OK, looks like there is a new Firefox security policy:
For all local files accessed via JavaScript, both the JAR file AND the HTML
file must be on the path to that file.
Pretty sure that's new.
The fix for me was to move the Jmol-12.... directory into the pages
directory, modify the files, and it worked. Of course, this is an
EXCEPTIONAL drag!!! Kind of removes the possibility of using the local
applet within anything more than a single-directory context. Actually, the
solution looks like using this path set:
.... /jmol
.............[all jar files here]
............./pages
.............[html here]
This basically makes impossible use of the unsigned applet on a local
machine.
On Tue, Jun 8, 2010 at 11:29 AM, Robert Hanson <[email protected]> wrote:
> UFF.txt is a resource within the Jar file. Specifically it is in:
>
> JmolApplet0_Minimize.jar/org/jmol/minimize/forcefield
>
> JmolAppletSigned0_Minimize.jar/org/jmol/minimize/forcefield
>
>
> If you use
>
> set debug
>
>
> you should see its contents listed when the minimizer runs.
>
> Very odd that the system can't find it. This could be an odd threading
> issue -- the thread that runs from a click of a button is not the same
> thread that runs when you use the Jmol console or menu.
>
> Local files -- sounds like a Java bug. But I could be doing something
> slightly wrong there.
>
> Suggestions:
>
> compare application and applet.
>
>
>
> 2010/6/8 Angel Herráez <[email protected]>
>
> This is the summary and a test case:
>>
>> 1. Problem is there only for local files, not from server. Seems to
>> be related to Jmol reading text files (either scripts or the UFF.txt
>> file embedded somehow inside Jmol) from a folder where the applet
>> jars are but the webpage is not.
>>
>> Main_folder
>> |
>> -- Pages_folder
>> |
>> -- mypage.htm
>> |
>> -- Jmol_folder
>> |
>> -- *.jar files
>> -- Jmol.js
>> -- model.mol
>> -- test.spt
>>
>> 2. The problem shows for reading script files (that do no model
>> loading, just simple commands) and also for running "minimize"
>>
>> 3. The same script commands or the minimize command work fine when
>> issued from teh script console. It'sonly calling them from a
>> jmolButton or an <input type="button" onClick="jmolScript()"> that
>> causes the problem.
>>
>> 4. Same behaviour in 11.6, 11.8.24 and 12.0.RC17
>>
>> 5. Errors are like:
>>
>> For loading a script file:
>>
>> FileManager opening
>> file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
>> 12.0.RC17/halos.spt
>> script ERROR: script ERROR:
>> io error reading
>> file:/F:/webs/_Proyectos/_pruebas/Jmol_local_scripts/Jmol-
>> 12.0.RC17/halos.spt:
>> java.security.AccessControlException:
>> access denied (java.io.FilePermission
>> F:\webs\_Proyectos\_pruebas\Jmol_local_scripts\Jmol-
>> 12.0.RC17\halos.spt read)
>>
>>
>
>> For running minimize:
>>
>> Minimizing 17 atoms
>> minimize: initializing (steps = 100 criterion =
>> 0.0010000000474974513) ...
>> minimize: using org.jmol.minimize.forcefield.ForceFieldUFF
>> 17 atoms will be minimized.
>> minimize: creating bonds...
>> minimize: setting atom types...
>> Couldn't find file: UFF.txt
>> Exception null in getResource UFF.txt
>> 0 force field parameters read
>>
>>
>>
> I don't think these are related, but they might be both security settings
> issues. Pretty much that's what we are seeing changing in browser updates
> these days.
>
>
>
>
>> Test case is avalable at
>> http://biomodel.uah.es/angel/test/Jmol_local_scripts.zip
>> Unzip and run from disk, not from server.
>> (Uses monolithic applet for simplicity; I've tested with the split
>> applet too)
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
>
> --
> 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, Lecture XXX, Monday, February 5, 1900
>
--
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, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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http://p.sf.net/sfu/thinkgeek-promo
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