[Jmol-users] Jmol permissions problem
Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
Hi Martin Yes, I know the feeling. It has happened to me occasionally. 1. Make sure you clear up the Java cache. Maybe try another browser to be sure it is not contaminated bu cached copies. 2. Check the paths of the files involved. Sister folders for example are a cause of security exceptions. But sometimes what used to work gives this error, often it is not permanent. I think it may well be a difference in Java's view between in-page scripts and external files scripts. Particularly for recent Java versions which are becoming more and more picky. If you can share the URL, I will happily try it. Good luck -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
@ Jaim and Angel Thanks for your feedback. It's exactly what I'm going through right now and its funny because the exact same application worked fine a couple of hours ago, when it was just in another location on the server. What fails is the loading of the structure from a Javascript call. However, if I issue the exact same command on the Jmol console, I can load the structure. Anyway, the applet is located at the following URL. http://www.biofetsim.org/ku_prototype.html Open the Jmol console before you hit Initialize, so you see the error message. Thanks again and looking forward to any feedback. Martin On 18.06.12 15:15, Jaime Prilusky wrote: Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
Just an update. It turns out, I was doing the load using jmolScriptWait(...). Using jmolScript(...), it seems to have no problem with permissions. On 18.06.12 15:15, Jaime Prilusky wrote: Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
I see no errors on Mac 10.6.8, FireFox 12.0 It draws a structure nicely, I'm able to change pH, redraw and plot the pH Response and BioFET-SIM graphs. No errors on the applet console nor on Java console. While testing from Safari 5.1.7 I got a python error, probably due to changes at the server side. Try clearing your browser cache. Jaim On Jun 18, 2012, at 4:29 PM, Martin Hediger wrote: @ Jaim and Angel Thanks for your feedback. It's exactly what I'm going through right now and its funny because the exact same application worked fine a couple of hours ago, when it was just in another location on the server. What fails is the loading of the structure from a Javascript call. However, if I issue the exact same command on the Jmol console, I can load the structure. Anyway, the applet is located at the following URL. http://www.biofetsim.org/ku_prototype.html Open the Jmol console before you hit Initialize, so you see the error message. Thanks again and looking forward to any feedback. Martin On 18.06.12 15:15, Jaime Prilusky wrote: Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
On 06/18/2012 03:29 PM, Martin Hediger wrote: @ Jaim and Angel Thanks for your feedback. It's exactly what I'm going through right now and its funny because the exact same application worked fine a couple of hours ago, when it was just in another location on the server. What fails is the loading of the structure from a Javascript call. However, if I issue the exact same command on the Jmol console, I can load the structure. Anyway, the applet is located at the following URL. http://www.biofetsim.org/ku_prototype.html Open the Jmol console before you hit Initialize, so you see the error message. I get the following error messages: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 130.225.101.52:80 connect,resolve) script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 130.225.101.52:80 connect,resolve) load ./bfs_pdb/aha.pdb File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 130.225.101.52:80 connect,resolve) script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 130.225.101.52:80 connect,resolve) load append ./bfs_pdb/aha-reo.pdb File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 130.225.101.52:80 connect,resolve) script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 130.225.101.52:80 connect,resolve) load append ./bfs_pdb/nw_aha.xyz If I resolve the hostname of 130.225.101.52 using the linux 'host' command I get propka.ki.ku.dk and not www.biofetsim.org. The names must match in a reverse lookup done by the browser. It doesn't help that 'host www.biofetsim.org' points to the same IP address. We ran into the same problem a few years ago after the security policy changed in this respect. Besides you are taking the 'jQuery' library from a different server (http://ajax.googleapis.com/ajax/libs/jquery/1.6.3/jquery.min.js). This might also provoke security problems. I would generally recommend to install it directly on your server. This way your website is not relying on the availability of another server and will not go down if the library file is moved/removed on that server. Regards, Rolf -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
It turns out, I was doing the load using jmolScriptWait(...). Using jmolScript(...), it seems to have no problem with permissions. Ah! That clicks a memory This is called use of threads. I have fixed security errors by setting useCommandThread Look for that word in the online scripting doc I used it like this: jmolInitialize(..); jmolSetCallback(UseCommandThread,true); jmolApplet(550); -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
Hi guys Thanks for your feedback. Yes, at the moment I think I just got it up and running. I did not rearrange any script locations, so all Javascript/JQuery scripts are still located in a sister directory of the Jmol directory. I cant really tell what the problem was/is. I'm doing all this anyway using Safari Develop/Disable Caches. Really appreciating the feedback here. Best regards Martin On 18.06.12 15:53, Jaime Prilusky wrote: I see no errors on Mac 10.6.8, FireFox 12.0 It draws a structure nicely, I'm able to change pH, redraw and plot the pH Response and BioFET-SIM graphs. No errors on the applet console nor on Java console. While testing from Safari 5.1.7 I got a python error, probably due to changes at the server side. Try clearing your browser cache. Jaim On Jun 18, 2012, at 4:29 PM, Martin Hediger wrote: @ Jaim and Angel Thanks for your feedback. It's exactly what I'm going through right now and its funny because the exact same application worked fine a couple of hours ago, when it was just in another location on the server. What fails is the loading of the structure from a Javascript call. However, if I issue the exact same command on the Jmol console, I can load the structure. Anyway, the applet is located at the following URL. http://www.biofetsim.org/ku_prototype.html Open the Jmol console before you hit Initialize, so you see the error message. Thanks again and looking forward to any feedback. Martin On 18.06.12 15:15, Jaime Prilusky wrote: Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il mailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___
Re: [Jmol-users] Jmol permissions problem
Ok, didn't know about it. Set the callback and using jmolScriptWait now. Looking fine, thanks again. Martin On 18.06.12 16:00, Angel Herráez wrote: It turns out, I was doing the load using jmolScriptWait(...). Using jmolScript(...), it seems to have no problem with permissions. Ah! That clicks a memory This is called use of threads. I have fixed security errors by setting useCommandThread Look for that word in the online scripting doc I used it like this: jmolInitialize(..); jmolSetCallback(UseCommandThread,true); jmolApplet(550); -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
