From: Nicolas V. <nve...@cl...> - 2006-04-26 20:26:59
|
Hi everyone, I have finished a first version of a fully functional version of a MediaWiki extension to add Jmol applets in MediaWiki wikis (like the well-known Wikipedia). Check the full description : http://wiki.jmol.org/index.php/MediaWiki and a simple example page: http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension Comments are welcome :) Nico |
From: Egon W. <ewi...@un...> - 2006-04-26 21:37:44
|
On Wednesday 26 April 2006 22:26, Nicolas Vervelle wrote: > I have finished a first version of a fully functional version of a > MediaWiki extension to add Jmol applets in MediaWiki wikis (like the > well-known Wikipedia). Looks good! Anyone who knows where to start lobbying to get this included in WikiPedia? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Brian Salter-D. <b_...@oc...> - 2006-04-26 23:52:50
|
On Wed, Apr 26, 2006 at 11:37:51PM +0200, Egon Willighagen wrote: > On Wednesday 26 April 2006 22:26, Nicolas Vervelle wrote: > > I have finished a first version of a fully functional version of a > > MediaWiki extension to add Jmol applets in MediaWiki wikis (like the > > well-known Wikipedia). > > Looks good! > > Anyone who knows where to start lobbying to get this included in WikiPedia? I have been discussing this with one of the senior Wikipedia developers but waiting until Nico had completed his extension. I will follow up on this today. I have only just seen the news this morning here in Australia. See:- http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_models and its talk page, where is information from Nico and others. I hope we can get a trial on Wikipedia soon. Cheers, Brian. > Egon > > -- > CUBIC > blog: http://chem-bla-ics.blogspot.com/ > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Brian Salter-Duke (Brian Duke) b_...@oc... Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. |
From: Bob H. <ha...@st...> - 2006-04-26 22:09:54
|
fascinating! Comments: 1. I suggest <onlineContents> be <inlineContents> 2. <size> : Size of the applet. Does that mean it's always square? 3. Two valuable options we should probably consider building into Jmol for this sort of public use might be: a) allowPopUpConsole b) allowShowFile realizing that a wiki may involve somewhat more control over the environment than a web site. Personally I've never been too thrilled with "show file" and its ability to deliver into the user's hands any file on the system. 4. One could imagine a system-wide defaultScript option. Nicolas Vervelle wrote: > Hi everyone, > > I have finished a first version of a fully functional version of a > MediaWiki extension to add Jmol applets in MediaWiki wikis (like the > well-known Wikipedia). > > Check the full description : > http://wiki.jmol.org/index.php/MediaWiki > > and a simple example page: > http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension > > > Comments are welcome :) > > Nico > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |
From: Nicolas V. <nve...@cl...> - 2006-04-27 04:31:32
|
Bob Hanson wrote: > fascinating! Comments: > > 1. I suggest > > <onlineContents> > > be > > <inlineContents> Ok > > 2. <size> : Size of the applet. Does that mean it's always square? Currently, yes. But that would be a thing to add. > > 3. Two valuable options we should probably consider building into Jmol > for this sort of public use might be: > > a) allowPopUpConsole > b) allowShowFile > > realizing that a wiki may involve somewhat more control over the > environment than a web site. Personally I've never been too thrilled > with "show file" and its ability to deliver into the user's hands any > file on the system. I am not sure about this: wikis are designed to be open, so even the files that are put there are openly accessible and can be changed by users. > > 4. One could imagine a system-wide defaultScript option. Yes Thanks for the ideas, Nico |
From: Nicolas V. <nve...@cl...> - 2006-04-27 16:31:41
|
Nicolas Vervelle wrote: > > > Bob Hanson wrote: >> fascinating! Comments: >> >> 1. I suggest >> >> <onlineContents> >> >> be >> >> <inlineContents> > Ok Done > >> >> 2. <size> : Size of the applet. Does that mean it's always square? > Currently, yes. But that would be a thing to add. Added in the TODO list >> >> 3. Two valuable options we should probably consider building into >> Jmol for this sort of public use might be: >> >> a) allowPopUpConsole >> b) allowShowFile >> >> realizing that a wiki may involve somewhat more control over the >> environment than a web site. Personally I've never been too thrilled >> with "show file" and its ability to deliver into the user's hands any >> file on the system. > I am not sure about this: wikis are designed to be open, so even the > files that are put there are openly accessible and can be changed by > users. > >> >> 4. One could imagine a system-wide defaultScript option. > Yes Done Nico |
From: Bob H. <ha...@st...> - 2006-04-26 22:25:55
|
Nico, you need a random number in that "windowTitle" variable. This is necessary because one needs to make sure that the window really DOES pop up -- if the user has hidden a previously popped up window and then press the button again (currently), then "nothing" (visible) happens. Actually, I think the window is loaded, but it doesn't come forward. So the classic solution to this is to assign a unique number in that second parameter of open(). Bob Nicolas Vervelle wrote: > Hi everyone, > > I have finished a first version of a fully functional version of a > MediaWiki extension to add Jmol applets in MediaWiki wikis (like the > well-known Wikipedia). > > Check the full description : > http://wiki.jmol.org/index.php/MediaWiki > > and a simple example page: > http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension > > > Comments are welcome :) > > Nico > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |
From: Nicolas V. <nve...@cl...> - 2006-04-27 04:15:50
|
Bob Hanson wrote: > Nico, you need a random number in that "windowTitle" variable. This is > necessary because one needs to make sure that the window really DOES > pop up -- if the user has hidden a previously popped up window and > then press the button again (currently), then "nothing" (visible) > happens. Actually, I think the window is loaded, but it doesn't come > forward. So the classic solution to this is to assign a unique number > in that second parameter of open(). Ok, I will add it this evening. Thanks > > Bob > > > Nicolas Vervelle wrote: > >> Hi everyone, >> >> I have finished a first version of a fully functional version of a >> MediaWiki extension to add Jmol applets in MediaWiki wikis (like the >> well-known Wikipedia). >> >> Check the full description : >> http://wiki.jmol.org/index.php/MediaWiki >> >> and a simple example page: >> http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension >> >> >> Comments are welcome :) >> >> Nico >> >> >> >> ------------------------------------------------------- >> Using Tomcat but need to do more? Need to support web services, >> security? >> Get stuff done quickly with pre-integrated technology to make your >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache >> Geronimo >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Angel H. <ang...@ua...> - 2006-04-27 10:47:21
|
El 26 Apr 2006 a las 17:25, Bob Hanson escribi=F3: > Nico, you need a random number in that "windowTitle" variable. [..snip..] > So the classic solution to this is to assign a unique number > in that second parameter of open(). Another choice is to bring tha pop-up window to the front (with the new content). This is done in javascript by popWin =3D window.open(....) popWin.focus() easy enough to implement in the Wiki extension, I guess. One or the other is better depending on the users' expertise and intentions. I find that most naive users get confused about new windows, so fewer would be better. And El 26 Apr 2006 a las 17:09, Bob Hanson escribi=F3: > 3. Two valuable options we should probably consider building into Jmol > for this sort of public use might be: > > a) allowPopUpConsole > b) allowShowFile We already have set DisablePopupMenu set HideNameInPopup The latter will probably also block file downloading, right? So, for consistency, the only need to be added could be: set DisablePopupConsole or just set DisableConsole Oh, I see Bob's ShowFile may be something different, "show file" as a script? But this is not available to the page user, or is it? |
From: Bob H. <ha...@st...> - 2006-04-27 11:23:54
|
Be aware that not all browsers support .focus(). I haven't looked at=20 this in a while, and maybe that's just "legacy browser" thinking. But=20 it's something to worry about. See http://www.quirksmode.org/js/support.html#focus The following quote from that site is a bit dated, so perhaps there is=20 no longer an issue: <quote> *Hotjava 3* has buggy support. The example on this page works, but=20 others on this site don't. I have no idea what the problem is. *Netscape 4 on Linux* does support it, but when you lay the focus on=20 something that's not currently on the screen, the page does not scroll=20 to show the element you laid the focus on. This is very confusing. *Opera 3 and 4* refuse to lay the focus on another window when you're=20 cross-window JavaScripting <http://www.quirksmode.org/js/croswin.html>,=20 although in other circumstances it does support the focus. This is=20 solved in Opera 5, except on *Linux*. *Opera 5 on Mac* says it supports focus() but in fact does nothing. </quote> So I recommend doing some further checking before using .focus() on=20 something as public as a wiki method. Angel Herraez wrote: >El 26 Apr 2006 a las 17:25, Bob Hanson escribi=F3: > > =20 > >>Nico, you need a random number in that "windowTitle" variable.=20 >> =20 >> > [..snip..] > =20 > >>So the classic solution to this is to assign a unique number=20 >>in that second parameter of open(). >> =20 >> > >Another choice is to bring tha pop-up window to the front (with the=20 >new content). This is done in javascript by > popWin =3D window.open(....) > popWin.focus() >easy enough to implement in the Wiki extension, I guess. > >One or the other is better depending on the users' expertise and=20 >intentions. I find that most naive users get confused about new=20 >windows, so fewer would be better. > >And=20 >El 26 Apr 2006 a las 17:09, Bob Hanson escribi=F3: > =20 > >>3. Two valuable options we should probably consider building into Jmol=20 >>for this sort of public use might be: >> >>a) allowPopUpConsole >>b) allowShowFile >> =20 >> > >We already have=20 >set DisablePopupMenu >set HideNameInPopup > >The latter will probably also block file downloading, right? >So, for consistency, the only need to be added could be: > set DisablePopupConsole >or just > set DisableConsole > >Oh, I see Bob's ShowFile may be something different, "show file" as a=20 >script? But this is not available to the page user, or is it? > > > >------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security= ? >Get stuff done quickly with pre-integrated technology to make your job e= asier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geroni= mo >http://sel.as-us.falkag.net/sel?cmd_____________________________________= __________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > =20 > |
From: Rzepa, H. <h....@im...> - 2006-04-27 11:34:22
|
Could someone please explain how to achieve the following code result <uploadedFileContents>Ethanol.xyz</uploadedFileContents> When I try to upload a file, mediawiki tells me its not a recognised image file, and refuses it. I guess a setting has to be tweaked somewhere (perhaps even setting a chemical/x-xyz MIME type?) to allow this? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rz...@ma... (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). |
From: Bob H. <ha...@st...> - 2006-04-27 12:14:58
|
On second thought, I think this probably is a legacy issue, at least=20 with Windows. The following should probably be checked by a variety of=20 Mac users: http://www.stolaf.edu/people/hansonr/jmol/test/testfocus.htm Bob Hanson wrote: > Be aware that not all browsers support .focus(). I haven't looked at=20 > this in a while, and maybe that's just "legacy browser" thinking. But=20 > it's something to worry about. See > > http://www.quirksmode.org/js/support.html#focus > > The following quote from that site is a bit dated, so perhaps there is=20 > no longer an issue: > <quote> > > *Hotjava 3* has buggy support. The example on this page works, but=20 > others on this site don't. I have no idea what the problem is. > > *Netscape 4 on Linux* does support it, but when you lay the focus on=20 > something that's not currently on the screen, the page does not scroll=20 > to show the element you laid the focus on. This is very confusing. > > *Opera 3 and 4* refuse to lay the focus on another window when you're=20 > cross-window JavaScripting=20 > <http://www.quirksmode.org/js/croswin.html>, although in other=20 > circumstances it does support the focus. This is solved in Opera 5,=20 > except on *Linux*. > > *Opera 5 on Mac* says it supports focus() but in fact does nothing. > </quote> > > So I recommend doing some further checking before using .focus() on=20 > something as public as a wiki method. > > > > > > Angel Herraez wrote: > >> El 26 Apr 2006 a las 17:25, Bob Hanson escribi=F3: >> >> =20 >> >>> Nico, you need a random number in that "windowTitle" variable. =20 >> >> [..snip..] >> =20 >> >>> So the classic solution to this is to assign a unique number in that=20 >>> second parameter of open(). >>> =20 >> >> >> Another choice is to bring tha pop-up window to the front (with the=20 >> new content). This is done in javascript by >> popWin =3D window.open(....) >> popWin.focus() >> easy enough to implement in the Wiki extension, I guess. >> >> One or the other is better depending on the users' expertise and=20 >> intentions. I find that most naive users get confused about new=20 >> windows, so fewer would be better. >> >> And El 26 Apr 2006 a las 17:09, Bob Hanson escribi=F3: >> =20 >> >>> 3. Two valuable options we should probably consider building into=20 >>> Jmol for this sort of public use might be: >>> >>> a) allowPopUpConsole >>> b) allowShowFile >>> =20 >> >> >> We already have set DisablePopupMenu >> set HideNameInPopup >> >> The latter will probably also block file downloading, right? >> So, for consistency, the only need to be added could be: >> set DisablePopupConsole >> or just >> set DisableConsole >> >> Oh, I see Bob's ShowFile may be something different, "show file" as a=20 >> script? But this is not available to the page user, or is it? >> >> >> >> ------------------------------------------------------- >> Using Tomcat but need to do more? Need to support web services,=20 >> security? >> Get stuff done quickly with pre-integrated technology to make your=20 >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache=20 >> Geronimo >> http://sel.as-us.falkag.net/sel?cmd___________________________________= ____________=20 >> >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> =20 >> > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, securit= y? > Get stuff done quickly with pre-integrated technology to make your job=20 > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache=20 > Geronimo > http://sel.as-us.falkag.net/sel?cmd____________________________________= ___________=20 > > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Frieda R. <fr...@ns...> - 2006-04-27 14:57:56
|
On Apr 27, 2006, at 8:15 AM, Bob Hanson wrote: > On second thought, I think this probably is a legacy issue, at > least with Windows. The following should probably be checked by a > variety of Mac users: > > http://www.stolaf.edu/people/hansonr/jmol/test/testfocus.htm Works perfectly for me in Safari 2 and Firefox 1.5 on OSX 10.4.6. Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Nicolas V. <nve...@cl...> - 2006-04-27 16:19:31
|
Bob Hanson wrote: > On second thought, I think this probably is a legacy issue, at least > with Windows. The following should probably be checked by a variety of > Mac users: > > http://www.stolaf.edu/people/hansonr/jmol/test/testfocus.htm Thanks for the test page. I will wait a little to see if people report problems with your test page. If no problem, I will use the focus approach for the wiki. Nico |
From: Nicolas V. <nve...@cl...> - 2006-05-08 10:01:49
|
Nicolas Vervelle wrote: > > > Bob Hanson wrote: >> On second thought, I think this probably is a legacy issue, at least >> with Windows. The following should probably be checked by a variety >> of Mac users: >> >> http://www.stolaf.edu/people/hansonr/jmol/test/testfocus.htm > > Thanks for the test page. > > I will wait a little to see if people report problems with your test > page. > If no problem, I will use the focus approach for the wiki. > No reports of problems, so I have just added the focus() call in the extension Nico |
From: Angel H. <ang...@ua...> - 2006-04-27 14:38:47
|
El 27 Apr 2006 a las 6:24, Bob Hanson escribi=F3: > Be aware that not all browsers support .focus(). I haven't looked at [..snip..] > *Hotjava 3* has buggy support. The example on this page works, but > *Netscape 4 on Linux* does support it, but when you lay the focus on > *Opera 3 and 4* refuse to lay the focus on another window when you're The note of caution is good. I have always defended that cross- browser compatibility is a priority. But I seriously doubt that 1) Anyone is still using those browsers 2) Those browsers would have the support to even **show** the Wiki pages and/or to run Java. My Netscape 4.7 (Win) crashed when I tried to enter the test page for Jmol extension in MediaWiki. > So I recommend doing some further checking before using .focus() on > something as public as a wiki method. A good advice anyway. Do you think we will find users with those specs? |
From: Bob H. <ha...@st...> - 2006-04-27 16:52:25
|
I think it's probably a dead issue. Angel Herraez wrote: > El 27 Apr 2006 a las 6:24, Bob Hanson escribi=F3: >=20 >>Be aware that not all browsers support .focus(). I haven't looked at=20 >=20 > [..snip..] >=20 >>*Hotjava 3* has buggy support. The example on this page works, but=20 >>*Netscape 4 on Linux* does support it, but when you lay the focus on=20 >>*Opera 3 and 4* refuse to lay the focus on another window when you're=20 >=20 >=20 > The note of caution is good. I have always defended that cross- > browser compatibility is a priority. But I seriously doubt that >=20 > 1) Anyone is still using those browsers > 2) Those browsers would have the support to even **show** the Wiki=20 > pages and/or to run Java. >=20 > My Netscape 4.7 (Win) crashed when I tried to enter the test page for=20 > Jmol extension in MediaWiki. >=20 >=20 >>So I recommend doing some further checking before using .focus() on=20 >>something as public as a wiki method. >=20 >=20 > A good advice anyway. Do you think we will find users with those=20 > specs? >=20 >=20 >=20 >=20 > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, securit= y? > Get stuff done quickly with pre-integrated technology to make your job = easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geron= imo > http://sel.as-us.falkag.net/sel?cmd____________________________________= ___________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users --=20 Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |