Merge pull request #722 from geneontology/dev

Updating Noctua Production

Author: kltm

config/startup.yaml.environment-development

@@ -81,8 +81,6 @@ WORKBENCHES:
   value:
     - '../noctua-form/workbenches'
     - '../noctua-landing-page/workbenches'
-    - '../noctua-annotation-review/workbenches'
-    - '../noctua-search/workbenches'
     - '../noctua-form-legacy/workbenches'
     - 'workbenches'
 ## Minerva operations preferences.

js/NoctuaEditor.js

@@ -739,7 +739,10 @@ var MMEnvInit = function(model_json, in_relations, in_token){
 		    });
 		    var vvm = new widgetry.contained_modal(
 			null, 'Violations',
-                        '<p>This feature is <strong>currently under development</strong>, with more user friendly error reports coming. If you have questions about the error messages you\'re seeing, please create a <a href="https://github.com/geneontology/noctua"><u>ticket</u></a>.</p>' +
+                      '<div class="alert alert-dismissable alert-warning">' +
+                        '<button type="button" class="close" data-dismiss="alert">&times;</button>' +
+                        'This feature is <strong>currently under development</strong>, with more user friendly error reports coming. If you have questions about the error messages you\'re seeing, please create a <a href="https://github.com/geneontology/noctua"><u>ticket</u></a>.' +
+                        '</div>' +
 			violation_renderings.join(' <hr /> '));
 		    vvm.show();
 		}

js/lib/noctua-widgetry/widgetry.js

@@ -104,11 +104,18 @@ function repaint_info(ecore, aid, info_div){
 	// Assemble a human-readable label.
 	var nid = v.node_id();
 	var node = ecore.get_node(nid);
-	var node_label = '';
-	var std_types = node.types();
-	us.each(std_types, function(in_type){
-	    node_label += type_to_span(in_type);
-	});
+	// This /could/ be a model.
+	// See: https://github.com/geneontology/noctua/issues/683
+	if( ! node ){
+	    // This is likely a model-level violation and cannot be
+	    // matched with a node.
+	}else{
+	    var node_label = '';
+	    var std_types = node.types();
+	    us.each(std_types, function(in_type){
+		node_label += type_to_span(in_type);
+	    });
+	}
 	if( node_label === '' ){
 	    node_label = nid;
 	}
@@ -971,6 +978,10 @@ function add_edge_modal(ecore, manager, relations, aid, source_id, target_id){
 	_fuse('positively regulates', 'RO:0002213', radio_name, 3),
 	_fuse('directly positively regulates', 'RO:0002629', radio_name, 4),
 	_fuse('has participant',  'RO:0000057', radio_name, 0),
+	_fuse('has small molecule regulator',  'RO:0012000', radio_name, 1),
+	_fuse('has small molecule activator',  'RO:0012001', radio_name, 2),
+	_fuse('has small molecular inhibitor',  'RO:0012002', radio_name, 2),
+	_fuse('acts on population of', 'RO:0012003', radio_name, 1),
 	_fuse('has input', 'RO:0002233', radio_name, 1),
 	_fuse('has output', 'RO:0002234', radio_name, 1),
 	_fuse('transports or maintains localization of', 'RO:0002313', radio_name, 1),

noctua.js

@@ -163,6 +163,8 @@ var NoctuaLauncher = function(){
     var workbenches_model = [];
     var workbenches_individual = [];
     var workbenches_edge = [];
+    var workbenches_universal_beta_test = [];
+    var workbenches_model_beta_test = [];
     each(workbench_maybe_dirs, function(dir){
 	//console.log('dir', dir);
 
@@ -258,7 +260,13 @@ var NoctuaLauncher = function(){
 			wb['public-directory'] = wbpath_try_public;
 
 			// Load workbench for later.
-			if( wb['type'] === 'universal' ){
+			if(wb['is-beta'] && wb['type'] === 'universal' ) {
+			    workbenches_universal_beta_test.push(wb);
+			    console.log('Added workbench (b: ' + wbid + ')');
+			}else if(wb['is-beta'] && wb['type'] === 'model' ) {
+				workbenches_model_beta_test.push(wb);
+			    console.log('Added workbench (b: ' + wbid + ')');
+			}else if( wb['type'] === 'universal' ){
 			    workbenches_universal.push(wb);
 			    console.log('Added workbench (u: '+wbid+')');
 			}else if( wb['type'] === 'model' ){
@@ -280,7 +288,12 @@ var NoctuaLauncher = function(){
     });
 
     // Apply external to internal variables.
-    var all_workbenches = workbenches_universal.concat(workbenches_model).concat(workbenches_individual).concat(workbenches_edge);
+	var all_workbenches = workbenches_universal
+		.concat(workbenches_model)
+		.concat(workbenches_individual)
+		.concat(workbenches_edge)
+		.concat(workbenches_universal_beta_test)
+		.concat(workbenches_model_beta_test);
     if( us.isEmpty(all_workbenches) ){
 	console.log('No workbenches defined.');
     }else{
@@ -617,6 +630,10 @@ var NoctuaLauncher = function(){
 		 value: workbenches_individual },
 		{name: 'global_workbenches_edge',
 		 value: workbenches_edge },
+		{name: 'global_workbenches_universal_beta_test',
+		 value: workbenches_universal_beta_test },
+		{name: 'global_workbenches_model_beta_test',
+		 value: workbenches_model_beta_test },
 		// SPARQL templates.
 		{name: 'global_sparql_templates_named',
 		 value: sparql_templates_named },
@@ -662,7 +679,9 @@ var NoctuaLauncher = function(){
 	    'noctua_workbenches_universal': workbenches_universal,
 	    'noctua_workbenches_model': workbenches_model,
 	    'noctua_workbenches_individual': workbenches_individual,
-	    'noctua_workbenches_edge': workbenches_edge
+	    'noctua_workbenches_edge': workbenches_edge,
+	    'noctua_workbenches_universal_beta_test': workbenches_universal_beta_test,
+	    'noctua_workbenches_model_beta_test': workbenches_model_beta_test
 	};
 
 	// Load in the additions.

workbenches/companion/Companion.js

@@ -33,7 +33,7 @@ var widgetry = require('noctua-widgetry');
 var jQuery = require('jquery');
 /* jshint ignore:end */
 
-// Items 
+// Items
 var barista_response = require('bbop-response-barista');
 var class_expression = require('class-expression');
 var minerva_requests = require('minerva-requests');
@@ -47,6 +47,7 @@ var gserv = global_golr_server;
 var defs = new amigo.data.definitions();
 var handler = new amigo.handler();
 var linker = new amigo.linker();
+linker.app_base = 'http://amigo.geneontology.org';
 //var dlimit = defs.download_limit();
 var dlimit = 1000;
 
@@ -113,7 +114,7 @@ var CompanionInit = function(user_token){
     var mmanager = new minerva_manager(global_barista_location,
 				       global_minerva_definition_name,
 				       user_token, engine, 'async');
-    
+
     // GOlr location and conf setup.
     var gconf = new bbop_legacy.golr.conf(amigo.data.golr);
 
@@ -211,15 +212,15 @@ var CompanionInit = function(user_token){
     ///
     /// AmiGO comms.
     ///
-    
+
     // Ready the primary widget manager.
     var widget_manager = new bbop_legacy.golr.manager.jquery(gserv, gconf);
     var confc = gconf.get_class('annotation');
     widget_manager.set_personality('annotation');
     widget_manager.add_query_filter('document_category',
 				    confc.document_category(), ['*']);
     widget_manager.add_query_filter('aspect', 'F'); // removable
-    
+
     // Attach filters to manager.
     var hargs = {
 	meta_label: 'Total documents: ',
@@ -230,24 +231,24 @@ var CompanionInit = function(user_token){
     var filters = new bbop_legacy.widget.live_filters(
 	'input-filter-accordion', widget_manager, gconf, hargs);
     filters.establish_display();
-    
+
     // Attach pager to manager.
     var pager_opts = {
     };
     var pager = new bbop_legacy.widget.live_pager('pager', widget_manager,
 						  pager_opts);
-    
-    // Describe the button that will attempt to compact the selected 
+
+    // Describe the button that will attempt to compact the selected
     // annotations and send macro commands to noctua/minerva.
     // The alrorithm is derived from a diagram here:
     // https://github.com/geneontology/noctua/issues/170#issuecomment-134414048
     var port_to_noctua_button = {
 	label: 'Import',
 	diabled_p: false,
-	click_function_generator: function(results_table, widget_manager){ // 
-	    
+	click_function_generator: function(results_table, widget_manager){ //
+
 	    return function(event){
-		
+
    		var selected_ids = results_table.get_selected_items();
    		var resp = results_table.last_response();
 
@@ -256,7 +257,7 @@ var CompanionInit = function(user_token){
 		    alert('No action can be taken currently.');
 		}else{
 		    //alert('Actionable input.');
-		    
+
 		    // Extract the documents that we'll operate on.
 		    var docs_to_run = [];
 		    each(selected_ids, function(sid){
@@ -265,11 +266,11 @@ var CompanionInit = function(user_token){
 			    docs_to_run.push(doc);
 			}
 		    });
-		    
+
 		    // Assemble a batch to run.
 		    var acls_set = {};
 		    each(docs_to_run, function(doc){
-			
+
 			// Who are we talking about?
 			var acls = doc['annotation_class'];
 			var bio = doc['bioentity'];
@@ -325,7 +326,7 @@ var CompanionInit = function(user_token){
 			    withs: withs
 			});
 		    });
-			
+
 		    // WARNING: Warn if we are going to be batching a lot.
 		    if( us.keys(acls_set).length > 3 ){
 			alert('You have a lot of requests from different ' +
@@ -342,45 +343,45 @@ var CompanionInit = function(user_token){
 			// Now let's actually assemble the /generic/ requests
 			// for the run.
 			var reqs = new minerva_requests.request_set(
-			    global_barista_token, global_id);			
+			    global_barista_token, global_id);
 			reqs.use_groups([
 			    // WARNING: We're minting money that we
 			    // might not honor here.
 			    'http://purl.obolibrary.org/go/groups/' + assby
 			]);
 
 			us.each(acls_assby_subset, function(bio_set, acls){
-			    
+
 			    var sub = reqs.add_individual(acls);
-			    
+
 			    us.each(bio_set, function(ev_list, bio){
-				
+
 				var obj = reqs.add_individual(bio);
 				var edge = reqs.add_fact(
 				    [sub, obj, 'RO:0002333']);
-			    
+
 				us.each(ev_list, function(ev_set){
-				    
+
 				    // Recover.
 				    var ev = ev_set['ev'];
 				    var refs = ev_set['refs'];
 				    var withs = ev_set['withs'];
 				    var assby = ev_set['assigned_by'];
-				    
+
 				    // Tag on the final evidence.
 				    reqs.add_evidence(
 					ev, refs, withs,
 					[sub, obj, 'RO:0002333']);
 				});
 			    });
-			    
-			    // ???			    
+
+			    // ???
 			});
 
 			// Fire and forget.
 			mmanager.request_with(reqs);
 		    });
-		    
+
 		}
 	    };
 	}
@@ -397,7 +398,7 @@ var CompanionInit = function(user_token){
     var results = new bbop_legacy.widget.live_results('results', widget_manager,
 						      confc, handler, linker,
 						      results_opts);
-    
+
     // Add pre and post run spinner (borrow filter's for now).
     widget_manager.register('prerun', 'foo', function(){
 	filters.spin_up();