Bugs item #3151350, was opened at 2011-01-04 13:12 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3151350&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Applet Group: None Status: Open Resolution: None Priority: 7 Private: No Submitted By: Andrew Dunn (adunn8) Assigned to: Bob Hanson (hansonr) Summary: Applet not loading files after Java 6 update 22 Initial Comment: We are having a problem with Jmol applet not being able to load new files via the javascript interface after the applet is instantiated. The initial file is loads fine, but when we switch to another model (see link), we get a java.security.AccessControlException. I have observed the issue only affects clients who are running Java 6 update 22 or higher. It was working fine previous to this update. Link to Jmol application (Protein Viewer): http://elsevier-apps.sciverse.com/ProteinViewer/ProteinViewer.html?pii=S0022283610004328# Steps to recreate (must have java 6 update 22 or higher installed): 1.) Access link above - Protein Viewer application will load the first structure in the film strip above (highlighted yellow) 2.) Click on any other structure in the filmstrip above the Jmol applet - The Jmol will try to load the structure's file for 10 seconds and then a custom error message will be displayed. The file has failed to load. 3.) Check java console. - You should see a stack trace similar to the one attched. 4.) If desired, uninstall java and install an update 21 or earlier to see Protein Viewer functioning correctly I have attached the Java console output. Notice that the first file (2VOA.pdb.gz) loads fine, but the second produces an error. Both use the same URI. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2011-01-04 18:38 Message: OK, I've pinned the problem down to your server. I don't know what it is, but something about that ProxyServlet call is what is doing it. This will fail: http://chemapps.stolaf.edu/jmol/docs/examples-12/t2.htm It calls your site using your JAR file and reads the first file, but then, as you say, the "test" link there fails to read that same file again. Here is the same thing, using St. Olaf site: http://chemapps.stolaf.edu/jmol/docs/examples-12/t2.htm?STOLAF Now clicking on "test" works. The only difference is the site -- yours versus mine. So I'm guessing it does not have to do with Java version 22 (I'm using 23 here). You must have also done something different in relation to that proxy server. ---------------------------------------------------------------------- Comment By: Andrew Dunn (adunn8) Date: 2011-01-04 16:12 Message: Thanks for the quick response, Bob. We are proxying the files from pdb.org, so they don't physically exist on our server. Sort of like the technique used by First Glance out lined here: http://molvis.sdsc.edu/fgij/datameth.htm . We don't use apache re-write, but a servlet that repackages the response, so it should appear to be coming from our server. It has worked up until the latest java updates came out. We were originally thinking it had something to do with the network plumbing, but we came to find that the file request was not even making it to server, like it was stuck on the client. What makes it even weirder is the fact that we can load the first model (on jmol initialization), no problem. Its only when we try to change the model. I will try your directory suggestion to see, if that changes anything. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-04 15:39 Message: I've tested this now at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm I think it's some sort of a proxy setting you might have on your server, because this is not a problem here, and I am having the problem at your server. So for example, at this site you can use javascript:jmolScript("load ../../data/1crn.pdb") That is, loading a file from a parallel set of directories from where JmolApplet.jar is found. That's the proper behavior. So what is different about your server? Do you by any chance have some sort of settings that would give a different IP address domain for the HTML file than for the loading file? It's got to be something like that. Bob ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-04 15:22 Message: Right, so there appears to be a new security model there. It seems to me we know about this... I'll have to do some looking. But the solution should be to move JmolApplet.jar (or JmolApplet*.jar) to the directory containing or above the directory containing the PDB files. Or switch to the signed applet. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3151350&group_id=23629 ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
