bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.5 to 0.0.6

lib/edit.js

@@ -35,3 +35,3 @@ /**
  * @constructor
- * @param {Object} kv_set - (optional) a set of keys and values; a simple object
+ * @param {Object} [kv_set] - optional a set of keys and values; a simple object
  * @returns {this} new instance
@@ -64,3 +64,2 @@ */
  *
- * @memberOf annotation
  * @returns {String} string
@@ -76,4 +75,4 @@ */
  * @param {String} key - string
- * @param {String} value - (optional) string
- * @param {String} value_type - (optional) string
+ * @param {String} [value] - string
+ * @param {String} [value_type] - string
  * @returns {String|null} returns property is key
@@ -108,3 +107,3 @@ */
  *
- * @param {String} key - (optional) string
+ * @param {String} [key] - string
  * @returns {String|null} returns string of annotation
@@ -121,3 +120,3 @@ */
  *
- * @param {String} value - (optional) string
+ * @param {String} [value] - string
  * @returns {String|null} returns string of annotation
@@ -134,3 +133,3 @@ */
  *
- * @param {String} value_type - (optional) string
+ * @param {String} [value_type] - string
  * @returns {String|null} returns string of annotation
@@ -195,3 +194,3 @@ */
  * @function
- * @param {Array} in_anns - (optional) list of annotations to clobber current list
+ * @param {Array} [in_anns] - list of annotations to clobber current list
  * @returns {Array} list of all annotations
@@ -297,3 +296,3 @@ */
  * @function
- * @param {Array} indivs - (optional) list of {node} to clobber current list
+ * @param {Array} [indivs] - list of {node} to clobber current list
  * @returns {Array} list of all referenced individuals
@@ -506,3 +505,3 @@ */
  * @alias graph
- * @param {String} new_id - (optional) new id; otherwise new unique generated
+ * @param {String} [new_id] - new id; otherwise new unique generated
  * @returns {this}
@@ -539,3 +538,3 @@ */
  * @param {string} object - node id string or node
- * @param {string} predicate - (optional) a user-friendly description of the node
+ * @param {string} [predicate] - a user-friendly description of the node
  * @returns {edge} bbop model edge
@@ -551,4 +550,4 @@ */
  * @param {string} id - a unique id for the node
- * @param {string} label - (optional) a user-friendly description of the node
- * @param {Array} types - (optional) list of types to pre-load
+ * @param {string} [label] - a user-friendly description of the node
+ * @param {Array} [types] - list of types to pre-load
  * @returns {node} new bbop model node
@@ -561,2 +560,32 @@ */
 /**
+ * Create a clone of the graph.
+ *
+ * @returns {graph} bbop model graph
+ */
+noctua_graph.prototype.clone = function(){
+    var anchor = this;
+
+    var new_graph = anchor.create_graph();
+
+    // Collect the nodes and edges.
+    each(anchor.all_nodes(), function(node){
+	new_graph.add_node(node.clone());
+    });
+    each(anchor.all_edges(), function(edge){
+	new_graph.add_edge(edge.clone());
+    });
+
+    // Collect other information.
+    new_graph.default_predicate = anchor.default_predicate;
+    new_graph._id = anchor._id;
+
+    // Copy new things: annotations.
+    each(anchor._annotations, function(annotation){
+	new_graph._annotations.push(annotation.clone());
+    });
+    
+    return new_graph;
+};
+
+/**
  * Create a graph for use in internal operations.
@@ -686,3 +715,3 @@ *
 /**
- * Return a node by its element id.
+ * Return a copy of a {node} by its element id.
  *
@@ -701,3 +730,4 @@ * @returns {node|null} node
 /**
- * Return a node by its corresponding Minerva JSON rep individual.
+ * Return a copy of a {node} by its corresponding Minerva JSON rep
+ * individual.
  *
@@ -735,3 +765,3 @@ * @returns {node|null} node
  * @param {String} node_id - the id for a node
- * @param {Boolean} clean_p - (optional) remove all edges connects to node (default false)
+ * @param {Boolean} [clean_p] - remove all edges connects to node (default false)
  * @returns {Boolean} true if node found and destroyed
@@ -867,3 +897,3 @@ */
  * @param {String} object_id - object by ID
- * @param {String} predicate_id - (Optional) predicate ID or default
+ * @param {String} [predicate_id] - predicate ID or default
  * @returns {Boolean} true if such an edge was found and deleted, false otherwise
@@ -1146,2 +1176,77 @@ */
 
+/**
+ * Load minerva data response. However, this time, in addition to
+ * everything we did for {load_data_evidence_fold}, we're going to
+ * search for nodes that have enabled_by and/or occurs_in targets
+ * (that are themselves leaves) fold them in to the contained subgraph
+ * item, and remove them from the top-level graph.
+ *
+ * TODO: inferred individuals
+ *
+ * @param {Object} the "data" portion of a Minerva graph-related response.
+ * @returns {Boolean} if data was loaded 
+ */
+noctua_graph.prototype.load_data_go_noctua = function(data){
+    var anchor = this;
+
+    // Start out with the evidence folded graph.
+    var ret = anchor.load_data_fold_evidence(data);
+    if( ! ret ){ return false; } // Early bail on bad upstream.
+    
+    // It is foldable if it is a root node (re: opposite of leaf--only
+    // target) and if it only has the one child (no way out--re: collapsible ).
+    function _foldable_p(node){
+	var ret = false;
+	if( anchor.is_root_node(node.id()) &&
+	    anchor.get_child_nodes(node.id()).length == 1 ){
+		//console.log("foldable: " + node.id());
+		ret = true;
+	    }
+	return ret;
+    }
+
+    // Okay, first scan all nodes for our pattern.
+    each(anchor.all_nodes(), function(ind){
+
+	// The possible base subgraph (seeding with current node--note
+	// the clone so we don't have infinite recursion) we might
+	// capture.
+	var subgraph = anchor.create_graph();
+	subgraph.add_node(ind.clone());
+
+	// Check a set of relations for completeness: enabled_by and
+	// occurs_in (location).
+	var collapsable_relations = ['RO:0002333', 'BFO:0000066'];
+	each(collapsable_relations, function(relation){
+	    
+	    var kids = anchor.get_parent_nodes(ind.id(), relation);
+	    each(kids, function(kid){
+		if( _foldable_p(kid) ){
+
+		    // Preserve it and its edge in the new subgraph.
+		    subgraph.add_node(kid.clone());
+		    subgraph.add_edge(
+			anchor.get_parent_edges(ind.id(), relation)[0].clone());
+
+		    // Remove same from the original graph, edge will be
+		    // destroyed in the halo.
+		    anchor.remove_node(kid.id(), true);
+		}
+	    });
+	});
+
+	// A usable folding subgraph only occurred when the are more
+	// than 1 node in it; i.e. we actually actually added things
+	// to our local subgraph and removed them from the master
+	// graph.
+	if( subgraph.all_nodes().length > 1 ){
+	    //console.log('slurpable subgraph for: ' + ind.id());
+	    ind.subgraph(subgraph);
+	}
+
+    });
+
+    return ret;
+};
+
 ///
@@ -1158,5 +1263,5 @@ /// Node subclass and overrides.
  * @alias node
- * @param {String} in_id - (optional) new id; otherwise new unique generated
- * @param {String} in_label - (optional) node "label"
- * @param {Array} in_types - (optional) list of Objects or strings--anything that can be parsed by class_expression
+ * @param {String} [in_id] - new id; otherwise new unique generated
+ * @param {String} [in_label] - node "label"
+ * @param {Array} [in_types] - list of Objects or strings--anything that can be parsed by class_expression
  * @returns {this}
@@ -1173,2 +1278,3 @@ */
     this._referenced_individuals = [];
+    this._embedded_subgraph = null;
 
@@ -1216,3 +1322,4 @@ // Incoming ID or generate ourselves.
 
-    // Transfer over the new goodies.
+    // Transfer over the new goodies, starting with annotations and
+    // referenced individuals.
     each(anchor._annotations, function(annotation){
@@ -1224,2 +1331,11 @@ new_clone._annotations.push(annotation.clone());
     });
+
+    // Embedded subgraph.
+    if( anchor._embedded_subgraph ){
+	new_clone._embedded_subgraph = anchor._embedded_subgraph.clone();
+    }else{
+	new_clone._embedded_subgraph = null;
+    }
+
+    // Coordinates.
     new_clone._x_init = anchor._x_init;
@@ -1235,3 +1351,3 @@ new_clone._y_init = anchor._y_init;
  * Parameters:
- * @param {Array} in_types - (optional) raw JSON type objects
+ * @param {Array} [in_types] - raw JSON type objects
  * @returns {Array} array of types
@@ -1299,2 +1415,21 @@ */
 /**
+ * Get/set the "contained" subgraph. This subgraph is still considered
+ * to be part of the graph, but is "hidden" under this node for most
+ * use cases except serialization.
+ * 
+ * To put it another way, unless you specifically load this with a
+ * specialized loader, it will remain unpopulated. During
+ * serialization, it should be recursively walked and dumped.
+ * 
+ * @param {graph} [subgraph] - the subgraph to "hide" inside this individual in the graph
+ * @returns {graph|null} contained subgraph
+ */
+noctua_node.prototype.subgraph = function(subgraph){
+    if( subgraph && bbop.what_is(subgraph) == 'bbop-graph-noctua.graph'){
+	this._embedded_subgraph = subgraph;
+    }
+    return this._embedded_subgraph;
+};
+
+/**
  * Get/set "x" value of node.
@@ -1334,3 +1469,3 @@ *
  * @param {String} object - required object id
- * @param {String} predicate - (optional) preidcate id; if not provided, will use defined default (you probably want to provide one--explicit is better)
+ * @param {String} [predicate] - preidcate id; if not provided, will use defined default (you probably want to provide one--explicit is better)
  * @returns {this}
@@ -1395,3 +1530,3 @@ */
  * @deprecated
- * @param {String} value - (optional) string
+ * @param {String} [value] - string
  * @returns {String} string
@@ -1408,3 +1543,3 @@ */
  * @deprecated
- * @param {String} value - (optional) string
+ * @param {String} [value] - string
  * @returns {String} string
@@ -1421,3 +1556,3 @@ */
  * @deprecated
- * @param {String} value - (optional) string
+ * @param {String} [value] - string
  * @returns {String} string
@@ -1424,0 +1559,0 @@ */

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.5",
+    "version": "0.0.6",
     "license": "BSD-3-Clause",
@@ -33,3 +33,3 @@ "description": "A subclass of bbop-graph that layers on a complete annotation and graph editing model for the Noctua set of tools.",
         "bbop-core": "0.0.4",
-        "bbop-graph": "0.0.12",
+        "bbop-graph": "0.0.13",
         "class-expression": "0.0.4",
@@ -36,0 +36,0 @@ "underscore": "1.8.3"

tests/noctua-basic.tests.js

@@ -251,2 +251,47 @@ ////
 
+describe('abbreviate graph as expected in go noctua loader', function(){
+
+    it('pull in many subgraphs', function(){	
+
+	// Setup.
+	var g = new model.graph();
+	var raw_resp = require('./minerva-01.json');
+	g.load_data_go_noctua(raw_resp['data']);	
+
+	// Basic structure count.
+	assert.equal(g.all_nodes().length, 7, 'only seven nodes left');
+	assert.equal(g.all_edges().length, 7, 'only seven edges left');
+
+	// Five subragphs, all containing the embedding individual as
+	// part of this loader's process.
+	var num_sub = 0;
+	var self_contained_sub = 0;
+	each(g.all_nodes(), function(n){
+	    if( n.subgraph() ){
+		num_sub++;
+		var s = n.subgraph();
+		//console.log('sub in: ' + n.id());
+		//console.log('sub is: ' + typeof(s.get_node));
+		if( s.get_node(n.id()) ){
+		    self_contained_sub++;
+		}
+	    }
+	});
+	assert.equal(num_sub, 5, 'five embedded subgraphs');
+	assert.equal(self_contained_sub, 5, 'five self-containing subgraphs');
+
+	// Close examination of a single subgraph.
+	var nid = 'gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023';
+	var n = g.get_node(nid);
+	assert.equal(n._is_a, 'bbop-graph-noctua.node', 'node is a node');
+	var s = n.subgraph();
+	//console.log(s);
+	assert.equal(s._is_a, 'bbop-graph-noctua.graph', 'graph is a graph');
+	assert.equal(s.all_nodes().length, 2, 'subgraph has two nodes');
+	assert.equal(s.all_edges().length, 1, 'subgraph has one edges');
+	assert.equal(s.all_edges()[0].predicate_id(), 'RO:0002333', 'correct subraph edge');
+	//console.log();
+    });
+});
+
 // var assert = require('chai').assert;
@@ -253,0 +298,0 @@ // var model = new require('..');

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Improved metrics

Total package byte prevSize

6331798

increased by0.09%

Lines of code

27070

increased by0.57%

Dependency changes

• + Addedbbop-graph@0.0.13(transitive)

• - Removedbbop-graph@0.0.12(transitive)

• Updatedbbop-graph@0.0.13