bbop-graph - npm Package Compare versions

Comparing version 0.0.2 to 0.0.3

lib/graph.js

@@ -1,2 +0,2 @@
-/* 
+/** 
  * Purpose: Basic edged graph and operations.
@@ -19,2 +19,3 @@ *
 var each = us.each;
+var bbop = require('bbop-core');
 
@@ -116,3 +117,3 @@ ///
  *
- * Get a fresh new copy of the current node (using bbop.core.clone for
+ * Get a fresh new copy of the current node (using bbop.clone for
  * metadata object).
@@ -126,3 +127,3 @@ *
     tmp_clone.label(this.label());
-    tmp_clone.metadata(bbop.core.clone(this.metadata()));
+    tmp_clone.metadata(bbop.clone(this.metadata()));
     return tmp_clone;
@@ -250,3 +251,3 @@ };
  *
- * Get a fresh new copy of the current edge (using bbop.core.clone for
+ * Get a fresh new copy of the current edge (using bbop.clone for
  * metadata object).
@@ -261,3 +262,3 @@ *
     // Metadata kind of needs to be duped separately.
-    tmp_clone.metadata(bbop.core.clone(this.metadata()));
+    tmp_clone.metadata(bbop.clone(this.metadata()));
     return tmp_clone;
@@ -928,3 +929,3 @@ };
     //if( nb_id_or_list.length && nb_id_or_list.index ){
-    if( bbop.core.is_array(nb_id_or_list) ){ // verify listy-ness
+    if( us.isArray(nb_id_or_list) ){ // verify listy-ness
 	for( var l = 0; l < nb_id_or_list.length; l++ ){	    
@@ -1011,5 +1012,3 @@ rec_up(nb_id_or_list[l]);
 	each(json_object.edges, function(edge_raw){
-	    var e = new edge(edge_raw.sub,
-					edge_raw.obj,
-					edge_raw.pred);
+	    var e = new edge(edge_raw.sub, edge_raw.obj, edge_raw.pred);
 	    // Copy out meta.
@@ -1043,3 +1042,3 @@ if(edge_raw.meta){ e.metadata(edge_raw.meta); }
 	
-	var node = bbop.core.clone(raw_node);
+	var node = bbop.clone(raw_node);
 	var ncopy = {};
@@ -1063,3 +1062,3 @@
     var eset = [];
-    var ecopy = bbop.core.clone(anchor._edges['array']);
+    var ecopy = bbop.clone(anchor._edges['array']);
     each(anchor.all_edges(), function(node){
@@ -1090,2 +1089,3 @@ var ecopy = {};
 
+    default_predicate: default_predicate,
     node: node,
@@ -1092,0 +1092,0 @@ edge: edge,

package.json

 {
     "name": "bbop-graph",
-    "version": "0.0.2",
-    "license": "BSD",
+    "version": "0.0.3",
+    "license": "BSD-3-Clause",
     "description": "General purpose (mathematical) graph library in JavaScript.",
@@ -6,0 +6,0 @@ "keywords": [

tests/core.tests.js

@@ -6,3 +6,2 @@ ////
 var assert = require('chai').assert;
-
 var model = new require('..');
@@ -12,5 +11,5 @@
 
-describe('trivial creations', function(){
+describe('node', function(){
 
-    it('works at all (thingy)', function(){
+    it('works at all', function(){
 
@@ -32,277 +31,321 @@ // Setup.
 
-// // Edges.
-// (function(){
+describe('edges', function(){
 
-//      // Setup.
-//      var n1 = new bbop.model.node('a');
-//      var n2 = new bbop.model.node('b');
-//      var n3 = new bbop.model.node('c');
+    // Setup.
+    var n1 = null;
+    var n2 = null;
+    var n3 = null;
+    var e1 = null;
+    var e2 = null;
+    var e3 = null;
+    
+    // Pre-run.    
+    before(function() {
+	// Setup.
+	n1 = new model.node('a');
+	n2 = new model.node('b');
+	n3 = new model.node('c');
+	
+	e1 = new model.edge(n1, n2);
+	e2 = new model.edge(n2, n3, 'foo');
+	e3 = new model.edge('d', 'e', 'bar');
+    });
 
-//      var e1 = new bbop.model.edge(n1, n2);
-//      var e2 = new bbop.model.edge(n2, n3, 'foo');
-//      var e3 = new bbop.model.edge('d', 'e', 'bar');
+    it('basically functional', function(){
+	
+	assert.isDefined(e1, 'at least this would be nice (edge 1)');
+	assert.isDefined(e2, 'at least this would be nice (edge 2)');
+	assert.isDefined(e2, 'at least this would be nice (edge 3)');
+	
+	assert.equal('a', e1.subject_id(), 'is a');
+	assert.equal('b', e1.object_id(), 'is b');
+	assert.equal('e', e3.object_id(), 'is e');
+	
+	assert.equal(model.default_predicate, e1.predicate_id(), 'is p');
+	assert.equal('foo', e2.predicate_id(), 'is p 2');
+	
+    });
+});
 
-//      mr_t.is_defined(e1, 'at least this would be nice (edge 1)');
-//      mr_t.is_defined(e2, 'at least this would be nice (edge 2)');
-//      mr_t.is_defined(e2, 'at least this would be nice (edge 3)');
+describe('simple model', function(){
 
-//      mr_t.is_same_atom('a', e1.subject_id(), 'is a');
-//      mr_t.is_same_atom('b', e1.object_id(), 'is b');
-//      mr_t.is_same_atom('e', e3.object_id(), 'is e');
+    var g = null;
+    var dpred = null;	
 
-//      mr_t.is_same_atom(bbop.model.default_predicate, e1.predicate_id(), 'is p');
-//      mr_t.is_same_atom('foo', e2.predicate_id(), 'is p 2');
+    // Pre-run.    
+    before(function() {
+	// Create graph described below.
+	//
+	//      a   n   x   z  
+	//     / \  |   |
+	//    b   c |   y?  <-- y is not extant, just referenced
+	//   ||  / \|
+	//   || e   d
+	//    \\___//  <-- non-default relationship (d is_a b)
+	//     \---/
+	//
+	g = new model.graph();
+	g.add_node(new model.node('a'));
+	g.add_node(new model.node('b'));
+	g.add_node(new model.node('c'));
+	g.add_node(new model.node('d'));
+	g.add_node(new model.node('e'));
+	g.add_node(new model.node('n'));
+	g.add_node(new model.node('x'));
+	g.add_node(new model.node('z'));
+	g.add_edge(new model.edge('b', 'a'));
+	g.add_edge(new model.edge('c', 'a'));
+	g.add_edge(new model.edge('d', 'c'));
+	g.add_edge(new model.edge('e', 'c'));
+	g.add_edge(new model.edge('d', 'n'));
+	g.add_edge(new model.edge('d', 'b', 'is_a'));
+	g.add_edge(new model.edge('y', 'x'));
 
-//  })();
+	dpred = model.default_predicate;
+    });	
+    
+    it('graph construction', function(){
 
-// // Check simple modelling.
-// (function(){
+	assert.isDefined(g, 'at least this would be nice (graph)');
+	assert.equal(8, g.all_nodes().length, '7 nodes');
+	assert.equal(7, g.all_edges().length, '7 edges');
+	assert.equal(7, g.all_edges().length, '7 edges');
+	assert.equal(1, g.get_singleton_nodes().length, 'just one single');
+	assert.equal('z', g.get_singleton_nodes()[0].id(), 'z alone');
+	assert.equal(1, g.all_dangling().length, 'just one dangle');
+	assert.equal(false, g.is_complete(), 'nope'); 
+    });
+    
+    it('leaf correctness', function(){
 
-//      // Create graph described below.
-//      //
-//      //      a   n   x   z  
-//      //     / \  |   |
-//      //    b   c |   y?  <-- y is not extant, just referenced
-//      //   ||  / \|
-//      //   || e   d
-//      //    \\___//  <-- non-default relationship (d is_a b)
-//      //     \---/
-//      //
-//      var g = new bbop.model.graph();
-//      g.add_node(new bbop.model.node('a'));
-//      g.add_node(new bbop.model.node('b'));
-//      g.add_node(new bbop.model.node('c'));
-//      g.add_node(new bbop.model.node('d'));
-//      g.add_node(new bbop.model.node('e'));
-//      g.add_node(new bbop.model.node('n'));
-//      g.add_node(new bbop.model.node('x'));
-//      g.add_node(new bbop.model.node('z'));
-//      g.add_edge(new bbop.model.edge('b', 'a'));
-//      g.add_edge(new bbop.model.edge('c', 'a'));
-//      g.add_edge(new bbop.model.edge('d', 'c'));
-//      g.add_edge(new bbop.model.edge('e', 'c'));
-//      g.add_edge(new bbop.model.edge('d', 'n'));
-//      g.add_edge(new bbop.model.edge('d', 'b', 'is_a'));
-//      g.add_edge(new bbop.model.edge('y', 'x'));
+	assert.equal(false, g.is_leaf_node('a'), '! leaf a');
+	assert.equal(false, g.is_leaf_node('b'), '! leaf b');
+	assert.equal(false, g.is_leaf_node('c'), '! leaf c');
+	assert.equal(true, g.is_leaf_node('d'), 'leaf d');
+	assert.equal(true, g.is_leaf_node('e'), 'leaf e');
+	assert.equal(false, g.is_leaf_node('n'), '! leaf n');
+	assert.equal(false, g.is_leaf_node('x'), '! leaf z');
+	assert.equal(false, g.is_leaf_node('y'), '! leaf y');
+	assert.equal(true, g.is_leaf_node('z'), 'leaf z');
+	assert.equal(3, g.get_leaf_nodes().length, '3 leaves');
+    });
+    
+    it('root correctness', function(){
 
-//      var dpred = bbop.model.default_predicate;
+	assert.equal(true, g.is_root_node('a'), 'root a');
+	assert.equal(false, g.is_root_node('b'), '! root b');
+	assert.equal(false, g.is_root_node('c'), '! root c');
+	assert.equal(false, g.is_root_node('d'), '! root d');
+	assert.equal(false, g.is_root_node('e'), '! root e');
+	assert.equal(true, g.is_root_node('n'), 'root n');
+	assert.equal(true, g.is_root_node('x'), 'root z');
+	assert.equal(false, g.is_root_node('y'), '! root y');
+	assert.equal(true, g.is_root_node('z'), 'root z');
+	assert.equal(4, g.get_root_nodes().length, '4 roots');
+    });
+    
+    it('graph structure up', function(){
 
-//      // Test graph construction.
-//      mr_t.is_defined(g, 'at least this would be nice (graph)');
-//      mr_t.is_same_atom(8, g.all_nodes().length, '7 nodes');
-//      mr_t.is_same_atom(7, g.all_edges().length, '7 edges');
-//      mr_t.is_same_atom(7, g.all_edges().length, '7 edges');
-//      mr_t.is_same_atom(1, g.get_singleton_nodes().length, 'just one single');
-//      mr_t.is_same_atom('z', g.get_singleton_nodes()[0].id(), 'z alone');
-//      mr_t.is_same_atom(1, g.all_dangling().length, 'just one dangle');
-//      mr_t.is_same_atom(false, g.is_complete(), 'nope'); 
+	assert.equal(0, g.get_parent_nodes('a').length, 'a is root');
+	assert.equal(1, g.get_parent_nodes('b').length, 'b under a (1)');
+	assert.equal('a', g.get_parent_nodes('b')[0].id(), 'b under a (2)');
+	assert.equal(3, g.get_parent_nodes('d').length, 'd: b c n');
+	assert.equal(2, g.get_parent_nodes('d', dpred).length, 'd: c n');
+	assert.equal(1, g.get_parent_nodes('d', 'is_a').length, 'd: b');
+    });
+    
+    it('graph structure down', function(){
 
-//      // Test leaf correctness.
-//      mr_t.is_same_atom(false, g.is_leaf_node('a'), '! leaf a');
-//      mr_t.is_same_atom(false, g.is_leaf_node('b'), '! leaf b');
-//      mr_t.is_same_atom(false, g.is_leaf_node('c'), '! leaf c');
-//      mr_t.is_same_atom(true, g.is_leaf_node('d'), 'leaf d');
-//      mr_t.is_same_atom(true, g.is_leaf_node('e'), 'leaf e');
-//      mr_t.is_same_atom(false, g.is_leaf_node('n'), '! leaf n');
-//      mr_t.is_same_atom(false, g.is_leaf_node('x'), '! leaf z');
-//      mr_t.is_same_atom(false, g.is_leaf_node('y'), '! leaf y');
-//      mr_t.is_same_atom(true, g.is_leaf_node('z'), 'leaf z');
-//      mr_t.is_same_atom(3, g.get_leaf_nodes().length, '3 leaves');
+	assert.equal(2, g.get_child_nodes('a').length, 'a has 2');
+	assert.equal(1, g.get_child_nodes('b').length, 'b has 1');
+	assert.equal('d', g.get_child_nodes('b')[0].id(), 'b: d 1');
+	assert.equal(0, g.get_child_nodes('b', dpred).length, 'b: d 2');
+	assert.equal('d', g.get_child_nodes('b', 'is_a')[0].id(), 'b: d 3');
+	assert.equal(0, g.get_child_nodes('d').length, 'd: -');
+	assert.equal(0, g.get_child_nodes('z').length, 'z: -');
+	assert.equal(0, g.get_child_nodes('x').length, 'x: -');
+    });
+    
+    it('edges and predicates', function(){
 
-//      // Test roots.
-//      mr_t.is_same_atom(true, g.is_root_node('a'), 'root a');
-//      mr_t.is_same_atom(false, g.is_root_node('b'), '! root b');
-//      mr_t.is_same_atom(false, g.is_root_node('c'), '! root c');
-//      mr_t.is_same_atom(false, g.is_root_node('d'), '! root d');
-//      mr_t.is_same_atom(false, g.is_root_node('e'), '! root e');
-//      mr_t.is_same_atom(true, g.is_root_node('n'), 'root n');
-//      mr_t.is_same_atom(true, g.is_root_node('x'), 'root z');
-//      mr_t.is_same_atom(false, g.is_root_node('y'), '! root y');
-//      mr_t.is_same_atom(true, g.is_root_node('z'), 'root z');
-//      mr_t.is_same_atom(4, g.get_root_nodes().length, '4 roots');
+	//g.add_edge(new model.edge('d', 'b', 'is_a'));
+	var med = g.get_edges('d', 'b');
+	assert.equal(med.length, 1, 'one edge');
+	assert.equal(med[0].predicate_id(), 'is_a', 'one edge is_a');
+	var mrel = g.get_predicates('d', 'b');
+	assert.equal(mrel.length, 1, 'one pred');
+	assert.equal(mrel[0], 'is_a', 'one pred is_a');
+    });
+    
+    it('subgraph test 1', function(){
 
-//      // Test graph structure up.
-//      mr_t.is_same_atom(0, g.get_parent_nodes('a').length, 'a is root');
-//      mr_t.is_same_atom(1, g.get_parent_nodes('b').length, 'b under a (1)');
-//      mr_t.is_same_atom('a', g.get_parent_nodes('b')[0].id(), 'b under a (2)');
-//      mr_t.is_same_atom(3, g.get_parent_nodes('d').length, 'd: b c n');
-//      mr_t.is_same_atom(2, g.get_parent_nodes('d', dpred).length, 'd: c n');
-//      mr_t.is_same_atom(1, g.get_parent_nodes('d', 'is_a').length, 'd: b');
+	var sub1 = g.get_ancestor_subgraph('d');
+	// Roots.
+	assert.equal(true, sub1.is_root_node('a'), 'root a');
+	assert.equal(true, sub1.is_root_node('n'), 'root n');
+	assert.equal(false, sub1.is_root_node('x'), '! root x');
+	assert.equal(2, sub1.get_root_nodes().length, '2 roots');
+	// Leaves.
+	assert.equal(1, sub1.get_leaf_nodes().length, '1 leaf');
+	assert.equal('d', sub1.get_leaf_nodes()[0].id(), 'd leaf');
+	// Graph structure up.
+	assert.equal(0, sub1.get_parent_nodes('a').length, 'a is root');
+	assert.equal(1, sub1.get_parent_nodes('b').length, 'b under a (1)');
+	assert.equal('a', sub1.get_parent_nodes('b')[0].id(), 'b under a (2)');
+	assert.equal(3, sub1.get_parent_nodes('d').length, 'd: b c n');
+	assert.equal(2, sub1.get_parent_nodes('d', dpred).length, 'd: c n');
+	assert.equal(1, sub1.get_parent_nodes('d', 'is_a').length, 'd: b');
+	// Graph structure down.
+	assert.equal(2, sub1.get_child_nodes('a').length, 'a has 2');
+	assert.equal(1, sub1.get_child_nodes('b').length, 'b has 1');
+	assert.equal('d', sub1.get_child_nodes('b')[0].id(), 'b: d 1');
+	assert.equal(0, sub1.get_child_nodes('b', dpred).length, 'b: d 2');
+	assert.equal('d', sub1.get_child_nodes('b', 'is_a')[0].id(), 'b: d 3');
+	assert.equal(0, sub1.get_child_nodes('d').length, 'd: -');
+    });
+    
+    it('subgraph test 2', function(){
 
-//      // Test graph structure down.
-//      mr_t.is_same_atom(2, g.get_child_nodes('a').length, 'a has 2');
-//      mr_t.is_same_atom(1, g.get_child_nodes('b').length, 'b has 1');
-//      mr_t.is_same_atom('d', g.get_child_nodes('b')[0].id(), 'b: d 1');
-//      mr_t.is_same_atom(0, g.get_child_nodes('b', dpred).length, 'b: d 2');
-//      mr_t.is_same_atom('d', g.get_child_nodes('b', 'is_a')[0].id(), 'b: d 3');
-//      mr_t.is_same_atom(0, g.get_child_nodes('d').length, 'd: -');
-//      mr_t.is_same_atom(0, g.get_child_nodes('z').length, 'z: -');
-//      mr_t.is_same_atom(0, g.get_child_nodes('x').length, 'x: -');
+	var sub2 = g.get_ancestor_subgraph('d', 'is_a');
+	// Roots.
+	assert.equal(false, sub2.is_root_node('a'), '! root a');
+	assert.equal(false, sub2.is_root_node('d'), '! root d');
+	assert.equal(true, sub2.is_root_node('b'), 'root b');
+	// Leaves.
+	assert.equal(1, sub2.get_leaf_nodes().length, '1 leaf');
+	assert.equal('d', sub2.get_leaf_nodes()[0].id(), 'd leaf');
+	// Graph structure up.
+	assert.equal(0, sub2.get_parent_nodes('b').length, 'b root');
+	assert.equal(1, sub2.get_parent_nodes('d').length, 'd: b');
+	assert.equal(0, sub2.get_parent_nodes('d', dpred).length, 'd: -');
+	assert.equal(1, sub2.get_parent_nodes('d', 'is_a').length, 'd: b');
+	// Graph structure down.
+	assert.equal('d', sub2.get_child_nodes('b')[0].id(), 'b: d 1');
+	assert.equal(0, sub2.get_child_nodes('b', dpred).length, 'b: d 2');
+	assert.equal('d', sub2.get_child_nodes('b', 'is_a')[0].id(), 'b:d 3');
+	assert.equal(0, sub2.get_child_nodes('d').length, 'd: -');
+    });
 
-//      // Test edges and predicates.
-//      //g.add_edge(new bbop.model.edge('d', 'b', 'is_a'));
-//      var med = g.get_edges('d', 'b');
-//      mr_t.is_same_atom(med.length, 1, 'one edge');
-//      mr_t.is_same_atom(med[0].predicate_id(), 'is_a', 'one edge is_a');
-//      var mrel = g.get_predicates('d', 'b');
-//      mr_t.is_same_atom(mrel.length, 1, 'one pred');
-//      mr_t.is_same_atom(mrel[0], 'is_a', 'one pred is_a');
+});
 
-//      ///
-//      /// Test subgraphs.
-//      ///
+// Test cases from owltools.graph.shunt junit test cases.
+describe('loading from JSON (good with Solr/GOlr)', function(){
 
-//      var sub1 = g.get_ancestor_subgraph('d');
-//      // Roots.
-//      mr_t.is_same_atom(true, sub1.is_root_node('a'), 'root a');
-//      mr_t.is_same_atom(true, sub1.is_root_node('n'), 'root n');
-//      mr_t.is_same_atom(false, sub1.is_root_node('x'), '! root x');
-//      mr_t.is_same_atom(2, sub1.get_root_nodes().length, '2 roots');
-//      // Leaves.
-//      mr_t.is_same_atom(1, sub1.get_leaf_nodes().length, '1 leaf');
-//      mr_t.is_same_atom('d', sub1.get_leaf_nodes()[0].id(), 'd leaf');
-//      // Graph structure up.
-//      mr_t.is_same_atom(0, sub1.get_parent_nodes('a').length, 'a is root');
-//      mr_t.is_same_atom(1, sub1.get_parent_nodes('b').length, 'b under a (1)');
-//      mr_t.is_same_atom('a', sub1.get_parent_nodes('b')[0].id(), 'b under a (2)');
-//      mr_t.is_same_atom(3, sub1.get_parent_nodes('d').length, 'd: b c n');
-//      mr_t.is_same_atom(2, sub1.get_parent_nodes('d', dpred).length, 'd: c n');
-//      mr_t.is_same_atom(1, sub1.get_parent_nodes('d', 'is_a').length, 'd: b');
-//      // Graph structure down.
-//      mr_t.is_same_atom(2, sub1.get_child_nodes('a').length, 'a has 2');
-//      mr_t.is_same_atom(1, sub1.get_child_nodes('b').length, 'b has 1');
-//      mr_t.is_same_atom('d', sub1.get_child_nodes('b')[0].id(), 'b: d 1');
-//      mr_t.is_same_atom(0, sub1.get_child_nodes('b', dpred).length, 'b: d 2');
-//      mr_t.is_same_atom('d', sub1.get_child_nodes('b', 'is_a')[0].id(), 'b: d 3');
-//      mr_t.is_same_atom(0, sub1.get_child_nodes('d').length, 'd: -');
+    var g1 = null;
+    var g2 = null;
 
-//      var sub2 = g.get_ancestor_subgraph('d', 'is_a');
-//      // Roots.
-//      mr_t.is_same_atom(false, sub2.is_root_node('a'), '! root a');
-//      mr_t.is_same_atom(false, sub2.is_root_node('d'), '! root d');
-//      mr_t.is_same_atom(true, sub2.is_root_node('b'), 'root b');
-//      // Leaves.
-//      mr_t.is_same_atom(1, sub2.get_leaf_nodes().length, '1 leaf');
-//      mr_t.is_same_atom('d', sub2.get_leaf_nodes()[0].id(), 'd leaf');
-//      // Graph structure up.
-//      mr_t.is_same_atom(0, sub2.get_parent_nodes('b').length, 'b root');
-//      mr_t.is_same_atom(1, sub2.get_parent_nodes('d').length, 'd: b');
-//      mr_t.is_same_atom(0, sub2.get_parent_nodes('d', dpred).length, 'd: -');
-//      mr_t.is_same_atom(1, sub2.get_parent_nodes('d', 'is_a').length, 'd: b');
-//      // Graph structure down.
-//      mr_t.is_same_atom('d', sub2.get_child_nodes('b')[0].id(), 'b: d 1');
-//      mr_t.is_same_atom(0, sub2.get_child_nodes('b', dpred).length, 'b: d 2');
-//      mr_t.is_same_atom('d', sub2.get_child_nodes('b', 'is_a')[0].id(), 'b:d 3');
-//      mr_t.is_same_atom(0, sub2.get_child_nodes('d').length, 'd: -');
+    // Pre-run.    
+    before(function() {
 
-//  })();
+	var jo = {"nodes":[{"id":"a","lbl":"A"},{"id":"b","lbl":"B"}],"edges":[{"sub":"a","obj":"b","pred":"is_a"}]};
+	g1 = new model.graph();
+	g1.load_json(jo);
 
-// // Check loading from JSON (good with Solr/GOlr).
-// // Test cases from owltools.graph.shunt junit test cases.
-// (function(){
+	// A bit of GO.
+	// Generate from:
+	//    cd ~/local/src/svn/owltools/OWLTools-Runner
+	//    ./bin/owltools --solr-shunt-test
+	var go = {"nodes":[{"id":"GO:0009987","lbl":"cellular process"},{"id":"GO:0048869","lbl":"cellular developmental process"},{"id":"GO:0048731","lbl":"system development"},{"id":"GO:0007275","lbl":"multicellular organismal development"},{"id":"GO:0030154","lbl":"cell differentiation"},{"id":"GO:0007399","lbl":"nervous system development"},{"id":"GO:0048856","lbl":"anatomical structure development"},{"id":"GO:0008150","lbl":"biological_process"},{"id":"GO:0022008","lbl":"neurogenesis"},{"id":"GO:0042063","lbl":"gliogenesis"},{"id":"GO:0032502","lbl":"developmental process"},{"id":"GO:0032501","lbl":"multicellular organismal process"},{"id":"GO:0048699","lbl":"generation of neurons"}],"edges":[{"sub":"GO:0022008","obj":"GO:0007399","pred":"part_of"},{"sub":"GO:0042063","obj":"GO:0022008","pred":"is_a"},{"sub":"GO:0022008","obj":"GO:0030154","pred":"is_a"},{"sub":"GO:0032501","obj":"GO:0008150","pred":"is_a"},{"sub":"GO:0032502","obj":"GO:0008150","pred":"is_a"},{"sub":"GO:0048731","obj":"GO:0048856","pred":"is_a"},{"sub":"GO:0007399","obj":"GO:0048731","pred":"is_a"},{"sub":"GO:0007275","obj":"GO:0032501","pred":"is_a"},{"sub":"GO:0007275","obj":"GO:0032502","pred":"is_a"},{"sub":"GO:0048856","obj":"GO:0032502","pred":"is_a"},{"sub":"GO:0048869","obj":"GO:0009987","pred":"is_a"},{"sub":"GO:0048699","obj":"GO:0022008","pred":"is_a"},{"sub":"GO:0048869","obj":"GO:0032502","pred":"is_a"},{"sub":"GO:0009987","obj":"GO:0008150","pred":"is_a"},{"sub":"GO:0030154","obj":"GO:0048869","pred":"is_a"},{"sub":"GO:0048731","obj":"GO:0007275","pred":"part_of"}]};
+	g2 = new model.graph();
+	g2.load_json(go);
+    });
 
-//      ///
-//      /// Trivial.
-//      ///
+    it('graph one okay', function(){
 
-//      var jo = {"nodes":[{"id":"a","lbl":"A"},{"id":"b","lbl":"B"}],"edges":[{"sub":"a","obj":"b","pred":"is_a"}]};
-//      var g1 = new bbop.model.graph();
-//      var result1 = g1.load_json(jo);
+	assert.isTrue(g1.is_root_node('b'), 'root b');
+	assert.isFalse(g1.is_root_node('a'), '! root a');
+	assert.equal('b', g1.get_parent_nodes('a')[0].id(), 'b under a');
+    });
 
-//      mr_t.is_same_atom(true, g1.is_root_node('b'), 'root b');
-//      mr_t.is_same_atom(false, g1.is_root_node('a'), '! root a');
-//      mr_t.is_same_atom('b', g1.get_parent_nodes('a')[0].id(), 'b under a');
-     
-//      ///
-//      /// A bit of GO.
-//      /// Generate from:
-//      ///    cd ~/local/src/svn/owltools/OWLTools-Runner
-//      ///    ./bin/owltools --solr-shunt-test
-//      ///
+    it('graph two okay', function(){
+	
+	var leaves = g2.get_child_nodes('GO:0022008');
+	assert.equal(leaves.length, 2, 'two children for GO:0022008');
+	
+	var leaf1 = leaves[0];
+	var leaf2 = leaves[1];
+	assert.includeMembers(['GO:0042063', 'GO:0048699'], [leaf1.id()],
+			      'either of the two kids (1)');
+	assert.includeMembers(['GO:0042063', 'GO:0048699'], [leaf2.id()],
+			      'either of the two kids (2)');
+	assert.notEqual(leaf1.id(), leaf2.id(),
+			'the children are different');
+	assert.equal(g2.get_child_nodes('GO:0022008', 'part_of').length, 0,
+		     'no part_of kids');
+	assert.equal(g2.get_child_nodes('GO:0022008', 'is_a').length, 2,
+		     'two is_a kids');
+    });
+});
 
-//      var go = {"nodes":[{"id":"GO:0009987","lbl":"cellular process"},{"id":"GO:0048869","lbl":"cellular developmental process"},{"id":"GO:0048731","lbl":"system development"},{"id":"GO:0007275","lbl":"multicellular organismal development"},{"id":"GO:0030154","lbl":"cell differentiation"},{"id":"GO:0007399","lbl":"nervous system development"},{"id":"GO:0048856","lbl":"anatomical structure development"},{"id":"GO:0008150","lbl":"biological_process"},{"id":"GO:0022008","lbl":"neurogenesis"},{"id":"GO:0042063","lbl":"gliogenesis"},{"id":"GO:0032502","lbl":"developmental process"},{"id":"GO:0032501","lbl":"multicellular organismal process"},{"id":"GO:0048699","lbl":"generation of neurons"}],"edges":[{"sub":"GO:0022008","obj":"GO:0007399","pred":"part_of"},{"sub":"GO:0042063","obj":"GO:0022008","pred":"is_a"},{"sub":"GO:0022008","obj":"GO:0030154","pred":"is_a"},{"sub":"GO:0032501","obj":"GO:0008150","pred":"is_a"},{"sub":"GO:0032502","obj":"GO:0008150","pred":"is_a"},{"sub":"GO:0048731","obj":"GO:0048856","pred":"is_a"},{"sub":"GO:0007399","obj":"GO:0048731","pred":"is_a"},{"sub":"GO:0007275","obj":"GO:0032501","pred":"is_a"},{"sub":"GO:0007275","obj":"GO:0032502","pred":"is_a"},{"sub":"GO:0048856","obj":"GO:0032502","pred":"is_a"},{"sub":"GO:0048869","obj":"GO:0009987","pred":"is_a"},{"sub":"GO:0048699","obj":"GO:0022008","pred":"is_a"},{"sub":"GO:0048869","obj":"GO:0032502","pred":"is_a"},{"sub":"GO:0009987","obj":"GO:0008150","pred":"is_a"},{"sub":"GO:0030154","obj":"GO:0048869","pred":"is_a"},{"sub":"GO:0048731","obj":"GO:0007275","pred":"part_of"}]};
+describe('failing case from the taxslim', function(){
 
-//      var g2 = new bbop.model.graph();
-//      var result2 = g2.load_json(go);
+    // Pre-run.    
+    before(function() {
+    });
 
-//      var leaves = g2.get_child_nodes('GO:0022008');
-//      mr_t.is_same_atom(2, leaves.length, 'two children for GO:0022008');
+    it('check', function(){
 
-//      var leaf1 = leaves[0];
-//      var leaf2 = leaves[1];
-//      mr_t.is_in_list(leaf1.id(), ['GO:0042063', 'GO:0048699'],
-// 		     'either of the two kids (1)');
-//      mr_t.is_in_list(leaf2.id(), ['GO:0042063', 'GO:0048699'],
-// 		     'either of the two kids (2)');
-//      mr_t.is_different_atom(leaf1.id(), leaf2.id(),
-// 			    'the children are different');
-//      mr_t.is_same_atom(g2.get_child_nodes('GO:0022008', 'part_of').length,
-// 			    0, 'no part_of kids');
-//      mr_t.is_same_atom(g2.get_child_nodes('GO:0022008', 'is_a').length,
-// 			    2, 'two is_a kids');
-// })();
+	var tax = 
+	    {"nodes": [
+		{"id":"NCBITaxon:33316","lbl":"Coelomata"},
+		{"id":"NCBITaxon:2759","lbl":"Eukaryota"},
+		{"id":"NCBITaxon:117565","lbl":"Hyperotreti"},
+		{"id":"NCBITaxon:33154","lbl":"Fungi/Metazoa group"},
+		{"id":"NCBITaxon:1","lbl":"root"},
+		{"id":"NCBITaxon:7742","lbl":"Vertebrata"},
+		{"id":"NCBITaxon:7711","lbl":"Chordata"},
+		{"id":"NCBITaxon:89593","lbl":"Craniata"},
+		{"id":"NCBITaxon:6072","lbl":"Eumetazoa"},
+		{"id":"NCBITaxon:131567","lbl":"cellular organisms"},
+		{"id":"NCBITaxon:33511","lbl":"Deuterostomia"},
+		{"id":"NCBITaxon:33213","lbl":"Bilateria"},
+		{"id":"NCBITaxon:33208","lbl":"Metazoa"}
+	    ],
+	     "edges": [
+		 {"sub":"NCBITaxon:33208","obj":"NCBITaxon:33154","pred":"is_a"},
+		 {"sub":"NCBITaxon:33154","obj":"NCBITaxon:2759","pred":"is_a"},
+		 {"sub":"NCBITaxon:6072","obj":"NCBITaxon:33208","pred":"is_a"},
+		 {"sub":"NCBITaxon:33316","obj":"NCBITaxon:33213","pred":"is_a"},
+		 {"sub":"NCBITaxon:2759","obj":"NCBITaxon:131567","pred":"is_a"},
+		 {"sub":"NCBITaxon:89593","obj":"NCBITaxon:7711","pred":"is_a"},
+		 {"sub":"NCBITaxon:33511","obj":"NCBITaxon:33316","pred":"is_a"},
+		 {"sub":"NCBITaxon:7711","obj":"NCBITaxon:33511","pred":"is_a"},
+		 {"sub":"NCBITaxon:33213","obj":"NCBITaxon:6072","pred":"is_a"},
+		 {"sub":"NCBITaxon:7742","obj":"NCBITaxon:89593","pred":"is_a"},
+		 {"sub":"NCBITaxon:131567","obj":"NCBITaxon:1","pred":"is_a"},
+		 {"sub":"NCBITaxon:117565","obj":"NCBITaxon:89593","pred":"is_a"}
+	     ]
+	    };
+	
+	var g = new model.graph();
+	var result2 = g.load_json(tax);
+	
+	assert.isTrue(g.is_complete(), 'tax is complete');
+	
+	var leaves = g.get_child_nodes('NCBITaxon:89593');
+	assert.equal(2, leaves.length, 'two children for NCBITaxon:89593');
+	var root_kids = g.get_child_nodes('NCBITaxon:1');
+	assert.equal(1, root_kids.length, 'one kid for root');
+	assert.equal('NCBITaxon:131567', root_kids[0].id(),
+		     'and the one root kid is NCBITaxon:131567');
+	
+    });
+});
 
+describe('roundtrip', function(){
 
-// // Here is a failing case from the taxslim
-// (function(){
+    // Pre-run.    
+    before(function() {
+    });
 
-// var tax = 
-//     {"nodes":
-//      [
-// 	 {"id":"NCBITaxon:33316","lbl":"Coelomata"},
-// 	 {"id":"NCBITaxon:2759","lbl":"Eukaryota"},
-// 	 {"id":"NCBITaxon:117565","lbl":"Hyperotreti"},
-// 	 {"id":"NCBITaxon:33154","lbl":"Fungi/Metazoa group"},
-// 	 {"id":"NCBITaxon:1","lbl":"root"},
-// 	 {"id":"NCBITaxon:7742","lbl":"Vertebrata"},
-// 	 {"id":"NCBITaxon:7711","lbl":"Chordata"},
-// 	 {"id":"NCBITaxon:89593","lbl":"Craniata"},
-// 	 {"id":"NCBITaxon:6072","lbl":"Eumetazoa"},
-// 	 {"id":"NCBITaxon:131567","lbl":"cellular organisms"},
-// 	 {"id":"NCBITaxon:33511","lbl":"Deuterostomia"},
-// 	 {"id":"NCBITaxon:33213","lbl":"Bilateria"},
-// 	 {"id":"NCBITaxon:33208","lbl":"Metazoa"}
-//      ],
-//      "edges":
-//      [
-// 	 {"sub":"NCBITaxon:33208","obj":"NCBITaxon:33154","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:33154","obj":"NCBITaxon:2759","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:6072","obj":"NCBITaxon:33208","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:33316","obj":"NCBITaxon:33213","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:2759","obj":"NCBITaxon:131567","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:89593","obj":"NCBITaxon:7711","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:33511","obj":"NCBITaxon:33316","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:7711","obj":"NCBITaxon:33511","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:33213","obj":"NCBITaxon:6072","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:7742","obj":"NCBITaxon:89593","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:131567","obj":"NCBITaxon:1","pred":"is_a"},
-// 	 {"sub":"NCBITaxon:117565","obj":"NCBITaxon:89593","pred":"is_a"}
-//      ]
-//     };
+    it('original obj and json', function(){
+	
+	var simp = {"nodes":[{"id":"a","lbl":"A"},{"id":"b","lbl":"B"}],"edges":[{"sub":"a","obj":"b","pred":"is_a"}]};
+	var g = new model.graph();
+	var l = g.load_json(simp);
+	var r = g.to_json();
+	assert.deepEqual(simp, r, 'round trip');
+    });
+    
+});
 
-//      var g = new bbop.model.graph();
-//      var result2 = g.load_json(tax);
-
-//      mr_t.is_true(g.is_complete(), 'tax is complete');
-
-//      var leaves = g.get_child_nodes('NCBITaxon:89593');
-//      mr_t.is_same_atom(2, leaves.length, 'two children for NCBITaxon:89593');
-//      var root_kids = g.get_child_nodes('NCBITaxon:1');
-//      mr_t.is_same_atom(1, root_kids.length, 'one kid for root');
-//      mr_t.is_same_atom('NCBITaxon:131567', root_kids[0].id(),
-// 		       'and the one root kid is NCBITaxon:131567');
-
-// })();
-
-
-// // Here is a failing case from the taxslim
-// // TODO: Cannot test until I get a better object testing function.
-// (function(){
-//      var simp = {"nodes":[{"id":"a","lbl":"A"},{"id":"b","lbl":"B"}],"edges":[{"sub":"a","obj":"b","pred":"is_a"}]};
-//      var g = new bbop.model.graph();
-//      var l = g.load_json(simp);
-//      var r = g.to_json();
-//      //mr_t.is_same_hash(simp, r, 'round trip');
-//      //var dump = bbop.core.dump;
-// });
-

tests/go.tests.js

@@ -8,7 +8,2 @@ ////
 
-// Remember, we are running from the project root, so relative to
-// there (?).
-var go_nodes = require('./go.nodes.json');
-var go_edges = require('./go.edges.json');
-
 ///
@@ -20,3 +15,15 @@ /// Start unit testing.
 
+    var go_nodes = null;
+    var go_edges = null;
+
+    // Pre-run.    
+    before(function() {
+	// Remember, we are running from the project root, so relative
+	// to there (?).
+	go_nodes = require('./go.nodes.json');
+	go_edges = require('./go.edges.json');
+    });
+
     it('all good', function(){
+	this.timeout(30000); // 30s
 
@@ -23,0 +30,0 @@ // Global testing graph.

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