User talk:A.l.brown

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Just realised I am a buerocrat and admin. cool...

Have you seen my pink box template?

This is a direct replacement for Adrian's html on the vaccinations page, which I think we should actively discourage, for reasons of consistency.Vk 00:51, 17 November (CET)

It was very nice, but its time has come! Rupert 16:35, 11 January (CET)

I agree. Didn't I make a remark about that on teh associated Talk page? Only criticism is the name - we may want float left etc as well. No bog. Midgley 20:07, 18 November (CET)

No problem, I actually noticed it last night before I logged off, but was too tired to sort it. Sorry. Vk 14:25, 17 November (CET)

All seems to be coming along nicely Dokane 16:57, 17 November (CET)

Yes it does rather! --A.l.brown 17:23, 17 November (CET)


Recent changes

Wikipedia shows only the last change rather than everyone's contribution to the very same page - the "recent changes" page looks a lot less cluttered as a consequence - is this fixable or is it an individual setting? Vk 19:40, 17 November (CET)

fixed by enabling javascript for recent changes! odd one... Vk 19:44, 17 November (CET)

Rejigged that main page. reserving the pink box for the disclaimer and not for potential authors. Moved it to the opening paragraph

Good idea! --A.l.brown 09:25, 21 November (CET)

Sorting out the registration page

Note for me: Sort out MySQL query for inserting into users table in DB (line 121, register2.php) --A.l.brown 18:06, 23 November (CET)

new messages on user talk pages

nice to see the progress!

have just had a message left on my user talk page. despite having read the message, i still get told that i have 'new messages'. is this a bug or is there a way of flagging the message as read? Mark ong Now fixed with upgrade - thanks. Mark ong

Alex, I don't know if you already worked this out, but I found that this is a known bug which affects users with spaces in their names. It was fixed only ten days ago by version 1.5.4 of MediaWiki. Rupert 17:39, 31 December (CET)
I've had the x.x.4 version installed on my test server at home, upgraded from x.x.2 - I've made a couple of changes to the code here so I'll have to upgrade carefully. ;-) --A.l.brown 15:36, 2 January (CET)
Now fixed. --A.l.brown 17:20, 18 January (CET)

Thanks for checking out the pertussis page! --Penglish 21:53, 12 December (CET)

It's easy to miss but I've posted a comment about adding ganfyd content to TRIP on Talk:TRIP Database - I have a feeling you're likely to know the answer! --Jb 10:59, 15 February (CET)

To do:

Sort out aminoglycosides & macrolides & glycopeptides & whatever else I've done into subcategories rather than pages.... --A.l.brown 19:25, 1 December (CET)

Finish Catalase test --A.l.brown 17:36, 13 December (CET)

Wonderful changes to main page !!!! Dokane 11:32, 21 December (CET)

Adam, thank you very much for making me a sysop. Rupert 09:58, 7 January (CET)

User templates

Student contributors & expert members? I know from reading the move log that you like consistent nomenclature! If you left this and then decided to change it later, it might be difficult because if you change the template, the categorisation of the pages that transclude the template won't be altered until the pages are edited. Also, is the student one finished? It might be nice to include a field for the mentor. Rupert 18:03, 9 January (CET)

Aha! Good point. It should be expert contributors! Mea culpa - I'll go and change it now...! And you are right about the mentors bit - I'm full of flu and finding abstract thinking a bit difficult at the moment so if you can add the mentors bit then be my guest :-) --A.l.brown 18:17, 9 January (CET)
Done! Rupert 19:04, 9 January (CET)

Hi. Adam. A few research grant deadlines coming up, so might not be so active around ganfyd over the next 3-4 weeks. Mark ong 23:04, 16 January (CET)


Good luck. Midgley 16:43, 18 January (CET)

Nice new (g) logo

A product of Revision Avoidance ;-) --A.l.brown 12:49, 23 January (CET)
How did you get on in the your exam? Rupert (Talk) 15:43, 15 June (BST)
I passed, amazingly. Now trying to sort out pre-final RITA audit and publications. --A.l.brown 17:46, 15 June (BST)
Well done! Good luck with those other things. Rupert (Talk) 18:32, 15 June (BST)


I observed a naive user approaching ganfy dfor the first time. She didn't spot the search. When she did, her first search failed through mis-spelling which is fair enough, but the text is small, and her second becuase the abbreviation picked didn't have a redirect to it. I've corrected the latter, and will carry on mkaing redirects for abbreviations commonly used as words (AF etc) When she had moved to another program, the button on th tskbar representing Ganfyd in the browser was not very evident it says "Main Page - Ganfyd" whereas ideally I think it would say soemthing like "ganfyd: Collaborative medical text book" or even the other way round. (Less obvious in Microsoft IE becuase that wants to tell you about Microsoft in every title IIRC)

The usability thing... Can we make the search slot a bit bigger and give it a text size slightly larger? I couldn't find the relevant bit. Is there any scope for putting a search slot either dead centre in the main page, or up on the top right, whcih is where Jakob Nielsen tells us all users expect it (I believe him).

And then categories not being searched .... Midgley 19:08, 8 February (CET)

The blue is better, in search. yes. Draws the eye. Do we need to point in the contents, or add search to contents - sending them tot eh advanced search age I wonder.Midgley 19:41, 9 February (CET)
I am working on adding search to the contents, however the inputbox extension needs so recoding to fit our board. --A.l.brown 09:45, 10 February (CET)
Good Google-esque approach. I had a look at some MediaWiki code and thought it good but fierce.
Incredibly fierce! I've managed to start work on custom parser hooks, but very early days at the moment. Large search thing now slap-bang in the middle of the Main Page.

Adam, I think Mlj could do with bureaucrat/sysop privileges. Mark ong 11:03, 13 February (CET)

I think you are right! --A.l.brown 11:47, 13 February (CET)
Thanks you both. What Trust. Off to do more content then.Mlj 21:21, 13 February (CET)

Can you please put Cochrane 'and' in capitals in code please. A bit of a pain that Template variables dont get parsed by the present php code, but apart from error detection my HACK in pharmacologybox isn't bad, if I say so myselfMlj 23:24, 14 February (CET)

Done :-) It is a pain isn't it. --A.l.brown 10:21, 15 February (CET)

Adam, I've written a references extension, which I've announced on Talk:Conjugate vaccines. I don't know if you'll think it's worthy of inclusion or not. I hope so. Tested so far only on Windows running MediaWiki: 1.5.5, PHP: 5.0.5 (apache2handler), MySQL: 4.0.21-nt, but it's simple stuff so I'm confident it'll work on any 1.5.5 MediaWiki. Rupert 13:28, 17 February (CET)

Immunity and Rabies

I wonder if this is up your street and possibly even within sight of revision Determining_immunity?

OK I will put country templates back - I can solve this issue another way. Thanks for the feed back Mlj 21:52, 21 February (CET)

<reference> syntax does not work with generation of reference list in Catalogue namespace yet :)Mlj 22:59, 21 February (CET) Ah problem solved was me...thanks for the good work of you and Rupert...I will improve Ruperts instructions Mlj 23:35, 21 February (CET)

New User Registration

Is this working okay? I gather bluedragon on DNUK had some trouble. Mark ong 23:46, 9 March (CET)

Yep it is now. My fault for missing off a single character. Shoddy really. --A.l.brown 17:19, 18 April (CEST)

Front page

Better. Midgley 00:17, 12 March (CET)

I've added a line stating that ganfyd is for healthcare professionals. --A.l.brown 13:53, 12 March (CET)


Thought you might be interested to see your that HubLog (Alf the guy who runs HubMed has a blog) has highlighted the ganfyd hubmed extensions [1].

Thanks for that. It is nice when various projects interlink. --A.l.brown 17:20, 18 April (CEST)


You might think that this is a silly little thing, but the way comments are timestamped in "Central European Summer Time" has really been getting on my nerves. I think timestamps should be in BST in the summer and GMT in the winter, ie. local time in the UK, rather than being an hour ahead. To do this you need to add the following lines to LocalSettings.php

$wgLocaltimezone = 'BST';  # Change this to GMT in the winter
$wgLocalTZoffset = 1;      # Probably not change this in the winter (It is local time on the server minus local time we want, in hours.)

I also had to make the following additions to function pstPass2( $text, &$user ) in Parser.php:

global $wgContLang, $wgLocaltimezone, $wgLocalTZoffset;
$d = $wgContLang->timeanddate( date( 'YmdHis', time() + $wgLocalTZoffset*3600 ) , false, false) .

I've done these on the dev-wiki and it works OK. They also fix the default timezone (for anonymous & new users) on the recent changes list, which was an hour behind local time in the UK. I hope you can use this - I've missed a lot of snooker to work it out. And the snooker's coming out of revision time! Rupert (Talk) 16:23, 18 April (CEST) or rather 15:23, 18 April (BST) ;)

Please, please, pretty please. Rupert (Talk) 16:39, 18 April (CEST)
Crikey. Looks like a job for our resident codemonkey (that would be you...!) - I've altered your ftp access so you have access to the web root. The main wiki is in /wiki - try not to break anything ;-) --A.l.brown 17:18, 18 April (CEST)
Righty ho. Thanks. I'll be careful! Rupert (Talk) 18:34, 18 April (CEST)
All done! Better, isn't it? Rupert (Talk) 17:46, 18 April (BST)
Yes it does. Do we have to remember to change things come the end of BST? --A.l.brown 17:48, 18 April (BST)
As it is at the moment, we will have to. (I have actually put it in my diary for the 29th October though so you don't need to worry.) Since the clocks go back in the UK and across the EU on the same day with no alteration, without adjustment, it will show the correct local time but incorrectly label it BST instead of GMT. Having just thought about it, it will require very little code to make the adjustment automatic, since PHP knows whether or not it's daylight saving time. I'm not sure it's worth doing though as I don't think Mediawiki is handling time zones as intended, so I should probably sort it out properly rather than a one-time fix for ganfyd. I'll need to get sorted with CVS and what-not though. The way it should work, is for the administrator to set the location/time zone for signatures and for unregistered and new users, and then each user to be able to set their own for page histories and so on. There probably should be an option to fudge it, if the PHP installation isn't working out GMT correctly. Rupert (Talk) 18:16, 18 April (BST)

Version 1.6.3 & ParserFunctions

Version 1.6.3 - I've got it working on my computer, found and fixed a small bug in it, and I'd really like it if ganfyd could be run on it. These are the improvements that are significant for ganfyd, some of which are taken directly from the release notes:

  • single tags supported for extensions- end to <ref></ref> and what-not.
  • Diffs in RSS and Atom feeds are now colored for improved readability. <- I would actually read the RSS summary, rather than always loading the article, if the diffs weren't in black and white. It's such an improvement!
  • Categories and "what links here" now update as expected when adding or removing links in a template.
  • Template parameters can now have default values, as default value
  • bug fixes

I know it's a lot to ask, so if you don't want to do it that's absolutely fine by me. I know your MRCPath exam is getting increasingly close so please don't feel like there's any pressure at all. I'm afraid, I'm too worried about buggering up the wiki to offer to do it myself. I thought about it, but having compared the dev wiki to the live wiki, I don't think a dummy run on the dev wiki would give me the confidence I need to go through with it. There is another little softwarey thingy - awake and articulate, aren't I?! - the ParserFunctions extension. Adrian was trying out the syntax yesterday and I think it would be a handy addition, enabling us to write much more intelligent templates. (More than making up for not having the support for default parameter values that 1.6 would bring.) Unlike upgrading the whole wiki, I would be quite happy to install this on the main wiki with your say-so. Rupert (Talk) 00:47, 20 April (BST)

Dummy runs? What are dummy runs!?! Tell you what, I'll lock the database mid-morning, back-up the whole thing, upgrade the wiki and make the necessary amendments and un-lock the database, then you can install the extension. --A.l.brown 09:54, 20 April (BST)
Great job. Shall I put the ParserFunctions extension on now then? Rupert (Talk) 11:20, 20 April (BST)
Go for it. --A.l.brown 11:25, 20 April (BST)
Nyaaaaaargh MediaWiki! 1.6.3 is only 10 days old, and I still had to patch Parser.php to get this extension to work with the same syntax as Wikipedia! Still, it's working now. I'm going to make a note of what I had to do on Ganfyd:MediaWiki customisations. Oh bollocks - the time stamp is wrong now! Rupert (Talk) 12:09, 20 April (BST)
But where would the fun be if it was straightforward!!! --A.l.brown 13:14, 20 April (BST)
By the way, you can still log into the mothballed forum, and if you go to the admin/sysop subforum you'll be able to put amendments there (use the Modifications to Mediawiki Source thread). Much of what is there is just me talking to myself! --A.l.brown 13:18, 20 April (BST)
Well you can see I've fixed it now. At least it demonstrates the need for the sort of reminder that I mentioned above - I'm clearly incapable of remembering that I patched Parser.php for even two days, so I'd be stuffed if I had to do it again after some weeks! Thanks for pointing me in the direction of the forum - I didn't realise I could still log-in or that I had access to that board. I will put the modifications on that thread. Rupert (Talk) 13:32, 20 April (BST)

Replace tag

There's a replace tag?? I'm shocked! I had absolutely no idea. How long has it been around for and how did you know about it? Rupert (Talk) 22:21, 30 April (BST)

Blimey thats quick. It has been in existence for about 5 minutes! A quick and dirty extension for Mlj to use when doing internet searches which don't like sp--A.l.brown 02:06, 1 May (BST)aces in them. The code is 60 lines long, and mostly comments!!! --A.l.brown 22:22, 30 April (BST)
You do know that I sit by my computer day & night, waiting for something to happen on ganfyd, right? Actually, when I woke up on saturday morning, although I can't ever remember my dreams, I'm positive the last one had something to do with wikis, because my waking thought was the word wikis. This is unhealthy. Rupert (Talk) 23:02, 30 April (BST)
You need to do more ballroom dancing! --A.l.brown 01:49, 1 May (BST)
I really need to do more revision, or at least some, but I find it so hard to motivate myself with a whole week before my exams start. Anyway, good night - I'm off to bed now. (a.k.a. the land of nodwiki!) Rupert (Talk) 02:02, 1 May (BST)
Ah yes - revision. The stuff I should be doing for my Part II MRCPath but aren't!--A.l.brown 02:06, 1 May (BST)

New Server

I see its two hours ahead of BST today.Mlj 02:07, 23 May (BST)....sorry, make that 3 hours. Mlj at really 23:08, 22 May (BST)

In localsettings.php, you need to change $wgLocalTZoffset = 1 to $wgLocalTZoffset = -2. I'd love to know how it's *3* hours out! Rupert (Talk) 02:20, 23 May (BST)
I think what we need to do is just SSH into the server and set its time, maybe pointing it at a time server somewhere? --A.l.brown 18:18, 23 May (BST)
Yes, the clock was wrong. The hardware clock is set to UTC. The linux timezone is correctly set to Europe/London, which it knows is BST atm. The two overrides in LocalSettings are not necessary any more, so I commented them out. Rupert (Talk) 16:44, 26 May (BST)

Upgrade problems

How awful.

Does this link help. Obviously I understand the theory of whats gone wrong if not the languageMlj 23:42, 24 May (BST)

Noted that you can't yet upload .png images...presumably a script problem.Mlj 01:41, 26 May (BST)
Gaaaahhh!!!! I hate computers. Its official. Sorry about that. I'll get on to it as soon as I can. D'you know, everything that was planned to work hasn't. --A.l.brown 11:57, 26 May (BST)

Excellent work Adam

And of course Adrian and Rupert. The database passes the tests I have thrown at it. It looks like you three have mutual expertise that mere mortals have to marvel at.Mlj 22:22, 2 June (BST)

That should be 'excellent work Adrian and Rupert despite Adam's feeble attempts'!!! --A.l.brown 18:04, 4 June (BST)

Possible Upload problem

Probably introduced if it exists on upgrade or when registration engine redone by Rupert. I thought all users could upload images but its been so long since I qualified as a bureaucrat myself who knows. Manville claims not allowed to at present. I have just upgraded Manville to a bureaucrat given his contributions and perhaps this will work. Any commentsMlj 21:57, 2 September (BST)

I've changed LocalSettings.php so that all users can upload. I expect it dates back to when we had to disable uploads for a move or upgrade. (Although we sysops would have been exempt from an alteration to the user permissions.) Rupert (Talk) 22:01, 2 September (BST)
My fault for forgetting to change that back. --A.l.brown 10:21, 3 September (BST)
Not to worry. For future reference, the "proper" way (easiest & most effective) to disable image uploading is to change $wgEnableUploads to false in LocalSettings.php Rupert (Talk) 12:08, 3 September (BST)

Search Facility

Having a bit of bother with searches. Was searching for TNM, but no hits (but see Breast_cancer#Staging). Unless there is a proxy caching problem on my side?

Also can't find MED/MED3/MED 3/Med3/Med 3 (or DWP), despite the fact that it is present in Incapacity assessment. I don't know if it is something to do with capitalised letters, but on the other hand, CD28 seems to be in the search database. Any ideas? Mark ong

I suspect this is the length of words that are indexed, and/or stopwords (words which are not indexed at all). We may need to expand the index to include TLAs. Midgley 15:29, 5 September (BST)
Adrian is right - how to expand the index. I can do it when I'm back at my own computer on Friday, or you could do it. (Before I left for the week, I copied down your username and password, which I tried to phone to you on Sunday evening, but you didn't answer. Ring me at a convenient time for you.) Rupert (Talk) 18:25, 5 September (BST)

Thanks for deleting my page with typo in title (SFA).

--Penglish 13:27, 12 September (BST)

My pleasure. You should now have a little 'delete' tab on pages, so you can do it yourself! :-) --A.l.brown 13:44, 12 September (BST)
Wow, cool! --Penglish 14:00, 12 September (BST)
Adam, the delete facility is only enabled for sysops. (I just checked that. Definitely true!) Peter, you actually will have the delete tab now. Rupert (Talk) 15:43, 12 September (BST)
Bugger. --A.l.brown 15:48, 12 September (BST)

Uploading Non-standard Files

How do you do it? Have an Excel spreadsheet file to calculate ROC curves which I'd like to upload. I take it you need special dispensation? ;) Mark ong 15:52, 22 November (GMT)

This is the file:
I'll upload it for you tonight - they get done via FTP to prevent accidental virus introduction. --A.l.brown 17:36, 22 November (GMT)

Failure to thrive comment

Ta for that. I know what you mean about it needing fleshing out. I suppose that's the problem with the wiki format. It's easy to create document titles and stubs, but much harder to create robust chapters. The fact that so many users of TRIP go to Ganfyd shows interest. Just unfortunate that some of the time they get very little. Interestingly the article on Chickungunya fever was also pretty popular!

I've been pretty quiet recently on ganfyd, with TRIP going free and also working on a new project - Gwagle (Welsh for space). It's very 'web 2.0' - think a cross between connotea and askville - with a bit of my-space thrown in! Should be available for alpha testing in March - if you're interested!

Have a great New Year --Jb 13:39, 27 December (GMT)

Good news!

Hooray! I passed all my exams and got the grade that I needed to get on an intercalated degree in clinical sciences. Off down the pub now. —Rupert (Talk) 18:40, 10 May (BST)

Good work! Enjoy the beer. Make sure there is plenty of it. --A.l.brown 18:44, 10 May (BST)

Dear Adam, Penglish, mlj and Midgley,

I'm writing to you all with my 'RUK editorial' hat on. RUK is the journal of RemedyUK, and has a circulation of around 2000 copies atm. I am hoping to write a piece about medical wikis, especially ganfyd, following last months mention of the US site, medpedia. I would be grateful if any of you would be willing to take part in an email interview, asking a few questions about ganfyd, your involvement, and how you think medical wikis will influence the medical profession.

If you would be happy to take part, please email me, fishgoth at gmail.

Best wishes,

Fishy aka Stephen O'Hanlon