bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.12 to 0.0.13

lib/edit.js

@@ -1154,3 +1154,6 @@ /**
  *
- * TODO: inferred individuals
+ * Currently, a single pass is run to fold evidence individuals into
+ * other nodes as referenced individuals. However, additional passes
+ * can very easily be added to fold away references to references as
+ * long as a matching function is provided.
  *
@@ -1201,6 +1204,15 @@ * @param {Object} the "data" portion of a Minerva graph-related response.
 
-	// Add the evidence singletons into the structure by
-	// scanning through the nodes and adding them as referenced
-	// individuals.
-	each(anchor.all_nodes(), function(node){
+	// 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){
@@ -1211,13 +1223,14 @@
 		// Is it an evidence annotation.
-		if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
+		//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 ev_ref = ann.value();
-		    if( singletons[ev_ref] ){
+		    var ref_node_id = ann.value();
+		    if( singletons[ref_node_id] ){
+			
+			// Remove node from the graph.
+			anchor.remove_node(ref_node_id);
 
-			// Remove
-			anchor.remove_node(ev_ref);
-
 			// Add as referenced individual.
-			var ev_indiv = singletons[ev_ref];
+			var ev_indiv = singletons[ref_node_id];
 			var c1 = node.add_referenced_individual(ev_indiv);
@@ -1227,6 +1240,13 @@ //console.log('<<' + node.id() + '>1>', c1.length);
 			//console.log('<<' + node.id() + '>2>', c2.length);
-//			console.log(node)
+			//			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);
 	});
@@ -1237,18 +1257,3 @@
 	each(anchor.all_edges(), function(edge){
-	    each(edge.annotations(), function(ann){
-
-		// Is it an evidence annotation.
-		if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
-		    // If so, add it in.
-		    var ev_ref = ann.value();
-		    if( singletons[ev_ref] ){
-			// Remove
-			anchor.remove_node(ev_ref);
-
-			// Add as referenced individual.
-			var ev_indiv = singletons[ev_ref];
-			edge.add_referenced_individual(ev_indiv);
-		    }
-		}
-	    });
+	    fold_in_reference(edge, is_iri_ev_p);
 	});
@@ -1259,3 +1264,3 @@
 
-//    console.log(anchor);
+    //    console.log(anchor);
 
@@ -1268,5 +1273,6 @@ return ret;
  * everything we did for {load_data_evidence_fold}, we're going to
- * search for nodes that have enabled_by and/or occurs_in targets
- * (that are themselves leaves) fold them in to the contained subgraph
- * item, and remove them from the top-level graph.
+ * 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.
  *
@@ -1276,5 +1282,6 @@ * TODO: inferred individuals
  * @param {Object} the "data" portion of a Minerva graph-related response.
+ * @param {Array} list of relations (as strings) to scan for for collapsing
  * @returns {Boolean} if data was loaded 
  */
-noctua_graph.prototype.load_data_go_noctua = function(data){
+noctua_graph.prototype.load_data_go_noctua = function(data, relation_list){
     var anchor = this;
@@ -1309,3 +1316,4 @@
 	// occurs_in (location).
-	var collapsable_relations = ['RO:0002333', 'BFO:0000066'];
+	//var collapsable_relations = ['RO:0002333', 'BFO:0000066'];
+	var collapsable_relations = relation_list || [];
 	each(collapsable_relations, function(relation){
@@ -1312,0 +1320,0 @@

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.12",
+    "version": "0.0.13",
     "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

@@ -258,3 +258,4 @@ ////
 	var raw_resp = require('./minerva-01.json');
-	g.load_data_go_noctua(raw_resp['data']);	
+	var rellist = ['RO:0002333', 'BFO:0000066'];
+	g.load_data_go_noctua(raw_resp['data'], rellist);
 
@@ -304,3 +305,4 @@ // Basic structure count.
 	var raw_resp = require('./minerva-01.json');
-	g.load_data_go_noctua(raw_resp['data']);	
+	var rellist = ['RO:0002333', 'BFO:0000066'];
+	g.load_data_go_noctua(raw_resp['data'], rellist);
 
@@ -332,3 +334,4 @@ var nid = 'gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023';
 	var raw_resp = require('./minerva-01.json');
-	g.load_data_go_noctua(raw_resp['data']);	
+	var rellist = ['RO:0002333', 'BFO:0000066'];
+	g.load_data_go_noctua(raw_resp['data'], rellist);
 
@@ -335,0 +338,0 @@ // Make a new graph to operate on.

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6333896

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27087

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