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Question types: Java Molecular Editor

qtype_jme
Question type created by Dan Stowell. The student draw a molecule as a response to a question using the editor and that response is graded by comparing against various model answers. The jme Moodle question type uses a java applet, the JMEMolecularEditor©. JMEMolecularEditor© is a freely-available molecule editor tool, but it is not open-source. Peter Ertl is JMEMolecularEditor's author. To use this question type you will need to obtain and install it separately.
Maintained by: Picture of Jean-Michel Védrine Jean-Michel Védrine

The JME editor can be used to design molecular structures, so you
can ask questions such as "Please draw the structure of
2,3-dichloro-but-2-ene". In order to mark responses, they need to
be converted to a simple text format called SMILES (see
http://www.daylight.com/smiles/ for more information).

So, the student must design the molecule, using the JME Java Applet.
The content of the student response is automatically saved when the
student change page in the quiz either by pressing on the "Next"
button, or using the quiz navigation panel. When quiz attempt is
submitted, this response is then marked in the same way as a
(case-sensitive) short-answer question.

You can use a similar process when designing the question. Using
the JME applet, design a molecule that is a possible (right or
wrong) answer and then press a button next to the answer boxes
to store the current design as a SMILES code.

This plugin contains potential privacy issues:
It is not possible to use this plugin without obtaining (see http://www.molinspiration.com/jme/getjme.html ) the JMEMolecularEditor© Java archive from Peter Ertl and installing it on your server (you need to put a copy of the JME.jar file in the question/type/jme/jme/ subfolder). This required code is closed source and as such has not been validated during plugin approval.

Screenshots

screenshot

Contributors

Picture of Dan Stowell
Dan Stowell: Original Author
Picture of Jean-Michel Védrine
Jean-Michel Védrine (Lead maintainer)
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  • MD shot of me from his iphone4
    Tue, Jul 2, 2013, 2:03 PM
    Ah you are right, JME.jar isn't GPL (http://www.molinspiration.com/jme/ states only 'free for non-commercial')

    However,
    http://peter-ertl.com/jsme/ -- contains BSD 3-clause license (GPL compatible) so there is hope that this can one day incorporate the open sourced version i hope.

    I've discussed this and, unfortunately, we feel that its better that this plugin be made to use an open source GPL compatible library instead of instructing others to obtain a non-GPL jar file at their own risks. So i'm unapproving it for now.

    Other changes needed are some urls for:
    - bug tracker url
    - website, documentation urls if any.
  • Picture of Jean-Michel Védrine
    Tue, Jul 2, 2013, 2:36 PM
    Hello Aparup,
    I am sorry but I don't understand your decision.
    Why should this plugin not be approved and pmatchjme (https://moodle.org/plugins/view.php?plugin=qtype_pmatchjme) be approved ? They are quite similar in their use of the JME library and qtype_jme is the "father" of all other plugins using JME molecule editor. without the jme question type maybe no other plugin like pmatchjme would exists today.
    You (not you personally by all the people involved in the discussion) must make your acts clear and either refuse all these plugins or accept all.
    I don't think I want to take the task to move this plugin (that I don't use) to another library just so it is accepted in the Directory
    Last thing: I offer this plugin a a service to other Moodle users (I don't understand anything to molecules) and having spend many hours on upgrading it to successive Moodle versions I am quite sad about this because it will force me to offer new versions of it in the forum as I have done until now without the comfort of the Moodle Directory. Why Anthony wrote me to submit my plugins to the plugins directory rather than offering them in the forum if after having done the work to do a proper release some are not accepted ? This is unfair !
    for the other changes
    - bug tracker url: once this plugin is approved (if it is) I will ask Anthony to create a CONTRIB component. Once this is done, I will fill the relevant foield on the submission form.
    - documentation: as I said I am not able to document it as I don't understand anything about molecule. A search in the Moodle docs returned nothing. I will do a Google search and also collect posts about jme in the quiz forum to sart a documentation. Another solution would be, if this plugin is approved, to ask users in the quiz forum to contribute to a page in the Moodle docs to better document it.
  • Picture of Jean-Michel Védrine
    Tue, Jul 2, 2013, 3:12 PM
    I forgot to say that you are surely right in saying that JSME is the way to go, but the problem is
    - my javascript abilities are rather limited
    - I have completely redone Dan stowell 's original code to integrate the JME applet in the student view and it is now inspired by Jamie's Pratt code fo the pmatchjme question type done for the OU, so it would be a lot easier for me to wait that pmatchjme itself is migrated to JSME smile
    - as I said jme question type is not a priority for me as I maintain a lot of other questions types that (contrary to this one) I use ( I still have to submit multichoiceset and formulas to the Plugins directory).
    That said, of course if you or someone else wants to help me with the port of qtype_jme to JSME I would glady accept smile
  • Picture of Jean-Michel Védrine
    Tue, Jul 2, 2013, 9:33 PM
    I hav estarted a Moodle docs page for this question type at http://docs.moodle.org/25/en/question/type/jme (I choose this page as it is the one linked to when a user press the "More help" link in the help of the "editing a java molecular editor question" Moodle page.
    Of course it is far from complete and the screenshot would need some update as it was taken with an old version of the JMe question type, but this is a start.
  • Picture of Jean-Michel Védrine
    Tue, Jul 2, 2013, 9:35 PM
    I have a problem: I don't know how to add Dan Stowell as a contributor as I am not able to find his username on moodle.com because he is no more subscribed to any course. Can you help me ?
  • Picture of Jean-Michel Védrine
    Wed, Jul 3, 2013, 2:07 AM
    I was able to contact Dan Stowell and to add him as a contributor. He was quite surprised to hear that jme question type is still alive smile
  • MD shot of me from his iphone4
    Wed, Jul 3, 2013, 11:45 AM
    Hi Jean-Michel,
    I understand and sympathise.
    Thanks for highlighting qtype_pmatchjme, i see it too relies on the closed JME.jar but doesn't distribute it.

    I will discuss this further as i do, personally, feel its not fair too.
  • Martin in black and white
    Wed, Jul 3, 2013, 12:00 PM
    In my opinion this is similar to any integration plugin that relies on extra things to work. As long as the plugin actually installs and uninstalls without the JME plugin, then I have no problem with it (ie the fact it isn't useful is not our concern).

    I'm OK to approve this IF (and only if):

    1) We give users FULL information on the dependency and what they need to do, in the description of this plugin and also qtype_pmatchjme.
    2) We make it explicit that JME is closed source and that we cannot vouch for it. The risk is all theirs to judge from the JME web site.
  • MD shot of me from his iphone4
    Wed, Jul 3, 2013, 2:07 PM
    Further to that, I've realised that the 'Potential privacy issues' field looks like a useful field to use to highlight the nature of risks involved here.

    I've added a FAQ here to clarify this: http://docs.moodle.org/dev/Plugin_validation#Q:_I.27ve_a_plugin_to_share_that_requires_closed_.28or_non-GPL_compatible.29_source_software._Can_i_share_this_in_the_plugins_directory.3F

    Jean-Michel, installation and using the plugin was no issue for me so i'll wait for the required changes to description before approving this.
  • Picture of Jean-Michel Védrine
    Wed, Jul 3, 2013, 2:46 PM
    Hello Aparup and Martin,
    I tried to modify description and Potential privacy issues accordingly to your comments. But as English is not my native language, I would feel more comfortable if somebody else can verify the text. Fell free to edit it.
  • Picture of Jean-Michel Védrine
    Wed, Jul 3, 2013, 2:50 PM
    Also thanks to Aparup for pointing me to the GPL compatible JSME javascript editor (I was not aware of it). I think it will be good to switch to JSME in a future version because it would be possible to use this plugin with mobiles.
    In fact I already started to do it, see https://moodle.org/mod/forum/discuss.php?d=231848 but I need some javascript help to finish the move.
  • MD shot of me from his iphone4
    Wed, Jul 3, 2013, 8:05 PM
    I think that works for me Jean-Michel smile , that and its a reddish field helps. ok, hitting the green light.

    Nice work on the quick start to change this!
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