On 2 Mar 2012, at 16:54, Robert Hanson wrote:
> Well, then I propose /*file*/"" within a script is adapted by MediaWiki
> to change that to a proper file name.
>
>
> On Fri, Mar 2, 2012 at 9:51 AM, Nicolas Vervelle wrote:
>
an alternative which by-passes the file path naming problem is to
Well, then I propose /*file*/"" within a script is adapted by MediaWiki
to change that to a proper file name.
On Fri, Mar 2, 2012 at 9:51 AM, Nicolas Vervelle wrote:
> Scripts can be used as you wish, there's just the limitation with paths to
> files.
>
> On Fri, Mar 2, 2012 at 4:46 PM, Robe
Scripts can be used as you wish, there's just the limitation with paths to
files.
On Fri, Mar 2, 2012 at 4:46 PM, Robert Hanson wrote:
> no scripts at all?
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.ed
no scripts at all?
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lectu
Shouldn't be hard to adapt that to the way Jmol finds file names in scripts:
load /*file*/"..."
isosurface /*file*/"."
next quoted phrase after /*file*/ needs to be replaced by full path to that
file.
On Fri, Mar 2, 2012 at 9:39 AM, Nicolas Vervelle wrote:
> Hi Bob,
>
> In short, it do
> How does MediaWiki know at all where to look for a file when the
> script is
>
> load xxx.xyz
Probably, the script can NEVER be that. Load is managed with the Jmol
MW Extension tags, not with scripts.
MW knows where to find the wiki file (handled like an
image)
external
external
MW
Hi Bob,
In short, it doesn't know.
When you want to display a file that has been previously uploaded, you can
use for example xxx.xyz.
The PHP code of the extension knows where xxx.xyz is stored and creates the
script that works.
See examples in http://wiki.jmol.org/index.php/MediaWiki/Basic_Examp
How does MediaWiki know at all where to look for a file when the script is
load xxx.xyz
?
On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson wrote:
> oh. never mind then. I thought they went into a specific directory. No,
> that would not work
>
>
>
> On Fri, Mar 2, 2012 at 7:02 AM, Nicolas V
oh. never mind then. I thought they went into a specific directory. No,
that would not work
On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle wrote:
> I have the impression that I'm missing a point in this discussion...
>
> The situation Henry is talking about is that he need to access severa
On 2 Mar 2012, at 13:23, Angel Herráez wrote:
> I agree with Nico. The location of uploades files in MW is uncertain.
>
> The .jmol file format is in my opinion the way out of this problem:
> upload a single file with everything included.
A single file as a zip (the same way that jar files ar
I agree with Nico. The location of uploades files in MW is uncertain.
The .jmol file format is in my opinion the way out of this problem:
upload a single file with everything included.
--
Virtualization & Cloud Managem
I have the impression that I'm missing a point in this discussion...
The situation Henry is talking about is that he need to access several
files that have been previously uploaded to the Wiki.
When you upload several files, they usually end up in different directories
(due to the md5 hash on the
My point was that if MediaWiki would just insert the Jmol script code for
defaultDirectory in the startup script, then the user can include numerous
files with no prefix and no concern over where they are.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfi
On Thu, Mar 1, 2012 at 6:02 PM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:
> On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote:
> The problem is that, depending on MediaWiki configuration, uploaded
> files can end up in different directories (to avoid putting thousands of
> files in
Hi Henry
I am senidng to you off-list a sample file I just created. That is a
.jmol file (really a zipfile, with contents added by Jmol; I'm not
sure if you can collate it manually).
This is the procedure I followed:
1. Load the molecule into Jmol app (I used 12.2.16)
2. Create the isosurface,
On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote:
The problem is that, depending on MediaWiki configuration, uploaded files can
end up in different directories (to avoid putting thousands of files in the
same directory)...
And the user has absolutely no control over which directory will be used
The problem is that, depending on MediaWiki configuration, uploaded files
can end up in different directories (to avoid putting thousands of files in
the same directory)...
And the user has absolutely no control over which directory will be used
for a file.
So there's not really a possible default
Couldn't you have the also set the default
directory? In face, one could imagine
might only set the default directory.
On Thu, Mar 1, 2012 at 9:51 AM, Rzepa, Henry S wrote:
>
> On 1 Mar 2012, at 15:09, Jaime Prilusky wrote:
>
> > On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote:
> > If you
On 1 Mar 2012, at 15:09, Jaime Prilusky wrote:
> On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote:
> If you have ideas of what syntax should be used in the extension to make
> using it simple, don't hesitate.
>
>
> If you keep the isosurface file together with the model file, then a simple
Hi,
The extension doesn't manage the path in which files are stored.
Depending on the configuration, MediaWiki stores them in several separate
folders and there's no way to be sure that 2 files will end up in the same
directory.
Maybe we can group ideas/suggestions about the syntax for Jmol exten
On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote:
If you have ideas of what syntax should be used in the extension to make using
it simple, don't hesitate.
If you keep the isosurface file together with the model file, then a simple
tag to indicate the name of the isosurface file (not the ful
Ok, that confirms the explanation.
Henry,
Yes, the tag was designed to hide such complexity
from the user (the call to Special:FilePath is done internally by the
extension).
But using this for scripts would be quite complex because the extension
would have to parse the Jmol script...
If you hav
I think the path is a good lead.
If you check the source of the generated wiki page, you should see a path
for isosurface.xyz.
You probably need to also have the path to isosurface.jvxl, but this is not
always obvious which one to use (try Special:FilePath)
Nico
On Thu, Mar 1, 2012 at 3:24 PM, Ja
On 1 Mar 2012, at 14:24, Jaime Prilusky wrote:
> On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote:
> The MediaWiki extension has the following form
> Overall, this amounts to
>
> load isosurface.xyz;isosurface color orange purple isosurface.jvxl
> translucent;
>
Yes, putting the full filenam
On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote:
The MediaWiki extension has the following form
Overall, this amounts to
load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent;
If your command is "isosurface surfile.iso", I understand that you don't need
to load the sur
Henry, maybe loading a .jmol file would help? It can contain the 2
files in it, and the state script.
You probably need to allow the new file type to be uploaded to the
wiki.
--
Virtualization & Cloud Management Usin
No problem,
Enjoy playing with the extension.
I hope to be able to work on it again soon.
Nico
On Thu, Dec 1, 2011 at 1:05 PM, Kilian Baerwinkel <
kilian.baerwin...@uni-bayreuth.de> wrote:
> Hi,
>
> Oh man I think i got it...
>
> Mediawiki on Ubuntu is split over three directories: /etc/med
Hi,
Oh man I think i got it...
Mediawiki on Ubuntu is split over three directories: /etc/mediawiki and
/etc/mediawiki-extensions, /usr/share/mediawiki and
/usr/share/mediawiki-extensions, /usr/share/mediawiki and
/usr/share/mediawiki-extensions and /var/lib/mediawiki.
Files are only directl
Nico,
sorry for double posting. The OS is Ubuntu Server. And I cannot access the
INSTALL file of the mediawiki itself, which is perfectly possible on the
jmol wiki.
There is something quite wrong here.,..
Best
Kilian
--
ayreuth.de>>
Reply-To:
mailto:jmol-users@lists.sourceforge.net>>
Date: Thu, 1 Dec 2011 12:09:54 +0100
To: mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] MediaWiki Plugin
Jaim,
its exactly the same. This is what i get:
Not Found
The requested URL /mediawiki/exten
Kilian,
The problem may be due to your web server configuration then (accessing of
text file is only done through web server not MW software).
What is your web server ? (Apache HTTPD, ...)
What version ?
On which OS ?
What is the content of your configuration files ?
Can you try putting the .txt
Jaim,
its exactly the same. This is what i get:
Not Found
The requested URL /mediawiki/extensions/UserMerge/blubb.txt was not found
on this server.
- same as for jmol files. Btw, rights are set as you told me (as for all
other extensions).
Kilian
-
n database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
From: Kilian Baerwinkel
mailto:kilian.baerwin...@uni-bayreuth.de>>
Reply-To:
mailto:jmol-users@lists.sourceforge.net>>
Date: Thu, 1 Dec 2011 11:02:21 +0100
To: mailto:jmol-users@lists.sourceforge.net>&
Hi,
I really dont get it...
a normal page on the wiki looks like http://
/mediawiki/index.php/Special:Version
and in the source, there is
Kilian,
I think you have a problem in your MW setup, because the file Jmol.js must
be accessible.
For example, on Jmol wiki, http://wiki.jmol.org/extensions/Jmol/Jmol.js
works.
It must be accessible otherwise, the HTML page can't retrieve the
Javascript functions that are necessary for Jmol.
On
e: Thu, 1 Dec 2011 09:45:22 +0100
To: mailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] MediaWiki Plugin
Nico,
I got the same in the source:
http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible - but
I would have expected this, as Jaime suggeste
Nico,
I got the same in the source:
http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible -
but I would have expected this, as Jaime suggested to try the
COPYRIGHT.txt, and i could not access this one as well.
Best
Kilian
On 30 November 2011 14:10, Nicolas Vervelle wrote
Ok,
So it seems that the extension is active (tags are correctly replaced), but
the Jmol part doesn't work at all :(
In one of your previous mail, you put a part of the source code of the page
for the tag.
Can you also send the part that contains the links to the Jmol .js files,
that is the part
;
>>>>> http://YouServerHere/mediawiki/extensions/Jmol/COPYRIGHT.txt
>>>>>
>>>>> If not, please either rename jmol-12.2.6 as Jmol or make a
>>>>> link/alias as needed.
>>>>>
>>>>> Jaim
>>>>> --
&g
Dear Angel,
You are completely right in asking first more information on versions,
before suggesting solutions :-)
We are, at this time, testing the latest stable Jmol (12.2.6) with the
latest stable MediaWiki (1.17.0) and found a problem similar to what
Kilian described, so I suggested the fix t
Hi Jaime
Do you think that is something that needs a permanent bug fix, or is
it just a per-case solution?
El 24 Nov 2011 a las 13:34, Jaime Prilusky escribió:
> On line 833 of the file Jmol.body.php remove the '&' from the third
> parameter of the functionjmolTag()
-
Hello Kilian
First, to be sure, please confirm that you are using the Jmol
Mediawiki Extension and what version it is.
Also, version of MediaWiki may be of relevance.
You mention a tag but that is not included in v.3.3 which
is the one documented at the Jmol Wiki.
So I guess you are using the
ailto:jmol-users@lists.sourceforge.net>>
Subject: Re: [Jmol-users] MediaWiki Plugin
Hello Jaime
Thank you very much for your answer... On line 833, there was no & at the third
parameter, but i fond some more &$parser and removed the &. This did not make
the applet appear, but now i ca
on database)
> Proteopedia, http://proteopedia.org (because life has more than 2D)
>
> From: Kilian Baerwinkel
> Reply-To:
> Date: Thu, 24 Nov 2011 14:15:24 +0100
> To:
> Subject: [Jmol-users] MediaWiki Plugin
>
> Dear all,
>
> I am trying to use Jmol within our Wiki.
y-To:
mailto:jmol-users@lists.sourceforge.net>>
Date: Thu, 24 Nov 2011 14:15:24 +0100
To: mailto:jmol-users@lists.sourceforge.net>>
Subject: [Jmol-users] MediaWiki Plugin
Dear all,
I am trying to use Jmol within our Wiki. I have installed the Mediawiki
extension according to the document
Dear all,
I am trying to use Jmol within our Wiki. I have installed the Mediawiki
extension according to the documentation, placing both the source files of
the extension and the files of Jmol in a Jmol folder within the extensions
folder of mediawiki.
Having set
require_once("extensions/Jmol/Jmo
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