[Wikitech-l] IRI for {{canonicalurl:}}?

2012-04-21 Thread Raimond Spekking
Looking at
https://en.wikipedia.org/w/index.php?title=Special:Cite&page=%C4%B0stanbul_B%C3%BCy%C3%BCk%C5%9Fehir_Belediyespor_%28football_team%29&id=483557138
you see a lot of unpretty URLs (Bug 7329 [0]).

With https://gerrit.wikimedia.org/r/#change,3897 a new global function
wfExpandIRI() was introduced for printer friendly URLs in unicode.

First and easiest solution for pretty URLs would be to run the function
which outputs {{canonicalurl:}} through wfExpandIRI().

Is this safe? Are all browsers able to handle IRIs [1]?

Otherwise I am thinking about creating a new magic word
{{canonicaliri:}}. This can be used in [2] for example.

Raimond.

[0] https://bugzilla.wikimedia.org/show_bug.cgi?id=7329
[1] https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier
[2] https://en.wikipedia.org/wiki/MediaWiki:Cite_text



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Re: [Wikitech-l] Git code review metrics

2012-04-21 Thread Platonides
On 21/04/12 04:18, MZMcBride wrote:
> Regarding help, is the Gerrit commit metadata available in some replicated
> form on WMF Labs? The Toolserver has a replicated copy of MediaWiki's
> CodeReview tables. Is there something similar for Gerrit/WMF Labs?
> 
> I almost asked about the Toolserver, but then I just got sad.
> 
> MZMcBride

Once a change is merged, there's a summary of the review stored in git
notes for that revision, but I don't know of any place where other
review info is being stored other than the manganese db.


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Re: [Wikitech-l] Git code review metrics

2012-04-21 Thread Chad
This information is fetchable from refs/notes/review.

-Chad
On Apr 21, 2012 9:51 AM, "Platonides"  wrote:

> On 21/04/12 04:18, MZMcBride wrote:
> > Regarding help, is the Gerrit commit metadata available in some
> replicated
> > form on WMF Labs? The Toolserver has a replicated copy of MediaWiki's
> > CodeReview tables. Is there something similar for Gerrit/WMF Labs?
> >
> > I almost asked about the Toolserver, but then I just got sad.
> >
> > MZMcBride
>
> Once a change is merged, there's a summary of the review stored in git
> notes for that revision, but I don't know of any place where other
> review info is being stored other than the manganese db.
>
>
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[Wikitech-l] Developing MediaWiki extension for WebGL-enabled interactive 3D models

2012-04-21 Thread emw
Hi all,

I'm in the process of developing a media handling extension for MediaWiki
that will allow users with WebGL-enabled browsers to manipulate 3D models
of large biological molecules, like proteins and DNA.  I'm new to MediaWiki
development, and I've got some questions about how I should go forward with
development of this extension if I want to ultimately get it into official
Wikimedia MediaWiki deployments.

My initial goal is to put the kind of interactive model available at
http://webglmol.sourceforge.jp/glmol/viewer.html into infoboxes like the
one in http://en.wikipedia.org/wiki/FOXP2.  The library enabling this
interactivity is called GLmol -- it's licensed under LGPL and described at
http://webglmol.sourceforge.jp/index-en.html.  There is some more
background discussion on the extension at
http://en.wikipedia.org/wiki/Portal:Gene_Wiki/Discussion#Enabling_molecular_structure_manipulation_with_WebGL.


I have a prototype of the extension working on a local deployment of
MediaWiki 1.18.1.  I've tried to organize the extension's code roughly
along the lines of http://www.mediawiki.org/wiki/Extension:OggHandler.  The
user workflow to get an interactive protein model into an article is to:

  1) Upload a PDB file (e.g. http://www.rcsb.org/pdb/files/2A07.pdb)
representing the protein structure through MediaWiki's standard file upload
UI.
  2) Add a wikilink to the resulting file, very similar to what's done with
images.  For example, [[File:2A07.pdb]].

If the user's browser has WebGL enabled, an interactive model of the
macromolecule similar to one in the linked GLmol demo is then loaded onto
the page via an asynchronous request to get the 3D model's atomic
coordinate data.  I've done work to decrease the time needed to render the
3D model and the size of the 3D model data (much beyond gzipping), so my
prototype loads faster than the linked demo.

A main element of this extension -- which I haven't yet developed -- is how
it will gracefully degrade for users without WebGL enabled.  IE8 and IE9
don't support WebGL, and IE10 probably won't either.  Safari 5.1.5 supports
WebGL, but not by default.  WebGL is also not supported on many smartphones.

One idea is to fall back to a 2D canvas representation of the model,
perhaps like the 3D-to-2D examples at https://github.com/mrdoob/three.js/.
I see several drawbacks to this.  First, it would not be a fall-back for
clients with JavaScript disabled.  Second, the GLmol molecular viewer
library doesn't currently support 2D canvas fall-back, and it would
probably take substantial time and effort to add that feature.  Third,
there are browser plug-ins for IE that enable WebGL, e.g.
http://iewebgl.com/.

Given that, my initial plan for handling browsers without WebGL enabled is
to fall back to a static image of the corresponding protein/DNA structure.
A few years ago I wrote a program to take in a PDB file and output a
high-quality static image of the corresponding structure.  This resulted in
PDBbot (http://commons.wikimedia.org/wiki/User:PDBbot,
http://code.google.com/p/pdbbot/).  That code could likely be repurposed in
this media handling extension to generate a static image upon the upload of
a PDB file.  The PDBbot code is mostly Python 3, and it interacts with GIMP
(via scripts in scheme) and PyMOL (http://en.wikipedia.org/wiki/PyMOL,
freely licensed:
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/LICENSE?revision=3882&view=markup
).

Would requiring Python, GIMP and PyMOL to be installed on the server be
workable for a WMF MediaWiki deployment?  If not, then there is a free web
service developed for Wikipedia (via Gene Wiki) available from the European
Bioinformatics Institute, which points to their pre-rendered static images
for macromolecules.  The static images could thus be retrieved from a
remote server if it wouldn't be feasible to generate them on locally on the
upload server.  I see a couple of disadvantages to this approac, e.g.
relying on a remote third-party web service, but I thought I'd put the idea
out for consideration.  If generating static images on the upload server
wouldn't be possible, would this be a workable alternative?

After I get an answer on the questions above, I can begin working on that
next major part of the extension.  This is a fairly blocking issue, so
feedback would definitely be appreciated.

Beyond that, and assuming this extension seems viable so far, I've got some
more questions:

1. Once I get the prototype more fully developed, what would be the
best next step to presenting it and getting it code reviewed?  Should I set
up a demo on a random domain/third-party VPN, or maybe something like
http://deployment.wikimedia.beta.wmflabs.org/wiki/Main_Page?  Or maybe the
former would come before the latter?

2. PDB (.pdb) is a niche file type that has a non-standard MIME type of
"chemical/x-pdb".  See
http://en.wikipedia.org/wiki/Protein_Data_Bank_%28file_format%29 for more.
To upload files with this MIME t

Re: [Wikitech-l] Developing MediaWiki extension for WebGL-enabled interactive 3D models

2012-04-21 Thread Platonides
On 21/04/12 17:07, emw wrote:
> Hi all,
> 
> I'm in the process of developing a media handling extension for MediaWiki
> that will allow users with WebGL-enabled browsers to manipulate 3D models
> of large biological molecules, like proteins and DNA.  I'm new to MediaWiki
> development, and I've got some questions about how I should go forward with
> development of this extension if I want to ultimately get it into official
> Wikimedia MediaWiki deployments.
(...)
> Given that, my initial plan for handling browsers without WebGL enabled is
> to fall back to a static image of the corresponding protein/DNA structure.
Seems the appropiate thing to do.

> Would requiring Python, GIMP and PyMOL to be installed on the server be
> workable for a WMF MediaWiki deployment? 

Not ideal, but is probably workable. Still much better than relying (and
potentially DDOSing) on a third party.
If you could drop GIMP requirement, that'd be even better (why is it
needed?).



> 1. Once I get the prototype more fully developed, what would be the
> best next step to presenting it and getting it code reviewed?  Should I set
> up a demo on a random domain/third-party VPN, or maybe something like
> http://deployment.wikimedia.beta.wmflabs.org/wiki/Main_Page?  Or maybe the
> former would come before the latter?

I'd go directly on labs.


> 2. PDB (.pdb) is a niche file type that has a non-standard MIME type of
> "chemical/x-pdb".  See
> http://en.wikipedia.org/wiki/Protein_Data_Bank_%28file_format%29 for more.

We could detect the format. Don't worry about that.


> 3. If at all possible, I'd like to have the molecular models be
> interactive by default, 
> Does having model interactivity by default for WebGL-enabled users
sound feasible?

Maybe, maybe not. Needs testing. I'd wait after having the prototype for
deciding that default.


Thanks for your contributions!


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[MediaWiki-CodeReview] [MediaWiki r114745]: Revision status changed

2012-04-21 Thread MediaWiki Mail
"SVG" changed the status of MediaWiki.r114745 to "ok"
URL: http://www.mediawiki.org/wiki/Special:Code/MediaWiki/114745

Old status:  new
New status: ok

Commit summary for MediaWiki.r114745:

Translation updates for SVN extensions from translatewiki.net

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[MediaWiki-CodeReview] [MediaWiki r114994]: Revision status changed

2012-04-21 Thread MediaWiki Mail
"SVG" changed the status of MediaWiki.r114994 to "ok"
URL: http://www.mediawiki.org/wiki/Special:Code/MediaWiki/114994

Old status:  new
New status: ok

Commit summary for MediaWiki.r114994:

Localisation updates from http://translatewiki.net.

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[MediaWiki-CodeReview] [MediaWiki r100315]: New comment added

2012-04-21 Thread MediaWiki Mail
"Bawolff" posted a comment on MediaWiki.r100315.
URL: http://www.mediawiki.org/wiki/Special:Code/MediaWiki/100315#c32713

Commit summary for MediaWiki.r100315:

* Made ?contribs=user actually show the results for the *user* if 'newbies' was 
given as the user.
* Added a link batch query to newbie contribs paging

Bawolff's comment:

*sigh*. This is really the issue that just never dies, isn't it.

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[MediaWiki-CodeReview] [MediaWiki r100315]: New comment added

2012-04-21 Thread MediaWiki Mail
"MZMcBride" posted a comment on MediaWiki.r100315.
URL: http://www.mediawiki.org/wiki/Special:Code/MediaWiki/100315#c32714

Commit summary for MediaWiki.r100315:

* Made ?contribs=user actually show the results for the *user* if 'newbies' was 
given as the user.
* Added a link batch query to newbie contribs paging

MZMcBride's comment:

Do you have any good ideas for finding links of this nature? It seems Special 
links aren't tracked very easily.

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Re: [Wikitech-l] Proposal to complete manually complete unification of all accounts

2012-04-21 Thread Thehelpfulone
On 6 April 2012 14:28, Platonides  wrote:

> Forwarding in behalf of the original user:
>
> > Platonides wrote:
> > K. Peachey wrote:
> >> Why would we not want blocked accounts to be processed?
> >
> > Presumably because an indefinetely blocked name (or worse, oversighted)
> > would then need a global block.
>
> Of course blocked accounts anywhere must not be processed.
>
> Is there a need to unify old blocked sock/vandal accounts to globally
> block them later? No.
>
> Is there a need to unify oversighted accounts via the wpHideUser
> function to globally oversight later? No.
>
> Do you know that before CentralAuth had the global oversight function
> accounts had to be locked at meta and then you need to go wiki by wiki
> manually blocking with 'wpHideUser', then manually oversight meta logs?
> - Creating global accounts for those users, most of them with personal
> information, would be appalling.
>
> Creating global accounts for blocked accounts creates no benefits but
> would be an absolute mistake and would indeed increase the level of work
> stewards (I am one) would have to do to fix the problems.
>
> So, I beg *not* to include blocked accounts anywhere into this proposal.
> Vandals, socks and abusive names does not need to be unified so they can
> continue vandalizing anywhere, or exposing personal information/libel, etc.
>
> Best regards.


As it's been over 2 weeks since there was activity on this thread, can the
developers get the ball rolling on completing the unification process for
these accounts?
-- 
Thehelpfulone
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[MediaWiki-CodeReview] [MediaWiki r100315]: New comment added

2012-04-21 Thread MediaWiki Mail
"Platonides" posted a comment on MediaWiki.r100315.
URL: http://www.mediawiki.org/wiki/Special:Code/MediaWiki/100315#c32715

Commit summary for MediaWiki.r100315:

* Made ?contribs=user actually show the results for the *user* if 'newbies' was 
given as the user.
* Added a link batch query to newbie contribs paging

Platonides's comment:

I think the best solution would be grepping the pages-meta-current xml dumps.

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Re: [Wikitech-l] Developing MediaWiki extension for WebGL-enabled interactive 3D models

2012-04-21 Thread Sumana Harihareswara
On 04/21/2012 08:07 AM, emw wrote:
> Hi all,
> 
> I'm in the process of developing a media handling extension for MediaWiki
> that will allow users with WebGL-enabled browsers to manipulate 3D models
> of large biological molecules, like proteins and DNA.  I'm new to MediaWiki
> development, and I've got some questions about how I should go forward with
> development of this extension if I want to ultimately get it into official
> Wikimedia MediaWiki deployments.

Eric, thank you for this contribution, and, like, wow, cool!  Let me
point you to
https://www.mediawiki.org/wiki/Writing_an_extension_for_deployment ,
which answers several of your questions, I think.

Please keep sharing your progress here.

-- 
Sumana Harihareswara
Volunteer Development Coordinator
Wikimedia Foundation

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