bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.16 to 0.0.17

lib/edit.js

@@ -1017,2 +1017,53 @@ /**
 /**
+ * Merge another graph into the current graph, with special overwrite
+ * rules. In essence, this could be used when trying to simulate a
+ * rebuild even though you got merge data.
+ * 
+ * Annotations in any top-level item (graph, node, edge), or lack
+ * thereof, from the incoming graph is preferred.
+ * 
+ * All extant edges and nodes in the incoming graph are clobbered.
+ *
+ * The incoming graph is considered to be "complete", so any edges
+ * where both the source and sink are in the incoming graph are
+ * considered to be the only edges between those node.
+ *
+ * Graph ID is /not/ copied.
+ *
+ * Beware that you're in the right folded mode.
+ *
+ * @param {graph} in_graph - the graph to merge in
+ * @returns {Boolean} if graph was loaded 
+ */
+noctua_graph.prototype.merge_special = function(in_graph){
+    var anchor = this;
+
+    // Since we can actually legally have an edge delete in the
+    // merge, let's go ahead and cycle through the "complete"
+    // graph and toss edges from individuals involved in the
+    // merge.
+    var involved_node = {};
+    each(in_graph.all_nodes(), function(node){
+	involved_node[node.id()] = true;
+    });
+    // Okay, now get rid of all edges that are defined by the
+    // involved nodes.
+    each(anchor.all_edges(), function(edge){
+	if(involved_node[edge.subject_id()] && involved_node[edge.object_id()]){
+	    anchor.remove_edge_by_id(edge.id());
+	}
+    });
+    
+    // Blitz our old annotations as all new will be incoming (and
+    // the merge just takes the superset). Will be fine with fix:
+    // https://github.com/geneontology/minerva/issues/5
+    anchor.annotations([]);
+    
+    var ret = anchor.merge_in(in_graph);
+    return ret;
+};
+
+/**
+ * DEPRECATED
+ *
  * This uses a subgraph to update the contents of the current
@@ -1044,2 +1095,3 @@ * graph. The update graph is considered to be an updated complete
  *
+ * @deprecated
  * @param {graph} in_graph - the graph to update with
@@ -1421,7 +1473,7 @@ * @returns {Boolean} if graph was loaded
     
-    // Optional layout hints.
-    this._x_init = null; // initial layout hint
-    this._y_init = null;
-    // this.xlast = null; // last known location
-    // this.ylast = null;
+    // // Optional layout hints.
+    // this._x_init = null; // initial layout hint
+    // this._y_init = null;
+    // // this.xlast = null; // last known location
+    // // this.ylast = null;
 };
@@ -1463,5 +1515,5 @@ bbop.extend(noctua_node, bbop_node);
 
-    // Coordinates.
-    new_clone._x_init = anchor._x_init;
-    new_clone._y_init = anchor._y_init;
+    // // Coordinates.
+    // new_clone._x_init = anchor._x_init;
+    // new_clone._y_init = anchor._y_init;
 
@@ -1633,23 +1685,23 @@ return new_clone;
 
-/**
- * Get/set "x" value of node.
- * 
- * @param {Number} value - number
- * @returns {Number|null} type or null
- */
-noctua_node.prototype.x_init = function(value){
-    if(value) this._x_init = value;
-    return this._x_init;
-};
+// /**
+//  * Get/set "x" value of node.
+//  * 
+//  * @param {Number} value - number
+//  * @returns {Number|null} type or null
+//  */
+// noctua_node.prototype.x_init = function(value){
+//     if(value) this._x_init = value;
+//     return this._x_init;
+// };
 
-/**
- * Get/set "y" value of node.
- * 
- * @param {Number} value - number
- * @returns {Number|null} type or null
- */
-noctua_node.prototype.y_init = function(value){
-    if(value) this._y_init = value;
-    return this._y_init;
-};
+// /**
+//  * Get/set "y" value of node.
+//  * 
+//  * @param {Number} value - number
+//  * @returns {Number|null} type or null
+//  */
+// noctua_node.prototype.y_init = function(value){
+//     if(value) this._y_init = value;
+//     return this._y_init;
+// };
 
@@ -1656,0 +1708,0 @@ ///

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.16",
+    "version": "0.0.17",
     "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

@@ -401,3 +401,3 @@ ////
 	assert.equal(g.all_nodes().length, 8, 'updated graph has eight nodes');
-	assert.equal(g.all_edges().length, 4, 'updated graph has seven edges');
+	assert.equal(g.all_edges().length, 4, 'updated graph has four edges');
 
@@ -407,2 +407,48 @@ });
 
+describe("special/dumb merge updating", function(){
+
+    it('updating with a subgraph to make it like a rebuild', function(){	
+
+	// Setup.
+	var g = new model.graph();
+	var raw_resp = require('./minerva-01.json');
+	var rellist = ['RO:0002333', 'BFO:0000066'];
+	g.load_data_basic(raw_resp['data']);
+	g.fold_go_noctua(rellist);
+
+	// Make a new graph to operate on.
+	var update_g = new model.graph();
+	// Graph annotations.
+	var an1 = new model.annotation({"key": "title",	"value": "meow"});
+	update_g.add_annotation(an1);
+	// Graph parts.
+	var un1 = new model.node('gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023');
+	var un2 = new model.node('gomodel_taxon_559292-5525a0fc0000001-GO-1990334-553ff9ed0000011');
+	var un3 = new model.node('blahblah');
+	var ue1 = new model.edge(un1.id(), un2.id(), 'RO:1234567');
+	update_g.add_node(un1);
+	update_g.add_node(un2);
+	update_g.add_node(un3);
+	update_g.add_edge(ue1);
+
+	// Double check.
+	assert.equal(update_g.all_nodes().length, 3, 'subgraph has 3 nodes');
+	assert.equal(update_g.all_edges().length, 1, 'subgraph has 1 edge');
+	assert.equal(update_g.annotations().length, 1, 'subgraph has 1 ann');
+
+	// Update our graph with new graph.
+	g.merge_special(update_g);
+
+	// Graph annotations clobbered.
+	assert.equal(g.annotations().length, 1, 'rebuild merge graph has 1 ann');
+	assert.equal(g.annotations()[0].key(), 'title', 'has title');
+	assert.equal(g.annotations()[0].value(), 'meow', 'title "meow"');
+
+	// We have one new node and same edges.
+	assert.equal(g.all_nodes().length, 8, 'updated graph has eight nodes');
+	assert.equal(g.all_edges().length, 7, 'updated graph has seven edges');
+
+    });
+});
+
 describe("unfolding works", function(){
@@ -409,0 +455,0 @@

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6341070

increased by0.05%

Lines of code

27273

increased by0.31%

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