User talk:NicolasVervelle

Hi Nicholas, its Kevin again. The two heparin models I put up on my Jmol userpage no longer show up. I've tried viewing the page with firefox and internet explorer and in both the page loads but with errors. Have you any idea whats caused this?

Thanks

Kevin

I found the problem. The link on the wikipedia page was going to wiki.jmol.org/, I changed this to wiki.jmol.org:81/ and the models on my user page show up fine

--NicolasVervelle 05:48, 11 December 2007 (CET)Hi Nicholas, I want to add a jmol model to the wikipedia page entitled 'heparin'. I've downloaded the model '1HPNmod.pdb' and I can view it in the Jmol simple model example page by changing the uploaded file contents to 1HPNmod.pdb from ethanol.xyz. When I try to transfer this to the heparin page instead of displaying the model it just displays the source code. What am I doing wrong? any suggestions?

Thanks

Kevin

The Jmol extension is not yet installed on wikipedia, so it can't work for the moment. We are discussing with the wikipedia team so that the Jmol extension is added to wikipedia: the current status is that I have to make some modifications to the extension (security and usability issues) before going any further.

How come I can view the ethanol model?

I am not sure I understand. On which page (url) can you see the ethanol model ?

At wiki.jmol.org/index.php/Jmol_MediaWikki_Extension

That's normal.

• On the Jmol wiki (wiki.jmol.org), the Jmol extension is installed because I am the one maintaining this wiki, so I installed it as soon as I got something working.
• On Wikipedia (en.wikipedia.org), the Jmol extension is not installed. Wikipedia team has asked me first to make some modifications to the extension before considering installing it on Wikipedia. I need to find some time to do the modifications, and then contact them again. Hopefully, in the next weeks, I'll be able to find some time to do this (I want to do this before the end of August).

OK, Thanks, I didn't realise they were two different wikis.

From Bduke

Thanks for your help. I replied on my talk page to keep the discussion together. --Bduke 22:14, 10 December 2007 (CET)

upload is now working for pdb files. Does Jmol support mol2 files? If so can upload be OK'ed for them. I have put everything back on my talk page whether it works or not. The incontents pdb files are identical to those uploaded. The former fails. The latter works. Thanks for the support. --Bduke 23:53, 10 December 2007 (CET)

A few small points. First, the popup window at Jmol MediaWiki Extension does not seem to be working. Second, I am wanting to look again at the JmolExtension.php. I do not see where I can get that. I see the link following "All the files for the extension .." and that leads to downloading three files. What is the relationship between those three files and JmolExtension.php? I am puzzled. I have just tested versions 11.2.14 and 11.3.54 on my server. They are fine. Again, thanks.

I have redesigned the extension, so now there's no more JmolExtension.php. It has been splitted in Jmol.php and Jmol.body.php, because I am using facilities provided by the StubManager extension, which also needs to be installed properly before using the extension (I forgot to mention that in the documentation). --NicolasVervelle 05:48, 11 December 2007 (CET)

OK, no wonder I was confused. In MediaWiki just after where it tells you get these, it has:-

Add the following line to the end of LocalSettings.php:

require_once('extensions/Jmol/JmolExtension.php');

I just fixed this line, thanks for pointing that.

I guess this needs changing. I have someone here in Australia who is prepared to look at the security issues and if necessary fight them out with Tim Starling, the WikiMedia Foundation Tech person, who lives in Australia (unfortunately not Melbourne anymore, where I am, but Sydney). I would appreciate it if you could complete the documentation so he can see where it all fits together. Do you think the new scripts are better from a security point of view? Regards, Brian. --Bduke 08:46, 11 December 2007 (CET)

That's great news ! Help is very very welcome

I am a complete beginner at PHP, JavaScript, ... so I am totally unsure if the security is better or not. I hope so, I added the escapeScript() and escapeAttribute() methods for this.

I don't think there's a need for a lot of documentation of the code, it's not very complex. Here are the basics :

• Jmol.php is using the StubManager to simply add the Jmol extension :
  • ParserBeforeStrip and ParserAfterStrip MediaWiki hooks
  • callbacks for jmol tag
• Jmol.body.php is the extension itself :
  • h... are the hooks implementation
  • tag_jmol is the callback for the Jmol tag
  • startElement, endElement, characterData are the callbacks called when parsing XML
  • render... are the methods creating the html for the jmol tags

If you need more details, don't hesitate to email me

--NicolasVervelle 20:43, 11 December 2007 (CET)

Contributors

NicolasVervelle, AngelHerraez, Bduke, K.murphy