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)

--NicolasVervelle 22:45, 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)

Many thanks. That is much clearer. I will pass it on and hope we can clear up the security concerns. The PopUp Window is still not working in Jmol MediaWiki Extension. It shows the Java image as it loads the applet and then just shows a little red cross in the top left of the pop up window. It occurs to me that we may use that a lot on Wikipedia. I think Tim suggested that it would be best to not load the applet every time a window was opened but leave the reader to discover s/he could use Jmol to see the molecule. That would certainly be appropriate for articles on specific molecules while in page use would be better for the teaching materials on molecular modelling on Wikiversity. --Bduke 22:15, 11 December 2007 (CET)

The PopUp window should work now, fix also committed to SVN. Delaying the applet loading would be good. I know it's possible, because it has been done (by Angel probably) but it needs to be integrated in the extension.

I also thought that a special page Special:Jmol could be useful as an easy way of displaying an uploaded chemical file in MediaWiki: either go to Special:Jmol/MyUploadedChemicalFile to see MyUploadedChemicalFile in Jmol, or go to where you can input the file name you want to see. What do you think ?

--NicolasVervelle 22:45, 11 December 2007 (CET)

Sorry, the PopUp window still does not work. It does what I described above. I did not mention that it also says "Downloading JmolApplet" at the bottom, but it is just hanging and not doing anything. What do you mean by Special:Jmol/MyUploadedChemicalFile and Special:Jmol? I copied these into the Go window but both gave "page not found". Could you give the actual URL link? You can see here if I link them that they do not go anywhere - Special:Jmol/MyUploadedChemicalFile and Special:Jmol. --Bduke 01:05, 12 December 2007 (CET)

Try cleaning your cache (it's a .js that has been modified and most browsers don't update them correctly). For the special page, it's just a thought, not something done. --NicolasVervelle 06:58, 12 December 2007 (CET)

Of course, I should have thought of clearing the cache. I am not sure what you intend with the Special:Jmol pages. I had misunderstood you before. Now I am just unclear. If you put say "Image:Artemisinin.pdb" in the Go/Search box it pulls up the page you see when you upload it with the details. File:Artemisinin.pdb also works, so we could have something like File:Artemisinin.pdb (but that does not work here, but should I think work on WP. Look at what I wrote). I think it would be useful if there was a way of getting this automatically. You can click on an image to see that page and that page shows the image as well as the details. It would be nice if that page, for say a pdb file, showed a small Jmol "picture" of the molecule. This is a bit fuzzy and I have no idea how to do it. For example is there any way we could double click on the Jmol image and bring up the details page, just like you can with a jpg image? All in all it would be good if the uploaded pdb files behaved just like uploaded images. This would be particularly important if that was the main or even only way of have Jmol images on Wikipedia, which I think might be the case and perhaps really should be the case. Another difference is that the details page for the pdb files has a list of pages that link to it which is empty. Is there any way of getting that to really show which pages were displaying it - i.e. just like images again? However, I am sure that will all get sorted out if we ever do get Jmol on WP. --Bduke 10:13, 12 December 2007 (CET)

Upload of MOL files

Nico, it seems that I cannot upload MOL files. A .png worked, but when I try .mol I get an error: "corrupted file or extension does not match the file type".

Can you check that .mol are allowed?

A .pdb file is not allowed either --AngelHerraez 12:18, 17 October 2010 (UTC)

Hi Angel, I currently have a very loosy internet connection in a hotel. I can't check the Wiki configuration right now. Can you send me an email to remind me to look after this when I get back (probably in a week or two) ? --NicolasVervelle 18:06, 17 October 2010 (UTC)

OK, I'll do that. Enjoy disconnection! --AngelHerraez 21:55, 17 October 2010 (UTC)

Website blacklist

Hi Nico, it seems that I cannot add a link to {lulu DOT com}. The edit is rejected based on antispam measures, but I cannot see that url listed either in the JmolWiki blacklist nor in the MediaWiki blacklist.

Do you know how that is regulated? Thanks --AngelHerraez 10:46, 9 May 2011 (CEST)

Hi Angel, I think it's blocked by enwiki blacklist. You can try adding it to MediaWiki:Spam-whitelist. --NicolasVervelle 13:48, 9 May 2011 (CEST)

OK, I had a look and it seems that they positively want lulu to be blacklisted. So I will resort to some other link. Don't bother with this. Thanks. --AngelHerraez 00:50, 10 May 2011 (CEST)

I tried adding it to the white list, and it seems to work : lulu.com. --NicolasVervelle 11:21, 10 May 2011 (CEST)

OK, thanks. I hadn't noticed that was a whitelist local to JmolWiki. --AngelHerraez 00:28, 11 May 2011 (CEST)

Contributors

NicolasVervelle, AngelHerraez, Bduke, K.murphy