From: Kilian B. <kil...@un...> - 2011-12-01 11:43:25
|
Nico, sorry for double posting. The OS is Ubuntu Server. And I cannot access the INSTALL file of the mediawiki itself, which is perfectly possible on the jmol wiki. There is something quite wrong here.,.. Best Kilian |
From: Kilian B. <kil...@un...> - 2011-12-01 12:05:27
|
Hi, Oh man.... I think i got it... Mediawiki on Ubuntu is split over three directories: /etc/mediawiki and /etc/mediawiki-extensions, /usr/share/mediawiki and /usr/share/mediawiki-extensions, /usr/share/mediawiki and /usr/share/mediawiki-extensions and /var/lib/mediawiki. Files are only directly accessibleis present or linked to the folders residing in var/lib. I linked the Jmol extension into /var/lib/mediawiki from /usr/share/mediawiki-extensions. Now it seems to work, at least the applet displays a molecule... So sorry for stealing you time that long. I really appreciate all your help. Best Kilian On 1 December 2011 12:43, Kilian Baerwinkel < kil...@un...> wrote: > Nico, > > sorry for double posting. The OS is Ubuntu Server. And I cannot access the > INSTALL file of the mediawiki itself, which is perfectly possible on the > jmol wiki. > There is something quite wrong here.,.. > > Best > > Kilian > > -- ______ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel: +49 921 55 - 4387 Fax: +49 921 55 - 2788 e-mail: kil...@un... http://www.senker.uni-bayreuth.de |
From: Nicolas V. <nve...@gm...> - 2011-12-01 12:54:44
|
No problem, Enjoy playing with the extension. I hope to be able to work on it again soon. Nico On Thu, Dec 1, 2011 at 1:05 PM, Kilian Baerwinkel < kil...@un...> wrote: > Hi, > > Oh man.... I think i got it... > > Mediawiki on Ubuntu is split over three directories: /etc/mediawiki and > /etc/mediawiki-extensions, /usr/share/mediawiki and > /usr/share/mediawiki-extensions, /usr/share/mediawiki and > /usr/share/mediawiki-extensions and /var/lib/mediawiki. > > Files are only directly accessibleis present or linked to the folders > residing in var/lib. > > I linked the Jmol extension into /var/lib/mediawiki from > /usr/share/mediawiki-extensions. > Now it seems to work, at least the applet displays a molecule... > > > So sorry for stealing you time that long. I really appreciate all your > help. > > Best > > Kilian > > > On 1 December 2011 12:43, Kilian Baerwinkel < > kil...@un...> wrote: > >> Nico, >> >> sorry for double posting. The OS is Ubuntu Server. And I cannot access >> the INSTALL file of the mediawiki itself, which is perfectly possible on >> the jmol wiki. >> There is something quite wrong here.,.. >> >> Best >> >> Kilian >> >> > > > -- > ______ > > MSc. Chem. Kilian Bärwinkel > > Lehrstuhl für Anorganische Chemie I > Fakultät NW 1 > Universität Bayreuth > Universitätsstr. 30 > 95447 Bayreuth > > Tel: +49 921 55 - 4387 > Fax: +49 921 55 - 2788 > > e-mail: kil...@un... > > http://www.senker.uni-bayreuth.de > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Rzepa, H. S <h....@im...> - 2012-03-01 13:35:26
|
On 1 Dec 2011, at 12:54, Nicolas Vervelle wrote: > No problem, > > Enjoy playing with the extension. > I hope to be able to work on it again soon. > The MediaWiki extension has the following form <jmol> <jmolApplet> <script>isosurface color orange purple isosurface.jvxl translucent;</script> <uploadedFileContents>isosurface.xyz;</uploadedFileContents> </jmolApplet> </jmol> Overall, this amounts to load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent; Because Jmol now separates the model (isosurface.xyz) from a second layer (the surface), two files need loading (older versions of Jmol supported one file containing both sets of data). So I need to load a file (the surface) using the script command. The above syntax however does not work (ie loading from a script is not supported?) Might Nico or someone tell us whether the above syntax is wrong, or whether the MediaWiki extension needs extending? |
From: Jaime P. <jai...@we...> - 2012-03-01 14:24:51
|
On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: The MediaWiki extension has the following form Overall, this amounts to load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent; If your command is "isosurface surfile.iso", I understand that you don't need to load the surfile.iso file in advance, but to provide the full path to the file (from the browser point of view), so the isosurface command can access and load the file, and render the content. Jaim |
From: Rzepa, H. S <h....@im...> - 2012-03-01 14:45:22
|
On 1 Mar 2012, at 14:24, Jaime Prilusky wrote: > On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: > The MediaWiki extension has the following form > Overall, this amounts to > > load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent; > Yes, putting the full filename path does work ( ie images/4/45/isosurface.jvxl ) but part of the reason for creating a Mediawiki extension was to hide such stuff from the user (our users are students, and bright though some of them are, others are bound to find locating the absolute path of a file a tad too much). |
From: Nicolas V. <nve...@gm...> - 2012-03-01 14:51:22
|
Ok, that confirms the explanation. Henry, Yes, the <uploadedFileContents> tag was designed to hide such complexity from the user (the call to Special:FilePath is done internally by the extension). But using this for scripts would be quite complex because the extension would have to parse the Jmol script... If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. I intend to work again on the extension some time in the future, still not sure when. Nico On Thu, Mar 1, 2012 at 3:45 PM, Rzepa, Henry S <h....@im...>wrote: > > On 1 Mar 2012, at 14:24, Jaime Prilusky wrote: > > > On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: > > The MediaWiki extension has the following form > > Overall, this amounts to > > > > load isosurface.xyz;isosurface color orange purple isosurface.jvxl > translucent; > > > > Yes, putting the full filename path does work ( ie > images/4/45/isosurface.jvxl ) but part of the reason for creating a > Mediawiki extension was to hide such stuff from the user (our users are > students, and bright though some of them are, others are bound to find > locating the absolute path of a file a tad too much). > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Jaime P. <jai...@we...> - 2012-03-01 15:09:27
|
On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple <isosurface> tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. Jaim -- Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: Jai...@we...<mailto:Jai...@we...> 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) |
From: Nicolas V. <nve...@gm...> - 2012-03-01 15:18:45
|
Hi, The extension doesn't manage the path in which files are stored. Depending on the configuration, MediaWiki stores them in several separate folders and there's no way to be sure that 2 files will end up in the same directory. Maybe we can group ideas/suggestions about the syntax for Jmol extension in the talk page of http://wiki.jmol.org/index.php/MediaWiki ? Nico On Thu, Mar 1, 2012 at 4:09 PM, Jaime Prilusky < jai...@we...> wrote: > On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: > If you have ideas of what syntax should be used in the extension to make > using it simple, don't hesitate. > > > If you keep the isosurface file together with the model file, then a > simple <isosurface> tag to indicate the name of the isosurface file (not > the full path) can be used to setup the internal default file path to the > location of the model file, and call the load. > > > Jaim > -- > Dr Jaime Prilusky > Head Bioinformatics > R&D Bioinformatics and Data Management > Department of Biological Services > Weizmann Institute of Science > 76100 Rehovot - Israel > > eml: Jai...@we... > 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) > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Rzepa, H. S <h....@im...> - 2012-03-01 15:51:58
|
On 1 Mar 2012, at 15:09, Jaime Prilusky wrote: > On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: > If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. > > > If you keep the isosurface file together with the model file, then a simple <isosurface> tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. > early versions of .jvxl used to include the coordinates as well as the surface, but (I might have mis-understood) the design nowadays is to keep these as separate files. If of course, it is still possible to write out a .jvxl file with both features, that would solve the immediate problem (but not the general one). |
From: Robert H. <ha...@st...> - 2012-03-01 16:15:37
|
Couldn't you have the <uploadedFileContents> also set the default directory? In face, one could imagine <uploadedFileContents></uploadedFileContents> might only set the default directory. On Thu, Mar 1, 2012 at 9:51 AM, Rzepa, Henry S <h....@im...>wrote: > > On 1 Mar 2012, at 15:09, Jaime Prilusky wrote: > > > On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: > > If you have ideas of what syntax should be used in the extension to make > using it simple, don't hesitate. > > > > > > If you keep the isosurface file together with the model file, then a > simple <isosurface> tag to indicate the name of the isosurface file (not > the full path) can be used to setup the internal default file path to the > location of the model file, and call the load. > > > > early versions of .jvxl used to include the coordinates as well as the > surface, but (I might have mis-understood) the design nowadays is to keep > these as separate files. If of course, it is still possible to write out a > .jvxl file with both features, that would solve the immediate problem (but > not the general one). > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Nicolas V. <nve...@gm...> - 2012-03-01 16:21:39
|
The problem is that, depending on MediaWiki configuration, uploaded files can end up in different directories (to avoid putting thousands of files in the same directory)... And the user has absolutely no control over which directory will be used for a file. So there's not really a possible default directory... For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while 1HPNmod.pdb is in images/4/49 Nico On Thu, Mar 1, 2012 at 5:15 PM, Robert Hanson <ha...@st...> wrote: > Couldn't you have the <uploadedFileContents> also set the default > directory? In face, one could imagine > > <uploadedFileContents></uploadedFileContents> > > might only set the default directory. > > > > On Thu, Mar 1, 2012 at 9:51 AM, Rzepa, Henry S <h....@im...>wrote: > >> >> On 1 Mar 2012, at 15:09, Jaime Prilusky wrote: >> >> > On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: >> > If you have ideas of what syntax should be used in the extension to >> make using it simple, don't hesitate. >> > >> > >> > If you keep the isosurface file together with the model file, then a >> simple <isosurface> tag to indicate the name of the isosurface file (not >> the full path) can be used to setup the internal default file path to the >> location of the model file, and call the load. >> > >> >> early versions of .jvxl used to include the coordinates as well as the >> surface, but (I might have mis-understood) the design nowadays is to keep >> these as separate files. If of course, it is still possible to write out a >> .jvxl file with both features, that would solve the immediate problem (but >> not the general one). >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Nicolas V. <nve...@gm...> - 2012-03-01 14:46:20
|
I think the path is a good lead. If you check the source of the generated wiki page, you should see a path for isosurface.xyz. You probably need to also have the path to isosurface.jvxl, but this is not always obvious which one to use (try Special:FilePath) Nico On Thu, Mar 1, 2012 at 3:24 PM, Jaime Prilusky < jai...@we...> wrote: > On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: > The MediaWiki extension has the following form > Overall, this amounts to > > load isosurface.xyz;isosurface color orange purple isosurface.jvxl > translucent; > > > If your command is "isosurface surfile.iso", I understand that you don't > need to load the surfile.iso file in advance, but to provide the full path > to the file (from the browser point of view), so the isosurface command can > access and load the file, and render the content. > > Jaim > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: A. H. <ang...@ua...> - 2012-03-01 14:07:38
|
Henry, maybe loading a .jmol file would help? It can contain the 2 files in it, and the state script. You probably need to allow the new file type to be uploaded to the wiki. |
From: Jaime P. <jai...@we...> - 2012-03-01 17:02:33
|
On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote: The problem is that, depending on MediaWiki configuration, uploaded files can end up in different directories (to avoid putting thousands of files in the same directory)... And the user has absolutely no control over which directory will be used for a file. So there's not really a possible default directory... For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while 1HPNmod.pdb is in images/4/49 Nico Nico, The subdirectories under images/ are computed from the md5 of the file name. $name = "1ALE.pdb"; $md5= md5(ucfirst($name)); $fullPath = "images/" . substr($md5,0,1) . "/" . substr($md5,0,2) . "/" . ucfirst($name); Jaim -- Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: Jai...@we...<mailto:Jai...@we...> 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) |
From: Nicolas V. <nve...@gm...> - 2012-03-02 07:35:26
|
On Thu, Mar 1, 2012 at 6:02 PM, Jaime Prilusky < jai...@we...> wrote: > On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote: > The problem is that, depending on MediaWiki configuration, uploaded > files can end up in different directories (to avoid putting thousands of > files in the same directory)... > And the user has absolutely no control over which directory will be used > for a file. > So there's not really a possible default directory... > For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while > 1HPNmod.pdb is in images/4/49 > Nico > > Nico, > > The subdirectories under images/ are computed from the md5 of the file > name. > > $name = "1ALE.pdb"; > > $md5= md5(ucfirst($name)); > > $fullPath = "images/" . substr($md5,0,1) . "/" . substr($md5,0,2) . > "/" . ucfirst($name); > > Jaim > > Thanks for the information, But, that still means there's no directory that can be set as default directory for Jmol. And the organization of the files depends also on the wiki configuration (with or without md5 hash, number of characters of the md5 taken into account) and uploads can be mixed between local and shared repository. So having to analyze the script to change file paths is really complex... Nico |
From: A. H. <ang...@ua...> - 2012-03-01 18:36:34
|
Hi Henry I am senidng to you off-list a sample file I just created. That is a .jmol file (really a zipfile, with contents added by Jmol; I'm not sure if you can collate it manually). This is the procedure I followed: 1. Load the molecule into Jmol app (I used 12.2.16) 2. Create the isosurface, color it etc. 3. Save the isosurface to disk 4. Zap 5. Load the molecule (load command or drag-and-drop) 6. Load the isosurface (isosurface command, drag-and-drop seems to work too) 7. "Save all" as .JMOL file (I did it from the popup menu) The .jmol file generated this way include both the model and the JVXL files, plus extra niceties like a png, the state script and a manifest). I moved it to a different folder and it loads into Jmol with everything. Note that if you skip step #6 and try to save with the isosurface just created, the file contains the command to generate it but not the isosurface data (as the state script included is recreating the history) So you must load the isosurface from disk. So I bet this is the safest and easiest way to go for the wiki. Good luck! |
From: Robert H. <ha...@st...> - 2012-03-02 12:49:43
|
My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Nicolas V. <nve...@gm...> - 2012-03-02 13:02:54
|
I have the impression that I'm missing a point in this discussion... The situation Henry is talking about is that he need to access several files that have been previously uploaded to the Wiki. When you upload several files, they usually end up in different directories (due to the md5 hash on the name), without any way to control it. So, I could easily add a code for defaultDirectory at the beginning of the script (even automatically by the Jmol extension). But my problem is to define this default directory so that it is useful : - there are no files in the root directory for uploads => not a good default directory - the directory where the uploaded file is (<uploadedFileContents> gives the atom coordinates file) is not the same directory where the surface file is => won't work to find the surface file - ... Nico On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson <ha...@st...> wrote: > My point was that if MediaWiki would just insert the Jmol script code for > defaultDirectory in the startup script, then the user can include numerous > files with no prefix and no concern over where they are. > > Bob > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: A. H. <ang...@ua...> - 2012-03-02 13:24:05
|
I agree with Nico. The location of uploades files in MW is uncertain. The .jmol file format is in my opinion the way out of this problem: upload a single file with everything included. |
From: Rzepa, H. S <h....@im...> - 2012-03-02 13:57:51
|
On 2 Mar 2012, at 13:23, Angel Herráez wrote: > I agree with Nico. The location of uploades files in MW is uncertain. > > The .jmol file format is in my opinion the way out of this problem: > upload a single file with everything included. A single file as a zip (the same way that jar files are considered single files). I am however intrigued that the .jvxl file is nowadays a proper XML file, and hence this can itself carry separate namespaces, amounting to different types of content. One can either package eg coordinate and surface files into a single zip archive, or one alternatively could express these components as a single XML file (which can be disentangled into its original components by suitable XML parsing into a DOM). I suppose both alternatives have their advantages and weaknesses. Anyway, Jmol adopts the former approach and this is what we have to find solutions for. |
From: Robert H. <ha...@st...> - 2012-03-02 15:32:54
|
oh. never mind then. I thought they went into a specific directory. No, that would not work.... On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle <nve...@gm...>wrote: > I have the impression that I'm missing a point in this discussion... > > The situation Henry is talking about is that he need to access several > files that have been previously uploaded to the Wiki. > When you upload several files, they usually end up in different > directories (due to the md5 hash on the name), without any way to control > it. > So, I could easily add a code for defaultDirectory at the beginning of the > script (even automatically by the Jmol extension). > But my problem is to define this default directory so that it is useful : > > - there are no files in the root directory for uploads => not a good > default directory > - the directory where the uploaded file is (<uploadedFileContents> > gives the atom coordinates file) is not the same directory where the > surface file is => won't work to find the surface file > - ... > > Nico > > On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson <ha...@st...> wrote: > >> My point was that if MediaWiki would just insert the Jmol script code for >> defaultDirectory in the startup script, then the user can include numerous >> files with no prefix and no concern over where they are. >> >> Bob >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2012-03-02 15:34:06
|
How does MediaWiki know at all where to look for a file when the script is load xxx.xyz ? On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson <ha...@st...> wrote: > oh. never mind then. I thought they went into a specific directory. No, > that would not work.... > > > > On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle <nve...@gm...>wrote: > >> I have the impression that I'm missing a point in this discussion... >> >> The situation Henry is talking about is that he need to access several >> files that have been previously uploaded to the Wiki. >> When you upload several files, they usually end up in different >> directories (due to the md5 hash on the name), without any way to control >> it. >> So, I could easily add a code for defaultDirectory at the beginning of >> the script (even automatically by the Jmol extension). >> But my problem is to define this default directory so that it is useful : >> >> - there are no files in the root directory for uploads => not a good >> default directory >> - the directory where the uploaded file is (<uploadedFileContents> >> gives the atom coordinates file) is not the same directory where the >> surface file is => won't work to find the surface file >> - ... >> >> Nico >> >> On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson <ha...@st...> wrote: >> >>> My point was that if MediaWiki would just insert the Jmol script code >>> for defaultDirectory in the startup script, then the user can include >>> numerous files with no prefix and no concern over where they are. >>> >>> Bob >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> ------------------------------------------------------------------------------ >>> Virtualization & Cloud Management Using Capacity Planning >>> Cloud computing makes use of virtualization - but cloud computing >>> also focuses on allowing computing to be delivered as a service. >>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Nicolas V. <nve...@gm...> - 2012-03-02 15:39:55
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Hi Bob, In short, it doesn't know. When you want to display a file that has been previously uploaded, you can use for example <jmolFile>xxx.xyz</jmolFile>. The PHP code of the extension knows where xxx.xyz is stored and creates the script that works. See examples in http://wiki.jmol.org/index.php/MediaWiki/Basic_Example Nico On Fri, Mar 2, 2012 at 4:33 PM, Robert Hanson <ha...@st...> wrote: > How does MediaWiki know at all where to look for a file when the script is > > load xxx.xyz > > ? > > > > On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson <ha...@st...> wrote: > >> oh. never mind then. I thought they went into a specific directory. No, >> that would not work.... >> >> >> >> On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle <nve...@gm...>wrote: >> >>> I have the impression that I'm missing a point in this discussion... >>> >>> The situation Henry is talking about is that he need to access several >>> files that have been previously uploaded to the Wiki. >>> When you upload several files, they usually end up in different >>> directories (due to the md5 hash on the name), without any way to control >>> it. >>> So, I could easily add a code for defaultDirectory at the beginning of >>> the script (even automatically by the Jmol extension). >>> But my problem is to define this default directory so that it is useful : >>> >>> - there are no files in the root directory for uploads => not a good >>> default directory >>> - the directory where the uploaded file is (<uploadedFileContents> >>> gives the atom coordinates file) is not the same directory where the >>> surface file is => won't work to find the surface file >>> - ... >>> >>> Nico >>> >>> On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson <ha...@st...>wrote: >>> >>>> My point was that if MediaWiki would just insert the Jmol script code >>>> for defaultDirectory in the startup script, then the user can include >>>> numerous files with no prefix and no concern over where they are. >>>> >>>> Bob >>>> >>>> >>>> -- >>>> Robert M. Hanson >>>> Professor of Chemistry >>>> St. Olaf College >>>> 1520 St. Olaf Ave. >>>> Northfield, MN 55057 >>>> http://www.stolaf.edu/people/hansonr >>>> phone: 507-786-3107 >>>> >>>> >>>> If nature does not answer first what we want, >>>> it is better to take what answer we get. >>>> >>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Virtualization & Cloud Management Using Capacity Planning >>>> Cloud computing makes use of virtualization - but cloud computing >>>> also focuses on allowing computing to be delivered as a service. >>>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Virtualization & Cloud Management Using Capacity Planning >>> Cloud computing makes use of virtualization - but cloud computing >>> also focuses on allowing computing to be delivered as a service. >>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Robert H. <ha...@st...> - 2012-03-02 15:46:07
|
Shouldn't be hard to adapt that to the way Jmol finds file names in scripts: load /*file*/"......." isosurface /*file*/"....." next quoted phrase after /*file*/ needs to be replaced by full path to that file. On Fri, Mar 2, 2012 at 9:39 AM, Nicolas Vervelle <nve...@gm...>wrote: > Hi Bob, > > In short, it doesn't know. > When you want to display a file that has been previously uploaded, you can > use for example <jmolFile>xxx.xyz</jmolFile>. > The PHP code of the extension knows where xxx.xyz is stored and creates > the script that works. > See examples in http://wiki.jmol.org/index.php/MediaWiki/Basic_Example > > Nico > > > On Fri, Mar 2, 2012 at 4:33 PM, Robert Hanson <ha...@st...> wrote: > >> How does MediaWiki know at all where to look for a file when the script is >> >> load xxx.xyz >> >> ? >> >> >> >> On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson <ha...@st...> wrote: >> >>> oh. never mind then. I thought they went into a specific directory. No, >>> that would not work.... >>> >>> >>> >>> On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle <nve...@gm...>wrote: >>> >>>> I have the impression that I'm missing a point in this discussion... >>>> >>>> The situation Henry is talking about is that he need to access several >>>> files that have been previously uploaded to the Wiki. >>>> When you upload several files, they usually end up in different >>>> directories (due to the md5 hash on the name), without any way to control >>>> it. >>>> So, I could easily add a code for defaultDirectory at the beginning of >>>> the script (even automatically by the Jmol extension). >>>> But my problem is to define this default directory so that it is useful >>>> : >>>> >>>> - there are no files in the root directory for uploads => not a >>>> good default directory >>>> - the directory where the uploaded file is (<uploadedFileContents> >>>> gives the atom coordinates file) is not the same directory where the >>>> surface file is => won't work to find the surface file >>>> - ... >>>> >>>> Nico >>>> >>>> On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson <ha...@st...>wrote: >>>> >>>>> My point was that if MediaWiki would just insert the Jmol script code >>>>> for defaultDirectory in the startup script, then the user can include >>>>> numerous files with no prefix and no concern over where they are. >>>>> >>>>> Bob >>>>> >>>>> >>>>> -- >>>>> Robert M. Hanson >>>>> Professor of Chemistry >>>>> St. Olaf College >>>>> 1520 St. Olaf Ave. >>>>> Northfield, MN 55057 >>>>> http://www.stolaf.edu/people/hansonr >>>>> phone: 507-786-3107 >>>>> >>>>> >>>>> If nature does not answer first what we want, >>>>> it is better to take what answer we get. >>>>> >>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Virtualization & Cloud Management Using Capacity Planning >>>>> Cloud computing makes use of virtualization - but cloud computing >>>>> also focuses on allowing computing to be delivered as a service. >>>>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>>>> _______________________________________________ >>>>> Jmol-users mailing list >>>>> Jmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>>> >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Virtualization & Cloud Management Using Capacity Planning >>>> Cloud computing makes use of virtualization - but cloud computing >>>> also focuses on allowing computing to be delivered as a service. >>>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |