bbop-graph-noctua - npm Package Compare versions

Comparing version 0.0.2 to 0.0.3

gulpfile.js

@@ -6,3 +6,3 @@ ////
 var gulp = require('gulp');
-var jsdoc = require('gulp-jsdoc');
+//var jsdoc = require('gulp-jsdoc');
 var mocha = require('gulp-mocha');
@@ -14,2 +14,3 @@ var uglify = require('gulp-uglify');
 var del = require('del');
+var shell = require('gulp-shell');
 
@@ -54,5 +55,13 @@ var paths = {
 // Completely dependent on clean before running doc.
+// gulp.task('jsdoc', ['clean'], function(cb) {
+//     gulp.src(paths.docable, paths.readme)
+//         .pipe(jsdoc('./doc'));
+//     cb(null);
+// });
+// TODO: Ugh--do this manually until gulp-jsdoc gets its act together.
 gulp.task('jsdoc', ['clean'], function(cb) {
-    gulp.src(paths.docable, paths.readme)
-        .pipe(jsdoc('./doc'));
+    gulp.src('')
+        .pipe(shell([
+	    './node_modules/.bin/jsdoc --verbose --template ./node_modules/jsdoc-baseline --readme ./README.md --destination ./doc/ ./lib/*.js'
+	]));
     cb(null);
@@ -59,0 +68,0 @@ });

lib/edit.js

@@ -63,2 +63,3 @@ /**
  *
+ * @memberOf annotation
  * @returns {String} string
@@ -278,2 +279,209 @@ */
 ///
+/// Generic internal evidence (reference individuals) operations;
+/// dynamically attached to node and edge.
+///
+
+/**
+ * Get/set referenced individual list.
+ *
+ * Also, changes type to "referenced" from (probably) node.
+ *
+ * @name referenced_individuals
+ * @function
+ * @param {Array} indivs - (optional) list of {node} to clobber current list
+ * @returns {Array} list of all referenced individuals
+ */
+function _referenced_individuals(indivs){
+
+    if( us.isArray(indivs) ){
+
+	// Convert type.
+	each(indivs, function(ind){
+	    ind.type('referenced');
+	});
+
+	// Not copies, so add by replacement.
+	this._referenced_individuals = indivs;
+    }
+    return this._referenced_individuals;
+}
+
+/**
+ * Add referenced individual.
+ *
+ * Also, changes type to "referenced" from (probably) node.
+ *
+ * @name add_referenced_individual
+ * @function
+ * @param {annotation} indiv - individual to add
+ * @returns {Array} list of all individuals
+ */
+function _add_referenced_individual(indiv){
+    if( ! us.isArray(indiv) ){	
+	indiv.type('referenced');
+	this._referenced_individuals.push(indiv);
+    }
+    return this._referenced_individuals;
+}
+
+/**
+ * Get a sublist of referenced individuals using the filter
+ * function. The filter function take a single individual as an
+ * argument, and adds to the return list if it evaluates to true.
+ *
+ * @name get_referenced_individuals_by_filter
+ * @function
+ * @param {Function} filter - function described above
+ * @returns {Array} list of passing individuals
+ */
+function _get_referenced_individuals_by_filter(filter){
+    var anchor = this;
+
+    var ret = [];
+    each(anchor._referenced_individuals, function(ind){
+	var res = filter(ind);
+	if( res && res == true ){
+	    ret.push(ind);
+	}
+    });
+
+    return ret;
+}
+
+/**
+ * Get sublist of referenced_individuals with a certain ID.
+ *
+ * @name get_referenced_individual_by_id
+ * @function
+ * @param {String} iid - referenced_individual ID to look for
+ * @returns {Array} list of referenced_individuals with that ID
+ */
+function _get_referenced_individual_by_id(iid){
+    var anchor = this;
+
+    var ret = null;
+    each(anchor._referenced_individuals, function(ind){
+	if( ind.id() == iid ){
+	    ret = ind;
+	}
+    });
+
+    return ret;
+}
+
+/**
+ * Returns a list with the following structure:
+ *
+ * : [ { id: <ID>,
+ * :     class_expressions: [{class_expression}, ...],
+ * :     anntations: [{annotation}, ...] },
+ * :   ...
+ * : ]
+ *
+ * Each top-level element in the list represents the core information
+ * of a single referenced individual for a node or edge in this model.
+ *
+ * Keep in mind that this may be most useful in the GO Noctua use case
+ * where evidence is uniformly modeled as (a) referenced
+ * individual(s), where the class(es) are evidence and the annotations
+ * keep things such as source (e.g. PMID), etc.
+ *
+ * @name get_referenced_individual_profiles
+ * @function
+ * @returns {Array} list of referenced_individual information.
+ */
+function _get_referenced_individual_profiles(){
+    var anchor = this;
+
+    var ret = [];
+    each(anchor.referenced_individuals(), function(ind){
+
+	// Base.
+	var prof = {
+	    id: null,
+	    class_expressions: [],
+	    annotations: []
+	}
+
+	// Referenced instance ID.
+	prof.id = ind.id();
+
+	// Collect class expressions and annotations.
+	each(ind.types(), function(ce){
+	    prof.class_expressions.push(ce);
+	});
+	each(ind.annotations(), function(ann){
+	    prof.annotations.push(ann);
+	});
+
+	//
+	ret.push(prof);
+    });
+
+    return ret;
+}
+
+/**
+ * Returns a list with the following structure:
+ *
+ * : [ { id: <ID>,
+ * :     cls: <ID>,
+ * :     source: <STRING>,
+ * :     date: <STRING>,
+ * :     etc
+ * :   },
+ * :   ...
+ * : ]
+ *
+ * Each top-level element in the list represents the core information
+ * in a simple (GO-style) element. This is essentially a distilled
+ * version of get_referenced_individual_profiles for cases where that
+ * is modelling simple piece of evidence (single non-nested class
+ * expression and a set know list of annotations).
+ *
+ * @name get_basic_evidence
+ * @function
+ * @param {Array} annotation_ids - list of strings that identify the annotation keys that will be captured--
+ * @returns {Array} list of referenced_individual simple evidence information.
+ */
+function _get_basic_evidence(annotation_ids){
+    var anchor = this;
+
+    var ret = [];
+
+    // Get hash of the annotation keys present.
+    var test = us.object(us.map(annotation_ids,
+				function(e){ return [e, true]}));
+
+    each(anchor.get_referenced_individual_profiles(), function(cmplx_prof){
+	//console.log(cmplx_prof);
+
+	// Only add conformant referenced individuals.
+	if( cmplx_prof.id && ! us.isEmpty(cmplx_prof.class_expressions) ){
+
+	    // Base.
+	    //console.log(cmplx_prof.class_expressions);
+	    var basic_prof = {
+		id: cmplx_prof.id,
+		cls: cmplx_prof.class_expressions[0].to_string()
+	    };
+	    
+	    // Match and clobber.
+	    each(cmplx_prof.annotations, function(ann){
+		//console.log(ann);
+		if( test[ann.key()] ){
+		    basic_prof[ann.key()] = ann.value();
+		}
+	    });
+
+	    //console.log(basic_prof);
+	    ret.push(basic_prof);
+	}
+	
+    });
+
+    return ret;
+}
+
+///
 /// Next, get some subclasses working for the core triumvirate: graph,
@@ -284,2 +492,12 @@ /// node, edge. Start with graph.
 var bbop_graph = bbop_model.graph;
+
+/**
+ * Sublcass of bbop-graph for use with Noctua ideas and concepts.
+ *
+ * @constructor
+ * @see module:bbop-graph
+ * @alias graph
+ * @param {String} new_id - (optional) new id; otherwise new unique generated
+ * @returns {this}
+ */
 function noctua_graph(new_id){
@@ -305,2 +523,3 @@ bbop_graph.call(this);
     this._annotations = [];
+    //this._referenced_individuals = []; // not for graph yet, or maybe ever
 };
@@ -719,6 +938,8 @@ bbop.extend(noctua_graph, bbop_graph);
  *
+ * TODO: inferred individuals
+ *
  * @param {Object} the "data" portion of a Minerva graph-related response.
- * @returns {this} 
+ * @returns {Boolean} if data was loaded 
  */
-noctua_graph.prototype.load_minerva_response_data = function(data){
+noctua_graph.prototype.load_data_base = function(data){
     var anchor = this;
@@ -730,12 +951,63 @@
 	
-	// TODO: Graph parts--annotations, etc.
+	// Add the graph metadata.
+	var graph_id = data['id'] || null;
+	var graph_anns = data['annotations'] || [];
+	if( graph_id ){ anchor.id(graph_id); }
+	if( ! us.isEmpty(graph_anns) ){
+	    each(graph_anns, function(ann_kv_set){
+		var na = new annotation(ann_kv_set);
+		anchor.add_annotation(na);
+	    });
+	}
+	
+	// Easy facts.
+	var facts = data['facts'];
+	each(facts, function(fact){
+	    anchor.add_edge_from_fact(fact);
+	});
 
+	// Build the structure of the graph in the most obvious way.
 	var inds = data['individuals'];
-	//var i_inds =raw_resp['data']['individuals-i'];
-	var facts = data['facts'];
-	
-	// This is likely to be the seed for the graph builders ;)
+	//var i_inds = raw_resp['data']['individuals-i'];
 	each(inds, function(ind){
 	    anchor.add_node_from_individual(ind);
 	});
+
+	ret = true;
+    }	
+
+    return ret;
+};
+
+/**
+ * Load minerva data response. However, this time, we're going to fold
+ * the evidence individuals into the edges and nodes that reference
+ * them under the referenced_individual functions.
+ *
+ * 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_fold_evidence = function(data){
+    var anchor = this;
+
+    var ret = false;
+
+    if( data ){
+	
+	// Load the graph parts as usual.
+	var graph_id = data['id'] || null;
+	var graph_anns = data['annotations'] || [];
+	if( graph_id ){ anchor.id(graph_id); }
+	if( ! us.isEmpty(graph_anns) ){
+	    each(graph_anns, function(ann_kv_set){
+		var na = new annotation(ann_kv_set);
+		anchor.add_annotation(na);
+	    });
+	}
+
+	// Currently, evidence does not have edges, and if they did,
+	// we wouldn't want to handle them here. All edges in.
+	var facts = data['facts'];
 	each(facts, function(fact){
@@ -745,5 +1017,67 @@ anchor.add_edge_from_fact(fact);
 
+	// Start by adding all of the individuals to the graph.
+	var inds = data['individuals'];
+	//var i_inds = raw_resp['data']['individuals-i'];
+	each(inds, function(ind){
+	    anchor.add_node_from_individual(ind);
+	});
+
+	// Find the evidence singletons and remove them from the
+	// graph.
+	var singletons = {};
+	each(anchor.get_singleton_nodes(), function(singleton){
+	    var sid = singleton.id();
+	    singletons[sid] = singleton;
+	    anchor.remove_node(sid);
+	});
+
+	//console.log('singletons');
+	//console.log(singletons);
+
+	// Add the evidence singletons back into the structure by
+	// scanning through the nodes and adding them as referenced
+	// individuals.
+	each(anchor.all_nodes(), function(node){
+	    each(node.annotations(), function(ann){
+
+		//console.log(ann.key(), ann.value_type(), ann.value());
+		
+		// Is it an evidence annotation.
+		if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
+		    // If so, add it in.
+		    var ev_ref = ann.value();
+		    if( singletons[ev_ref] ){
+			var ev_indiv = singletons[ev_ref];
+			var c1 = node.add_referenced_individual(ev_indiv);
+//			console.log('<<' + node.id() + '>1>', c1.length);
+			var c2 = node.referenced_individuals();
+//			console.log('<<' + node.id() + '>2>', c2.length);
+//			console.log(node)
+		    }
+		}
+	    });
+	});
+
+	// We also need to do the same thing with the edges, adding
+	// back in the evidence as referenced individuals.
+	each(anchor.all_edges(), function(edge){
+	    each(edge.annotations(), function(ann){
+
+		// Is it an evidence annotation.
+		if( ann.key() == 'evidence' && ann.value_type() == 'IRI' ){
+		    // If so, add it in.
+		    var ev_ref = ann.value();
+		    if( singletons[ev_ref] ){
+			var ev_indiv = singletons[ev_ref];
+			edge.add_referenced_individual(ev_indiv);
+		    }
+		}
+	    });
+	});
+
 	ret = true;
     }	
 
+//    console.log(anchor);
+
     return ret;
@@ -757,2 +1091,13 @@ };
 var bbop_node = bbop_model.node;
+/**
+ * Sublcass of bbop-graph.node for use with Noctua ideas and concepts.
+ *
+ * @constructor
+ * @see module:bbop-graph
+ * @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
+ * @returns {this}
+ */
 function noctua_node(in_id, in_label, in_types){
@@ -766,2 +1111,3 @@ bbop_node.call(this, in_id, in_label);
     this._annotations = [];
+    this._referenced_individuals = [];
 
@@ -813,2 +1159,5 @@ // Incoming ID or generate ourselves.
     });
+    each(anchor._referenced_individuals, function(ind){
+	new_clone._referenced_individuals.push(ind.clone());
+    });
     new_clone._x_init = anchor._x_init;
@@ -913,2 +1262,13 @@ new_clone._y_init = anchor._y_init;
 var bbop_edge = bbop_model.edge;
+/**
+ * Sublcass of bbop-graph.edge for use with Noctua ideas and concepts.
+ *
+ * @constructor
+ * @see module:bbop-graph
+ * @alias edge
+ * @param {String} subject - required subject id
+ * @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)
+ * @returns {this}
+ */
 function noctua_edge(subject, object, predicate){
@@ -922,2 +1282,3 @@ bbop_edge.call(this, subject, object, predicate);
     this._annotations = [];
+    this._referenced_individuals = [];
 };
@@ -951,2 +1312,5 @@ bbop.extend(noctua_edge, bbop_edge);
     });
+    each(anchor._referenced_individuals, function(ind){
+	new_clone._referenced_individuals.push(ind.clone());
+    });
 
@@ -1001,6 +1365,3 @@ return new_clone;
 
-///
-/// Add generic bulk annotation operations to: graph, edge, and node.
-///
-
+// Add generic bulk annotation operations to: graph, edge, and node.
 each([noctua_graph, noctua_node, noctua_edge], function(constructr){
@@ -1014,2 +1375,19 @@ constructr.prototype.annotations = _annotations;
 
+// Add generic evidence (referenced individuals) operations to: edge
+// and node.
+each([noctua_node, noctua_edge], function(constructr){
+    constructr.prototype.referenced_individuals =
+	_referenced_individuals;
+    constructr.prototype.add_referenced_individual =
+	_add_referenced_individual;
+    constructr.prototype.get_referenced_individuals_by_filter =
+	_get_annotations_by_filter;
+    constructr.prototype.get_referenced_individual_by_id =
+	_get_referenced_individual_by_id;
+    constructr.prototype.get_referenced_individual_profiles
+	= _get_referenced_individual_profiles;
+    constructr.prototype.get_basic_evidence
+	= _get_basic_evidence;
+});
+
 ///
@@ -1016,0 +1394,0 @@ /// Exportable body.

package.json

 {
     "name": "bbop-graph-noctua",
-    "version": "0.0.2",
+    "version": "0.0.3",
     "license": "BSD-3-Clause",
@@ -34,3 +34,3 @@ "description": "A subclass of bbop-graph that layers on a complete annotation and graph editing model for the Noctua set of tools.",
         "bbop-graph": "0.0.12",
-        "class-expression": "0.0.3",
+        "class-expression": "0.0.4",
         "underscore": "1.8.3"
@@ -48,3 +48,6 @@ },
         "gulp-rename": "^1.2.2",
-        "gulp-uglify": "^1.2.0"
+        "gulp-shell": "^0.4.2",
+        "gulp-uglify": "^1.2.0",
+        "jsdoc": "^3.3.0",
+        "jsdoc-baseline": "git://github.com/hegemonic/jsdoc-baseline.git#74d1dc8075"
     },
@@ -56,3 +59,3 @@ "bundleDependencies": [],
         "lib": "lib",
-        "test": "tests"
+        "tests": "tests"
     },
@@ -59,0 +62,0 @@ "main": "lib/edit.js",

README.md

@@ -5,3 +5,5 @@ # bbop-graph-noctua
 
-General purpose (mathematical) graph library in JavaScript.
+A Noctua-specific subclass of the bbop-graph general graph library.
+The purpose is to add named edges, evidence, types, and other features
+found in a Noctua environment.
 
@@ -8,0 +10,0 @@ ### Availability

tests/minerva-01.json

@@ -7,8 +7,7 @@ {
                     {
-                        "label": "in vitro binding evidence",
-                        "id": "ECO:0000148",
+                        "id": "SGD:S000004659",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000148-553ff9ed0000013"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004659-553ff9ed0000010"
             },
@@ -18,7 +17,8 @@ {
                     {
-                        "id": "SGD:S000004659",
+                        "label": "GTPase inhibitor activity",
+                        "id": "GO:0005095",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004659-553ff9ed0000010"
+                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0005095-5525a0fc0000009"
             },
@@ -33,3 +33,3 @@ {
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000005"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000017"
             },
@@ -39,12 +39,2 @@ {
                     {
-                        "label": "GTPase inhibitor activity",
-                        "id": "GO:0005095",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel:taxon_559292-5525a0fc0000001-GO-0005095-5525a0fc0000009"
-            },
-            {
-                "type": [
-                    {
                         "label": "enzyme assay evidence",
@@ -79,7 +69,8 @@ "id": "ECO:0000005",
                     {
-                        "id": "SGD:S000003814",
+                        "label": "direct assay evidence",
+                        "id": "ECO:0000002",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000005"
             },
@@ -98,2 +89,11 @@ {
                     {
+                        "id": "SGD:S000003814",
+                        "type": "class"
+                    }
+                ],
+                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
+            },
+            {
+                "type": [
+                    {
                         "label": "physical interaction evidence",
@@ -147,8 +147,8 @@ "id": "ECO:0000021",
                     {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
+                        "label": "in vitro binding evidence",
+                        "id": "ECO:0000148",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000017"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000148-553ff9ed0000013"
             },
@@ -266,18 +266,2 @@ {
                     {
-                        "value": "PMID:12048186",
-                        "key": "source"
-                    }
-                ],
-                "type": [
-                    {
-                        "label": "in vitro binding evidence",
-                        "id": "ECO:0000148",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000148-553ff9ed0000013"
-            },
-            {
-                "annotations": [
-                    {
                         "value": "2015-04-14",
@@ -302,18 +286,3 @@ "key": "date"
                     {
-                        "value": "PMID:12048186",
-                        "key": "source"
-                    }
-                ],
-                "type": [
-                    {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
-                        "type": "class"
-                    }
-                ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000005"
-            },
-            {
-                "annotations": [
-                    {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000005-553ff9ed0000001",
@@ -349,2 +318,18 @@ "key": "evidence"
                     {
+                        "label": "direct assay evidence",
+                        "id": "ECO:0000002",
+                        "type": "class"
+                    }
+                ],
+                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000017"
+            },
+            {
+                "annotations": [
+                    {
+                        "value": "PMID:12048186",
+                        "key": "source"
+                    }
+                ],
+                "type": [
+                    {
                         "label": "enzyme assay evidence",
@@ -395,2 +380,18 @@ "id": "ECO:0000005",
                     {
+                        "value": "PMID:12048186",
+                        "key": "source"
+                    }
+                ],
+                "type": [
+                    {
+                        "label": "direct assay evidence",
+                        "id": "ECO:0000002",
+                        "type": "class"
+                    }
+                ],
+                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000005"
+            },
+            {
+                "annotations": [
+                    {
                         "value": "http://orcid.org/0000-0001-7476-6306",
@@ -410,3 +411,3 @@ "key": "contributor"
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000002"
             },
@@ -430,3 +431,3 @@ {
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000002"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000007"
             },
@@ -452,2 +453,3 @@ {
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000148-553ff9ed0000013",
@@ -541,8 +543,8 @@ "key": "evidence"
                     {
-                        "label": "direct assay evidence",
-                        "id": "ECO:0000002",
+                        "label": "in vitro binding evidence",
+                        "id": "ECO:0000148",
                         "type": "class"
                     }
                 ],
-                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000017"
+                "id": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000148-553ff9ed0000013"
             },
@@ -631,2 +633,3 @@ {
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000005",
@@ -652,2 +655,3 @@ "key": "evidence"
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000005-553ff9ed0000003",
@@ -673,2 +677,3 @@ "key": "evidence"
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000021-553ff9ed0000009",
@@ -753,5 +758,5 @@ "key": "evidence"
                 ],
-                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000014",
+                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004",
                 "property": "RO:0002333",
-                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005525-5525a0fc0000010"
+                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008"
             },
@@ -761,12 +766,12 @@ {
                     {
-                        "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"
@@ -781,9 +786,9 @@ },
                     {
-                        "value": "2015-04-14",
+                        "value": "2015-04-13",
                         "key": "date"
                     }
                 ],
-                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000003814-553ff9ed0000012",
-                "property": "RO:0002233",
-                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023"
+                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000014",
+                "property": "RO:0002333",
+                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005525-5525a0fc0000010"
             },
@@ -823,2 +828,3 @@ {
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000017",
@@ -843,13 +849,13 @@ "key": "evidence"
                     {
-                        "value": "http://orcid.org/0000-0001-7476-6306",
+                        "value": "GOC:kmv",
                         "key": "contributor"
                     },
                     {
-                        "value": "2015-04-13",
+                        "value": "2015-04-20",
                         "key": "date"
                     }
                 ],
-                "object": "gomodel_taxon_559292-5525a0fc0000001-SGD-S000004529-553ff9ed0000004",
-                "property": "RO:0002333",
-                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0003924-5525a0fc0000008"
+                "object": "gomodel:taxon_559292-5525a0fc0000001-GO-0005096-5525a0fc0000012",
+                "property": "RO:0002406",
+                "subject": "gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023"
             },
@@ -874,2 +880,3 @@ {
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000015",
@@ -894,2 +901,3 @@ "key": "evidence"
                     {
+                        "value-type": "IRI",
                         "value": "gomodel_taxon_559292-5525a0fc0000001-ECO-0000002-553ff9ed0000016",
@@ -952,3 +960,3 @@ "key": "evidence"
     "uid": "GOC:kltm",
-    "packet-id": "587a9e87c34a51a"
+    "packet-id": "5b87bdc7d497b3"
 }

tests/noctua-basic.tests.js

@@ -96,3 +96,3 @@ ////
 	var g = new model.graph();
-	g.load_minerva_response_data(raw_resp['data']);
+	g.load_data_base(raw_resp['data']);
 
@@ -109,4 +109,11 @@ // Right?
 	var g = new model.graph();
-	g.load_minerva_response_data(raw_resp['data']);
+	g.load_data_base(raw_resp['data']);
 
+	assert.equal(g.id(),'gomodel:taxon_559292-5525a0fc0000001_all_indivdual',
+		     'graph id');
+	assert.equal(g.annotations().length, 4, '4 graph annotation');
+	var anns = g.get_annotations_by_key('date');
+	assert.equal(anns.length, 1, 'one date annotation');
+	assert.equal(anns[0].value(), '2015-04-10', 'correct date annotation');
+
 	// Wee tests.
@@ -127,3 +134,3 @@ assert.equal(g.all_nodes().length, 22, 'right num nodes');
 	var g = new model.graph();
-	g.load_minerva_response_data(raw_resp['data']);
+	g.load_data_base(raw_resp['data']);
 	
@@ -158,2 +165,45 @@ // Head up from our one leaf
 
+    it("evidence that evidence works", function(){
+
+	// Setup.
+	var raw_resp = require('./minerva-01.json');
+	var g = new model.graph();
+	g.load_data_fold_evidence(raw_resp['data']);
+	
+	// Okay, we should have a lot less nodes now.
+	assert.equal(g.all_nodes().length, 14, '22 - 8 ev nodes = 14');
+	
+	// Let's track down the evidence for one node.
+	var nid = 'gomodel:taxon_559292-5525a0fc0000001-GO-0005515-5525a0fc0000023';
+	var n = g.get_node(nid);
+	assert.equal(n.id(), nid, 'some weirdness here at one point');
+
+	// The hard way.
+	var ri = n.referenced_individuals();
+	assert.equal(ri.length, 1, 'one piece of ev');
+	var ev_ind = ri[0];
+	var types = ev_ind.types();
+	assert.equal(types.length, 1, 'one class exp');
+	var t = types[0];
+	assert.equal(t.class_id(), 'ECO:0000021', 'say hi');
+
+	// The easy way.
+	var profs = n.get_referenced_individual_profiles();
+	assert.equal(profs.length, 1, 'one profile using this method');
+	var first_prof = profs[0];
+	assert.isNotNull(first_prof.id, 'has id using this method');
+	assert.equal(first_prof.class_expressions.length, 1,
+		     'one ce using this method');
+	assert.equal(first_prof.annotations.length, 1,
+		     'one ann using this method');
+
+	// The overly easy super-simple (GO) way.
+	var evs = n.get_basic_evidence(['source']);
+	//console.log(evs);
+	assert.equal(evs.length, 1, 'one evs');
+	var ev = evs[0];
+	assert.isString(ev['id'], 'got RI id');
+	assert.equal(ev['cls'], 'ECO:0000021', 'got ev class');
+	assert.equal(ev['source'], 'PMID:12048186', 'got source ref');
+    });
 });
@@ -169,2 +219,2 @@
 // var g = new model.graph();
-// g.load_minerva_response_data(raw_resp['data']);
+// g.load_data_fold_evidence(raw_resp['data']);

No alert changes

Improved metrics

Total package byte prevSize

6323765

increased by0.21%

Lines of code

26840

increased by1.48%

Number of lines in readme file

18

increased by12.5%

Worsened metrics

Dev dependency count

13

increased by30%

Dependency changes

• + Addedclass-expression@0.0.4(transitive)

• - Removedclass-expression@0.0.3(transitive)

• Updatedclass-expression@0.0.4