Ok. I'm not sure this will add any helpful info, but this is what I tested
this morning on Mac OS X 10.6.4 with Firefox 3.6.8 and Java 1.6.0_20.
Went to Java Preferences.app and cleared the cache. Started up Firefox and
loaded NT1. Clicked the Load Chlorophyll button. Worked fine. Closed Firefox
and reopened it. Loaded NT1 and clicked the button. Now chlorophyll doesn't
load (file access error). Went to Java Preferences and cleared the cache.
Reloaded NT1. Still doesn't work. Closed Firefox, reopened it, and loaded
NT1. Now it works. Reloaded NT1, still works. As long as I keep the browser
open and reload the page or open it in a new tab, it works. As soon as I close
Firefox and restart it, it doesn't work unless the cache has first been
cleared. When the chlorophyll is not loading by the button, it loads from the
console as Phil has already noted. NT3 works fine in all situations.
I downloaded Firefox 3.6.7, 3.6.6, 3.5.11, 3.5.10, and 3.0.19 and observed the
same behavior with all of them.
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[email protected]
***********************************************
On Jul 25, 2010, at 1:55 PM, Philip Bays wrote:
> Go to Application/Utilities/Java Preferences.ap. Once open go to the network
> tab. Toward the bottom there is a button to view cache files.
> If you select them all, and there may be many, click the X at the top to
> delete them. Or, if you really want to demonstrate the issue, only remove
> the one for the chlorophyll file.
>
> I have used Cocktail, Firefox, and applejack which each claims to clear the
> Java cache. None of them do:-(
> This is the only way I have found to do it.
>
> If you have your system set to clear java cache when the browser is shut down
> (however you do that -- I can't figure it out) then you will not observe the
> error.
>
>
>
> Phil
>
> On Jul 25, 2010, at 1:47 PM, Jeff Hansen wrote:
>
>> Sorry, not sure where to find that. I cleared them from the Firefox Tools
>> menu.
>>
>>
>> ***********************************************
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> [email protected]
>> ***********************************************
>>
>>
>> On Jul 25, 2010, at 1:25 PM, Philip Bays wrote:
>>
>>> Did you clear the Java cache from the java preferences panel? That seems
>>> to be the key.
>>>
>>> On Jul 25, 2010, at 1:15 PM, Jeff Hansen wrote:
>>>
>>>> Under no circumstances am I now able to get the chlorophyll model to load.
>>>> I cleared the cache and restarted Firefox and it didn't load chlorophyll.
>>>>
>>>> Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.8)
>>>> Gecko/20100722 Firefox/3.6.8
>>>> Java 1.6.0_20
>>>>
>>>>
>>>> ***********************************************
>>>> Jeff Hansen
>>>> Department of Chemistry and Biochemistry
>>>> DePauw University
>>>> 602 S. College Ave.
>>>> Greencastle, IN 46135
>>>> [email protected]
>>>> ***********************************************
>>>>
>>>>
>>>> On Jul 25, 2010, at 11:24 AM, Robert Hanson wrote:
>>>>
>>>>> OK, I've tested this on my Mac with a freshly downloaded Firefox 3.6.8.
>>>>>
>>>>> No such problem.
>>>>>
>>>>> Phil, it looks to me like it might be a bad early version of 3.6.8.
>>>>>
>>>>> Mac users -- we need you to try this on Firefox 3.6.8:
>>>>>
>>>>> 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html
>>>>> 2. click on the link under the applet to display chlorophyl
>>>>> 3. close the browser
>>>>> 4. open the browser
>>>>> 5 repeat steps 1 and 2.
>>>>>
>>>>> Phil's experience is that in step 5 the click will not work.
>>>>> My experience is that it will work.
>>>>>
>>>>> Please report EXACT Firefox version.
>>>>>
>>>>> Bob
>>>>>
>>>>>
>>>>>
>>>>> On Sun, Jul 25, 2010 at 10:00 AM, Robert Hanson <[email protected]>
>>>>> wrote:
>>>>> Phil, I went ahead and added a comment to that bug report to see what
>>>>> they say. I'll try to dig up Firefox 3.6.8 on a Mac around here to get
>>>>> additional specifics.
>>>>>
>>>>> Bob
>>>>>
>>>>>
>>>>> On Sun, Jul 25, 2010 at 8:30 AM, Robert Hanson <[email protected]> wrote:
>>>>> Phil, wait, there are a couple more issues before you go back to them.
>>>>>
>>>>> 1) Did you say in that bug report that the signed applet has the same
>>>>> problem? That would be a BIG and different issue.
>>>>>
>>>>> 2) The first structure always loads, right? That indicates that Java can
>>>>> access its cache appropriately.
>>>>>
>>>>> 3) If only the second structure loading does not work, what we have is a
>>>>> JavaScript thread issue. It is the JavaScript/LiveConnect THREAD that is
>>>>> being blocked.
>>>>>
>>>>> 4) Tests you need to do:
>>>>>
>>>>> I. Try opening a console and issuing the load command from there. If it
>>>>> loads, then it is DEFINITELY a browser liveConnect thread blocking issue.
>>>>>
>>>>> II. Try that again using the useCommandThread TRUE.
>>>>>
>>>>> Bob
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Sun, Jul 25, 2010 at 8:11 AM, Robert Hanson <[email protected]> wrote:
>>>>> You should be able to get any version of Firefox, and in fact, if you
>>>>> search your Mac applications directory you will probably find it. Just
>>>>> start it.
>>>>>
>>>>> OK, I have run a little test:
>>>>>
>>>>> 1. Monitor the Java Cache before and after starting the browser and
>>>>> loading http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>>>>>
>>>>> 2. Close the browser
>>>>>
>>>>> 3. Repeat step 1.
>>>>>
>>>>> 4. Close the browser
>>>>>
>>>>> 5. Upload a NEW caffeine.xyz
>>>>>
>>>>> 6. Repeat step 1.
>>>>>
>>>>> Findings:
>>>>>
>>>>> 1. Java never "clears its cache." It just stores the file and the header
>>>>> that came from the server associated with that file. That header contains
>>>>> a date.
>>>>>
>>>>> 2. It looks like Java just first sends a message to a server asking for a
>>>>> header, and if the header matches the one in the cache, then the file is
>>>>> not downloaded, and the cached file is used instead. This is pretty
>>>>> standard operation.
>>>>>
>>>>>
>>>>> OK, so why the security bug? Obviously it is a Firefox bug. Doesn't
>>>>> happen in older browsers; only appears with Mac 3.6.8. You need to
>>>>> respond to that bug report reply and be very clear about that. It would
>>>>> be especially good if you have verified that it all works with
>>>>> Firefox/Mac 3.5.7.
>>>>>
>>>>>
>>>>> The bug is this (if you can confirm it on your Mac, Phil)
>>>>>
>>>>> Observation: Java applet running in Firefox 3.6.8/Mac specifically hit a
>>>>> security violation when trying to read a file that was previously cached
>>>>> in a prior browser session.
>>>>>
>>>>> Comments: This bug is specific to Firefox 3.6.8/Mac. It does not appear
>>>>> with other operating systems and it does not appear with Firefox 3.5.7.
>>>>> All works appropriately within one browser session, but after the browser
>>>>> is closed and then re-opened, the applet cannot access any locally cached
>>>>> data file from that previous session opened using Java's
>>>>> URL.openConnection() method.
>>>>>
>>>>>
>>>>> Bob
>>>>>
>>>>>
>>>>> On Sun, Jul 25, 2010 at 7:08 AM, Robert Hanson
>>>>>
>>>>> <[email protected]> wrote:
>>>>> Right - that does make sense -- submit a Java bug report, then. Make sure
>>>>> you have the latest Java available.
>>>>>
>>>>> On Sun, Jul 25, 2010 at 6:27 AM, Philip Bays <[email protected]> wrote:
>>>>> Does this response make sense to anyone? If Firefox does not look at
>>>>> java cache, how can adjusting the cache (removing a file, turning it on
>>>>> or off) have any affect? Because it is a bug in java that does not affect
>>>>> non-mozilla browsers???
>>>>>
>>>>> Phil
>>>>>
>>>>> Begin forwarded message:
>>>>>
>>>>>> From: [email protected]
>>>>>> Date: July 25, 2010 4:52:35 AM EDT
>>>>>> To: [email protected]
>>>>>> Subject: [Bug 581717] Firefox does not read java cache correctly
>>>>>>
>>>>>> Do not reply to this email. You can add comments to this bug at
>>>>>> https://bugzilla.mozilla.org/show_bug.cgi?id=581717
>>>>>>
>>>>>> Jo Hermans <[email protected]> changed:
>>>>>>
>>>>>> What |Removed |Added
>>>>>> ----------------------------------------------------------------------------
>>>>>> Status|UNCONFIRMED |RESOLVED
>>>>>> CC| |[email protected]
>>>>>> Resolution| |INVALID
>>>>>>
>>>>>> --- Comment #1 from Jo Hermans <[email protected]> 2010-07-25
>>>>>> 01:52:33 PDT ---
>>>>>> That is a problem in your version of Java, Firefox doesn't read that
>>>>>> cache at
>>>>>> all. That's why you see the problem on Mac, but not on Windows (different
>>>>>> versions).
>>>>>>
>>>>>> --
>>>>>> Configure bugmail: https://bugzilla.mozilla.org/userprefs.cgi?tab=email
>>>>>> ------- You are receiving this mail because: -------
>>>>>> You reported the bug.
>>>>>
>>>>> J. Philip Bays
>>>>> Professor of Chemistry
>>>>> Department of Chemistry and Physics
>>>>> Saint Mary's College
>>>>> Notre Dame, IN 46556
>>>>> (574) 284-4663
>>>>> [email protected]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by Sprint
>>>>> What will you do first with EVO, the first 4G phone?
>>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>>> _______________________________________________
>>>>> Jmol-users mailing list
>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
>>>>> http://www.stolaf.edu/people/hansonr
>>>>> phone: 507-786-3107
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
>>>>> http://www.stolaf.edu/people/hansonr
>>>>> phone: 507-786-3107
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
>>>>> http://www.stolaf.edu/people/hansonr
>>>>> phone: 507-786-3107
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
>>>>> http://www.stolaf.edu/people/hansonr
>>>>> phone: 507-786-3107
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
>>>>> http://www.stolaf.edu/people/hansonr
>>>>> phone: 507-786-3107
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by Sprint
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>>>>> Visit sprint.com/first --
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>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Sprint
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>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>> J. Philip Bays
>>> Professor of Chemistry
>>> Department of Chemistry and Physics
>>> Saint Mary's College
>>> Notre Dame, IN 46556
>>> (574) 284-4663
>>> [email protected]
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Sprint
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>>> Visit sprint.com/first --
>>> http://p.sf.net/sfu/sprint-com-first_______________________________________________
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>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first --
>> http://p.sf.net/sfu/sprint-com-first_______________________________________________
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>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> J. Philip Bays
> Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> (574) 284-4663
> [email protected]
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first --
> http://p.sf.net/sfu/sprint-com-first_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
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