tripal/tripal_analysis/tripal_analysis.module

<?php
// $Id:
// Copyright 2009 Clemson University
/*******************************************************************************
 * Note: When we pull information for an analysis from chado database. We use
 * 'analysisname' instead of just 'name' to avoid name collision with drupal's
 * node->name variable. Therefore, the SQL statement used is 'SELECT name AS
 * analysisname FROM Analysis', instead of 'SELECT name FROM Analysis'. All
 * other node variables have exact same name as the column name.
 ******************************************************************************/

/*************************************************************************
*
*/
function tripal_analysis_register_child($modulename){
   $sql = "INSERT INTO {tripal_analysis} (modulename) VALUES ('%s')";
   db_query($sql, $modulename);
}
/*************************************************************************
*
*/
function tripal_analysis_unregister_child($modulename){
   if (db_table_exists('tripal_analysis')) {
      $sql = "DELETE FROM {tripal_analysis} WHERE modulename = '%s'";
      db_query($sql, $modulename);
   }
}
/******************************************************************************
 * Tripal Analysis lets users display/hide analysis results associated
 * with a tripal feature. Load javascript when module initialized
 */
function tripal_analysis_init(){
   drupal_add_js(drupal_get_path('theme', 'tripal').
                                 '/js/tripal_analysis.js');
}
/*******************************************************************************
 * tripal_analysis_menu()
 * HOOK: Implementation of hook_menu()
 * Entry points and paths of the module
 */
function tripal_analysis_menu() {
	// Display available analyses
	$items['analyses'] = array(
      'menu_name' => ('primary-links'), //Enable the 'Analysis' primary link
      'title' => t('Analyses'),
      'page callback' => 'tripal_analysis_show_analyses',
      'access arguments' => array('access chado_analysis content'),
      'type' => MENU_NORMAL_ITEM
	);
	//Sync analysis
	$items['chado_sync_analyses'] = array(
     'title' => t('Sync Data'),
     'page callback' => 'tripal_analysis_sync_analyses',
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK
	);
	// Tripal Analysis administrative settings
	$items['admin/tripal/tripal_analysis'] = array(
      'title' => 'Analyses',
      'description' => 'Settings for the displays of analysis results.',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_analysis_admin'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,
      'file' => 'tripal_analysis.admin.inc',
	);
	return $items;
}

/*******************************************************************************
 * Display the summary view of analyses when click on the 'Analyses'
 * primary-link
 */
function tripal_analysis_show_analyses (){
	// Show libraries stored in Drupal's {chado_analysis} table
	$sql = "SELECT COUNT(analysis_id) FROM {chado_analysis}";
	$no_ana = db_result(db_query ($sql));
	if($no_ana != 0) {
		$analyses = get_chado_analyses ();
		return theme('tripal_analysis_analysis_page', $analyses);
	} else {
		return t("No analysis available at this time.");
	}

}

/*******************************************************************************
 *  Provide information to drupal about the node types that we're creating
 *  in this module
 */
function tripal_analysis_node_info() {
	$nodes = array();
	$nodes['chado_analysis'] = array(
      'name' => t('Analysis'),
      'module' => 'chado_analysis',
      'description' => t('An analysis from the chado database'),
      'has_title' => FALSE,
      'title_label' => t('Analysis'),
      'has_body' => FALSE,
      'body_label' => t('Analysis Description'),
      'locked' => TRUE
	);
	return $nodes;
}
/*******************************************************************************
 *  When a new chado_analysis node is created we also need to add information
 *  to our chado_analysis table.  This function is called on insert of a new
 *  node of type 'chado_analysis' and inserts the necessary information.
 */
function chado_analysis_insert($node){
	global $user;
	// Create a timestamp so we can insert it into the chado database
	$time = $node->timeexecuted;
	$month = $time['month'];
	$day = $time['day'];
	$year = $time['year'];
	$timestamp = $month.'/'.$day.'/'.$year;

	// If this analysis already exists then don't recreate it in chado
	$analysis_id = $node->analysis_id;
	if ($analysis_id) {
		$sql = "SELECT analysis_id ".
               "FROM {Analysis} ".
               "WHERE analysis_id = %d ";
		$previous_db = db_set_active('chado');
		$analysis = db_fetch_object(db_query($sql, $node->analysis_id));
		db_set_active($previous_db);
	}

	// If the analysis doesn't exist then let's create it in chado.
	if(!$analysis){
		// First add the item to the chado analysis table
		$sql = "INSERT INTO {analysis} ".
             "  (name, description, program, programversion, algorithm, ".
             "   sourcename, sourceversion, sourceuri, timeexecuted) ".
             "VALUES ('%s','%s','%s','%s','%s','%s','%s','%s','%s')";
		$previous_db = db_set_active('chado');  // use chado database
		db_query($sql,$node->analysisname, $node->description,
		$node->program,$node->programversion,$node->algorithm,
		$node->sourcename, $node->sourceversion, $node->sourceuri,
		$timestamp);
      db_set_active($previous_db);
	}

	// Make sure the entry for this analysis doesn't already exist in the
	// chado_analysis table if it doesn't exist then we want to add it.
	$node_check_sql = "SELECT * FROM {chado_analysis} ".
                     "WHERE analysis_id = %d";
	$node_check = db_fetch_object(db_query($node_check_sql, $analysis_id));
	if(!$node_check){
		// next add the item to the drupal table
		$sql = "INSERT INTO {chado_analysis} (nid, vid, analysis_id) ".
             "VALUES (%d, %d, %d)";
		db_query($sql,$node->nid,$node->vid,$analysis_id);
		// Create a title for the analysis node using the unique keys so when the
		// node is saved, it will have a title
		$record = new stdClass();
		// If the analysis has a name, use it as the node title. If not, construct
		// the title using program, programversion, and sourcename
		if ($node->analysisname) {
			$record->title = $node->analysisname;
		} else {
			//Construct node title as "program (version)
			$record->title = "$node->program ($node->programversion)";
		}
		$record->nid = $node->nid;
		drupal_write_record('node',$record,'nid');
		drupal_write_record('node_revisions',$record,'nid');
	}
}
/*******************************************************************************
 */
function chado_analysis_delete($node){
	// Before removing, get analysis_id so we can remove it from chado database
	// later
	$sql_drupal = "SELECT analysis_id ".
                 "FROM {chado_analysis} ".
                 "WHERE nid = %d ".
                 "AND vid = %d";
	$analysis_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));

	// Remove data from the {chado_analysis}, {node}, and {node_revisions} tables
	$sql_del = "DELETE FROM {chado_analysis} ".
              "WHERE nid = %d ".
              "AND vid = %d";
	db_query($sql_del, $node->nid, $node->vid);
	$sql_del = "DELETE FROM {node} ".
              "WHERE nid = %d ".
              "AND vid = %d";
	db_query($sql_del, $node->nid, $node->vid);
	$sql_del = "DELETE FROM {node_revisions} ".
              "WHERE nid = %d ".
              "AND vid = %d";
	db_query($sql_del, $node->nid, $node->vid);

	//Remove from analysis and analysisprop tables of chado database as well
	$previous_db = db_set_active('chado');
	db_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
	db_set_active($previous_db);
}

/*******************************************************************************
 * Update analyses
 */
function chado_analysis_update($node){
	global $user;
	if($node->revision){
		// TODO -- decide what to do about revisions
	} else {
		// Create a timestamp so we can insert it into the chado database
		$time = $node->timeexecuted;
		$month = $time['month'];
		$day = $time['day'];
		$year = $time['year'];
		$timestamp = $month.'/'.$day.'/'.$year;

		// get the analysis_id for this node:
		$sql = "SELECT analysis_id ".
             "FROM {chado_analysis} ".
             "WHERE vid = %d";
		$analysis_id = db_fetch_object(db_query($sql, $node->vid))->analysis_id;

		$sql = "UPDATE {analysis} ".
             "SET name = '%s', ".
             "    description = '%s', ".
             "    program = '%s', ".
             "    programversion = '%s', ".
             "    algorithm = '%s', ".
             "    sourcename = '%s', ".
             "    sourceversion = '%s', ".
             "    sourceuri = '%s', ".
             "    timeexecuted = '%s' ".
             "WHERE analysis_id = %d ";

		$previous_db = db_set_active('chado');  // use chado database
		db_query($sql, $node->analysisname, $node->description, $node->program,
		$node->programversion,$node->algorithm,$node->sourcename,
		$node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
      db_set_active($previous_db);  // switch back to drupal database
		
		// Create a title for the analysis node using the unique keys so when the
		// node is saved, it will have a title
		$record = new stdClass();
		// If the analysis has a name, use it as the node title. If not, construct
		// the title using program, programversion, and sourcename
		if ($node->analysisname) {
			$record->title = $node->analysisname;
		} else {
			//Construct node title as "program (version)
			$record->title = "$node->program ($node->programversion)";
		}
		$record->nid = $node->nid;
		drupal_write_record('node',$record,'nid');
		drupal_write_record('node_revisions',$record,'nid');
	}
}

/*******************************************************************************
 *  When editing or creating a new node of type 'chado_analysis' we need
 *  a form.  This function creates the form that will be used for this.
 */
function chado_analysis_form ($node){

	$type = node_get_types('type', $node);
	$form = array();
	$form['title']= array(
      '#type' => 'hidden',
      '#default_value' => $node->title,
	);
	$form['analysisname']= array(
      '#type' => 'textfield',
      '#title' => t('Analysis Name'),
      '#required' => FALSE,
      '#default_value' => $node->analysisname,
      '#weight' => 1
	);
	$form['program']= array(
      '#type' => 'textfield',
      '#title' => t('Program'),
      '#required' => TRUE,
      '#default_value' => $node->program,
      '#weight' => 2
	);
	$form['programversion']= array(
      '#type' => 'textfield',
      '#title' => t('Program Version'),
      '#required' => TRUE,
      '#default_value' => $node->programversion,
      '#weight' => 3
	);
	$form['algorithm']= array(
      '#type' => 'textfield',
      '#title' => t('Algorithm'),
      '#required' => FALSE,
      '#default_value' => $node->algorithm,
      '#weight' => 4
	);
	$form['sourcename']= array(
      '#type' => 'textfield',
      '#title' => t('Source Name'),
      '#required' => FALSE,
      '#default_value' => $node->sourcename,
      '#weight' => 5
	);
	$form['sourceversion']= array(
      '#type' => 'textfield',
      '#title' => t('Source Version'),
      '#required' => FALSE,
      '#default_value' => $node->sourceversion,
      '#weight' => 6
	);
	$form['sourceuri']= array(
      '#type' => 'textfield',
      '#title' => t('Source URI'),
      '#required' => FALSE,
      '#default_value' => $node->sourceuri,
      '#weight' => 7
	);
	// Get time saved in chado
	$default_time = $node->timeexecuted;
	$year = preg_replace("/^(\d+)-\d+-\d+ .*/", "$1", $default_time);
	$month = preg_replace("/^\d+-0?(\d+)-\d+ .*/", "$1", $default_time);
	$day = preg_replace("/^\d+-\d+-0?(\d+) .*/", "$1", $default_time);
	// If the time is not set, use current time
	if (!$default_time) {
		$default_time = time();
		$year = format_date($default_time, 'custom', 'Y');
		$month = format_date($default_time, 'custom', 'n');
		$day = format_date($default_time, 'custom', 'j');
	}
	$form['timeexecuted']= array(
      '#type' => 'date',
      '#title' => t('Time Executed'),
      '#required' => TRUE,
      '#default_value' => array(
         'year' => $year,
         'month' => $month,
         'day' => $day,
	),
      '#weight' => 8
	);
	$form['description']= array(
      '#type' => 'textarea',
      '#rows' => 15,
      '#title' => t('Description and/or Program Settings'),
      '#required' => FALSE,
      '#default_value' => check_plain($node->description),
      '#weight' => 9
	);
	
	return $form;
}

/*******************************************************************************
 *  When a node is requested by the user this function is called to allow us
 *  to add auxiliary data to the node object.
 */
function chado_analysis_load($node){
	// get the analysis_id for this node:
	$sql = "SELECT analysis_id FROM {chado_analysis} WHERE vid = %d";
	$ana_node = db_fetch_object(db_query($sql, $node->vid));
	$additions = new stdClass();
	if ($ana_node) {
		// get analysis information
		$sql = "SELECT Analysis_id, name AS analysisname, description, program, ".
             "  programversion, algorithm, sourcename, sourceversion, ".
             "  sourceuri, timeexecuted ".
             "FROM {Analysis} ".
             "WHERE Analysis_id = $ana_node->analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$additions = db_fetch_object(db_query($sql));
		db_set_active($previous_db);  // now use drupal database
	}
	// If the analysis has a name, use it as the node title. If not, construct
	// the title using program programversion, and sourcename
	if ($additions->analysisname) {
		$additions->title = $additions->analysisname;
	} else {
		// Construct node title as "program version (source)
		$additions->title = "$additions->program ($additions->programversion)";
	}
	return $additions;
}

/*******************************************************************************
 *  This function customizes the view of the chado_analysis node.  It allows
 *  us to generate the markup.
 */
function chado_analysis_view ($node, $teaser = FALSE, $page = FALSE) {
	// use drupal's default node view:
	if (!$teaser) {
		$node = node_prepare($node, $teaser);
		// When previewing a node submitting form, it shows 'Array' instead of
		// correct date format. We need to format the date here
		$time = $node->timeexecuted;
		if(is_array($time)){
			$month = $time['month'];
			$day = $time['day'];
			$year = $time['year'];
			$timestamp = $year.'-'.$month.'-'.$day;
			$node->timeexecuted = $timestamp;
		}
	}
	return $node;
}

/*******************************************************************************
 * Synchronize analyses from chado to drupal
 */
function tripal_analysis_sync_analyses ($analysis_id = NULL, $job_id = NULL){
	global $user;
	$page_content = '';

	if(!$analysis_id){
		$sql = "SELECT Analysis_id, name AS analysisname, description, program, ".
   		 "  programversion, algorithm, sourcename, sourceversion, sourceuri, ".
          "  timeexecuted ".
          "FROM {Analysis} ".
          "ORDER BY analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$results = db_query($sql);
		db_set_active($previous_db);  // now use drupal database
	} else {
		$sql = "SELECT Analysis_id, name AS analysisname, description, program, ".
   		  "  programversion, algorithm, sourcename, sourceversion, sourceuri, ".
          "  timeexecuted ".
          "FROM {Analysis} ".
          "WHERE analysis_id = %d";
          "ORDER BY analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$results = db_query($sql,$analysis_id);
		db_set_active($previous_db);  // now use drupal database
	}

	// We'll use the following SQL statement for checking if the analysis
	// already exists as a drupal node.
	$sql = "SELECT * FROM {chado_analysis} ".
          "WHERE analysis_id = %d";

	while($analysis = db_fetch_object($results)){
		// check if this analysis already exists in the drupal database. if it
		// does then skip this analysis and go to the next one.
		if(!db_fetch_object(db_query($sql,$analysis->analysis_id))){
			
			$new_node = new stdClass();
			// try to access analysisprop for this analysis
			$sql = "SELECT * FROM {analysisprop} WHERE analysis_id = %d";
			$previous_db = db_set_active('chado');
			$analysisprop = db_fetch_object(db_query($sql, $analysis->analysis_id));
			// If analysisprop exists, this analysis can be a blast analysis or 
			// interpro analysis. Get its type using cvterm_id
			if ($analysisprop) {
				$sql = "SELECT name, definition FROM {cvterm} WHERE cvterm_id = %d";
				$result = db_fetch_object(db_query($sql, $analysisprop->type_id));
				// This is a blast analysis
				if ($result->name == 'analysis_blast_settings') {
					$new_node->type = 'chado_analysis_blast';
			   // This is a interpro analysis
				} else if ($result->name == 'analysis_interpro_settings') {
					$new_node->type = 'chado_analysis_interpro';
			   // This is a kegg analysis
				} else if ($result->name == 'analysis_kegg_settings' ||
	              		  $result->name == 'kegg_brite_data' ||
				           preg_match("/KEGG BRITE term:/", $result->definition)) {
				   $new_node->type = 'chado_analysis_kegg';
				} else {
				   $new_node->type = 'chado_analysis';
				}
			// If it doesn't exist, this analysis is generic
			} else {
				$new_node->type = 'chado_analysis';
			}
			db_set_active($previous_db);
			
			$new_node->uid = $user->uid;
			$new_node->analysis_id = $analysis->analysis_id;
			$new_node->analysisname = $analysis->analysisname;
			$new_node->description = $analysis->description;
			$new_node->program = $analysis->program;
			$new_node->programversion = $analysis->programversion;
			$new_node->algorithm = $analysis->algorithm;
			$new_node->sourcename = $analysis->sourcename;
			$new_node->sourceversion = $analysis->sourceversion;
			$new_node->sourceuri = $analysis->sourceuri;
			$new_node->timeexecuted = $analysis->timeexecuted;

			// If the analysis has a name, use it as the node title. If not,
			// construct the title using program, programversion, and sourcename
			if ($new_node->analysisname) {
				$new_node->title = $new_node->analysisname;
			} else {
				//Construct node title as "program (version)
				$new_node->title = "$analysis->program ($analysis->programversion)";
			}
			node_validate($new_node);
			if(!form_get_errors()){
				$node = node_submit($new_node);
				node_save($node);
				if($node->nid){
					$page_content .= "Added $new_node->title<br>";
				}
			}
		} else {
			$page_content .= "Skipped $new_node->title<br>";
		}
	}
	return $page_content;
}
/*******************************************************************************
 * Display help and module information
 * @param path which path of the site we're displaying help
 * @param arg array that holds the current path as would be returned from arg()
 * function
 * @return help text for the path
 */
function tripal_analysis_help($path, $arg) {
	$output = '';
	switch ($path) {
		case "admin/help#tripal_analysis":
			$output = '<p>'.
			t("Displays links to nodes created on this date").
                '</p>';
			break;
	}
	return $output;
}
/*******************************************************************************
 *  The following function proves access control for users trying to
 *  perform actions on data managed by this module
 */
function chado_analysis_access($op, $node, $account){
	if ($op == 'create') {
		return user_access('create chado_analysis content', $account);
	}

	if ($op == 'update') {
		if (user_access('edit chado_analysis content', $account)) {
			return TRUE;
		}
	}
	if ($op == 'delete') {
		if (user_access('delete chado_analysis content', $account)) {
			return TRUE;
		}
	}
	if ($op == 'view') {
		if (user_access('access chado_analysis content', $account)) {
			return TRUE;
		}
	}
	return FALSE;
}

/*******************************************************************************
 *  Set the permission types that the chado module uses.  Essentially we
 *  want permissionis that protect creation, editing and deleting of chado
 #  data objects
 */
function tripal_analysis_perm(){
	return array(
      'access chado_analysis content',
      'create chado_analysis content',
      'delete chado_analysis content',
      'edit chado_analysis content',
	);
}

/*******************************************************************************
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 */
function tripal_analysis_theme () {
	return array(
      'tripal_analysis_analysis_page' => array (
         'arguments' => array('analyses'),
	),
	);
}

/*******************************************************************************
 * This function uses analysis_id's of all drupal analysis nodes as input and
 * pull the analysis information (name, description, program, programversion,
 * algorithm, sourcename, sourceversion, sourceuri, timeexecuted) from
 * chado database. The return type is an object array that stores $analysis
 * objects sorted by program
 */
function get_chado_analyses() {
	$sql_drupal = "SELECT COUNT (analysis_id) FROM {chado_analysis}";
	$no_orgs = db_result(db_query($sql_drupal));
	if ($no_orgs != 0) {
		$sql = "SELECT analysis_id, CA.nid, type FROM {chado_analysis} CA INNER JOIN node ON CA.nid = node.nid";
		$result = db_query($sql);
		$previous_db = db_set_active('chado');
		$sql = "SELECT Analysis_id, name AS analysisname, description, program, 
		                       programversion, algorithm, sourcename, sourceversion, 
		                       sourceuri, timeexecuted
		           FROM {Analysis} 		           WHERE analysis_id=%d";
		$analyses = array();
		$count = 0;
		while ($data = db_fetch_object($result)) {
			$analysis = db_fetch_object(db_query($sql, $data->analysis_id));
			$analysis->node_id = $data->nid;
			$analysis->node_type = $data->type;
			// Use node_type as the key so we can sort by node type
			// Since node_type is not unique by itself, we need to add
			// $count to the key
			$sortedBy = $analysis->timeexecuted;
			$analyses ["$sortedBy$count"] = $analysis;
			$count ++;
		}
		db_set_active($previous_db);

		//Sort analyses by time, descending order
		krsort($analyses, SORT_STRING);
		return $analyses;
	}
}
/************************************************************************
 *
 */
function theme_tripal_analysis_analysis_page($analyses) {
   
	$output = "<br>Analyses are listed in the descending order of their execution time.<br><a id=\"tripal_expandableBox_toggle_button\" onClick=\"toggleExpandableBoxes()\">[-] Collapse All</a>";
	
   foreach($analyses as $analysis){
		// Prepare information for html output
		$ana_node_url = url("node/$analysis->node_id");
	   if ($analysis->sourceversion) {
         $ver = "($analysis->sourceversion)";
      }
      $date =  preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted);
      
      // Generate html output
		$output .= "<div class=\"tripal_chado_analysis-info-box\" style=\"padding:5px\">
                         <div class=\"tripal_expandableBox\">
                           <h3>$analysis->analysisname ($date)</h3>
                         </div>
                         <div class=\"tripal_expandableBoxContent\">
                           <span>
                             <table class=\"tripal_chado_analysis_content\">
                               <tr><td>
                                 Name: <a href=\"$ana_node_url\">$analysis->analysisname</a>
                               </td></tr>
                               <tr><td>
                                 Program: $analysis->program ($analysis->programversion)
                               </td></tr>
                               <tr><td>
                                 Algorithm: $analysis->algorithm
                               </td></tr>
		                         <tr><td>
                                 Source: $analysis->sourcename $ver
		                         </td></tr>
		                         <tr><td>
                                 Source URI: $analysis->sourceuri
                               </td></tr>
                               <tr><td>
                                 Executed Time:$date
                               </td></tr>
                               <tr><td>
                                 Description: $analysis->description
                               </td></tr>
                             </table>
                           </span>
                         </div>
                       </div>";
	}

	return $output;
}

/************************************************************************
 *
 */
function tripal_analyses_cleanup($dummy = NULL, $job_id = NULL) {

	// build the SQL statments needed to check if nodes point to valid analyses
	$dsql = "SELECT * FROM {node} WHERE type = 'chado_analysis' order by nid";
	$nsql = "SELECT * FROM {node} WHERE nid = %d";
	$csql = "SELECT * FROM {chado_analysis} where nid = %d ";
	$cosql= "SELECT * FROM {chado_analysis}";
	$tsql = "SELECT * FROM {analysis} O ".
           "WHERE analysis_id = %d";

	// load into nodes array
	$results = db_query($dsql);
	$count = 0;
	$nodes = array();
	while($node = db_fetch_object($results)){
		$nodes[$count] = $node;
		$count++;
	}

	// load the chado_analyses into an array
	$results = db_query($cosql);
	$cnodes = array();
	while($node = db_fetch_object($results)){
		$cnodes[$count] = $node;
		$count++;
	}
	$interval = intval($count * 0.01);

	// iterate through all of the chado_analysis nodes and delete those that aren't valid
	foreach($nodes as $nid){

		// update the job status every 1% analyses
		if($job_id and $i % $interval == 0){
			tripal_job_set_progress($job_id,intval(($i/$count)*100));
		}

		// first check to see if the node has a corresponding entry
		// in the chado_analysis table. If not then delete the node.
		$analysis = db_fetch_object(db_query($csql,$nid->nid));
		if(!$analysis){
			node_delete($nid->nid);
			$message = "Missing in chado_analysis table.... DELETING: $nid->nid\n";
			watchdog('tripal_analysis',$message,array(),WATCHDOG_WARNING);
			continue;
		}
		$i++;
	}

	// iterate through all of the chado_analysis nodes and delete those  that aren't valid
	foreach($cnodes as $nid){
		// update the job status every 1% analyses
		if($job_id and $i % $interval == 0){
			tripal_job_set_progress($job_id,intval(($i/$count)*100));
		}
		$node = db_fetch_object(db_query($nsql,$nid->nid));
		if(!$node){
			db_query("DELETE FROM {chado_analysis} WHERE nid = $nid->nid");
			$message = "chado_analysis missing node.... DELETING: $nid->nid\n";
			watchdog('tripal_analysis',$message,array(),WATCHDOG_WARNING);
		}

		$i++;
	}
	return '';
}
/*******************************************************************************
 *
 */
function tripal_analysis_reindex_features ($analysis_id = NULL, $job_id = NULL){
	$i = 0;

	// if the caller provided a analysis_id then get all of the features
	// associated with the analysis. Otherwise get all sequences assoicated
	// with all libraries.
	if(!$analysis_id){
		$sql = "SELECT Analysis_id, Feature_id ".
          "FROM {Analysisfeature} ".
          "ORDER BY analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$results = db_query($sql);
		db_set_active($previous_db);  // now use drupal database
	} else {
		$sql = "SELECT Analysis_id, Feature_id ".
             "FROM {Analysisfeature} ".
             "WHERE analysis_id = %d";
             "ORDER BY analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$results = db_query($sql,$analysis_id);
		db_set_active($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++;
	}

	$interval = intval($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));
		}
		tripal_feature_sync_feature ($feature_id);
		$i++;
	}
}
/*******************************************************************************
 *
 */
function tripal_analysis_taxonify_features ($analysis_id = NULL, $job_id = NULL){
	$i = 0;

	// if the caller provided a analysis_id then get all of the features
	// associated with the analysis. Otherwise get all sequences assoicated
	// with all libraries.
	if(!$analysis_id){
		$sql = "SELECT Analysis_id, Feature_id ".
          "FROM {Analysisfeature} ".
          "ORDER BY analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$results = db_query($sql);
		db_set_active($previous_db);  // now use drupal database
	} else {
		$sql = "SELECT Analysis_id, Feature_id ".
             "FROM {Analysisfeature} ".
             "WHERE analysis_id = %d";
             "ORDER BY analysis_id";
		$previous_db = db_set_active('chado');  // use chado database
		$results = db_query($sql,$analysis_id);
		db_set_active($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();

	// use this SQL for getting the nodes
	$nsql =  "SELECT * FROM {chado_feature} CF ".
            "  INNER JOIN {node} N ON N.nid = CF.nid ".
            "WHERE feature_id = %d";

	// iterate through the features and set the taxonomy
	$interval = intval($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));
		}
		$node = db_fetch_object(db_query($nsql,$feature_id));
		tripal_feature_set_taxonomy($node,$feature_id);
		$i++;
	}
}