jmol on notebook blocked in firefox

[Luis Finotti]

Dear all,

I am making a presentation of Sage for undergraduate math students next week, and when trying some old example I see that I cannot make a 3D graph interactive anymore.

The first error is that the java plugin is "out of date and vulnerable".  I've installed the latest plugin (from http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html, namely Java Plug-in 1.7.0_25) and the problem persists.  (I had tried open-jdk and icedtea in the past, and they seemed not to work well with sage/jmol, at least at the time).

I'm running sage-6.1.1, on 64-bit up to date Debian Unstable (Linux), with Firefox 27 and Chromium 32.

If I try to allow (by clicking on "run once"), I get a message "Your security setting have blocked an application from running with an out-of-date or expired version of Java."

BTW, it works fine from the command line.  But is there a way to run it from the notebook?

Thanks,

Luis

[kcrisman]

On Thursday, March 6, 2014 9:48:28 AM UTC-5, Luis Finotti wrote:

Dear all,

I am making a presentation of Sage for undergraduate math students next week, and when trying some old example I see that I cannot make a 3D graph interactive anymore.

The first error is that the java plugin is "out of date and vulnerable".  I've installed the latest plugin (from http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html, namely Java Plug-in 1.7.0_25) and the problem persists.  (I had tried open-jdk and icedtea in the past, and they seemed not to work well with sage/jmol, at least at the time).

I'm running sage-6.1.1, on 64-bit up to date Debian Unstable (Linux), with Firefox 27 and Chromium 32.

If I try to allow (by clicking on "run once"), I get a message "Your security setting have blocked an application from running with an out-of-date or expired version of Java."

With those security settings, I'm not sure there is.  This is a real problem we've been encountering, also with respect to the certificates.  In fact, I downgraded my Java on my computer just so I can keep running the applets in class for now.  This isn't only an issue with Jmol, by the way - I have students encountering the same issue with some Geogebra-type applets embedded inside of WeBWorK.

- kcrisman 

[Luis Finotti]

Thanks for the reply!

That is too bad, as it will make it seem less user friendly to new users...

Is it possible to tell the notebook to open jmol in its own window (like if it were called from the command line)?

Thanks again,

Luis

[P Purkayastha]

This  should work:

sage.plot.plot.EMBEDDED_MODE=False  # show plot in jmol/other window
sphere().show()
sage.plot.plot.EMBEDDED_MODE=True   # show other plots in notebook again
plot(x)

[kcrisman]

Hey, nice idea!  But one would have to go back and forth if one wanted to show 2d plots.   Otherwise you could just put this at the very top of a page...

[kcrisman]

On Friday, March 7, 2014 10:47:54 AM UTC-5, kcrisman wrote:

Hey, nice idea!  But one would have to go back and forth if one wanted to show 2d plots.   Otherwise you could just put this at the very top of a page...

And this wouldn't work for people viewing it off a notebook server somewhere else, right?  Or would it?

[ssin...@coe.edu]

Hello,

On Thursday, March 6, 2014 8:48:28 AM UTC-6, Luis Finotti wrote:

Dear all,

The first error is that the java plugin is "out of date and vulnerable".  I've installed the latest plugin (from http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html, namely Java Plug-in 1.7.0_25) and the problem persists.  (I had tried open-jdk and icedtea in the past, and they seemed not to work well with sage/jmol, at least at the time).

I'm running sage-6.1.1, on 64-bit up to date Debian Unstable (Linux), with Firefox 27 and Chromium 32.

I had a similar problem with the sage cell server. My system: Ubuntu 12.04-32, Chromium 32, FF 27, java-7-oracle. The fix for me: found an application called jcontrol; I used "locate jcontrol" and found it hiding at:

/usr/bin/jcontrol
/usr/lib/jvm/java-7-oracle/bin/jcontrol
/usr/lib/jvm/java-7-oracle/jre/bin/jcontrol

Run jcontrol; click the "Security" tab; click "Enable Java content in the browser", lower the security slider to "Medium", add "https://cloud.sagemath.com" to the Exception Site List.   I still get various security warnings, but jmol now works inline. The slider and exception list are probably redundant, but now java works on other sites, too.

Hope it works for you!
SSingleton

[ssin...@coe.edu]

I'll try this again; google groups just gave me a "This message has been deleted" after I posted...anyone know why this happened?

On Thursday, March 6, 2014 8:48:28 AM UTC-6, Luis Finotti wrote:

Dear all,

I am making a presentation of Sage for undergraduate math students next week, and when trying some old example I see that I cannot make a 3D graph interactive anymore.

The first error is that the java plugin is "out of date and vulnerable".  I've installed the latest plugin (from http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html, namely Java Plug-in 1.7.0_25) and the problem persists.  (I had tried open-jdk and icedtea in the past, and they seemed not to work well with sage/jmol, at least at the time).

I'm running sage-6.1.1, on 64-bit up to date Debian Unstable (Linux), with Firefox 27 and Chromium 32.

If I try to allow (by clicking on "run once"), I get a message "Your security setting have blocked an application from running with an out-of-date or expired version of Java."

I have a similar Ubuntu setup with java-7-oracle and saw the same problems with sage cell server 3d plots trying to start jmol.  Here was what worked for me:
- Run the "jconfig" application (mine was in the path at /usr/bin/jconfig; "locate" might find it elsewhere)
- Click Security tab, click "Enable Java content in the browser", lower Security Level to "Medium",
- I also added "https://cloud.sagemath.com" to the Exception Site List, but if you're running a "local install", may not need this.

Starting jmol will give some warning messages, but it seems to work fine.

Hope this works for you, too.
SSingleton

[Luis Finotti]

On Friday, March 7, 2014 1:46:43 AM UTC-5, P Purkayastha wrote:

That works great for me!  It's too bad it cannot run embedded, but this is great.   Thanks for the reply!

Luis

[Luis Finotti]

On Saturday, March 8, 2014 12:49:24 PM UTC-5, ssin...@coe.edu wrote:

Hello,

 

I had a similar problem with the sage cell server. My system: Ubuntu 12.04-32, Chromium 32, FF 27, java-7-oracle. The fix for me: found an application called jcontrol; I used "locate jcontrol" and found it hiding at:

/usr/bin/jcontrol
/usr/lib/jvm/java-7-oracle/bin/jcontrol
/usr/lib/jvm/java-7-oracle/jre/bin/jcontrol

Run jcontrol; click the "Security" tab; click "Enable Java content in the browser", lower the security slider to "Medium", add "https://cloud.sagemath.com" to the Exception Site List.   I still get various security warnings, but jmol now works inline. The slider and exception list are probably redundant, but now java works on other sites, too.

Hope it works for you!
SSingleton

Thanks for the reply.  For me, the tab "Security" (in Java's control panel -- jcontrol) did not have the  "Enable Java content in the browser" option.

Although this might a good solution if set up correctly, I feel a bit nervous about messing with security settings.  I will stick with running jmol outside of the browser for now.  But I greatly appreciate your reply.

Thanks,

Luis

[Luis Finotti]

You original post shows up to me...  I also would like to note that I think you mean jcontrol instead of jconfig (as in the orignial post).  (At least I don't seem to have jconfig.)

Best,

Luis