User talk:Physchim62

Wikichem proposal

Hi PC, Can you sign up here if you're officially on this grant application? We can do copyedits there. Thanks! Martin A. Walker 21:32, 29 July 2009 (UTC)

WP articles on wikichem

Hey PC, thanks for all your behind-the-scenes work getting templates and categories organised here. I hope that things like image files are working for you now.

My friend Kelson - one of the organisers of the Paris wiki conference - should be able to help create a collection of the articles from the English Wikipedia for us on wikichem. We just need to supply him with a list of the articles, and ideally the versionIDs as well, and he will upload them onto wikichem for us. (Do you know which list(s) would be best to use?) However, I know that for now we need a few test articles to play with - and I think Kelson is perhaps away right now (see his WP homepage. Cheers, Martin A. Walker 17:01, 1 August 2009 (UTC)

Yes, I think we're still quite a way from any sort of automated upload of articles. I've been trying to organise what is here already, although I have turned my attention to the more urgent task of the grant proposal for the time being. Physchim62 00:04, 6 August 2009 (UTC)

Note to self

We're having problems with the display and uploading of long pages from Wikipedia (more than about 50k of wikitext). I am systematically blanking any long pages which can't be viewed. Physchim62 12:47, 9 August 2009 (UTC)

I'll ask Greg to look into this tomorrow. They switched servers earlier in the summer, and some of the settings got messed up in the switch. Thanks, Martin A. Walker 20:04, 9 August 2009 (UTC)

Any chance of nudging him about the extensions at the same time? ;) Physchim62 20:07, 9 August 2009 (UTC)

I've sent an email regarding both. I'm not sure if I asked about the other extensions - I remember composing the email, but maybe I didn't hit send? (Last week was very busy!) Greg is usually very good at responding to my requests within 24 hours, but one of us must've dropped the ball there. I also asked him last week for specifics on expected hardware needs, to put in the grant- his boss is helping him with that. Martin A. Walker 21:42, 9 August 2009 (UTC)

I love the new templates linking straight over to WP - beautiful! Didn't know we could do that so easily! Thanks, Martin A. Walker 17:22, 10 August 2009 (UTC)

BTW, the tech people are still looking at the 50k+ issue, but the others have been resolved. Martin A. Walker 17:23, 10 August 2009 (UTC)

Sulfuric acid

PC, do you know why the sulfuric acid article on Wikichem is "hanging"? Other articles seem fine, but this one isn't working for some reason? Is there a template in an infinite loop or something?

Driving to Washington, DC today for the ACS conference - about 11 hours on the road, so leaving soon. Martin A. Walker 15:06, 14 August 2009 (UTC)

I'm afraid I seem to be driving the servers to the limit today. Sulfuric acid is not the only page that's been hanging for me. In my defense, I have been installing the chembox, which will have been hard on the servers during the installation but less hard once it's nice and stable (the heaviest bits are done now). I've a couple of quick tech points for you as well, but they can wait until after the weekend. Physchim62 21:58, 14 August 2009 (UTC)

Sulfuric acid

PC, do you know why the sulfuric acid article on Wikichem is "hanging"? Other articles seem fine, but this one isn't working for some reason? Is there a template in an infinite loop or something?

Driving to Washington, DC today for the ACS conference - about 11 hours on the road, so leaving soon. Martin A. Walker 17:33, 14 August 2009 (UTC)

Thanks

Thanks for getting the copyrights cleaned up here. I can see it's been a major task, but it'll be worth it in the long run. Martin A. Walker 04:36, 17 August 2009 (UTC)

More notes to self

Or rather things to ask the Potsdam techies!

StringFunctions

To add/set $wgPFEnableStringFunctions = true; in LocalSettings.php; see http://www.mediawiki.org/wiki/Extension:StringFunctions

Subpages

To enable subpages in the Template and Template talk namespaces; see http://www.mediawiki.org/wiki/Manual:$wgNamespacesWithSubpages In LocalSettings.php

# Enable subpages in selected namespaces
$wgNamespacesWithSubpages[NS_TEMPLATE] = true;
$wgNamespacesWithSubpages[NS_TEMPLATE_TALK] = true;

There may also be an easier way to do it, that's just the way that seemed obvious from the MediaWiki manual! Question? Do we want subpages in the Main namespace?

Image considerations

Do we want to be able to directly access images on Wikimedia Commons?

We can do this by adding the following code to LocalSettings.php see http://www.mediawiki.org/wiki/Manual:$wgForeignFileRepos#Using_files_from_Wikimedia_Commons_:_ForeignAPIRepo

$wgForeignFileRepos[] = array(
   'class'                   => 'ForeignAPIRepo',
   'name'                    => 'shared',
   'apibase'                 => 'http://commons.wikimedia.org/w/api.php',
   'fetchDescription'        => true, // Optional
   'descriptionCacheExpiry'  => 43200, // 12 hours, optional
   'apiThumbCacheExpiry'     => 43200, // 12 hours, optional, but required for local thumb caching
);

but do we want to? We would have more control over image validation if we stored the images locally, and it would cost us less in bandwidth, but it would be much more work to upload all the images we need.

SVG images

See http://www.mediawiki.org/wiki/Manual:Image_Administration#SVG

• To enable uploading of SVG images, we simply need to add 'svg' to the $wgFileExtensions array
• However, to use SVG images, we need to choose a renderer. The default is ImageMagick: do we want to change this? Batik is supposedly better, but more expensive in server-time.

I asked Greg to enable SVG for us, and I also gave him the details you mention here. I suggested Batik (1st choice) or Librsvg (the Wikimedia servers use the latter). Martin A. Walker 04:54, 21 September 2009 (UTC)

Wow!

What a can of worms we keep finding! Kudos to you for taking that on! Martin A. Walker 20:02, 20 September 2009 (UTC)

How are things?

Hi PC, Looks like you're having fun here! Are you piloting things here for use on WP, or ready for us to open up this site next year?

I've been pretty quiet on WP, though I have been involved with the offline task force; I've just been busy with organising our conference and with work in general. Things will be easier after December 21st. I have also been doing stuff at work that I hope can be added to the wikichem site, including a large set of pages from my Advanced Organic class that I plan to put up here ready for teaching it in Spring 2010.

Have you done anything on the paper for J Cheminf. yet? I was hoping to start thinking about that this week, and do some writing next week. Cheers, Martin A. Walker 21:10, 14 December 2009 (UTC)

Both pilot work and preparation, really. I am trying to put new stuff for WP up here first, so that it doesn't get stuck with a "share-alike" restriction. But also, I'm trying to sort out some of the less obvious bits of a categorization system for WikiChem, so that new articles will have somewhere obvious to go when the site goes public.

Much of the classification is pretty obvious at first sight, but don't forget that it took WP:PHARM nearly nine months to introduce an ATC-based calssification for drugs – it's so much easier to do things correctly from the start than to have to change them later. Next on my list are pesticides and POPs, although I notice you want me to do organic reactions as well ;) Physchim62 14:33, 15 December 2009 (UTC)

We can, of course, learn some of the lessons from WP, and copy over some of the standards. Of course once we start on new things, we will have to learn the hard way like we did on WP! Re organic reactions, you can let me do those cats if you like :) Martin A. Walker 20:21, 15 December 2009 (UTC)

Merry Christmas!

Have a great Christmas! I'll be in touch soon about the paper. Martin A. Walker 05:57, 19 December 2009 (UTC)

Collapsible tables

Hi PC,

I'm using this site as a testbed for ChemSpider Education materials.

I was really wanting to use collapsible tables, and/or collapsible NavFrames, but I can't get them to work. It looks to me as if you made the necessary changes but I am still not seeing the Hide/Show button. Do you know why? Do you see Hide/Show? Should I ask for help from the IT people at SUNY Potsdam?

BTW, I've also asked for the data transclusion extension to be added here, so we can try transcluding certain data (InChIs and SMILES) directly from ChemSpider: http://www.mediawiki.org/wiki/Extension:DataTransclusion

Regards, Martin A. Walker 02:33, 11 August 2010 (UTC)