Initial import of version 0.2

tripal_analysis/tripal_analysis.admin.inc

@@ -0,0 +1,384 @@
+<?php
+//
+// Copyright 2009 Clemson University
+//
+
+/*******************************************************************************
+ * Administration page callbacks for the Tripal Analysis module
+ * We have defined a hook_get_settings() function. When a sub-module
+ * is enabled, we'll look for this function to provide a form for the
+ * administrative setting.
+ */
+function tripal_analysis_admin() {
+	// Create a new administrative form. We'll add main functions to the form
+	// first (Sync, Reindex, Clean, Taxonify). Thereafter, any sub-module that
+	// has a setting will be added.
+	$form = array();
+
+	// before proceeding check to see if we have any
+	// currently processing jobs. If so, we don't want
+	// to give the opportunity to sync libraries
+	$active_jobs = FALSE;
+	if(tripal_get_module_active_jobs('tripal_organism')){
+		$active_jobs = TRUE;
+	}
+
+	// add the field set for syncing libraries
+	if(!$active_jobs){
+		// add the field set for syncing analyses
+		get_tripal_analysis_admin_form_sync_set($form);
+		get_tripal_analysis_admin_form_reindex_set($form);
+		get_tripal_analysis_admin_form_taxonomy_set($form);
+		get_tripal_analysis_admin_form_cleanup_set($form);
+	} else {
+		$form['notice'] = array(
+		   '#type' => 'fieldset',
+		   '#title' => t('Analysis Management Temporarily Unavailable')
+		);
+		$form['notice']['message'] = array(
+          '#value' => t('Currently, analysis management jobs are waiting or are running. . Managemment features have been hidden until these jobs complete.  Please check back later once these jobs have finished.  You can view the status of pending jobs in the Tripal jobs page.'),
+		);
+	}
+
+	// Add sub-module settings. Pull all sub-module information from
+	// {tripal_analysis} table
+	$sql = "SELECT modulename FROM {tripal_analysis}";
+	$result = db_query($sql);
+	$counter = 0;  //keep track of the number of sub-modules
+	while ($data = db_fetch_object($result)) {
+
+		// Check if the hook_get_settings() function is already defined.
+		$func = $data->modulename."_get_settings";
+		$functions = get_defined_functions();
+		$settings;
+		foreach($functions['user'] as $function) {
+			if ($function == $func) {
+				$settings = $func();
+			}
+		}
+		
+		// Add sub-module's specific settings to the administrative view
+		if ($settings) {
+			// Define a fieldset for the sub-module
+			$form["field$counter"] = array(
+            '#type' => 'fieldset',
+            '#title' => "$settings->title",
+            '#collapsible' => TRUE
+			);
+			$form["field$counter"]["$settings->title"] = $settings->form;
+		}
+		$counter ++;
+	}
+	return system_settings_form($form);
+}
+
+/************************************************************************
+ *
+ */
+function get_tripal_analysis_admin_form_taxonomy_set(&$form) {
+	$form['taxonify'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Assign Drupal Taxonomy to Analysis Features')
+	);
+
+	// get the list of analyses
+	$sql = "SELECT * FROM {Analysis} ORDER BY name";
+	$previous_db = db_set_active('chado');  // use chado database
+	$lib_rset = db_query($sql);
+	db_set_active($previous_db);  // now use drupal database
+
+	// iterate through all of the libraries
+	$lib_boxes = array();
+	while($analysis = db_fetch_object($lib_rset)){
+		$lib_boxes[$analysis->analysis_id] = "$analysis->name";
+	}
+
+	$form['taxonify']['description'] = array(
+       '#type' => 'item',
+       '#value' => t("Drupal allows for assignment of \"taxonomy\" or catagorical terms to " .
+          "nodes. These terms allow for advanced filtering during searching. This option allows ".
+          "for setting taxonomy only for features that belong to the selected analyses below.  All other features will be unaffected.  To set taxonomy for all features in the site see the Feature Administration page."),
+		 '#weight' => 1,
+	);
+
+	$form['taxonify']['tx-analyses'] = array (
+     '#title'       => t('Analyses'),
+     '#type'        => t('checkboxes'),
+     '#description' => t("Check the analyses whose features you want to reset taxonomy.  Note: this list contains all analyses, even those that may not be synced."),
+     '#required'    => FALSE,
+     '#prefix'      => '<div id="lib_boxes">',
+     '#suffix'      => '</div>',
+     '#options'     => $lib_boxes,
+     '#weight'      => 2
+	);
+	$form['taxonify']['tx-button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Set Feature Taxonomy'),
+      '#weight'      => 3
+	);
+}
+/************************************************************************
+ *
+ */
+function get_tripal_analysis_admin_form_reindex_set(&$form) {
+	// define the fieldsets
+	$form['reindex'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Reindex Analysis Features')
+	);
+
+	// get the list of libraries
+	$sql = "SELECT * FROM {Analysis} ORDER BY name";
+	$previous_db = db_set_active('chado');  // use chado database
+	$lib_rset = db_query($sql);
+	db_set_active($previous_db);  // now use drupal database
+
+	// iterate through all of the libraries
+	$lib_boxes = array();
+	while($analysis = db_fetch_object($lib_rset)){
+		$lib_boxes[$analysis->analysis_id] = "$analysis->name";
+	}
+	$form['reindex']['description'] = array(
+       '#type' => 'item',
+       '#value' => t("This option allows for reindexing of only those features that belong to the selected analyses below. All other features will be unaffected.  To reindex all features in the site see the Feature Administration page."),
+		 '#weight' => 1,
+	);
+
+	$form['reindex']['re-analyses'] = array (
+     '#title'       => t('Libraries'),
+     '#type'        => t('checkboxes'),
+     '#description' => t("Check the analyses whoee features you want to reindex. Note: this list contains all analyses, even those that may not be synced."),
+     '#required'    => FALSE,
+     '#prefix'      => '<div id="lib_boxes">',
+     '#suffix'      => '</div>',
+     '#options'     => $lib_boxes,
+     '#weight' => 2,
+	);
+	$form['reindex']['re-button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Reindex Features'),
+      '#weight' => 3,
+	);
+}
+/************************************************************************
+ *
+ */
+function get_tripal_analysis_admin_form_cleanup_set(&$form) {
+	$form['cleanup'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Clean Up')
+	);
+	$form['cleanup']['description'] = array(
+       '#type' => 'item',
+       '#value' => t("With Drupal and chado residing in different databases ".
+          "it is possible that nodes in Drupal and analyses in Chado become ".
+          "\"orphaned\".  This can occur if an analysis node in Drupal is ".
+          "deleted but the corresponding chado analysis is not and/or vice ".
+          "versa. Click the button below to resolve these discrepancies."),
+       '#weight' => 1,
+	);
+	$form['cleanup']['button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Clean up orphaned analyses'),
+      '#weight' => 2,
+	);
+}
+/************************************************************************
+ *
+ */
+function get_tripal_analysis_admin_form_sync_set (&$form) {
+	// define the fieldsets
+	$form['sync'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Sync Analyses')
+	);
+
+	// before proceeding check to see if we have any
+	// currently processing jobs. If so, we don't want
+	// to give the opportunity to sync analyses
+	$active_jobs = FALSE;
+	if(tripal_get_module_active_jobs('tripal_analysis')){
+		$active_jobs = TRUE;
+	}
+
+	if(!$active_jobs){
+			
+		// get the list of analyses
+		$sql = "SELECT * FROM {analysis} ORDER BY name";
+		$previous_db = db_set_active('chado');  // use chado database
+		$ana_rset = db_query($sql);
+		db_set_active($previous_db);  // now use drupal database
+			
+		// if we've added any analyses to the list that can be synced
+		// then we want to build the form components to allow the user
+		// to select one or all of them.  Otherwise, just present
+		// a message stating that all analyses are currently synced.
+		$ana_boxes = array();
+		$added = 0;
+		while($analysis = db_fetch_object($ana_rset)){
+			// check to see if the analysis is already present as a node in drupal.
+			// if so, then skip it.
+			$sql = "SELECT * FROM {chado_analysis} WHERE analysis_id = %d";
+			if(!db_fetch_object(db_query($sql,$analysis->analysis_id))){
+				$ana_boxes[$analysis->analysis_id] = "$analysis->name";
+				$added++;
+			}
+		}
+
+		// if we have analyses we need to add to the checkbox then
+		// build that form element
+		if($added > 0){
+			$ana_boxes['all'] = "All analyses";
+
+			$form['sync']['analyses'] = array (
+           '#title'       => t('Available analyses'),
+           '#type'        => t('checkboxes'),
+           '#description' => t("Check the analyses you want to sync.  Drupal ".
+              "content will be created for each of the analyses listed above. ".
+              "Select 'All analyses' to sync all of them."),
+           '#required'    => FALSE,
+           '#prefix'      => '<div id="ana_boxes">',
+           '#suffix'      => '</div>',
+           '#options'     => $ana_boxes,
+			);
+			$form['sync']['button'] = array(
+            '#type' => 'submit',
+            '#value' => t('Submit Sync Job')
+			);
+		}
+		// we don't have any analyses to select from
+		else {
+			$form['sync']['value'] = array(
+            '#value' => t('All analyses in Chado are currently synced with Drupal.')
+			);
+		}
+	}
+	// we don't want to present a form since we have an active job running
+	else {
+		$form['sync']['value'] = array(
+          '#value' => t('Currently, jobs exist related to chado analyses. Please check back later for analyses that can by synced once these jobs have finished.  You can view the status of pending jobs in the Tripal jobs page.')
+		);
+	}
+}
+/************************************************************************
+ *
+ */
+function tripal_analysis_admin_validate($form, &$form_state) {
+	global $user;  // we need access to the user info
+	$job_args = array();
+
+	if ($form_state['values']['op'] == t('Submit Sync Job')) {
+
+		// check to see if the user wants to sync chado and drupal.  If
+		// so then we need to register a job to do so with tripal
+		$analyses = $form_state['values']['analyses'];
+		$do_all = FALSE;
+		$to_sync = array();
+
+		foreach ($analyses as $analysis_id){
+			if(preg_match("/^all$/i",$analysis_id)){
+				$do_all = TRUE;
+			}
+			if($analysis_id and preg_match("/^\d+$/i",$analysis_id)){
+				// get the list of analyses
+				$sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
+				$previous_db = db_set_active('chado');  // use chado database
+				$analysis = db_fetch_object(db_query($sql,$analysis_id));
+				db_set_active($previous_db);  // now use drupal database
+				$to_sync[$analysis_id] = $analysis->name;
+			}
+		}
+
+		// submit the job the tripal job manager
+		if($do_all){
+			tripal_add_job('Sync all analyses','tripal_analysis','tripal_analysis_sync_analyses',$job_args,$user->uid);
+		}
+		else{
+			foreach($to_sync as $analysis_id => $name){
+				$job_args[0] = $analysis_id;
+				tripal_add_job("Sync analysis: $name",'tripal_analysis','tripal_analysis_sync_analyses',$job_args,$user->uid);
+			}
+		}
+	}
+	// -------------------------------------
+	// Submit the Reindex Job if selected
+	if ($form_state['values']['op'] == t('Reindex Features')) {
+		global $user;  // we need access to the user info
+		$job_args = array();
+		$analyses = $form_state['values']['re-analyses'];
+		foreach ($analyses as $analysis_id){
+			if($analysis_id and preg_match("/^\d+$/i",$analysis_id)){
+				// get the analysis info
+				$sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
+				$previous_db = db_set_active('chado');  // use chado database
+				$analysis = db_fetch_object(db_query($sql,$analysis_id));
+				db_set_active($previous_db);  // now use drupal database
+				$job_args[0] = $analysis_id;
+				tripal_add_job("Reindex features for analysis: $analysis->name",'tripal_analysis',
+             'tripal_analysis_reindex_features',$job_args,$user->uid);
+			}
+		}
+	}
+
+	// -------------------------------------
+	// Submit the Taxonomy Job if selected
+	if ($form_state['values']['op'] == t('Set Feature Taxonomy')) {
+		global $user;  // we need access to the user info
+		$job_args = array();
+		$analyses = $form_state['values']['tx-analyses'];
+		foreach ($analyses as $analysis_id){
+			if($analysis_id and preg_match("/^\d+$/i",$analysis_id)){
+				// get the analysis info
+				$sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
+				$previous_db = db_set_active('chado');  // use chado database
+				$analysis = db_fetch_object(db_query($sql,$analysis_id));
+				db_set_active($previous_db);  // now use drupal database
+				$job_args[0] = $analysis_id;
+				tripal_add_job("Set taxonomy for features in analysis: $analysis->name",'tripal_analysis',
+             'tripal_analysis_taxonify_features',$job_args,$user->uid);
+			}
+		}
+	}
+
+	// -------------------------------------
+	// Submit the Cleanup Job if selected
+	if ($form_state['values']['op'] == t('Clean up orphaned analyses')) {
+		tripal_add_job('Cleanup orphaned analyses','tripal_analysis',
+         'tripal_analyses_cleanup',$job_args,$user->uid);
+	}
+
+	// -------------------------------------
+	// Save blast regular expression settings
+	if ($form_state['values']['op'] == t('Save settings')) {
+		$db_id = $form_state['values']['blastdb'];
+		$name = $form_state['values']['displayname'];
+		$gbstyle = $form_state['values']['gb_style_parser'];
+		$reg1 = $form_state['values']['hit_id'];
+		$reg2 = $form_state['values']['hit_def'];
+		$reg3 = $form_state['values']['hit_accession'];
+		
+		// Check if the blast settings exists
+		
+		$sql = "SELECT db_id FROM {tripal_analysis_blast} WHERE db_id=%d";
+		$check = db_result(db_query($sql, $db_id));
+
+		// If setting exists, update it
+		if ($check) {
+			$sql = "UPDATE {tripal_analysis_blast} ".
+   	          "SET displayname = '%s', ".
+   	          "    regex_hit_id = '%s', ".
+   	          "    regex_hit_def = '%s', ".
+   	          "    regex_hit_accession = '%s', ".
+			       "    genbank_style = %d ".
+   	          "WHERE db_id=%d";
+			db_query($sql, $name, $reg1, $reg2, $reg3, $gbstyle, $db_id);
+			// Otherwise, insert a new setting for the db
+		} else {
+			$sql = "INSERT INTO {tripal_analysis_blast} (db_id, displayname, ".
+   		       "           regex_hit_id, regex_hit_def, regex_hit_accession, genbank_style) ".
+   		       "VALUES (%d, '%s', '%s', '%s', '%s', %d) ";
+			db_query($sql, $db_id, $name, $reg1, $reg2, $reg3, $gbstyle);
+		}
+	}
+}
+

tripal_analysis/tripal_analysis.info

@@ -0,0 +1,9 @@
+; $Id:
+name = Tripal Analysis
+description = A module that controls the display of all analysis sub-modules. This module also interfaces the GMOD chado database with Drupal, providing viewing, inserting and editing of chado analyses.
+core = 6.x
+project = tripal_analysis
+package = Tripal
+version = 6.x-0.2b-m0.2
+dependencies[] = tripal_core
+dependencies[] = tripal_feature

tripal_analysis/tripal_analysis.install

@@ -0,0 +1,127 @@
+<?php
+//$Id:
+
+/*******************************************************************************
+ * Implementation of hook_install().
+ */
+function tripal_analysis_install() {
+
+	// create the module's data directory
+	tripal_create_moddir('tripal_analysis');
+
+	// Use schema API to create database table.
+	drupal_install_schema('tripal_analysis');
+	
+	// Create analysisfeatureprop table in chado. This cannot be accomplished
+	// by calling drupal_install_schema because it's not in the drupal db. This
+	// table is used to store Blast xml and Interpro html/goterms
+	$previous_db = db_set_active('chado');
+	if (!db_table_exists('analysisfeatureprop')) {
+	   $sql = "CREATE TABLE {analysisfeatureprop} (".
+	          "  analysisfeatureprop_id SERIAL PRIMARY KEY, ".
+	          "  analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, ".
+	          "  type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, ".
+	          "  value TEXT, ".
+	          "  rank INTEGER NOT NULL, ".
+	          "  CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)".
+	          ")";
+	   db_query($sql);
+	}
+	db_set_active($previous_db);
+
+   tripal_add_cvterms('analysis_type','The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go).');
+	tripal_add_cvterms('analysis_date','The date that an analysis was performed.');
+	tripal_add_cvterms('analysis_short_name','A computer legible (no spaces '.
+      'or special characters) abbreviation for the analysis.');
+}
+
+/*******************************************************************************
+ * Implementation of hook_uninstall().
+ */
+function tripal_analysis_uninstall() {
+	// Use schema API to delete database table.
+	drupal_uninstall_schema('tripal_analysis');
+	// Remove analysis nodes from drupal.
+	$sql_ana_id = "SELECT nid, vid ".
+                 "FROM {node} ".
+                 "WHERE type like 'chado_analysi%'";
+	$result = db_query($sql_ana_id);
+	while ($ana = db_fetch_object($result)) {
+		node_delete($ana->nid);
+	}
+}
+
+/*******************************************************************************
+ * Implementation of hook_schema() creates two tables. chado_analysis table
+ * stores nodes that are also saved in the analysis table of chado database.
+ * tripal_analysis table stores the sub-module names, such as
+ * tripal_analysis_blast, that are registered with this module.
+ */
+function tripal_analysis_schema() {
+	// chado_analysis table
+	$schema['chado_analysis'] = array(
+      'fields' => array(
+         'vid' => array(
+            'type' => 'int',
+            'unsigned' => TRUE,
+            'not null' => TRUE,
+            'default' => 0
+	),
+         'nid' => array(
+            'type' => 'int',
+            'unsigned' => TRUE,
+            'not null' => TRUE,
+            'default' => 0
+	),
+         'analysis_id' => array(
+            'type' => 'int',
+            'not null' => TRUE,
+            'default' => 0
+	)
+	),
+      'indexes' => array(
+         'analysis_id' => array('analysis_id')
+	),
+      'unique keys' => array(
+         'nid_vid' => array('nid','vid'),
+         'vid' => array('vid')
+	),
+      'primary key' => array('nid'),
+	);
+
+	// tripal_analysis table
+	$schema['tripal_analysis'] = array(
+      'description' => t('Table to store analysis sub-modules'),
+      'fields' => array(
+         'modulename' => array(
+            'type' => 'text',
+            'size' => 'small',
+            'not null' => TRUE,
+            'description' => t('The module name. Tripal Analysis will use the '.
+                               'module name to call module_setting_form()')
+	)
+	),
+      'unique keys' => array(
+         'modulename' => array('modulename')
+	)
+	);
+	return $schema;
+}
+
+/*******************************************************************************
+ * Implementation of hook_requirements(). Make sure 'Tripal Core' is enabled
+ * before installation
+ */
+function tripal_analysis_requirements($phase) {
+   $requirements = array();
+   if ($phase == 'install') {
+      if (!function_exists('tripal_create_moddir')) {
+         $requirements ['tripal_analysis'] = array(
+            'title' => "tripal_analysis",
+            'value' => "error. Some required modules are just being installed. Please try again.",
+            'severity' => REQUIREMENT_ERROR,
+         );
+      }
+   }
+   return $requirements;
+}

tripal_analysis/tripal_analysis.module

@@ -0,0 +1,837 @@
+<?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_table', $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_table' => 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 $analyses;
+	}
+}
+/************************************************************************
+ *
+ */
+function theme_tripal_analysis_analysis_table (&$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++;
+	}
+}