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Javascript Dot-Syntax function disappears in listen callback

I'm trying to update Annotorious (https://annotorious.github.io/#) to the latest version of Closure / Javascript.
When I compile it with "SIMPLE" optimizations, dot-syntax functions seem to disappear when goog.events.listen callbacks are invoked. Here's an example:
Here's the "main":
goog.provide('annotorious.Annotorious');
...
/**
* The main entrypoint to the application. The Annotorious class is instantiated exactly once,
* and added to the global window object as 'window.anno'. It exposes the external JavaScript API
* and internally manages the 'modules'. (Each module is responsible for one particular media
* type - image, OpenLayers, etc.)
* #constructor
*/
annotorious.Annotorious = function() {
/** #private **/
this._isInitialized = false;
/** #private **/
this._modules = [ new annotorious.mediatypes.image.ImageModule() ];
...
In another file (they're all compiled together), we have this:
goog.provide('annotorious.Annotation');
goog.require('annotorious.shape');
/**
* A 'domain class' implementation of the external annotation interface.
* #param {string} src the source URL of the annotated object
* #param {string} text the annotation text
* #param {annotorious.shape.Shape} shape the annotated fragment shape
* #constructor
*/
annotorious.Annotation = function(src, text, shape) {
this.src = src;
this.text = text;
this.shapes = [ shape ];
this['context'] = document.URL; // Prevents dead code removal
}
So we start up the code, and at some point we end in the editor for the annotation, listening for a "Save" button:
goog.provide('annotorious.Editor');
....
/**
* Annotation edit form.
* #param {Object} annotator reference to the annotator
* #constructor
*/
annotorious.Editor = function(annotator) {
this.element = goog.soy.renderAsElement(annotorious.templates.editform);
....
/** #private **/
//this._btnSave = goog.dom.query('.annotorious-editor-button-save', this.element)[0];
this._btnSave = this.element.querySelector('.annotorious-editor-button-save');
...
goog.events.listen(this._btnSave, goog.events.EventType.CLICK, function(event) {
event.preventDefault();
var annotation = self.getAnnotation();
annotator.addAnnotation(annotation);
annotator.stopSelection();
if (self._original_annotation)
annotator.fireEvent(annotorious.events.EventType.ANNOTATION_UPDATED, annotation, annotator.getItem());
else
annotator.fireEvent(annotorious.events.EventType.ANNOTATION_CREATED, annotation, annotator.getItem());
self.close();
});
If I put a breakpoint at "goog.events.listen(this._btnSave...", and type "annotorious.Annotation", I get what I expect:
In fact, it has all kinds of methods:
Then I let the code go, and break in the listener (event.preventDefault();, etc, above):
Now, all the dot-syntax methods are gone.
This of course causes crashes later on.
All of these files are compiled together.
This happens for all callbacks - 'load' events, other ux callbacks, etc.
This must have worked in prior versions of Closure / JS.
What could be causing this?
Thanks!

Ok, I was able to resolve the problem by adding "--assume_function_wrapper" to the closure compiler command line.
Previously, I was compiling the package using Plovr. However, since Plovr hasn't been updated in a long time, I switched to using the closure compiler natively.
Apparently either Plovr provided '--assume_function_wrapper' internally or the version of the compiler Plovr used didn't break the functions as described.
As #john suggests above I'll bet '--assume_function_wrapper' keeps goog.provide from "destroying" namespaces by re-declaring them.

Wrangling Javascript Members into the correct Namespace in Netbeans

I have several modules organized in my app's namespace. I'm new to Netbeans, and having trouble getting it to properly recognize where they fit.
/**
* Provides general utilities.
* #param {object} util - window.myNamespace.util
*/
(function (util) {
/** #private */
var uniqueCounter = 0;
/** Returns unique incrementing integer. */
util.uniqueID = function() {
uniqueCounter++;
return uniqueCounter;
};
}(window.myNamespace.util = window.myNamespace.util || {}));
I've tried several permutations of JSDoc #name, #namespace, #alias, #memberOf, etc on the IIFE and on the individual members, but nothing seems to move it correctly to window.vltTDT.util from Global util.
Product Version: NetBeans IDE 8.1 (Build 201510222201)

How do I document NodeJS native (V8) modules?

I have developed a native NodeJS module (using the NAN helpers). Now I am wondering what is the best way to document it.
The methods the module exports exist only in the C++ source code, however I wish to export Javascript documentation.

EDIT: I found another way that I think is better:
All JSDoc needs is to be able to attach the doclet to SOMETHING, so you can actually just do this (if you ignore JSHint warning about expecting an assignment or call instead of expression):
var nativeStuff = require('some/native/stuff');
/**
* My Cool Class
* #class
*/
nativeStuff.MyCoolClass;
/**
* My Cool Method
* #function
* #param {String} [name] The argument
*/
nativeStuff.MyCoolClass.prototype.CoolMethod;
/**
* Some Other Value
* #type {String}
*/
nativeStuff.someStringValue;
module.exports = nativeStuff;
This has the advantage of working with IDE's (at least WebStorm) and not requiring you to copy or proxy the object itself. Note though that you have to explicitly tell it what kind of field each entry is (with #function or #class or #type) because it can't infer it automatically otherwise.
Original Answer
There are a couple ways I know of, though I admit none seem particularly elegant.
In the small adapter file where you require() the native parts of the code and make it available as a module, you can assign each component individually and document them that way:
var nativeStuff = require('some/native/stuff');
// If your module only has one thing
/**
* My Cool Class
* #class MyCoolClass
*/
module.exports = nativeStuff;
// If it has several things
module.exports = {
/**
* My cool class
* #class
*/
MyCoolClass: nativeStuff.MyCoolClass,
/**
* My Other Cool Member
*/
OtherCoolMember: nativeStuff.OtherCoolMember
};
You could document members of the class this way too if you want to pick apart the class and re-assemble it, but it gets kinda unwieldy the deeper you go.
The other way I know of is to wrap every class method in native JS, which comes with a (almost negligible) performance hit:
var nativeStuff = require('some/native/stuff');
/**
* My Cool Class
*/
class MyCoolClass {
constructor() {
this._nativeObj = new nativeStuff.MyCoolClass();
}
/**
* Some Cool Method
* #param {String} [name] My name
*/
coolMethod(name) {
return this._nativeObj(name);
}
}
module.exports = MyCoolClass;
(Note this also works in older JS versions, but ES6 classes make stuff way easier to understand visually :)
You also can try using the #typedef directive to define things since a doclet about a typedef can be separate from the object it describes, but I don't think typedef's can document methods or classes in general, they're just for data objects.

I had to create a simple documentation generator to scan comments in source code in Javadoc-like style: https://github.com/aspectron/gendoc
Here is a part of such documentation, that looks like this:
/**
#module crypto
**/
/**
#class Hash
Hash generator
#function Hash(algorithm)
#param algorithm {String}
Constructor. Initiaize hash generator with specified algorithm, see #getHashes
Throws exception on unknown algorithm
**/
v8pp::class_<hash_generator> hash_class(bindings.isolate(), v8pp::v8_args_ctor);
hash_class
/**
#function reset([algorithm])
#param [algorithm] {String}
#return {Hash}
Reset hash generator to initial state optionaly changing generator algorithm.
Throws exception on unknown algorithm.
**/
.set("reset", &hash_generator::reset_v8)
...

Finally I opted for a not very elegant solution. I have created a separate JavaScript file which only has methods that are exported by my native API.
This file looks like this:
/** #namespace AwesomeLibrary
*
* #description API overview
*/
AwesomeLibrary = {
/**
* #param {string} param Input parameter
* #return combobulates {#link param}
*/
combobulate: function (param) {}
}
Then I am using JsDoc to generate the documentation of the project and passing this JavaScript file as an input rather than my native code. Finally I bundle the documentation with the binary distribution of my module.
This solution is not ideal as the documentation and the source code have to be maintained separately, however it has the advantage of zero overhead and a (rather) clean file. I have also disabled the source code generation in JsDoc as this would be obviously quite useless and only show the empty stubs.

typedef of this variable doesn't produce warning

I want to produce a warning for a number if a string is assigned to it. So, I thought typedef of Closure might do this for me. I tried the following -
var Widget = function()
{
/** #typedef {number} */
this.size = null;
};
new Widget().size = "kaboom!"
When I compile it using http://closure-compiler.appspot.com/home it doesn't throw a warning or error. What am I doing wrong? And/or what other tool should I be using?

Turn the optimization up to Advanced in the closure compiler service to catch these warnings. You still won't see any for your example (well, you will see some, but not what you are expecting), because typedefs are used to define custom types. Also, you need to annotate your constructor. Run the following example in advanced mode and you will see your warnings. Instead of making a typedef for a simple thing like number, I would just use #type, but this example is to show you the proper use of typedef.
/** #typedef {number} */
var customType;
/** #constructor */
var Widget = function()
{
/** #type {customType} */
this.size = null;
};
new Widget().size = "kaboom!"

What is the best way to export library method, when using Closure Compiler?

Closure Compiler documentation clearly states: "Don't use Externs instead of Exports". Because Externs are very handy to use, I came down with a problem:
function Lib(){
//some initialization
}
Lib.prototype = {
invoke : function(str){
//this function is called from outside to invoke some of Lib's events
}
}
When using Closure Compiler with ADVANCED_OPTIMIZATIONS, function invoke is removed from the source. This could be prevented in two ways:
Adding the line after prototype definition:
Lib.prototype['invoke'] = Lib.prototype.invoke;
But this adds an ugly peace of code at the end of the output code:
Lib.prototype.invoke = Lib.prototype.g;
I managed to get rid of this by adding this line to the constructor:
this.invoke = this.invoke;
And this line to the externs file:
/**
* #param {String} str
*/
Lib.prototype.invoke = function(str){};
This way, Closure Compiler can't remove invoke function from the output code, because it is assigned by itself in the constructor, and also, it can't rename it, because it is defined in the externs file.
So witch method is better?

If you use JSDoc consistently, you could use the #export tag:
/**
* #param {String} str
* #export
*/
Lib.prototype.invoke = function(str){
//this function is called from outside to invoke some of Lib's events
};
and call the compiler with the --generate_exports flag.
This requires you to either include base.js from the Google Closure library, or to copy goog.exportSymbol and goog.exportProperty to your codebase.

Personally, I like defining interfaces in externs file and having my internal classes implement them.
// Externs
/** #interface */
function IInvoke {};
IInvoke.prototype.invoke;
/**
* #constructor
* #implements {IInvoke}
*/
function Lib(){
//some initialization
}
Lib.prototype = {
invoke : function(str){
//this function is called from outside to invoke some of Lib's events
}
}
You still export the constructor itself, but not the interface methods.