#12299: Upgrade Jmol to 12.3.27, Advance Jmol Interactive Features in Flask
Notebook
--------------------------------------------------------------+-------------
Reporter: gutow | Owner:
jason, mpatel, was
Type: enhancement | Status:
needs_work
Priority: major | Milestone:
sage-pending
Component: notebook | Resolution:
Keywords: Jmol, 3D, notebook | Work issues:
Report Upstream: Fixed upstream, in a later stable release. | Reviewers:
Karl-Dieter Crisman, Steven Trogdon, Punarbasu Purkayastha, John Palmieri
Authors: Jonathan Gutow | Merged in:
Dependencies: #11080,#11078,#11503,#13121 | Stopgaps:
--------------------------------------------------------------+-------------
Changes (by jhpalmieri):
* status: positive_review => needs_work
Comment:
Running on a Mac, remotely logged in, I see this error when doctesting:
{{{
sage -t --long -force_lib "devel/sage/sage/interfaces/jmoldata.py"
Exception in thread "main" java.lang.InternalError: Can't connect to
window server - not enough permissions.
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
at java.lang.Runtime.loadLibrary0(Runtime.java:823)
at java.lang.System.loadLibrary(System.java:1045)
at
sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.image.ColorModel.loadLibraries(ColorModel.java:188)
at java.awt.image.ColorModel.<clinit>(ColorModel.java:196)
at org.jmol.awt.Image.<clinit>(Unknown Source)
at org.jmol.awt.Platform.newBufferedRgbImage(Unknown Source)
at org.jmol.g3d.Platform3D.allocateOffscreenImage(Unknown Source)
at org.jmol.g3d.Platform3D.createInstance(Unknown Source)
at org.jmol.g3d.Graphics3D.<init>(Unknown Source)
at org.jmol.viewer.Viewer.<init>(Unknown Source)
at org.jmol.viewer.Viewer.allocateViewer(Unknown Source)
at org.jmol.api.JmolViewer.allocateViewer(Unknown Source)
at org.openscience.jmol.app.JmolData.<init>(Unknown Source)
at org.openscience.jmol.app.JmolData.main(Unknown Source)
**********************************************************************
File
"/Users/palmieri/Desktop/Sage_stuff/sage_builds/6495plus13121/sage-5.1.rc0-6495/devel/sage/sage/interfaces/jmoldata.py",
line 165:
sage: print os.path.exists(testfile)
Expected:
True
Got:
False
**********************************************************************
}}}
When I'm sitting at the same machine, I see JMol open up as a separate
application; perhaps there is a problem doing this when remotely logged
in.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:126>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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