Re: [Jmol-users] Jmol extension for Mediawiki
Then it would be wise to pass this by the Wikipedia Team to see how they feel about it. If there's no JavaScript, that pretty much excludes JSmol. On Tue, Apr 23, 2013 at 2:39 PM, Herráez Sánchez Ángel angel.herr...@uah.es wrote: - Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? Time ago, one of the objections to include Jmol in Wikipedia was that arbitrary Javascript should not be allowed to execute from within a malicious Jmol Script. A flag was implemented to block javascript calls within Jmol scripts (and it is enabled by default, or may be enforced, in the Jmol MediaWiki Extension). Yes, it sounds funny now, but still there may be a basis for it. Don't know... -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Hi, I don't think they would have trouble with the requirement for JavaScript (if we can still have a still image when JavaScript is disabled). It seems less constraining that having Java... There's a lot of extensions, tools, gadgets, ... in MediaWiki that requires users to have JavaScript enabled. Nico On Wed, Apr 24, 2013 at 4:25 PM, Robert Hanson hans...@stolaf.edu wrote: Then it would be wise to pass this by the Wikipedia Team to see how they feel about it. If there's no JavaScript, that pretty much excludes JSmol. On Tue, Apr 23, 2013 at 2:39 PM, Herráez Sánchez Ángel angel.herr...@uah.es wrote: - Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? Time ago, one of the objections to include Jmol in Wikipedia was that arbitrary Javascript should not be allowed to execute from within a malicious Jmol Script. A flag was implemented to block javascript calls within Jmol scripts (and it is enabled by default, or may be enforced, in the Jmol MediaWiki Extension). Yes, it sounds funny now, but still there may be a basis for it. Don't know... -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol extension for Mediawiki
Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? - Switching between Jmol and JSmol depending on the browser capabilities - Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it - Opening Jmol in a new window, that would be scalable - Disabling javascript in Jmol script - ... - anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? * Switching between Jmol and JSmol depending on the browser capabilities * Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it * Opening Jmol in a new window, that would be scalable * Disabling javascript in Jmol script * ... * anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
What I've learned... On Tue, Apr 23, 2013 at 10:13 AM, Nicolas Vervelle nverve...@gmail.comwrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? - Switching between Jmol and JSmol depending on the browser capabilities Doesn't work from a page-side perspective. You can't detect if Java is available any more, and when it is, the page holds until it is functional. So that's a real problem. From the server, you can certainly find out if it is mobile or not, and guess that only HTML5 will work. WebGL development is still minimal -- doesn't seem to be a future in that for the iPad; only minimally supported in JSmol. There's an image only option that I thought might allow the server to create the view and send it, but that turns out to require too much dead time waiting for the server to process the script. The only clear autoswitching that works from the page is If no HTML5, use Java for older browsers. - Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it That's all set. It's a couple of flags in the Info block. This does work well. - Opening Jmol in a new window, that would be scalable All set, but not built in. I know someone was doing this. - Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? - ... - anything you can think of Basically JSmol is precisely the same as Jmol, just all in JavaScript. Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
- Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? Time ago, one of the objections to include Jmol in Wikipedia was that arbitrary Javascript should not be allowed to execute from within a malicious Jmol Script. A flag was implemented to block javascript calls within Jmol scripts (and it is enabled by default, or may be enforced, in the Jmol MediaWiki Extension). Yes, it sounds funny now, but still there may be a basis for it. Don't know... winmail.dat-- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
On Tue, Apr 23, 2013 at 9:39 PM, Herráez Sánchez Ángel angel.herr...@uah.es wrote: - Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? Time ago, one of the objections to include Jmol in Wikipedia was that arbitrary Javascript should not be allowed to execute from within a malicious Jmol Script. A flag was implemented to block javascript calls within Jmol scripts (and it is enabled by default, or may be enforced, in the Jmol MediaWiki Extension). Yes, it sounds funny now, but still there may be a basis for it. Don't know... Yes, that's what I meant by disabling javascript in Jmol script. I think it would still be an objection to include Jmol in a wiki if arbitrary Javascript could be executed through Jmol script. Since every user would be able to create the Jmol script, it should be safe for others to view it. Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Hi Jaime, Good to hear that you have kept working on this That would be great to have this packaged :) Is there anything I can do to help ? If I can, I would like to try to go the Wikimedia hackathon[1] at the end of May in Amsterdam to discuss about what should be done to the extension to have it integrated in wikipedia. But I'm not sure I will be in Europe at this time. I think that security is an important issue to cope with if you want a slight chance of seeing Jmol used. Nico [1] http://www.mediawiki.org/wiki/Amsterdam_Hackathon_2013 On Tue, Apr 23, 2013 at 5:36 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? - Switching between Jmol and JSmol depending on the browser capabilities - Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it - Opening Jmol in a new window, that would be scalable - Disabling javascript in Jmol script - ... - anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Thank you for offering your help. Your expertise on Jmol extension will certainly become very handy. Regarding Wikipedia: Joel Sussman and myself took part of Wikimania 2011, and had the opportunity to meet and discuss with key MediaWiki developers and Wikipedia leaders. They got inside information on Proteopedia, it's integration with Jmol, and understood that Jmol never caused problems to Proteopedia. We offered our help and Proteopedia code. No progress after that. All this considering a Java based Jmol. I assume that today they might be more reluctant to using a Javascript centered JSmol. Still, we are willing to share our experience with Jmol/JSmol over MediaWiki in Proteopedia in case they changed their mind. Jaim On Apr 24, 2013, at 12:47 AM, Nicolas Vervelle wrote: Hi Jaime, Good to hear that you have kept working on this That would be great to have this packaged :) Is there anything I can do to help ? If I can, I would like to try to go the Wikimedia hackathon[1] at the end of May in Amsterdam to discuss about what should be done to the extension to have it integrated in wikipedia. But I'm not sure I will be in Europe at this time. I think that security is an important issue to cope with if you want a slight chance of seeing Jmol used. Nico [1] http://www.mediawiki.org/wiki/Amsterdam_Hackathon_2013 On Tue, Apr 23, 2013 at 5:36 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.ilhttp://oca.weizmann.ac.il/ (the protein structure/function database) Proteopedia, http://proteopedia.orghttp://proteopedia.org/ (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? * Switching between Jmol and JSmol depending on the browser capabilities * Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it * Opening Jmol in a new window, that would be scalable * Disabling javascript in Jmol script * ... * anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol extension for Mediawiki
Xavier Prat-Resina a écrit : Jmol people, does anyone know the current status of the jmol extension for Mediawiki? The Jmol extension I downloaded from the svn server is using an external Mediawiki extension called StubManager which is not mentioned in the installation instructions http://wiki.jmol.org:81/index.php/MediaWiki#Installation StubManager can be downloaded from here, so no problem http://jldupont.com/Extension:StubManager (even though the name of the extension doesn't seem to be used for something very stable :) ) I forgot to update the documentation for this one. The documentation and links for it can be found at http://www.mediawiki.org/wiki/Extension:StubManager It also explains the name ;) In addition, I think that the file Jmol.body.php needs to be modified for every Mediawiki installation, since the variable $wgJmolExtensionPath can change. No, Jmol.body.php shouldn't be modified. It's explained in http://wiki.jmol.org:81/index.php/MediaWiki#Installation You can configure the Jmol extension with several _*settings added after the above line*_ $wgJmolExtensionPath can be changed in LocalSettings.php Now it's working for me but I just wanted to know, before I update the documentation myself, if there is anyone working on that. Thanks I haven't worked on it for quite some time and haven't much time and less motivation. Feel free to update the documentation. Nico - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
