set_message(t("$feature_id: The node is missing, but has a chado_feature entry... correcting"));
+         $df_sql = "DELETE FROM {chado_feature} WHERE feature_id = %d";
+         db_query($df_sql,$feature_id);
+      } else {
+         drupal_set_message(t("$feature_id: A corresponding node exists"));
+         $create_node = 0;
+      }
+   }
+
+   // if we've encountered an error then just return.
+   if($error_msg = db_error()){
+      //print "$error_msg\n";
+      return '';
+   }
+
+   // if a drupal node does not exist for this feature then we want to
+   // create one.  Note that the node_save call in this block
+   // will call the hook_submit function which
+   if($create_node){
+      drupal_set_message(t("$feature_id: Creating node $feature->name"));
+      $new_node = new stdClass();
+      $new_node->type = 'chado_feature';
+      $new_node->uid = $user->uid;
+      $new_node->title = "$feature->name";
+      $new_node->feature_id = $feature->feature_id;
+      $new_node->residues = $feature->residues;
+      $new_node->organism_id = $feature->organism_id;
+      $new_node->feature_type = $feature->cvname;
+
+      // validate the node and if okay then submit
+      node_validate($new_node);
+      if ($errors = form_get_errors()) {
+         foreach($errors as $key => $msg){
+            drupal_set_message($msg);
+         }
+         return $errors;
+      } else {
+         $node = node_submit($new_node);
+         node_save($node);
+      }
+
+   }
+   else {
+      $node = $chado_feature;
+   }
+
+
+   // set the taxonomy for this node
+   drupal_set_message(t("$feature_id ($node->nid): setting taxonomy"));
+   tripal_feature_set_taxonomy($node,$feature_id);
+
+   // reindex the node
+   // drupal_set_message(t("$feature_id( $node->nid): indexing"));
+   // tripal_feature_index_feature ($feature_id,$node->nid);
+
+   // remove any URL alias that may already exist and recreate
+   drupal_set_message(t("$feature_id ($node->nid): setting URL alias"));
+   db_query("DELETE FROM {url_alias} WHERE dst = '%s'", "$aprefix$feature_id");
+   path_set_alias("node/$node->nid","$aprefix$feature_id");
+
+   return '';
+}
+
+
+
+/*******************************************************************************
+ *  Returns a list of organisms that are currently synced with Drupal
+ */
+function organism_get_synced() {
+
+   // use this SQL for getting synced organisms
+   $dsql =  "SELECT * FROM {chado_organism}";
+   $orgs = db_query($dsql);
+
+   // use this SQL statement for getting the organisms
+   $csql =  "SELECT * FROM {Organism} ".
+            "WHERE organism_id = %d";
+
+   $org_list = array();
+
+   // iterate through the organisms and build an array of those that are synced
+   while($org = db_fetch_object($orgs)){
+      $previous_db = db_set_active('chado');  // use chado database
+      $info = db_fetch_object(db_query($csql,$org->organism_id));
+      db_set_active($previous_db);  // now use drupal database
+      $org_list[] = $info;
+   }    
+   return $org_list;
+}
+
+
+
+
+
+?>

tripal_feature/tripal_feature.module

@@ -4,6 +4,9 @@
 // Copyright 2009 Clemson University
 //
 
+require_once "syncFeatures.php";
+require_once "indexFeatures.php";
+
 /*************************************************************************
 *
 */
@@ -1211,203 +1214,6 @@ function theme_tripal_feature_search_results ($node) {
 
    return $content;
 }
-/************************************************************************
- *
- */
-function tripal_feature_sync_features ($max_sync = 0, $job_id = NULL){
-   $i = 0;
-
-   // get the list of available sequence ontology terms for which
-   // we will build drupal pages from features in chado.  If a feature
-   // is not one of the specified typse we won't build a node for it.
-   $allowed_types = variable_get('chado_feature_types','EST contig');
-   $allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
-   $so_terms = split(' ',$allowed_types);
-   $where_cvt = "";
-   foreach ($so_terms as $term){
-      $where_cvt .= "CVT.name = '$term' OR ";
-   }
-   $where_cvt = substr($where_cvt,0,strlen($where_cvt)-3);  # strip trailing 'OR'
-
-   // get the list of organisms that are synced and only include features from
-   // those organisms
-   $orgs = tripal_organism_get_synced();
-   $where_org = "";
-   foreach($orgs as $org){
-      $where_org .= "F.organism_id = $org->organism_id OR ";
-   }
-   $where_org = substr($where_org,0,strlen($where_org)-3);  # strip trailing 'OR'
-
-   // use this SQL statement to get the features that we're going to upload
-   $sql = "SELECT feature_id ".
-          "FROM {FEATURE} F ".
-          "   INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
-          "WHERE ($where_cvt) AND ($where_org) ".
-          "ORDER BY feature_id";
-   // get the list of features
-   $previous_db = db_set_active('chado');  // use chado database
-   $results = db_query($sql);
-
-   db_set_active($previous_db);  // now use drupal database
-
-   // load into ids array
-   $count = 0;
-   $ids = array();
-   while($id = db_fetch_object($results)){
-      $ids[$count] = $id->feature_id;
-      $count++;
-   }
-
-   // make sure our vocabularies are set before proceeding
-   tripal_feature_set_vocabulary();
-
-   // pre-create the SQL statement that will be used to check
-   // if a feature has already been synced.  We skip features
-   // that have been synced
-   $sql = "SELECT * FROM {chado_feature} WHERE feature_id = %d";
-
-   // Iterate through features that need to be synced
-   $interval = intval($count * 0.01);
-   foreach($ids as $feature_id){
-      // update the job status every 1% features
-      if($job_id and $i % $interval == 0){
-         tripal_job_set_progress($job_id,intval(($i/$count)*100));
-      }
-      // if we have a maximum number to sync then stop when we get there
-      // if not then just continue on
-      if($max_sync and $i == $max_sync){
-         return '';
-      }
-      if(!db_fetch_object(db_query($sql,$feature_id))){
-         tripal_feature_sync_feature ($feature_id);
-      }
-      $i++;
-   }
-
-   return '';
-}
-
-/************************************************************************
- *
- */
-function tripal_feature_sync_feature ($feature_id){
-
-   global $user;
-   $create_node = 1;   // set to 0 if the node exists and we just sync and not create
-
-   // get the accession prefix
-   $aprefix = variable_get('chado_feature_accession_prefix','ID');
-
-   // if we don't have a feature_id then return
-   if(!$feature_id){
-      drupal_set_message(t("Please provide a feature_id to sync"));
-      return '';
-   }
-
-   // get information about this feature
-   $fsql = "SELECT F.feature_id, F.name, F.uniquename,O.genus, ".
-           "    O.species,CVT.name as cvname,F.residues,F.organism_id ".
-           "FROM {FEATURE} F ".
-           "  INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
-           "  INNER JOIN Organism O ON F.organism_id = O.organism_ID ".
-           "WHERE F.feature_id = %d";
-   $previous_db = db_set_active('chado');  // use chado database
-   $feature = db_fetch_object(db_query($fsql,$feature_id));
-   db_set_active($previous_db);  // now use drupal database
-
-   // check to make sure that we don't have any nodes with this feature name as a title
-   // but without a corresponding entry in the chado_feature table if so then we want to
-   // clean up that node.  (If a node is found we don't know if it belongs to our feature or
-   // not since features can have the same name/title.)
-   $tsql =  "SELECT * FROM {node} N ".
-            "WHERE title = '%s'";
-   $cnsql = "SELECT * FROM {chado_feature} ".
-            "WHERE nid = %d";
-   $nodes = db_query($tsql,$feature->name);
-   // cycle through all nodes that may have this title
-   while($node = db_fetch_object($nodes)){
-      $feature_nid = db_fetch_object(db_query($cnsql,$node->nid));
-      if(!$feature_nid){
-         drupal_set_message(t("$feature_id: A node is present but the chado_feature entry is missing... correcting"));
-         node_delete($node->nid);
-      }
-   }
-
-   // check if this feature already exists in the chado_feature table.
-   // if we have a chado feature, we want to check to see if we have a node
-   $cfsql = "SELECT * FROM {chado_feature} ".
-            "WHERE feature_id = %d";
-   $nsql =  "SELECT * FROM {node} ".
-            "WHERE nid = %d";
-   $chado_feature = db_fetch_object(db_query($cfsql,$feature->feature_id));
-   if($chado_feature){
-      drupal_set_message(t("$feature_id: A chado_feature entry exists"));
-      $node = db_fetch_object(db_query($nsql,$chado_feature->nid));
-      if(!$node){
-         // if we have a chado_feature but not a node then we have a problem and
-         // need to cleanup
-         drupal_set_message(t("$feature_id: The node is missing, but has a chado_feature entry... correcting"));
-         $df_sql = "DELETE FROM {chado_feature} WHERE feature_id = %d";
-         db_query($df_sql,$feature_id);
-      } else {
-         drupal_set_message(t("$feature_id: A corresponding node exists"));
-         $create_node = 0;
-      }
-   }
-
-   // if we've encountered an error then just return.
-   if($error_msg = db_error()){
-      //print "$error_msg\n";
-      return '';
-   }
-
-   // if a drupal node does not exist for this feature then we want to
-   // create one.  Note that the node_save call in this block
-   // will call the hook_submit function which
-   if($create_node){
-      drupal_set_message(t("$feature_id: Creating node $feature->name"));
-      $new_node = new stdClass();
-      $new_node->type = 'chado_feature';
-      $new_node->uid = $user->uid;
-      $new_node->title = "$feature->name";
-      $new_node->feature_id = $feature->feature_id;
-      $new_node->residues = $feature->residues;
-      $new_node->organism_id = $feature->organism_id;
-      $new_node->feature_type = $feature->cvname;
-
-      // validate the node and if okay then submit
-      node_validate($new_node);
-      if ($errors = form_get_errors()) {
-         foreach($errors as $key => $msg){
-            drupal_set_message($msg);
-         }
-         return $errors;
-      } else {
-         $node = node_submit($new_node);
-         node_save($node);
-      }
-
-   }
-   else {
-      $node = $chado_feature;
-   }
-
-
-   // set the taxonomy for this node
-   drupal_set_message(t("$feature_id ($node->nid): setting taxonomy"));
-   tripal_feature_set_taxonomy($node,$feature_id);
-
-   // reindex the node
-   drupal_set_message(t("$feature_id( $node->nid): indexing"));
-   tripal_feature_index_feature ($feature_id,$node->nid);
-
-   // remove any URL alias that may already exist and recreate
-   drupal_set_message(t("$feature_id ($node->nid): setting URL alias"));
-   db_query("DELETE FROM {url_alias} WHERE dst = '%s'", "$aprefix$feature_id");
-   path_set_alias("node/$node->nid","$aprefix$feature_id");
-
-   return '';
-}
 /************************************************************************
  *
  */
@@ -1688,94 +1494,6 @@ function tripal_feature_set_taxonomy ($node,$feature_id){
    }
 
 }
-/************************************************************************
- *
- */
-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 synced
-   $interval = intval($count * 0.01);
-   foreach($chado_features as $chado_feature){
-
-      // update the job status every 1% features
-      if($job_id and $i % $interval == 0){
-         tripal_job_set_progress($job_id,intval(($i/$count)*100));
-      }
-
-      // sync only the max requested
-      if($max_sync and $i == $max_sync){
-         return '';
-      }
-      tripal_feature_index_feature ($chado_feature->feature_id,$chado_feature->nid);
-      $i++;
-   }
-
-   return '';
-}
-
-/************************************************************************
- *
- */
-function tripal_feature_index_feature ($feature_id,$nid){
-   // return if we haven't been provided with a feature_id
-   if(!$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);
-   return 1;
-}
 /************************************************************************
  *
  */