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From: Xavier Prat-R. <xa...@ch...> - 2008-06-10 19:08:02
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Dear jmol-users,
This topic has already been discussed on this list, but it's still unclear
to me how
to solve the problem.
java 1.6.0_nn (default in windows) seems to give some problems with some of
my web pages.
Sometimes, when jmol displays a coordinates file, java will store it in the
cache. After that,
when I load the same page jmol will try to read from the cache which gives a
security error
eval ERROR: java.security.AccessControlException: access denied
(java.io.FilePermission C:\Documents and Settings\Administrator\Application
Data\Sun\Java\Deployment\cache\6.0\24\26e704d8-5b2c453d.idx read)
----line 1 command 1 of file null:
load >> "cumene.pdb" <<
If I reload the page the file is read from the web and the problem
disappears.
If I empty the java cache the problem disappears also, but it will show up
the next time.
If I work with java 1.4.2 or 1.5 the problem doesn't show up at all.
(Windows and Ubuntu/linux show similar behaviour)
I don't think I need any signed applet for this case.
I would like to be able to tell jmol to avoid reading from the cache and
download it
every time I access the page. Is that possible?
Another issue I don't understand is that the same web on a different server
doesn't
give this problem because the coordinate file is never stored in the cache.
Any idea?
Thanks
Xavier
--
Xavier Prat-Resina
Research Associate
Journal of Chemical Education and University of Wisconsin
209 N. Brooks St. Madison, WI 53715-1116
Tel: 608 8901702 // Fax: 608 2627145
e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
http://x.prat.resina.googlepages.com
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From: <rh...@fl...> - 2008-06-10 21:13:03
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Quoting Xavier Prat-Resina <xa...@ch...>: > Dear jmol-users, > > This topic has already been discussed on this list, but it's still unclear > to me how > to solve the problem. > > java 1.6.0_nn (default in windows) seems to give some problems with some of > my web pages. > Sometimes, when jmol displays a coordinates file, java will store it in the > cache. After that, > when I load the same page jmol will try to read from the cache which gives a > security error > > eval ERROR: java.security.AccessControlException: access denied > (java.io.FilePermission C:\Documents and Settings\Administrator\Application > Data\Sun\Java\Deployment\cache\6.0\24\26e704d8-5b2c453d.idx read) > ----line 1 command 1 of file null: > load >> "cumene.pdb" << > > If I reload the page the file is read from the web and the problem > disappears. > If I empty the java cache the problem disappears also, but it will show up > the next time. > If I work with java 1.4.2 or 1.5 the problem doesn't show up at all. > (Windows and Ubuntu/linux show similar behaviour) > I don't think I need any signed applet for this case. > I would like to be able to tell jmol to avoid reading from the cache and > download it > every time I access the page. Is that possible? > Another issue I don't understand is that the same web on a different server > doesn't > give this problem because the coordinate file is never stored in the cache. > Any idea? > Thanks Q: Have you looked at the HTTP headers from the two different servers? With some luck the web servers are configured differently regarding caching directives. Then you might be able to fix the problem by changing the configuration on the problematic server. (One easy way to look at the HTTP headers is to use the extremely useful 'Web Developer' extension in Firefox: Information->View Response Headers) Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
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From: Bob H. <ha...@st...> - 2008-06-10 21:35:02
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Xavier, this sounds like a problem others may start seeing as well. I think it's safe to say that it is impossible to "tell Jmol to not read the cache." Jmol just reads the file; it has no capability of knowing whether that file is cached or not. I'm using Java build 1.6.0_05-b13, and I have not seen this problem. It's possible that it's a problem Sun has fixed -- or not. To avoid the problem entirely, just use the signed applet. Bob Xavier Prat-Resina wrote: > Dear jmol-users, > > This topic has already been discussed on this list, but it's still > unclear to me how > to solve the problem. > > java 1.6.0_nn (default in windows) seems to give some problems with > some of my web pages. > Sometimes, when jmol displays a coordinates file, java will store it > in the cache. After that, > when I load the same page jmol will try to read from the cache which > gives a security error > > eval ERROR: java.security.AccessControlException: access denied > (java.io.FilePermission C:\Documents and > Settings\Administrator\Application > Data\Sun\Java\Deployment\cache\6.0\24\26e704d8-5b2c453d.idx read) > ----line 1 command 1 of file null: > load >> "cumene.pdb" << > > If I reload the page the file is read from the web and the problem > disappears. > If I empty the java cache the problem disappears also, but it will > show up the next time. > If I work with java 1.4.2 or 1.5 the problem doesn't show up at all. > (Windows and Ubuntu/linux show similar behaviour) > I don't think I need any signed applet for this case. > I would like to be able to tell jmol to avoid reading from the cache > and download it > every time I access the page. Is that possible? > Another issue I don't understand is that the same web on a different > server doesn't > give this problem because the coordinate file is never stored in the > cache. Any idea? > Thanks > > Xavier > > > -- > Xavier Prat-Resina > Research Associate > Journal of Chemical Education and University of Wisconsin > 209 N. Brooks St. Madison, WI 53715-1116 > > Tel: 608 8901702 // Fax: 608 2627145 > e-mail: xavier ( ) chem.wisc.edu <http://chem.wisc.edu> ; skype: > xavierprat > http://x.prat.resina.googlepages.com > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services for >just about anything Open Source. >http://sourceforge.net/services/buy/index.php > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
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From: Xavier Prat-R. <xa...@ch...> - 2008-06-13 12:05:02
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Thanks to Rolf and Bob for their reply. Just for those who have had the same problem. A fast way to solve the problem is to use the signed applet, even though the signed applet it's not designed for that, right? I don't know if it's a bug in java 1.6 or (most probably) I'm missing something. The problem shows up when Apache activates the expires_module (ExpiresActive On) which comes in the configuration file by default. In this case, I have seen an inconsistency between what my Apache web server has configured (by default no cache: ExpiresDefault A0) and what java 1.6 does. The headers that java gets are OK, but then it seems that it doesn't read the headers correctly... Anyway, one way to solve this is to remove the line "ExpiresDefault". After that, even if I explicitly set a long expiration time e.g. ExpiresByType chemical/x-pdb "access plus 12 months" everything works, the pdb is downloaded from the server and java does what it's supposed to. Maybe I'm looking at the wrong spot, but that's the best I came up with. Xavier On Tue, Jun 10, 2008 at 4:34 PM, Bob Hanson <ha...@st...> wrote: > Xavier, this sounds like a problem others may start seeing as well. I > think it's safe to say that it is impossible to "tell Jmol to not read > the cache." Jmol just reads the file; it has no capability of knowing > whether that file is cached or not. I'm using Java build 1.6.0_05-b13, > and I have not seen this problem. It's possible that it's a problem Sun > has fixed -- or not. > > To avoid the problem entirely, just use the signed applet. > > Bob > > > > Xavier Prat-Resina wrote: > > > Dear jmol-users, > > > > This topic has already been discussed on this list, but it's still > > unclear to me how > > to solve the problem. > > > > java 1.6.0_nn (default in windows) seems to give some problems with > > some of my web pages. > > Sometimes, when jmol displays a coordinates file, java will store it > > in the cache. After that, > > when I load the same page jmol will try to read from the cache which > > gives a security error > > > > eval ERROR: java.security.AccessControlException: access denied > > (java.io.FilePermission C:\Documents and > > Settings\Administrator\Application > > Data\Sun\Java\Deployment\cache\6.0\24\26e704d8-5b2c453d.idx read) > > ----line 1 command 1 of file null: > > load >> "cumene.pdb" << > > > > If I reload the page the file is read from the web and the problem > > disappears. > > If I empty the java cache the problem disappears also, but it will > > show up the next time. > > If I work with java 1.4.2 or 1.5 the problem doesn't show up at all. > > (Windows and Ubuntu/linux show similar behaviour) > > I don't think I need any signed applet for this case. > > I would like to be able to tell jmol to avoid reading from the cache > > and download it > > every time I access the page. Is that possible? > > Another issue I don't understand is that the same web on a different > > server doesn't > > give this problem because the coordinate file is never stored in the > > cache. Any idea? > > Thanks > > > > Xavier > > > > > > -- > > Xavier Prat-Resina > > Research Associate > > Journal of Chemical Education and University of Wisconsin > > 209 N. Brooks St. Madison, WI 53715-1116 > > > > Tel: 608 8901702 // Fax: 608 2627145 > > e-mail: xavier ( ) chem.wisc.edu <http://chem.wisc.edu> ; skype: > > xavierprat > > http://x.prat.resina.googlepages.com > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >Check out the new SourceForge.net Marketplace. > >It's the best place to buy or sell services for > >just about anything Open Source. > >http://sourceforge.net/services/buy/index.php > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Jmol-users mailing list > >Jmo...@li... > >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Xavier Prat-Resina Research Associate Journal of Chemical Education and University of Wisconsin 209 N. Brooks St. Madison, WI 53715-1116 Tel: 608 8901702 // Fax: 608 2627145 e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat http://x.prat.resina.googlepages.com |
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