Re: [Jmol-users] Jmol mediawiki extension
Something's not right.
mayscript = false in no way prevents jmolButton from being created,
and with mayscript=false, the jmolButton still works fine.
Something else is going on there.
Bob
On Wed, Dec 10, 2008 at 3:14 PM, Angel Herráez [EMAIL PROTECTED] wrote:
On 10 Dec 2008 at 7:36, Robert Hanson wrote:
But, really, it's simpler than that if you want to disallow all
callbacks and every last bit of JavaScript capability of the applet --
just don't have mayscript in the applet tag.
Ah, interesting.
But then jmolButton() et al. do nothing. I mean, the button is not written
to the page*. A
very safe mode indeed, but not what we need for the Wiki. So I will go with
the
_jmol.noEval method.
*) Rightly so, since they would not be able to send scripts to the applet.
Oh, not exactly! If I add a button using
input type=button value=cpk off onClick=jmolScript('cpk off')
it does send the script to the applet.
So mayscript is unidirectional: its absence blocks Jmol from talking to
javascript, and
blocks Jmol.js from generating UI controls, but does not block Jmol from
listening to
javascript. Intriguing...
(tested in WinXP, Firefox, IE7 and Opera)
This is the reference I recalled:
http://www.javasonics.com/support/check_liveconnect.php
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Re: [Jmol-users] Jmol mediawiki extension
Hi, On Tue, Dec 9, 2008 at 1:21 PM, Angel Herraez [EMAIL PROTECTED] wrote: I'd like to keep this discussion going, so here is a little bit more, picking up on the possibilities to have Jmol supported in Wikipedia and other Wikis: On 30 Nov 2008 22:53, Nicolas Vervelle wrote: On the matter of security issues, there are at least 2 things to do : * Being able to entirely deactivate the possibility to let arbitrary Javascript being called by Jmol. I don't know if there's a way in Jmol to disable this. There's a need to completely disable the 'javascript' command in Jmol scripts. The problem is demonstrated by http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_dem o Do we still need this? (see below) * Ensuring that the extension doesn't allow for true Javascript injection (whatever text is entered by someone in the jmoltags, this only creates Jmol applet and Jmol scripts, nothing else). I think this means ensuring that in the generated page, the text is always correctly escaped to prevent Javascript injection. This is implemented in the last update. The second problem nees to be treated in the extension. My knowledge on PHP and the security issues is limited (and I don't have much time avaiable), so some help from someone knowing how to deal with the script injection would be very useful. The way I've implemented it, any script passed to the Extension (inside the extension's script tag) containing the word javascript (case-insensitive) will be completely ignored. I gues it can be done so that only the javascript part is removed and the remaining script is preserved, but I don't know so much PHP as to do so. And the idea is that users-editors of wiki pages should not try at all to use javascript in the wiki pages. This approach is interesting but I am not sure it covers all the possibilities. For example, I think you can still run Javascript with scripts calling other scripts : - Create a wiki page with contents corresponding to a Jmol script with Javascript in it. - Add a jmol tag in a page with a script calling the other script As a side effect, the text, title, name... tags of the extension cannot contain the forbidden word either (they are all parsed via the same function as script is). Not a big sacrifice. Not a problem :) And on 1 Dec 2008 9:49, Brian Salter-Duke wrote: The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. This needs further work, but is related to the above config. settings. I am not sure using Jmol files on Commons needs any change. I thought that files in the Image namespace in Commons are simply exported to other wikis and kept up to date. Nico -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió: For example, I think you can stillrun Javascriptwithscripts calling other scripts: * Create a wiki page with contents corresponding to a Jmol script with Javascript in it. * Add a jmol tag in a page with a script calling the other script Aha, that's the sort of idea I wanted to hear (but had not imagined). Then maybe we should block the use of the script command too. After all, we shouldn't need too much Jmol scripting flexibility inside a Wiki; just basic display options that can be pasted in the page, not in independent files. I will test it this evening. -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Angel Herraez wrote: El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió: For example, I think you can stillrun Javascriptwithscripts calling other scripts: * Create a wiki page with contents corresponding to a Jmol script with Javascript in it. * Add a jmol tag in a page with a script calling the other script Aha, that's the sort of idea I wanted to hear (but had not imagined). Then maybe we should block the use of the script command too. After all, we shouldn't need too much Jmol scripting flexibility inside a Wiki; just basic display options that can be pasted in the page, not in independent files. I will test it this evening. I think the only way to guarantee that no Javascript can be injected by Jmol would be to add a non-reversible switch to Jmol itself. I would expect only this kind of solution might convince the Wikipedia people that Jmol is save enough. Regards, Rolf -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Tue, Dec 9, 2008 at 2:41 PM, Angel Herraez [EMAIL PROTECTED] wrote: El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió: For example, I think you can stillrun Javascriptwithscripts calling other scripts: * Create a wiki page with contents corresponding to a Jmol script with Javascript in it. * Add a jmol tag in a page with a script calling the other script Aha, that's the sort of idea I wanted to hear (but had not imagined). Then maybe we should block the use of the script command too. After all, we shouldn't need too much Jmol scripting flexibility inside a Wiki; just basic display options that can be pasted in the page, not in independent files. I will test it this evening. I am rather thinking as Rolf does, that to convince Wikipedia people it would be better to really deactivate Javascript in Jmol itself (would it be possible to pass an option to Jmol applet when starting it ?), rather than trying to block several things. I don't know if scripts would be used much, but using independent files can help apply similar display options to a lot of a pages. I haven't tested if inserting templates inside jmol tags works : that could be an other way of running the same script on a lot of pages. Nico -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On 9 Dec 2008 at 17:14, Nicolas Vervelle wrote: I am rather thinking as Rolf does, that to convince Wikipedia people it would be better to really deactivate Javascript in Jmol itself (would it be possible to pass an option to Jmol applet whenstarting it ?), rather than trying to block several things. As usual, Bob had the rabbit ready in his hat. There is an option to avoid evaluation of javascript from inside Jmol. This prevents javascript injection in the wiki both from script tags and from called scripts contained in another wiki page. Tested and commited (revision 10478). Aggressive testers are welcome. Nico, you were right: scripts can be invoked that are the contents of another wiki page. Sometimes the name or path of that page gives trouble, but it is possible (I still have to learn the intricacies of namespaces, subpages, categories). I don't know if scripts would be used much, but using independent files can help apply similar display options to a lot of a pages. I haven't tested if inserting templates inside jmol tags works : that could be an other way of running the same script on a lot of pages. It seems not possible to use templates for this. -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Tue, Dec 09, 2008 at 01:21:01PM +0100, Angel Herraez wrote: I'd like to keep this discussion going, so here is a little bit more, picking up on the possibilities to have Jmol supported in Wikipedia and other Wikis: [Nico's message snipped] And on 1 Dec 2008 9:49, Brian Salter-Duke wrote: I am just thinking aloud here. I think there could be a solution to add a chaneg to medciawiki itself to have some specific Jmol tags, something like: jmolimage ... /jmolimage We already have the jmol tag added by the extension. Is there any difference intended? avoiding all calls to Jmol itself. I don't quite understand. There is no call to Jmol until the extension inserts the Jmol code. And by using jmolAppletButton or jmolAppletLink one avoids Jmol to be loaded until the visitor requests it. This is an example of an image inserted on wikipedia:- [[Image:Meissner effect zoom.jpg|thumb|200px|right|A [[magnet]] levitating above a [[high-temperature superconductor]] demonstrates the [[Meissner effect]].]] Everything is together. I presume the bits are handled by mediawiki. In contrast, a simple Jmol call is full of html/javascript like stuff. jmoljmolAppletscriptset spin X 10; spin on/script nameethane_s1/namecolorpalegreen/colorsize250/size uploadedFileContentsethane_s.pdb/uploadedFileContents /jmolApplet jmolButtonscriptspin on/scriptnameethane_s1/nametextStart spinning/text/jmolButton jmolButtonscriptspin off/scriptnameethane_s1/nametextStop spinning/text/jmolButton /jmol What if it was like this:- [[Jmolimage:ethane_s.pdb|color=palegreen|script=spin X 10|script=spin on|size=250|button=(spin on,Start spinning)|button=(spin off,Stop spining)]] Jmolimage:ethane_s.pdb starts it all off and includes:- uploadedFileContentsethane_s.pdb/uploadedFileContents color=palegreen includes colorpalegreen/color size=250 includes colorpalegreen/color script=spin X 10| script=spin on would generate:- scriptset spin X 10; spin on/script button=(spin on,Start spinning) is interpreted as:- jmolButtonscriptspin on/scriptnameethane_s1/nametextStart spinning/text/jmolButton button=(spin off,Stop spining) is interpreted as:- jmolButtonscriptspin off/scriptnameethane_s1/nametextStop spinning/text/jmolButton I suspect this would be easier for users and could likely be made more secure. However, I have no idea how this would be implemented. The mediawiki language seems to aim to remove as much direct html use as possible. The parameters for jmolimage would give everything that was needed, method, file names, etc. Mediawiki itself would then be doing any chaecks that were needed. It would also be easier for wikipedia editors and I suspect the wikipedia techs would prefer this solution. Is this worth following up? I do noptset spin X 10; spin on/scriptt know mediawiki and could be just talking nonsense. I think it is the JmolMediaWiki Extension that must do all this anyway, not the generic MediaWiki software. And it is doing so already, by using the different sub-tags of the jmol tag. Do you envisage any differences, Brian? Please ellaborate on that. The configuration in the server (LocalSettings.php) may block the use of external URLs for models, or of uploaded files, may block or impose the use of signed applet. The rest of the task in inside the Extension. Another advantage of this approach is that wikipedia could limit the mehtods available and perhaps limit them to file upload only. Already possible (see above). I understand this. When the extension was first written, it was understandable that a number of different approaches were tried. Maybe it is time to limit these choices and make it simpler. Particularly on wikipedia, which has a large number of editors who are likely to be less familiar with Jmol than users on say the Jmol wiki, I think we have to decide. The choice is I think really between an uploaded file (on either wikipedia or Commons) and inline data. The latter will be seen as clumsy, but it makes it all self contained and does not mean that the whole upload business has to be altered - see below. The former would be better, but changes would be needed. The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. This needs further work, but is related to the above config. settings. Whether Commons or the home wiki (say wikipedia or wikiversity) many changes would be needed. First, upload is restricted to files with certain extensions. We would have to decide which file types we wanted and allow those extensions to the upload. Second, we need to think about copyright issues on uploaded files and how these are going to be added. If you click on an image, it brings up the image page that displays both the image and all the upload, copyright, etc. details. How would this work for say a pdb file. So, third, we have a different image page. Adding an new prefix Jmolimage may
Re: [Jmol-users] Jmol mediawiki extension
On Tue, Dec 09, 2008 at 02:03:17PM +0100, Nicolas Vervelle wrote: Hi, On Tue, Dec 9, 2008 at 1:21 PM, Angel Herraez [EMAIL PROTECTED] wrote: I'd like to keep this discussion going, so here is a little bit more, picking up on the possibilities to have Jmol supported in Wikipedia and other Wikis: On 30 Nov 2008 22:53, Nicolas Vervelle wrote: On the matter of security issues, there are at least 2 things to do : * Being able to entirely deactivate the possibility to let arbitrary Javascript being called by Jmol. I don't know if there's a way in Jmol to disable this. There's a need to completely disable the 'javascript' command in Jmol scripts. The problem is demonstrated by http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_dem o Do we still need this? (see below) * Ensuring that the extension doesn't allow for true Javascript injection (whatever text is entered by someone in the jmoltags, this only creates Jmol applet and Jmol scripts, nothing else). I think this means ensuring that in the generated page, the text is always correctly escaped to prevent Javascript injection. This is implemented in the last update. The second problem nees to be treated in the extension. My knowledge on PHP and the security issues is limited (and I don't have much time avaiable), so some help from someone knowing how to deal with the script injection would be very useful. The way I've implemented it, any script passed to the Extension (inside the extension's script tag) containing the word javascript (case-insensitive) will be completely ignored. I gues it can be done so that only the javascript part is removed and the remaining script is preserved, but I don't know so much PHP as to do so. And the idea is that users-editors of wiki pages should not try at all to use javascript in the wiki pages. This approach is interesting but I am not sure it covers all the possibilities. For example, I think you can still run Javascript with scripts calling other scripts : - Create a wiki page with contents corresponding to a Jmol script with Javascript in it. - Add a jmol tag in a page with a script calling the other script As a side effect, the text, title, name... tags of the extension cannot contain the forbidden word either (they are all parsed via the same function as script is). Not a big sacrifice. Not a problem :) And on 1 Dec 2008 9:49, Brian Salter-Duke wrote: The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. This needs further work, but is related to the above config. settings. I am not sure using Jmol files on Commons needs any change. I thought that files in the Image namespace in Commons are simply exported to other wikis and kept up to date. I am fairly sure that this is not right. The code looks at Commons first for the image, and then on the local wiki. I could however be mistaken. Wikipedia images confuse me. Brian. Nico -- next part -- An HTML attachment was scrubbed... -- -- The PROPER way to handle HTML postings is to cancel the article, then hire a hitman to kill the poster, his wife and kids, and fuck his dog and smash his computer into little bits. Anything more is just extremism. -- Paul Tomblin Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Hi Gerard Thanks for the suggestions. Jmol is already fully internationalized and localized, over 10 languages: http://wiki.jmol.org:81/index.php/Internationalisation/Current_Status I'm not sure if the MediaWiki extension would need any further localization. Does the testing environment that you mention need a web Wiki setup, or can it be tested locally? I would be interested on it, but haven't got a Wiki to implement it --nor the time to involvemyself into such a task--. El 1 Dec 2008 a las 11:24, Brian Salter-Duke escribió: Hi folks, Gerard Meijssen [EMAIL PROTECTED] has asked me to pass this on to the Jmol list. I responded to this discussion on the Commons-l list:- [Commons-l] Support for Chemical Markup Language - followup -- Hoi, If you want to get the JMOL software internationalised and localised, you may want to consider talking to the Betawiki people. We do the localisation of MediaWiki and we do the localisation of many of its extensions. We would be interested in working on JMOL as it is a lively and relevant software / community. I am also involved in a testing envirionment for MediaWiki extensions, if you are interested in using this environment, let me know.. I take it that you will convey my message to the JMOL mailing list ? Thanks, Gerard - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Take a look at this blog:- http://ultimategerardm.blogspot.com/2008/12/jmol.html More publicity to get Jmol properly working on wikis. Brian. -- First they ignore you, then they laugh at you, then they fight you, then you win. -- Gandhi, being prophetic about Linux. Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Hi everyone, I have been quite busy for several months on other matters than Jmol, so I haven't worked at all on the extension. I am happy to see people interested in making it work, and bringing it to Wikipedia. On the matter of security issues, there are at least 2 things to do : - Being able to entirely deactivate the possibility to let arbitrary Javascript being called by Jmol. I don't know if there's a way in Jmol to disable this. There's a need to completely disable the 'javascript' command in Jmol scripts. The problem is demonstrated by http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_demo - Ensuring that the extension doesn't allow for true Javascript injection (whatever text is entered by someone in the jmol tags, this only creates Jmol applet and Jmol scripts, nothing else). I think this means ensuring that in the generated page, the text is always correctly escaped to prevent Javascript injection. Both things clearly need to be done in order to hope to see Jmol on Wikipedia : having every editor being able to add arbitrary Javascript that will be run by everyone viewing a page is a security issue. The first problem needs first to be answered in the Jmol applet itself. Is there a way to add an option in the applet construction to remove the 'javascript' command in Jmol scripts ? Bob ? The second problem nees to be treated in the extension. My knowledge on PHP and the security issues is limited (and I don't have much time avaiable), so some help from someone knowing how to deal with the script injection would be very useful. Nico - 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=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Sun, Nov 30, 2008 at 10:53:29PM +0100, Nicolas Vervelle wrote: Hi everyone, I have been quite busy for several months on other matters than Jmol, so I haven't worked at all on the extension. I am happy to see people interested in making it work, and bringing it to Wikipedia. On the matter of security issues, there are at least 2 things to do : - Being able to entirely deactivate the possibility to let arbitrary Javascript being called by Jmol. I don't know if there's a way in Jmol to disable this. There's a need to completely disable the 'javascript' command in Jmol scripts. The problem is demonstrated by http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_demo - Ensuring that the extension doesn't allow for true Javascript injection (whatever text is entered by someone in the jmol tags, this only creates Jmol applet and Jmol scripts, nothing else). I think this means ensuring that in the generated page, the text is always correctly escaped to prevent Javascript injection. Both things clearly need to be done in order to hope to see Jmol on Wikipedia : having every editor being able to add arbitrary Javascript that will be run by everyone viewing a page is a security issue. The first problem needs first to be answered in the Jmol applet itself. Is there a way to add an option in the applet construction to remove the 'javascript' command in Jmol scripts ? Bob ? The second problem nees to be treated in the extension. My knowledge on PHP and the security issues is limited (and I don't have much time avaiable), so some help from someone knowing how to deal with the script injection would be very useful. Nico I am just thinking aloud here. I think there could be a solution to add a chaneg to medciawiki itself to have some specific Jmol tags, something like: jmolimage ... /jmolimage avoiding all calls to Jmol itself. The parameters for jmolimage would give everything that was needed, method, file names, etc. Mediawiki itself would then be doing any chaecks that were needed. It would also be easier for wikipedia editors and I suspect the wikipedia techs would prefer this solution. Is this worth following up? I do not know mediawiki and could be just talking nonsense. Another advantage of this approach is that wikipedia could limit the mehtods available and perhaps limit them to file upload only. The mediawiki code would need changing anyway to allow use of Jmol files on Commons as well as wikipedia. Some mediawiki changes are going to be needed anyway. Brian. -- Real Programmers can write FORTRAN in any language. -- unknown Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Hi folks, Gerard Meijssen [EMAIL PROTECTED] has asked me to pass this on to the Jmol list. I responded to this discussion on the Commons-l list:- [Commons-l] Support for Chemical Markup Language - followup -- Hoi, If you want to get the JMOL software internationalised and localised, you may want to consider talking to the Betawiki people. We do the localisation of MediaWiki and we do the localisation of many of its extensions. We would be interested in working on JMOL as it is a lively and relevant software / community. I am also involved in a testing envirionment for MediaWiki extensions, if you are interested in using this environment, let me know.. I take it that you will convey my message to the JMOL mailing list ? Thanks, Gerard -- This does seem to be a useful idea. I'll have a look at betawiki but I'm very busy this week and early next week. Cheers, Brian. -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: [EMAIL PROTECTED]Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Brian, We are currently running courses with no issue using the old implementation http://www.ch.ic.ac.uk/wiki/ (which has proved VERY robust. We often have classes of 50 students all hammering pages with 10 or more embedded Jmols, with no issues). but have also been struggling to implement the new version http://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol I currently have it down to a silly mistake somewhere, probably a variable in LocalSettings.php. The correct source code is being generated, including the Jmolinitialize script etc, but it just does not start (if someone CAN spot a mistake in the source for the page above, I would be very grateful!) The current environment is as usual at http://www.ch.ic.ac.uk/wiki2/index.php/Special:Version Perhaps its an issue with the combinationin of Jmol and StubManager? Although I love Mediawiki (and its use HAS revolutionalized how we grade student molecular modelling), it remains a very fragile environment. Thus a single misbehaving extension and mediawiki has a propensity for displaying NOTHING. I am very keen to extend our course so that the wiki can start to display eg MO surfaces, vibrations, etc, but all this is predicated on being able to update the Jmol. Oh, and I need to get all this working, since I hope to present on this topic at the ACS next spring! One final question. Students are asked to paste a boiler plate 3 lines to include their own molecules. Inevitably, they sometimes truncate this, missing out either the start or the end of the syntax. MediaWiki contrives to accept this without issue, but then complains inevitably that the XML is broken and will refuse to allow the broken page to be edited. One then has to access the history list manually, and revert to a working version. Its messy. But why cannot the php parser validate the XML in the first place, and refused to deposit it into the MySQL if it does not validate? On 29 Nov 2008, at 01:41, Brian Salter-Duke wrote: The question of having Jmol used on wikipedia has again been raised on the commons email list. On contributor to the discussion says that the jmol mediawiki extension now only works with an older version of mediawiki. Certainly my examples at:- http://wiki.jmol.org:81/index.php/User:Bduke are not working. I still very much want to get jmol working on wikipedia and would like to also get it on wikiversity for some teaching materials I have started to add there. However, I have been very much out of touch recently. Could someone please update me on what the situation is with the jmol mediawiki extension and point me to an example of it working, so I can point the wikipedia technical folks to have a look at the examples? Also, last time I tried to get jmol on wikipedia I was told there were security issues with the extension. Have these been addressed? - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On 29 Nov 2008 at 8:12, Rzepa, Henry wrote: http://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol I currently have it down to a silly mistake somewhere, probably a variable in LocalSettings.php. The correct source code is being generated, including the Jmolinitialize script etc, but it just does not start (if someone CAN spot a mistake in the source for the page above, I would be very grateful!) Henry, I'm probably been naïve, but your page source code says script language='Javascript' type='text/javascript' src='/extensions/Jmol/Jmol.js'/script and when I try the url http://www.ch.ic.ac.uk/extensions/Jmol/Jmol.js I get an error: The requested URL /extensions/Jmol/Jmol.js was not found on this server. So where am I confused? That explains the js console errors I get: Error: jmolInitialize is not defined Archivo de origen: http://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol Línea: 58 Error: jmolCheckBrowser is not defined Archivo de origen: http://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol Línea: 75 - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On 29 Nov 2008, at 01:41, Brian Salter-Duke wrote: The question of having Jmol used on wikipedia has again been raised on the commons email list. On contributor to the discussion says that the jmol mediawiki extension now only works with an older version of mediawiki. Certainly my examples at:- http://wiki.jmol.org:81/index.php/User:Bduke I have gotten things to work myself (Thanks Angel for the remark that gave the clue). In the distribution http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki/MediaWiki/ edit the file Jmol.php to make the change from $wgJmolExtensionPath = /extensions/Jmol; to $wgJmolExtensionPath = $wgScriptPath./extensions/Jmol; - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
I have gotten the Jmol Mediawiki to display a variety of more interesting modes: https://www.ch.ic.ac.uk/wiki2/index.php/Mod:jmol (although I dont think it can do everything a conventionally invoked applet can). - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Henry, I'm glad that you found the cure for your problem, and to have been a catalyst in that cure :) On 29 Nov 2008 at 14:53, Rzepa, Henry wrote: In the distribution http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki/MediaWiki/ edit the file Jmol.php to make the change from $wgJmolExtensionPath = /extensions/Jmol; to $wgJmolExtensionPath = $wgScriptPath./extensions/Jmol; I have commited this change to SVN. The discussion has also prompted me to update several pages in Jmol Wiki related to wiki extensions. - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On 29 Nov 2008, at 18:43, Angel Herráez wrote: Henry, I'm glad that you found the cure for your problem, and to have been a catalyst in that cure :) On 29 Nov 2008 at 14:53, Rzepa, Henry wrote: In the distribution http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki/MediaWiki/ edit the file Jmol.php to make the change from $wgJmolExtensionPath = /extensions/Jmol; to $wgJmolExtensionPath = $wgScriptPath./extensions/Jmol; I have commited this change to SVN. Thanks for the above! - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Sat, Nov 29, 2008 at 02:53:18PM +, Rzepa, Henry wrote: On 29 Nov 2008, at 01:41, Brian Salter-Duke wrote: The question of having Jmol used on wikipedia has again been raised on the commons email list. On contributor to the discussion says that the jmol mediawiki extension now only works with an older version of mediawiki. Certainly my examples at:- http://wiki.jmol.org:81/index.php/User:Bduke I have gotten things to work myself (Thanks Angel for the remark that gave the clue). In the distribution http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-extensions/wiki/MediaWiki/ edit the file Jmol.php to make the change from $wgJmolExtensionPath = /extensions/Jmol; to $wgJmolExtensionPath = $wgScriptPath./extensions/Jmol; That is great news. Thanks, Henry. My page on the Jmol wiki is now working and I have something I can point the wikipedia tech folks to so that they can look at Jmol. The question of security still remains. Has this been addresed by anyone? Does anyone on this list think it is an issue? It is quite clear that Kmol will never be added to wikipedia until the tech folks are totally convinced that there are no security issues. I just do not know much about security and I do not speak php. Regards, Brian. -- On two occasions I have been asked [by members of Parliament], Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?. I am not able rightly to comprehend the kind of confusion of ideas that could provoke such a question. -- Charles Babbage Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On 30 Nov 2008 at 9:48, Brian Salter-Duke wrote: That is great news. Thanks, Henry. My page on the Jmol wiki is now working and I have something I can point the wikipedia tech folks to so that they can look at Jmol. Brian, I'm quite surprised that your page has started to work NOW. Unless Nico has updated the Wiki without saying a word, what I updated earlier this evening was the php file in the Jmol SVN pages. I would not expect that to affect the Wiki automatically. The question of security still remains. Has this been addresed by anyone? Does anyone on this list think it is an issue? A recent addition to the Wiki questions security on the basis that any javascript can be run from Jmol script. I'm not sure, though, what security issues that raises. See http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_demo The latest post in the Talk page http://wiki.jmol.org:81/index.php/User_talk:Ilmari_Karonen/JS_injection_demo sounds very threatening, but I don't understand it fully. It may, however, be a big obstacle for Wikipedia adoption. - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
On Sun, Nov 30, 2008 at 01:16:21AM +0100, Angel Herráez wrote: On 30 Nov 2008 at 9:48, Brian Salter-Duke wrote: That is great news. Thanks, Henry. My page on the Jmol wiki is now working and I have something I can point the wikipedia tech folks to so that they can look at Jmol. Brian, I'm quite surprised that your page has started to work NOW. Unless Nico has updated the Wiki without saying a word, what I updated earlier this evening was the php file in the Jmol SVN pages. I would not expect that to affect the Wiki automatically. The question of security still remains. Has this been addresed by anyone? Does anyone on this list think it is an issue? A recent addition to the Wiki questions security on the basis that any javascript can be run from Jmol script. I'm not sure, though, what security issues that raises. See http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_demo The latest post in the Talk page http://wiki.jmol.org:81/index.php/User_talk:Ilmari_Karonen/JS_injection_demo sounds very threatening, but I don't understand it fully. It may, however, be a big obstacle for Wikipedia adoption. Discussion has been going on at both:- Wikimedia Commons Discussion List [EMAIL PROTECTED] and Wikimedia developers [EMAIL PROTECTED] This discussion may illustrate the problem:- [Post to commons list] See https://bugzilla.wikimedia.org/show_bug.cgi?id=16491 That users can embed javascript is not acceptable to run it on Wikipedia. Other parameters, like urlContents or signed wouldn't be used but at least they can be disabled. [Me] I am afraid this is all beyond my expertise. Are you saying that there is no way Jmol can ever be used on WMF projects? [Reply from someone else] There is, as soon as the Javascript embedding possibility gets disabled and the extension gets a proper review (TM). This link:- https://bugzilla.wikimedia.org/show_bug.cgi?id=16491 mentioned there is interesting but the question of the CML extension is getting confused with the Jmol extension as both were mentioned in the original post on the Commons list. While Jmol on wikipedia would be great, I would really like it on wikiversity to illustrate some teeaching materials I have started to put there. Brian. -- If people are good only because they fear punishment, and hope for reward, then we are a sorry lot indeed. -- Albert Einstein Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au - 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=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Hi folks. It works now! Details follow.
My group's wiki is behind a corporate proxy so it's unreachable from your
ends. Thanks Nico for providing the new JmolExtension.php on
wiki.jmol.org and for your LocalSettings.php excerpts. No significant
differences between our LocalSettings.php files. Regarding the
JmolExtension.php diffs, they were as follows:
-bash-3.00$ diff JmolExtension.php.old JmolExtension.php
611a612
$wgParser-disableCache();
637a639
$wgParser-disableCache();
...one disableCache() call in wfJmolRender() as discussed on Friday, and
another in wfJmolDevRender() which is new but may or may not be relevant
for nondevelopment use. That said, I did have to save the wiki page one
more time after updating JmolExtension.php before it would work, perhaps
to remove some cache data within the wiki that disableCache() couldn't
reach. I'm really not sure, and it's possible if I had done this on
Friday it would have worked then. At any rate, live/normal page views do
work consistently now.
Thanks Nico and everyone for your help!
--JRM
Nicolas Vervelle [EMAIL PROTECTED]
24-Mar-2007 06:22
To
jmol-users@lists.sourceforge.net
cc
[EMAIL PROTECTED]
Subject
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on
live page
Hi Joseph,
Can you give an URL to your wiki so that I can check myself ?
I have uploaded the latest version of JmolExtension.php on the Jmol Wiki:
http://wiki.jmol.org:81/index.php/MediaWiki/JmolExtension.php
At the end of the mail, I have put a stripped version of my
LocalSettings.php file.
You can compare it with your own (for example, do you use MemCached ?)
If I have new ideas before monday, I will try to implement them.
Have a nice weekend
Nico
[EMAIL PROTECTED] wrote:
Regarding updating the argument list for onBeforePageDisplay() to be just
$out -- PHP was satisfied but otherwise no change.
Regarding your tests -- sorry I didn't include mention of purge tests from
my end. But yes, our results matched: edit/preview ok, normal/live nok,
purge ok.
Now regarding your latest suggestion regarding disableCache() in
wfJmolRender(), it's no dice on my end. I tried it together with our
earlier edits up to and including above, and then I tried inserting the
$wgParser-disableCache(); statement into a stock JmolExtension.php -- the
results were the same (live nok).
That includes Firefox 2.0.0.3 and IE7 with empty local caches, and after
using the purge mode to clear MediaWiki's cache. Touching or otherwise
updating MediaWiki's LocalSettings.php also forces MediaWiki to clear its
cache, and I did so -- still nok on the live page. I was beginning to
think this was a cache issue within MediaWiki and we could work around it
with suitable tweaks to LocalSettings.php, now I don't know.
All the test pages on wiki.jmol.org do work for me -- I think before today
only the uploaded XYZ example worked properly, now all three upload
examples work, as does the Inlined CML File example.
FYI, I'm heading home for the day and won't be able to revisit this until
Monday. Thanks for your attention and suggestions today,
--JRM
LocalSettings.php:
?php
# This file was automatically generated by the MediaWiki installer.
# If you make manual changes, please keep track in case you need to
# recreate them later.
#
# See includes/DefaultSettings.php for all configurable settings
# and their default values, but don't forget to make changes in _this_
# file, not there.
# If you customize your file layout, set $IP to the directory that
contains
# the other MediaWiki files. It will be used as a base to locate files.
if( defined( 'MW_INSTALL_PATH' ) ) {
$IP = MW_INSTALL_PATH;
} else {
$IP = dirname( __FILE__ );
}
$path = array( $IP, $IP/includes, $IP/languages );
set_include_path( implode( PATH_SEPARATOR, $path ) . PATH_SEPARATOR .
get_include_path() );
require_once( includes/DefaultSettings.php );
# If PHP's memory limit is very low, some operations may fail.
# ini_set( 'memory_limit', '20M' );
if ( $wgCommandLineMode ) {
if ( isset( $_SERVER ) array_key_exists( 'REQUEST_METHOD', $_SERVER
) ) {
die( This script must be run from the command line\n );
}
} elseif ( empty( $wgNoOutputBuffer ) ) {
## Compress output if the browser supports it
if( !ini_get( 'zlib.output_compression' ) ) @ob_start( 'ob_gzhandler'
);
}
$wgSitename = Jmol;
$wgScriptPath = ;
$wgScript = $wgScriptPath/index.php;
$wgRedirectScript = $wgScriptPath/redirect.php;
## For more information on customizing the URLs please see:
## http://meta.wikimedia.org/wiki/Eliminating_index.php_from_the_url
## If using PHP as a CGI module, the ?title= style usually must be used.
$wgArticlePath = $wgScript/$1;
# $wgArticlePath = $wgScript?title=$1;
$wgStylePath= $wgScriptPath/skins;
$wgStyleDirectory = $IP/skins;
#$wgLogo = $wgStylePath/common/images/wiki.png;
$wgLogo
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Hi Joseph,
Can you give an URL to your wiki so that I can check myself ?
I have uploaded the latest version of JmolExtension.php on the Jmol
Wiki:
http://wiki.jmol.org:81/index.php/MediaWiki/JmolExtension.php
At the end of the mail, I have put a stripped version of my
LocalSettings.php file.
You can compare it with your own (for example, do you use MemCached ?)
If I have new ideas before monday, I will try to implement them.
Have a nice weekend
Nico
[EMAIL PROTECTED] wrote:
Regarding updating the argument list for
onBeforePageDisplay() to be just $out -- PHP was satisfied but
otherwise
no change.
Regarding your tests -- sorry I didn't
include
mention of purge tests from my end. But yes, our results matched:
edit/preview ok, normal/live nok, purge ok.
Now regarding your latest suggestion
regarding
disableCache() in wfJmolRender(), it's no dice on my end. I tried
it together with our earlier edits up to and including above, and then
I tried inserting the $wgParser-disableCache(); statement into a
stock
JmolExtension.php -- the results were the same (live nok).
That includes Firefox 2.0.0.3 and IE7
with
empty local caches, and after using the purge mode to clear MediaWiki's
cache. Touching or otherwise updating MediaWiki's LocalSettings.php
also forces MediaWiki to clear its cache, and I did so -- still nok on
the live page. I was beginning to think this was a cache issue within
MediaWiki and we could work around it with suitable tweaks to
LocalSettings.php,
now I don't know.
All the test pages on wiki.jmol.org do
work
for me -- I think before today only the uploaded XYZ example worked
properly,
now all three upload examples work, as does the "Inlined CML File"
example.
FYI, I'm heading home for the day and
won't
be able to revisit this until Monday. Thanks for your attention and
suggestions today,
--JRM
LocalSettings.php:
?php
# This file was automatically generated by the MediaWiki installer.
# If you make manual changes, please keep track in case you need to
# recreate them later.
#
# See includes/DefaultSettings.php for all configurable settings
# and their default values, but don't forget to make changes in _this_
# file, not there.
# If you customize your file layout, set $IP to the directory that
contains
# the other MediaWiki files. It will be used as a base to locate files.
if( defined( 'MW_INSTALL_PATH' ) ) {
$IP = MW_INSTALL_PATH;
} else {
$IP = dirname( __FILE__ );
}
$path = array( $IP, "$IP/includes", "$IP/languages" );
set_include_path( implode( PATH_SEPARATOR, $path ) . PATH_SEPARATOR .
get_include_path() );
require_once( "includes/DefaultSettings.php" );
# If PHP's memory limit is very low, some operations may fail.
# ini_set( 'memory_limit', '20M' );
if ( $wgCommandLineMode ) {
if ( isset( $_SERVER ) array_key_exists(
'REQUEST_METHOD', $_SERVER ) ) {
die( "This script must be run from the command line\n" );
}
} elseif ( empty( $wgNoOutputBuffer ) ) {
## Compress output if the browser supports it
if( !ini_get( 'zlib.output_compression' ) ) @ob_start(
'ob_gzhandler' );
}
$wgSitename = "Jmol";
$wgScriptPath = "";
$wgScript = "$wgScriptPath/index.php";
$wgRedirectScript = "$wgScriptPath/redirect.php";
## For more information on customizing the URLs please see:
## http://meta.wikimedia.org/wiki/Eliminating_index.php_from_the_url
## If using PHP as a CGI module, the ?title= style usually must be used.
$wgArticlePath = "$wgScript/$1";
# $wgArticlePath = "$wgScript?title=$1";
$wgStylePath = "$wgScriptPath/skins";
$wgStyleDirectory = "$IP/skins";
#$wgLogo = "$wgStylePath/common/images/wiki.png";
$wgLogo = "$wgScriptPath/Jmol_smallLogo.gif";
$wgUploadPath = "$wgScriptPath/images";
$wgUploadDirectory = "$IP/images";
$wgEnableEmail = true;
$wgEnableUserEmail = true;
## For a detailed description of the following switches see
## http://meta.wikimedia.org/Enotif and
http://meta.wikimedia.org/Eauthent
## There are many more options for fine tuning available see
## /includes/DefaultSettings.php
## UPO means: this is also a user preference option
$wgEnotifUserTalk = true; # UPO
$wgEnotifWatchlist = true; # UPO
$wgEmailAuthentication = true;
# Experimental charset support for MySQL 4.1/5.0.
$wgDBmysql5 = false;
## Shared memory settings
$wgMainCacheType = CACHE_NONE;
$wgMemCachedServers = array();
## To enable image uploads, make sure the 'images' directory
## is writable, then set this to true:
$wgEnableUploads = true;
$wgUseImageResize = true;
# $wgUseImageMagick = true;
# $wgImageMagickConvertCommand = "/usr/bin/convert";
## If you want to use image uploads under safe mode,
## create the directories images/archive, images/thumb and
## images/temp, and make them all writable. Then uncomment
## this, if it's not already uncommented:
$wgHashedUploadDirectory = false;
## If you have the appropriate support software installed
## you can enable inline LaTeX equations:
$wgUseTeX = false;
$wgMathPath =
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior is
the same.
--JRM
Nicolas Vervelle [EMAIL PROTECTED]
23-Mar-2007 15:33
To
jmol-users@lists.sourceforge.net
cc
[EMAIL PROTECTED]
Subject
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on
live page
Hi,
Since several months, I have a lot of work and didn't get the courage of
working again on the Jmol extension.
I think a simple fix should be the following : in function
onParserAfterStrip(), try replacing the if ($this-mJmolTagPresent ==
true) { line by if (true) {.
Tell me if it works ...
Nico
[EMAIL PROTECTED] wrote:
Hi folks. I support a small internal wiki for group use within my
company. Recently a chemist inquired about embedding Jmol within a
wiki page, and I found the Jmol MediaWiki extension:
http://wiki.jmol.org:81/index.php/MediaWiki
I installed the extension according to the instructions and found
that, while I can get the Jmol applet to display properly in the
wiki's Show Preview mode while editing the page, viewing the live
page gets no applet at all. It seems the Javacript lines to include
Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being
included in the live page. This is with Jmol 11.0.1 and MediaWiki
1.7.1. I think my problem is similar to Kevin Murphy's situation,
posted here on 2007-01-23:
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html
I couldn't find a resolution in the list archive. Is this a problem
within the Jmol extension, or MediaWiki itself? I'd appreciate any
suggestions and am willing to test tweaks to the extension. Thanks,
--JRM
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Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
If you can easily test modifications, I can try to help you with ideas
to make the extension working.
I have some problems with understanding the internal workings of
MediaWiki, and this part is really difficult (finding how to include
the links to Jmol _javascript_ files only once per page, and only if the
page is really using the Jmol extension).
To easily test on my side, I need to setup a wiki on my computer rather
than using Jmol wiki, and it requires some time.
An other idea to make it work is to use the BeforePageDisplay hook.
Try the following :
- like the onParserAfterScript() function, create a
onBeforePageDisplay() function with the same content, using the
modified version of the "if".
- in the wfJmolExtension() function, comment out the
"$wgHooks['ParserAfterStrip'][] = $wgJmolExtension;" line and add a new
line "$wgHooks['BeforePageDisplay'][] = $wgJmolExtension;" line
Tell me if you have better result
It may require purging the page to have the modification taken into
account (use the purge action: go into edit mode, and replace edit by
purge in the URL).
Nico
[EMAIL PROTECTED] wrote:
Hi Nico. Changed line 576 as you
suggested,
but no joy -- the behavior is the same.
--JRM
Hi,
Since several months, I have a lot of work and didn't get the courage
of
working again on the Jmol extension.
I think a simple fix should be the following : in function
onParserAfterStrip(), try replacing the "if ($this-mJmolTagPresent
==
true) {" line by "if (true) {".
Tell me if it works ...
Nico
[EMAIL PROTECTED] wrote:
Hi folks. I support a small internal wiki for group use within
my
company. Recently a chemist inquired about embedding Jmol within
a
wiki page, and I found the Jmol MediaWiki extension:
http://wiki.jmol.org:81/index.php/MediaWiki
I installed the extension according to the instructions and found
that, while I can get the Jmol applet to display properly in the
wiki's "Show Preview" mode while editing the page, viewing
the live
page gets no applet at all. It seems the Javacript lines to
include
Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not
being
included in the live page. This is with Jmol 11.0.1 and MediaWiki
1.7.1. I think my problem is similar to Kevin Murphy's situation,
posted here on 2007-01-23:
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html
I couldn't find a resolution in the list archive. Is this a
problem
within the Jmol extension, or MediaWiki itself? I'd appreciate
any
suggestions and am willing to test tweaks to the extension.
Thanks,
--JRM
-
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Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Okay, so the resulting diff on JmolExtension.php is as follows. No
change, aside from PHP complaining about not having a second argument to
pass to onBeforePageDisplay().
Incidentally I do have $wgAllowUserCss = true and $wgAllowUserJs = true in
MediaWiki's LocalSettings.php to encourage the wiki not to strip out any
contributed JavaScript or CSS, though I'd think the wiki would consider
code coming from an extension as being non-user in origin.
--JRM
586a587,601
// Experimental callback called before display
function onBeforePageDisplay($parser, $text, $x) {
global $wgJmolExtensionPath,$wgOut;
if (true) {
$this-includeScript($wgOut, $wgJmolExtensionPath./Jmol.js);
$this-includeScript($wgOut,
$wgJmolExtensionPath./JmolMediaWiki.js);
if ($this-mValSigned) {
$this-addScript($wgOut,
jmolInitialize('.$wgJmolExtensionPath.', true););
} else {
$this-addScript($wgOut,
jmolInitialize('.$wgJmolExtensionPath.', false););
}
}
$this-mJmolTagPresent = false;
}
606c621,622
$wgHooks['ParserAfterStrip'][] = $wgJmolExtension;
---
// $wgHooks['ParserAfterStrip'][] = $wgJmolExtension;
$wgHooks['BeforePageDisplay'][] = $wgJmolExtension;
Nicolas Vervelle [EMAIL PROTECTED]
23-Mar-2007 16:34
To
jmol-users@lists.sourceforge.net
cc
[EMAIL PROTECTED]
Subject
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on
live page
If you can easily test modifications, I can try to help you with ideas to
make the extension working.
I have some problems with understanding the internal workings of
MediaWiki, and this part is really difficult (finding how to include the
links to Jmol javascript files only once per page, and only if the page is
really using the Jmol extension).
To easily test on my side, I need to setup a wiki on my computer rather
than using Jmol wiki, and it requires some time.
An other idea to make it work is to use the BeforePageDisplay hook.
Try the following :
- like the onParserAfterScript() function, create a onBeforePageDisplay()
function with the same content, using the modified version of the if.
- in the wfJmolExtension() function, comment out the
$wgHooks['ParserAfterStrip'][] = $wgJmolExtension; line and add a new
line $wgHooks['BeforePageDisplay'][] = $wgJmolExtension; line
Tell me if you have better result
It may require purging the page to have the modification taken into
account (use the purge action: go into edit mode, and replace edit by
purge in the URL).
Nico
[EMAIL PROTECTED] wrote:
Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior is
the same.
--JRM
Hi,
Since several months, I have a lot of work and didn't get the courage of
working again on the Jmol extension.
I think a simple fix should be the following : in function
onParserAfterStrip(), try replacing the if ($this-mJmolTagPresent ==
true) { line by if (true) {.
Tell me if it works ...
Nico
[EMAIL PROTECTED] wrote:
Hi folks. I support a small internal wiki for group use within my
company. Recently a chemist inquired about embedding Jmol within a
wiki page, and I found the Jmol MediaWiki extension:
http://wiki.jmol.org:81/index.php/MediaWiki
I installed the extension according to the instructions and found
that, while I can get the Jmol applet to display properly in the
wiki's Show Preview mode while editing the page, viewing the live
page gets no applet at all. It seems the Javacript lines to include
Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being
included in the live page. This is with Jmol 11.0.1 and MediaWiki
1.7.1. I think my problem is similar to Kevin Murphy's situation,
posted here on 2007-01-23:
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html
I couldn't find a resolution in the list archive. Is this a problem
within the Jmol extension, or MediaWiki itself? I'd appreciate any
suggestions and am willing to test tweaks to the extension. Thanks,
--JRM
-
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Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
I have managed to set up a local wiki for testing.
Here's what I see :
- in edit mode: ok
- in normal mode: nok
- in purge mode (replace edit by purge in the edit mode URL): ok
I am going to try to find help on the Mediawiki irc channel
Nico
[EMAIL PROTECTED] wrote:
Okay, so the resulting diff on
JmolExtension.php
is as follows. No change, aside from PHP complaining about not having
a second argument to pass to onBeforePageDisplay().
Incidentally I do have $wgAllowUserCss =
true and $wgAllowUserJs = true in MediaWiki's LocalSettings.php to
encourage
the wiki not to strip out any contributed _javascript_ or CSS, though I'd
think the wiki would consider code coming from an extension as being
non-user
in origin.
--JRM
586a587,601
// Experimental callback called
before display
function
onBeforePageDisplay($parser,
$text, $x) {
global
$wgJmolExtensionPath,$wgOut;
if (true) {
$this-includeScript($wgOut,
$wgJmolExtensionPath."/Jmol.js");
$this-includeScript($wgOut,
$wgJmolExtensionPath."/JmolMediaWiki.js");
if ($this-mValSigned)
{
$this-addScript($wgOut,
"jmolInitialize('".$wgJmolExtensionPath."', true);");
} else {
$this-addScript($wgOut,
"jmolInitialize('".$wgJmolExtensionPath."', false);");
}
}
$this-mJmolTagPresent
= false;
}
606c621,622
$wgHooks['ParserAfterStrip'][]
= $wgJmolExtension;
---
//
$wgHooks['ParserAfterStrip'][]
= $wgJmolExtension;
$wgHooks['BeforePageDisplay'][]
= $wgJmolExtension;
"Nicolas
Vervelle"
[EMAIL PROTECTED]
23-Mar-2007 16:34
To
jmol-users@lists.sourceforge.net
cc
[EMAIL PROTECTED]
Subject
Re: [Jmol-users]
Jmol MediaWiki extension,
works in preview but not on live page
If you can easily test modifications, I can try to
help
you with ideas to make the extension working.
I have some problems with understanding the internal workings of
MediaWiki,
and this part is really difficult (finding how to include the links to
Jmol _javascript_ files only once per page, and only if the page is
really
using the Jmol extension).
To easily test on my side, I need to setup a wiki on my computer rather
than using Jmol wiki, and it requires some time.
An other idea to make it work is to use the BeforePageDisplay hook.
Try the following :
- like the onParserAfterScript() function, create a
onBeforePageDisplay()
function with the same content, using the modified version of the "if".
- in the wfJmolExtension() function, comment out the
"$wgHooks['ParserAfterStrip'][]
= $wgJmolExtension;" line and add a new line
"$wgHooks['BeforePageDisplay'][]
= $wgJmolExtension;" line
Tell me if you have better result
It may require purging the page to have the modification taken into
account
(use the purge action: go into edit mode, and replace edit by purge in
the URL).
Nico
[EMAIL PROTECTED]
wrote:
Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior
is the same.
--JRM
Hi,
Since several months, I have a lot of work and didn't get the courage
of
working again on the Jmol extension.
I think a simple fix should be the following : in function
onParserAfterStrip(), try replacing the "if ($this-mJmolTagPresent
==
true) {" line by "if (true) {".
Tell me if it works ...
Nico
[EMAIL PROTECTED]
wrote:
Hi folks. I support a small internal wiki for group use within
my
company. Recently a chemist inquired about embedding Jmol within
a
wiki page, and I found the Jmol MediaWiki extension:
http://wiki.jmol.org:81/index.php/MediaWiki
I installed the extension according to the instructions and found
that, while I can get the Jmol applet to display properly in the
wiki's "Show Preview" mode while editing the page, viewing
the live
page gets no applet at all. It seems the Javacript lines to
include
Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not
being
included in the live page. This is with Jmol 11.0.1 and MediaWiki
1.7.1. I think my problem is similar to Kevin Murphy's situation,
posted here on 2007-01-23:
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html
I couldn't find a resolutio
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Nicolas Vervelle wrote:
If you can easily test modifications, I can try to help you with ideas
to make the extension working.
I have some problems with understanding the internal workings of
MediaWiki, and this part is really difficult (finding how to include
the links to Jmol javascript files only once per page, and only if the
page is really using the Jmol extension).
Nico -- note that now with the automatic initialization, in the
MediaWiki business you would not do the initialization at all, and that
at least takes care of the problem that you might have 0 or multiple
initializations.
To easily test on my side, I need to setup a wiki on my computer
rather than using Jmol wiki, and it requires some time.
An other idea to make it work is to use the BeforePageDisplay hook.
Try the following :
- like the onParserAfterScript() function, create a
onBeforePageDisplay() function with the same content, using the
modified version of the if.
- in the wfJmolExtension() function, comment out the
$wgHooks['ParserAfterStrip'][] = $wgJmolExtension; line and add a
new line $wgHooks['BeforePageDisplay'][] = $wgJmolExtension; line
Tell me if you have better result
It may require purging the page to have the modification taken into
account (use the purge action: go into edit mode, and replace edit by
purge in the URL).
Nico
[EMAIL PROTECTED] wrote:
Hi Nico. Changed line 576 as you suggested, but no joy -- the
behavior is the same.
--JRM
Hi,
Since several months, I have a lot of work and didn't get the courage of
working again on the Jmol extension.
I think a simple fix should be the following : in function
onParserAfterStrip(), try replacing the if ($this-mJmolTagPresent ==
true) { line by if (true) {.
Tell me if it works ...
Nico
[EMAIL PROTECTED] wrote:
Hi folks. I support a small internal wiki for group use within my
company. Recently a chemist inquired about embedding Jmol within a
wiki page, and I found the Jmol MediaWiki extension:
http://wiki.jmol.org:81/index.php/MediaWiki
I installed the extension according to the instructions and found
that, while I can get the Jmol applet to display properly in the
wiki's Show Preview mode while editing the page, viewing the live
page gets no applet at all. It seems the Javacript lines to include
Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being
included in the live page. This is with Jmol 11.0.1 and MediaWiki
1.7.1. I think my problem is similar to Kevin Murphy's situation,
posted here on 2007-01-23:
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html
I couldn't find a resolution in the list archive. Is this a problem
within the Jmol extension, or MediaWiki itself? I'd appreciate any
suggestions and am willing to test tweaks to the extension. Thanks,
--JRM
-
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Take
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Regarding updating the argument list for onBeforePageDisplay() to be just $out -- PHP was satisfied but otherwise no change. Regarding your tests -- sorry I didn't include mention of purge tests from my end. But yes, our results matched: edit/preview ok, normal/live nok, purge ok. Now regarding your latest suggestion regarding disableCache() in wfJmolRender(), it's no dice on my end. I tried it together with our earlier edits up to and including above, and then I tried inserting the $wgParser-disableCache(); statement into a stock JmolExtension.php -- the results were the same (live nok). That includes Firefox 2.0.0.3 and IE7 with empty local caches, and after using the purge mode to clear MediaWiki's cache. Touching or otherwise updating MediaWiki's LocalSettings.php also forces MediaWiki to clear its cache, and I did so -- still nok on the live page. I was beginning to think this was a cache issue within MediaWiki and we could work around it with suitable tweaks to LocalSettings.php, now I don't know. All the test pages on wiki.jmol.org do work for me -- I think before today only the uploaded XYZ example worked properly, now all three upload examples work, as does the Inlined CML File example. FYI, I'm heading home for the day and won't be able to revisit this until Monday. Thanks for your attention and suggestions today, --JRM Nicolas Vervelle [EMAIL PROTECTED] 23-Mar-2007 19:06 To jmol-users@lists.sourceforge.net cc [EMAIL PROTECTED], [EMAIL PROTECTED] Subject Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page Bob Hanson wrote: Nicolas Vervelle wrote: If you can easily test modifications, I can try to help you with ideas to make the extension working. I have some problems with understanding the internal workings of MediaWiki, and this part is really difficult (finding how to include the links to Jmol javascript files only once per page, and only if the page is really using the Jmol extension). Nico -- note that now with the automatic initialization, in the MediaWiki business you would not do the initialization at all, and that at least takes care of the problem that you might have 0 or multiple initializations. Ok, that could help but I am also trying to include Jmol.js only once by putting the script tag in the header. This is rather difficult to understand how MediaWiki works. I got an answer from mediawiki irc channel, seems to work better. Joseph, can you try the following modification (it seems to work for me) ? in the wfJmolRender() function, try adding $wgParser-disableCache(); as the second line in the function I have added this modification to Jmol wiki and it seems to work. Any tester to check that it works on different platforms ? Nico - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
