bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.13 to 0.0.14

lib/edit.js

@@ -1113,3 +1113,3 @@ /**
  */
-noctua_graph.prototype.load_data_base = function(data){
+noctua_graph.prototype.load_data_basic = function(data){
     var anchor = this;
@@ -1151,5 +1151,4 @@
 /**
- * Load minerva data response. However, this time, we're going to fold
- * the evidence individuals into the edges and nodes that reference
- * them under the referenced_individual functions.
+ * Fold the evidence individuals into the edges and nodes that
+ * reference them under the referenced_individual functions.
  *
@@ -1164,3 +1163,3 @@ * Currently, a single pass is run to fold evidence individuals into
  */
-noctua_graph.prototype.load_data_fold_evidence = function(data){
+noctua_graph.prototype.fold_evidence = function(){
     var anchor = this;
@@ -1170,96 +1169,67 @@
 
-    if( data ){
-	
-	// Load the graph parts as usual.
-	var graph_id = data['id'] || null;
-	var graph_anns = data['annotations'] || [];
-	if( graph_id ){ anchor.id(graph_id); }
-	if( ! us.isEmpty(graph_anns) ){
-	    each(graph_anns, function(ann_kv_set){
-		var na = new annotation(ann_kv_set);
-		anchor.add_annotation(na);
-	    });
-	}
+    // Find the evidence singletons for future lookup.
+    var singletons = {};
+    each(anchor.get_singleton_nodes(), function(singleton){
+	var sid = singleton.id();
+	singletons[sid] = singleton;
+    });
 
-	// Currently, evidence does not have edges, and if they did,
-	// we wouldn't want to handle them here. All edges in.
-	var facts = data['facts'];
-	each(facts, function(fact){
-	    anchor.add_edge_from_fact(fact);
-	});
+    //console.log('singletons');
+    //console.log(us.keys(singletons).length);
 
-	// Start by adding all of the individuals to the graph.
-	var inds = data['individuals'];
-	each(inds, function(ind){
-	    anchor.add_node_from_individual(ind);
-	});
-
-	// Find the evidence singletons for future lookup.
-	var singletons = {};
-	each(anchor.get_singleton_nodes(), function(singleton){
-	    var sid = singleton.id();
-	    singletons[sid] = singleton;
-	});
-
-	//console.log('singletons');
-	//console.log(us.keys(singletons).length);
-
-	// Take and, and see if it is an evidence reference.
-	function is_iri_ev_p(ann){
-	    var ret = false;
-	    if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
-		ret = true;
-	    }
-	    return ret;
+    // Take and, and see if it is an evidence reference.
+    function is_iri_ev_p(ann){
+	var ret = false;
+	if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
+	    ret = true;
 	}
+	return ret;
+    }
 
-	// For any node, look at all of the annotations, and fold in
-	// ones that 1) pass the test and 2) reference a singleton
-	// node.
-	function fold_in_reference(node, test_p){
-	    each(node.annotations(), function(ann){
-
-		//console.log(ann.key(), ann.value_type(), ann.value());
-		
-		// Is it an evidence annotation.
-		//if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
-		if( test_p(ann) ){
-		    // If so, and the individual in question is a
-		    // singleton (if not, we don't fold it).
-		    var ref_node_id = ann.value();
-		    if( singletons[ref_node_id] ){
-			
-			// Remove node from the graph.
-			anchor.remove_node(ref_node_id);
-
-			// Add as referenced individual.
-			var ev_indiv = singletons[ref_node_id];
-			var c1 = node.add_referenced_individual(ev_indiv);
-			//console.log('<<' + node.id() + '>1>', c1.length);
-			//var c2 = node.referenced_individuals();
-			//console.log('<<' + node.id() + '>2>', c2.length);
-			//			console.log(node)
-		    }
+    // For any node, look at all of the annotations, and fold in
+    // ones that 1) pass the test and 2) reference a singleton
+    // node.
+    function fold_in_reference(node, test_p){
+	each(node.annotations(), function(ann){
+	    
+	    //console.log(ann.key(), ann.value_type(), ann.value());
+	    
+	    // Is it an evidence annotation.
+	    //if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
+	    if( test_p(ann) ){
+		// If so, and the individual in question is a
+		// singleton (if not, we don't fold it).
+		var ref_node_id = ann.value();
+		if( singletons[ref_node_id] ){
+		    
+		    // Remove node from the graph.
+		    anchor.remove_node(ref_node_id);
+		    
+		    // Add as referenced individual.
+		    var ev_indiv = singletons[ref_node_id];
+		    var c1 = node.add_referenced_individual(ev_indiv);
+		    //console.log('<<' + node.id() + '>1>', c1.length);
+		    //var c2 = node.referenced_individuals();
+		    //console.log('<<' + node.id() + '>2>', c2.length);
+		    //			console.log(node)
 		}
-	    });
-	}
-
-	// Add the evidence singletons into the structure by
-	// scanning through the nodes and adding them as referenced
-	// individuals.
-	each(anchor.all_nodes(), function(node){
-	    fold_in_reference(node, is_iri_ev_p);
+	    }
 	});
+    }
+    
+    // Add the evidence singletons into the structure by
+    // scanning through the nodes and adding them as referenced
+    // individuals.
+    each(anchor.all_nodes(), function(node){
+	fold_in_reference(node, is_iri_ev_p);
+    });
+    
+    // We also need to do the same thing with the edges, adding
+    // back in the evidence as referenced individuals.
+    each(anchor.all_edges(), function(edge){
+	fold_in_reference(edge, is_iri_ev_p);
+    });
+    
+    ret = true;
 
-	// We also need to do the same thing with the edges, adding
-	// back in the evidence as referenced individuals.
-	each(anchor.all_edges(), function(edge){
-	    fold_in_reference(edge, is_iri_ev_p);
-	});
-
-	ret = true;
-    }	
-
-    //    console.log(anchor);
-
     return ret;
@@ -1269,8 +1239,7 @@ };
 /**
- * Load minerva data response. However, this time, in addition to
- * everything we did for {load_data_evidence_fold}, we're going to
- * search for nodes that have enabled_by and/or occurs_in (or any
- * other specified relation) targets (that are themselves leaves) fold
- * them in to the contained subgraph item, and remove them from the
- * top-level graph.
+ * In addition to everything we did for {load_data_evidence_fold},
+ * we're going to search for nodes that have enabled_by and/or
+ * occurs_in (or any other specified relation) targets (that are
+ * themselves leaves) fold them in to the contained subgraph item, and
+ * remove them from the top-level graph.
  *
@@ -1283,7 +1252,7 @@ * TODO: inferred individuals
  */
-noctua_graph.prototype.load_data_go_noctua = function(data, relation_list){
+noctua_graph.prototype.fold_go_noctua = function(relation_list){
     var anchor = this;
 
     // Start out with the evidence folded graph.
-    var ret = anchor.load_data_fold_evidence(data);
+    var ret = anchor.fold_evidence();
     if( ! ret ){ return false; } // Early bail on bad upstream.
@@ -1290,0 +1259,0 @@

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.13",
+    "version": "0.0.14",
     "license": "BSD-3-Clause",
@@ -5,0 +5,0 @@ "description": "A subclass of bbop-graph that layers on a complete annotation and graph editing model for the Noctua set of tools.",

tests/noctua-basic.tests.js

@@ -115,3 +115,3 @@ ////
 	var g = new model.graph();
-	g.load_data_base(raw_resp['data']);
+	g.load_data_basic(raw_resp['data']);
 
@@ -128,3 +128,3 @@ // Right?
 	var g = new model.graph();
-	g.load_data_base(raw_resp['data']);
+	g.load_data_basic(raw_resp['data']);
 
@@ -153,3 +153,3 @@ assert.equal(g.id(),'gomodel:taxon_559292-5525a0fc0000001_all_indivdual',
 	var g = new model.graph();
-	g.load_data_base(raw_resp['data']);
+	g.load_data_basic(raw_resp['data']);
 	
@@ -189,3 +189,4 @@ // Head up from our one leaf
 	var g = new model.graph();
-	g.load_data_fold_evidence(raw_resp['data']);
+	g.load_data_basic(raw_resp['data']);
+	g.fold_evidence();
 	
@@ -238,3 +239,4 @@ // Okay, we should have a lot less nodes now.
 	var g_new = new model.graph();
-	g_new.load_data_fold_evidence(raw_resp['data']);	
+	g_new.load_data_basic(raw_resp['data']);	
+	g_new.fold_evidence();
 
@@ -264,3 +266,4 @@ // Empty g_base should now essentially be g_new.
 	var rellist = ['RO:0002333', 'BFO:0000066'];
-	g.load_data_go_noctua(raw_resp['data'], rellist);
+	g.load_data_basic(raw_resp['data']);
+	g.fold_go_noctua(rellist);
 
@@ -311,3 +314,4 @@ // Basic structure count.
 	var rellist = ['RO:0002333', 'BFO:0000066'];
-	g.load_data_go_noctua(raw_resp['data'], rellist);
+	g.load_data_basic(raw_resp['data']);
+	g.fold_go_noctua(rellist);
 
@@ -340,3 +344,4 @@ var nid = 'gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023';
 	var rellist = ['RO:0002333', 'BFO:0000066'];
-	g.load_data_go_noctua(raw_resp['data'], rellist);
+	g.load_data_basic(raw_resp['data']);
+	g.fold_go_noctua(rellist);
 
@@ -343,0 +348,0 @@ // Make a new graph to operate on.

No alert changes

Worsened metrics

Total package byte prevSize

6333147

decreased by-0.01%

Lines of code

27066

decreased by-0.08%

No dependency changes