The syncing method now tries to figure out what type of analysis is being synchronized by checking the cvterm "analysis_type". This cvterm should be added to each analysis by the individual analysis modules or the user if the upload is directly into chado. The value for this cvterm should reflect the name of the module, "tripal_analysis_unigene", "tripal_analysis_blast", etc.

tripal_analysis/tripal_analysis.module

@@ -369,6 +369,12 @@ function chado_analysis_load($node){
              "WHERE Analysis_id = $ana_node->analysis_id";
 		$previous_db = db_set_active('chado');  // use chado database
 		$additions = db_fetch_object(db_query($sql));
+        // get number of features assc with this analysis
+        $sql = "SELECT count(feature_id) as featurecount ".
+             "FROM {Analysisfeature} ".
+             "WHERE Analysis_id = %d";
+        $additions->featurecount = db_result(db_query($sql, $ana_node->analysis_id));
+
 		db_set_active($previous_db);  // now use drupal database
 	}
 	// If the analysis has a name, use it as the node title. If not, construct
@@ -410,7 +416,7 @@ function chado_analysis_view ($node, $teaser = FALSE, $page = FALSE) {
 function tripal_analysis_sync_analyses ($analysis_id = NULL, $job_id = NULL){
 	global $user;
 	$page_content = '';
-
+    
 	if(!$analysis_id){
 		$sql = "SELECT Analysis_id, name AS analysisname, description, program, ".
    		 "  programversion, algorithm, sourcename, sourceversion, sourceuri, ".
@@ -430,10 +436,6 @@ function tripal_analysis_sync_analyses ($analysis_id = NULL, $job_id = NULL){
 		db_set_active($previous_db);  // now use drupal database
 	}
 
-    ##REMOVE 
-    print "results:\n";
-    print $results;
-    print "\n";
 
 	// We'll use the following SQL statement for checking if the analysis
 	// already exists as a drupal node.
@@ -441,40 +443,43 @@ function tripal_analysis_sync_analyses ($analysis_id = NULL, $job_id = NULL){
           "WHERE analysis_id = %d";
 
 	while($analysis = db_fetch_object($results)){
+        print "syncing analysis ";
+        print $analysis->analysisname;
+        print ", ";
+        print $analysis->analysis_id;
+        print "\n";
+
 		// check if this analysis already exists in the drupal database. if it
 		// does then skip this analysis and go to the next one.
 		if(!db_fetch_object(db_query($sql,$analysis->analysis_id))){
-			
+
 			$new_node = new stdClass();
         
-			// try to access analysisprop for this analysis
-			$sql = "SELECT * FROM {analysisprop} WHERE analysis_id = %d";
+			// try to access analysis type for this analysis
+			$sql = "SELECT * FROM {analysisprop} 
+                    WHERE analysis_id = %d 
+                    AND type_id =  
+                        (SELECT cvterm_id from {cvterm} where name = '%s')
+            ";
 			$previous_db = db_set_active('chado');
-			$analysisprop = db_fetch_object(db_query($sql, $analysis->analysis_id));
+			$analysis_type = db_fetch_object(db_query($sql, $analysis->analysis_id, "analysis_type"));
 			db_set_active($previous_db);
 
 			// Get the type of analysis using cvterm_id
             // Current possibilities: kegg, unigene, interpro, blast
-			if ($analysisprop) {
-
-				$sql = "SELECT name, definition FROM {cvterm} WHERE cvterm_id = %d";
-			    $previous_db = db_set_active('chado');
-				$result = db_fetch_object(db_query($sql, $analysisprop->type_id));
-			    db_set_active($previous_db);
+			if ($analysis_type) {
 
 				// This is a unigene analysis
-				if ($result->name == 'analysis_unigene_settings') {
-					$new_node->type = 'chado_unigene_blast';
+				if ($analysis_type->value == 'tripal_analysis_unigene') {
+					$new_node->type = 'chado_analysis_unigene';
 				// This is a blast analysis
-				} else if ($result->name == 'analysis_blast_settings') {
+				} else if ($result->name == 'tripal_analysis_blast') {
 					$new_node->type = 'chado_analysis_blast';
 			   // This is a interpro analysis
-				} else if ($result->name == 'analysis_interpro_settings') {
+				} else if ($result->name == 'tripal_analysis_interpro') {
 					$new_node->type = 'chado_analysis_interpro';
 			   // This is a kegg analysis
-				} else if ($result->name == 'analysis_kegg_settings' ||
-	              		  $result->name == 'kegg_brite_data' ||
-				           preg_match("/KEGG BRITE term:/", $result->definition)) {
+				} else if ($result->name == 'tripal_analysis_kegg' ){
 				   $new_node->type = 'chado_analysis_kegg';
 				} else {
 				   $new_node->type = 'chado_analysis';
@@ -484,6 +489,8 @@ function tripal_analysis_sync_analyses ($analysis_id = NULL, $job_id = NULL){
 				$new_node->type = 'chado_analysis';
 			}
 
+            print "analysis type is $new_node->type\n";
+
 			$new_node->uid = $user->uid;
 			$new_node->analysis_id = $analysis->analysis_id;
 			$new_node->analysisname = $analysis->analysisname;
@@ -607,6 +614,7 @@ function tripal_analysis_theme () {
  * 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) {
@@ -634,6 +642,7 @@ function get_chado_analyses() {
 
 		//Sort analyses by time, descending order
 		krsort($analyses, SORT_STRING);
+
 		return $analyses;
 	}
 }