bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.14 to 0.0.15

lib/edit.js

@@ -1235,3 +1235,3 @@ /**
 /**
- * In addition to everything we did for {load_data_evidence_fold},
+ * In addition to everything we did for {fold_evidence},
  * we're going to search for nodes that have enabled_by and/or
@@ -1312,2 +1312,56 @@ * occurs_in (or any other specified relation) targets (that are
 
+/**
+ * Essentially, undo anything that could be done in a folding
+ * step--return the graph to its most expanded form.
+ *
+ * @returns {Boolean} if unfolded (should always be true)
+ */
+noctua_graph.prototype.unfold = function(){
+    var anchor = this;
+
+    // For any entity, remove its referenced individuals and re-add
+    // them to the graph.
+    function _unfold_reference(item){
+	// Get.
+	var refd = item.referenced_individuals();
+
+	// Restore to graph.
+	each(refd, function(r){
+	    anchor.add_node(r);
+	});
+
+	// Remove references.
+	item.referenced_individuals([]);
+    }
+    // Apply to all nodes.
+    each(anchor.all_nodes(), function(node){ _unfold_reference(node); });
+    // Apply to all edges.
+    each(anchor.all_edges(), function(edge){ _unfold_reference(edge); });
+
+    // For all individuals, apply its subgraph back to the main graph
+    // and reset.
+    each(anchor.all_nodes(), function(node){
+
+	// Get the subgraph.
+	var sub = node.subgraph();
+
+	// If extant, walk it and apply all parts to outer graph.
+	if( sub ){
+	    each(sub.all_nodes(), function(node){
+		anchor.add_node(node);
+	    });
+	    each(sub.all_edges(), function(edge){
+		anchor.add_edge(edge);
+	    });
+	}
+
+	// Destroy the reference.
+	var sub = node.subgraph(null);
+    });
+
+    // Revisit if we want something meaningful out of here.
+    var retval = true;
+    return retval;
+};
+
 ///
@@ -1561,7 +1615,13 @@ /// Node subclass and overrides.
  * 
- * @param {graph} [subgraph] - the subgraph to "hide" inside this individual in the graph
+ * @param {graph|null} [subgraph] - the subgraph to "hide" inside this individual in the graph, or null to reset it
  * @returns {graph|null} contained subgraph
  */
 noctua_node.prototype.subgraph = function(subgraph){
-    if( subgraph && bbop.what_is(subgraph) == 'bbop-graph-noctua.graph'){
+    if( typeof(subgraph) === 'undefined' ){
+	// Just return current state.
+    }else if( subgraph == null ){
+	// Reset state (and return).
+	this._embedded_subgraph = null;
+    }else if(bbop.what_is(subgraph) == 'bbop-graph-noctua.graph'){
+	// Update state (and return).
 	this._embedded_subgraph = subgraph;
@@ -1568,0 +1628,0 @@ }

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.14",
+    "version": "0.0.15",
     "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

@@ -375,2 +375,55 @@ ////
 
+describe("unfolding works", function(){
+
+    it('basic unfolded graph checks', function(){
+
+	// Setup.
+	var raw_resp = require('./minerva-01.json');
+	var g = new model.graph();
+	g.load_data_basic(raw_resp['data']);
+
+	// Double-check fold.
+	var rellist = ['RO:0002333', 'BFO:0000066'];
+	g.fold_go_noctua(rellist);
+	assert.equal(g.all_nodes().length, 7, 'only seven nodes left');
+	assert.equal(g.all_edges().length, 7, 'only seven edges left');
+
+	// Unfold and check.
+	g.unfold();
+	assert.equal(g.all_nodes().length, 22, 'return to right num nodes');
+	assert.equal(g.all_edges().length, 14, 'return to right num edges');
+
+	///
+	/// The next three examples are from various tests
+	/// above--copied to ensure.
+	///
+
+	// Deeper check.
+	assert.equal(g.id(),'gomodel:taxon_559292-5525a0fc0000001_all_indivdual',
+		     'graph id');
+	assert.equal(g.annotations().length, 4, '4 graph annotation');
+	var anns = g.get_annotations_by_key('date');
+	assert.equal(anns.length, 1, 'one date annotation');
+	assert.equal(anns[0].value(), '2015-04-10', 'correct date annotation');
+
+	// More exploring.
+	assert.equal(g.get_singleton_nodes().length, 8, 'ev makes singletons');
+	assert.equal(g.get_root_nodes().length, 17, 'technically lots of roots');
+	assert.equal(g.get_leaf_nodes().length, 9, 'leaves are ev + 1 here');
+	
+	// S'more.
+	var nid =
+	    'gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023';
+	var n = g.get_node(nid);	
+	assert.equal(n.types().length, 1, 'one std');
+	assert.equal(n.inferred_types().length, 2, 'two inferred');
+	assert.equal(n.get_unique_inferred_types().length, 1,
+		     'one unique inferred');
+	assert.equal(n.types()[0].class_id(), 'GO:0005515',
+		     'std class id');
+	assert.equal(n.get_unique_inferred_types()[0].class_id(), 'GO:0098772',
+		     'one unique inferred class id');
+    });
+});
+
 // var assert = require('chai').assert;
@@ -377,0 +430,0 @@ // var model = new require('..');

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Improved metrics

Total package byte prevSize

6336552

increased by0.05%

Lines of code

27161

increased by0.35%

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