my first serious commit to this integration project

.gitignore

 # Created by .ignore support plugin (hsz.mobi)
+.idea/
+node_modules/
+morpheus.js
+morpheus-external.js
+morpheus-external.min.js

Gruntfile.js

@@ -66,7 +66,8 @@ module.exports = function (grunt) {
 					'js/hopscotch.min.js', 'js/typed.min.js',
 					'js/jquery.event.drag-2.2.js',
 					'js/clipboard.min.js', 'js/slick.min.js',
-					'js/js.cookie.js', 'js/d3.layout.cloud.js']
+					'js/js.cookie.js', 'js/d3.layout.cloud.js',
+					'js/long.js', 'js/bytebuffer.js', 'js/protobuf.js']
 			},
 			morpheus: {
 				nonull: true,

message.proto

+// Originally written by Saptarshi Guha for RHIPE (http://www.rhipe.org)
+// Released under Apache License 2.0, and reused with permission here
+// Extended in November 2014 with new types to support encoding
+// language, environment, and function types from R.
+
+package rexp;
+
+option java_package = "org.godhuli.rhipe";
+option java_outer_classname = "REXPProtos";
+
+// TODO(mstokely): Refine this using the new protobuf 2.6 oneof field
+// for unions.
+message REXP {
+    enum RClass {
+        STRING = 0;
+        RAW = 1;
+        REAL = 2;
+        COMPLEX = 3;
+        INTEGER = 4;
+        LIST = 5;
+        LOGICAL = 6;
+        NULLTYPE = 7;
+        NATIVE = 8;
+    }
+    enum RBOOLEAN {
+        F=0;
+        T=1;
+        NA=2;
+    }
+
+
+    required RClass rclass = 1;
+    repeated double realValue = 2 [packed=true];
+    repeated sint32 intValue = 3 [packed=true];
+    repeated RBOOLEAN booleanValue = 4;
+    repeated STRING stringValue = 5;
+
+    optional bytes rawValue = 6;
+    repeated CMPLX complexValue = 7;
+    repeated REXP rexpValue = 8;
+
+    repeated string attrName = 11;
+    repeated REXP attrValue = 12;
+    optional bytes nativeValue = 13;
+}
+message STRING {
+    optional string strval = 1;
+    optional bool isNA = 2 [default=false];
+}
+message CMPLX {
+    optional double real = 1 [default=0];
+    required double imag = 2;
+}
\ No newline at end of file

package.json

@@ -33,6 +33,7 @@
     "grunt-contrib-jshint": "~1.0.0",
     "grunt-contrib-uglify": "~1.0.1",
     "grunt-contrib-watch": "~1.0.0",
-    "serve-static": "^1.10.2"
+    "serve-static": "^1.10.2",
+    "protobufjs": "~3.7"
   }
 }

src/tools/test_tool.js

+morpheus.TestTool = function () {
+};
+morpheus.TestTool.prototype = {
+    toString : function () {
+        return 'Test';
+    },
+    gui : function () {
+        return [
+
+        ];
+    },
+    execute : function (options) {
+        var project = options.project;
+        var dataset = project.getFullDataset();
+        var matrix = dataset.seriesArrays;
+
+        ocpu.seturl("http://localhost:7120/ocpu/library/base/R");
+        var req = ocpu.call("ncol", {
+            "x" : matrix
+        }, function (session) {
+            session.getConsole(function (output) {
+                console.log(output);
+            });
+        });
+        req.fail(function () {
+            console.log("test tool failed");
+        });
+    }
+};
+

src/ui/heat_map_toolbar.js

@@ -140,6 +140,10 @@ morpheus.HeatMapToolBar = function (controller) {
 		toolbarHtml
 		.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Reset Zoom" name="resetZoom">100%</button>');
 	}
+
+
+
+
 	toolbarHtml.push('<div class="morpheus-button-divider"></div>');
 	if (controller.options.toolbar.sort) {
 		toolbarHtml
@@ -243,6 +247,73 @@ morpheus.HeatMapToolBar = function (controller) {
 		toolbarHtml.push('</div>');
 	}
 
+	toolbarHtml.push('<div class="morpheus-button-divider"></div>');
+
+	toolbarHtml.push('<button type="button" class="btn btn-default btn-xs" data-toggle="tooltip" title="Test" name="test">Test</button>');
+
+	$buttons.on('click', '[name=test]', function (e) {
+		console.log("test button clicked");
+		var project = controller.getProject();
+		var dataset = project.getFullDataset();
+		var matrix = dataset.seriesArrays[0];
+		console.log(dataset);
+
+		var rows = dataset.rows;
+		var columns = dataset.columns;
+		var array = [];
+		for (var i = 0; i < rows; i++) {
+			for (var j = 0; j < columns; j++) {
+				array.push(matrix[i][j]);
+			}
+		}
+
+
+		ProtoBuf = dcodeIO.ProtoBuf;
+		var builder = ProtoBuf.loadProtoFile("./message.proto"),
+			rexp = builder.build("rexp"),
+			REXP = rexp.REXP;
+
+		var msgMatrix2 = new REXP({
+			rclass : REXP.RClass.LIST,
+			rexpValue : [{
+				rclass: REXP.RClass.REAL,
+				realValue: array,
+				attrName: "dim",
+				attrValue: {
+					rclass: REXP.RClass.INTEGER,
+					intValue: [rows, columns]
+				}
+			},
+				{
+					rclass : REXP.RClass.REAL,
+					realValue : 1
+				}, {
+					rclass : REXP.RClass.REAL,
+					realValue : 2
+				}],
+			attrName : "names",
+			attrValue : {
+				rclass : REXP.RClass.STRING,
+				stringValue : [{
+					strval : "es"
+				},
+					{
+						strval : "c1"
+					}, {
+						strval : "c2"
+					}]
+			}
+		});
+		var res = morpheus.ocpu.call(msgMatrix2, {
+			library : "testproject",
+			fun : "pcaPlot",
+			host : "localhost:5721"
+		});
+		if (res != -1) {
+			alert(res);
+		}
+	});
+
 	var $lineOneColumn = $el.find('[data-name=lineOneColumn]');
 	$search.appendTo($lineOneColumn);
 	var $toolbarForm = $(toolbarHtml.join(''));

src/util/my_opencpu_call.js

+/**
+ * Created by baba_beda on 8/16/16.
+ */
+morpheus.ocpu = function () {
+};
+
+morpheus.ocpu.call = function(obj, settings) {
+    settings.host = settings.host || "localhost:8004";
+    if (settings.library == null) {
+        alert("Library is not specified. Call terminated");
+        return -1;
+    }
+    if (settings.fun == null) {
+        alert("Function is not specified. Call terminated");
+        return -1;
+    }
+    if (obj == null) {
+        alert("No arguments for function presented. Call terminated");
+        return -1;
+    }
+    var http = new XMLHttpRequest();
+    var url = "http://" + settings.host + "/ocpu/library/" + settings.library + "/R/" + settings.fun;
+    http.open("POST", url, false);
+    settings.contentType = settings.contentType || "application/x-protobuf";
+    http.setRequestHeader("Content-Type", settings.contentType);
+
+    var params = new Uint8Array(obj.toArrayBuffer());
+    http.send(params);
+
+    var loc;
+    if (http.status == 201) {
+        loc = http.getResponseHeader("Location");
+    }
+    else {
+        alert("Some problems occurred during POST request. Call terminated");
+        return -1;
+    }
+
+    var url2 = loc + "R/.val/print";
+    var http2 = new XMLHttpRequest();
+    http2.open("GET", url2, false);
+    http2.send(null);
+    if (http2.status == 200) {
+        return http2.responseText;
+    }
+    else {
+        alert("Some problems occurred during GET request. Call terminated");
+        return -1;
+    }
+};
\ No newline at end of file