bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.6 to 0.0.7

lib/edit.js

@@ -402,3 +402,3 @@ /**
 	    annotations: []
-	}
+	};
 
@@ -543,6 +543,7 @@ // Referenced instance ID.
  * @param {Array} [types] - list of types to pre-load
+ * @param {Array} [inferred_types] - list of inferred types to pre-load
  * @returns {node} new bbop model node
  */
-noctua_graph.prototype.create_node = function(id, label, types){
-    return new noctua_node(id, label, types);
+noctua_graph.prototype.create_node = function(id, label, types, inferred_types){
+    return new noctua_node(id, label, types, inferred_types);
 };
@@ -668,3 +669,4 @@
 	var itypes = indv['type'] || [];
-	new_node = anchor.create_node(iid, null, itypes);
+	var inf_itypes = indv['inferred-type'] || [];
+	new_node = anchor.create_node(iid, null, itypes, inf_itypes);
 
@@ -1049,3 +1051,2 @@ // See if there is type info that we want to add.
 	var inds = data['individuals'];
-	//var i_inds = raw_resp['data']['individuals-i'];
 	each(inds, function(ind){
@@ -1098,3 +1099,2 @@ anchor.add_node_from_individual(ind);
 	var inds = data['individuals'];
-	//var i_inds = raw_resp['data']['individuals-i'];
 	each(inds, function(ind){
@@ -1254,5 +1254,6 @@ anchor.add_node_from_individual(ind);
  * @param {Array} [in_types] - list of Objects or strings--anything that can be parsed by class_expression
+ * @param {Array} [in_inferred_types] - list of Objects or strings--anything that can be parsed by class_expression
  * @returns {this}
  */
-function noctua_node(in_id, in_label, in_types){
+function noctua_node(in_id, in_label, in_types, in_inferred_types){
     bbop_node.call(this, in_id, in_label);
@@ -1262,4 +1263,6 @@ this._is_a = 'bbop-graph-noctua.node';
 
+    // Let's make this an OWL-like world.
     this._types = [];
-    this._id2type = {};
+    this._inferred_types = [];
+    this._id2type = {}; // contains map to both types and inferred types
     this._annotations = [];
@@ -1273,3 +1276,2 @@ this._referenced_individuals = [];
     }else{
-	//this._id = in_id;
 	this._id = in_id;
@@ -1285,2 +1287,10 @@ }
 	});
+    }    
+    // Same with inferred types.
+    if( us.isArray(in_inferred_types) ){
+	each(in_inferred_types, function(in_inferred_type){
+	    var new_type = new class_expression(in_inferred_type);
+	    anchor._id2type[new_type.id()] = new_type;
+	    anchor._inferred_types.push(new class_expression(in_inferred_type));
+	});
     }
@@ -1306,3 +1316,4 @@
     // Fresh.
-    var new_clone = new noctua_node(anchor.id(), anchor.label(), anchor.types());
+    var new_clone = new noctua_node(anchor.id(), anchor.label(),
+				    anchor.types(), anchor.inferred_types());
 
@@ -1349,5 +1360,8 @@ // Base class stuff.
 	// Wipe previous type set.
-	anchor._id2type = {};
+	each(anchor._types, function(t){
+	    delete anchor._id2type[t.id()];
+	});
 	anchor._types = [];
 
+	// Serially add new ondes.
 	each(in_types, function(in_type){
@@ -1359,2 +1373,3 @@ var new_type = new class_expression(in_type);
     }
+
     return this._types;
@@ -1364,2 +1379,31 @@ };
 /**
+ * Get current inferred types; replace current inferred types.
+ * 
+ * Parameters:
+ * @param {Array} [in_types] - raw JSON type objects
+ * @returns {Array} array of types
+ */
+noctua_node.prototype.inferred_types = function(in_types){
+    var anchor = this;    
+
+    if( us.isArray(in_types) ){
+
+	// Wipe previous type set.
+	each(anchor._inferred_types, function(t){
+	    delete anchor._id2type[t.id()];
+	});
+	anchor._inferred_types = [];
+
+	// Serially add new ondes.
+	each(in_types, function(in_type){
+	    var new_type = new class_expression(in_type);
+	    anchor._id2type[new_type.id()] = new_type;
+	    anchor._inferred_types.push(new_type);
+	});
+    }
+
+    return this._inferred_types;
+};
+
+/**
  * Add types to current types.
@@ -1380,5 +1424,9 @@ *
 	each(in_types, function(in_type){
-	    var new_type = new class_expression(in_type, inf_p);
+	    var new_type = new class_expression(in_type);
 	    anchor._id2type[new_type.id()] = new_type;
-	    anchor._types.push(new_type);
+	    if( ! inferred_p ){
+		anchor._types.push(new_type);
+	    }else{
+		anchor._inferred_types.push(new_type);
+	    }
 	    
@@ -1392,3 +1440,4 @@ ret = true; // return true if did something
 /**
- * If extant, get the type by its unique identifier.
+ * If extant, get the type by its unique identifier. This works for
+ * both inferred and non-inferred types generally.
  * 
@@ -1408,2 +1457,35 @@ * @param {String} type_id - type id
 /**
+ * Essentially, get all of the "uneditable" inferred types from the
+ * reasoner that are not duplicated in the regular (editable) types
+ * listing.
+ * 
+ * Returns originals.
+ * 
+ * Note: the matching here is awful and should be redone (going by
+ * very lossy string rep).
+ * 
+ * @returns {Array} of {class_expression}
+ */
+noctua_node.prototype.get_unique_inferred_types = function(){
+    var anchor = this;
+
+    var ret = [];
+
+    // Create a checkable representation of the types.
+    var type_cache = {};
+    each(anchor.types(), function(t){
+	type_cache[t.to_string()] = true;
+    });
+
+    // Do a lookup.
+    each(anchor.inferred_types(), function(t){
+	if( ! type_cache[t.to_string()] ){
+	    ret.push(t);
+	}
+    });
+
+    return ret;
+};
+
+/**
  * Get/set the "contained" subgraph. This subgraph is still considered
@@ -1410,0 +1492,0 @@ * to be part of the graph, but is "hidden" under this node for most

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.6",
+    "version": "0.0.7",
     "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/minerva-01.json

 {
     "data": {
-        "individuals-i": [
+        "properties": [
             {
-                "type": [
-                    {
-                        "id": "SGD:S000004659",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004659-553ff9ed0000010"
+                "label": "has input",
+                "id": "RO:0002233",
+                "type": "property"
             },
             {
-                "type": [
-                    {
-                        "label": "GTPase inhibitor activity",
-                        "id": "GO:0005095",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0005095-5525a0fc0000009"
-            },
-            {
-                "type": [
-                    {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000017"
-            },
-            {
-                "type": [
-                    {
-                        "label": "enzyme assay evidence",
-                        "id": "ECO:0000005",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000005-553ff9ed0000003"
-            },
-            {
-                "type": [
-                    {
-                        "id": "SGD:S000004529",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004"
-            },
-            {
-                "type": [
-                    {
-                        "label": "enzyme assay evidence",
-                        "id": "ECO:0000005",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000005-553ff9ed0000001"
-            },
-            {
-                "type": [
-                    {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000005"
-            },
-            {
-                "type": [
-                    {
-                        "id": "SGD:S000003814",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000002"
-            },
-            {
-                "type": [
-                    {
-                        "id": "SGD:S000003814",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
-            },
-            {
-                "type": [
-                    {
-                        "label": "physical interaction evidence",
-                        "id": "ECO:0000021",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000021-553ff9ed0000009"
-            },
-            {
-                "type": [
-                    {
-                        "label": "GTP binding",
-                        "id": "GO:0005525",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0005525-5525a0fc0000010"
-            },
-            {
-                "type": [
-                    {
-                        "id": "SGD:S000004659",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004659-553ff9ed0000006"
-            },
-            {
-                "type": [
-                    {
-                        "label": "Bfa1-Bub2 complex",
-                        "id": "GO:1990334",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-GO-1990334-553ff9ed0000011"
-            },
-            {
-                "type": [
-                    {
-                        "id": "SGD:S000004529",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000014"
-            },
-            {
-                "type": [
-                    {
-                        "label": "in vitro binding evidence",
-                        "id": "ECO:0000148",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000148-553ff9ed0000013"
-            },
-            {
-                "type": [
-                    {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000016"
-            },
-            {
-                "type": [
-                    {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000015"
-            },
-            {
-                "type": [
-                    {
-                        "label": "GTPase activator complex",
-                        "id": "GO:1902773",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-GO-1902773-553ff9ed0000008"
-            },
-            {
-                "type": [
-                    {
-                        "id": "SGD:S000003814",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000012"
-            },
-            {
-                "type": [
-                    {
-                        "label": "GTPase activator activity",
-                        "id": "GO:0005096",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0005096-5525a0fc0000012"
-            },
-            {
-                "type": [
-                    {
-                        "label": "GTPase activity",
-                        "id": "GO:0003924",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008"
-            },
-            {
-                "type": [
-                    {
-                        "label": "molecular function regulator",
-                        "id": "GO:0098772",
-                        "type": "class"
-                    },
-                    {
-                        "label": "protein binding",
-                        "id": "GO:0005515",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023"
-            }
-        ],
-        "properties": [
-            {
                 "label": "occurs in",
@@ -230,7 +15,2 @@ "id": "BFO:0000066",
             {
-                "label": "has input",
-                "id": "RO:0002233",
-                "type": "property"
-            },
-            {
                 "label": "directly inhibits",
@@ -336,8 +116,8 @@ "id": "RO:0002408",
                     {
+                        "value": "http://orcid.org/0000-0001-7476-6306",
+                        "key": "contributor"
+                    },
+                    {
                         "value": "2015-04-13",
                         "key": "date"
-                    },
-                    {
-                        "value": "http://orcid.org/0000-0001-7476-6306",
-                        "key": "contributor"
                     }
@@ -347,7 +127,7 @@ ],
                     {
-                        "id": "SGD:S000004529",
+                        "id": "SGD:S000003814",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
             },
@@ -408,8 +188,8 @@ {
                     {
+                        "value": "2015-04-13",
+                        "key": "date"
+                    },
+                    {
                         "value": "http://orcid.org/0000-0001-7476-6306",
                         "key": "contributor"
-                    },
-                    {
-                        "value": "2015-04-13",
-                        "key": "date"
                     }
@@ -419,7 +199,7 @@ ],
                     {
-                        "id": "SGD:S000003814",
+                        "id": "SGD:S000004529",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004"
             },
@@ -678,2 +458,14 @@ {
                 ],
+                "inferred-type": [
+                    {
+                        "label": "molecular function regulator",
+                        "id": "GO:0098772",
+                        "type": "class"
+                    },
+                    {
+                        "label": "protein binding",
+                        "id": "GO:0005515",
+                        "type": "class"
+                    }
+                ],
                 "type": [
@@ -731,20 +523,5 @@ {
                 ],
-                "object": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008",
-                "property": "RO:0002406",
-                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005096-5525a0fc0000012"
-            },
-            {
-                "annotations": [
-                    {
-                        "value": "http://orcid.org/0000-0001-7476-6306",
-                        "key": "contributor"
-                    },
-                    {
-                        "value": "2015-04-13",
-                        "key": "date"
-                    }
-                ],
-                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004",
+                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000014",
                 "property": "RO:0002333",
-                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008"
+                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005525-5525a0fc0000010"
             },
@@ -754,12 +531,12 @@ {
                     {
-                        "value": "http://orcid.org/0000-0001-7476-6306",
+                        "value": "GOC:kmv",
                         "key": "contributor"
                     },
                     {
-                        "value": "2015-04-14",
+                        "value": "2015-04-20",
                         "key": "date"
                     }
                 ],
-                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000012",
-                "property": "RO:0002233",
+                "object": "gomodel:taxon_559292-5525a0fc0000001-GO-0005096-5525a0fc0000012",
+                "property": "RO:0002406",
                 "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023"
@@ -778,5 +555,5 @@ },
                 ],
-                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000014",
-                "property": "RO:0002333",
-                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005525-5525a0fc0000010"
+                "object": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008",
+                "property": "RO:0002406",
+                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005096-5525a0fc0000012"
             },
@@ -836,12 +613,12 @@ {
                     {
-                        "value": "GOC:kmv",
+                        "value": "http://orcid.org/0000-0001-7476-6306",
                         "key": "contributor"
                     },
                     {
-                        "value": "2015-04-20",
+                        "value": "2015-04-14",
                         "key": "date"
                     }
                 ],
-                "object": "gomodel:taxon_559292-5525a0fc0000001-GO-0005096-5525a0fc0000012",
-                "property": "RO:0002406",
+                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000012",
+                "property": "RO:0002233",
                 "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023"
@@ -856,2 +633,17 @@ },
                     {
+                        "value": "2015-04-13",
+                        "key": "date"
+                    }
+                ],
+                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004",
+                "property": "RO:0002333",
+                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008"
+            },
+            {
+                "annotations": [
+                    {
+                        "value": "http://orcid.org/0000-0001-7476-6306",
+                        "key": "contributor"
+                    },
+                    {
                         "value": "2015-04-14",
@@ -946,3 +738,3 @@ "key": "date"
     "uid": "GOC:kltm",
-    "packet-id": "5b87bdc7d497b3"
+    "packet-id": "6fcd5414a08834"
 }

tests/noctua-basic.tests.js

@@ -296,2 +296,29 @@ ////
 
+describe("let's take a close look at types and inferred types", function(){
+
+    it('are they working as expected?', function(){	
+
+	// Setup.
+	var g = new model.graph();
+	var raw_resp = require('./minerva-01.json');
+	g.load_data_go_noctua(raw_resp['data']);	
+
+	var nid = 'gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023';
+	var n = g.get_node(nid);	
+
+	//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');
+
+    });
+});
+
 // var assert = require('chai').assert;
@@ -298,0 +325,0 @@ // var model = new require('..');

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Found 1 instance in 1 package

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Worsened metrics

Total package byte prevSize

6327852

decreased by-0.06%

Lines of code

26953

decreased by-0.43%

No dependency changes