modify template and validator to new structure of the dosuments

the documents have not any longer fields:

gene.full_score
gene.evalue
gene.best_domain_score
gene.best_domain_evalue
gene.c_value
gene.coverage_profile

but there are now new fields:

replicon.ncbi_id
gene.score
gene.i_evalue
gene.coverage

src/couchapp/secreton/templates/secretion_system.html

@@ -269,10 +269,12 @@
 	<h2>Replicon</h2>
 	<ul>
 		{{#replicon}}
+		<li>name: {{name}}</li>
+		<li>ncbi_id: {{ncbi_id}}</li>
 		<li>taxid: {{taxid}}</li>
+		<li>strain: {{strain}}</li>
 		<li>taxonomy: {{taxonomy}}</li>
-		<li>type: {{type}}</li> 
-		<li>name: {{name}}</li>
+		<li>type: {{type}}</li>
 		{{/replicon}}
 	</ul>
 	
@@ -291,12 +293,9 @@
 				<th>Begin</th>
 				<th>End</th>
 				<th>Match</th>
-				<th>Full-score</th>
-				<th>Evalue</th>
-				<th>Best-domain-score</th>
-				<th>Best-domain-evalue</th>
-				<th>c-Evalue</th>
-				<th>Coverage-profile</th>
+				<th>Score</th>
+				<th>i-evalue</th>
+				<th>Coverage</th>
 				<th>Match-begin</th>
 				<th>Match-end</th>
 				<th>Gene-name</th>
@@ -313,12 +312,9 @@
 				<td>{{begin}}</td>
 				<td>{{end}}</td>
 				<td>{{match}}</td>
-				<td>{{full_score}}</td>
-				<td>{{e_value}}</td>
-				<td>{{best_domain_score}}</td>
-				<td>{{best_domain_evalue}}</td>
-				<td>{{c_value}}</td>
-				<td>{{coverage_profile}}</td>
+				<td>{{score}}</td>
+				<td>{{i_evalue}}</td>
+				<td>{{coverage}}</td>
 				<td>{{match_begin}}</td>
 				<td>{{match_end}}</td>
 				<td>{{name}}</td>

src/couchapp/secreton/validate_doc_update.js

@@ -5,11 +5,15 @@ function(newDoc, oldDoc, userCtx, secObj) {
       } else {
     	  if (!newDoc.code) throw({forbidden : "Secretion system must have a code"});
     	  if (!newDoc.genes) throw({forbidden : "Secretion system must have a genes"});
-    	  if (!newDoc.T3SS_family) throw({forbidden : "Secretion system must have a T3SS_family"});
+    	  if (!newDoc.predicted_system) throw({forbidden : "Secretion system must have a predicted system"});
+    	  if (!newDoc.system_status) throw({forbidden : "Secretion system must have a system_status"});
     	  if (!newDoc.replicon) throw({forbidden : "Secretion system must have a replicon"});
+    	  if (!newDoc.replicon.name) throw({forbidden : "Replicon must have a name"});
+    	  if (!newDoc.replicon.ncbi_id) throw({forbidden : "Replicon must have a ncbi_id"});
+    	  if (!newDoc.replicon.taxid) throw({forbidden : "Replicon must have a taxid"});
     	  if (!newDoc.replicon.strain) throw({forbidden : "Replicon must have a strain"});
+    	  if (!newDoc.replicon.taxonomy) throw({forbidden : "Replicon must have a taxonomy"});
     	  if (!newDoc.replicon.type) throw({forbidden : "Replicon must have a type"});
-    	  if (!newDoc.replicon.name) throw({forbidden : "Replicon must have a name"});
       }
 }