On 2012.07.16. 16:31, Robert Hanson wrote:
Just to confirm, Gusts, I'm totally with you on this. I've wanted to learn more about  jQuery for a long time, and this seems like a great opportunity.
Superb, I'll be more than glad to help you there.
My key points:

--Anything you want to do in relation to JmolCore/Applet/Api is great. Jmol.js is history.
Noted
--We don't want to remove any of the functionality of  JmolCore/Aplept/Api/Controls/CD/JME/JSpeView, but certainly a new JQueryApi.js, for example, that would extend that functionality would be terrific.
I think it would be for the best to just keep them separated for a while, because my approach is not fully finished yet and as I said, it's intended as a lightweight buildingblock (just like JmolApplet.js is now). As you saw previously, there are some things I didn't know that were kinda deprecated around here (like <param name="script"...> etc.), so I have to address these issues first, and maybe we should think about the opportunities with events and data objects (pre-parsed callback message strings).
--I'm more than happy to share my experience with issues. Others on this list know a lot about this as well. Some of these I'm sure jQuery addresses; maybe some (like "a div containing an applet may not ever be set to display:none") are less obvious.
Removing the element or setting it to display=none will crash Java, am I right?
--ChemDoodleWeb.js must not be adjusted -- or if it is, that must be done in collaboration with Kevin Theissen (who is probably reading this)
I think I'll go for JME first, which as much as I saw, does not have a jQuery wrapper at all, but ChemDoodle is somewhere in between, so it can stay as is for now. Only afterwards we'll need some wrapper API (like Jmol is now). I just don't understand why it's still called Jmol, if it's so much more than just Jmol, it should have been named Online Chem Toolkit or something. :)


So I say there is no problems with writing simple HTML with data attributes containing some hard core scripts. Maybe, if you have some really nasty examples, that have strict indenting and line breaks, that you could show me and I could test them, then, please, show me them.


We just can't put scripts in HTML as tag attributes. Period. Find some other way. Trust me on that one.
I'm still sceptical about that, I really need to do some proof of concept testing, that it does not work, because it's thee data, that HTML is all about.
 
As for quotes - always escape them. If the site is running with some kinda CMS, that can be done automatically in WYSIWYG, if the site is prepared with some authoring tool, like, for example, Dreamweaver, then it will also do it for you.

First of all, scripts could run hundreds of lines. Second, we have tried escaping these, and besides being a royal pain, mostly it hasn't worked. HTML tags and <param.  values are just not adequate for holders of scripts. It's totally unnecessary anyway, I think. the solution has been around for years, and we have had no problem with it. It seems to me you will quickly find a different way. Perhaps the "data-script" simply points to a key in an associative array that is created in the head using an API, for example.
This still breaks the separation attempt. I know that it would be a painfull, in case, if somebody would like to write HTML by hand, but with authoring tools today it should not be that kind of pain anymore, especially when HTML5 introduced special attributes for raw and crazy data to be held inline. 

I should note that Jmol.js and JmolApi.js both  allow simple

<div id="xxxx"></div>

within the body and all Jmol calls in the head to populate those. Most developers I've talked with just don't find that any easier. I actually like it, because it nicely separates the page formatting (in the body) from the dynamics (in the head). But still, I rarely do it unless I really have to. Jmol calls within the body are really just implementing static code anyway, so one could argue that's where they should be. But that's probably old school...
Yes, I was not paying enough attention to whole inner workings of Jmol.js and JmolApplet.js, maybe beause I was more looking at example code that used inline scripting, and that kinda made me a wee bit angry :)

Coding web pages is an evolving art. All you see there are best practices from pre-jQuery days. Some of us have seen the entire process from the start (no CSS, no DIV, no document.getElementById, etc.). So it's hard to imagine what you would be angry about. You are blessed to have missed all that, I think. Welcome to the club.
Don't worry, when I started working as webdev it was all about tables, spacer images and inline DHTML (buzzword at the time, now it's all bout jQuery, MVC, and whatever not.), but I just saw the potential in so called semantic web, and I jumped the train, although at the time the browser support for all this was really bad. :)
 

We could probably do a lot more with jQuery, but since it's only needed for the AJAX, we haven't felt it necessary to do more with it.
 
var jmol; // This is the Jmol object on which we are working on
function myclick_listener_function(e){
  e.preventDefault(); // If it's a link tag for example, we kill it's default behaviour
  var scriptStr = $(this).data('script'); // We could store all the scripting in HTML code in HTML5 data attributes
  Jmol.script(jmol, scriptStr); // This is where we call Jmol OOP framework and send some commands to our Jmol applet
}
$(document).ready(function(){
    $('#mybutton').bind('click', myclick_listener_function);
});


And this is easier than

Jmol.jmolButton(jmol, "myscript", "mytag")

? What makes that particularly appealing to you?
Jmol.jmolButton() returns HTML instead of HTML already being prepared in the body, that's it. Basically, the main concern I see is that JavaScript is doing stuff it could be freed of - like generating HTML where it's not really necessary. JavaScript is great for adding action to static HTML, but why should one use it create HTML?

Well, for one thing, that was pretty much the original function of JavaScript -- to create HTML on the fly for a page. Newer browser capability has allowed that original function to be expanded greatly, and the combination of CSS and DOM in particular has greatly extended the use of JavaScript. If you are saying you never want to use .innerHTML =, that seems rather unnecessarily harsh. Even jQuery must use innerHTML, I think.

If you mean, "Never use document.write," then what you are basically saying is simply, "Let's move this to XHTML standards." That's certainly of interest to some Jmol page developers. We explored this three years ago, and mostly it didn't go anywhere.
Not really. I like whole clean and correct concept, but browsers still don't care (especially IE) about XHTML, and it will interpret it as HTML. But still, I tend to write my HTML as strictly as XHTML (always close tags, use double quotes for attributes, use lower case tag names, etc.).

And so, innerHtml is not the same as document.write, for one, it will allow you to fill a specific element from different location in the source, where document.write on the other hand writes right in the place from where it was called.
Q: Is jQuery XHTML compliant?
I think yes, because, it doesn't really matter, as JavaScript is working with DOM, and if DOM has been initialized as XHTML then JavaScript will work with it. If I'm not mistaken, the same innerHtml, just sends some kind of eval() to the browsers DOM parser, where it turns into a DOM fragment, whereas it really does not matter anymore weather it is XHTML or just plain old HTML.
If you want to remove all document.write, it seems to me you might as well go to XHTML compliance. That might require hacking of jQuery, though....
I think it's not really a matter of concern with jQuery. jQuery is just a mild abstraction over native JavaScript, so if you use innerHtml in XHTML, the only thing you might have to worry is that the innerHTML receives correctly formed XHTML source (which I tend to use anyway).
 
Let's say we have my one and only example:

 

<p><a href="some_molecule.pdb" class="jmol-load">DNA</a></p>

If Jmol didn't load properly or JavaScript has been disabled, this allows user to download a PDB file and open it up in whatever software he likes. If JavaScript is disabled Jmol.jmolButton(jmol, 'load some_molecule.pdb', 'DNA'); would not even show up.


Agreed. But also, if JavaScript is disabled, for just about all Jmol web apps, the app is toast. jQuery is dead, Jmol is dead, the page is probably totally malformed. I've never seen a need to cater to users who turn off JavaScript. Have you ever turned that off and seen how far you can get? But you are right, probably something more than a blank page is advisable.

In any case, no one wants to download a pdb file as last resort. That's way too esoteric. (Anyone who could read that file will not want it this way.) If the applet doesn't load, the best solution is to provide an image. That's what JmolApplet.js does, upon request. 
I'd propose a different approach and throw in one more buzzword - accessibility :) neither Flash nor Java is good with all the screen readers for blind people, but they are not my main concern here. My approach would be to show a static image in the placeholder in the first place and then gradually replace it with Jmol applet (instantly or with a mouse click). By the way, it's the approach http://www.pdb.org/ are using, which, I must say, is really thought trough. I think it's called degrading gracefully. And throwing in an option for file download if Jmol could not be started is one of them.

You would be surprised how many people in Russia disable JavaScript in their browsers, I was visiting St. Petersburg two years ago and this guy, I stayed with, told me that they are kind of paranoid about the hacker scene there.

-- 
Gusts Kaksis