From: Robert H. <ha...@st...> - 2008-08-30 04:15:56
|
I'd like to propose a change to Jmol.js. The change would be an addition. If the page URL contains "JMOLJAR=" then Jmol.js would be instructed to ignore the jmolInitialize() command and instead use the codebase directory and jar file as defined after that tag. For example: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar This would allow quick checking of sites with different JAR files. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: A. H. <ang...@ua...> - 2008-08-30 10:12:47
|
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar > > This would allow quick checking of sites with different JAR files. Ah! interesting. No need to edit the html file. I like it |
From: Robert H. <ha...@st...> - 2008-08-30 12:12:20
|
One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Bob On Sat, Aug 30, 2008 at 5:24 AM, Angel Herráez <ang...@ua...> wrote: > > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar > > > > This would allow quick checking of sites with different JAR files. > > Ah! interesting. No need to edit the html file. I like it > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: <rh...@fl...> - 2008-08-30 17:56:30
|
Quoting Robert Hanson <ha...@st...>: > One of the interesting aspects is that I could use > > JMOLJAR= > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar > > for example to go to the PDB website and use MY applet instead of theirs. > Bob, have you tried that already? If this is allowed it would be exactly what should pe prevented within Jmol.js! It should only be allowed to load a different Jmol version from the same server! Otherwise anyone could use your/our service by 'URL Spoofing' to deliver an "evil" Jmol applet (or even a totally different applet) to the user!!! Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
From: Robert H. <ha...@st...> - 2008-08-30 18:04:38
|
that's why I'm asking. Yes, I have tried this. We could make it only the applet from the server -- in other words not allow a new codebase -- if you think that is a major concern. How would you see the spoof working, Rolf? Bob On Sat, Aug 30, 2008 at 12:56 PM, <rh...@fl...> wrote: > Quoting Robert Hanson <ha...@st...>: > > > One of the interesting aspects is that I could use > > > > JMOLJAR= > > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar > > > > for example to go to the PDB website and use MY applet instead of theirs. > > > > Bob, > have you tried that already? > If this is allowed it would be exactly what should pe prevented within > Jmol.js! > It should only be allowed to load a different Jmol version from the > same server! > > Otherwise anyone could use your/our service by 'URL Spoofing' to > deliver an "evil" Jmol applet (or even a totally different applet) to > the user!!! > > Regards, > Rolf > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: <rh...@fl...> - 2008-08-30 19:16:33
|
Quoting Robert Hanson <ha...@st...>: > that's why I'm asking. Yes, I have tried this. We could make it only the > applet from the server -- in other words not allow a new codebase -- if you > think that is a major concern. > > How would you see the spoof working, Rolf? > The HTML code shown below just hides the 'JMOLJAR=...' extension within the status line. Althugh my Firefox 3 does show the real URL, even when I exceptionally allow status line changes, it still works with my Internet Eplorer 7. And this is just the most simple way. There are more sophisticated techniques possible. <a href="http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&MODE=biological1&JMOLJAR=http://www.fakejenalib.com/fakejmol.jar" onmouseout="window.status='';return true" onmouseover="window.status='http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&MODE=biological1';return true">JenaLib Jmol Viewer</a> Since it may be possible that the complete version is only shown as links here is a (modified) repeat of the Javascript portion: onmouseout="window.status='';return true" onmouseover="window.status='original_URL';return true" Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
From: Robert H. <ha...@st...> - 2008-08-30 19:24:24
|
ok. Shucks. That's convincing. OK if it allows same-server jar changes? Bob On Sat, Aug 30, 2008 at 2:16 PM, <rh...@fl...> wrote: > Quoting Robert Hanson <ha...@st...>: > > > that's why I'm asking. Yes, I have tried this. We could make it only the > > applet from the server -- in other words not allow a new codebase -- if > you > > think that is a major concern. > > > > How would you see the spoof working, Rolf? > > > > The HTML code shown below just hides the 'JMOLJAR=...' extension > within the status line. Althugh my Firefox 3 does show the real URL, > even when I exceptionally allow status line changes, it still works > with my Internet Eplorer 7. And this is just the most simple way. > There are more sophisticated techniques possible. > > <a > href=" > http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&MODE=biological1&JMOLJAR=http://www.fakejenalib.com/fakejmol.jar" > onmouseout="window.status='';return true" onmouseover="window.status=' > http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&MODE=biological1';return<http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&MODE=biological1%27;return>true">JenaLib Jmol > Viewer</a> > > Since it may be possible that the complete version is only shown as > links here is a (modified) repeat of the Javascript portion: > > onmouseout="window.status='';return true" > onmouseover="window.status='original_URL';return true" > > Regards, > Rolf > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: <rh...@fl...> - 2008-08-30 19:43:31
|
Quoting Robert Hanson <ha...@st...>: > ok. Shucks. That's convincing. OK if it allows same-server jar changes? > Yes, I think so. If the server is compromised then I guess it won't make much difference anyhow. Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
From: Robert H. <ha...@st...> - 2008-08-31 15:29:42
|
One more thought on this: What about an option that allows the replacement of the Jar file but first prompts the user for an OK (using JavaScript prompt() ) and explains why this might be an issue? If the user says it is OK, then the Jar file is used? Bob On Sat, Aug 30, 2008 at 2:43 PM, <rh...@fl...> wrote: > Quoting Robert Hanson <ha...@st...>: > > > ok. Shucks. That's convincing. OK if it allows same-server jar changes? > > > > Yes, I think so. If the server is compromised then I guess it won't > make much difference anyhow. > > Regards, > Rolf > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: A. H. <ang...@ua...> - 2008-08-30 12:18:20
|
> One of the interesting aspects is that I could use > > JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar > > for example to go to the PDB website and use MY applet instead of theirs. Assuming that they update their Jmol.js file!!! They are still using 10.2, and I think there have been requests for update already, to no avail |
From: Paul P. <pau...@ac...> - 2008-08-30 12:32:39
|
I am setting up a web page with the ability to load local files as well as external files (for example, files coming from the pdb) When I run the page locally, the applet is able to load any local file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari): java.security.AccessControlException: access denied (java.net.SocketPermission www.rcsb.org:80 connect,resolve) openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms eval ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission www.rcsb.org:80 connect,resolve) ----line 1 command 1 of file null: load >> "http://www.rcsb.org/pdb/files/1gzx.pdb" << When the page is loaded from a webserver, the applet is unable to load any local file, as well as remote files coming from elsewhere than the webserver : FileManager.openFile(''file:////Users/paul/Desktop/ ac.pdb'') //''file:////Users/paul/Desktop/ac.pdb'' FileManager opening http://ordinateur-de-judith-ciosi.local/~paul/ JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' file ERROR: http://ordinateur-de-judith-ciosi.local/~paul/ JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' java.io.FileNotFoundException: http://ordinateur-de-judith- ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' openFile(''file:////Users/paul/Desktop/ac.pdb''): 3 ms eval ERROR: java.io.FileNotFoundException: http://ordinateur-de- judith-ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' ----line 1 command 1 of file null: load >> "''file:////Users/paul/Desktop/ac.pdb''" << I searched the mailing list archive for this issue and found a one year old thread, which stated that this behavior is linked to the inability to accept loading external files when the command is issued by an unsigned javascript. A workaround is to reload the jmol applet with the new file. I would like to know if there is any other solution to make the signed applet accept an external file ? I am also wondering at how this problem has been dealt with in jmol protein explorer ? Thanks in advance, Paul |
From: Robert H. <ha...@st...> - 2008-08-30 13:07:13
|
Paul, check out this page to see how yours might be different. http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm It's using the signed applet and working just fine. Maybe has to be newer than 11.6.RC8, but I don't think so. It should load files from the PDB using "load =xxxx" and files from your hard drive using, for example: load c:/temp/caffeine.xyz Also, the Jmol Protein Explorer is using using the signed applet without a hitch. Bob On Sat, Aug 30, 2008 at 7:32 AM, Paul Pillot < pau...@ac...> wrote: > I am setting up a web page with the ability to load local files as > well as external files (for example, files coming from the pdb) > > When I run the page locally, the applet is able to load any local > file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari): > java.security.AccessControlException: access denied > (java.net.SocketPermission www.rcsb.org:80 connect,resolve) > openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms > eval ERROR: java.security.AccessControlException: access denied > (java.net.SocketPermission www.rcsb.org:80 connect,resolve) > ----line 1 command 1 of file null: > load >> "http://www.rcsb.org/pdb/files/1gzx.pdb" << > > When the page is loaded from a webserver, the applet is unable to > load any local file, as well as remote files coming from elsewhere > than the webserver : > FileManager.openFile(''file:////Users/paul/Desktop/ > ac.pdb'') //''file:////Users/paul/Desktop/ac.pdb'' > FileManager opening http://ordinateur-de-judith-ciosi.local/~paul/<http://ordinateur-de-judith-ciosi.local/%7Epaul/> > JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > file ERROR: http://ordinateur-de-judith-ciosi.local/~paul/<http://ordinateur-de-judith-ciosi.local/%7Epaul/> > JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > java.io.FileNotFoundException: http://ordinateur-de-judith- > ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > openFile(''file:////Users/paul/Desktop/ac.pdb''): 3 ms > eval ERROR: java.io.FileNotFoundException: http://ordinateur-de- > judith-ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > ----line 1 command 1 of file null: > load >> "''file:////Users/paul/Desktop/ac.pdb''" << > > I searched the mailing list archive for this issue and found a one > year old thread, which stated that this behavior is linked to the > inability to accept loading external files when the command is issued > by an unsigned javascript. A workaround is to reload the jmol applet > with the new file. > I would like to know if there is any other solution to make the > signed applet accept an external file ? I am also wondering at how > this problem has been dealt with in jmol protein explorer ? > > Thanks in advance, > Paul > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Robert H. <ha...@st...> - 2008-08-30 13:08:14
|
I'm working with them -- they are mostly waiting for 11.6 to be stable. Then they will go to that. Bob On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez <ang...@ua...> wrote: > > One of the interesting aspects is that I could use > > > > JMOLJAR= > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar > > > > for example to go to the PDB website and use MY applet instead of theirs. > > > Assuming that they update their Jmol.js file!!! > > They are still using 10.2, and I think there have been requests for update > already, to no > avail > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Robert H. <ha...@st...> - 2008-08-30 13:13:40
|
RCSB beta site is using Jmol 11.4. See for example: http://betastaging.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1O1I Current version there is 11.4.6, I think. On Sat, Aug 30, 2008 at 8:08 AM, Robert Hanson <ha...@st...> wrote: > I'm working with them -- they are mostly waiting for 11.6 to be stable. > Then they will go to that. > > Bob > > > > On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez <ang...@ua...>wrote: > >> > One of the interesting aspects is that I could use >> > >> > JMOLJAR= >> http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar >> > >> > for example to go to the PDB website and use MY applet instead of >> theirs. >> >> >> Assuming that they update their Jmol.js file!!! >> >> They are still using 10.2, and I think there have been requests for update >> already, to no >> avail >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Paul P. <pau...@ac...> - 2008-08-30 14:28:57
|
Thanks Bob, I narrowed down the problem to the jmolScriptWaitAsArray() function : surprisingly when I replace it by jmolScript(), I can load whatever file I want. On the contrary jmolScriptWaitAsArray() gives me access denial errors... Paul Le 30 août 08 à 15:07, Robert Hanson a écrit : > Paul, check out this page to see how yours might be different. > > http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm > > It's using the signed applet and working just fine. Maybe has to be > newer than 11.6.RC8, but I don't think so. It should load files > from the PDB using "load =xxxx" and files from your hard drive > using, for example: > > load c:/temp/caffeine.xyz > > > Also, the Jmol Protein Explorer is using using the signed applet > without a hitch. > > Bob > > > > On Sat, Aug 30, 2008 at 7:32 AM, Paul Pillot <paul.pillot@ac- > orleans-tours.fr> wrote: > I am setting up a web page with the ability to load local files as > well as external files (for example, files coming from the pdb) > > When I run the page locally, the applet is able to load any local > file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari): > java.security.AccessControlException: access denied > (java.net.SocketPermission www.rcsb.org:80 connect,resolve) > openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms > eval ERROR: java.security.AccessControlException: access denied > (java.net.SocketPermission www.rcsb.org:80 connect,resolve) > ----line 1 command 1 of file null: > load >> "http://www.rcsb.org/pdb/files/1gzx.pdb" << > > When the page is loaded from a webserver, the applet is unable to > load any local file, as well as remote files coming from elsewhere > than the webserver : > FileManager.openFile(''file:////Users/paul/Desktop/ > ac.pdb'') //''file:////Users/paul/Desktop/ac.pdb'' > FileManager opening http://ordinateur-de-judith-ciosi.local/~paul/ > JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > file ERROR: http://ordinateur-de-judith-ciosi.local/~paul/ > JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > java.io.FileNotFoundException: http://ordinateur-de-judith- > ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' > openFile(''file:////Users/paul/Desktop/ac.pdb''): 3 ms > eval ERROR: java.io.FileNotFoundException: http://ordinateur-de- > judith-ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ > ac.pdb'' > ----line 1 command 1 of file null: > load >> "''file:////Users/paul/Desktop/ac.pdb''" << > > I searched the mailing list archive for this issue and found a one > year old thread, which stated that this behavior is linked to the > inability to accept loading external files when the command is issued > by an unsigned javascript. A workaround is to reload the jmol applet > with the new file. > I would like to know if there is any other solution to make the > signed applet accept an external file ? I am also wondering at how > this problem has been dealt with in jmol protein explorer ? > > Thanks in advance, > Paul > > ---------------------------------------------------------------------- > --- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2008-08-31 15:10:31
|
right, that actually makes sense. In communicating with the applet, particularly the signed applet, you have to be very careful about threads. When you use jmolScript() you pass the command to one of two free-running script processors within Jmol. Commands involving the JavaScript command must run on one thread; commands doing any sort of file opening from restricted domains must run on a thread special thread created at the time the applet was created. When you use jmolScriptWait() you use the thread that gave the command, and since that is of browser origin it does not have the security rights of the signed applet. So the lesson here is that one cannot use jmolScriptWait() to open files with the signed applet, and one should always use callbacks if further processing in that case is required. The note I have in the code reads: /* * CommandWatcher thread handles processing of * command scripts independently of the user thread. * This is important for the signed applet, where the * thread opening remote files cannot be the browser's, * and commands that utilize JavaScript must be the browser's. * * We need two threads for the signed applet, because commands * that involve JavaScript -- the "javascript" command or math javascript() -- * must run on a thread created by the thread generating the applet call. * * This CommandWatcher thread, on the other hand, is created by the applet at * start up -- it can cross domains, but it can't run JavaScript. * * */ It's quite possible that there are methods of making all this work that I just don't know of. But that's the way it is set up currently. I suspect that someone with more Java experience could set this up so that the JmolScriptWait() lets its thread sleep while the other processor is working. Something like that. Bob On Sat, Aug 30, 2008 at 9:28 AM, Paul Pillot < pau...@ac...> wrote: > Thanks Bob,I narrowed down the problem to the jmolScriptWaitAsArray() > function : surprisingly when I replace it by jmolScript(), I can load > whatever file I want. On the contrary jmolScriptWaitAsArray() gives me > access denial errors... > > Paul > > Le 30 août 08 à 15:07, Robert Hanson a écrit : > > Paul, check out this page to see how yours might be different. > > http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm > > It's using the signed applet and working just fine. Maybe has to be newer > than 11.6.RC8, but I don't think so. It should load files from the PDB using > "load =xxxx" and files from your hard drive using, for example: > > load c:/temp/caffeine.xyz > > > Also, the Jmol Protein Explorer is using using the signed applet without a > hitch. > > Bob > > > > On Sat, Aug 30, 2008 at 7:32 AM, Paul Pillot < > pau...@ac...> wrote: > >> I am setting up a web page with the ability to load local files as >> well as external files (for example, files coming from the pdb) >> >> When I run the page locally, the applet is able to load any local >> file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari): >> java.security.AccessControlException: access denied >> (java.net.SocketPermission www.rcsb.org:80 connect,resolve) >> openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms >> eval ERROR: java.security.AccessControlException: access denied >> (java.net.SocketPermission www.rcsb.org:80 connect,resolve) >> ----line 1 command 1 of file null: >> load >> "http://www.rcsb.org/pdb/files/1gzx.pdb" << >> >> When the page is loaded from a webserver, the applet is unable to >> load any local file, as well as remote files coming from elsewhere >> than the webserver : >> FileManager.openFile(''file:////Users/paul/Desktop/ >> ac.pdb'') //''file:////Users/paul/Desktop/ac.pdb'' >> FileManager opening http://ordinateur-de-judith-ciosi.local/~paul/<http://ordinateur-de-judith-ciosi.local/%7Epaul/> >> JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' >> file ERROR: http://ordinateur-de-judith-ciosi.local/~paul/<http://ordinateur-de-judith-ciosi.local/%7Epaul/> >> JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' >> java.io.FileNotFoundException: http://ordinateur-de-judith- >> ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' >> openFile(''file:////Users/paul/Desktop/ac.pdb''): 3 ms >> eval ERROR: java.io.FileNotFoundException: http://ordinateur-de- >> judith-ciosi.local/~paul/JMolUSc/''file:////Users/paul/Desktop/ac.pdb'' >> ----line 1 command 1 of file null: >> load >> "''file:////Users/paul/Desktop/ac.pdb''" << >> >> I searched the mailing list archive for this issue and found a one >> year old thread, which stated that this behavior is linked to the >> inability to accept loading external files when the command is issued >> by an unsigned javascript. A workaround is to reload the jmol applet >> with the new file. >> I would like to know if there is any other solution to make the >> signed applet accept an external file ? I am also wondering at how >> this problem has been dealt with in jmol protein explorer ? >> >> Thanks in advance, >> Paul >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Rolf H. <rh...@fl...> - 2008-09-01 14:58:22
|
Robert Hanson wrote: > One more thought on this: What about an option that allows the replacement > of the Jar file but first prompts the user for an OK (using JavaScript > prompt() ) and explains why this might be an issue? If the user says it is > OK, then the Jar file is used? > Accepting should not be the default and then I think it should be ok. If it is integrated the possible consequences should be pointed out clearly in the documentation of 'Jmol.js'. And it should be easily removable by people who don't like to take the risk. Regards, Rolf |
From: Robert H. <ha...@st...> - 2008-09-01 15:03:19
|
OK. Others have comments on this? Bob On Mon, Sep 1, 2008 at 9:58 AM, Rolf Huehne <rh...@fl...> wrote: > Robert Hanson wrote: > > One more thought on this: What about an option that allows the > replacement > > of the Jar file but first prompts the user for an OK (using JavaScript > > prompt() ) and explains why this might be an issue? If the user says it > is > > OK, then the Jar file is used? > > > > Accepting should not be the default and then I think it should be ok. > > If it is integrated the possible consequences should be pointed out > clearly in the documentation of 'Jmol.js'. And it should be easily > removable by people who don't like to take the risk. > > Regards, > Rolf > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Robert H. <ha...@st...> - 2008-09-21 17:53:42
|
I've put up a proposed change to Jmol.js. Please check it out. The idea is that we would be able to test sites using different Jar files. The comment in the Jar file reads: // Note added 12:41 PM 9/21/2008 by Bob Hanson, ha...@st...: // JMOLJAR=xxxxx.jar on the URL for this page will override // the JAR file specified in the jmolInitialize() call. // The idea is that it can be very useful to test a web page with different JAR files // Or for an expert user to substitute a signed applet for an unsigned one // so as to use a broader range of models or to create JPEG files, for example. // If the JAR file is not in the current directory (has any sort of "/" in its name) // then the user is presented with a warning and asked whether it is OK to change Jar files. // The default action, if the user just presses "OK" is to NOT allow the change. // The user must type the word "yes" in the prompt box for the change to be approved. // If you don't want people to be able to switch in their own JAR file on your page, // simply set this next line to read "var allowJMOLJAR = false". You can try it out using URLs such as these: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolApplet.jar http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar Bob On Mon, Sep 1, 2008 at 10:03 AM, Robert Hanson <ha...@st...> wrote: > OK. Others have comments on this? > > Bob > > > > On Mon, Sep 1, 2008 at 9:58 AM, Rolf Huehne <rh...@fl...>wrote: > >> Robert Hanson wrote: >> > One more thought on this: What about an option that allows the >> replacement >> > of the Jar file but first prompts the user for an OK (using JavaScript >> > prompt() ) and explains why this might be an issue? If the user says it >> is >> > OK, then the Jar file is used? >> > >> >> Accepting should not be the default and then I think it should be ok. >> >> If it is integrated the possible consequences should be pointed out >> clearly in the documentation of 'Jmol.js'. And it should be easily >> removable by people who don't like to take the risk. >> >> Regards, >> Rolf >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 Northfield, MN http://www.stolaf.edu/people/hansonr 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 |