bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.18 to 0.0.19

lib/edit.js

@@ -569,2 +569,8 @@ /**
     //this._referenced_subgraphs = []; // not for graph yet, or maybe ever
+
+    // Some things that come up in live noctua environments. These are
+    // graph properties that may or may not be there. If unknown,
+    // null; if positively true (bad), true; may be false otherwise.
+    this._inconsistent_p = null;
+    this._modified_p = null;
 }
@@ -626,3 +632,7 @@ bbop.extend(noctua_graph, bbop_graph);
     });
-    
+
+    // Copy other properties over.
+    new_graph._inconsistent_p = anchor._inconsistent_p;
+    new_graph._modified_p = anchor._modified_p;
+
     return new_graph;
@@ -668,2 +678,22 @@ };
 /**
+ * Returns true if the model had the "inconsistent-p" property when
+ * built.
+ *
+ * @returns {Boolean|null} inconsistent or not; null if unknown
+ */
+noctua_graph.prototype.inconsistent_p = function(){
+    return this._inconsistent_p;
+};
+
+/**
+ * Returns true if the model had the "modified-p" property when
+ * built.
+ *
+ * @returns {Boolean|null} inconsistent or not; null if unknown
+ */
+noctua_graph.prototype.modified_p = function(){
+    return this._modified_p;
+};
+
+/**
  * Get the ID from the graph.
@@ -1236,2 +1266,10 @@ *
 	
+	// Add the additional metadata.
+	if( typeof(data['inconsistent-p']) !== 'undefined' ){
+	    anchor._inconsistent_p = data['inconsistent-p'];
+	}
+	if( typeof(data['modified-p']) !== 'undefined' ){
+	    anchor._modified_p = data['modified-p'];
+	}
+
 	// Easy facts.
@@ -1238,0 +1276,0 @@ var facts = data['facts'];

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.18",
+    "version": "0.0.19",
     "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

@@ -22,3 +22,3 @@ ////
 function _get_standard_graph(){
-    var raw_resp = require('./minerva-02.json');
+    var raw_resp = require('./minerva-03.json');
     var g = new model.graph();
@@ -31,8 +31,7 @@ g.load_data_basic(raw_resp['data']);
 var model_a = 'gomodel:5525a0fc00000001';
-var seed_a =
-	"http://purl.obolibrary.org/obo/#5525a0fc00000001%2F5595c4cb00000425";
+var seed_a = "obo:#5525a0fc00000001%2F5595c4cb00000425";
 // The one leaf in the graph ("protein binding").
-var leaf_a = 'http://model.geneontology.org/5525a0fc00000001/5525a0fc0000023';
+var leaf_a = 'gomodel:5525a0fc00000001\/5525a0fc0000023';
 // Bub2.
-var node_a = 'http://purl.obolibrary.org/obo/#5525a0fc00000001%2F5595c4cb00000431';
+var node_a = 'obo:#5525a0fc00000001%2F5595c4cb00000431';
 
@@ -374,28 +373,28 @@ ///
 
-// describe("let's take a close look at types and inferred types", function(){
+describe("let's take a close look at types and inferred types", function(){
 
-//     it('are they working as expected?', function(){	
+    it('are they working as expected?', function(){	
 
-// 	// Setup.
-// 	var g = _get_standard_graph();
-// 	var rellist = ['RO:0002333', 'BFO:0000066'];
-// 	g.fold_go_noctua(rellist);
+	// Setup.
+	var g = _get_standard_graph();
+	var rellist = ['RO:0002333', 'BFO:0000066'];
+	g.fold_go_noctua(rellist);
 
-// 	var nid = leaf_a;
-// 	var n = g.get_node(nid);	
+	var nid = leaf_a;
+	var n = g.get_node(nid);	
 
-// 	//console.log('type:', n.types());
-// 	//console.log('inferred type:', n.inferred_types());
+	//console.log('type:', n.types());
+	//console.log('inferred type:', n.inferred_types());
 
-// 	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');
+	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');
 
-//     });
-// });
+    });
+});
 
@@ -537,8 +536,6 @@ describe("clobbering updating", function(){
 	// Currently dealing with possibly bad data in minerva-02.json
-	//assert.equal(n.inferred_types().length, 2, 'two inferred');
-	assert.equal(n.inferred_types().length, 0, 'two inferred');
+	assert.equal(n.inferred_types().length, 2, 'two inferred');
+
 	// Ditto
-	// assert.equal(n.get_unique_inferred_types().length, 1,
-	// 	     'one unique inferred');
-	assert.equal(n.get_unique_inferred_types().length, 0,
+	assert.equal(n.get_unique_inferred_types().length, 1,
 		     'one unique inferred');
@@ -548,4 +545,4 @@ assert.equal(n.types()[0].class_id(), 'GO:0005515',
 	// Ditto.
-	// assert.equal(n.get_unique_inferred_types()[0].class_id(), 'GO:0098772',
-	// 	     'one unique inferred class id');
+	assert.equal(n.get_unique_inferred_types()[0].class_id(), 'GO:0098772',
+		     'one unique inferred class id');
     });
@@ -648,2 +645,61 @@ });
 
+describe("inconsistent_p and modified_p", function(){
+
+    it('would expect them not to usually be defined', function(){
+
+	// Setup.
+	var g = _get_standard_graph();
+
+	//
+	assert.equal(g.inconsistent_p(), null, "consistency unknown");
+	assert.equal(g.modified_p(), null, "modification unknown");
+    });
+
+    it('goose setup so they are false', function(){
+
+	// Setup.
+	var raw_resp = require('./minerva-03.json');
+	raw_resp['data']['inconsistent-p'] = false;
+	raw_resp['data']['modified-p'] = false;
+	var g = new model.graph();
+	g.load_data_basic(raw_resp['data']);
+
+	//
+	assert.equal(g.inconsistent_p(), false, "consistency false");
+	assert.equal(g.modified_p(), false, "modification false");
+    });
+
+    it('goose setup so they are true', function(){
+
+	// Setup.
+	var raw_resp = require('./minerva-03.json');
+	raw_resp['data']['inconsistent-p'] = true;
+	raw_resp['data']['modified-p'] = true;
+	var g = new model.graph();
+	g.load_data_basic(raw_resp['data']);
+
+	//
+	assert.equal(g.inconsistent_p(), true, "consistency true");
+	assert.equal(g.modified_p(), true, "modification true");
+    });
+
+    it('make sure truth survives a cloning', function(){
+
+	// Setup.
+	var raw_resp = require('./minerva-03.json');
+	raw_resp['data']['inconsistent-p'] = true;
+	raw_resp['data']['modified-p'] = true;
+	var g = new model.graph();
+	g.load_data_basic(raw_resp['data']);
+
+	var c = g.clone()
+
+	//
+	assert.equal(c.inconsistent_p(), true, "clone consistency true");
+	assert.equal(c.modified_p(), true, "clone modification true");
+    });
+
+});
+
+
 // var assert = require('chai').assert;
@@ -650,0 +706,0 @@ // var model = new require('..');

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Improved metrics

Total package byte prevSize

6407489

increased by0.43%

Number of package files

17

increased by6.25%

Lines of code

29179

increased by2.84%

No dependency changes