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 nverve...@gmail.comwrote:
an alternative which by-passes the file path naming
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.
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
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
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 are
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 nverve...@gmail.comwrote:
I have the impression that I'm missing a point in this discussion...
The situation Henry is talking about is that he need
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 hans...@stolaf.edu 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
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 jmolFilexxx.xyz/jmolFile.
The PHP code of the extension knows where xxx.xyz is stored and creates the
script that works.
See examples in
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.
jmolFile MW knows where to find the wiki file (handled like an
image)
jmolPdb external
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 nverve...@gmail.comwrote:
Hi Bob,
In
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,
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 hans...@stolaf.edu wrote:
no scripts at all?
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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 nverve...@gmail.comwrote:
Scripts can be used as you wish, there's just the limitation with paths to
files.
On Fri, Mar 2, 2012 at
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
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 filename path
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,
Ok, that confirms the explanation.
Henry,
Yes, the uploadedFileContents 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
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
isosurface tag to indicate the name of the isosurface file
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
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
Couldn't you have the uploadedFileContents also set the default
directory? In face, one could imagine
uploadedFileContents/uploadedFileContents
might only set the default directory.
On Thu, Mar 1, 2012 at 9:51 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote:
On 1 Mar 2012, at 15:09, Jaime
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
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
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
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 the
Nico,
I got the same in the source:
/scriptscript
src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript
src=/mediawiki/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script/headbody
http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible -
but I would have
@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Thu, 1 Dec 2011 09:45:22 +0100
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] MediaWiki Plugin
Nico,
I got the same in the source:
/scriptscript
src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1
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
Hi,
I really dont get it...
a normal page on the wiki looks like http://
IP/mediawiki/index.php/Special:Version
and in the source, there is /scriptscript src=/mediawiki/extensions/
Jmol/Jmol.js?version=3.3_dev_1
so i assume, it should be possible to access Jmo.js via http://
@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] MediaWiki Plugin
Hi,
I really dont get it...
a normal page on the wiki looks like
http://IP/mediawiki/index.php/Special:Version
and in the source, there is /scriptscript
src=/mediawiki/extensions/Jmol/Jmol.js
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
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
-bayreuth.de
Reply-To:
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Thu, 1 Dec 2011 12:09:54 +0100
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] MediaWiki Plugin
Jaim,
its exactly the same. This is what i get
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
--
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
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/mediawiki
/function
database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de
Reply-To: jmol-users@lists.sourceforge.net
Date: Thu, 24 Nov 2011 18:34:12 +0100
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users
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 jmol tag.
Can you also send the part that contains the links to the Jmol .js files,
that is the
On line 833 of the file Jmol.body.php remove the '' from the third parameter
of the function jmolTag()
Jaim
--
Dr Jaime Prilusky
Head Bioinformatics
RD Bioinformatics and Data Management
Department of Biological Services
Weizmann Institute of Science
76100 Rehovot – Israel
mail:
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 can see a link if I insert a
jmolfile. Still nothing happens if the link is clicked.
Any ideas?
: Thu, 24 Nov 2011 15:23:43 +0100
To: jmol-users@lists.sourceforge.netmailto: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
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 jmolfile tag but that is not included in v.3.3 which
is the one documented at the Jmol Wiki.
So I guess you are
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()
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
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