#9238: J. Gutow's update to Jmol in the notebook...
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Reporter: gutow |
Owner: gutow
Type: enhancement |
Status: needs_review
Priority: major |
Milestone: sage-4.7.2
Component: notebook |
Keywords: sd31, sd32
Work_issues: |
Upstream: N/A
Reviewer: Jason Grout, Karl-Dieter Crisman, William Stein |
Author: Jonathan Gutow
Merged: |
Dependencies:
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Comment(by gutow):
First, take note of the first paragraph of this ticket. Because this
involves working with the notebook interface all development since June
2011 has been on the Flask notebook version. That means the package and
patches here have not been updated since about 4.7.1. They are up
primarily so that people using 4.7.1 and older can get the controls that
allow changing the display of surfaces. Development has been limited to
the Flask version of the notebook. I have very limited time to work on
this (I'm a chemistry professor), but if the Flask notebook is going to be
severely delayed could try to package a version to work with the older
notebook. If you really want to test this you should test it in a Flask
install (see the appropriate tickets).
That said your concerns about the patch warnings are valid. I did not
know that any of it had been folded into 4.7.2. This is odd.
The pop-up warnings are because your server connection is relatively slow.
The notebook now allows about 15 seconds for an applet to load. If it
hasn't loaded by that time, one of these warnings pops up. The idea is to
provide some feedback when it takes a long time to load. The reason for
the async load code is that worksheets with lots of applets in them can
overwhelm the browsers if too many applets try to load simultaneously.
This code requires them to load sequentially and limits worksheets to 4
running Jmol applets at a time. Those that are not running are replaced
with a picture and a button to wake them. The primary reason for this is
constraints on the memory available for applets within browsers. The
async code is for all browsers. There are warnings associated with
specific browsers that we have had difficulty with (e.g. MS IE and certain
versions of FF and Safari).
If your worksheets worked without the async code, that suggests you were:
1) lucky; 2) had only one or very few applets in your worksheet. If your
worksheet did not work at all with the async code could you package it up
so that we could test it in the latest code? Thanks.
Does this answer your questions? I think the key message is that without
more work on my part the enhanced Jmol interface may be tied to the Flask
notebook.
Replying to [comment:172 strogdon]:
> I've tested some of the features of this ticket on vanilla
sage-4.7.2.alpha2 and I have some questions. I installed
Jmol_for_SageNoteBook-1.1.6.spkg and applied the patches {{{
trac_9238_interactive_js.patch trac_9238-add-help.patch
trac_9238_jmol_lib_async.patch }}} The add-help patch would not apply with
the response that a JmolHelp.html file already existed. I did not attempt
to apply the IE patches. After applying the patches I issued "sage -b" and
started sage and the notebook. Now when I load a worksheet that has Jmol
applets I get pop-ups. If there are numerous applets, I get numerous pop-
ups. These pop-ups seem to be triggered by the follow alerts in
trac_9238_jmol_lib_async.patch {{{ + if(loading>=0){//we found a
loading applet + jmolStatus.attempts[loading]+=1; //update number
of checks for load completion. +
if(jmolStatus.defaultdirectory[loading]=="done"){//Applet is ready. +
jmolAppletLive(loading); + }else{ //Applet not ready. How many
checks have we done? + if(jmolStatus.attempts[loading]==10){ +
alert("Jmol Applet #"+loading+" is having trouble loading. Will retry
once."); + var scriptStr = 'x=defaultdirectory; data
"directory @x";'; + scriptStr += 'set MessageCallback
"jmolMessageHandler"; show defaultdirectory;'; +
jmolScript(scriptStr); + } +
if(jmolStatus.attempts[loading]==20){ + alert("Second
attempt to finish launch of Jmol Applet #"+loading+" failed. Recommend
reevaluating the cell manually."); +
jmolStatus.jmolArray[loading]=-2; //launch failed. + } +
} + }else{//no loading applets. Search for queued applet. }}} since
the quoted expressions in the alerts appear in the pop-ups. Loading the
applets is extremely slow and the pop-ups have to be "clicked" before
loading continues. Now if I do not install trac_9238_jmol_lib_async.patch
then I do not get the pop-ups and the loading of the applets is much
faster. I have used Firefox 3 and Firefox 6 with the same result. Are the
pop-ups a feature or is the jmol_lib_async only intended for safari
browsers?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9238#comment:173>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
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