bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.11 to 0.0.12

lib/edit.js

		@@ -980,4 +980,5 @@ /**
		* Merge another graph (addition) into the current graph. Includes the
		* copying of annotations for the graph.
		* Graph ID is /not/ copied.
		* copying of annotations for the graph. This is an /additive/
		* operation (e.g. annotations and other non-unique entities
		* accumulate). Graph ID is /not/ copied.
		*
		@@ -1017,2 +1018,91 @@ * @param {graph} in_graph - the graph to merge in
		/**
		* This uses a subgraph to update the contents of the current
		* graph. The update graph is considered to be an updated complete
		* self-contained subsection of the graph, clobbering nodes, edges,
		* and the graph annotations. In the case of edges, all edges for the
		* incoming nodes are deleted, and the ones described in the incoming
		* graph are added (again, update).
		*
		* For example: you can think of it like this: if we have a graph:
		* A, B, C, and A.1, where A, B, and C are nodes and A.1 is an annotation for A.
		* And we have an argument subgraph:
		* A, B, and edge (A,B), and A.2, B.1.
		* The final graph would be:
		* A, B, C and edge (A,B), and A.2, B.1.
		*
		* Essentially, any entity in the new graph clobbers the "old"
		* version; nodes not mentioned are left alone, the subgraph edges are
		* assumed to be complete with reference to the contained nodes. This
		* can express removal of things like annotations and sometimes edges,
		* but not of nodes and edges not contained in within the subgraph.
		*
		* See the unit tests for examples.
		*
		* Be careful of what happens when using with the various loaders as
		* the contents of top-level entities can be very different--you
		* probably want to apply the right loader first.
		*
		* @param {graph} in_graph - the graph to update with
		* @returns {Boolean} if graph was loaded
		*/
		noctua_graph.prototype.update_with = function(update_graph){
		var anchor = this;

		// Prefer the new graph annotations by nuking the old.
		anchor._annotations = [];
		var update_graph_anns = update_graph.annotations();
		each(update_graph_anns, function(ann){
		anchor.add_annotation(ann.clone());
		});

		// Next, look at individuals/nodes for addition or updating.
		var updatable_nodes = {};
		each(update_graph.all_nodes(), function(ind){
		// Update node by clobbering. This is preferred since deleting
		// it would mean that all the connections would have to be
		// reconstructed as well.
		var update_node = anchor.get_node(ind.id());
		if( update_node ){
		//console.log('update node: ' + ind.id());
		}else{
		//console.log('add new node' + ind.id());
		}
		// Mark as a modified node.
		updatable_nodes[ind.id()] = true;
		// Add new node to edit core.
		anchor.add_node(ind.clone());
		});

		// Now look at edges (by individual) for purging and
		// reinstating--no going to try and update edges, just clobber.
		each(update_graph.all_nodes(), function(source_node){
		//console.log('looking at node: ' + source_node.id());

		// Look up what edges it has in /core/, as they will be the
		// ones to update.
		var snid = source_node.id();
		var src_edges = anchor.get_edges_by_subject(snid);

		// Delete all edges for said node in model. We cannot
		// (apparently?) go from connection ID to connection easily,
		// so removing from UI is a separate step.
		each(src_edges, function(src_edge){
		// Remove from model.
		var removed_p = anchor.remove_edge_by_id(src_edge.id());
		//console.log('remove edge (' + removed_p + '): ' + src_edge.id());
		});
		});

		// All edges should have IDs, so get them out of the graph if they
		// are incoming.
		each(update_graph.all_edges(), function(edge){
		var in_id = edge.id();
		anchor.remove_edge_by_id(in_id);
		anchor.add_edge(edge.clone());
		});

		return true;
		};

		/**
		* Load minerva data response.
		@@ -1109,4 +1199,4 @@ *

		console.log('singletons');
		console.log(us.keys(singletons).length);
		//console.log('singletons');
		//console.log(us.keys(singletons).length);

		@@ -1113,0 +1203,0 @@ // Add the evidence singletons into the structure by

package.json

		{
		"name": "bbop-graph-noctua",
		"version": "0.0.11",
		"version": "0.0.12",
		"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

		@@ -323,2 +323,46 @@ ////

		describe("clobbering updating", function(){

		it('updating with a subgraph is not the same as a merge', function(){

		// Setup.
		var g = new model.graph();
		var raw_resp = require('./minerva-01.json');
		g.load_data_go_noctua(raw_resp['data']);

		// 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.update_with(update_g);

		// Graph annotations clobbered to one.
		assert.equal(g.annotations().length, 1, 'updated 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, 4, 'updated graph has seven edges');

		});
		});

		// var assert = require('chai').assert;
		@@ -325,0 +369,0 @@ // var model = new require('..');

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