add a universal workbench for noctua for doing arbitrary sparql queri…

…es; as this can be very easily transferred to a model workbench (would need to extend bbop-manager-sparql to just return filled templates) this is essentially completion for geneontology/go-graphstore#9 and #465; TODO: track down cross-site issue

workbenches/gosling/Gosling.js

@@ -0,0 +1,164 @@
+////
+//// A little fun driving a view with YAS*.
+////
+
+// Let jshint pass over over our external globals (browserify takes
+// care of it all).
+/* global YASQE */
+/* global YASR */
+/* global jQuery */
+/* global global_barista_token */
+/* global global_barista_location */
+/* global global_sparql_templates_universal */
+
+var us = require('underscore');
+var bbop = require('bbop-core');
+//var bbop = require('bbop').bbop;
+//var bbopx = require('bbopx');
+var amigo_inst = require('amigo2-instance-data');
+var amigo = new amigo_inst();
+var bbop_legacy = require('bbop').bbop;
+
+// Help with strings and colors--configured separately.
+var aid = new bbop_legacy.context(amigo.data.context);
+
+var widgetry = require('noctua-widgetry');
+
+// Aliases
+var each = us.each;
+var uuid = bbop.uuid;
+
+// Code here will be ignored by JSHint, as we are technically
+// "redefining" jQuery (although we are not).
+/* jshint ignore:start */
+var jQuery = require('jquery');
+/* jshint ignore:end */
+
+//
+var json_response = require('bbop-rest-response');
+var jquery_engine = require('bbop-rest-manager').jquery;
+var sparql_manager = require('bbop-manager-sparql');
+
+///
+/// ...
+///
+
+var sparql_select_id = 'spqlsel';
+var yasqe_id = 'yasqe';
+var yasr_id = 'yasr';
+
+// Make the default ours at least.
+YASQE.defaults.sparql.endpoint = "http://rdf.geneontology.org/sparql";
+
+///
+var GoslingInit = function(){
+
+    var logger = new bbop.logger('gosling');
+    logger.DEBUG = true;
+    function ll(str){ logger.kvetch(str); }
+
+    ///
+    /// Add option to dropdown.
+    ///
+
+    // Attach to interface.
+    var app_map = {};
+    var selopts_str = [];
+    us.each(global_sparql_templates_universal, function(tmpl){
+	var uuid = bbop.uuid();
+
+	// Mental.
+	app_map[uuid] = tmpl;
+
+	// Physical.
+	var str = '<option value="' + uuid + '">' + tmpl.title + '</option>';
+	selopts_str.push(str);
+    });
+    jQuery('#'+sparql_select_id).append(selopts_str.join(''));
+
+    ///
+    /// Setup and glue YAS*.
+    ///
+
+    var yasqe = YASQE(document.getElementById("yasqe"), {
+	sparql: {
+	    showQueryButton: true,
+	    endpoint: 'http://rdf.geneontology.org/sparql'
+	}
+    });
+    var yasr = YASR(document.getElementById("yasr"), {
+	//this way, the URLs in the results are prettified using the
+	//defined prefixes in the query
+	getUsedPrefixes: yasqe.getPrefixesFromQuery
+    });
+
+    //link both together
+    yasqe.options.sparql.callbacks.complete = yasr.setResponse;
+
+    ///
+    /// ...
+    ///
+
+    function _insertion(tmpl){
+
+	var prefixes = '';
+	us.each(tmpl['prefixes'], function(prefix){
+	    prefixes +=
+		'PREFIX '+ prefix['prefix'] +':'+ prefix['expansion'] +'\n';
+	});
+	var qstr = prefixes + tmpl['query'];
+
+	yasqe.setValue(qstr);
+	if( tmpl['endpoint'] ){
+	    var ep = tmpl['endpoint'];
+	    //yasqe.endpoint(tmpl['endpoint']);
+	    //YASQE.defaults.sparql.endpoint = ep;
+	    //yasqe.defaults.sparql.endpoint = ep;
+	}
+    }
+
+    // Make the interface live.
+    jQuery("#"+sparql_select_id).change(function(){
+        var tmpl_id = jQuery(this).val();
+	console.log(tmpl_id);
+	var tmpl = app_map[tmpl_id];
+	console.log(tmpl);
+	console.log(app_map);
+	_insertion(tmpl);
+    });
+
+    // Insert first item.
+    var stu = global_sparql_templates_universal;
+    if( stu && stu[0] ){
+	_insertion(stu[0]);
+    }
+};
+
+// Start the day the jQuery way.
+jQuery(document).ready(function(){
+    console.log('jQuery ready');
+
+    // Try to define token.
+    var start_token = null;
+    if( global_barista_token ){
+	start_token = global_barista_token;
+    }
+
+    // Next we need a manager to try and pull in the model.
+    if( typeof(global_minerva_definition_name) === 'undefined' ||
+	typeof(global_barista_location) === 'undefined' ){
+	    alert('environment not ready');
+	}else{
+	    // Only roll if the env is correct.
+	    // Will use the above variables internally (sorry).
+	    GoslingInit();
+
+	    // When all is said and done, let's also fillout the user
+	    // name just for niceness. This is also a test of CORS in
+	    // express.
+	    if( start_token ){
+		widgetry.user_check(global_barista_location,
+				    start_token, 'user_name_info', false);
+	    }
+	}
+});

workbenches/gosling/README.md

@@ -0,0 +1,4 @@
+```
+npm install
+npm run build
+```

workbenches/gosling/config.yaml

@@ -0,0 +1,11 @@
+menu-name: "Gosling (Noctua's little GOOSE)"
+page-name: "Gosling (Noctua's little GOOSE)"
+type: "universal"
+help-link: "http://github.com/geneontology/noctua/issues"
+javascript:
+  - http://cdn.jsdelivr.net/yasqe/2.11.10/yasqe.bundled.min.js
+  - http://cdn.jsdelivr.net/yasr/2.10.8/yasr.bundled.min.js
+  - GoslingBundle.js
+css:
+  - http://cdn.jsdelivr.net/yasqe/2.11.10/yasqe.min.css
+  - http://cdn.jsdelivr.net/yasr/2.10.8/yasr.min.css

workbenches/gosling/package.json

@@ -0,0 +1,91 @@
+{
+    "name": "workbench-go-gosling",
+    "version": "0.0.1",
+    "license": "BSD-3-Clause",
+    "description": "Experimental GOOOSE-like Noctua interface for the Gene Ontology.",
+    "keywords": [
+	"workbench",
+	"gene ontology",
+	"GO",
+	"bbop",
+	"SPARQL",
+	"GOOSE",
+	"YASGUI",
+	"noctua"
+    ],
+    "author": "SJC <[email protected]> (http://berkeleybop.org/)",
+    "homepage": "http://berkeleybop.org/",
+    "repository": {
+	"type": "git",
+	"url": "git+https://github.com/geneontology/noctua.git"
+    },
+    "engines": {
+	"node": ">= 4.4",
+	"npm": ">= 2.15"
+    },
+    "dependencies": {
+	"amigo2-instance-data": "2.5.7",
+	"amigo2": "2.4.3",
+	"bbop": "2.4.3",
+	"bbop-core": "0.0.5",
+	"bbop-graph-noctua": "0.0.32",
+	"bbop-manager-sparql": "0.0.5",
+	"bbop-rest-manager": "0.0.17",
+	"bbop-rest-response": "0.0.4",
+	"gulp": "^3.9.1",
+	"jquery": "^2.2.4",
+	"underscore": "1.8.3"
+    },
+    "devDependencies": {
+	"browserify": "^13.0.1",
+	"browserify-shim": "^3.8.12",
+	"chai": "^3.5.0",
+	"eslint": "^2.13.1",
+	"gulp-bump": "^2.1.0",
+	"gulp-git": "^1.7.2",
+	"gulp-jsdoc": "^0.1.5",
+	"gulp-jshint": "^2.0.1",
+	"gulp-mocha": "^2.2.0",
+	"gulp-streamify": "^1.0.2",
+	"gulp-uglify": "^1.5.3",
+	"jsdoc": "^3.4.0",
+	"jshint": "^2.9.3",
+	"uglifyify": "^3.0.2",
+	"vinyl-source-stream": "1.1.0",
+	"wait-on": "^1.5.2",
+	"watchify": "^3.7.0"
+    },
+    "browserify": {
+	"transform": [
+	    "browserify-shim"
+	]
+    },
+    "browser": {
+	"jquery": "./node_modules/jquery/dist/jquery.min.js",
+	"bootstrap": "./node_modules/bootstrap/dist/js/bootstrap.min.js",
+	"jquery-ui": "./external_js/jquery-ui-1.10.3.custom.min.js",
+	"noctua-widgetry": "../../js/lib/noctua-widgetry/widgetry.js"
+    },
+    "browserify-shim": {
+	"jquery": {
+	    "exports": "global:jQuery"
+	},
+	"jquery-ui": {
+	    "depends": [
+		"jquery"
+	    ]
+	}
+    },
+    "bundleDependencies": [],
+    "private": false,
+    "main": null,
+    "bugs": {
+	"url": "https://github.com/geneontology/noctua/issues"
+    },
+    "directories": {
+    },
+    "scripts": {
+	"build": "./node_modules/.bin/browserify Gosling.js -o public/GoslingBundle.js --exclude ringo/httpclient",
+	"test": "echo \"Error: no test specified\" && exit 1"
+    }
+}