#12299: Upgrade Jmol to 12.3.27, Advance Jmol Interactive Features in Flask
Notebook
--------------------------------------------------------------+-------------
Reporter: gutow | Owner:
jason, mpatel, was
Type: enhancement | Status:
needs_info
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:
--------------------------------------------------------------+-------------
Comment (by gutow):
The first is the expected error on machines without JVMs installed. I
had trouble writing doctests for this because of the multiple possible
outcomes. Could we rewrite the doctests to output something like: "JVM
was/was not detected, thus an image was/was not generated?" If I
understand the doctest mechanism correctly it is flexible enough to check
for just the "JVM was..." part, right? Then it could produce some other
text if the JVM was found, but image generation failed. This last case
would be the only failure mode. Would that be better?
The second one looks as if you did not get this patch installed:
http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/12299/trac_12299_headless_java.patch
Replying to [comment:139 jdemeyer]:
> On arando, I get the doctest failure:
> {{{
> sage -t --long -force_lib devel/sage/sage/interfaces/jmoldata.py
> **********************************************************************
> File
"/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.2.beta1/devel
/sage-main/sage/interfaces/jmoldata.py", line 164:
> sage: JData.export_image(targetfile =testfile,datafile = script,
image_type="PNG")
> Exception raised:
> Traceback (most recent call last):
> File
"/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.2.beta1/local/bin/ncadoctest.py",
line 1231, in run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File
"/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.2.beta1/local/bin/sagedoctest.py",
line 38, in run_one_example
> OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
> File
"/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.2.beta1/local/bin/ncadoctest.py",
line 1172, in run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_6[14]>", line 1, in <module>
> JData.export_image(targetfile =testfile,datafile = script,
image_type="PNG")###line 164:
> sage: JData.export_image(targetfile =testfile,datafile = script,
image_type="PNG")
> File
"/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.2.beta1/local/lib/python
/site-packages/sage/interfaces/jmoldata.py", line 195, in export_image
> raise JmolDataError(errStr)
> JmolDataError: 'Java Virtual Machine not available.\nThis should be
checked before calling JmolData().export_image().\nUse
JmolData().is_jvm_available() to check.\nAdministrator should install
JVM.'
> **********************************************************************
> File
"/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.2.beta1/devel
/sage-main/sage/interfaces/jmoldata.py", line 165:
> sage: print os.path.exists(testfile)
> Expected:
> True
> Got:
> False
> **********************************************************************
> }}}
>
> On rosemary, the doctest failure
> {{{
> sage -t --long -force_lib devel/sage/sage/interfaces/jmoldata.py
>
> (.:323): Gtk-WARNING **: cannot open display:
> **********************************************************************
> File
"/home/buildbot/build/sage/rosemary-1/rosemary_full/build/sage-5.2.beta1/devel
/sage-main/sage/interfaces/jmoldata.py", line 165:
> sage: print os.path.exists(testfile)
> Expected:
> True
> Got:
> False
> **********************************************************************
> }}}
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:140>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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